Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold51
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: 3712191
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.32
Warning! 131352 characters in sequence are not A, C, G, or T
File 12 of 23
Found at i:1689719 original size:126 final size:127
Alignment explanation
Indices: 1689550--1689794 Score: 395
Period size: 126 Copynumber: 1.9 Consensus size: 127
1689540 CTAAGACCAT
* *
1689550 TGTCGCTGGCCTTGAACCAGTACATTGGCATAAACCCAATATCGCTGGCCTTGAATCAGCATATT
1 TGTCGCTGGCCTTGAACCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAATCAGCATATT
*
1689615 GGCACCTT-GTCTTTAAGACC-ATTGTCGCTGGCCTTGAATCAGCACATTAGCACAAGCCCAA
66 GGCACCTTCATCTTTAAGACCGA-TGTCGCTGGCCTTGAATCAGCACATTAGCACAAGCCCAA
* *
1689676 TGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATT
1 TGTCGCTGGCCTTGAACCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAATCAGCATATT
* * *
1689741 GGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCATCACATTGGCAC
66 GGCACCTTCATCTTTAAGACCGATGTCGCTGGCCTTGAATCAGCACATTAGCAC
1689795 CTTAACCATC
Statistics
Matches: 109, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
126 69 0.63
127 39 0.36
128 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (127 bp):
TGTCGCTGGCCTTGAACCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAATCAGCATATT
GGCACCTTCATCTTTAAGACCGATGTCGCTGGCCTTGAATCAGCACATTAGCACAAGCCCAA
Found at i:1689898 original size:101 final size:98
Alignment explanation
Indices: 1689722--1690142 Score: 319
Period size: 101 Copynumber: 4.2 Consensus size: 98
1689712 CAATATCGCT
* * * * *
1689722 GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCATCAC
1 GGCCTTGAATCAGCACATTGGCACCTTCATCTGTAAGACCGATATCGCTGGCCTTGAATCAGCAC
* * *
1689787 ATTGGCACCTTAACCATCTTTAAGTCCAATGTC-TCC
66 ATTAGAACCTT---CATCTTTAAGACCAATGTCGT-C
* * *
1689823 GGCCTTGAATCAGCACATTGGCATCTTCATCTGTAAGTCCGATATCGCTGGCCTTGAATCAGCAT
1 GGCCTTGAATCAGCACATTGGCACCTTCATCTGTAAGACCGATATCGCTGGCCTTGAATCAGCAC
* *
1689888 ATTAGAACCTTCATCTTTAAGACCGATGTCGTT
66 ATTAGAACCTTCATCTTTAAGACCAATGTCGTC
* * * * * * * * **
1689921 GGTCTAGAATCAGCACATTAGCACCATAACCATCTTTAAGTCCAATGTCGCCAGCCTTGAATCAG
1 GGCCTTGAATCAGCACATTGGCACC-T--TCATCTGTAAGACCGATATCGCTGGCCTTGAATCAG
* * * * * * *
1689986 CACATTGGCATCTTCATCTGTAAGTCCGATATCG-C
63 CACATTAGAACCTTCATCTTTAAGACCAATGTCGTC
* * * * * *
1690021 TGGCCTTGAATTAGCATATTGGCACCGTTAAT-TTTAAGACCAATGTCGC-GAGCCTTGAATCAG
1 -GGCCTTGAATCAGCACATTGGCACC-TTCATCTGTAAGACCGATATCGCTG-GCCTTGAATCAG
* * * * ** * *
1690084 CACATTGGCATCTTCATCTTTAAGTCCGGTATCGTT
63 CACATTAGAACCTTCATCTTTAAGACCAATGTCGTC
*
1690120 GGCCTTGAATCAGCATATTGGCA
1 GGCCTTGAATCAGCACATTGGCA
1690143 TCTTTAACAT
Statistics
Matches: 268, Mismatches: 45, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
98 120 0.45
99 4 0.01
101 144 0.54
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (98 bp):
GGCCTTGAATCAGCACATTGGCACCTTCATCTGTAAGACCGATATCGCTGGCCTTGAATCAGCAC
ATTAGAACCTTCATCTTTAAGACCAATGTCGTC
Found at i:1689985 original size:150 final size:149
Alignment explanation
Indices: 1689714--1690146 Score: 622
Period size: 150 Copynumber: 2.9 Consensus size: 149
1689704 CACAAGCCCA
1689714 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
* *
1689779 ATCATCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCTCCGGCCTTGAATCAGCACATTGG
66 ATCAGCACATTGGCACC-TAACCATCTTTAAGTCCAATGTCGCCGGCCTTGAATCAGCACATTGG
1689844 CATCTTCATCTGTAAGTCCG
130 CATCTTCATCTGTAAGTCCG
* * * *
1689864 ATATCGCTGGCCTTGAATCAGCATATTAGAACCTTCATCTTTAAGACCGATGTCGTTGGTCTAGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
* *
1689929 ATCAGCACATTAGCACCATAACCATCTTTAAGTCCAATGTCGCCAGCCTTGAATCAGCACATTGG
66 ATCAGCACATTGGCACC-TAACCATCTTTAAGTCCAATGTCGCCGGCCTTGAATCAGCACATTGG
1689994 CATCTTCATCTGTAAGTCCG
130 CATCTTCATCTGTAAGTCCG
* * * *
1690014 ATATCGCTGGCCTTGAATTAGCATATTGGCACCGTTAAT-TTTAAGACCAATGTCG-CGAGCCTT
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTCATCTTTAAGACCGATGTCGTTG-GCCTT
* * ** * ** *
1690077 GAATCAGCACATTGGCATCT--TCATCTTTAAGTCCGGTATCGTTGGCCTTGAATCAGCATATTG
64 GAATCAGCACATTGGCACCTAACCATCTTTAAGTCCAATGTCGCCGGCCTTGAATCAGCACATTG
1690140 GCATCTT
129 GCATCTT
1690147 TAACATTCTT
Statistics
Matches: 254, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
147 42 0.17
149 2 0.01
150 206 0.81
151 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (149 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
ATCAGCACATTGGCACCTAACCATCTTTAAGTCCAATGTCGCCGGCCTTGAATCAGCACATTGGC
ATCTTCATCTGTAAGTCCG
Found at i:1690171 original size:150 final size:147
Alignment explanation
Indices: 1689707--1690194 Score: 588
Period size: 150 Copynumber: 3.3 Consensus size: 147
1689697 ACATTGGCAC
1689707 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTG
*
1689772 GCCTTGAATCATCACATTGGCACCTTAACCATCTTTAAGTCCAATGTC-TCCGGCCTTGAATCAG
66 GCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGTCCAATGTCGT-CGGCCTTGAATCAG
1689836 CACATTGGCATCTTCATCTGT
127 CACATTGGCATCTTCATCTGT
* * * *
1689857 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTAGAACCTTCATCTTTAAGACCGATGTCGTTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTG
* * * * * *
1689922 GTCTAGAATCAGCACATTAGCACCATAACCATCTTTAAGTCCAATGTCGCCAGCCTTGAATCAGC
66 GCCTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGTCCAATGTCGTCGGCCTTGAATCAGC
1689987 ACATTGGCATCTTCATCTGT
128 ACATTGGCATCTTCATCTGT
* * * * * *
1690007 AAGTCCGATATCGCTGGCCTTGAATTAGCATATTGGCACCGTTAAT-TTTAAGACCAATGTCG-C
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTCATCTTTAAGACCGATGTCGTT
* ** * *
1690070 GAGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCGTTGGCCTTGAATCAGCA
65 G-GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGTCGGCCTTGAATCAGCA
*
1690135 TATTGGCATCTTTAACATTCT-T
129 CATTGGCATC-TT--CA-TCTGT
* ** *
1690157 AAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1690195 TTCTTCTATA
Statistics
Matches: 292, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
147 40 0.14
148 2 0.01
149 2 0.01
150 240 0.82
151 8 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (147 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTG
GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGTCGGCCTTGAATCAGCACA
TTGGCATCTTCATCTGT
Found at i:1691160 original size:32 final size:32
Alignment explanation
Indices: 1691124--1691188 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1691114 TTCAACGATT
1691124 TGTATCGATAC-TAAAATGTTGTATCGATACAA
1 TGTATCGATACAT-AAATGTTGTATCGATACAA
** *
1691156 TGTATCGATACATATTTTTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
1691188 T
1 T
1691189 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTGTATCGATACAA
Found at i:1691161 original size:13 final size:13
Alignment explanation
Indices: 1691143--1691167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1691133 ACTAAAATGT
1691143 TGTATCGATACAA
1 TGTATCGATACAA
1691156 TGTATCGATACA
1 TGTATCGATACA
1691168 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1691250 original size:13 final size:13
Alignment explanation
Indices: 1691232--1691256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1691222 ATTACTCACA
1691232 TGTATCGATACAG
1 TGTATCGATACAG
1691245 TGTATCGATACA
1 TGTATCGATACA
1691257 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1691370 original size:51 final size:53
Alignment explanation
Indices: 1691265--1691385 Score: 210
Period size: 51 Copynumber: 2.3 Consensus size: 53
1691255 CACTGATCTT
*
1691265 TGTATCGATACATGCAGGCCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1691318 TGTATCGATACATGCAGG-C-AATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCCAAATTTGCCCAGATGTATCGATACACTATAAAA
1691369 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1691386 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 47 0.71
52 1 0.02
53 18 0.27
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (53 bp):
TGTATCGATACATGCAGGCCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1698671 original size:13 final size:13
Alignment explanation
Indices: 1698653--1698677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1698643 CCTACTCTTC
1698653 ACAAAAAAAAAAA
1 ACAAAAAAAAAAA
1698666 ACAAAAAAAAAA
1 ACAAAAAAAAAA
1698678 GGGGAAAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
ACAAAAAAAAAAA
Found at i:1699658 original size:30 final size:31
Alignment explanation
Indices: 1699621--1699705 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 31
1699611 CAAATACCTT
*
1699621 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
1 TTCAAAGTCCACAACTCAGTGGCATTTTGTC
* *
1699652 -TCAAAGTCCACAACTTAGTGGCATTTTTTC
1 TTCAAAGTCCACAACTCAGTGGCATTTTGTC
* * *
1699682 TTTAAAGCCCACAACTCTGTGGCA
1 TTCAAAGTCCACAACTCAGTGGCA
1699706 CACTTTTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
30 27 0.59
31 19 0.41
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (31 bp):
TTCAAAGTCCACAACTCAGTGGCATTTTGTC
Found at i:1699763 original size:34 final size:33
Alignment explanation
Indices: 1699659--1700205 Score: 440
Period size: 34 Copynumber: 16.6 Consensus size: 33
1699649 GTCTCAAAGT
** *
1699659 CCACAACTTAGTGGCA-TTTTTTCT-TTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
* * * *
1699690 CCACAACTCTGTGGCACACTTTTTCTTTTTAAAAC
1 CCACAACTCCGTGGCAC-TTTTTTCTCTTT-AAGC
* * *
1699725 CCACAATTCTGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-TCTTTAAGC
1699759 CCACAACTCCGTGGCAC------C-CGTTTAAGC
1 CCACAACTCCGTGGCACTTTTTTCTC-TTTAAGC
* *
1699786 CCACAACTCCGTGGCACCTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
*
1699820 CCACAACTCCGTGGCACCTTTTTCT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* *
1699853 CCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGC
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTT--AAGC
* *
1699890 CCACAACTCCGTGGCACCTTTTTCTGTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
*
1699924 CCACAACTCCGTGGCAC-----TCT-TTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
* * *
1699951 CCACAACTCCGTGGCACCTTCTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* *
1699985 CCACAACTCTGTGGCACTCTTTTTC-CTCCTAAGC
1 CCACAACTCCGTGGCACT-TTTTTCTCT-TTAAGC
*
1700019 CCACAACTCTGTGGCACTCTTTTTC-CTTCTAAGC
1 CCACAACTCCGTGGCACT-TTTTTCTCTT-TAAGC
*
1700053 CCACAACTCCGTGGCA-----TCCT-TTTAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
* *
1700080 CCATAACTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-TCTTTAAGC
* *
1700114 CCATAACTCCGTGGCACCTTTTTTTTCTTTTAAAGC
1 CCACAACTCCGTGGCA-CTTTTTTCTC-TTT-AAGC
* *
1700150 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTTAAGC
1700185 CCACAACTCCGTGGCATCTTT
1 CCACAACTCCGTGGCA-CTTT
1700206 CTCCCTTTCT
Statistics
Matches: 435, Mismatches: 40, Indels: 78
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.00
27 64 0.15
28 7 0.02
29 3 0.01
31 14 0.03
32 5 0.01
33 38 0.09
34 178 0.41
35 65 0.15
36 39 0.09
37 21 0.05
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (33 bp):
CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
Found at i:1699790 original size:27 final size:27
Alignment explanation
Indices: 1699752--1699803 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1699742 TTTTTTCATC
*
1699752 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
1699779 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
1699804 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:1699800 original size:61 final size:63
Alignment explanation
Indices: 1699654--1700166 Score: 271
Period size: 61 Copynumber: 7.9 Consensus size: 63
1699644 ATTTTGTCTC
* ** *
1699654 AAAGTCCACAACTTAGTGGCA--TTTTT-TCTTTAAAGCCCACAACTCTGTGGCACACTTTTTCT
1 AAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCAC-C----TC-
*
1699716 TTTT
60 GTTT
* * * *
1699720 AAAACCCACAATTCTGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACC-CGTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAAGCCCACAACTCCGTGGCACCTCGTTT
* * *
1699782 -AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 AAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACC----TCGT
1699846 TT
62 TT
* *
1699848 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 AAAGCCCACAACTCCGTGGCACT-TTTTTCTC-TTT-AAAGCCCACAACTCCGTGGCACC----T
1699913 CTGTTT
59 C-GTTT
*
1699919 AAAGCCCACAACTCCGTGGCA-------CTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTT
1 AAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCA-C--C-TC-G
1699977 TTT
61 TTT
* * *
1699980 AAAGCCCACAACTCTGTGGCACTCTTTTTC-CTCCT-AAGCCCACAACTCTGTGGCACTCTTTTT
1 AAAGCCCACAACTCCGTGGCACT-TTTTTCTCT-TTAAAGCCCACAACTCCGTGGCAC-C----T
*
1700043 CCTTCT
59 CGTT-T
* * * *
1700049 -AAGCCCACAACTCCGTGGCA------TC-CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCAT
1 AAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCAC----CTCGT
1700106 CTT
62 -TT
* * * *
1700109 TAAGTCCATAACTCCGTGGCACCTTTTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC
1 AAAGCCCACAACTCCGTGGCA-CTTTTTTCTC-TTTAAAGCCCACAACTCCGTGGCAC
1700167 TCTTTTTCCC
Statistics
Matches: 363, Mismatches: 38, Indels: 88
0.74 0.08 0.18
Matches are distributed among these distances:
60 9 0.02
61 135 0.37
62 7 0.02
63 3 0.01
64 2 0.01
66 22 0.06
67 21 0.06
68 55 0.15
69 29 0.08
70 57 0.16
71 23 0.06
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.33
Consensus pattern (63 bp):
AAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAAGCCCACAACTCCGTGGCACCTCGTTT
Found at i:1699953 original size:165 final size:161
Alignment explanation
Indices: 1699654--1700225 Score: 628
Period size: 165 Copynumber: 3.5 Consensus size: 161
1699644 ATTTTGTCTC
* ** * * *
1699654 AAAGTCCACAACTTAGTGGCA-T-TTTTT-CTTTAAAGCCCACAACTCTGTGGCACACTTTTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCTGTGGCACTCTTTTTCC
* * * * * * *
1699716 TTTTAAAACCCACAATTCTGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCGTT
66 TTTCAAAGCCCACAACTCCGTGGCAC-TTTTTC-T-TTTAAGCCCACAACTCCGTGGCACTCATT
1699781 TAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
128 TAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1699815 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT-AAGCCCACAACTCTGTGGCACTCTTTTT-
1699878 CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTC
64 CC-TTTCAAAGCCCACAACTCCGTGGCA-CTTTTTCT-TTT-AAGCCCACAACTCCGTGGCACTC
*
1699943 -TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTT
125 ATTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* **
1699980 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCTGTGGCACTCTTTTTCC
* * *
1700045 -TTCTAAGCCCACAACTCCGTGGCA----TCCTTTTAAGCCCATAACTCCGTGGCACTTTTTTCA
66 TTTCAAAGCCCACAACTCCGTGGCACTTTTTCTTTTAAGCCCACAACTCCGTGGCAC-----TCA
* * *
1700105 TCTTTAAGTCCATAACTCCGTGGCACCTTTTTTTTCTTTT
126 --TTTAAGCCCACAACTCCGTGGCACC-TTTTTCT-TTTT
* * *
1700145 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA-TCTTTCTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTTAAGCCCACAACTCTGTGGCACTCTTT-TT
1700209 CCTTTCTAAAGCCCACA
64 CCTTTC-AAAGCCCACA
1700226 CAAGTCGGTG
Statistics
Matches: 356, Mismatches: 31, Indels: 41
0.83 0.07 0.10
Matches are distributed among these distances:
156 20 0.06
157 3 0.01
158 3 0.01
161 20 0.06
162 9 0.03
163 70 0.20
164 16 0.04
165 140 0.39
166 60 0.17
167 6 0.02
168 9 0.03
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (161 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCTGTGGCACTCTTTTTCC
TTTCAAAGCCCACAACTCCGTGGCACTTTTTCTTTTAAGCCCACAACTCCGTGGCACTCATTTAA
GCCCACAACTCCGTGGCACCTTTTTCTTTTT
Found at i:1699954 original size:27 final size:27
Alignment explanation
Indices: 1699916--1700006 Score: 110
Period size: 27 Copynumber: 3.1 Consensus size: 27
1699906 CCTTTTTCTG
1699916 TTTAAAGCCCACAACTCCGTGGCACTC
1 TTTAAAGCCCACAACTCCGTGGCACTC
1699943 TTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTTAAAGCCCACAACTCCGTGGCA----C-TC
*
1699975 TTTTTAAAGCCCACAACTCTGTGGCACTC
1 --TTTAAAGCCCACAACTCCGTGGCACTC
1700004 TTT
1 TTT
1700007 TTCCTCCTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
27 27 0.48
29 2 0.04
30 1 0.02
31 1 0.02
32 2 0.04
34 23 0.41
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (27 bp):
TTTAAAGCCCACAACTCCGTGGCACTC
Found at i:1700102 original size:27 final size:27
Alignment explanation
Indices: 1700042--1700095 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1700032 GCACTCTTTT
*
1700042 TCCTTCTAAGCCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
*
1700069 TCCTTTTAAGCCCATAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
1700096 CTTTTTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (27 bp):
TCCTTTTAAGCCCACAACTCCGTGGCA
Found at i:1700146 original size:35 final size:34
Alignment explanation
Indices: 1700071--1700205 Score: 155
Period size: 35 Copynumber: 3.9 Consensus size: 34
1700061 CCGTGGCATC
*
1700071 CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCAT
1 CTTTTAAGCCCACAACTCCGTGGCACTTTTTT-AT
* * *
1700106 C-TTTAAGTCCATAACTCCGTGGCACCTTTTTTTT
1 CTTTTAAGCCCACAACTCCGTGGCA-CTTTTTTAT
**
1700140 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 CTTTT-AAGCCCACAACTCCGTGGCACT-TTTTTAT
*
1700176 CTTTTAAGTCCACAACTCCGTGGCATCTTT
1 CTTTTAAGCCCACAACTCCGTGGCA-CTTT
1700206 CTCCCTTTCT
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
34 24 0.27
35 34 0.39
36 30 0.34
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (34 bp):
CTTTTAAGCCCACAACTCCGTGGCACTTTTTTAT
Found at i:1700211 original size:34 final size:34
Alignment explanation
Indices: 1700070--1700225 Score: 161
Period size: 36 Copynumber: 4.4 Consensus size: 34
1700060 TCCGTGGCAT
* *
1700070 CCTTTTAAGCCCATAACTCCGTGGCA-CTTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTTC
* * * * *
1700103 CATCTTTAAGTCCATAACTCCGTGGCACCTTTTTTT
1 CCT-TTTAAGCCCACAACTCCGTGGCATC-TTTTTC
*
1700139 TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 CCTTTT-AAGCCCACAACTCCGTGGCA-TCTTTTTC
* *
1700175 CCTTTTAAGTCCACAACTCCGTGGCATCTTTCTC
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTTC
1700209 CCTTTCTAAAGCCCACA
1 CCTTT-T-AAGCCCACA
1700226 CAAGTCGGTG
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
33 2 0.02
34 34 0.33
35 24 0.23
36 43 0.41
37 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.11, T:0.37
Consensus pattern (34 bp):
CCTTTTAAGCCCACAACTCCGTGGCATCTTTTTC
Found at i:1700219 original size:71 final size:70
Alignment explanation
Indices: 1700070--1700225 Score: 201
Period size: 71 Copynumber: 2.2 Consensus size: 70
1700060 TCCGTGGCAT
* *
1700070 CCTTTT-AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTAAGTCCATAACTCCGTGGCACCTT
1 CCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTT
* *
1700134 TTTTT
66 TTCTC
* * *
1700139 TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATC
1 CCTTTTAAAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACC
1700203 -TTTCTC
64 TTTTCTC
1700209 CCTTTCTAAAGCCCACA
1 CCTTT-TAAAGCCCACA
1700226 CAAGTCGGTG
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
69 5 0.07
70 30 0.40
71 40 0.53
ACGTcount: A:0.20, C:0.33, G:0.11, T:0.37
Consensus pattern (70 bp):
CCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTT
TTCTC
Found at i:1700258 original size:33 final size:34
Alignment explanation
Indices: 1700216--1700279 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
1700206 CTCCCTTTCT
1700216 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTTCC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCC
1700249 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1700280 AAGCCCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.17
Consensus pattern (34 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCC
Found at i:1700286 original size:30 final size:31
Alignment explanation
Indices: 1700212--1700286 Score: 107
Period size: 33 Copynumber: 2.4 Consensus size: 31
1700202 CTTTCTCCCT
1700212 TTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
1 TTCT-AAGCCCACACAAGTCGGTGGCAACC-TC
*
1700245 TTCCAAAGCCCACACAAGTCGGTGGCAACC-C
1 TT-CTAAGCCCACACAAGTCGGTGGCAACCTC
1700276 TTCTAAGCCCA
1 TTCTAAGCCCA
1700287 ATATAGCTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 8 0.21
31 3 0.08
33 27 0.69
34 1 0.03
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (31 bp):
TTCTAAGCCCACACAAGTCGGTGGCAACCTC
Found at i:1700390 original size:43 final size:43
Alignment explanation
Indices: 1700325--1700594 Score: 333
Period size: 43 Copynumber: 6.0 Consensus size: 43
1700315 GCATCTTCAT
* *
1700325 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* * *
1700368 CTTTAAGCCCAATATAGTTGGCCCTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C
* *
1700415 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
1700460 CTTTAAGTCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C
* *
1700507 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
1700552 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1700595 ATCTCCATCT
Statistics
Matches: 196, Mismatches: 19, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
43 116 0.59
45 2 0.01
47 2 0.01
49 76 0.39
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:1700436 original size:92 final size:92
Alignment explanation
Indices: 1700274--1700637 Score: 629
Period size: 92 Copynumber: 3.9 Consensus size: 92
1700264 CGGTGGCAAC
*
1700274 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1700339 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
1700367 CCTTTAAGCCCAATATAGTTGGCCCTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1700432 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
1700459 CCTTTAAGTCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1700524 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
1700551 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATCTCCATCTTTAAGTTCAAT
1 CCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGG--CATCTTCATCTTTAAGTCCAAT
1700616 GTAGCTGGCCTTGAATCAGCAC
64 GTAGCTGGCCTTGAATCAGCAC
1700638 GTTGACATCC
Statistics
Matches: 261, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
92 215 0.82
93 4 0.02
94 42 0.16
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
CCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1701555 original size:33 final size:33
Alignment explanation
Indices: 1701518--1701584 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1701508 TTCAACGATT
1701518 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1701551 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1701584 T
1 T
1701585 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1701556 original size:13 final size:13
Alignment explanation
Indices: 1701538--1701562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1701528 CATAAAATGT
1701538 TGTATCGATACAA
1 TGTATCGATACAA
1701551 TGTATCGATACA
1 TGTATCGATACA
1701563 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1701645 original size:13 final size:13
Alignment explanation
Indices: 1701627--1701651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1701617 ATTACTCACA
1701627 TGTATCGATACAT
1 TGTATCGATACAT
1701640 TGTATCGATACA
1 TGTATCGATACA
1701652 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1701788 original size:52 final size:52
Alignment explanation
Indices: 1701660--1701780 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1701650 CACTGATCTT
*
1701660 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1701712 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1701764 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1701781 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1705158 original size:13 final size:13
Alignment explanation
Indices: 1705140--1705167 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1705130 CATTATTCAA
1705140 TGTATCGATACAT
1 TGTATCGATACAT
1705153 TGTATCGATACAT
1 TGTATCGATACAT
1705166 TG
1 TG
1705168 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1705166 original size:33 final size:33
Alignment explanation
Indices: 1705120--1705185 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1705110 GCCAAGGAAA
1705120 TGTATCGAGACATT-ATTCAATGTATCGATACAT
1 TGTATCGAGACATTGA-TCAATGTATCGATACAT
* **
1705153 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGAGACATTGATCAATGTATCGATACAT
1705186 CAGGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGAGACATTGATCAATGTATCGATACAT
Found at i:1706119 original size:20 final size:20
Alignment explanation
Indices: 1706094--1706143 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1706084 TCAACCTTGA
*
1706094 TCATGCTTTTTTACTATGCT
1 TCATGCATTTTTACTATGCT
1706114 TCATGCATTTTTACTATGCT
1 TCATGCATTTTTACTATGCT
1706134 TCATGCATTT
1 TCATGCATTT
1706144 ATGGCATGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.10, T:0.52
Consensus pattern (20 bp):
TCATGCATTTTTACTATGCT
Found at i:1710274 original size:19 final size:18
Alignment explanation
Indices: 1710249--1710313 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
1710239 CTTTCAACGA
1710249 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1710267 TGTTGTATCGATACA-AA-
1 T-TTGTATCGATACATAAG
1710284 ---GTATCGATACATAAG
1 TTTGTATCGATACATAAG
1710299 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1710314 ATGTATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
14 2 0.05
18 3 0.08
19 24 0.60
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1710288 original size:32 final size:32
Alignment explanation
Indices: 1710252--1710321 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
1710242 TCAACGATTT
1710252 GTATCGATACATAAGTGTTGTATCGATACAAA
1 GTATCGATACATAAGTGTTGTATCGATACAAA
* *
1710284 GTATCGATACATAAGTTTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAA
1710316 GTATCG
1 GTATCG
1710322 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (32 bp):
GTATCGATACATAAGTGTTGTATCGATACAAA
Found at i:1710289 original size:13 final size:14
Alignment explanation
Indices: 1710271--1710299 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1710261 CATAAGTGTT
1710271 GTATCGATACA-AA
1 GTATCGATACATAA
1710284 GTATCGATACATAA
1 GTATCGATACATAA
1710298 GT
1 GT
1710300 TTTGTATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (14 bp):
GTATCGATACATAA
Found at i:1710384 original size:13 final size:13
Alignment explanation
Indices: 1710366--1710390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1710356 ATTATTCAAA
1710366 TGTATCGATACAT
1 TGTATCGATACAT
1710379 TGTATCGATACA
1 TGTATCGATACA
1710391 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1710444 original size:52 final size:52
Alignment explanation
Indices: 1710399--1710527 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
1710389 CACTGATCTT
***
1710399 TGTATCGATACATGTGGGCAAATTTGCCCAGATGTATCAATACACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCAATACACTATGAAA
* *
1710451 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATAGACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCAATACACTATGAAA
*
1710503 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATACAGGCAAATTT
1710528 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCAATACACTATGAAA
Found at i:1717152 original size:15 final size:15
Alignment explanation
Indices: 1717134--1717175 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1717124 AGTCAAAAGT
1717134 AAACACAAAAAAACA
1 AAACACAAAAAAACA
*
1717149 AAACAAAAAAAAACA
1 AAACACAAAAAAACA
**
1717164 ACGCACAAAAAA
1 AAACACAAAAAA
1717176 GTGCAAAGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.79, C:0.19, G:0.02, T:0.00
Consensus pattern (15 bp):
AAACACAAAAAAACA
Found at i:1718450 original size:30 final size:30
Alignment explanation
Indices: 1718380--1718559 Score: 211
Period size: 31 Copynumber: 5.9 Consensus size: 30
1718370 ATACCTTCTT
* *
1718380 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCCC
*
1718411 AAAGCCCACGACTCAGTGGCAT-TTTGTCCC
1 AAAGTCCACGACTCAGTGGCATCTTT-TCCC
*
1718441 AAAGTCCACGACTCAGTGGCATCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATCTTTTC-CC
1718472 AAAGTCCACGACTCAGTGGCATCTCTTT-CC
1 AAAGTCCACGACTCAGTGGCATCT-TTTCCC
* *
1718502 AAAGTCCACGACTCAGAGGCATCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATCTTTTC-CC
* * * *
1718533 AAAGCCCACCACTCCGTGGCACCTTTT
1 AAAGTCCACGACTCAGTGGCATCTTTT
1718560 TCTTTTCTCC
Statistics
Matches: 130, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.04
30 52 0.40
31 70 0.54
32 3 0.02
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.27
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCCC
Found at i:1718455 original size:61 final size:61
Alignment explanation
Indices: 1718380--1718553 Score: 255
Period size: 61 Copynumber: 2.9 Consensus size: 61
1718370 ATACCTTCTT
*
1718380 AAAGTCCACGACTCAGTGGCAATCTCTTC-TCAAAGCCCACGACTCAGTGGCAT-T-TTGTCCC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGCCCACGACTCAGTGGCATCTCTT-T-CC
*
1718441 AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCATCTCTTTCC
1 AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACGACTCAGTGGCATCTCTTTCC
* * *
1718502 AAAGTCCACGACTCAGAGGCATCTTTTCTTCAAAGCCCACCACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACGACTCAGTGGCA
1718554 CCTTTTTCTT
Statistics
Matches: 104, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
60 7 0.07
61 93 0.89
62 2 0.02
63 2 0.02
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACGACTCAGTGGCATCTCTTTCC
Found at i:1718573 original size:37 final size:36
Alignment explanation
Indices: 1718523--1718700 Score: 152
Period size: 37 Copynumber: 4.9 Consensus size: 36
1718513 CTCAGAGGCA
*
1718523 TCTTTTCTTCAAAGCCCACCACTCCGTGGCACCTTTT
1 TCTTTTC-TCAAAGCCCACAACTCCGTGGCACCTTTT
* * *
1718560 TCTTTTCTCCAAAGCCCATAAATCCATGGCACCTTTT
1 TCTTTTCT-CAAAGCCCACAACTCCGTGGCACCTTTT
1718597 TCTTTT-T-AAAGCCCACAACTCCGTGGCACTCTTTT
1 TCTTTTCTCAAAGCCCACAACTCCGTGGCAC-CTTTT
* * *
1718632 TCCCTTT-T--AAGTCCACAACTCCGTGGCATCTTTCT
1 T-CTTTTCTCAAAGCCCACAACTCCGTGGCACCTTT-T
* * * * *
1718667 CCTTTTC-AAAAGCCCATAAGTCAGTGGCAACCTT
1 TCTTTTCTCAAAGCCCACAACTCCGTGGC-ACCTT
1718701 CAAAAGCCCA
Statistics
Matches: 116, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
34 27 0.23
35 26 0.22
36 22 0.19
37 41 0.35
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.34
Consensus pattern (36 bp):
TCTTTTCTCAAAGCCCACAACTCCGTGGCACCTTTT
Found at i:1719159 original size:102 final size:98
Alignment explanation
Indices: 1718732--1719600 Score: 862
Period size: 102 Copynumber: 8.9 Consensus size: 98
1718722 GGCATCTTCT
* * * * * * *
1718732 TTTAAGTCTAATATCGCCGGCCTTGAATCAGCATATTGGCGCCTTT-GTCTTTAAGACCAATGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC-ACTTTCATCTTTAAGTCCAATATC
* *
1718796 GCTAGCCTTGAATCAACATATTGGCA----C--C
65 GCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
1718824 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-GTCTTTAAGACCAATGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTTTAAGTCCAATATC
*
1718888 GCTGGCCTTGAATCAGCACATTGGCA----C--C
65 GCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
1718916 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-GTCTTTAAGACCAATGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTTTAAGTCCAATATC
*
1718980 GCTGGCCTTGAATCAGCACATTGGCA----C--C
65 GCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
1719008 TTTAAGTCCAAAATCGCTGGCCTTGAATCATCATATTGGTGC-CTTTGTCATCTTTTAAGTCCAA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCAC-TT-TCATC-TTTAAGTCCAA
* * * *
1719072 TGTCGTTGGCCTTGAATCAGCACATTGGCACATTCATC
61 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
1719110 TTTAAGTCCAATATCGCTGGCCTT-ACATCAGCATATTGGCATCTTTGTCATCTTTTAAGTCCAA
1 TTTAAGTCCAATATCGCTGGCCTTGA-ATCAGCACATTGGCA-C-TT-TCATC-TTTAAGTCCAA
*
1719174 -AGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
61 TA-TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
1719212 TTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC-AC-TT-TCATC-TTTAAGTCCAAT
* * * **
1719277 ATCGCTAGCCTTGAATCGGCAAATTGGCACCTTTGTC
62 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
1719314 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATCG
*
1719373 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
66 CTGGCCTTGAATCAGCATATTGGCACC--T-TCATC
* * * *
1719409 TTTTAAGTCCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATC
* *
1719474 GCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCATC
65 GCTGGCCTTGAATCAGCATATTGGCACC--T-TCATC
* *
1719511 TTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATC
*
1719576 GTTGGCCTTGAATCAGCATATTGGC
65 GCTGGCCTTGAATCAGCATATTGGC
1719601 GCCTGTCGTA
Statistics
Matches: 705, Mismatches: 42, Indels: 50
0.88 0.05 0.06
Matches are distributed among these distances:
92 252 0.36
93 4 0.01
94 4 0.01
95 6 0.01
96 77 0.11
100 4 0.01
101 2 0.00
102 354 0.50
103 2 0.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (98 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATCG
CTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:1719362 original size:247 final size:247
Alignment explanation
Indices: 1718732--1719600 Score: 990
Period size: 247 Copynumber: 3.6 Consensus size: 247
1718722 GGCATCTTCT
* * * *
1718732 TTTAAGTCTAATATCGCCGGCCTTGAATCAGCATATTGGCGCCTTTG--TC-TTTAAGACCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGCATCTTTTAAGTCCAATA
*
1718794 TCGCTAGCCTTGAATCAACATATTGGCA-C-----CTTTAAGTCCAATATCGCTGGCCTTGAATC
66 TCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCTTGAATC
* * * * *
1718853 AGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----
131 AGCACATTGGCA----TCTCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTT
* **
1718914 --C--C-TTTAAGTCCAATA-TCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
192 GTCATCTTTTAAGTCCAA-AGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * * *
1718965 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT---G-----GCA-CCTTTAAGTCCAAAA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGCATCTTTTAAGTCCAATA
* * ** * *
1719021 TCGCTGGCCTTGAATCATCATATTGGTGCCTTTGTCATCTTTTAAGTCCAATGTCGTTGGCCTTG
66 TCGCTAGCCTTGAATCAGCATATTGGCACCTTTG---TC-TTTAAGTCCAATATCGCTGGCCTTG
1719086 AATCAGCACATTGGCACATTCATCTTTAAGTCCAATATCGCTGGCCTT-ACATCAGCATATTGGC
127 AATCAGCACATTGG--CA-TC-TCTTTAAGTCCAATATCGCTGGCCTTGA-ATCAGCATATTGGC
1719150 ATCTTTGTCATCTTTTAAGTCCAAAGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
187 A-CTTTGTCATCTTTTAAGTCCAAAGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
1719212 TTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTG-CATCTTTTAAGTCCAAT
* * * *
1719277 ATCGCTAGCCTTGAATCGGCAAATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAAT
65 ATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCTTGAAT
*
1719342 CAGCACATTGGCA-C-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGT
130 CAGCACATTGGCATCTCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-ACTTTGT
* * *
1719405 CATCTTTTAAGTCCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTCATC
194 CATCTTTTAAGTCCAAAGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
1719459 TTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTG-CATCTTTTAAGTCCAAT
* * * ** *
1719524 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAAT
65 ATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCTTGAAT
*
1719589 CAGCATATTGGC
130 CAGCACATTGGC
1719601 GCCTGTCGTA
Statistics
Matches: 544, Mismatches: 52, Indels: 66
0.82 0.08 0.10
Matches are distributed among these distances:
225 1 0.00
226 1 0.00
227 34 0.06
228 1 0.00
230 1 0.00
233 32 0.06
236 4 0.01
237 74 0.14
239 2 0.00
244 1 0.00
246 2 0.00
247 303 0.56
248 1 0.00
249 1 0.00
250 1 0.00
251 2 0.00
253 37 0.07
254 2 0.00
255 1 0.00
256 2 0.00
257 41 0.08
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (247 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGCATCTTTTAAGTCCAATA
TCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCTTGAATC
AGCACATTGGCATCTCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCA
TCTTTTAAGTCCAAAGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
Found at i:1719459 original size:349 final size:345
Alignment explanation
Indices: 1718729--1719605 Score: 1250
Period size: 349 Copynumber: 2.6 Consensus size: 345
1718719 GGTGGCATCT
* * ** * * * ** * *
1718729 TCTTTTAAGTCTAATATCGCCGGCCTTGAATCAGCATATTGGCGCCTTTGTCTTTAAGACCAATG
1 TCTTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACATTCATCTTTAAGTCCAATA
* *
1718794 TCGCTAGCCTTGAATCAACATATTGGCA-------C--C-TTTAAGTCCAATA-TCGCTGGCCTT
66 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTTAAGTCCAA-AGTCGCTGGCCTT
* ** * * * *
1718848 GAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT---
130 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGC
* *
1718910 G---GCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGA
195 GCCTGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCAAATTGGCACCTTTGTCTTTAAGA
1718972 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAAATCGCTGGCCTTGAATC
260 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAAATCGCTGGCCTTGAATC
* *
1719037 ATCATATTGGTGCCTTTGTCA
325 AGCATATTGGCGCCTTTGTCA
* *
1719058 TCTTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACATTCATCTTTAAGTCCAATA
1 TCTTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACATTCATCTTTAAGTCCAATA
*
1719123 TCGCTGGCCTT-ACATCAGCATATTGGCATCTTTGTCATCTTTTAAGTCCAAAGTCGCTGGCCTT
66 TCGCTGGCCTTGA-ATCAGCATATTGGCACCTTTGTCATCTTTTAAGTCCAAAGTCGCTGGCCTT
1719187 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGC
130 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGC
* *
1719252 GCCTTTGTCATCTTTTAAGTCCAATATCGCTAGCCTTGAATCGGCAAATTGGCACCTTTGTCTTT
195 GCC--TG-CA-CCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCAAATTGGCACCTTTGTCTTT
*
1719317 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTG
256 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAAATCGCTGGCCTTG
1719382 AATCAGCATATTGGCGCCTTTGTCA
321 AATCAGCATATTGGCGCCTTTGTCA
* *
1719407 TCTTTTAAGTCCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATA
1 TCTTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACATTCATCTTTAAGTCCAATA
* * *
1719472 TCGCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTG
66 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTTAAGTCCAAAGTCGCTGGCCTTG
*
1719537 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCG
131 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCG
1719602 CCTG
196 CCTG
1719606 TCGTAACGTG
Statistics
Matches: 489, Mismatches: 36, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
328 1 0.00
329 78 0.16
336 1 0.00
338 2 0.00
339 77 0.16
342 1 0.00
347 3 0.01
348 2 0.00
349 323 0.66
350 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (345 bp):
TCTTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACATTCATCTTTAAGTCCAATA
TCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTTAAGTCCAAAGTCGCTGGCCTTG
AATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCG
CCTGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCAAATTGGCACCTTTGTCTTTAAGAC
CAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAAATCGCTGGCCTTGAATCA
GCATATTGGCGCCTTTGTCA
Found at i:1723263 original size:53 final size:53
Alignment explanation
Indices: 1723184--1723742 Score: 747
Period size: 53 Copynumber: 11.0 Consensus size: 53
1723174 AGTGTCTACA
*
1723184 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTA
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
* *
1723237 GCGCCTTTGTCATCTTTTAAGTCCAATATCGCTGGCCTTGAATCGGCATATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
* ** *
1723290 GCACCTTTG---TC-TTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATT-
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
* * *
1723338 --G-----G-CA-CCTTTAAGTCCAATATCGCCGGCCTTGAATCAGCATATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
*
1723382 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
* *
1723435 GCACC--TG-CATC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
*
1723484 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
* *
1723537 GCACC--T-TCATC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
* *
1723586 GCGCCTTTGTCATCTTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
* *
1723639 GCACC--T-TCATC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
*
1723688 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
1723741 GC
1 GC
1723743 ACTTTCATCT
Statistics
Matches: 442, Mismatches: 39, Indels: 50
0.83 0.07 0.09
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 32 0.07
46 1 0.00
49 151 0.34
50 16 0.04
51 9 0.02
52 16 0.04
53 215 0.49
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (53 bp):
GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
Found at i:1723487 original size:102 final size:102
Alignment explanation
Indices: 1723184--1723756 Score: 941
Period size: 102 Copynumber: 5.7 Consensus size: 102
1723174 AGTGTCTACA
* * *
1723184 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGCGCCTTTGTCA
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCA
*
1723249 TCTTTTAAGTCCAATATCGCTGGCCTTGAATCGGCATATTG
63 TC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
* **
1723290 GCACCTTTG---TC-TTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CT
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
*
1723345 TTAAGTCCAATATCGCCGGCCTTGAATCAGCATATTG
66 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
*
1723382 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTGCATCT
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1723447 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
66 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1723484 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1723549 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
66 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
*
1723586 GCGCCTTTGTCATCTTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1723651 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
66 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
*
1723688 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCT
1 GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1723753 TTAA
66 TTAA
1723757 CATTCCTAAG
Statistics
Matches: 441, Mismatches: 16, Indels: 24
0.92 0.03 0.05
Matches are distributed among these distances:
92 44 0.10
93 1 0.00
95 3 0.01
96 39 0.09
100 1 0.00
102 343 0.78
103 2 0.00
106 8 0.02
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.34
Consensus pattern (102 bp):
GCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
Found at i:1724597 original size:13 final size:13
Alignment explanation
Indices: 1724579--1724635 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1724569 TTCAACGATT
1724579 TGTATCGATACAA
1 TGTATCGATACAA
1724592 TGTATCGATACATAA
1 TGTATCGATAC--AA
1724607 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1724624 TGTATCGATACA
1 TGTATCGATACA
1724636 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1724616 original size:19 final size:18
Alignment explanation
Indices: 1724592--1724654 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1724582 ATCGATACAA
1724592 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1724611 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1724624 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1724643 TGTATCGATACA
1 TGTATCGATACA
1724655 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1724619 original size:32 final size:32
Alignment explanation
Indices: 1724578--1724662 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
1724568 TTTCAACGAT
1724578 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
1724610 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
1724642 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
1724663 CTACGAAGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:1727740 original size:27 final size:27
Alignment explanation
Indices: 1727708--1727763 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1727698 AAAATTAAAA
1727708 TTAG-AAT-AAATAATCATAAACAAAATC
1 TTAGAAATGAAATAATCA-AAA-AAAATC
*
1727735 TTAGAAATGAAATAATGAAAAAAAATC
1 TTAGAAATGAAATAATCAAAAAAAATC
1727762 TT
1 TT
1727764 GATTAGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 12 0.46
28 6 0.23
29 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (27 bp):
TTAGAAATGAAATAATCAAAAAAAATC
Found at i:1727806 original size:15 final size:16
Alignment explanation
Indices: 1727784--1727819 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1727774 CCAAAACTAT
1727784 AAAA-TCTTATA-AGA
1 AAAATTCTTATAGAGA
1727798 AAAATTCTTATAGAGA
1 AAAATTCTTATAGAGA
1727814 AAAATT
1 AAAATT
1727820 AATATATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 9 0.45
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (16 bp):
AAAATTCTTATAGAGA
Found at i:1730633 original size:99 final size:95
Alignment explanation
Indices: 1730466--1730656 Score: 285
Period size: 99 Copynumber: 2.0 Consensus size: 95
1730456 AATTCTTTCG
* * *
1730466 GGATTCAATTTTGGCTATCTTAAATACTGAAAATTTGAAAAAGAAAATTGTTATAGCATCTTTTC
1 GGATTCAATTTTGGCAACCTTAAATACTGAAAATTTGAAAAAAAAAATTGTTATAGCATCTTTTC
*
1730531 TGAAATATTACCTCATCATAGACATCACAA
66 TGAAACATTACCTCATCATAGACATCACAA
1730561 GGATTCAATTTTGGCAACCTTAAATACTGAAAATAAAAATT-AAAAAAAAAATTGTTATAGCATC
1 GGATTCAATTTTGGCAACCTTAAATACTGAAAAT-----TTGAAAAAAAAAATTGTTATAGCATC
*
1730625 TTTTCTGAAACATTACCTCATTATAGACATCA
61 TTTTCTGAAACATTACCTCATCATAGACATCA
1730657 TAATTTGTAT
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
95 32 0.37
99 52 0.60
100 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (95 bp):
GGATTCAATTTTGGCAACCTTAAATACTGAAAATTTGAAAAAAAAAATTGTTATAGCATCTTTTC
TGAAACATTACCTCATCATAGACATCACAA
Found at i:1731635 original size:49 final size:49
Alignment explanation
Indices: 1731578--1731677 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
1731568 TTTGTATTTA
1731578 AACTTGACCTAAAATTGCTATCTTCTTCTCAATACTAAAAGTAATAAAT
1 AACTTGACCTAAAATTGCTATCTTCTTCTCAATACTAAAAGTAATAAAT
1731627 AACTTGACCTAAAATTGCTATCTTCTTCTCAATACTAAAAGTAATAAAT
1 AACTTGACCTAAAATTGCTATCTTCTTCTCAATACTAAAAGTAATAAAT
1731676 AA
1 AA
1731678 TACATATTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (49 bp):
AACTTGACCTAAAATTGCTATCTTCTTCTCAATACTAAAAGTAATAAAT
Found at i:1745916 original size:16 final size:16
Alignment explanation
Indices: 1745890--1745931 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1745880 ATTTTTAAAT
*
1745890 TTAAA-AAATATT-TT
1 TTAAATAAATATTATA
1745904 TTAAAATAAATATTATA
1 TT-AAATAAATATTATA
1745921 TTAAATAAATA
1 TTAAATAAATA
1745932 AAATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 16 0.67
17 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAATAAATATTATA
Found at i:1746060 original size:24 final size:23
Alignment explanation
Indices: 1746033--1746087 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1746023 TGAATGAACT
* *
1746033 AATTTTATTATCTTTATATATTTA
1 AATTTTATTAT-TTTAAATATATA
1746057 AATTTTTATTATTTTAAATATATA
1 AA-TTTTATTATTTTAAATATATA
1746081 ATATTTT
1 A-ATTTT
1746088 CACATTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTTTATTATTTTAAATATATA
Found at i:1746063 original size:25 final size:25
Alignment explanation
Indices: 1746035--1746087 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1746025 AATGAACTAA
* *
1746035 TTTTATTATCTTTATATATTTAA-AT
1 TTTTATTAT-TTTAAATATATAATAT
1746060 TTTTATTATTTTAAATATATAATAT
1 TTTTATTATTTTAAATATATAATAT
1746085 TTT
1 TTT
1746088 CACATTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTTATTATTTTAAATATATAATAT
Found at i:1748715 original size:141 final size:141
Alignment explanation
Indices: 1748556--1749133 Score: 525
Period size: 141 Copynumber: 3.9 Consensus size: 141
1748546 TGTAAATTTT
*
1748556 AAAAATCTCATTTCGTACCTTAATGGAGAACCGAAAAGGTACGAAAAGTTTTGAAGATTTCTATA
1 AAAAAT-TCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATA
* * * *
1748621 CTCCTATAGAAAACTATAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTCTATTTAAT
65 CCCCTACAGAAAACTATAAGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTCTATTTAAT
1748686 TTTTAATTTTCA
130 TTTTAATTTTCA
* ** * *
1748698 AAAAATTCATTTCGTACCTTAATAGAGAATTGAAAAGATATGAAAGGTTTTGAAGATTTCTATAC
1 AAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATAC
* * *
1748763 CCCTACAGAAAA-TCATAGGAATATTAGAAATCTTGAAAAATGAAGATAATAATTTTTATTTAAT
66 CCCTACAGAAAACT-ATAAGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTCTATTTAAT
*
1748827 TTTTAATTTCCA
130 TTTTAATTTTCA
* * *** * * *
1748839 AAATATTCATTTCGTTAATTTCCAAAATATTCATTTTGTACCTTAATGGAGA-ACTGAAAAGATA
1 AAAAATTCATTTCG-T-A---CC------TTAATGGAGAACC-GAA--AAGATAC-G--A-----
* * * * *
1748903 TAAAAAGTTTTAAAGATTTTTATACCTCTACAAAAAACTATAAGAATATTAGAAATCTTGAATAA
44 ---AAAGTTTTGAAGATTTCTATACCCCTACAGAAAACTATAAGAATATTAGAAATCTTGAAAAA
*
1748968 TTAAGAT-ATGAATTTCTACTTAAATTTTTTTAATTTTCA
106 TTAAGATAAT-AATTTCTA-TTTAA--TTTTTAATTTTCA
* *
1749007 AAAAATTCATTTCTTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAATATTTCTATAC
1 AAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATAC
* * * * *
1749072 CCCTAC-GAAAAACCATAAAAATATTAGAAATCTTGAATAATTAAGAAAATAATTTTTATTTA
66 CCCTACAG-AAAACTATAAGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTCTATTTA
1749134 GTGATAAAAC
Statistics
Matches: 349, Mismatches: 53, Indels: 67
0.74 0.11 0.14
Matches are distributed among these distances:
140 1 0.00
141 134 0.38
142 7 0.02
143 4 0.01
144 67 0.19
145 2 0.01
146 2 0.01
152 7 0.02
153 2 0.01
154 5 0.01
155 6 0.02
156 2 0.01
157 9 0.03
163 2 0.01
164 2 0.01
165 66 0.19
166 6 0.02
167 1 0.00
168 24 0.07
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (141 bp):
AAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATAC
CCCTACAGAAAACTATAAGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTCTATTTAATT
TTTAATTTTCA
Found at i:1748856 original size:24 final size:24
Alignment explanation
Indices: 1748829--1748874 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1748819 TATTTAATTT
1748829 TTAATTTCCAAAATATTCATTTCG
1 TTAATTTCCAAAATATTCATTTCG
1748853 TTAATTTCCAAAATATTCATTT
1 TTAATTTCCAAAATATTCATTT
1748875 TGTACCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (24 bp):
TTAATTTCCAAAATATTCATTTCG
Found at i:1748960 original size:165 final size:167
Alignment explanation
Indices: 1748688--1749019 Score: 447
Period size: 165 Copynumber: 2.0 Consensus size: 167
1748678 TATTTAATTT
* * * * *
1748688 TTAATTTTCAAAAAATTCATTTCGTACCTTAATAGAGAATTGAAAAGATATGAAAGGTTTTGAAG
1 TTAATTTCCAAAAAATTCATTTCGTACCTTAATAGAGAACTGAAAAGATATAAAAAGTTTTAAAG
* *
1748753 ATTTCTATACCCCTACAGAAAATCATAGGAATATTAGAAATCTTGAAAAATGAAGATAAT-AATT
66 ATTTCTATACCCCTACAAAAAATCATAAGAATATTAGAAATCTTGAAAAATGAAGAT-ATGAATT
* * *
1748817 TTTA-TTTAA-TTTTTAATTTCCAAAATATTCATTTCG
130 TCTACTTAAATTTTTTAATTTCCAAAAAATTCATTTCG
* * *
1748853 TTAATTTCCAAAATATTCATTTTGTACCTTAATGGAGAACTGAAAAGATATAAAAAGTTTTAAAG
1 TTAATTTCCAAAAAATTCATTTCGTACCTTAATAGAGAACTGAAAAGATATAAAAAGTTTTAAAG
* * * *
1748918 ATTTTTATACCTCTACAAAAAA-CTATAAGAATATTAGAAATCTTGAATAATTAAGATATGAATT
66 ATTTCTATACCCCTACAAAAAATC-ATAAGAATATTAGAAATCTTGAAAAATGAAGATATGAATT
*
1748982 TCTACTTAAATTTTTTTAATTTTCAAAAAATTCATTTC
130 TCTACTTAAA-TTTTTTAATTTCCAAAAAATTCATTTC
1749020 TTACCTTAAT
Statistics
Matches: 144, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
164 3 0.02
165 113 0.78
166 4 0.03
168 24 0.17
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (167 bp):
TTAATTTCCAAAAAATTCATTTCGTACCTTAATAGAGAACTGAAAAGATATAAAAAGTTTTAAAG
ATTTCTATACCCCTACAAAAAATCATAAGAATATTAGAAATCTTGAAAAATGAAGATATGAATTT
CTACTTAAATTTTTTAATTTCCAAAAAATTCATTTCG
Found at i:1749113 original size:144 final size:144
Alignment explanation
Indices: 1748853--1749117 Score: 406
Period size: 144 Copynumber: 1.8 Consensus size: 144
1748843 ATTCATTTCG
* * *
1748853 TTAATTTCCAAAATATTCATTTTGTACCTTAATGGAGAACTGAAAAGATATAAAAAGTTTTAAAG
1 TTAATTTCCAAAAAATTCATTTTGTACCTTAATGGAGAACCGAAAAGATACAAAAAGTTTTAAAG
* * * *
1748918 ATTTTTATACCTCTACAAAAAACTATAAGAATATTAGAAATCTTGAATAATTAAGATATGAATTT
66 ATTTCTATACCCCTACAAAAAACCATAAAAATATTAGAAATCTTGAATAATTAAGATATGAATTT
1748983 CTACTTAAATTTTT
131 CTACTTAAATTTTT
* * *
1748997 TTAATTTTCAAAAAATTCATTTCT-TACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAA
1 TTAATTTCCAAAAAATTCATTT-TGTACCTTAATGGAGAACCGAAAAGATACAAAAAGTTTTAAA
* *
1749061 TATTTCTATACCCCTACGAAAAACCATAAAAATATTAGAAATCTTGAATAATTAAGA
65 GATTTCTATACCCCTACAAAAAACCATAAAAATATTAGAAATCTTGAATAATTAAGA
1749118 AAATAATTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
144 107 0.99
145 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (144 bp):
TTAATTTCCAAAAAATTCATTTTGTACCTTAATGGAGAACCGAAAAGATACAAAAAGTTTTAAAG
ATTTCTATACCCCTACAAAAAACCATAAAAATATTAGAAATCTTGAATAATTAAGATATGAATTT
CTACTTAAATTTTT
Found at i:1749126 original size:309 final size:306
Alignment explanation
Indices: 1748563--1749133 Score: 833
Period size: 309 Copynumber: 1.9 Consensus size: 306
1748553 TTTAAAAATC
* * * *
1748563 TCATTTCGTACCTTAATGGAGAACCGAAAAGGTACGAAAAGTTTTGAAGATTTCTATACTCCTAT
1 TCATTTCGTACCTTAATGGAGAACCGAAAAGATACAAAAAGTTTTAAAGATTTCTATACTCCTAC
* * *
1748628 AGAAAACTATAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTCTATTTAATTTTTAAT
66 AAAAAACTATAAGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTCTATTAAATTTTTAAT
** * *
1748693 TTTCAAAAAATTCATTTCGTACCTTAATAGAGAATTGAAAAGATATGAAAGGTTTTGAAGATTTC
131 TTTCAAAAAATTCATTTCGTACCTTAATAGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTC
* ** *
1748758 TATACCCCTACAGAAAATCATAGGAATATTAGAAATCTTGAAAAATGAAGATAATAATTTTTATT
196 TATACCCCTACAGAAAACCATAAAAATATTAGAAATCTTGAAAAATGAAGAAAATAATTTTTATT
1748823 TAATTTTTAATTTCCAAAATATTCATTTCGTTAATTTCCAAAATAT
261 TAATTTTTAATTTCCAAAATATTCATTTCGTTAATTTCCAAAATAT
* * * *
1748869 TCATTTTGTACCTTAATGGAGAACTGAAAAGATATAAAAAGTTTTAAAGATTTTTATAC-CTCTA
1 TCATTTCGTACCTTAATGGAGAACCGAAAAGATACAAAAAGTTTTAAAGATTTCTATACTC-CTA
* *
1748933 CAAAAAACTATAAGAATATTAGAAATCTTGAATAATTAAGAT-ATGAATTTCTACTTAAATTTTT
65 CAAAAAACTATAAGAATATTAAAAATCTTGAAAAATTAAGATAAT-AATTTCTA-TTAAA--TTT
* * *
1748997 TTAATTTTCAAAAAATTCATTTCTTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAT
126 TTAATTTTCAAAAAATTCATTTCGTACCTTAATAGAGAACCGAAAAGATACGAAAAGTTTTGAAG
* *
1749062 ATTTCTATACCCCTAC-GAAAAACCATAAAAATATTAGAAATCTTGAATAATTAAGAAAATAATT
191 ATTTCTATACCCCTACAG-AAAACCATAAAAATATTAGAAATCTTGAAAAATGAAGAAAATAATT
1749126 TTTATTTA
255 TTTATTTA
1749134 GTGATAAAAC
Statistics
Matches: 233, Mismatches: 26, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
305 3 0.01
306 100 0.43
307 4 0.02
308 1 0.00
309 125 0.54
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (306 bp):
TCATTTCGTACCTTAATGGAGAACCGAAAAGATACAAAAAGTTTTAAAGATTTCTATACTCCTAC
AAAAAACTATAAGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTCTATTAAATTTTTAAT
TTTCAAAAAATTCATTTCGTACCTTAATAGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTC
TATACCCCTACAGAAAACCATAAAAATATTAGAAATCTTGAAAAATGAAGAAAATAATTTTTATT
TAATTTTTAATTTCCAAAATATTCATTTCGTTAATTTCCAAAATAT
Found at i:1750941 original size:166 final size:167
Alignment explanation
Indices: 1750569--1750987 Score: 501
Period size: 166 Copynumber: 2.5 Consensus size: 167
1750559 CAAAATTCAT
* ** * * * *
1750569 AAAATAAATTG-AATTTCTAAAAATTGATTTAATGGGAGTTCAATGACAATATTAT-ATGAATTT
1 AAAATAAA-TGAAATTT-T-AAAACTGATTTAATATGAGTTAAATAATAATATT-TGATGAATAT
* * *
1750632 TAAAAATTTTAAACCGAGAAAAATCCCCCCTTAAAACCTTTATAGAATAGAAAACTTAGTTTCAC
62 TAAAAATTTCAAACCAAGAAAAATCCCCCCTTAAAACCTTTATAGAATAGAAAACTCAGTTTCAC
**
1750697 CGAAATAGAAAAATTTCAAGGAAAAAAATGAAAAATTCATG
127 CGAAATAGAAAAATTTCAAGGAAAAAAATGAAAAACACATG
* *
1750738 AAAATAAATAAAAGTTTTAAAACTGATTTATTATGAGTTAAATAATAATATTTGATGAATATTAA
1 AAAATAAATGAAA-TTTTAAAACTGATTTAATATGAGTTAAATAATAATATTTGATGAATATTAA
** * * *
1750803 AAATTTCAAACCAAGAAACCTCCCCCC-TAAAACCTTTATGGAATAGAAAACTCAGTTTTTA-GG
65 AAATTTCAAACCAAGAAAAATCCCCCCTTAAAACCTTTATAGAATAGAAAACTCAG-TTTCACCG
*
1750866 AAATA-ATAAAATTTTAAGG-AAAAAATGAAAAACACATG
129 AAATAGA-AAAATTTCAAGGAAAAAAATGAAAAACACATG
*
1750904 AAAATAAATGAAATTTTCAAAACTGATTTAATATGAGTTAAATAATAATATTTGATGAACATT-A
1 AAAATAAATGAAATTTT-AAAACTGATTTAATATGAGTTAAATAATAATATTTGATGAATATTAA
**
1750968 AAATTTTGAACCAATGAAAA
65 AAATTTCAAACCAA-GAAAA
1750988 TCCTCTTAAA
Statistics
Matches: 217, Mismatches: 26, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
165 17 0.08
166 77 0.35
167 44 0.20
168 65 0.30
169 11 0.05
170 3 0.01
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (167 bp):
AAAATAAATGAAATTTTAAAACTGATTTAATATGAGTTAAATAATAATATTTGATGAATATTAAA
AATTTCAAACCAAGAAAAATCCCCCCTTAAAACCTTTATAGAATAGAAAACTCAGTTTCACCGAA
ATAGAAAAATTTCAAGGAAAAAAATGAAAAACACATG
Found at i:1751791 original size:13 final size:13
Alignment explanation
Indices: 1751773--1751799 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1751763 ACATCATGCT
1751773 TTGTATCGATACA
1 TTGTATCGATACA
1751786 TTGTATCGATACA
1 TTGTATCGATACA
1751799 T
1 T
1751800 GTTCATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1751808 original size:19 final size:19
Alignment explanation
Indices: 1751784--1751839 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1751774 TGTATCGATA
*
1751784 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
* *
1751803 CATTGTTTCGATACATACT
1 CATTGTATCGATACATGCT
1751822 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1751840 AAAGTGACAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:1756253 original size:22 final size:22
Alignment explanation
Indices: 1756221--1756273 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1756211 TGTGGGAGCT
*
1756221 GAGCTGCTGGAGGCTACCGTGG
1 GAGCTGTTGGAGGCTACCGTGG
1756243 GAGCTGTTGGAGGCTACCGTGG
1 GAGCTGTTGGAGGCTACCGTGG
*
1756265 AAGCTGTTG
1 GAGCTGTTG
1756274 AAGCTGTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.15, C:0.19, G:0.43, T:0.23
Consensus pattern (22 bp):
GAGCTGTTGGAGGCTACCGTGG
Found at i:1756348 original size:22 final size:22
Alignment explanation
Indices: 1756314--1756373 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
1756304 CATGGTTGTT
* *
1756314 GAGCTGTTGGAGGCTACCGTGG
1 GAGCTGCTGGAGGCTACCGTAG
* *
1756336 GAGCTGCTAGAGGCTATCGTAG
1 GAGCTGCTGGAGGCTACCGTAG
*
1756358 AAGCTGCTGGA-GCTAC
1 GAGCTGCTGGAGGCTAC
1756374 TGGAAGTTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (22 bp):
GAGCTGCTGGAGGCTACCGTAG
Found at i:1756390 original size:18 final size:19
Alignment explanation
Indices: 1756357--1756395 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1756347 GGCTATCGTA
1756357 GAAGCTGCTGGAGCTACTG
1 GAAGCTGCTGGAGCTACTG
*
1756376 GAAGTTGCT-GAGCTACTG
1 GAAGCTGCTGGAGCTACTG
1756394 GA
1 GA
1756396 GGCTACAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (19 bp):
GAAGCTGCTGGAGCTACTG
Found at i:1757063 original size:43 final size:41
Alignment explanation
Indices: 1756985--1757067 Score: 103
Period size: 43 Copynumber: 2.0 Consensus size: 41
1756975 CCAATTTCAT
* * * * *
1756985 GCATGAATGCATGCATTGCCACCTTATTGATTTAGGTGGCA
1 GCATGAATGCATGCAATGCCACCTAAATCAATTAGGTGGCA
1757026 GCATGCAATGCAATGCAATGCCACCTAAATCAATTAGGTGGC
1 GCATG-AATGC-ATGCAATGCCACCTAAATCAATTAGGTGGC
1757068 TACAAATCGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 5 0.14
42 5 0.14
43 25 0.71
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (41 bp):
GCATGAATGCATGCAATGCCACCTAAATCAATTAGGTGGCA
Found at i:1757157 original size:7 final size:7
Alignment explanation
Indices: 1757111--1757141 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1757101 AAATTAATTT
1757111 TTTTTTA
1 TTTTTTA
1757118 TTTTTTA
1 TTTTTTA
1757125 TTTTTTA
1 TTTTTTA
*
1757132 TTTTTAA
1 TTTTTTA
1757139 TTT
1 TTT
1757142 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:1760666 original size:34 final size:35
Alignment explanation
Indices: 1760628--1760694 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1760618 CCTTACAACA
1760628 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1760662 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1760695 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1761181 original size:13 final size:13
Alignment explanation
Indices: 1761163--1761202 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1761153 TACTATTTAT
1761163 AGTGTATCGATAC
1 AGTGTATCGATAC
1761176 AGTGTATCGATAC
1 AGTGTATCGATAC
*
1761189 AATGTATCGATAC
1 AGTGTATCGATAC
1761202 A
1 A
1761203 TGAATAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (13 bp):
AGTGTATCGATAC
Found at i:1763849 original size:17 final size:17
Alignment explanation
Indices: 1763827--1763861 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1763817 TTCATTTTGA
1763827 CTAGTTTAAGTTGGCAT
1 CTAGTTTAAGTTGGCAT
*
1763844 CTAGTTTAGGTTGGCAT
1 CTAGTTTAAGTTGGCAT
1763861 C
1 C
1763862 CAATTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (17 bp):
CTAGTTTAAGTTGGCAT
Found at i:1764147 original size:12 final size:12
Alignment explanation
Indices: 1764139--1764171 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1764129 TAAAAAAGAG
1764139 GAGAA-AAAAAA
1 GAGAAGAAAAAA
1764150 GAGAAAGAAAAAA
1 GAG-AAGAAAAAA
1764163 GAGAAGAAA
1 GAGAAGAAA
1764172 TAGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 8 0.40
13 9 0.45
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
GAGAAGAAAAAA
Found at i:1764189 original size:27 final size:27
Alignment explanation
Indices: 1764130--1764188 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
1764120 AGGTTCAACT
*
1764130 AAAAAAGAGGAGAAAAAAAAGAGAAAG
1 AAAAAAGAGAAGAAAAAAAAGAGAAAG
*
1764157 AAAAAAGAGAAGAAATAGAAA-A-AAAG
1 AAAAAAGAGAAGAAA-AAAAAGAGAAAG
1764183 AAAAAA
1 AAAAAA
1764189 AAAATAAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 10 0.34
27 15 0.52
28 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (27 bp):
AAAAAAGAGAAGAAAAAAAAGAGAAAG
Found at i:1767394 original size:61 final size:61
Alignment explanation
Indices: 1767244--1767386 Score: 250
Period size: 61 Copynumber: 2.3 Consensus size: 61
1767234 GCTATGTGCC
*
1767244 TTCGTGAGTAACTCTCCGCATAGGCATAGTAATAACTTCCATGATGTAAATTACCTATGCT
1 TTCGTGAGTAACCCTCCGCATAGGCATAGTAATAACTTCCATGATGTAAATTACCTATGCT
* *
1767305 CTCATGAGTAACCCTCCGCATAGGCATAGTAATAACTTCCATGATGTAAATTACCTATGCT
1 TTCGTGAGTAACCCTCCGCATAGGCATAGTAATAACTTCCATGATGTAAATTACCTATGCT
*
1767366 TTCGTGAGTAACCCTCTGCAT
1 TTCGTGAGTAACCCTCCGCAT
1767387 TTCCATAGGG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 76 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (61 bp):
TTCGTGAGTAACCCTCCGCATAGGCATAGTAATAACTTCCATGATGTAAATTACCTATGCT
Found at i:1770847 original size:22 final size:23
Alignment explanation
Indices: 1770813--1770876 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 23
1770803 TCAAAATGAC
* * *
1770813 AAAAAAGTTAAAAGGAAAAGCAT
1 AAAAAAGTGAAAAGGAAAAACAA
1770836 AAAAAA-TGAAAA-GAAAAACAA
1 AAAAAAGTGAAAAGGAAAAACAA
*
1770857 AAAAAAGTGCAAAAGCAAAA
1 AAAAAAGTG-AAAAGGAAAA
1770877 TAAAAAGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 13 0.38
22 7 0.21
23 10 0.29
24 4 0.12
ACGTcount: A:0.72, C:0.06, G:0.14, T:0.08
Consensus pattern (23 bp):
AAAAAAGTGAAAAGGAAAAACAA
Found at i:1770870 original size:23 final size:22
Alignment explanation
Indices: 1770813--1770882 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
1770803 TCAAAATGAC
* * *
1770813 AAAAAAGTTAAAAGGAAAAGCAT
1 AAAAAAGTGAAAA-GAAAAACAA
1770836 AAAAAA-TGAAAAGAAAAACAA
1 AAAAAAGTGAAAAGAAAAACAA
* *
1770857 AAAAAAGTGCAAAAGCAAAATAA
1 AAAAAAGTG-AAAAGAAAAACAA
1770880 AAA
1 AAA
1770883 GGGAACAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 13 0.32
22 7 0.17
23 20 0.50
ACGTcount: A:0.73, C:0.06, G:0.13, T:0.09
Consensus pattern (22 bp):
AAAAAAGTGAAAAGAAAAACAA
Found at i:1772391 original size:82 final size:82
Alignment explanation
Indices: 1772223--1772848 Score: 800
Period size: 82 Copynumber: 7.7 Consensus size: 82
1772213 CAGCGGCATT
* * *
1772223 CCTTTTAAAGTCCACAAGTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGT
* *
1772288 CCACAAGTCTGTGGCAT
66 CCACAACTCTGTGGCAC
* * * *
1772305 CCTTTT-AAGTCCACAACTCCGTGGCATCTTTTTAAGTCCACAAGTTCGTGGTACCCTTTTAAAG
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCCTTTT-AAG
1772369 TCCACAACTCTGTGGCAC
65 TCCACAACTCTGTGGCAC
* * * *
1772387 CCTTTT-AAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAAGTCCGTGGCATCCTTTTAAGT
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGT
* * *
1772451 CCACAAGTCCGCGG-AC
66 CCACAACTCTGTGGCAC
* *
1772467 CCTTTTAAAGTCCACAACTCCG-GGACACCCTTTTAAAGTTCACAACTTCGTGGAACCCTTTTAA
1 CCTTTTAAAGTCCACAACTCCGTGG-CACCCTTTT-AAGTCCACAACTTCGTGGCACCCTTTTAA
* *
1772531 ATCCATAACTCTGTGGCAC
64 GTCCACAACTCTGTGGCAC
* * * * * * *
1772550 CTTTTTAAAGTCCATAACTCTGTGGCACCCTTTTAAGTCCACAAGTCCGTGGCATCGTTTTAAGT
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGT
* *
1772615 TCATAACTCTGTGGCAC
66 CCACAACTCTGTGGCAC
* *
1772632 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTTTGTGGCACCCTTTTAAGT
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAG-
*
1772697 TCC-C-ACGTCTGTGGCAT
65 TCCACAAC-TCTGTGGCAC
*
1772714 CCTTTT-AAGTCCACAAGTCCGTGGCACCCTTTTAAAGTCCACAACTTCGTGGCACCCTTTTAAG
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTTCGTGGCACCCTTTTAAG
*
1772778 TCCACAACTCTGTGGTAC
65 TCCACAACTCTGTGGCAC
* * * *
1772796 CCTTTT-AAGTCCACAACTCCGTGGCATCCTTTTATGACCACAACTCCGTGGCA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCA
1772849 TTCTACAAAT
Statistics
Matches: 473, Mismatches: 60, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
80 10 0.02
81 135 0.29
82 292 0.62
83 34 0.07
84 2 0.00
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (82 bp):
CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGT
CCACAACTCTGTGGCAC
Found at i:1772393 original size:109 final size:108
Alignment explanation
Indices: 1772223--1772848 Score: 733
Period size: 109 Copynumber: 5.7 Consensus size: 108
1772213 CAGCGGCATT
* *
1772223 CCTTTTAAAGTCCACAAGTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CCTTTT-AAGTCCACAAGTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* * * *
1772288 CCACAAGTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAT
65 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCAC
* * *
1772332 CTTTTTAAGTCCACAAGTTCGTGGTACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGT
1 CCTTTTAAGTCCACAAGTTCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGT
* * *
1772397 CCACAACTCCATGGCACCCTTTTAAGTCCACAAGTCCGTGGCAT
65 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCAC
* *
1772441 CCTTTTAAGTCCACAAGTCCGCGG-ACCCTTTTAAAGTCCACAACTCCG-GGACACCCTTTTAAA
1 CCTTTTAAGTCCACAAGTTCGTGGCACCCTTTT-AAGTCCACAACTCCGTGG-CACCCTTTT-AA
* * * * * *
1772504 GTTCACAACTTCGTGGAACCCTTTTAAATCCATAACTCTGTGGCAC
63 GTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCAC
* * * * * *
1772550 CTTTTTAAAGTCCATAA-CTCTGTGGCACCCTTTTAAGTCCACAAGTCCGTGGCATCGTTTTAAG
1 CCTTTT-AAGTCCACAAGTTC-GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
* * *
1772614 TTCATAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCAC
64 TCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCAC
* * * * *
1772660 CCTTTTAAGTCCATAACTTTGTGGCACCCTTTTAAGTTCC-C-ACGTCTGTGGCATCCTTTTAAG
1 CCTTTTAAGTCCACAAGTTCGTGGCACCCTTTTAAG-TCCACAAC-TCCGTGGCACCCTTTTAAG
* *
1772723 TCCACAAGTCCGTGGCACCCTTTTAAAGTCCACAACTTCGTGGCAC
64 TCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCAC
* * * * *
1772769 CCTTTTAAGTCCACAA-CTCTGTGGTACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTATGA
1 CCTTTTAAGTCCACAAGTTC-GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1772833 CCACAACTCCGTGGCA
65 CCACAACTCCGTGGCA
1772849 TTCTACAAAT
Statistics
Matches: 446, Mismatches: 57, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
107 2 0.00
108 61 0.14
109 311 0.70
110 62 0.14
111 10 0.02
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (108 bp):
CCTTTTAAGTCCACAAGTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:1772849 original size:27 final size:27
Alignment explanation
Indices: 1772223--1772848 Score: 747
Period size: 27 Copynumber: 23.0 Consensus size: 27
1772213 CAGCGGCATT
* *
1772223 CCTTTTAAAGTCCACAAGTCCGTGGCAT
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
1772251 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* * *
1772278 CCTTTTAAGTCCACAAGTCTGTGGCAT
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1772305 CCTTTTAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* * * *
1772332 CTTTTTAAGTCCACAAGTTCGTGGTAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1772359 CCTTTTAAAGTCCACAACTCTGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
1772387 CCTTTTAAGTCCACAACTCCATGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
1772414 CCTTTTAAGTCCACAAGTCCGTGGCAT
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
1772441 CCTTTTAAGTCCACAAGTCCGCGG-AC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1772467 CCTTTTAAAGTCCACAACTCCG-GGACAC
1 CCTTTT-AAGTCCACAACTCCGTGG-CAC
* * *
1772495 CCTTTTAAAGTTCACAACTTCGTGGAAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* * *
1772523 CCTTTTAAATCCATAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* * *
1772550 CTTTTTAAAGTCCATAACTCTGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1772578 CCTTTTAAGTCCACAAGTCCGTGGCAT
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* * * *
1772605 CGTTTTAAGTTCATAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1772632 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* **
1772660 CCTTTTAAGTCCATAACTTTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
1772687 CCTTTTAAGTTCC-C-ACGTCTGTGGCAT
1 CCTTTTAAG-TCCACAAC-TCCGTGGCAC
*
1772714 CCTTTTAAGTCCACAAGTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1772741 CCTTTTAAAGTCCACAACTTCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1772769 CCTTTTAAGTCCACAACTCTGTGGTAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1772796 CCTTTTAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
1772823 CCTTTTATGACCACAACTCCGTGGCA
1 CCTTTTAAGTCCACAACTCCGTGGCA
1772849 TTCTACAAAT
Statistics
Matches: 516, Mismatches: 70, Indels: 25
0.84 0.11 0.04
Matches are distributed among these distances:
26 14 0.03
27 363 0.70
28 137 0.27
29 2 0.00
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:1779458 original size:13 final size:13
Alignment explanation
Indices: 1779440--1779465 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1779430 CAATTTTTTG
1779440 TGTATCGATACAT
1 TGTATCGATACAT
1779453 TGTATCGATACAT
1 TGTATCGATACAT
1779466 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1779530 original size:21 final size:21
Alignment explanation
Indices: 1779504--1779579 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1779494 CTGCCAAGAA
*
1779504 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1779525 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1779545 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1779566 ATGTATCGATACAT
1 ATGTATCGATACAT
1779580 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1779550 original size:20 final size:20
Alignment explanation
Indices: 1779525--1779597 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1779515 CATCTTTTTT
1779525 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1779545 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1779566 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1779586 ATGTATCGATAC
1 ATGTATCGATAC
1779598 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1779561 original size:41 final size:41
Alignment explanation
Indices: 1779504--1779597 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1779494 CTGCCAAGAA
*
1779504 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1779545 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1779586 ATGTATCGATAC
1 ATGTATCGATAC
1779598 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1780226 original size:36 final size:36
Alignment explanation
Indices: 1780183--1780255 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1780173 ATAAGGTAAT
1780183 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
1 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
1780219 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
1 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
1780255 T
1 T
1780256 AAATCTCCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.16, C:0.36, G:0.05, T:0.42
Consensus pattern (36 bp):
TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
Found at i:1782094 original size:13 final size:13
Alignment explanation
Indices: 1782076--1782114 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1782066 ATAATCACCC
*
1782076 TGTATCGATACAG
1 TGTATCGATACAA
1782089 TGTATCGATACAA
1 TGTATCGATACAA
1782102 TGTATCGATACAA
1 TGTATCGATACAA
1782115 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1782125 original size:20 final size:20
Alignment explanation
Indices: 1782100--1782178 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1782090 GTATCGATAC
1782100 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
1782120 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
1782145 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
1782164 ACATGTATCGATACA
1 A-ATGTATCGATACA
1782179 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:1784213 original size:15 final size:15
Alignment explanation
Indices: 1784193--1784223 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1784183 ATTTCGTTTG
*
1784193 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1784208 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1784223 G
1 G
1784224 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1788303 original size:13 final size:13
Alignment explanation
Indices: 1788285--1788310 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1788275 CAATTTTTTG
1788285 TGTATCGATACAT
1 TGTATCGATACAT
1788298 TGTATCGATACAT
1 TGTATCGATACAT
1788311 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1788375 original size:21 final size:21
Alignment explanation
Indices: 1788349--1788424 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1788339 CTGCCAAGAA
*
1788349 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1788370 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1788390 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1788411 ATGTATCGATACAT
1 ATGTATCGATACAT
1788425 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1788395 original size:20 final size:20
Alignment explanation
Indices: 1788370--1788442 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1788360 CATCTTTTTT
1788370 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1788390 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1788411 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1788431 ATGTATCGATAC
1 ATGTATCGATAC
1788443 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1788406 original size:41 final size:41
Alignment explanation
Indices: 1788349--1788442 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1788339 CTGCCAAGAA
*
1788349 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1788390 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1788431 ATGTATCGATAC
1 ATGTATCGATAC
1788443 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1789306 original size:79 final size:78
Alignment explanation
Indices: 1789127--1789370 Score: 253
Period size: 79 Copynumber: 3.1 Consensus size: 78
1789117 AACGGGGCTA
** *
1789127 GAGTATCCCTGATTATGGAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTA-CCTCCTCG
1 GAGTATCCCCAATTATGGAAAATCGATGTTTTGAAAATAAAATAG-GGTTGGAGTATCCT-CTCG
*
1789191 GAAATAACAAGGTTG
64 GAAATAACGAGGTTG
* *** * *
1789206 GAGTTTCCTTGATTATAGAAAATCGATGTTTTGAAAATAAAATTAGGGTTGGAGTATCCTCTCGA
1 GAGTATCCCCAATTATGGAAAATCGATGTTTTGAAAATAAAA-TAGGGTTGGAGTATCCTCTCGG
1789271 AAATAACGAGGTTG
65 AAATAACGAGGTTG
* **** *
1789285 GAGTATCCCCAATTGA-GGAAAATCGATGCTTT-AGAAATAAGGCCGGGGTTGG-GTATCCCCTC
1 GAGTATCCCCAATT-ATGGAAAATCGATGTTTTGA-AAATAA-AATAGGGTTGGAGTATCCTCTC
*
1789347 GGAAATAACGGGGTTG
63 GGAAATAACGAGGTTG
1789363 GAGTATCC
1 GAGTATCC
1789371 TTGATGAAAT
Statistics
Matches: 141, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
78 32 0.23
79 103 0.73
80 6 0.04
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (78 bp):
GAGTATCCCCAATTATGGAAAATCGATGTTTTGAAAATAAAATAGGGTTGGAGTATCCTCTCGGA
AATAACGAGGTTG
Found at i:1791767 original size:13 final size:13
Alignment explanation
Indices: 1791749--1791778 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1791739 GTAAACCCAG
*
1791749 AATGTATCGATAT
1 AATGTATCGATAC
1791762 AATGTATCGATAC
1 AATGTATCGATAC
1791775 AATG
1 AATG
1791779 AACCATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1791788 original size:20 final size:20
Alignment explanation
Indices: 1791762--1791816 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1791752 GTATCGATAT
1791762 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
* *
1791782 CATGTATTGATACAATGAAC
1 AATGTATCGATACAATGAAC
1791802 AATGTATCGATACAA
1 AATGTATCGATACAA
1791817 CTTGTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:1793946 original size:13 final size:13
Alignment explanation
Indices: 1793928--1793955 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1793918 TCCTTTGTGG
1793928 ATTCATCCATTTC
1 ATTCATCCATTTC
1793941 ATTCATCCATTTC
1 ATTCATCCATTTC
1793954 AT
1 AT
1793956 CCGGAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTCATCCATTTC
Found at i:1794536 original size:84 final size:85
Alignment explanation
Indices: 1794425--1794664 Score: 277
Period size: 84 Copynumber: 2.8 Consensus size: 85
1794415 ACAAAAGTTG
* * * * ****
1794425 ACCAGGATTGAATTGACAAGTTAACAAAGGATAAAAGGATTTATCGGTTACTAAGCCGACAAGTA
1 ACCAGAATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACCCAAGACTAAGCCGACAAGTA
*
1794490 AATAAA-GGATAAAACGGCT-
66 AACAAATGG-TAAAACGGCTA
* * **
1794509 ACTAGAATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACCCAAGACTGAGTTGACAAGTA
1 ACCAGAATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACCCAAGACTAAGCCGACAAGTA
* *
1794574 AACAAATGGTAAAATGGTTA
66 AACAAATGGTAAAACGGCTA
* * * * *
1794594 ACCAGGATTGAACCGACAAGTCAACAAAGGTTAAAAGGATTTACCCAAGACTAAGCCGATAGGTA
1 ACCAGAATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACCCAAGACTAAGCCGACAAGTA
1794659 AACAAA
66 AACAAA
1794665 GGATTCAAAG
Statistics
Matches: 130, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
84 66 0.51
85 64 0.49
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (85 bp):
ACCAGAATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACCCAAGACTAAGCCGACAAGTA
AACAAATGGTAAAACGGCTA
Found at i:1794578 original size:43 final size:43
Alignment explanation
Indices: 1794439--1794668 Score: 150
Period size: 43 Copynumber: 5.4 Consensus size: 43
1794429 GGATTGAATT
* * **** *
1794439 GACAAGTTAACAAAGGATAAAAGGATTTATCGGTTACTAAGCC
1 GACAAGTAAACAAAGGATAAAAGGATTTACCCAAGACTGAGCC
* * * * * *
1794482 GACAAGTAAATAAAGGATAAAACGG--CTA--CTAGAATTGAACT
1 GACAAGTAAACAAAGGATAAAA-GGATTTACCCAAG-ACTGAGCC
* **
1794523 GACAAGTCAACAAAGGATAAAAGGATTTACCCAAGACTGAGTT
1 GACAAGTAAACAAAGGATAAAAGGATTTACCCAAGACTGAGCC
* * * *
1794566 GACAAGTAAACAAATGG-TAAAATGG--TTAACCAGGATTGAACC
1 GACAAGTAAACAAA-GGATAAAA-GGATTTACCCAAGACTGAGCC
* * *
1794608 GACAAGTCAACAAAGGTTAAAAGGATTTACCCAAGACTAAGCC
1 GACAAGTAAACAAAGGATAAAAGGATTTACCCAAGACTGAGCC
* *
1794651 GATAGGTAAACAAAGGAT
1 GACAAGTAAACAAAGGAT
1794669 TCAAAGGTTG
Statistics
Matches: 141, Mismatches: 35, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
40 2 0.01
41 28 0.20
42 33 0.23
43 69 0.49
44 9 0.06
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (43 bp):
GACAAGTAAACAAAGGATAAAAGGATTTACCCAAGACTGAGCC
Found at i:1794635 original size:85 final size:83
Alignment explanation
Indices: 1794387--1794714 Score: 316
Period size: 85 Copynumber: 3.9 Consensus size: 83
1794377 GAGGTTACCG
* * * * *
1794387 AGACTAAATTGACAAGTAAACAAGGGATACAAAAGTTGACCAGGATTGAATTGACAAGTTAACAA
1 AGACTAAGTTGACAAGTAAACAAAGGATA-AAAGGTT-ACCAGGATTGAACTGACAAGTCAACAA
* **
1794452 AGGATAAAAGGATTTATCGG
64 AGGATAAAAGGATTTACCCA
** ** * * * *
1794472 TTACTAAGCCGACAAGTAAATAAAGGATAAAACGGCTACTAGAATTGAACTGACAAGTCAACAAA
1 AGACTAAGTTGACAAGTAAACAAAGGATAAAA-GGTTACCAGGATTGAACTGACAAGTCAACAAA
1794537 GGATAAAAGGATTTACCCA
65 GGATAAAAGGATTTACCCA
* *
1794556 AGACTGAGTTGACAAGTAAACAAATGG-TAAAATGGTTAACCAGGATTGAACCGACAAGTCAACA
1 AGACTAAGTTGACAAGTAAACAAA-GGATAAAA-GGTT-ACCAGGATTGAACTGACAAGTCAACA
*
1794620 AAGGTTAAAAGGATTTACCCA
63 AAGGATAAAAGGATTTACCCA
** * * * *** * *
1794641 AGACTAAGCCGATAGGTAAACAAAGGATTCAAAGGTTGATTGGGATTAAACTGACAAGTCAATAA
1 AGACTAAGTTGACAAGTAAACAAAGGA-TAAAAGGTT-ACCAGGATTGAACTGACAAGTCAACAA
1794706 AGGATAAAA
64 AGGATAAAA
1794715 AGCGATACCT
Statistics
Matches: 196, Mismatches: 42, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
84 71 0.36
85 121 0.62
86 4 0.02
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.20
Consensus pattern (83 bp):
AGACTAAGTTGACAAGTAAACAAAGGATAAAAGGTTACCAGGATTGAACTGACAAGTCAACAAAG
GATAAAAGGATTTACCCA
Found at i:1794910 original size:46 final size:46
Alignment explanation
Indices: 1794822--1795117 Score: 218
Period size: 46 Copynumber: 6.5 Consensus size: 46
1794812 TGCTAATTGA
* * * *
1794822 AGAA-GAAAAGAGTTTGACTAGGGTGATAA-CTGATACAGTCAAACG
1 AGAATGAAAAGGGTTTGACCAAGGTGGTAATC-GATACAGTCAAACG
* * * *
1794867 AGAACGAAAAGGGTTTAACCAAGGTGGTAATCGATATAGTCAAATG
1 AGAATGAAAAGGGTTTGACCAAGGTGGTAATCGATACAGTCAAACG
* ** *
1794913 AGAATGAAAAGGGTTTGACCAAGGTGGTAATAGATTTAGTCGAACG
1 AGAATGAAAAGGGTTTGACCAAGGTGGTAATCGATACAGTCAAACG
* * * * * *
1794959 AGGATGAAAAGGGTTTGACTAAAGTGGTAACCAATACAGTCAAATG
1 AGAATGAAAAGGGTTTGACCAAGGTGGTAATCGATACAGTCAAACG
* * ** * * * * * * *
1795005 AGAGTGGAAAGAATGTGACTAGGGTAGTAACCGATACAGTTAAACA
1 AGAATGAAAAGGGTTTGACCAAGGTGGTAATCGATACAGTCAAACG
* * * * * * *
1795051 AGGATGAAAAGGGTTTGACCAGGGTGGCAACCGATATAGTTAAACA
1 AGAATGAAAAGGGTTTGACCAAGGTGGTAATCGATACAGTCAAACG
* * *
1795097 AGGATGAAAAGAGTTGGACCA
1 AGAATGAAAAGGGTTTGACCA
1795118 TATACAACCA
Statistics
Matches: 201, Mismatches: 48, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
45 4 0.02
46 196 0.98
47 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (46 bp):
AGAATGAAAAGGGTTTGACCAAGGTGGTAATCGATACAGTCAAACG
Found at i:1795138 original size:35 final size:35
Alignment explanation
Indices: 1795099--1795340 Score: 252
Period size: 35 Copynumber: 6.9 Consensus size: 35
1795089 GTTAAACAAG
* * * *
1795099 GATGAAAAGAGTTGGACCATATACAACCAAATGAT
1 GATGAAAAGAGTTTGACCAAATACAATCAAACGAT
* *
1795134 GATGAAAAGAGTTTGACCAGATACAA-CTAAACGAC
1 GATGAAAAGAGTTTGACCAAATACAATC-AAACGAT
* * * *
1795169 AATGAAAAGAGTTTGACCAGATACGATCAAACAAT
1 GATGAAAAGAGTTTGACCAAATACAATCAAACGAT
* *** *
1795204 GATGAAAAGAGTTTGACCAAAAATGGTCAAACGTT
1 GATGAAAAGAGTTTGACCAAATACAATCAAACGAT
* * * ** *
1795239 GATAAAAAGAGTTTGACTAGATACAGCCAAACAAT
1 GATGAAAAGAGTTTGACCAAATACAATCAAACGAT
* *
1795274 GATGAAAAGAGTTTGACCAAATATAGTCAAACGAT
1 GATGAAAAGAGTTTGACCAAATACAATCAAACGAT
*
1795309 GATGAAAAGAATTTGACCAAATACAATCAAAC
1 GATGAAAAGAGTTTGACCAAATACAATCAAAC
1795341 AAAGGTAGAA
Statistics
Matches: 172, Mismatches: 33, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
34 1 0.01
35 170 0.99
36 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (35 bp):
GATGAAAAGAGTTTGACCAAATACAATCAAACGAT
Found at i:1795339 original size:105 final size:105
Alignment explanation
Indices: 1795084--1795358 Score: 300
Period size: 105 Copynumber: 2.6 Consensus size: 105
1795074 GTGGCAACCG
* * * * * * *
1795084 ATATAGTTAAACAAGGATGAAAAGAGTTGGACCATATACAACCAAATGATGATGAAAAGAGTTTG
1 ATATAGTCAAACAATGATGAAAAGAGTTTGACCAAATACAATCAAACGATGATAAAAAGAGTTTG
* * *
1795149 ACCAGATACAACTAAACGACAATGAAAAGAGTTTGACCAG
66 ACCAGATACAACCAAACAACAATGAAAAGAGTTTGACCAA
* * *** *
1795189 ATA-CGATCAAACAATGATGAAAAGAGTTTGACCAAAAATGGTCAAACGTTGATAAAAAGAGTTT
1 ATATAG-TCAAACAATGATGAAAAGAGTTTGACCAAATACAATCAAACGATGATAAAAAGAGTTT
* * **
1795253 GACTAGATACAGCCAAACAATGATGAAAAGAGTTTGACCAA
65 GACCAGATACAACCAAACAACAATGAAAAGAGTTTGACCAA
* * * * * *
1795294 ATATAGTCAAACGATGATGAAAAGAATTTGACCAAATACAATCAAACAAAGGTAGAAAGAGTTTG
1 ATATAGTCAAACAATGATGAAAAGAGTTTGACCAAATACAATCAAACGATGATAAAAAGAGTTTG
1795359 GCTAGGACTA
Statistics
Matches: 136, Mismatches: 32, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
104 1 0.01
105 134 0.99
106 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (105 bp):
ATATAGTCAAACAATGATGAAAAGAGTTTGACCAAATACAATCAAACGATGATAAAAAGAGTTTG
ACCAGATACAACCAAACAACAATGAAAAGAGTTTGACCAA
Found at i:1795358 original size:70 final size:70
Alignment explanation
Indices: 1795084--1795342 Score: 295
Period size: 70 Copynumber: 3.7 Consensus size: 70
1795074 GTGGCAACCG
* * * * * * **
1795084 ATATAGTTAAACAAGGATGAAAAGAGTTGGACCATATACAACCAAATGATGATGAAAAGAGTTTG
1 ATATAGTCAAACGATGATGAAAAGAGTTTGACCAGATACAATCAAACAATGATGAAAAGAGTTTG
*
1795149 ACCAG
66 ACCAA
* * ** *
1795154 ATACA-ACTAAACGACAATGAAAAGAGTTTGACCAGATACGATCAAACAATGATGAAAAGAGTTT
1 ATATAGTC-AAACGATGATGAAAAGAGTTTGACCAGATACAATCAAACAATGATGAAAAGAGTTT
1795218 GACCAA
65 GACCAA
* * * * * **
1795224 AAATGGTCAAACGTTGATAAAAAGAGTTTGACTAGATACAGCCAAACAATGATGAAAAGAGTTTG
1 ATATAGTCAAACGATGATGAAAAGAGTTTGACCAGATACAATCAAACAATGATGAAAAGAGTTTG
1795289 ACCAA
66 ACCAA
* *
1795294 ATATAGTCAAACGATGATGAAAAGAATTTGACCAAATACAATCAAACAA
1 ATATAGTCAAACGATGATGAAAAGAGTTTGACCAGATACAATCAAACAA
1795343 AGGTAGAAAG
Statistics
Matches: 153, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
70 152 0.99
71 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (70 bp):
ATATAGTCAAACGATGATGAAAAGAGTTTGACCAGATACAATCAAACAATGATGAAAAGAGTTTG
ACCAA
Found at i:1795493 original size:47 final size:46
Alignment explanation
Indices: 1795392--1795528 Score: 139
Period size: 47 Copynumber: 2.9 Consensus size: 46
1795382 CAAACTAAGG
* * *
1795392 AAAAGTTTGACCAGGTCTTAATGCCAATACAGTCAAATGAAGGTAA
1 AAAAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAAGATAA
* * * **
1795438 AAAGAGTTTAACCAGGTCCTAATGCTAATACATTCAAACGGCGATAGA
1 AAA-AGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAAGATA-A
* * * * *
1795486 AAAAGTTTGACTAGGTCCTTACGCCAATATAGTCAAACAAAGA
1 AAAAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAAGA
1795529 AAGACTTGAC
Statistics
Matches: 71, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
46 3 0.04
47 64 0.90
48 4 0.06
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (46 bp):
AAAAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAAGATAA
Found at i:1796159 original size:88 final size:88
Alignment explanation
Indices: 1795995--1796162 Score: 243
Period size: 88 Copynumber: 1.9 Consensus size: 88
1795985 TGCCCCTAGG
*
1795995 AAATCAAGTTTTGTGATGCATCAATACCATCTAGTGGCTTGATGAAGGAGATATGATTGGGAATG
1 AAATCAAGTTTTGTGATGCATCAATACCATCTAGTGGCTTGATGAAGGAGATACGATTGGGAATG
*
1796060 TGTTGTCTGCACCCTCCCCAATA
66 TGTGGTCTGCACCCTCCCCAATA
* * *
1796083 AAATCAGGTTTTGTGATGCATCAATACCATTTAGTGG-TTGAGTGAAAGG-GATACGATTGTGAA
1 AAATCAAGTTTTGTGATGCATCAATACCATCTAGTGGCTTGA-TG-AAGGAGATACGATTGGGAA
1796146 TGTGTGGGT-TGCACCCT
64 TGTGT-GGTCTGCACCCT
1796163 TTCCCTTTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
87 4 0.06
88 62 0.86
89 6 0.08
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (88 bp):
AAATCAAGTTTTGTGATGCATCAATACCATCTAGTGGCTTGATGAAGGAGATACGATTGGGAATG
TGTGGTCTGCACCCTCCCCAATA
Found at i:1797140 original size:111 final size:111
Alignment explanation
Indices: 1796989--1797306 Score: 386
Period size: 111 Copynumber: 2.9 Consensus size: 111
1796979 TTGGCTTAAA
* * **
1796989 AATTTCAAAATTGATAGGGTACATGCCTTATTTTCCTAGGCACGAATGGATCAGAATGTATAAAA
1 AATTTCAAAATTCATAGGATATGTGCCTTA-TTTCCTAGGCACGAATGGATCAGAATGTATAAAA
* *
1797054 TATGAATTTATTGAAAATTAGACAAATTTGACGTTGTTGGGCTCAAG
65 TATGAATTTCTTGAAAATTAGACAAATTTGACGTTGTTGAGCTCAAG
* * * * *
1797101 AATTTCAAAATTTATAGGATATGTGCCCTATTTCCTAGGCACAAATCGATCATAATGTATAAAAT
1 AATTTCAAAATTCATAGGATATGTGCCTTATTTCCTAGGCACGAATGGATCAGAATGTATAAAAT
** * *
1797166 ATGAATTTCTCAAAAATCT-GACAAATCTGATGTTGTTGAGCTCAAG
66 ATGAATTTCTTGAAAAT-TAGACAAATTTGACGTTGTTGAGCTCAAG
* * * * * * *
1797212 AATTTCAAAACTCATAGGATATGTGCCTTATGTCTTAGGCATGAATGGTTCGGAATATATAAAAT
1 AATTTCAAAATTCATAGGATATGTGCCTTATTTCCTAGGCACGAATGGATCAGAATGTATAAAAT
* * *
1797277 ATGAATTTCCTGAAAATCAGAAAAATTTGA
66 ATGAATTTCTTGAAAATTAGACAAATTTGA
1797307 TATTCTTTTA
Statistics
Matches: 172, Mismatches: 32, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
111 146 0.85
112 26 0.15
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (111 bp):
AATTTCAAAATTCATAGGATATGTGCCTTATTTCCTAGGCACGAATGGATCAGAATGTATAAAAT
ATGAATTTCTTGAAAATTAGACAAATTTGACGTTGTTGAGCTCAAG
Found at i:1797919 original size:21 final size:21
Alignment explanation
Indices: 1797887--1797959 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 21
1797877 CTATCTGCAC
1797887 TTTTTTCA-TTTTATGCTTT-T
1 TTTTTTCATTTTTAT-CTTTCT
1797907 TTTTTTCATTTTTTATCTTTCT
1 TTTTTTCA-TTTTTATCTTTCT
* * *
1797929 TTTTCTC-TTTTT-TTTTTAT
1 TTTTTTCATTTTTATCTTTCT
1797948 TTTTTTCTATTT
1 TTTTTTC-ATTT
1797960 GTTTTAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 11 0.25
20 13 0.30
21 7 0.16
22 13 0.30
ACGTcount: A:0.08, C:0.11, G:0.01, T:0.79
Consensus pattern (21 bp):
TTTTTTCATTTTTATCTTTCT
Found at i:1797920 original size:22 final size:22
Alignment explanation
Indices: 1797887--1797959 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 22
1797877 CTATCTGCAC
1797887 TTTTTTCA--TTTTATGCTTT-T
1 TTTTTTCATTTTTTAT-CTTTCT
1797907 TTTTTTCATTTTTTATCTTTCT
1 TTTTTTCATTTTTTATCTTTCT
* *
1797929 TTTTCTC-TTTTTT-T-TTTAT
1 TTTTTTCATTTTTTATCTTTCT
1797948 TTTTTTCTATTT
1 TTTTTTC-ATTT
1797960 GTTTTAGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 10 0.22
20 9 0.20
21 13 0.29
22 13 0.29
ACGTcount: A:0.08, C:0.11, G:0.01, T:0.79
Consensus pattern (22 bp):
TTTTTTCATTTTTTATCTTTCT
Found at i:1797958 original size:10 final size:10
Alignment explanation
Indices: 1797906--1797964 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
1797896 TTTATGCTTT
1797906 TTTTTTTC-A
1 TTTTTTTCTA
1797915 TTTTTTATCT-
1 TTTTTT-TCTA
*
1797925 TTCTTTTTCTCT
1 TT-TTTTTCT-A
*
1797937 TTTTTTTTTA
1 TTTTTTTCTA
1797947 TTTTTTTCTA
1 TTTTTTTCTA
1797957 TTTGTTTT
1 TTT-TTTT
1797965 AGAAAGAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
9 6 0.15
10 19 0.46
11 14 0.34
12 2 0.05
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (10 bp):
TTTTTTTCTA
Found at i:1801361 original size:13 final size:13
Alignment explanation
Indices: 1801343--1801368 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1801333 ACATTTGGTC
1801343 ATGTATCGATACA
1 ATGTATCGATACA
1801356 ATGTATCGATACA
1 ATGTATCGATACA
1801369 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1801363 original size:33 final size:32
Alignment explanation
Indices: 1801321--1801388 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
1801311 CGTTACAAGC
* *
1801321 CAATGTATCGGTACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCAATA
1801354 CAATGTATCGATACATCTTGTATGTATCAATA
1 CAATGTATCGATACATCTTGTATGTATCAATA
1801386 CAA
1 CAA
1801389 ACAATTAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 17 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCAATA
Found at i:1801475 original size:13 final size:13
Alignment explanation
Indices: 1801457--1801481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1801447 TATAGTGGTC
1801457 ATGTATCGATACA
1 ATGTATCGATACA
1801470 ATGTATCGATAC
1 ATGTATCGATAC
1801482 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1801600 original size:21 final size:21
Alignment explanation
Indices: 1801571--1801629 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1801561 ATGTATCATT
*
1801571 ACAAATATCGATACATTCTTA
1 ACAAGTATCGATACATTCTTA
1801592 ACAAGTATCGATACA-T-TTA
1 ACAAGTATCGATACATTCTTA
1801611 A-AAGTGTATCGATACATTC
1 ACAA--GTATCGATACATTC
1801630 AAGGGTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 12 0.36
21 15 0.45
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (21 bp):
ACAAGTATCGATACATTCTTA
Found at i:1802236 original size:22 final size:22
Alignment explanation
Indices: 1802160--1802238 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
1802150 TAATCAAATA
*
1802160 AAAAAAATTTCTCCCCCTTAAT
1 AAAAAAATTTCTTCCCCTTAAT
* * *
1802182 AAAACAATTTCCTTTAATCAC-TAA-
1 AAAAAAATTT-C-TT--CCCCTTAAT
1802206 AAAAAAATTTCTTCCCCTTAAT
1 AAAAAAATTTCTTCCCCTTAAT
*
1802228 AAAACAATTTC
1 AAAAAAATTTC
1802239 CTTTAATTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
20 2 0.05
21 3 0.07
22 21 0.49
23 2 0.05
24 10 0.23
25 3 0.07
26 2 0.05
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAAAATTTCTTCCCCTTAAT
Found at i:1809225 original size:13 final size:13
Alignment explanation
Indices: 1809207--1809322 Score: 52
Period size: 13 Copynumber: 7.5 Consensus size: 13
1809197 AGCTTCGTAG
1809207 CGATACATTGTAT
1 CGATACATTGTAT
1809220 CGATACAAAATTTATGTAT
1 CGATAC---A-TT--GTAT
*
1809239 CAATACATTGTAT
1 CGATACATTGTAT
1809252 CGATACAACACCTATGTAT
1 CGAT---ACA--T-TGTAT
1809271 CGATACATTGTAT
1 CGATACATTGTAT
*
1809284 CGTTACAACACCTATGTAT
1 CG--A-TACA--T-TGTAT
1809303 CGATACATTGTAT
1 CGATACATTGTAT
1809316 CGATACA
1 CGATACA
1809323 ACACTTATGT
Statistics
Matches: 81, Mismatches: 4, Indels: 36
0.67 0.03 0.30
Matches are distributed among these distances:
13 32 0.40
14 2 0.02
15 3 0.04
16 14 0.17
17 3 0.04
18 2 0.02
19 25 0.31
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1809250 original size:32 final size:32
Alignment explanation
Indices: 1809207--1809341 Score: 216
Period size: 32 Copynumber: 4.2 Consensus size: 32
1809197 AGCTTCGTAG
* **
1809207 CGATACATTGTATCGATACAAAATTTATGTAT
1 CGATACATTGTATCGATACAACACCTATGTAT
*
1809239 CAATACATTGTATCGATACAACACCTATGTAT
1 CGATACATTGTATCGATACAACACCTATGTAT
*
1809271 CGATACATTGTATCGTTACAACACCTATGTAT
1 CGATACATTGTATCGATACAACACCTATGTAT
*
1809303 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACCTATGTAT
1809335 CGATACA
1 CGATACA
1809342 GTTACTGTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 95 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACCTATGTAT
Found at i:1809271 original size:19 final size:18
Alignment explanation
Indices: 1809247--1809341 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
1809237 ATCAATACAT
1809247 TGTATCGATACAACACCTA
1 TGTATCGATACAACA-CTA
1809266 TGTATCGAT---ACA-T-
1 TGTATCGATACAACACTA
*
1809279 TGTATCGTTACAACACCTA
1 TGTATCGATACAACA-CTA
1809298 TGTATCGAT---ACA-T-
1 TGTATCGATACAACACTA
1809311 TGTATCGATACAACACTTA
1 TGTATCGATACAACAC-TA
1809330 TGTATCGATACA
1 TGTATCGATACA
1809342 GTTACTGTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 24
0.70 0.02 0.27
Matches are distributed among these distances:
13 17 0.27
14 2 0.03
16 12 0.19
18 2 0.03
19 29 0.47
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAACACTA
Found at i:1813878 original size:13 final size:13
Alignment explanation
Indices: 1813860--1813885 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1813850 ACATTTGGTC
1813860 ATGTATCGATACA
1 ATGTATCGATACA
1813873 ATGTATCGATACA
1 ATGTATCGATACA
1813886 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1813880 original size:33 final size:32
Alignment explanation
Indices: 1813838--1813905 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
1813828 CGTTACAAGC
1813838 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
1813871 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
1813903 CAA
1 CAA
1813906 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:1813992 original size:13 final size:13
Alignment explanation
Indices: 1813974--1813998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1813964 TACAGTGGTC
1813974 ATGTATCGATACA
1 ATGTATCGATACA
1813987 ATGTATCGATAC
1 ATGTATCGATAC
1813999 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1815050 original size:21 final size:21
Alignment explanation
Indices: 1815026--1815070 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1815016 CGATCTTCAT
1815026 TTAAAAAAGGATATCTCCTTA
1 TTAAAAAAGGATATCTCCTTA
*
1815047 TTAAAAAAGGATATCTCTTTA
1 TTAAAAAAGGATATCTCCTTA
1815068 TTA
1 TTA
1815071 GAATAATCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (21 bp):
TTAAAAAAGGATATCTCCTTA
Found at i:1818791 original size:79 final size:79
Alignment explanation
Indices: 1818659--1818951 Score: 256
Period size: 79 Copynumber: 3.7 Consensus size: 79
1818649 ACAACAAGGC
* * * * *
1818659 TGGAGTATCCCCTAATTATGGAAAATCGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATTCCCT
1 TGGAGTAT-CCCTGATTATAGAAAATCGGTGTTTTAGAAATAAAATCGAGGTTGGACTATCCCCT
1818724 CGAAAATAACAGGGT
65 CGAAAATAACAGGGT
* *
1818739 TGGAGCATCCCTGATTATAGAAAATTGGTGTTTT-GAAAATAAAATCGAGGTTGGACTATCCCCT
1 TGGAGTATCCCTGATTATAGAAAATCGGTGTTTTAG-AAATAAAATCGAGGTTGGACTATCCCCT
* *
1818803 CGAAGATAACGGGGT
65 CGAAAATAACAGGGT
* * *** * *** *
1818818 TGGAGTATCCCCGATTGT-GAAAAATCAAAGCTTTAGAAATAAGGCCG-GGTTTGGAGTAT-CCC
1 TGGAGTATCCCTGATTATAG-AAAATCGGTGTTTTAGAAATAAAATCGAGG-TTGGACTATCCCC
*
1818880 TGCAAAAATAAC-GAGGT
64 T-CGAAAATAACAG-GGT
* * * * *
1818897 TGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTAGAAATAAAATAGGGGTTGGA
1 TGGAGTATCCCTGATTATAG-AAAATCGGTGTTTTAGAAATAAAATCGAGGTTGGA
1818952 TCCCCGATTA
Statistics
Matches: 174, Mismatches: 32, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
78 9 0.05
79 155 0.89
80 10 0.06
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
TGGAGTATCCCTGATTATAGAAAATCGGTGTTTTAGAAATAAAATCGAGGTTGGACTATCCCCTC
GAAAATAACAGGGT
Done.