Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003279.1 Hibiscus syriacus cultivar Beakdansim tig00006894_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 109898
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:4171 original size:18 final size:18
Alignment explanation
Indices: 4148--4191 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
4138 TTTGAAGATT
4148 CTTACTCGTGTTGAAATC
1 CTTACTCGTGTTGAAATC
4166 CTTACTCGTGTTGAAATC
1 CTTACTCGTGTTGAAATC
4184 CTTACTCG
1 CTTACTCG
4192 CGTTTTCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (18 bp):
CTTACTCGTGTTGAAATC
Found at i:7814 original size:34 final size:34
Alignment explanation
Indices: 7767--7844 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
7757 TTGAGAGTTA
*
7767 TTTTCTCATTTTTATCAAGAGAGAATTGTCATTG
1 TTTTCTCCTTTTTATCAAGAGAGAATTGTCATTG
*
7801 TTTTTTCCTTTTTATCAAGAGAGAATTGTCATTG
1 TTTTCTCCTTTTTATCAAGAGAGAATTGTCATTG
7835 TTTTCTCCTT
1 TTTTCTCCTT
7845 GTTAGATCGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (34 bp):
TTTTCTCCTTTTTATCAAGAGAGAATTGTCATTG
Found at i:7858 original size:36 final size:34
Alignment explanation
Indices: 7767--7858 Score: 121
Period size: 34 Copynumber: 2.6 Consensus size: 34
7757 TTGAGAGTTA
* *
7767 TTTTCTCATTTTTATCAAGAGAGAATTGTCATTG
1 TTTTCTCCTTTTGATCAAGAGAGAATTGTCATTG
* *
7801 TTTTTTCCTTTTTATCAAGAGAGAATTGTCATTG
1 TTTTCTCCTTTTGATCAAGAGAGAATTGTCATTG
*
7835 TTTTCTCCTTGTTAGATCGAGAGA
1 TTTTCTCCTT-TT-GATCAAGAGA
7859 AGTTATATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 41 0.80
35 2 0.04
36 8 0.16
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (34 bp):
TTTTCTCCTTTTGATCAAGAGAGAATTGTCATTG
Found at i:12598 original size:65 final size:64
Alignment explanation
Indices: 12444--12609 Score: 174
Period size: 65 Copynumber: 2.6 Consensus size: 64
12434 AAATAGCCTG
* * *
12444 AGTGCATTGATACATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTA
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAACTCCA
* ** * ** *
12509 AGTGCATCGATGCATAGTACGTGCATCGATGCATGAAATGCATTCGATG-TTCA-ATTTATTCCA
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATA-AAACTCCA
* *
12572 TGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 -AGTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
12610 CTTTGAAAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
62 1 0.01
63 8 0.10
64 15 0.18
65 58 0.71
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAACTCCA
Found at i:15836 original size:16 final size:17
Alignment explanation
Indices: 15815--15847 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
15805 TTACTGTTTA
15815 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
15831 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
15848 TGTTGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:21157 original size:19 final size:19
Alignment explanation
Indices: 21135--21186 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
21125 TTTTTAAACT
21135 TAAATCAAAATAATTAA-AA
1 TAAAT-AAAATAATTAATAA
21154 TAAATATAAA-AATTAATAA
1 TAAATA-AAATAATTAATAA
*
21173 TATATAAAATAATT
1 TAAATAAAATAATT
21187 TATATGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATAAAATAATTAATAA
Found at i:21224 original size:20 final size:20
Alignment explanation
Indices: 21201--21294 Score: 68
Period size: 20 Copynumber: 4.5 Consensus size: 20
21191 TGATATAAAA
21201 TAAATTTAAAAAATTAATAT
1 TAAATTTAAAAAATTAATAT
* * **
21221 TAAAATTAATATCTATAATA-
1 TAAATTTAAAAAAT-TAATAT
21241 T-AATATT-AAAAATTAATATT
1 TAAAT-TTAAAAAATTAATA-T
21261 TAATTTATTTAAAAAATTAATAT
1 TAA---ATTTAAAAAATTAATAT
*
21284 TAAAATTAAAA
1 TAAATTTAAAA
21295 TCAAATATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
18 5 0.09
19 5 0.09
20 21 0.38
21 6 0.11
23 6 0.11
24 13 0.23
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATTTAAAAAATTAATAT
Found at i:21225 original size:12 final size:12
Alignment explanation
Indices: 21210--21315 Score: 85
Period size: 12 Copynumber: 8.7 Consensus size: 12
21200 ATAAATTTAA
21210 AAAATTAATATT
1 AAAATTAATATT
21222 AAAATTAATATCT
1 AAAATTAATAT-T
*
21235 ATAATATAATATT
1 AAAAT-TAATATT
21248 AAAAATTAATATT
1 -AAAATTAATATT
* *
21261 -TAATTTAT-TT
1 AAAATTAATATT
21271 AAAAAATTAATATT
1 --AAAATTAATATT
*
21285 AAAATTAA-AAT
1 AAAATTAATATT
*
21296 CAAATATAATA-T
1 AAAAT-TAATATT
21308 AAAATTAA
1 AAAATTAA
21316 ATATAAAACC
Statistics
Matches: 76, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
10 2 0.03
11 15 0.20
12 27 0.36
13 20 0.26
14 12 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:21318 original size:12 final size:12
Alignment explanation
Indices: 21273--21323 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
21263 ATTTATTTAA
21273 AAAATT-AATATT
1 AAAATTAAATA-T
21285 AAAATTAAA-AT
1 AAAATTAAATAT
*
21296 CAAA-TATAATAT
1 AAAATTA-AATAT
21308 AAAATTAAATAT
1 AAAATTAAATAT
21320 AAAA
1 AAAA
21324 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:21780 original size:18 final size:18
Alignment explanation
Indices: 21757--21812 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
21747 TTCAATTTAT
21757 TTTGATCAATAATTTAAA
1 TTTGATCAATAATTTAAA
21775 TTTGAT---TGAA-TT-AA
1 TTTGATCAAT-AATTTAAA
21789 TTTGATCAATAATTTAAA
1 TTTGATCAATAATTTAAA
21807 TTTGAT
1 TTTGAT
21813 ATTAAATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 8 0.25
15 3 0.09
16 4 0.12
17 3 0.09
18 14 0.44
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (18 bp):
TTTGATCAATAATTTAAA
Found at i:21820 original size:18 final size:17
Alignment explanation
Indices: 21766--21817 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 17
21756 TTTTGATCAA
21766 TAATTTAAATTTGAT-T
1 TAATTTAAATTTGATAT
* *
21782 GAA-TT-AATTTGATCAA
1 TAATTTAAATTTGAT-AT
21798 TAATTTAAATTTGATAT
1 TAATTTAAATTTGATAT
21815 TAA
1 TAA
21818 ATTCAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 8 0.29
15 2 0.07
16 4 0.14
17 6 0.21
18 8 0.29
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (17 bp):
TAATTTAAATTTGATAT
Found at i:23052 original size:21 final size:21
Alignment explanation
Indices: 23012--23066 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
23002 GATTCTTGAC
23012 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
23032 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
23054 AATCGCAACGCGA
1 AATCGCAATGCGA
23067 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:23079 original size:20 final size:20
Alignment explanation
Indices: 23054--23246 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
23044 GATTTTACAG
* ** *
23054 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
23074 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
23094 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23114 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23134 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23154 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23174 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
23194 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
23215 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23235 AATCGCAACGCG
1 AATCGCAACGCG
23247 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:23664 original size:33 final size:33
Alignment explanation
Indices: 23625--23695 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
23615 TTCACTTAGA
23625 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
23658 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
23691 TTTCA
1 TTTCA
23696 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:23845 original size:20 final size:20
Alignment explanation
Indices: 23775--23847 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
23765 TGCAGAAGAG
*
23775 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAAAAATG-AAA
* *
23796 TCGCAACGTG-AAAATGACTA
1 TCGCAACGAGAAAAATGA-AA
23816 TCTGCAACGAGAAAAATGAAA
1 TC-GCAACGAGAAAAATGAAA
23837 TCGCAACGAGA
1 TCGCAACGAGA
23848 GAATCGCAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.02
20 17 0.39
21 19 0.43
22 7 0.16
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAAATGAAA
Found at i:23892 original size:19 final size:19
Alignment explanation
Indices: 23870--23920 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
23860 GAAACCAAAA
*
23870 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
23889 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
23908 TCGCGTTGCGATT
1 TCGCATTGCGATT
23921 CTCTCGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:23945 original size:21 final size:21
Alignment explanation
Indices: 23919--23983 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
23909 CGCGTTGCGA
23919 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
23940 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
23960 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
23981 TTC
1 TTC
23984 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:23980 original size:20 final size:20
Alignment explanation
Indices: 23879--23981 Score: 96
Period size: 19 Copynumber: 5.5 Consensus size: 20
23869 ATCGCATTGT
*
23879 GATTTTCATT-TCGCGTTGC
1 GATTTTCATTCTCTCGTTGC
*
23898 GATTTTCATT-TCGCGTTGC
1 GATTTTCATTCTCTCGTTGC
23917 G------ATTCTCTCGTTGC
1 GATTTTCATTCTCTCGTTGC
23931 GATTTTCATTTCTCTCGTTGC
1 GATTTTCA-TTCTCTCGTTGC
***
23952 GACAGTCATTCTCTCGTTGC
1 GATTTTCATTCTCTCGTTGC
23972 GATTTTCATT
1 GATTTTCATT
23982 TCAACCAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
13 3 0.04
14 9 0.13
19 20 0.29
20 20 0.29
21 17 0.25
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (20 bp):
GATTTTCATTCTCTCGTTGC
Found at i:25824 original size:93 final size:93
Alignment explanation
Indices: 25665--26073 Score: 800
Period size: 93 Copynumber: 4.4 Consensus size: 93
25655 TAGATTGCTT
*
25665 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25730 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
25758 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACCGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25823 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
25851 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
25916 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
25944 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26009 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26037 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
26074 AATACCCTGA
Statistics
Matches: 313, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 313 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:26208 original size:14 final size:14
Alignment explanation
Indices: 26189--26245 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
26179 CGAAACTTAA
26189 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
26203 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
26222 AATCGCAACGACAG
1 AATCGCAACGAGAG
26236 AATCGCAACG
1 AATCGCAACG
26246 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:26227 original size:19 final size:18
Alignment explanation
Indices: 26203--26294 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
26193 GCAACGAGAG
26203 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
26222 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
26236 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
26255 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
26269 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
26288 AATCGCA
1 AATCGCA
26295 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:26229 original size:33 final size:33
Alignment explanation
Indices: 26171--26294 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
26161 TAGTTTACTT
* * *
26171 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
26205 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
26238 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
26271 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
26295 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:26271 original size:14 final size:14
Alignment explanation
Indices: 26220--26278 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
26210 ACGCGAAATG
26220 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
26234 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
26253 AAAATCGCAACGAC
1 AAAATCGCAACGAC
26267 AAAATCGCAACG
1 AAAATCGCAACG
26279 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:26312 original size:19 final size:19
Alignment explanation
Indices: 26290--26462 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
26280 GAAACCAAAA
*
26290 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
26309 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
26323 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
26342 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
26358 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
26375 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
26394 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
26413 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
26432 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
26452 TCGTGTTGCGA
1 TCGCGTTGCGA
26463 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:26331 original size:14 final size:14
Alignment explanation
Indices: 26312--26368 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
26302 TTTCATTTCG
26312 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
26326 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
26343 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
26359 CGTTGCGATT
1 CGTTGCGATT
26369 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:26420 original size:38 final size:38
Alignment explanation
Indices: 26290--26462 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
26280 GAAACCAAAA
*
26290 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
26325 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
26358 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
26394 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
26432 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
26463 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:28401 original size:14 final size:14
Alignment explanation
Indices: 28382--28408 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28372 ATTGTTTAAT
28382 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
28396 TGATTTGTAAAAG
1 TGATTTGTAAAAG
28409 TTAATTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:28415 original size:14 final size:14
Alignment explanation
Indices: 28384--28417 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28374 TGTTTAATTG
*
28384 ATTTGTAAAAGATG
1 ATTTGTAAAAGATA
*
28398 ATTTGTAAAAGTTA
1 ATTTGTAAAAGATA
28412 ATTTGT
1 ATTTGT
28418 GTAATTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGATA
Found at i:28532 original size:19 final size:19
Alignment explanation
Indices: 28508--28595 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
28498 GCATTATGTT
28508 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
28527 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
28544 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
28560 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
28579 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
28596 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:28599 original size:53 final size:52
Alignment explanation
Indices: 28508--28614 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 52
28498 GCATTATGTT
28508 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
28560 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
28613 GA
1 GA
28615 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (52 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:28730 original size:105 final size:107
Alignment explanation
Indices: 28604--28860 Score: 395
Period size: 105 Copynumber: 2.4 Consensus size: 107
28594 AACGAGAGAA
*
28604 TCGCAATGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
28669 TTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATT
66 TTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTC--T
28709 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
*
28774 TTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCT
66 TTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTCT
*
28818 T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
28861 GTAATTTCCG
Statistics
Matches: 143, Mismatches: 3, Indels: 12
0.91 0.02 0.08
Matches are distributed among these distances:
105 108 0.76
106 14 0.10
107 3 0.02
108 3 0.02
109 4 0.03
111 11 0.08
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (107 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
TTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCT
Found at i:28734 original size:72 final size:70
Alignment explanation
Indices: 28610--28846 Score: 263
Period size: 72 Copynumber: 3.4 Consensus size: 70
28600 AGAATCGCAA
* *
28610 TGCGATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGAT
1 TGCGATTTGCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
28669 TTTCAT
65 TTTCAT
* * *
28675 TTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
1 TGCG-ATTTGC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
*
28739 ATTCTCTCGT
63 ATT-T-TCAT
*
28749 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
*
28814 TTCTTGT
66 TTC--AT
* *
28821 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTGCATTTCGCATTGCGATT
28847 CTCTCGTTGC
Statistics
Matches: 147, Mismatches: 11, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
65 6 0.04
66 12 0.08
67 1 0.01
68 3 0.02
69 4 0.03
70 2 0.01
71 16 0.11
72 89 0.61
73 5 0.03
74 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (70 bp):
TGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
TTCAT
Found at i:28875 original size:53 final size:52
Alignment explanation
Indices: 28604--28860 Score: 380
Period size: 53 Copynumber: 4.9 Consensus size: 52
28594 AACGAGAGAA
*
28604 TCGCAATGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
28657 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
28709 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
28762 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC--T
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
28818 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
28861 GTAATTTCCG
Statistics
Matches: 193, Mismatches: 4, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.02
52 62 0.32
53 95 0.49
54 3 0.02
55 3 0.02
56 4 0.02
58 11 0.06
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:31159 original size:12 final size:12
Alignment explanation
Indices: 31142--31166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31132 TCTTCGGGGA
31142 CTTTTTCTTCTT
1 CTTTTTCTTCTT
31154 CTTTTTCTTCTT
1 CTTTTTCTTCTT
31166 C
1 C
31167 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:31375 original size:24 final size:24
Alignment explanation
Indices: 31341--31387 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31331 CTGAAACATC
31341 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
31365 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
31388 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:32108 original size:20 final size:20
Alignment explanation
Indices: 32080--32308 Score: 226
Period size: 20 Copynumber: 11.4 Consensus size: 20
32070 AAATTTCAGT
* * *
32080 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
32100 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* **
32120 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
**
32140 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
32160 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
32180 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
32200 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
32220 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
32240 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
32260 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
32280 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
32300 GTTGCGATT
1 GTTGCGATT
32309 CTTGAAAATC
Statistics
Matches: 183, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 182 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:32361 original size:21 final size:20
Alignment explanation
Indices: 32276--32373 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
32266 ATTTATGTGT
* *
32276 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
32296 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
32317 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
32338 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
32359 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
32374 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:32369 original size:42 final size:43
Alignment explanation
Indices: 32276--32374 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
32266 ATTTATGTGT
* *
32276 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
32317 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
32359 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
32375 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:36100 original size:12 final size:12
Alignment explanation
Indices: 36083--36109 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
36073 TATTTGTGAA
36083 AAATTGAAATTT
1 AAATTGAAATTT
36095 AAATTGAAATTT
1 AAATTGAAATTT
36107 AAA
1 AAA
36110 AACTCGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:36206 original size:23 final size:24
Alignment explanation
Indices: 36169--36224 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
36159 AATGTTATAT
* *
36169 AAAAAATGAATAAATAAATCAAAG
1 AAAAAAAGAATAAATAAATAAAAG
*
36193 AAAAAAAGAA-AAATAAATAAAAT
1 AAAAAAAGAATAAATAAATAAAAG
*
36216 AAAATAAGA
1 AAAAAAAGA
36225 TAATGAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (24 bp):
AAAAAAAGAATAAATAAATAAAAG
Found at i:38721 original size:84 final size:84
Alignment explanation
Indices: 38597--39397 Score: 698
Period size: 84 Copynumber: 9.7 Consensus size: 84
38587 ACTTGATTTA
* * * * * * * * *
38597 CCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCCTCGGTTGGCAGATAGCTCTTCTCGACTTAAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
* **
38662 CTATGCTGCAGATGACGTG
66 CTATGCTGCAAATGATATG
* * *
38681 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCATATAACCCTTCTAGTCTTGAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
** *
38746 CTATATTGTAAATGATATG
66 CTATGCTGCAAATGATATG
*** * * ** * *
38765 CCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAA
1 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAA
* * *
38826 GGTATGCTACAAATGATGTG
65 GCTATGCTGCAAATGATATG
* * *
38846 CCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAA
1 CC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAA
* *
38910 GTTGTGCTGCAAATGATATG
65 GCTATGCTGCAAATGATATG
* ** *
38930 CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG-TGATAGATAACCCTTCTAGACTTGAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
* **
38994 TTATGCTGTGAATGATATG
66 CTATGCTGCAAATGATATG
* * * * ** * * *
39013 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCTCTTCTCGACTTAA
1 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAA
*
39074 GCTATGCTGCAAATGATGTG
65 GCTATGCTGCAAATGATATG
* * *
39094 CCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAA
1 CC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAA
* * *
39158 GTTGTGCTGCAAATTATATG
65 GCTATGCTGCAAATGATATG
** *
39178 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TAACAGATAACCCTTCTAGACTTGAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
* * **
39242 TTATGATGTGAATGATATG
66 CTATGCTGCAAATGATATG
*** * * * ** * * * *
39261 CCCTCAAAGTTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAAATAGCTCTTCTCGACTTAA
1 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAA
* * *
39322 GCTATGCTACAAATGATGTA
65 GCTATGCTGCAAATGATATG
* * *
39342 CCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCT
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
39398 TGTCTTAAAA
Statistics
Matches: 564, Mismatches: 132, Indels: 42
0.76 0.18 0.06
Matches are distributed among these distances:
80 73 0.13
81 103 0.18
82 5 0.01
83 79 0.14
84 278 0.49
85 26 0.05
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
CTATGCTGCAAATGATATG
Found at i:39054 original size:164 final size:162
Alignment explanation
Indices: 38600--39379 Score: 568
Period size: 164 Copynumber: 4.7 Consensus size: 162
38590 TGATTTACCT
* * * * * * * * * *
38600 TTGAGCTGAGTGTAATCGAACTCAAAGGTCCTCGGTTGGCAGATAGCTCTTCTCGACTTAAGCTA
1 TTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG-TGACAGACAACCCTTCTAGACTTAAGTTA
* ** * * * *
38665 TGCTGCAGATGACGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCATATAA
65 TGCTGCAAATGATATGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTC--T--TTGGCAGATAA
* * * ** *
38730 CCCTTCTAGTCTTGAGCTATATTGTAAATGATATGCCC
126 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CC
** * ** * * * *
38768 TCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGGTA
1 T-TGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGACAGACAACCCTTCTAGACTTAAGTTA
* * * * * *
38830 TGCTACAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
65 TGCTGCAAATGATATGCC-TCGAAGCTGAGCGTAATCGAACTCGAAGGTC---T-TTGGCAGATA
*
38894 ACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCC
125 ACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC
* * *
38932 TTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGATAGATAACCCTTCTAGACTTGAGTTA
1 TT-GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGACAGACAACCCTTCTAGACTTAAGTTA
** * ** * *
38997 TGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCTC
65 TGCTGCAAATGATATG-CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCC
* * *
39062 TTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
129 TTCTAGACTTAAGTTATGCTGCAAATGATATGCC
* * * *
39096 GTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
1 -TTGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGGTGACAGACAACCCTTCTAGACTTAAGTT
* * * * *
39161 GTGCTGCAAATTATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTAACAGATAA
64 ATGCTGCAAATGATATGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG---CAGATAA
* * **
39226 CCCTTCTAGACTTGAGTTATGATGTGAATGATATGCCC
126 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CC
** * * ** * * * * * *
39264 TCAAAGTTGAGTGTAATCGAACTCGGGGGTCTTT-G-G-CAAATAGCTCTTCTCGACTTAAGCTA
1 T-TGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGACAGACAACCCTTCTAGACTTAAGTTA
* * * * *
39326 TGCTACAAATGATGTACCTTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
65 TGCTGCAAATGATATGCC-TCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG
39380 TTGGCAAATA
Statistics
Matches: 500, Mismatches: 95, Indels: 38
0.79 0.15 0.06
Matches are distributed among these distances:
164 194 0.39
165 152 0.30
166 8 0.02
167 72 0.14
168 49 0.10
169 25 0.05
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (162 bp):
TTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGACAGACAACCCTTCTAGACTTAAGTTAT
GCTGCAAATGATATGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTT
CTAGACTTAAGTTATGCTGCAAATGATATGCC
Found at i:39089 original size:248 final size:248
Alignment explanation
Indices: 38600--39385 Score: 1241
Period size: 248 Copynumber: 3.2 Consensus size: 248
38590 TGATTTACCT
* * * * * * * * * *
38600 TTGAGCTGAGTGTAATCGAACTCAAAGGTCCTCGGTTGGCAGATAGCTCTTCTCGACTTAAGCTA
1 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTG
* ** * *
38665 TGCTGCAGATGACGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCATATAA
66 TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAA
* * *
38730 CCCTTCTAGTCTTGAGCTAT-ATTGTAAATGATATGCCCTCAAAGCTGAGTGTAATCGAACTCGG
130 CCCTTCTAGACTTGAGTTATGA-TGTGAATGATATGCCCTCAAAGCTGAGTGTAATCGAACTCGG
* *
38794 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGGTATGCTACAAATGATGTGCCG
194 GGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCG
*
38849 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
1 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTG
* *
38914 TGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGATAGATAAC
66 TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAAC
* *
38979 CCTTCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGG
131 CCTTCTAGACTTGAGTTATGATGTGAATGATATGCCCTCAAAGCTGAGTGTAATCGAACTCGGGG
*
39044 GTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCG
196 GTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCG
*
39097 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
1 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTG
* *
39162 TGCTGCAAATTATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTAACAGATAAC
66 TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAAC
*
39227 CCTTCTAGACTTGAGTTATGATGTGAATGATATGCCCTCAAAGTTGAGTGTAATCGAACTCGGGG
131 CCTTCTAGACTTGAGTTATGATGTGAATGATATGCCCTCAAAGCTGAGTGTAATCGAACTCGGGG
* * *
39292 GTCTTTGGCAAATAGCTCTTCTCGACTTAAGCTATGCTACAAATGATGTACCT
196 GTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCG
*
39345 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCA
1 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCA
39386 AATAGCCCTT
Statistics
Matches: 497, Mismatches: 39, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
248 393 0.79
249 104 0.21
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (248 bp):
TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTG
TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAAC
CCTTCTAGACTTGAGTTATGATGTGAATGATATGCCCTCAAAGCTGAGTGTAATCGAACTCGGGG
GTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCG
Found at i:42826 original size:18 final size:19
Alignment explanation
Indices: 42786--42830 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
42776 AGTTAATGTG
*
42786 AATGTAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
42805 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
42823 AATGCAAA
1 AATGCAAA
42831 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:43467 original size:17 final size:17
Alignment explanation
Indices: 43441--43473 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43431 TGCAAACGAT
*
43441 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
43458 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
43474 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:46548 original size:3 final size:3
Alignment explanation
Indices: 46542--46571 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
46532 AAATTATTAT
*
46542 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46572 CATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:47656 original size:15 final size:15
Alignment explanation
Indices: 47633--47662 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47623 ACGAGGCTAG
47633 AATTACAAAAACAAC
1 AATTACAAAAACAAC
*
47648 AATTCCAAAAACAAC
1 AATTACAAAAACAAC
47663 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAAAAACAAC
Found at i:53413 original size:125 final size:126
Alignment explanation
Indices: 53190--53440 Score: 441
Period size: 125 Copynumber: 2.0 Consensus size: 126
53180 ATTTGTTTAT
* * *
53190 GGATTTGGATGTGGGTTTTGTTCTTTTTTCTTCTTCTGTGATTTCCATTTCCTGATTGTTCGTTG
1 GGATTTGGATGTGGGTTTTGTTCTTATTTCTTCTTCTGTGATTTCCATTGCCTGATTGTTCGTTC
* *
53255 GACATGCCTCCTTAGTGTGTCCATAAATCCCGCATGTGAAACAGATGTGTTGGAGTCCCTC
66 GACACGCCTCCTTAGTGTGGCCATAAATCCCGCATGTGAAACAGATGTGTTGGAGTCCCTC
53316 GGATTTGGATGTGGGTTTTGTTCTTATTT-TTCTTCTGTGATTTCCATTGCCTGATTGTTCGTTC
1 GGATTTGGATGTGGGTTTTGTTCTTATTTCTTCTTCTGTGATTTCCATTGCCTGATTGTTCGTTC
*
53380 GACACGCCTTCTTAGTGTGGCCATAAATCCCGCATGTGAAACAGATGTGTTGGAGTCCCTC
66 GACACGCCTCCTTAGTGTGGCCATAAATCCCGCATGTGAAACAGATGTGTTGGAGTCCCTC
53441 CTATTCCAGC
Statistics
Matches: 119, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 91 0.76
126 28 0.24
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (126 bp):
GGATTTGGATGTGGGTTTTGTTCTTATTTCTTCTTCTGTGATTTCCATTGCCTGATTGTTCGTTC
GACACGCCTCCTTAGTGTGGCCATAAATCCCGCATGTGAAACAGATGTGTTGGAGTCCCTC
Found at i:54359 original size:3 final size:3
Alignment explanation
Indices: 54351--54419 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
54341 AACTAACGAT
54351 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54399 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
54420 ATATCATATG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:74653 original size:59 final size:59
Alignment explanation
Indices: 74126--74635 Score: 878
Period size: 59 Copynumber: 8.6 Consensus size: 59
74116 GAATTACCAA
74126 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
74185 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
74244 AGGGCATTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCAAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
74303 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACAAAGGGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
74362 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAACTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
74421 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* **
74480 AGGGCACTTTGTGTGCTCAAATGGTAAGGAAATCATACTAAGTGTATGAATTTATAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
74539 ATGGCACTTTGTGTGCTAAAA-GAGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATG-GTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
74598 AGGGCACTCTGTGTGCTAAAATGATAAAGAAATCATAC
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
74636 CGTTTTTATG
Statistics
Matches: 426, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
58 1 0.00
59 424 1.00
60 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:76490 original size:15 final size:15
Alignment explanation
Indices: 76469--76504 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
76459 AGCACCTAAT
76469 AGAAGCAGAGGGAGA
1 AGAAGCAGAGGGAGA
*
76484 GGAAGCAGAGGGAGA
1 AGAAGCAGAGGGAGA
76499 AGAAGC
1 AGAAGC
76505 TCTGGTGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.08, G:0.47, T:0.00
Consensus pattern (15 bp):
AGAAGCAGAGGGAGA
Found at i:77876 original size:12 final size:12
Alignment explanation
Indices: 77859--77888 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
77849 TTATATATAC
77859 ATTATAAAAATT
1 ATTATAAAAATT
77871 ATTATAAAAATT
1 ATTATAAAAATT
77883 ATTATA
1 ATTATA
77889 TGATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTATAAAAATT
Found at i:80329 original size:5 final size:5
Alignment explanation
Indices: 80319--80344 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
80309 TGTTGAGTCT
80319 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
80345 ATTGTCTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:92038 original size:36 final size:36
Alignment explanation
Indices: 91991--92065 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
91981 GTAGGGGAAA
*
91991 ATTCAAGCCATAATAGATTGGCAATCTCCCAAGAAT
1 ATTCAAGCCATAATAGATTGGCAATCACCCAAGAAT
*
92027 ATTCAAGCCATAATAGATTGGCAATCACCCAATAAT
1 ATTCAAGCCATAATAGATTGGCAATCACCCAAGAAT
92063 ATT
1 ATT
92066 ACGGAAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (36 bp):
ATTCAAGCCATAATAGATTGGCAATCACCCAAGAAT
Found at i:95193 original size:22 final size:21
Alignment explanation
Indices: 95160--95219 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
95150 TACATGAAGA
* *
95160 GGGTATCAATACCCTAA-TAG
1 GGGTATCGATACCATAAGTAG
95180 GGTAGTATCGATACCATAAGTAG
1 GG--GTATCGATACCATAAGTAG
95203 GGGTATCGATACC-TAAG
1 GGGTATCGATACCATAAG
95220 GGCTGAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.17
21 11 0.31
22 13 0.37
23 5 0.14
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (21 bp):
GGGTATCGATACCATAAGTAG
Found at i:95210 original size:21 final size:20
Alignment explanation
Indices: 95160--95219 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
95150 TACATGAAGA
*
95160 GGGTATCAATACCCTAA-TAG
1 GGGTATCGATA-CCTAAGTAG
95180 GGTAGTATCGATACCATAAGTAG
1 GG--GTATCGATACC-TAAGTAG
95203 GGGTATCGATACCTAAG
1 GGGTATCGATACCTAAG
95220 GGCTGAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 6 0.17
21 13 0.37
22 11 0.31
23 5 0.14
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCTAAGTAG
Found at i:95853 original size:59 final size:59
Alignment explanation
Indices: 95444--95836 Score: 635
Period size: 59 Copynumber: 6.7 Consensus size: 59
95434 GAATTACCAA
* *
95444 AGGGCACTTTGTGTGCTAGAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
95503 AGGGCACATTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
95562 ATGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTACAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
95621 AGGGCACATTGTGTTCTAAAATGGTAAGCAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
95680 AGGGCACTTTGTGTGCTAAAATGGTAAGGAGATCATACTAAGTGTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
95739 AGGGCACTTTGTGTGCTAAAA-GATTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATG-GTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
95798 AGGGCACTCTATGTGCTAAAATGATAAGGAAATCATACT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACT
95837 GTTTGTATGA
Statistics
Matches: 308, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
58 1 0.00
59 306 0.99
60 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:97457 original size:117 final size:118
Alignment explanation
Indices: 97289--97510 Score: 358
Period size: 117 Copynumber: 1.9 Consensus size: 118
97279 ACGAGCTAAG
97289 GTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCTCATTATGAA
* * **
97354 CTC-TCCACTT-GAGATGTTGATCCACCTTTTTCTGTGATGAAATTGATGTGAA
66 CCCTTCCA-TTGGAAATGTTGATCCACCTCATTCTGTGATGAAATTGATGTGAA
* * *
97406 GTTGAACAAGTTCTTCTCATTATGAACTTGTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCTCATTATGAA
97471 CCCTTCCATTGGAAATGTTGATCCACCTCATTCTGTGATG
66 CCCTTCCATTGGAAATGTTGATCCACCTCATTCTGTGATG
97511 GAATCGAACA
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
117 66 0.69
118 30 0.31
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (118 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCTCATTATGAA
CCCTTCCATTGGAAATGTTGATCCACCTCATTCTGTGATGAAATTGATGTGAA
Found at i:97546 original size:321 final size:321
Alignment explanation
Indices: 96959--97721 Score: 1079
Period size: 321 Copynumber: 2.4 Consensus size: 321
96949 GGTGTAGTAC
* * * *
96959 CAAGATAAGGTTGAGAAAGATCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCT
1 CAAGCTAAGGTTGA-AAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCT
* * **
97024 CATTACGAACACTCCACTAGAAATGTCAATCCACCTCATTCTGTGAT-AGAATCGATCCAAGGTT
65 CATTATGAACTCTCCACTAGAAATGTTGATCCACCTCATTCTGTGATGAGAATCGATCCAAGGTT
** *
97088 GAACAAGTTCTTCCCATTATGAACTTCTTCTCTTTCATCAGTTGAGTTCTTCTCATTATGAACCC
130 GAACAAGTTCTTCCCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACCC
* * **
97153 TTTCATTGGAAATATTGATCCACATTCTTATGTGATGGAATCAAACAAAGTGATGATGTTGATTT
195 TTCCATTGGAAATATTGATCCACACTCTTATGTGATGGAATCAAACAAAGTGATGATGTTGATCC
*
97218 AACTCCATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATATGATGGAAA
260 AACTCCATATGCGATGGATGAGCCAAGTATTAGTGTTGTTCCAACTCCTTATATGATGGAAA
*
97280 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCT
1 CAAGCTAAGGTTGAA-AAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCT
* * ** * **
97345 CATTATGAACTCTCCACTTGAGATGTTGATCCACCTTTTTCTGTGATGA-AATTGATGTGAA-GT
65 CATTATGAACTCTCCACTAGAAATGTTGATCCACCTCATTCTGTGATGAGAATCGAT-CCAAGGT
* * **
97408 TGAACAAGTTCTTCTCATTATGAACTTGTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACC
129 TGAACAAGTTCTTCCCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACC
* * *
97473 CTTCCATTGGAAATGTTGATCCAC-CTCATTCTGTGATGGAATCGAACAAAGTGATGATGTTGAT
194 CTTCCATTGGAAATATTGATCCACACTC-TTATGTGATGGAATCAAACAAAGTGATGATGTTGAT
* * *
97537 CCAACTCCATATGCTATGGATGAGCCAAGTATTAGTGTTGTTCCAACTTCTTATGTGATGGAAA
258 CCAACTCCATATGCGATGGATGAGCCAAGTATTAGTGTTGTTCCAACTCCTTATATGATGGAAA
*
97601 CAAGCTAAGGTTGAAAAAGTTCTTCTCATTATGAATTTCTTCAT-CCTCATCGGATGAGTTCTTC
1 CAAGCTAAGGTTG-AAAAGTTCTTCTCATTATGAACTTCTT-ATCCCTCATCGGATGAGTTCTTC
* * *
97665 TCATTATGAACTTCACCACTAGAAATGTTGATCTACCTCCTTCTGTGATG-GAATCGA
64 TCATTATGAAC-TCTCCACTAGAAATGTTGATCCACCTCATTCTGTGATGAGAATCGA
97722 ACAAAGTGAT
Statistics
Matches: 391, Mismatches: 43, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
320 3 0.01
321 344 0.88
322 44 0.11
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (321 bp):
CAAGCTAAGGTTGAAAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCTC
ATTATGAACTCTCCACTAGAAATGTTGATCCACCTCATTCTGTGATGAGAATCGATCCAAGGTTG
AACAAGTTCTTCCCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACCCT
TCCATTGGAAATATTGATCCACACTCTTATGTGATGGAATCAAACAAAGTGATGATGTTGATCCA
ACTCCATATGCGATGGATGAGCCAAGTATTAGTGTTGTTCCAACTCCTTATATGATGGAAA
Found at i:97743 original size:204 final size:202
Alignment explanation
Indices: 97406--97923 Score: 790
Period size: 204 Copynumber: 2.5 Consensus size: 202
97396 TTGATGTGAA
* *
97406 GTTGAACAAGTTCTTCTCATTATGAACTTGTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAA
* * * *
97471 CCCTT-CCATTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCGAACAAAGTGATGATGTTG
66 --CTTCCCACT-GAAATGTTGATCTACCTCCTTCTGTGATGGAATCGAACAAAGTGATGATGCTG
* * *
97535 ATCCAACTCCATATGCTATGGATGAGCCAAGTATTAGTGTTGTTCCAACTTCTTATGTGATGGAA
128 ATCCAACTCCATATGCGATGGATGAGCCAAGTATTAGTGTTGTTCCAACTCCTTATGTGAGGGAA
97600 ACAAGCTAAG
193 ACAAGCTAAG
* * *
97610 GTTGAAAAAGTTCTTCTCATTATGAATTTCTTCAT-CCTCATCGGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTATTC-TCCCTCATCGGATGAGTTCTTCTCATTATGA
97674 ACTTCACCACTAGAAATGTTGATCTACCTCCTTCTGTGATGGAATCGAACAAAGTGATGATGCTG
65 ACTTC-CCACT-GAAATGTTGATCTACCTCCTTCTGTGATGGAATCGAACAAAGTGATGATGCTG
*
97739 ATCCAACTCCATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGAGGGAA
128 ATCCAACTCCATATGCGATGGATGAGCCAAGTATTAGTGTTGTTCCAACTCCTTATGTGAGGGAA
*
97804 ACGAGCTAAG
193 ACAAGCTAAG
* *
97814 GTTGAACAAGTTCTTCTTATTATGAACTTATTCTCCCTCATCGAATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAA
*
97879 C-TCTCCACTGAAAATGTTGATCTACCTCCTTCTATGATGGAATCG
66 CTTC-CCACTG-AAATGTTGATCTACCTCCTTCTGTGATGGAATCG
97924 TGCTAAGGTT
Statistics
Matches: 288, Mismatches: 21, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
202 4 0.01
203 41 0.14
204 242 0.84
205 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (202 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAA
CTTCCCACTGAAATGTTGATCTACCTCCTTCTGTGATGGAATCGAACAAAGTGATGATGCTGATC
CAACTCCATATGCGATGGATGAGCCAAGTATTAGTGTTGTTCCAACTCCTTATGTGAGGGAAACA
AGCTAAG
Found at i:99418 original size:52 final size:54
Alignment explanation
Indices: 99293--99420 Score: 163
Period size: 52 Copynumber: 2.4 Consensus size: 54
99283 TTACAGTTAT
*
99293 CATCAAGAAACCCCTAAAAAATTAGGCTTAGCTTATTTTAAAAAAACAATTGAAAA
1 CATCAAGAAA-CCCT-GAAAATTAGGCTTAGCTTATTTTAAAAAAACAATTGAAAA
* **
99349 CATCAAGAAACCTTGAAAATTAGGCTTAGCTTA-TTT-AAAATTC-ATTAGAAAA
1 CATCAAGAAACCCTGAAAATTAGGCTTAGCTTATTTTAAAAAAACAATT-GAAAA
*
99401 CATTAAGAAACCCTGAAAAT
1 CATCAAGAAACCCTGAAAAT
99421 CAATTTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
51 3 0.05
52 28 0.43
53 3 0.05
54 18 0.28
55 3 0.05
56 10 0.15
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.27
Consensus pattern (54 bp):
CATCAAGAAACCCTGAAAATTAGGCTTAGCTTATTTTAAAAAAACAATTGAAAA
Found at i:100807 original size:28 final size:28
Alignment explanation
Indices: 100776--100838 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
100766 GAAAGTAGAG
*
100776 TGTTTCAATTTAATTTG-GGGAGGTAATA
1 TGTTTCAAGTTAATTTGAGGG-GGTAATA
*
100804 TGTTTCAGGTTAATTTGAGGGGGTAATA
1 TGTTTCAAGTTAATTTGAGGGGGTAATA
100832 TGTTTCA
1 TGTTTCA
100839 TGTTGGCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.27, T:0.43
Consensus pattern (28 bp):
TGTTTCAAGTTAATTTGAGGGGGTAATA
Found at i:101577 original size:25 final size:23
Alignment explanation
Indices: 101514--101577 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
101504 TGATATGGTT
*
101514 TTTCTTTTTTGCTTTCTTTTCTA
1 TTTCTTTTTTACTTTCTTTTCTA
*
101537 TCTCTTTTTTTACTTTCTTTTTCTA
1 TTTC-TTTTTTACTTTC-TTTTCTA
101562 TATTCTTTCTTT-CTTT
1 T-TTCTTT-TTTACTTT
101578 TCTCTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 3 0.09
24 11 0.32
25 15 0.44
26 5 0.15
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTCTTTTTTACTTTCTTTTCTA
Found at i:101609 original size:25 final size:28
Alignment explanation
Indices: 101562--101620 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
101552 TCTTTTTCTA
* *
101562 TATTCTTTCTTTCTTTT--CTCTATTTTT
1 TATT-TTTCTTTCTTTTAGCTATATCTTT
101589 TATTTTTC-TTCTTTTAGCTATATCTTT
1 TATTTTTCTTTCTTTTAGCTATATCTTT
101616 TATTT
1 TATTT
101621 CTCTCTCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.25
26 4 0.14
27 17 0.61
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (28 bp):
TATTTTTCTTTCTTTTAGCTATATCTTT
Found at i:103003 original size:13 final size:13
Alignment explanation
Indices: 102985--103016 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
102975 TGCAAATATA
102985 CAAAATTGGAATG
1 CAAAATTGGAATG
102998 CAAAATTGGAATG
1 CAAAATTGGAATG
*
103011 CGAAAT
1 CAAAAT
103017 GCCAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (13 bp):
CAAAATTGGAATG
Done.