Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006831.1 Hibiscus syriacus cultivar Beakdansim tig00017367_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: 178850
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:113215 original size:19 final size:19
Alignment explanation
Indices: 113121--113255 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
113111 TAGTTTACTT
* *
113121 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
113141 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
113160 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
113179 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
113193 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
113212 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
113226 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
113245 TCGCAATGCGA
1 TCGCAACGCGA
113256 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:113273 original size:19 final size:19
Alignment explanation
Indices: 113251--113379 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
113241 AAAATCGCAA
113251 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
113270 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
113284 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
113303 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
113317 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
113336 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
113355 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
113375 TGCGA
1 TGCGA
113380 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:113293 original size:33 final size:33
Alignment explanation
Indices: 113251--113342 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
113241 AAAATCGCAA
113251 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
113284 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
113317 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
113343 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:113576 original size:93 final size:93
Alignment explanation
Indices: 113427--113988 Score: 1099
Period size: 93 Copynumber: 6.1 Consensus size: 93
113417 ATGGATTGCA
113427 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
113491 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
113519 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
113584 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
113612 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
113677 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
113705 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
113770 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
113798 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAATT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
113863 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
113891 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
113956 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
113984 TTACT
1 TTACT
113989 AAGCAATCTA
Statistics
Matches: 466, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 30 0.06
93 436 0.94
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:115714 original size:14 final size:14
Alignment explanation
Indices: 115695--115784 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
115685 TTGAAATGAA
115695 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
115709 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
*
115728 AATCGCAACGAGAT
1 AATCGCAACGAGAG
*
115742 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
115761 AATCGCAACGAGAG
1 AATCGCAACGAGAG
115775 AATCGCAACG
1 AATCGCAACG
115785 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:115732 original size:33 final size:33
Alignment explanation
Indices: 115687--115801 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
115677 TCTTTTGGTT
115687 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
115720 GAAATGACAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
115753 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
115786 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
115802 TGCGAAATGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:115733 original size:19 final size:19
Alignment explanation
Indices: 115709--115813 Score: 104
Period size: 19 Copynumber: 6.1 Consensus size: 19
115699 GCAACGAGAG
*
115709 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
115728 AATCGCAA--CG--A-GAT
1 AATCGCAACGCGAAATGAA
115742 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
115761 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
115775 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
115794 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
115813 A
1 A
115814 TCTAAGTGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
14 20 0.28
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 39 0.55
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:116047 original size:22 final size:22
Alignment explanation
Indices: 115995--116049 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
115985 TGGTTGTGAG
**
115995 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
116017 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
116039 GGATTTCTTCG
1 GGATTTCTTCG
116050 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:116221 original size:20 final size:20
Alignment explanation
Indices: 116196--116349 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
116186 CTTTAAATAT
116196 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
116216 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
116238 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
116257 CGCGTTGCGATTAACGGATA
1 CGCGTTGCGATTTACGGATA
*
116277 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
116297 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
116317 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
116337 CGCGTTGCGATTT
1 CGCGTTGCGATTT
116350 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:116323 original size:40 final size:40
Alignment explanation
Indices: 116195--116349 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
116185 GCTTTAAATA
*
116195 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
116236 TATCGTTGCGATTTACGGATACGCGTTGCGATTAACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
116276 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
116316 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
116350 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:116366 original size:21 final size:21
Alignment explanation
Indices: 116336--116418 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
116326 ATTTTCATAT
*
116336 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
116357 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
116378 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
116399 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
116419 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:116409 original size:42 final size:43
Alignment explanation
Indices: 116316--116414 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
116306 ATTTATGTGT
* *
116316 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
116357 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
116399 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
116415 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:116548 original size:79 final size:79
Alignment explanation
Indices: 116465--116630 Score: 332
Period size: 79 Copynumber: 2.1 Consensus size: 79
116455 ATTTCGCGTT
116465 GCGATTTTGTTGGTCATTTTGGCAAATCCAAAAAAAGTTGGTTAAAATCGTATATTATAACTTTT
1 GCGATTTTGTTGGTCATTTTGGCAAATCCAAAAAAAGTTGGTTAAAATCGTATATTATAACTTTT
116530 TTTTGGTCACTGAG
66 TTTTGGTCACTGAG
116544 GCGATTTTGTTGGTCATTTTGGCAAATCCAAAAAAAGTTGGTTAAAATCGTATATTATAACTTTT
1 GCGATTTTGTTGGTCATTTTGGCAAATCCAAAAAAAGTTGGTTAAAATCGTATATTATAACTTTT
116609 TTTTGGTCACTGAG
66 TTTTGGTCACTGAG
116623 GCGATTTT
1 GCGATTTT
116631 CTCTCTTTAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 87 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.41
Consensus pattern (79 bp):
GCGATTTTGTTGGTCATTTTGGCAAATCCAAAAAAAGTTGGTTAAAATCGTATATTATAACTTTT
TTTTGGTCACTGAG
Found at i:121598 original size:31 final size:30
Alignment explanation
Indices: 121563--121626 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
121553 TTTAAAAATA
*
121563 TAAGATATAATCACTTTTGTTTTTATTTAAT
1 TAAGATAT-ATCACTTTCGTTTTTATTTAAT
* *
121594 TAAGATATGTTACTTTCGTTTTTATTTAAT
1 TAAGATATATCACTTTCGTTTTTATTTAAT
121624 TAA
1 TAA
121627 ACGTGGTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (30 bp):
TAAGATATATCACTTTCGTTTTTATTTAAT
Found at i:121824 original size:27 final size:27
Alignment explanation
Indices: 121794--121864 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 27
121784 AAATAAAAAT
121794 AAAATATTTTTAAATTAAGTTAAT-AA
1 AAAATATTTTTAAATTAAGTTAATCAA
* *
121820 GAAAATATATTT-AA-TAAGTTAATCTA
1 -AAAATATTTTTAAATTAAGTTAATCAA
*
121846 AAAGTATTTTTTAAATTAA
1 AAAATA-TTTTTAAATTAA
121865 TATATATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 14 0.39
26 7 0.19
27 12 0.33
28 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (27 bp):
AAAATATTTTTAAATTAAGTTAATCAA
Found at i:123840 original size:21 final size:21
Alignment explanation
Indices: 123814--123867 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
123804 GCGTTGCATT
123814 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
123835 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
123856 TCTCGTTGCGAT
1 TCGCGTTGCGAT
123868 TTTCCAGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:123884 original size:20 final size:20
Alignment explanation
Indices: 123858--123956 Score: 78
Period size: 22 Copynumber: 4.8 Consensus size: 20
123848 GTTGAAAATC
123858 TCGTTGCGATTTTCCAGTTCG
1 TCGTTGCGATTTTCCAGTT-G
* *
123879 -CGTTGCGATAGTCTACAGTTG
1 TCGTTGCGAT--TTTCCAGTTG
*
123900 TCGTTGCGATTTTCCAAATTG
1 TCGTTGCGATTTTCC-AGTTG
* *
123921 --GTTGCGATAGTCTACAGTTG
1 TCGTTGCGAT--TTTCCAGTTG
123941 TCGTTGCGATTTTCCA
1 TCGTTGCGATTTTCCA
123957 AATTCGTTAC
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
19 8 0.13
20 20 0.33
21 8 0.13
22 24 0.40
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGTTGCGATTTTCCAGTTG
Found at i:123904 original size:22 final size:22
Alignment explanation
Indices: 123879--123950 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
123869 TTCCAGTTCG
123879 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
** * *
123901 CGTTGCGATTTTCCA-AATTG-
1 CGTTGCGATAGTCTACAGTTGT
123921 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
123942 CGTTGCGAT
1 CGTTGCGAT
123951 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:123925 original size:41 final size:41
Alignment explanation
Indices: 123858--124044 Score: 214
Period size: 41 Copynumber: 4.7 Consensus size: 41
123848 GTTGAAAATC
*
123858 TCGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTG
*
123900 TCGTTGCGATTTTCCAAATTGGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
* *
123941 TCGTTGCGATTTTCCAAATTCGTTACGA-A----A-A-TCG
1 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
* *
123975 -CATTGCGATTTTCC-AGTTCACGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTG
124016 TCGTTGCGATTTTCCAAATTCGTTGCGAT
1 TCGTTGCGATTTTCCAAATTCGTTGCGAT
124045 TTTCCAAATT
Statistics
Matches: 122, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
32 3 0.02
33 13 0.11
34 9 0.07
35 2 0.02
36 1 0.01
39 1 0.01
40 2 0.02
41 57 0.47
42 28 0.23
43 6 0.05
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
Found at i:123926 original size:19 final size:20
Alignment explanation
Indices: 123859--124063 Score: 92
Period size: 19 Copynumber: 10.4 Consensus size: 20
123849 TTGAAAATCT
*
123859 CGTTGCGATTTTCC-AGTTCG
1 CGTTGCGATTTTCCAAATT-G
** * *
123879 CGTTGCGATAGTCTACAGTTG
1 CGTTGCGATTTTCCA-AATTG
123900 TCGTTGCGATTTTCCAAATTG
1 -CGTTGCGATTTTCCAAATTG
** * *
123921 -GTTGCGATAGTCTACAGTTG
1 CGTTGCGATTTTCCA-AATTG
123941 TCGTTGCGATTTTCCAAATT-
1 -CGTTGCGATTTTCCAAATTG
* *
123961 CGTTACGA------AAATCG
1 CGTTGCGATTTTCCAAATTG
* * *
123975 CATTGCGATTTTCC-AGTTCA
1 CGTTGCGATTTTCCAAATT-G
** * *
123995 CGTTGCGATAGTCTACAGTTG
1 CGTTGCGATTTTCCA-AATTG
124016 TCGTTGCGATTTTCCAAATT-
1 -CGTTGCGATTTTCCAAATTG
124036 CGTTGCGATTTTCCAAATT-
1 CGTTGCGATTTTCCAAATTG
124055 CGTTGCGAT
1 CGTTGCGAT
124064 AGTTAAAAAA
Statistics
Matches: 137, Mismatches: 31, Indels: 35
0.67 0.15 0.17
Matches are distributed among these distances:
13 4 0.03
14 6 0.04
19 48 0.35
20 25 0.18
21 11 0.08
22 43 0.31
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCCAAATTG
Found at i:124663 original size:6 final size:6
Alignment explanation
Indices: 124647--124720 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
124637 GTCCGTCTCG
124647 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
124694 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
124721 AATACGTGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:124850 original size:22 final size:22
Alignment explanation
Indices: 124821--124871 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 22
124811 AATTTGGAAA
124821 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
124843 TTCGC-A--ACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
124862 ATCGCAACGA
1 ATCGCAACGA
124872 ATTTGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 17 0.71
20 1 0.04
21 1 0.04
22 5 0.21
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:124930 original size:41 final size:42
Alignment explanation
Indices: 124857--124979 Score: 150
Period size: 41 Copynumber: 3.0 Consensus size: 42
124847 CAACAACTGT
*
124857 AGACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-A-TTGC
1 AGACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTGC
* *
124897 AGACTATCGCAACGCGAAATGGAAAATCCCAACGCGATTTTC
1 AGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTGC
124939 A-ACTATCGCAACGCGAAATGG-AAATCGCAACGCGAATTTGC
1 AGACTATCGCAACGCGAAATGGAAAATCGCAACGCG-ATTTGC
124980 GATAGTGGAA
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
40 25 0.34
41 40 0.55
42 8 0.11
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (42 bp):
AGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTGC
Found at i:124930 original size:60 final size:59
Alignment explanation
Indices: 124806--124930 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 59
124796 TTAACTATCG
* * * ** *
124806 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTTTCGCAACAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGCAGACTATCGCAACAAATG-AGAAAATCC
*
124866 CAACGAATTTGGAAAATCGCAACGAC-ATTGCAGACTATCGCAACGCGAAATG-GAAAATCC
1 CAACGAATTTGGAAAATCGCAACGACAACTGCAGACTATCGCAA--C-AAATGAGAAAATCC
124926 CAACG
1 CAACG
124931 CGATTTTCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 14 0.25
60 36 0.65
61 1 0.02
62 4 0.07
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (59 bp):
CAACGAATTTGGAAAATCGCAACGACAACTGCAGACTATCGCAACAAATGAGAAAATCC
Found at i:124967 original size:19 final size:19
Alignment explanation
Indices: 124902--124974 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
124892 ATTGCAGACT
124902 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGG-AA
* ** **
124922 ATCCCAACGCGATTTTCAA
1 ATCGCAACGCGAAATGGAA
124941 CTATCGCAACGCGAAATGGAA
1 --ATCGCAACGCGAAATGGAA
124962 ATCGCAACGCGAA
1 ATCGCAACGCGAA
124975 TTTGCGATAG
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.37
20 12 0.29
21 14 0.34
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGGAA
Found at i:125143 original size:22 final size:21
Alignment explanation
Indices: 125117--125157 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
125107 TATAAAAAAT
125117 TATTTTTATTAAATATTTTTGA
1 TATTTTTATTAAAT-TTTTTGA
*
125139 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
125158 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:126572 original size:20 final size:20
Alignment explanation
Indices: 126543--126587 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
126533 CATATATAGT
126543 CGTTGAGGATGTTTTGGAGC
1 CGTTGAGGATGTTTTGGAGC
*
126563 CGTTGTGGATGTTTTGGAGC
1 CGTTGAGGATGTTTTGGAGC
*
126583 AGTTG
1 CGTTG
126588 GGGGATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.09, G:0.40, T:0.38
Consensus pattern (20 bp):
CGTTGAGGATGTTTTGGAGC
Found at i:126872 original size:22 final size:22
Alignment explanation
Indices: 126811--126874 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
126801 TGTTTGAGCC
* * *
126811 TTCATAGGAGTATTGATACCCA
1 TTCATAGGGGTATTGGTACCAA
126833 TTCATAGGGGTATTGGTACCAA
1 TTCATAGGGGTATTGGTACCAA
*
126855 TTCATAGGGGTATCGGTACC
1 TTCATAGGGGTATTGGTACC
126875 TATTAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (22 bp):
TTCATAGGGGTATTGGTACCAA
Found at i:131456 original size:2 final size:2
Alignment explanation
Indices: 131449--131502 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
131439 CAATTGTTAC
*
131449 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131491 AT AT AT AT AT AT
1 AT AT AT AT AT AT
131503 TAATCTAGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134508 original size:22 final size:22
Alignment explanation
Indices: 134480--134536 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
134470 ATTTTCAATT
134480 TTGTAAAAAAAAATTATATTCC
1 TTGTAAAAAAAAATTATATTCC
134502 TTGTAAAAAAAAATTATATTCC
1 TTGTAAAAAAAAATTATATTCC
134524 TTGTAAAAAAAAA
1 TTGTAAAAAAAAA
134537 CAAATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.33
Consensus pattern (22 bp):
TTGTAAAAAAAAATTATATTCC
Found at i:134581 original size:14 final size:14
Alignment explanation
Indices: 134562--134590 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
134552 GACAATTTGG
134562 TCAAATATACATTC
1 TCAAATATACATTC
134576 TCAAATATACATTC
1 TCAAATATACATTC
134590 T
1 T
134591 AATAATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (14 bp):
TCAAATATACATTC
Found at i:137068 original size:20 final size:19
Alignment explanation
Indices: 137045--137087 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
137035 CCAGAGGGGG
*
137045 AGAGAGAGAATATGAGAGAA
1 AGAGAGAGAACAT-AGAGAA
*
137065 AGAGAGAGAACGTAGAGAA
1 AGAGAGAGAACATAGAGAA
137084 AGAG
1 AGAG
137088 TGTGTGTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.53, C:0.02, G:0.37, T:0.07
Consensus pattern (19 bp):
AGAGAGAGAACATAGAGAA
Found at i:140936 original size:21 final size:20
Alignment explanation
Indices: 140904--140942 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
140894 ATGTAAGATT
140904 TAAAATTAAATTTAAAACAC
1 TAAAATTAAATTTAAAACAC
*
140924 TAAAATCTAAATTTTAAAC
1 TAAAAT-TAAATTTAAAAC
140943 CCTAGTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATTAAATTTAAAACAC
Found at i:141094 original size:33 final size:33
Alignment explanation
Indices: 141052--141120 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
141042 GATCATATTT
*
141052 CGTCCATTGACCCCTTATTATCCGTCCACCCTC
1 CGTCCATTGACCCCTTATTATCCGCCCACCCTC
* *
141085 CGTCCATTGACCCCTTATTTTTCGCCCACCCTC
1 CGTCCATTGACCCCTTATTATCCGCCCACCCTC
141118 CGT
1 CGT
141121 TCACGGAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.13, C:0.45, G:0.10, T:0.32
Consensus pattern (33 bp):
CGTCCATTGACCCCTTATTATCCGCCCACCCTC
Found at i:145335 original size:20 final size:20
Alignment explanation
Indices: 145310--145378 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
145300 GAACACTAGT
* *
145310 TTCGCAACACAGTTTTTAAA
1 TTCGCAACACGGTTTTCAAA
* *
145330 TTCGCAACGCGGTTCTCCAAA
1 TTCGCAACACGGTT-TTCAAA
*
145351 ATCGCAACACGGTTTTCAAA
1 TTCGCAACACGGTTTTCAAA
145371 TTCGCAAC
1 TTCGCAAC
145379 GTGAATTTCG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 24 0.60
21 16 0.40
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (20 bp):
TTCGCAACACGGTTTTCAAA
Found at i:145506 original size:111 final size:111
Alignment explanation
Indices: 145312--145672 Score: 569
Period size: 111 Copynumber: 3.3 Consensus size: 111
145302 ACACTAGTTT
* * * * *
145312 CGCAACACAGTTTTTAAATTCGCAACGCGGTTCTCCAAAATCGCAACACGGTTTTCAAATTCGCA
1 CGCAACTCAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGAAACGCGGTTTTCAAATTCGCA
*
145377 ACGTGAATTTCGTTTTCGCAACGCTAATTACCGATATAGGTAAACA
66 ACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAGGTAAACA
* * *
145423 CGCAATTCAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCAAAACGCGGTTTTTAAATTCGCA
1 CGCAACTCAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGAAACGCGGTTTTCAAATTCGCA
*
145488 ATGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAGGTAAACA
66 ACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAGGTAAACA
* * *
145534 CGCAACTCAGTTTTCAAATTCGCAACACGATTCTCCAAAATCGTAATGCGGTTTTCAAATTCGCA
1 CGCAACTCAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGAAACGCGGTTTTCAAATTCGCA
* *
145599 ACGCGAATTTCATTTTCGCAATGCTAATTACCGATATAGGTAAACA
66 ACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAGGTAAACA
* *
145645 CGCAACGCGGTTTTCAAATTCGCAACGC
1 CGCAACTCAGTTTTCAAATTCGCAACGC
145673 TAATTACCGA
Statistics
Matches: 228, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 228 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (111 bp):
CGCAACTCAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGAAACGCGGTTTTCAAATTCGCA
ACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAGGTAAACA
Found at i:145609 original size:20 final size:19
Alignment explanation
Indices: 145545--145610 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
145535 GCAACTCAGT
*
145545 TTTCAAATTCGCAACACGA
1 TTTCAAATTCGCAACGCGA
* * * *
145564 TTCTCCAAAATCGTAATGCGGT
1 TT-T-CAAATTCGCAACGC-GA
145586 TTTCAAATTCGCAACGCGAA
1 TTTCAAATTCGCAACGCG-A
145606 TTTCA
1 TTTCA
145611 TTTTCGCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 7
0.68 0.18 0.14
Matches are distributed among these distances:
19 3 0.09
20 17 0.50
21 11 0.32
22 3 0.09
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (19 bp):
TTTCAAATTCGCAACGCGA
Found at i:145675 original size:50 final size:50
Alignment explanation
Indices: 145595--145716 Score: 172
Period size: 50 Copynumber: 2.4 Consensus size: 50
145585 TTTTCAAATT
** ** *
145595 CGCAACGCGAATTTCATTTTCGCAATGCTAATTACCGATATAGGTAAACA
1 CGCAACGCGGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACA
*
145645 CGCAACGCGGTTTTCAAATTCGCAACGCTAATTACCGATATATGTAAACA
1 CGCAACGCGGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACA
* *
145695 AGCAACGTGGTTTTCAAATTCG
1 CGCAACGCGGTTTTCAAATTCG
145717 TGTTGCGAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (50 bp):
CGCAACGCGGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACA
Found at i:145869 original size:21 final size:21
Alignment explanation
Indices: 145842--145907 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 21
145832 TTGCGAAAAC
*
145842 GAAAATCGCGTTGAGATTTTG
1 GAAAATCGCGTTGCGATTTTG
* *
145863 GAGAATCGCGTTGCGAATTT-
1 GAAAATCGCGTTGCGATTTTG
*
145883 GAAAACCGCGTTGCGATTTT-
1 GAAAATCGCGTTGCGATTTTG
145903 GAAAA
1 GAAAA
145908 CTGTGTTGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (21 bp):
GAAAATCGCGTTGCGATTTTG
Found at i:148667 original size:25 final size:24
Alignment explanation
Indices: 148608--148680 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
148598 AACAAGCTTT
148608 TAAACGAGCTTGTTCATGAACATA
1 TAAACGAGCTTGTTCATGAACATA
148632 TAAACGAGCTTGTTCATGAACATA
1 TAAACGAGCTTGTTCATGAACATA
*
148656 TAAAACGAGCTTGTTCGTGAACATA
1 T-AAACGAGCTTGTTCATGAACATA
148681 AACGAAATGA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 25 0.53
25 22 0.47
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
TAAACGAGCTTGTTCATGAACATA
Found at i:149290 original size:24 final size:24
Alignment explanation
Indices: 149233--149290 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
149223 TGGGTATGGA
*
149233 GAACATAAACAAACATTAACGAAC
1 GAACATAAATAAACATTAACGAAC
149257 GAACATAAATAAACA-TAACCGAAC
1 GAACATAAATAAACATTAA-CGAAC
*
149281 GAATATAAAT
1 GAACATAAAT
149291 GAACGAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.59, C:0.17, G:0.09, T:0.16
Consensus pattern (24 bp):
GAACATAAATAAACATTAACGAAC
Found at i:149294 original size:14 final size:14
Alignment explanation
Indices: 149253--149308 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
149243 AAACATTAAC
149253 GAACGAACATAAAT
1 GAACGAACATAAAT
**
149267 --A--AACATAACC
1 GAACGAACATAAAT
*
149277 GAACGAATATAAAT
1 GAACGAACATAAAT
149291 GAACGAACATAAAT
1 GAACGAACATAAAT
149305 GAAC
1 GAAC
149309 AGATTATGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
10 7 0.22
12 2 0.06
14 23 0.72
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.14
Consensus pattern (14 bp):
GAACGAACATAAAT
Found at i:151075 original size:13 final size:13
Alignment explanation
Indices: 151043--151078 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
151033 CAATCCAGGC
151043 GACATACG-GGGT
1 GACATACGAGGGT
151055 GACAATACGAGGGT
1 GAC-ATACGAGGGT
151069 GACATACGAG
1 GACATACGAG
151079 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 12 0.55
14 7 0.32
ACGTcount: A:0.33, C:0.17, G:0.36, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:151115 original size:13 final size:13
Alignment explanation
Indices: 151097--151123 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
151087 GAGCCATATG
151097 GGGTGACATACGA
1 GGGTGACATACGA
151110 GGGTGACATACGA
1 GGGTGACATACGA
151123 G
1 G
151124 CCATATACGA
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:0.41, T:0.15
Consensus pattern (13 bp):
GGGTGACATACGA
Found at i:151115 original size:45 final size:46
Alignment explanation
Indices: 151045--151134 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 46
151035 ATCCAGGCGA
151045 CATACGGGGTGACAATACGAGGGTGACATACGAGCCATATACGAGC
1 CATACGGGGTGACAATACGAGGGTGACATACGAGCCATATACGAGC
*
151091 CATATGGGGTGAC-ATACGAGGGTGACATACGAGCCATATACGAG
1 CATACGGGGTGACAATACGAGGGTGACATACGAGCCATATACGAG
151135 GGGAGCATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 31 0.72
46 12 0.28
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (46 bp):
CATACGGGGTGACAATACGAGGGTGACATACGAGCCATATACGAGC
Found at i:151188 original size:29 final size:29
Alignment explanation
Indices: 151155--151234 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
151145 AGGAATAGAG
* *
151155 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGCAGTCC-AGGCGACCCTCT
* *
151184 AGGTCGCCATGTAGTCCCGGCGACCCTCT
1 AGGTCGCCATGCAGTCCAGGCGACCCTCT
* *
151213 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGCAGTCCAGGCG
151235 CCATTCCCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 44 0.96
30 2 0.04
ACGTcount: A:0.15, C:0.34, G:0.31, T:0.20
Consensus pattern (29 bp):
AGGTCGCCATGCAGTCCAGGCGACCCTCT
Found at i:151335 original size:27 final size:27
Alignment explanation
Indices: 151303--151358 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
151293 CCTACAGCTC
151303 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
*
151330 CCAATGCATGCATGTGAACCGTTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
151357 CC
1 CC
151359 GTGAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:151503 original size:23 final size:23
Alignment explanation
Indices: 151475--151520 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
151465 AAAAGAAAGA
151475 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
151498 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
151521 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:151535 original size:25 final size:23
Alignment explanation
Indices: 151475--151535 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
151465 AAAAGAAAGA
**
151475 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
151498 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
151521 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
151536 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:151549 original size:21 final size:21
Alignment explanation
Indices: 151525--151577 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
151515 TTGCAGCCGA
151525 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
151546 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
151567 GAAAGTAAGAA
1 GAAAGAAAGAA
151578 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:151571 original size:17 final size:16
Alignment explanation
Indices: 151523--151554 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
151513 GATTGCAGCC
151523 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
151539 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
151555 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:151757 original size:41 final size:41
Alignment explanation
Indices: 151712--151800 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
151702 TATATGATTG
* *
151712 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
151753 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
151794 TTAGTTT
1 TTAGTTT
151801 GTTTTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:151824 original size:47 final size:47
Alignment explanation
Indices: 151781--151872 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 47
151771 TTATATAGTT
*
151781 AAAAAA-TAATTAATTAGTTTGT-TTTGTT-AATAGTTAGTTATATA
1 AAAAAATTAATTAATTAGTTTGTGTTAGTTAAATAGTTAGTTATATA
*
151825 AAAAAATTTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TTAATTAATTAGTTTGTGTTAGTTAAATAGTT-AGTTATAT
151873 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
44 6 0.15
46 15 0.37
47 5 0.12
48 7 0.17
49 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (47 bp):
AAAAAATTAATTAATTAGTTTGTGTTAGTTAAATAGTTAGTTATATA
Found at i:152064 original size:16 final size:16
Alignment explanation
Indices: 152032--152078 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
152022 TTTAAAAAGT
*
152032 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
152048 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
152064 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
152079 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:152073 original size:15 final size:14
Alignment explanation
Indices: 152053--152083 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
152043 GTTTATTAGT
152053 TTATTATATTATAAG
1 TTATTATATTA-AAG
152068 TTATTATATTAAAG
1 TTATTATATTAAAG
152082 TT
1 TT
152084 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:153119 original size:20 final size:21
Alignment explanation
Indices: 153082--153122 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
153072 CCTCTATTTT
153082 AATATAAAATATTAATTAAAA
1 AATATAAAATATTAATTAAAA
* *
153103 AATA-AAAATTTTGATTAAAA
1 AATATAAAATATTAATTAAAA
153123 TTATTGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AATATAAAATATTAATTAAAA
Found at i:154202 original size:26 final size:25
Alignment explanation
Indices: 154162--154498 Score: 288
Period size: 26 Copynumber: 13.4 Consensus size: 25
154152 ACAACAATTG
*
154162 TAAACTCATTTTTATAATGATTATTA
1 TAAA-TCATTATTATAATGATTATTA
154188 CTAAATCATTATTATAATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
*
154214 TCAAATCATTACTATAATGATTATTA
1 T-AAATCATTATTATAATGATTATTA
* * * *
154240 TCAAATCATTACTA-AATCATCAAATCA
1 T-AAATCATTATTATAATGAT--TATTA
*
154267 TTAAAT-A-T-TTA-AATCATTA-T-
1 -TAAATCATTATTATAATGATTATTA
*
154287 TAAATCATTTTTATAATGATTATTA
1 TAAATCATTATTATAATGATTATTA
154312 CTAAATCATTATTATAATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
*
154338 TCAAATCATTACTATAATGATTATTA
1 T-AAATCATTATTATAATGATTATTA
* * * *
154364 TCAAATCATTACTA-AATCATCAAATCA
1 T-AAATCATTATTATAATGAT--TATTA
*
154391 TTAAAT-A-T-TTA-AATCATTA-T-
1 -TAAATCATTATTATAATGATTATTA
*
154411 TAAATCATTTTTATAATGATTATTA
1 TAAATCATTATTATAATGATTATTA
154436 CTAAATCATTATTATAATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
*
154462 TCAAATCATTACTATAATGATTATTA
1 T-AAATCATTATTATAATGATTATTA
154488 TCAAATCATTA
1 T-AAATCATTA
154499 CTAAATCATC
Statistics
Matches: 267, Mismatches: 20, Indels: 47
0.80 0.06 0.14
Matches are distributed among these distances:
19 10 0.04
20 2 0.01
21 2 0.01
22 8 0.03
23 14 0.05
24 18 0.07
25 15 0.06
26 178 0.67
27 18 0.07
28 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (25 bp):
TAAATCATTATTATAATGATTATTA
Found at i:154387 original size:124 final size:124
Alignment explanation
Indices: 154162--154556 Score: 781
Period size: 124 Copynumber: 3.2 Consensus size: 124
154152 ACAACAATTG
154162 TAAACTCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACT
1 TAAA-TCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACT
154227 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
65 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
154287 TAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
1 TAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
154352 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
66 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
154411 TAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
1 TAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
154476 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
66 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
154535 TAAATCATTTTTATAATGATTA
1 TAAATCATTTTTATAATGATTA
154557 ATAAATACAT
Statistics
Matches: 270, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
124 266 0.99
125 4 0.01
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (124 bp):
TAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
Found at i:157444 original size:26 final size:24
Alignment explanation
Indices: 157386--157444 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
157376 CTAATAAATC
*
157386 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
157410 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
157438 TAATAAT
1 TAATAAT
157445 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:157744 original size:16 final size:15
Alignment explanation
Indices: 157710--157740 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
157700 CAATGTAAAA
157710 TAAACAAAATATTTT
1 TAAACAAAATATTTT
*
157725 TAAACACAATATTTT
1 TAAACAAAATATTTT
157740 T
1 T
157741 TAAAACGGAA
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:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAACAAAATATTTT
Found at i:158189 original size:28 final size:30
Alignment explanation
Indices: 158149--158211 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
158139 ATTTTTTATA
*
158149 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
158179 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
158207 TAATA
1 TAATA
158212 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:158218 original size:28 final size:28
Alignment explanation
Indices: 158153--158218 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
158143 TTTATATAAT
*
158153 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
158181 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
158209 ATAATTTATA
1 ATAATATATA
158219 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:158221 original size:21 final size:21
Alignment explanation
Indices: 158188--158236 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
158178 CTAATATAAT
158188 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
158209 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
158230 ATTAACT
1 A-TAACT
158237 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:158856 original size:29 final size:29
Alignment explanation
Indices: 158814--158876 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
158804 TTTGCAAAAT
* *
158814 ACCTCCAAGGTCGCCGGGATTACATGGCG
1 ACCTACAAGGTCGCCGGGACTACATGGCG
158843 ACCTACAAGGTCGCCGGGACTACATGGCG
1 ACCTACAAGGTCGCCGGGACTACATGGCG
158872 ACCTA
1 ACCTA
158877 TGGCGATCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.24, C:0.32, G:0.29, T:0.16
Consensus pattern (29 bp):
ACCTACAAGGTCGCCGGGACTACATGGCG
Found at i:169826 original size:14 final size:14
Alignment explanation
Indices: 169807--169837 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
169797 AGTTAAGAAC
*
169807 CATGTAAACCGTGG
1 CATGTAAACCATGG
169821 CATGTAAACCATGG
1 CATGTAAACCATGG
169835 CAT
1 CAT
169838 TGCCAACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (14 bp):
CATGTAAACCATGG
Found at i:170909 original size:12 final size:12
Alignment explanation
Indices: 170892--170920 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
170882 ATAAATTTAA
170892 TTAAATAATAAT
1 TTAAATAATAAT
170904 TTAAATAATAAT
1 TTAAATAATAAT
170916 TTAAA
1 TTAAA
170921 AGTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAAATAATAAT
Done.