Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2284141 original size:28 final size:26
Alignment explanation
Indices: 2284104--2284165 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
2284094 TTTTGAAAAC
*
2284104 GTTTTT-AATATATATATAATATATA
1 GTTTTTGAAAATATATATAATATATA
*
2284129 GTTTTTGAAAATATATATAATATTTA
1 GTTTTTGAAAATATATATAATATATA
2284155 GTTTTTGAAAA
1 GTTTTTGAAAA
2284166 CATTTTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 6 0.18
26 28 0.82
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
GTTTTTGAAAATATATATAATATATA
Found at i:2284150 original size:37 final size:37
Alignment explanation
Indices: 2284078--2284151 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
2284068 GGTGTCGACA
* * *
2284078 ATATATAATATATAGTTTTTGAAAACGTTTTTAATAT
1 ATATATAATATATAGTTTTTGAAAACATATATAATAT
*
2284115 ATATATAATATATAGTTTTTGAAAATATATATAATAT
1 ATATATAATATATAGTTTTTGAAAACATATATAATAT
2284152 TTAGTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTGAAAACATATATAATAT
Found at i:2284180 original size:63 final size:61
Alignment explanation
Indices: 2284078--2284200 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 61
2284068 GGTGTCGACA
* *
2284078 ATATATAATATATAGTTTTTGAAAACGTTTTTAATATATATATAATATATAGTTTTTGAAAAT
1 ATATATAATATATAGTTTTTGAAAACATTTTGAA-A-ATATATAATATATAGTTTTTGAAAAT
*
2284141 ATATATAATATTTAGTTTTTGAAAACATTTTGAAAATATATAATATATAGTTTTTGAAAA
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATAATATATAGTTTTTGAAAA
2284201 CATTTTTGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 25 0.44
62 1 0.02
63 31 0.54
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (61 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATAATATATAGTTTTTGAAAAT
Found at i:2284208 original size:12 final size:12
Alignment explanation
Indices: 2284191--2284215 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2284181 TAATATATAG
2284191 TTTTTGAAAACA
1 TTTTTGAAAACA
2284203 TTTTTGAAAACA
1 TTTTTGAAAACA
2284215 T
1 T
2284216 ATATAAAATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:2284218 original size:36 final size:35
Alignment explanation
Indices: 2284143--2284218 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 35
2284133 TTGAAAATAT
* *
2284143 ATATAATATTTAGTTTTTGAAAACATTTTGAAAAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAAC
2284178 ATATAATATATAGTTTTTGAAAACATTTTTGAAAAC
1 ATATAATATATAGTTTTTGAAAACA-TTTTGAAAAC
2284214 ATATA
1 ATATA
2284219 TAAAATATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 24 0.63
36 14 0.37
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (35 bp):
ATATAATATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:2284224 original size:47 final size:47
Alignment explanation
Indices: 2284156--2284299 Score: 128
Period size: 47 Copynumber: 3.2 Consensus size: 47
2284146 TAATATTTAG
*
2284156 TTTTTGAAAACAT-TTTGAAAATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAACATATAT-AAAATATATAATATATAGTTTTTGAAAACA
* * *
2284203 TTTTTGAAAACATATATAAAATATAGT-TTAAATTGTTTTTTGAAAACA
1 TTTTTGAAAACATATATAAAATATA-TAATATATAG-TTTTTGAAAACA
* * *
2284251 --TTT---AATATATAT-ATATATATAATATATAG-TTTT-AAAATA
1 TTTTTGAAAACATATATAAAATATATAATATATAGTTTTTGAAAACA
2284290 TTTTTGAAAA
1 TTTTTGAAAA
2284300 AAGTATATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
39 5 0.06
40 4 0.05
41 4 0.05
42 11 0.14
43 8 0.10
44 2 0.03
46 3 0.04
47 26 0.33
48 15 0.19
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (47 bp):
TTTTTGAAAACATATATAAAATATATAATATATAGTTTTTGAAAACA
Found at i:2284312 original size:35 final size:39
Alignment explanation
Indices: 2284261--2284349 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 39
2284251 TTTAATATAT
* * *
2284261 ATATATATATAATATATAGTTTT-AAAATATTTTTGAAA
1 ATATATGTATATTATATAGTTTTGAAAATATATTTGAAA
*
2284299 A-A-A-GTATATTATATAGTTTTGGAAATATATTTGAAA
1 ATATATGTATATTATATAGTTTTGAAAATATATTTGAAA
2284335 ATATATGTATATTAT
1 ATATATGTATATTAT
2284350 TATTATTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
35 15 0.35
36 15 0.35
37 2 0.05
38 2 0.05
39 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (39 bp):
ATATATGTATATTATATAGTTTTGAAAATATATTTGAAA
Found at i:2284312 original size:52 final size:51
Alignment explanation
Indices: 2284214--2284313 Score: 121
Period size: 51 Copynumber: 1.9 Consensus size: 51
2284204 TTTTGAAAAC
* * * *
2284214 ATATATAAAATATAGTTTAAATTGTTTTTTGAAAACATTTAATATATATAT
1 ATATATAAAATATAGTTTAAAATGATTTTTGAAAAAATATAATATATATAT
* *
2284265 ATATATAATATATAGTTTTAAAAT-ATTTTTGAAAAAAGTATATTATATA
1 ATATATAAAATATAG-TTTAAAATGATTTTTGAAAAAA-TATAATATATA
2284314 GTTTTGGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 25 0.61
52 16 0.39
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (51 bp):
ATATATAAAATATAGTTTAAAATGATTTTTGAAAAAATATAATATATATAT
Found at i:2286170 original size:156 final size:156
Alignment explanation
Indices: 2285885--2286191 Score: 474
Period size: 156 Copynumber: 2.0 Consensus size: 156
2285875 TAAAATTCTG
2285885 AAACCATAGTAATCCCTCCAGAACAACACATCATAATGTGTAGGTTCCCTAGAACCATACACCCA
1 AAACCATAGTAATCCCTCCAGAACAACACATCATAATGTGTAGGTTCCCTAGAACCATACACCCA
* * *
2285950 CTGTCAAATCGAGTAAAGCCCTGAGCATAAAGCCGAGGAACCTGCAAGTATACTTCATCCAACAA
66 CCGTCAAATCGAGTAAAGCCCTGAGCACAAAGCCGAGGAACCTGCAAGTATACTTCATACAACAA
2286015 TA-CCTCCCAAATAAAACATTTATCAA
131 TATCC-CCCAAATAAAACATTTATCAA
* * *
2286041 AAACCATAGTAATCCTTCCA-ACCGAACACATCATAATGTGTAGGTTCCCTAGAACTATACACCC
1 AAACCATAGTAATCCCTCCAGAAC-AACACATCATAATGTGTAGGTTCCCTAGAACCATACACCC
* * * * * *
2286105 ACCGTCATATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATTCTTCCTATAACA
65 ACCGTCAAATCGAGTAAAGCCCTGAGCACAAAGCCGAGGAACCTGCAAGTATACTTCATACAACA
2286170 ATATCCCCCAAATAAAACATTT
130 ATATCCCCCAAATAAAACATTT
2286192 TCCATCCGTA
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
155 2 0.01
156 133 0.97
157 2 0.01
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.21
Consensus pattern (156 bp):
AAACCATAGTAATCCCTCCAGAACAACACATCATAATGTGTAGGTTCCCTAGAACCATACACCCA
CCGTCAAATCGAGTAAAGCCCTGAGCACAAAGCCGAGGAACCTGCAAGTATACTTCATACAACAA
TATCCCCCAAATAAAACATTTATCAA
Found at i:2286267 original size:24 final size:24
Alignment explanation
Indices: 2286212--2286269 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
2286202 AACGGATATA
* *
2286212 TCAAAAATCAAAACATAATTCAGG
1 TCAAATATCAAAACATAATCCAGG
*
2286236 TCAAATATCAGAACATAATCCAGG
1 TCAAATATCAAAACATAATCCAGG
2286260 T-AAGATATCA
1 TCAA-ATATCA
2286270 CAATAGAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.22
Consensus pattern (24 bp):
TCAAATATCAAAACATAATCCAGG
Found at i:2286488 original size:20 final size:20
Alignment explanation
Indices: 2286465--2286520 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2286455 GATACATTCC
2286465 CTTCGGTATCGATACTCCAT
1 CTTCGGTATCGATACTCCAT
* *
2286485 CTTCGATATCGATACTCCTT
1 CTTCGGTATCGATACTCCAT
*
2286505 TTTCGGTATCGATACT
1 CTTCGGTATCGATACT
2286521 TTTTAAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (20 bp):
CTTCGGTATCGATACTCCAT
Found at i:2295167 original size:46 final size:46
Alignment explanation
Indices: 2295112--2295351 Score: 381
Period size: 46 Copynumber: 5.2 Consensus size: 46
2295102 TTTATGCAAG
*
2295112 TTTAATTATGACATCCTTTCATGCCTTAATGTATCCTTTCATGCAT
1 TTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCAT
* ** *
2295158 TTTAATTATGGCATCCTTTCATAACTTAATGTATCCTTTCATGCAT
1 TTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCAT
*
2295204 TTTAATTATGATATCCTTTCATGCCTTAATGCATCCTTTCATGCAT
1 TTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCAT
* *
2295250 TTTAATTATGTCATCCTTTCATGCCTTAATGCATCCTTTCATACAT
1 TTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCAT
* * *
2295296 TTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGTAT
1 TTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCAT
2295342 TTTAATTATG
1 TTTAATTATG
2295352 TATTCGATTT
Statistics
Matches: 179, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 179 1.00
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (46 bp):
TTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCAT
Found at i:2295335 original size:20 final size:20
Alignment explanation
Indices: 2295123--2295338 Score: 117
Period size: 20 Copynumber: 9.6 Consensus size: 20
2295113 TTAATTATGA
2295123 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
2295143 TATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
**
2295169 CATCCTTTCATAACTTAATG
1 CATCCTTTCATGCCTTAATG
* *
2295189 TATCCTTTCATGCATTTTAATTATG
1 CATCCTTTCATGC--CTT-A--ATG
*
2295214 ATATCCTTTCATGCCTTAATG
1 -CATCCTTTCATGCCTTAATG
*
2295235 CATCCTTTCATGCATTTTAATTATG
1 CATCCTTTCATGC--CTT-A--ATG
2295260 TCATCCTTTCATGCCTTAATG
1 -CATCCTTTCATGCCTTAATG
* *
2295281 CATCCTTTCATACATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
2295307 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
2295327 CATCATTTCATG
1 CATCCTTTCATG
2295339 TATTTTAATT
Statistics
Matches: 153, Mismatches: 19, Indels: 48
0.70 0.09 0.22
Matches are distributed among these distances:
20 59 0.39
21 10 0.07
22 8 0.05
23 8 0.05
24 8 0.05
25 10 0.07
26 50 0.33
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.45
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:2295865 original size:20 final size:18
Alignment explanation
Indices: 2295840--2295890 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 18
2295830 GTTTTGAAAT
*
2295840 GGTATCGATACCTTGCCTTC
1 GGTATCGATACCCT--CTTC
2295860 GGTATCGATAATCCCTCTTC
1 GGTATCGAT-A-CCCTCTTC
2295880 GGTATCGATAC
1 GGTATCGATAC
2295891 AGATTGAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 1 0.04
20 22 0.79
21 1 0.04
22 3 0.11
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (18 bp):
GGTATCGATACCCTCTTC
Found at i:2297521 original size:2 final size:2
Alignment explanation
Indices: 2297477--2297508 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2297467 ATAAAACAAT
2297477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2297509 CACACACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2298268 original size:15 final size:14
Alignment explanation
Indices: 2298248--2298281 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2298238 CGACCGGGTC
2298248 AACTCGAACTGAGTT
1 AACTCG-ACTGAGTT
*
2298263 AACTCGGCTGAGTT
1 AACTCGACTGAGTT
2298277 AACTC
1 AACTC
2298282 ACCAGATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (14 bp):
AACTCGACTGAGTT
Found at i:2298342 original size:13 final size:13
Alignment explanation
Indices: 2298319--2298358 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2298309 AGTCAATCCA
*
2298319 TTGACCTTTGACTG
1 TTGA-CTTTGACCG
2298333 TTGACTTTGACCG
1 TTGACTTTGACCG
*
2298346 TTAACTTTGACCG
1 TTGACTTTGACCG
2298359 AGTCAACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGACTTTGACCG
Found at i:2306004 original size:29 final size:29
Alignment explanation
Indices: 2305972--2306030 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2305962 TTAGTAGGAC
2305972 TTAGTTTGTGACATTAGTTATAGTTATGG
1 TTAGTTTGTGACATTAGTTATAGTTATGG
* *
2306001 TTAGTTTGTGACATTAGTTCTAGTTGTGG
1 TTAGTTTGTGACATTAGTTATAGTTATGG
2306030 T
1 T
2306031 GAAAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.49
Consensus pattern (29 bp):
TTAGTTTGTGACATTAGTTATAGTTATGG
Found at i:2318537 original size:44 final size:45
Alignment explanation
Indices: 2318470--2318563 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 45
2318460 ATTTTTATTT
2318470 GATTTTTTTAATTCGGTAGATATTTGGTTGGATTTGCCGACATGA
1 GATTTTTTTAATTCGGTAGATATTTGGTTGGATTTGCCGACATGA
* * *
2318515 GATTTTTTT-ATTTGGTTGATATTTGGTTGGATTTGCTGACATGA
1 GATTTTTTTAATTCGGTAGATATTTGGTTGGATTTGCCGACATGA
*
2318559 TATTT
1 GATTT
2318564 ATTGGTGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 36 0.80
45 9 0.20
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.50
Consensus pattern (45 bp):
GATTTTTTTAATTCGGTAGATATTTGGTTGGATTTGCCGACATGA
Found at i:2319897 original size:26 final size:27
Alignment explanation
Indices: 2319841--2319897 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
2319831 AATTTTTTTG
* * ** *
2319841 TCCTCCTGAAGTTTTATAAGTTCGTTT
1 TCCTCCTGAAATTTTATAAATTCACTC
2319868 TCCT-CTGAAATTTTATAAATTCACTC
1 TCCTCCTGAAATTTTATAAATTCACTC
2319894 TCCT
1 TCCT
2319898 AGTATAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (27 bp):
TCCTCCTGAAATTTTATAAATTCACTC
Found at i:2320705 original size:44 final size:45
Alignment explanation
Indices: 2320571--2320793 Score: 319
Period size: 44 Copynumber: 5.0 Consensus size: 45
2320561 ACATGCATAT
*
2320571 CCAATAT-TTTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATT--CCATAAGCTCGTAAGCTTATTTTA
* * *
2320617 CCAAAATACTTACCATTTATTCCCACAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTA
2320663 CC-ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
2320707 CC-ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* * * *
2320751 CCAACATACTTTCCA-TTATTTCGTAAGCTCGTAAGCTTATTTT
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
2320794 CATGCTTACA
Statistics
Matches: 163, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
44 94 0.58
45 27 0.17
46 30 0.18
47 12 0.07
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (45 bp):
CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
Found at i:2320711 original size:24 final size:24
Alignment explanation
Indices: 2320683--2320753 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
2320673 ACCATTTATT
2320683 CCATAAGCTCGTAAGCTTATTTTA
1 CCATAAGCTCGTAAGCTTATTTTA
* *
2320707 CCATATA-CT--T-A-C-CATTTATT
1 CCATA-AGCTCGTAAGCTTATTT-TA
2320727 CCATAAGCTCGTAAGCTTATTTTA
1 CCATAAGCTCGTAAGCTTATTTTA
2320751 CCA
1 CCA
2320754 ACATACTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
19 5 0.14
20 9 0.26
21 1 0.03
22 2 0.06
23 1 0.03
24 12 0.34
25 5 0.14
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (24 bp):
CCATAAGCTCGTAAGCTTATTTTA
Found at i:2320948 original size:40 final size:40
Alignment explanation
Indices: 2320904--2321065 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
2320894 ACCGTAGTGC
2320904 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2320944 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2320984 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2321024 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2321064 TA
1 TA
2321066 TAAACCTGCA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 119 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2343155 original size:22 final size:22
Alignment explanation
Indices: 2343103--2343157 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2343093 TGACCGAGCC
**
2343103 GACCAAGCCAATCGAGTTGTAT
1 GACCAAGCTGATCGAGTTGTAT
*
2343125 GACCGAGCTGATCGAGTTGTAT
1 GACCAAGCTGATCGAGTTGTAT
*
2343147 GACTAAGCTGA
1 GACCAAGCTGA
2343158 CCAAGTCGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (22 bp):
GACCAAGCTGATCGAGTTGTAT
Found at i:2344343 original size:18 final size:18
Alignment explanation
Indices: 2344316--2344350 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2344306 AAAACTAAAA
* *
2344316 TAAATGATAAGTTTGAAT
1 TAAATAATAAGATTGAAT
2344334 TAAATAATAAGATTGAA
1 TAAATAATAAGATTGAA
2344351 ATACCTTGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
TAAATAATAAGATTGAAT
Found at i:2345880 original size:31 final size:30
Alignment explanation
Indices: 2345845--2345945 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 30
2345835 GTGACTATTA
* *
2345845 GGTAGGCTATGCGGCCCCAAGATCATTCTTG
1 GGTAGGCCAT-CGGCCCTAAGATCATTCTTG
* ** **
2345876 GGTAGGCCCTACGGCCCTGGGATTTTTCTTG
1 GGTAGGCCAT-CGGCCCTAAGATCATTCTTG
2345907 GGTAGGCCCCAT-GGCCCTAAGATCATTCTTG
1 GGTAGG--CCATCGGCCCTAAGATCATTCTTG
2345938 GGTAGGCC
1 GGTAGGCC
2345946 CTGTAGCCCT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
29 2 0.04
31 50 0.91
33 3 0.05
ACGTcount: A:0.16, C:0.27, G:0.31, T:0.27
Consensus pattern (30 bp):
GGTAGGCCATCGGCCCTAAGATCATTCTTG
Found at i:2345929 original size:62 final size:62
Alignment explanation
Indices: 2345857--2346003 Score: 186
Period size: 62 Copynumber: 2.4 Consensus size: 62
2345847 TAGGCTATGC
* * ** **
2345857 GGCCCCAAGATCATTCTTGGGTAGGCCCTACGGCCCTGGGATTTTTCTTGGGTAGGCCCCAT
1 GGCCCTAAGATCATTCTTGGGTAGGCCCTACAGCCCTGACAACTTTCTTGGGTAGGCCCCAT
** *
2345919 GGCCCTAAGATCATTCTTGGGTAGGCCCTGTAGCCCTGACAACTTTCTTGGGTAGGCCCCGT
1 GGCCCTAAGATCATTCTTGGGTAGGCCCTACAGCCCTGACAACTTTCTTGGGTAGGCCCCAT
* * *
2345981 GGCCCTGAGAACTTTCTTGGGTA
1 GGCCCTAAGATCATTCTTGGGTA
2346004 AGCTCTCAGG
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 73 1.00
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (62 bp):
GGCCCTAAGATCATTCTTGGGTAGGCCCTACAGCCCTGACAACTTTCTTGGGTAGGCCCCAT
Found at i:2345946 original size:31 final size:31
Alignment explanation
Indices: 2345857--2346022 Score: 145
Period size: 31 Copynumber: 5.4 Consensus size: 31
2345847 TAGGCTATGC
* * * *
2345857 GGCCCCAAGATCATTCTTGGGTAGGCCCTAC
1 GGCCCTAAGATCTTTCTTGGGTAGGCCCCAT
** *
2345888 GGCCCTGGGATTTTTCTTGGGTAGGCCCCAT
1 GGCCCTAAGATCTTTCTTGGGTAGGCCCCAT
* **
2345919 GGCCCTAAGATCATTCTTGGGTAGGCCCTGT
1 GGCCCTAAGATCTTTCTTGGGTAGGCCCCAT
* * * * *
2345950 AGCCCTGACAACTTTCTTGGGTAGGCCCCGT
1 GGCCCTAAGATCTTTCTTGGGTAGGCCCCAT
* * * *
2345981 GGCCCTGAGAACTTTCTTGGGTAAGCTCTCA-
1 GGCCCTAAGATCTTTCTTGGGTAGGC-CCCAT
2346012 GGCCCTAAGAT
1 GGCCCTAAGAT
2346023 GCTCCTTTAG
Statistics
Matches: 108, Mismatches: 26, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
31 106 0.98
32 2 0.02
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27
Consensus pattern (31 bp):
GGCCCTAAGATCTTTCTTGGGTAGGCCCCAT
Found at i:2352844 original size:21 final size:21
Alignment explanation
Indices: 2352819--2352861 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2352809 GAGGGGATCG
*
2352819 AAAAAACACATAAAGCATTCAT
1 AAAAAA-ACAGAAAGCATTCAT
*
2352841 AAAAAAACAGAGAGCATTCAT
1 AAAAAAACAGAAAGCATTCAT
2352862 CAACATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAAAAACAGAAAGCATTCAT
Found at i:2354811 original size:17 final size:19
Alignment explanation
Indices: 2354781--2354819 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
2354771 CGCATACCTC
2354781 AAATTTATTTA-TTTTATT
1 AAATTTATTTATTTTTATT
2354799 AAATTTA-TTATTTTTATT
1 AAATTTATTTATTTTTATT
2354817 AAA
1 AAA
2354820 ATGGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AAATTTATTTATTTTTATT
Found at i:2366804 original size:23 final size:23
Alignment explanation
Indices: 2366778--2366822 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2366768 ATACCTGACC
* *
2366778 TGACCTGGATTCTGATTTGATAT
1 TGACATGGATTCTGATATGATAT
2366801 TGACATGGATTCTGATATGATA
1 TGACATGGATTCTGATATGATA
2366823 CTTAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (23 bp):
TGACATGGATTCTGATATGATAT
Found at i:2366952 original size:35 final size:35
Alignment explanation
Indices: 2366905--2366979 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
2366895 TGGAGGAAGA
* *
2366905 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCAGCTTTGTGCTCAGGGCC
2366940 TTACTTGCAGGCTCCTCAGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCAGCTTTGTGCTCAGGGCC
2366975 TTACT
1 TTACT
2366980 GTTCGTGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.11, C:0.29, G:0.27, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCAGCTTTGTGCTCAGGGCC
Found at i:2373826 original size:5 final size:5
Alignment explanation
Indices: 2373807--2373868 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
2373797 TTACATAGTA
2373807 TATAT TATAT ATATAT TATAT TAT-T GTATTAT TAT-T ATATAT TAT-T
1 TATAT TATAT -TATAT TATAT TATAT -TA-TAT TATAT -TATAT TATAT
*
2373853 TTTA- TATAT TATAT TA
1 TATAT TATAT TATAT TA
2373869 AAGTATATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
4 8 0.17
5 29 0.62
6 9 0.19
7 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:2373836 original size:8 final size:8
Alignment explanation
Indices: 2373807--2373868 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
2373797 TTACATAGTA
2373807 TATATTA-
1 TATATTAT
2373814 TATATATAT
1 TATAT-TAT
2373823 TATATTAT
1 TATATTAT
*
2373831 TGTATTAT
1 TATATTAT
2373839 TATTATATAT
1 TA-TAT-TAT
2373849 TAT-TT-T
1 TATATTAT
2373855 TATA-TAT
1 TATATTAT
2373862 TATATTA
1 TATATTA
2373869 AAGTATATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
6 5 0.11
7 11 0.24
8 16 0.35
9 9 0.20
10 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (8 bp):
TATATTAT
Found at i:2373848 original size:39 final size:38
Alignment explanation
Indices: 2373805--2373931 Score: 102
Period size: 39 Copynumber: 3.2 Consensus size: 38
2373795 TATTACATAG
2373805 TATATATTATATATATATTATATTATTGTATTATTATTA
1 TATATATTATATATATATTATATTA-TGTATTATTATTA
* * *
2373844 TATATTATT-TTTATATATTATATTAAAGTA-TATTCTTAAA
1 TATA-TATTATATATATATTATATT-ATGTATTATTATT--A
*
2373884 CTTATATATGTATATACCAT-TTATATTAT-TATTATTATTA
1 --TATATAT-TATATA-TATATTATATTATGTATTATTATTA
2373924 T-TATATTA
1 TATATATTA
2373932 ATGTTTTCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
36 2 0.03
37 5 0.07
38 7 0.10
39 21 0.30
40 7 0.10
41 5 0.07
42 12 0.17
43 10 0.14
44 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (38 bp):
TATATATTATATATATATTATATTATGTATTATTATTA
Found at i:2373849 original size:13 final size:12
Alignment explanation
Indices: 2373789--2373868 Score: 81
Period size: 13 Copynumber: 6.3 Consensus size: 12
2373779 CGTCCGTGAC
2373789 ATTATATATTACAT
1 ATTATATATT--AT
*
2373803 AGTATATATTAT
1 ATTATATATTAT
2373815 A-TATATATTAT
1 ATTATATATTAT
*
2373826 ATTATTGTATTATT
1 ATTA-TATATTA-T
2373840 ATTATATATTATT
1 ATTATATATTA-T
*
2373853 TTTATATATTAT
1 ATTATATATTAT
2373865 ATTA
1 ATTA
2373869 AAGTATATTC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
11 11 0.19
12 9 0.16
13 24 0.41
14 14 0.24
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (12 bp):
ATTATATATTAT
Found at i:2375363 original size:31 final size:31
Alignment explanation
Indices: 2375325--2375390 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
2375315 TGCTGAGCAG
*
2375325 AATGGAAATACCAACTCAGACAATATTTTGA
1 AATGGAAATACCAACACAGACAATATTTTGA
*
2375356 AATGGAAATACCAACACAGACAATATTTTTA
1 AATGGAAATACCAACACAGACAATATTTTGA
2375387 AATG
1 AATG
2375391 AAAAACAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (31 bp):
AATGGAAATACCAACACAGACAATATTTTGA
Found at i:2381320 original size:24 final size:24
Alignment explanation
Indices: 2381293--2381339 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2381283 AGCAAAAACT
*
2381293 TCATCAATTGCAAAAACACAAGCC
1 TCATCAACTGCAAAAACACAAGCC
* *
2381317 TCATCTACTGCAAAATCACAAGC
1 TCATCAACTGCAAAAACACAAGC
2381340 TTCTATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.30, G:0.09, T:0.19
Consensus pattern (24 bp):
TCATCAACTGCAAAAACACAAGCC
Found at i:2385273 original size:18 final size:18
Alignment explanation
Indices: 2385250--2385287 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2385240 ACCGGTCATA
* *
2385250 ACCCGACCCGACCCATTG
1 ACCCGACACAACCCATTG
2385268 ACCCGACACAACCCATTG
1 ACCCGACACAACCCATTG
2385286 AC
1 AC
2385288 TGTTGACCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.47, G:0.13, T:0.11
Consensus pattern (18 bp):
ACCCGACACAACCCATTG
Found at i:2387736 original size:24 final size:24
Alignment explanation
Indices: 2387718--2387833 Score: 139
Period size: 24 Copynumber: 4.8 Consensus size: 24
2387708 TTTGATTTAA
*
2387718 ATTCTGATCTGATACTTGATATGG
1 ATTCTGATCTGATACTTGACATGG
*
2387742 ATTCTTATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
2387766 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
2387790 ATTCTGATCT-ATTACTTGACCT-G
1 ATTCTGATCTGA-TACTTGACATGG
*
2387813 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
2387834 CTGATTTATG
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.05
24 75 0.93
25 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.42
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:2389954 original size:18 final size:18
Alignment explanation
Indices: 2389928--2389972 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2389918 ACCGGTTATA
* * *
2389928 ACCCAACCCAACCCGTTT
1 ACCCGACCCAACACGTTG
2389946 ACCCGACCCAACACGTTG
1 ACCCGACCCAACACGTTG
2389964 ACCCGACCC
1 ACCCGACCC
2389973 GTTGAGCCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.51, G:0.11, T:0.11
Consensus pattern (18 bp):
ACCCGACCCAACACGTTG
Found at i:2392453 original size:24 final size:24
Alignment explanation
Indices: 2392416--2392531 Score: 121
Period size: 24 Copynumber: 4.8 Consensus size: 24
2392406 TCTGATTTAA
*
2392416 ATTCTGATCAGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
2392440 ATTTTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* * *
2392464 ATTCTGATCTGAGACTTGACTTTG
1 ATTCTGATCTGATACTTGACATGG
*
2392488 ATTCTGATCT-ATTACTTGACCT-G
1 ATTCTGATCTGA-TACTTGACATGG
*
2392511 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
2392532 CTGATTTATG
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
23 4 0.05
24 72 0.92
25 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:2394211 original size:39 final size:38
Alignment explanation
Indices: 2394167--2394297 Score: 174
Period size: 39 Copynumber: 3.3 Consensus size: 38
2394157 CGCTACGACA
* *
2394167 AGGGTAAGTCATTACCAG-AGGCTCCTTTGTTTTGTGCAT
1 AGGGTAAGTC-TTACC-GCAGACTCCTTTGTTTTGTGCAC
2394206 AGGGTAAGTCCTTACCGCAGACTCCTTTGTTTTGTGCAC
1 AGGGTAAGT-CTTACCGCAGACTCCTTTGTTTTGTGCAC
* *
2394245 AGGGTAAGTTCTTACCGTATACTCCTTTGTTTTGTGCAC
1 AGGGTAAG-TCTTACCGCAGACTCCTTTGTTTTGTGCAC
2394284 AGGGTAAGTTCTTA
1 AGGGTAAG-TCTTA
2394298 TCGTAATCTC
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
38 1 0.01
39 82 0.96
40 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (38 bp):
AGGGTAAGTCTTACCGCAGACTCCTTTGTTTTGTGCAC
Found at i:2399738 original size:30 final size:30
Alignment explanation
Indices: 2399683--2399752 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2399673 AAAAAATGTT
* * *
2399683 AAATTTTAATTTGACCTCTGAATTTAGACA
1 AAATATTAATTTGACCTCTAAATTTACACA
*
2399713 AAATATTAATTTGACCT-TAACATTTACATA
1 AAATATTAATTTGACCTCTAA-ATTTACACA
*
2399743 AAATACTAAT
1 AAATATTAAT
2399753 CTAACTCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATATTAATTTGACCTCTAAATTTACACA
Found at i:2404052 original size:59 final size:59
Alignment explanation
Indices: 2403959--2404508 Score: 796
Period size: 59 Copynumber: 9.3 Consensus size: 59
2403949 ATTCATAATT
* * * * * *
2403959 TTAGCACACAATGTGCCCAATAAGGAAATTCATACACTTAGTATGAACTTCTTACCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * *
2404018 TTAGCACACGAAGTGCCCTATACGAAAATCCATACACTTAGTATGAATTTCTTCTCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* *
2404077 TTAGCACACAAAGTGCCCTATATGGAAATCCGTACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * *
2404136 TTAGTACACAAAGTGTCATATACGGAAATCCATACACTTAGTATGGATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * * *
2404195 TTAGCACACAAAGTGCCCTATACAGAAATCCATACACTTAATATGATTTTTTTCTCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* *
2404254 TTAGCACACAAATTGCCCTATACGGAAATCCATACACTTAGTATAAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* **
2404313 TTAGCACACAAAGTGCCCTATACAGAAATCCATACACTTAGTACAAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * *
2404372 TTAGCACACAAAGTGCCTTAAATGGAAATCAATACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* *
2404431 GTAGCACACAAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
*
2404490 TTCA-CTCACAAAGTGCCCT
1 TT-AGCACACAAAGTGCCCT
2404509 CTAGTAATCA
Statistics
Matches: 436, Mismatches: 54, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
59 435 1.00
60 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (59 bp):
TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
Found at i:2410318 original size:59 final size:59
Alignment explanation
Indices: 2410220--2410768 Score: 789
Period size: 59 Copynumber: 9.3 Consensus size: 59
2410210 TTTCATAATT
* * ** * *
2410220 TTAGCACACAAGGTGCCCAATACATAAATTCATACACTTAGTATGAACTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * *
2410279 TTAGCACACGAAGTTCCCTATACGAAAATCCATACACTTAGTATGAATTTCTTCTCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* *
2410338 TTAGCACACAAAGTACCCGATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * *
2410397 TTAGCACACAAAGTGCCCTATACGGAAATCCATATACATAGTATGAATTTCTTATAATA
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * *
2410456 TTAGCACACAAAGTGCCCTATATGGAAATCCATACACTTAGTATAAATGTT-TTCTCGTG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAAT-TTCTTATCATG
* *
2410515 TTAGAACACAAAGTTCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* *
2410574 TTAGCACAAAAAGTGCCCTATAC-GAAAGTCCATACACTTAATATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAA-TCCATACACTTAGTATGAATTTCTTATCATG
* * *
2410633 TTAGAACACAAATTGCCCTATACAG-AATCCATACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * *
2410691 TTAGCGCACAAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTATCATT
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
2410750 TTAGCACACAAAGTGCCCT
1 TTAGCACACAAAGTGCCCT
2410769 CTGGTAATCA
Statistics
Matches: 436, Mismatches: 49, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
58 57 0.13
59 376 0.86
60 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (59 bp):
TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
Found at i:2418141 original size:13 final size:13
Alignment explanation
Indices: 2418125--2418159 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2418115 TAAGATTTTC
2418125 TTTTTGAAAATCA
1 TTTTTGAAAATCA
2418138 TTTTTG-AAATCA
1 TTTTTGAAAATCA
*
2418150 ATTTTGAAAA
1 TTTTTGAAAA
2418160 ATTACTCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:2420486 original size:23 final size:21
Alignment explanation
Indices: 2420451--2420505 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
2420441 CCCTCTAGGG
*
2420451 GTATCGATGCACATTCAAGGAAT
1 GTATCGATACACATTCAAGG--T
* *
2420474 GTATCGGTACACATTTAAGGT
1 GTATCGATACACATTCAAGGT
2420495 GTATCGATACA
1 GTATCGATACA
2420506 TAGAAAGGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (21 bp):
GTATCGATACACATTCAAGGT
Found at i:2424693 original size:47 final size:47
Alignment explanation
Indices: 2424636--2424755 Score: 170
Period size: 47 Copynumber: 2.6 Consensus size: 47
2424626 TTTACCATTT
*
2424636 ATCCCATAAGCTCGTAAGCTTATTTTA-CCAAAATACTTAACATATAA
1 ATCCCATAAGCTCGTAAGCTTATTTTATACAAAATACTTAACAT-TAA
* * * *
2424683 ATTCCATAAGCTCATAAGCTTATTTTATACAAAATACTTACCATTTA
1 ATCCCATAAGCTCGTAAGCTTATTTTATACAAAATACTTAACATTAA
*
2424730 ATCCCATAAGCTCGTAAGGTTATTTT
1 ATCCCATAAGCTCGTAAGCTTATTTT
2424756 TCCCATATAC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 50 0.78
48 14 0.22
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (47 bp):
ATCCCATAAGCTCGTAAGCTTATTTTATACAAAATACTTAACATTAA
Found at i:2424947 original size:40 final size:40
Alignment explanation
Indices: 2424903--2425062 Score: 293
Period size: 40 Copynumber: 4.0 Consensus size: 40
2424893 ACCGTAGTGC
*
2424903 TACACATAAAGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2424943 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2424983 TACACATAAGGCCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2425023 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2425063 ATAAACCTGC
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2431713 original size:47 final size:45
Alignment explanation
Indices: 2431648--2431819 Score: 193
Period size: 47 Copynumber: 3.8 Consensus size: 45
2431638 ATAAAATCTT
* *
2431648 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
2431693 TTACCATATAAATTCCATAAGCTCATAAGCTTATTTTATACAAAATAC
1 TTACCAT-T-AATTCCATAAGCTCGTAAGCTTATTTTA-CCAAAATAC
* * * * *
2431741 TTATCATTTAATCCCATAAGCTCGTAAGCTTATTTTTCCCATATAC
1 TTACCA-TTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
2431787 TTGCCATT-ATTCCAAAAGCTTGTAAGCTTATTT
1 TTACCATTAATTCCATAAGCTCGTAAGCTTATTT
2431820 GCATGGTTAC
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
44 22 0.21
45 9 0.08
46 11 0.10
47 50 0.47
48 14 0.13
49 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (45 bp):
TTACCATTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:2431759 original size:94 final size:90
Alignment explanation
Indices: 2431652--2431819 Score: 237
Period size: 94 Copynumber: 1.8 Consensus size: 90
2431642 AATCTTTTAC
*
2431652 CATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATATAAATTCCATAAGCTC
1 CATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAT-T--ATTCCAAAAGCTC
2431717 ATAAGCTTATTTTATACAAAATACTTAT
63 ATAAGCTTATTTTATACAAAATACTTAT
* * * * **
2431745 CATTTAATCCCATAAGCTCGTAAGCTTATTTTTCCCATATACTTGCCATTATTCCAAAAGCTTGT
1 CATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCCAAAAGCTCAT
2431810 AAGCTTATTT
65 AAGCTTATTT
2431820 GCATGGTTAC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
91 22 0.33
93 6 0.09
94 39 0.58
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.38
Consensus pattern (90 bp):
CATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCCAAAAGCTCATA
AGCTTATTTTATACAAAATACTTAT
Found at i:2431968 original size:40 final size:40
Alignment explanation
Indices: 2431924--2432085 Score: 270
Period size: 40 Copynumber: 4.0 Consensus size: 40
2431914 ACCGTAGTGC
2431924 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
2431964 TACACATAAGGTCGTGTCCACCATATACATCGAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* **
2432004 TACACATAAGGTTGTGCCCACCATATACACTAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2432044 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2432084 TA
1 TA
2432086 TAAACCTGCA
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 110 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2438688 original size:13 final size:14
Alignment explanation
Indices: 2438670--2438707 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2438660 TATCTATTTA
2438670 TTTATTT-TAAATC
1 TTTATTTATAAATC
2438683 TTTATTTGATAAATC
1 TTTATTT-ATAAATC
2438698 TATTATTTAT
1 T-TTATTTAT
2438708 TTCTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTATTTATAAATC
Found at i:2440855 original size:16 final size:18
Alignment explanation
Indices: 2440836--2440872 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2440826 AGCTCTAGGG
2440836 ACTAAA-TCAAAAGG-AA
1 ACTAAATTCAAAAGGTAA
*
2440852 ACTAAATTTAAAAGGTAA
1 ACTAAATTCAAAAGGTAA
2440870 ACT
1 ACT
2440873 TAAAGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
ACTAAATTCAAAAGGTAA
Found at i:2441247 original size:2 final size:2
Alignment explanation
Indices: 2441240--2441269 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2441230 ATACGTGTGA
2441240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2441270 TATTAGGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2442270 original size:2 final size:2
Alignment explanation
Indices: 2442263--2442292 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2442253 CATGTATGTT
2442263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2442293 AGTTTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2446359 original size:23 final size:23
Alignment explanation
Indices: 2446332--2446375 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2446322 TAACCGGTTC
*
2446332 CGACCTGACCC-ACCCCGTTGACT
1 CGACCCGACCCGA-CCCGTTGACT
2446355 CGACCCGACCCGACCCGTTGA
1 CGACCCGACCCGACCCGTTGA
2446376 ACGTTGACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (23 bp):
CGACCCGACCCGACCCGTTGACT
Found at i:2446572 original size:29 final size:30
Alignment explanation
Indices: 2446516--2446573 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2446506 TTTAGTAAAT
**
2446516 ATTTTGAAAATGGTGCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTCATAATTA
*
2446546 ATTTT-AAAATGGTGCTATTTTCATAATT
1 ATTTTGAAAATGGTGCTATATTCATAATT
2446574 TTGAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.47
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTCATAATTA
Found at i:2447923 original size:17 final size:19
Alignment explanation
Indices: 2447898--2447936 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2447888 ATATCTGTAT
2447898 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
2447916 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
2447935 TA
1 TA
2447937 AGTTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:2450893 original size:13 final size:13
Alignment explanation
Indices: 2450872--2450915 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
2450862 GGTTCCAACC
*
2450872 TGACTCGACCCGT
1 TGACCCGACCCGT
2450885 TGACCCGACCCGT
1 TGACCCGACCCGT
*
2450898 TGACCCGACCCAT
1 TGACCCGACCCGT
2450911 TGACC
1 TGACC
2450916 GTTAACCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.18, C:0.43, G:0.20, T:0.18
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:2453932 original size:85 final size:85
Alignment explanation
Indices: 2453736--2454011 Score: 423
Period size: 85 Copynumber: 3.2 Consensus size: 85
2453726 CGTTATAGCT
* **
2453736 GGTCCCTTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTT--TTAGGTCCCTTTGCTGTGTGCAAG
1 GGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAG
2453799 GGTAAGCCTTACAGTTTTCCCA
65 GGTAAGCCTTACAG-TTTCCCA
* *
2453821 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGCCCCTTTGCTGTGTGCAGGG
1 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGG
2453886 GTAAGCCTTACAGTTTCCCA
66 GTAAGCCTTACAGTTTCCCA
*
2453906 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTACTGTGTGCAAGG
1 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGG
*
2453971 ATAAGCCTTACAGTTTCCCA
66 GTAAGCCTTACAGTTTCCCA
* *
2453991 GG-CTCTTTTGCTATGTGCAAG
1 GGTC-CCTTTGCTGTGTGCAAG
2454012 TATAAGACCT
Statistics
Matches: 177, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
84 32 0.18
85 111 0.63
86 34 0.19
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.33
Consensus pattern (85 bp):
GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGG
GTAAGCCTTACAGTTTCCCA
Found at i:2454023 original size:43 final size:42
Alignment explanation
Indices: 2453736--2454011 Score: 412
Period size: 43 Copynumber: 6.5 Consensus size: 42
2453726 CGTTATAGCT
* **
2453736 GGTCCCTTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTT-TTA
1 GGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCA
2453778 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCCCA
1 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCCCA
2453821 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
1 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCA
* *
2453864 GGCCCCTTTGCTGTGTGCAGGGGTAAGCCTTACAGTTTCCCA
1 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCA
2453906 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
1 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCA
* *
2453949 GGTCCCTTTACTGTGTGCAAGGATAAGCCTTACAGTTTCCCA
1 GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCA
* *
2453991 GG-CTCTTTTGCTATGTGCAAG
1 GGTC-CCTTTGCTGTGTGCAAG
2454012 TATAAGACCT
Statistics
Matches: 217, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
41 29 0.13
42 72 0.33
43 116 0.53
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.33
Consensus pattern (42 bp):
GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCA
Found at i:2454023 original size:128 final size:127
Alignment explanation
Indices: 2453739--2454011 Score: 440
Period size: 128 Copynumber: 2.1 Consensus size: 127
2453729 TATAGCTGGT
* **
2453739 CCCTTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTTTAGGTCCCTTTGCTGTGTGCAAGGGTAA
1 CCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCAGGTCCCTTTGCTGTGTGCAAGGGTAA
* * *
2453804 GCCTTACAGTTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG
66 GCCTTACAGTTTCCCCAGGTCCCTTTACTGTGTGCAAGGATAAGCCTTACAGTTTCCCCAGG
* *
2453866 CCCCTTTGCTGTGTGCAGGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTA
1 CCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCAGGTCCCTTTGCTGTGTGCAAGGGTA
2453931 AGCCTTACAGTTTCCCCAGGTCCCTTTACTGTGTGCAAGGATAAGCCTTACAGTTT-CCCAGG
65 AGCCTTACAGTTTCCCCAGGTCCCTTTACTGTGTGCAAGGATAAGCCTTACAGTTTCCCCAGG
* *
2453993 CTCTTTTGCTATGTGCAAG
1 CCCTTTTGCTGTGTGCAAG
2454012 TATAAGACCT
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
127 54 0.41
128 79 0.59
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (127 bp):
CCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCAGGTCCCTTTGCTGTGTGCAAGGGTAA
GCCTTACAGTTTCCCCAGGTCCCTTTACTGTGTGCAAGGATAAGCCTTACAGTTTCCCCAGG
Found at i:2456011 original size:13 final size:13
Alignment explanation
Indices: 2455993--2456024 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2455983 TACCATACCT
2455993 GACCCGTTAACCC
1 GACCCGTTAACCC
*
2456006 GACCCGTTGACCC
1 GACCCGTTAACCC
2456019 GACCCG
1 GACCCG
2456025 ACTCGTTGAT
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:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (13 bp):
GACCCGTTAACCC
Found at i:2456025 original size:18 final size:18
Alignment explanation
Indices: 2455966--2456033 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 18
2455956 ACCGGTTCTA
*
2455966 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
** *
2455984 ACCATACCTGACCCGTT-
1 ACCCGACCCGACCCGTTG
2456001 A----ACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2456015 ACCCGACCCGACTCGTTG
1 ACCCGACCCGACCCGTTG
2456033 A
1 A
2456034 TTGTTAACCA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
17 1 0.03
18 27 0.68
ACGTcount: A:0.21, C:0.44, G:0.18, T:0.18
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2458970 original size:43 final size:43
Alignment explanation
Indices: 2458879--2459170 Score: 399
Period size: 43 Copynumber: 6.8 Consensus size: 43
2458869 ACCGTTACAG
* *
2458879 CAGGTCCCTTTTGCTATGTACAAGGGTAAGCCTTACAGTTT-CC
1 CAGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * * *
2458922 TAGGTCCCTTTGTTGTGTGAAAGGGTAAGCATTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
2458965 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * *
2459008 CAGGCCCCTTTGTTGTGTTCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
2459051 CAGGTCCCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
2459094 CAGGTCCCTTTACTGTGTGCAAGGATAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * * * *
2459137 AAGCT-CTTTTGCTATGTGCAAGGATAAGACCTTA
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
2459171 TCCTTTTTGC
Statistics
Matches: 224, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 47 0.21
43 177 0.79
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (43 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:2459063 original size:21 final size:21
Alignment explanation
Indices: 2459039--2459106 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
2459029 AGGGTAAGCC
2459039 TTACAGTTTCCCCAGGTCCCT
1 TTACAGTTTCCCCAGGTCCCT
* * * * *
2459060 TTACTGTGT-GCAAGGGTAAGCCT
1 TTACAGTTTCCCCA-GGT--CCCT
2459083 -TACAGTTTCCCCAGGTCCCT
1 TTACAGTTTCCCCAGGTCCCT
2459103 TTAC
1 TTAC
2459107 TGTGTGCAAG
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
20 5 0.16
21 13 0.41
22 9 0.28
23 5 0.16
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.32
Consensus pattern (21 bp):
TTACAGTTTCCCCAGGTCCCT
Found at i:2461417 original size:43 final size:43
Alignment explanation
Indices: 2461310--2461559 Score: 360
Period size: 43 Copynumber: 5.8 Consensus size: 43
2461300 CCGTTACAAT
* *
2461310 AGGTCCCTTTTACTGTGTGCAAGGGTAAGCCTTACAGTTT-CCT
1 AGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
2461353 AGATCCTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
2461396 AGGTCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
2461438 AGGTCCCTTTACTATGTGCAAGGGTAAGCCTTACAGTTTCCCT
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
2461481 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
2461524 AAGTCCCTTTGCTGTGTGAAAGGATAAGACCTTACA
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAG-CCTTACA
2461560 TTTTGTTTTA
Statistics
Matches: 187, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
42 69 0.37
43 111 0.59
44 7 0.04
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (43 bp):
AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
Found at i:2461456 original size:85 final size:85
Alignment explanation
Indices: 2461310--2461559 Score: 365
Period size: 85 Copynumber: 2.9 Consensus size: 85
2461300 CCGTTACAAT
* * * * *
2461310 AGGTCCCTTTTACTGTGTGCAAGGGTAAGCCTTACAGTTTCCTAGATCCTTTTGTTGTGTGCAAG
1 AGGT-CCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAG
2461375 GGTAAGCCTTACAGTTTCCCC
65 GGTAAGCCTTACAGTTTCCCC
* *
2461396 AGGTCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTACTATGTGCAAGG
1 AGGTCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGG
*
2461461 GTAAGCCTTACAGTTTCCCT
66 GTAAGCCTTACAGTTTCCCC
* * *
2461481 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTCCCTTTGCTGTGTGAAAG
1 AGGTCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTCCCTTTGCTGTGTGCAAG
*
2461546 GATAAGACCTTACA
65 GGTAAG-CCTTACA
2461560 TTTTGTTTTA
Statistics
Matches: 148, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
85 111 0.75
86 30 0.20
87 7 0.05
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (85 bp):
AGGTCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGG
GTAAGCCTTACAGTTTCCCC
Found at i:2462037 original size:18 final size:18
Alignment explanation
Indices: 2462014--2462058 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2462004 GGTCGGTCAA
2462014 CAGGTCAAAGGGTC-AGAT
1 CAGGTCAAAGGGTCGAG-T
*
2462032 CAGGTCAACGGGTCGAGT
1 CAGGTCAAAGGGTCGAGT
*
2462050 CGGGTCAAA
1 CAGGTCAAA
2462059 CTGGGTCGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.29, C:0.20, G:0.36, T:0.16
Consensus pattern (18 bp):
CAGGTCAAAGGGTCGAGT
Found at i:2469286 original size:18 final size:18
Alignment explanation
Indices: 2469173--2469268 Score: 75
Period size: 18 Copynumber: 5.2 Consensus size: 18
2469163 GTCGTTCAAA
* *
2469173 GGTCAATGGGTTGGATCG
1 GGTCAACGGGTTGGGTCG
*
2469191 GGTGAACGGGTTGGGTCG
1 GGTCAACGGGTTGGGTCG
* * *
2469209 AGTCAAACCAGGTCGGGTCG
1 GGTC-AA-CGGGTTGGGTCG
* * *
2469229 GGTCAAAGGGTTGGATCA
1 GGTCAACGGGTTGGGTCG
* *
2469247 GGTCAACGAGTCGGGTCG
1 GGTCAACGGGTTGGGTCG
2469265 GGTC
1 GGTC
2469269 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
18 41 0.71
19 4 0.07
20 13 0.22
ACGTcount: A:0.19, C:0.17, G:0.44, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTTGGGTCG
Found at i:2471285 original size:3 final size:3
Alignment explanation
Indices: 2471272--2471323 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
2471262 TCTCTGGGTC
2471272 TTA TT- 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
2471319 TTA TT
1 TTA TT
2471324 TATAACATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2490813 original size:13 final size:13
Alignment explanation
Indices: 2490795--2490826 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2490785 AGTCATTCCC
2490795 TTCCATCCAATCT
1 TTCCATCCAATCT
2490808 TTCCATCCAATCT
1 TTCCATCCAATCT
2490821 TTCCAT
1 TTCCAT
2490827 TTAATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.41
Consensus pattern (13 bp):
TTCCATCCAATCT
Found at i:2491584 original size:22 final size:22
Alignment explanation
Indices: 2491556--2491603 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
2491546 CAATGGCCAA
*
2491556 TCAATGCTCGATCATTACCCGG
1 TCAATGCTCGATCATTACCCAG
2491578 TCAATGCTCGATCATTACCCAG
1 TCAATGCTCGATCATTACCCAG
2491600 TCAA
1 TCAA
2491604 CACCTGGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (22 bp):
TCAATGCTCGATCATTACCCAG
Found at i:2493401 original size:17 final size:15
Alignment explanation
Indices: 2493361--2493406 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 15
2493351 GAATCACATG
2493361 AAATATAAAAGAA-T
1 AAATATAAAAGAATT
*
2493375 AAACATAAAAGAATCT
1 AAATATAAAAGAAT-T
2493391 AAAATATAAAAGAATT
1 -AAATATAAAAGAATT
2493407 TGAGAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 12 0.44
16 2 0.07
17 13 0.48
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (15 bp):
AAATATAAAAGAATT
Found at i:2494637 original size:39 final size:39
Alignment explanation
Indices: 2494583--2494674 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 39
2494573 ATAGGGGAAT
* *
2494583 TTAAGAGTCTATTGGGAGTTAGAGCGTTTTATTGTGAAA
1 TTAAGAGTCTATTGGGAGTTAGAGCATTTTATTATGAAA
* * * *
2494622 TTAAGATTCTCTTGGGAGTTAGAGTATTTTATTATGAAT
1 TTAAGAGTCTATTGGGAGTTAGAGCATTTTATTATGAAA
2494661 TTAAGAGT-TATTGG
1 TTAAGAGTCTATTGG
2494675 AATATGGAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 5 0.11
39 40 0.89
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.42
Consensus pattern (39 bp):
TTAAGAGTCTATTGGGAGTTAGAGCATTTTATTATGAAA
Found at i:2499064 original size:27 final size:27
Alignment explanation
Indices: 2499026--2499087 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
2499016 AGTGCTTAGG
* * *
2499026 GTATTTTGGTCATTTTATAGTTTAAGA
1 GTATTTTAGTCATTTTAGAGTTCAAGA
*
2499053 GTATTTTAGTCATTTTAGAGTTCAAGG
1 GTATTTTAGTCATTTTAGAGTTCAAGA
2499080 GTATTTTA
1 GTATTTTA
2499088 ATCCTTTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (27 bp):
GTATTTTAGTCATTTTAGAGTTCAAGA
Found at i:2501629 original size:21 final size:22
Alignment explanation
Indices: 2501603--2501655 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
2501593 ATAAGGGGCC
2501603 ATTTTCCTTTGACTGGGAAAA-
1 ATTTTCCTTTGACTGGGAAAAT
*
2501624 ATTTTCCTTTGGCTGGGAAAAT
1 ATTTTCCTTTGACTGGGAAAAT
2501646 ATTTTCCTTT
1 ATTTTCCTTT
2501656 CACCAACCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (22 bp):
ATTTTCCTTTGACTGGGAAAAT
Found at i:2501837 original size:20 final size:20
Alignment explanation
Indices: 2501781--2501847 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
2501771 TCGATTTGGA
* * * *
2501781 TTGACTCAGACCGGTTCGGG
1 TTGACTCAGTCTGATTCGAG
* * *
2501801 TTAACTCAGTTTAATTCGAG
1 TTGACTCAGTCTGATTCGAG
*
2501821 TTGACTCAGTCTGATTCAAG
1 TTGACTCAGTCTGATTCGAG
2501841 TTGACTC
1 TTGACTC
2501848 GGATCAATTC
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (20 bp):
TTGACTCAGTCTGATTCGAG
Found at i:2507164 original size:30 final size:30
Alignment explanation
Indices: 2507120--2507184 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
2507110 AAAAATGGTT
* * ** *
2507120 AAATTTTAATTTGACCTTTGAATTTAGATA
1 AAATATTAAGTTGACCTTAAAATTTACATA
2507150 AAATATTAAGTTGACCTTAAAATTTACATA
1 AAATATTAAGTTGACCTTAAAATTTACATA
2507180 AAATA
1 AAATA
2507185 GTAATGTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (30 bp):
AAATATTAAGTTGACCTTAAAATTTACATA
Found at i:2514099 original size:46 final size:45
Alignment explanation
Indices: 2514048--2514137 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
2514038 TTCTTTTCGT
* *
2514048 TTGTAACCTCCATTTTTGTTTATAATACA-CCATTATGCACTTTAAA
1 TTGTAACAT-CATTTTTGTTGATAATACACCCA-TATGCACTTTAAA
* * *
2514094 TTGTAACATCTTTTTTGTTGATAATGCACCCATATGCATTTTAA
1 TTGTAACATCATTTTTGTTGATAATACACCCATATGCACTTTAA
2514138 CTATAGTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 27 0.71
46 11 0.29
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (45 bp):
TTGTAACATCATTTTTGTTGATAATACACCCATATGCACTTTAAA
Found at i:2514476 original size:34 final size:33
Alignment explanation
Indices: 2514415--2514485 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
2514405 ACCTTACAAC
* *
2514415 TCCCTAGTTTTTCACGGGTTAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGCTAAACTAGAACCTT
*
2514448 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTACACGGGCTAAACTAGAACCTT
2514482 TCCC
1 TCCC
2514486 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 7 0.21
34 27 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGCTAAACTAGAACCTT
Found at i:2514897 original size:21 final size:21
Alignment explanation
Indices: 2514850--2514925 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
2514840 TTGCAGCCTT
*
2514850 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
*
2514870 GAGGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
*
2514891 GATGCATGGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
2514912 GATGCATCGATGCA
1 GATGCATCGATGCA
2514926 CTAATTGCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 16 0.32
21 34 0.68
ACGTcount: A:0.28, C:0.17, G:0.37, T:0.18
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:2515014 original size:21 final size:21
Alignment explanation
Indices: 2514988--2515045 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
2514978 CATTAGTGTA
2514988 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
*
2515009 GATGCATGGTTGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
2515030 GATGCATGGATGCACT
1 GATGCATGGATGCACT
2515046 TTGACACCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:2515184 original size:30 final size:30
Alignment explanation
Indices: 2515127--2515186 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2515117 AACTTTGAAT
2515127 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
2515157 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
2515187 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:2515780 original size:45 final size:45
Alignment explanation
Indices: 2515545--2515781 Score: 296
Period size: 45 Copynumber: 5.3 Consensus size: 45
2515535 TGTTTTTAAC
* **
2515545 ACATTTCAACCATAATATACTTTTCTGTTGATAATGTACCCATAT
1 ACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCATAT
* * *
2515590 ACATTTCAACTCTAGCAT-GTTATTCTGTTGATAATGCACCCATAT
1 ACATTTCAACTATAGCATACTT-TTCTGTTGATAATGTACCCATAT
* * * *
2515635 GCATTTCAACTCTAGCACACTTTTCTGTTGATAATGCACCCATAT
1 ACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCATAT
* * *
2515680 GCATTTCAACTTTAGCATACTTTTCTGTGGATAATGTACCCATAT
1 ACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCATAT
** ** *
2515725 ACATTTCAACTATAATATGTTTTTCCGTTGATAATGTACCCATAT
1 ACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCATAT
2515770 ACATTTCAACTA
1 ACATTTCAACTA
2515782 CAACATCCTT
Statistics
Matches: 169, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
44 2 0.01
45 165 0.98
46 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (45 bp):
ACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCATAT
Found at i:2515804 original size:45 final size:43
Alignment explanation
Indices: 2515564--2515819 Score: 235
Period size: 45 Copynumber: 5.7 Consensus size: 43
2515554 CCATAATATA
* *
2515564 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCAT
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTC-AACAT
* *
2515608 GTTATTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCACA-
1 CTT-TTCTGTTGATAATGCACCCATATACATTTCAACTC-A--ACAT
* * *
2515654 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTTTAGCAT
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAAC-TCAACAT
* * * *
2515698 ACTTTTCTGTGGATAATGTACCCATATACATTTCAACTATAATAT
1 -CTTTTCTGTTGATAATGCACCCATATACATTTCAACT-CAACAT
* * *
2515743 GTTTTTCCGTTGATAATGTACCCATATACATTTCAACTACAACAT
1 -CTTTTCTGTTGATAATGCACCCATATACATTTCAACT-CAACAT
* * * * *
2515788 CCTTTCATGCTAATAATGCACCTATATGCATT
1 CTTTTC-TGTTGATAATGCACCCATATACATT
2515820 AATATTTTCA
Statistics
Matches: 178, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
43 2 0.01
44 7 0.04
45 164 0.92
46 3 0.02
47 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (43 bp):
CTTTTCTGTTGATAATGCACCCATATACATTTCAACTCAACAT
Found at i:2515804 original size:90 final size:87
Alignment explanation
Indices: 2515545--2515819 Score: 298
Period size: 90 Copynumber: 3.1 Consensus size: 87
2515535 TGTTTTTAAC
* *
2515545 ACATTTCAACCATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATGT
1 ACATTTCAACTATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTC-AGCATCT
2515610 TATTCTGTTGATAATGCACCCATAT
65 T-TTCTG-TGATAATGCACCCATAT
* * ** * * * *
2515635 GCATTTCAACTCTAGCACACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTTTAGCATAC
1 ACATTTCAACTATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC-TCAGCAT-C
*
2515700 TTTTCTGTGGATAATGTACCCATAT
64 TTTTCTGT-GATAATGCACCCATAT
** * * *
2515725 ACATTTCAACTATAATATGTTTTTCCGTTGATAATGTACCCATATACATTTCAACTACAACATCC
1 ACATTTCAACTATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAACT-CAGCATCT
* *
2515790 TTTCATGCTAATAATGCACCTATAT
65 TTTC-TG-TGATAATGCACCCATAT
*
2515815 GCATT
1 ACATT
2515820 AATATTTTCA
Statistics
Matches: 151, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
89 7 0.05
90 140 0.93
91 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.38
Consensus pattern (87 bp):
ACATTTCAACTATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCAGCATCTT
TTCTGTGATAATGCACCCATAT
Found at i:2515804 original size:135 final size:134
Alignment explanation
Indices: 2515561--2515819 Score: 360
Period size: 135 Copynumber: 1.9 Consensus size: 134
2515551 CAACCATAAT
* * * *
2515561 ATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATGTTATTCTGTTGATAATG
1 ATACTTTTCTGTGGATAATGTACCCATATACATTTCAACTATAACATGTTATTCCGTTGATAATG
* * * *
2515626 CACCCATATGCATTTCAACTCTAGCACACTTTTCTGTTGATAATGCACCCATATGCATTTCAACT
66 CACCCATATACATTTCAACTCTA-CACACCTTTCTGCTAATAATGCACCCATATGCATTTCAACT
2515691 TTAGC
130 TTAGC
* *
2515696 ATACTTTTCTGTGGATAATGTACCCATATACATTTCAACTATAATATGTTTTTCCGTTGATAATG
1 ATACTTTTCTGTGGATAATGTACCCATATACATTTCAACTATAACATGTTATTCCGTTGATAATG
* *
2515761 TACCCATATACATTTCAA--CTACAACATCCTTTCATGCTAATAATGCACCTATATGCATT
66 CACCCATATACATTTCAACTCTAC-ACA-CCTTTC-TGCTAATAATGCACCCATATGCATT
2515820 AATATTTTCA
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
132 1 0.01
133 6 0.06
134 5 0.05
135 97 0.89
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (134 bp):
ATACTTTTCTGTGGATAATGTACCCATATACATTTCAACTATAACATGTTATTCCGTTGATAATG
CACCCATATACATTTCAACTCTACACACCTTTCTGCTAATAATGCACCCATATGCATTTCAACTT
TAGC
Found at i:2516430 original size:94 final size:95
Alignment explanation
Indices: 2516268--2516448 Score: 267
Period size: 94 Copynumber: 1.9 Consensus size: 95
2516258 ACTACCCTAT
* * *
2516268 TATGGTATCGAGACCCCCTTCGAGTATTAATACCAAAATTAGCTTCGATGTAGTCTGCTATCGAT
1 TATGGTATCGAGACCCCCTTAGAGTATCAATACCAAAATTAGATTCGATGTAGTCTGCTATCGAT
2516333 ACCCTCACCATGGTATCGATACCAATATGC
66 ACCCTCACCATGGTATCGATACCAATATGC
* * * *
2516363 TATGGTATCGATACCCCCTTAG-GTATCGATACCAAAATTAGATTCGATGT-TTACTGGTATCGA
1 TATGGTATCGAGACCCCCTTAGAGTATCAATACCAAAATTAGATTCGATGTAGT-CTGCTATCGA
*
2516426 TACCCTTACCATGGTATCGATAC
65 TACCCTCACCATGGTATCGATAC
2516449 TGATTCAATC
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 1 0.01
94 56 0.73
95 20 0.26
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (95 bp):
TATGGTATCGAGACCCCCTTAGAGTATCAATACCAAAATTAGATTCGATGTAGTCTGCTATCGAT
ACCCTCACCATGGTATCGATACCAATATGC
Found at i:2518348 original size:180 final size:180
Alignment explanation
Indices: 2518138--2518577 Score: 423
Period size: 180 Copynumber: 2.5 Consensus size: 180
2518128 CTAAAAATAT
* * *
2518138 AATTTGTCA-AAAAACGTGAATATAATTATTT-TTGTGACAATATTTTTTGTAATAATTATTAAC
1 AATTTGTCATAAAAACTTGAATCTCATTATTTGTTGTGACAATATTTTTTGTAATAATTATTAAC
** * *
2518201 ATTTATAGTTACAAAATTTGTCACTATATTACTTTT-TTGGTGCA-AAAAAATATGGAGGGA-AA
66 ATTTATAGTTACAAAACATGTCACTATATGA-TTTTGTTGGTACATAAAAAAT-T-G-GGGATAA
* * *
2518263 TC-TTAGTGACAATATATTTTGTCACTATAATTAAAACATATAACGACAAACAT
127 TCATTACTGACAATACATTTTGTCACTATAATTAAAACATATAACGACAAACAA
** * * * *
2518316 TGTTTGTTACTAAAAACTTGAATCTCATTATTTGTTGTGACAA-ATTTTTTATAACAATAATTAT
1 AATTTGTCA-TAAAAACTTGAATCTCATTATTTGTTGTGACAATATTTTTTGTAATAATTATTA-
* ** *
2518380 AGC--TTATTGTTACAAAACATGTCACTATATGATTTTGTTTTTATATAAAAAATTGGGGATAAT
64 A-CATTTATAGTTACAAAACATGTCACTATATGATTTTGTTGGTACATAAAAAATTGGGGATAAT
* * * **
2518443 CATTTCTGACTATACATTTTGTCACTATAATTAAAATATATAATTACAAACAA
128 CATTACTGACAATACATTTTGTCACTATAATTAAAACATATAACGACAAACAA
* * * * * * * *
2518496 AATTTGTCATAACAAATTTAAATCTCTTTATTTGTTATGACAATTTTTTTTGTCATAGTTACTAA
1 AATTTGTCATAA-AAACTTGAATCTCATTATTTGTTGTGACAATATTTTTTGTAATAATTATTAA
*
2518561 AACTTT-TAGTTACAAAA
65 CA-TTTATAGTTACAAAA
2518578 GTAGTCACCC
Statistics
Matches: 207, Mismatches: 41, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
178 10 0.05
179 12 0.06
180 142 0.69
181 40 0.19
182 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (180 bp):
AATTTGTCATAAAAACTTGAATCTCATTATTTGTTGTGACAATATTTTTTGTAATAATTATTAAC
ATTTATAGTTACAAAACATGTCACTATATGATTTTGTTGGTACATAAAAAATTGGGGATAATCAT
TACTGACAATACATTTTGTCACTATAATTAAAACATATAACGACAAACAA
Found at i:2527466 original size:24 final size:24
Alignment explanation
Indices: 2527439--2527529 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
2527429 TCTGATTTGA
* *
2527439 ATTATGTTATGATACCTGACCTGG
1 ATTATGATATGATACTTGACCTGG
* *
2527463 ATTATGATTTGATA-TTGACATGG
1 ATTATGATATGATACTTGACCTGG
* * *
2527486 ATTCTGATCTGATACATGACCTGG
1 ATTATGATATGATACTTGACCTGG
*
2527510 ATTCTGATATGATACTTGAC
1 ATTATGATATGATACTTGAC
2527530 TTAAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.34
24 37 0.66
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTATGATATGATACTTGACCTGG
Found at i:2527654 original size:35 final size:35
Alignment explanation
Indices: 2527606--2527680 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
2527596 TGGAGGAAGA
*
2527606 TTACTTGGTGGCTCATCGGCTTTGTGCTTAGGGCC
1 TTACTTGGTGGCTCATCGGCTTTGTGCTCAGGGCC
*
2527641 TTACTT-GTAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGGT-GGCTCATCGGCTTTGTGCTCAGGGCC
2527676 TTACT
1 TTACT
2527681 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.09, C:0.25, G:0.28, T:0.37
Consensus pattern (35 bp):
TTACTTGGTGGCTCATCGGCTTTGTGCTCAGGGCC
Found at i:2532191 original size:23 final size:24
Alignment explanation
Indices: 2532144--2532234 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
2532134 TCTGATTTGA
* *
2532144 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
2532168 ATTCTGATTTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
2532191 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
2532215 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
2532235 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:2532204 original size:47 final size:48
Alignment explanation
Indices: 2532144--2532234 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
2532134 TCTGATTTGA
* * *
2532144 ATTCTGTTATGATACCTGACCTGGATTCTGATTTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
2532191 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
2532235 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:2532359 original size:35 final size:35
Alignment explanation
Indices: 2532311--2532385 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
2532301 TGGAGGAAGA
** *
2532311 TTACTTGGTGGCTCATCGGCTTTGTGCTTAGGGCC
1 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
*
2532346 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
2532381 TTACT
1 TTACT
2532386 GTTCGTGACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.09, C:0.27, G:0.28, T:0.36
Consensus pattern (35 bp):
TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
Found at i:2534293 original size:23 final size:24
Alignment explanation
Indices: 2534246--2534336 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
2534236 TCTGATTTGA
* *
2534246 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
2534270 ATTCTGATTTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * * *
2534293 ATTCTAATCTGATACATGACCTAG
1 ATTCTGATATGATACTTGACCTGG
2534317 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
2534337 TTGAATTATG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:2542241 original size:7 final size:7
Alignment explanation
Indices: 2542215--2542289 Score: 75
Period size: 7 Copynumber: 11.0 Consensus size: 7
2542205 CATCCGTGAC
2542215 ATTATAT
1 ATTATAT
*
2542222 ATTACAT
1 ATTATAT
*
2542229 AGTATAT
1 ATTATAT
*
2542236 ATTATAC
1 ATTATAT
2542243 A-TATTAT
1 ATTA-TAT
2542250 ATTATAT
1 ATTATAT
2542257 ATTAT-T
1 ATTATAT
*
2542263 AATATAT
1 ATTATAT
2542270 ATTAT-T
1 ATTATAT
*
2542276 TTTATAT
1 ATTATAT
2542283 ATTATAT
1 ATTATAT
2542290 TAAAGTATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
6 12 0.22
7 40 0.74
8 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (7 bp):
ATTATAT
Found at i:2542243 original size:16 final size:14
Alignment explanation
Indices: 2542215--2542291 Score: 56
Period size: 13 Copynumber: 5.6 Consensus size: 14
2542205 CATCCGTGAC
2542215 ATTATA-TATTACAT
1 ATTATATTA-TACAT
2542229 AGTATATATTATACAT
1 A-T-TATATTATACAT
2542245 ATTATATTAT--AT
1 ATTATATTATACAT
* *
2542257 ATTAT-TAATATAT
1 ATTATATTATACAT
* *
2542270 ATTAT-TTTTATAT
1 ATTATATTATACAT
2542283 ATTATATTA
1 ATTATATTA
2542292 AAGTATATTC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
11 3 0.06
12 7 0.13
13 18 0.34
14 11 0.21
15 2 0.04
16 10 0.19
17 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (14 bp):
ATTATATTATACAT
Found at i:2542288 original size:18 final size:18
Alignment explanation
Indices: 2542215--2542291 Score: 61
Period size: 18 Copynumber: 4.2 Consensus size: 18
2542205 CATCCGTGAC
* *
2542215 ATTATATATTACATAGTAT
1 ATTAT-TATTATATATTAT
*
2542234 A-TATTA-TACATATTAT
1 ATTATTATTATATATTAT
2542250 ATTATATATTAT-TAATATAT
1 ATTAT-TATTATAT-AT-TAT
*
2542270 ATTATTTTTATATATTAT
1 ATTATTATTATATATTAT
2542288 ATTA
1 ATTA
2542292 AAGTATATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
16 10 0.20
17 5 0.10
18 13 0.27
19 12 0.24
20 9 0.18
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (18 bp):
ATTATTATTATATATTAT
Found at i:2553726 original size:18 final size:18
Alignment explanation
Indices: 2553701--2553746 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2553691 ACTGGTCATA
2553701 ACCCGACCCGACCCGATG
1 ACCCGACCCGACCCGATG
* * *
2553719 ATCCGACCCAACCCGTTG
1 ACCCGACCCGACCCGATG
2553737 ACCCGACCCG
1 ACCCGACCCG
2553747 TTGACTCGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.50, G:0.20, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCCGATG
Found at i:2556203 original size:24 final size:24
Alignment explanation
Indices: 2556171--2556282 Score: 97
Period size: 24 Copynumber: 4.7 Consensus size: 24
2556161 ATCTGATTTA
*
2556171 TGATCTGATACTTGACATGGAATC
1 TGATATGATACTTGACATGGAATC
* *
2556195 TGATATGATA-TCTGATATGGATTC
1 TGATATGATACT-TGACATGGAATC
* *
2556219 TGATATGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGAATC
* *
2556243 TGATCT-ATTACTTGACCT--AATTTC
1 TGATATGA-TACTTGACATGGAA--TC
2556267 TGATATGATACTTGAC
1 TGATATGATACTTGAC
2556283 CTGATTTATG
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
22 1 0.01
23 2 0.03
24 68 0.93
25 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (24 bp):
TGATATGATACTTGACATGGAATC
Found at i:2556209 original size:12 final size:12
Alignment explanation
Indices: 2556192--2556228 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
2556182 TTGACATGGA
2556192 ATCTGATATGAT
1 ATCTGATATGAT
2556204 ATCTGATATGGAT
1 ATCTGATAT-GAT
2556217 -TCTGATATGAT
1 ATCTGATATGAT
2556228 A
1 A
2556229 CTTGACTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (12 bp):
ATCTGATATGAT
Found at i:2556283 original size:24 final size:24
Alignment explanation
Indices: 2556163--2556289 Score: 93
Period size: 24 Copynumber: 5.3 Consensus size: 24
2556153 AATATTTTAT
* *
2556163 CTGATTTATGATCTGATACTTGAC
1 CTGATTTCTGATATGATACTTGAC
* * *
2556187 ATGGA-ATCTGATATGATA-TCTGAT
1 CT-GATTTCTGATATGATACT-TGAC
*
2556211 ATGGA-TTCTGATATGATACTTGAC
1 CT-GATTTCTGATATGATACTTGAC
* *
2556235 TTGGA-TTCTGATCT-ATTACTTGAC
1 CT-GATTTCTGATATGA-TACTTGAC
*
2556259 CTAATTTCTGATATGATACTTGAC
1 CTGATTTCTGATATGATACTTGAC
2556283 CTGATTT
1 CTGATTT
2556290 ATGTTTTGAT
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
23 3 0.04
24 77 0.92
25 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (24 bp):
CTGATTTCTGATATGATACTTGAC
Found at i:2558444 original size:18 final size:18
Alignment explanation
Indices: 2558391--2558446 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
2558381 ACCGATCATA
*
2558391 ACCCGACCCAACCCGTTA
1 ACCCGACCCAACCCGTTG
*
2558409 ACCCGACCAAACCCGTTG
1 ACCCGACCCAACCCGTTG
2558427 ACCCGACCCAACCCGTTG
1 ACCCGACCCAACCCGTTG
2558445 AC
1 AC
2558447 ATTGTAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.27, C:0.48, G:0.14, T:0.11
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTG
Found at i:2562897 original size:30 final size:30
Alignment explanation
Indices: 2562858--2562927 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2562848 AAAAATGGTT
* * *
2562858 AAATTTTAATTTCACCTCTGA-ATTTAGATA
1 AAATATTAATTTCACCT-TAACATTTACATA
*
2562888 AAATATTAATTTGACCTTAACATTTACATA
1 AAATATTAATTTCACCTTAACATTTACATA
*
2562918 AAATACTAAT
1 AAATATTAAT
2562928 CTAACTCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (30 bp):
AAATATTAATTTCACCTTAACATTTACATA
Found at i:2564461 original size:59 final size:59
Alignment explanation
Indices: 2564362--2564903 Score: 789
Period size: 59 Copynumber: 9.2 Consensus size: 59
2564352 TTTCATAATT
* * * * *
2564362 TTAGCACACAAGGTGCCCAATACAGAAATTCATACACTTAGTATGAACTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
** * * *
2564421 TTAGCACATGAAGTTCCCTATACGAAAATCCATACACTTAGTATGAATTTCTTCTCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * *
2564480 TGAGCACACAAAGTGTCCGATACGGAAATTCATACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * *
2564539 TTAGCGCACAAAGTGCCCTATACGGAAATCCATATACATAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * *
2564598 TTAGCACACAAAGTGCCCTATATGGAAATCCATACACTTAGTATAAATTTCTTCTCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
*
2564657 TTAGAACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * *
2564716 TTAGCACAAAAAGTGCCCTATACGGAAGTCCATACACTTAATATGAATTTATTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* * * * *
2564775 TTAGCACACAAATTTCCCTATACAG-AATCCATACACTTAGTATGAATTTTTTTTCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
* *
2564833 TTAGCACACAAAGTGCCCTATATGGAAATTCATACACTTAGTATGAATTTCTTATCATG
1 TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
2564892 TTAGCACACAAA
1 TTAGCACACAAA
2564904 CACATATATC
Statistics
Matches: 426, Mismatches: 56, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
58 50 0.12
59 376 0.88
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (59 bp):
TTAGCACACAAAGTGCCCTATACGGAAATCCATACACTTAGTATGAATTTCTTATCATG
Found at i:2575820 original size:15 final size:15
Alignment explanation
Indices: 2575800--2575830 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2575790 CAATTTCTCT
2575800 ATCGTTATCTAAACC
1 ATCGTTATCTAAACC
*
2575815 ATCGTTATCTAGACC
1 ATCGTTATCTAAACC
2575830 A
1 A
2575831 AATGTCCTAG
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:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (15 bp):
ATCGTTATCTAAACC
Found at i:2576935 original size:23 final size:21
Alignment explanation
Indices: 2576903--2576957 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
2576893 CCCTCTAGGG
2576903 GTATCGATACACATTCAAGGAAT
1 GTATCGATACACATTCAAGG--T
* * *
2576926 GTATCAATACATATTTAAGGT
1 GTATCGATACACATTCAAGGT
2576947 GTATCGATACA
1 GTATCGATACA
2576958 TAGAAATGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (21 bp):
GTATCGATACACATTCAAGGT
Found at i:2580563 original size:13 final size:13
Alignment explanation
Indices: 2580547--2580594 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
2580537 TTTATGAATA
2580547 GTGAACAGTACCC
1 GTGAACAGTACCC
* *
2580560 GTGAACAGTAACA
1 GTGAACAGTACCC
2580573 GTG-ACTAGTACCC
1 GTGAAC-AGTACCC
2580586 GTGAACAGT
1 GTGAACAGT
2580595 GGGGGAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 25 0.86
14 2 0.07
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (13 bp):
GTGAACAGTACCC
Found at i:2581134 original size:47 final size:45
Alignment explanation
Indices: 2581066--2581237 Score: 152
Period size: 47 Copynumber: 3.8 Consensus size: 45
2581056 ATAAAATCTT
* *
2581066 TTACCATT-TATCCCATAAGCTCGTAAGCATATTTTACTAAAATAC
1 TTACCATTAAATCCCATAAGCTCGTAAGCTTATTTTAC-AAAATAC
* * *
2581111 TTACCATATAAATTCCTTAAGCTCATAAGCTTAATTTATACAAAATAC
1 TTACCAT-TAAATCCCATAAGCTCGTAAGCTT-ATTT-TACAAAATAC
* * * * *
2581159 TTATCATTTAATCCCATAAGCTCGTAAGCTTATTTTTTCCATATAC
1 TTACCATTAAATCCCATAAGCTCGTAAGCTTA-TTTTACAAAATAC
* * * *
2581205 TTGCCATT--ATTCCAAAAGCTTGTAAGCTTATTT
1 TTACCATTAAATCCCATAAGCTCGTAAGCTTATTT
2581238 GTATGCTTAC
Statistics
Matches: 104, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
43 3 0.03
44 19 0.18
45 7 0.07
46 15 0.14
47 40 0.38
48 17 0.16
49 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (45 bp):
TTACCATTAAATCCCATAAGCTCGTAAGCTTATTTTACAAAATAC
Found at i:2581386 original size:40 final size:40
Alignment explanation
Indices: 2581342--2581463 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
2581332 ACCGTAGTGC
2581342 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2581382 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2581422 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2581462 TA
1 TA
2581464 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2588131 original size:47 final size:45
Alignment explanation
Indices: 2588077--2588236 Score: 178
Period size: 47 Copynumber: 3.5 Consensus size: 45
2588067 ATCATTTATC
*
2588077 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTTCCATATAAATT
1 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAT-T-AATT
* * * *
2588124 CCATAAGCTCATAAGCTTATTTTATACAAAATTCTTACCATTTAATC
1 CCATAAGCTCGTAAGCTTATTTTA-CCAAAATACTTACCA-TTAATT
* * * *
2588171 CCATAAGCTCGTAAGCTTATTTTTCCCATATACTTGCCATT-ATT
1 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTAATT
* *
2588215 CCAAAAGCTTGTAAGCTTATTT
1 CCATAAGCTCGTAAGCTTATTT
2588237 GTATGCTTAC
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
44 22 0.23
45 2 0.02
46 10 0.10
47 48 0.50
48 13 0.14
49 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTAATT
Found at i:2588395 original size:40 final size:40
Alignment explanation
Indices: 2588341--2588502 Score: 288
Period size: 40 Copynumber: 4.0 Consensus size: 40
2588331 ACCGTAGTGC
2588341 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
2588381 TACATATAAGGTCGTGCACACCATATACACAGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2588421 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2588461 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2588501 TA
1 TA
2588503 TAAACCTGCA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2594997 original size:13 final size:14
Alignment explanation
Indices: 2594979--2595016 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2594969 TATCTATTTA
2594979 TTTATTT-TAAATC
1 TTTATTTATAAATC
2594992 TTTATTTGATAAATC
1 TTTATTT-ATAAATC
2595007 TATTATTTAT
1 T-TTATTTAT
2595017 TTCTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTATTTATAAATC
Found at i:2597169 original size:16 final size:18
Alignment explanation
Indices: 2597150--2597186 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2597140 AGCTCTAGGG
2597150 ACTAAA-TCAAAAGG-AA
1 ACTAAATTCAAAAGGTAA
*
2597166 ACTAAATTTAAAAGGTAA
1 ACTAAATTCAAAAGGTAA
2597184 ACT
1 ACT
2597187 TAAAGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
ACTAAATTCAAAAGGTAA
Found at i:2603207 original size:26 final size:27
Alignment explanation
Indices: 2603150--2603225 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 27
2603140 AAAAGGGTTA
* * *
2603150 TATTTTTGTAATTTTTTTAAAAAATGC
1 TATTTTAGTAAATTTTTGAAAAAATGC
2603177 TATTTTCA-T-AATTTTTGAAAAAATGAC
1 TATTTT-AGTAAATTTTTGAAAAAATG-C
2603204 -ATTTTAGTAAATATTTTGAAAA
1 TATTTTAGTAAAT-TTTTGAAAA
2603226 TGGTGCTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.02
26 20 0.49
27 11 0.27
28 9 0.22
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (27 bp):
TATTTTAGTAAATTTTTGAAAAAATGC
Found at i:2603271 original size:29 final size:29
Alignment explanation
Indices: 2603204--2603273 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
2603194 AAAAAATGAC
*
2603204 ATTTTAGTAAATATTTTGAAAATGGTGCT
1 ATTTTAGTAATTATTTTGAAAATGGTGCT
* * *
2603233 ATATTGGTAATTAATTTT-AAAATGGTGTT
1 ATTTTAGTAATT-ATTTTGAAAATGGTGCT
2603262 ATTTTAGTAATT
1 ATTTTAGTAATT
2603274 TTGAAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (29 bp):
ATTTTAGTAATTATTTTGAAAATGGTGCT
Found at i:2604632 original size:17 final size:19
Alignment explanation
Indices: 2604607--2604645 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2604597 ATATTTGTAT
2604607 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
2604625 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
2604644 TA
1 TA
2604646 AGTTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Done.