Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 51
Found at i:4364492 original size:3 final size:3
Alignment explanation
Indices: 4364484--4364539 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
4364474 TATGTAAAAT
*
4364484 TAA TAA TAA TAGT TAA TAA TAA TTAA TAA TAA -AA -AA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
*
4364529 -AA TAA AAA TAA
1 TAA TAA TAA TAA
4364540 ATATAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.13
3 34 0.76
4 5 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:4364502 original size:10 final size:10
Alignment explanation
Indices: 4364487--4364526 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
4364477 GTAAAATTAA
*
4364487 TAATAATAGT
1 TAATAATAAT
4364497 TAATAATAAT
1 TAATAATAAT
*
4364507 TAATAATAAA
1 TAATAATAAT
*
4364517 AAATAATAAT
1 TAATAATAAT
4364527 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (10 bp):
TAATAATAAT
Found at i:4364513 original size:13 final size:12
Alignment explanation
Indices: 4364484--4364539 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 12
4364474 TATGTAAAAT
*
4364484 TAATAATAATAGT
1 TAATAATAATA-A
4364497 TAATAATAATTAA
1 TAATAATAA-TAA
4364510 TAATAA-AA-AA
1 TAATAATAATAA
4364520 TAATAATAA-AA
1 TAATAATAATAA
*
4364531 TAAAAATAA
1 TAATAATAA
4364540 ATATAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 8 0.21
11 12 0.31
12 2 0.05
13 15 0.38
14 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:4364521 original size:17 final size:17
Alignment explanation
Indices: 4364498--4364553 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
4364488 AATAATAGTT
4364498 AATAATAATTAATAATAAAA
1 AATAATAA-TAA-AAT-AAA
4364518 AATAATAATAAAATAAA
1 AATAATAATAAAATAAA
4364535 AATAA-ATATAAATATAAA
1 AATAATA-ATAAA-ATAAA
4364553 A
1 A
4364554 GACTCGGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
18 9 0.26
19 3 0.09
20 8 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAATAAAATAAA
Found at i:4370352 original size:49 final size:49
Alignment explanation
Indices: 4370280--4370378 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
4370270 ACTAGCTTAT
4370280 CAAAAGGTAAAATTTTGTTATTAGTCTCTTTACTATTTGTAAATTGTGA
1 CAAAAGGTAAAATTTTGTTATTAGTCTCTTTACTATTTGTAAATTGTGA
4370329 CAAAAGGTAAAATTTTGTTATTAGTCTCTTTACTATTTGTAAATTGTGA
1 CAAAAGGTAAAATTTTGTTATTAGTCTCTTTACTATTTGTAAATTGTGA
4370378 C
1 C
4370379 CTTAATATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (49 bp):
CAAAAGGTAAAATTTTGTTATTAGTCTCTTTACTATTTGTAAATTGTGA
Found at i:4379860 original size:42 final size:42
Alignment explanation
Indices: 4379813--4379897 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
4379803 ATGTCTTTCA
* * *
4379813 TATGCTTCAATCAAAAAACTTTCACCTAGGCAAATATTTTTG
1 TATGCTACAATCAAAAAACTTTCACCTAGGCAAAAATTATTG
** ** *
4379855 TATGCTACGTTCAGTAAACTTTCGCCTAGGCAAAAATTATTG
1 TATGCTACAATCAAAAAACTTTCACCTAGGCAAAAATTATTG
4379897 T
1 T
4379898 GTTTCTTAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (42 bp):
TATGCTACAATCAAAAAACTTTCACCTAGGCAAAAATTATTG
Found at i:4391031 original size:2 final size:2
Alignment explanation
Indices: 4391026--4391065 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4391016 AAAAATATGA
4391026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4391066 TGTATAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4391894 original size:2 final size:2
Alignment explanation
Indices: 4391860--4391884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4391850 CCCTTTTAAT
4391860 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4391885 TAATTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4391906 original size:29 final size:29
Alignment explanation
Indices: 4391855--4391941 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
4391845 GCGAACCCTT
* *
4391855 TTAATTATATATA-TATATATATATATATA
1 TTAATTATATAAATTAAAT-TATATATATA
4391884 TTAATTATATAAATTAAATTATAT-TCATA
1 TTAATTATATAAATTAAATTATATAT-ATA
* * *
4391913 TTTATAATATAAACATTAAATTATTTATA
1 TTAATTATAT-AA-ATTAAATTATATATA
4391942 ATATAAACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.02
29 28 0.58
30 6 0.12
31 12 0.25
32 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAATTATATAAATTAAATTATATATATA
Found at i:4391966 original size:28 final size:23
Alignment explanation
Indices: 4391911--4391954 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
4391901 ATTATATTCA
4391911 TATTTATAATATAAACATTAAAT
1 TATTTATAATATAAACATTAAAT
4391934 TATTTATAATATAAACATTAA
1 TATTTATAATATAAACATTAA
4391955 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTTATAATATAAACATTAAAT
Found at i:4392451 original size:36 final size:35
Alignment explanation
Indices: 4392386--4392468 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
4392376 AATGTTTATA
** *
4392386 ATATAAATATAAAATAATTTATATTTATATTTATATT
1 ATATAAAT-TAAAATAATTTATAAATATATATA-ATT
*
4392423 ATATAAATTAAAATATTTTATAAATATATATAATT
1 ATATAAATTAAAATAATTTATAAATATATATAATT
*
4392458 AAATACAATTA
1 ATATA-AATTA
4392469 TAATTTACTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 7 0.17
36 25 0.62
37 8 0.20
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (35 bp):
ATATAAATTAAAATAATTTATAAATATATATAATT
Found at i:4392861 original size:14 final size:14
Alignment explanation
Indices: 4392838--4392869 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4392828 ATATATTTTA
4392838 TTATAATTATATTT
1 TTATAATTATATTT
*
4392852 TTATATTTATATTT
1 TTATAATTATATTT
4392866 TTAT
1 TTAT
4392870 TATAGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATAATTATATTT
Found at i:4392878 original size:24 final size:25
Alignment explanation
Indices: 4392829--4392887 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
4392819 TTATATAAAA
*
4392829 TATATTT-TATTATAATTATATTTT
1 TATATTTATATTATAATTATATGTT
* *
4392853 TATATTTATATTTTTATTATA-GTT
1 TATATTTATATTATAATTATATGTT
* *
4392877 TAAATTGATAT
1 TATATTTATAT
4392888 AATTTATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (25 bp):
TATATTTATATTATAATTATATGTT
Found at i:4394063 original size:39 final size:39
Alignment explanation
Indices: 4394020--4394102 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
4394010 GCTAAATATT
* * *
4394020 AAGACTCCATGACTGCATGGCGTCTTCAGGAAAATGAAG
1 AAGACTCCACGACTGCAAGGCGTATTCAGGAAAATGAAG
* * *
4394059 AAGACTCTACGACTGCAAGGCGTATTCAGGTAAATGGAG
1 AAGACTCCACGACTGCAAGGCGTATTCAGGAAAATGAAG
4394098 AAGAC
1 AAGAC
4394103 CCCAGGAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (39 bp):
AAGACTCCACGACTGCAAGGCGTATTCAGGAAAATGAAG
Found at i:4397331 original size:16 final size:16
Alignment explanation
Indices: 4397310--4397342 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4397300 TACTATTCAT
*
4397310 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
4397326 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
4397342 G
1 G
4397343 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:4405503 original size:2 final size:2
Alignment explanation
Indices: 4405496--4405534 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4405486 CGAATTTTTA
4405496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4405535 GTTAGTAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4405862 original size:19 final size:20
Alignment explanation
Indices: 4405816--4405873 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
4405806 ATTTGCCAAA
4405816 AATATGTGGGTAAGGATTAC
1 AATATGTGGGTAAGGATTAC
* ** *
4405836 AATTTGTGGGTCTGG-TTTC
1 AATATGTGGGTAAGGATTAC
4405855 AATATGTGGGTAAGGATTA
1 AATATGTGGGTAAGGATTA
4405874 ATTTGCCAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (20 bp):
AATATGTGGGTAAGGATTAC
Found at i:4408098 original size:35 final size:35
Alignment explanation
Indices: 4408059--4408134 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
4408049 TTGTAATCTT
4408059 ACATTCATGATAAACGAACCAAACACAACAATGCA
1 ACATTCATGATAAACGAACCAAACACAACAATGCA
* * *
4408094 ACATTCCTGCTAATCGAACCAAACACAACAATGCA
1 ACATTCATGATAAACGAACCAAACACAACAATGCA
4408129 ACATTC
1 ACATTC
4408135 TCAATAATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.46, C:0.29, G:0.08, T:0.17
Consensus pattern (35 bp):
ACATTCATGATAAACGAACCAAACACAACAATGCA
Found at i:4408166 original size:18 final size:18
Alignment explanation
Indices: 4408139--4408188 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
4408129 ACATTCTCAA
* *
4408139 TAATCTTATTTCCGTCGG
1 TAATCCTATTCCCGTCGG
*
4408157 TAATTCTATTCCCGTCGG
1 TAATCCTATTCCCGTCGG
4408175 TAATCCTATTCCCG
1 TAATCCTATTCCCG
4408189 CCGATAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.40
Consensus pattern (18 bp):
TAATCCTATTCCCGTCGG
Found at i:4408196 original size:18 final size:18
Alignment explanation
Indices: 4408138--4408197 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
4408128 AACATTCTCA
* *
4408138 ATAATCTTATTTCCGTCG
1 ATAATCCTATTCCCGTCG
* *
4408156 GTAATTCTATTCCCGTCG
1 ATAATCCTATTCCCGTCG
* *
4408174 GTAATCCTATTCCCGCCG
1 ATAATCCTATTCCCGTCG
4408192 ATAATC
1 ATAATC
4408198 TTACATTCCG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (18 bp):
ATAATCCTATTCCCGTCG
Found at i:4409876 original size:2 final size:2
Alignment explanation
Indices: 4409869--4409895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4409859 ATGAAAATTA
4409869 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4409896 CATCACGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4415938 original size:15 final size:15
Alignment explanation
Indices: 4415910--4415944 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4415900 AGAACCTCTA
* *
4415910 AATCATTCAGCGCTT
1 AATCAATCAACGCTT
4415925 AATCAATCAACGCTT
1 AATCAATCAACGCTT
4415940 AATCA
1 AATCA
4415945 TTCTGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.29
Consensus pattern (15 bp):
AATCAATCAACGCTT
Found at i:4416065 original size:45 final size:45
Alignment explanation
Indices: 4416001--4416135 Score: 252
Period size: 45 Copynumber: 3.0 Consensus size: 45
4415991 ATAACATTCC
*
4416001 TGAGATATTTTACCAATTAAATATGTATAGACGGGTACGGGTGCA
1 TGAGATATTTTACCAATTAAATATGTATAGACTGGTACGGGTGCA
4416046 TGAGATATTTTACCAATTAAATATGTATAGACTGGTACGGGTGCA
1 TGAGATATTTTACCAATTAAATATGTATAGACTGGTACGGGTGCA
*
4416091 TGAGATATTTTACCAATTAAATATGTATAGACTGGTATGGGTGCA
1 TGAGATATTTTACCAATTAAATATGTATAGACTGGTACGGGTGCA
4416136 ATTCAACATA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (45 bp):
TGAGATATTTTACCAATTAAATATGTATAGACTGGTACGGGTGCA
Found at i:4417787 original size:36 final size:36
Alignment explanation
Indices: 4417735--4417851 Score: 189
Period size: 36 Copynumber: 3.2 Consensus size: 36
4417725 TAATTTACTG
4417735 AAAACAAAGTTTTGTCTCTCTTGAGACGGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACGGTTTCTCTT
**
4417772 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACGGTTTCTCTT
*
4417808 AAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACGGTTTCTCTT
*
4417844 GAAACAAA
1 AAAACAAA
4417852 AAACTTTGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
36 66 0.89
37 8 0.11
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACGGTTTCTCTT
Found at i:4417896 original size:22 final size:22
Alignment explanation
Indices: 4417871--4417934 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
4417861 ATTTGTTTTC
4417871 CTTGAAACAAAGTTTTGTCTCT
1 CTTGAAACAAAGTTTTGTCTCT
*
4417893 CTTGAGAC--AG--TT-TCT-T
1 CTTGAAACAAAGTTTTGTCTCT
4417909 -TTAGAAACAAA-TTTTGTCTCT
1 CTT-GAAACAAAGTTTTGTCTCT
4417930 CTTGA
1 CTTGA
4417935 GACATTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 17
0.63 0.04 0.33
Matches are distributed among these distances:
15 2 0.06
16 5 0.16
17 3 0.09
18 3 0.09
19 2 0.06
20 5 0.16
21 3 0.09
22 9 0.28
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (22 bp):
CTTGAAACAAAGTTTTGTCTCT
Found at i:4418014 original size:139 final size:136
Alignment explanation
Indices: 4417736--4418344 Score: 920
Period size: 139 Copynumber: 4.5 Consensus size: 136
4417726 AATTTACTGA
* *
4417736 AAACAAAGTTTTGTCTCTCTTGAGACGGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
* *
4417801 TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAAACTTTGAATTTG
66 TTCTCTT-AAA-AATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAAACTTTGAATTTG
4417866 TTTTCCTTG
128 TTTTCCTTG
4417875 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAGAAACAAATTTTGTCTCTCTTGAGACAT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTA-AAACAAATTTTGTCTCTCTTGAGACAT
*
4417940 TTTCTCTTAAAAAATTTTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTG
65 TTTCTCTT-AAAAA-TTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATTTG
4418005 TTTTCCTTG
128 TTTTCCTTG
4418014 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTATAAACAAATTTTGTCTCTCTTGAGACAT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTA-AAACAAATTTTGTCTCTCTTGAGACAT
* *
4418079 TTTCTCTTAAAAATTTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGTT
65 TTTCTCTTAAAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATTTGTT
4418144 TTCCTTG
130 TTCCTTG
* * * * *
4418151 AAACAAA-TCTCGTCTCCCTTGAAACAATTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
** * *
4418215 TTCTCTTAAACTTTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTTAATTTGTTT
66 TTCTCTTAAAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATTTGTTT
*
4418280 TCCTTT
131 TCCTTG
* * * * * *
4418286 AAACAAA-TTTCGTCTCTCTCGAGACTGTTTCTCTT-GAA-AAATTTTGTCTCCCTTGAGAC
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGAC
4418345 GGTTTCTTTT
Statistics
Matches: 442, Mismatches: 26, Indels: 10
0.92 0.05 0.02
Matches are distributed among these distances:
133 20 0.05
134 2 0.00
135 122 0.28
136 24 0.05
137 63 0.14
138 5 0.01
139 134 0.30
140 72 0.16
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (136 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
TTCTCTTAAAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATTTGTTT
TCCTTG
Found at i:4418065 original size:37 final size:35
Alignment explanation
Indices: 4418006--4418128 Score: 142
Period size: 34 Copynumber: 3.4 Consensus size: 35
4417996 TTGAATTTGT
4418006 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTT-AAACAAA-TTTTGTCTCTCTTGAGACAG
* *
4418042 TTTCTTTTATAAACAAATTTTGTCTCTCTTGAGACAT
1 TTTC-TCT-TAAACAAATTTTGTCTCTCTTGAGACAG
* *
4418079 TTTCTCTTAAA-AATTTTTGTCTCTCTTAAGACAG
1 TTTCTCTTAAACAAATTTTGTCTCTCTTGAGACAG
*
4418113 TTTCCCTTGAAACAAA
1 TTTCTCTT-AAACAAA
4418129 ATCTTTGAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
34 27 0.36
35 7 0.09
36 8 0.11
37 23 0.31
38 8 0.11
39 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (35 bp):
TTTCTCTTAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:4418191 original size:36 final size:36
Alignment explanation
Indices: 4418143--4418224 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
4418133 TTGAATTTGT
*
4418143 TTTC-CTTGAAACAAATCTCGTCTCCCTTGAAACAA
1 TTTCTCTTAAAACAAATCTCGTCTCCCTTGAAACAA
* * * * * *
4418178 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTTAAAACAAATCTCGTCTCCCTTGAAACAA
4418214 TTTCTCTTAAA
1 TTTCTCTTAAA
4418225 CTTTTTTGTC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 4 0.11
36 34 0.89
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.41
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATCTCGTCTCCCTTGAAACAA
Found at i:4418237 original size:34 final size:35
Alignment explanation
Indices: 4418194--4418260 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
4418184 TTAAAACAAA
* *
4418194 TTTTGTCTCTCTTGAGACATTTTCTCTT-AAACTT
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACTT
4418228 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
4418261 AAAATCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACTT
Found at i:4418301 original size:99 final size:101
Alignment explanation
Indices: 4418178--4418393 Score: 260
Period size: 99 Copynumber: 2.1 Consensus size: 101
4418168 CTTGAAACAA
* * * ** *
4418178 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAT-TTTCTCTT-AAACTTTTTTGTCTCTCTT
1 TTTCCTTT-AAACAAATTTCGTCTCTCTCGAGAC-TGTTTCTCTTGAAA-AATTTTGTCTCCCTT
* *
4418241 GAGACAGTTTCCCTTG-AA-ACAAAATCTTTTAATTTGT
63 GAGACAGTTTCCCTTGAAACACAAAATCTTTGAATTTAT
4418278 TTTCCTTTAAACAAATTTCGTCTCTCTCGAGACTGTTTCTCTTGAAAAATTTTGTCTCCCTTGAG
1 TTTCCTTTAAACAAATTTCGTCTCTCTCGAGACTGTTTCTCTTGAAAAATTTTGTCTCCCTTGAG
* **
4418343 ACGGTTTCTTTTGAAACACAAAATCTTTGAATTTAT
66 ACAGTTTCCCTTGAAACACAAAATCTTTGAATTTAT
* *
4418379 TTCCCTTAAAACAAA
1 TTTCCTTTAAACAAA
4418394 ATTTTGTTTA
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
98 1 0.01
99 56 0.57
100 12 0.12
101 30 0.30
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (101 bp):
TTTCCTTTAAACAAATTTCGTCTCTCTCGAGACTGTTTCTCTTGAAAAATTTTGTCTCCCTTGAG
ACAGTTTCCCTTGAAACACAAAATCTTTGAATTTAT
Found at i:4418328 original size:34 final size:34
Alignment explanation
Indices: 4418290--4418358 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
4418280 TCCTTTAAAC
* *
4418290 AAATTTCGTCTCTCTCGAGACTGTTTCTCTTGAA
1 AAATTTCGTCTCCCTCGAGACGGTTTCTCTTGAA
* * *
4418324 AAATTTTGTCTCCCTTGAGACGGTTTCTTTTGAA
1 AAATTTCGTCTCCCTCGAGACGGTTTCTCTTGAA
4418358 A
1 A
4418359 CACAAAATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (34 bp):
AAATTTCGTCTCCCTCGAGACGGTTTCTCTTGAA
Found at i:4420052 original size:3 final size:3
Alignment explanation
Indices: 4420044--4420083 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4420034 CGTATATATG
4420044 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4420084 TCATTTTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4420221 original size:42 final size:42
Alignment explanation
Indices: 4420175--4420275 Score: 98
Period size: 41 Copynumber: 2.4 Consensus size: 42
4420165 ATTTTATTCA
4420175 TTTTTTTATTTTTTTTATTTCTACCATTT-TATTTATTTTGT-
1 TTTTTTTATTTTTTTTATTT-TACCATTTATATTTATTTTGTG
* ** * *
4420216 TTTTTTCATCTTCATTTATTTTACCATTTATTTTTATTTTTTTG
1 TTTTTTTAT-TTTTTTTATTTTACCATTTATATTTA-TTTTGTG
*
4420260 TTTTGTTTATTATTTT
1 TTTT-TTTATTTTTTT
4420276 CATATTTATG
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
41 16 0.35
42 14 0.30
43 5 0.11
44 7 0.15
45 4 0.09
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (42 bp):
TTTTTTTATTTTTTTTATTTTACCATTTATATTTATTTTGTG
Found at i:4422188 original size:29 final size:29
Alignment explanation
Indices: 4422146--4422205 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
4422136 TTATTATTAA
4422146 ACATAATCGACATTGATTTTGGTTCAACT
1 ACATAATCGACATTGATTTTGGTTCAACT
4422175 ACATAATCGACATTGATTTTGGTTCAACT
1 ACATAATCGACATTGATTTTGGTTCAACT
4422204 AC
1 AC
4422206 CGAATCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (29 bp):
ACATAATCGACATTGATTTTGGTTCAACT
Found at i:4427162 original size:12 final size:12
Alignment explanation
Indices: 4427145--4427199 Score: 92
Period size: 12 Copynumber: 4.6 Consensus size: 12
4427135 CCATCCCATC
4427145 CCATCCCTACTA
1 CCATCCCTACTA
*
4427157 CCATCCCTACTG
1 CCATCCCTACTA
4427169 CCATCCCTACTA
1 CCATCCCTACTA
*
4427181 CCATCCCTACTT
1 CCATCCCTACTA
4427193 CCATCCC
1 CCATCCC
4427200 CTAAGCCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.20, C:0.53, G:0.02, T:0.25
Consensus pattern (12 bp):
CCATCCCTACTA
Found at i:4432598 original size:21 final size:21
Alignment explanation
Indices: 4432572--4432612 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4432562 ACAATAGGAC
*
4432572 CTTGTCAAATTTTGACTCTAG
1 CTTGTCAAATGTTGACTCTAG
*
4432593 CTTGTCGAATGTTGACTCTA
1 CTTGTCAAATGTTGACTCTA
4432613 TTTTAGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (21 bp):
CTTGTCAAATGTTGACTCTAG
Found at i:4436215 original size:60 final size:60
Alignment explanation
Indices: 4436122--4436303 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 60
4436112 ATACTCTTGA
** * * * *
4436122 GTTAGAAATCACTTCAAAACCCTTGGCCGCAATAACTATATTATGTCT-ATTGCTTCTTTC
1 GTTAGAAGGCACTTCGAAGCCCTCGGCTGCAATAACTATATTATGT-TGATTGCTTCTTTC
* * *
4436182 GTTAGAAGGCACTTCGAAGCCCTCGGCTGCAATAACTAAATTATGTTGAGTGTTTCTTTC
1 GTTAGAAGGCACTTCGAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTTCTTTC
* ** *
4436242 GTTAGAAGGCATTTCGAAGCCCTCGTATGC---AACTATATTATGTTGATTGCTCCTTTC
1 GTTAGAAGGCACTTCGAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTTCTTTC
*
4436299 TTTAG
1 GTTAG
4436304 TGACAGTTTC
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
57 27 0.26
59 1 0.01
60 76 0.73
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (60 bp):
GTTAGAAGGCACTTCGAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTTCTTTC
Found at i:4438058 original size:21 final size:21
Alignment explanation
Indices: 4438034--4438084 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
4438024 GCTTGATCAT
4438034 TATCGATACTATGCTTCATGG
1 TATCGATACTATGCTTCATGG
*
4438055 TATCGATATTATGCTTCATGG
1 TATCGATACTATGCTTCATGG
4438076 TATCGATAC
1 TATCGATAC
4438085 GACTGTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
TATCGATACTATGCTTCATGG
Found at i:4439063 original size:22 final size:22
Alignment explanation
Indices: 4439022--4439065 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4439012 TATAATGAAC
4439022 AAACTATTATGAAAAATCATTA
1 AAACTATTATGAAAAATCATTA
4439044 AAACT-TTA-GAAAATATTCATTA
1 AAACTATTATGAAAA-A-TCATTA
4439066 CAATTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.25
21 4 0.20
22 11 0.55
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (22 bp):
AAACTATTATGAAAAATCATTA
Found at i:4439673 original size:20 final size:21
Alignment explanation
Indices: 4439648--4439699 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4439638 TTTTCCCAAT
*
4439648 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4439668 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
4439689 TCGCAATGCGA
1 TCGCAATGCGA
4439700 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:4439713 original size:20 final size:20
Alignment explanation
Indices: 4439688--4439801 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
4439678 AATTGGGAAA
*
4439688 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
4439708 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
4439728 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
4439749 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
4439769 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
4439789 TTCGCAACGCGAT
1 ATCGCAACGCGAT
4439802 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:4439732 original size:61 final size:61
Alignment explanation
Indices: 4439685--4439801 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
4439675 GCGAATTGGG
* * * * *
4439685 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
4439746 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
4439802 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:4440358 original size:19 final size:19
Alignment explanation
Indices: 4440320--4440375 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
4440310 TTCGAGAATG
4440320 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
4440340 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
4440359 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
4440376 CCAAAATCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:4440428 original size:20 final size:19
Alignment explanation
Indices: 4440387--4440547 Score: 126
Period size: 20 Copynumber: 8.8 Consensus size: 19
4440377 CAAAATCACA
4440387 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
4440406 TTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGC-G
4440426 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
4440445 TTGCGATTGTC---T-G-G
1 TTGCGATTTTCATTTCGCG
** **
4440459 TCACGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
4440478 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
4440492 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
4440512 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
4440532 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
4440548 AACCAAAAGA
Statistics
Matches: 113, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 36 0.32
20 49 0.43
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:4440477 original size:33 final size:33
Alignment explanation
Indices: 4440435--4440522 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
4440425 GTTGCGATTT
* *
4440435 TCATTTCGCGTTGCGATTGTCTGGTCACGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
**
4440468 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
4440501 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
4440523 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
Found at i:4442494 original size:42 final size:42
Alignment explanation
Indices: 4442433--4442516 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
4442423 GCCCGACTCG
* * *
4442433 CCTATAATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATAATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * *
4442475 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATAATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
4442517 ACTGTCATCG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATAATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:4442513 original size:21 final size:21
Alignment explanation
Indices: 4442489--4442555 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4442479 TCATTCCTCG
4442489 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
4442510 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
4442531 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
4442552 AGAG
1 AGAG
4442556 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:4443933 original size:14 final size:14
Alignment explanation
Indices: 4443914--4443949 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4443904 ATTGTTTAAT
4443914 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4443928 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4443942 TGATTTGT
1 TGATTTGT
4443950 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:4444150 original size:19 final size:19
Alignment explanation
Indices: 4444128--4444212 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
4444118 CGAAATTAAA
4444128 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4444147 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4444162 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
4444180 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
4444199 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4444213 GAACATTAAG
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
14 8 0.16
16 3 0.06
17 3 0.06
19 25 0.51
20 10 0.20
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4446502 original size:12 final size:12
Alignment explanation
Indices: 4446485--4446509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4446475 TCTTCGGGGA
4446485 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4446497 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4446509 C
1 C
4446510 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:4446718 original size:24 final size:24
Alignment explanation
Indices: 4446684--4446737 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4446674 CTGAAACATC
* *
4446684 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
4446708 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
4446732 ATCAAA
1 ATCAAA
4446738 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:4447812 original size:20 final size:20
Alignment explanation
Indices: 4447755--4447805 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
4447745 ATTCATTTGA
4447755 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
4447775 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
4447795 CTATCGCAACG
1 CTATCGCAACG
4447806 AGGAAATCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:4447855 original size:14 final size:14
Alignment explanation
Indices: 4447836--4447889 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
4447826 GAAAATCGCA
4447836 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
4447850 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
4447867 CATTACGATTTTCTCG
1 --TTGCGATTTTCTCG
4447883 TTGCGAT
1 TTGCGAT
4447890 AGCCATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:4447855 original size:33 final size:33
Alignment explanation
Indices: 4447818--4447888 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
4447808 GAAATCGCAA
*
4447818 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTACGATTTTCTCGT
** ** **
4447851 TGCGATTTTCATTTCGCATTACGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTACGATTTTCTCGT
4447884 TGCGA
1 TGCGA
4447889 TAGCCATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTACGATTTTCTCGT
Found at i:4447897 original size:33 final size:33
Alignment explanation
Indices: 4447831--4447897 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4447821 GAAATGAAAA
* ***
4447831 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTACGATTTTCTCGTTGCGATAGCCATT
4447864 TCGCATTACGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTACGATTTTCTCGTTGCGATAGCCATT
4447897 T
1 T
4447898 TCGCGTTGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
TCGCATTACGATTTTCTCGTTGCGATAGCCATT
Found at i:4447899 original size:20 final size:20
Alignment explanation
Indices: 4447874--4447911 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4447864 TCGCATTACG
*
4447874 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
4447894 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
4447912 TCTGTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:4448016 original size:14 final size:14
Alignment explanation
Indices: 4447997--4448033 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4447987 CATCAATTAA
4447997 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
4448011 ACAAATCATCTTTT
1 ACAAATCAACATTT
4448025 ACAAATCAA
1 ACAAATCAA
4448034 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:4449943 original size:20 final size:19
Alignment explanation
Indices: 4449908--4449974 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
4449898 GAAACTTAAA
*
4449908 ATCGCAACGTGAAATGACT
1 ATCGCAACGCGAAATGACT
*
4449927 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
4449947 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4449966 ATCGCAACG
1 ATCGCAACG
4449975 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4449982 original size:14 final size:14
Alignment explanation
Indices: 4449963--4450052 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
4449953 ATGCGAAATG
4449963 AAAATCGCAACGAC
1 AAAATCGCAACGAC
4449977 AAAATCGCAACGCGAAAC
1 AAAATCGCAA--CG--AC
*
4449995 GAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4450009 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
4450025 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
4450041 AAAATCGCAACG
1 AAAATCGCAACG
4450053 CGAAATACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 32 0.50
16 12 0.19
18 20 0.31
ACGTcount: A:0.48, C:0.27, G:0.18, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4450001 original size:18 final size:18
Alignment explanation
Indices: 4449947--4450068 Score: 88
Period size: 14 Copynumber: 7.3 Consensus size: 18
4449937 GGAAATGGCT
* *
4449947 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAA-CAAA
4449966 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAACAAA
*
4449980 ATCGCAACGCGAAACGAA
1 ATCGCAACGCGAAACAAA
4449998 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAACAAA
**
4450012 ATCGCAACGCGAAATGAA
1 ATCGCAACGCGAAACAAA
4450030 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAACAAA
*
4450044 ATCGCAACGCGAAATACAA
1 ATCGCAACGCGAAACA-AA
4450063 ATCGCA
1 ATCGCA
4450069 TTGTGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
14 31 0.38
15 1 0.01
16 10 0.12
17 2 0.02
18 23 0.28
19 15 0.18
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (18 bp):
ATCGCAACGCGAAACAAA
Found at i:4450005 original size:32 final size:32
Alignment explanation
Indices: 4449947--4450068 Score: 199
Period size: 32 Copynumber: 3.8 Consensus size: 32
4449937 GGAAATGGCT
*
4449947 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
4449980 ATCGCAACGCGAAACGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
4450012 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
*
4450044 ATCGCAACGCGAAATACAAATCGCA
1 ATCGCAACGCGAAAT-GAAATCGCA
4450069 TTGTGATTTT
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
32 62 0.74
33 22 0.26
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:4450064 original size:19 final size:18
Alignment explanation
Indices: 4449889--4450068 Score: 87
Period size: 14 Copynumber: 10.3 Consensus size: 18
4449879 TAGTTTACTT
*
4449889 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA--TAAAA
* **
4449909 TCGCAACGTGAAATGACTA
1 TCGCAACGCGAAAT-AAAA
***
4449928 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAAT-AAAA
*
4449948 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAAT-AAAA
*
4449967 TCGCAA--CG--ACAAAA
1 TCGCAACGCGAAATAAAA
**
4449981 TCGCAACGCGAAACGAAA
1 TCGCAACGCGAAATAAAA
*
4449999 TCGCAA--CG--ACAAAA
1 TCGCAACGCGAAATAAAA
*
4450013 TCGCAACGCGAAATGAAA
1 TCGCAACGCGAAATAAAA
*
4450031 TCGCAA--CG--ACAAAA
1 TCGCAACGCGAAATAAAA
4450045 TCGCAACGCGAAATACAAA
1 TCGCAACGCGAAATA-AAA
4450064 TCGCA
1 TCGCA
4450069 TTGTGATTTT
Statistics
Matches: 127, Mismatches: 18, Indels: 31
0.72 0.10 0.18
Matches are distributed among these distances:
14 31 0.24
15 1 0.01
16 10 0.08
17 2 0.02
18 24 0.19
19 31 0.24
20 28 0.22
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (18 bp):
TCGCAACGCGAAATAAAA
Found at i:4450105 original size:14 final size:14
Alignment explanation
Indices: 4450086--4450143 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4450076 TTTCATTTCG
4450086 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4450100 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4450116 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4450132 CGTTGCGATTTT
1 CGTTGCGATTTT
4450144 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4450150 original size:33 final size:33
Alignment explanation
Indices: 4450073--4450159 Score: 158
Period size: 32 Copynumber: 2.7 Consensus size: 33
4450063 ATCGCATTGT
*
4450073 GATTTTCATTTCGCGTTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
4450106 GA-TTTCATTTCGCATTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
4450138 GATTTTCATTTCGCATTGCGAT
1 GATTTTCATTTCGCATTGCGAT
4450160 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 31 0.60
33 21 0.40
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
Found at i:4450178 original size:20 final size:19
Alignment explanation
Indices: 4450144--4450198 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
4450134 TTGCGATTTT
*
4450144 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4450163 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
4450183 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
4450199 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:4450712 original size:18 final size:18
Alignment explanation
Indices: 4450686--4450730 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4450676 GTCGATCAGA
*
4450686 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
4450704 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4450722 TGATGGCTC
1 TGATGGCTC
4450731 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:4452051 original size:20 final size:20
Alignment explanation
Indices: 4452026--4452063 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4452016 AATAGTTTCT
4452026 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
4452046 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
4452064 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:4452345 original size:20 final size:21
Alignment explanation
Indices: 4452320--4452368 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
4452310 TCTGAGAGAT
4452320 GGAGAT-AGACGGATTTCGTC
1 GGAGATGAGACGGATTTCGTC
4452340 GGAGATGGAGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGTC
*
4452362 AGAGATG
1 GGAGATG
4452369 GGTGAGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.23
21 1 0.04
22 19 0.73
ACGTcount: A:0.27, C:0.12, G:0.39, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGTC
Found at i:4452353 original size:22 final size:22
Alignment explanation
Indices: 4452326--4452369 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4452316 AGATGGAGAT
*
4452326 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGTCAGAGATGG
4452348 AGACGGATTTCGTCAGAGATGG
1 AGACGGATTTCGTCAGAGATGG
4452370 GTGAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.23
Consensus pattern (22 bp):
AGACGGATTTCGTCAGAGATGG
Found at i:4452586 original size:20 final size:20
Alignment explanation
Indices: 4452558--4452606 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
4452548 GATTATGTAT
*
4452558 TATCACGTTGCGAAAGTCAG
1 TATCACGTTGCGAAAGTAAG
*
4452578 TATCGCGTTGCGAAAGTAAG
1 TATCACGTTGCGAAAGTAAG
*
4452598 TATCTCGTT
1 TATCACGTT
4452607 ACGATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCACGTTGCGAAAGTAAG
Found at i:4452665 original size:20 final size:20
Alignment explanation
Indices: 4452621--4452713 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
4452611 TTTTTTATTA
* **
4452621 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
4452642 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
4452662 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
4452683 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
4452703 TCGCATTGCGA
1 TCGCATTGCGA
4452714 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:4452666 original size:41 final size:41
Alignment explanation
Indices: 4452614--4452713 Score: 186
Period size: 41 Copynumber: 2.5 Consensus size: 41
4452604 GTTACGATTT
4452614 TTTA-TTA-TCGCATTGCGATTTTCCCAATTCGCGTTGCGA
1 TTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGA
4452653 TTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGA
1 TTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGA
4452694 TTTACTTATTCGCATTGCGA
1 TTTACTTATTCGCATTGCGA
4452714 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
39 4 0.07
40 3 0.05
41 52 0.88
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (41 bp):
TTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGA
Found at i:4453099 original size:20 final size:20
Alignment explanation
Indices: 4453051--4453098 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
4453041 TCAAAACCAT
4453051 TTTTCAAAATTTCATTTTGC
1 TTTTCAAAATTTCATTTTGC
4453071 TTTTCAAAATTTCATTTTGC
1 TTTTCAAAATTTCATTTTGC
4453091 -TTTCAAAA
1 TTTTCAAAA
4453099 ACCAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTGC
Found at i:4454372 original size:21 final size:21
Alignment explanation
Indices: 4454340--4454382 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4454330 CAAGACAGAT
*
4454340 AGTATCGATACTCCTTTAATA
1 AGTATCGATACTACTTTAATA
*
4454361 AGTATC-AGTACTACTTTTATA
1 AGTATCGA-TACTACTTTAATA
4454382 A
1 A
4454383 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
AGTATCGATACTACTTTAATA
Found at i:4457395 original size:20 final size:20
Alignment explanation
Indices: 4457372--4457434 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
4457362 ATCTAAATTC
4457372 TAAACAGATTACCTAACAAT
1 TAAACAGATTACCTAACAAT
* **
4457392 TAAACATATTATAGATAAACAAT
1 TAAACAGA-T-TACCT-AACAAT
4457415 TAAACAGATTACCTTAACAA
1 TAAACAGATTACC-TAACAA
4457435 AATAACAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 5 0.15
23 13 0.39
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAACAGATTACCTAACAAT
Found at i:4457590 original size:24 final size:27
Alignment explanation
Indices: 4457529--4457582 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
4457519 CCAATATATA
*
4457529 AACAATTAAACAAATTACATTGAAGAT
1 AACAATTAAACAAATTACAGTGAAGAT
4457556 GAAGCAATTAAACAAATTACAGTGAAG
1 -AA-CAATTAAACAAATTACAGTGAAG
4457583 TAAATTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (27 bp):
AACAATTAAACAAATTACAGTGAAGAT
Found at i:4460792 original size:19 final size:22
Alignment explanation
Indices: 4460754--4460797 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
4460744 TTATATTTCA
4460754 AATTATTTTTTTGTGTTTAAAG
1 AATTATTTTTTTGTGTTTAAAG
*
4460776 AATT-TTTTTTT-TGTTAAAAG
1 AATTATTTTTTTGTGTTTAAAG
4460796 AA
1 AA
4460798 GATATCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 7 0.33
22 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (22 bp):
AATTATTTTTTTGTGTTTAAAG
Found at i:4460906 original size:17 final size:18
Alignment explanation
Indices: 4460884--4460918 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4460874 ATGATTTTTT
4460884 TAAAATATA-TTTTTAAA
1 TAAAATATACTTTTTAAA
*
4460901 TAAAATTTACTTTTTAAA
1 TAAAATATACTTTTTAAA
4460919 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAAATATACTTTTTAAA
Found at i:4461432 original size:16 final size:16
Alignment explanation
Indices: 4461411--4461445 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4461401 ATCAACTAAT
4461411 ATTTTATATTT-ATTTA
1 ATTTTA-ATTTCATTTA
4461427 ATTTTAATTTCATTTA
1 ATTTTAATTTCATTTA
4461443 ATT
1 ATT
4461446 CTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTAATTTCATTTA
Found at i:4461924 original size:25 final size:24
Alignment explanation
Indices: 4461887--4461937 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
4461877 TTAGATAATG
*
4461887 GAGATTTGTAGATTTAGGATTTAGA
1 GAGATTTGTAGATTTAAG-TTTAGA
4461912 GAGATTT-TAAGATTTAAGTTTAGA
1 GAGATTTGT-AGATTTAAGTTTAGA
4461936 GA
1 GA
4461938 TTTAAGAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.39
Consensus pattern (24 bp):
GAGATTTGTAGATTTAAGTTTAGA
Found at i:4483035 original size:20 final size:20
Alignment explanation
Indices: 4482998--4483040 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4482988 ATTCCACCAC
*
4482998 ATGCAACTATATGCTCCTAA
1 ATGCAACTACATGCTCCTAA
* *
4483018 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
4483038 ATG
1 ATG
4483041 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:4486716 original size:2 final size:2
Alignment explanation
Indices: 4486709--4486734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4486699 ATTTATAATC
4486709 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
4486735 AAATGTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4486785 original size:9 final size:10
Alignment explanation
Indices: 4486760--4486787 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
4486750 TATCTTAATA
4486760 TATTTTTTAT
1 TATTTTTTAT
4486770 TATTTTTTAT
1 TATTTTTTAT
4486780 TATTTTTT
1 TATTTTTT
4486788 TAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:4486968 original size:51 final size:51
Alignment explanation
Indices: 4486863--4486990 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
4486853 ACCGGAATAG
* * **
4486863 GTATGTATTAAGTGATACATTTTTTTTATTTCATTCACTTACATTAGTGCAA
1 GTATGTATTAAGTGATACA-CTTTTTGATTTCATTCACTTACACCAGTGCAA
* * *
4486915 GTATGTATTAAGTGTTACACTTTTTGATTTTATTCACTTACACCAGTGTAA
1 GTATGTATTAAGTGATACACTTTTTGATTTCATTCACTTACACCAGTGCAA
* *
4486966 GTATGTGTTAAGTGCTACACTTTTT
1 GTATGTATTAAGTGATACACTTTTT
4486991 TGTAGTATGA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 49 0.73
52 18 0.27
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (51 bp):
GTATGTATTAAGTGATACACTTTTTGATTTCATTCACTTACACCAGTGCAA
Found at i:4492445 original size:32 final size:32
Alignment explanation
Indices: 4492409--4492484 Score: 152
Period size: 32 Copynumber: 2.4 Consensus size: 32
4492399 TGAGTTTGAG
4492409 TCGAGTTGAGCTTACTTTTAAAGTTTTCAAGT
1 TCGAGTTGAGCTTACTTTTAAAGTTTTCAAGT
4492441 TCGAGTTGAGCTTACTTTTAAAGTTTTCAAGT
1 TCGAGTTGAGCTTACTTTTAAAGTTTTCAAGT
4492473 TCGAGTTGAGCT
1 TCGAGTTGAGCT
4492485 CAGCAATACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (32 bp):
TCGAGTTGAGCTTACTTTTAAAGTTTTCAAGT
Found at i:4497873 original size:17 final size:17
Alignment explanation
Indices: 4497851--4497883 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4497841 GTAAGCTAAA
4497851 AGAAAT-GATTATGGTAT
1 AGAAATGGA-TATGGTAT
4497868 AGAAATGGATATGGTA
1 AGAAATGGATATGGTA
4497884 AAGGTAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (17 bp):
AGAAATGGATATGGTAT
Found at i:4500776 original size:2 final size:2
Alignment explanation
Indices: 4500769--4500816 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4500759 CATATGCTCA
4500769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4500811 AT AT AT
1 AT AT AT
4500817 TGTAAATTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4502862 original size:54 final size:54
Alignment explanation
Indices: 4502804--4503387 Score: 889
Period size: 54 Copynumber: 10.8 Consensus size: 54
4502794 GATACGGTCT
* * * * * * * *
4502804 TTCATAAACATATTATGTATTCCGTGGGTTGCACACATAGTGCCAATTCGAAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
*
4502858 TTCATAAACTTATTATGAATTTCTTATGTTGCACACACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
* ** *
4502912 TTCATAAACTTATGATGAATTTCTTAGGTTGCACACGGAGTGGCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
* * *
4502966 TTCATAAACTTATTATGAATTTATTAGGTTGTACACAGAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
* *
4503020 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
* * *
4503074 TTCATAAACTTATTATAAATTTCTTAGGTTACATACACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
* *
4503128 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
* *
4503182 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACATTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
*
4503236 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACATTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
* *
4503290 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACATTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
* * *
4503344 TTCATAAACTTATTATGAATTTCTTAAGTTTCACACATAGTGCC
1 TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCC
4503388 CATTCGGTAA
Statistics
Matches: 486, Mismatches: 44, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 486 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (54 bp):
TTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAA
Found at i:4506133 original size:23 final size:23
Alignment explanation
Indices: 4506102--4506170 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
4506092 CACCACAGCT
* *
4506102 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
4506125 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
4506148 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
4506171 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:4506359 original size:103 final size:103
Alignment explanation
Indices: 4506186--4506398 Score: 363
Period size: 103 Copynumber: 2.1 Consensus size: 103
4506176 TAATGTCCAT
* * * *
4506186 AAGGACTACATATCATTCCTTAAGAATCATATATATATAATAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
4506251 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
**
4506289 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
*
4506354 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
4506392 AAGGACC
1 AAGGACC
4506399 GCGTAGACCC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:4508099 original size:21 final size:21
Alignment explanation
Indices: 4508075--4508119 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4508065 TTTTGTTCGT
* *
4508075 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
4508096 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
4508117 TTG
1 TTG
4508120 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:4508991 original size:2 final size:2
Alignment explanation
Indices: 4508984--4509010 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4508974 CTTTTTCCTT
4508984 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4509011 TCATATCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4511347 original size:23 final size:23
Alignment explanation
Indices: 4511321--4511389 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
4511311 CACCACAGCT
*
4511321 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
4511344 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
4511367 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
4511390 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:4511576 original size:103 final size:103
Alignment explanation
Indices: 4511405--4511617 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
4511395 TAATGTCCAT
* * * *
4511405 AAGGACTACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
4511470 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
4511508 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
4511573 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
4511611 AAGGACC
1 AAGGACC
4511618 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:4513306 original size:21 final size:21
Alignment explanation
Indices: 4513282--4513326 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4513272 ATTTGTTCGT
4513282 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
4513303 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
4513324 TTG
1 TTG
4513327 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:4518270 original size:3 final size:3
Alignment explanation
Indices: 4518255--4518292 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
4518245 TCTATAAAAA
4518255 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAAT TAT T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT T-AT TAT T
4518293 TTTTATACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.03
3 27 0.84
4 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4525504 original size:6 final size:6
Alignment explanation
Indices: 4525493--4525523 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
4525483 TCTCTCGCTA
4525493 TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
1 TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
4525524 GTGCGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCCCT
Found at i:4533586 original size:2 final size:2
Alignment explanation
Indices: 4533579--4533617 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4533569 TAACAAATGC
4533579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4533618 CTAATATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4534044 original size:21 final size:21
Alignment explanation
Indices: 4534006--4534045 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4533996 CCGAAGTACC
**
4534006 ACATATATGTTTCAAAGAATT
1 ACATATATGTCCCAAAGAATT
*
4534027 ACATATATGTCCCGAAGAA
1 ACATATATGTCCCAAAGAA
4534046 CCACGTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (21 bp):
ACATATATGTCCCAAAGAATT
Found at i:4537335 original size:23 final size:24
Alignment explanation
Indices: 4537274--4537336 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
4537264 AAAGGGCTAT
4537274 TAAATCTATTTTAAATAAAATGGGAAA
1 TAAATCTATTTT-AATAAAA--GGAAA
* *
4537301 TAAATATGTTTTAATAAAA-GAAA
1 TAAATCTATTTTAATAAAAGGAAA
4537324 TAAATCTATTTTA
1 TAAATCTATTTTA
4537337 TCTTTATCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 15 0.47
26 7 0.22
27 10 0.31
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (24 bp):
TAAATCTATTTTAATAAAAGGAAA
Found at i:4538414 original size:20 final size:20
Alignment explanation
Indices: 4538345--4538414 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 20
4538335 TATATTTTAT
* *
4538345 AAAATAATTATAAAATTATA
1 AAAATAATTAAAAAAATATA
* *
4538365 AATAT-ATGTATGAAAAATATTA
1 AAAATAAT-TA-AAAAAATA-TA
**
4538387 AATTTAATTAAAAAAATATA
1 AAAATAATTAAAAAAATATA
4538407 AAAATAAT
1 AAAATAAT
4538415 AATTTTGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.05
20 14 0.36
21 13 0.33
22 8 0.21
23 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATAATTAAAAAAATATA
Found at i:4538730 original size:9 final size:9
Alignment explanation
Indices: 4538713--4538757 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
4538703 GATTAAAAGA
*
4538713 TAAAATAAT
1 TAAATTAAT
4538722 TAAATTAAT
1 TAAATTAAT
4538731 TAAAATTAAGAT
1 T-AAATT-A-AT
4538743 TAAATTAAT
1 TAAATTAAT
4538752 TAAATT
1 TAAATT
4538758 TATATGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 17 0.53
10 6 0.19
11 6 0.19
12 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
TAAATTAAT
Found at i:4538919 original size:29 final size:30
Alignment explanation
Indices: 4538881--4538941 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
4538871 ATAGGATAAA
4538881 TTATATA-TTTAGTACCTAAA-TTATTAATT
1 TTATATATTTTAGTACCTAAACTT-TTAATT
* *
4538910 TTATCTATTTTAGTACTTAAACTTTTAATT
1 TTATATATTTTAGTACCTAAACTTTTAATT
4538940 TT
1 TT
4538942 TTTAAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 6 0.21
30 20 0.71
31 2 0.07
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (30 bp):
TTATATATTTTAGTACCTAAACTTTTAATT
Found at i:4547081 original size:2 final size:2
Alignment explanation
Indices: 4547069--4547122 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
4547059 AAATAAACAC
*
4547069 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4547111 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4547123 TATTTTATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4548233 original size:16 final size:17
Alignment explanation
Indices: 4548214--4548246 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4548204 TTTTCCCTCA
4548214 TATTATTTTTTA-GTAT
1 TATTATTTTTTATGTAT
4548230 TATTATTTTTTATGTAT
1 TATTATTTTTTATGTAT
4548247 ATACATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
TATTATTTTTTATGTAT
Found at i:4548345 original size:14 final size:14
Alignment explanation
Indices: 4548326--4548356 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4548316 TATATTTTGT
4548326 TTTATTCCTTAATA
1 TTTATTCCTTAATA
*
4548340 TTTATTTCTTAATA
1 TTTATTCCTTAATA
4548354 TTT
1 TTT
4548357 TTTAGTTTAC
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:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATTCCTTAATA
Found at i:4548489 original size:13 final size:13
Alignment explanation
Indices: 4548396--4548507 Score: 52
Period size: 13 Copynumber: 8.5 Consensus size: 13
4548386 TATATATGTA
*
4548396 TATTTTATTTCTT
1 TATTTTATTTATT
*
4548409 TTTTTTACTTT-TT
1 TATTTTA-TTTATT
** *
4548422 CGTTTTGTTTATT
1 TATTTTATTTATT
*
4548435 CATTTTATTGCTATT
1 TATTTTATT--TATT
** *
4548450 TCCTCTATTT-TT
1 TATTTTATTTATT
4548462 TATTTTATTTATT
1 TATTTTATTTATT
*
4548475 TATCTTT-TTTCTT
1 TAT-TTTATTTATT
4548488 TA-TTTATCTTATT
1 TATTTTAT-TTATT
4548501 CTATTTT
1 -TATTTT
4548508 GTCTTTATTC
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
11 3 0.04
12 13 0.18
13 38 0.51
14 8 0.11
15 12 0.16
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.72
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:4548489 original size:17 final size:17
Alignment explanation
Indices: 4548464--4548497 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4548454 CTATTTTTTA
4548464 TTTTATTTATTTATCTT
1 TTTTATTTATTTATCTT
*
4548481 TTTTCTTTATTTATCTT
1 TTTTATTTATTTATCTT
4548498 ATTCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTATTTATCTT
Found at i:4548499 original size:26 final size:25
Alignment explanation
Indices: 4548465--4548527 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 25
4548455 TATTTTTTAT
4548465 TTTATTTAT-TTA-TCT-TTTT-TC
1 TTTATTTATCTTATTCTATTTTGTC
4548486 TTTATTTATCTTATTCTATTTTGTC
1 TTTATTTATCTTATTCTATTTTGTC
*
4548511 TTTATTCTTTCTTATTC
1 TTTATT-TATCTTATTC
4548528 CTTTCATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 9 0.25
22 3 0.08
23 3 0.08
24 4 0.11
25 8 0.22
26 9 0.25
ACGTcount: A:0.14, C:0.13, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTATTTATCTTATTCTATTTTGTC
Found at i:4552386 original size:95 final size:95
Alignment explanation
Indices: 4552218--4552396 Score: 306
Period size: 95 Copynumber: 1.9 Consensus size: 95
4552208 ATATTATTTA
*
4552218 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAAGCCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAAGCCCCGGCTTTATGGATAAG
*
4552283 ATTCAGCTAGCCTGATAAATGTGATTATAC
66 ATTCAGCTAACCTGATAAATGTGATTATAC
*
4552313 TATACAATAAAGCTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTTAAAAGCCCCGGCTTTATGGATAA
*
4552377 GATTTAGCTAACCTGATAAA
65 GATTCAGCTAACCTGATAAA
4552397 GGTATTTACA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 1 0.01
95 78 0.99
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAAGCCCCGGCTTTATGGATAAG
ATTCAGCTAACCTGATAAATGTGATTATAC
Found at i:4553798 original size:21 final size:22
Alignment explanation
Indices: 4553766--4553808 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
4553756 TAATTTACTC
4553766 AAAACAAAATTTTGTCTCTCTT
1 AAAACAAAATTTTGTCTCTCTT
4553788 AAAAC-AAATTTTGTCTCTCTT
1 AAAACAAAATTTTGTCTCTCTT
4553809 GAGAAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (22 bp):
AAAACAAAATTTTGTCTCTCTT
Found at i:4554029 original size:36 final size:36
Alignment explanation
Indices: 4553948--4554108 Score: 149
Period size: 36 Copynumber: 4.6 Consensus size: 36
4553938 AATATGTTGT
* *
4553948 CCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
** * **
4553984 TTTTAAAACAAATTTTGTCTCTCTTGAGATGGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
* * *
4554020 CCTTGAAACAAA------ATCT-TTGA-ATATGTTTT
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACA-GTTTC
*
4554049 CCTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
4554085 CCTTGAAACAAAGTTTTGTCTCTC
1 CCTTGAAACAAA-TTTTGTCTCTC
4554109 AACAAAGTTT
Statistics
Matches: 97, Mismatches: 18, Indels: 19
0.72 0.13 0.14
Matches are distributed among these distances:
28 2 0.02
29 19 0.20
30 3 0.03
35 3 0.03
36 57 0.59
37 13 0.13
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
Found at i:4554041 original size:101 final size:101
Alignment explanation
Indices: 4553786--4554108 Score: 488
Period size: 101 Copynumber: 3.2 Consensus size: 101
4553776 TTTGTCTCTC
*
4553786 TTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
4553851 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTT
66 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTT
** * * * *
4553887 TTGGAACTAA--TTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTGTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
*
4553950 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTT
66 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTT
**
4553986 TTAAAACAAATTTTGTCTCTCTTGAGATGGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
* * **
4554051 TTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
66 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTT
*
4554087 TTGAAACAAAGTTTTGTCTCTC
1 TTAAAACAAA-TTTTGTCTCTC
4554109 AACAAAGTTT
Statistics
Matches: 198, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
99 91 0.46
101 96 0.48
102 11 0.06
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (101 bp):
TTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTT
Found at i:4554114 original size:18 final size:18
Alignment explanation
Indices: 4554091--4554126 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4554081 TTTCCCTTGA
4554091 AACAAAGTTTTGTCTCTC
1 AACAAAGTTTTGTCTCTC
4554109 AACAAAGTTTTGTCTCTC
1 AACAAAGTTTTGTCTCTC
4554127 TTGAGACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
AACAAAGTTTTGTCTCTC
Found at i:4554118 original size:35 final size:35
Alignment explanation
Indices: 4554044--4554118 Score: 80
Period size: 36 Copynumber: 2.1 Consensus size: 35
4554034 CTTTGAATAT
* * * * *
4554044 GTTTTCCTTTAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTC-TAACAAA
4554080 GTTTCCCTTGAAACAAAGTTTTGTCTCTC-AACAAA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTAACAAA
4554115 GTTT
1 GTTT
4554119 TGTCTCTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
35 7 0.21
36 15 0.45
37 11 0.33
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (35 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTAACAAA
Found at i:4554192 original size:33 final size:33
Alignment explanation
Indices: 4554155--4554246 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
4554145 AAGCACCAAT
4554155 CTTTGAAATTGTTTCTCTTGAAACACAAAAAAC
1 CTTTGAAATTGTTTCTCTTGAAACACAAAAAAC
**
4554188 CTTTGAAACAGTTTCTCTTGAAACACAAAAAAC
1 CTTTGAAATTGTTTCTCTTGAAACACAAAAAAC
4554221 CTATTGAAATTGTTTCTCTTGAAACA
1 CT-TTGAAATTGTTTCTCTTGAAACA
4554247 TTATTCTTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 33 0.61
34 21 0.39
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (33 bp):
CTTTGAAATTGTTTCTCTTGAAACACAAAAAAC
Found at i:4555655 original size:14 final size:14
Alignment explanation
Indices: 4555636--4555666 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4555626 TATATTTTGT
4555636 TTTATTCCTTAATA
1 TTTATTCCTTAATA
*
4555650 TTTATTTCTTAATA
1 TTTATTCCTTAATA
4555664 TTT
1 TTT
4555667 TTTAGTTTAC
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:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATTCCTTAATA
Found at i:4555779 original size:21 final size:22
Alignment explanation
Indices: 4555762--4555822 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 22
4555752 TATTTTTTAT
4555762 TTTATTTAT-TTATCTTTTTTC
1 TTTATTTATCTTATCTTTTTTC
4555783 TTTATTTATCTTATTCTATTTTGTC
1 TTTATTTATCTTA-TCT-TTTT-TC
*
4555808 TTTATTCTTTCTTAT
1 TTTATT-TATCTTAT
4555823 TTATTTCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 9 0.26
22 3 0.09
23 3 0.09
24 4 0.12
25 9 0.26
26 6 0.18
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTATTTATCTTATCTTTTTTC
Found at i:4555786 original size:17 final size:17
Alignment explanation
Indices: 4555761--4555794 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4555751 CTATTTTTTA
4555761 TTTTATTTATTTATCTT
1 TTTTATTTATTTATCTT
*
4555778 TTTTCTTTATTTATCTT
1 TTTTATTTATTTATCTT
4555795 ATTCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTATTTATCTT
Found at i:4555790 original size:25 final size:25
Alignment explanation
Indices: 4555762--4555828 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
4555752 TATTTTTTAT
4555762 TTTATTTAT-TTA-TCT-TTTT-TC
1 TTTATTTATCTTATTCTATTTTGTC
4555783 TTTATTTATCTTATTCTATTTTGTC
1 TTTATTTATCTTATTCTATTTTGTC
*
4555808 TTTATTCTTTCTTATT-TATTT
1 TTTATT-TATCTTATTCTATTT
4555829 CATTTTCACT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
21 9 0.22
22 3 0.08
23 3 0.08
24 4 0.10
25 13 0.32
26 8 0.20
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.73
Consensus pattern (25 bp):
TTTATTTATCTTATTCTATTTTGTC
Done.