Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007735.1 Hibiscus syriacus cultivar Beakdansim tig00109992_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: 534668
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:179840 original size:37 final size:36
Alignment explanation
Indices: 179786--179857 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
179776 TTATTATCAG
179786 TTTTATTAATTTATATATATATATATACTATTTTTT
1 TTTTATTAATTTATATATATATATATACTATTTTTT
** *
179822 TTTTATTTTTTTATTATATATATATATATTATTTTT
1 TTTTATTAATTTA-TATATATATATATACTATTTTT
179858 ACTTTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 11 0.34
37 21 0.66
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTTATTAATTTATATATATATATATACTATTTTTT
Found at i:179864 original size:43 final size:42
Alignment explanation
Indices: 179733--179879 Score: 138
Period size: 43 Copynumber: 3.4 Consensus size: 42
179723 TTAGCATATA
179733 TTTTTATTTTTTTAGATTATATATATATATA-TA-TATTATTTT
1 TTTTTATTTTTTT--ATTATATATATATATATTATTATTATTTT
** * *
179775 TTTATTATCAGTTTTATTA-ATTTATATATATATATATACTATTTTT
1 TTT-TTAT-TTTTTTATTATATATATATATAT-TAT-TATTA-TTTT
*
179821 TTTTTATTTTTTTATTATATATATATATATTATTTTTACTTTT
1 TTTTTATTTTTTTATTATATATATATATATTATTATTA-TTTT
* *
179864 TTATTATTATTTTATT
1 TTTTTATTTTTTTATT
179880 TATTTGTTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
41 10 0.12
42 7 0.08
43 27 0.32
44 15 0.18
45 19 0.22
46 7 0.08
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (42 bp):
TTTTTATTTTTTTATTATATATATATATATTATTATTATTTT
Found at i:179865 original size:88 final size:82
Alignment explanation
Indices: 179733--179907 Score: 217
Period size: 88 Copynumber: 2.0 Consensus size: 82
179723 TTAGCATATA
*
179733 TTTTTATTTTTTTAGATTATATATATATATATATATTATTTTTTTATTATCAGTTTTATTAATTT
1 TTTTTATTTTTTTA-ATTATATATATATATATATATTACTTTTTTATTATCA-TTTTATTAATTT
179798 ATATATATATATATACTATTTTT
64 AT-T-T-TATATATA-TATTTTT
* * *
179821 TTTTTATTTTTTT-ATTATATATATATATATTATTTTTACTTTTTTATTATTATTTTATTTATTT
1 TTTTTATTTTTTTAATTATATATATATATA-TA-TATTACTTTTTTATTATCATTTTATTAATTT
* *
179885 GTTTTATTTATATATTTTT
64 ATTTTATATATATATTTTT
179904 TTTT
1 TTTT
179908 CTTCTTTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
83 11 0.14
84 7 0.09
85 1 0.01
86 17 0.22
87 14 0.18
88 29 0.37
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (82 bp):
TTTTTATTTTTTTAATTATATATATATATATATATTACTTTTTTATTATCATTTTATTAATTTAT
TTTATATATATATTTTT
Found at i:179890 original size:32 final size:31
Alignment explanation
Indices: 179805--179890 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 31
179795 TTTATATATA
*
179805 TATATATACTATTT-TTTTTTTATTTTTTTAT
1 TATATATA-TATTTATTTTTTTACTTTTTTAT
*
179836 TATATATATATATATTATTTTTACTTTTTTAT
1 TATATATATATTTATT-TTTTTACTTTTTTAT
*
179868 TAT-TATTTTATTTATTTGTTTTA
1 TATATA-TATATTTATTT-TTTTA
179891 TTTATATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.09
31 13 0.28
32 30 0.64
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (31 bp):
TATATATATATTTATTTTTTTACTTTTTTAT
Found at i:179897 original size:51 final size:50
Alignment explanation
Indices: 179822--179992 Score: 143
Period size: 51 Copynumber: 3.3 Consensus size: 50
179812 ACTATTTTTT
* * *
179822 TTTTATTTTTTTATTATATATATATATATTATTTTTACTTTTTTAT-TATTA
1 TTTTATTTATTTATTTTATTTATATAT-TTATTTTTACTTTTTTATCT-TTA
* *
179873 TTTTATTTATTTGTTTTATTTATATATTT-TTTTTTCTTCTTTT-TCTTTA
1 TTTTATTTATTTATTTTATTTATATATTTATTTTTACTT-TTTTATCTTTA
* * * * *
179922 TTTTTTTATATTTATTTTACTTA-ATATTTTATCTTTGCTTTCTTTATCTTATC
1 TTTTATT-TATTTATTTTATTTATATA-TTTATTTTTACTTT-TTTATCTT-TA
*
179975 TTTTATTTAATTTGTTTT
1 TTTTATTT-ATTTATTTT
179993 TTCTTCATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
49 21 0.21
50 24 0.24
51 33 0.34
52 5 0.05
53 15 0.15
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.73
Consensus pattern (50 bp):
TTTTATTTATTTATTTTATTTATATATTTATTTTTACTTTTTTATCTTTA
Found at i:179907 original size:43 final size:42
Alignment explanation
Indices: 179756--179907 Score: 112
Period size: 43 Copynumber: 3.5 Consensus size: 42
179746 AGATTATATA
* * * *
179756 TATATATATATATTATTTTTTTATTATCAGTTTTATTAATTTAT
1 TATATTTATATATTTTTTTTTTATTATTA-TTTTATTTATTT-T
* * * * *
179800 ATATATATATATACTATTTTTTTT-TTATTTTTTTATTATATATA
1 -TATATTTATATA-TTTTTTTTTTATTATTATTTTATT-TATTTT
*
179844 TATATATTAT-T-TTTACTTTTTTATTATTATTTTATTTATTTGT
1 TATAT-TTATATATTT-TTTTTTTATTATTATTTTATTTATTT-T
*
179887 TTTATTTATATATTTTTTTTT
1 TATATTTATATATTTTTTTTT
179908 CTTCTTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
41 2 0.02
42 14 0.17
43 28 0.33
44 13 0.15
45 19 0.23
46 8 0.10
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (42 bp):
TATATTTATATATTTTTTTTTTATTATTATTTTATTTATTTT
Found at i:179923 original size:49 final size:49
Alignment explanation
Indices: 179844--179992 Score: 133
Period size: 49 Copynumber: 2.9 Consensus size: 49
179834 ATTATATATA
* *
179844 TATATATTATTTTTACTT-TTTTAT-TATTATTTTATTTATTTGTTTTATT
1 TATATATTTTTTTTACTTCTTTT-TCT-TTATTTTATTTATTTGTTTTACT
* * *
179893 TATATATTTTTTTTTCTTCTTTTTCTTTATTTTTTTATATTTATTTTACT
1 TATATATTTTTTTTACTTCTTTTTCTTTATTTTATT-TATTTGTTTTACT
* * *
179943 TA-ATATTTTATCTTTGCTTTCTTTATCTTATCTTTTATTTAATTTGTTTT
1 TATATATTTT-T-TTTAC-TTCTTTTTCTT-TATTTTATTT-ATTTGTTTT
179993 TTCTTCATTT
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
49 33 0.40
50 19 0.23
51 4 0.05
52 11 0.13
53 15 0.18
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (49 bp):
TATATATTTTTTTTACTTCTTTTTCTTTATTTTATTTATTTGTTTTACT
Found at i:179928 original size:13 final size:13
Alignment explanation
Indices: 179816--179939 Score: 69
Period size: 13 Copynumber: 9.2 Consensus size: 13
179806 ATATATACTA
179816 TTTTTTT-TTTA-
1 TTTTTTTATTTAT
179827 TTTTTTTA-TTAT
1 TTTTTTTATTTAT
* * *
179839 ATATATATATATTAT
1 -TTTTTTTAT-TTAT
179854 TTTTACTTT-TTTAT
1 TTTT--TTTATTTAT
179868 TATTATTTTATTTAT
1 T-TT-TTTTATTTAT
*
179883 TTGTTTTATTTAT
1 TTTTTTTATTTAT
*
179896 ATATTTTTT-TTTCT
1 -T-TTTTTTATTTAT
* *
179910 TCTTTTTCTTTAT
1 TTTTTTTATTTAT
179923 TTTTTTATATTTAT
1 TTTTTT-TATTTAT
179937 TTT
1 TTT
179940 ACTTAATATT
Statistics
Matches: 86, Mismatches: 13, Indels: 25
0.69 0.10 0.20
Matches are distributed among these distances:
11 10 0.12
12 5 0.06
13 25 0.29
14 25 0.29
15 18 0.21
16 3 0.03
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (13 bp):
TTTTTTTATTTAT
Found at i:179951 original size:24 final size:24
Alignment explanation
Indices: 179847--179951 Score: 72
Period size: 24 Copynumber: 4.3 Consensus size: 24
179837 ATATATATAT
*
179847 ATATTATTTTTACTT-TTTTA-TTA
1 ATATT-TTTTTATTTATTTTACTTA
* * *
179870 TTATTTTATTTATTTGTTTTATTTA
1 ATATTTT-TTTATTTATTTTACTTA
* * * *
179895 TATATTTTTTTTTCTTCTTTTTCTTT
1 -ATATTTTTTTAT-TTATTTTACTTA
179921 AT-TTTTTTATATTTATTTTACTTA
1 ATATTTTTT-TATTTATTTTACTTA
179945 ATATTTT
1 ATATTTT
179952 ATCTTTGCTT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
22 2 0.03
23 10 0.16
24 22 0.35
25 15 0.24
26 14 0.22
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (24 bp):
ATATTTTTTTATTTATTTTACTTA
Found at i:183032 original size:7 final size:7
Alignment explanation
Indices: 183016--183059 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
183006 AGATTTAATC
*
183016 AAAGAAA
1 AAAGAGA
183023 AAAGAGA
1 AAAGAGA
*
183030 AAAAAGA
1 AAAGAGA
183037 AAAGAGA
1 AAAGAGA
*
183044 AAATA-A
1 AAAGAGA
183050 AAAGAGA
1 AAAGAGA
183057 AAA
1 AAA
183060 AAACAAAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAGAGA
Found at i:183052 original size:13 final size:13
Alignment explanation
Indices: 183020--183072 Score: 72
Period size: 13 Copynumber: 4.0 Consensus size: 13
183010 TTAATCAAAG
183020 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
183033 AAGAAAAGAGAAAA
1 AA-AAAAGAGAAAA
*
183047 TAAAAAGAGAAAA
1 AAAAAAGAGAAAA
183060 AAACAAAG-GAAAA
1 AAA-AAAGAGAAAA
183073 TTGAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
13 20 0.56
14 16 0.44
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:183057 original size:27 final size:26
Alignment explanation
Indices: 183021--183073 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
183011 TAATCAAAGA
183021 AAAAAGAGAAAAAAGA-AAAGAGAAAAT
1 AAAAAGAGAAAAAA-ACAAAG-GAAAAT
183048 AAAAAGAGAAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAAACAAAGGAAAAT
183074 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAAAGAGAAAAAAACAAAGGAAAAT
Found at i:183263 original size:69 final size:69
Alignment explanation
Indices: 183145--183282 Score: 188
Period size: 69 Copynumber: 2.0 Consensus size: 69
183135 GATTCAAACT
* *
183145 ATGAGATTGGTCAAGCAAAATCATTTTCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCAAAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
183210 TCAA
66 TCAA
* * * ** *
183214 ATGAGATTTATCAAGCACAATCA-TTTCTGAATTACTGAGTCACTCCACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCAAAATCATTTTC-GAATCACTGAACCACTCCACTCGAAGATCATAGAGC
183278 ATCAA
65 ATCAA
183283 GAGAGAGACA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 4 0.07
69 56 0.93
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGCAAAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:184244 original size:32 final size:32
Alignment explanation
Indices: 184208--184327 Score: 134
Period size: 32 Copynumber: 3.8 Consensus size: 32
184198 GGAACAATTA
* *
184208 GGGCATCTTTGAAGATTCAACATCAAATGTTT
1 GGGCATCTTTGTAGATTCAACATCAAATGTTG
* * *
184240 GGGCATTTTTTTAGATTTAACATCAAATGTTG
1 GGGCATCTTTGTAGATTCAACATCAAATGTTG
* * * *
184272 GGGCATTTTTTTAGATTCAACATCGAATATTG
1 GGGCATCTTTGTAGATTCAACATCAAATGTTG
*
184304 GGGCATCTTTG-GGAATTCAACATC
1 GGGCATCTTTGTAG-ATTCAACATC
184328 CTGATGCAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
31 1 0.01
32 75 0.99
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
GGGCATCTTTGTAGATTCAACATCAAATGTTG
Found at i:185040 original size:106 final size:106
Alignment explanation
Indices: 184913--185238 Score: 436
Period size: 106 Copynumber: 3.1 Consensus size: 106
184903 CCACTTGAGT
* *
184913 CAACACAAGTTTAACTCCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCTCAATTTCAG
1 CAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCTCAATTTCAG
*
184978 AGCCAATTTCAACTTCATAGTGAAGGATATTGGACTCGAGA
66 AGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGA
* *
185019 CAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAG
1 CAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCTCAATTTCAG
*
185084 AGCCAATTTCAACTTCACAGTGAATGATATTGGACTCGAGA
66 AGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGA
* * * * * * * * * * *
185125 CAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTAGCTATCAACAAACAATTTCTTAGTTCCAG
1 CAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCTCAATTTCAG
* * * * * *
185190 AGCCAATTTTAACTTCACGGCGGAGGATATTGGAATCGAAA
66 AGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGA
*
185231 CAATACAA
1 CAACACAA
185239 CTTACTTGGA
Statistics
Matches: 192, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
106 192 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (106 bp):
CAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCTCAATTTCAG
AGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGA
Found at i:185682 original size:87 final size:87
Alignment explanation
Indices: 185484--185660 Score: 318
Period size: 87 Copynumber: 2.0 Consensus size: 87
185474 GACAGTTTCT
*
185484 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
185549 CTTGAAACAAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
* * *
185571 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
185636 CTTGAAACAAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
185658 CTT
1 CTT
185661 AAGACAGTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCC
Found at i:185682 original size:102 final size:102
Alignment explanation
Indices: 185571--185810 Score: 363
Period size: 102 Copynumber: 2.4 Consensus size: 102
185561 TTTTGTCTCC
* * *
185571 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTCATCTCGCTTGAGATAGTTTCC
185636 CTTGAAACAAAATTTTGTCTCCCTTAAGACAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTAAGACAGTTTCT
* * * *
185673 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTCGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTCATCTCGCTTGAGATAGTTTCC
* * * *
185738 CTTGTAATAAAATTTTGTCTCCCTTGAGATAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTAAGACAGTTTCT
* *
185775 CTTGAAACACAAACCTTGAAAACATTTCCCTTGAAA
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
185811 CATAAAATAT
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 124 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTCATCTCGCTTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCCCTTAAGACAGTTTCT
Found at i:185898 original size:37 final size:37
Alignment explanation
Indices: 185848--185950 Score: 181
Period size: 36 Copynumber: 2.8 Consensus size: 37
185838 AAAATGAGTT
185848 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
*
185885 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
*
185921 TTGATACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
185951 TGAATATCTT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 34 0.55
37 28 0.45
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:186018 original size:102 final size:102
Alignment explanation
Indices: 185861--186047 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
185851 AGACAGTTTC
* *
185861 CCTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAT
1 CCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
185926 ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
66 ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * *
185963 CCTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTT
1 CCTTGAAACAAAATCTT-GTCTCCCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTCTCTT
* **
186025 GAGATAGTTTCTTTTGAAACAAA
63 GAGACAGTTTCCCTTGAAACAAA
186048 TTTTGTCCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 6 0.08
101 25 0.34
102 43 0.58
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (102 bp):
CCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:186060 original size:36 final size:36
Alignment explanation
Indices: 185848--186081 Score: 168
Period size: 36 Copynumber: 6.6 Consensus size: 36
185838 AAAATGAGTT
** * *
185848 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCTTTTGAAAC-AAATTTTGTCCCTC
** *
185885 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
* ** *
185921 TTGATACAGTTTCCCTTGAAACAAA----AT--CT-
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
* *
185950 TTGA-ATA-TCTT-TTCCTTGAAACAAATTTCGTCTCC-C
1 TTGAGACAGT-TTCTT--TTGAAACAAATTTTGTC-CCTC
* *
185986 TTGAGACAGTTTCTTTT-AGAACTAAGTTTTGTCTCTC
1 TTGAGACAGTTTCTTTTGA-AAC-AAATTTTGTCCCTC
*
186023 TTGAGATAGTTTCTTTTGAAACAAATTTTGTCCCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
*
186059 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCTTTTGAAACA
186082 TAAAAAAACC
Statistics
Matches: 163, Mismatches: 16, Indels: 37
0.75 0.07 0.17
Matches are distributed among these distances:
27 1 0.01
28 4 0.02
29 14 0.09
30 2 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 81 0.50
37 54 0.33
38 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
Found at i:186312 original size:84 final size:85
Alignment explanation
Indices: 186165--186322 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 85
186155 TACCAAACCC
* * * * * *
186165 TCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTATAAGGGT
1 TCGAGTTTGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGC
186230 TATCTGTCACCAAAACACCT
66 TATCTGTCACCAAAACACCT
** * *
186250 TCGAGTTTGACTATGCTCAGC-TCTAAGGCACGTCATTTACAGCATAACTCAAGGCAAGAAGGGC
1 TCGAGTTTGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGC
186314 TATCTGTCA
66 TATCTGTCA
186323 ATAAAATTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 45 0.71
85 18 0.29
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (85 bp):
TCGAGTTTGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGC
TATCTGTCACCAAAACACCT
Found at i:187325 original size:2 final size:2
Alignment explanation
Indices: 187318--187356 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
187308 TTTATTAATT
*
187318 TA TA TA TA TA TT TA CTA T- 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 TA TA TA TA TA TA T
187357 TATTTTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:187331 original size:20 final size:19
Alignment explanation
Indices: 187271--187348 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
187261 ATTTTTTTAG
*
187271 ATTATATATATATATATATT
1 ATTATTTATATATATAT-TT
* *
187291 ATT-TTTTTATTATCATTTTT
1 ATTATTTATA-TAT-ATATTT
187311 ATTAATTTATATATATATTT
1 ATT-ATTTATATATATATTT
*
187331 ACTATTATATATATATAT
1 ATTATT-TATATATATAT
187349 ATATATATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
19 7 0.15
20 29 0.62
21 6 0.13
22 5 0.11
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATTTATATATATATTT
Found at i:187398 original size:38 final size:39
Alignment explanation
Indices: 187272--187448 Score: 121
Period size: 39 Copynumber: 4.4 Consensus size: 39
187262 TTTTTTTAGA
* * * *
187272 TTATATATATATATATATTATTTTTTTATTATCATTT-TT
1 TTATTTATATATTTATTTTATTATTTTATTAT-ATTTATT
* * * *
187311 ATTAATTTATATATATATTTACTATTATATATATATATATATATA
1 -TT-ATTTATATATTTATTT--TATTAT-TTTAT-TATATTTATT
*
187356 TTATTT-T-TACTTTATTATTATTATTTTATT-TATTTGTT
1 TTATTTATATA-TTTATT-TTATTATTTTATTATATTTATT
* *
187394 TTATTTATATATTTGTTTTATTATTTTTTTATATTTATT
1 TTATTTATATATTTATTTTATTATTTTATTATATTTATT
*
187433 TTACTTACTAT-TTTAT
1 TTATTTA-TATATTTAT
187449 CTTTGCTATC
Statistics
Matches: 109, Mismatches: 16, Indels: 25
0.73 0.11 0.17
Matches are distributed among these distances:
38 23 0.21
39 24 0.22
40 11 0.10
41 22 0.20
42 6 0.06
43 10 0.09
44 9 0.08
45 4 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (39 bp):
TTATTTATATATTTATTTTATTATTTTATTATATTTATT
Found at i:187406 original size:17 final size:17
Alignment explanation
Indices: 187380--187415 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
187370 TTATTATTAT
*
187380 TTTATTTATTTGTTTTA
1 TTTATATATTTGTTTTA
187397 TTTATATATTTGTTTTA
1 TTTATATATTTGTTTTA
187414 TT
1 TT
187416 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTATATATTTGTTTTA
Found at i:187429 original size:22 final size:23
Alignment explanation
Indices: 187395--187453 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
187385 TTATTTGTTT
*
187395 TATTTATATATTTGTTTTA-TTAT
1 TATTT-TATATTTGTTTTACTTAC
* *
187418 TTTTTTATATTTATTTTACTTAC
1 TATTTTATATTTGTTTTACTTAC
*
187441 TATTTTATCTTTG
1 TATTTTATATTTG
187454 CTATCTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (23 bp):
TATTTTATATTTGTTTTACTTAC
Found at i:187434 original size:13 final size:13
Alignment explanation
Indices: 187376--187448 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
187366 TTTATTATTA
187376 TTATTTTATTTAT
1 TTATTTTATTTAT
*
187389 TTGTTTTATTTAT
1 TTATTTTATTTAT
*
187402 ATATTTGT-TTTA-
1 TTATTT-TATTTAT
*
187414 TTATTTTTTTATAT
1 TTATTTTATT-TAT
*
187428 TTATTTTACTTA-
1 TTATTTTATTTAT
*
187440 CTATTTTAT
1 TTATTTTAT
187449 CTTTGCTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
11 1 0.02
12 14 0.29
13 24 0.50
14 9 0.19
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:188922 original size:17 final size:18
Alignment explanation
Indices: 188886--188926 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
188876 ATATTATGTA
*
188886 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
188904 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
188921 TTTACT
1 TTTACT
188927 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:191185 original size:26 final size:24
Alignment explanation
Indices: 191114--191185 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
191104 TTATATTTGT
191114 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
191139 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
191161 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
191186 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:191253 original size:35 final size:33
Alignment explanation
Indices: 191214--191298 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
191204 GTATTTTAGT
191214 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
191249 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
191284 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
191299 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:199735 original size:18 final size:18
Alignment explanation
Indices: 199712--199754 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
199702 CCCTTACTTT
199712 AACACTTCTCCCATTTAA
1 AACACTTCTCCCATTTAA
199730 AACACTTCTCCCATTTAA
1 AACACTTCTCCCATTTAA
199748 AACACTT
1 AACACTT
199755 AACACTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (18 bp):
AACACTTCTCCCATTTAA
Found at i:202029 original size:21 final size:21
Alignment explanation
Indices: 202004--202060 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
201994 CAGAACCCCA
*
202004 GGGGGTATCGATTCCCCT-GT
1 GGGGGTATCGATTCCCCTCAT
* *
202024 GGGGGGAATCGGTT-CCCTCAT
1 -GGGGGTATCGATTCCCCTCAT
202045 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
202061 TCTGCACCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.12, C:0.25, G:0.37, T:0.26
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTCAT
Found at i:209437 original size:30 final size:30
Alignment explanation
Indices: 209403--209475 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
209393 CCCGAAGGAC
209403 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
* *
209433 CTATCCAGAGATCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
* *
209463 CTGTCCATAGGTC
1 CTATCCAGAGGTC
209476 CTGAAGAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAAATCCTCGGTAA
Found at i:209501 original size:31 final size:31
Alignment explanation
Indices: 209461--209534 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
209451 GATCCTCGGT
* *
209461 AACTGTCCATA-GGTCCTGAAGAACCTAGGTA
1 AACTATCCATATGGTCCT-AAGAACATAGGTA
* *
209492 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGGTCCTAAGAACATAGGTA
*
209523 TACTATCCATAT
1 AACTATCCATAT
209535 ATCTCGAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (31 bp):
AACTATCCATATGGTCCTAAGAACATAGGTA
Found at i:210167 original size:24 final size:20
Alignment explanation
Indices: 210110--210167 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
210100 TTCCCCTTGA
210110 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
210130 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
210153 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
210168 CTACTCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:210783 original size:3 final size:3
Alignment explanation
Indices: 210775--210802 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
210765 GCTTACGGGG
210775 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
210803 AATAAGCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:213561 original size:30 final size:30
Alignment explanation
Indices: 213527--213654 Score: 175
Period size: 30 Copynumber: 4.2 Consensus size: 30
213517 CCCGAATGAC
213527 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
213557 CTATCCAGAGGTCAAAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
213587 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * * *
213617 CTGTCCATAGGTCCTGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
213648 CTATCCA
1 CTATCCA
213655 TATGTTCCTT
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
30 78 0.91
31 8 0.09
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:214321 original size:24 final size:20
Alignment explanation
Indices: 214264--214321 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
214254 TTCCCCTTGA
214264 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
214284 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
214307 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
214322 CTACTCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:214937 original size:3 final size:3
Alignment explanation
Indices: 214929--214953 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
214919 GCTTACGGGG
214929 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
214954 AATAAGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:217551 original size:13 final size:13
Alignment explanation
Indices: 217510--217555 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
217500 AACCTATATC
217510 ATACATATATCAT
1 ATACATATATCAT
217523 AT-CATGCA-ATTCAT
1 ATACAT--ATA-TCAT
217537 ATACATATATCAT
1 ATACATATATCAT
217550 ATACAT
1 ATACAT
217556 TGATTTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 3 0.11
13 14 0.50
14 8 0.29
15 3 0.11
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.37
Consensus pattern (13 bp):
ATACATATATCAT
Found at i:217711 original size:30 final size:30
Alignment explanation
Indices: 217677--217779 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
217667 CCCGAATTAC
217677 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
217707 CTATCCAGAGGTCAAAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
217737 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
217767 CTGTCCATAGGTC
1 CTATCCAGAGGTC
217780 CTGAAGAACC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:218469 original size:20 final size:20
Alignment explanation
Indices: 218441--218478 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
218431 TTCCCCTTGA
218441 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
*
218461 AGTGTATCGATGCATTCT
1 AGTGCATCGATGCATTCT
218479 TTAACATGTG
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:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:218498 original size:24 final size:20
Alignment explanation
Indices: 218441--218498 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
218431 TTCCCCTTGA
*
218441 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAC
*
218461 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
218484 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
218499 CTACTCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:218511 original size:19 final size:19
Alignment explanation
Indices: 218487--218536 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
218477 CTTTAACATG
*
218487 TGCATCGATGCACTACTCA
1 TGCATCGATACACTACTCA
218506 TGCATCGATACACTACTCA
1 TGCATCGATACACTACTCA
218525 TGCATCGATACA
1 TGCATCGATACA
218537 TAAATTACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (19 bp):
TGCATCGATACACTACTCA
Found at i:218592 original size:64 final size:63
Alignment explanation
Indices: 218505--218645 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
218495 TGCACTACTC
* * * *
218505 ATGCATCGATACACTACTCATGCATCGATACATAAATTACCTTCGATGTTTTCATT-TTAAAGGG
1 ATGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATG-TTTC-TTATTAAAGAG
* * * * *
218569 ATGCATCGATGCATTCCTTATGCATCGATGCACCAATTACATTCGATGTTTCTTCATTAAAGAG
1 ATGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTT-ATTAAAGAG
218633 -TGCATCGATGCAC
1 ATGCATCGATGCAC
218646 ATTTAATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
62 2 0.03
63 16 0.25
64 47 0.72
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTATTAAAGAG
Found at i:223960 original size:18 final size:18
Alignment explanation
Indices: 223919--224020 Score: 69
Period size: 18 Copynumber: 5.5 Consensus size: 18
223909 GGCTTAGGTC
* * *
223919 AAGAAGGATCCGAAGAAG
1 AAGAAGAATCGGAAGGAG
* *
223937 ACGAAGAATCGGAAGGCG
1 AAGAAGAATCGGAAGGAG
* * *
223955 AGGAAGCATCTGAAGGAG
1 AAGAAGAATCGGAAGGAG
*
223973 AAGAAGAAGCATCCGAAGGAG
1 AAGAAG-A--ATCGGAAGGAG
* * *
223994 CAGAAGAATCTGAAAGAG
1 AAGAAGAATCGGAAGGAG
224012 AAGAAGAAT
1 AAGAAGAAT
224021 TGGAGGAAAG
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
18 49 0.75
20 1 0.02
21 15 0.23
ACGTcount: A:0.47, C:0.12, G:0.33, T:0.08
Consensus pattern (18 bp):
AAGAAGAATCGGAAGGAG
Found at i:223976 original size:39 final size:39
Alignment explanation
Indices: 223932--224019 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
223922 AAGGATCCGA
* * * * *
223932 AGAAGACGAAGAATCGGAAGGCG-AGGAAGCATCTGAAGG
1 AGAAGAAGAAGAATCCGAAGGAGCA-GAAGAATCTGAAAG
*
223971 AGAAGAAGAAGCATCCGAAGGAGCAGAAGAATCTGAAAG
1 AGAAGAAGAAGAATCCGAAGGAGCAGAAGAATCTGAAAG
224010 AGAAGAAGAA
1 AGAAGAAGAA
224020 TTGGAGGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 41 0.98
40 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.34, T:0.07
Consensus pattern (39 bp):
AGAAGAAGAAGAATCCGAAGGAGCAGAAGAATCTGAAAG
Found at i:223983 original size:21 final size:21
Alignment explanation
Indices: 223957--224019 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
223947 GGAAGGCGAG
223957 GAAGCATCTGAAGGAGAAGAA
1 GAAGCATCTGAAGGAGAAGAA
* *
223978 GAAGCATCCGAAGGAGCAGAA
1 GAAGCATCTGAAGGAGAAGAA
*
223999 G-A--ATCTGAAAGAGAAGAA
1 GAAGCATCTGAAGGAGAAGAA
224017 GAA
1 GAA
224020 TTGGAGGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.39
19 1 0.03
20 1 0.03
21 20 0.56
ACGTcount: A:0.49, C:0.11, G:0.32, T:0.08
Consensus pattern (21 bp):
GAAGCATCTGAAGGAGAAGAA
Found at i:231988 original size:2 final size:2
Alignment explanation
Indices: 231983--232014 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
231973 TTTTTTGGTG
*
231983 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
232015 GACAACTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:234019 original size:35 final size:30
Alignment explanation
Indices: 233952--234022 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
233942 TGATGAAGGA
* *
233952 GTCATGTCATCGCCGTCATGGAATAAAGAT
1 GTCATGTCATCGCCGTCACGGAACAAAGAT
233982 GTCATGTCATCGCCGTCACGGAACAAAGAT
1 GTCATGTCATCGCCGTCACGGAACAAAGAT
*
234012 ATCATGTCATC
1 GTCATGTCATC
234023 ATCCCTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
GTCATGTCATCGCCGTCACGGAACAAAGAT
Found at i:234193 original size:80 final size:79
Alignment explanation
Indices: 234052--234201 Score: 239
Period size: 80 Copynumber: 1.9 Consensus size: 79
234042 GACGGAGTGA
*
234052 CAAAATTACAGGAAAACATAAATGTCCGTGCTAAAATTGATAAAATTAAAACATCAGTGGCATTT
1 CAAAATTACAGGAAAACATAAATGTCCGTGCTAAAATTGATAAAATTAAAACATCAATGGCA-TT
234117 TTCGAGCCTGAGCGG
65 TTCGAGCCTGAGCGG
* * *
234132 CAAAATTGCAGTG-AAACATAAATGTCCTTGCTAAAATTGATAAAATTAAAACTTCAATGGCATT
1 CAAAATTACAG-GAAAACATAAATGTCCGTGCTAAAATTGATAAAATTAAAACATCAATGGCATT
234196 TTCGAG
65 TTCGAG
234202 TCCGAACTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
79 8 0.12
80 56 0.86
81 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (79 bp):
CAAAATTACAGGAAAACATAAATGTCCGTGCTAAAATTGATAAAATTAAAACATCAATGGCATTT
TCGAGCCTGAGCGG
Found at i:235371 original size:21 final size:21
Alignment explanation
Indices: 235345--235388 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
235335 GATTATTGTA
235345 GTTCAATACGCATCACTCATC
1 GTTCAATACGCATCACTCATC
235366 GTTCAATACGCATCACTCATC
1 GTTCAATACGCATCACTCATC
235387 GT
1 GT
235389 GTATTGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (21 bp):
GTTCAATACGCATCACTCATC
Found at i:238208 original size:28 final size:30
Alignment explanation
Indices: 238177--238232 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
238167 CAAAAATAAC
*
238177 ATACAGAAGA-AA-ACACACTCCTACAAAA
1 ATACAGAAGACAAGAAACACTCCTACAAAA
**
238205 ATACTTAAGACAAGAAACACTCCTACAA
1 ATACAGAAGACAAGAAACACTCCTACAA
238233 TACCTCACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 2 0.09
30 13 0.57
ACGTcount: A:0.54, C:0.25, G:0.07, T:0.14
Consensus pattern (30 bp):
ATACAGAAGACAAGAAACACTCCTACAAAA
Found at i:247554 original size:22 final size:23
Alignment explanation
Indices: 247515--247561 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
247505 AACCCTAAAC
247515 AAGCCCAAGAATCATATCTGCTA
1 AAGCCCAAGAATCATATCTGCTA
* *
247538 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAGAATCATATCTGCTA
247560 AA
1 AA
247562 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGCCCAAGAATCATATCTGCTA
Found at i:251064 original size:33 final size:33
Alignment explanation
Indices: 251022--251104 Score: 157
Period size: 33 Copynumber: 2.5 Consensus size: 33
251012 ACTAAACGTT
*
251022 ACAGCCTCAATGCCTTGGTTCATGTTTCAATGG
1 ACAGCCTCAATGCCTTAGTTCATGTTTCAATGG
251055 ACAGCCTCAATGCCTTAGTTCATGTTTCAATGG
1 ACAGCCTCAATGCCTTAGTTCATGTTTCAATGG
251088 ACAGCCTCAATGCCTTA
1 ACAGCCTCAATGCCTTA
251105 ATACAATATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (33 bp):
ACAGCCTCAATGCCTTAGTTCATGTTTCAATGG
Found at i:258608 original size:34 final size:34
Alignment explanation
Indices: 258565--258669 Score: 122
Period size: 34 Copynumber: 3.1 Consensus size: 34
258555 TATTAATTAA
*
258565 CCTGAATTACATAAGATACAAAATGCACTCAAAC
1 CCTGAATTACATAAGATACAAAATACACTCAAAC
* * *
258599 CCTGAATTACATAAGATACACATTACACTCTAAC
1 CCTGAATTACATAAGATACAAAATACACTCAAAC
* * * *
258633 CCTAAAATACATAAGATACACATTACACT-ATAAC
1 CCTGAATTACATAAGATACAAAATACACTCA-AAC
258667 CCT
1 CCT
258670 CCTTGATTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.24
Consensus pattern (34 bp):
CCTGAATTACATAAGATACAAAATACACTCAAAC
Found at i:269106 original size:21 final size:21
Alignment explanation
Indices: 269080--269130 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
269070 ACCGTTATAG
*
269080 TGCTGATGTAACAATTCATGT
1 TGCTGATGTAACAATTCATGA
*
269101 TGCTGATGTAACAATTTATGA
1 TGCTGATGTAACAATTCATGA
*
269122 TGTTGATGT
1 TGCTGATGT
269131 GACAGTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (21 bp):
TGCTGATGTAACAATTCATGA
Found at i:269324 original size:23 final size:22
Alignment explanation
Indices: 269255--269337 Score: 64
Period size: 22 Copynumber: 3.7 Consensus size: 22
269245 AATATTTAGA
* *
269255 TATTCAAAAAAATAAATATAAG
1 TATTCAAAAATATAAATATAAT
* *
269277 AATTCTAAAAATAAAAAT-TAAAT
1 TATTC-AAAAATATAAATAT-AAT
*
269300 TATTCAAAAATTTAAATATATAT
1 TATTCAAAAATATAAATATA-AT
269323 TA-T-AAAAATAGTAAA
1 TATTCAAAAATA-TAAA
269338 AATACTATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
21 6 0.12
22 21 0.44
23 21 0.44
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
TATTCAAAAATATAAATATAAT
Found at i:271061 original size:2 final size:2
Alignment explanation
Indices: 271056--271080 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
271046 TTTTTAATAA
271056 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 A
271081 ATTTTTAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:271787 original size:4 final size:4
Alignment explanation
Indices: 271778--271870 Score: 69
Period size: 4 Copynumber: 21.8 Consensus size: 4
271768 GGAGGTAATT
* * *
271778 TTTA TTTA TTTA TTTA CTTTTA ATTA TTTA TTTA TTTCAA ATAA TTTA
1 TTTA TTTA TTTA TTTA --TTTA TTTA TTTA TTTA TTT--A TTTA TTTA
* * * *
271826 TTTA TTTA TGTA ATAA TTTA TTTTGA ATTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTT
271871 GAAGGGATAC
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
4 57 0.83
5 5 0.07
6 7 0.10
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:271804 original size:18 final size:17
Alignment explanation
Indices: 271777--271866 Score: 85
Period size: 18 Copynumber: 5.2 Consensus size: 17
271767 TGGAGGTAAT
*
271777 TTTTATTTATTTATTTA
1 TTTTAATTATTTATTTA
271794 CTTTTAATTATTTATTTA
1 -TTTTAATTATTTATTTA
* *
271812 TTTCAAATAATTTATTTA
1 TTT-TAATTATTTATTTA
* *
271830 -TTT-ATGTAATAATTTA
1 TTTTAAT-TATTTATTTA
271846 TTTTGAATTATTTATTTA
1 TTTT-AATTATTTATTTA
271864 TTT
1 TTT
271867 ATTTGAAGGG
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
15 2 0.03
16 7 0.12
17 8 0.14
18 39 0.67
19 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTAATTATTTATTTA
Found at i:271826 original size:22 final size:21
Alignment explanation
Indices: 271778--271848 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
271768 GGAGGTAATT
**
271778 TTTATTTATTTATTTACTTTTAA
1 TTTATTTATTTATTT-C-AATAA
271801 -TTATTTATTTATTTCAAATAA
1 TTTATTTATTTATTTC-AATAA
*
271822 TTTATTTATTTATGT-AATAA
1 TTTATTTATTTATTTCAATAA
271842 TTTATTT
1 TTTATTT
271849 TGAATTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 12 0.28
21 4 0.09
22 27 0.63
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (21 bp):
TTTATTTATTTATTTCAATAA
Found at i:273970 original size:33 final size:34
Alignment explanation
Indices: 273932--274005 Score: 132
Period size: 33 Copynumber: 2.2 Consensus size: 34
273922 AAATTTGTAA
273932 TTTTTTAGTTAATCGAACTCCATTTTC-TTTTCT
1 TTTTTTAGTTAATCGAACTCCATTTTCTTTTTCT
273965 TTTTTTAGTTAATCGAACTCCATTTTCTTTTTTCT
1 TTTTTTAGTTAATCGAACTCCATTTTC-TTTTTCT
274000 TTTTTT
1 TTTTTT
274006 TTACTTAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 27 0.69
35 12 0.31
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.62
Consensus pattern (34 bp):
TTTTTTAGTTAATCGAACTCCATTTTCTTTTTCT
Found at i:274119 original size:17 final size:17
Alignment explanation
Indices: 274073--274124 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
274063 TACTTTTTTA
274073 AAATTTGTTTAAATTAT
1 AAATTTGTTTAAATTAT
*
274090 AAATTAAGTTTAAATTAT
1 AAATT-TGTTTAAATTAT
* *
274108 TAATTTGTTTAAGTTAT
1 AAATTTGTTTAAATTAT
274125 CCTTGAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (17 bp):
AAATTTGTTTAAATTAT
Found at i:278844 original size:171 final size:172
Alignment explanation
Indices: 278542--278890 Score: 526
Period size: 171 Copynumber: 2.0 Consensus size: 172
278532 ACAATATCTA
* *
278542 ATATGTCTTGATAATGGCCTCAACTAAAAGAAAATTTCTAATATTACGCCTCTAATATTATAAAT
1 ATATGTCTTGATAATGGCCTCAACTAAAAGAAAATTTATAATACTACGCCTCTAATATTATAAAT
* * *
278607 TATGAAAAATATGATATTAAATACCCGAATATGCCCCCCGAACATGCCTGTAAGCACTTATGATT
66 TATGAAAAATATGAGATTAAATACCCGAATATGCCCCCCGAACATGCCTATAAACACTTATGATT
*
278672 TGGGATGGAAAACTAAATACCTCGCTCTTTGGAAAACACAAG
131 TGGGATGGAAAACTAAATACCTCGCTCTTTAGAAAACACAAG
*
278714 -TATGTCTTGATAATGGCCTCAACTAAAAGATAAA-TTATAATACT-C-CACTACTAATCTTATA
1 ATATGTCTTGATAATGGCCTCAACTAAAAGA-AAATTTATAATACTACGC-CT-CTAATATTATA
* * * *
278775 AATTATGAAAATTTTGAGATTAAATACCCGAATATGCCCCCCGAACATGCTTATAAACACTTGTG
63 AATTATGAAAAATATGAGATTAAATACCCGAATATGCCCCCCGAACATGCCTATAAACACTTATG
* *
278840 ATTTGGGCTGGAAAACTAAATACCTCGCTCTTTAGAAAACACGAG
128 ATTTGGGATGGAAAACTAAATACCTCGCTCTTTAGAAAACACAAG
278885 ATATGT
1 ATATGT
278891 TGAATGCTAT
Statistics
Matches: 160, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
169 1 0.01
170 3 0.02
171 148 0.93
172 8 0.05
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30
Consensus pattern (172 bp):
ATATGTCTTGATAATGGCCTCAACTAAAAGAAAATTTATAATACTACGCCTCTAATATTATAAAT
TATGAAAAATATGAGATTAAATACCCGAATATGCCCCCCGAACATGCCTATAAACACTTATGATT
TGGGATGGAAAACTAAATACCTCGCTCTTTAGAAAACACAAG
Found at i:286269 original size:13 final size:13
Alignment explanation
Indices: 286251--286276 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
286241 AGAGTTATCT
286251 CTCTTTATATAGG
1 CTCTTTATATAGG
286264 CTCTTTATATAGG
1 CTCTTTATATAGG
286277 ATAATACATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
CTCTTTATATAGG
Found at i:287948 original size:27 final size:27
Alignment explanation
Indices: 287917--288026 Score: 220
Period size: 27 Copynumber: 4.1 Consensus size: 27
287907 ATTGTACAAC
287917 TGGATAATACTCTTTGGATGCATGATT
1 TGGATAATACTCTTTGGATGCATGATT
287944 TGGATAATACTCTTTGGATGCATGATT
1 TGGATAATACTCTTTGGATGCATGATT
287971 TGGATAATACTCTTTGGATGCATGATT
1 TGGATAATACTCTTTGGATGCATGATT
287998 TGGATAATACTCTTTGGATGCATGATT
1 TGGATAATACTCTTTGGATGCATGATT
288025 TG
1 TG
288027 CTACAAGAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (27 bp):
TGGATAATACTCTTTGGATGCATGATT
Found at i:287961 original size:14 final size:14
Alignment explanation
Indices: 287917--288016 Score: 56
Period size: 14 Copynumber: 7.4 Consensus size: 14
287907 ATTGTACAAC
287917 TGGATAATACTCTT
1 TGGATAATACTCTT
*
287931 TGGATGCATGA---TT
1 TGGAT-AAT-ACTCTT
287944 TGGATAATACTCTT
1 TGGATAATACTCTT
*
287958 TGGATGCATGA---TT
1 TGGAT-AAT-ACTCTT
287971 TGGATAATACTCTT
1 TGGATAATACTCTT
*
287985 TGGATGCATGA---TT
1 TGGAT-AAT-ACTCTT
287998 TGGATAATACTCTT
1 TGGATAATACTCTT
288012 TGGAT
1 TGGAT
288017 GCATGATTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 30
0.64 0.06 0.30
Matches are distributed among these distances:
11 3 0.05
12 6 0.09
13 21 0.32
14 26 0.40
15 6 0.09
16 3 0.05
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (14 bp):
TGGATAATACTCTT
Found at i:289675 original size:66 final size:66
Alignment explanation
Indices: 289569--289709 Score: 273
Period size: 66 Copynumber: 2.1 Consensus size: 66
289559 TACAGAAGAA
289569 ACTTGAGTGTCCTCAGTGTCATCCTTAGCAATAGCTTTCTCAAGTTTCACACACTGTCGACTCTA
1 ACTTGAGTGTCCTCAGTGTCATCCTTAGCAATAGCTTTCTCAAGTTTCACACACTGTCGACTCTA
289634 G
66 G
*
289635 ACTTGAGTGTCCTCAGTGTCATCCTTAGCAATAGCTTTCTCAAGTTTCACACACTGTTGACTCTA
1 ACTTGAGTGTCCTCAGTGTCATCCTTAGCAATAGCTTTCTCAAGTTTCACACACTGTCGACTCTA
289700 G
66 G
289701 ACTTGAGTG
1 ACTTGAGTG
289710 GGTCAAATAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.34
Consensus pattern (66 bp):
ACTTGAGTGTCCTCAGTGTCATCCTTAGCAATAGCTTTCTCAAGTTTCACACACTGTCGACTCTA
G
Found at i:292524 original size:10 final size:10
Alignment explanation
Indices: 292495--292532 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
292485 GAAATTTGTG
292495 AAAAATAAAT
1 AAAAATAAAT
* *
292505 -ATATTAAAT
1 AAAAATAAAT
292514 AAAAATAAAT
1 AAAAATAAAT
292524 AAAAATAAA
1 AAAAATAAA
292533 GTTAATCCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:294182 original size:16 final size:16
Alignment explanation
Indices: 294153--294193 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
294143 CGTTCATTTA
294153 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
294167 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
294183 ATAAACGAACA
1 ATAAATGAACA
294194 AATTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 2 0.08
16 16 0.67
ACGTcount: A:0.61, C:0.17, G:0.10, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:294274 original size:10 final size:10
Alignment explanation
Indices: 294259--294333 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
294249 CATTTAATAA
294259 ATAAACGAAC
1 ATAAACGAAC
294269 ATAAACG-A-
1 ATAAACGAAC
*
294277 AT--ACAAAC
1 ATAAACGAAC
294285 ATAAACGAAC
1 ATAAACGAAC
** *
294295 ACGAAC-ATAA
1 ATAAACGA-AC
294305 ATGAACACGAAC
1 AT-AA-ACGAAC
294317 ATAAACGAAC
1 ATAAACGAAC
294327 ATAAACG
1 ATAAACG
294334 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 2 0.04
7 1 0.02
8 4 0.08
9 2 0.04
10 31 0.63
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:294287 original size:16 final size:16
Alignment explanation
Indices: 294263--294327 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
294253 TAATAAATAA
*
294263 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
*
294279 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
*
294295 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
294311 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
294327 A
1 A
294328 TAAACGTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:295095 original size:14 final size:14
Alignment explanation
Indices: 295078--295133 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
295068 AATGAACATA
*
295078 AACGAACATAATCG
1 AACGAACATAACCG
295092 AACGAACAT-A---
1 AACGAACATAACCG
*
295102 AACGAACATAACCA
1 AACGAACATAACCG
295116 AACGAACATAACCG
1 AACGAACATAACCG
295130 AACG
1 AACG
295134 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:295098 original size:24 final size:24
Alignment explanation
Indices: 295058--295132 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
295048 GATTGTGTTA
*
295058 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
295082 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
295106 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
295130 AAC
1 AAC
295133 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:296372 original size:29 final size:29
Alignment explanation
Indices: 296330--296386 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
296320 AATGTTGGCC
*
296330 GTAGGTTGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
296359 GTAGGTCGCCATGCACTCCGGGTGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
296387 ACCCTGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.32, G:0.32, T:0.23
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:296420 original size:12 final size:12
Alignment explanation
Indices: 296403--296427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
296393 CTCAAACAGA
296403 GAGAATGAACGT
1 GAGAATGAACGT
296415 GAGAATGAACGT
1 GAGAATGAACGT
296427 G
1 G
296428 TTGCATGGCA
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:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:296521 original size:33 final size:33
Alignment explanation
Indices: 296484--296546 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
296474 GGGCGACCTA
*
296484 CCCTCGCATAGCTCGCTCGGTTGCCCTCGGATG
1 CCCTCGCATAGCTCGCTCGGATGCCCTCGGATG
* *
296517 CCCTCGCATAGCTCGTTCGGATGGCCTCGG
1 CCCTCGCATAGCTCGCTCGGATGCCCTCGG
296547 TCGGATGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.10, C:0.38, G:0.29, T:0.24
Consensus pattern (33 bp):
CCCTCGCATAGCTCGCTCGGATGCCCTCGGATG
Found at i:296550 original size:14 final size:14
Alignment explanation
Indices: 296528--296560 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
296518 CCTCGCATAG
*
296528 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
296542 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
296556 CTCGG
1 CTCGG
296561 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:296640 original size:29 final size:29
Alignment explanation
Indices: 296603--296660 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
296593 GCAATCTCTT
*
296603 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
296632 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
296661 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:299936 original size:291 final size:291
Alignment explanation
Indices: 299392--299957 Score: 738
Period size: 291 Copynumber: 1.9 Consensus size: 291
299382 ATTTTTATTC
* *
299392 AATATATGAATTAGAAACCCGACACGACACAAAATAAAAAAAAAATATTTTTATTCAATAAAAAT
1 AATATATGAATTAGAAACCCAACACGACACAAAATAAAAAAAAAATATTTTTATTCAATAAAAAC
* * * * *
299457 ATTGACTTAATTGAAAAAATATATATATATATAAGGGTATTATTGTAATTATTCCTAAATATATA
66 AATGACTTAATTG-AAAAATATATATAGAGAGAAGGGTATTATTGTAATTATTCATAAATATATA
* *
299522 AGGTAAAATTATATATTTTTTCGGGTTGGTCTGGTTTTTTTCACCCTAAACCCGAACCGACCCGA
130 AGGTAAAATTATATATATTTTCGGGTTGG--TGGTATTTTTCACCCTAAACCCGAACCGACCCGA
* *
299587 ATATCACACTTAAAAAAACTCAACCCGACTAGATCCGAATATTACAGTTAAAAAACCCGATCCGA
193 ATATCACACTTAAAAAAACTCAACCCGACTAGACCCGAATATTACAGTTAAAAAACCCGACCCGA
299652 CCCGAACAAAATAAAATTTCACCCGACCCGACCCG
258 CCCGAA-AAAATAAAATTTCACCCGACCCGACCCG
** * * * * *
299687 AATATATGAATTAGAAATTCAACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAAC
1 AATATATGAATTAGAAACCCAACACGACACAAAATAAAAAAAAAATATTTTTATTCAATAAAAAC
* *
299752 AATGACTTAATTG-AAAA-A-ATATAGAGAGAGGGGTGTTATTGTAATTATTCATAAATATATAA
66 AATGACTTAATTGAAAAATATATATAGAGAGAAGGGTATTATTGTAATTATTCATAAATATATAA
*
299814 GGTAAAATTATATATATTTTCGGGTT-G-GGTATTTTTCACCTTAAACCCGAACTCGACCCGACC
131 GGTAAAATTATATATATTTTCGGGTTGGTGGTATTTTTCACCCTAAACCCG-A----A-CCGACC
*
299877 CGAATATCACACTTAAAAAAACT-AACCCGACCT-GACCCGAATATATGA-A-TT-AGAAACCCG
190 CGAATATCACACTTAAAAAAACTCAACCCGA-CTAGACCCGAATAT-T-ACAGTTAAAAAACCCG
*
299937 ACCCGACCCGAAATAATAAAA
252 ACCCGACCCGAAAAAATAAAA
299958 AATATTTTTA
Statistics
Matches: 239, Mismatches: 23, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
287 20 0.08
288 1 0.00
290 9 0.04
291 82 0.34
292 21 0.09
293 37 0.15
294 1 0.00
295 68 0.28
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (291 bp):
AATATATGAATTAGAAACCCAACACGACACAAAATAAAAAAAAAATATTTTTATTCAATAAAAAC
AATGACTTAATTGAAAAATATATATAGAGAGAAGGGTATTATTGTAATTATTCATAAATATATAA
GGTAAAATTATATATATTTTCGGGTTGGTGGTATTTTTCACCCTAAACCCGAACCGACCCGAATA
TCACACTTAAAAAAACTCAACCCGACTAGACCCGAATATTACAGTTAAAAAACCCGACCCGACCC
GAAAAAATAAAATTTCACCCGACCCGACCCG
Found at i:301467 original size:214 final size:215
Alignment explanation
Indices: 300857--301678 Score: 1207
Period size: 217 Copynumber: 3.8 Consensus size: 215
300847 TTAAGAATTG
*
300857 AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAATACACATTGATGAGGG
1 AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGG
300922 ATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
66 ATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
* * * * * *
300987 ATTTAAATAGTTATGTGCAAATTAAAAAAATAGAATTAAGTAATAAGTATG-GATCAATTTCATA
131 ATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGAG-TCAATTTCAGA
301051 TGCAAATAAAATTTGGAGGACT
194 TGCAAATAAAATTTGGAGGACT
* *
301073 GAATTGAACAAATAAGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGG
1 -AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGG
* * * * *
301138 GATTAAATCGAAATAATTTTAAATCGTGATGTTGAAATTAATACAAAAAAATACTAAATTATACA
65 GATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACC
* *
301203 CATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTATTAAGTATGAGTCAATTTCAGAC
130 CATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGAGTCAATTTCAGAT
301268 GCAAATAAAATTTGGAGGACT
195 GCAAATAAAATTTGGAGGACT
* *
301289 AATTTGAATAAATATGAAATTACAAATAAAAATTTAAATATATTAAA-AACACACATTGATGAGG
1 AA-TTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGG
* * *
301353 GATCAAATCGAACTAATTTTAAATTGTGAAGTTGAAATTAATAC-GAAAAGTACTAAATTATACC
65 GATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACC
* * *
301417 CATTTAAAAAGTTATGGGCCAATTTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGGT
130 CATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGAGTCAATTTCAGAT
*
301482 GCAAATAAATTTTGGAGGACT
195 GCAAATAAAATTTGGAGGACT
* *
301503 AAATTGAACAAATATAAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A---A--AGG
1 -AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGG
* * * * *
301562 GTTCAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATACT
65 GATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACC
* *
301627 CATATAAAAAGTTATGGGTCAA-TTAATAAATAGAAATAAGTAATAAGT-TGAG
130 CATTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGTATGAG
301679 AAAAAAATTA
Statistics
Matches: 552, Mismatches: 47, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
209 49 0.09
210 57 0.10
211 1 0.00
214 140 0.25
215 67 0.12
216 95 0.17
217 143 0.26
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.30
Consensus pattern (215 bp):
AATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGG
ATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
ATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGAGTCAATTTCAGATG
CAAATAAAATTTGGAGGACT
Found at i:301703 original size:2 final size:2
Alignment explanation
Indices: 301698--301783 Score: 86
Period size: 2 Copynumber: 42.0 Consensus size: 2
301688 AAAACAACTA
*
301698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
301740 AT AGT AT AT GT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
301782 AT
1 AT
301784 TATGTATAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
1 2 0.03
2 63 0.90
3 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:301747 original size:29 final size:30
Alignment explanation
Indices: 301699--302024 Score: 110
Period size: 29 Copynumber: 11.2 Consensus size: 30
301689 AAACAACTAA
*
301699 TATATATATATA-TATATA-TATATATATA
1 TATATATATAAACTATATAGTATATATATA
*
301727 TA-ATATA--AACTATATAGTATATGTAT-
1 TATATATATAAACTATATAGTATATATATA
*
301753 TATATATATAAACTATATAGTTTATATATA
1 TATATATATAAACTATATAGTATATATATA
* * * * *
301783 T-TATGTATAAAGTATAAACTATATATACCATG
1 TATATATATAAACTATATAGTATATAT---ATA
*
301815 TATAAACTATAATACTATATAGT-T-TATATA
1 TATATA-TATAA-ACTATATAGTATATATATA
* *
301845 TGA-ACTAT-TGAACTATATA-TA-A-ACTACA
1 T-ATA-TATATAAACTATATAGTATATA-TATA
*
301873 TAGT-TCATATATA-TATATAGTATATATGA-A
1 TA-TAT-ATATAAACTATATAGTATATAT-ATA
* * * *
301903 T-TATATATAAACTATACAATTTATATTTA
1 TATATATATAAACTATATAGTATATATATA
* *
301932 TATATTATGTATAA-T-TATA-AATA-ATATA
1 TATA-TATATA-AACTATATAGTATATATATA
* * *
301960 TAT-TGTATAAATTATATAGTTTAT-TA-A
1 TATATATATAAACTATATAGTATATATATA
* * * *
301987 TATAAATTATACAGTTTATA-TATATATATA
1 TATATA-TATAAACTATATAGTATATATATA
302017 GTATATAT
1 -TATATAT
302025 GGTTTAGGGT
Statistics
Matches: 216, Mismatches: 42, Indels: 78
0.64 0.12 0.23
Matches are distributed among these distances:
25 3 0.01
26 13 0.06
27 30 0.14
28 44 0.20
29 71 0.33
30 17 0.08
31 15 0.07
32 5 0.02
33 5 0.02
34 6 0.03
35 7 0.03
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
TATATATATAAACTATATAGTATATATATA
Found at i:301806 original size:27 final size:28
Alignment explanation
Indices: 301775--301835 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
301765 CTATATAGTT
** *
301775 TATATATATTATGTATAAAGTATAA-AC
1 TATATATACCATGTATAAACTATAATAC
301802 TATATATACCATGTATAAACTATAATAC
1 TATATATACCATGTATAAACTATAATAC
301830 TATATA
1 TATATA
301836 GTTTATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (28 bp):
TATATATACCATGTATAAACTATAATAC
Found at i:301934 original size:46 final size:44
Alignment explanation
Indices: 301815--301936 Score: 111
Period size: 46 Copynumber: 2.6 Consensus size: 44
301805 ATATACCATG
*
301815 TATAAACTATAATACTATATAGTTTATATATGAACTATTGAACTATA
1 TATAAACTATAA-A-TTTATA-TTTATATATGAACTATTGAACTATA
* * * * * *
301862 TATAAACTACATAGTTCATATATATATATAGTA-TATATGAATTATA
1 TATAAACTATA-AATTTATATTTATATAT-GAACTAT-TGAACTATA
301908 TATAAACTATACAATTTATATTTATATAT
1 TATAAACTATA-AATTTATATTTATATAT
301937 TATGTATAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
45 11 0.18
46 38 0.63
47 10 0.17
48 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (44 bp):
TATAAACTATAAATTTATATTTATATATGAACTATTGAACTATA
Found at i:302052 original size:21 final size:20
Alignment explanation
Indices: 302022--302065 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
302012 ATATAGTATA
*
302022 TATGGTTTAGGGTTTAGGATT
1 TATGGCTTA-GGTTTAGGATT
*
302043 TATGGCTTAGGTTTAGGGTT
1 TATGGCTTAGGTTTAGGATT
302063 TAT
1 TAT
302066 ATTTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.18, C:0.02, G:0.32, T:0.48
Consensus pattern (20 bp):
TATGGCTTAGGTTTAGGATT
Found at i:302109 original size:22 final size:22
Alignment explanation
Indices: 302083--302148 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
302073 TAAACTACAT
*
302083 ATTATAATTTATATTTATATAT
1 ATTATAATTTATATTTATATAA
* *
302105 TTTAT-TTTATACTATTTATATAA
1 ATTATAATT-TA-TATTTATATAA
*
302128 ACTA-AAGTTTATATTTATATA
1 ATTATAA-TTTATATTTATATA
302149 CTATATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
21 2 0.06
22 16 0.47
23 14 0.41
24 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTATAATTTATATTTATATAA
Found at i:302110 original size:13 final size:15
Alignment explanation
Indices: 302084--302125 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
302074 AAACTACATA
302084 TTATA-ATTTATA-T
1 TTATATATTTATATT
302097 TTATATATTT-TATT
1 TTATATATTTATATT
302111 TTATACTATTTATAT
1 TTATA-TATTTATAT
302126 AAACTAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
15 5 0.20
16 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATATATTTATATT
Found at i:302158 original size:33 final size:33
Alignment explanation
Indices: 302107--302173 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
302097 TTATATATTT
*
302107 TATTTTATACTATTTATATA-AACTAAAGTTTA
1 TATTTTATACTATATATATAGAACTAAAGTTTA
*
302139 TATTTATATACTATATATATATGAACTATAGTTTA
1 TATTT-TATACTATATATATA-GAACTAAAGTTTA
302174 CATATAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 5 0.17
33 14 0.47
35 11 0.37
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (33 bp):
TATTTTATACTATATATATAGAACTAAAGTTTA
Found at i:302172 original size:35 final size:32
Alignment explanation
Indices: 302100--302173 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 32
302090 TTTATATTTA
302100 TATA-TTT-TATTTTATACTATTTATATAAAC
1 TATAGTTTATATTTTATACTATTTATATAAAC
* *
302130 TAAAGTTTATATTTATATACTATATATATATGAAC
1 TATAGTTTATATTT-TATACTAT-T-TATATAAAC
302165 TATAGTTTA
1 TATAGTTTA
302174 CATATAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 3 0.08
31 3 0.08
32 5 0.14
33 8 0.22
34 1 0.03
35 16 0.44
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.51
Consensus pattern (32 bp):
TATAGTTTATATTTTATACTATTTATATAAAC
Found at i:302183 original size:18 final size:18
Alignment explanation
Indices: 302157--302227 Score: 81
Period size: 18 Copynumber: 3.8 Consensus size: 18
302147 TACTATATAT
*
302157 ATATGAACTATAGTTTAC
1 ATATAAACTATAGTTTAC
*
302175 ATATAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTTAC
302195 ATACT-AACTATAGTTTAC
1 ATA-TAAACTATAGTTTAC
*
302213 ATATAAACTGTAGTT
1 ATATAAACTATAGTT
302228 GATATTTACG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.02
18 28 0.62
20 15 0.33
21 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (18 bp):
ATATAAACTATAGTTTAC
Found at i:302285 original size:24 final size:24
Alignment explanation
Indices: 302258--302338 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 24
302248 ATATATAAAC
302258 TATATAGTTTACATA-TGAACTATA
1 TATATAGTTTA-ATAGTGAACTATA
*
302282 TATATAGTTTATTAGTGAACTATA
1 TATATAGTTTAATAGTGAACTATA
* *
302306 TACACTA-TTTATATAGTATATACTATA
1 TATA-TAGTTTA-ATAGT-GA-ACTATA
302333 TATATA
1 TATATA
302339 AACTATAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
23 2 0.04
24 27 0.57
25 6 0.13
26 3 0.06
27 9 0.19
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (24 bp):
TATATAGTTTAATAGTGAACTATA
Found at i:302330 original size:18 final size:18
Alignment explanation
Indices: 302304--302338 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
302294 TAGTGAACTA
*
302304 TATACACTATTTATATAG
1 TATACACTATATATATAG
*
302322 TATATACTATATATATA
1 TATACACTATATATATA
302339 AACTATAGTT
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:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (18 bp):
TATACACTATATATATAG
Found at i:302338 original size:20 final size:20
Alignment explanation
Indices: 302300--302379 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
302290 TTATTAGTGA
302300 ACTATATAC-ACTATTTATAT
1 ACTATATACTA-TATTTATAT
* * *
302320 AGTATATACTATATATATAA
1 ACTATATACTATATTTATAT
*
302340 ACTATAGT-TTATATTTATAT
1 ACTATA-TACTATATTTATAT
*
302360 ACTACATACTATAGTTTATA
1 ACTATATACTATA-TTTATA
302380 AATTATATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 38 0.81
21 8 0.17
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (20 bp):
ACTATATACTATATTTATAT
Found at i:302343 original size:40 final size:40
Alignment explanation
Indices: 302299--302402 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
302289 TTTATTAGTG
*
302299 AACTATATACACTATTTATATAGTATATACTATA-TATATA
1 AACTATATATA-TATTTATATAGTATATACTATAGTATATA
* * * *
302339 AACTATAGTTTATATTTATATACTACATACTATAGTTTATA
1 AACTATA-TATATATTTATATAGTATATACTATAGTATATA
302380 AA-T-TATATATA-TTATATAGTATA
1 AACTATATATATATTTATATAGTATA
302403 ATTTACAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
37 10 0.19
38 5 0.09
39 2 0.04
40 28 0.52
41 9 0.17
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (40 bp):
AACTATATATATATTTATATAGTATATACTATAGTATATA
Found at i:302352 original size:27 final size:27
Alignment explanation
Indices: 302322--302391 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
302312 ATTTATATAG
*
302322 TATATACTATATATATAAACTATAGTT
1 TATATATTATATATATAAACTATAGTT
* *
302349 TATAT-TTATATACTACATACTATAGTT
1 TATATATTATATA-TATAAACTATAGTT
*
302376 TATAAATTATATATAT
1 TATATATTATATATAT
302392 TATATAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 6 0.17
27 23 0.64
28 7 0.19
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (27 bp):
TATATATTATATATATAAACTATAGTT
Found at i:302545 original size:17 final size:17
Alignment explanation
Indices: 302523--302580 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
302513 AACTATACAT
302523 TATATATAGTTCATTAG
1 TATATATAGTTCATTAG
**
302540 TATATATA-AAC-TATA-
1 TATATATAGTTCAT-TAG
302555 TACTATATAGTTCATTAG
1 TA-TATATAGTTCATTAG
302573 TATATATA
1 TATATATA
302581 AACTATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (17 bp):
TATATATAGTTCATTAG
Found at i:302562 original size:33 final size:33
Alignment explanation
Indices: 302454--302687 Score: 245
Period size: 33 Copynumber: 7.2 Consensus size: 33
302444 CTTAAACTAT
* *
302454 TATATAGTTTATTAGTATATATAAACTATATGATA
1 TATATAGTTCATTAGTATATATAAACTATAT-A-G
* *
302489 TATATAG-ACTATATGGTATATATAAACTATACATTA-
1 TATATAGTTC-AT-TAGTATATATAAACTAT--A-TAG
*
302525 TATATAGTTCATTAGTATATATAAACTATATAC
1 TATATAGTTCATTAGTATATATAAACTATATAG
*
302558 TATATAGTTCATTAGTATATATAAACTATATAT
1 TATATAGTTCATTAGTATATATAAACTATATAG
* *
302591 TATATAGTTTATTAGTATATATAACCTATATAG
1 TATATAGTTCATTAGTATATATAAACTATATAG
* *
302624 TATAT-G-------GTATATACAAACTATATAT
1 TATATAGTTCATTAGTATATATAAACTATATAG
302649 TATATAGTTCATTAGTATATATAAACTATATAG
1 TATATAGTTCATTAGTATATATAAACTATATAG
302682 TATATA
1 TATATA
302688 TAAACTATAT
Statistics
Matches: 170, Mismatches: 14, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
25 21 0.12
26 1 0.01
32 3 0.02
33 91 0.54
35 25 0.15
36 25 0.15
37 1 0.01
38 2 0.01
39 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (33 bp):
TATATAGTTCATTAGTATATATAAACTATATAG
Found at i:302563 original size:18 final size:18
Alignment explanation
Indices: 302466--302698 Score: 143
Period size: 18 Copynumber: 13.1 Consensus size: 18
302456 TATAGTTTAT
302466 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
302484 T-GATATATATAGACTATA
1 TAG-TATATATAAACTATA
*
302502 TGGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * **
302520 CATTATATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
302537 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* *
302555 TACTATATAGT--TC-AT-
1 TAGTATATA-TAAACTATA
302570 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
***
302588 TA-T-TATATAGTTTAT-
1 TAGTATATATAAACTATA
*
302603 TAGTATATATAACCTATA
1 TAGTATATATAAACTATA
302621 TAGTATATGGTATATACAAACTATA
1 TAG--TA---TATAT--AAACTATA
**
302646 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
302661 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
302679 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
302697 TA
1 TA
302699 TTACTTTATA
Statistics
Matches: 164, Mismatches: 26, Indels: 50
0.68 0.11 0.21
Matches are distributed among these distances:
14 1 0.01
15 14 0.09
16 16 0.10
17 33 0.20
18 81 0.49
19 2 0.01
20 2 0.01
22 1 0.01
23 5 0.03
25 9 0.05
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:302628 original size:51 final size:51
Alignment explanation
Indices: 302570--302701 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 51
302560 TATAGTTCAT
* *
302570 TAGTATATATAAACTATATATTATATAGTTTATTAGTATATATAACCTATA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATA
302621 TAGTATATGGTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATA
1 TAG--TA---TATAT--AAACTATATATTATATAGTTCATTAGTATATATAAACTATA
302679 TAGTATATATAAACTATATATTA
1 TAGTATATATAAACTATATATTA
302702 CTTTATAACC
Statistics
Matches: 72, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
51 16 0.22
53 7 0.10
56 7 0.10
58 42 0.58
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (51 bp):
TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATA
Found at i:302644 original size:25 final size:25
Alignment explanation
Indices: 302591--302656 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
302581 AACTATATAT
* * *
302591 TATATAGTTTATTAGTATATATAACC
1 TATATAGTATA-TAGTATATACAAAC
*
302617 TATATAGTATATGGTATATACAAAC
1 TATATAGTATATAGTATATACAAAC
*
302642 TATATATTATATAGT
1 TATATAGTATATAGT
302657 TCATTAGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 24 0.71
26 10 0.29
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (25 bp):
TATATAGTATATAGTATATACAAAC
Found at i:302645 original size:58 final size:58
Alignment explanation
Indices: 302572--302686 Score: 203
Period size: 58 Copynumber: 2.0 Consensus size: 58
302562 TAGTTCATTA
* * *
302572 GTATATATAAACTATATATTATATAGTTTATTAGTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATG
302630 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATAT
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATAT
302687 ATAAACTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (58 bp):
GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATG
Found at i:302733 original size:91 final size:90
Alignment explanation
Indices: 302541--302744 Score: 245
Period size: 91 Copynumber: 2.2 Consensus size: 90
302531 GTTCATTAGT
* ***
302541 ATATATAAACTATATACTATATAGTTCATTAGTATATATAAACTATATATTATATAGTTTATTAG
1 ATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATATTATATAAACTATTAG
*
302606 TATATATAACCTATATAGTATATGGT
66 TATATATAACCTATATAGTATAT-GA
*
302632 ATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATAAACTATA
1 ATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATA-T-TATATAAACTAT-
* *
302697 TATTACTTTATAACCTAT-T-GTATAT-A
63 TAGTA-TATATAACCTATATAGTATATGA
*
302723 ATTTATAAACTATAGT-TTATAT
1 ATATATAAACTATA-TATTATAT
302745 TAATGTTAAT
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
91 65 0.66
92 2 0.02
93 15 0.15
94 5 0.05
95 11 0.11
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (90 bp):
ATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATATTATATAAACTATTAG
TATATATAACCTATATAGTATATGA
Found at i:302743 original size:21 final size:21
Alignment explanation
Indices: 302686--302831 Score: 81
Period size: 21 Copynumber: 6.9 Consensus size: 21
302676 ATATAGTATA
*
302686 TATAAACTATA-TAT-TACTT
1 TATAAACTATAGTATATAATT
* *
302705 TATAACCTATTGTATATAATT
1 TATAAACTATAGTATATAATT
302726 TATAAACTATAGTTTATATTAATGT
1 TATAAACTATAG--TATA-TAAT-T
* *
302751 TAATTATCT-TA--ACTATAATT
1 T-ATAAACTATAGTA-TATAATT
*
302771 TATATTAA-TATAGTATATAGTT
1 TATA--AACTATAGTATATAATT
**
302793 TATAAACTATACAATATAATT
1 TATAAACTATAGTATATAATT
*
302814 TAT-AACATATAGTTTATA
1 TATAAAC-TATAGTATATA
302832 TTAATATTAA
Statistics
Matches: 96, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
19 11 0.11
20 11 0.11
21 44 0.46
22 12 0.12
23 5 0.05
24 4 0.04
25 4 0.04
26 5 0.05
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (21 bp):
TATAAACTATAGTATATAATT
Found at i:302818 original size:88 final size:88
Alignment explanation
Indices: 302718--302958 Score: 242
Period size: 88 Copynumber: 2.9 Consensus size: 88
302708 AACCTATTGT
*
302718 ATATAATTTATAA-ACTATAGTTTATATTAATGTTAATTATCT-TA-ACTATAATTTATATTAAT
1 ATATAATTTATAACA-TATAGTTTATATTAATATTAATT-T-TATAGACTATAATTTATATTAAT
* **
302780 A-TAGTATATAGTTTATAAACTATACA
63 ATTAAT-TATAAATTATAAACTATACA
*
302806 ATATAATTTATAACATATAGTTTATATTAATATTAATTTTATAGACTATATTTTATATTAATATT
1 ATATAATTTATAACATATAGTTTATATTAATATTAATTTTATAGACTATAATTTATATTAATATT
302871 AATTATAAATTATAAACTAT---
66 AATTATAAATTATAAACTATACA
* * * * *
302891 AT-T-ATAT-TAATATA-AGTTAATATTAATATTAA--TTATA-A-TATATACTTATTTTAATAT
1 ATATAATTTATAACATATAGTTTATATTAATATTAATTTTATAGACTATA-ATTTATATTAATAT
302948 TAATTATAAAT
65 TAATTATAAAT
302959 ACCATTTTTT
Statistics
Matches: 137, Mismatches: 11, Indels: 20
0.82 0.07 0.12
Matches are distributed among these distances:
77 4 0.03
78 23 0.17
79 5 0.04
81 17 0.12
82 6 0.04
83 3 0.02
84 1 0.01
85 2 0.01
86 1 0.01
87 3 0.02
88 68 0.50
89 4 0.03
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (88 bp):
ATATAATTTATAACATATAGTTTATATTAATATTAATTTTATAGACTATAATTTATATTAATATT
AATTATAAATTATAAACTATACA
Found at i:302912 original size:44 final size:44
Alignment explanation
Indices: 302863--302947 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 44
302853 ATATTTTATA
302863 TTAATATTAATTATAAATTATAA-ACTATA-TTATATTAATATAAG
1 TTAATATTAA-TATAAATTATAATA-TATACTTATATTAATATAAG
* *
302907 TTAATATTAATATTAATTATAATATATACTTATTTTAATAT
1 TTAATATTAATATAAATTATAATATATACTTATATTAATAT
302948 TAATTATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 15 0.41
44 22 0.59
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (44 bp):
TTAATATTAATATAAATTATAATATATACTTATATTAATATAAG
Found at i:304625 original size:19 final size:20
Alignment explanation
Indices: 304591--304632 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
304581 AGTTACCCTC
304591 ATAAGTCATATCTTGTTAGA
1 ATAAGTCATATCTTGTTAGA
304611 ATAAGTCAT-TCTTGTTAGA
1 ATAAGTCATATCTTGTTAGA
304630 ATA
1 ATA
304633 TTTGTGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (20 bp):
ATAAGTCATATCTTGTTAGA
Found at i:305770 original size:23 final size:23
Alignment explanation
Indices: 305720--305773 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
305710 CTTAATGCAG
* *
305720 GATGCTTGTTGAATTGATGCAAT
1 GATGCTTGATGAATTGATACAAT
* * *
305743 AATGCTTGATGAATTGGTACATT
1 GATGCTTGATGAATTGATACAAT
305766 GATGCTTG
1 GATGCTTG
305774 TTGGTTGCTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (23 bp):
GATGCTTGATGAATTGATACAAT
Found at i:306599 original size:16 final size:16
Alignment explanation
Indices: 306578--306612 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
306568 TCAATTACAT
*
306578 GTCAGGTTCATAACAG
1 GTCAGGTTCAAAACAG
*
306594 GTCAGGTTGAAAACAG
1 GTCAGGTTCAAAACAG
306610 GTC
1 GTC
306613 GAGTAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (16 bp):
GTCAGGTTCAAAACAG
Found at i:311347 original size:5 final size:5
Alignment explanation
Indices: 311337--311385 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
311327 GAACCGGTCT
*
311337 GACCC GACCC GA-CC GACCC GACCC GA-CC GACCGTT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACC
311386 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 8 0.21
5 26 0.68
7 4 0.11
ACGTcount: A:0.20, C:0.53, G:0.22, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:311356 original size:14 final size:14
Alignment explanation
Indices: 311337--311368 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
311327 GAACCGGTCT
311337 GACCCGACCCGACC
1 GACCCGACCCGACC
311351 GACCCGACCCGACC
1 GACCCGACCCGACC
311365 GACC
1 GACC
311369 GTTGACCCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (14 bp):
GACCCGACCCGACC
Found at i:313218 original size:2 final size:2
Alignment explanation
Indices: 313211--313242 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
313201 AATAACCAGG
313211 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
313243 AAACACACAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:318961 original size:24 final size:24
Alignment explanation
Indices: 318929--318976 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
318919 ATGCAACATA
318929 GATTACTACCATCACTATATCCTG
1 GATTACTACCATCACTATATCCTG
318953 GATTACTACCATCACTATATCCTG
1 GATTACTACCATCACTATATCCTG
318977 CAAAACTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (24 bp):
GATTACTACCATCACTATATCCTG
Found at i:324687 original size:21 final size:20
Alignment explanation
Indices: 324663--324704 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
324653 GTCATACAAC
*
324663 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
324684 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
324704 T
1 T
324705 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:324930 original size:21 final size:20
Alignment explanation
Indices: 324890--324931 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
324880 CCAACTTACA
*
324890 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
324910 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
324931 A
1 A
324932 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:332184 original size:16 final size:16
Alignment explanation
Indices: 332165--332211 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
332155 AAAATTGAAT
*
332165 AATTAAAACAAATTTA
1 AATTAAAATAAATTTA
332181 AATTAAAATAAATTTA
1 AATTAAAATAAATTTA
332197 AATTAAAATAAATTT
1 AATTAAAATAAATTT
332212 TATAGTTTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTAAAATAAATTTA
Found at i:334575 original size:28 final size:30
Alignment explanation
Indices: 334543--334611 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
334533 GTTGTATCGT
334543 TTATACCACTAAAATTTAATTTT-G-TCAA
1 TTATACCACTAAAATTTAATTTTCGTTCAA
* * * *
334571 TTATAACACTCAACTTTGATTTTCGTTTCAA
1 TTATACCACTAAAATTTAATTTTCG-TTCAA
334602 TTATACCACT
1 TTATACCACT
334612 GGACCGTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 19 0.58
29 1 0.03
31 13 0.39
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.43
Consensus pattern (30 bp):
TTATACCACTAAAATTTAATTTTCGTTCAA
Found at i:335837 original size:18 final size:19
Alignment explanation
Indices: 335799--335837 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
335789 GTATAATATT
335799 TTTATATCTTTAAACTAAA
1 TTTATATCTTTAAACTAAA
335818 TTTATATCTTTAAA-TAAA
1 TTTATATCTTTAAACTAAA
335836 TT
1 TT
335838 CAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTATATCTTTAAACTAAA
Found at i:336682 original size:36 final size:35
Alignment explanation
Indices: 336601--336740 Score: 192
Period size: 36 Copynumber: 3.9 Consensus size: 35
336591 AGATGAACAA
*
336601 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
* * *
336636 TTGAATCGAAAGTGTCGGTGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC-AC
*
336672 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
*
336707 TTTGAATCGAAAGTG-CTGATGCTTCCTTTCGTTC
1 -TTGAATCGAAAGTGTC-GATGCTTCCTTCCGTTC
336741 TTCTTATTCA
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.34
36 61 0.66
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
Done.