Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 94 of 133
Found at i:18348501 original size:30 final size:30
Alignment explanation
Indices: 18348467--18348552 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 30
18348457 TTTTTCTAGG
* *
18348467 TTTTCTAGAAATTTTTG-GTTTTTCGATCAA
1 TTTTCTAGAAA-GTTTGAATTTTTCGATCAA
18348497 TTTTCCT-GCAAAGTTTGAATTTTTCGATCAA
1 TTTT-CTAG-AAAGTTTGAATTTTTCGATCAA
* *
18348528 TTTTCTAGAAGGTTTAAATTTTTCG
1 TTTTCTAGAAAGTTTGAATTTTTCG
18348553 GTAGGATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
30 26 0.54
31 22 0.46
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (30 bp):
TTTTCTAGAAAGTTTGAATTTTTCGATCAA
Found at i:18348859 original size:18 final size:18
Alignment explanation
Indices: 18348832--18348866 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
18348822 TTTTCAATTC
18348832 TTTTTATTGTT-TTTTAT
1 TTTTTATTGTTATTTTAT
18348849 TTTTTATTTGTTATTTTA
1 TTTTTA-TTGTTATTTTA
18348867 ATTATTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTTATTGTTATTTTAT
Found at i:18349469 original size:16 final size:17
Alignment explanation
Indices: 18349430--18349473 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
18349420 TCCATTAAGC
*
18349430 CTTAAAATTTTACGCAT
1 CTTAAAATTTTACACAT
*
18349447 ATTAAAATTTTACAC-T
1 CTTAAAATTTTACACAT
18349463 CTTAAAATTTT
1 CTTAAAATTTT
18349474 CTTAACTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (17 bp):
CTTAAAATTTTACACAT
Found at i:18349799 original size:54 final size:53
Alignment explanation
Indices: 18349617--18349955 Score: 226
Period size: 54 Copynumber: 6.2 Consensus size: 53
18349607 AAAAAACTTA
* * * ** ***
18349617 ATTTTGAGAAAAAATTAATATTTTAACATTTTTCCCAAAAGCTTGAAATTATTTT
1 ATTTTAAGAAAAAATTGATATTTCAAC-TTTTTCTTAAATTTTTGAAATTA-TTT
* * * *
18349672 CATTTTAAGGAAAATTTGATATTTCAA-TTTTT-TTCAAAATCTTGAAATTATTT
1 -ATTTTAAGAAAAAATTGATATTTCAACTTTTTCTT-AAATTTTTGAAATTATTT
* * *
18349725 -TTTTAAGAAAAAATTAATATTTCAACTTTTCCTTACATTTTTGAAATTATTT
1 ATTTTAAGAAAAAATTGATATTTCAACTTTTTCTTAAATTTTTGAAATTATTT
* * ** *
18349777 CACTTTATGAAAAAATTGATA-TTCTAACTTTCTTCTTGATTTTTTTTTTAAATTATTT
1 -ATTTTAAGAAAAAATTGATATTTC-AACTTT-TTCTT-A--AATTTTTGAAATTATTT
* * * * *
18349835 TTATTTAAGGAAAAATTCATATTTCAAATTTTTTCTT-GATTTTTGAAATTATTT
1 AT-TTTAAGAAAAAATTGATATTTC-AACTTTTTCTTAAATTTTTGAAATTATTT
* *
18349889 -TTTTAAAAAAAAAATTTGATATTTCAACTTTTTTCTCAAATTTTTGAAA-TATTT
1 ATTTT-AAGAAAAAA-TTGATATTTCAAC-TTTTTCTTAAATTTTTGAAATTATTT
*
18349943 TTGTTTAA-AAAAA
1 AT-TTTAAGAAAAA
18349956 GCTCACTAAA
Statistics
Matches: 227, Mismatches: 38, Indels: 38
0.75 0.13 0.13
Matches are distributed among these distances:
51 22 0.10
52 22 0.10
53 18 0.08
54 81 0.36
55 17 0.07
56 25 0.11
58 34 0.15
59 8 0.04
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (53 bp):
ATTTTAAGAAAAAATTGATATTTCAACTTTTTCTTAAATTTTTGAAATTATTT
Found at i:18349933 original size:112 final size:110
Alignment explanation
Indices: 18349659--18349933 Score: 253
Period size: 112 Copynumber: 2.5 Consensus size: 110
18349649 TCCCAAAAGC
* * ** *
18349659 TTGAAATTATTTTCATTTTAAGGAAAATTTGATATTTCAA-TTTTTT-TCAAA---ATCTTGAAA
1 TTGAAATTATTTAC-TTTAAAAAAAAATTTGATATTTCAACTTTTTTCTCAAATTTTTCTTGAAA
18349719 TTATTTTTTTAAGAAAAAATTAATATTTCAACTTTTCCTTACATTT
65 TTATTTTTTTAAGAAAAAATTAATATTTCAACTTTTCCTTACATTT
** * ** * * *
18349765 TTGAAATTATTTCACTTTATGAAAAAA-TTGATA-TTCTAACTTTCTTCTTGATTTTTTTTTTAA
1 TTGAAATTATTT-ACTTTAAAAAAAAATTTGATATTTC-AACTTTTTTCTCAAATTTTTCTTGAA
* * * * *
18349828 ATTATTTTTATTTAAGGAAAAATTCATATTTCAAATTTTTTCTT-GATTT
64 ATTA-TTTT-TTTAAGAAAAAATTAATATTTC-AACTTTTCCTTACATTT
*
18349877 TTGAAATTATTT-TTTTAAAAAAAAAATTTGATATTTCAACTTTTTTCTCAAATTTTT
1 TTGAAATTATTTACTTT-AAAAAAAAATTTGATATTTCAACTTTTTTCTCAAATTTTT
18349934 GAAATATTTT
Statistics
Matches: 131, Mismatches: 25, Indels: 20
0.74 0.14 0.11
Matches are distributed among these distances:
104 3 0.02
105 8 0.06
106 24 0.18
107 3 0.02
110 12 0.09
111 11 0.08
112 58 0.44
113 12 0.09
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (110 bp):
TTGAAATTATTTACTTTAAAAAAAAATTTGATATTTCAACTTTTTTCTCAAATTTTTCTTGAAAT
TATTTTTTTAAGAAAAAATTAATATTTCAACTTTTCCTTACATTT
Found at i:18354546 original size:22 final size:22
Alignment explanation
Indices: 18354491--18354543 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
18354481 TTAAAAGACC
*
18354491 ATGCCTAAAGTTTTTATAGATA
1 ATGCCTAAAGTTTTTATAAATA
* *
18354513 ATGCCTGGAAGTTTTTA-AAATT
1 ATGCCT-AAAGTTTTTATAAATA
18354535 ATGCCTAAA
1 ATGCCTAAA
18354544 AGTCTTACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 15 0.58
23 9 0.35
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
ATGCCTAAAGTTTTTATAAATA
Found at i:18354886 original size:22 final size:22
Alignment explanation
Indices: 18354855--18354897 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18354845 AAAGATTATC
18354855 TAGAGATTTTAAAAAATGATAT
1 TAGAGATTTTAAAAAATGATAT
* * *
18354877 TAGAGGTTTTTAAAATTGATA
1 TAGAGATTTTAAAAAATGATA
18354898 ATCGAAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (22 bp):
TAGAGATTTTAAAAAATGATAT
Found at i:18355000 original size:412 final size:412
Alignment explanation
Indices: 18354533--18355355 Score: 1178
Period size: 412 Copynumber: 2.0 Consensus size: 412
18354523 GTTTTTAAAA
*
18354533 TTATGCCTAAAAGTCTTACAAATCAAACTTTGAAAAAAGTTTTGAAAATCATGCTCGAAGATCTC
1 TTATGCCCAAAAGTCTTACAAATCAAACTTTGAAAAAAGTTTTGAAAATCATGCTCGAAGATC-C
* * * *
18354598 -ATAAATCATGTCT-GGAGGTCTTATA-ACTAATGCTTGAAGGTCTTTGAGATTATGCTTAGAGG
65 AATAAATCATG-CTAGAAGGTCTTATAGA-TAATGCTTGAAGGTCTTTGAGATAATGCTCAAAGG
* * * *
18354660 TATTACAAATCAAACTTTGAAAAAGGTTTTGAAATCATGTTTAAAGGTTTTATAGATCA-AGTCC
128 TATTACAAATCAAACTTTGAAAAAGGTTTTGAAATCATGCTTAAAGGTCTTATAAATCATACT-C
* * * * *
18354724 A-AGTTTTTTGAAGATAGTAATTAAAA-GTTTTGAAGATGTACCCGAATG-TTTGACAAGAATAC
192 AGAGGTCTTTGAAGATAGTAA-TAAAATGTTTTGAAAATGTA-CCGAAAGATTTGACAAAAATAC
* * * *
18354786 ATATAAGTTTTAAAGATAACACCCAAAGGTTTTGAAGAAGATTACCTAGAGGTATAAAGAAAGAT
255 ATATAAATTTTAAAGATAACACCCAAAGGTTTTGAAAAAGATTACCTAAAGGTATAAAAAAAGAT
* **
18354851 TA-TCTAGAGATTTTAAAAAATGATATTAGAGGTTTTTAAAATTGATAATCGAAAGTTTTAACAA
320 TATTC-AAAGATTTTAAAAAATGATATTAGAGGTTTCCAAAATTGATAATC-AAAGTTTTAACAA
*
18354915 AAATA-CTCAGAGGTAAATTCTTATTTGGCT
383 AAATACCT-AGAGGTAAAGTCTTATTTGGCT
* *
18354945 TTATGCCCAAAAGTCTTACAAATCAAACTTTGAAAAAGGTTTTGAAAATCATGCTCGAAGGTCCA
1 TTATGCCCAAAAGTCTTACAAATCAAACTTTGAAAAAAGTTTTGAAAATCATGCTCGAAGATCCA
* * * *
18355010 ATAGATCATGCTAGAATGTCTTATAGATAATGCTTGAAGGTTTTTGAGATAATGCTCAAAGGTCT
66 ATAAATCATGCTAGAAGGTCTTATAGATAATGCTTGAAGGTCTTTGAGATAATGCTCAAAGGTAT
* * *
18355075 TATAAATCAAACTTTGAAAAAGGTTTTGAAATCATGCTTAGAGGTCTTATAAATCATACTTAGAG
131 TACAAATCAAACTTTGAAAAAGGTTTTGAAATCATGCTTAAAGGTCTTATAAATCATACTCAGAG
*
18355140 GTCTTTGAAGATAGTAATAAAATGTTTTGAAAATGTACCGAAAGATTTGACAAAAATACATGTAA
196 GTCTTTGAAGATAGTAATAAAATGTTTTGAAAATGTACCGAAAGATTTGACAAAAATACATATAA
* * *
18355205 ATTTTAAAGATAATACCCAAAGGTTTTGAAAAAGATTACTTAAAGGTTTAAAAAAAGATTATTCA
261 ATTTTAAAGATAACACCCAAAGGTTTTGAAAAAGATTACCTAAAGGTATAAAAAAAGATTATTCA
*
18355270 AAGATTTTAGAAAATGATATTAGAGGTTTCCAAAATTGATAATCAAAGTTTTAACAAAAATACCT
326 AAGATTTTAAAAAATGATATTAGAGGTTTCCAAAATTGATAATCAAAGTTTTAACAAAAATACCT
18355335 AGAGGTAAAGTCTTATTTGGC
391 AGAGGTAAAGTCTTATTTGGC
18355356 CTTCTTATCA
Statistics
Matches: 366, Mismatches: 36, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
411 3 0.01
412 213 0.58
413 148 0.40
414 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (412 bp):
TTATGCCCAAAAGTCTTACAAATCAAACTTTGAAAAAAGTTTTGAAAATCATGCTCGAAGATCCA
ATAAATCATGCTAGAAGGTCTTATAGATAATGCTTGAAGGTCTTTGAGATAATGCTCAAAGGTAT
TACAAATCAAACTTTGAAAAAGGTTTTGAAATCATGCTTAAAGGTCTTATAAATCATACTCAGAG
GTCTTTGAAGATAGTAATAAAATGTTTTGAAAATGTACCGAAAGATTTGACAAAAATACATATAA
ATTTTAAAGATAACACCCAAAGGTTTTGAAAAAGATTACCTAAAGGTATAAAAAAAGATTATTCA
AAGATTTTAAAAAATGATATTAGAGGTTTCCAAAATTGATAATCAAAGTTTTAACAAAAATACCT
AGAGGTAAAGTCTTATTTGGCT
Found at i:18355017 original size:22 final size:22
Alignment explanation
Indices: 18354992--18355050 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
18354982 GGTTTTGAAA
*
18354992 ATCATGCTCGAAGGTCCAATAG
1 ATCATGCTAGAAGGTCCAATAG
* **
18355014 ATCATGCTAGAATGTCTTATAG
1 ATCATGCTAGAAGGTCCAATAG
* *
18355036 ATAATGCTTGAAGGT
1 ATCATGCTAGAAGGT
18355051 TTTTGAGATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (22 bp):
ATCATGCTAGAAGGTCCAATAG
Found at i:18355130 original size:22 final size:22
Alignment explanation
Indices: 18355103--18355144 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18355093 AAAGGTTTTG
*
18355103 AAATCATGCTTAGAGGTCTTAT
1 AAATCATACTTAGAGGTCTTAT
18355125 AAATCATACTTAGAGGTCTT
1 AAATCATACTTAGAGGTCTT
18355145 TGAAGATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (22 bp):
AAATCATACTTAGAGGTCTTAT
Found at i:18355167 original size:114 final size:114
Alignment explanation
Indices: 18354947--18355167 Score: 243
Period size: 114 Copynumber: 1.9 Consensus size: 114
18354937 ATTTGGCTTT
*
18354947 ATGCCCAAAAGTCTTACAAATCAAACTTTGAAAAAGGTTTTGAAAATCATGCTCGAAGGTCCAAT
1 ATGCCCAAAAGTCTTACAAATCAAACTTTGAAAAAGGTTTTGAAAATCATGCTAGAAGGTCCAAT
* * * ** **
18355012 AGATCATGCTAGAATGTCTTATAGATAATGCTTGAAGGTTTTTGAGATA
66 AAATCATACTAGAAGGTCTTATAGATAATAATAAAAGGTTTTTGAGATA
* * * **
18355061 ATGCTCAAAGGTCTTATAAATCAAACTTTGAAAAAGGTTTTG-AAATCATGCTTAG-AGGTCTTA
1 ATGCCCAAAAGTCTTACAAATCAAACTTTGAAAAAGGTTTTGAAAATCATGC-TAGAAGGTCCAA
* *
18355124 TAAATCATACTTAG-AGGTCTT-TGAAGATAGTAATAAAATGTTTT
65 TAAATCATAC-TAGAAGGTCTTAT--AGATAATAATAAAAGGTTTT
18355168 GAAAATGTAC
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
112 1 0.01
113 29 0.33
114 58 0.66
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (114 bp):
ATGCCCAAAAGTCTTACAAATCAAACTTTGAAAAAGGTTTTGAAAATCATGCTAGAAGGTCCAAT
AAATCATACTAGAAGGTCTTATAGATAATAATAAAAGGTTTTTGAGATA
Found at i:18355251 original size:23 final size:23
Alignment explanation
Indices: 18355222--18355283 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
18355212 AGATAATACC
18355222 CAAAGGTTTTGAAAAAGATTACTT
1 CAAAGGTTTTGAAAAAGATTA-TT
**
18355246 -AAAGGTTTAAAAAAAGATTATT
1 CAAAGGTTTTGAAAAAGATTATT
*
18355268 CAAAGATTTTAGAAAA
1 CAAAGGTTTT-GAAAA
18355284 TGATATTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 2 0.06
23 25 0.81
24 4 0.13
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.31
Consensus pattern (23 bp):
CAAAGGTTTTGAAAAAGATTATT
Found at i:18355507 original size:18 final size:18
Alignment explanation
Indices: 18355468--18355507 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18355458 GGAAGTAAGC
*
18355468 AATGAATGTAATACATGG
1 AATGAATGTAATACATAG
* *
18355486 AATGAATGTGATACATAT
1 AATGAATGTAATACATAG
18355504 AATG
1 AATG
18355508 CATGAAATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
AATGAATGTAATACATAG
Found at i:18358792 original size:17 final size:18
Alignment explanation
Indices: 18358752--18358799 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
18358742 ATGAATGCAT
18358752 TACATGAATG-ATGATGA
1 TACATGAATGAATGATGA
18358769 T-CTATGAATGAATGA-GA
1 TAC-ATGAATGAATGATGA
18358786 TACATGAAATGAAT
1 TACATG-AATGAAT
18358800 AAAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 14 0.52
18 12 0.44
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (18 bp):
TACATGAATGAATGATGA
Found at i:18359836 original size:18 final size:18
Alignment explanation
Indices: 18359812--18359849 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
18359802 TATGAAATTC
18359812 CAAAAAAATTTAAT-TTT
1 CAAAAAAATTTAATATTT
*
18359829 CAAAAAAATTTGATATTT
1 CAAAAAAATTTAATATTT
18359847 CAA
1 CAA
18359850 CTTTTTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (18 bp):
CAAAAAAATTTAATATTT
Found at i:18359961 original size:55 final size:54
Alignment explanation
Indices: 18359831--18360083 Score: 235
Period size: 55 Copynumber: 4.6 Consensus size: 54
18359821 TTAATTTTCA
* * *
18359831 AAAAAATTTGATATTTCAACTTTTTCC-CAAAATCTTGAAATTATTTTTGTTTCAAG
1 AAAAAA-TTGATATTTCAAC-TTTTCCTCAAATTTTTGAAATTATTTTTATTT-AAG
* * * *
18359887 --AAAATTAATATTTCAACTTTTCCTTAAATTTTTGAAATTATTATCATTTAAAG
1 AAAAAATTGATATTTCAACTTTTCCTCAAATTTTTGAAATTATTTTTATTT-AAG
* * **
18359940 AAAAAATTGATATTTTAACTTTCTCCTTGATTTTTTTGAAATTATTTTTA-TTAAG
1 AAAAAATTGATATTTCAACTTT-TCC-TCAAATTTTTGAAATTATTTTTATTTAAG
* * * ** *
18359995 AAAAAAGTGATATTTTAAATATTTCCTCAAAAATTTGAAATTATTGTTATTTAAG
1 AAAAAATTGATATTTCAACT-TTTCCTCAAATTTTTGAAATTATTTTTATTTAAG
* *
18360050 GAAAAACTGATATTTCAACTTTTTCCTCAAATTT
1 AAAAAATTGATATTTCAAC-TTTTCCTCAAATTT
18360084 GCAAGAGAGA
Statistics
Matches: 160, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
52 6 0.04
53 34 0.21
54 21 0.13
55 73 0.46
56 8 0.05
57 18 0.11
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (54 bp):
AAAAAATTGATATTTCAACTTTTCCTCAAATTTTTGAAATTATTTTTATTTAAG
Found at i:18360409 original size:20 final size:20
Alignment explanation
Indices: 18360372--18360412 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18360362 AATGCTCTAA
** *
18360372 GGTCAAATTTAGTTAAACTT
1 GGTCAAATAAAGTCAAACTT
18360392 GGTCAAATAAAGTCAAACTT
1 GGTCAAATAAAGTCAAACTT
18360412 G
1 G
18360413 ATAAAATTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
GGTCAAATAAAGTCAAACTT
Found at i:18363367 original size:17 final size:17
Alignment explanation
Indices: 18363345--18363386 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
18363335 AAGAAAAAAG
*
18363345 GAACAAAGGAAAAGGAA
1 GAACAAAGGAAAAGAAA
18363362 GAACAAAGGAAAAGAAA
1 GAACAAAGGAAAAGAAA
*
18363379 GAAAAAAG
1 GAACAAAG
18363387 AAGAAAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.69, C:0.05, G:0.26, T:0.00
Consensus pattern (17 bp):
GAACAAAGGAAAAGAAA
Found at i:18363739 original size:10 final size:10
Alignment explanation
Indices: 18363724--18363755 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
18363714 GTATAATATT
18363724 AAAAAAAAGA
1 AAAAAAAAGA
18363734 AAAAAAAAGA
1 AAAAAAAAGA
18363744 AAAAAAAAGA
1 AAAAAAAAGA
18363754 AA
1 AA
18363756 GAAAGATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:18364772 original size:13 final size:12
Alignment explanation
Indices: 18364735--18364773 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
18364725 AATACTTCTT
* *
18364735 AAGAAGAAACTA
1 AAGAAAAAATTA
18364747 AAGAAAAAATTA
1 AAGAAAAAATTA
18364759 AAGAAAAGAATTA
1 AAGAAAA-AATTA
18364772 AA
1 AA
18364774 AAAGAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.72, C:0.03, G:0.13, T:0.13
Consensus pattern (12 bp):
AAGAAAAAATTA
Found at i:18365058 original size:49 final size:47
Alignment explanation
Indices: 18364847--18365434 Score: 398
Period size: 49 Copynumber: 12.1 Consensus size: 47
18364837 ACCTTTTCAA
* * * * * *
18364847 AAAGAAATTTTTAAAG-TTGCTACCTATTTTCATAAAAGACATTTTC
1 AAAGAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
* * * * * *
18364893 AAAAAATGAAAATTTTAATGTTTATTACATATTTTCATAAGAGCCCTTTATA
1 ---AAA-GAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAG-CCTTTTTC
* * * *
18364945 AAAGAAATTTTTAAA-TTTGTTGCCTATTTTCATAGGAGTCTTTTCC
1 AAAGAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
* * * *
18364991 AAAAGGAAATTTTTAAGTTTGTTGTCTATTTTCATATGAGCCTTTTTC
1 -AAAGAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
* ** * **
18365039 AAAGAAACATTTTAAAAGTTTGTTGCCTATCTAT-ATGGGAACCCTTTTAAA
1 AAAGAAA-ATTTT-AAAGTTTGTTGCCTAT-TTTCATAAG-AGCCTTTT-TC
* * * *
18365090 AAAGAAAAATTTTAAAGTTTGTCGACTATTTTCATAGGAGCCATTTTTAA
1 AAAG-AAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCC-TTTTT-C
* * ** *
18365140 AAAGATATTTTTAAAGTTTGTCACCTATTTTCATAAGAG-CTCTTTC
1 AAAGAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
*** * *
18365186 AAA-AAAAAAAT-AAGTTTGTTGCCTATTTTCATATGAGCCATTTTC
1 AAAGAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
* ** * *
18365231 ATAAAGAAACTTTTAAAGTTTGTAACCTATTTTCATAAGAACCCTTTTC
1 --AAAGAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
* * * *
18365280 AAAAAAGAAAAATTTAAAGTTTGTTGCCTATTTTTATAAAAGCATTTTTC
1 ---AAAGAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
* *
18365330 AAAAAGAAAATTTTAAAGTTTGTTACCTATCTTT-ATAAGAGCCCTCTTTTTTAA
1 --AAAGAAAATTTTAAAGTTTGTTGCCTAT-TTTCATAAGAG--C-C-TTTTT-C
* *
18365384 AAAGAAAAATTTTAAAGTTTGTTGCCTATTTTCATAGGAGCCCTTTTC
1 AAAG-AAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
18365432 AAA
1 AAA
18365435 ATGAGATTTT
Statistics
Matches: 424, Mismatches: 87, Indels: 57
0.75 0.15 0.10
Matches are distributed among these distances:
44 23 0.05
45 8 0.02
46 7 0.02
47 44 0.10
48 50 0.12
49 125 0.29
50 90 0.21
51 29 0.07
52 14 0.03
53 34 0.08
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (47 bp):
AAAGAAAATTTTAAAGTTTGTTGCCTATTTTCATAAGAGCCTTTTTC
Found at i:18365121 original size:99 final size:98
Alignment explanation
Indices: 18364847--18365434 Score: 480
Period size: 99 Copynumber: 6.0 Consensus size: 98
18364837 ACCTTTTCAA
* * * *
18364847 AAAGAAA-TTTTTAAAG-TTGCTACCTATTTTCATAA-AAGACATTTTCAAAAAATG-AAAATTT
1 AAAGAAACATTTTAAAGTTTGTTACCTATTTTCATAAGAA-CCCTTTT-AAAAAA-GAAAAATTT
* * * * * * *
18364908 TAATGTTTATTACATATTTTCATAAGAGCCCTTTATA
63 TAAAGTTTGTTGCCTATTTTCATAGGAG-CCTTTTTC
* * * ** ** * *
18364945 AAAGAAA-TTTTTAAA-TTTGTTGCCTATTTTCAT-AGGAGTCTTTTCCAAAAG-GAAATTTTTA
1 AAAGAAACATTTTAAAGTTTGTTACCTATTTTCATAAGAACCCTTTTAAAAAAGAAAAATTTTAA
* *
18365006 AGTTTGTTGTCTATTTTCATATGAGCCTTTTTC
66 AGTTTGTTGCCTATTTTCATAGGAGCCTTTTTC
* * **
18365039 AAAGAAACATTTTAAAAGTTTGTTGCCTATCTAT-ATGGGAACCCTTTTAAAAAAGAAAAATTTT
1 AAAGAAACATTTT-AAAGTTTGTTACCTAT-TTTCATAAGAACCCTTTTAAAAAAGAAAAATTTT
* *
18365103 AAAGTTTGTCGACTATTTTCATAGGAGCCATTTTT-
64 AAAGTTTGTTGCCTATTTTCATAGGAGCC-TTTTTC
* * * * *
18365138 AAA-AAGATATTTTTAAAGTTTGTCACCTATTTTCATAAGAGCTC-TTTCAAAAA-AAAAA---T
1 AAAGAA-ACA-TTTTAAAGTTTGTTACCTATTTTCATAAGAACCCTTTTAAAAAAGAAAAATTTT
* *
18365197 -AAGTTTGTTGCCTATTTTCATATGAGCCATTTTC
64 AAAGTTTGTTGCCTATTTTCATAGGAGCCTTTTTC
*
18365231 ATAAAGAAAC-TTTTAAAGTTTGTAACCTATTTTCATAAGAACCCTTTTCAAAAAAGAAAAA-TT
1 --AAAGAAACATTTTAAAGTTTGTTACCTATTTTCATAAGAACCCTTTT-AAAAAAGAAAAATTT
* ** *
18365294 TAAAGTTTGTTGCCTATTTTTATAAAAGCATTTTTC
63 TAAAGTTTGTTGCCTATTTTCATAGGAGCCTTTTTC
* *
18365330 AAAAAGAAA-ATTTTAAAGTTTGTTACCTATCTTT-ATAAGAGCCCTCTTTTTTAAAAAGAAAAA
1 --AAAGAAACATTTTAAAGTTTGTTACCTAT-TTTCATAAGA-ACC-C-TTTTAAAAAAGAAAAA
*
18365393 TTTTAAAGTTTGTTGCCTATTTTCATAGGAGCCCTTTTC
60 TTTTAAAGTTTGTTGCCTATTTTCATAGGAGCCTTTTTC
18365432 AAA
1 AAA
18365435 ATGAGATTTT
Statistics
Matches: 399, Mismatches: 63, Indels: 54
0.77 0.12 0.10
Matches are distributed among these distances:
92 4 0.01
93 56 0.14
94 17 0.04
95 41 0.10
96 14 0.04
97 24 0.06
98 58 0.15
99 119 0.30
100 17 0.04
101 12 0.03
102 37 0.09
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (98 bp):
AAAGAAACATTTTAAAGTTTGTTACCTATTTTCATAAGAACCCTTTTAAAAAAGAAAAATTTTAA
AGTTTGTTGCCTATTTTCATAGGAGCCTTTTTC
Found at i:18365217 original size:192 final size:191
Alignment explanation
Indices: 18364847--18365434 Score: 581
Period size: 192 Copynumber: 3.0 Consensus size: 191
18364837 ACCTTTTCAA
* * * *
18364847 AAAGAAATTTTTAAAG-TTGCT-ACCTATTTTCATAA-AAGACATTTTCAAAAAATG-AAAATTT
1 AAAGAAACTTTTAAAGTTTG-TAACCTATTATCATAAGAA-CCCTTTTCAAAAAA-GAAAAATTT
* * * * * *
18364908 TAATGTTTATTACATATTTTCATAAGAGCCCTTTAT-AAAAGAAATTTTTAAA-TTTGTTGCCTA
63 TAAAGTTTGTGAC-TATTTTCATAAGAGCCATTTTTAAAAAGAAATTTTTAAAGTTTGTTACCTA
* *** * *
18364971 TTTTCATAGGAG-TCTTTTCCAAAAGGAAATTTTTAAGTTTGTTGTCTATTTTCATATGAGCCTT
127 TTTTCATAAGAGCTCTTTT-CAAAA--AAA-AAATAAGTTTGTTGCCTATTTTCATATGAGCCAT
18365035 TTTC
188 TTTC
** **
18365039 AAAGAAACATTTTAAAAGTTTGTTGCCTATCTAT-ATGGGAACCCTTTT-AAAAAAGAAAAATTT
1 AAAGAAAC-TTTT-AAAGTTTGTAACCTAT-TATCATAAGAACCCTTTTCAAAAAAGAAAAATTT
* * *
18365102 TAAAGTTTGTCGACTATTTTCATAGGAGCCATTTTTAAAAAGATATTTTTAAAGTTTGTCACCTA
63 TAAAGTTTGT-GACTATTTTCATAAGAGCCATTTTTAAAAAGAAATTTTTAAAGTTTGTTACCTA
18365167 TTTTCATAAGAGCTC-TTTCAAAAAAAAAATAAGTTTGTTGCCTATTTTCATATGAGCCATTTTC
127 TTTTCATAAGAGCTCTTTTCAAAAAAAAAATAAGTTTGTTGCCTATTTTCATATGAGCCATTTTC
*
18365231 ATAAAGAAACTTTTAAAGTTTGTAACCTATTTTCATAAGAACCCTTTTCAAAAAAGAAAAA-TTT
1 --AAAGAAACTTTTAAAGTTTGTAACCTATTATCATAAGAACCCTTTTCAAAAAAGAAAAATTTT
* * * *
18365295 AAAGTTTGTTGCCTATTTTTATAAAAG-CATTTTTCAAAAAGAAAATTTTAAAGTTTGTTACCTA
64 AAAGTTTG-TGACTATTTTCATAAGAGCCATTTTT-AAAAAGAAATTTTTAAAGTTTGTTACCTA
* *
18365359 TCTTT-ATAAGAGCCCTCTTTTTTAAAAAGAAAAATTTTAAAGTTTGTTGCCTATTTTCATAGGA
127 T-TTTCATAAGAG--CTC-TTTTCAAAAA-AAAAA---T-AAGTTTGTTGCCTATTTTCATATGA
*
18365423 GCCCTTTTC
183 GCCATTTTC
18365432 AAA
1 AAA
18365435 ATGAGATTTT
Statistics
Matches: 332, Mismatches: 37, Indels: 47
0.80 0.09 0.11
Matches are distributed among these distances:
191 9 0.03
192 124 0.37
193 28 0.08
194 56 0.17
195 37 0.11
196 35 0.11
197 7 0.02
199 3 0.01
200 1 0.00
201 32 0.10
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (191 bp):
AAAGAAACTTTTAAAGTTTGTAACCTATTATCATAAGAACCCTTTTCAAAAAAGAAAAATTTTAA
AGTTTGTGACTATTTTCATAAGAGCCATTTTTAAAAAGAAATTTTTAAAGTTTGTTACCTATTTT
CATAAGAGCTCTTTTCAAAAAAAAAATAAGTTTGTTGCCTATTTTCATATGAGCCATTTTC
Found at i:18367819 original size:16 final size:18
Alignment explanation
Indices: 18367798--18367835 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
18367788 TTACATGCAT
18367798 AATTCC-ATGAAA-CCCA
1 AATTCCTATGAAATCCCA
18367814 AATTCCTATGAAATCCCA
1 AATTCCTATGAAATCCCA
18367832 AATT
1 AATT
18367836 TGAAGCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 6 0.30
18 8 0.40
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (18 bp):
AATTCCTATGAAATCCCA
Found at i:18367870 original size:29 final size:29
Alignment explanation
Indices: 18367828--18367883 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
18367818 CCTATGAAAT
18367828 CCCAAATTTGAAGCCTTATA-CCCTAAAAC
1 CCCAAATTTGAAGCCTTA-AGCCCTAAAAC
18367857 CCCAAATTTGAAGCCTTAAGCCCTAAA
1 CCCAAATTTGAAGCCTTAAGCCCTAAA
18367884 CCCTAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (29 bp):
CCCAAATTTGAAGCCTTAAGCCCTAAAAC
Found at i:18367887 original size:7 final size:7
Alignment explanation
Indices: 18367877--18367931 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
18367867 AAGCCTTAAG
18367877 CCCTAAA
1 CCCTAAA
18367884 CCCTAAAA
1 CCCT-AAA
*
18367892 TCCTAAA
1 CCCTAAA
*
18367899 CCTTAAA
1 CCCTAAA
18367906 CCCTAAA
1 CCCTAAA
* *
18367913 -AC-ATA
1 CCCTAAA
18367918 CCCTAAA
1 CCCTAAA
18367925 CCCTAAA
1 CCCTAAA
18367932 AGCAACCCCT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
5 2 0.05
6 2 0.05
7 27 0.73
8 6 0.16
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.18
Consensus pattern (7 bp):
CCCTAAA
Found at i:18367892 original size:29 final size:29
Alignment explanation
Indices: 18367831--18367914 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
18367821 ATGAAATCCC
*
18367831 AAATTTGAAGCCTTATACCCTAAAACCCC
1 AAATTTGAAGCCTTATACCCTAAAACCCA
18367860 AAATTTGAAGCCTTA-AGCCCT-AAACCCTA
1 AAATTTGAAGCCTTATA-CCCTAAAACCC-A
* * *
18367889 AAATCCT-AAACCTTAAACCCTAAAAC
1 AAAT-TTGAAGCCTTATACCCTAAAAC
18367915 ATACCCTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 7 0.15
29 34 0.72
30 6 0.13
ACGTcount: A:0.42, C:0.30, G:0.06, T:0.23
Consensus pattern (29 bp):
AAATTTGAAGCCTTATACCCTAAAACCCA
Found at i:18367939 original size:19 final size:18
Alignment explanation
Indices: 18367877--18367939 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 18
18367867 AAGCCTTAAG
18367877 CCCTAAACCCTAAAATCCTAAA
1 CCCTAAACCCTAAAA--C--AA
*
18367899 CCTTAAACCCTAAAACATA
1 CCCTAAACCCTAAAACA-A
18367918 CCCTAAACCCTAAAAGCAA
1 CCCTAAACCCTAAAA-CAA
18367937 CCC
1 CCC
18367940 CTAACCCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 3 0.08
22 14 0.38
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.16
Consensus pattern (18 bp):
CCCTAAACCCTAAAACAA
Found at i:18367946 original size:19 final size:19
Alignment explanation
Indices: 18367877--18367932 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
18367867 AAGCCTTAAG
*
18367877 CCCTAAACCCTAAAATCCTAAA
1 CCCTAAACCCTAAAA--C-ATA
*
18367899 CCTTAAACCCTAAAACATA
1 CCCTAAACCCTAAAACATA
18367918 CCCTAAACCCTAAAA
1 CCCTAAACCCTAAAA
18367933 GCAACCCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.52
20 1 0.03
22 14 0.45
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (19 bp):
CCCTAAACCCTAAAACATA
Found at i:18373077 original size:18 final size:18
Alignment explanation
Indices: 18373054--18373088 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18373044 ATGAAAGTTG
18373054 AATTGAGAGAAACAATAA
1 AATTGAGAGAAACAATAA
*
18373072 AATTGATAGAAACAATA
1 AATTGAGAGAAACAATA
18373089 TTACATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (18 bp):
AATTGAGAGAAACAATAA
Found at i:18374330 original size:19 final size:19
Alignment explanation
Indices: 18374308--18374367 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
18374298 GATAATTTGA
18374308 GGTTATGGGTTAGATTTAG
1 GGTTATGGGTTAGATTTAG
* * *
18374327 GGTT-TGGATCAAATTTAG
1 GGTTATGGGTTAGATTTAG
* * *
18374345 GGTTATAGGCTAGGTTTAG
1 GGTTATGGGTTAGATTTAG
18374364 GGTT
1 GGTT
18374368 CAATGTTTGC
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.22, C:0.03, G:0.35, T:0.40
Consensus pattern (19 bp):
GGTTATGGGTTAGATTTAG
Found at i:18376263 original size:144 final size:142
Alignment explanation
Indices: 18375996--18376504 Score: 523
Period size: 144 Copynumber: 3.6 Consensus size: 142
18375986 TATGATCTGG
* * * * ** * *
18375996 AGCTTTTCACAAAAAACTAACCTCGAAAAA-GTTAAATTATGAAATTATCC-CTAAAAGGTA-TT
1 AGCTTTTCACGAAAAACTTACC-CTAAAAAGGTCAAATTACAAAAATA-CCTCTAAAAGGCATTT
* *
18376058 TGGTAATTTTACCTTTTTCAA-GTGCAATCAAGGTTTTCAATACATCAAAATTCATGGAATAATA
64 TGGTAATTTCACCTTTTT-AAGGTGCAATCAAGGTTTTCAATACATC-AAATTCATGAAATAATA
*
18376122 TTAAAACATAATCTAT
127 TTAAAACATAATCTAA
* * *
18376138 AGCTTTTCACGAAAAACTTACCCTAAGAAGGTCAAATTACAAAAATACCTCTAAAGGGTATTTTG
1 AGCTTTTCACGAAAAACTTACCCTAAAAAGGTCAAATTACAAAAATACCTCTAAAAGGCATTTTG
* * * * *
18376203 GTAATTTCATTCTTTTTTAGGTGCAATCAAGGTTTTCAATGCATCTTAATTCATGAAATAATGTT
66 GTAATTTCA-CCTTTTTAAGGTGCAATCAAGGTTTTCAATACATC-AAATTCATGAAATAATATT
**
18376268 AAAACATAATCTGC
129 AAAACATAATCTAA
* * * *
18376282 AGCTTTTCAC-AAAAAGC-TAACCTAAAAAAGGTCAAATTAC-AAAATATCTTTAAGAGGCATTT
1 AGCTTTTCACGAAAAA-CTTACCCT-AAAAAGGTCAAATTACAAAAATACCTCTAAAAGGCATTT
* * * *
18376344 TGATAGTTTCAACCTTTTTAAGGTGCAATCAAGATTTTCAATACATCAAATTTTAT-AGAATAAT
64 TGGTAATTTC-ACCTTTTTAAGGTGCAATCAAGGTTTTCAATACATCAAA-TTCATGA-AATAAT
*
18376408 ATTAAAACATGATCTAA
126 ATTAAAACATAATCTAA
* * * * *
18376425 AGTTTTTTTATGAAAAA-TTGACCTTAAAAAGGCCAAATTACAAAAATACCTCTAAAAGGCATTT
1 AG-CTTTTCACGAAAAACTT-ACCCTAAAAAGGTCAAATTACAAAAATACCTCTAAAAGGCATTT
18376489 TGGTAATTTCACCTTT
64 TGGTAATTTCACCTTT
18376505 ATGAAGCGCA
Statistics
Matches: 303, Mismatches: 49, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
141 7 0.02
142 45 0.15
143 104 0.34
144 112 0.37
145 35 0.12
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (142 bp):
AGCTTTTCACGAAAAACTTACCCTAAAAAGGTCAAATTACAAAAATACCTCTAAAAGGCATTTTG
GTAATTTCACCTTTTTAAGGTGCAATCAAGGTTTTCAATACATCAAATTCATGAAATAATATTAA
AACATAATCTAA
Found at i:18376518 original size:287 final size:286
Alignment explanation
Indices: 18375990--18376525 Score: 686
Period size: 287 Copynumber: 1.9 Consensus size: 286
18375980 ATTAACTATG
* * * * * *
18375990 ATCTGGAGCTTTTCACAAAAAACTAACCTCGAAAAAGTTAAATTATGAAATTATCCCTAAAAGGT
1 ATCTGCAGCTTTTCACAAAAAACTAACCTCAAAAAAGTCAAATTATCAAAATATCCCTAAAAGGC
* * * *
18376055 ATTTGGTAATTTTACCTTTTTCAAGTGCAATCAAGGTTTTCAATACATCAAAATTCATGGAATAA
66 ATTTGATAATTTAACCTTTTTCAAGTGCAATCAAGATTTTCAATACATCAAAATTCATAGAATAA
* * *
18376120 TATTAAAACATAATCTATAGCTTTTCACGAAAAACTTACCCTAAGAAGGTCAAATTACAAAAATA
131 TATTAAAACATAATCTAAAGCTTTTCACGAAAAACTTACCCTAAAAAGGCCAAATTACAAAAATA
* * * * * * * *
18376185 CCTCTAAAGGGTATTTTGGTAATTTCATTCTTTTTTAGGTGCAATCAAGGTTTTCAATGCATCTT
196 CCTCTAAAAGGCATTTTGGTAATTTCATCCTTTATGAAGCGCAATCAAGATTTTCAATGCATCTT
18376250 AATTCATGAAATAATGTTAAAACATA
261 AATTCATGAAATAATGTTAAAACATA
* ** *
18376276 ATCTGCAGCTTTTCACAAAAAGCTAACCT-AAAAAAGGTCAAATTA-CAAAATATCTTTAAGAGG
1 ATCTGCAGCTTTTCACAAAAAACTAACCTCAAAAAA-GTCAAATTATCAAAATATCCCTAAAAGG
* * *
18376339 CATTTTGATAGTTTCAACCTTTTT-AAGGTGCAATCAAGATTTTCAATACATCAAATTTTATAGA
65 CA-TTTGATAATTT-AACCTTTTTCAA-GTGCAATCAAGATTTTCAATACATCAAAATTCATAGA
* * * * *
18376403 ATAATATTAAAACATGATCTAAAGTTTTTTTATGAAAAA-TTGACCTTAAAAAGGCCAAATTACA
127 ATAATATTAAAACATAATCTAAAG-CTTTTCACGAAAAACTT-ACCCTAAAAAGGCCAAATTACA
18376467 AAAATACCTCTAAAAGGCATTTTGGTAATTTCA-CCTTTATGAAGCGCAATCAAGATTTT
190 AAAATACCTCTAAAAGGCATTTTGGTAATTTCATCCTTTATGAAGCGCAATCAAGATTTT
18376526 TAAGAATCCA
Statistics
Matches: 211, Mismatches: 33, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
285 19 0.09
286 46 0.22
287 85 0.40
288 61 0.29
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (286 bp):
ATCTGCAGCTTTTCACAAAAAACTAACCTCAAAAAAGTCAAATTATCAAAATATCCCTAAAAGGC
ATTTGATAATTTAACCTTTTTCAAGTGCAATCAAGATTTTCAATACATCAAAATTCATAGAATAA
TATTAAAACATAATCTAAAGCTTTTCACGAAAAACTTACCCTAAAAAGGCCAAATTACAAAAATA
CCTCTAAAAGGCATTTTGGTAATTTCATCCTTTATGAAGCGCAATCAAGATTTTCAATGCATCTT
AATTCATGAAATAATGTTAAAACATA
Found at i:18376679 original size:29 final size:29
Alignment explanation
Indices: 18376624--18376679 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
18376614 TTCTTATCAA
* * **
18376624 GTTTGACCATTTTTGACCGTATTGCATAC
1 GTTTGACCATGTTTGACCATAGAGCATAC
*
18376653 GTTTGATCATGTTTGACCATAGAGCAT
1 GTTTGACCATGTTTGACCATAGAGCAT
18376680 TTTGGTTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (29 bp):
GTTTGACCATGTTTGACCATAGAGCATAC
Found at i:18377481 original size:21 final size:21
Alignment explanation
Indices: 18377456--18377496 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18377446 TAATCATATT
18377456 ACATATAACAAAGTAAAGTAA
1 ACATATAACAAAGTAAAGTAA
* *
18377477 ACATATAAGAAAGTAGAGTA
1 ACATATAACAAAGTAAAGTA
18377497 TACTTAATCT
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:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (21 bp):
ACATATAACAAAGTAAAGTAA
Found at i:18391017 original size:18 final size:19
Alignment explanation
Indices: 18390994--18391029 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18390984 AATTCATCAA
*
18390994 TAAAATAACAA-ACAAAAG
1 TAAAATAAAAATACAAAAG
18391012 TAAAATAAAAATACAAAA
1 TAAAATAAAAATACAAAA
18391030 AACCAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (19 bp):
TAAAATAAAAATACAAAAG
Found at i:18399455 original size:10 final size:11
Alignment explanation
Indices: 18399420--18399476 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
18399410 ACCACTTGTG
*
18399420 ATTTTATTTCT
1 ATTTTATTTAT
18399431 ATTTTA-TTAT
1 ATTTTATTTAT
18399441 ATTTTATTTAT
1 ATTTTATTTAT
*
18399452 TTTTTCA-TTAT
1 ATTTT-ATTTAT
18399463 -TGTTT-TTTAT
1 AT-TTTATTTAT
18399473 ATTT
1 ATTT
18399477 CTTTATTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 16 0.41
11 22 0.56
12 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (11 bp):
ATTTTATTTAT
Found at i:18399456 original size:21 final size:22
Alignment explanation
Indices: 18399420--18399476 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
18399410 ACCACTTGTG
*
18399420 ATTTTATTTCTATTTT-ATTAT
1 ATTTTATTTATATTTTCATTAT
*
18399441 ATTTTATTTATTTTTTCATTAT
1 ATTTTATTTATATTTTCATTAT
18399463 -TGTTT-TTTATATTT
1 AT-TTTATTTATATTT
18399477 CTTTATTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTTATTTATATTTTCATTAT
Found at i:18400082 original size:14 final size:14
Alignment explanation
Indices: 18400063--18400095 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
18400053 AAACAAATAA
*
18400063 AAAAAGTAAAAAAG
1 AAAAAGAAAAAAAG
18400077 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
18400091 AAAAA
1 AAAAA
18400096 AATATAATAA
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:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:18400097 original size:8 final size:8
Alignment explanation
Indices: 18400061--18400097 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
18400051 TCAAACAAAT
18400061 AAAAAAAG
1 AAAAAAAG
*
18400069 TAAAAAAG
1 AAAAAAAG
18400077 --AAAAAG
1 AAAAAAAG
18400083 AAAAAAAG
1 AAAAAAAG
18400091 AAAAAAA
1 AAAAAAA
18400098 TATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:18404254 original size:2 final size:2
Alignment explanation
Indices: 18404238--18404283 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
18404228 TCGGACAATA
* *
18404238 AT AT AT A- AT ACT AT AT AT AT AT AT AT AT CT AT CT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18404280 AT AT
1 AT AT
18404284 GTATGGCTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18404281 original size:18 final size:18
Alignment explanation
Indices: 18404238--18404283 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
18404228 TCGGACAATA
18404238 ATATATA-ATA-CTATAT
1 ATATATATATATCTATAT
*
18404254 ATATATATATATCTATCT
1 ATATATATATATCTATAT
18404272 ATATATATATAT
1 ATATATATATAT
18404284 GTATGGCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 7 0.26
17 3 0.11
18 17 0.63
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATATATATATCTATAT
Found at i:18405754 original size:3 final size:3
Alignment explanation
Indices: 18405746--18405774 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18405736 TCAGTGGAGC
18405746 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
18405775 AGATGATGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:18413594 original size:17 final size:18
Alignment explanation
Indices: 18413561--18413594 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18413551 AGCCACAGGA
18413561 ACAGAATCAAGGTCAAAG
1 ACAGAATCAAGGTCAAAG
*
18413579 ACAGAATGAA-GTCAAA
1 ACAGAATCAAGGTCAAA
18413595 AAGTGTTGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.15, G:0.21, T:0.12
Consensus pattern (18 bp):
ACAGAATCAAGGTCAAAG
Found at i:18416335 original size:21 final size:22
Alignment explanation
Indices: 18416309--18416349 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18416299 ATATTAGAGA
*
18416309 CAAAGA-CAAATTTGTTTTGTC
1 CAAAGATCAAATATGTTTTGTC
*
18416330 CAAAGATGAAATATGTTTTG
1 CAAAGATCAAATATGTTTTG
18416350 GAAAAAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
CAAAGATCAAATATGTTTTGTC
Found at i:18416931 original size:27 final size:27
Alignment explanation
Indices: 18416901--18416952 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
18416891 AAATAAATAA
*
18416901 TTTGATAACATAAATATTAATATATTT
1 TTTGATAACACAAATATTAATATATTT
***
18416928 TTTGATATTGCAAATATTAATATAT
1 TTTGATAACACAAATATTAATATAT
18416953 AAAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (27 bp):
TTTGATAACACAAATATTAATATATTT
Found at i:18418136 original size:16 final size:16
Alignment explanation
Indices: 18418075--18418137 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 16
18418065 ATTATGTGGT
18418075 ATTATATTTAGTAAAA
1 ATTATATTTAGTAAAA
18418091 A--ATA-TTA--AAAA
1 ATTATATTTAGTAAAA
* *
18418102 ATTGA-ATTAAGT-GAA
1 ATT-ATATTTAGTAAAA
18418117 ATTATATTTAGTAAAA
1 ATTATATTTAGTAAAA
18418133 ATTAT
1 ATTAT
18418138 TATAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
11 5 0.14
13 4 0.11
14 7 0.20
15 11 0.31
16 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (16 bp):
ATTATATTTAGTAAAA
Found at i:18420107 original size:2 final size:2
Alignment explanation
Indices: 18420100--18420126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18420090 TAAACTCAAC
18420100 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
18420127 AGCTGGCCAT
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:18422626 original size:2 final size:2
Alignment explanation
Indices: 18422619--18422651 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18422609 TAATTCTTGA
18422619 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 A
18422652 CACACCAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18422853 original size:16 final size:17
Alignment explanation
Indices: 18422832--18422879 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
18422822 AGTTCTTTAA
18422832 TAATTTAATATGTA-GT
1 TAATTTAATATGTATGT
*
18422848 TAATTTTATAT-TATGT
1 TAATTTAATATGTATGT
18422864 TAAAATTTAATATGTA
1 T--AATTTAATATGTA
18422880 ATTTAGTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 13 0.50
18 9 0.35
19 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (17 bp):
TAATTTAATATGTATGT
Found at i:18424343 original size:131 final size:132
Alignment explanation
Indices: 18424091--18424374 Score: 301
Period size: 131 Copynumber: 2.2 Consensus size: 132
18424081 ATAATATGAG
* * * * *
18424091 GGTATTATAGTAAATAATTGTAAGAGAAAAAGTATTTTTATAATTATGGTATAAGAGCATAATAG
1 GGTATTATAGTAAATAATTATAAGAGAAAAAGTATTTTGATAACTATGATATAAGAGCATAATAA
* * * * * * * * *
18424156 TCAATTTGGCAATGTGTTAATTTTTTATCAAGCAATGGAAATGGTATTTTAGTAAATTCATAGGA
66 TCAATTTGGCAATATATCAATTTCTTACCAAACAATGAAAAAGGCATTTTAGTAAATTCATAGGA
18424221 GA
131 GA
* * *
18424223 GGTATTATGGTTAATAATTATAAGAG-AAATGATATTTTGATAACTATGAT-TGAAGA-CATAAT
1 GGTATTATAGTAAATAATTATAAGAGAAAAAG-TATTTTGATAACTATGATAT-AAGAGCATAAT
* * *
18424285 AATCAATTTGGCCATATATCAATTTCTTACCAAATAATGAAAAAGGCATTTT-GATAAATTCTTA
64 AATCAATTTGGCAATATATCAATTTCTTACCAAACAATGAAAAAGGCATTTTAG-TAAATTCATA
18424349 GGAGA
128 GGAGA
* *
18424354 -TTATT-TAATAAATAATTATAA
1 GGTATTATAGTAAATAATTATAA
18424375 AAAATATTGT
Statistics
Matches: 125, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
129 13 0.10
130 5 0.04
131 65 0.52
132 42 0.34
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (132 bp):
GGTATTATAGTAAATAATTATAAGAGAAAAAGTATTTTGATAACTATGATATAAGAGCATAATAA
TCAATTTGGCAATATATCAATTTCTTACCAAACAATGAAAAAGGCATTTTAGTAAATTCATAGGA
GA
Found at i:18424637 original size:24 final size:25
Alignment explanation
Indices: 18424608--18424672 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
18424598 AATGGTAATG
18424608 ATATTTTAATAATTTTTTAAAAAAT
1 ATATTTTAATAATTTTTTAAAAAAT
18424633 -TA-TTTAATAAATAATTTTTAAAAAAT
1 ATATTTTAAT-AAT--TTTTTAAAAAAT
* *
18424659 ATATATTCATAATT
1 ATATTTTAATAATT
18424673 ATAATATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
23 6 0.18
24 5 0.15
25 1 0.03
26 12 0.36
27 5 0.15
28 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTTTAATAATTTTTTAAAAAAT
Found at i:18429853 original size:17 final size:18
Alignment explanation
Indices: 18429803--18429853 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
18429793 TTTTAATTTT
*
18429803 ATATTATATTTATAAAAAA
1 ATATTATA-TTATAATAAA
* * *
18429822 ATATTATTTTTTAATATA
1 ATATTATATTATAATAAA
18429840 A-ATTATATTATAAT
1 ATATTATATTATAAT
18429854 TATATATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 11 0.42
18 8 0.31
19 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTATATTATAATAAA
Found at i:18429942 original size:24 final size:25
Alignment explanation
Indices: 18429915--18429962 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
18429905 ATAATTTTAT
* *
18429915 TAATATAATATATAATT-AAATAAA
1 TAATAAAAAATATAATTCAAATAAA
18429939 TAATAAAAAATATAATTCAAATAA
1 TAATAAAAAATATAATTCAAATAA
18429963 CTCAAGATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
TAATAAAAAATATAATTCAAATAAA
Found at i:18430981 original size:24 final size:25
Alignment explanation
Indices: 18430937--18430995 Score: 102
Period size: 24 Copynumber: 2.4 Consensus size: 25
18430927 ATCAAGCAAA
18430937 AATATCATAATAAAAATCATACAAT
1 AATATCATAATAAAAATCATACAAT
*
18430962 AATATTATAAT-AAAATCATACAAT
1 AATATCATAATAAAAATCATACAAT
18430986 AATATCATAA
1 AATATCATAA
18430996 ATCATGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 22 0.69
25 10 0.31
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (25 bp):
AATATCATAATAAAAATCATACAAT
Found at i:18430992 original size:13 final size:13
Alignment explanation
Indices: 18430898--18430994 Score: 57
Period size: 13 Copynumber: 7.8 Consensus size: 13
18430888 TATTTACAAG
*
18430898 ATAATGTCATACA
1 ATAATATCATACA
*
18430911 AAAATA-C-TATCA
1 ATAATATCATA-CA
18430923 A-AATATCA-AGCA
1 ATAATATCATA-CA
*
18430935 AAAATATCAT--A
1 ATAATATCATACA
*
18430946 ATAAAAATCATACA
1 AT-AATATCATACA
*
18430960 ATAATAT--TATA
1 ATAATATCATACA
*
18430971 ATAAAATCATACA
1 ATAATATCATACA
18430984 ATAATATCATA
1 ATAATATCATA
18430995 AATCATGCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
11 17 0.27
12 16 0.25
13 28 0.44
14 3 0.05
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (13 bp):
ATAATATCATACA
Found at i:18431014 original size:28 final size:28
Alignment explanation
Indices: 18430983--18431054 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 28
18430973 AAAATCATAC
18430983 AATAATATCATA-AATCATGCAAAAAAAA
1 AATAATATCATACAATCATGC-AAAAAAA
*
18431011 AATAATATCATCATCAATCATGCAAAAATA
1 AATAATATCAT-A-CAATCATGCAAAAAAA
18431041 AATAAT-TCATACAA
1 AATAATATCATACAA
18431055 ATAACATCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 3 0.08
28 12 0.30
29 5 0.12
30 12 0.30
31 8 0.20
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (28 bp):
AATAATATCATACAATCATGCAAAAAAA
Found at i:18431030 original size:31 final size:29
Alignment explanation
Indices: 18430989--18431050 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
18430979 ATACAATAAT
18430989 ATCATAAATCATGCAAAAAAAAAATAATATC
1 ATCATAAATCATGC-AAAAAAAAATAAT-TC
* *
18431020 ATCATCAATCATGCAAAAATAAATAATTC
1 ATCATAAATCATGCAAAAAAAAATAATTC
18431049 AT
1 AT
18431051 ACAAATAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 12 0.41
31 13 0.45
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (29 bp):
ATCATAAATCATGCAAAAAAAAATAATTC
Found at i:18431126 original size:49 final size:47
Alignment explanation
Indices: 18431027--18431137 Score: 125
Period size: 49 Copynumber: 2.3 Consensus size: 47
18431017 ATCATCATCA
* * * *
18431027 ATCATGCAAAA-ATAAATAATTCATACAAATAACATCTATATATAAC
1 ATCATGCAAAATATAAATAAATCATACAAATAAAATCTATACAAAAC
* * *
18431073 ATCATGCAAAATATAGTAATAAATCATGCAAATAAAATCTGTACAAAAT
1 ATCATGCAAAATATA--AATAAATCATACAAATAAAATCTATACAAAAC
18431122 ATCATGCAAATATATA
1 ATCATGCAAA-ATATA
18431138 TTATAATTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 11 0.20
47 3 0.06
49 35 0.65
50 5 0.09
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (47 bp):
ATCATGCAAAATATAAATAAATCATACAAATAAAATCTATACAAAAC
Found at i:18431213 original size:27 final size:27
Alignment explanation
Indices: 18431154--18431210 Score: 91
Period size: 25 Copynumber: 2.2 Consensus size: 27
18431144 TTATGCATTC
18431154 AAAAATATCATATAAATATCATGCAAA
1 AAAAATATCATATAAATATCATGCAAA
*
18431181 TAAAATATCATA-AAA-ATCATGCAAA
1 AAAAATATCATATAAATATCATGCAAA
18431206 AAAAA
1 AAAAA
18431211 AATGCAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 14 0.50
26 3 0.11
27 11 0.39
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.23
Consensus pattern (27 bp):
AAAAATATCATATAAATATCATGCAAA
Found at i:18431304 original size:17 final size:16
Alignment explanation
Indices: 18431275--18431343 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 16
18431265 ATTTTAATTC
*
18431275 AATCATAATAAAA-AA
1 AATCAAAATAAAATAA
18431290 AACTCAAACATAAAA-AA
1 AA-TCAAA-ATAAAATAA
18431307 AATCAAAATAAAATCAAA
1 AATCAAAATAAAAT--AA
18431325 AATCAAAAATAAAATAA
1 AATC-AAAATAAAATAA
18431342 AA
1 AA
18431344 AAAACCTATG
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
15 8 0.17
16 9 0.19
17 14 0.30
18 6 0.13
19 10 0.21
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (16 bp):
AATCAAAATAAAATAA
Found at i:18431307 original size:18 final size:17
Alignment explanation
Indices: 18431275--18431344 Score: 74
Period size: 16 Copynumber: 4.1 Consensus size: 17
18431265 ATTTTAATTC
*
18431275 AATCATAATAAAA-AAA
1 AATCAAAATAAAATAAA
*
18431291 ACTCAAACAT-AAA-AAA
1 AATCAAA-ATAAAATAAA
18431307 AATCAAAATAAAATCAAA
1 AATCAAAATAAAAT-AAA
18431325 AATCAAAAATAAAATAAA
1 AATC-AAAATAAAATAAA
18431343 AA
1 AA
18431345 AAACCTATGA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.04
16 20 0.43
17 2 0.04
18 12 0.26
19 10 0.22
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (17 bp):
AATCAAAATAAAATAAA
Found at i:18432107 original size:22 final size:22
Alignment explanation
Indices: 18432075--18432117 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18432065 TTACATACTT
*
18432075 TTCAAAAGTTCCCAACTTGAAA
1 TTCAAAAGTTCACAACTTGAAA
* *
18432097 TTCAAAGGTTCACAATTTGAA
1 TTCAAAAGTTCACAACTTGAA
18432118 TTTTAAGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (22 bp):
TTCAAAAGTTCACAACTTGAAA
Found at i:18432119 original size:21 final size:21
Alignment explanation
Indices: 18432075--18432150 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
18432065 TTACATACTT
* * *
18432075 TTCAAAAGTTCCCAACTTGAAA
1 TTCAAAGGTTCACAAATTG-AA
*
18432097 TTCAAAGGTTCACAATTTGAA
1 TTCAAAGGTTCACAAATTGAA
** * *
18432118 TTTTAAGGTTTA-ATAATTAAA
1 TTCAAAGGTTCACA-AATTGAA
18432139 TTCAAAGGTTCA
1 TTCAAAGGTTCA
18432151 TAAGATTTCA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 25 0.60
22 16 0.38
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (21 bp):
TTCAAAGGTTCACAAATTGAA
Found at i:18432248 original size:18 final size:18
Alignment explanation
Indices: 18432181--18432241 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
18432171 AAAAGTCAAA
*
18432181 GCAAGAATTGAAAGATTC
1 GCAAGAATTCAAAGATTC
* *
18432199 ACAAGAATTCAAA-ATTTT
1 GCAAGAATTCAAAGA-TTC
*
18432217 GCAAGATTTCAAAGATTC
1 GCAAGAATTCAAAGATTC
18432235 GCAAGAA
1 GCAAGAA
18432242 GTTAAAGGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.94
19 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (18 bp):
GCAAGAATTCAAAGATTC
Found at i:18432303 original size:37 final size:37
Alignment explanation
Indices: 18432255--18432467 Score: 173
Period size: 37 Copynumber: 5.6 Consensus size: 37
18432245 AAAGGGTTGT
* * * *
18432255 AAGATTTAAGATTCGCAAAAGATTTAAAGGTTCACAA
1 AAGATTCAAAATTCACAAAAGATTTAAAGATTCACAA
* *
18432292 AAGATTCAAGATTCACAAAAAGATTCAAAGATTCACAA
1 AAGATTCAAAATTCAC-AAAAGATTTAAAGATTCACAA
* ** * * *
18432330 AAAATTCACAAAAGATTCGTAAAAGA-TTCAATATTC-GAA
1 AAGATT--C-AAA-ATTCACAAAAGATTTAAAGATTCACAA
* *
18432369 AAGATTCAAAAGTTTACACAAGATTT-AAGATTCACAA
1 AAGATTCAAAA-TTCACAAAAGATTTAAAGATTCACAA
*
18432406 AAGATTCAAAAATTCACAAAAGATTTAAA-ATTCATAA
1 AAGATTC-AAAATTCACAAAAGATTTAAAGATTCACAA
* *
18432443 AAGATTTAAAATTTCGCAAAAGATT
1 AAGATTCAAAA-TTCACAAAAGATT
18432468 CAAAAATAAT
Statistics
Matches: 141, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
35 1 0.01
36 20 0.14
37 63 0.45
38 30 0.21
39 7 0.05
40 8 0.06
41 8 0.06
42 4 0.03
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (37 bp):
AAGATTCAAAATTCACAAAAGATTTAAAGATTCACAA
Found at i:18432359 original size:22 final size:22
Alignment explanation
Indices: 18432299--18432347 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
18432289 CAAAAGATTC
18432299 AAGATTCACAAAAAGATT--C-A
1 AAGATTCACAAAAA-ATTCACAA
18432319 AAGATTCACAAAAAATTCACAA
1 AAGATTCACAAAAAATTCACAA
18432341 AAGATTC
1 AAGATTC
18432348 GTAAAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.12
20 14 0.54
21 1 0.04
22 8 0.31
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.20
Consensus pattern (22 bp):
AAGATTCACAAAAAATTCACAA
Found at i:18432409 original size:11 final size:11
Alignment explanation
Indices: 18432395--18432430 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
18432385 CACAAGATTT
18432395 AAGATTCACAA
1 AAGATTCACAA
18432406 AAGATT--CAA
1 AAGATTCACAA
18432415 AA-ATTCACAA
1 AAGATTCACAA
18432425 AAGATT
1 AAGATT
18432431 TAAAATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.14
9 5 0.23
10 5 0.23
11 9 0.41
ACGTcount: A:0.56, C:0.14, G:0.08, T:0.22
Consensus pattern (11 bp):
AAGATTCACAA
Found at i:18432472 original size:19 final size:18
Alignment explanation
Indices: 18432255--18432472 Score: 168
Period size: 19 Copynumber: 11.6 Consensus size: 18
18432245 AAAGGGTTGT
* * *
18432255 AAGATTTAAGATTCGCAA
1 AAGATTCAAAATTCACAA
* *
18432273 AAGATTTAAAGGTTCACAA
1 AAGATTCAAA-ATTCACAA
*
18432292 AAGATTCAAGATTCACAAA
1 AAGATTCAAAATTCAC-AA
18432311 AAGATTCAAAGATTCACAA
1 AAGATTCAAA-ATTCACAA
* **
18432330 AAAATTCACAAAAGATTCGTAA
1 AAGATT--C-AAA-ATTCACAA
* *
18432352 AAGATTCAATATTC-GAA
1 AAGATTCAAAATTCACAA
* *
18432369 AAGATTCAAAAGTTTACAC
1 AAGATTCAAAA-TTCACAA
* *
18432388 AAGATTTAAGATTCACAA
1 AAGATTCAAAATTCACAA
18432406 AAGATTCAAAAATTCACAA
1 AAGATTC-AAAATTCACAA
* *
18432425 AAGATTTAAAATTCATAA
1 AAGATTCAAAATTCACAA
* *
18432443 AAGATTTAAAATTTCGCAA
1 AAGATTCAAAA-TTCACAA
18432462 AAGATTCAAAA
1 AAGATTCAAAA
18432473 ATAATTTTAA
Statistics
Matches: 162, Mismatches: 28, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
17 12 0.07
18 52 0.32
19 75 0.46
20 7 0.04
21 1 0.01
22 15 0.09
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (18 bp):
AAGATTCAAAATTCACAA
Found at i:18432548 original size:24 final size:24
Alignment explanation
Indices: 18432516--18432599 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 24
18432506 AATTCAAAAT
* *
18432516 TTCATATTCAAAAATATTTTGAGA
1 TTCACATTCAAAAATATTTAGAGA
* *
18432540 TTCACATTC-AAAAT-TTTAAATA
1 TTCACATTCAAAAATATTTAGAGA
18432562 TTCACATT-AAAAA-ATCTTAGAGA
1 TTCACATTCAAAAATAT-TTAGAGA
* *
18432585 TTCATATCCAAAAAT
1 TTCACATTCAAAAAT
18432600 TCAAAAATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
22 18 0.38
23 16 0.34
24 13 0.28
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (24 bp):
TTCACATTCAAAAATATTTAGAGA
Found at i:18432567 original size:22 final size:22
Alignment explanation
Indices: 18432539--18432700 Score: 76
Period size: 22 Copynumber: 7.2 Consensus size: 22
18432529 ATATTTTGAG
18432539 ATTCACATTCAAAATTTTAAAT
1 ATTCACATTCAAAATTTTAAAT
* * * *
18432561 ATTCACATTAAAAAATCTTAGAG
1 ATTCACATT-CAAAATTTTAAAT
* * * * *
18432584 ATTCATATCCAAAAATTCAAAA
1 ATTCACATTCAAAATTTTAAAT
** * *
18432606 ATTTTCATTTGAAAAATTTTAAAA
1 ATTCACA-TT-CAAAATTTTAAAT
18432630 ATTCACA-TCTAAAA-TTTAAAT
1 ATTCACATTC-AAAATTTTAAAT
* * ***
18432651 ATTCTCATTTTAAAATTTTAGGG
1 ATTCACA-TTCAAAATTTTAAAT
* *
18432674 ATTCACATCCAAAATTTCAAAT
1 ATTCACATTCAAAATTTTAAAT
*
18432696 TTTCA
1 ATTCA
18432701 AACTTTGTCC
Statistics
Matches: 97, Mismatches: 36, Indels: 14
0.66 0.24 0.10
Matches are distributed among these distances:
21 12 0.12
22 42 0.43
23 28 0.29
24 15 0.15
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.38
Consensus pattern (22 bp):
ATTCACATTCAAAATTTTAAAT
Found at i:18432575 original size:23 final size:22
Alignment explanation
Indices: 18432539--18432670 Score: 72
Period size: 23 Copynumber: 5.9 Consensus size: 22
18432529 ATATTTTGAG
*
18432539 ATTCACATTCAAAATTTTAAAT
1 ATTCACATTAAAAATTTTAAAT
* * *
18432561 ATTCACATTAAAAAATCTTAGAG
1 ATTCACATT-AAAAATTTTAAAT
* * **
18432584 ATTCATATCCAAAAATTCAAAAAT
1 ATTCACAT-TAAAAATT-TTAAAT
* * *
18432608 TTTCA-TTTGAAAAATTTTAAAA
1 ATTCACATT-AAAAATTTTAAAT
18432630 ATTCACATCT-AAAA-TTTAAAT
1 ATTCACAT-TAAAAATTTTAAAT
* *
18432651 ATTCTCATTTTAAAATTTTA
1 ATTCACA-TTAAAAATTTTA
18432671 GGGATTCACA
Statistics
Matches: 80, Mismatches: 21, Indels: 17
0.68 0.18 0.14
Matches are distributed among these distances:
21 13 0.16
22 25 0.31
23 35 0.44
24 7 0.09
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTCACATTAAAAATTTTAAAT
Found at i:18432585 original size:45 final size:45
Alignment explanation
Indices: 18432504--18432700 Score: 168
Period size: 45 Copynumber: 4.4 Consensus size: 45
18432494 TGAAGCTTCT
* *
18432504 AAAA-TTCAAA-ATTTCATATTCAAAAATATTTT-GAGATTCACATTC
1 AAAATTTCAAATA-TTCACATT-AAAAA-ATTTTAGAGATTCACATCC
* * *
18432549 AAAATTTTAAATATTCACATTAAAAAATCTTAGAGATTCATATCC
1 AAAATTTCAAATATTCACATTAAAAAATTTTAGAGATTCACATCC
* * ** * * * *
18432594 AAAAATTCAAAAATTTTCATTTGAAAAATTTTAAAAATTCACATCT
1 AAAATTTCAAATATTCACA-TTAAAAAATTTTAGAGATTCACATCC
* ** *
18432640 AAAATTT-AAATATTCTCATTTTAAAATTTTAGGGATTCACATCC
1 AAAATTTCAAATATTCACATTAAAAAATTTTAGAGATTCACATCC
*
18432684 AAAATTTCAAATTTTCA
1 AAAATTTCAAATATTCA
18432701 AACTTTGTCC
Statistics
Matches: 120, Mismatches: 27, Indels: 10
0.76 0.17 0.06
Matches are distributed among these distances:
44 31 0.26
45 50 0.42
46 38 0.32
47 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (45 bp):
AAAATTTCAAATATTCACATTAAAAAATTTTAGAGATTCACATCC
Found at i:18432677 original size:90 final size:92
Alignment explanation
Indices: 18432504--18432694 Score: 230
Period size: 90 Copynumber: 2.1 Consensus size: 92
18432494 TGAAGCTTCT
** *
18432504 AAAATTC-AAAATTTCATATTCAAAAATATTTTGAGATTCACATTCAAAATTTTAAATATTCACA
1 AAAATTCAAAAATTTCATATTCAAAAATATTTAAAAATTCACATTCAAAATTTTAAATATTCACA
*
18432568 TTAAAAAATCTTAGAGATTCATATCCA
66 TTAAAAAATCTTAGAGATTCACATCCA
* *
18432595 AAAATTCAAAAATTTTCAT-TTGAAAAAT-TTTAAAAATTCACA-TCTAAAA-TTTAAATATTCT
1 AAAATTCAAAAA-TTTCATATTCAAAAATATTTAAAAATTCACATTC-AAAATTTTAAATATTCA
** * *
18432656 CATTTTAAAATTTTAGGGATTCACATCCA
64 CATTAAAAAATCTTAGAGATTCACATCCA
*
18432685 AAATTTCAAA
1 AAAATTCAAA
18432695 TTTTCAAACT
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
90 46 0.53
91 22 0.26
92 12 0.14
93 6 0.07
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (92 bp):
AAAATTCAAAAATTTCATATTCAAAAATATTTAAAAATTCACATTCAAAATTTTAAATATTCACA
TTAAAAAATCTTAGAGATTCACATCCA
Found at i:18433985 original size:20 final size:21
Alignment explanation
Indices: 18433962--18434000 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18433952 AGGTTTTTTG
18433962 TTTCCATTACTTTT-TTTTAT
1 TTTCCATTACTTTTCTTTTAT
* *
18433982 TTTCCTTTCCTTTTCTTTT
1 TTTCCATTACTTTTCTTTT
18434001 CCTCTTCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTCCATTACTTTTCTTTTAT
Found at i:18437003 original size:44 final size:45
Alignment explanation
Indices: 18436948--18437066 Score: 134
Period size: 45 Copynumber: 2.7 Consensus size: 45
18436938 ATGCCAATCC
* * * * *
18436948 AAATAATCAAATAAATTAGTGCACAT-GAAAAGTCGA-AATCTACA
1 AAATAAACAAATAAATTAGTGCACATAAAAAAATC-ATAAGCTAAA
18436992 AAATAAACAAATAAATTAGTGCACATAAAAAAATCATAAGCTAAA
1 AAATAAACAAATAAATTAGTGCACATAAAAAAATCATAAGCTAAA
*** *
18437037 AAATAAACAAATGGGTTAATGCACATAAAA
1 AAATAAACAAATAAATTAGTGCACATAAAA
18437067 TCATAAATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 26 0.41
45 38 0.59
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.21
Consensus pattern (45 bp):
AAATAAACAAATAAATTAGTGCACATAAAAAAATCATAAGCTAAA
Found at i:18437725 original size:23 final size:24
Alignment explanation
Indices: 18437695--18437753 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
18437685 TAGAACATGC
18437695 AATCATGCAAA-TATCATAATAAA
1 AATCATGCAAAGTATCATAATAAA
*
18437718 AATCATGCTAAAGTATTATAATAAA
1 AATCATGC-AAAGTATCATAATAAA
* *
18437743 AACCATACAAA
1 AATCATGCAAA
18437754 AAATCATGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.26
24 6 0.19
25 17 0.55
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (24 bp):
AATCATGCAAAGTATCATAATAAA
Found at i:18437892 original size:31 final size:35
Alignment explanation
Indices: 18437857--18437922 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
18437847 TTTGTAATAC
18437857 ATCATGC-AA-ATAAATTA-AA-TTCATGCAAAAT
1 ATCATGCAAATATAAATTATAAGTTCATGCAAAAT
18437888 ATCATGCAAATATAAATTATAAGTTTCATGCAAAA
1 ATCATGCAAATATAAATTATAAG-TTCATGCAAAA
18437923 ATATTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 7 0.23
32 2 0.07
33 8 0.27
34 2 0.07
36 11 0.37
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (35 bp):
ATCATGCAAATATAAATTATAAGTTCATGCAAAAT
Found at i:18437954 original size:24 final size:24
Alignment explanation
Indices: 18437884--18437977 Score: 59
Period size: 24 Copynumber: 3.9 Consensus size: 24
18437874 AATTCATGCA
* *
18437884 AAATATCATGCAAATATAAAT-TAT
1 AAATATTATGCAAA-ATACATATAT
* *
18437908 AAGT-TTCATGCAAAAATA-TTATAT
1 AAATATT-ATGC-AAAATACATATAT
*
18437932 AAATATTATGCAAAATACATATAA
1 AAATATTATGCAAAATACATATAT
* * *
18437956 AAAAATAATGCCAAATATCATA
1 AAATATTATGCAAAATA-CATA
18437978 AAAAATGTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
23 8 0.15
24 38 0.69
25 9 0.16
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (24 bp):
AAATATTATGCAAAATACATATAT
Found at i:18438081 original size:14 final size:13
Alignment explanation
Indices: 18438062--18438137 Score: 71
Period size: 14 Copynumber: 5.3 Consensus size: 13
18438052 AATCACTATT
18438062 AAAAATAAAATATAA
1 AAAAATAAAA-AT-A
18438077 AAAATATAAAAAATCA
1 AAAA-AT-AAAAAT-A
*
18438093 AAAAATCAAAATCA
1 AAAAATAAAAAT-A
*
18438107 AAAAATAAAAAAA
1 AAAAATAAAAATA
18438120 TAAAAATAAAAATA
1 -AAAAATAAAAATA
18438134 AAAA
1 AAAA
18438138 CCTGCTATCT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
13 5 0.09
14 29 0.55
15 6 0.11
16 9 0.17
17 4 0.08
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:18438087 original size:8 final size:8
Alignment explanation
Indices: 18438068--18438131 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 8
18438058 TATTAAAAAT
18438068 AAAATATAA
1 AAAATAT-A
18438077 AAAATATA
1 AAAATATA
18438085 AAAA-ATCA
1 AAAATAT-A
*
18438093 AAAA-ATC
1 AAAATATA
18438100 AAAATCA-A
1 AAAAT-ATA
18438108 AAAATA-A
1 AAAATATA
18438115 AAAA-ATA
1 AAAATATA
18438122 AAAATA-A
1 AAAATATA
18438129 AAA
1 AAA
18438132 TAAAAACCTG
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
6 1 0.02
7 21 0.44
8 18 0.38
9 8 0.17
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAATATA
Found at i:18438116 original size:6 final size:6
Alignment explanation
Indices: 18438061--18438137 Score: 54
Period size: 6 Copynumber: 13.0 Consensus size: 6
18438051 CAATCACTAT
* * * *
18438061 TAAAAA T-AAAA TATAAA -AAATA TAAAAAA TCAAAAAA TCAAAA TCAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA T-AAAAA T--AAAAA TAAAAA TAAAAA
*
18438110 -AATAA -AAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
18438138 CCTGCTATCT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
5 15 0.26
6 31 0.53
7 5 0.09
8 7 0.12
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:18439870 original size:62 final size:61
Alignment explanation
Indices: 18439784--18439953 Score: 198
Period size: 61 Copynumber: 2.8 Consensus size: 61
18439774 TTTACTAATA
* * * *
18439784 GTTGACTATTGGTGGCATCGGTATAGACTAAAATATTCTAACAAAAAAAGTTTTTACCAACG
1 GTTGACTATTGGTGGCATCAGTATAGCCTAAAATATTCCAACAAAAAAAG-GTTTACCAACG
* ** * *
18439846 GTTGACTATTGGTGGCATCAGTATAGCCTAAAATATTCCAATAAAATGAGGTTTACTAATG
1 GTTGACTATTGGTGGCATCAGTATAGCCTAAAATATTCCAACAAAAAAAGGTTTACCAACG
* ** *
18439907 GTTGA-TGATTAGTGGTGTCAATATAGCCTAAAATATTCCAACAAAAA
1 GTTGACT-ATTGGTGGCATCAGTATAGCCTAAAATATTCCAACAAAAA
18439954 CGGGCATCAG
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
60 1 0.01
61 47 0.51
62 44 0.48
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (61 bp):
GTTGACTATTGGTGGCATCAGTATAGCCTAAAATATTCCAACAAAAAAAGGTTTACCAACG
Found at i:18441099 original size:19 final size:19
Alignment explanation
Indices: 18441075--18441112 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18441065 TGTTAGAAAA
18441075 TTATCTTTGAAGTAATGAC
1 TTATCTTTGAAGTAATGAC
18441094 TTATCTTTGAAGTAATGAC
1 TTATCTTTGAAGTAATGAC
18441113 AAGATGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
TTATCTTTGAAGTAATGAC
Found at i:18441494 original size:11 final size:11
Alignment explanation
Indices: 18441477--18441510 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18441467 TTCTATTTTT
18441477 ACGTGTACAAG
1 ACGTGTACAAG
*
18441488 GCGTGTACAAG
1 ACGTGTACAAG
*
18441499 ATGTGTACAAG
1 ACGTGTACAAG
18441510 A
1 A
18441511 AAAAATATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (11 bp):
ACGTGTACAAG
Found at i:18446268 original size:3 final size:3
Alignment explanation
Indices: 18446262--18446297 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
18446252 GTAGTAGTAG
18446262 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18446298 AAGGGAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18449837 original size:19 final size:19
Alignment explanation
Indices: 18449802--18449838 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18449792 ACGTTACACT
*
18449802 CTTAAAATGATAGAGAAGG
1 CTTAAAATGATAAAGAAGG
*
18449821 CTTAAAATGGTAAAGAAG
1 CTTAAAATGATAAAGAAG
18449839 AGATATTGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (19 bp):
CTTAAAATGATAAAGAAGG
Found at i:18454865 original size:31 final size:29
Alignment explanation
Indices: 18454823--18454893 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
18454813 GCTTGAGAAG
18454823 AAAGAAAAAAACAAAACTAAAGAAAAAATAA
1 AAAGAAAAAAACAAAAC-AAA-AAAAAATAA
* * * *
18454854 TAATAAAAAAACATAACAAAACAAAATAA
1 AAAGAAAAAAACAAAACAAAAAAAAATAA
18454883 AAAGAAAAAAA
1 AAAGAAAAAAA
18454894 TGAAAGAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.50
30 3 0.09
31 14 0.41
ACGTcount: A:0.80, C:0.07, G:0.04, T:0.08
Consensus pattern (29 bp):
AAAGAAAAAAACAAAACAAAAAAAAATAA
Found at i:18455913 original size:41 final size:41
Alignment explanation
Indices: 18455866--18455945 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
18455856 GATTTCAAAG
18455866 TTTC-AAAGCCTCTATTTAAGGAGAACCATTTTCAAACAAGA
1 TTTCAAAAGCCTCTATTT-AGGAGAACCATTTTCAAACAAGA
* * *
18455907 TTTCAAAAGCCTCTATTTAGGAGGAGCTTTTTCAAACAA
1 TTTCAAAAGCCTCTATTTAGGAGAACCATTTTCAAACAA
18455946 AACCTTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 22 0.63
42 13 0.37
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (41 bp):
TTTCAAAAGCCTCTATTTAGGAGAACCATTTTCAAACAAGA
Found at i:18456118 original size:96 final size:97
Alignment explanation
Indices: 18456001--18456237 Score: 308
Period size: 96 Copynumber: 2.5 Consensus size: 97
18455991 AAATAAAAAC
* * *
18456001 TTTT-AAAGTTTTAATGCCTCTATTACGAGGAGCATTCAAAGATTTTTAAGACCTCTAGGCATAA
1 TTTTCAAAGTTTCAATGCCTCTATTACGAGGAGAATTCAAAGATTTTTAAGACCTATAGGCATAA
* * * *
18456065 TTTTCAAGACCT-TCGAGCAAAATA-TTTTAAA
66 CTTCCAAGACCTATAG-GCAAAACATTTTTAAA
* * *
18456096 TTTTTGAAA-TTTCAATGCCTCTATTACGAGGAGTATTCAAAGATTTTTAAGACCTATGGGCATA
1 -TTTTCAAAGTTTCAATGCCTCTATTACGAGGAGAATTCAAAGATTTTTAAGACCTATAGGCATA
18456160 ACTTCCAAGACCTATAGGCAAAACATTTTTAAA
65 ACTTCCAAGACCTATAGGCAAAACATTTTTAAA
*
18456193 TTTTCAAAGTTTCAA--CCTCTA-TACAAGGAGAATTCAAAGATTTTT
1 TTTTCAAAGTTTCAATGCCTCTATTACGAGGAGAATTCAAAGATTTTT
18456238 TAGATTCATA
Statistics
Matches: 126, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
94 22 0.17
95 6 0.05
96 80 0.63
97 18 0.14
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (97 bp):
TTTTCAAAGTTTCAATGCCTCTATTACGAGGAGAATTCAAAGATTTTTAAGACCTATAGGCATAA
CTTCCAAGACCTATAGGCAAAACATTTTTAAA
Found at i:18456377 original size:127 final size:125
Alignment explanation
Indices: 18456155--18456403 Score: 329
Period size: 127 Copynumber: 2.0 Consensus size: 125
18456145 AGACCTATGG
*
18456155 GCATAACTTCCAAGACCTATAGGCAAAACATTTTTAAATTTTCAAAGTTTCAACCTCTATACAAG
1 GCATAACTTCCAAAACCTATAGGCAAAACATTTTTAAATTTTCAAAGTTTCAACCTCTATACAAG
* *
18456220 GAGAATTCAAAGATTTTTTAGATTCATAAGACCTTTGGGCATAATCTTTAAAACCTCCAA
66 GAGAATTCAAAGAGTTTTTAGATTCATAAGACCTTTGGGCACAATCTTTAAAACCTCCAA
* * * * *
18456280 GCATAATTTTCAAAACCTCTAGGCAAAACA-TTTTAAATTTTTAAAGTTTCAACACCTCTATTAT
1 GCATAACTTCCAAAACCTATAGGCAAAACATTTTTAAATTTTCAAAGTTTC-A-ACCTCTA-TAC
* * ** ** *
18456344 GAGGAGCATTCAAAGAGTTTTTAGATTTTTAAGACCTTTGGGTGCAATCTTTAAGACCTC
63 AAGGAGAATTCAAAGAGTTTTTAGATTCATAAGACCTTTGGGCACAATCTTTAAAACCTC
18456404 TGGGCAAACC
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
124 19 0.18
125 27 0.25
126 7 0.07
127 53 0.50
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (125 bp):
GCATAACTTCCAAAACCTATAGGCAAAACATTTTTAAATTTTCAAAGTTTCAACCTCTATACAAG
GAGAATTCAAAGAGTTTTTAGATTCATAAGACCTTTGGGCACAATCTTTAAAACCTCCAA
Found at i:18456660 original size:17 final size:15
Alignment explanation
Indices: 18456631--18456675 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
18456621 TTATTAATTC
18456631 ACAAAAAAAAAATCA
1 ACAAAAAAAAAATCA
18456646 ACAAAAAAATCAAATCA
1 ACAAAAAAA--AAATCA
*
18456663 AGAAAAAATAAAA
1 ACAAAAAA-AAAA
18456676 AAAAAATCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 13 0.50
18 1 0.04
ACGTcount: A:0.78, C:0.11, G:0.02, T:0.09
Consensus pattern (15 bp):
ACAAAAAAAAAATCA
Found at i:18458209 original size:21 final size:21
Alignment explanation
Indices: 18458185--18458225 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18458175 TATTTACTTA
*
18458185 TTATTTTAATTTAGTTTCATG
1 TTATTTTAATATAGTTTCATG
*
18458206 TTATTTTACTATAGTTTCAT
1 TTATTTTAATATAGTTTCAT
18458226 TATAGTTTAG
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:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (21 bp):
TTATTTTAATATAGTTTCATG
Found at i:18463402 original size:3 final size:3
Alignment explanation
Indices: 18463394--18463418 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18463384 TCCAAAGAAA
18463394 AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT A
18463419 ATAATAATAA
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:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:18463423 original size:3 final size:3
Alignment explanation
Indices: 18463417--18463485 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
18463407 GTAGTAGTAG
18463417 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18463465 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
18463486 AGTAAAAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18464557 original size:19 final size:18
Alignment explanation
Indices: 18464533--18464594 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
18464523 AGCCAAACAA
18464533 TAAACAATTATATGTAATC
1 TAAACAATTATAT-TAATC
18464552 TAAAC-A--ATA-T-A--
1 TAAACAATTATATTAATC
18464563 TAAACAATTATATATAATC
1 TAAACAATTATAT-TAATC
18464582 TAAACAATTATAT
1 TAAACAATTATAT
18464595 AAAACTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
11 5 0.14
12 1 0.03
13 1 0.03
14 4 0.11
16 4 0.11
17 1 0.03
18 1 0.03
19 18 0.51
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (18 bp):
TAAACAATTATATTAATC
Found at i:18464566 original size:30 final size:31
Alignment explanation
Indices: 18464532--18464597 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
18464522 AAGCCAAACA
*
18464532 ATAAACAATTATATGTAATCTAAACAA-TAT
1 ATAAACAATTATATATAATCTAAACAATTAT
18464562 ATAAACAATTATATATAATCTAAACAATTAT
1 ATAAACAATTATATATAATCTAAACAATTAT
18464593 ATAAA
1 ATAAA
18464598 ACTTATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (31 bp):
ATAAACAATTATATATAATCTAAACAATTAT
Found at i:18465676 original size:3 final size:3
Alignment explanation
Indices: 18465670--18465705 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
18465660 TCATTTTATT
*
18465670 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
18465706 CAAATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:18468005 original size:17 final size:18
Alignment explanation
Indices: 18467985--18468023 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
18467975 TAAAAATGAA
18467985 TTTTTA-GAAAAAGAAAT
1 TTTTTATGAAAAAGAAAT
18468002 TTTTTATTTGAAAAAGAAAT
1 TTTTTA--TGAAAAAGAAAT
18468022 TT
1 TT
18468024 GATGAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
20 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTTTATGAAAAAGAAAT
Found at i:18470711 original size:16 final size:16
Alignment explanation
Indices: 18470690--18470720 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18470680 TCTTGATAAC
*
18470690 ATATCTTTAACAATTG
1 ATATCTATAACAATTG
18470706 ATATCTATAACAATT
1 ATATCTATAACAATT
18470721 AGTATAAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (16 bp):
ATATCTATAACAATTG
Found at i:18471329 original size:37 final size:38
Alignment explanation
Indices: 18471259--18471330 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
18471249 GTTGTGTTGA
*
18471259 ATTAGGATGCATAAATTGAGGGGGAGTTTTGCCATAGG
1 ATTAGGATGCACAAATTGAGGGGGAGTTTTGCCATAGG
18471297 ATTAGGATGCACAAATTGA-GGGGAGTTTTGCCAT
1 ATTAGGATGCACAAATTGAGGGGGAGTTTTGCCAT
18471331 GCATTGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (38 bp):
ATTAGGATGCACAAATTGAGGGGGAGTTTTGCCATAGG
Found at i:18472270 original size:21 final size:21
Alignment explanation
Indices: 18472224--18472297 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
18472214 TTTTCCAGAA
*
18472224 AAGGGATCGATCCCCTA-CGT
1 AAGGGATCGATCCCCTATCGC
* *
18472244 AAGGGATCGATCACCTATGGC
1 AAGGGATCGATCCCCTATCGC
* **
18472265 AAGGGATCGATCCCCTCTTTC
1 AAGGGATCGATCCCCTATCGC
18472286 AAGGGATCGATC
1 AAGGGATCGATC
18472298 GGTTGTTCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.22
Consensus pattern (21 bp):
AAGGGATCGATCCCCTATCGC
Found at i:18474138 original size:3 final size:3
Alignment explanation
Indices: 18474132--18474158 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18474122 GTAGTAGTAG
18474132 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
18474159 AGTAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18475228 original size:19 final size:18
Alignment explanation
Indices: 18475204--18475265 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
18475194 AGCCAAACAA
18475204 TAAACAATTATATGTAATC
1 TAAACAATTATAT-TAATC
18475223 TAAAC-A--ATA-T-A--
1 TAAACAATTATATTAATC
18475234 TAAACAATTATATATAATC
1 TAAACAATTATAT-TAATC
18475253 TAAACAATTATAT
1 TAAACAATTATAT
18475266 AAAACTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
11 5 0.14
12 1 0.03
13 1 0.03
14 4 0.11
16 4 0.11
17 1 0.03
18 1 0.03
19 18 0.51
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (18 bp):
TAAACAATTATATTAATC
Found at i:18475237 original size:30 final size:31
Alignment explanation
Indices: 18475203--18475268 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
18475193 AAGCCAAACA
*
18475203 ATAAACAATTATATGTAATCTAAACAA-TAT
1 ATAAACAATTATATATAATCTAAACAATTAT
18475233 ATAAACAATTATATATAATCTAAACAATTAT
1 ATAAACAATTATATATAATCTAAACAATTAT
18475264 ATAAA
1 ATAAA
18475269 ACTTATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (31 bp):
ATAAACAATTATATATAATCTAAACAATTAT
Found at i:18476348 original size:3 final size:3
Alignment explanation
Indices: 18476342--18476377 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
18476332 TCATTTTATT
*
18476342 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
18476378 CAAATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:18478692 original size:17 final size:18
Alignment explanation
Indices: 18478672--18478710 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
18478662 TAAAAATGAA
18478672 TTTTTA-GAAAAAGAAAT
1 TTTTTATGAAAAAGAAAT
18478689 TTTTTATTTGAAAAAGAAAT
1 TTTTTA--TGAAAAAGAAAT
18478709 TT
1 TT
18478711 GATGAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
20 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTTTATGAAAAAGAAAT
Found at i:18482015 original size:37 final size:38
Alignment explanation
Indices: 18481941--18482016 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 38
18481931 TTAAGTTGTG
18481941 TTGGATTAGGATGCCTAAATTGAGGGGGAGTTTTGCCA
1 TTGGATTAGGATGCCTAAATTGAGGGGGAGTTTTGCCA
18481979 TTGGATTAGGATGCAC-AAATTGA-GGGGAGTTTTGCCA
1 TTGGATTAGGATGC-CTAAATTGAGGGGGAGTTTTGCCA
18482016 T
1 T
18482017 GCATTGATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
37 15 0.41
38 21 0.57
39 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.33, T:0.32
Consensus pattern (38 bp):
TTGGATTAGGATGCCTAAATTGAGGGGGAGTTTTGCCA
Found at i:18482962 original size:21 final size:21
Alignment explanation
Indices: 18482916--18482989 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
18482906 TTTTCCAGAA
*
18482916 AAGGGATCGATCCCCTA-CGT
1 AAGGGATCGATCCCCTATCGC
* *
18482936 AAGGGATCGATCACCTATGGC
1 AAGGGATCGATCCCCTATCGC
* **
18482957 AAGGGATCGATCCCCTCTTTC
1 AAGGGATCGATCCCCTATCGC
18482978 AAGGGATCGATC
1 AAGGGATCGATC
18482990 GGTTGTTCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.22
Consensus pattern (21 bp):
AAGGGATCGATCCCCTATCGC
Found at i:18483179 original size:111 final size:111
Alignment explanation
Indices: 18483040--18483265 Score: 418
Period size: 111 Copynumber: 2.0 Consensus size: 111
18483030 AAAAGGGATC
18483040 GATCACCTAAAGAGCAAATCAATCCCCTCAAGCAAGGGATCAATCGGGTAAGGCTTTTTGTGCAT
1 GATCACCTAAAGAGCAAATCAATCCCCTCAAGCAAGGGATCAATCGGGTAAGGCTTTTTGTGCAT
*
18483105 AATTTCTGGGTGTCTCAAAGCTGAATCAATCGATCCCTTGCTTG-AG
66 AATTTCTAGGTGTCTCAAA-CTGAATCAATCGATCCCTTGCTTGAAG
*
18483151 GATCACCTAAAGAGCAAATCAATCCCCTCAAGTAAGGGATCAATCGGGTAAGGCTTTTTGTGCAT
1 GATCACCTAAAGAGCAAATCAATCCCCTCAAGCAAGGGATCAATCGGGTAAGGCTTTTTGTGCAT
18483216 AATTTCTAGGTGTCTCAAACTGAATCAATCGATCCCTTGCTTGAAG
66 AATTTCTAGGTGTCTCAAACTGAATCAATCGATCCCTTGCTTGAAG
18483262 GATC
1 GATC
18483266 GATCTATTCT
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
110 24 0.21
111 88 0.79
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (111 bp):
GATCACCTAAAGAGCAAATCAATCCCCTCAAGCAAGGGATCAATCGGGTAAGGCTTTTTGTGCAT
AATTTCTAGGTGTCTCAAACTGAATCAATCGATCCCTTGCTTGAAG
Found at i:18483422 original size:20 final size:21
Alignment explanation
Indices: 18483357--18483430 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
18483347 TTGAACAACC
* *
18483357 GATCGATCCCTTGAAAGAGGG
1 GATCGATCCCTTGACATAGGG
* *
18483378 GATCGATCCCTTGCCATAGGT
1 GATCGATCCCTTGACATAGGG
*
18483399 GATCGATCCCTT-ACGTAGGG
1 GATCGATCCCTTGACATAGGG
18483419 GATCGATCCCTT
1 GATCGATCCCTT
18483431 TTCTGGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.22, C:0.26, G:0.27, T:0.26
Consensus pattern (21 bp):
GATCGATCCCTTGACATAGGG
Found at i:18490792 original size:2 final size:2
Alignment explanation
Indices: 18490785--18490822 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18490775 AACCTGTTGG
18490785 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
18490823 TGTGATCTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18491092 original size:22 final size:22
Alignment explanation
Indices: 18491057--18491101 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
18491047 CCTAAGATTA
*
18491057 AAAAAAATAAAAAATAAAAAGG
1 AAAAAAATAAAAAAAAAAAAGG
* *
18491079 AAAAAACTACAAAAAAAAAAGG
1 AAAAAAATAAAAAAAAAAAAGG
18491101 A
1 A
18491102 GCAAATTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07
Consensus pattern (22 bp):
AAAAAAATAAAAAAAAAAAAGG
Found at i:18491156 original size:18 final size:18
Alignment explanation
Indices: 18491129--18491167 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
18491119 AATATAAATG
*
18491129 TTATAGAAATTTACTATT
1 TTATAGAAATTTACTACT
*
18491147 TTATATAAATTTACTACT
1 TTATAGAAATTTACTACT
18491165 TTA
1 TTA
18491168 CTACATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATAGAAATTTACTACT
Found at i:18491484 original size:14 final size:13
Alignment explanation
Indices: 18491449--18491487 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
18491439 AGATTTTTGG
18491449 TATATAGTAAAAA
1 TATATAGTAAAAA
*
18491462 CAT-TAGTAAGAAA
1 TATATAGTAA-AAA
18491475 TATATAGTAAAAA
1 TATATAGTAAAAA
18491488 ATTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 6 0.27
13 10 0.45
14 6 0.27
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (13 bp):
TATATAGTAAAAA
Found at i:18491489 original size:14 final size:14
Alignment explanation
Indices: 18491449--18491489 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
18491439 AGATTTTTGG
18491449 TATATAGT-AAAAA
1 TATATAGTAAAAAA
* *
18491462 CAT-TAGTAAGAAA
1 TATATAGTAAAAAA
18491475 TATATAGTAAAAAA
1 TATATAGTAAAAAA
18491489 T
1 T
18491490 TAAAATAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 4 0.18
13 8 0.36
14 10 0.45
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (14 bp):
TATATAGTAAAAAA
Found at i:18492814 original size:14 final size:14
Alignment explanation
Indices: 18492763--18492815 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
18492753 GAATTTTAAA
*
18492763 AAATTTTAAAAATT
1 AAATTATAAAAATT
* *
18492777 ACATTATATAAATT
1 AAATTATAAAAATT
*
18492791 AAATTA-AAAAATC
1 AAATTATAAAAATT
18492804 AAATTATAAAAA
1 AAATTATAAAAA
18492816 GTAAGATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATTATAAAAATT
Found at i:18495903 original size:22 final size:23
Alignment explanation
Indices: 18495875--18495955 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 23
18495865 CTTAATTTTT
18495875 ATTATT-ATTTAAACATTTTTGG
1 ATTATTAATTTAAACATTTTTGG
*
18495897 ATTATTAATTTATTACTTAATTTTT--
1 ATTATTAATTTA-AAC---ATTTTTGG
18495922 ATTATT-ATTTAAACATTTTTGG
1 ATTATTAATTTAAACATTTTTGG
18495944 ATTATTAATTTA
1 ATTATTAATTTA
18495956 TTATTATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
20 6 0.12
22 12 0.24
23 12 0.24
24 7 0.14
25 6 0.12
27 6 0.12
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (23 bp):
ATTATTAATTTAAACATTTTTGG
Found at i:18495932 original size:47 final size:47
Alignment explanation
Indices: 18495863--18495958 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
18495853 GGCATGATGA
18495863 TACTTAATTTTTATTATTATTTAAACATTTTTGGATTATTAATTTAT
1 TACTTAATTTTTATTATTATTTAAACATTTTTGGATTATTAATTTAT
18495910 TACTTAATTTTTATTATTATTTAAACATTTTTGGATTATTAATTTAT
1 TACTTAATTTTTATTATTATTTAAACATTTTTGGATTATTAATTTAT
18495957 TA
1 TA
18495959 TTATTATTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (47 bp):
TACTTAATTTTTATTATTATTTAAACATTTTTGGATTATTAATTTAT
Found at i:18505276 original size:12 final size:13
Alignment explanation
Indices: 18505261--18505297 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
18505251 ATATATATAT
18505261 ATGTATGTATG-G
1 ATGTATGTATGTG
18505273 ATGTATGTATGTG
1 ATGTATGTATGTG
*
18505286 -TGTATGTGTGTG
1 ATGTATGTATGTG
18505298 TGTGTGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 22 0.96
13 1 0.04
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (13 bp):
ATGTATGTATGTG
Done.