Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007914.1 Hibiscus syriacus cultivar Beakdansim tig00110317_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: 500553
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:1398 original size:7 final size:7
Alignment explanation
Indices: 1386--1411 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1376 AACCAGGCGT
1386 TTTCAAA
1 TTTCAAA
1393 TTTCAAA
1 TTTCAAA
1400 TTTCAAA
1 TTTCAAA
1407 TTTCA
1 TTTCA
1412 GGCGATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTCAAA
Found at i:13485 original size:15 final size:15
Alignment explanation
Indices: 13465--13510 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
13455 ACTTTTCTTC
13465 TTCTTTCT-TTCTCT
1 TTCTTTCTCTTCTCT
13479 TTACTTT-TCTTCTCT
1 TT-CTTTCTCTTCTCT
*
13494 TTCTTTCTCTTCACT
1 TTCTTTCTCTTCTCT
13509 TT
1 TT
13511 TCTTCATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.25
15 21 0.75
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCTTTCTCTTCTCT
Found at i:13500 original size:25 final size:26
Alignment explanation
Indices: 13444--13515 Score: 119
Period size: 25 Copynumber: 2.8 Consensus size: 26
13434 CCATTCCCCA
*
13444 TCTTTTTCTTCACTTTTCTTCTTCTT
1 TCTTTCTCTTCACTTTTCTTCTTCTT
*
13470 TCTTTCTCTTTACTTTTCTTC-TCTT
1 TCTTTCTCTTCACTTTTCTTCTTCTT
13495 TCTTTCTCTTCACTTTTCTTC
1 TCTTTCTCTTCACTTTTCTTC
13516 ATTGTTCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
25 24 0.56
26 19 0.44
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (26 bp):
TCTTTCTCTTCACTTTTCTTCTTCTT
Found at i:14482 original size:23 final size:22
Alignment explanation
Indices: 14447--14515 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
14437 CACCACAGCT
*
14447 CGTATAATTGCACATAAGTGCCA
1 CGTAGAATTGCACAT-AGTGCCA
* ** *
14470 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCA-CATAGTGCCA
14493 CGTAGAATTGCACCATAGTGCCA
1 CGTAGAATTGCA-CATAGTGCCA
14516 TATAATAATG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
CGTAGAATTGCACATAGTGCCA
Found at i:14652 original size:103 final size:103
Alignment explanation
Indices: 14531--14748 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
14521 TAATGTCCAT
* * *
14531 AAGGACCACATATTATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
*
14596 GACCTCACACATGTTCCAAAGAATGCATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
14634 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
*
14699 TACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
14737 AAGGACCACATA
1 AAGGACCACATA
14749 GACCCTCTAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:15493 original size:13 final size:13
Alignment explanation
Indices: 15475--15501 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15465 GAATAATAGT
15475 ATGTTTACCTTAG
1 ATGTTTACCTTAG
15488 ATGTTTACCTTAG
1 ATGTTTACCTTAG
15501 A
1 A
15502 AATTGGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (13 bp):
ATGTTTACCTTAG
Found at i:16629 original size:25 final size:24
Alignment explanation
Indices: 16587--16647 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
16577 GCATTGTTTA
16587 TATTTTAATTTTAAATATTTTTTT
1 TATTTTAATTTTAAATATTTTTTT
* *
16611 TATTTTTATTTTATGATATTTTTAATT
1 TATTTTAATTTTA-AATATTTTT--TT
*
16638 TAGTTTAATT
1 TATTTTAATT
16648 AATTTTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.40
25 8 0.27
27 10 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (24 bp):
TATTTTAATTTTAAATATTTTTTT
Found at i:18205 original size:45 final size:46
Alignment explanation
Indices: 18155--18280 Score: 193
Period size: 45 Copynumber: 2.8 Consensus size: 46
18145 AATAAATGCT
18155 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTC-GAACAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCTGAACAAGCA
*
18200 TGCGAACTAGATATCATGCGGTTAGGTTTA-TTTTCTGAATAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCTGAACAAGCA
* * *
18245 TGCGAATTAGATATCATGAGGTTAGGATTTCTTTTT
1 TGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT
18281 GTGGATAACA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
44 5 0.07
45 62 0.84
46 3 0.04
47 4 0.05
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (46 bp):
TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCTGAACAAGCA
Found at i:27947 original size:8 final size:8
Alignment explanation
Indices: 27936--27973 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
27926 AAATAAAAGA
27936 GAAAAAAT
1 GAAAAAAT
27944 GAAAAAAT
1 GAAAAAAT
*
27952 GAGAAAAAA
1 GA-AAAAAT
27961 G-AAAAAT
1 GAAAAAAT
27968 GAAAAA
1 GAAAAA
27974 TGATGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 14 0.54
9 6 0.23
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:27957 original size:18 final size:16
Alignment explanation
Indices: 27930--27966 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
27920 AAGAAGAAAT
27930 AAAAGAGAAAAAATGAA
1 AAAAGAGAAAAAA-GAA
27947 AAAATGAGAAAAAAGAA
1 AAAA-GAGAAAAAAGAA
27964 AAA
1 AAA
27967 TGAAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAGAGAAAAAAGAA
Found at i:27970 original size:24 final size:25
Alignment explanation
Indices: 27938--27995 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
27928 ATAAAAGAGA
*
27938 AAAAATGAAAAAATGA-GAAAAAAG
1 AAAAATGAAAAAATGAGGAAAAAAC
27962 AAAAATG-AAAAATGATGGAAAAAAC
1 AAAAATGAAAAAATGA-GGAAAAAAC
27987 AAAAA-GAAA
1 AAAAATGAAA
27996 GAAAAAGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.27
24 8 0.27
25 14 0.47
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.09
Consensus pattern (25 bp):
AAAAATGAAAAAATGAGGAAAAAAC
Found at i:28017 original size:18 final size:18
Alignment explanation
Indices: 27930--28028 Score: 52
Period size: 18 Copynumber: 5.7 Consensus size: 18
27920 AAGAAGAAAT
*
27930 AAAAG-AGAAAAAATGAA
1 AAAAGAAGAAAAAATGGA
27947 AAAATG-AGAAAAAA--GA
1 AAAA-GAAGAAAAAATGGA
**
27963 AAAATGAA-AAATGATGGA
1 AAAA-GAAGAAAAAATGGA
*
27981 AAAA-ACA-AAAAGAA-AGA
1 AAAAGA-AGAAAA-AATGGA
27998 AAAAGAAGAAAAAATGGA
1 AAAAGAAGAAAAAATGGA
*
28016 AAAGGGAAGAAAA
1 AAA-AGAAGAAAA
28029 CGTATGTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
16 12 0.19
17 18 0.28
18 26 0.41
19 8 0.12
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (18 bp):
AAAAGAAGAAAAAATGGA
Found at i:29717 original size:159 final size:159
Alignment explanation
Indices: 29389--29860 Score: 720
Period size: 159 Copynumber: 3.0 Consensus size: 159
29379 TTGAGTCCTA
** * *
29389 TACTCTCTGA-AGGAATAGAGAGCGGACAAGTTCGTTGAA----GATTGAGTCCTATACTCTCTG
1 TACTCTCTGATA-GAATAGAGAGCGGACCCGTTCGTTGAAGTTTGTTTGAGTCC--TGCTCTCTG
* * * * * * *
29449 AAGGAATAGGGAGCGGACAAGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGC
63 AAGGAATAGGGAGCGGACATGTTTATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGC
* * *
29514 GGACCCGTTTTGTTGAAGATTGTTCGAGTTCTG
128 AGACACG-TTTGTTGAAGATTGTTCGAGTTATG
*
29547 TACTCTCTGATAGAATAGAGAGCGGACCCGTTCGTTGAAGTTTGTTTGAGTCCTGCTCTCAGAAG
1 TACTCTCTGATAGAATAGAGAGCGGACCCGTTCGTTGAAGTTTGTTTGAGTCCTGCTCTCTGAAG
29612 GAATAGGGAGCGGACATGTTTATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGA
66 GAATAGGGAGCGGACATGTTTATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGA
29677 CACGTTTGTTGAAGATTGTTCGAGTTATG
131 CACGTTTGTTGAAGATTGTTCGAGTTATG
*
29706 TACTCTCTGATAGAATAGAGAGCGAACCCGTTCGTTGAAGTTTGTTTGAGTCCTGCTCTCTGAAG
1 TACTCTCTGATAGAATAGAGAGCGGACCCGTTCGTTGAAGTTTGTTTGAGTCCTGCTCTCTGAAG
29771 GAATAGGGAGCGGACATGTTTATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGA
66 GAATAGGGAGCGGACATGTTTATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGA
*
29836 CACGTTTGTTGAAGATTGTTTGAGT
131 CACGTTTGTTGAAGATTGTTCGAGT
29861 CTTATACTCC
Statistics
Matches: 291, Mismatches: 18, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
158 35 0.12
159 177 0.61
160 70 0.24
162 9 0.03
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (159 bp):
TACTCTCTGATAGAATAGAGAGCGGACCCGTTCGTTGAAGTTTGTTTGAGTCCTGCTCTCTGAAG
GAATAGGGAGCGGACATGTTTATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGA
CACGTTTGTTGAAGATTGTTCGAGTTATG
Found at i:29849 original size:104 final size:104
Alignment explanation
Indices: 29367--29861 Score: 363
Period size: 104 Copynumber: 4.7 Consensus size: 104
29357 AAGCAAATTA
* * * * *
29367 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGA--
1 GTTCATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATT
* *
29430 --TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
66 GTTTGAGTCC--TGCTCTCTGAAGGAATAGGGAGCGGACAC
* * *
29469 GTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGAT
1 GTTCATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACG-TTTGTTGAAGAT
* * * *
29534 TGTTCGAGTTCTGTACTCTCTGATA-GAATAGAGAGCGGACCC
65 TGTTTGAGTCCTG--CTCTCTGA-AGGAATAGGGAGCGGACAC
* ** * * * *
29576 GTTCGTTGAAG-T-TTGT-TTGAGTCCTGCTCTCAGAAGGAATAGGGAGCGGACATGTTTATTGA
1 GTTCATTGAAGATCGAGTCTT-A-TACT-CTCT--GAAGGAATAGAGAGCGGACACGTTTGTTGA
* * * *
29638 AGATCGAGTCTT-A-TACT-C-C-CTGAACGAATAGGGAGCAGACAC
61 AGAT--TGT-TTGAGTCCTGCTCTCTGAAGGAATAGGGAGCGGACAC
** * * * *
29680 GTTTGTTGAAGATTGTTCGAGT-TATGTACTCTCTGATA-GAATAGAGAGCGAACCCGTTCGTTG
1 GTTCATTGAAGA----TCGAGTCT-TATACTCTCTGA-AGGAATAGAGAGCGGACACGTTTGTTG
* *
29743 AAGTTTGTTTGAGTCCTGCTCTCTGAAGGAATAGGGAGCGGACAT
60 AAGATTGTTTGAGTCCTGCTCTCTGAAGGAATAGGGAGCGGACAC
* * * * *
29788 GTTTATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATT
1 GTTCATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATT
29853 GTTTGAGTC
66 GTTTGAGTC
29862 TTATACTCCC
Statistics
Matches: 310, Mismatches: 51, Indels: 62
0.73 0.12 0.15
Matches are distributed among these distances:
102 49 0.16
103 14 0.05
104 82 0.26
105 9 0.03
106 31 0.10
107 44 0.14
108 47 0.15
109 26 0.08
110 6 0.02
111 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (104 bp):
GTTCATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATT
GTTTGAGTCCTGCTCTCTGAAGGAATAGGGAGCGGACAC
Found at i:29886 original size:55 final size:55
Alignment explanation
Indices: 29379--29942 Score: 442
Period size: 51 Copynumber: 10.6 Consensus size: 55
29369 TCGTTGAAGA
* * * *
29379 TTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGA----
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * **
29430 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGA----
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * *
29481 TTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGT
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACG-TTTGTTGAAGATTGT
* * * * * *
29537 TCGAGT-TCTGTACTCTCTGATA-GAATAGAGAGCGGACCCGTTCGTTGAAGTTTGT
1 TTGAGTCT-TATACTCTCTGA-AGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * *
29592 TTGAGTC--CTGCTCTCAGAAGGAATAGGGAGCGGACATGTTTATTGAAGA----
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * *
29641 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * * * *
29696 TCGAGT-TATGTACTCTCTGATA-GAATAGAGAGCGAACCCGTTCGTTGAAGTTTGT
1 TTGAGTCT-TATACTCTCTGA-AGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * *
29751 TTGAGTC--CTGCTCTCTGAAGGAATAGGGAGCGGACATGTTTATTGAAGA----
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * *
29800 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * ** **
29855 TTGAGTCTTATACTCCCTGAATGAATAGGGAGAAGACACGTTTG-CCAAGGATTGT
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAA-GATTGT
**
29910 TCAAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 TTGAGTCTTATACTCT-CTGAAGGAATAGGGAGC
29943 AGGCTCGTCA
Statistics
Matches: 419, Mismatches: 67, Indels: 50
0.78 0.12 0.09
Matches are distributed among these distances:
49 12 0.03
51 155 0.37
52 11 0.03
53 62 0.15
54 3 0.01
55 140 0.33
56 35 0.08
57 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (55 bp):
TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
Found at i:30660 original size:13 final size:13
Alignment explanation
Indices: 30644--30670 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30634 GAATAATAGT
30644 ATGTTTACCTTAG
1 ATGTTTACCTTAG
30657 ATGTTTACCTTAG
1 ATGTTTACCTTAG
30670 A
1 A
30671 AATTGGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (13 bp):
ATGTTTACCTTAG
Found at i:31764 original size:14 final size:15
Alignment explanation
Indices: 31732--31794 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
31722 GCATTGTTTA
* **
31732 TATTTTAATTTTAAA
1 TATTTTTATTTTATT
31747 TATTTTT-TTTTATT
1 TATTTTTATTTTATT
*
31761 TATTTTTATTTTATGA
1 TATTTTTATTTTAT-T
*
31777 TATTTTTAATTTAGTT
1 TATTTTTATTTTA-TT
31793 TA
1 TA
31795 ATTAATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 12 0.31
15 12 0.31
16 14 0.36
17 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTTTTATTTTATT
Found at i:31780 original size:16 final size:15
Alignment explanation
Indices: 31730--31789 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
31720 AAGCATTGTT
*
31730 TATATTTTAATTTTA
1 TATATTTTTATTTTA
*
31745 AATATTTTT-TTTTA
1 TATATTTTTATTTTA
*
31759 TTTATTTTTATTTTA
1 TATATTTTTATTTTA
*
31774 TGATATTTTTAATTTA
1 T-ATATTTTTATTTTA
31790 GTTTAATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.32
15 13 0.35
16 12 0.32
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TATATTTTTATTTTA
Found at i:32950 original size:19 final size:20
Alignment explanation
Indices: 32912--32949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32902 CTTTTTTTTA
*
32912 TGGGGGAATCGGTTCCCCCT
1 TGGGGGAATCGATTCCCCCT
*
32932 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
32950 TCTATAGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.29, G:0.34, T:0.26
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCT
Found at i:39155 original size:23 final size:23
Alignment explanation
Indices: 39068--39155 Score: 110
Period size: 23 Copynumber: 3.8 Consensus size: 23
39058 CAGCTCATAT
39068 AATTGCACC-TAAGTGCCACT-TAG
1 AATTGCACCGT-AGTGCCA-TGTAG
**
39091 AATTGCACCAG-AGTGCCGCGTAG
1 AATTGCACC-GTAGTGCCATGTAG
39114 AATTGCACCGTAGTGCCATGTAG
1 AATTGCACCGTAGTGCCATGTAG
39137 AATTGCACCGTAGTGCCAT
1 AATTGCACCGTAGTGCCAT
39156 ATAATAATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
22 1 0.02
23 56 0.98
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCATGTAG
Found at i:39295 original size:103 final size:103
Alignment explanation
Indices: 39162--39387 Score: 382
Period size: 103 Copynumber: 2.2 Consensus size: 103
39152 CCATATAATA
* * *
39162 ATGTCCAT-AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGT
1 ATGTCC-TGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGT
*
39226 GTCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACCTCACACATATTCCAAAGAATACATAT
39265 ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTG
1 ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTG
39330 TCTCACCAGACCTCACACATATTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATATTCCAAAGAATACATAT
* *
39368 ATGTCCCGAAGGATCACATA
1 ATGTCCTGAAGGACCACATA
39388 GACCCTCTAC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
102 1 0.01
103 115 0.99
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTG
TCTCACCAGACCTCACACATATTCCAAAGAATACATAT
Found at i:39905 original size:19 final size:20
Alignment explanation
Indices: 39867--39904 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39857 CTTTTTTTTA
*
39867 TGGGGGAATCGGTTCCCCCT
1 TGGGGGAATCGATTCCCCCT
*
39887 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
39905 TCTAGCGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.29, G:0.34, T:0.26
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCT
Found at i:39956 original size:21 final size:21
Alignment explanation
Indices: 39932--39974 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
39922 TCATATTCGT
*
39932 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
39953 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
39974 T
1 T
39975 AGCCCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:41770 original size:15 final size:15
Alignment explanation
Indices: 41748--41811 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
41738 GATGCGAAAG
41748 AAGAAAAGTGAAGAGA
1 AAGAAAAGTGAAGA-A
41764 AAG-AAAGTGAAGAA
1 AAGAAAAGTGAAGAA
** *
41778 AAGTGAAGAGAAAGAAA
1 AAGAAAAGTG-AAG-AA
41795 AAGAAAAGTGAAGAA
1 AAGAAAAGTGAAGAA
41810 AA
1 AA
41812 AAGATGGGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
14 4 0.10
15 18 0.45
16 9 0.22
17 9 0.22
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (15 bp):
AAGAAAAGTGAAGAA
Found at i:41776 original size:25 final size:23
Alignment explanation
Indices: 41743--41808 Score: 107
Period size: 25 Copynumber: 2.8 Consensus size: 23
41733 GATTCGATGC
41743 GAAAGAAGAAAAGTGAAGAGAAA
1 GAAAGAAGAAAAGTGAAGAGAAA
41766 GAAAGTGAAGAAAAGTGAAGAGAAA
1 GAAA--GAAGAAAAGTGAAGAGAAA
41791 GAAA-AAGAAAAGTGAAGA
1 GAAAGAAGAAAAGTGAAGA
41809 AAAAAGATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
22 14 0.34
23 4 0.10
25 23 0.56
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (23 bp):
GAAAGAAGAAAAGTGAAGAGAAA
Found at i:41780 original size:10 final size:10
Alignment explanation
Indices: 41767--41811 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
41757 GAAGAGAAAG
41767 AAAGTGAAGA
1 AAAGTGAAGA
41777 AAAGTGAAGA
1 AAAGTGAAGA
**
41787 GAAAGAAAAAGA
1 -AAAG-TGAAGA
41799 AAAGTGAAGA
1 AAAGTGAAGA
41809 AAA
1 AAA
41812 AAGATGGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 17 0.59
11 8 0.28
12 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (10 bp):
AAAGTGAAGA
Found at i:53136 original size:53 final size:53
Alignment explanation
Indices: 53038--53245 Score: 321
Period size: 53 Copynumber: 3.9 Consensus size: 53
53028 TCTTCGAATG
* * * *
53038 ACGGGTTTGCTCCCTCTTG-TTCAGGGAGTAGAATTTGAATAATCTTCTGCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTT
* *
53090 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTT
* *
53143 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTTTG-TCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCT-T
53196 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
53246 GTGTGATTCT
Statistics
Matches: 144, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
52 18 0.12
53 126 0.88
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTT
Found at i:53666 original size:41 final size:41
Alignment explanation
Indices: 53612--53703 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 41
53602 ACTATTCCGA
* *
53612 AAAGGCTTA-AAATGGCCCGAAGGACTTATCATC-TCA-CTCG
1 AAAGACTTACAAATGACCCGAAGGA-TT-TCATCATCAGCTCG
53652 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCA-GCTCG
53694 AAAGACTTAC
1 AAAGACTTAC
53704 TGATGAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
39 5 0.11
40 13 0.28
41 14 0.30
42 14 0.30
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAGACTTACAAATGACCCGAAGGATTTCATCATCAGCTCG
Found at i:53697 original size:42 final size:42
Alignment explanation
Indices: 53612--53825 Score: 137
Period size: 42 Copynumber: 5.2 Consensus size: 42
53602 ACTATTCCGA
* *
53612 AAAGGCTTA-AAATGGCCCGAAGGACTTATCATC-TCA--CTCG
1 AAAGACTTACAAATGACCCGAAGGA-TT-TCATCATCATGCTCG
53652 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
* ** * * *
53694 AAAGACTTAC---TGA--TGAATTTACTTCA-CTACTCTTCGGT-G
1 AAAGACTTACAAATGACCCGAA-GGATTTCATC-A-TCAT-GCTCG
* *** *
53733 -AAGGCTTACAAATTTTCCGAAGGATTTAATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
** * *
53774 AAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCA
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
53816 AAAGACTTAC
1 AAAGACTTAC
53826 TGATGGCACT
Statistics
Matches: 132, Mismatches: 26, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
37 4 0.03
38 14 0.11
39 12 0.09
40 17 0.13
41 19 0.14
42 62 0.47
43 4 0.03
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
Found at i:53826 original size:42 final size:42
Alignment explanation
Indices: 53749--53832 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
53739 TACAAATTTT
*
53749 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
*
53791 CCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATGGC
1 CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
53833 ACTTACTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
Found at i:53838 original size:13 final size:13
Alignment explanation
Indices: 53820--53844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53810 TGCTCAAAAG
53820 ACTTACTGATGGC
1 ACTTACTGATGGC
53833 ACTTACTGATGG
1 ACTTACTGATGG
53845 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:54075 original size:41 final size:40
Alignment explanation
Indices: 54029--54152 Score: 113
Period size: 42 Copynumber: 3.0 Consensus size: 40
54019 CTTTTGAAAA
* *
54029 CATCTTACCCGAAGGTTTTACAGATGGCCCGAAGGACTTAT
1 CATCTTGCCCGAAGG-CTTACAGATGGCCCGAAGGACTTAT
** * * *
54070 CATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAG
1 CATCTTGC-CCGAAGGCTTACAGATGGCCCGAAGGACTT-AT
* * * *
54112 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAT
1 CATCTTGCCCG-AAGGCTTACAGATGGCCCGAAGGACTTAT
54153 AAATTGTGAA
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
41 28 0.44
42 36 0.56
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (40 bp):
CATCTTGCCCGAAGGCTTACAGATGGCCCGAAGGACTTAT
Found at i:54118 original size:214 final size:214
Alignment explanation
Indices: 53868--54258 Score: 692
Period size: 214 Copynumber: 1.8 Consensus size: 214
53858 CTCTTCGGTG
* *
53868 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
* *
53933 ACTTATAAATTGTGAAATTTTGAAAATCGCATTATTTGTTTTCAAAAATTTCATCTTCTCAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
*
53998 ATCGTTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACAGATGGCCCGAAG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACAGATGGCCCGAAG
54063 GACTTATCATCTTGCTCTA
196 GACTTATCATCTTGCTCTA
* *
54082 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
* *
54147 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
*
54212 ATCATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGT
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGT
54259 CTTATGGATG
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
214 167 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (214 bp):
AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
ACTTATAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACAGATGGCCCGAAG
GACTTATCATCTTGCTCTA
Found at i:54143 original size:42 final size:41
Alignment explanation
Indices: 54046--54151 Score: 140
Period size: 42 Copynumber: 2.6 Consensus size: 41
54036 CCCGAAGGTT
* * * *
54046 TTACAGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGAC
* *
54087 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGAC
*
54129 TTACTGATGGCCCGAAGGACTTA
1 TTACAGATGGCCCGAAGGACTTA
54152 TAAATTGTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 21 0.38
42 34 0.62
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGAC
Found at i:72559 original size:15 final size:15
Alignment explanation
Indices: 72539--72569 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
72529 GCAAAATTTC
72539 AAAATTGCTATTTAT
1 AAAATTGCTATTTAT
*
72554 AAAATTGCTGTTTAT
1 AAAATTGCTATTTAT
72569 A
1 A
72570 CCATTAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (15 bp):
AAAATTGCTATTTAT
Found at i:73122 original size:153 final size:153
Alignment explanation
Indices: 72839--73123 Score: 543
Period size: 153 Copynumber: 1.9 Consensus size: 153
72829 ACAGTAGAAA
*
72839 AATTGTTTTTATATTTACCATATGATAATGTTATTTTTCATTAATGAGCTAACAGTAAATATTAT
1 AATTATTTTTATATTTACCATATGATAATGTTATTTTTCATTAATGAGCTAACAGTAAATATTAT
*
72904 TTTTGTATTTACCATATGATAAAATCAAAAACATGTAATTTATATTCTATTCAAAGACTGGACTT
66 TTTTGTATTTACCATATGATAAAATCAAAAACATATAATTTATATTCTATTCAAAGACTGGACTT
72969 TTAAAAATCTATTGTGTTAGATC
131 TTAAAAATCTATTGTGTTAGATC
*
72992 AATTATTTTTATATTTACCATATGATAATGTTATTTTTCATTAATGATCTAACAGTAAATATTAT
1 AATTATTTTTATATTTACCATATGATAATGTTATTTTTCATTAATGAGCTAACAGTAAATATTAT
73057 TTTTGTATTTACCATATGATAAAATCAAAAACATATAATTTATATTCTATTCAAAGACTGGACTT
66 TTTTGTATTTACCATATGATAAAATCAAAAACATATAATTTATATTCTATTCAAAGACTGGACTT
73122 TT
131 TT
73124 TAAGACTTTT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 129 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (153 bp):
AATTATTTTTATATTTACCATATGATAATGTTATTTTTCATTAATGAGCTAACAGTAAATATTAT
TTTTGTATTTACCATATGATAAAATCAAAAACATATAATTTATATTCTATTCAAAGACTGGACTT
TTAAAAATCTATTGTGTTAGATC
Found at i:76853 original size:18 final size:19
Alignment explanation
Indices: 76809--76856 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
76799 AATAAAAAAA
76809 TAAACAAAA-TAAATTAAG
1 TAAACAAAATTAAATTAAG
*
76827 TAATA-AAAATTAAA-TAAT
1 TAA-ACAAAATTAAATTAAG
76845 TAAACAAAATTA
1 TAAACAAAATTA
76857 CAAGTGTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.04
18 20 0.77
19 5 0.19
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAACAAAATTAAATTAAG
Found at i:76901 original size:16 final size:13
Alignment explanation
Indices: 76867--76892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76857 CAAGTGTTGG
76867 TAAATAAAAAAAT
1 TAAATAAAAAAAT
76880 TAAATAAAAAAAT
1 TAAATAAAAAAAT
76893 AATGAAATAT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAATAAAAAAAT
Found at i:80998 original size:16 final size:16
Alignment explanation
Indices: 80942--80998 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 16
80932 TAAAATATTA
*
80942 TAGAAAAACATAAAAAGT
1 TAGAAAATC-TAAAAA-T
*
80960 TAGAAAATTGTAAAAA-
1 TAGAAAA-TCTAAAAAT
*
80976 TATAAAATCTAAAAAT
1 TAGAAAATCTAAAAAT
80992 TAGAAAA
1 TAGAAAA
80999 CAAAAATATC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 7 0.22
16 12 0.38
18 13 0.41
ACGTcount: A:0.65, C:0.04, G:0.09, T:0.23
Consensus pattern (16 bp):
TAGAAAATCTAAAAAT
Found at i:81631 original size:14 final size:14
Alignment explanation
Indices: 81609--81658 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
81599 AATATGATTG
*
81609 TTTATGTTCGTTCA
1 TTTACGTTCGTTCA
81623 TTTACGTTCG----
1 TTTACGTTCGTTCA
*
81633 TTTATGTTCGTTCA
1 TTTACGTTCGTTCA
81647 TTTACGTTCGTT
1 TTTACGTTCGTT
81659 TATGTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
10 9 0.31
14 20 0.69
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.56
Consensus pattern (14 bp):
TTTACGTTCGTTCA
Found at i:81636 original size:24 final size:24
Alignment explanation
Indices: 81608--81698 Score: 137
Period size: 24 Copynumber: 3.8 Consensus size: 24
81598 TAATATGATT
81608 GTTTATGTTCGTTCATTTACGTTC
1 GTTTATGTTCGTTCATTTACGTTC
81632 GTTTATGTTCGTTCATTTACGTTC
1 GTTTATGTTCGTTCATTTACGTTC
* * * *
81656 GTTTATGTTCATTCGTTTATGTTT
1 GTTTATGTTCGTTCATTTACGTTC
*
81680 GTTTATGTACGTTCATTTA
1 GTTTATGTTCGTTCATTTA
81699 TGTTTAGCCC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.14, C:0.13, G:0.16, T:0.56
Consensus pattern (24 bp):
GTTTATGTTCGTTCATTTACGTTC
Found at i:81699 original size:24 final size:24
Alignment explanation
Indices: 81601--81703 Score: 134
Period size: 24 Copynumber: 4.3 Consensus size: 24
81591 CGTTCGGTAA
*
81601 TATGATTGTTTATGTTCGTTCATT
1 TATGTTTGTTTATGTTCGTTCATT
* *
81625 TACGTTCGTTTATGTTCGTTCATT
1 TATGTTTGTTTATGTTCGTTCATT
* * * *
81649 TACGTTCGTTTATGTTCATTCGTT
1 TATGTTTGTTTATGTTCGTTCATT
*
81673 TATGTTTGTTTATGTACGTTCATT
1 TATGTTTGTTTATGTTCGTTCATT
81697 TATGTTT
1 TATGTTT
81704 AGCCCAATCT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.57
Consensus pattern (24 bp):
TATGTTTGTTTATGTTCGTTCATT
Found at i:81891 original size:10 final size:10
Alignment explanation
Indices: 81873--81998 Score: 90
Period size: 10 Copynumber: 11.2 Consensus size: 10
81863 TCTATTTTCA
81873 TTTATGTTCG
1 TTTATGTTCG
* *
81883 TTTACGTTCA
1 TTTATGTTCG
*
81893 TTTATGTTCA
1 TTTATGTTCG
81903 TTTATTGTGTTCG
1 TTTA---TGTTCG
81916 TTTACGTTCGTTCG
1 TTTA---T-GTTCG
81930 TTTATGTTCG
1 TTTATGTTCG
*
81940 TTTACGTTCG
1 TTTATGTTCG
81950 TTTATTGTGTTCG
1 TTTA---TGTTCG
81963 TTTATGTTCG
1 TTTATGTTCG
81973 TTTACATCCGTTCG
1 TTT--AT--GTTCG
81987 TTTATGTTCG
1 TTTATGTTCG
81997 TT
1 TT
81999 CATTTATGTT
Statistics
Matches: 96, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
10 55 0.57
11 1 0.01
12 4 0.04
13 19 0.20
14 17 0.18
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.56
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:81894 original size:20 final size:20
Alignment explanation
Indices: 81869--81906 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
81859 AAAATCTATT
*
81869 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCATTTACG
81889 TTCATTTATGTTCATTTA
1 TTCATTTATGTTCATTTA
81907 TTGTGTTCGT
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:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACG
Found at i:81930 original size:14 final size:14
Alignment explanation
Indices: 81911--81951 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
81901 CATTTATTGT
81911 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
81925 GTTCGTTTA---T-
1 GTTCGTTTACGTTC
81935 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
81949 GTT
1 GTT
81952 TATTGTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
13 1 0.04
14 12 0.52
ACGTcount: A:0.07, C:0.17, G:0.22, T:0.54
Consensus pattern (14 bp):
GTTCGTTTACGTTC
Found at i:81942 original size:24 final size:22
Alignment explanation
Indices: 81883--82014 Score: 102
Period size: 24 Copynumber: 5.6 Consensus size: 22
81873 TTTATGTTCG
* * * *
81883 TTTACGTTCATTTATGTTCATT
1 TTTATGTTCGTTTACGTTCGTT
*
81905 TATTGTGTTCGTTTACGTTCGTT
1 T-TTATGTTCGTTTACGTTCGTT
81928 CGTTTATGTTCGTTTACGTTCGTT
1 --TTTATGTTCGTTTACGTTCGTT
* *
81952 TATTGTGTTCGTTTATGTTCGTT
1 T-TTATGTTCGTTTACGTTCGTT
** *
81975 TACATCCGTTCGTTTATGTTCGTT
1 TTTAT--GTTCGTTTACGTTCGTT
81999 CATTTATGTTCGTTTA
1 --TTTATGTTCGTTTA
82015 TCATTTAAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
22 3 0.03
23 36 0.40
24 46 0.52
25 1 0.01
26 3 0.03
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.56
Consensus pattern (22 bp):
TTTATGTTCGTTTACGTTCGTT
Found at i:81954 original size:47 final size:47
Alignment explanation
Indices: 81878--81974 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 47
81868 TTTCATTTAT
*
81878 GTTCGTTTACGTTCATTTATGTTCATTTATTGTGTTCGTTTACGTTC
1 GTTCGTTTACGTTCATTTACGTTCATTTATTGTGTTCGTTTACGTTC
* * * *
81925 GTTCGTTTATGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTC
1 GTTCGTTTACGTTCATTTACGTTCATTTATTGTGTTCGTTTACGTTC
81972 GTT
1 GTT
81975 TACATCCGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (47 bp):
GTTCGTTTACGTTCATTTACGTTCATTTATTGTGTTCGTTTACGTTC
Found at i:81971 original size:57 final size:55
Alignment explanation
Indices: 81873--81998 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 55
81863 TCTATTTTCA
* *
81873 TTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGTGTTCGTTTACGTTCGTTCG
1 TTTATGTTCGTTTACGTTCATTTATGTTCATTTA-T-TGTTCGTTTACATCCGTTCG
* *
81930 TTTATGTTCGTTTACGTTCGTTTATTGTGTTCGTTTA-TGTTCGTTTACATCCGTTCG
1 TTTATGTTCGTTTACGTTCATTTA---TGTTCATTTATTGTTCGTTTACATCCGTTCG
81987 TTTATGTTCGTT
1 TTTATGTTCGTT
81999 CATTTATGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
57 53 0.85
60 9 0.15
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.56
Consensus pattern (55 bp):
TTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGTTCGTTTACATCCGTTCG
Found at i:82021 original size:17 final size:14
Alignment explanation
Indices: 81981--82012 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
81971 CGTTTACATC
*
81981 CGTTCGTTTATGTT
1 CGTTCATTTATGTT
81995 CGTTCATTTATGTT
1 CGTTCATTTATGTT
82009 CGTT
1 CGTT
82013 TATCATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.19, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:94237 original size:29 final size:29
Alignment explanation
Indices: 94195--94253 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
94185 ATTTTCACCT
94195 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
94224 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
94253 A
1 A
94254 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:98921 original size:29 final size:29
Alignment explanation
Indices: 98879--98937 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
98869 ATTTTCACCT
98879 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
98908 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
98937 A
1 A
98938 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:100859 original size:16 final size:18
Alignment explanation
Indices: 100827--100861 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
100817 ATATAAAAAC
100827 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
100845 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
100861 A
1 A
100862 AATAAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:102384 original size:105 final size:105
Alignment explanation
Indices: 102197--102646 Score: 703
Period size: 105 Copynumber: 4.3 Consensus size: 105
102187 GCATTGTTCA
* * ** *
102197 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
102257 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
102297 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
102362 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
102402 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGAAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
102467 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
102507 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
102572 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
102612 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
102647 CGCGGATGGC
Statistics
Matches: 323, Mismatches: 19, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
100 37 0.11
101 1 0.00
102 1 0.00
104 5 0.02
105 254 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:103411 original size:65 final size:66
Alignment explanation
Indices: 103209--103560 Score: 262
Period size: 65 Copynumber: 5.2 Consensus size: 66
103199 AAAGAGATAG
* * * * * *
103209 AATTCGTTTCAAGGGAAAT-GATCTCAAAGATATATGTTGTTTCATGAGAAACGGTCTCAAGGGA
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-T-T-TTGTTTCAAGAGAAACTGTCTCAAGAGA
* *
103273 AACAA
62 GACGA
** *
103278 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGAGAGA
1 AATT-TGTTTTAAGGGAAATAAATTCAAAGATTTT-TGTTTCAAGAGAAACTGTCTCAAGAGAGA
103343 CGA
64 CGA
* * *
103346 AATTTGTTTTAGGGGAAATAAATTCAAAGA-TTTTGTTTCAAGGGAAACTGTCTCAAGATAGACG
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACG
103410 A
66 A
* * *** * ** * * * *
103411 AATTTGTTTCAAGAGAAACTGTCTTAAGAGAGACAAACTTAGTTCCAAGGGAAACTATCTCAAGA
1 AATTTGTTTTAAGGGAAA-TAAATTCA-A-AG---ATTTTTGTTTCAAGAGAAACTGTCTCAAGA
103476 GAGACGA
60 GAGACGA
* * *** * *
103483 AATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC-
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACG
103546 A
66 A
103547 AATCTTGTTTTAAG
1 AAT-TTGTTTTAAG
103561 AAAAACAATC
Statistics
Matches: 229, Mismatches: 43, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
64 4 0.02
65 79 0.34
66 7 0.03
67 25 0.11
68 33 0.14
69 6 0.03
70 20 0.09
71 9 0.04
72 46 0.20
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (66 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACG
A
Found at i:103429 original size:36 final size:36
Alignment explanation
Indices: 103377--103500 Score: 169
Period size: 36 Copynumber: 3.4 Consensus size: 36
103367 ATTCAAAGAT
*
103377 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* *
103413 TTTGTTTCAAGAGAAACTGTCTTAAGAGAGAC-AAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * *
103448 CTTAGTTCCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
103485 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
103501 TGTTTTCAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
35 3 0.04
36 69 0.92
37 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
Found at i:104020 original size:18 final size:18
Alignment explanation
Indices: 103993--104028 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
103983 TGTTGAATCC
* *
103993 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
104011 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
104029 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:104497 original size:22 final size:22
Alignment explanation
Indices: 104420--104490 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
104410 TTGTGTTTGG
*
104420 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
104442 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
104464 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
104486 TCAAA
1 TCAAA
104491 AGATTGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:105149 original size:7 final size:7
Alignment explanation
Indices: 105116--105200 Score: 64
Period size: 7 Copynumber: 11.1 Consensus size: 7
105106 TTTTTGTCCA
105116 TTTTTCT
1 TTTTTCT
*
105123 TTTTGCTT
1 TTTTTC-T
*
105131 TTTGCTTTT
1 TTT--TTCT
105140 TTTTTCT
1 TTTTTCT
105147 TTTATTCT
1 TTT-TTCT
*
105155 TGTTTCT
1 TTTTTCT
105162 CTTTTTCT
1 -TTTTTCT
105170 TTGTTT-T
1 TT-TTTCT
105177 TTTTTCT
1 TTTTTCT
105184 TTTTTGCT
1 TTTTT-CT
105192 TCTTTTCT
1 T-TTTTCT
105200 T
1 T
105201 CTTGATTGGA
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
6 3 0.05
7 26 0.41
8 25 0.40
9 8 0.13
10 1 0.02
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:105149 original size:8 final size:8
Alignment explanation
Indices: 105116--105200 Score: 54
Period size: 8 Copynumber: 11.0 Consensus size: 8
105106 TTTTTGTCCA
105116 TTTTTC-T
1 TTTTTCTT
*
105123 TTTTGCTT
1 TTTTTCTT
105131 TTTGCTT-TT
1 TTT--TTCTT
105140 TTTTTCTT
1 TTTTTCTT
*
105148 TTATTC-T
1 TTTTTCTT
* *
105155 TGTTTCTC
1 TTTTTCTT
105163 TTTTTC-T
1 TTTTTCTT
*
105170 TTGTT-TT
1 TTTTTCTT
105177 TTTTTCTT
1 TTTTTCTT
*
105185 TTTTGCTT
1 TTTTTCTT
*
105193 CTTTTCTT
1 TTTTTCTT
105201 CTTGATTGGA
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
7 21 0.36
8 31 0.53
9 5 0.09
10 1 0.02
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (8 bp):
TTTTTCTT
Found at i:106398 original size:8 final size:8
Alignment explanation
Indices: 106382--106420 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
106372 ATTGTAGATG
106382 AAAATGCA
1 AAAATGCA
*
106390 AAAAGGCA
1 AAAATGCA
106398 AAAATGC-
1 AAAATGCA
106405 AAAATGCA
1 AAAATGCA
*
106413 AGAATGCA
1 AAAATGCA
106421 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:106408 original size:15 final size:15
Alignment explanation
Indices: 106382--106420 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
106372 ATTGTAGATG
106382 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
106398 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
106413 AGAATGCA
1 AAAATGCA
106421 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:109109 original size:15 final size:17
Alignment explanation
Indices: 109079--109111 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
109069 AATATAAAAC
109079 ATAAATATAGGATAAAT
1 ATAAATATAGGATAAAT
109096 ATAAA-ATA-GATAAAT
1 ATAAATATAGGATAAAT
109111 A
1 A
109112 AATAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (17 bp):
ATAAATATAGGATAAAT
Found at i:109147 original size:20 final size:20
Alignment explanation
Indices: 109121--109172 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
109111 AAATAAGTAA
109121 AATATATAAAAAAGTAAAAG
1 AATATATAAAAAAGTAAAAG
* * * *
109141 CATATATATATAAGTAAAAT
1 AATATATAAAAAAGTAAAAG
109161 AATA-ATAAAAAA
1 AATATATAAAAAA
109173 AAGAAAATCA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
AATATATAAAAAAGTAAAAG
Found at i:112337 original size:23 final size:22
Alignment explanation
Indices: 112299--112346 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
112289 TTTGTATGTA
* *
112299 TTTTTATATTTTTATGGCACGCT
1 TTTTTATATTTCTATGACACG-T
*
112322 TTTTTATGTTTCTATGACACGT
1 TTTTTATATTTCTATGACACGT
112344 TTT
1 TTT
112347 CGGTTGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.58
Consensus pattern (22 bp):
TTTTTATATTTCTATGACACGT
Found at i:112763 original size:2 final size:2
Alignment explanation
Indices: 112756--112786 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
112746 ATTAGAGGAT
112756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
112787 TCTACCAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:114258 original size:20 final size:20
Alignment explanation
Indices: 114233--114283 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
114223 TGGAGCGTGG
114233 GGGGAATCGGTACCCCTTAT
1 GGGGAATCGGTACCCCTTAT
*
114253 GGGGAATCAGTACCCCTTAT
1 GGGGAATCGGTACCCCTTAT
114273 GGGGAATCGGT
1 GGGGAATCGGT
114284 TCCCTAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGGAATCGGTACCCCTTAT
Found at i:115519 original size:27 final size:29
Alignment explanation
Indices: 115461--115520 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
115451 GATATACGTC
115461 AGCTTCTGGTGGAGCTTAAGAGAAGAGCT
1 AGCTTCTGGTGGAGCTTAAGAGAAGAGCT
115490 AGCTTCTGGTGGAGCTT-A-AGAAGAGCT
1 AGCTTCTGGTGGAGCTTAAGAGAAGAGCT
115517 AGCT
1 AGCT
115521 CCCGGAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 13 0.42
28 1 0.03
29 17 0.55
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (29 bp):
AGCTTCTGGTGGAGCTTAAGAGAAGAGCT
Found at i:117098 original size:22 final size:23
Alignment explanation
Indices: 117053--117112 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
117043 ATTCCCCTAA
117053 GGGGAATCGGTTCCCATTCAAAG
1 GGGGAATCGGTTCCCATTCAAAG
*
117076 GGGGAATCGGTTCCCCTTC-AAG
1 GGGGAATCGGTTCCCATTCAAAG
* *
117098 GGGGTATCGATTCCC
1 GGGGAATCGGTTCCC
117113 TCTACCCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (23 bp):
GGGGAATCGGTTCCCATTCAAAG
Found at i:122752 original size:155 final size:158
Alignment explanation
Indices: 122495--122807 Score: 605
Period size: 155 Copynumber: 2.0 Consensus size: 158
122485 GAAATGCTCA
122495 AACTTGAGGTTTGATGCTTTCTCTTTGATTCTCTATTGATTCTAGTTGCTTGATGTTTCTTGTTA
1 AACTTGAGGTTTGATGCTTTCTCTTTGATTCTCTATTGATTCTAGTTGCTTGATGTTTCTTGTTA
122560 TTGATCAATGGCTTCTAAGCTTGCTTAAATACACCTTGAATCACTTCTGAACGTTGGGGATCATT
66 TTGATCAATGGCTTCTAAGCTTGCTTAAATACACCTTGAATCACTTCTGAACGTTGGGGATCATT
122625 AATGAAG-TATTGGAGCCGTTTAAGTGT
131 AATGAAGTTATTGGAGCCGTTTAAGTGT
122652 AACTTGAGGTTTGATGCTTTCTCTTTGATTCTCTATTGATTCTAG-TGCTTGATG-TTCTTGTTA
1 AACTTGAGGTTTGATGCTTTCTCTTTGATTCTCTATTGATTCTAGTTGCTTGATGTTTCTTGTTA
122715 TTGATCAATGGCTTCTAAGCTTGCTTAAATACACCTTGAATCACTTCTGAACGTTGGGGATCATT
66 TTGATCAATGGCTTCTAAGCTTGCTTAAATACACCTTGAATCACTTCTGAACGTTGGGGATCATT
122780 AATGAAGTTATTGGAGCCGTTTAAGTGT
131 AATGAAGTTATTGGAGCCGTTTAAGTGT
122808 GAAAACAATT
Statistics
Matches: 155, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
155 81 0.52
156 29 0.19
157 45 0.29
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.42
Consensus pattern (158 bp):
AACTTGAGGTTTGATGCTTTCTCTTTGATTCTCTATTGATTCTAGTTGCTTGATGTTTCTTGTTA
TTGATCAATGGCTTCTAAGCTTGCTTAAATACACCTTGAATCACTTCTGAACGTTGGGGATCATT
AATGAAGTTATTGGAGCCGTTTAAGTGT
Found at i:128152 original size:18 final size:19
Alignment explanation
Indices: 128129--128166 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
128119 TTCGTTGTTA
128129 TCTTTATTGGAT-GGACAC
1 TCTTTATTGGATAGGACAC
128147 TCTTTATTGGATAGGACAC
1 TCTTTATTGGATAGGACAC
128166 T
1 T
128167 AGAGAAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (19 bp):
TCTTTATTGGATAGGACAC
Found at i:134965 original size:48 final size:49
Alignment explanation
Indices: 134874--134968 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
134864 GCAGGATATG
* *
134874 AATTTAAAATTTATTTTTTTAAAGATATTTAAGAATATGGAAAAAAGGA
1 AATTTAAAATTCATTTTTTAAAAGATATTTAAGAATATGGAAAAAAGGA
*
134923 AATTTAAAATTCATTTTTTAAAAGATATTTAAGCATAT-GAAAAAAG
1 AATTTAAAATTCATTTTTTAAAAGATATTTAAGAATATGGAAAAAAG
134969 AGAGGAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 8 0.19
49 35 0.81
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (49 bp):
AATTTAAAATTCATTTTTTAAAAGATATTTAAGAATATGGAAAAAAGGA
Found at i:138672 original size:21 final size:22
Alignment explanation
Indices: 138622--138673 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
138612 GTCAATGGTT
* *
138622 CTATTTGGTCCTTCGGGGCAAA
1 CTATGTGGTCCTTCGGGACAAA
*
138644 CCTATGTGGTCTTTCGGGACAAA
1 -CTATGTGGTCCTTCGGGACAAA
138667 -TATGTGG
1 CTATGTGG
138674 CACTTCGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 7 0.27
23 19 0.73
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGACAAA
Found at i:146172 original size:21 final size:21
Alignment explanation
Indices: 146148--146201 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 21
146138 ATTAATTTGA
146148 TATTAATTTTAATTTATCT-TT
1 TATTAATTTTAATTTAT-TATT
146169 TATTAA-TTTAATTT-TTATT
1 TATTAATTTTAATTTATTATT
146188 T-TT-ATTTTAATTTA
1 TATTAATTTTAATTTA
146202 ATAAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.03
18 11 0.37
19 4 0.13
20 8 0.27
21 6 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTAATTTTAATTTATTATT
Found at i:146189 original size:32 final size:32
Alignment explanation
Indices: 146130--146194 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
146120 TCATTACCTA
*
146130 TATCCTTTATTAATTTGATATTAATTTTAATT
1 TATCCTTTATTAATTTAATATTAATTTTAATT
* * * *
146162 TATCTTTTATTAATTTAATTTTTATTTTTATT
1 TATCCTTTATTAATTTAATATTAATTTTAATT
146194 T
1 T
146195 TAATTTAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (32 bp):
TATCCTTTATTAATTTAATATTAATTTTAATT
Found at i:152380 original size:23 final size:23
Alignment explanation
Indices: 152354--152415 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 23
152344 CACCGAAGTG
*
152354 CCACATATAATTGTCCAGAAGGA
1 CCACATATAATTATCCAGAAGGA
* * * *
152377 CCACGTAGAATTTATCCCGATGGA
1 CCACATATAA-TTATCCAGAAGGA
*
152401 CCATATATAATTATC
1 CCACATATAATTATC
152416 TCCAATGACC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (23 bp):
CCACATATAATTATCCAGAAGGA
Found at i:152448 original size:23 final size:23
Alignment explanation
Indices: 152354--152448 Score: 66
Period size: 23 Copynumber: 4.1 Consensus size: 23
152344 CACCGAAGTG
* *
152354 CCACATATAATTGTC-CAGAAGGA
1 CCACATAGAATTATCTC-GAAGGA
* * *
152377 CCACGTAGAATTTATCCCGATGGA
1 CCACATAGAA-TTATCTCGAAGGA
* * * *
152401 CCATATATAATTATCTCCAATGA
1 CCACATAGAATTATCTCGAAGGA
* *
152424 CCACATAGATTTGTCTCGAAGGA
1 CCACATAGAATTATCTCGAAGGA
152447 CC
1 CC
152449 GCGTAGAACC
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 36 0.68
24 16 0.30
25 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (23 bp):
CCACATAGAATTATCTCGAAGGA
Found at i:153565 original size:20 final size:20
Alignment explanation
Indices: 153542--153611 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
153532 ATATGAACAA
153542 TATCGATACTGCTCATGAGG
1 TATCGATACTGCTCATGAGG
* * **
153562 TATCGATACT-AT-AAGAACAT
1 TATCGATACTGCTCATG-A-GG
*
153582 TATTGATACTGCTCATGAGG
1 TATCGATACTGCTCATGAGG
153602 TATCGATACT
1 TATCGATACT
153612 ATAAGAACAT
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 28 0.78
21 2 0.06
22 2 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (20 bp):
TATCGATACTGCTCATGAGG
Found at i:153580 original size:40 final size:40
Alignment explanation
Indices: 153520--153631 Score: 179
Period size: 40 Copynumber: 2.8 Consensus size: 40
153510 CCTTACCTTT
* * * *
153520 GGTATCGGTACCATATGAACAATATCGATACTGCTCATGA
1 GGTATCGATACTATAAGAACATTATCGATACTGCTCATGA
*
153560 GGTATCGATACTATAAGAACATTATTGATACTGCTCATGA
1 GGTATCGATACTATAAGAACATTATCGATACTGCTCATGA
153600 GGTATCGATACTATAAGAACATTATCGATACT
1 GGTATCGATACTATAAGAACATTATCGATACT
153632 TCTTGTATGT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (40 bp):
GGTATCGATACTATAAGAACATTATCGATACTGCTCATGA
Found at i:157667 original size:64 final size:63
Alignment explanation
Indices: 157576--157696 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 63
157566 CAAATCAATG
* *
157576 AACATCGAATGCCATTAGTGCATCGATGCATAAGGAGTGCATCGATGCACCCGCTTAAAATACA
1 AACATCGAATGCCATTAGTGCACCGATGCACAAGGAGTGCATCGATGCACCCG-TTAAAATACA
** * * * *
157640 AACATCGAATGGGATTTGTGTACCGATGCACATGTAGTGCATCGATGCACCCGTTAA
1 AACATCGAATGCCATTAGTGCACCGATGCACAAGGAGTGCATCGATGCACCCGTTAA
157697 GGAATGCATC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 4 0.08
64 45 0.92
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (63 bp):
AACATCGAATGCCATTAGTGCACCGATGCACAAGGAGTGCATCGATGCACCCGTTAAAATACA
Found at i:158272 original size:18 final size:18
Alignment explanation
Indices: 158249--158283 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
158239 AGGGATTATC
*
158249 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
158267 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
158284 AATATTCAGT
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:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:161601 original size:23 final size:23
Alignment explanation
Indices: 161571--161617 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
161561 ACTCAATCAT
* *
161571 ACACAATCCCAAGACTTTCGCAA
1 ACACAATCCCAAAACTTTCACAA
161594 ACACAATCCCAAAACTTTCACAA
1 ACACAATCCCAAAACTTTCACAA
161617 A
1 A
161618 ACTTTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
ACACAATCCCAAAACTTTCACAA
Found at i:184290 original size:21 final size:21
Alignment explanation
Indices: 184264--184320 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
184254 TTTTACACTT
184264 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
184285 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
184306 AGGGTACCGATTCCC
1 AGGGAACCGATTCCC
184321 CCACGCTCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:184537 original size:13 final size:13
Alignment explanation
Indices: 184516--184570 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
184506 AAGTTCGATA
*
184516 AATTCAAATACTT
1 AATTGAAATACTT
184529 AATTGAAATACTT
1 AATTGAAATACTT
* *
184542 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
184556 AATTGAAATACTT
1 AATTGAAATACTT
184569 AA
1 AA
184571 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:184652 original size:32 final size:33
Alignment explanation
Indices: 184556--184654 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
184546 AACTCAACAT
* * *
184556 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
184589 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
184622 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
184654 A
1 A
184655 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:184673 original size:21 final size:21
Alignment explanation
Indices: 184649--184690 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
184639 ACTTCAAGTT
184649 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
184670 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
184691 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:187067 original size:14 final size:13
Alignment explanation
Indices: 187032--187070 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
187022 GGTTTTTTAT
187032 CCGG-TAAAAAAA
1 CCGGTTAAAAAAA
*
187044 CCGGTTAAAATAA
1 CCGGTTAAAAAAA
187057 CCGGTTTAAAAAAA
1 CCGG-TTAAAAAAA
187071 TCCGATCCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (13 bp):
CCGGTTAAAAAAA
Found at i:187096 original size:14 final size:14
Alignment explanation
Indices: 187037--187096 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 14
187027 TTTATCCGGT
187037 AAAAAAACCGGTT-
1 AAAAAAACCGGTTA
*
187050 AAAATAACCGGTTTA
1 AAAAAAACCGG-TTA
187065 AAAAAATCCGATCCGGTTA
1 AAAAAA----A-CCGGTTA
187084 AAAAAAACCGGTT
1 AAAAAAACCGGTT
187097 TTTCCCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.26
14 8 0.21
15 6 0.16
19 10 0.26
20 4 0.11
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (14 bp):
AAAAAAACCGGTTA
Found at i:188536 original size:45 final size:46
Alignment explanation
Indices: 188440--188544 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 46
188430 ATGCTCATAC
* * *
188440 CATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCAATCAGGTTGTTATGAAAACATCGAATGCACTT
* * *
188486 GATGCATCGATGCAATCTGGCTTGTT-TG-AAACATTGAATGCACTT
1 CATGCATCGATGCAATCAGG-TTGTTATGAAAACATCGAATGCACTT
188531 CATGCATCGATGCA
1 CATGCATCGATGCA
188545 CTAAGAGTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 28 0.55
46 19 0.37
47 4 0.08
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (46 bp):
CATGCATCGATGCAATCAGGTTGTTATGAAAACATCGAATGCACTT
Found at i:193957 original size:44 final size:43
Alignment explanation
Indices: 193902--194003 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 43
193892 TTGTGCTTAA
* * *
193902 TGCATCGATACA-ATTAACAGTGCATCGATGCACCCCTTTGTATG
1 TGCATCGATACACATGAACA-TGCACCGATGCACCCC-TTGAATG
* *
193946 TGCATCGATACATCATGAAGATGCACCGATGCACTCCTTGAATG
1 TGCATCGATACA-CATGAACATGCACCGATGCACCCCTTGAATG
*
193990 TGCATCGATGCACA
1 TGCATCGATACACA
194004 AAGCCATGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.04
44 29 0.58
45 14 0.28
46 5 0.10
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (43 bp):
TGCATCGATACACATGAACATGCACCGATGCACCCCTTGAATG
Found at i:207117 original size:14 final size:14
Alignment explanation
Indices: 207100--207168 Score: 92
Period size: 14 Copynumber: 5.2 Consensus size: 14
207090 AATGAACATA
*
207100 AACGAACATAACCG
1 AACGAACATAAACG
207114 AACGAACATAAACG
1 AACGAACATAAACG
207128 AACGAACAT--A--
1 AACGAACATAAACG
*
207138 AACGAACATAACCG
1 AACGAACATAAACG
207152 AACGAACATAAACG
1 AACGAACATAAACG
207166 AAC
1 AAC
207169 ATAACGAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.19
12 1 0.02
14 38 0.79
ACGTcount: A:0.55, C:0.25, G:0.13, T:0.07
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:207135 original size:38 final size:38
Alignment explanation
Indices: 207080--207168 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
207070 GATTGAGTTA
* *
207080 AACATAAATGAATGAACATAAACGAACATAACCGAACG
1 AACATAAACGAACGAACATAAACGAACATAACCGAACG
207118 AACATAAACGAACGAACATAAACGAACATAACCGAACG
1 AACATAAACGAACGAACATAAACGAACATAACCGAACG
207156 AACATAAACGAAC
1 AACATAAACGAAC
207169 ATAACGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.10
Consensus pattern (38 bp):
AACATAAACGAACGAACATAAACGAACATAACCGAACG
Found at i:207141 original size:24 final size:24
Alignment explanation
Indices: 207114--207178 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
207104 AACATAACCG
207114 AACGAACATAAACGAACGAACATA
1 AACGAACATAAACGAACGAACATA
*
207138 AACGAACATAACCGAACGAACATA
1 AACGAACATAAACGAACGAACATA
207162 AACGAACAT-AACGAACG
1 AACGAACATAAACGAACG
207179 TTCACGAACC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 7 0.18
24 32 0.82
ACGTcount: A:0.55, C:0.23, G:0.14, T:0.08
Consensus pattern (24 bp):
AACGAACATAAACGAACGAACATA
Found at i:216412 original size:20 final size:20
Alignment explanation
Indices: 216387--216435 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
216377 TTTAAAACAT
216387 TATTTAAATATGTGTAACGC
1 TATTTAAATATGTGTAACGC
*
216407 TATTT-AA-ATGTGTAATGC
1 TATTTAAATATGTGTAACGC
216425 TATTTAAATAT
1 TATTTAAATAT
216436 TAAACTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 15 0.58
19 4 0.15
20 7 0.27
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (20 bp):
TATTTAAATATGTGTAACGC
Found at i:227978 original size:2 final size:2
Alignment explanation
Indices: 227971--228000 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
227961 CCTGGTTTTG
227971 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
228001 ATCTTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:233726 original size:21 final size:21
Alignment explanation
Indices: 233697--233748 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
233687 ATTCTGACTA
233697 TCGCATTGCGA-TTTCCTAAAT
1 TCGCATTGCGATTTTCCT-AAT
*
233718 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
*
233739 TCGCAATGCG
1 TCGCATTGCG
233749 TATACGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:233764 original size:20 final size:20
Alignment explanation
Indices: 233739--233832 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
233729 TTTTCCTAAT
*
233739 TCGCAATGCGTATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
233759 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
233780 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
233800 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
233820 TCGCAATGCGAAT
1 TCGCAATGCGAAT
233833 CTGACTATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 47 0.73
21 17 0.27
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:233785 original size:41 final size:40
Alignment explanation
Indices: 233739--233832 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
233729 TTTTCCTAAT
* **
233739 TCGCAATGCGTATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAA
* * *
233780 TCGCAACGCGAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
233820 TCGCAATGCGAAT
1 TCGCAATGCGAAT
233833 CTGACTATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 17 0.37
41 29 0.63
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
Found at i:234053 original size:22 final size:22
Alignment explanation
Indices: 234028--234089 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 22
234018 GGCGACATCC
234028 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
234050 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
234068 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
234090 ATCACGGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.50
22 16 0.50
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:234503 original size:20 final size:20
Alignment explanation
Indices: 234480--234526 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
234470 CAAATTCGCC
234480 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
** *
234500 TTGCGATTTTTATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
234520 TTGCGAT
1 TTGCGAT
234527 TTAAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.51
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:234527 original size:20 final size:20
Alignment explanation
Indices: 234491--234528 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
234481 TGCGATAGTC
234491 ATTTTCGTGTTGCGATTTTT
1 ATTTTCGTGTTGCGATTTTT
234511 ATTTTCGTGTTGCGATTT
1 ATTTTCGTGTTGCGATTT
234529 AAAGTTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.58
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTT
Found at i:234536 original size:20 final size:20
Alignment explanation
Indices: 234493--234536 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
234483 CGATAGTCAT
** *
234493 TTTCGTGTTGCGATTTTTAT
1 TTTCGTGTTGCGATTTAAAG
234513 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
234533 TTTC
1 TTTC
234537 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:236148 original size:33 final size:34
Alignment explanation
Indices: 236089--236181 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 34
236079 ATGACAATGG
*
236089 TGCGATTTTCATTTTCGCATTGCGATTCACTCGT
1 TGCGATTTTCATTTTCGCATTACGATTCACTCGT
*
236123 TGCGATTTTCA-TTTCGCATTACGATTCTCTCGT
1 TGCGATTTTCATTTTCGCATTACGATTCACTCGT
** *
236156 TGCGATAGTCATTTTCGCGTTACGAT
1 TGCGATTTTCATTTTCGCATTACGAT
236182 AGTCAATTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (34 bp):
TGCGATTTTCATTTTCGCATTACGATTCACTCGT
Found at i:236181 original size:20 final size:20
Alignment explanation
Indices: 236153--236221 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
236143 ACGATTCTCT
236153 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * *
236173 CGTTACGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTTCG
*
236193 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTTCG
236213 CGTTGCGAT
1 CGTTGCGAT
236222 TTCCGCGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:238548 original size:23 final size:23
Alignment explanation
Indices: 238522--238582 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
238512 CTCATATAAA
*
238522 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
238545 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
238568 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
238583 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:238761 original size:103 final size:103
Alignment explanation
Indices: 238598--238918 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
238588 TAATGTCCAT
238598 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
* *
238663 GACTTCACACATGTTCCAAAGAATATATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
238701 AAGAACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
238766 GAATTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
238804 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
238869 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
238907 AAGGACCACATA
1 AAGGACCACATA
238919 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:243850 original size:103 final size:103
Alignment explanation
Indices: 243731--244051 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
243721 ACAGCTCCAT
*
243731 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCATCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
243796 GACTTCACACATGTTTCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
243834 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTATGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
243899 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
243937 AAGGACCACATATCATTCCTTAAGAATTATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
244002 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
244040 AATGACCACATA
1 AAGGACCACATA
244052 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:247225 original size:24 final size:24
Alignment explanation
Indices: 247191--247244 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
247181 CTAAAAAATC
247191 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
247215 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
247239 ATCAAA
1 ATCAAA
247245 TTTCAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:248133 original size:20 final size:21
Alignment explanation
Indices: 248110--248191 Score: 102
Period size: 20 Copynumber: 4.1 Consensus size: 21
248100 ATCTCGTTGT
248110 GATTTACAG-ATTCGCATTGC
1 GATTTACAGTATTCGCATTGC
248130 GATTTAC-GTATTCGCATTGC
1 GATTTACAGTATTCGCATTGC
*
248150 GATAGT-CAG-ATTCGCATTGC
1 GAT-TTACAGTATTCGCATTGC
*
248170 GATTTA-TGTATTCGCATTGC
1 GATTTACAGTATTCGCATTGC
248190 GA
1 GA
248192 ATCTGGAAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
19 3 0.06
20 49 0.91
21 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (21 bp):
GATTTACAGTATTCGCATTGC
Found at i:248160 original size:40 final size:40
Alignment explanation
Indices: 248116--248191 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
248106 TTGTGATTTA
248116 CAGATTCGCATTGCGATTTACGTATTCGCATTGCGATAGT
1 CAGATTCGCATTGCGATTTACGTATTCGCATTGCGATAGT
*
248156 CAGATTCGCATTGCGATTTATGTATTCGCATTGCGA
1 CAGATTCGCATTGCGATTTACGTATTCGCATTGCGA
248192 ATCTGGAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (40 bp):
CAGATTCGCATTGCGATTTACGTATTCGCATTGCGATAGT
Found at i:257316 original size:111 final size:108
Alignment explanation
Indices: 257134--257556 Score: 680
Period size: 111 Copynumber: 3.9 Consensus size: 108
257124 ATTACAAAAA
* * *
257134 TTAAGTCTCAATCTAATAATCATGCATTAAATAAATCTAATTATTATTAATAATTTAAATTAAAT
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCTAATTATTACTAATAATTTAAATTAAAT
*
257199 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATAT
66 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
257242 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT---CTAATTATTACTAATAATTTAAATTA
257307 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
63 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
257353 TTAATTCTTAATCTAATAATCATGCATTAAATAAATC-----A--ACTAATAATTTAAATTAAAT
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCTAATTATTACTAATAATTTAAATTAAAT
257411 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
257454 TTAATTCTTAATCTAATGATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT---CTAATTATTACTAATAATTTAAATTA
*
257519 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGT
63 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
257557 AGATATATAT
Statistics
Matches: 296, Mismatches: 6, Indels: 23
0.91 0.02 0.07
Matches are distributed among these distances:
101 98 0.33
103 1 0.00
104 1 0.00
108 35 0.12
109 1 0.00
111 160 0.54
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (108 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCTAATTATTACTAATAATTTAAATTAAAT
TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:257517 original size:212 final size:214
Alignment explanation
Indices: 257134--257556 Score: 724
Period size: 212 Copynumber: 2.0 Consensus size: 214
257124 ATTACAAAAA
*
257134 TTAAGTCTCAATCTAATAATCATGCATTAAATAAATCTAATTATTATTAATAATTTAAATTAAAT
1 TTAAGTCTCAATCTAATAATCATGCATTAAATAAATC----TA-TACTAATAATTTAAATTAAAT
*
257199 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATATTTAATTCTTAATCTAATAATCA
61 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTCTTAATCTAATAATCA
*
257264 TGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATTAAAACGTTAAAATGTTAC
126 TGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAAACGTTAAAATGTTAC
*
257329 CGTATCAGCAAAGTGTCGAGATAT
191 CGTATCAACAAAGTGTCGAGATAT
* *
257353 TTAATTCTTAATCTAATAATCATGCATTAAATAAATC-A-ACTAATAATTTAAATTAAATTAAAA
1 TTAAGTCTCAATCTAATAATCATGCATTAAATAAATCTATACTAATAATTTAAATTAAATTAAAA
*
257416 CGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTCTTAATCTAATGATCATGCAT
66 CGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTCTTAATCTAATAATCATGCAT
257481 TAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAAACGTTAAAATGTTACCGTAT
131 TAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAAACGTTAAAATGTTACCGTAT
257546 CAACAAAGTGT
196 CAACAAAGTGT
257557 AGATATATAT
Statistics
Matches: 197, Mismatches: 7, Indels: 7
0.93 0.03 0.03
Matches are distributed among these distances:
212 161 0.82
214 1 0.01
219 35 0.18
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (214 bp):
TTAAGTCTCAATCTAATAATCATGCATTAAATAAATCTATACTAATAATTTAAATTAAATTAAAA
CGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTCTTAATCTAATAATCATGCAT
TAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAAACGTTAAAATGTTACCGTAT
CAACAAAGTGTCGAGATAT
Found at i:257669 original size:17 final size:18
Alignment explanation
Indices: 257626--257666 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
257616 GAATTATATT
257626 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
257643 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
257661 ATTAAA
1 AGTAAA
257667 TACATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:257720 original size:12 final size:10
Alignment explanation
Indices: 257707--257747 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
257697 CCTTAAAAGA
*
257707 GAGAGTATTT
1 GAGAGAATTT
257717 GAGAGAAATTT
1 GAGAG-AATTT
257728 -AGAGAATTT
1 GAGAGAATTT
257737 GAGAGAATTT
1 GAGAGAATTT
257747 G
1 G
257748 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:257937 original size:50 final size:48
Alignment explanation
Indices: 257870--257993 Score: 158
Period size: 50 Copynumber: 2.5 Consensus size: 48
257860 AGATACTCAG
*
257870 GTATGGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
1 GTATAGCGCGGA-CAGGGGGCGCGCTATACCCACG-GGCACCAAATCACC
* * * *
257920 GTATATCGCAGGACAGGGGGCGCACTATACCCACGGGCGCCAAATCAGC
1 GTATAGCGC-GGACAGGGGGCGCGCTATACCCACGGGCACCAAATCACC
**
257969 GTATAGCGCGTTCAGGGGGCGCGCT
1 GTATAGCGCGGACAGGGGGCGCGCT
257994 TTACTGCTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 13 0.20
49 20 0.31
50 28 0.44
51 3 0.05
ACGTcount: A:0.22, C:0.30, G:0.34, T:0.15
Consensus pattern (48 bp):
GTATAGCGCGGACAGGGGGCGCGCTATACCCACGGGCACCAAATCACC
Found at i:258352 original size:36 final size:34
Alignment explanation
Indices: 258264--258470 Score: 234
Period size: 35 Copynumber: 5.8 Consensus size: 34
258254 AAAAAAACAT
*
258264 ATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 ATATATAATATATAGTTTTTAAAACAT-TTTGAAA
*
258299 ACTTTTATATATTATATAGTTTTTAAAACATTTTGAAA
1 A----TATATAATATATAGTTTTTAAAACATTTTGAAA
*
258337 ATAAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 AT--ATATAATATATAGTTTTTAAAACA-TTTTGAAA
* * **
258374 ATATATATTATATAGTTTTTAAAATATTTCAAAA
1 ATATATAATATATAGTTTTTAAAACATTTTGAAA
*
258408 ATAAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 AT--ATATAATATATAGTTTTTAAAACA-TTTTGAAA
*
258445 ATATATATTATATAGTTTTTAAAACA
1 ATATATAATATATAGTTTTTAAAACA
258471 ACAACAACAA
Statistics
Matches: 150, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
34 9 0.06
35 46 0.31
36 45 0.30
37 18 0.12
38 8 0.05
39 24 0.16
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (34 bp):
ATATATAATATATAGTTTTTAAAACATTTTGAAA
Found at i:258374 original size:12 final size:11
Alignment explanation
Indices: 258354--258448 Score: 57
Period size: 11 Copynumber: 8.1 Consensus size: 11
258344 TAATATATAG
258354 TTTTTAAAATA
1 TTTTTAAAATA
258365 TTTTTGAAAATA
1 TTTTT-AAAATA
* *
258377 TATATT-ATATA
1 T-TTTTAAAATA
258388 GTTTTTAAAATA
1 -TTTTTAAAATA
**
258400 TTTCAAAAATA
1 TTTTTAAAATA
** *
258411 AATATAATATATA
1 TTTTTAA-A-ATA
258424 GTTTTTAAAATA
1 -TTTTTAAAATA
258436 TTTTTGAAAATA
1 TTTTT-AAAATA
258448 T
1 T
258449 ATATTATATA
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
11 29 0.46
12 23 0.37
13 7 0.11
14 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:258387 original size:37 final size:37
Alignment explanation
Indices: 258221--258468 Score: 233
Period size: 36 Copynumber: 6.7 Consensus size: 37
258211 TTATATATAT
* * *
258221 ATATATACATATATATAG-TTTGAAAATATTTTTAAAAAAA
1 ATATATA-TTATATATAGTTTTTAAAATATTTTT---GAAA
* * * *
258261 CATATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 -ATATATATTATATATAGTTTTTAAAATATTTTTGAAA
* *
258299 ACT-TTTATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 A-TATATAT-TA-TATATAGTTTTTAAAATATTTTTGAAA
* *
258337 ATAAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATATATATTATATATAGTTTTTAAAATATTTTTGAAA
**
258374 ATATATA-T-TATATAGTTTTTAAAATA-TTTCAAAA
1 ATATATATTATATATAGTTTTTAAAATATTTTTGAAA
* *
258408 ATAAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATATATATTATATATAGTTTTTAAAATATTTTTGAAA
258445 ATATATA-T-TATATAGTTTTTAAAA
1 ATATATATTATATATAGTTTTTAAAA
258469 CAACAACAAC
Statistics
Matches: 175, Mismatches: 23, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
34 12 0.07
35 34 0.19
36 35 0.20
37 33 0.19
38 16 0.09
39 17 0.10
40 8 0.05
41 20 0.11
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATATTATATATAGTTTTTAAAATATTTTTGAAA
Found at i:258409 original size:71 final size:71
Alignment explanation
Indices: 258257--258470 Score: 320
Period size: 71 Copynumber: 2.9 Consensus size: 71
258247 TATTTTTAAA
* * * *
258257 AAAACATATATATAATATATAGTTTTGAAAACATGTTTGAAAACTTTTATATATTATATAGTTTT
1 AAAA-ATAAATATAATATATAGTTTTTAAAATATTTTTGAAAA----TATATATTATATAGTTTT
*
258322 TAAAACATTTT
61 TAAAACATTTC
*
258333 GAAAATAAATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATTATATAGTTTTTAAAA
1 AAAAATAAATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATTATATAGTTTTTAAAA
*
258398 TATTTC
66 CATTTC
258404 AAAAATAAATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATTATATAGTTTTTAAAA
1 AAAAATAAATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATTATATAGTTTTTAAAA
258469 CA
66 CA
258471 ACAACAACAA
Statistics
Matches: 129, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
71 92 0.71
75 34 0.26
76 3 0.02
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (71 bp):
AAAAATAAATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATTATATAGTTTTTAAAA
CATTTC
Found at i:258973 original size:39 final size:37
Alignment explanation
Indices: 258919--259012 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 37
258909 ATATATATAG
* * *
258919 TTTTGAAAACATATATATATTATATAATTTTGAAATCAT
1 TTTTGAAAACATATATA-A-TATATAATTTTAAAAACAA
*
258958 TTTTGAAAA-ATTATATAATATATAGTTTTAAAAACAA
1 TTTTGAAAACA-TATATAATATATAATTTTAAAAACAA
258995 TTTTGAAAAC-TATATAAT
1 TTTTGAAAACATATATAAT
259013 TTTTGAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
36 8 0.16
37 24 0.49
38 2 0.04
39 15 0.31
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (37 bp):
TTTTGAAAACATATATAATATATAATTTTAAAAACAA
Found at i:259125 original size:5 final size:5
Alignment explanation
Indices: 259106--259169 Score: 69
Period size: 5 Copynumber: 12.4 Consensus size: 5
259096 TATAATAATA
259106 TTATT ATTA-T TTATT TTATT TTATT TTATT TTATT TTATCT TT-TAT
1 TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTAT-T TTAT-T
*
259152 TAATT TTATT TTCATT TT
1 TTATT TTATT TT-ATT TT
259170 TATTGTCAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
4 3 0.06
5 36 0.71
6 12 0.24
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Done.