Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007129.1 Hibiscus syriacus cultivar Beakdansim tig00018629_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: 146715
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2573 original size:37 final size:37
Alignment explanation
Indices: 2497--2573 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
2487 TTTTTATATT
*
2497 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
2534 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
2571 TTT
1 TTT
2574 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:2754 original size:20 final size:20
Alignment explanation
Indices: 2718--2755 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2708 ATCTTATTCT
**
2718 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
2738 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2756 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:7302 original size:21 final size:21
Alignment explanation
Indices: 7278--7320 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
7268 ATGCTTCACC
*
7278 TGAGATTACATGTATCTAACA
1 TGAGATGACATGTATCTAACA
*
7299 TGAGATGACCTGTATCTAACA
1 TGAGATGACATGTATCTAACA
7320 T
1 T
7321 TACACCTTGA
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:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
TGAGATGACATGTATCTAACA
Found at i:11749 original size:33 final size:33
Alignment explanation
Indices: 11711--11777 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
11701 GTTTAGTAGG
** * *
11711 TAGTGGATTTTTATTTAATATATATTGAGTTTT
1 TAGTGGATGATTATTTAATAGATAATGAGTTTT
*
11744 TAGTGGATGATTATTTAATAGGTAATGAGTTTT
1 TAGTGGATGATTATTTAATAGATAATGAGTTTT
11777 T
1 T
11778 TAGATTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.52
Consensus pattern (33 bp):
TAGTGGATGATTATTTAATAGATAATGAGTTTT
Found at i:12444 original size:3 final size:3
Alignment explanation
Indices: 12431--12512 Score: 128
Period size: 3 Copynumber: 26.7 Consensus size: 3
12421 GAAAAAATAC
12431 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
12477 TAT TAT TAT TAT TAT CAT TAT CAT TAT TAAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
12513 CATAATCTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
3 67 0.92
4 6 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:12561 original size:33 final size:33
Alignment explanation
Indices: 12522--12608 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
12512 ACATAATCTA
* ** *
12522 AAAAACTCACTACCAATTAAATAATCATCCACT
1 AAAAACTCACTACCTATTAAATAAAAACCCACT
*
12555 AAAAACTCAATACCTATTAAATAAAAACCCACT
1 AAAAACTCACTACCTATTAAATAAAAACCCACT
*
12588 AAAAACTAACTACCTATTAAA
1 AAAAACTCACTACCTATTAAA
12609 CAAATAAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.23
Consensus pattern (33 bp):
AAAAACTCACTACCTATTAAATAAAAACCCACT
Found at i:15558 original size:23 final size:24
Alignment explanation
Indices: 15514--15560 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
15504 ATTTTAATTT
15514 TTTTAGATATTTTAAATCTAAATA
1 TTTTAGATATTTTAAATCTAAATA
* * *
15538 TTTTA-ATTTTTTTAATTTAAATA
1 TTTTAGATATTTTAAATCTAAATA
15561 ATCTCTATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTAGATATTTTAAATCTAAATA
Found at i:16576 original size:20 final size:20
Alignment explanation
Indices: 16551--16595 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
16541 ATCATCCAAT
16551 TTTTTAAAACCCAGACCGGA
1 TTTTTAAAACCCAGACCGGA
* *
16571 TTTTTAAACCCCATACCGGA
1 TTTTTAAAACCCAGACCGGA
16591 TTTTT
1 TTTTT
16596 TTCCGAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTTTAAAACCCAGACCGGA
Found at i:20845 original size:10 final size:10
Alignment explanation
Indices: 20827--20856 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20817 ATCTATCTTG
20827 TAATTTAATC
1 TAATTTAATC
*
20837 TACTTTAATC
1 TAATTTAATC
20847 TAATTTAATC
1 TAATTTAATC
20857 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (10 bp):
TAATTTAATC
Found at i:20972 original size:10 final size:10
Alignment explanation
Indices: 20954--20983 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20944 ATCTATATTG
20954 TAATTTAATC
1 TAATTTAATC
*
20964 TACTTTAATC
1 TAATTTAATC
20974 TAATTTAATC
1 TAATTTAATC
20984 ATTAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (10 bp):
TAATTTAATC
Found at i:20974 original size:27 final size:25
Alignment explanation
Indices: 20930--20982 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
20920 TTTATCTAAT
* * *
20930 TTTAATGTATTTTTATCTATATTGTAA
1 TTTAATCTACTTTAATCTA-ATT-TAA
20957 TTTAATCTACTTTAATCTAATTTAA
1 TTTAATCTACTTTAATCTAATTTAA
20982 T
1 T
20983 CATTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 16 0.70
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTAATCTACTTTAATCTAATTTAA
Found at i:21686 original size:13 final size:13
Alignment explanation
Indices: 21668--21692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21658 CAAAATAAAA
21668 TAAAATTAATAAT
1 TAAAATTAATAAT
21681 TAAAATTAATAA
1 TAAAATTAATAA
21693 AATATCATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAATTAATAAT
Found at i:24010 original size:25 final size:25
Alignment explanation
Indices: 23948--24012 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
23938 GGGTACTCGA
*
23948 AGCCCCTGTACTTAA-AAAATAATGT
1 AGCCCTTGTAC-TAATAAAATAATGT
23973 AGCCCTTGTACTAATAAAATAATGT
1 AGCCCTTGTACTAATAAAATAATGT
23998 AGCCCTTGTACTAAT
1 AGCCCTTGTACTAAT
24013 TTTTCTCTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 3 0.08
25 35 0.92
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (25 bp):
AGCCCTTGTACTAATAAAATAATGT
Found at i:24395 original size:11 final size:11
Alignment explanation
Indices: 24379--24403 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24369 AAAAAGTACG
24379 AATGTCAATTA
1 AATGTCAATTA
24390 AATGTCAATTA
1 AATGTCAATTA
24401 AAT
1 AAT
24404 CTTTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
AATGTCAATTA
Found at i:24557 original size:60 final size:60
Alignment explanation
Indices: 24464--24587 Score: 178
Period size: 60 Copynumber: 2.1 Consensus size: 60
24454 TCGTGTGGGT
* * * *
24464 CACGTGAAGTTAATAAACCGCTGCTTTTATCTTTCATTAA-TGTCCGTGTGGGTCATACAC
1 CACGTGAAATTAATAAAACACTGCTTTTATCTTTCATTAATTG-CCGTGTGGGTCAAACAC
* *
24524 CACGTGAAATTAATAAAACACTGCTTTTATCTTTCGTTAATTGCCGTGTGGTTCAAACAC
1 CACGTGAAATTAATAAAACACTGCTTTTATCTTTCATTAATTGCCGTGTGGGTCAAACAC
24584 CACG
1 CACG
24588 ATTCAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 55 0.96
61 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (60 bp):
CACGTGAAATTAATAAAACACTGCTTTTATCTTTCATTAATTGCCGTGTGGGTCAAACAC
Found at i:25707 original size:9 final size:9
Alignment explanation
Indices: 25671--25707 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
25661 TATTAGATGA
25671 TATTTTATT
1 TATTTTATT
* *
25680 AATTTTAAT
1 TATTTTATT
25689 TATTTTATT
1 TATTTTATT
25698 TATTTTATT
1 TATTTTATT
25707 T
1 T
25708 TGCAACCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTTATT
Found at i:29296 original size:17 final size:17
Alignment explanation
Indices: 29262--29298 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29252 TGGTGGATTA
*
29262 AAAATTTAAATTCGAAT
1 AAAATTTAAATTCAAAT
*
29279 AAAATTTAAATTTAAAT
1 AAAATTTAAATTCAAAT
29296 AAA
1 AAA
29299 CCATAGCAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAATTTAAATTCAAAT
Found at i:29909 original size:31 final size:30
Alignment explanation
Indices: 29874--29931 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
29864 CCGCCGATAT
29874 TCTTTATTTTCTTTTTCTTTTTTATATTGTA
1 TCTTTATTTTCTTTTTCTTTTTT-TATTGTA
*
29905 TCTTTATTTTCTTTTTGTTTTTTTATT
1 TCTTTATTTTCTTTTTCTTTTTTTATT
29932 TTCAATCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.10, C:0.09, G:0.03, T:0.78
Consensus pattern (30 bp):
TCTTTATTTTCTTTTTCTTTTTTTATTGTA
Found at i:31759 original size:3 final size:3
Alignment explanation
Indices: 31753--31811 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
31743 TGATATTTTG
* * *
31753 TAA TAA TAA TAA TAA TAA TAA TATT TTA TAA T-A TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* *
31798 TGA TGA TAA TAA TA
1 TAA TAA TAA TAA TA
31812 GGATGGTTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.93
4 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:31771 original size:28 final size:27
Alignment explanation
Indices: 31730--31801 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
31720 AATGAGTTTG
*
31730 TAATAAATAATAATGATATTTTGTAATAA
1 TAAT-AATAATAATGATATTTTATAAT-A
*
31759 TAATAATAATAATAATATTTTATAATA
1 TAATAATAATAATGATATTTTATAATA
*
31786 TAATAAAAATAATGAT
1 TAATAATAATAATGAT
31802 GATAATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 15 0.38
28 20 0.51
29 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
TAATAATAATAATGATATTTTATAATA
Found at i:34082 original size:69 final size:69
Alignment explanation
Indices: 33971--35000 Score: 1411
Period size: 69 Copynumber: 14.9 Consensus size: 69
33961 GCTGCTAAGT
* * * * *
33971 CTTTTCTCAAGGATTTCGACCCAAATCGTCCTCAGTATAATTACCTGTCGCAGGAGGCCATGAAA
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
*
34036 AAAG
66 AACG
* * *
34040 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAATACAATTATCTGTCTCAGGAGGCCATGAAG
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
34105 AACG
66 AACG
* * * * * * * * * *
34109 CCTTCCTTAAGGATTTTGACTCTAACCGTCCTCAATACAATTATCTGTCTCAGGAGGCAATGAAG
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
*
34174 AATG
66 AACG
* * * *
34178 CATTCCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACTTGTCTCAGGAGGCCATGAAG
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
34243 AACG
66 AACG
* * *
34247 CTTTTCTCAAGGACTTCGACCCCAACCGTCCTCAGTACAATTACTTGTCTCAGGAGGCCATGAAG
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
34312 AACG
66 AACG
* * *
34316 CTTTCCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACTTGTCTCAGGAGGCCATGAAG
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
34381 AACG
66 AACG
* * * * *
34385 CTTTCCTCAAGGATTTTGACCCCAACCGTCCCCAGTACAATTACCTGTCTCAGGAGGCCATGAAA
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
34450 AACG
66 AACG
* * *
34454 CTTTCCTTAAGGACTTT-GACCCCAACCGTCCCCAGTACAATTACCTGTCCCAGGAGGCCATGAA
1 CTTTTCTCAAGGA-TTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAA
*
34518 GAACT
65 GAACG
* *
34523 CTTTTCTCAAGGACTTCGACCCCAACCGTCCCCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
*
34588 AACT
66 AACG
* *
34592 CTTTTCTCAAGGACTTCGACCCCAACCGTCCCCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
*
34657 AACT
66 AACG
* *
34661 CTTTTCTCAAGGACTTCGACCCCAACCGTCCCCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
*
34726 AACT
66 AACG
* * *
34730 CTTTTCTCAAGGACTTT-GACGCCAACCGTCCCCAGTACAATTACCTGTCCCAGGAAGCCATGAA
1 CTTTTCTCAAGGA-TTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAA
*
34794 GAACT
65 GAACG
* * *
34799 CTTTTCTCAAGGACTTT-GACGCCAACCGTCCCCAGTACAATTACCTGTCCCAGGAAGCCATGAA
1 CTTTTCTCAAGGA-TTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAA
*
34863 GAACT
65 GAACG
* *
34868 CTTTTCTCAAGGACTTT-GACGCCAACCGTCCTCAGTACAATTACTTGTCCCAGGAGGCCATGAA
1 CTTTTCTCAAGGA-TTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAA
*
34932 AAACG
65 GAACG
* * * * * *
34937 CTTTTCTCAATGATTTCAACCCCAACCGTCCTCAATACAATTATCTATCCCAAGAGGCCATGAA
1 CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAA
35001 CTCTTTGAAG
Statistics
Matches: 899, Mismatches: 58, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
68 5 0.01
69 889 0.99
70 5 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (69 bp):
CTTTTCTCAAGGATTTCGACCCCAACCGTCCTCAGTACAATTACCTGTCCCAGGAGGCCATGAAG
AACG
Found at i:40844 original size:31 final size:32
Alignment explanation
Indices: 40801--40865 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
40791 ACGATGTAAT
40801 TTACCCTTAATTTAATTACT-TAACTTTCAAA
1 TTACCCTTAATTTAATTACTCTAACTTTCAAA
* *
40832 TTACTCTTAATTTAATTACTCTAGCTTTCAAA
1 TTACCCTTAATTTAATTACTCTAACTTTCAAA
40864 TT
1 TT
40866 TATTTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (32 bp):
TTACCCTTAATTTAATTACTCTAACTTTCAAA
Found at i:40850 original size:15 final size:15
Alignment explanation
Indices: 40801--40853 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
40791 ACGATGTAAT
*
40801 TTACCCTTAATTTAA
1 TTACTCTTAATTTAA
40816 TTA--CTTAACTTTCAAA
1 TTACTCTTAA-TTT--AA
40832 TTACTCTTAATTTAA
1 TTACTCTTAATTTAA
40847 TTACTCT
1 TTACTCT
40854 AGCTTTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.15
14 3 0.09
15 12 0.36
16 5 0.15
17 3 0.09
18 5 0.15
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (15 bp):
TTACTCTTAATTTAA
Found at i:41455 original size:37 final size:35
Alignment explanation
Indices: 41383--41455 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 35
41373 ATCTTTGTTC
* *
41383 TTAAATTTTTAATATTTTGAAATATTAAAAATTTA
1 TTAAATTTTAAATATTTTGAAATATGAAAAATTTA
* * *
41418 TTAAATTATTAAATTATTTTGAATTATGATAATTTTA
1 TTAAATT-TTAAA-TATTTTGAAATATGAAAAATTTA
41455 T
1 T
41456 AAAAAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 7 0.23
36 4 0.13
37 20 0.65
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (35 bp):
TTAAATTTTAAATATTTTGAAATATGAAAAATTTA
Found at i:48296 original size:24 final size:24
Alignment explanation
Indices: 48264--48309 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
48254 TCTTCCATTT
48264 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
48288 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
48310 TATATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:50220 original size:31 final size:31
Alignment explanation
Indices: 50185--50269 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
50175 CCATATACTA
*
50185 GTCAGGTTTGTATTAAGATAATGTACAATAT
1 GTCAGGTTTATATTAAGATAATGTACAATAT
* * * *
50216 GTCAGGTTTACATTCAGATAATGTATAGTAT
1 GTCAGGTTTATATTAAGATAATGTACAATAT
* * *
50247 GTCAAGTTCATATTTAGATAATG
1 GTCAGGTTTATATTAAGATAATG
50270 CAGTAGCATT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (31 bp):
GTCAGGTTTATATTAAGATAATGTACAATAT
Found at i:56636 original size:27 final size:27
Alignment explanation
Indices: 56565--56623 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 27
56555 GAACCGAGTA
56565 AAACGGTTCGGTTCGGTTCGGTTCGGCTTT
1 AAACGGTTCGGTT---TTCGGTTCGGCTTT
56595 AAACGGTTCGGTTTTCGGTTCGG-TTT
1 AAACGGTTCGGTTTTCGGTTCGGCTTT
56621 AAA
1 AAA
56624 GGCTTCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 6 0.21
27 10 0.34
30 13 0.45
ACGTcount: A:0.15, C:0.17, G:0.31, T:0.37
Consensus pattern (27 bp):
AAACGGTTCGGTTTTCGGTTCGGCTTT
Found at i:68056 original size:17 final size:16
Alignment explanation
Indices: 68034--68123 Score: 60
Period size: 14 Copynumber: 6.2 Consensus size: 16
68024 TGAATCGAAT
68034 ATCATTACTATTATTAA
1 ATCATTA-TATTATTAA
68051 ATCA-T-TATTATTAA
1 ATCATTATATTATTAA
68065 ATCATTA-A--AGTTAA
1 ATCATTATATTA-TTAA
*
68079 ATTA-T-TATTATTAA
1 ATCATTATATTATTAA
68093 ATCATTA-A--AGTTAA
1 ATCATTATATTA-TTAA
68107 ATCA-T-TATTATTAA
1 ATCATTATATTATTAA
68121 ATC
1 ATC
68124 GTTAAAGTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 27
0.67 0.02 0.31
Matches are distributed among these distances:
13 6 0.10
14 42 0.71
15 6 0.10
16 1 0.02
17 4 0.07
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (16 bp):
ATCATTATATTATTAA
Found at i:68061 original size:14 final size:14
Alignment explanation
Indices: 68047--68272 Score: 169
Period size: 14 Copynumber: 15.9 Consensus size: 14
68037 ATTACTATTA
*
68047 TTAAATCATTATTA-
1 TTAAATCATTA-AAG
68061 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
68075 TTAAATTATTATTA-
1 TTAAATCATTA-AAG
68089 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
68103 TTAAATCATTATTA-
1 TTAAATCATTA-AAG
*
68117 TTAAATCGTTAAAG
1 TTAAATCATTAAAG
68131 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
68145 TTAAATTATTATTA-
1 TTAAATCATTA-AAG
68159 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
68173 TGAAATTATTAAAG
1 TTAAATCATTAAAG
* *
68187 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
68201 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
68215 TTAACTACCAATTATTA-
1 TTAA--ATC-ATTA-AAG
68232 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
68246 CTAACTCATTATTA-
1 TTAAATCATTA-AAG
68260 TTAAATCATTAAA
1 TTAAATCATTAAA
68273 TCATTTTGAT
Statistics
Matches: 167, Mismatches: 30, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
13 7 0.04
14 142 0.85
15 7 0.04
16 2 0.01
17 8 0.05
18 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:68087 original size:28 final size:28
Alignment explanation
Indices: 68047--68272 Score: 269
Period size: 28 Copynumber: 8.0 Consensus size: 28
68037 ATTACTATTA
68047 TTAAATCATTATTATTAAATCATTAAAG
1 TTAAATCATTATTATTAAATCATTAAAG
*
68075 TTAAATTATTATTATTAAATCATTAAAG
1 TTAAATCATTATTATTAAATCATTAAAG
*
68103 TTAAATCATTATTATTAAATCGTTAAAG
1 TTAAATCATTATTATTAAATCATTAAAG
* * *
68131 TTAAATCATTA-AAGTTAAATTATTATTA-
1 TTAAATCATTATTA-TTAAATCATTA-AAG
* * *
68159 TTAAATCATTA-AAGTGAAATTATTAAAG
1 TTAAATCATTATTA-TTAAATCATTAAAG
*
68187 TTAAATAATTATTATTAAATCATTAAAG
1 TTAAATCATTATTATTAAATCATTAAAG
*
68215 TTAACTACCAATTATTATTAAATCATTAAAG
1 TTAA--ATC-ATTATTATTAAATCATTAAAG
* *
68246 CTAACTCATTATTATTAAATCATTAAA
1 TTAAATCATTATTATTAAATCATTAAA
68273 TCATTTTGAT
Statistics
Matches: 173, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.01
28 143 0.83
29 3 0.02
30 1 0.01
31 24 0.14
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (28 bp):
TTAAATCATTATTATTAAATCATTAAAG
Found at i:68121 original size:42 final size:42
Alignment explanation
Indices: 68047--68218 Score: 215
Period size: 42 Copynumber: 4.1 Consensus size: 42
68037 ATTACTATTA
* * * *
68047 TTAAATCATTATTA-TTAAATCATTA-AAGTTAAATTATTATTA-
1 TTAAATCATTA-AAGTTAAATCATTATTA-TTAAATCATTA-AAG
*
68089 TTAAATCATTAAAGTTAAATCATTATTATTAAATCGTTAAAG
1 TTAAATCATTAAAGTTAAATCATTATTATTAAATCATTAAAG
*
68131 TTAAATCATTAAAGTTAAATTATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTTAAATCATTATTATTAAATCATTAAAG
* * *
68173 TGAAATTATTAAAGTTAAATAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTTAAATCATTATTATTAAATCATTAAAG
68215 TTAA
1 TTAA
68219 CTACCAATTA
Statistics
Matches: 116, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.02
42 113 0.97
43 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (42 bp):
TTAAATCATTAAAGTTAAATCATTATTATTAAATCATTAAAG
Found at i:71815 original size:30 final size:32
Alignment explanation
Indices: 71781--71851 Score: 114
Period size: 30 Copynumber: 2.3 Consensus size: 32
71771 GAAGATGTCG
71781 AGACCTCCATG-A-ATTGTGTTAAAGACGCCT
1 AGACCTCCATGCACATTGTGTTAAAGACGCCT
71811 AGACCT-C-TGCACATTGTGTTAAAGACGCCT
1 AGACCTCCATGCACATTGTGTTAAAGACGCCT
71841 AGACCTCCATG
1 AGACCTCCATG
71852 TTTAAATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 2 0.05
29 2 0.05
30 30 0.81
31 1 0.03
32 2 0.05
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (32 bp):
AGACCTCCATGCACATTGTGTTAAAGACGCCT
Found at i:74698 original size:39 final size:39
Alignment explanation
Indices: 74633--74741 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 39
74623 AATTAAAAGA
* * *
74633 AATAATTTAGATTGCTAAGGTAAAATAATTTAAAAAATT
1 AATAATTTAGAATGTTAAGGTGAAATAATTTAAAAAATT
*
74672 AATAATTTAGAATGTTACAGG-GAAATAATTTAAGAAATT
1 AATAATTTAGAATGTTA-AGGTGAAATAATTTAAAAAATT
* *
74711 AA-AATTTTAGAAGGTTAGGGTGAAATAATTT
1 AATAA-TTTAGAATGTTAAGGTGAAATAATTT
74742 GAGAATTAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
38 4 0.07
39 54 0.89
40 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.35
Consensus pattern (39 bp):
AATAATTTAGAATGTTAAGGTGAAATAATTTAAAAAATT
Found at i:76352 original size:35 final size:36
Alignment explanation
Indices: 76305--76400 Score: 106
Period size: 37 Copynumber: 2.7 Consensus size: 36
76295 CACATACATT
* *
76305 AATTACATTCTAAACCCCAAATTTC-AAAATACTTC
1 AATTACAATCTAAACCCCAAATTCCAAAAATACTTC
* *
76340 AATTACAATCTAAACCTCAAATTCCAAAAAATGCTTC
1 AATTACAATCTAAACCCCAAATTCC-AAAAATACTTC
**
76377 AATTAC-ATGCCCAACCCCAAATTC
1 AATTACAAT-CTAAACCCCAAATTC
76401 ATAATCCGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
35 22 0.43
36 2 0.04
37 27 0.53
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.27
Consensus pattern (36 bp):
AATTACAATCTAAACCCCAAATTCCAAAAATACTTC
Found at i:76993 original size:13 final size:13
Alignment explanation
Indices: 76975--77001 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
76965 GATTTAAATT
76975 TTATAAACTGAAC
1 TTATAAACTGAAC
76988 TTATAAACTGAAC
1 TTATAAACTGAAC
77001 T
1 T
77002 GAATTAGAAT
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:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TTATAAACTGAAC
Found at i:77387 original size:34 final size:35
Alignment explanation
Indices: 77317--77395 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 35
77307 AGGGTTGGGT
*
77317 ATGTAATTGAAGTATTTTGGAATTTGAGGTTCAGA
1 ATGTAATTGAAGCATTTTGGAATTTGAGGTTCAGA
* *
77352 ATGTAATTGAAGCATTTTGG-ATTTGGGGTTTAGA
1 ATGTAATTGAAGCATTTTGGAATTTGAGGTTCAGA
77386 ATGTAATTGA
1 ATGTAATTGA
77396 TGATTGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 22 0.54
35 19 0.46
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.41
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTGGAATTTGAGGTTCAGA
Found at i:80519 original size:81 final size:81
Alignment explanation
Indices: 79790--80484 Score: 1102
Period size: 81 Copynumber: 8.6 Consensus size: 81
79780 CCTCCGTTGG
* * *
79790 TGATTTTGAACCGAGGCCAAGCACAACGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
*
79855 AGAAATCATTCGTTAA
66 AGAAATCATTCGCTAA
* * * * *
79871 TGATTTTGAACCGAGGCCAAGCACAACGGCCTACGGAGACAATGATGTTGGCTTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
79936 AGAAATCATTCGCTAA
66 AGAAATCATTCGCTAA
* * *
79952 TGATTTTGAACCGAGACCAAGCGTATCGGCCTACGAAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
80017 AGAAATCATTCGCTAA
66 AGAAATCATTCGCTAA
* * *
80033 TGATTTTGAATCAAGACCAAGCGTATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
80098 AGAAATCATTCGCTAA
66 AGAAATCATTCGCTAA
*
80114 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGTCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
80179 AGAAATCATTCGCTAA
66 AGAAATCATTCGCTAA
80195 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
* * *
80260 ATAAATTATTCACTAA
66 AGAAATCATTCGCTAA
* * *
80276 TGATTTTGAACCGAGACCAAGCTTATCGGCCTATGGAGACAATGATGTTGGTCTTAAAGAAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
* *
80341 AGAAATCGTTCACTAA
66 AGAAATCATTCGCTAA
* *
80357 TGATTTTGAACCGAGACCAAGCGTATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGTAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
* *
80422 AGAAATTATTCACTAA
66 AGAAATCATTCGCTAA
* * * *
80438 TGATTTTGAACCGAGACCAAGCACAACGGCCTAGGGAGACGATGATG
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATG
80485 CTGATCTTAA
Statistics
Matches: 576, Mismatches: 38, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 576 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (81 bp):
TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
AGAAATCATTCGCTAA
Found at i:81333 original size:29 final size:31
Alignment explanation
Indices: 81272--81347 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 31
81262 TAAATTCTAT
*
81272 AAAATAATAT--TATAAT-TTATAAATATTA
1 AAAATAATATAATATAATATTATAAACATTA
*
81300 AAAAT-CTATAAT-TAATATTATAAACA-TA
1 AAAATAATATAATATAATATTATAAACATTA
81328 ACAAATAATATAATATAATA
1 A-AAATAATATAATATAATA
81348 ATATTATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 3 0.08
28 12 0.31
29 13 0.33
30 6 0.15
31 5 0.13
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAATAATATAATATAATATTATAAACATTA
Found at i:82436 original size:255 final size:255
Alignment explanation
Indices: 81985--82727 Score: 1378
Period size: 255 Copynumber: 2.9 Consensus size: 255
81975 AGCAAGCAAT
* *
81985 TGGGATGTTGGAGTTGGTTCCCAAACAGTTCATGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
1 TGGGATGTTGGAGTTGGTTCCCAGACAGTTCGTGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
82050 GAGGAGTGGCTCTACGAATGTTATGGAGACAAATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
66 GAGGAGTGGCTCTACGAATGTTATGGAGACAAATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
82115 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
131 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
*
82180 ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTCCCAAACAGTAAACCAA
196 ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTCCCAAACAATAAACCAA
82240 TGGGATGTTGGAGTTGGTTCCCAGACAGTTCGTGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
1 TGGGATGTTGGAGTTGGTTCCCAGACAGTTCGTGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
* *
82305 GAGGAGTGGCTCTACGAATGTTATGGAGACATATTGTAGGGAGCATGTAGTCGTAGAGCTGGATT
66 GAGGAGTGGCTCTACGAATGTTATGGAGACAAATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
82370 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
131 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
* * *
82435 ATGGAAACTGCTGTTTTTGATGTTAATGCTTATAGTACGGGTTCCCAGACAATAAACTAA
196 ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTCCCAAACAATAAACCAA
*
82495 TGGGATGTTGGAGTTGGTTCCCAGACAGTTCGTGATGGGGTAGCAACGCATGCTTCAATTTGTCA
1 TGGGATGTTGGAGTTGGTTCCCAGACAGTTCGTGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
* *
82560 GAGGAGTGGCTCTACGAATGTTATGGAGACAGATTGTAGGGAGCATGTAGTCGCAGGGCTGGATT
66 GAGGAGTGGCTCTACGAATGTTATGGAGACAAATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
82625 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
131 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
*
82690 ATGTAAACTGCTGCTTTTGATGTTAATGCTTATAGTAC
196 ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTAC
82728 AACTAATTTG
Statistics
Matches: 474, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
255 474 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (255 bp):
TGGGATGTTGGAGTTGGTTCCCAGACAGTTCGTGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
GAGGAGTGGCTCTACGAATGTTATGGAGACAAATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTCCCAAACAATAAACCAA
Found at i:84183 original size:22 final size:22
Alignment explanation
Indices: 84158--84204 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
84148 ATGACATGTA
*
84158 TTTCTCTATTTTATAGCACGTT
1 TTTCTCTATTTTATAACACGTT
* * *
84180 TTTCTTTGTTTTCTAACACGTT
1 TTTCTCTATTTTATAACACGTT
84202 TTT
1 TTT
84205 TTATCTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTCTCTATTTTATAACACGTT
Found at i:84213 original size:22 final size:22
Alignment explanation
Indices: 84174--84216 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
84164 TATTTTATAG
*
84174 CACGTTTTTCTTTGTTTTCTAA
1 CACGTTTTTCTTTCTTTTCTAA
84196 CACGTTTTT-TTATCTTTTCTA
1 CACGTTTTTCTT-TCTTTTCTA
84217 TCAGTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.14, C:0.19, G:0.07, T:0.60
Consensus pattern (22 bp):
CACGTTTTTCTTTCTTTTCTAA
Found at i:95445 original size:17 final size:17
Alignment explanation
Indices: 95423--95458 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
95413 TTATTAGTTT
95423 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
95440 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
95457 GT
1 GT
95459 AAAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (17 bp):
GTTAGTTTAGGGTTAGG
Found at i:95665 original size:30 final size:30
Alignment explanation
Indices: 95602--95701 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 30
95592 TAATTAATTT
* *
95602 TTTAGTAG-TGAA-TTATAATTAAAAAATAT
1 TTTATTAGTTGAAGTTAT-ATTAAAAAATAG
* *
95631 TTTATTAGTTTAAGTTATATTAAAGAATAG
1 TTTATTAGTTGAAGTTATATTAAAAAATAG
95661 TTTATTAGTTGAAGTTATATTAAAAAATAG
1 TTTATTAGTTGAAGTTATATTAAAAAATAG
95691 TTTATTAGTTG
1 TTTATTAGTTG
95702 TTTAAACAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
29 7 0.11
30 52 0.83
31 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (30 bp):
TTTATTAGTTGAAGTTATATTAAAAAATAG
Found at i:95782 original size:15 final size:16
Alignment explanation
Indices: 95754--95787 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
95744 GTTTGTTACT
95754 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
95770 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
95785 TTA
1 TTA
95788 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:96426 original size:49 final size:50
Alignment explanation
Indices: 96360--96764 Score: 325
Period size: 60 Copynumber: 7.4 Consensus size: 50
96350 CACAACTTTC
*
96360 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTC------A-T--T
*
96419 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT
1 -ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTC------A-T--T
*
96479 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
1 -ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
96530 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAACTTCATT
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
96579 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
96628 ATTACT-AATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCAATATT
1 ATTACTAAATCATTACT--ATCA--AATCATTAAAT-ATT--A-A-TAA---TAATTTC---A-T
96691 ACTAAT
50 -----T
*
96697 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
1 -ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
96748 ATTACT-AATCATTACTA
1 ATTACTAAATCATTACTA
96765 AATCTTATAA
Statistics
Matches: 311, Mismatches: 10, Indels: 59
0.82 0.03 0.16
Matches are distributed among these distances:
49 115 0.37
50 12 0.04
51 5 0.02
52 5 0.02
53 7 0.02
54 1 0.00
55 1 0.00
56 2 0.01
57 4 0.01
60 119 0.38
63 4 0.01
64 2 0.01
65 1 0.00
67 6 0.02
68 6 0.02
69 5 0.02
70 6 0.02
71 10 0.03
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (50 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:96429 original size:60 final size:60
Alignment explanation
Indices: 96358--96546 Score: 360
Period size: 60 Copynumber: 3.1 Consensus size: 60
96348 GGCACAACTT
96358 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
1 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
96418 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
1 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
* *
96478 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAA
1 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
96538 TCATTACTA
1 TCATTACTA
96547 TCAAATCATT
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 127 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.41
Consensus pattern (60 bp):
TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
Found at i:96434 original size:21 final size:22
Alignment explanation
Indices: 96360--96768 Score: 75
Period size: 18 Copynumber: 19.5 Consensus size: 22
96350 CACAACTTTC
96360 ATTACTAAATCATTACT-ATCAA
1 ATTACTAAATCATTACTAATC-A
* * *
96382 ATCATTAAAT-ATTAATAA-CA
1 ATTACTAAATCATTACTAATCA
* *
96402 ATT--T-CATTATTACTAATC-
1 ATTACTAAATCATTACTAATCA
96420 ATTACTAAATCATTACT-ATCAA
1 ATTACTAAATCATTACTAATC-A
* * *
96442 ATCATTAAAT-ATTAATAA-CA
1 ATTACTAAATCATTACTAATCA
* *
96462 ATT--T-CATTATTACTAATC-
1 ATTACTAAATCATTACTAATCA
96480 ATTACTAAATCATTACT-ATCAA
1 ATTACTAAATCATTACTAATC-A
* * *
96502 ATCATTAAAT-ATTAATAAT-A
1 ATTACTAAATCATTACTAATCA
* *
96522 ATT--T-TATTATTACTAATC-
1 ATTACTAAATCATTACTAATCA
** *
96540 ATTACTATCAAATCATTAAAAATTA
1 ATTAC--T-AAATCATTACTAATCA
** *
96565 ATAATAACTTCATTATTACTAATC-
1 AT--T-ACTAAATCATTACTAATCA
** *
96589 ATTACTATCAAATCATTAAAAATTA
1 ATTAC--T-AAATCATTACTAATCA
* *
96614 A-TAATAATTTCATTATTACTAATC-
1 ATTACTAA-ATCA-T--TACTAATCA
*
96638 ATTACTAAATCATTAAT-ATCAA
1 ATTACTAAATCATTACTAATC-A
* * *
96660 ATCATTAAAT-ATTAATAAT-A
1 ATTACTAAATCATTACTAATCA
*
96680 ATT--TCAAT-ATTACTAATC-
1 ATTACTAAATCATTACTAATCA
96698 ATTACTAAATCATTACT-ATCAA
1 ATTACTAAATCATTACTAATC-A
* * *
96720 ATCATTAAAT-ATTAATAAT-A
1 ATTACTAAATCATTACTAATCA
*
96740 ATT--T-CATCATTACTAATC-
1 ATTACTAAATCATTACTAATCA
96758 ATTACTAAATC
1 ATTACTAAATC
96769 TTATAAATAC
Statistics
Matches: 274, Mismatches: 60, Indels: 107
0.62 0.14 0.24
Matches are distributed among these distances:
17 8 0.03
18 61 0.22
19 2 0.01
20 34 0.12
21 60 0.22
22 54 0.20
23 3 0.01
24 26 0.09
25 22 0.08
26 1 0.00
27 1 0.00
28 2 0.01
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTACTAAATCATTACTAATCA
Found at i:96627 original size:120 final size:109
Alignment explanation
Indices: 96420--96764 Score: 412
Period size: 109 Copynumber: 3.2 Consensus size: 109
96410 ATTACTAATC
* * * *
96420 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAACTTCAATATTACTAATCATTAC
* *
96485 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
65 TAAATCATTACTATAAAATCATTAAATATTAATAATAATTTCATT
*
96530 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAACTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAACTTCAATATTACTAATCATTAC-
* * * * * * * * *
96595 ATCAAATCATTA--A-AAATTAATAATAAT-TTCATTATTA-CTAATC
65 -T-AAATCATTACTATAAAATCATTA-AATATTAATAATAATTTCATT
* * *
96638 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCAATATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAACTTCAATATTACTAATCATTAC
* *
96703 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
65 TAAATCATTACTATAAAATCATTAAATATTAATAATAATTTCATT
96748 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
96765 AATCTTATAA
Statistics
Matches: 198, Mismatches: 27, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
106 9 0.05
107 1 0.01
108 13 0.07
109 145 0.73
110 20 0.10
111 1 0.01
112 9 0.05
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (109 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAACTTCAATATTACTAATCATTACT
AAATCATTACTATAAAATCATTAAATATTAATAATAATTTCATT
Found at i:96650 original size:11 final size:10
Alignment explanation
Indices: 96628--96765 Score: 53
Period size: 10 Copynumber: 13.8 Consensus size: 10
96618 TAATTTCATT
96628 ATTACTAATC
1 ATTACTAATC
96638 ATTACTAAATC
1 ATTACT-AATC
*
96649 ATTAATATCAAATC
1 A-T--TA-CTAATC
96663 ATTA--AAT-
1 ATTACTAATC
* *
96670 ATTAATAATA
1 ATTACTAATC
*
96680 ATTTC-AAT-
1 ATTACTAATC
96688 ATTACTAATC
1 ATTACTAATC
96698 ATTACTAAATC
1 ATTACT-AATC
96709 ATTACTATCAAATC
1 ATTAC--T--AATC
96723 ATTA--AAT-
1 ATTACTAATC
* *
96730 ATTAATAATA
1 ATTACTAATC
*
96740 ATT--TCATC
1 ATTACTAATC
96748 ATTACTAATC
1 ATTACTAATC
96758 ATTACTAA
1 ATTACTAA
96766 ATCTTATAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 38
0.69 0.05 0.26
Matches are distributed among these distances:
7 8 0.08
8 16 0.16
9 12 0.12
10 30 0.29
11 16 0.16
12 1 0.01
13 2 0.02
14 16 0.16
15 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTACTAATC
Found at i:96658 original size:60 final size:60
Alignment explanation
Indices: 96579--96768 Score: 337
Period size: 60 Copynumber: 3.2 Consensus size: 60
96569 TAACTTCATT
*
96579 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
96638 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCAATATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
96698 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
96758 ATTACTAAATC
1 ATTACTAAATC
96769 TTATAAATAC
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
59 6 0.05
60 118 0.95
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:96739 original size:218 final size:219
Alignment explanation
Indices: 96360--96764 Score: 740
Period size: 218 Copynumber: 1.9 Consensus size: 219
96350 CACAACTTTC
*
96360 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTAC
* *
96425 TAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAAT
66 TAAATCATTAATATCAAATCATTAAATATTAATAACAATTTCAATATTACTAATCATTACTAAAT
* *
96490 CATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATCATTACTATCAAATCA
131 CATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTATCAAATCA
96555 TTAAAAATTAATAATAACTTCATT
196 TTAAAAATTAATAATAACTTCATT
*
96579 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTAC
*
96643 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCAATATTACTAATCATTACTAAAT
66 TAAATCATTAATATCAAATCATTAAATATTAATAACAATTTCAATATTACTAATCATTACTAAAT
96708 CATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTA
131 CATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTA
96765 AATCTTATAA
Statistics
Matches: 179, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
218 173 0.97
219 6 0.03
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (219 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTAC
TAAATCATTAATATCAAATCATTAAATATTAATAACAATTTCAATATTACTAATCATTACTAAAT
CATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTATCAAATCA
TTAAAAATTAATAATAACTTCATT
Found at i:96751 original size:39 final size:39
Alignment explanation
Indices: 96586--96754 Score: 100
Period size: 39 Copynumber: 4.3 Consensus size: 39
96576 ATTATTACTA
*
96586 ATCATTACTATCAAATCATTAAAAATTAATAATAATTTC
1 ATCATTACTATCAAATCATTAAATATTAATAATAATTTC
* * *
96625 ATTATTACTAATC--ATTACTAAATCATTAAT-ATCAA----
1 ATCATTACT-ATCAAATCATTAAAT-ATTAATAAT-AATTTC
* * * * * * *
96660 ATCATTAAATATTAATAATAATTTCAATATTACTAATCATTACTAA
1 ATCATT-ACTA-TCA-AATCA-TTAAATATTAATAATAATT--T-C
96706 ATCATTACTATCAAATCATTAAATATTAATAATAATTTC
1 ATCATTACTATCAAATCATTAAATATTAATAATAATTTC
96745 ATCATTACTA
1 ATCATTACTA
96755 ATCATTACTA
Statistics
Matches: 94, Mismatches: 19, Indels: 34
0.64 0.13 0.23
Matches are distributed among these distances:
35 6 0.06
36 3 0.03
38 9 0.10
39 35 0.37
40 10 0.11
42 16 0.17
43 4 0.04
44 2 0.02
45 3 0.03
46 6 0.06
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (39 bp):
ATCATTACTATCAAATCATTAAATATTAATAATAATTTC
Found at i:104227 original size:2 final size:2
Alignment explanation
Indices: 104220--104247 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
104210 TTAGTTTAAA
104220 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
104248 TTAAGATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110530 original size:16 final size:15
Alignment explanation
Indices: 110495--110528 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
110485 ATATTCATGA
110495 ATATAATTTTTACAT
1 ATATAATTTTTACAT
*
110510 GTATAATTTTTA-AT
1 ATATAATTTTTACAT
110524 ATATA
1 ATATA
110529 TATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATAATTTTTACAT
Found at i:111150 original size:2 final size:2
Alignment explanation
Indices: 111143--111175 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
111133 AACGTCGTTG
111143 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
111176 AAGAGGTTCG
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:111635 original size:20 final size:20
Alignment explanation
Indices: 111612--111663 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
111602 ACAGGTTCCA
111612 AAATCGCAACGCGAATA-GAT
1 AAATCGCAACGCGAATATG-T
*
111632 AAATCGCAACTCGAATATGT
1 AAATCGCAACGCGAATATGT
111652 AAATCGCAACGC
1 AAATCGCAACGC
111664 AATTTTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:111749 original size:57 final size:58
Alignment explanation
Indices: 111654--111855 Score: 345
Period size: 57 Copynumber: 3.5 Consensus size: 58
111644 GAATATGTAA
* * *
111654 ATCGCAACGCAATTTTCCAAAATCGCAACACTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAACGCGATTTTCCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
**
111712 ATCGCAACGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTT
1 ATCGCAACGCGATTTTCCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
111769 ATCGCAACGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAACGCGATTTTCCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
111826 ATCGCAACGCGATTTTCCAAATTCGCAACG
1 ATCGCAACGCGATTTTCCAAATTCGCAACG
111856 AGATTTTCAA
Statistics
Matches: 136, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
57 108 0.79
58 28 0.21
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (58 bp):
ATCGCAACGCGATTTTCCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
Found at i:111868 original size:20 final size:21
Alignment explanation
Indices: 111827--111875 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
111817 AACAGTACTA
*
111827 TCGCAACGCGATTTTCCAAAT
1 TCGCAACGAGATTTTCCAAAT
111848 TCGCAACGAGATTTT-CAAAT
1 TCGCAACGAGATTTTCCAAAT
111868 TCGCAACG
1 TCGCAACG
111876 CTAATTACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (21 bp):
TCGCAACGAGATTTTCCAAAT
Found at i:111937 original size:20 final size:20
Alignment explanation
Indices: 111914--111952 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
111904 ATTGCAACTC
111914 GATTTTCAAATTCGCAACGA
1 GATTTTCAAATTCGCAACGA
111934 GATTTTCAAATTCGCAACG
1 GATTTTCAAATTCGCAACG
111953 CTAATTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (20 bp):
GATTTTCAAATTCGCAACGA
Found at i:111968 original size:77 final size:77
Alignment explanation
Indices: 111770--112359 Score: 416
Period size: 77 Copynumber: 7.6 Consensus size: 77
111760 AACAGTGTTA
*
111770 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
1 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
111835 CGATTTTCCAAAT
66 CGATTTT-CAAAT
* * * *
111848 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGCTATAGGTAAACAATACTATTGCAACT
1 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
111913 CGATTTTCAAAT
66 CGATTTTCAAAT
* **
111925 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACAGATATAGGTAAACAGTGTTATCGCAACG
1 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
*
111990 CGATTTACAAAT
66 CGATTTTCAAAT
** * ** * * * * *** *
112002 TCGCAACGCTA-ATTACCGATATAGGTAAACAG-T-ACTATCGCA-A-CGCGATTTTCA--AAT-
1 TCGCAACG--AGATTTTC-AAATTCG-CAAC-GCTAATTACCG-ATATAG-G-TAAACAGTACTA
* ** *
112059 TCGCAACGCTAATTACCGATAT
58 TCGCAACGC-GATTTTC-AAAT
* * ** * * * * *
112081 AT-GTAAAC-AG-TGTTATCGCAACACG-AACAG-T-GTTATCGCA-A-A-GTGAATAGGTA-AA
1 -TCG-CAACGAGAT-TT-TC-AAATTCGCAAC-GCTAATTACCG-ATATAGGTAAACA-GTACTA
112136 TCGCAACGC-AGTTTTCCAAAT
58 TCGCAACGCGA-TTTT-CAAAT
*
112157 TCGCAACGAGATTTTCAAATTTGCAAC-CTTAATTACCGATATAGGTAAACAGTACTATCGCAAC
1 TCGCAACGAGATTTTCAAATTCGCAACGC-TAATTACCGATATAGGTAAACAGTACTATCGCAAC
*
112221 ACGATTTAT-AAAT
65 GCGATTT-TCAAAT
*
112234 TCGCAAC-ACGATTTTCAAATTCGCAATGCTAATTACCGATATAGGTAAACAGTACTATCGCAAC
1 TCGCAACGA-GATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAC
* *
112298 ACGATTTACAAAT
65 GCGATTTTCAAAT
* *
112311 TCGCAAC-ACGATTTTTAAATTCGCAATGCTAATTACCGATATAGGTAAA
1 TCGCAACGA-GATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAA
112360 AAATCGCAAC
Statistics
Matches: 410, Mismatches: 65, Indels: 75
0.75 0.12 0.14
Matches are distributed among these distances:
74 5 0.01
75 13 0.03
76 17 0.04
77 244 0.60
78 96 0.23
79 22 0.05
80 12 0.03
81 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (77 bp):
TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
CGATTTTCAAAT
Found at i:111986 original size:57 final size:57
Alignment explanation
Indices: 111925--112102 Score: 302
Period size: 57 Copynumber: 3.1 Consensus size: 57
111915 ATTTTCAAAT
* *
111925 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACAGATATAGGTAAACAGTGTTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTA
* **
111982 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTA
*
112039 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATATGTAAACAGTGTTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTA
112096 TCGCAAC
1 TCGCAAC
112103 ACGAACAGTG
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 112 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (57 bp):
TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTA
Found at i:112156 original size:20 final size:19
Alignment explanation
Indices: 112133--112176 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
112123 GTGAATAGGT
112133 AAATCGCAACGCAG-TTTTCC
1 AAATCGCAACG-AGATTTT-C
112153 AAATTCGCAACGAGATTTTC
1 AAA-TCGCAACGAGATTTTC
112173 AAAT
1 AAAT
112177 TTGCAACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.05
20 9 0.41
21 12 0.55
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (19 bp):
AAATCGCAACGAGATTTTC
Found at i:112177 original size:20 final size:21
Alignment explanation
Indices: 112136--112183 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
112126 AATAGGTAAA
112136 TCGCAACGCAGTTTTCCAAAT
1 TCGCAACGCAGTTTTCCAAAT
112157 TCGCAACG-AGATTTT-CAAAT
1 TCGCAACGCAG-TTTTCCAAAT
*
112177 TTGCAAC
1 TCGCAAC
112184 CTTAATTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (21 bp):
TCGCAACGCAGTTTTCCAAAT
Found at i:112239 original size:20 final size:20
Alignment explanation
Indices: 112214--112259 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
112204 AACAGTACTA
112214 TCGCAACACGATTTAT-AAAT
1 TCGCAACACGATTT-TCAAAT
112234 TCGCAACACGATTTTCAAAT
1 TCGCAACACGATTTTCAAAT
112254 TCGCAA
1 TCGCAA
112260 TGCTAATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (20 bp):
TCGCAACACGATTTTCAAAT
Found at i:112316 original size:20 final size:20
Alignment explanation
Indices: 112291--112336 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
112281 AACAGTACTA
112291 TCGCAACACGATTTACAAAT
1 TCGCAACACGATTTACAAAT
**
112311 TCGCAACACGATTTTTAAAT
1 TCGCAACACGATTTACAAAT
112331 TCGCAA
1 TCGCAA
112337 TGCTAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (20 bp):
TCGCAACACGATTTACAAAT
Found at i:112457 original size:37 final size:37
Alignment explanation
Indices: 112331--112480 Score: 166
Period size: 37 Copynumber: 4.2 Consensus size: 37
112321 ATTTTTAAAT
* * *
112331 TCGCAATGCTAATTACCGATATAGGTAAA-A--A--A
1 TCGCAACGCTAATTACCGATGTACGTAAACAGTACTA
* * * **
112363 TCGCAACGCTAATTACCGATATAGGTATACAGTGTTA
1 TCGCAACGCTAATTACCGATGTACGTAAACAGTACTA
*
112400 TCGCAACGCTAATTACCGATGTACGTACACAGTACTA
1 TCGCAACGCTAATTACCGATGTACGTAAACAGTACTA
* *
112437 TCGCAACGCTAATTACCGATGTACATAAATAGTACTA
1 TCGCAACGCTAATTACCGATGTACGTAAACAGTACTA
112474 TCGCAAC
1 TCGCAAC
112481 ACGATTTTGG
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
32 27 0.26
33 1 0.01
37 74 0.73
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (37 bp):
TCGCAACGCTAATTACCGATGTACGTAAACAGTACTA
Found at i:115479 original size:21 final size:21
Alignment explanation
Indices: 115453--115495 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
115443 TGATTTTAAA
115453 AAAATTAAAAATTTAAATATT
1 AAAATTAAAAATTTAAATATT
* * *
115474 AAAATTGATAATTTAGATATT
1 AAAATTAAAAATTTAAATATT
115495 A
1 A
115496 GTAGTTTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAATTAAAAATTTAAATATT
Found at i:116559 original size:20 final size:20
Alignment explanation
Indices: 116536--116597 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
116526 TTTATGTTTA
116536 TATTAAGTTCTATATAAATT
1 TATTAAGTTCTATATAAATT
*
116556 TATTAA-TT-TATGT---TT
1 TATTAAGTTCTATATAAATT
116571 ATATTAAGTTCTATATAAATT
1 -TATTAAGTTCTATATAAATT
116592 TATTAA
1 TATTAA
116598 TTTATGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 2 0.06
16 6 0.18
17 2 0.06
18 8 0.24
19 2 0.06
20 12 0.35
21 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
TATTAAGTTCTATATAAATT
Found at i:116572 original size:36 final size:36
Alignment explanation
Indices: 116477--116621 Score: 256
Period size: 36 Copynumber: 4.0 Consensus size: 36
116467 TGTTTTTGGT
116477 TAAATTTATTAATTTATGTTTATATTAAGTTCTATA
1 TAAATTTATTAATTTATGTTTATATTAAGTTCTATA
*
116513 T-AATATTAGTATATTTATGTTTATATTAAGTTCTATA
1 TAAAT-TTATTA-ATTTATGTTTATATTAAGTTCTATA
116550 TAAATTTATTAATTTATGTTTATATTAAGTTCTATA
1 TAAATTTATTAATTTATGTTTATATTAAGTTCTATA
116586 TAAATTTATTAATTTATGTTTATATTAAGTTCTATA
1 TAAATTTATTAATTTATGTTTATATTAAGTTCTATA
116622 CAATATTAAG
Statistics
Matches: 104, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
35 3 0.03
36 67 0.64
37 31 0.30
38 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (36 bp):
TAAATTTATTAATTTATGTTTATATTAAGTTCTATA
Found at i:117317 original size:13 final size:13
Alignment explanation
Indices: 117301--117326 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
117291 AAAAAGTATC
117301 ATTAATTTAAATA
1 ATTAATTTAAATA
117314 ATTAATTTAAATA
1 ATTAATTTAAATA
117327 TTTTATTAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTAATTTAAATA
Found at i:117865 original size:24 final size:24
Alignment explanation
Indices: 117838--117901 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
117828 CACGATATCG
*
117838 TCAAAAATATTAACATTATCAACA
1 TCAAAATTATTAACATTATCAACA
* * *
117862 TCAACATTATTAGGC-TTATCAATA
1 TCAAAATTATTA-ACATTATCAACA
*
117886 TCAAAATTATAAACAT
1 TCAAAATTATTAACAT
117902 CAACATGCTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
23 1 0.03
24 29 0.94
25 1 0.03
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (24 bp):
TCAAAATTATTAACATTATCAACA
Found at i:118516 original size:64 final size:65
Alignment explanation
Indices: 118415--118544 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 65
118405 ATTCTTATTC
* * *
118415 TTCTTCTTGAATTTGAATGAATTGAATTGTGAGTATGGTATA-AAAATGAATAATATAAGAATAT
1 TTCTTCTTGAATTTGAATGAAGTGAATGGTGAGTATGGTATATAAAAGGAATAATATAAGAATAT
* *
118479 TTCTTTTTGAATTTGAATGAAGTGAATGGT-AGGTATGGTATATAAAAGGAATAATTTAAGAATA
1 TTCTTCTTGAATTTGAATGAAGTGAATGGTGA-GTATGGTATATAAAAGGAATAATATAAGAATA
118543 T
65 T
118544 T
1 T
118545 AAATTAGAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
63 1 0.02
64 37 0.63
65 21 0.36
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.39
Consensus pattern (65 bp):
TTCTTCTTGAATTTGAATGAAGTGAATGGTGAGTATGGTATATAAAAGGAATAATATAAGAATAT
Found at i:119567 original size:21 final size:20
Alignment explanation
Indices: 119537--119577 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
119527 TAAGGCGCAG
*
119537 GGGATCGATCCTTTTACCAAA
1 GGGATCGATCATTTT-CCAAA
*
119558 GGGATTGATCATTTTCCAAA
1 GGGATCGATCATTTTCCAAA
119578 TATTCCGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (20 bp):
GGGATCGATCATTTTCCAAA
Found at i:119665 original size:20 final size:20
Alignment explanation
Indices: 119640--119694 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
119630 AGTTTCCTCG
*
119640 AGGGATCAATCCTTTTG-TCA
1 AGGGATCGATCCTTTTGCT-A
*
119660 AGGGATCGATCATTTTGCTA
1 AGGGATCGATCCTTTTGCTA
*
119680 AGGGGTCGATCCTTT
1 AGGGATCGATCCTTT
119695 GAGCCAGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (20 bp):
AGGGATCGATCCTTTTGCTA
Found at i:120693 original size:22 final size:21
Alignment explanation
Indices: 120643--120697 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
120633 AACCCTCTAT
*
120643 ATATTATTTTTTTCAATTAAA
1 ATATTATTTTTTTCAATAAAA
* * *
120664 TTACTATTTTTATTGAATAAAA
1 ATATTATTTTT-TTCAATAAAA
120686 ATATTATTTTTT
1 ATATTATTTTTT
120698 ATTATTTTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATTATTTTTTTCAATAAAA
Found at i:120868 original size:2 final size:2
Alignment explanation
Indices: 120861--120902 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
120851 TTCTCATCCC
120861 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
120903 CACACACACG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:125606 original size:111 final size:112
Alignment explanation
Indices: 125412--125671 Score: 353
Period size: 111 Copynumber: 2.3 Consensus size: 112
125402 CATACATACA
* ** * * *
125412 TGAGGGTGCTCTTTGTAGACAAAGGGAGCTTCAAAA-ATTCATTGACACACACATACATACATAC
1 TGAGGGTGCTCTTTGTAAACAAAGGGAGCTTCAAAATAAGCACTGACACACACACACACACATAC
* * *
125476 ATGCATGCATAACTCTTTTGTTTGCCATCTTTCCATATGCAGGCACT
66 ATACATACATAACTCTTTTGCTTGCCATCTTTCCATATGCAGGCACT
* * *
125523 TGAGGGTGCTCTTTTTAAACAAA-GAAGCTTCAAAATAAGCCCTGACACACACACACACACATAC
1 TGAGGGTGCTCTTTGTAAACAAAGGGAGCTTCAAAATAAGCACTGACACACACACACACACATAC
*
125587 ATACATACATAACTCTTTTGCTTGCTATCTTTCCATATGCAGGCACT
66 ATACATACATAACTCTTTTGCTTGCCATCTTTCCATATGCAGGCACT
* * *
125634 TAAGGATGCTCTTGGTAAACAAAGGGAGCTTCAGAAAT
1 TGAGGGTGCTCTTTGTAAACAAAGGGAGCTTCA-AAAT
125672 TCATCGACAG
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
110 11 0.09
111 105 0.82
112 8 0.06
113 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (112 bp):
TGAGGGTGCTCTTTGTAAACAAAGGGAGCTTCAAAATAAGCACTGACACACACACACACACATAC
ATACATACATAACTCTTTTGCTTGCCATCTTTCCATATGCAGGCACT
Found at i:126426 original size:19 final size:19
Alignment explanation
Indices: 126394--126430 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
126384 ATGACCAACA
*
126394 AAATCACAATGCGATCTCT
1 AAATCACAACGCGATCTCT
*
126413 AAATCGCAACGCGATCTC
1 AAATCACAACGCGATCTC
126431 CAGTATCGCA
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:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCACAACGCGATCTCT
Found at i:131154 original size:21 final size:21
Alignment explanation
Indices: 131128--131176 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
131118 CACATCAAAT
131128 CGTCCCCAAATAAACTTTGAC
1 CGTCCCCAAATAAACTTTGAC
*
131149 CGTCCCCAAGTAAACTTTGAC
1 CGTCCCCAAATAAACTTTGAC
*
131170 CATCCCC
1 CGTCCCC
131177 GAATTTAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.39, G:0.10, T:0.22
Consensus pattern (21 bp):
CGTCCCCAAATAAACTTTGAC
Found at i:134458 original size:41 final size:41
Alignment explanation
Indices: 134374--134633 Score: 149
Period size: 41 Copynumber: 6.3 Consensus size: 41
134364 TTTTATGTAA
*
134374 AAACGCCGCTAAA-ACT-CGTACTTTAGTGGCGTTTATACGAC
1 AAACGCCGCTAAAGA-TACGTACTTTAGTGGCGTTTATA-AAC
* * *
134415 AAACGCCGCTAAAGATAAGTACTTTAGTAGCGTTTGTAAAC
1 AAACGCCGCTAAAGATACGTACTTTAGTGGCGTTTATAAAC
* * * * *
134456 AAACGCCACCATAGA-ATCGTTCTTTAGTGGCGTTTTTAAAC
1 AAACGCCGCTAAAGATA-CGTACTTTAGTGGCGTTTATAAAC
* * * * * * *
134497 AAACGCCGC-AATAGGGTACATA-TATCGTTGCGTTTTTAAAT
1 AAACGCCGCTAA-A-GATACGTACTTTAGTGGCGTTTATAAAC
*** ** *
134538 AAACGCCGCTAAACCCAAATACTTTAGTGGCGTTTTATTCAA-
1 AAACGCCGCTAAAGATACGTACTTTAGTGGCG-TTTA-TAAAC
* * * *
134580 AAACGCCGCTAAATACT-CATACTTTAGTGACGATTT-TAGAC
1 AAACGCCGCTAAAGA-TACGTACTTTAGTGGCG-TTTATAAAC
134621 AAACGCCGCTAAA
1 AAACGCCGCTAAA
134634 ACCTAGTACT
Statistics
Matches: 170, Mismatches: 37, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
40 8 0.05
41 102 0.60
42 56 0.33
43 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (41 bp):
AAACGCCGCTAAAGATACGTACTTTAGTGGCGTTTATAAAC
Found at i:134644 original size:41 final size:40
Alignment explanation
Indices: 134538--134646 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 40
134528 GTTTTTAAAT
* * *
134538 AAACGCCGCTAAACCCAAATACTTTAGTGGCGTTTTATTCAA
1 AAACGCCGCTAAAACC-TATACTTTAGTGACGTTTTA-TCAA
* *
134580 AAACGCCGCTAAATA-CTCATACTTTAGTGACGATTTTA-GAC
1 AAACGCCGCTAAA-ACCT-ATACTTTAGTGACG-TTTTATCAA
134621 AAACGCCGCTAAAACCTAGTACTTTA
1 AAACGCCGCTAAAACCTA-TACTTTA
134647 TTGGCATTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
40 2 0.04
41 23 0.40
42 27 0.47
43 5 0.09
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (40 bp):
AAACGCCGCTAAAACCTATACTTTAGTGACGTTTTATCAA
Found at i:137216 original size:43 final size:43
Alignment explanation
Indices: 137163--137448 Score: 373
Period size: 43 Copynumber: 6.7 Consensus size: 43
137153 GTTTGTATAG
* *
137163 AAAAACGCCGCTATAAATCTCGACCTTTTGCAGCATTTGTTCA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
137206 AAAAACGCCGCTATAGATCT-AACCTTTTGCGGCATTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
137248 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
137291 AAAAACGCCGCTATAGATCT-GACCTTTTACGGCATTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* ** * *
137333 AAAAACGCCACTATAAATCTTTACCTTTAGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* * ** *
137376 AAAAGCGCCGCTATAGATCTCGACCTTTTGCGGTGTTTGTTCA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
*
137419 AAAAACGCCGCTAT--ATCTCGACTTTTTGCG
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCG
137449 TTTTTGTTCT
Statistics
Matches: 213, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
41 15 0.07
42 75 0.35
43 123 0.58
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (43 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
Found at i:137298 original size:85 final size:85
Alignment explanation
Indices: 137163--137470 Score: 403
Period size: 85 Copynumber: 3.7 Consensus size: 85
137153 GTTTGTATAG
* * *
137163 AAAAACGCCGCTATAAATCTCGACCTTTTGC-AGCATTTGTTCAAAAAACGCCGCTATAGATCTA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGA-CTTTTGTTCCAAAAACGCCGCTATAGATCTG
137227 ACCTTTTGCGGCATTTGTTCC
65 ACCTTTTGCGGCATTTGTTCC
137248 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCCAAAAACGCCGCTATAGATCTGA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCCAAAAACGCCGCTATAGATCTGA
*
137313 CCTTTTACGGCATTTGTTCC
66 CCTTTTGCGGCATTTGTTCC
* ** * * * *
137333 AAAAACGCCACTATAAATCTTTACCTTTAGCGGCGTTTGTTCCAAAAGCGCCGCTATAGATCTCG
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCCAAAAACGCCGCTATAGATCT-G
** *
137398 ACCTTTTGCGGTGTTTGTTCA
65 ACCTTTTGCGGCATTTGTTCC
* *
137419 AAAAACGCCGCTAT--ATCTCGACTTTTTGCG-TTTTTGTTCTC--AAACGCCGCTA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTC-CAAAAACGCCGCTA
137471 ACTTTAGCGG
Statistics
Matches: 197, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
82 10 0.05
83 7 0.04
84 13 0.07
85 135 0.69
86 32 0.16
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (85 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCCAAAAACGCCGCTATAGATCTGA
CCTTTTGCGGCATTTGTTCC
Found at i:137396 original size:128 final size:128
Alignment explanation
Indices: 137163--137445 Score: 394
Period size: 128 Copynumber: 2.2 Consensus size: 128
137153 GTTTGTATAG
* * *
137163 AAAAACGCCGCTATAAATCTCGACCTTTTGCAGCATTTGTTCAAAAAACGCCGCTATAGATCTAA
1 AAAAACGCCGCTATAAATCTCGACCTTTTACAGCATTTGTTCAAAAAACGCCACTATAAATCTAA
* *
137228 CCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAAATCTCGACCTTTTGCGACT-TTTGTTCC
66 CCTTTAGCGGCATTTGTTCCAAAAACGCCGCTATAAATCTCGACCTTTTGCG-CTGTTTGTTCA
* * * *
137291 AAAAACGCCGCTATAGATCT-GACCTTTTACGGCATTTGTTCCAAAAACGCCACTATAAATCTTT
1 AAAAACGCCGCTATAAATCTCGACCTTTTACAGCATTTGTTCAAAAAACGCCACTATAAATC-TA
* * * *
137355 ACCTTTAGCGGCGTTTGTTCCAAAAGCGCCGCTATAGATCTCGACCTTTTGCGGTGTTTGTTCA
65 ACCTTTAGCGGCATTTGTTCCAAAAACGCCGCTATAAATCTCGACCTTTTGCGCTGTTTGTTCA
*
137419 AAAAACGCCGCTAT--ATCTCGACTTTTT
1 AAAAACGCCGCTATAAATCTCGACCTTTT
137446 GCGTTTTTGT
Statistics
Matches: 138, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
126 4 0.03
127 44 0.32
128 90 0.65
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (128 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTACAGCATTTGTTCAAAAAACGCCACTATAAATCTAA
CCTTTAGCGGCATTTGTTCCAAAAACGCCGCTATAAATCTCGACCTTTTGCGCTGTTTGTTCA
Found at i:142254 original size:6 final size:6
Alignment explanation
Indices: 142243--142294 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
142233 TTTTTATATC
* *
142243 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTCTAA ATTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
142291 TTTT
1 TTTT
142295 TAAATATCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:145241 original size:29 final size:30
Alignment explanation
Indices: 145199--145280 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 30
145189 CGTACTGAAA
*
145199 TAAAATAA-AA-TTAAACATT-AAATATGATT
1 TAAAATAATAATTTAAATATTAAAATA-GA-T
145228 TAAAA-AAT-ATTTAAATATTAAAATAGAT
1 TAAAATAATAATTTAAATATTAAAATAGAT
145256 TAAAATTAATAATTTAAATATTAAA
1 TAAAA-TAATAATTTAAATATTAAA
145281 GTTATATTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
28 9 0.20
29 15 0.33
30 8 0.17
31 14 0.30
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (30 bp):
TAAAATAATAATTTAAATATTAAAATAGAT
Found at i:146351 original size:2 final size:2
Alignment explanation
Indices: 146344--146416 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
146334 ATTAAACAAG
146344 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
146385 AT AT AT AT AT AT AT AT AT -T AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
146417 CATGTATGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 65 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.