Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008697.1 Hibiscus syriacus cultivar Beakdansim tig00111727_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: 196991
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:2264 original size:22 final size:21
Alignment explanation
Indices: 2234--2278 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2224 AATCTCCATT
2234 TCATCATCAACACCA-ACAACA
1 TCATCATCAACACCATA-AACA
*
2255 TCATCCATCAAGACCATAAACA
1 TCAT-CATCAACACCATAAACA
2277 TC
1 TC
2279 TTCTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 16 0.76
23 1 0.05
ACGTcount: A:0.44, C:0.36, G:0.02, T:0.18
Consensus pattern (21 bp):
TCATCATCAACACCATAAACA
Found at i:2627 original size:21 final size:18
Alignment explanation
Indices: 2598--2640 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
2588 TCAAGATAAA
2598 AAGAAAAAAAATCAGAAAAG
1 AAGAAAAAAAA--AGAAAAG
2618 AAGAAAAAAAAAGAAAAG
1 AAGAAAAAAAAAGAAAAG
2636 AAGAA
1 AAGAA
2641 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 12 0.52
20 11 0.48
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAAAAGAAAAG
Found at i:12936 original size:33 final size:33
Alignment explanation
Indices: 12894--12962 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
12884 TGTTGATGAA
*
12894 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
12927 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
12960 GAA
1 GAA
12963 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:13003 original size:36 final size:36
Alignment explanation
Indices: 12933--13047 Score: 160
Period size: 38 Copynumber: 3.2 Consensus size: 36
12923 AATGGAAGGA
* *
12933 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
12968 TGATGATATAGGCGTGATAATGGTGATGGACTATGGTG
1 TGATGATATAGGCGTGATAATGGTGATGGAATAT-G-G
* *
13006 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
13042 TGATGA
1 TGATGA
13048 AAAATAGTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 16 0.22
36 21 0.29
37 2 0.03
38 33 0.46
ACGTcount: A:0.27, C:0.03, G:0.37, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:13005 original size:13 final size:11
Alignment explanation
Indices: 12947--13047 Score: 53
Period size: 13 Copynumber: 8.3 Consensus size: 11
12937 GTTATTGGCG
12947 TGATATGGTGA
1 TGATATGGTGA
12958 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
12971 TGATATAGGCG-
1 TGATAT-GGTGA
12982 TGATAATGGTGA
1 TGAT-ATGGTGA
12994 TGGACTATGGTGTGA
1 T-GA-TAT-G-GTGA
*
13009 TGATATAGGCG-
1 TGATAT-GGTGA
*
13020 TGATAATGGAGA
1 TGAT-ATGGTGA
13032 TGGATTATGGTGA
1 T-GA-TATGGTGA
13045 TGA
1 TGA
13048 AAAATAGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 25
0.70 0.06 0.25
Matches are distributed among these distances:
11 19 0.27
12 15 0.21
13 27 0.38
14 5 0.07
15 5 0.07
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:14590 original size:33 final size:33
Alignment explanation
Indices: 14553--14616 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
14543 TGATGAATGA
*
14553 ATGAT-TTAATGGTGATGAAATGGTAATGGAAGG
1 ATGATGTTAATGGCG-TGAAATGGTAATGGAAGG
* * *
14586 ATGATGTTATTGGCGTGATATGGTGATGGAA
1 ATGATGTTAATGGCGTGAAATGGTAATGGAA
14617 TATGGTGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 19 0.73
34 7 0.27
ACGTcount: A:0.31, C:0.02, G:0.34, T:0.33
Consensus pattern (33 bp):
ATGATGTTAATGGCGTGAAATGGTAATGGAAGG
Found at i:14648 original size:35 final size:36
Alignment explanation
Indices: 14587--14696 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 36
14577 AATGGAAGGA
* *
14587 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
14622 TG-TGATATAGGCGTGATAATGGTGATGG-CTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
14656 TGATGATATAGGCGTG-TAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
14691 TGATGA
1 TGATGA
14697 AAATAGTATC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
34 31 0.46
35 36 0.54
ACGTcount: A:0.25, C:0.04, G:0.37, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:21669 original size:45 final size:45
Alignment explanation
Indices: 21578--21669 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
21568 TTCTTCCAAA
* * * **
21578 GACACGTTCATTGAATGGAAAATGGTGTCCTTTTGCTGTTTGATG
1 GACACGTCCATTGAATGAAAAATGGTATCCTTTTGCTGTTCAATG
* *
21623 GACACGTCCTTTGAATGAAAAA-GTGTATCCTTTTGTTGTTCAATG
1 GACACGTCCATTGAATGAAAAATG-GTATCCTTTTGCTGTTCAATG
21668 GA
1 GA
21670 TATTTCTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (45 bp):
GACACGTCCATTGAATGAAAAATGGTATCCTTTTGCTGTTCAATG
Found at i:24590 original size:36 final size:35
Alignment explanation
Indices: 24505--24596 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
24495 GCGTGAAACG
* * * * *
24505 GTGATAGAAGATGGTAATGATATAGACATGCAATG
1 GTGATGGAAGATGGTGATGTTATAGACATGAAATA
* * *
24540 GTAATGGAATATGGTGATGTTATAGTCATGAAAATA
1 GTGATGGAAGATGGTGATGTTATAGACATG-AAATA
24576 GTGATGGAAGATGGTGATGTT
1 GTGATGGAAGATGGTGATGTT
24597 TAGGTAGTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
35 24 0.52
36 22 0.48
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.30
Consensus pattern (35 bp):
GTGATGGAAGATGGTGATGTTATAGACATGAAATA
Found at i:25143 original size:117 final size:117
Alignment explanation
Indices: 24937--25162 Score: 452
Period size: 117 Copynumber: 1.9 Consensus size: 117
24927 GTCTTAAAAT
24937 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
1 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
25002 CTTGGCGCCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAGGGTTCAAC
66 CTTGGCGCCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAGGGTTCAAC
25054 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
1 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
25119 CTTGGCGCCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAG
66 CTTGGCGCCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAG
25163 AGAACCCTCT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 109 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (117 bp):
GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
CTTGGCGCCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAGGGTTCAAC
Found at i:47761 original size:36 final size:33
Alignment explanation
Indices: 47688--47761 Score: 78
Period size: 36 Copynumber: 2.2 Consensus size: 33
47678 TATCTTCACT
* * *
47688 TTCTTATTATTTCATTTCCTTTTCTTTCATCTT
1 TTCTTATTATTTCATATCCTTTTCTTCCATCTC
47721 TTCTTATTTCATTATCATATCCTTTTCTTACCAT-TC
1 TTCTTA-TT-ATT-TCATATCCTTTTCTT-CCATCTC
47757 TTCTT
1 TTCTT
47762 TCCTACCCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 6 0.18
34 2 0.06
35 3 0.09
36 20 0.59
37 3 0.09
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (33 bp):
TTCTTATTATTTCATATCCTTTTCTTCCATCTC
Found at i:54132 original size:22 final size:21
Alignment explanation
Indices: 54097--54138 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
54087 AGCCTTTTTC
*
54097 TTCTAAATATCTTTATCTCAAG
1 TTCTAAATAACTTTA-CTCAAG
*
54119 TTCTAAGTAACTTTACTCAA
1 TTCTAAATAACTTTACTCAA
54139 ATCTGTACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (21 bp):
TTCTAAATAACTTTACTCAAG
Found at i:54436 original size:11 final size:11
Alignment explanation
Indices: 54420--54444 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54410 TTTTTATTCT
54420 TTCACTTGCAC
1 TTCACTTGCAC
54431 TTCACTTGCAC
1 TTCACTTGCAC
54442 TTC
1 TTC
54445 TTTTGTATTT
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:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:57707 original size:19 final size:19
Alignment explanation
Indices: 57685--57733 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
57675 AAAATAAAAG
*
57685 AAAAAGACA-AAAAGAAGA
1 AAAAAAACAGAAAAGAAGA
*
57703 AAAAAATCAGAAAAGAAGA
1 AAAAAAACAGAAAAGAAGA
*
57722 AAAGAAA-AGAAA
1 AAAAAAACAGAAA
57734 TTCAAAAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAAAACAGAAAAGAAGA
Found at i:64764 original size:19 final size:20
Alignment explanation
Indices: 64740--64782 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
64730 AGCATTTATC
*
64740 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
64759 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
64779 TTCA
1 TTCA
64783 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:66993 original size:23 final size:26
Alignment explanation
Indices: 66967--67021 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 26
66957 AAATCCAGCA
66967 AAGAAAATT-AAAGCACTCAAA-A-G
1 AAGAAAATTGAAAGCACTCAAAGAGG
66990 AAG-AAATTGAAAGCACTCAAAGAGG
1 AAGAAAATTGAAAGCACTCAAAGAGG
67015 AAGAAAA
1 AAGAAAA
67022 AAAGAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.18
23 15 0.54
24 1 0.04
25 4 0.14
26 3 0.11
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (26 bp):
AAGAAAATTGAAAGCACTCAAAGAGG
Found at i:67031 original size:5 final size:5
Alignment explanation
Indices: 67021--67049 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
67011 GAGGAAGAAA
67021 AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
67050 TTGAAAGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:69819 original size:11 final size:13
Alignment explanation
Indices: 69787--69816 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
69777 TGGCCAAAGA
69787 TGAAAAGGTATGT
1 TGAAAAGGTATGT
69800 TGAAAAGGTATG-
1 TGAAAAGGTATGT
69812 TGAAA
1 TGAAA
69817 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:71775 original size:65 final size:65
Alignment explanation
Indices: 71671--71801 Score: 208
Period size: 65 Copynumber: 2.0 Consensus size: 65
71661 TATACTAGCC
*
71671 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGTTCTCTCCCTATTCGGCCAAG
1 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
* *** *
71736 CCATGTGCCTTGCATGTGGTTTATTTAGGTGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
1 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
71801 C
1 C
71802 ACCATTTCCC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (65 bp):
CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:72918 original size:13 final size:12
Alignment explanation
Indices: 72898--72936 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
72888 TGCTGCAACA
72898 AAAGAGAAAAAG
1 AAAGAGAAAAAG
72910 AAAGAAGAAAAAG
1 AAAG-AGAAAAAG
* *
72923 AAACAGAAACAG
1 AAAGAGAAAAAG
72935 AA
1 AA
72937 GAAAAGACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAAG
Found at i:74492 original size:33 final size:33
Alignment explanation
Indices: 74450--74518 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
74440 GTTGATGAAT
*
74450 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
74483 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
74516 GAA
1 GAA
74519 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:74523 original size:13 final size:12
Alignment explanation
Indices: 74504--74600 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
74494 TTATTGGCGT
74504 GATATGGTGATG
1 GATATGGTGATG
74516 GAATATGGTGAT-
1 G-ATATGGTGATG
*
74528 GATATAGGCG-T-
1 GATAT-GGTGATG
74539 GATAATGGTGATG
1 GAT-ATGGTGATG
74552 GACTATGGTGAT-
1 GA-TATGGTGATG
*
74564 GATATAGGCG-T-
1 GATAT-GGTGATG
*
74575 GATAATGGAGATG
1 GAT-ATGGTGATG
74588 GATTATGGTGATG
1 GA-TATGGTGATG
74601 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:74559 original size:36 final size:36
Alignment explanation
Indices: 74489--74601 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
74479 AATGGAAGGA
* *
74489 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
74524 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
74560 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
74596 TGATGA
1 TGATGA
74602 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:78998 original size:33 final size:33
Alignment explanation
Indices: 78956--79024 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
78946 GTTGATGAAT
*
78956 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
78989 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
79022 GAA
1 GAA
79025 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:79029 original size:13 final size:12
Alignment explanation
Indices: 79010--79074 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
79000 TTATTGGCGT
79010 GATATGGTGATG
1 GATATGGTGATG
79022 GAATATGGTGAT-
1 G-ATATGGTGATG
*
79034 GATATAGGCG-T-
1 GATAT-GGTGATG
79045 GATAATGGTGATG
1 GAT-ATGGTGATG
79058 GACTATGGTGAT-
1 GA-TATGGTGATG
79070 GATAT
1 GATAT
79075 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:79065 original size:36 final size:36
Alignment explanation
Indices: 78995--79107 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
78985 AATGGAAGGA
* *
78995 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
79030 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
79066 TGATGATATAGGCGTGATAATGGAGACGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
79102 TGATGA
1 TGATGA
79108 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:81136 original size:33 final size:33
Alignment explanation
Indices: 81094--81162 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
81084 GTTGATGAAT
*
81094 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
81127 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
81160 GAA
1 GAA
81163 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:81167 original size:13 final size:12
Alignment explanation
Indices: 81148--81244 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
81138 TTATTGGCGT
81148 GATATGGTGATG
1 GATATGGTGATG
81160 GAATATGGTGAT-
1 G-ATATGGTGATG
*
81172 GATATAGGCG-T-
1 GATAT-GGTGATG
81183 GATAATGGTGATG
1 GAT-ATGGTGATG
81196 GACTATGGTGAT-
1 GA-TATGGTGATG
*
81208 GATATAGGCG-T-
1 GATAT-GGTGATG
*
81219 GATAATGGAGATG
1 GAT-ATGGTGATG
81232 GATTATGGTGATG
1 GA-TATGGTGATG
81245 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:81203 original size:36 final size:36
Alignment explanation
Indices: 81133--81245 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
81123 AATGGAAGGA
* *
81133 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
81168 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
81204 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
81240 TGATGA
1 TGATGA
81246 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:84635 original size:15 final size:15
Alignment explanation
Indices: 84604--84650 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
84594 TTTTGCTTCA
*
84604 CTTTTTCTTTGCTTT
1 CTTTTTCTTTTCTTT
*
84619 -TTTTT-TATTC-TT
1 CTTTTTCTTTTCTTT
84631 CTTTTTCTTTTCTTT
1 CTTTTTCTTTTCTTT
84646 CTTTT
1 CTTTT
84651 GCACTCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
12 2 0.08
13 8 0.31
14 9 0.35
15 7 0.27
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (15 bp):
CTTTTTCTTTTCTTT
Found at i:85094 original size:33 final size:33
Alignment explanation
Indices: 85052--85120 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
85042 GTTGATGAAT
*
85052 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
85085 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
85118 GAA
1 GAA
85121 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:85125 original size:13 final size:12
Alignment explanation
Indices: 85106--85202 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
85096 TTATTGGCGT
85106 GATATGGTGATG
1 GATATGGTGATG
85118 GAATATGGTGAT-
1 G-ATATGGTGATG
*
85130 GATATAGGCG-T-
1 GATAT-GGTGATG
85141 GATAATGGTGATG
1 GAT-ATGGTGATG
85154 GACTATGGTGAT-
1 GA-TATGGTGATG
*
85166 GATATAGGCG-T-
1 GATAT-GGTGATG
*
85177 GATAATGGAGATG
1 GAT-ATGGTGATG
85190 GATTATGGTGATG
1 GA-TATGGTGATG
85203 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:85161 original size:36 final size:36
Alignment explanation
Indices: 85091--85203 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
85081 AATGGAAGGA
* *
85091 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
85126 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
85162 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
85198 TGATGA
1 TGATGA
85204 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:90336 original size:21 final size:21
Alignment explanation
Indices: 90311--90358 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
90301 ATCCTGCAAG
90311 TCAAAGAAAAAATCTGCATGT
1 TCAAAGAAAAAATCTGCATGT
90332 TCAAAGAAAAAATCTGCATGT
1 TCAAAGAAAAAATCTGCATGT
90353 TCAAAG
1 TCAAAG
90359 TTAGAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.23
Consensus pattern (21 bp):
TCAAAGAAAAAATCTGCATGT
Found at i:92137 original size:36 final size:36
Alignment explanation
Indices: 92085--92197 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
92075 GATACTATTT
*
92085 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
92121 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
92157 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
92192 ACATCA
1 TCATCA
92198 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:92140 original size:13 final size:11
Alignment explanation
Indices: 92085--92183 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
92075 GATACTATTT
92085 TCATCACCATAA
1 TCATCACCAT-A
*
92097 TCCATCTCCATTA
1 T-CATCACCA-TA
*
92110 TCA-CGCCTATA
1 TCATCACC-ATA
92121 TCATCACCATA
1 TCATCACCATA
92132 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
92146 TCA-CGCCTATA
1 TCATCACC-ATA
92157 TCATCACCATA
1 TCATCACCATA
92168 TTCCATCACCATA
1 -T-CATCACCATA
92181 TCA
1 TCA
92184 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:92212 original size:33 final size:33
Alignment explanation
Indices: 92097--92236 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
92087 ATCACCATAA
* * *
92097 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
92131 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
92169 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
92202 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
92235 TC
1 TC
92237 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:94602 original size:22 final size:21
Alignment explanation
Indices: 94561--94604 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
94551 CACCATCTCC
*
94561 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
94582 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
94604 A
1 A
94605 TTCCGTAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:94971 original size:13 final size:12
Alignment explanation
Indices: 94923--94977 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 12
94913 GTGCAAAAAG
94923 AAAGAAAAAGACAA
1 AAAG-AAAAGA-AA
*
94937 AAAGAAGAGAAA
1 AAAGAAAAGAAA
94949 AATCAGAAAAGAATA
1 AA--AGAAAAGAA-A
94964 AAAGAAAAGAAA
1 AAAGAAAAGAAA
94976 AA
1 AA
94978 GAATTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 7 0.19
13 14 0.39
14 12 0.33
15 3 0.08
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:94977 original size:19 final size:19
Alignment explanation
Indices: 94955--94994 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
94945 GAAAAATCAG
94955 AAAAGAA-TAAAAGAAAAGA
1 AAAAGAATTAAAA-AAAAGA
*
94974 AAAAGAATTTAAAAAAAGA
1 AAAAGAATTAAAAAAAAGA
94993 AA
1 AA
94995 GCAAGCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAGAATTAAAAAAAAGA
Found at i:98987 original size:22 final size:21
Alignment explanation
Indices: 98946--98989 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
98936 CACCATCTCC
*
98946 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
98967 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
98989 A
1 A
98990 TTCCGCAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:101299 original size:17 final size:17
Alignment explanation
Indices: 101239--101302 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 17
101229 AATTCGAGTG
101239 AAAAAAGAAAGAAAAG-A
1 AAAAAAG-AAGAAAAGAA
*
101256 CAAAAAGAA-AAAA-AA
1 AAAAAAGAAGAAAAGAA
*
101271 ATCAGAATAGAAGAAAAGAA
1 A--A-AAAAGAAGAAAAGAA
101291 AAAAAAGAAGAA
1 AAAAAAGAAGAA
101303 TTTCAAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
15 5 0.14
16 2 0.05
17 16 0.43
18 7 0.19
19 4 0.11
20 3 0.08
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAGAAAAGAA
Found at i:101302 original size:25 final size:25
Alignment explanation
Indices: 101239--101303 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 25
101229 AATTCGAGTG
*
101239 AAAAAAGAAAGAAAAGACAAAAAGAA
1 AAAAAAG-AAGAATAGACAAAAAGAA
101265 AAAAAA-ATCAGAATAGA-AGAAAAGAA
1 AAAAAAGA--AGAATAGACA-AAAAGAA
101291 AAAAAAGAAGAAT
1 AAAAAAGAAGAAT
101304 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
24 1 0.03
25 6 0.18
26 26 0.76
27 1 0.03
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (25 bp):
AAAAAAGAAGAATAGACAAAAAGAA
Found at i:104351 original size:32 final size:32
Alignment explanation
Indices: 104310--104382 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
104300 CTTCCCATCC
104310 TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
1 TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
104342 TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
1 TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
104374 TTAGCCGAA
1 TTAGCCGAA
104383 CCATCACAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (32 bp):
TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
Found at i:106135 original size:18 final size:19
Alignment explanation
Indices: 106095--106135 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
106085 ATGTAGGAGT
* *
106095 CTTTTTCTTTTCTTTTTTG
1 CTTTTTCTCTTCTTTGTTG
106114 -TTTTTCTCTT-TTTGTTG
1 CTTTTTCTCTTCTTTGTTG
106131 CTTTT
1 CTTTT
106136 GTTGCAGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (19 bp):
CTTTTTCTCTTCTTTGTTG
Found at i:106521 original size:23 final size:24
Alignment explanation
Indices: 106495--106541 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
106485 GGATAATTCA
106495 ATGGTTAA-GGAATGGTGAT-GAAT
1 ATGG-TAATGGAATGGTGATAGAAT
*
106518 ATGGTAATGGGATGGTGATAGAAT
1 ATGGTAATGGAATGGTGATAGAAT
106542 TGGCGTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 14 0.67
24 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (24 bp):
ATGGTAATGGAATGGTGATAGAAT
Found at i:106580 original size:14 final size:14
Alignment explanation
Indices: 106561--106588 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
106551 AGAGATGAAT
106561 GATGGTGATGGAAA
1 GATGGTGATGGAAA
106575 GATGGTGATGGAAA
1 GATGGTGATGGAAA
106589 TAGTATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:108666 original size:35 final size:36
Alignment explanation
Indices: 108586--108668 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
108576 AGATACTATC
* *
108586 TATTCATCACCACCTTCCATCACCATTTTCACGCCTA
1 TATT-ATCACCACATTCCATCACCATTATCACGCCTA
** * *
108623 TAACATCACCATATTCCATTACCA-TATCACGCCTA
1 TATTATCACCACATTCCATCACCATTATCACGCCTA
108658 TATTATCACCA
1 TATTATCACCA
108669 ACTTATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 19 0.50
36 17 0.45
37 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TATTATCACCACATTCCATCACCATTATCACGCCTA
Found at i:109074 original size:26 final size:23
Alignment explanation
Indices: 109045--109092 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
109035 AAAGTGCTAC
109045 AACAAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAAG-AA-AAGAAA-AAGAA
*
109071 AACAAAAGAGAAAAGAAAAAGA
1 AACAAAAAAGAAAAGAAAAAGA
109093 CTCCTACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 2 0.10
26 9 0.43
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (23 bp):
AACAAAAAAGAAAAGAAAAAGAA
Found at i:109148 original size:14 final size:15
Alignment explanation
Indices: 109114--109160 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
109104 AATTTGGAGT
109114 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
109129 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
109143 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
109160 G
1 G
109161 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:113046 original size:35 final size:36
Alignment explanation
Indices: 112966--113048 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
112956 AGATACTATC
* *
112966 TATTCATCACCACCTTCCATCACCATTTTCACGCCTA
1 TATT-ATCACCACATTCCATCACCATTATCACGCCTA
** * *
113003 TAACATCACCATATTCCATTACCA-TATCACGCCTA
1 TATTATCACCACATTCCATCACCATTATCACGCCTA
113038 TATTATCACCA
1 TATTATCACCA
113049 ACTTATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 19 0.50
36 17 0.45
37 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TATTATCACCACATTCCATCACCATTATCACGCCTA
Found at i:115518 original size:35 final size:36
Alignment explanation
Indices: 115452--115520 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
115442 CACCACCACC
*
115452 TTCCATCACCATTTTCACGCCTATAACATCACCATA
1 TTCCATCACCATTATCACGCCTATAACATCACCATA
* **
115488 TTCCATTACCA-TATCACGCCTATATTATCACCA
1 TTCCATCACCATTATCACGCCTATAACATCACCA
115521 ACTTATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (36 bp):
TTCCATCACCATTATCACGCCTATAACATCACCATA
Found at i:122476 original size:24 final size:25
Alignment explanation
Indices: 122430--122477 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
122420 CACCATGATC
* * *
122430 TGCATTTTCTTCAGTTTCTTCATCT
1 TGCATTGTCTTCAGGTTCCTCATCT
122455 TGCATTGT-TTCAGGTTCCTCATC
1 TGCATTGTCTTCAGGTTCCTCATC
122478 AAAAATAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCATCT
Found at i:124013 original size:15 final size:15
Alignment explanation
Indices: 123978--124006 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
123968 GTGCTTCAAC
123978 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
123992 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
124007 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:129748 original size:5 final size:5
Alignment explanation
Indices: 129713--129741 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
129703 CTTTTTGAAC
129713 TTCTT TT-TT TTCTT TTCTT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
129742 CTTTTCTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTCTT
Found at i:131151 original size:16 final size:16
Alignment explanation
Indices: 131130--131161 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
131120 TCTTCCACCA
131130 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
131146 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
131162 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:133869 original size:23 final size:23
Alignment explanation
Indices: 133843--134016 Score: 87
Period size: 23 Copynumber: 7.3 Consensus size: 23
133833 ACAATCTATC
*
133843 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
133866 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
133889 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCACCATA-T
*
133914 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
* *
133938 CATCACCATAACCCATCACCATTAT
1 CATCACCATTA-TCATCACCA-TAT
*
133963 CAT-GCC-TATATCATCACCATATT
1 CATCACCAT-TATCATCACCATA-T
*
133986 CCATCACCA-TATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
*
134009 TATCACCA
1 CATCACCA
134017 ACTTATAAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 41
0.69 0.08 0.24
Matches are distributed among these distances:
22 16 0.14
23 44 0.37
24 26 0.22
25 25 0.21
26 2 0.02
27 5 0.04
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:133884 original size:13 final size:11
Alignment explanation
Indices: 133843--133999 Score: 97
Period size: 11 Copynumber: 13.2 Consensus size: 11
133833 ACAATCTATC
133843 CATCACCATTAT
1 CATCACCA-TAT
*
133855 CA-CGCCTATAT
1 CATCACC-ATAT
133866 CATCACCATAGT
1 CATCACCATA-T
133878 CCATCACCATTAT
1 -CATCACCA-TAT
*
133891 CA-CGCCTATAT
1 CATCACC-ATAT
133902 CATCACCATAGT
1 CATCACCATA-T
133914 CCATCACCATTAT
1 -CATCACCA-TAT
*
133927 CA-CGCCTATAT
1 CATCACC-ATAT
*
133938 CATCACCATAACC
1 CATCACCAT-A-T
133951 CATCACCATTAT
1 CATCACCA-TAT
*
133963 CATGC-CTATAT
1 CAT-CACCATAT
133974 CATCACCATATT
1 CATCACCATA-T
133986 CCATCACCATAT
1 -CATCACCATAT
133998 CA
1 CA
134000 CGCCTATATT
Statistics
Matches: 116, Mismatches: 10, Indels: 39
0.70 0.06 0.24
Matches are distributed among these distances:
10 1 0.01
11 44 0.38
12 28 0.24
13 38 0.33
14 5 0.04
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:133888 original size:36 final size:36
Alignment explanation
Indices: 133841--134016 Score: 300
Period size: 36 Copynumber: 4.9 Consensus size: 36
133831 ATACAATCTA
133841 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
133877 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
133913 TCCATCACCATTATCACGCCTATATCATCACCATAA
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
133949 CCCATCACCATTATCATGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
133985 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
134017 ACTTATAAAT
Statistics
Matches: 133, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 20 0.15
36 113 0.85
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:134872 original size:33 final size:35
Alignment explanation
Indices: 134834--134914 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
134824 ATGGTGATGA
* * *
134834 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGG-TGATGATATAGGCGTGAT
134868 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
134903 AATGGTGATGGA
1 AATGGTGATGGA
134915 CAGATTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 9 0.22
34 1 0.03
35 18 0.45
36 12 0.30
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:140513 original size:33 final size:33
Alignment explanation
Indices: 140471--140539 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
140461 GTTGATGAAT
140471 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGTG-TGAAATGGTAATG
* * *
140504 GAAGGATGATGTTATTGGTGTGATATGGTGATG
1 GAAGGATGATGTTAATGGTGTGAAATGGTAATG
140537 GAA
1 GAA
140540 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGTGTGAAATGGTAATG
Found at i:146358 original size:24 final size:21
Alignment explanation
Indices: 146323--146365 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
146313 GGCTCATTCT
*
146323 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
146346 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
146366 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:150380 original size:24 final size:21
Alignment explanation
Indices: 150345--150387 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
150335 GGCTCATTCT
*
150345 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
150368 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
150388 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:157331 original size:19 final size:20
Alignment explanation
Indices: 157307--157357 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
157297 CGGCCAAGAG
* *
157307 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
157326 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
157346 CATGTATTTTCA
1 CATGTATTTTCA
157358 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:158086 original size:18 final size:18
Alignment explanation
Indices: 158063--158115 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
158053 AATTGGAGTG
158063 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAAGAAAAAGA
158081 CAAAAAG-AAGAAGAAAAGA
1 CAAAAAGAAAG-A-AAAAGA
158100 -AGAAAAGAAAAGAAAA
1 CA-AAAAG-AAAGAAAA
158116 GAATTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
17 3 0.10
18 9 0.30
19 14 0.47
20 1 0.03
21 3 0.10
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAAGA
Found at i:158091 original size:11 final size:11
Alignment explanation
Indices: 158070--158118 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
158060 GTGCAAAAAG
*
158070 AAAGAAAAAGA
1 AAAGAAGAAGA
158081 CAAA-AAGAAGA
1 -AAAGAAGAAGA
158092 AGAA-AAGAAGA
1 A-AAGAAGAAGA
158103 AAAGAA-AAGA
1 AAAGAAGAAGA
158113 AAAGAA
1 AAAGAA
158119 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 13 0.38
11 18 0.53
12 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAGA
Found at i:158116 original size:18 final size:17
Alignment explanation
Indices: 158064--158118 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
158054 ATTGGAGTGC
158064 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAG-AAAAGA
158081 CAAAAAGAAGAAGAAAAGA
1 -AAAAAGAA-AAGAAAAGA
158100 AGAAAAGAAAAGAAAAGA
1 A-AAAAGAAAAGAAAAGA
158118 A
1 A
158119 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 17 0.50
19 14 0.41
20 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAGA
Found at i:161540 original size:19 final size:20
Alignment explanation
Indices: 161516--161566 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
161506 CGGCCAAGAG
* *
161516 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
161535 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
161555 CATGTATTTTCA
1 CATGTATTTTCA
161567 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:164231 original size:16 final size:16
Alignment explanation
Indices: 164210--164243 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
164200 TTGAACTTCA
164210 CTTTTTCTT-TTCTTTT
1 CTTTTT-TTCTTCTTTT
164226 CTTTTTTTCTTCTTTT
1 CTTTTTTTCTTCTTTT
164242 CT
1 CT
164244 GATTTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
CTTTTTTTCTTCTTTT
Found at i:165571 original size:76 final size:76
Alignment explanation
Indices: 165445--165596 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
165435 AAAAGGTACG
165445 TGATGTGAGGCTAACCAGGCTTCTTCAATGATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
1 TGATGTGAGGCTAACCAGGCTTCTTCAATGATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
165510 AGGAGAGACAC
66 AGGAGAGACAC
165521 TGATGTGAGGCTAACCAGGCTTCTTCAATGATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
1 TGATGTGAGGCTAACCAGGCTTCTTCAATGATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
165586 AGGAGAGACAC
66 AGGAGAGACAC
165597 CAAATGCTAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (76 bp):
TGATGTGAGGCTAACCAGGCTTCTTCAATGATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
AGGAGAGACAC
Found at i:165859 original size:33 final size:33
Alignment explanation
Indices: 165817--165885 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
165807 GTTGATGAAT
*
165817 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
165850 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
165883 GAA
1 GAA
165886 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:165890 original size:13 final size:11
Alignment explanation
Indices: 165870--166004 Score: 87
Period size: 13 Copynumber: 11.3 Consensus size: 11
165860 GTTATTGGCG
165870 TGATATGGTGA
1 TGATATGGTGA
165881 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
165894 TGATATAGGCG-
1 TGATAT-GGTGA
165905 TGATAATGGTGA
1 TGAT-ATGGTGA
165917 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
165930 TGATATAGGCG-
1 TGATAT-GGTGA
165941 TGATAATGGTGA
1 TGAT-ATGGTGA
165953 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
165966 TGATATAGGCG-
1 TGATAT-GGTGA
*
165977 TGATAATGGAGA
1 TGAT-ATGGTGA
165989 TGGATTATGGTGA
1 T-GA-TATGGTGA
166002 TGA
1 TGA
166005 AAATAGTATC
Statistics
Matches: 100, Mismatches: 7, Indels: 33
0.71 0.05 0.24
Matches are distributed among these distances:
11 32 0.32
12 26 0.26
13 39 0.39
14 3 0.03
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:165915 original size:23 final size:23
Alignment explanation
Indices: 165887--165990 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
165877 GTGATGGAAT
165887 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
*
165910 ATGGTGATGGACTAT-GGTGATGAT-
1 ATGGTGAT-GA-TATAGGCG-TGATA
* *
165934 ATAGGCG-TGATA-ATG-GTGATGGA
1 AT-GGTGATGATATAGGCGTGAT--A
165957 CTATGGTGATGATATAGGCGTGATA
1 --ATGGTGATGATATAGGCGTGATA
*
165982 ATGGAGATG
1 ATGGTGATG
165991 GATTATGGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 26
0.66 0.06 0.28
Matches are distributed among these distances:
20 4 0.06
21 1 0.02
22 3 0.05
23 18 0.29
24 11 0.18
25 18 0.29
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.30
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:165926 original size:36 final size:36
Alignment explanation
Indices: 165856--166004 Score: 246
Period size: 36 Copynumber: 4.2 Consensus size: 36
165846 AATGGAAGGA
* * *
165856 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
165891 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
165927 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
* *
165963 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
165999 TGATGA
1 TGATGA
166005 AAATAGTATC
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 16 0.15
36 92 0.85
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:166390 original size:19 final size:20
Alignment explanation
Indices: 166343--166393 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
166333 GAAATCCCTT
**
166343 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
166363 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
166382 TGAAGATACATG
1 TGAAAATACATG
166394 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:167807 original size:33 final size:33
Alignment explanation
Indices: 167765--167833 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
167755 GTTGATGAAT
167765 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGTG-TGAAATGGTAATG
* * *
167798 GAAGGATGATGTTATTGGTGTGATATGGTGATG
1 GAAGGATGATGTTAATGGTGTGAAATGGTAATG
167831 GAA
1 GAA
167834 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGTGTGAAATGGTAATG
Found at i:173475 original size:33 final size:33
Alignment explanation
Indices: 173433--173501 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
173423 GTTGATGAAT
*
173433 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
173466 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
173499 GAA
1 GAA
173502 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:175882 original size:5 final size:5
Alignment explanation
Indices: 175872--175897 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
175862 CTTCAACTTC
175872 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
175898 CTTTTGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:180294 original size:22 final size:21
Alignment explanation
Indices: 180253--180296 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
180243 CACCATCTCC
*
180253 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
180274 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
180296 A
1 A
180297 TTCTGCAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:182147 original size:23 final size:24
Alignment explanation
Indices: 182121--182167 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
182111 GGATAATTCA
182121 ATGGTTAA-GGAATGGTGAT-GAAT
1 ATGG-TAATGGAATGGTGATAGAAT
*
182144 ATGGTAATGGGATGGTGATAGAAT
1 ATGGTAATGGAATGGTGATAGAAT
182168 TGGCGTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 14 0.67
24 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (24 bp):
ATGGTAATGGAATGGTGATAGAAT
Found at i:182206 original size:14 final size:14
Alignment explanation
Indices: 182178--182214 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
182168 TGGCGTGAAA
*
182178 GTGAT-GAATGATG
1 GTGATGGAAAGATG
182191 GTGATGGAAAGATG
1 GTGATGGAAAGATG
182205 GTGATGGAAA
1 GTGATGGAAA
182215 TAGTATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.35, C:0.00, G:0.41, T:0.24
Consensus pattern (14 bp):
GTGATGGAAAGATG
Found at i:191301 original size:13 final size:13
Alignment explanation
Indices: 191277--191309 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
191267 ATACTAAACA
191277 CTTTTC-ACATAC
1 CTTTTCAACATAC
191289 CTTTTCAACATAC
1 CTTTTCAACATAC
191302 CTTTTCAA
1 CTTTTCAA
191310 TTTTGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (13 bp):
CTTTTCAACATAC
Found at i:196323 original size:19 final size:19
Alignment explanation
Indices: 196299--196348 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
196289 CGGCCAAGAG
* *
196299 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATCAAAAT
196318 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
196337 CATGTATTTTCA
1 CATGTATTTTCA
196349 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Done.