Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006336.1 Hibiscus syriacus cultivar Beakdansim tig00015144_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: 363990
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:300 original size:64 final size:62
Alignment explanation
Indices: 232--381 Score: 180
Period size: 64 Copynumber: 2.4 Consensus size: 62
222 GAATAAATTG
* * * *
232 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATTGATGCAC-C-AGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACAT-CCATGCATCGATGCACTCTAG-CTATT-TG-
295 A
62 A
* * *
296 AACATCGAATGCATTTGATCCATCGATGCCCATCCATGCATCGATGCACTCTAGCTATTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACATCCATGCATCGATGCACTCTAGCTATTTGA
358 AACATCGAATGCA-TTCATGCATCG
1 AACATCGAATGCATTTCATGCATCG
382 TTGCCCTCTT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
61 9 0.12
62 14 0.19
63 16 0.21
64 34 0.45
65 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (62 bp):
AACATCGAATGCATTTCATGCATCGATGCACATCCATGCATCGATGCACTCTAGCTATTTGA
Found at i:6189 original size:21 final size:21
Alignment explanation
Indices: 6160--6216 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
6150 CCTTTTAATA
6160 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCATGAAGG
* * * *
6181 TGCACCGATGCACGCCTTGAATG
1 TGCATCGAT--ACACCATGAAGG
6204 TGCATCGATACAC
1 TGCATCGATACAC
6217 AAGGCCATGC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
TGCATCGATACACCATGAAGG
Found at i:7785 original size:21 final size:21
Alignment explanation
Indices: 7743--7786 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
7733 ACTCCGGGAG
*
7743 CTAGTTCTTCATGAGCTGCTC
1 CTAGTTCTTCATGAGCTCCTC
*
7764 CTAGTTCTTC-TCGTGCTCCTC
1 CTAGTTCTTCAT-GAGCTCCTC
7785 CT
1 CT
7787 CCTCCGGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.09, C:0.34, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCATGAGCTCCTC
Found at i:8319 original size:2 final size:2
Alignment explanation
Indices: 8312--8342 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8302 CAGCTTAAGC
8312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8343 CAATTGGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10236 original size:20 final size:20
Alignment explanation
Indices: 10213--10250 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10203 CAAAGGAAGC
*
10213 AAGAATAAGAAAAAGAATAA
1 AAGAACAAGAAAAAGAATAA
*
10233 AAGAACAATAAAAAGAAT
1 AAGAACAAGAAAAAGAAT
10251 GAGGTATGAG
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:0.74, C:0.03, G:0.13, T:0.11
Consensus pattern (20 bp):
AAGAACAAGAAAAAGAATAA
Found at i:10501 original size:19 final size:19
Alignment explanation
Indices: 10477--10522 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
10467 AATGATTTTC
*
10477 TTTTGAAAGC-AAAATTAAA
1 TTTTGAAA-CAAAAATGAAA
10496 TTTTGAAACAAAAATGAAA
1 TTTTGAAACAAAAATGAAA
*
10515 ATTTGAAA
1 TTTTGAAA
10523 AATAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.30
Consensus pattern (19 bp):
TTTTGAAACAAAAATGAAA
Found at i:12713 original size:13 final size:13
Alignment explanation
Indices: 12695--12734 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
12685 ATAAAAATGT
12695 ATAATATAATTAA
1 ATAATATAATTAA
*
12708 ATAATATAAAGTAA
1 ATAATAT-AATTAA
*
12722 ATAATTTAATTAA
1 ATAATATAATTAA
12735 CTATTTACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
ATAATATAATTAA
Found at i:19333 original size:52 final size:52
Alignment explanation
Indices: 19272--19375 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
19262 AGATTGGGCA
* *
19272 CACATAAATATGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTACAAGG
1 CACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTACAAGG
19324 CACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTACAAGG
1 CACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTACAAGG
19376 ATATTTACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (52 bp):
CACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTACAAGG
Found at i:19427 original size:74 final size:74
Alignment explanation
Indices: 19306--19454 Score: 280
Period size: 74 Copynumber: 2.0 Consensus size: 74
19296 AGTTGGGGGA
19306 TTACAACTAATTACAAGGCACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTA
1 TTACAACTAATTACAAGGCACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTA
19371 CAAGGATAT
66 CAAGGATAT
* *
19380 TTACAACTAATTACAAGGCACAGAAATAGGAAACTAGCTTATAGTTGGGGGATTACAACTAATTA
1 TTACAACTAATTACAAGGCACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTA
19445 CAAGGATAT
66 CAAGGATAT
19454 T
1 T
19455 ATAATTATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (74 bp):
TTACAACTAATTACAAGGCACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTA
CAAGGATAT
Found at i:23945 original size:10 final size:10
Alignment explanation
Indices: 23930--23968 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
23920 GAGTTGGAGG
23930 ATTACAACTA
1 ATTACAACTA
*
23940 ATTACAAGTA
1 ATTACAACTA
23950 TATTTACAACTA
1 -A-TTACAACTA
23962 ATTACAA
1 ATTACAA
23969 GGCACATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 15 0.60
11 2 0.08
12 8 0.32
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (10 bp):
ATTACAACTA
Found at i:29835 original size:18 final size:19
Alignment explanation
Indices: 29800--29836 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
29790 TACGGAATGT
29800 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
29820 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
29837 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:30556 original size:3 final size:3
Alignment explanation
Indices: 30548--30616 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
30538 ATGCTAACCT
30548 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30596 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
30617 GCCGCTCTCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30665 original size:17 final size:17
Alignment explanation
Indices: 30639--30672 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30629 TCCCCTCCCC
30639 CTTTTCTTTCTTTCTTT
1 CTTTTCTTTCTTTCTTT
*
30656 CTTTTGTTTCTTTCTTT
1 CTTTTCTTTCTTTCTTT
30673 ATAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (17 bp):
CTTTTCTTTCTTTCTTT
Found at i:36974 original size:21 final size:23
Alignment explanation
Indices: 36959--37004 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
36949 ATGTATCAAT
*
36959 ATATCTTGAATGTGTATCGATAC
1 ATATCTTGAATATGTATCGATAC
*
36982 ATTTCTTGAATATGTATCGATAC
1 ATATCTTGAATATGTATCGATAC
37005 CCCTCGAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (23 bp):
ATATCTTGAATATGTATCGATAC
Found at i:40898 original size:16 final size:17
Alignment explanation
Indices: 40867--40900 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40857 CATATTGCCG
*
40867 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
40884 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
40900 A
1 A
40901 TATGAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:42598 original size:19 final size:19
Alignment explanation
Indices: 42570--42617 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
42560 TGTCATGGGT
42570 GTACTGATACCCCTGGGAG
1 GTACTGATACCCCTGGGAG
*
42589 GTACTAATACCCCTGGGAG
1 GTACTGATACCCCTGGGAG
42608 GTACTGATAC
1 GTACTGATAC
42618 ACTTGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (19 bp):
GTACTGATACCCCTGGGAG
Found at i:49458 original size:15 final size:15
Alignment explanation
Indices: 49434--49463 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49424 GTCGAATCCC
49434 TTGACACTATATGAT
1 TTGACACTATATGAT
*
49449 TTGACTCTATATGAT
1 TTGACACTATATGAT
49464 ATATGTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (15 bp):
TTGACACTATATGAT
Found at i:49636 original size:25 final size:26
Alignment explanation
Indices: 49599--49647 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
49589 AGAAACTTAA
* *
49599 AAACTTGACTCGACTC-AAATTTTAT
1 AAACTCGAATCGACTCGAAATTTTAT
49624 AAACTCGAATCGACTCGAAATTTT
1 AAACTCGAATCGACTCGAAATTTT
49648 TTTAAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (26 bp):
AAACTCGAATCGACTCGAAATTTTAT
Found at i:52395 original size:21 final size:21
Alignment explanation
Indices: 52348--52446 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
52338 GAAATTATAA
* * * *
52348 AGTATTGATACTCGACTAGGT
1 AGTATAGATACTCCACCAAGT
* * *
52369 ATTATAGATATTCCACCATGT
1 AGTATAGATACTCCACCAAGT
* *
52390 AGTATAGGTACTCCTCCAAGT
1 AGTATAGATACTCCACCAAGT
* *
52411 AGTACA-AGTACTCCACTAAGT
1 AGTATAGA-TACTCCACCAAGT
* *
52432 AGTACAAATACTCCA
1 AGTATAGATACTCCA
52447 AGAGGAGTAC
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 60 0.98
22 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (21 bp):
AGTATAGATACTCCACCAAGT
Found at i:54626 original size:21 final size:21
Alignment explanation
Indices: 54602--54650 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
54592 CGAAATACTT
54602 AGATTCATTTCCATTAAATGA
1 AGATTCATTTCCATTAAATGA
54623 AGATTCATTTCCATTAAATGA
1 AGATTCATTTCCATTAAATGA
*
54644 AGTTTCA
1 AGATTCA
54651 ATAGCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (21 bp):
AGATTCATTTCCATTAAATGA
Found at i:55979 original size:10 final size:10
Alignment explanation
Indices: 55951--55984 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
55941 TGCTATTTTT
55951 AAAAAAAAA-
1 AAAAAAAAAC
*
55960 ATAAAAAAAC
1 AAAAAAAAAC
55970 AAAAAAAAAC
1 AAAAAAAAAC
55980 AAAAA
1 AAAAA
55985 GCCAAAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.91, C:0.06, G:0.00, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:60868 original size:30 final size:30
Alignment explanation
Indices: 60825--60918 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
60815 AGAGGTCATA
* * *
60825 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
60855 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
60886 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
60917 AA
1 AA
60919 AGACATTGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:67305 original size:14 final size:14
Alignment explanation
Indices: 67286--67318 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
67276 AAAGCACTCA
67286 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
67300 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
67314 AAAAG
1 AAAAG
67319 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:70087 original size:11 final size:13
Alignment explanation
Indices: 70055--70084 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
70045 TGGCCAAAGA
70055 TGAAAAGGTATGT
1 TGAAAAGGTATGT
70068 TGAAAAGGTATG-
1 TGAAAAGGTATGT
70080 TGAAA
1 TGAAA
70085 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:76975 original size:22 final size:24
Alignment explanation
Indices: 76948--77000 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
76938 AAAAACAGCA
* *
76948 AAGAAAT-TGAAGTACTC-AAAAG
1 AAGAAATATCAAGCACTCAAAAAG
76970 AAGAAAATATCAAGCACTCAAAAAG
1 AAG-AAATATCAAGCACTCAAAAAG
76995 AAGAAA
1 AAGAAA
77001 AAGAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 3 0.12
23 4 0.15
24 11 0.42
25 8 0.31
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.13
Consensus pattern (24 bp):
AAGAAATATCAAGCACTCAAAAAG
Found at i:78899 original size:23 final size:25
Alignment explanation
Indices: 78873--78927 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
78863 AAATCCAGCA
78873 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
78896 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
78921 AAGAAAA
1 AAGAAAA
78928 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:81631 original size:22 final size:24
Alignment explanation
Indices: 81604--81656 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
81594 AAAATCAGCA
*
81604 AAGAAA-TTGAAGCACTC-AAAAG
1 AAGAAATTTCAAGCACTCAAAAAG
81626 AAGAAAATTTCAAGCACTCAAAAAG
1 AAG-AAATTTCAAGCACTCAAAAAG
81651 AAGAAA
1 AAGAAA
81657 AAGAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 13 0.48
25 8 0.30
ACGTcount: A:0.58, C:0.13, G:0.15, T:0.13
Consensus pattern (24 bp):
AAGAAATTTCAAGCACTCAAAAAG
Found at i:83552 original size:23 final size:25
Alignment explanation
Indices: 83526--83580 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
83516 AAATCCAGCA
83526 AAGAAAATCAAAGCACTCAAA-AG-
1 AAGAAAATCAAAGCACTCAAAGAGT
* *
83549 AAGAAATTGAAAGCACTCAAAGAGT
1 AAGAAAATCAAAGCACTCAAAGAGT
83574 AAGAAAA
1 AAGAAAA
83581 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.60, C:0.13, G:0.16, T:0.11
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGT
Found at i:91688 original size:30 final size:31
Alignment explanation
Indices: 91654--91713 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
91644 CTTAGCTTTA
**
91654 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
91684 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
91714 GGAAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:92626 original size:19 final size:21
Alignment explanation
Indices: 92602--92653 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
92592 CGGCCAAGAG
*
92602 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
92621 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
92642 CATGTATTTTCA
1 CATGTATTTTCA
92654 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:93090 original size:19 final size:20
Alignment explanation
Indices: 93066--93105 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
93056 TATCCTTTCT
93066 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
93085 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
93105 T
1 T
93106 ATTATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:93413 original size:19 final size:18
Alignment explanation
Indices: 93374--93441 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
93364 TTGGAGTGCA
93374 AAAAGAA-AGAAAAAGTC
1 AAAAGAAGAGAAAAAGTC
* *
93391 AAAAGAAGAGAAAAATTAG
1 AAAAGAAGAGAAAAAGT-C
93410 AAAAGAAGA-AAAGAA-T-
1 AAAAGAAGAGAAA-AAGTC
*
93426 AAAAGAAAAGAAAAAG
1 AAAAGAAGAGAAAAAG
93442 AGAAGTTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
16 10 0.23
17 10 0.23
18 12 0.28
19 11 0.26
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAGAAGAGAAAAAGTC
Found at i:96784 original size:21 final size:19
Alignment explanation
Indices: 96744--96795 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
96734 CGGCCAAGAG
*
96744 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
96763 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
*
96784 CATATATTTTCA
1 CATGTATTTTCA
96796 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:97231 original size:19 final size:20
Alignment explanation
Indices: 97207--97246 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
97197 TATCCTTTCT
97207 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
97226 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
97246 T
1 T
97247 ATTATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:99241 original size:15 final size:15
Alignment explanation
Indices: 99207--99244 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
99197 GAAATGGAAG
99207 AAGAAATGAAATGAT
1 AAGAAATGAAATGAT
*
99222 AAGAATTGAAATGGAT
1 AAGAAATGAAAT-GAT
99238 -AGAAATG
1 AAGAAATG
99245 TTATCAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (15 bp):
AAGAAATGAAATGAT
Found at i:99877 original size:21 final size:21
Alignment explanation
Indices: 99838--99877 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
99828 AAGGAAGATT
*
99838 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
99859 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
99878 AGGCTAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:99926 original size:22 final size:21
Alignment explanation
Indices: 99900--99940 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
99890 GCTATGGAAT
99900 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
99922 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
99941 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:101207 original size:2 final size:2
Alignment explanation
Indices: 101190--101227 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
101180 TTATAATAAC
*
101190 TA TA GA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
101228 GAAAATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:103044 original size:22 final size:21
Alignment explanation
Indices: 103007--103047 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
102997 CCATCTCCGT
103007 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
103028 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
103048 ATTCTGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:109501 original size:24 final size:21
Alignment explanation
Indices: 109467--109509 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
109457 TCCACAAGAC
*
109467 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
109489 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
109510 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:113250 original size:22 final size:21
Alignment explanation
Indices: 113213--113254 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
113203 CCATCTCCAT
113213 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
113234 TTCATCCATCAAGACCATCAT
1 TTCAT-CATCAACACCATCAT
113255 TTTTCGTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.29
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:119159 original size:11 final size:11
Alignment explanation
Indices: 119151--119181 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
119141 TCCGAAAATT
119151 AAAGAAAAAAA
1 AAAGAAAAAAA
*
119162 AAAGAAAAGAA
1 AAAGAAAAAAA
119173 AAAGAAAAA
1 AAAGAAAAA
119182 GAATTCTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:119169 original size:6 final size:6
Alignment explanation
Indices: 119151--119184 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
119141 TCCGAAAATT
119151 AAAGAA AAA-AA AAAG-A AAAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
119185 TTCTGGTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:130669 original size:133 final size:133
Alignment explanation
Indices: 130431--130693 Score: 508
Period size: 133 Copynumber: 2.0 Consensus size: 133
130421 TAATATGATT
130431 ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
1 ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
*
130496 GCATGAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTA
66 GCATGAATATCATATAAAATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTA
130561 AGA
131 AGA
130564 ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
1 ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
*
130629 GCATGAATATCATATAAAATGGTATTCTTAAATGATAAATGGAAACATGTAATAATAATATCCTA
66 GCATGAATATCATATAAAATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTA
130694 TGAAATGATA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 128 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (133 bp):
ATAAGACTATCCTAATATGCTTATAACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTAT
GCATGAATATCATATAAAATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTA
AGA
Found at i:132379 original size:19 final size:20
Alignment explanation
Indices: 132355--132405 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
132345 CGGCCAAGAG
* *
132355 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
132374 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
132394 CATGTATTTTCA
1 CATGTATTTTCA
132406 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:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:132842 original size:19 final size:20
Alignment explanation
Indices: 132818--132857 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
132808 TATCCTTTCT
132818 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
132837 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
132857 T
1 T
132858 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:152544 original size:2 final size:2
Alignment explanation
Indices: 152537--152576 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
152527 TATCACCAAC
152537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
152577 CCGCTTCCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153978 original size:14 final size:14
Alignment explanation
Indices: 153959--153988 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
153949 TAAGTAGTGG
153959 GATCCTCCTTGTAA
1 GATCCTCCTTGTAA
153973 GATCCTCCTTGTAA
1 GATCCTCCTTGTAA
153987 GA
1 GA
153989 AAATTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (14 bp):
GATCCTCCTTGTAA
Found at i:157014 original size:21 final size:22
Alignment explanation
Indices: 156972--157015 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
156962 GGATGAATAT
**
156972 TCTAGATAATTTTGGGGATGAA
1 TCTAGATAATTTTGAAGATGAA
*
156994 TCTAGATAA-TTTGAAGTTGAA
1 TCTAGATAATTTTGAAGATGAA
157015 T
1 T
157016 ATGGCCTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (22 bp):
TCTAGATAATTTTGAAGATGAA
Found at i:158839 original size:20 final size:18
Alignment explanation
Indices: 158816--158863 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
158806 TTGGCTTGCG
158816 TTCTCTTTTTGAATTTCTT
1 TTCTCTTTTTGAATTT-TT
158835 TT-TCTTTTCTGAATTTTT
1 TTCTCTTTT-TGAATTTTT
158853 TTCTTCTTTTT
1 TTC-TCTTTTT
158864 ATCTTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.38
19 10 0.38
20 6 0.23
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.73
Consensus pattern (18 bp):
TTCTCTTTTTGAATTTTT
Found at i:158849 original size:19 final size:19
Alignment explanation
Indices: 158819--158863 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
158809 GCTTGCGTTC
158819 TCTTTTTGAATTTCTTT-T
1 TCTTTTTGAATTTCTTTCT
*
158837 TCTTTTCTGAATTTTTTTCT
1 TCTTTT-TGAATTTCTTTCT
158857 TCTTTTT
1 TCTTTTT
158864 ATCTTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 11 0.46
20 7 0.29
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.73
Consensus pattern (19 bp):
TCTTTTTGAATTTCTTTCT
Found at i:178242 original size:42 final size:43
Alignment explanation
Indices: 178183--178267 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
178173 CTTGCTTCAG
178183 GTTCTGTAATTCTGAAAC-TGTCCCAGTGATAATGAGTAGGAA
1 GTTCTGTAATTCTGAAACATGTCCCAGTGATAATGAGTAGGAA
178225 GTTCTGTAATTCTGAAACATGTCCCAGTGATAATGAGTAGGAA
1 GTTCTGTAATTCTGAAACATGTCCCAGTGATAATGAGTAGGAA
178268 TAAAACATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 18 0.43
43 24 0.57
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (43 bp):
GTTCTGTAATTCTGAAACATGTCCCAGTGATAATGAGTAGGAA
Found at i:181293 original size:19 final size:20
Alignment explanation
Indices: 181269--181319 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
181259 CGGCCAAGAG
* *
181269 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
181288 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
181308 CGTGTATTTTCA
1 CATGTATTTTCA
181320 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:182265 original size:35 final size:37
Alignment explanation
Indices: 182197--182276 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
182187 ATACTATTTC
* *
182197 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
182234 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
182269 CATCACCA
1 CATCACCA
182277 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:184369 original size:36 final size:36
Alignment explanation
Indices: 184319--184423 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
184309 GATACAATCT
*
184319 GTCCATCACTATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
184355 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
184391 TTTCATCACCA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
184424 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.30, C:0.34, G:0.05, T:0.31
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:184398 original size:13 final size:13
Alignment explanation
Indices: 184340--184404 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
184330 TTATCACGCC
184340 TATATCATCACCA
1 TATATCATCACCA
*
184353 TAGT-CCATCACCA
1 TA-TATCATCACCA
*
184366 T-TATCA-CGCC-
1 TATATCATCACCA
184376 TATATCATCACCA
1 TATATCATCACCA
*
184389 TATTTCATCACCA
1 TATATCATCACCA
184402 TAT
1 TAT
184405 CACGCCTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
10 1 0.02
11 9 0.21
12 5 0.12
13 26 0.62
14 1 0.02
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (13 bp):
TATATCATCACCA
Found at i:187702 original size:22 final size:20
Alignment explanation
Indices: 187677--187716 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
187667 ATGTTTGTTT
187677 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
187699 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
187717 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:193125 original size:22 final size:20
Alignment explanation
Indices: 193100--193139 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
193090 ATGTTTGTTT
193100 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
193122 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
193140 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:201811 original size:13 final size:11
Alignment explanation
Indices: 201770--201855 Score: 68
Period size: 11 Copynumber: 7.3 Consensus size: 11
201760 ACAATCTGTC
201770 CATCACCATTAT
1 CATCACCA-TAT
*
201782 CA-CGCCTATAT
1 CATCACC-ATAT
201793 CATCACCATAGT
1 CATCACCATA-T
201805 CCATCACCATTAT
1 -CATCACCA-TAT
*
201818 CA-CGCCTATAT
1 CATCACC-ATAT
201829 CATCACCATATT
1 CATCACCATA-T
201841 CCATCACCATAT
1 -CATCACCATAT
201853 CAT
1 CAT
201856 GCCTATTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
11 25 0.41
12 15 0.25
13 19 0.31
14 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:201814 original size:36 final size:36
Alignment explanation
Indices: 201767--201871 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
201757 GATACAATCT
201767 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
201803 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
201839 TTCCATCACCA-TATCATGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
201872 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:207977 original size:8 final size:8
Alignment explanation
Indices: 207966--207999 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
207956 ATTTTTTTTT
207966 CAAAAAAA
1 CAAAAAAA
207974 CAAAAAAA
1 CAAAAAAA
207982 GGCAAAAAAA
1 --CAAAAAAA
207992 CAAAAAAA
1 CAAAAAAA
208000 GCCAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:208006 original size:9 final size:9
Alignment explanation
Indices: 207966--208015 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
207956 ATTTTTTTTT
*
207966 CAAAAAAAC
1 CAAAAAAGC
* *
207975 AAAAAAAGG
1 CAAAAAAGC
*
207984 CAAAAAAAC
1 CAAAAAAGC
*
207993 AAAAAAAGC
1 CAAAAAAGC
208002 CAAAAAAGC
1 CAAAAAAGC
208011 CAAAA
1 CAAAA
208016 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (9 bp):
CAAAAAAGC
Found at i:208015 original size:18 final size:18
Alignment explanation
Indices: 207966--208008 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
207956 ATTTTTTTTT
*
207966 CAAAAAAACAAAAAAAGG
1 CAAAAAAACAAAAAAAGC
207984 CAAAAAAACAAAAAAAGC
1 CAAAAAAACAAAAAAAGC
208002 CAAAAAA
1 CAAAAAA
208009 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (18 bp):
CAAAAAAACAAAAAAAGC
Found at i:214893 original size:35 final size:37
Alignment explanation
Indices: 214825--214904 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
214815 ATACTATTTC
* *
214825 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
214862 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
214897 CATCACCA
1 CATCACCA
214905 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:215517 original size:26 final size:27
Alignment explanation
Indices: 215470--215533 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
215460 CTTGGCTTGC
*
215470 TTTC-TCTTTT-TGAATTTCTTTTTCT
1 TTTCTTCTTTTCTGAATTTCTTTTCCT
215495 TTTCTTCTTTTCTGAATTT-TTTTCCT
1 TTTCTTCTTTTCTGAATTTCTTTTCCT
215521 TTT-TATCTTTTCT
1 TTTCT-TCTTTTCT
215534 TTTCTTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 5 0.14
26 23 0.66
27 7 0.20
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (27 bp):
TTTCTTCTTTTCTGAATTTCTTTTCCT
Found at i:219527 original size:23 final size:25
Alignment explanation
Indices: 219501--219555 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
219491 AAATCCAGCA
*
219501 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAACACTCAAAGAGG
* *
219524 AAGAAATTGAAAACACTCAAAGAGG
1 AAGAAAATCAAAACACTCAAAGAGG
219549 AAGAAAA
1 AAGAAAA
219556 AGAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAACACTCAAAGAGG
Found at i:219560 original size:25 final size:23
Alignment explanation
Indices: 219514--219561 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
219504 AAAATCAAAG
**
219514 CACTCAAAAGAAGAAATTGAAAA
1 CACTCAAAAGAAGAAAAAGAAAA
219537 CACTCAAAGAGGAAGAAAAAGAAAA
1 CACTCAAA-A-GAAGAAAAAGAAAA
219562 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 12 0.57
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.08
Consensus pattern (23 bp):
CACTCAAAAGAAGAAAAAGAAAA
Found at i:219563 original size:5 final size:5
Alignment explanation
Indices: 219553--219594 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
219543 AAGAGGAAGA
219553 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
219595 GTTGAAGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:222259 original size:11 final size:13
Alignment explanation
Indices: 222227--222256 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
222217 TAGCCAAAGA
222227 TGAAAAGGTATGT
1 TGAAAAGGTATGT
222240 TGAAAAGGTATG-
1 TGAAAAGGTATGT
222252 TGAAA
1 TGAAA
222257 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:228911 original size:23 final size:23
Alignment explanation
Indices: 228883--229056 Score: 98
Period size: 23 Copynumber: 7.3 Consensus size: 23
228873 ACAATCTGTC
*
228883 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
228906 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
228929 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
228954 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
228978 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
229001 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
229026 CCATCACCA-TATCA-CACCTATAT
1 -CATCACCATTATCATCACC-ATAT
*
229049 TATCACCA
1 CATCACCA
229057 ACTTATAAAT
Statistics
Matches: 121, Mismatches: 8, Indels: 45
0.70 0.05 0.26
Matches are distributed among these distances:
22 21 0.17
23 45 0.37
24 22 0.18
25 20 0.17
26 3 0.02
27 10 0.08
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:228924 original size:13 final size:11
Alignment explanation
Indices: 228883--229056 Score: 115
Period size: 11 Copynumber: 14.7 Consensus size: 11
228873 ACAATCTGTC
228883 CATCACCATTAT
1 CATCACCA-TAT
*
228895 CA-CGCCTATAT
1 CATCACC-ATAT
228906 CATCACCATAGT
1 CATCACCATA-T
228918 CCATCACCATTAT
1 -CATCACCA-TAT
*
228931 CA-CGCCTATAT
1 CATCACC-ATAT
228942 CATCACCATATT
1 CATCACCATA-T
228954 CCATCACCATTAT
1 -CATCACCA-TAT
*
228967 CA-CGCCTATAT
1 CATCACC-ATAT
228978 CATCACCATAGT
1 CATCACCATA-T
228990 CCATCACCATTAT
1 -CATCACCA-TAT
*
229003 CA-CGCCTATAT
1 CATCACC-ATAT
229014 CATCACCATATT
1 CATCACCATA-T
229026 CCATCACCATAT
1 -CATCACCATAT
229038 CA-CACCTATAT
1 CATCACC-ATAT
*
229049 TATCACCA
1 CATCACCA
229057 ACTTATAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 43
0.72 0.05 0.23
Matches are distributed among these distances:
10 4 0.03
11 52 0.39
12 33 0.25
13 37 0.28
14 6 0.05
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:228927 original size:36 final size:36
Alignment explanation
Indices: 228880--229056 Score: 311
Period size: 36 Copynumber: 4.9 Consensus size: 36
228870 GATACAATCT
228880 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
228916 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
228952 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
228988 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
229024 TTCCATCACCA-TATCACACCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
229057 ACTTATAAAT
Statistics
Matches: 136, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
35 20 0.15
36 116 0.85
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:243212 original size:13 final size:12
Alignment explanation
Indices: 243193--243289 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
243183 TACGCCTATA
243193 TCATCACCATAT
1 TCATCACCATAT
243205 TCCATCACC--AT
1 T-CATCACCATAT
*
243216 T-ATCACGCCTAT
1 TCATCAC-CATAT
243228 ATCATCACCATAGT
1 -TCATCACCATA-T
*
243242 CCATCACC--AT
1 TCATCACCATAT
*
243252 T-ATCACTCCTAT
1 TCATCAC-CATAT
243264 ATCATCACCATAT
1 -TCATCACCATAT
243277 TCCATCACCATAT
1 T-CATCACCATAT
243290 CACGCCTATA
Statistics
Matches: 68, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
9 10 0.15
10 3 0.04
11 4 0.06
12 6 0.09
13 34 0.50
14 11 0.16
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:243224 original size:36 final size:36
Alignment explanation
Indices: 243135--243308 Score: 266
Period size: 36 Copynumber: 4.9 Consensus size: 36
243125 GATACAATCT
*
243135 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
243171 GT-C--CACCATTATTACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
243204 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
243240 GTCCATCACCATTATCACTCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
243276 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
243309 ACTTATAAAT
Statistics
Matches: 126, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
33 29 0.23
34 1 0.01
35 21 0.17
36 75 0.60
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:247747 original size:19 final size:19
Alignment explanation
Indices: 247723--247760 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
247713 GATGCTTTAA
247723 ATGTCTTGGGAGGGGCCAC
1 ATGTCTTGGGAGGGGCCAC
247742 ATGTCTTGGGAGGGGCCAC
1 ATGTCTTGGGAGGGGCCAC
247761 GTATCTACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.42, T:0.21
Consensus pattern (19 bp):
ATGTCTTGGGAGGGGCCAC
Found at i:252252 original size:19 final size:19
Alignment explanation
Indices: 252228--252265 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
252218 GATGCTTTAA
252228 ATGTCTTGGGAGGGGCCAC
1 ATGTCTTGGGAGGGGCCAC
252247 ATGTCTTGGGAGGGGCCAC
1 ATGTCTTGGGAGGGGCCAC
252266 GTATCTACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.42, T:0.21
Consensus pattern (19 bp):
ATGTCTTGGGAGGGGCCAC
Found at i:259236 original size:24 final size:21
Alignment explanation
Indices: 259201--259243 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
259191 GGCTCAATCT
*
259201 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
259224 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
259244 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:263823 original size:19 final size:19
Alignment explanation
Indices: 263799--263844 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
263789 CACTTGAGCT
263799 GGACTTTTGAGCTAGCTAG
1 GGACTTTTGAGCTAGCTAG
263818 GGACTTTTGAGCTAGCTAG
1 GGACTTTTGAGCTAGCTAG
*
263837 AGACTTTT
1 GGACTTTT
263845 TTTCAGCTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (19 bp):
GGACTTTTGAGCTAGCTAG
Found at i:268087 original size:35 final size:36
Alignment explanation
Indices: 268040--268107 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
268030 ATTTAGAAGT
268040 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
268075 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
268108 TAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:273149 original size:24 final size:25
Alignment explanation
Indices: 273120--273169 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
273110 TAGAAAAGGT
*
273120 TAAGAAAAGGAT-AAAG-TAAGGAAA
1 TAAGAAAA-GATGAAAGAAAAGGAAA
273144 TAAGAAAAGATGAAAGAAAAGGAAA
1 TAAGAAAAGATGAAAGAAAAGGAAA
273169 T
1 T
273170 GAAATAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 12 0.52
25 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (25 bp):
TAAGAAAAGATGAAAGAAAAGGAAA
Found at i:273415 original size:22 final size:22
Alignment explanation
Indices: 273390--273434 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
273380 TGTAGGAGTC
* * *
273390 TTTTCTTTTCTTTTTGTTTTTT
1 TTTTCTTCTCTTGTTGCTTTTT
273412 TTTTCTTCTCTTGTTGCTTTTT
1 TTTTCTTCTCTTGTTGCTTTTT
273434 T
1 T
273435 GTTGTAGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTTCTTCTCTTGTTGCTTTTT
Found at i:281860 original size:26 final size:26
Alignment explanation
Indices: 281789--281863 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
281779 TGGCTGCAAC
* *
281789 AAAGATAAGAAAAGGAAGATG-ATTAAT
1 AAAGATAAG-AAATGAA-ATGAAATAAT
*
281816 AAAG-GAAG-AAT-AAATGAAATAAT
1 AAAGATAAGAAATGAAATGAAATAAT
281839 AAAGATAAGAAATGAAATGAAATAA
1 AAAGATAAGAAATGAAATGAAATAA
281864 AGAAGGGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 3 0.08
23 11 0.28
24 5 0.12
25 3 0.08
26 14 0.35
27 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (26 bp):
AAAGATAAGAAATGAAATGAAATAAT
Found at i:288253 original size:21 final size:21
Alignment explanation
Indices: 288214--288253 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
288204 AAGGAAGATT
*
288214 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
288235 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
288254 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:288302 original size:22 final size:21
Alignment explanation
Indices: 288276--288316 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
288266 GTTGCGGAAT
288276 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
288298 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
288317 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:290932 original size:35 final size:37
Alignment explanation
Indices: 290863--290942 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
290853 ATACTATTTC
* * *
290863 CATCCCCATAATCCATCTTCCATTATCATGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
290900 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
290935 CATCACCA
1 CATCACCA
290943 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:296611 original size:35 final size:37
Alignment explanation
Indices: 296543--296622 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
296533 ATACTATTTC
* *
296543 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
296580 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
296615 CATCACCA
1 CATCACCA
296623 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:302321 original size:19 final size:19
Alignment explanation
Indices: 302299--302361 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
302289 AAATTTTGGC
*
302299 TTTTTGGCTTTTTTTTTTG
1 TTTTTTGCTTTTTTTTTTG
*
302318 TTTTTTTGC-CTTTTTTTTG
1 -TTTTTTGCTTTTTTTTTTG
*
302337 TTTTTTGTTTTTTTTTTTG
1 TTTTTTGCTTTTTTTTTTG
302356 TTTTTT
1 TTTTTT
302362 TGAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 7 0.18
19 24 0.63
20 7 0.18
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (19 bp):
TTTTTTGCTTTTTTTTTTG
Found at i:303868 original size:19 final size:21
Alignment explanation
Indices: 303817--303860 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
303807 GAAACCCCCT
303817 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
303838 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
303857 TGAA
1 TGAA
303861 GATGCATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 13 0.57
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:305742 original size:24 final size:24
Alignment explanation
Indices: 305692--305741 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
305682 AACACAACCC
* *
305692 TTGGCACTTCAAATGACATTTCTT
1 TTGGAACTTCAAATGACATATCTT
*
305716 TTGGAACTTCAAATGGCATCATCTT
1 TTGGAACTTCAAATGACAT-ATCTT
305741 T
1 T
305742 GAAACATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (24 bp):
TTGGAACTTCAAATGACATATCTT
Found at i:307026 original size:8 final size:8
Alignment explanation
Indices: 307013--307047 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
307003 GAATTTCTTT
307013 TTCTTTTC
1 TTCTTTTC
307021 TTCTTTTC
1 TTCTTTTC
307029 -T-TTTTC
1 TTCTTTTC
307035 TTCTTTTC
1 TTCTTTTC
307043 TTCTT
1 TTCTT
307048 CATTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.20
7 2 0.08
8 18 0.72
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:307026 original size:14 final size:14
Alignment explanation
Indices: 307007--307070 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
306997 CTTTTTGAAT
307007 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTC
307021 TTC-TTTTCTTTTTC
1 TTCTTTTTC-TTTTC
307035 TTC-TTTTCTTCTTC
1 TTCTTTTTCTT-TTC
* *
307049 AT-TTTTTATTTTC
1 TTCTTTTTCTTTTC
307062 TTTCTTTTT
1 -TTCTTTTT
307071 GTACTCCAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 10 0.24
14 27 0.64
15 5 0.12
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:307030 original size:19 final size:19
Alignment explanation
Indices: 307006--307069 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
306996 TCTTTTTGAA
307006 TTTCTTTTTCTTTTCTTCT
1 TTTCTTTTTCTTTTCTTCT
307025 TTTCTTTTTCTTCTT-TTCT
1 TTTCTTTTTCTT-TTCTTCT
*
307044 TCTTCATTTTTTATTTTCTTTCT
1 T-TTC--TTTTTCTTTTC-TTCT
307067 TTT
1 TTT
307070 TGTACTCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 17 0.45
20 5 0.13
21 2 0.05
22 9 0.24
23 5 0.13
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTTCT
Found at i:307054 original size:22 final size:20
Alignment explanation
Indices: 307005--307055 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
306995 TTCTTTTTGA
307005 ATTTCTTTTTCTTTTCTTCTT
1 ATTT-TTTTTCTTTTCTTCTT
*
307026 TTCTTTTTCTTCTTTTCTTCTT
1 AT-TTTTT-TTCTTTTCTTCTT
307048 CATTTTTT
1 -ATTTTTT
307056 ATTTTCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.16
22 20 0.80
23 1 0.04
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTTTTTCTTTTCTTCTT
Found at i:307823 original size:19 final size:21
Alignment explanation
Indices: 307783--307831 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
307773 ACCCCCTTGT
307783 AAATACATGACTTTTAAATGA
1 AAATACATGACTTTTAAATGA
307804 AAATACATGA-TTTT-AATGA
1 AAATACATGACTTTTAAATGA
*
307823 AGATACATG
1 AAATACATG
307832 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 13 0.48
20 4 0.15
21 10 0.37
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
AAATACATGACTTTTAAATGA
Found at i:313623 original size:13 final size:12
Alignment explanation
Indices: 313601--313631 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
313591 AAAATTTGGC
313601 TTTTTTTTGCCT
1 TTTTTTTTGCCT
313613 TTTTATTTTGCCT
1 TTTT-TTTTGCCT
313626 TTTTTT
1 TTTTTT
313632 GTTTTTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.03, C:0.13, G:0.06, T:0.77
Consensus pattern (12 bp):
TTTTTTTTGCCT
Found at i:317969 original size:14 final size:14
Alignment explanation
Indices: 317940--317978 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
317930 TTTTTTGAAA
*
317940 TTTTTTTTTTGTCT
1 TTTTTTTTTTGCCT
317954 TTTTTTTTTTGCCT
1 TTTTTTTTTTGCCT
317968 TTTTTTGTTTT
1 TTTTTT-TTTT
317979 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTGCCT
Found at i:322275 original size:10 final size:10
Alignment explanation
Indices: 322262--322303 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
322252 TTTTTGAAAA
322262 TTTGGCTTTT
1 TTTGGCTTTT
322272 TTTGGCTTTT
1 TTTGGCTTTT
*
322282 TTTTG-TTTT
1 TTTGGCTTTT
322291 TTTGGCTTTT
1 TTTGGCTTTT
322301 TTT
1 TTT
322304 TTTGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.00, C:0.07, G:0.17, T:0.76
Consensus pattern (10 bp):
TTTGGCTTTT
Found at i:322290 original size:19 final size:20
Alignment explanation
Indices: 322268--322314 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
322258 AAAATTTGGC
322268 TTTTTTTGGC-TTTTTTTTG
1 TTTTTTTGGCTTTTTTTTTG
322287 TTTTTTTGGCTTTTTTTTTTG
1 TTTTTTTGGC-TTTTTTTTTG
322308 TTTTTTT
1 TTTTTTT
322315 TTGTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 10 0.38
21 16 0.62
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (20 bp):
TTTTTTTGGCTTTTTTTTTG
Found at i:322303 original size:13 final size:11
Alignment explanation
Indices: 322268--322323 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
322258 AAAATTTGGC
**
322268 TTTTTTTGGCT
1 TTTTTTTGTTT
322279 TTTTTTTG--T
1 TTTTTTTGTTT
*
322288 TTTTTTGGCTTT
1 TTTTTTTG-TTT
322300 TTTTTTTG-TT
1 TTTTTTTGTTT
322310 TTTTTTTGTTT
1 TTTTTTTGTTT
322321 TTT
1 TTT
322324 GAAAAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.21
10 10 0.26
11 13 0.33
12 8 0.21
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:322311 original size:10 final size:10
Alignment explanation
Indices: 322268--322323 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
322258 AAAATTTGGC
* *
322268 TTTTTTTGGC
1 TTTTTTTTGT
322278 TTTTTTTTG-
1 TTTTTTTTGT
*
322287 TTTTTTTGGCTT
1 TTTTTTTTG--T
322299 TTTTTTTTGT
1 TTTTTTTTGT
322309 TTTTTTTTGT
1 TTTTTTTTGT
322319 TTTTT
1 TTTTT
322324 GAAAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.20
10 24 0.60
12 8 0.20
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:322321 original size:19 final size:19
Alignment explanation
Indices: 322268--322323 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
322258 AAAATTTGGC
*
322268 TTTTTTTGGCTTTTTTTTGT
1 TTTTTTTTG-TTTTTTTTGT
322288 TTTTTTGGCTT-TTTTTTTTGT
1 TTTTTT---TTGTTTTTTTTGT
322309 TTTTTTTTGTTTTTT
1 TTTTTTTTGTTTTTT
322324 GAAAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
19 6 0.19
20 6 0.19
21 16 0.52
23 1 0.03
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (19 bp):
TTTTTTTTGTTTTTTTTGT
Found at i:325067 original size:21 final size:22
Alignment explanation
Indices: 325036--325077 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
325026 TTTTTGAAAT
**
325036 TTTGGCTTTTTTGGCTTTTTTG
1 TTTGGCTTTTTTACCTTTTTTG
325058 TTTGG-TTTTTTACCTTTTTT
1 TTTGGCTTTTTTACCTTTTTT
325078 TGCCTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.02, C:0.10, G:0.17, T:0.71
Consensus pattern (22 bp):
TTTGGCTTTTTTACCTTTTTTG
Found at i:329678 original size:13 final size:12
Alignment explanation
Indices: 329658--329690 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
329648 TTTTTTTTTG
329658 TTTTTTTGCCTT
1 TTTTTTTGCCTT
329670 TTTTCTTTGCCTT
1 TTTT-TTTGCCTT
329683 TTTTTTTG
1 TTTTTTTG
329691 TTTTTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:333034 original size:17 final size:18
Alignment explanation
Indices: 333008--333055 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
332998 TTGATTTTGC
*
333008 CCTTTTACATACT-AACA
1 CCTTTCACATACTAAACA
333025 CCTTTCACATACTAAACA
1 CCTTTCACATACTAAACA
333043 CCTTTTCACATAC
1 CC-TTTCACATAC
333056 CTTTTCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 12 0.43
18 6 0.21
19 10 0.36
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (18 bp):
CCTTTCACATACTAAACA
Found at i:333051 original size:19 final size:18
Alignment explanation
Indices: 333008--333055 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
332998 TTGATTTTGC
333008 CCTTTT-ACATACTAACA
1 CCTTTTCACATACTAACA
333025 CC-TTTCACATACTAAACA
1 CCTTTTCACATACT-AACA
333043 CCTTTTCACATAC
1 CCTTTTCACATAC
333056 CTTTTCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.11
17 9 0.32
18 6 0.21
19 10 0.36
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (18 bp):
CCTTTTCACATACTAACA
Found at i:333070 original size:13 final size:13
Alignment explanation
Indices: 333042--333075 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
333032 CATACTAAAC
333042 ACCTTTTC-ACAT
1 ACCTTTTCAACAT
*
333054 ACCTTTTCAATAT
1 ACCTTTTCAACAT
333067 ACCTTTTCA
1 ACCTTTTCA
333076 TATTTGGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.44
Consensus pattern (13 bp):
ACCTTTTCAACAT
Found at i:333078 original size:12 final size:12
Alignment explanation
Indices: 333042--333078 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
333032 CATACTAAAC
*
333042 ACCTTTTCACAT
1 ACCTTTTCATAT
333054 ACCTTTTCAATAT
1 ACCTTTTC-ATAT
333067 ACCTTTTCATAT
1 ACCTTTTCATAT
333079 TTGGCCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (12 bp):
ACCTTTTCATAT
Found at i:333578 original size:242 final size:238
Alignment explanation
Indices: 333116--333594 Score: 890
Period size: 242 Copynumber: 2.0 Consensus size: 238
333106 TACCAAGATT
333116 TTCGACTCCAAAGTGTCCCATGAGTCCTCCTTCATGCGCTTCTTTGGTTAACACTTCTGTATAGA
1 TTCGACTCCAAAGTGTCCCATGAGTCCTCCTTCATGCGCTTCTTTGGTTAACACTTCTGTATAGA
333181 ACCTTGTGGAATATATAGTCGTCTTCTTCGAAAAGATATCCATCATGCTGATAATATTGTCATGA
66 ACCTTGTGGAATATATAGTCGTCTTCTTCGAAAAGATATCCATCATGCTGATAATATTGTCATGA
333246 GCTGTTTCACATAACATATACTTCTCCAAAGTCCAAATCGTAGCATAATGTTCCTTAATGAATGA
131 GCTGTTTCACATAACATATACTTCTCCAAAGTCCAAATCGTAGCATAATGTTCCTTAATGAATGA
333311 AAAACCAAGAAGTTTTGAATCCAAAGTGTTAAGTAAGACATAC
196 AAAACCAAGAAGTTTTGAATCCAAAGTGTTAAGTAAGACATAC
333354 TTCGACTCCAAAG-GTCCCATGAGTCCTCCTTCATGCGCTTCTTTGGTTAACACTTCTCGTATAG
1 TTCGACTCCAAAGTGTCCCATGAGTCCTCCTTCATGCGCTTCTTTGGTTAACACTTCT-GTATAG
333418 AACCTTGTGGAATATATAGTCGTCCTTCTTCGAAAAGATATCCATCATGCTGATAATATTTGTCA
65 AACCTTGTGGAATATATAGTCGT-CTTCTTCGAAAAGATATCCATCATGCTGATAATA-TTGTCA
333483 TGAGCTGTTTCACATAACATATACCTTTCTCCAAAGTCCAAATCAGTAGCATAATGTTCCTTAAT
128 TGAGCTGTTTCACATAACATATA-C-TTCTCCAAAGTCCAAATC-GTAGCATAATGTTCCTTAAT
333548 GAATG-AAAACCAAGAAGTTTTGAATCCAAAGTGTTAAGTAAGACATA
190 GAATGAAAAACCAAGAAGTTTTGAATCCAAAGTGTTAAGTAAGACATA
333595 TAACATATAC
Statistics
Matches: 235, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
237 44 0.19
238 42 0.18
239 34 0.14
240 29 0.12
241 1 0.00
242 60 0.26
243 25 0.11
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (238 bp):
TTCGACTCCAAAGTGTCCCATGAGTCCTCCTTCATGCGCTTCTTTGGTTAACACTTCTGTATAGA
ACCTTGTGGAATATATAGTCGTCTTCTTCGAAAAGATATCCATCATGCTGATAATATTGTCATGA
GCTGTTTCACATAACATATACTTCTCCAAAGTCCAAATCGTAGCATAATGTTCCTTAATGAATGA
AAAACCAAGAAGTTTTGAATCCAAAGTGTTAAGTAAGACATAC
Found at i:333606 original size:98 final size:99
Alignment explanation
Indices: 333496--333693 Score: 389
Period size: 98 Copynumber: 2.0 Consensus size: 99
333486 GCTGTTTCAC
333496 ATAACATATACCTTTCTCCAAAGTCCAAATCAGTAGCATAATGTTCCTTAATGAATG-AAAACCA
1 ATAACATATACCTTTCTCCAAAGTCCAAATCAGTAGCATAATGTTCCTTAATGAATGAAAAACCA
333560 AGAAGTTTTGAATCCAAAGTGTTAAGTAAGACAT
66 AGAAGTTTTGAATCCAAAGTGTTAAGTAAGACAT
333594 ATAACATATACCTTTCTCCAAAGTCCAAATCAGTAGCATAATGTTCCTTAATGAATGAAAAACCA
1 ATAACATATACCTTTCTCCAAAGTCCAAATCAGTAGCATAATGTTCCTTAATGAATGAAAAACCA
333659 AGAAGTTTTGAATCCAAAGTGTTAAGTAAGACAT
66 AGAAGTTTTGAATCCAAAGTGTTAAGTAAGACAT
333693 A
1 A
333694 CCTGCGTGAA
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 57 0.58
99 42 0.42
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (99 bp):
ATAACATATACCTTTCTCCAAAGTCCAAATCAGTAGCATAATGTTCCTTAATGAATGAAAAACCA
AGAAGTTTTGAATCCAAAGTGTTAAGTAAGACAT
Found at i:346898 original size:18 final size:18
Alignment explanation
Indices: 346877--346936 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
346867 TTTGAATTTC
*
346877 TTTTTCTTTTCTTTTATT
1 TTTTTCTTTTCTTTTCTT
*
346895 TTTTTCTGATTTTTTCTTCTT
1 TTTTTCT--TTTCTT-TTCTT
*
346916 TTTGTCTTTTCTTTTCTT
1 TTTTTCTTTTCTTTTCTT
346934 TTT
1 TTT
346937 GCACTCTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 15 0.43
19 5 0.14
20 5 0.14
21 10 0.29
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTCTT
Found at i:347277 original size:22 final size:21
Alignment explanation
Indices: 347251--347291 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
347241 GCTGTGGAAT
347251 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
347273 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
347292 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:351217 original size:35 final size:35
Alignment explanation
Indices: 351178--351269 Score: 184
Period size: 35 Copynumber: 2.6 Consensus size: 35
351168 CATCTTCCAT
351178 TATCACGCCTATATCATCACCATAGTCCATCACCA
1 TATCACGCCTATATCATCACCATAGTCCATCACCA
351213 TATCACGCCTATATCATCACCATAGTCCATCACCA
1 TATCACGCCTATATCATCACCATAGTCCATCACCA
351248 TATCACGCCTATATCATCACCA
1 TATCACGCCTATATCATCACCA
351270 AATTCTGAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (35 bp):
TATCACGCCTATATCATCACCATAGTCCATCACCA
Found at i:351228 original size:11 final size:11
Alignment explanation
Indices: 351188--351269 Score: 78
Period size: 11 Copynumber: 7.1 Consensus size: 11
351178 TATCACGCCT
351188 ATATCATCACC
1 ATATCATCACC
351199 ATAGTCCATCACC
1 ATA-T-CATCACC
*
351212 ATATCA-CGCC
1 ATATCATCACC
351222 TATATCATCACC
1 -ATATCATCACC
351234 ATAGTCCATCACC
1 ATA-T-CATCACC
*
351247 ATATCA-CGCC
1 ATATCATCACC
351257 TATATCATCACC
1 -ATATCATCACC
351269 A
1 A
351270 AATTCTGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
10 6 0.10
11 23 0.39
12 10 0.17
13 20 0.34
ACGTcount: A:0.33, C:0.37, G:0.05, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:351266 original size:22 final size:22
Alignment explanation
Indices: 351188--351269 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 22
351178 TATCACGCCT
351188 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATA-T-CATCACC
*
351212 ATATCA-CGCCTATATCATCACC
1 ATATCATCACC-ATATCATCACC
*
351234 ATAGTCCATCACCATATCA-CGCC
1 ATA-T-CATCACCATATCATCACC
351257 TATATCATCACCA
1 -ATATCATCACCA
351270 AATTCTGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
22 18 0.36
23 9 0.18
24 20 0.40
25 3 0.06
ACGTcount: A:0.33, C:0.37, G:0.05, T:0.26
Consensus pattern (22 bp):
ATATCATCACCATATCATCACC
Found at i:361954 original size:22 final size:24
Alignment explanation
Indices: 361913--361958 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
361903 AAGAGGAGAA
361913 TGAAGAACCATATTTTTAACTAAC
1 TGAAGAACCATATTTTTAACTAAC
361937 TGAAGAA-CATA-TTTTAACTAAC
1 TGAAGAACCATATTTTTAACTAAC
361959 CTTATTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 4 0.18
24 7 0.32
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (24 bp):
TGAAGAACCATATTTTTAACTAAC
Done.