Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001107.1 Hibiscus syriacus cultivar Beakdansim tig00002189_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: 73316
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:5974 original size:17 final size:16
Alignment explanation
Indices: 5866--5987 Score: 68
Period size: 16 Copynumber: 6.9 Consensus size: 16
5856 ATAACAAAAC
5866 AAGTAAAAAATAATAAA
1 AAGTAAAAAA-AATAAA
5883 AA-TAAATAAAAATAAA
1 AAGTAAA-AAAAATAAA
*
5899 AATGTTAAAAAAAAGACACA
1 AA-G-TAAAAAAAATA-A-A
5919 AA-TAAAAGGAAAATATTAA
1 AAGTAAAA--AAAATA--AA
*
5938 TGGAGTAAAAAAAATAAA
1 --AAGTAAAAAAAATAAA
*
5956 AAGTAAAAGAAATTAAA
1 AAGTAAAA-AAAATAAA
* *
5973 AAGGAATAAAAATAA
1 AAGTAAAAAAAATAA
5988 TGTGTACATA
Statistics
Matches: 83, Mismatches: 9, Indels: 27
0.70 0.08 0.23
Matches are distributed among these distances:
16 25 0.30
17 23 0.28
18 8 0.10
19 11 0.13
20 10 0.12
21 1 0.01
22 5 0.06
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (16 bp):
AAGTAAAAAAAATAAA
Found at i:6114 original size:18 final size:18
Alignment explanation
Indices: 6091--6128 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6081 ATTAAGAAAA
6091 AAAATAATAG-AAAAAGAT
1 AAAATAA-AGTAAAAAGAT
*
6109 AAAATAAAGTAAAAATAT
1 AAAATAAAGTAAAAAGAT
6127 AA
1 AA
6129 TATATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (18 bp):
AAAATAAAGTAAAAAGAT
Found at i:6264 original size:2 final size:2
Alignment explanation
Indices: 6257--6303 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
6247 TTAATACATC
*
6257 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
6300 TA TA
1 TA TA
6304 AAAAAATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:8774 original size:67 final size:66
Alignment explanation
Indices: 8655--8975 Score: 247
Period size: 65 Copynumber: 4.8 Consensus size: 66
8645 AAGATATCTG
* * * **
8655 TTGTTTCATGA-AAACAGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGAT
8719 TT
65 TT
8721 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTT-AGGGAAAATAAATTCAAAGA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGG-AAATAAATTCAAAGA
8785 TTT
64 TTT
* * * * * **
8788 TT-TTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAAT-TGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAAT-TC-A-A-A
**
8851 GACAAAACT
62 G----ATTT
* * * * * *** * * * *
8860 TAGTTCCAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAATAAAACATATTCAAATA-A
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
8924 T
66 T
* * *
8925 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
8976 CTGTCTCAAA
Statistics
Matches: 204, Mismatches: 37, Indels: 29
0.76 0.14 0.11
Matches are distributed among these distances:
64 1 0.00
65 85 0.42
66 11 0.05
67 35 0.17
68 23 0.11
70 1 0.00
71 1 0.00
72 4 0.02
73 41 0.20
74 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
T
Found at i:8843 original size:36 final size:36
Alignment explanation
Indices: 8790--9011 Score: 226
Period size: 36 Copynumber: 6.3 Consensus size: 36
8780 AAAGATTTTT
*
8790 TTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
* * *
8826 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTG
* ** * *
8863 TTCCAAAAGAAACTATCTCAAGGGAGACAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
*** * *
8899 TTTCAAATAAAACATAT-TC-----A-A-ATAATTTG
1 TTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATTTG
8928 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
* *
8964 TTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
9000 TTTCAAGGGAAA
1 TTTCAAGGGAAA
9012 TATTTTCAAT
Statistics
Matches: 155, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 19 0.12
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 97 0.63
37 33 0.21
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:8846 original size:15 final size:16
Alignment explanation
Indices: 8818--8850 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
8808 CAAGAGAGAC
*
8818 GAAATTTGTTTCAAGA
1 GAAATTTGTCTCAAGA
8834 GAAA-TTGTCTCAAGA
1 GAAATTTGTCTCAAGA
8849 GA
1 GA
8851 GACAAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (16 bp):
GAAATTTGTCTCAAGA
Found at i:8889 original size:138 final size:138
Alignment explanation
Indices: 8732--8995 Score: 402
Period size: 138 Copynumber: 1.9 Consensus size: 138
8722 GTGTTTCAAG
* * ** * * *
8732 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGAAAATAAATTCAAAGATTTTTTTTCAAG
1 AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* * *
8797 GGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTA
8862 GTTCCAAA
131 GTTCCAAA
* * *
8870 AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
*
8935 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA
8996 TTTATTTCAA
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 112 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (138 bp):
AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTA
GTTCCAAA
Found at i:9020 original size:101 final size:101
Alignment explanation
Indices: 8820--9077 Score: 320
Period size: 101 Copynumber: 2.5 Consensus size: 101
8810 AGAGAGACGA
* * * ** *
8820 AATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAA
* * *
8885 GGAGACAAAATTTGTTTCAAATAAAACATATTCAAAT
66 AGAGACAAAATTTATTTCAAAGAAAACATATTC-AAT
* *
8922 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAA
* * * *
8986 AGAGACAAAATTTATTTCAAGGGAAATATTTTCAAT
66 AGAGACAAAATTTATTTCAAAGAAAACATATTCAAT
** * *
9022 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAA
9078 TGTTTTCAAT
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
100 5 0.04
101 78 0.58
102 52 0.39
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (101 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAA
AGAGACAAAATTTATTTCAAAGAAAACATATTCAAT
Found at i:9100 original size:66 final size:66
Alignment explanation
Indices: 8962--9144 Score: 305
Period size: 66 Copynumber: 2.8 Consensus size: 66
8952 AGACAAAATT
* ** *
8962 TGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA-TTTATTTCAAGGGAAATATTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATATTTTCAATGTTT
9026 A
66 A
*
9027 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATATTTTCAATGTTT
9092 A
66 A
*
9093 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAT
9145 TATCTCAAGC
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 31 0.28
66 80 0.72
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATATTTTCAATGTTT
A
Found at i:9151 original size:37 final size:38
Alignment explanation
Indices: 9084--9158 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
9074 GAAATGTTTT
* * *
9084 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
* *
9122 CAATATTT-TGTTTCAAGGGAAATTATCTCAAGCGAGA
1 CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
9159 TAAAATATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (38 bp):
CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
Found at i:10743 original size:69 final size:69
Alignment explanation
Indices: 10627--10764 Score: 233
Period size: 69 Copynumber: 2.0 Consensus size: 69
10617 TGTCTCTCTC
*
10627 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGCGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGCGATTCAGAAATGATTGTGCTTGATCAATC
10692 TCAT
66 TCAT
* *
10696 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTC-GAAAATGATTGTGCTTGATCAAT
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGCGATTCAG-AAATGATTGTGCTTGATCAAT
10760 CTCAT
65 CTCAT
10765 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGCGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:10872 original size:25 final size:26
Alignment explanation
Indices: 10839--10892 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
10829 TTTCTTCAAT
10839 TTTGTTTTTTCTCT-TTTTATTTTCTC
1 TTTGTTTTTTCTCTCTTTT-TTTTCTC
10865 TTTGTTTTTT-TCTCTTTTTTTTCTC
1 TTTGTTTTTTCTCTCTTTTTTTTCTC
10890 TTT
1 TTT
10893 TTGTTCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (26 bp):
TTTGTTTTTTCTCTCTTTTTTTTCTC
Found at i:10873 original size:27 final size:24
Alignment explanation
Indices: 10839--10892 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 24
10829 TTTCTTCAAT
10839 TTTGTTTTTTCTCTTTTTATTTTCTC
1 TTTGTTTTTTCTC-TTTT-TTTTCTC
10865 TTTGTTTTTTTCTCTTTTTTTTCTC
1 TTTG-TTTTTTCTCTTTTTTTTCTC
10890 TTT
1 TTT
10893 TTGTTCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 10 0.37
26 8 0.30
27 9 0.33
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (24 bp):
TTTGTTTTTTCTCTTTTTTTTCTC
Found at i:10883 original size:11 final size:12
Alignment explanation
Indices: 10843--10894 Score: 70
Period size: 13 Copynumber: 4.2 Consensus size: 12
10833 TTCAATTTTG
10843 TTTTTTCTCTTT
1 TTTTTTCTCTTT
10855 TTATTTTCTCTTT
1 TT-TTTTCTCTTT
10868 GTTTTTT-TCTCTT
1 -TTTTTTCTCT-TT
10881 TTTTTTCTCTTT
1 TTTTTTCTCTTT
10893 TT
1 TT
10895 GTTCTGATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
12 15 0.42
13 19 0.53
14 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:10895 original size:27 final size:27
Alignment explanation
Indices: 10838--10897 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
10828 TTTTCTTCAA
10838 TTTTG-TTTTTTCTCTTTTTATTTTCT
1 TTTTGTTTTTTTCTCTTTTTATTTTCT
*
10864 CTTTGTTTTTTTCTCTTTTT-TTTCTCT
1 TTTTGTTTTTTTCTCTTTTTATTT-TCT
10891 TTTTGTT
1 TTTTGTT
10898 CTGATTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (27 bp):
TTTTGTTTTTTTCTCTTTTTATTTTCT
Found at i:12107 original size:7 final size:7
Alignment explanation
Indices: 12095--12135 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
12085 TGAAATGTAG
12095 ATGCAAA
1 ATGCAAA
12102 ATGCAAA
1 ATGCAAA
12109 ATGCAAA
1 ATGCAAA
12116 ATGCAAA
1 ATGCAAA
12123 ATGCAAAA
1 ATGC-AAA
12131 ATGCA
1 ATGCA
12136 TGAAATGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGCAAA
Found at i:12883 original size:17 final size:18
Alignment explanation
Indices: 12843--12883 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
12833 CTTTTAAATG
12843 ATGAAAATGATGAAAAAA
1 ATGAAAATGATGAAAAAA
12861 AT-AAAA-GA-GAACAAAA
1 ATGAAAATGATGAA-AAAA
12877 ATGAAAA
1 ATGAAAA
12884 AGGTTAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 8 0.38
18 2 0.10
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (18 bp):
ATGAAAATGATGAAAAAA
Found at i:14042 original size:26 final size:26
Alignment explanation
Indices: 13972--14044 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 26
13962 ACGTGAGAAT
13972 AATAAATAAAACA-AGAAAAAAATGAAA
1 AATAAATAAAA-ATA-AAAAAAATGAAA
13999 AATAACA-AAACAAGTAAAAAATAAT-AAA
1 AATAA-ATAAA-AA-TAAAAAA-AATGAAA
14027 AATAAATAAAAATAAAAA
1 AATAAATAAAAATAAAAA
14045 TGTTAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
26 6 0.15
27 12 0.30
28 18 0.45
29 4 0.10
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (26 bp):
AATAAATAAAAATAAAAAAAATGAAA
Found at i:14111 original size:20 final size:20
Alignment explanation
Indices: 14088--14126 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14078 ATATTAATGG
14088 AGTAAAAAAAAAATAAAAAA
1 AGTAAAAAAAAAATAAAAAA
* *
14108 AGTAAAAAGAAATTAAAAA
1 AGTAAAAAAAAAATAAAAA
14127 GGAATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (20 bp):
AGTAAAAAAAAAATAAAAAA
Found at i:14289 original size:41 final size:40
Alignment explanation
Indices: 14244--14326 Score: 91
Period size: 40 Copynumber: 2.0 Consensus size: 40
14234 TAAGAAAAAA
14244 AATAATAGAAAAAGCTAAAATA-AAGTA-AAAATATA-ATATAT
1 AATAA-AGAAAAA-C-AAAATAGAA-TATAAAATATATATATAT
*
14285 AATAAATAAAAACAAAATAGAATATTAAAATATATATATAT
1 AATAAAGAAAAACAAAATAGAATA-TAAAATATATATATAT
14326 A
1 A
14327 TATATATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
38 8 0.22
39 3 0.08
40 14 0.38
41 12 0.32
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (40 bp):
AATAAAGAAAAACAAAATAGAATATAAAATATATATATAT
Found at i:14321 original size:2 final size:2
Alignment explanation
Indices: 14314--14354 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
14304 GAATATTAAA
14314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14355 AACGTATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14426 original size:8 final size:8
Alignment explanation
Indices: 14413--14474 Score: 53
Period size: 8 Copynumber: 8.4 Consensus size: 8
14403 AGAAAAATTA
*
14413 ATACATCT
1 ATACATAT
14421 ATACATAT
1 ATACATAT
14429 ATACATAT
1 ATACATAT
*
14437 ATATATAT
1 ATACATAT
*
14445 ATATATA-
1 ATACATAT
14452 ATA-ATA-
1 ATACATAT
14458 ATA-ATAT
1 ATACATAT
*
14465 A-AGATAT
1 ATACATAT
14472 ATA
1 ATA
14475 TAATAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
6 10 0.20
7 9 0.18
8 30 0.61
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (8 bp):
ATACATAT
Found at i:14438 original size:2 final size:2
Alignment explanation
Indices: 14420--14476 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
14410 TTAATACATC
* *
14420 TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA -A TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
14459 TA -A TA TA -A GA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
14477 ATAAAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
1 5 0.11
2 40 0.89
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (2 bp):
TA
Found at i:14476 original size:25 final size:25
Alignment explanation
Indices: 14443--14491 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
14433 ATATATATAT
*
14443 ATATATATAATAATAATAATATAAG
1 ATATATATAATAAAAATAATATAAG
14468 ATATATATAATAAAAATAATATAA
1 ATATATATAATAAAAATAATATAA
14492 TATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATATATATAATAAAAATAATATAAG
Found at i:14494 original size:23 final size:24
Alignment explanation
Indices: 14437--14505 Score: 88
Period size: 25 Copynumber: 2.9 Consensus size: 24
14427 ATATACATAT
* *
14437 ATATATATATATATAATAATAATA
1 ATATAGATATATATAATAAAAATA
14461 ATATAAGATATATATAATAAAAATA
1 ATAT-AGATATATATAATAAAAATA
*
14486 ATATA-ATATAAATAA-AAAAA
1 ATATAGATATATATAATAAAAA
14506 GGAATATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
22 5 0.12
23 9 0.22
24 5 0.12
25 22 0.54
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (24 bp):
ATATAGATATATATAATAAAAATA
Found at i:14498 original size:14 final size:14
Alignment explanation
Indices: 14427--14500 Score: 71
Period size: 14 Copynumber: 5.1 Consensus size: 14
14417 ATCTATACAT
*
14427 ATATACATATATAT-
1 ATATA-ATATAAATA
14441 ATAT-ATATATAATA
1 ATATAATATA-AATA
14455 ATAATAATATAAGATA
1 AT-ATAATATAA-ATA
*
14471 TATATAATAAAAATA
1 -ATATAATATAAATA
14486 ATATAATATAAATA
1 ATATAATATAAATA
14500 A
1 A
14501 AAAAAGGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
12 5 0.10
13 2 0.04
14 20 0.39
15 6 0.12
16 16 0.31
17 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (14 bp):
ATATAATATAAATA
Found at i:14503 original size:21 final size:20
Alignment explanation
Indices: 14443--14526 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
14433 ATATATATAT
*
14443 ATATATATAATAATAATAATATA
1 ATATATAT-A-AATAA-AAAATA
*
14466 AGATATATATAAT-AAAAATA
1 ATATATATA-AATAAAAAATA
*
14486 ATATAATATAAATAAAAAAAGGA
1 ATAT-ATATAAAT-AAAAAA-TA
14509 ATATA-ATAAATAAAAAAT
1 ATATATATAAATAAAAAAT
14527 TATAATTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
20 17 0.33
21 12 0.23
22 11 0.21
23 12 0.23
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
ATATATATAAATAAAAAATA
Found at i:14511 original size:23 final size:21
Alignment explanation
Indices: 14468--14525 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
14458 ATAATATAAG
* *
14468 ATATATATAATAAAAATAATAT
1 ATATAAATAA-AAAAAGAATAT
14490 AATATAAATAAAAAAAGGAATAT
1 -ATATAAATAAAAAAA-GAATAT
14513 A-ATAAATAAAAAA
1 ATATAAATAAAAAA
14526 TTATAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.38
22 6 0.19
23 14 0.44
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (21 bp):
ATATAAATAAAAAAAGAATAT
Found at i:17275 original size:64 final size:65
Alignment explanation
Indices: 17141--17287 Score: 181
Period size: 64 Copynumber: 2.3 Consensus size: 65
17131 TTATGGGCGG
* * * *
17141 AGGGTATCGATACCCTATGAAGGCGTATCGATACCCCTTTTTAAAGAAAAATTTTAGAATGTCAG
1 AGGGTATCGATACCCTATGAAGGCGTATCGATACCCC-TGTGAAAGAAAAAATTCAGAATGTCAG
17206 T
65 T
* * * *
17207 AGGGTATCGATACCCTAT-AGGGGGTATCGATACCCC-GTGAAGATAAAAAATTCAGAATGTCAT
1 AGGGTATCGATACCCTATGAAGGCGTATCGATACCCCTGTGAA-AGAAAAAATTCAGAATGTCAG
17270 T
65 T
*
17271 AGGGTATCTATACCCTA
1 AGGGTATCGATACCCTA
17288 GACATGGTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
63 3 0.04
64 34 0.48
65 16 0.23
66 18 0.25
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (65 bp):
AGGGTATCGATACCCTATGAAGGCGTATCGATACCCCTGTGAAAGAAAAAATTCAGAATGTCAGT
Found at i:18211 original size:2 final size:2
Alignment explanation
Indices: 18204--18234 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18194 AGTTATGAGA
18204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18235 ACAAGCTATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18758 original size:39 final size:39
Alignment explanation
Indices: 18704--18781 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
18694 AGTGGAGAGT
18704 TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
18743 TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
18782 ATTTCAGTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.26
Consensus pattern (39 bp):
TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
Found at i:18780 original size:18 final size:18
Alignment explanation
Indices: 18707--18772 Score: 89
Period size: 18 Copynumber: 3.5 Consensus size: 18
18697 GGAGAGTTAC
18707 AGTGGTCCTATGGGACAT
1 AGTGGTCCTATGGGACAT
18725 AGTGGTCCT-TCGGGACAAT
1 AGTGGTCCTAT-GGGAC-AT
18744 ACAGTGGTCCTATGGGACAT
1 --AGTGGTCCTATGGGACAT
18764 AGTGGTCCT
1 AGTGGTCCT
18773 TCGGGACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.02
18 23 0.53
19 2 0.05
20 2 0.05
21 14 0.33
22 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTATGGGACAT
Found at i:19056 original size:18 final size:18
Alignment explanation
Indices: 19035--19088 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
19025 TACATGATCG
19035 TGATAGAGATCATGATAA
1 TGATAGAGATCATGATAA
** **
19053 TGATATTGATGTTGATAA
1 TGATAGAGATCATGATAA
*
19071 TGATAGAGATCATTATAA
1 TGATAGAGATCATGATAA
19089 AGATGTTTGT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (18 bp):
TGATAGAGATCATGATAA
Found at i:19082 original size:36 final size:36
Alignment explanation
Indices: 19035--19109 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
19025 TACATGATCG
*
19035 TGATAGAGATCATGATAATGAT-ATTGATGTTGATAA
1 TGATAGAGATCATGATAAAGATGATTG-TGTTGATAA
* *
19071 TGATAGAGATCATTATAAAGATGTTTGTGTTGATAA
1 TGATAGAGATCATGATAAAGATGATTGTGTTGATAA
19107 TGA
1 TGA
19110 GGGTATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 32 0.91
37 3 0.09
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (36 bp):
TGATAGAGATCATGATAAAGATGATTGTGTTGATAA
Found at i:23651 original size:18 final size:18
Alignment explanation
Indices: 23628--23665 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
23618 TATGTTATTC
*
23628 TATATG-TTATGTGATGAA
1 TATATGATTATATG-TGAA
23646 TATATGATTATATGTGAA
1 TATATGATTATATGTGAA
23664 TA
1 TA
23666 AGATAGGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (18 bp):
TATATGATTATATGTGAA
Found at i:24011 original size:18 final size:18
Alignment explanation
Indices: 23988--24022 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23978 CGAGGGTTAC
*
23988 AGTGGTCCTACGGGACAT
1 AGTGGTCATACGGGACAT
*
24006 AGTGGTCATTCGGGACA
1 AGTGGTCATACGGGACA
24023 AATTTCAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCATACGGGACAT
Found at i:24292 original size:18 final size:18
Alignment explanation
Indices: 24269--24335 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
24259 AATGTTAATA
*
24269 CATGATAGTGATAGAGAT
1 CATGATAATGATAGAGAT
**
24287 CATGATAATGATATTGAT
1 CATGATAATGATAGAGAT
**
24305 GTTGATAATGATAGAGAT
1 CATGATAATGATAGAGAT
*
24323 CATGATAAAGATA
1 CATGATAATGATA
24336 TTTGTGTTGA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.31
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:24318 original size:36 final size:36
Alignment explanation
Indices: 24271--24349 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
24261 TGTTAATACA
* *
24271 TGATAGTGATAGAGATCATGATAATGATA-TTGATGT
1 TGATAATGATAGAGATCATGATAAAGATATTTG-TGT
24307 TGATAATGATAGAGATCATGATAAAGATATTTGTGT
1 TGATAATGATAGAGATCATGATAAAGATATTTGTGT
24343 TGATAAT
1 TGATAAT
24350 TAGAGTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 37 0.93
37 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (36 bp):
TGATAATGATAGAGATCATGATAAAGATATTTGTGT
Found at i:26986 original size:35 final size:35
Alignment explanation
Indices: 26929--27008 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
26919 TAATATGTAC
*
26929 TACTATATACTAAACTACTTAATATGAAGACTATA
1 TACTATATACTAAACTACTTAATATGAAAACTATA
* * *
26964 TACTATATATTATACTATTTAATATGAAAACTATA
1 TACTATATACTAAACTACTTAATATGAAAACTATA
26999 TACTATATAC
1 TACTATATAC
27009 GTACTATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (35 bp):
TACTATATACTAAACTACTTAATATGAAAACTATA
Found at i:28083 original size:14 final size:14
Alignment explanation
Indices: 28064--28108 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
28054 TCTTTTGTTT
28064 TCTCTTTCTTCTTC
1 TCTCTTTCTTCTTC
28078 TCTCTTTCTTCTTC
1 TCTCTTTCTTCTTC
28092 TCT-TTCTCTTCTTC
1 TCTCTT-TCTTCTTC
28106 TCT
1 TCT
28109 TATTTATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 2 0.07
14 28 0.93
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTCTTTCTTCTTC
Found at i:28095 original size:8 final size:8
Alignment explanation
Indices: 28066--28109 Score: 53
Period size: 7 Copynumber: 6.1 Consensus size: 8
28056 TTTTGTTTTC
28066 TCTT-TCT
1 TCTTCTCT
28073 TCTTCTC-
1 TCTTCTCT
28080 TCTT-TCT
1 TCTTCTCT
28087 TCTTCTC-
1 TCTTCTCT
28094 T-TTCTCT
1 TCTTCTCT
28101 TCTTCTCT
1 TCTTCTCT
28109 T
1 T
28110 ATTTATTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
6 7 0.22
7 14 0.44
8 11 0.34
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (8 bp):
TCTTCTCT
Found at i:28109 original size:14 final size:13
Alignment explanation
Indices: 28054--28109 Score: 71
Period size: 14 Copynumber: 4.3 Consensus size: 13
28044 TTGGTTTTTT
*
28054 TCTTTTGTT-TTC
1 TCTTTTCTTCTTC
28066 TC-TTTCTTCTTC
1 TCTTTTCTTCTTC
28078 TCTCTTTCTTCTTC
1 TCT-TTTCTTCTTC
28092 TCTTTCTCTTCTTC
1 TCTTT-TCTTCTTC
28106 TCTT
1 TCTT
28110 ATTTATTCTC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
11 5 0.13
12 7 0.18
13 2 0.05
14 25 0.64
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (13 bp):
TCTTTTCTTCTTC
Found at i:28118 original size:26 final size:26
Alignment explanation
Indices: 28063--28120 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
28053 TTCTTTTGTT
*
28063 TTCTCTTTCTTCTTCTCTCTTTCTTC
1 TTCTCTTTCTTCTTCTCTCTTTCTTA
28089 TTCTCTTTC-TCTTCTTCTCTTAT-TTA
1 TTCTCTTTCTTCTTC-TCTCTT-TCTTA
28115 TTCTCT
1 TTCTCT
28121 ACTTCTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 5 0.17
26 23 0.79
27 1 0.03
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (26 bp):
TTCTCTTTCTTCTTCTCTCTTTCTTA
Found at i:28126 original size:28 final size:28
Alignment explanation
Indices: 28063--28118 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
28053 TTCTTTTGTT
* *
28063 TTCTC-TT-TCTTCTTCTCTCTTTCTTC
1 TTCTCTTTCTCTTCTTCTCTATTTATTC
28089 TTCTCTTTCTCTTCTTCTCTTATTTATTC
1 TTCTCTTTCTCTTCTTCTC-TATTTATTC
28118 T
1 T
28119 CTACTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 2 0.08
28 10 0.40
29 8 0.32
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (28 bp):
TTCTCTTTCTCTTCTTCTCTATTTATTC
Found at i:35685 original size:18 final size:18
Alignment explanation
Indices: 35662--35696 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35652 TTCCATCCGG
*
35662 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
35680 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
35697 GTCCTTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:36870 original size:19 final size:19
Alignment explanation
Indices: 36848--36929 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
36838 CTAGGCGGCT
*
36848 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
36867 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
36886 CGGCTCGGCT----T-AAA
1 CGGCTCGGCTCAGCTCAAA
*
36900 CGGCTCGGCTCAGCTC-AG
1 CGGCTCGGCTCAGCTCAAA
36918 CGGCTCGGCTCA
1 CGGCTCGGCTCA
36930 AACGGCTCCT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 14 0.25
19 28 0.50
ACGTcount: A:0.17, C:0.35, G:0.29, T:0.18
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:36877 original size:14 final size:14
Alignment explanation
Indices: 36872--36937 Score: 69
Period size: 14 Copynumber: 4.4 Consensus size: 14
36862 TCAAACGGCT
*
36872 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
36886 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
*
36900 CGGCTCGGCTCAGCTCAG
1 CGGCTCGGCTCA----AA
36918 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
36932 CGGCTC
1 CGGCTC
36938 CTCAGGCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
14 30 0.70
18 13 0.30
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:40704 original size:18 final size:18
Alignment explanation
Indices: 40681--40715 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40671 TTCCATCCGG
*
40681 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
40699 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
40716 GTCCTTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:41889 original size:14 final size:14
Alignment explanation
Indices: 41890--41956 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
41880 TCAAACGGCT
*
41890 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
41904 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
41918 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
41936 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
41951 CGGCTC
1 CGGCTC
41957 CTCAGGCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.16
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:41896 original size:19 final size:19
Alignment explanation
Indices: 41867--41948 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
41857 CTAGGCGGCT
41867 CGGCT-GGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
41885 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
41904 CGGCTCGGCT----T-AAA
1 CGGCTCGGCTCAGCTCAAA
*
41918 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
41937 CGGCTCGGCTCA
1 CGGCTCGGCTCA
41949 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 6 0.11
19 37 0.65
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:41919 original size:33 final size:33
Alignment explanation
Indices: 41872--41956 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
41862 CGGCTCGGCT
*
41872 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
41905 GGCTCGGCTTAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
41938 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
41957 CTCAGGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.16
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:43209 original size:27 final size:27
Alignment explanation
Indices: 43148--43268 Score: 106
Period size: 27 Copynumber: 4.6 Consensus size: 27
43138 TATTTATAAG
* * * *
43148 AATTAAAAGAAATAAAGATTTAAAGGCG
1 AATTAAAAGGAATAAACATTAAAAGG-A
*
43176 AA-TAAAAGGAATAAACATTAAAAAGA
1 AATTAAAAGGAATAAACATTAAAAGGA
* * *
43202 AATCAAAAGGAA-AAATATT-ATAGGA
1 AATTAAAAGGAATAAACATTAAAAGGA
* * *
43227 AGTTAAAAAGAATAAAGATTAAAAGGA
1 AATTAAAAGGAATAAACATTAAAAGGA
43254 AATTAAAA-GAATAAA
1 AATTAAAAGGAATAAA
43269 AAATTAAATA
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
25 13 0.17
26 21 0.28
27 39 0.52
28 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.15, T:0.19
Consensus pattern (27 bp):
AATTAAAAGGAATAAACATTAAAAGGA
Found at i:43283 original size:26 final size:25
Alignment explanation
Indices: 43178--43276 Score: 74
Period size: 26 Copynumber: 3.8 Consensus size: 25
43168 TAAAGGCGAA
*
43178 TAAAAGGAATAAACATTAAAAAGAAAT
1 TAAAA-GAATAAAAATT-AAAAGAAAT
* * * * *
43205 CAAAAGGAA-AAATATTATAGGAAGT
1 TAAAA-GAATAAAAATTAAAAGAAAT
*
43230 TAAAAAGAATAAAGATTAAAAGGAAAT
1 T-AAAAGAATAAAAATTAAAA-GAAAT
43257 TAAAAGAATAAAAAATTAAA
1 TAAAAGAAT-AAAAATTAAA
43277 TAAAATTGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
25 9 0.16
26 26 0.46
27 22 0.39
ACGTcount: A:0.66, C:0.02, G:0.13, T:0.19
Consensus pattern (25 bp):
TAAAAGAATAAAAATTAAAAGAAAT
Found at i:45514 original size:21 final size:21
Alignment explanation
Indices: 45489--45528 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45479 AAGACTCTAT
45489 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
45510 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
45529 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:47342 original size:19 final size:20
Alignment explanation
Indices: 47305--47345 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
47295 TCCAACCATT
47305 AGGGGGTACCAATTCCCCCC
1 AGGGGGTACCAATTCCCCCC
* *
47325 AGGGGGTATCGATTCCCCCC
1 AGGGGGTACCAATTCCCCCC
47345 A
1 A
47346 CTGTTCAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.17
Consensus pattern (20 bp):
AGGGGGTACCAATTCCCCCC
Found at i:51172 original size:10 final size:10
Alignment explanation
Indices: 51157--51181 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
51147 GATTAAGCAT
51157 TTTAGTTGCA
1 TTTAGTTGCA
51167 TTTAGTTGCA
1 TTTAGTTGCA
51177 TTTAG
1 TTTAG
51182 GACATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:52575 original size:55 final size:55
Alignment explanation
Indices: 52495--52988 Score: 634
Period size: 55 Copynumber: 9.0 Consensus size: 55
52485 ATTACCAAAT
* * * * *
52495 GGCACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
1 GGCACTGTGTGTG-TAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * ** *
52552 GGCACTATATGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTATGTACG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
52607 GGCATTGTGTGTGAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * *
52662 GGCACTGTGTGTGAAAAACCAATAAATTCGTAATAAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* ** *
52717 GGCACTGTGTGTGCAAAACTAAGAAATTTGTAAGAAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
52772 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
52827 GGCACTGTATGTGTAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * * * *
52882 GGCTCTGTGTATG-CAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATT
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
52936 GGCACTGTGTGTG--CAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
1 GGCACTGTGTGTGTAAAAC-TAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
52989 CGAAACTAAG
Statistics
Matches: 388, Mismatches: 48, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
53 3 0.01
54 80 0.21
55 290 0.75
56 4 0.01
57 11 0.03
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (55 bp):
GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:52808 original size:165 final size:165
Alignment explanation
Indices: 52495--52984 Score: 700
Period size: 165 Copynumber: 3.0 Consensus size: 165
52485 ATTACCAAAT
* * * * *
52495 GGCACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTAT
1 GGCACTGTGTGTG-AAAAA-CTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCACTGT
* * * * * * *
52560 ATGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTATGTACGGGCATTGTGTGTGAAAAA
64 GTGTGCAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAA
52625 CTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
129 CTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
* * *
52662 GGCACTGTGTGTGAAAAACCAATAAATTCGTAATAAGTTTATGAATTTCCGTATGGGCACTGTGT
1 GGCACTGTGTGTGAAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
** *
52727 GTGCAAAACTAAGAAATTTGTAAGAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAAAACT
66 GTGCAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACT
52792 AAGAAATTCATAATAAGTTTATGAATTTCCATATG
131 AAGAAATTCATAATAAGTTTATGAATTTCCATATG
* * *
52827 GGCACTGTATGTGTAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCTCTGTGT
1 GGCACTGTGTGTGAAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
* *
52892 ATGC-AAACTAAGAAATTCATAATG-AGTTTATGAATTTCTGTATTGGCACTGTGTGTGC--AAC
66 GTGCAAAACTAAGAAATTCATAA-GAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAAC
*
52953 TTAAGAAATTCATAATGAGTTTATGAATTTCC
130 -TAAGAAATTCATAATAAGTTTATGAATTTCC
52985 GTATCGAAAC
Statistics
Matches: 291, Mismatches: 30, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
162 3 0.01
163 30 0.10
164 48 0.16
165 193 0.66
166 5 0.02
167 12 0.04
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (165 bp):
GGCACTGTGTGTGAAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
GTGCAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACT
AAGAAATTCATAATAAGTTTATGAATTTCCATATG
Found at i:57630 original size:2 final size:2
Alignment explanation
Indices: 57625--57675 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
57615 ACACACACAA
57625 AT 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 AT
57667 AT AT AT AT A
1 AT AT AT AT A
57676 CCATTTCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58141 original size:23 final size:23
Alignment explanation
Indices: 58108--58170 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
58098 CAGCTCGTAT
*
58108 AAATGCACCAAAGTGCCGTGTAG
1 AAATGCACCAAAGTGCCGTGCAG
*
58131 AATTGCACCAAAGTGCCGTGCAG
1 AAATGCACCAAAGTGCCGTGCAG
58154 AAATGCACCAAAGTGCC
1 AAATGCACCAAAGTGCC
58171 ATACAAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCGTGCAG
Found at i:58865 original size:19 final size:18
Alignment explanation
Indices: 58821--58865 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
58811 CACTATCCTA
* *
58821 AATTTATACATATCATTT
1 AATTTATACATAACATAT
*
58839 AATCTATACTATAACATAT
1 AATTTATAC-ATAACATAT
58858 AATTTATA
1 AATTTATA
58866 TCACTTATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTATACATAACATAT
Found at i:59420 original size:31 final size:31
Alignment explanation
Indices: 59384--59443 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
59374 AACTTAAAAG
* *
59384 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
59415 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
59444 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:59940 original size:28 final size:28
Alignment explanation
Indices: 59909--60041 Score: 151
Period size: 24 Copynumber: 5.1 Consensus size: 28
59899 TATATGATAT
59909 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATATCTATAATATAATATTAA
*
59938 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
59962 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATATCTATAATATAATATTAA
*
59990 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
* *
60014 AAAATTAATAT-TAAAAT-TAAAATTAA
1 AAAATTAATATCTATAATATAATATTAA
60040 AA
1 AA
60042 TCAAATATAA
Statistics
Matches: 92, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
24 31 0.34
25 12 0.13
26 18 0.20
27 5 0.05
28 20 0.22
29 6 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATTAATATCTATAATATAATATTAA
Found at i:59942 original size:24 final size:24
Alignment explanation
Indices: 59915--59994 Score: 65
Period size: 26 Copynumber: 3.2 Consensus size: 24
59905 ATATAAAATT
59915 AAATATCTATAATATAATATTAAA
1 AAATATCTATAATATAATATTAAA
* * *
59939 AAATTAATATTTAAT-TTAT-TTAAAAA
1 AAA-T-ATCTATAATATAATATT--AAA
59965 ATTAATATCTATAATATAATATTAAA
1 A--AATATCTATAATATAATATTAAA
59991 AAAT
1 AAAT
59995 TAATATTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
24 8 0.19
25 4 0.10
26 22 0.52
27 4 0.10
28 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATATCTATAATATAATATTAAA
Found at i:59981 original size:52 final size:52
Alignment explanation
Indices: 59909--60041 Score: 225
Period size: 52 Copynumber: 2.6 Consensus size: 52
59899 TATATGATAT
59909 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
59962 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
* *
60014 AAAATTAATAT-TAAAAT-TAAAATTAAAA
1 AAAATTAATATCTATAATATAATATTAAAA
60042 TCAAATATAA
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
50 10 0.13
51 5 0.06
52 57 0.73
53 6 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (52 bp):
AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
Found at i:60032 original size:6 final size:6
Alignment explanation
Indices: 60014--60063 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
60004 ATTTATTTAA
* * *
60014 AAAATT AATATT AAAATT AAAATT AAAA-T CAAA-T ATAATAT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT-T AAAATT
60061 AAA
1 AAA
60064 TATAAAACCT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 7 0.19
6 24 0.67
7 5 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:63795 original size:2 final size:2
Alignment explanation
Indices: 63788--63812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63778 CCAAACATAA
63788 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
63813 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:64314 original size:23 final size:23
Alignment explanation
Indices: 64260--64321 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
64250 CAGCTTGTAT
*
64260 AAATGCACCGAAGTACCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
64283 AATTACACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
64306 AAATGCACCAAAGTGC
1 AAATGCACCGAAGTGC
64322 TATATAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.37, C:0.26, G:0.23, T:0.15
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Done.