Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004122.1 Hibiscus syriacus cultivar Beakdansim tig00009020_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: 41299
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8408 original size:24 final size:24
Alignment explanation
Indices: 8376--8424 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
8366 AGTCTTCCTG
8376 ATGATGTATAAAACATCCATGTAC
1 ATGATGTATAAAACATCCATGTAC
*
8400 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCCATGTAC
8424 A
1 A
8425 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (24 bp):
ATGATGTATAAAACATCCATGTAC
Found at i:9019 original size:30 final size:31
Alignment explanation
Indices: 8962--9022 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
8952 CAACCATTCA
8962 TAACTTTTGCAAAATTGAAAAATTGGTCCCC
1 TAACTTTTGCAAAATTGAAAAATTGGTCCCC
8993 TAACTTTT-CAAAAATT-ACAAAA-TGGTCCCC
1 TAACTTTTGC-AAAATTGA-AAAATTGGTCCCC
9023 AAATTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (31 bp):
TAACTTTTGCAAAATTGAAAAATTGGTCCCC
Found at i:13636 original size:7 final size:7
Alignment explanation
Indices: 13624--13659 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
13614 TTTGGTCAGA
13624 GTTGACC
1 GTTGACC
13631 GTTGACC
1 GTTGACC
13638 GTTGACC
1 GTTGACC
13645 GGTCTGACC
1 -GT-TGACC
13654 GTTGAC
1 GTTGAC
13660 TTTGACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 18 0.67
8 4 0.15
9 5 0.19
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (7 bp):
GTTGACC
Found at i:13654 original size:16 final size:14
Alignment explanation
Indices: 13624--13659 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
13614 TTTGGTCAGA
13624 GTTGACCGTTGACC
1 GTTGACCGTTGACC
13638 GTTGACCGGTCTGACC
1 GTTGACC-GT-TGACC
13654 GTTGAC
1 GTTGAC
13660 TTTGACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
16 11 0.55
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (14 bp):
GTTGACCGTTGACC
Found at i:18148 original size:3 final size:3
Alignment explanation
Indices: 18140--18195 Score: 85
Period size: 3 Copynumber: 18.0 Consensus size: 3
18130 GATTCATTTG
*
18140 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT AAT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT AT-T ATT
18187 ATT ATT ATT
1 ATT ATT ATT
18196 TAATAAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:18930 original size:13 final size:13
Alignment explanation
Indices: 18912--18940 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18902 CCACCGTTCA
18912 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
18925 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
18938 CGG
1 CGG
18941 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:19806 original size:96 final size:93
Alignment explanation
Indices: 19657--19829 Score: 211
Period size: 96 Copynumber: 1.8 Consensus size: 93
19647 ATTATTTTAA
* * * * * *
19657 TATTTATTTTTCAATATCGAAGAAAAGGGCAGTCTTAATACAACTGGATGTCCTATTCTGGTATT
1 TATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATT
19722 TTAAAATTAAATATTAATAAAAAAAATAT
66 TTAAAA-TAAATATTAATAAAAAAAATAT
* * * * *
19751 TATTTAATTTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATA
1 TATTT-ATTTT-TCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATA
*
19816 TTTTTAAATAAATA
64 TTTTAAAATAAATA
19830 AATATATTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
94 5 0.08
95 11 0.17
96 49 0.75
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (93 bp):
TATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATT
TTAAAATAAATATTAATAAAAAAAATAT
Found at i:22011 original size:14 final size:14
Alignment explanation
Indices: 21976--22026 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
21966 TTAAATAATG
* *
21976 TACATTTACATTTT
1 TACATTTGCATATT
21990 TACATTTGCATATT
1 TACATTTGCATATT
*
22004 TACATTTGGCATCTT
1 TACATTT-GCATATT
*
22019 TGCATTTG
1 TACATTTG
22027 TATTGCACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.51
Consensus pattern (14 bp):
TACATTTGCATATT
Found at i:22024 original size:15 final size:15
Alignment explanation
Indices: 21988--22026 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
21978 CATTTACATT
21988 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
22002 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
22017 TTTGCATTTG
1 TTTACATTTG
22027 TATTGCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:24989 original size:2 final size:2
Alignment explanation
Indices: 24982--25011 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24972 TTATCCTTTA
24982 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
25012 CCTTTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25325 original size:22 final size:22
Alignment explanation
Indices: 25299--25342 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25289 TATTATACTC
25299 ATCCAGCAAAGAAAGAAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAA
*
25321 ATCCAGCAAAGAAAGGAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAA
25343 GAAAAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.66, C:0.14, G:0.16, T:0.05
Consensus pattern (22 bp):
ATCCAGCAAAGAAAGAAAAAAA
Found at i:25348 original size:7 final size:7
Alignment explanation
Indices: 25336--25425 Score: 74
Period size: 7 Copynumber: 12.0 Consensus size: 7
25326 GCAAAGAAAG
25336 GAAAAAA
1 GAAAAAA
25343 GAAAAAAGA
1 G-AAAAA-A
25352 GGAAAAAA
1 -GAAAAAA
25360 GAAAAAA
1 GAAAAAA
25367 GAAAAAA
1 GAAAAAA
25374 GAAAAAAA
1 G-AAAAAA
**
25382 GAGGAAA
1 GAAAAAA
25389 GAAATAGAAA
1 G-AA-A-AAA
*
25399 AAAAAAA
1 GAAAAAA
*
25406 CAAAAAA
1 GAAAAAA
25413 G-AAAAA
1 GAAAAAA
25419 GAAAAAA
1 GAAAAAA
25426 ATTAAATCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
6 6 0.09
7 35 0.51
8 15 0.22
9 8 0.12
10 4 0.06
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (7 bp):
GAAAAAA
Found at i:25356 original size:17 final size:17
Alignment explanation
Indices: 25334--25388 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
25324 CAGCAAAGAA
25334 AGGAAAAAAGAAAAAAG
1 AGGAAAAAAGAAAAAAG
25351 AGGAAAAAAG-AAAAA-
1 AGGAAAAAAGAAAAAAG
25366 A-GAAAAAAGAAAAAAAG
1 AGGAAAAAAG-AAAAAAG
25383 AGGAAA
1 AGGAAA
25389 GAAATAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.24
15 1 0.03
16 10 0.29
17 11 0.32
18 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AGGAAAAAAGAAAAAAG
Found at i:25363 original size:24 final size:22
Alignment explanation
Indices: 25336--25426 Score: 103
Period size: 24 Copynumber: 4.0 Consensus size: 22
25326 GCAAAGAAAG
25336 GAAAAAAGAAAAAAGAGGAAAAAA
1 GAAAAAAGAAAAAAGA--AAAAAA
25360 GAAAAAAGAAAAAAGAAAAAAA
1 GAAAAAAGAAAAAAGAAAAAAA
** *
25382 GAGGAAAGAAATAGAAAAAAAAAA
1 GAAAAAAGAAA-A-AAGAAAAAAA
*
25406 CAAAAAAG-AAAAAGAAAAAAA
1 GAAAAAAGAAAAAAGAAAAAAA
25427 TTAAATCAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
21 9 0.16
22 16 0.28
23 3 0.05
24 30 0.52
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (22 bp):
GAAAAAAGAAAAAAGAAAAAAA
Found at i:25380 original size:32 final size:33
Alignment explanation
Indices: 25336--25412 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 33
25326 GCAAAGAAAG
25336 GAAAAAAG-AAAAAAGAGGAAA-AAAGAAAAAA
1 GAAAAAAGAAAAAAAGAGGAAAGAAAGAAAAAA
* *
25367 GAAAAAAGAAAAAAAGAGGAAAGAAATAGAAAA
1 GAAAAAAGAAAAAAAGAGGAAAGAAAGAAAAAA
*
25400 -AAAAAACAAAAAA
1 GAAAAAAGAAAAAA
25413 GAAAAAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
31 8 0.20
32 25 0.61
33 8 0.20
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (33 bp):
GAAAAAAGAAAAAAAGAGGAAAGAAAGAAAAAA
Found at i:25380 original size:39 final size:39
Alignment explanation
Indices: 25327--25426 Score: 98
Period size: 39 Copynumber: 2.6 Consensus size: 39
25317 AAAAATCCAG
* *
25327 CAAAGAAAGGAAAAAAGAAAAAAGAGGAA-A-AAAGAAAAAA
1 CAAA-AAAGAAAAAAAGAAAAAAGA--AATAGAAAAAAAAAA
* **
25367 GAAAAAAGAAAAAAAGAGGAAAGAAATAGAAAAAAAAAA
1 CAAAAAAGAAAAAAAGAAAAAAGAAATAGAAAAAAAAAA
*
25406 CAAAAAAGAAAAAGA-AAAAAA
1 CAAAAAAGAAAAAAAGAAAAAA
25427 TTAAATCAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
37 2 0.04
38 5 0.10
39 39 0.80
40 3 0.06
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.01
Consensus pattern (39 bp):
CAAAAAAGAAAAAAAGAAAAAAGAAATAGAAAAAAAAAA
Found at i:29038 original size:76 final size:75
Alignment explanation
Indices: 28955--29203 Score: 313
Period size: 75 Copynumber: 3.3 Consensus size: 75
28945 ATTAACAAGA
* * **
28955 AGCAAATGTTAGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATTTTGAA
* **
29020 TGTTTATATC
66 CGTTCGTATC
* * *
29030 AGCAAAATGCTGGGGCATGCTGAAAGCCCCTTTT-AATCAGAATGAAGAATGTTGATGTATTTTG
1 AGC-AAATGTTGGGGCATGCTGAAA-ACCCTTTTCAATCAGAATCAAGAATGTTGATGTATTTTG
29094 AACGTTCGTATC
64 AACGTTCGTATC
* * * * *
29106 AACAATTGATGGGGCATGCTG-AAAGCCTATTTCAATCAGAATCAAGAATATTGATGTATTTTGA
1 AGCAAATGTTGGGGCATGCTGAAAACCCT-TTTCAATCAGAATCAAGAATGTTGATGTATTTTGA
29170 ACGTTCGTATC
65 ACGTTCGTATC
*
29181 AGCAATTGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
29204 GGCCCACAAC
Statistics
Matches: 150, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
73 3 0.02
74 5 0.03
75 78 0.52
76 57 0.38
77 7 0.05
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATTTTGAA
CGTTCGTATC
Found at i:30518 original size:22 final size:22
Alignment explanation
Indices: 30489--30543 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
30479 ATCTACACTC
*
30489 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
30511 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
30533 TTCAAAGATGA
1 TTCAAAGATGA
30544 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:31050 original size:40 final size:40
Alignment explanation
Indices: 30979--31082 Score: 172
Period size: 40 Copynumber: 2.6 Consensus size: 40
30969 CAGTTTTTCC
* * *
30979 AGAAAAAGTTCATAATGAGAAGAATTTATCTGAAGAAGGA
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
31019 AGAAGAAGTCCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
31059 AGAAGAAGTTCATAATGAGAAGAA
1 AGAAGAAGTTCATAATGAGAAGAA
31083 TTTGTTCAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.18
Consensus pattern (40 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:31307 original size:40 final size:40
Alignment explanation
Indices: 31241--31339 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
31231 TTTCCAGAGA
* *
31241 AAGTTCATAATGAGAAGAATTTATCTGAAGAAGGAA-GAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATG-AG
* *
31281 AAGTCCATAATAAGAAGAACTCATCTGAAGAAGGAATGAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATGAG
*
31321 AAATTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
31340 TTTGTTCAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 50 0.98
41 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.20
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATGAG
Found at i:31411 original size:111 final size:111
Alignment explanation
Indices: 31276--31686 Score: 548
Period size: 111 Copynumber: 3.7 Consensus size: 111
31266 TGAAGAAGGA
* * *
31276 AGAAGAAGTCCATAATAAGAAGAACTCATCTGAAGAAGGAATG-AGAAATTCATAATGAGAAGAA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-GAAGAAATTCATAATGAGAAGAA
*
31340 TTTGTTCAACCTTTTGCAAATCCATCACTTGATGGATCAGCTTTTGC
65 TTTGTTCAACCTTTTGCAAATCCATCACTTGATGGATCAGCTTTTAC
* * *
31387 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
* *
31452 TTGTTCAA-CTTTTCGCTTGAAT-CATCA-TTCGAT-GATTCAG-TATTAC
66 TTGTTCAACCTTTT-GC--AAATCCATCACTT-GATGGA-TCAGCTTTTAC
** * *
31498 AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGGAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
*
31563 TTGTTCAACC-TTTGCAAATCCATCACTTGATGGATCAGCTTTTCC
66 TTGTTCAACCTTTTGCAAATCCATCACTTGATGGATCAGCTTTTAC
* * * * *
31608 AGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
31673 TTGTTCAACCTTTT
66 TTGTTCAACCTTTT
31687 ACATGACTCT
Statistics
Matches: 261, Mismatches: 27, Indels: 24
0.84 0.09 0.08
Matches are distributed among these distances:
108 3 0.01
109 12 0.05
110 83 0.32
111 147 0.56
112 13 0.05
113 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (111 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCAAATCCATCACTTGATGGATCAGCTTTTAC
Found at i:31679 original size:221 final size:223
Alignment explanation
Indices: 31286--31686 Score: 707
Period size: 221 Copynumber: 1.8 Consensus size: 223
31276 AGAAGAAGTC
*
31286 CATAATAAGAAGAACTCATCTGAAGAAGGAATGAGAAATTCATAATGAGAAGAATTTGTTCAACC
1 CATAATAAGAAGAACTCATCTGAAGAAGGAAGGAGAAATTCATAATGAGAAGAATTTGTTCAACC
*
31351 TTTTGCAAATCCATCACTTGATGGATCAGCTTTTGCAGAAAAAGTTCATAATGAGAAGAACTCAT
66 TTTTGCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAT
31416 CTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATCATCAT
131 CTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTGAATCATCAT
31480 TCGATGATTCAGTATTACAGGTAGAGTT
196 TCGATGATTCAGTATTACAGGTAGAGTT
*
31508 CATAATGAGAAGAACTCATCTGAAGAAGGAAGGAGAAATTCATAATGAGAAGAATTTGTTCAACC
1 CATAATAAGAAGAACTCATCTGAAGAAGGAAGGAGAAATTCATAATGAGAAGAATTTGTTCAACC
* * *
31573 -TTTGCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAATTTAT
66 TTTTGCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAT
* **
31637 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTT
131 CTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
31687 ACATGACTCT
Statistics
Matches: 169, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
221 101 0.60
222 68 0.40
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (223 bp):
CATAATAAGAAGAACTCATCTGAAGAAGGAAGGAGAAATTCATAATGAGAAGAATTTGTTCAACC
TTTTGCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAT
CTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCGCTTGAATCATCAT
TCGATGATTCAGTATTACAGGTAGAGTT
Found at i:31795 original size:84 final size:83
Alignment explanation
Indices: 31648--31840 Score: 260
Period size: 84 Copynumber: 2.3 Consensus size: 83
31638 TGAAGAAGGA
** * *
31648 AGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTACATGACTCTATCACAGAATTAGATA
1 AGAA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATAACTCTATCACAGAAGTAGATA
*
31713 GATCAACATCAACTTTTCC
65 GATCAACATCAACATTTCC
* *** * *
31732 AGAGAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTTAACTCTATCACATAAGTAGATG
1 AGA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATAACTCTATCACAGAAGTAGATA
31797 GATCAACATCAACATTTCC
65 GATCAACATCAACATTTCC
*
31816 AGAAATGTTCATAATGAGAAGAACT
1 AGAAAAGTTCATAATGAGAAGAACT
31841 CATCTGAAAG
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
83 21 0.22
84 74 0.77
85 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (83 bp):
AGAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATAACTCTATCACAGAAGTAGATAG
ATCAACATCAACATTTCC
Found at i:32096 original size:3 final size:3
Alignment explanation
Indices: 32088--32155 Score: 100
Period size: 3 Copynumber: 22.0 Consensus size: 3
32078 GATTCATTTG
*
32088 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
*
32134 AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT
32156 TAATAAATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:32229 original size:51 final size:51
Alignment explanation
Indices: 32153--32255 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
32143 TATTATTATT
32153 ATTTAATAAATAATTACAAAACCCAGAGCCCAATAATCAGGCCCATTTTAC
1 ATTTAATAAATAATTACAAAACCCAGAGCCCAATAATCAGGCCCATTTTAC
32204 ATTTAATAAATAATTACAAAACCCAGAGCCCAATAATCAGGCCCATTTTAC
1 ATTTAATAAATAATTACAAAACCCAGAGCCCAATAATCAGGCCCATTTTAC
32255 A
1 A
32256 AGCCCAACCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (51 bp):
ATTTAATAAATAATTACAAAACCCAGAGCCCAATAATCAGGCCCATTTTAC
Done.