Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006167.1 Hibiscus syriacus cultivar Beakdansim tig00014651_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: 101905
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3481 original size:21 final size:23
Alignment explanation
Indices: 3448--3507 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
3438 TACTTATTGT
*
3448 TTATTATGATTATTG-AAAAATA
1 TTATTATGTTTATTGTAAAAATA
*
3470 TTA-TATGTTTATGTGTAAAAATT
1 TTATTATGTTTAT-TGTAAAAATA
3493 TTATTATGTTATATT
1 TTATTATGTT-TATT
3508 TTCGTTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 8 0.25
22 5 0.16
23 9 0.28
24 7 0.22
25 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (23 bp):
TTATTATGTTTATTGTAAAAATA
Found at i:7847 original size:17 final size:17
Alignment explanation
Indices: 7821--7858 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
7811 AATTAAATAC
*
7821 AATA-TTAAATAATTTA
1 AATACTTAAATAAATTA
7837 AATACTTAAATAAATTA
1 AATACTTAAATAAATTA
7854 AATAC
1 AATAC
7859 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AATACTTAAATAAATTA
Found at i:7863 original size:24 final size:24
Alignment explanation
Indices: 7836--7881 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
7826 TAAATAATTT
*
7836 AAATACTTAAATA-AATTAAATACA
1 AAATA-TTAAATATAATAAAATACA
7860 AAATATTAAATATAATAAAATA
1 AAATATTAAATATAATAAAATA
7882 TACCTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATATTAAATATAATAAAATACA
Found at i:14638 original size:18 final size:19
Alignment explanation
Indices: 14617--14654 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
14607 TATTTAAGTG
*
14617 ATAAAAGCGA-TTAAATAA
1 ATAAAAGCAATTTAAATAA
14635 ATAAAAGCAATTTAAATAA
1 ATAAAAGCAATTTAAATAA
14654 A
1 A
14655 AATAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATAAAAGCAATTTAAATAA
Found at i:16681 original size:2 final size:2
Alignment explanation
Indices: 16676--16706 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16666 AATCAATTTG
16676 AC AC AC 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 AC AC AC A
16707 GAGACAGGCA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:24605 original size:45 final size:47
Alignment explanation
Indices: 24553--24641 Score: 146
Period size: 45 Copynumber: 1.9 Consensus size: 47
24543 TCGAATAAAT
24553 GCATGCGAACTAGATATCATACGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATACGGTTAGGATTTATTTTTGTGAACAA
* *
24598 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATACGGTTAGGATTTATTTTTGTGAA
24642 TAACAAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 27 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATACGGTTAGGATTTATTTTTGTGAACAA
Found at i:34364 original size:28 final size:28
Alignment explanation
Indices: 34333--34398 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
34323 TAAAAATGAG
34333 AAGAAGAAAAA-GA-AAAAATATGAGAAAA
1 AAGAAGAAAAATGAGAAAAA-ATGA-AAAA
34361 AAGAA-AAAAATGAGAAAAAATGAAAAA
1 AAGAAGAAAAATGAGAAAAAATGAAAAA
**
34388 GGGAAGAAAAA
1 AAGAAGAAAAA
34399 ATAAAACGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 12 0.36
28 16 0.48
29 5 0.15
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (28 bp):
AAGAAGAAAAATGAGAAAAAATGAAAAA
Found at i:34368 original size:40 final size:39
Alignment explanation
Indices: 34281--34387 Score: 107
Period size: 40 Copynumber: 2.7 Consensus size: 39
34271 ATTTCGCTTG
*
34281 AAGAAGAAATAGAAGAGAAAAAATGAAAAAAATGAATAAT
1 AAGAA-AAATAGAAGAGAAAAAATGAAAAAAATGAATAAA
*
34321 AATAAAAATGAGAAGA-AGAAAAA-GAAAAAATATGAGA-AAA
1 AAGAAAAAT-AGAAGAGA-AAAAATGAAAAAA-ATGA-ATAAA
*
34361 AAGAAAAA-A-ATGAGAAAAAATGAAAAA
1 AAGAAAAATAGAAGAGAAAAAATGAAAAA
34388 GGGAAGAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
37 8 0.14
38 8 0.14
39 12 0.21
40 28 0.49
41 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (39 bp):
AAGAAAAATAGAAGAGAAAAAATGAAAAAAATGAATAAA
Found at i:34380 original size:18 final size:19
Alignment explanation
Indices: 34339--34387 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
34329 TGAGAAGAAG
34339 AAAAAGAAAAAATATGAGA
1 AAAAAGAAAAAATATGAGA
34358 AAAAAGAAAAAA-ATGAGA
1 AAAAAGAAAAAATATGAGA
34376 AAAAATGAAAAA
1 AAAAA-GAAAAA
34388 GGGAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAAGAAAAAATATGAGA
Found at i:34381 original size:10 final size:9
Alignment explanation
Indices: 34298--34387 Score: 69
Period size: 9 Copynumber: 9.4 Consensus size: 9
34288 AATAGAAGAG
34298 AAAAAATGA
1 AAAAAATGA
34307 AAAAAATGA
1 AAAAAATGA
*
34316 ATAATAAT-A
1 A-AAAAATGA
*
34325 AAAATGAGAAGA
1 AAAA--A-ATGA
34337 AGAAAAA-GA
1 A-AAAAATGA
34346 AAAAATATGA
1 AAAAA-ATGA
34356 GAAAAAA-GA
1 -AAAAAATGA
34365 AAAAAATGA
1 AAAAAATGA
34374 GAAAAAATGA
1 -AAAAAATGA
34384 AAAA
1 AAAA
34388 GGGAAGAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
8 12 0.18
9 24 0.36
10 19 0.28
11 7 0.10
12 2 0.03
13 3 0.04
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (9 bp):
AAAAAATGA
Found at i:36012 original size:162 final size:161
Alignment explanation
Indices: 35811--36221 Score: 549
Period size: 162 Copynumber: 2.5 Consensus size: 161
35801 TTTATGAAGA
* *
35811 TCAAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTAAAGATTGAGTCCTATACT
1 TCAAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTAAAGATCGAGTCCTATACT
* *
35876 CTCTGAAAGAATAGGGAGCGGAC-CTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGA
66 CTCTGAAAGAATAGGGAGCGGACTC-GGTTATTGAAGATTATTCGAGTTCTATACTCTCTGAAGA
*
35940 AATAGAGAGCGGACCCGTTT-TATGGAAGATTGT
130 AATAGAGAGCGGACCCGTTTGT-T-GAAGATTAT
* * *
35973 TCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGATCGAGTCTTATACT
1 TCAAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTAAAGATCGAGTCCTATACT
* *
36038 CTCTGAAGGAATAGGGAGCGGACTCGGTTATTGAAGATTATTCGAGTTCTATACTCTCTGAAGGA
66 CTCTGAAAGAATAGGGAGCGGACTCGGTTATTGAAGATTATTCGAGTTCTATACTCTCTGAAGAA
36103 ATAGAGAGCGGACCCGTTTGTTGAAGATTAT
131 ATAGAGAGCGGACCCGTTTGTTGAAGATTAT
** * * * * * * *
36134 TTGAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTCGAGTCTTA
1 TCAAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACAC-GTTTATTAA-A--GATCGAGTCCTA
*
36199 TACT-TCCTGAAGGAATAGGGAGC
62 TACTCT-CTGAAAGAATAGGGAGC
36222 AGACCCGCCA
Statistics
Matches: 222, Mismatches: 20, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
161 41 0.18
162 145 0.65
163 3 0.01
164 1 0.00
165 32 0.14
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (161 bp):
TCAAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTAAAGATCGAGTCCTATACT
CTCTGAAAGAATAGGGAGCGGACTCGGTTATTGAAGATTATTCGAGTTCTATACTCTCTGAAGAA
ATAGAGAGCGGACCCGTTTGTTGAAGATTAT
Found at i:36240 original size:55 final size:55
Alignment explanation
Indices: 35814--36228 Score: 449
Period size: 55 Copynumber: 7.7 Consensus size: 55
35804 ATGAAGATCA
* * * *
35814 AGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTT-AA-A-GATT-G
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTATTCG
* * * * *
35865 AGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTATTCG
* * * *
35920 AGT-TCTATACTCTCTGAAGAAATAGAGAGCGGACCCGTTTTATGGAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCG-TTTATTGAAGATTATTCG
* * *
35976 AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAG---A-TCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTATTCG
* * *
36027 AGTCTTATACTCTCTGAAGGAATAGGGAGCGGACTCGGTTATTGAAGATTATTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTATTCG
* *
36082 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTATTTG
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTATTCG
* * * * *
36137 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTT-TATGAAGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTATTCG
* *
36192 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGACCCG
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCGGACCCG
36229 CCATTTGAAG
Statistics
Matches: 309, Mismatches: 40, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
51 84 0.27
52 2 0.01
53 1 0.00
54 6 0.02
55 168 0.54
56 48 0.16
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTATTCG
Found at i:39521 original size:29 final size:31
Alignment explanation
Indices: 39460--39521 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
39450 AATTTTGGTT
* *
39460 AAATTTAAGAGTTAAATTGATATTTTATTTA
1 AAATTTAAGAGTTAAATTGATATTTCATCTA
39491 AAATTT-AGAGGTT-AA-TGATATTTCATCTA
1 AAATTTAAGA-GTTAAATTGATATTTCATCTA
39520 AA
1 AA
39522 GAGAATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 14 0.50
30 5 0.18
31 9 0.32
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (31 bp):
AAATTTAAGAGTTAAATTGATATTTCATCTA
Found at i:43206 original size:22 final size:23
Alignment explanation
Indices: 43158--43207 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
43148 GAGCAACACT
43158 AGATGATTTTAGTTTCAAATGTC
1 AGATGATTTTAGTTTCAAATGTC
43181 -GATGA-TTTAGTTTTCAAATG-C
1 AGATGATTTTAG-TTTCAAATGTC
43202 AGATGA
1 AGATGA
43208 GGAGAAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (23 bp):
AGATGATTTTAGTTTCAAATGTC
Found at i:55372 original size:35 final size:35
Alignment explanation
Indices: 55296--55373 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
55286 TTAAATACAA
55296 AAAACTTACAATAAGTATTAAATGGTAAATGATAAC
1 AAAA-TTACAATAAGTATTAAATGGTAAATGATAAC
*
55332 CAAATTACAATAACTGATATTAAATGGT-AAT-A-AAC
1 AAAATTACAATAA--G-TATTAAATGGTAAATGATAAC
55367 AAAATTA
1 AAAATTA
55374 ACTGAAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 18 0.49
36 4 0.11
37 4 0.11
38 11 0.30
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (35 bp):
AAAATTACAATAAGTATTAAATGGTAAATGATAAC
Found at i:57987 original size:41 final size:41
Alignment explanation
Indices: 57938--58039 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 41
57928 GACCTCTGAT
*
57938 CCGCGCTATACCCCTATGTGA-CGTATAGCGCGGATCAGGGG
1 CCGCGCTATACCCC-ATGTGAGCGTATAGCGCGGAGCAGGGG
* * * *
57979 CCGTGCTATACCCACGTGTTAGCGTATAGCGCGGGGCAGGGG
1 CCGCGCTATACCC-CATGTGAGCGTATAGCGCGGAGCAGGGG
*
58021 GCGCGCTATACCCCATGTG
1 CCGCGCTATACCCCATGTG
58040 GCGCCAAATC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
41 20 0.40
42 30 0.60
ACGTcount: A:0.18, C:0.29, G:0.33, T:0.20
Consensus pattern (41 bp):
CCGCGCTATACCCCATGTGAGCGTATAGCGCGGAGCAGGGG
Found at i:59070 original size:16 final size:16
Alignment explanation
Indices: 59049--59079 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59039 ATAAATAAAT
59049 GAACATAAACGAACAC
1 GAACATAAACGAACAC
59065 GAACATAAACGAACA
1 GAACATAAACGAACA
59080 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:59169 original size:16 final size:16
Alignment explanation
Indices: 59148--59208 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
59138 TAATAAATAA
**
59148 ACGAACATAAACGCGC
1 ACGAACATAAACGAAC
*
59164 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
59180 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
59196 ACGAACATAAACG
1 ACGAACATAAACG
59209 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.54, C:0.25, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:59400 original size:16 final size:16
Alignment explanation
Indices: 59379--59425 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
59369 TGAAACTCGT
59379 CTCGAACTCAAAAAGG
1 CTCGAACTCAAAAAGG
*
59395 CTCGAACTCTAAAAGG
1 CTCGAACTCAAAAAGG
59411 CTCGAACTCTAAAAA
1 CTCGAACTC-AAAAA
59426 CAAATTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 24 0.86
17 4 0.14
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.17
Consensus pattern (16 bp):
CTCGAACTCAAAAAGG
Found at i:60324 original size:24 final size:24
Alignment explanation
Indices: 60289--60363 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
60279 GATTGGGTTA
* *
60289 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACGAACATAAACG
60313 AACATAACTGAACGAACATAAACG
1 AACATAACTGAACGAACATAAACG
* *
60337 AACATAACCGAACGAACATAACCG
1 AACATAACTGAACGAACATAAACG
60361 AAC
1 AAC
60364 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:60326 original size:14 final size:14
Alignment explanation
Indices: 60309--60364 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
60299 AATGAACATA
*
60309 AACGAACATAACTG
1 AACGAACATAACCG
60323 AACGAACAT-A---
1 AACGAACATAACCG
60333 AACGAACATAACCG
1 AACGAACATAACCG
60347 AACGAACATAACCG
1 AACGAACATAACCG
60361 AACG
1 AACG
60365 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:60363 original size:10 final size:10
Alignment explanation
Indices: 60302--60349 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
60292 ATAAATGAAT
60302 GAACATAAAC
1 GAACATAAAC
60312 GAACATAACTGAAC
1 GAACAT-A---AAC
60326 GAACATAAAC
1 GAACATAAAC
*
60336 GAACATAACC
1 GAACATAAAC
60346 GAAC
1 GAAC
60350 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:61007 original size:2 final size:2
Alignment explanation
Indices: 61002--61027 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60992 ATTAAAATTT
61002 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
61028 AAAGAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64619 original size:20 final size:20
Alignment explanation
Indices: 64577--64620 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
64567 GGAGTCGATG
* **
64577 GCGACGATCCGGACGGCGAA
1 GCGACGACCCGGACAACGAA
*
64597 GCGACGACCCGGACAACGGA
1 GCGACGACCCGGACAACGAA
64617 GCGA
1 GCGA
64621 TGGTCGGGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.39, T:0.02
Consensus pattern (20 bp):
GCGACGACCCGGACAACGAA
Found at i:68407 original size:31 final size:30
Alignment explanation
Indices: 68348--68417 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 30
68338 ACAAGCCTTA
* * *
68348 GAAAAATTAGGGGACCATTTTGTAATTTTT
1 GAAAAGTTAGGGGACCATTTGGTAATTTTG
68378 GAAAAGTTAGGGGACCAATTTGGTAATTTTG
1 GAAAAGTTAGGGGACC-ATTTGGTAATTTTG
68409 GAAAAGTTA
1 GAAAAGTTA
68418 TGAATGATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 15 0.42
31 21 0.58
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (30 bp):
GAAAAGTTAGGGGACCATTTGGTAATTTTG
Found at i:69232 original size:26 final size:26
Alignment explanation
Indices: 69203--69255 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
69193 GAAAATGGGT
*
69203 ATATGTGTCATATGTTATTATATGTG
1 ATATGTGTCACATGTTATTATATGTG
* * *
69229 ATATGTTTGACATGTTATTTTATGTG
1 ATATGTGTCACATGTTATTATATGTG
69255 A
1 A
69256 CATGATTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (26 bp):
ATATGTGTCACATGTTATTATATGTG
Found at i:69264 original size:26 final size:26
Alignment explanation
Indices: 69214--69264 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
69204 TATGTGTCAT
* *
69214 ATGTTATTATATGTGATATGTTTGAC
1 ATGTTATTATATGTGACATGATTGAC
*
69240 ATGTTATTTTATGTGACATGATTGA
1 ATGTTATTATATGTGACATGATTGA
69265 TATGAACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (26 bp):
ATGTTATTATATGTGACATGATTGAC
Found at i:69689 original size:20 final size:20
Alignment explanation
Indices: 69661--69706 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
69651 TTGGGATAAT
* *
69661 TTTACATGCCTTAATGGGAA
1 TTTATATGCCTTAATGGAAA
*
69681 TTTATATGCCTTAGTGGAAA
1 TTTATATGCCTTAATGGAAA
69701 TTTATA
1 TTTATA
69707 CGAGCTGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (20 bp):
TTTATATGCCTTAATGGAAA
Found at i:69798 original size:30 final size:30
Alignment explanation
Indices: 69764--69826 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
69754 CCTTGAGTTC
* *
69764 TCAGTAATGTACATGGGCTTATAAAAGATA
1 TCAGTAATGTACATGGGCCTACAAAAGATA
* *
69794 TCAGTACTGTATATGGGCCTACAAAAGATA
1 TCAGTAATGTACATGGGCCTACAAAAGATA
69824 TCA
1 TCA
69827 AAAGTATGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (30 bp):
TCAGTAATGTACATGGGCCTACAAAAGATA
Found at i:77539 original size:21 final size:21
Alignment explanation
Indices: 77513--77557 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
77503 GATTTCTGGG
* *
77513 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
77534 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
77555 CAA
1 CAA
77558 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:78426 original size:32 final size:32
Alignment explanation
Indices: 78385--78480 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
78375 GAGTCGAGGG
78385 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
78417 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* * *
78448 TATACCTATGTTCTAAGGAACATATGGAAAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
78480 T
1 T
78481 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
31 25 0.46
32 29 0.54
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:78597 original size:29 final size:30
Alignment explanation
Indices: 78472--78594 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
78462 AAGGAACATA
* *
78472 TGGAAAGTTACCGAGGATCTTTATGACCTT
1 TGGACAGTTACCGAGGATCTTTATGACCTC
78502 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
78532 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
78562 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
78591 TGGA
1 TGGA
78595 TAGGTCCTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 18 0.20
30 70 0.80
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:81707 original size:18 final size:18
Alignment explanation
Indices: 81684--81735 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
81674 GAGAGTCCCC
*
81684 AGCCTGCTGAACCTGAAG
1 AGCCTGATGAACCTGAAG
* **
81702 AGCCTGTTGATGCTGAAG
1 AGCCTGATGAACCTGAAG
* *
81720 AGACTGATGACCCTGA
1 AGCCTGATGAACCTGA
81736 CCCCGTCCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (18 bp):
AGCCTGATGAACCTGAAG
Done.