Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002148.1 Hibiscus syriacus cultivar Beakdansim tig00004389_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: 85529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5872 original size:21 final size:21
Alignment explanation
Indices: 5848--5928 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
5838 TAAAGCAAGG
*
5848 GAAGCAGAGAGAGAAGTAGCA
1 GAAGCAGAGAGAGAAGCAGCA
* *
5869 GAAGCA-ACTAGAGCAGCAGC-
1 GAAGCAGA-GAGAGAAGCAGCA
*
5889 GAAAGCAGAGAAAGAAGCAGCA
1 G-AAGCAGAGAGAGAAGCAGCA
* *
5911 GCAGCACAGAGAGAAGCA
1 GAAGCAGAGAGAGAAGCA
5929 TCATATCAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
20 2 0.04
21 43 0.91
22 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.33, T:0.02
Consensus pattern (21 bp):
GAAGCAGAGAGAGAAGCAGCA
Found at i:6430 original size:43 final size:43
Alignment explanation
Indices: 6383--6553 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 43
6373 ACATTTTAGC
* *
6383 GAAAAACGCCACTAAACATCATA-ACCTATTGCGGCGTTTGTCT
1 GAAAAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTGTCT
** * * *
6426 GAAAAACGTTGCTAAATATTAACACCTATTGCGGCGTTTTTAT
1 GAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCT
* * * *
6469 GACAAACTCCGCTAAATATCAATACCTACTGCGGCGTTTG--T
1 GAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCT
*
6510 GAAAGAAACGTCGCTAAATATCAACACCTATTGCGGCGTTTGTC
1 G-AA-AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTC
6554 ACACAAAATT
Statistics
Matches: 103, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 99 0.96
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (43 bp):
GAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCT
Found at i:6498 original size:129 final size:129
Alignment explanation
Indices: 6348--6595 Score: 288
Period size: 129 Copynumber: 1.9 Consensus size: 129
6338 ATCAGAAGCG
*
6348 CCGCAAAACATCAACACCTACTGCGACATTT-TAGCGAA-AAACGCCACTAAACATCATA-ACCT
1 CCGCAAAACATCAACACCTACTGCGACATTTGT-G-AAAGAAACGCCACTAAACATCA-ACACCT
** * * *
6410 ATTGCGGCGTTTGTCTGA-AAAACGTTGCTAAATATTAACACCTATTGCGGCGTTTTTATGACAA
63 ATTGCGGCGTTTGTCACACAAAA-GTTGCTAAATATCAACACATATTGCGACGTTTTTATGACAA
6474 ACT
127 ACT
* * * * * * * *
6477 CCGCTAAATATCAATACCTACTGCGGCGTTTGTGAAAGAAACGTCGCTAAATATCAACACCTATT
1 CCGCAAAACATCAACACCTACTGCGACATTTGTGAAAGAAACGCCACTAAACATCAACACCTATT
* *
6542 GCGGCGTTTGTCACACAAAATTTGCTAAATATCAATACATATTGCGACGTTTTT
66 GCGGCGTTTGTCACACAAAAGTTGCTAAATATCAACACATATTGCGACGTTTTT
6596 TGTGAAAAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
128 3 0.03
129 91 0.92
130 5 0.05
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (129 bp):
CCGCAAAACATCAACACCTACTGCGACATTTGTGAAAGAAACGCCACTAAACATCAACACCTATT
GCGGCGTTTGTCACACAAAAGTTGCTAAATATCAACACATATTGCGACGTTTTTATGACAAACT
Found at i:6560 original size:86 final size:85
Alignment explanation
Indices: 6406--6593 Score: 236
Period size: 86 Copynumber: 2.2 Consensus size: 85
6396 AAACATCATA
* * * *
6406 ACCTATTGCGGCGTTTGTCTGAAAAACGTTGCTAAATATTAACACCTATTGCGGCGTTTTTATGA
1 ACCTATTGCGGCGTTTG-CTGAAAAACGTCGCTAAATATCAACACCTATTGCGGCGTTTTCATCA
*
6471 CAAACTCCGCTAAATATCAAT
65 CAAAATCCGCTAAATATCAAT
*
6492 ACCTACTGCGGCGTTTG-TGAAAGAAACGTCGCTAAATATCAACACCTATTGCGGCGTTTGTCA-
1 ACCTATTGCGGCGTTTGCTG-AA-AAACGTCGCTAAATATCAACACCTATTGCGGCGTTT-TCAT
**
6555 CACAAAATTTGCTAAATATCAAT
63 CACAAAATCCGCTAAATATCAAT
* *
6578 ACATATTGCGACGTTT
1 ACCTATTGCGGCGTTT
6594 TTTGTGAAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
84 2 0.02
85 2 0.02
86 82 0.93
87 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (85 bp):
ACCTATTGCGGCGTTTGCTGAAAAACGTCGCTAAATATCAACACCTATTGCGGCGTTTTCATCAC
AAAATCCGCTAAATATCAAT
Found at i:6569 original size:43 final size:43
Alignment explanation
Indices: 6406--6593 Score: 175
Period size: 43 Copynumber: 4.4 Consensus size: 43
6396 AAACATCATA
* * *
6406 ACCTATTGCGGCGTTTGTCTGA-AAAACGTTGCTAAATATTAAC
1 ACCTATTGCGGCGTTTGTCAGACAAAA-GTCGCTAAATATCAAC
* * *
6449 ACCTATTGCGGCGTTT-TTATGAC-AAACTCCGCTAAATATCAAT
1 ACCTATTGCGGCGTTTGTCA-GACAAAAGT-CGCTAAATATCAAC
* * * * *
6492 ACCTACTGCGGCGTTTGTGAAAGAAACGTCGCTAAATATCAAC
1 ACCTATTGCGGCGTTTGTCAGACAAAAGTCGCTAAATATCAAC
* * * *
6535 ACCTATTGCGGCGTTTGTCACACAAAATTTGCTAAATATCAAT
1 ACCTATTGCGGCGTTTGTCAGACAAAAGTCGCTAAATATCAAC
* *
6578 ACATATTGCGACGTTT
1 ACCTATTGCGGCGTTT
6594 TTTGTGAAAA
Statistics
Matches: 117, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
42 2 0.02
43 110 0.94
44 5 0.04
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (43 bp):
ACCTATTGCGGCGTTTGTCAGACAAAAGTCGCTAAATATCAAC
Found at i:6848 original size:20 final size:20
Alignment explanation
Indices: 6820--6859 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6810 ATTTTAATTA
6820 AAAACAAT-ATTTAAAATATT
1 AAAACAATAATTT-AAATATT
*
6840 AAAATAATAATTTAAATATT
1 AAAACAATAATTTAAATATT
6860 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAACAATAATTTAAATATT
Found at i:7562 original size:10 final size:10
Alignment explanation
Indices: 7543--7607 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
7533 TTAAAATTAC
*
7543 ATTATAAAAA
1 ATTATTAAAA
7553 ATTATTAAAAAA
1 ATTATT--AAAA
* *
7565 ATTATTGATA
1 ATTATTAAAA
7575 ATTA-T-AAA
1 ATTATTAAAA
7583 ATT-TTAAAA
1 ATTATTAAAA
7592 ATATATTAAAA
1 AT-TATTAAAA
7603 ATTAT
1 ATTAT
7608 ATAATACTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
8 6 0.13
9 6 0.13
10 15 0.33
11 8 0.18
12 10 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
ATTATTAAAA
Found at i:7565 original size:12 final size:13
Alignment explanation
Indices: 7543--7575 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
7533 TTAAAATTAC
7543 ATTATAAAAAATT
1 ATTATAAAAAATT
7556 ATTA-AAAAAATT
1 ATTATAAAAAATT
7568 ATTGATAA
1 ATT-ATAA
7576 TTATAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.61
13 5 0.28
14 2 0.11
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (13 bp):
ATTATAAAAAATT
Found at i:7598 original size:28 final size:30
Alignment explanation
Indices: 7550--7608 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
7540 TACATTATAA
* *
7550 AAAATTATTAAAAAAATTATTGATAATTAT
1 AAAATTATTAAAAAAATTATTAAAAATTAT
*
7580 AAAATT-TTAAAAATA-TATTAAAAATTAT
1 AAAATTATTAAAAAAATTATTAAAAATTAT
7608 A
1 A
7609 TAATACTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 12 0.46
29 8 0.31
30 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTATTAAAAAAATTATTAAAAATTAT
Found at i:7747 original size:7 final size:7
Alignment explanation
Indices: 7727--7776 Score: 66
Period size: 7 Copynumber: 7.3 Consensus size: 7
7717 GTTAGATTAC
7727 ACCCTAA
1 ACCCTAA
7734 A-CCTAA
1 ACCCTAA
7740 ACCCTAA
1 ACCCTAA
*
7747 ACTCTAA
1 ACCCTAA
7754 ACCCTAA
1 ACCCTAA
*
7761 AACCTAA
1 ACCCTAA
*
7768 GCCCTAA
1 ACCCTAA
7775 AC
1 AC
7777 ACATGTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.16
Consensus pattern (7 bp):
ACCCTAA
Found at i:7755 original size:14 final size:13
Alignment explanation
Indices: 7727--7776 Score: 73
Period size: 14 Copynumber: 3.7 Consensus size: 13
7717 GTTAGATTAC
7727 ACCCTAAACCTAA
1 ACCCTAAACCTAA
7740 ACCCTAAACTCTAA
1 ACCCTAAAC-CTAA
7754 ACCCTAAAACCTAA
1 ACCCT-AAACCTAA
*
7768 GCCCTAAAC
1 ACCCTAAAC
7777 ACATGTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.38
14 17 0.50
15 4 0.12
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.16
Consensus pattern (13 bp):
ACCCTAAACCTAA
Found at i:9254 original size:11 final size:11
Alignment explanation
Indices: 9238--9301 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
9228 TACTTACCTG
*
9238 TCGAGCTTGAA
1 TCGAGCTTAAA
*
9249 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
9261 TCGAGCTTGAA
1 TCGAGCTTAAA
* *
9272 CCGAGCTCAAAA
1 TCGAGCT-TAAA
*
9284 TCGAGCTTCAA
1 TCGAGCTTAAA
9295 TCGAGCT
1 TCGAGCT
9302 CGAGTCTCGA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 24 0.59
12 17 0.41
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (11 bp):
TCGAGCTTAAA
Found at i:9264 original size:23 final size:23
Alignment explanation
Indices: 9238--9302 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
9228 TACTTACCTG
9238 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCAAAA
*
9261 TCGAGCTTGAACCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCAAAA
*
9284 TCGAGCTTCAATCGAGCTC
1 TCGAGCTTGAATCGAGCTC
9303 GAGTCTCGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCAAAA
Found at i:9897 original size:61 final size:59
Alignment explanation
Indices: 9818--10024 Score: 219
Period size: 61 Copynumber: 3.5 Consensus size: 59
9808 ATAGGTCGAA
* * * **
9818 ATTTGACAAATCCGATTTCATTTTGACAAAACATGTATCAAATTTGACAAAACCGATTGAT
1 ATTTGACAAAACCAATTTCAATTTGACAAAACCGGTAT-AAATTTGACAAAACCG-TTGAT
* * * *
9879 ATTTGACAAAACCAATTTCAATTTGAGAAAACCGGTA-AAGAGTT-AC---A-TGTTGAA
1 ATTTGACAAAACCAATTTCAATTTGACAAAACCGGTATAA-ATTTGACAAAACCGTTGAT
* *
9933 ATTTGACAAATCCAATTTCAATTTGACAAAACCGGTAGTGAATTTGACAAAACCTGTTGAT
1 ATTTGACAAAACCAATTTCAATTTGACAAAACCGGTA-TAAATTTGACAAAACC-GTTGAT
*
9994 ATTTGACAAAACCAATTTCAATTTGATAAAA
1 ATTTGACAAAACCAATTTCAATTTGACAAAA
10025 TCGATAAAGA
Statistics
Matches: 120, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
54 39 0.32
55 4 0.03
56 4 0.03
59 5 0.04
60 3 0.03
61 65 0.54
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (59 bp):
ATTTGACAAAACCAATTTCAATTTGACAAAACCGGTATAAATTTGACAAAACCGTTGAT
Found at i:9902 original size:20 final size:20
Alignment explanation
Indices: 9817--9912 Score: 90
Period size: 20 Copynumber: 4.8 Consensus size: 20
9807 AATAGGTCGA
*
9817 AATTTGACAAATCCGATTTC
1 AATTTGACAAAACCGATTTC
*
9837 ATTTTGACAAAA-C-ATGTATC
1 AATTTGACAAAACCGAT-T-TC
*
9857 AAATTTGACAAAACCGA-TTG
1 -AATTTGACAAAACCGATTTC
*
9877 ATATTTGACAAAACCAATTTC
1 A-ATTTGACAAAACCGATTTC
*
9898 AATTTGAGAAAACCG
1 AATTTGACAAAACCG
9913 GTAAAGAGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 39 0.64
21 15 0.25
22 1 0.02
23 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (20 bp):
AATTTGACAAAACCGATTTC
Found at i:9957 original size:20 final size:21
Alignment explanation
Indices: 9932--10024 Score: 77
Period size: 20 Copynumber: 4.6 Consensus size: 21
9922 TACATGTTGA
*
9932 AATTTGACAAATCCAAT-TTC
1 AATTTGACAAAACCAATATTC
** * *
9952 AATTTGACAAAACCGGTAGTG
1 AATTTGACAAAACCAATATTC
* *
9973 AATTTGACAAAACC--TGTTG
1 AATTTGACAAAACCAATATTC
9992 ATATTTGACAAAACCAAT-TTC
1 A-ATTTGACAAAACCAATATTC
*
10013 AATTTGATAAAA
1 AATTTGACAAAA
10025 TCGATAAAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.07
20 37 0.62
21 18 0.30
22 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (21 bp):
AATTTGACAAAACCAATATTC
Found at i:9978 original size:21 final size:19
Alignment explanation
Indices: 9952--10006 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 19
9942 ATCCAATTTC
9952 AATTTGACAAAACCGGTAGTG
1 AATTTGACAAAACCGGT--TG
*
9973 AATTTGACAAAACCTGTTG
1 AATTTGACAAAACCGGTTG
9992 ATATTTGACAAAACC
1 A-ATTTGACAAAACC
10007 AATTTCAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 16 0.50
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
AATTTGACAAAACCGGTTG
Found at i:10017 original size:115 final size:115
Alignment explanation
Indices: 9815--10035 Score: 338
Period size: 115 Copynumber: 1.9 Consensus size: 115
9805 ATAATAGGTC
* * *
9815 GAAATTTGACAAATCCGATTTCATTTTGACAAAACATGTATCAAATTTGACAAAACCGATTGATA
1 GAAATTTGACAAATCCAATTTCAATTTGACAAAACAGGTATCAAATTTGACAAAACCGATTGATA
*
9880 TTTGACAAAACCAATTTCAATTTGAGAAAACCGGTAAAGAGTTACATGTT
66 TTTGACAAAACCAATTTCAATTTGAGAAAACCGATAAAGAGTTACATGTT
* *
9930 GAAATTTGACAAATCCAATTTCAATTTGACAAAACCGGTAGT-GAATTTGACAAAACCTG-TTGA
1 GAAATTTGACAAATCCAATTTCAATTTGACAAAACAGGTA-TCAAATTTGACAAAACC-GATTGA
* *
9993 TATTTGACAAAACCAATTTCAATTTGATAAAATCGATAAAGAG
64 TATTTGACAAAACCAATTTCAATTTGAGAAAACCGATAAAGAG
10036 CTACTGGAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
115 94 0.98
116 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (115 bp):
GAAATTTGACAAATCCAATTTCAATTTGACAAAACAGGTATCAAATTTGACAAAACCGATTGATA
TTTGACAAAACCAATTTCAATTTGAGAAAACCGATAAAGAGTTACATGTT
Found at i:13909 original size:200 final size:196
Alignment explanation
Indices: 13372--14036 Score: 678
Period size: 200 Copynumber: 3.3 Consensus size: 196
13362 TGCATTGTAG
* * * *
13372 AAGTAATATGTAAATTTACAATGTAAACGATAAAAGTATATCAGTATAATGATAATAGCGTA-A-
1 AAGTAATAGGTAAATTTACAATGTAAACGGTAAAAGTATACCGGTATAATGATAATAGCGTATAT
* * * * *
13435 ACACATCGTATCAATACTTTGTTATATCGGTGTCGATACTTTAATTCCAGTATGCATCTCAAACA
66 AC-CA-CGTATCGATACTTT-TTATAT--ATATCGATAATTTTATTCCAGTATGCATCTCAAACA
* * * *
13500 ATTTGGACGCAAAAAGTATCGATACACATATATAAAATATCGATATACTCAGAATTTTGAAACCT
126 ATTTGCACGCAAAAAGTATCGATACACATATAT-AAATATC-A-ATACTTATAATTTCGAAACCT
13565 A-TACTTTA
188 ATTACTTTA
* * * * *
13573 AAGTAATAGGTAAATTTATAATGTAAACGGTAAAAATCTACTGGTTTAATGATAATAG-GTATAA
1 AAGTAATAGGTAAATTTACAATGTAAACGGTAAAAGTATACCGGTATAATGATAATAGCGTAT--
** * * * *
13637 ATATAATGTATCGATACTTTTTTTTATAGGTATCGATAATTTTATTCCAGTAAGCTTCTCAAACA
64 ATACCACGTATCGATAC-TTTTTATATA--TATCGATAATTTTATTCCAGTATGCATCTCAAACA
* * * * *
13702 ATTTGCACGCAAAAAGTATCGATTCACATGTACAAAGTATCAATACTTTTAATTCCGAAACCTAT
126 ATTTGCACGCAAAAAGTATCGATACACATATATAAA-TATCAATACTTATAATTTCGAAACCTAT
*
13767 TACTATA
190 TACTTTA
* * * * **
13774 AAATAATAGGTAAATTAACAATGTAAAGGGTAAAAGTTTACCGGTATAATGACCATAAGCGTATA
1 AAGTAATAGGTAAATTTACAATGTAAACGGTAAAAGTATACCGGTATAATGATAAT-AGCGTATA
* *
13839 TACCACGTATCGATACTTTATATATATATATCGATAATTTTATTCCAATATGCATCTTAAACAAT
65 TACCACGTATCGATACTTT-T-TATATATATCGATAATTTTATTCCAGTATGCATCTCAAACAAT
* * *
13904 TTGCACGCAAAATGTATCGATACACATATATAAATCTTCGATACTTATAATTTCG-AACCTATTA
128 TTGCACGCAAAAAGTATCGATACACATATATAAAT-ATCAATACTTATAATTTCGAAACCTATTA
13968 CTTTA
192 CTTTA
* * * *
13973 AAGTAATAGGTTAATTTACAAT-TAAAAACGGTAAAAATCA-ATCTGTATAATGATAATAGGCGT
1 AAGTAATAGGTAAATTTACAATGT--AAACGGTAAAAGT-ATACCGGTATAATGATAATA-GCGT
14036 A
62 A
14037 AACATCAAAT
Statistics
Matches: 379, Mismatches: 67, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
198 1 0.00
199 34 0.09
200 130 0.34
201 120 0.32
202 84 0.22
203 9 0.02
204 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (196 bp):
AAGTAATAGGTAAATTTACAATGTAAACGGTAAAAGTATACCGGTATAATGATAATAGCGTATAT
ACCACGTATCGATACTTTTTATATATATCGATAATTTTATTCCAGTATGCATCTCAAACAATTTG
CACGCAAAAAGTATCGATACACATATATAAATATCAATACTTATAATTTCGAAACCTATTACTTT
A
Found at i:14459 original size:118 final size:117
Alignment explanation
Indices: 14291--14671 Score: 340
Period size: 118 Copynumber: 3.3 Consensus size: 117
14281 ATAACAAATT
* * *
14291 AAGTAATT-AACTTATTTTGTTATCATCTG-ATTTCTAAGGCTCCACCAGCTTTAAACAAGCGCT
1 AAGTAATTAAAC-TATTTTGTTATCGTC-GAATTTCTAAGGTTCCATCAGCTTTAAACAAG-GCT
* * * *
14354 ACCTATTACATTAAATAAGCGCTATTTGATATGTTATTATGGTTAATAATGCTTC
63 ACCTATTACATTAAATAAGCGCTACTTGATATGTTATTATGATTGATAATGATTC
* * * **
14409 CAGTAATTAAACTATTTTGTTATCGTCGAATTTATAAGGTTCCATTAGC-TTAAACTTTGG----
1 AAGTAATTAAACTATTTTGTTATCGTCGAATTTCTAAGGTTCCATCAGCTTTAAAC-AAGGCTAC
* * * * * ** *
14469 -TA--ACATT--TTAGGCGCTACCTAATATGTTGATAAT-ATTGATAACAAATC
65 CTATTACATTAAATAAGCGCTACTTGATATGTT-ATTATGATTGATAATGATTC
* * * *
14517 AAGTAATTAACCTATTTTGTTATCGTCCAATTTCTAAGGTCCCATCAGCTTTAAACAGGTGCTAC
1 AAGTAATTAAACTATTTTGTTATCGTCGAATTTCTAAGGTTCCATCAGCTTTAAACAAG-GCTAC
* * *
14582 CTATTACATTAAATAAGCGTTACTTGTTATGTTATTATGATTGATAATGTTTC
65 CTATTACATTAAATAAGCGCTACTTGATATGTTATTATGATTGATAATGATTC
* *
14635 TAGTAATTAATCTATTTTGTTATCGTC-AGATTTCTAA
1 AAGTAATTAAACTATTTTGTTATCGTCGA-ATTTCTAA
14672 AGCTCTATCA
Statistics
Matches: 205, Mismatches: 41, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
108 68 0.33
109 11 0.05
110 5 0.02
112 2 0.01
114 2 0.01
116 5 0.02
117 13 0.06
118 96 0.47
119 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (117 bp):
AAGTAATTAAACTATTTTGTTATCGTCGAATTTCTAAGGTTCCATCAGCTTTAAACAAGGCTACC
TATTACATTAAATAAGCGCTACTTGATATGTTATTATGATTGATAATGATTC
Found at i:14781 original size:216 final size:222
Alignment explanation
Indices: 14262--14871 Score: 740
Period size: 226 Copynumber: 2.8 Consensus size: 222
14252 ATGTACACGG
* * *
14262 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACTTATTTTGTTATCATCTGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTA
* * *
14327 AGGCTCCACCAGCTTTAAACAAGCGCTACCTATTACATTAAATAAGCGCTATTTGATATGTTATT
66 AGGTTCCATCAGCTTTAAACAAGCGCTACCTATTACATTAAATAAGCGCTACTTGATATGTTATT
* * * * *
14392 ATGGTTAATAATGCTTCCAGTAATTAAACTATTTTGTTATCGTCGAATTTATAAGGTTCCATTAG
131 ATGATTGATAATGTTTCCAGTAATTAATCTATTTTGTTATCGTCGAATTTATAAAG-T-CA-TA-
**
14457 CTTAAACTTTGGTAACATTTTAGGCGCTACC
192 CTTAAACTAGGGTAACATTTTAGGCGCTACC
* *
14488 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCCA-ATTTCT
1 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCGT-CAGATTTCT
* * * * *
14552 AAGGTCCCATCAGCTTTAAACAGGTGCTACCTATTACATTAAATAAGCGTTACTTGTTATGTTAT
65 AAGGTTCCATCAGCTTTAAACAAGCGCTACCTATTACATTAAATAAGCGCTACTTGATATGTTAT
* *
14617 TATGATTGATAATGTTTCTAGTAATTAATCTATTTTGTTATCGTC-AGATTTCTAAAG-C-T-C-
130 TATGATTGATAATGTTTCCAGTAATTAATCTATTTTGTTATCGTCGA-ATTTATAAAGTCATACT
* * *
14677 T-ATC-AGGGTAACATTTTATGCTCTACC
194 TAAACTAGGGTAACATTTTAGGCGCTACC
*
14704 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTTTT
1 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGA-TTTCT
* * * * * *
14769 AA-GTTCCATCAGCTTTAAA-ATAACGCTACCTATTACGTTACATAAACACTACCT-ATATGTTA
65 AAGGTTCCATCAGCTTTAAACA-AGCGCTACCTATTACATTAAATAAGCGCTACTTGATATGTTA
* * *
14831 TTAT-AGTTGATAATGTTTCCAATAATTAATCGATTATGTTA
129 TTATGA-TTGATAATGTTTCCAGTAATTAATCTATTTTGTTA
14872 AAATTAATAT
Statistics
Matches: 336, Mismatches: 42, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
214 1 0.00
215 45 0.13
216 113 0.34
217 8 0.02
218 1 0.00
219 1 0.00
221 1 0.00
223 1 0.00
225 1 0.00
226 163 0.49
227 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (222 bp):
TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTA
AGGTTCCATCAGCTTTAAACAAGCGCTACCTATTACATTAAATAAGCGCTACTTGATATGTTATT
ATGATTGATAATGTTTCCAGTAATTAATCTATTTTGTTATCGTCGAATTTATAAAGTCATACTTA
AACTAGGGTAACATTTTAGGCGCTACC
Found at i:23414 original size:32 final size:35
Alignment explanation
Indices: 23352--23428 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 35
23342 GATTAAAATG
*
23352 AAATTAAAATATAATAATAATAATAATAATAATTTAA
1 AAATTAAAATATAATAAT-ATAATAATAAT-AGTTAA
23389 AAATTAAAAT-TAA-AAT-TAA-AATAATAGTTAA
1 AAATTAAAATATAATAATATAATAATAATAGTTAA
23420 ATAATTAAA
1 A-AATTAAA
23429 TACATAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 6 0.16
32 13 0.34
33 3 0.08
35 3 0.08
36 3 0.08
37 10 0.26
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (35 bp):
AAATTAAAATATAATAATATAATAATAATAGTTAA
Found at i:23442 original size:20 final size:20
Alignment explanation
Indices: 23367--23442 Score: 52
Period size: 20 Copynumber: 3.8 Consensus size: 20
23357 AAAATATAAT
*
23367 AATAATAATAATAATAATTTAAA
1 AATAATAAT-TTAATAA-TT-AA
23390 AATTAA-AA-TTAA-AATTAA
1 AA-TAATAATTTAATAATTAA
* *
23408 AATAATAGTTAAATAATT-A
1 AATAATAATTTAATAATTAA
23427 AATACATAATTTAATA
1 AATA-ATAATTTAATA
23443 TTTTTATTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
17 3 0.07
18 5 0.12
19 10 0.23
20 15 0.35
21 3 0.07
23 4 0.09
24 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (20 bp):
AATAATAATTTAATAATTAA
Found at i:25617 original size:30 final size:30
Alignment explanation
Indices: 25577--25642 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
25567 CCTACTGATA
*
25577 ATCTTTCATTGCGTGAACCAAATACACTAT
1 ATCTTCCATTGCGTGAACCAAATACACTAT
*
25607 ATCTTCCATTGCGTGAACCAAATGCACTAT
1 ATCTTCCATTGCGTGAACCAAATACACTAT
25637 ATCTTC
1 ATCTTC
25643 TGCCCCTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (30 bp):
ATCTTCCATTGCGTGAACCAAATACACTAT
Found at i:28991 original size:3 final size:3
Alignment explanation
Indices: 28983--29011 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28973 TGTAATTATA
28983 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29012 AAGACCCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30459 original size:38 final size:40
Alignment explanation
Indices: 30374--30459 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
30364 CTTCGCCAAT
*
30374 AAATATTATGAAGAATGAAATATTTTCGAGTGCCAACCGA
1 AAATATTATGAAGAATGAAATATTTTCGAGTGCAAACCGA
*
30414 AAATATTATGAAGAAT-ACAATATTTTTGA-T-CAAACCGA
1 AAATATTATGAAGAATGA-AATATTTTCGAGTGCAAACCGA
30452 AAATATTA
1 AAATATTA
30460 GGAAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 15 0.35
39 2 0.05
40 26 0.60
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (40 bp):
AAATATTATGAAGAATGAAATATTTTCGAGTGCAAACCGA
Found at i:31966 original size:41 final size:43
Alignment explanation
Indices: 31904--31988 Score: 156
Period size: 41 Copynumber: 2.0 Consensus size: 43
31894 AGCATATGCG
31904 CATATATATGCATGTTATATATTTGGATAAAAATCAATATAAC
1 CATATATATGCATGTTATATATTTGGATAAAAATCAATATAAC
31947 CATATATATGCATG-T-TATATTTGGATAAAAATCAATATAAC
1 CATATATATGCATGTTATATATTTGGATAAAAATCAATATAAC
31988 C
1 C
31989 GACTCAACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 27 0.64
42 1 0.02
43 14 0.33
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (43 bp):
CATATATATGCATGTTATATATTTGGATAAAAATCAATATAAC
Found at i:37137 original size:153 final size:153
Alignment explanation
Indices: 36859--37140 Score: 489
Period size: 152 Copynumber: 1.8 Consensus size: 153
36849 CTTTCACCAT
*
36859 TTATTATGAGAAATTTTACTTCTCGCGTTTATCGAAATGGTTCATTTTGCAGGCATGAAACTTTT
1 TTATTATGAGAAAATTTACTTCTCGCGTTTATCGAAATGGTTCATTTTGCAGGCATGAAACTTTT
*
36924 TCTTGCAATTGGAAATTTGAGGTGTTTTAGAACATTACCATAATTGTTGTCATGGCGAAGTACTA
66 TCTTGCAATTGAAAATTTGAGGTGTTTTAGAACATTACCATAATTGTTGTCATGGCGAAGTACTA
36989 TGAATTAGGATGAAGTTCTTTCA
131 TGAATTAGGATGAAGTTCTTTCA
*
37012 TTATTATGAGAAAATTTACTTCTCG-TTTATATCGAAATGGTTCATTTATGCAGGCATG-AAC-T
1 TTATTATGAGAAAATTTACTTCTCGCGTT-TATCGAAATGGTTCATTT-TGCAGGCATGAAACTT
37074 TTTCTTGCAATTGAAAATTTGAGGTGTTTTAGAACATTACCATAATTGTTGTCATGAGCGAAGTA
64 TTTCTTGCAATTGAAAATTTGAGGTGTTTTAGAACATTACCATAATTGTTGTCATG-GCGAAGTA
37139 CT
128 CT
37141 TGTTTGTGTT
Statistics
Matches: 123, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
152 58 0.47
153 55 0.45
154 10 0.08
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (153 bp):
TTATTATGAGAAAATTTACTTCTCGCGTTTATCGAAATGGTTCATTTTGCAGGCATGAAACTTTT
TCTTGCAATTGAAAATTTGAGGTGTTTTAGAACATTACCATAATTGTTGTCATGGCGAAGTACTA
TGAATTAGGATGAAGTTCTTTCA
Found at i:45256 original size:17 final size:17
Alignment explanation
Indices: 45234--45267 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
45224 AAACCACTTC
45234 GTTTTTCCATTCTTTTG
1 GTTTTTCCATTCTTTTG
45251 GTTTTTCCATTCTTTTG
1 GTTTTTCCATTCTTTTG
45268 TGTACCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.12, T:0.65
Consensus pattern (17 bp):
GTTTTTCCATTCTTTTG
Found at i:47797 original size:18 final size:18
Alignment explanation
Indices: 47774--47809 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
47764 AAAGGCGATG
47774 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
47792 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
47810 ACGGTGGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:49459 original size:111 final size:111
Alignment explanation
Indices: 49320--49541 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
49310 ATTACAAAAA
* *
49320 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
49385 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
49431 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
49496 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
49542 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:49623 original size:17 final size:18
Alignment explanation
Indices: 49603--49638 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
49593 GAATTATATT
49603 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
49620 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
49638 A
1 A
49639 TTATATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:55671 original size:21 final size:21
Alignment explanation
Indices: 55632--55673 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55622 AAGCAGAATC
* *
55632 TGCTACCCTATTTTTTGGTCT
1 TGCTACCCTATTCTCTGGTCT
*
55653 TGCTACCCTGTTCTCTGGTCT
1 TGCTACCCTATTCTCTGGTCT
55674 AGCCTCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.29, G:0.17, T:0.48
Consensus pattern (21 bp):
TGCTACCCTATTCTCTGGTCT
Found at i:58567 original size:21 final size:22
Alignment explanation
Indices: 58541--58582 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
58531 AATAAAAAAG
*
58541 AATGAAATTTAAAATT-TTAAT
1 AATGAAATTGAAAATTGTTAAT
58562 AATGAAATTGAAAATTGTTAA
1 AATGAAATTGAAAATTGTTAA
58583 AGTTGAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (22 bp):
AATGAAATTGAAAATTGTTAAT
Found at i:60869 original size:17 final size:18
Alignment explanation
Indices: 60847--60881 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
60837 GGGGGAGGAG
60847 CGAA-GGGAATTAGGGAT
1 CGAAGGGGAATTAGGGAT
*
60864 CGAAGGGGGATTAGGGAT
1 CGAAGGGGAATTAGGGAT
60882 TGAAATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.06, G:0.46, T:0.17
Consensus pattern (18 bp):
CGAAGGGGAATTAGGGAT
Found at i:63928 original size:75 final size:77
Alignment explanation
Indices: 63841--64040 Score: 248
Period size: 75 Copynumber: 2.6 Consensus size: 77
63831 AACCGTTGAA
* * * * *
63841 TAGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGATTCCCTCCGAGCATACTGGAATTCTCGGA
1 TAGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCTGAGCATACTGGAAATCTCGGA
*
63905 -ACAAA-AATGTT
66 GACAAACAAT-TC
* **
63916 TAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCTGAGCATTTTGGAAATCTCGGA
1 TAGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCTGAGCATACTGGAAATCTCGGA
* *
63980 GCCAAACCATTC
66 GACAAACAATTC
63992 T-GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 TAGGGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCTGAGCA
64041 ATCTGTAATT
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
75 76 0.70
76 12 0.11
77 20 0.19
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.24
Consensus pattern (77 bp):
TAGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCTGAGCATACTGGAAATCTCGGA
GACAAACAATTC
Found at i:64686 original size:16 final size:15
Alignment explanation
Indices: 64655--64695 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
64645 ACCATTCATA
*
64655 AATCCAAAATCCAAC
1 AATCCAAAATCAAAC
64670 AATCCACAAATCAAAC
1 AATCCA-AAATCAAAC
*
64686 AATTCAAAAT
1 AATCCAAAAT
64696 GTTGAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.17
Consensus pattern (15 bp):
AATCCAAAATCAAAC
Found at i:66675 original size:20 final size:20
Alignment explanation
Indices: 66646--66683 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
66636 CATAACCCCA
*
66646 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
66666 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
66684 TCAAAGGGGG
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:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:66718 original size:20 final size:21
Alignment explanation
Indices: 66666--66726 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
66656 ATTCCCCTGT
66666 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
66689 GGGGGAATCGGTTCCCTC-AG
1 GGGGGAATCGGTTCCCTCAAA
* *
66709 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
66727 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.36, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:72574 original size:74 final size:75
Alignment explanation
Indices: 72488--72685 Score: 256
Period size: 74 Copynumber: 2.6 Consensus size: 75
72478 GACCGTTGAA
* * * *
72488 TAGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCTGAGCATACTGGAATTCTCGGAA
1 TAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGGAA
**
72552 CAAAAATGTT
66 CAAAAACATT
* * *
72562 TAGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 TAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGGAA
* *
72626 CCAAACCATT
66 CAAAAACATT
*
72636 CAGGGGGGAATCGGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 TA-GGGGGAATC-GGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
72686 ATCTGTAATT
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
74 62 0.58
75 10 0.09
76 12 0.11
77 23 0.21
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.24
Consensus pattern (75 bp):
TAGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGGAA
CAAAAACATT
Found at i:84142 original size:21 final size:19
Alignment explanation
Indices: 84115--84162 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
84105 AATAAGATAA
84115 CAAAAGATAAGAAATGAAAT
1 CAAAAGATAAGAAA-GAAAT
* *
84135 GAATAAGATAATAAAGAAAT
1 CAA-AAGATAAGAAAGAAAT
84155 CAAAAGAT
1 CAAAAGAT
84163 CCTCTTAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 9 0.38
21 10 0.42
ACGTcount: A:0.65, C:0.04, G:0.15, T:0.17
Consensus pattern (19 bp):
CAAAAGATAAGAAAGAAAT
Done.