Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, 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: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 14 of 14
Found at i:5429613 original size:14 final size:14
Alignment explanation
Indices: 5429594--5429622 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5429584 TGAAATTACA
5429594 ATAATAATAATAAT
1 ATAATAATAATAAT
5429608 ATAATAATAATAAT
1 ATAATAATAATAAT
5429622 A
1 A
5429623 ATTCTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:5456762 original size:22 final size:22
Alignment explanation
Indices: 5456737--5456781 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5456727 CCTTTTTCCC
*
5456737 TTTTCTTTTTGTTA-TTTCTTAT
1 TTTTCTTTCT-TTAGTTTCTTAT
*
5456759 TTTTGTTTCTTTAGTTTCTTAT
1 TTTTCTTTCTTTAGTTTCTTAT
5456781 T
1 T
5456782 GGACCACCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTCTTTCTTTAGTTTCTTAT
Found at i:5471697 original size:49 final size:49
Alignment explanation
Indices: 5471644--5471762 Score: 125
Period size: 49 Copynumber: 2.4 Consensus size: 49
5471634 ATCCACTTAT
* **
5471644 GGAACATACATATCTCAC-TTCAAGTCATCGTTTGAAATCATCTAC-AGAC
1 GGAACATACATATCTCACATCCAA-TCATCGTCCGAAATCATCTACTA-AC
** * * *
5471693 GGAACATATGTATCTGACATCCTATCATCGTCCGAAATCATCTACTAAT
1 GGAACATACATATCTCACATCCAATCATCGTCCGAAATCATCTACTAAC
*
5471742 GAAACATACATATCTCACATC
1 GGAACATACATATCTCACATC
5471763 ATATCNNNNN
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
49 52 0.93
50 4 0.07
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (49 bp):
GGAACATACATATCTCACATCCAATCATCGTCCGAAATCATCTACTAAC
Found at i:5474700 original size:21 final size:19
Alignment explanation
Indices: 5474676--5474755 Score: 54
Period size: 21 Copynumber: 3.8 Consensus size: 19
5474666 CTTCTTCTTT
5474676 TTCATTTTTTTTAATTTTTCA
1 TTCA-TTTTTTTAATTTTT-A
* *
5474697 TTCAGTTTTTCAATTTTTTA
1 TTCATTTTTTTAA-TTTTTA
5474717 TTTTCCATTTTTTT-ATTTTTA
1 --TT-CATTTTTTTAATTTTTA
*
5474738 TTACTTTTTTTTCAATTT
1 TT-CATTTTTTT-AATTT
5474756 AATTATTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
19 10 0.21
20 8 0.17
21 19 0.40
22 3 0.06
23 7 0.15
ACGTcount: A:0.17, C:0.10, G:0.01, T:0.71
Consensus pattern (19 bp):
TTCATTTTTTTAATTTTTA
Found at i:5474726 original size:14 final size:15
Alignment explanation
Indices: 5474703--5474735 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5474693 TTCATTCAGT
5474703 TTTTCAA-TTTTTTA
1 TTTTCAATTTTTTTA
*
5474717 TTTTCCATTTTTTTA
1 TTTTCAATTTTTTTA
5474732 TTTT
1 TTTT
5474736 TATTACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCAATTTTTTTA
Found at i:5474747 original size:20 final size:19
Alignment explanation
Indices: 5474724--5474773 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
5474714 TTATTTTCCA
* *
5474724 TTTTTTTATTTTTATTACTT
1 TTTTTTTAATTTAATTA-TT
*
5474744 TTTTTTCAATTTAATTATT
1 TTTTTTTAATTTAATTATT
5474763 TTATTTTTAAT
1 TT-TTTTTAAT
5474774 ATATTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTAATTTAATTATT
Found at i:5475709 original size:21 final size:20
Alignment explanation
Indices: 5475673--5475718 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
5475663 CTAGAGCCTA
5475673 AAGAAGAAGAAGAAGA-AGG
1 AAGAAGAAGAAGAAGAGAGG
5475692 CAAGAGAGAAGCAA-AAGAGAGG
1 -AAGA-AGAAG-AAGAAGAGAGG
5475714 AAGAA
1 AAGAA
5475719 AAATATTGNN
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.61, C:0.04, G:0.35, T:0.00
Consensus pattern (20 bp):
AAGAAGAAGAAGAAGAGAGG
Found at i:5478991 original size:8 final size:8
Alignment explanation
Indices: 5478963--5479042 Score: 72
Period size: 8 Copynumber: 9.2 Consensus size: 8
5478953 TAAATAACTG
5478963 AATAAAAA
1 AATAAAAA
5478971 AAGTAATAAA
1 AA-TAA-AAA
5478981 AATAAAAA
1 AATAAAAA
5478989 AAT-AAAA
1 AATAAAAA
5478996 AATAAAAA
1 AATAAAAA
* *
5479004 ATTGAAAA
1 AATAAAAA
5479012 AATGAATGAAA
1 AAT-AA--AAA
5479023 AATCAAGAAA
1 AAT-AA-AAA
5479033 AATAAAAA
1 AATAAAAA
5479041 AA
1 AA
5479043 AAAGAAGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
7 7 0.11
8 25 0.41
9 9 0.15
10 12 0.20
11 8 0.13
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:5478994 original size:14 final size:15
Alignment explanation
Indices: 5478963--5479061 Score: 65
Period size: 15 Copynumber: 6.0 Consensus size: 15
5478953 TAAATAACTG
5478963 AATAAAAAAAGTAATAAA
1 AATAAAAAAA-T-A-AAA
5478981 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
*
5478996 AATAAAAAATTGAAAA
1 AATAAAAAAAT-AAAA
5479012 AATGAATGAAAAATCAAGAAA
1 AAT-AA--AAAAAT--A-AAA
*
5479033 AATAAAAAAA-AAAG
1 AATAAAAAAATAAAA
* *
5479047 AAGAAAAAAAGAAAA
1 AATAAAAAAATAAAA
5479062 CAAATGAGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 17
0.75 0.07 0.19
Matches are distributed among these distances:
14 11 0.16
15 17 0.25
16 8 0.12
17 3 0.04
18 15 0.22
19 5 0.07
20 3 0.04
21 6 0.09
ACGTcount: A:0.79, C:0.01, G:0.08, T:0.12
Consensus pattern (15 bp):
AATAAAAAAATAAAA
Found at i:5479012 original size:42 final size:42
Alignment explanation
Indices: 5478966--5479059 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 42
5478956 ATAACTGAAT
5478966 AAAAAAAGTAAT-AAAAAT-AA-AAAAATAAAAAATAAAA-AATTG
1 AAAAAAAG-AATGAAAAATCAAGAAAAATAAAAAA-AAAAGAA--G
*
5479008 AAAAAATGAATGAAAAATCAAGAAAAATAAAAAAAAAAGAAG
1 AAAAAAAGAATGAAAAATCAAGAAAAATAAAAAAAAAAGAAG
5479050 AAAAAAAGAA
1 AAAAAAAGAA
5479060 AACAAATGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
41 3 0.07
42 23 0.50
43 6 0.13
44 14 0.30
ACGTcount: A:0.79, C:0.01, G:0.09, T:0.12
Consensus pattern (42 bp):
AAAAAAAGAATGAAAAATCAAGAAAAATAAAAAAAAAAGAAG
Found at i:5479018 original size:53 final size:51
Alignment explanation
Indices: 5478947--5479055 Score: 123
Period size: 52 Copynumber: 2.1 Consensus size: 51
5478937 AAAATATATT
* * *
5478947 AAAAATTAAATAACTGAATAAAAAAAGT-AATAAAAATAAAAAAATAAAAAATA
1 AAAAATTAAATAAATGAAT-AAAAAA-TCAAGAAAAATAAAAAAA-AAAAAAGA
* *
5479000 AAAAATTGAAA-AAATGAATGAAAAATCAAGAAAAATAAAAAAAAAAGAAGA
1 AAAAATT-AAATAAATGAATAAAAAATCAAGAAAAATAAAAAAAAAAAAAGA
5479051 AAAAA
1 AAAAA
5479056 AGAAAACAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
51 12 0.24
52 20 0.41
53 14 0.29
54 3 0.06
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (51 bp):
AAAAATTAAATAAATGAATAAAAAATCAAGAAAAATAAAAAAAAAAAAAGA
Found at i:5482564 original size:22 final size:20
Alignment explanation
Indices: 5482506--5482594 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
5482496 GCCCTAGCCC
* * *
5482506 TTTCTCATTTGTTTTCTTTT
1 TTTCTTATTTTTTTTCATTT
* *
5482526 TTTCTTCTTCTTTTTCATTT
1 TTTCTTATTTTTTTTCATTT
5482546 TTTCTTATTTTTTCATTCATTT
1 TTTCTTATTTTTT--TTCATTT
*
5482568 TTTCAATTTTTTATTTTTCATATT
1 TTTC--TTATTT-TTTTTCAT-TT
5482592 TTT
1 TTT
5482595 ATTTTTATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
20 26 0.47
22 11 0.20
23 5 0.09
24 10 0.18
25 3 0.05
ACGTcount: A:0.11, C:0.13, G:0.01, T:0.74
Consensus pattern (20 bp):
TTTCTTATTTTTTTTCATTT
Found at i:5482567 original size:12 final size:12
Alignment explanation
Indices: 5482539--5482572 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5482529 CTTCTTCTTT
5482539 TTCATTTTTTC-
1 TTCATTTTTTCA
5482550 TT-ATTTTTTCA
1 TTCATTTTTTCA
5482561 TTCATTTTTTCA
1 TTCATTTTTTCA
5482573 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 4 0.19
12 9 0.43
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (12 bp):
TTCATTTTTTCA
Found at i:5482585 original size:16 final size:16
Alignment explanation
Indices: 5482564--5482600 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5482554 TTTTTCATTC
5482564 ATTTTTTCA-ATTTTT
1 ATTTTTTCATATTTTT
5482579 -TATTTTTCATATTTTT
1 AT-TTTTTCATATTTTT
5482595 ATTTTT
1 ATTTTT
5482601 ATTACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 7 0.37
16 10 0.53
17 1 0.05
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTTCATATTTTT
Found at i:5482586 original size:15 final size:15
Alignment explanation
Indices: 5482566--5482600 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
5482556 TTTCATTCAT
5482566 TTTTTCA-ATTTTTTA
1 TTTTTCATA-TTTTTA
5482581 TTTTTCATATTTTTA
1 TTTTTCATATTTTTA
5482596 TTTTT
1 TTTTT
5482601 ATTACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCATATTTTTA
Found at i:5485008 original size:20 final size:20
Alignment explanation
Indices: 5484963--5485029 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
5484953 GGCCTTTCTC
5484963 ATTTATTTTC-TTATTTTCTT-
1 ATTT-TTTTCATT-TTTTCTTA
5484983 ATTTTTTTCATTTTTTCTTA
1 ATTTTTTTCATTTTTTCTTA
5485003 ATTTTTCATTCATTTTTTC--A
1 ATTTTT--TTCATTTTTTCTTA
5485023 ATTTTTT
1 ATTTTTT
5485030 ATTTTTATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.02
19 12 0.28
20 19 0.44
22 11 0.26
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTTTTCATTTTTTCTTA
Found at i:5485065 original size:20 final size:19
Alignment explanation
Indices: 5485000--5485066 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
5484990 TCATTTTTTC
* *
5485000 TTAATTTTTCATTCATTTT
1 TTAATTTTTTATTCATTAT
*
5485019 TTCAATTTTTTATT-TTTA-
1 TT-AATTTTTTATTCATTAT
*
5485037 TTACTTTTTTTATTCAGTTAT
1 TTA-ATTTTTTATTCA-TTAT
5485058 TTAATTTTT
1 TTAATTTTT
5485067 AATATATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.03
18 11 0.30
19 4 0.11
20 18 0.49
21 3 0.08
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.70
Consensus pattern (19 bp):
TTAATTTTTTATTCATTAT
Found at i:5528607 original size:27 final size:27
Alignment explanation
Indices: 5528577--5528635 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 27
5528567 GGGCCATGGT
* *
5528577 TTGTGATATATGTGGCAAGGCCACAGG
1 TTGTGATATATGTGACAAGGCCACAAG
*
5528604 TTGT--TATATGTGACTAGGCCACAAG
1 TTGTGATATATGTGACAAGGCCACAAG
5528629 TTGTGAT
1 TTGTGAT
5528636 GCGCGGTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 22 0.81
27 5 0.19
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (27 bp):
TTGTGATATATGTGACAAGGCCACAAG
Found at i:5531823 original size:25 final size:25
Alignment explanation
Indices: 5531775--5531824 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5531765 TGGTCTGTGA
* **
5531775 TATATGTGGCAAGGCCACGGGTTGT
1 TATATGTGACAAGGCCACAAGTTGT
*
5531800 TATATGTGACTAGGCCACAAGTTGT
1 TATATGTGACAAGGCCACAAGTTGT
5531825 GATGCCCGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (25 bp):
TATATGTGACAAGGCCACAAGTTGT
Found at i:5566590 original size:22 final size:22
Alignment explanation
Indices: 5566550--5566592 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5566540 ATCTACCTTT
** *
5566550 CTCTCTTAACTTATTTATAAAG
1 CTCTCTTAAAATATATATAAAG
5566572 CTCTCTTAAAATATATATAAA
1 CTCTCTTAAAATATATATAAA
5566593 AATANNNNNN
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (22 bp):
CTCTCTTAAAATATATATAAAG
Found at i:5572842 original size:3 final size:3
Alignment explanation
Indices: 5572834--5572887 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
5572824 ATCTTTGGTC
* *
5572834 ATT ATT ATT ATT GTT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5572882 ATT ATT
1 ATT ATT
5572888 GTCACTTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5584839 original size:3 final size:3
Alignment explanation
Indices: 5584831--5584863 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5584821 ATCTTTGGTC
*
5584831 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5584864 GTNNNNNNNN
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5608914 original size:29 final size:29
Alignment explanation
Indices: 5608835--5609048 Score: 156
Period size: 29 Copynumber: 7.6 Consensus size: 29
5608825 TTTAACCTTG
* * *
5608835 TTAGGTGCCTTTGCACCTTCTGAGCTTTA
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* *
5608864 TTAGGTGCTTTTGCA-CTGTTTGAACTTTA
1 TTAGGTGCCTTAGCACCT-TTTGAACTTTA
** *
5608893 TTAGGTGCCTTAGTGCCTTTTGAACTTTG
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
** * * *
5608922 TTAGGTTTCTTAGCACCTATGGAACTTTG
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* * *
5608951 TAAGGTG---T-GTACCTTTTGAACTTTG
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
*
5608976 TTAGGTGCCTTAGCACCGTTTG-ACTTTA
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* * *
5609004 GTAGGCGCCTTAGCACCTTTAG-ACTTT-
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* * *
5609031 GTAAGTGCCATAGCACCT
1 TTAGGTGCCTTAGCACCT
5609049 ATGGATTTTG
Statistics
Matches: 149, Mismatches: 30, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
25 20 0.13
26 1 0.01
27 15 0.10
28 31 0.21
29 80 0.54
30 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (29 bp):
TTAGGTGCCTTAGCACCTTTTGAACTTTA
Found at i:5610117 original size:19 final size:19
Alignment explanation
Indices: 5610077--5610117 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5610067 NNNNNNNNNN
** *
5610077 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
5610096 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
5610115 AAT
1 AAT
5610118 CCGATAGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:5612836 original size:23 final size:24
Alignment explanation
Indices: 5612793--5612838 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5612783 TTTTTATACT
* *
5612793 TTTTTTTTAAAATGTTGTTGAAAA
1 TTTTTGTTAAAATGTTATTGAAAA
5612817 TTTTTGTTAAAA-GTTATTGAAA
1 TTTTTGTTAAAATGTTATTGAAA
5612839 CAAAGATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTTTGTTAAAATGTTATTGAAAA
Found at i:5613149 original size:23 final size:24
Alignment explanation
Indices: 5613103--5613149 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5613093 TTTTTATAAT
* * *
5613103 TTTTTTTTAAAATGTTGTTGAAAA
1 TTTTTGTTAAAATGTTATTAAAAA
5613127 TTTTTGTTAAAA-GTTATTAAAAA
1 TTTTTGTTAAAATGTTATTAAAAA
5613150 AAGATGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTTTGTTAAAATGTTATTAAAAA
Found at i:5620427 original size:23 final size:24
Alignment explanation
Indices: 5620384--5620430 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5620374 GTTTTTATAC
* *
5620384 TTTTTTTTAAAATGTTGTTGAAAA
1 TTTTTGTTAAAATGTTATTGAAAA
5620408 TTTTTGTTAAAA-GTTATTGAAAA
1 TTTTTGTTAAAATGTTATTGAAAA
5620431 AATGATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (24 bp):
TTTTTGTTAAAATGTTATTGAAAA
Found at i:5623007 original size:17 final size:17
Alignment explanation
Indices: 5622985--5623019 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5622975 ATTGAAAGAA
5622985 TGAATTATTAATTTTAT
1 TGAATTATTAATTTTAT
5623002 TGAATTATTAATTTTAT
1 TGAATTATTAATTTTAT
5623019 T
1 T
5623020 CTCTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
TGAATTATTAATTTTAT
Found at i:5635953 original size:28 final size:29
Alignment explanation
Indices: 5635874--5636086 Score: 174
Period size: 29 Copynumber: 7.6 Consensus size: 29
5635864 TTTAACCCTG
* * *
5635874 TTAGGTGCCTTTGCACCTTCTGAGCTTTA
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* *
5635903 TTAGGTGCCTTTGCACCGTTTGAACTTTA
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* *
5635932 TTAGGT-CCTTAGTACCTTTTGAACTTTG
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* * *
5635960 TTAGGTGCCTTAGCATCTGTGGAACTTT-
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* * *
5635988 GTACGGT--C-T-GTACCTTTTGAACTTTG
1 TTA-GGTGCCTTAGCACCTTTTGAACTTTA
*
5636014 TTAGGTGCCTTAGCACCATTTG-ACTTTA
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* * *
5636042 GTAGGCGCCTTAGCACC-TTTAAACTTT-
1 TTAGGTGCCTTAGCACCTTTTGAACTTTA
* * *
5636069 GTAAGTGCCATAGCACCT
1 TTAGGTGCCTTAGCACCT
5636087 ATGGATTTTG
Statistics
Matches: 149, Mismatches: 26, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
25 15 0.10
26 3 0.02
27 19 0.13
28 52 0.35
29 60 0.40
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.39
Consensus pattern (29 bp):
TTAGGTGCCTTAGCACCTTTTGAACTTTA
Found at i:5645979 original size:29 final size:29
Alignment explanation
Indices: 5645928--5646128 Score: 155
Period size: 29 Copynumber: 7.1 Consensus size: 29
5645918 GTTTTCGCAT
* *
5645928 TTTTTAACCTTATTAGGTGCCTTTGCACC
1 TTTTGAACTTTATTAGGTGCCTTTGCACC
* *
5645957 TTCTGAGCTTTATTAGGTGCCTTTGCA-C
1 TTTTGAACTTTATTAGGTGCCTTTGCACC
* *
5645985 TGTTTCAACTTTATTAGGTGCCTTTGTACC
1 T-TTTGAACTTTATTAGGTGCCTTTGCACC
* * *
5646015 TTTTGAACTTTGTTAGGAGCCTTAGCACC
1 TTTTGAACTTTATTAGGTGCCTTTGCACC
* * * * *
5646044 TATGGAACTTTGTAAGGTG----TGTACC
1 TTTTGAACTTTATTAGGTGCCTTTGCACC
* * *
5646069 TTTTGAACTTTGTTAAGTGCCTTAGCA-C
1 TTTTGAACTTTATTAGGTGCCTTTGCACC
* * *
5646097 TGTTTG-ACTTTAGTACGTGCCTTAGCACC
1 T-TTTGAACTTTATTAGGTGCCTTTGCACC
5646126 TTT
1 TTT
5646129 AGACTTTGTA
Statistics
Matches: 136, Mismatches: 28, Indels: 17
0.75 0.15 0.09
Matches are distributed among these distances:
25 19 0.14
28 24 0.18
29 91 0.67
30 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.42
Consensus pattern (29 bp):
TTTTGAACTTTATTAGGTGCCTTTGCACC
Found at i:5646031 original size:58 final size:57
Alignment explanation
Indices: 5645930--5646137 Score: 192
Period size: 58 Copynumber: 3.7 Consensus size: 57
5645920 TTTCGCATTT
* * * * *
5645930 TTTAACCTTATTAGGTGCCTTTGCACCTTCTGAGCTTTATTAGGTGCCTTTGCACTG
1 TTTAACTTTATTAGGTGCCTTTGCACCTTTTGAACTTTGTTAGGTGCCTTAGCACTG
* * *
5645987 TTTCAACTTTATTAGGTGCCTTTGTACCTTTTGAACTTTGTTAGGAGCCTTAGCACCTA
1 TTT-AACTTTATTAGGTGCCTTTGCACCTTTTGAACTTTGTTAGGTGCCTTAGCA-CTG
** * * * *
5646046 TGGAACTTTGTAAGGTG----TGTACCTTTTGAACTTTGTTAAGTGCCTTAGCACTG
1 TTTAACTTTATTAGGTGCCTTTGCACCTTTTGAACTTTGTTAGGTGCCTTAGCACTG
* * * * *
5646099 TTTGACTTTAGTACGTGCCTTAGCACCTTTAG-ACTTTGT
1 TTTAACTTTATTAGGTGCCTTTGCACCTTTTGAACTTTGT
5646138 AAGTGCCATA
Statistics
Matches: 120, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
53 12 0.10
54 31 0.26
56 7 0.06
57 11 0.09
58 56 0.47
59 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.42
Consensus pattern (57 bp):
TTTAACTTTATTAGGTGCCTTTGCACCTTTTGAACTTTGTTAGGTGCCTTAGCACTG
Found at i:5646152 original size:27 final size:27
Alignment explanation
Indices: 5646002--5646153 Score: 98
Period size: 28 Copynumber: 5.5 Consensus size: 27
5645992 ACTTTATTAG
* * *
5646002 GTGCCTTTGTACCTTTTGAACTTTGTTAG
1 GTGCCTTAGCACCTTTTG-ACTTTG-TAA
* * *
5646031 GAGCCTTAGCACCTATGGAACTTTGTAA
1 GTGCCTTAGCACCTTTTG-ACTTTGTAA
*
5646059 G-G--TGT-GTACCTTTTGAACTTTGTTAA
1 GTGCCT-TAGCACCTTTTG-ACTTTG-TAA
*
5646085 GTGCCTTAGCA-CTGTTTGACTTTAGTAC
1 GTGCCTTAGCACCT-TTTGACTTT-GTAA
*
5646113 GTGCCTTAGCACCTTTAGACTTTGTAA
1 GTGCCTTAGCACCTTTTGACTTTGTAA
* *
5646140 GTGCCATAACACCT
1 GTGCCTTAGCACCT
5646154 ATGGATTTTG
Statistics
Matches: 99, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
25 15 0.15
26 5 0.05
27 17 0.17
28 32 0.32
29 30 0.30
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (27 bp):
GTGCCTTAGCACCTTTTGACTTTGTAA
Found at i:5647833 original size:29 final size:29
Alignment explanation
Indices: 5647717--5647879 Score: 120
Period size: 29 Copynumber: 5.8 Consensus size: 29
5647707 TACAAAATCT
* * *
5647717 AAAGGTGCCAAGGCGCCTACTAAAGT-CA
1 AAAGGTGCTAAGGCACCTAATAAAGTACA
* * * **
5647745 AACGGTGCTAAAGCACCTAACAAAGTTTA
1 AAAGGTGCTAAGGCACCTAATAAAGTACA
* * * * *
5647774 AAAGGTAC--A--CACCTTAGAAAGTTCT
1 AAAGGTGCTAAGGCACCTAATAAAGTACA
* *
5647799 ATAGGTGCTAAGCCACCTAATAAAGTACA
1 AAAGGTGCTAAGGCACCTAATAAAGTACA
* *
5647828 AAAGGTACTAAGGCACCTAATAAAGTTCA
1 AAAGGTGCTAAGGCACCTAATAAAGTACA
* *
5647857 AACGGTGCAAAGGCACCTAATAA
1 AAAGGTGCTAAGGCACCTAATAA
5647880 NNNNNNNNNN
Statistics
Matches: 104, Mismatches: 26, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
25 18 0.17
27 2 0.02
28 20 0.19
29 64 0.62
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (29 bp):
AAAGGTGCTAAGGCACCTAATAAAGTACA
Found at i:5653391 original size:3 final size:3
Alignment explanation
Indices: 5653383--5653409 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5653373 ACATGAAAAA
5653383 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5653410 TTTCTAAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5663870 original size:25 final size:26
Alignment explanation
Indices: 5663837--5663918 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 26
5663827 CAAACGGTGC
*
5663837 TAAGGCACCTAACAAAGTTCAAAAGG
1 TAAGACACCTAACAAAGTTCAAAAGG
* * *
5663863 TAA-ACACCTTACAAAGTTCCATAGGTG
1 TAAGACACCTAACAAAGTT-CAAAAG-G
*
5663890 CTAAGGCACCTAACAAAGTTCAAAAGG
1 -TAAGACACCTAACAAAGTTCAAAAGG
5663917 TA
1 TA
5663919 CTAAGGCGCC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
25 13 0.30
26 9 0.20
27 2 0.05
28 7 0.16
29 13 0.30
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.20
Consensus pattern (26 bp):
TAAGACACCTAACAAAGTTCAAAAGG
Found at i:5663909 original size:29 final size:28
Alignment explanation
Indices: 5663792--5663975 Score: 155
Period size: 29 Copynumber: 6.5 Consensus size: 28
5663782 TGTGGCACTT
**
5663792 ACAAAG-TCTAAAGGTGCTAAGGTGCCT-
1 ACAAAGTTC-AAAGGTGCTAAGGCACCTA
5663819 ACTAAAG-TCAAACGGTGCTAAGGCACCTA
1 AC-AAAGTTCAAA-GGTGCTAAGGCACCTA
* * *
5663848 ACAAAGTTCAAAAG-G-TAA-ACACCTT
1 ACAAAGTTCAAAGGTGCTAAGGCACCTA
*
5663873 ACAAAGTTCCATAGGTGCTAAGGCACCTA
1 ACAAAGTT-CAAAGGTGCTAAGGCACCTA
* *
5663902 ACAAAGTTCAAAAGGTACTAAGGCGCCTA
1 ACAAAGTTC-AAAGGTGCTAAGGCACCTA
* *
5663931 ATAAAGTTCAAATGGTGCAAAGGCACCTA
1 ACAAAGTTCAAA-GGTGCTAAGGCACCTA
* *
5663960 ATAAAGCTCAGAAGGT
1 ACAAAGTTCA-AAGGT
5663976 TGAAAGGCAC
Statistics
Matches: 129, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
25 13 0.10
26 7 0.05
27 7 0.05
28 31 0.24
29 69 0.53
30 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (28 bp):
ACAAAGTTCAAAGGTGCTAAGGCACCTA
Found at i:5663975 original size:112 final size:109
Alignment explanation
Indices: 5663771--5663975 Score: 275
Period size: 112 Copynumber: 1.9 Consensus size: 109
5663761 ACGGCCAAAA
** * * * * *
5663771 TCCATAGGTGCTGTGGCACTTACAAAGTCTAAAGGTGCTAAGGTGCCTACTAAAGTCAAACGGTG
1 TCCATAGGTGCTAAGGCACTAACAAAGTCAAAAGGTACTAAGGCGCCTAATAAAGTCAAACGGTG
* *
5663836 CTAAGGCACCTAACAAAGTTCAAAAGGTAAACACCTTACAAAGT
66 CAAAGGCACCTAACAAAGCTCAAAAGGTAAACACCTTACAAAGT
*
5663880 TCCATAGGTGCTAAGGCACCTAACAAAGTTCAAAAGGTACTAAGGCGCCTAATAAAGTTCAAATG
1 TCCATAGGTGCTAAGGCA-CTAACAAAG-TCAAAAGGTACTAAGGCGCCTAATAAAG-TCAAACG
* *
5663945 GTGCAAAGGCACCTAATAAAGCTCAGAAGGT
63 GTGCAAAGGCACCTAACAAAGCTCAAAAGGT
5663976 TGAAAGGCAC
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
109 16 0.20
110 8 0.10
111 24 0.30
112 33 0.41
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (109 bp):
TCCATAGGTGCTAAGGCACTAACAAAGTCAAAAGGTACTAAGGCGCCTAATAAAGTCAAACGGTG
CAAAGGCACCTAACAAAGCTCAAAAGGTAAACACCTTACAAAGT
Found at i:5663983 original size:58 final size:57
Alignment explanation
Indices: 5663810--5663983 Score: 171
Period size: 58 Copynumber: 3.1 Consensus size: 57
5663800 TAAAGGTGCT
* * *
5663810 AAGGTGCCTACTAAAG-TCAAACGGTGCTAAGGCACCTAACAAAGTTCAAAAGG-TA
1 AAGGCGCCTAATAAAGTTCAAATGGTGCTAAGGCACCTAACAAAGTTCAAAAGGTTA
* * * *
5663865 AA--CACCTTACAAAGTTC-CATAGGTGCTAAGGCACCTAACAAAGTTCAAAAGG-TA
1 AAGGCGCCTAATAAAGTTCAAAT-GGTGCTAAGGCACCTAACAAAGTTCAAAAGGTTA
* * * *
5663919 CTAAGGCGCCTAATAAAGTTCAAATGGTGCAAAGGCACCTAATAAAGCTCAGAAGGTTGA
1 --AAGGCGCCTAATAAAGTTCAAATGGTGCTAAGGCACCTAACAAAGTTCAAAAGGTT-A
5663979 AAGGC
1 AAGGC
5663984 ACTTAACAGG
Statistics
Matches: 95, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
53 8 0.08
54 35 0.37
55 2 0.02
56 2 0.02
58 44 0.46
59 3 0.03
60 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (57 bp):
AAGGCGCCTAATAAAGTTCAAATGGTGCTAAGGCACCTAACAAAGTTCAAAAGGTTA
Done.