Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008036.1 Hibiscus syriacus cultivar Beakdansim tig00110523_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: 266387
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1940 original size:11 final size:13
Alignment explanation
Indices: 1908--1937 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1898 TGGCCAAAGA
1908 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1921 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1933 TGAAA
1 TGAAA
1938 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:7453 original size:11 final size:13
Alignment explanation
Indices: 7421--7450 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
7411 TGGCCAAAGA
7421 TGAAAAGGTATGT
1 TGAAAAGGTATGT
7434 TGAAAAGGTATG-
1 TGAAAAGGTATGT
7446 TGAAA
1 TGAAA
7451 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:13938 original size:35 final size:36
Alignment explanation
Indices: 13873--13940 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
13863 ATACAATCTG
*
13873 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATAACGCCTATATCATCACCATAT
*
13909 TCCATCACCA-TATAACGCCTATATTATCACCA
1 TCCATCACCATTATAACGCCTATATCATCACCA
13941 ACTTCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATAACGCCTATATCATCACCATAT
Found at i:17888 original size:19 final size:20
Alignment explanation
Indices: 17850--17897 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
17840 ACCCCTTTAT
* *
17850 AAATATATGATTTTTGATGA
1 AAATACATGATTTTTAATGA
17870 AAATACATGA-TTTTAATGA
1 AAATACATGATTTTTAATGA
*
17889 AGATACATG
1 AAATACATG
17898 CTCTTGGACG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (20 bp):
AAATACATGATTTTTAATGA
Found at i:33459 original size:14 final size:13
Alignment explanation
Indices: 33442--33491 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
33432 GTGCAAAAAG
33442 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
33456 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
33469 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
33480 AAAGAAAAAGAA
1 AAAGAAAAAGAA
33492 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:33488 original size:19 final size:18
Alignment explanation
Indices: 33436--33491 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
33426 ATTGGAGTGC
33436 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
33453 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
33472 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
33491 A
1 A
33492 TTCAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:38516 original size:35 final size:37
Alignment explanation
Indices: 38447--38526 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
38437 ATACTATTTC
*
38447 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
38484 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
38519 CATCACCA
1 CATCACCA
38527 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:47116 original size:19 final size:20
Alignment explanation
Indices: 47078--47120 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
47068 GAAACCCCTT
47078 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
47098 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
47117 TGAA
1 TGAA
47121 GACACATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:47127 original size:19 final size:20
Alignment explanation
Indices: 47078--47128 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
47068 GAAACCCCTT
*
47078 TGAAAATACATGATTTTTAA
1 TGAAAACACATGATTTTTAA
*
47098 TGAAAATACATGA-TTTTAA
1 TGAAAACACATGATTTTTAA
*
47117 TGAAGACACATG
1 TGAAAACACATG
47129 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAACACATGATTTTTAA
Found at i:75346 original size:13 final size:13
Alignment explanation
Indices: 75324--75353 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
75314 ACTAAACACC
75324 TTTC-ACATACCT
1 TTTCAACATACCT
75336 TTTCAACATACCT
1 TTTCAACATACCT
75349 TTTCA
1 TTTCA
75354 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:79904 original size:24 final size:24
Alignment explanation
Indices: 79875--79947 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
79865 GACCGTGTGG
79875 CATGACCTCCGGATCTGGTGTAGA
1 CATGACCTCCGGATCTGGTGTAGA
** * *
79899 CATGA-CT--ATATC-AGTGT-GG
1 CATGACCTCCGGATCTGGTGTAGA
79918 CATGACCTCCGGATCTGGTGTAGA
1 CATGACCTCCGGATCTGGTGTAGA
*
79942 CGTGAC
1 CATGAC
79948 TATATCATTG
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
19 6 0.17
20 6 0.17
21 3 0.09
22 3 0.09
23 6 0.17
24 11 0.31
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (24 bp):
CATGACCTCCGGATCTGGTGTAGA
Found at i:79930 original size:43 final size:43
Alignment explanation
Indices: 79869--79954 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
79859 TAATGGGACC
79869 GTGTGGCATGACCTCCGGATCTGGTGTAGACATGACTATATCA
1 GTGTGGCATGACCTCCGGATCTGGTGTAGACATGACTATATCA
*
79912 GTGTGGCATGACCTCCGGATCTGGTGTAGACGTGACTATATCA
1 GTGTGGCATGACCTCCGGATCTGGTGTAGACATGACTATATCA
79955 TTGATACTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (43 bp):
GTGTGGCATGACCTCCGGATCTGGTGTAGACATGACTATATCA
Found at i:80787 original size:16 final size:16
Alignment explanation
Indices: 80743--80799 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
80733 GAGTTGTAAG
*
80743 TTATCTTCATTTTCTTAC
1 TTAT-TTCATTTT-TTTC
80761 -TATTTCA-TTTTTT-
1 TTATTTCATTTTTTTC
*
80774 TTCTTTCATTTTTTTC
1 TTATTTCATTTTTTTC
80790 TTATTTCATT
1 TTATTTCATT
80800 ACCTTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 8 0.24
15 9 0.27
16 13 0.39
17 3 0.09
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTCATTTTTTTC
Found at i:86810 original size:36 final size:36
Alignment explanation
Indices: 86758--86870 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
86748 GATACTATTT
*
86758 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
86794 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
86830 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
86865 ACATCA
1 TCATCA
86871 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:86813 original size:13 final size:11
Alignment explanation
Indices: 86758--86856 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
86748 GATACTATTT
86758 TCATCACCATAA
1 TCATCACCAT-A
*
86770 TCCATCTCCATTA
1 T-CATCACCA-TA
*
86783 TCA-CGCCTATA
1 TCATCACC-ATA
86794 TCATCACCATA
1 TCATCACCATA
86805 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
86819 TCA-CGCCTATA
1 TCATCACC-ATA
86830 TCATCACCATA
1 TCATCACCATA
86841 TTCCATCACCATA
1 -T-CATCACCATA
86854 TCA
1 TCA
86857 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:86885 original size:33 final size:33
Alignment explanation
Indices: 86759--86885 Score: 112
Period size: 36 Copynumber: 3.6 Consensus size: 33
86749 ATACTATTTT
* * *
86759 CATCACCATAATCCATCTCCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
* *
86795 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
86831 CATCACCATATTCCATCACCATATCACGCCAATAA
1 CATCACC--ATTCCATCACCATATCACGCCAATAA
*
86866 CATCATCC-TTCCATTACCAT
1 CATCA-CCATTCCATCACCAT
86886 TTCATCAACA
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
33 11 0.13
35 17 0.20
36 53 0.64
38 2 0.02
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.28
Consensus pattern (33 bp):
CATCACCATTCCATCACCATATCACGCCAATAA
Found at i:87781 original size:19 final size:20
Alignment explanation
Indices: 87734--87784 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
87724 GAAACCACTT
**
87734 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
87754 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
87773 TGAAGATACATG
1 TGAAAATACATG
87785 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:91065 original size:22 final size:22
Alignment explanation
Indices: 91015--91057 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
91005 GATGTAGGAG
91015 TCTT-TTTCTTTTCTCTATTTT
1 TCTTCTTTCTTTTCTCTATTTT
*
91036 TCTTCTTTCTTTT-TCTCTTTT
1 TCTTCTTTCTTTTCTCTATTTT
91057 T
1 T
91058 GTTGCTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (22 bp):
TCTTCTTTCTTTTCTCTATTTT
Found at i:91284 original size:17 final size:16
Alignment explanation
Indices: 91232--91297 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
91222 AAAATTAAAG
*
91232 AAAA-AAATGATTA-A
1 AAAAGAAATGATAAGA
*
91246 AATAGAATATGA-AAGA
1 AAAAGAA-ATGATAAGA
91262 AGAAAGGAAATGATAAGA
1 A-AAA-GAAATGATAAGA
91280 AAAAGAAATAGAT-AGA
1 AAAAGAAAT-GATAAGA
91296 AA
1 AA
91298 TGTTATCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 16 0.38
17 12 0.29
18 8 0.19
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAAGAAATGATAAGA
Found at i:99506 original size:11 final size:11
Alignment explanation
Indices: 99490--99531 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
99480 TTGGAGTGCA
99490 AAAAGAAGAAG
1 AAAAGAAGAAG
99501 AAAAGAAG-A-
1 AAAAGAAGAAG
*
99510 AAAAGAAAAAG
1 AAAAGAAGAAG
99521 AAAAGAA-AAG
1 AAAAGAAGAAG
99531 A
1 A
99532 GAAGTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 7 0.25
10 6 0.21
11 15 0.54
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:99514 original size:20 final size:20
Alignment explanation
Indices: 99489--99527 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
99479 ATTGGAGTGC
*
99489 AAAAAGAAGAAGAAAAGAAG
1 AAAAAGAAAAAGAAAAGAAG
99509 AAAAAGAAAAAGAAAAGAA
1 AAAAAGAAAAAGAAAAGAA
99528 AAGAGAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAGAAAAGAAG
Found at i:100094 original size:33 final size:33
Alignment explanation
Indices: 100052--100120 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
100042 GTTGATGAAT
*
100052 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
100085 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
100118 GAA
1 GAA
100121 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:100125 original size:13 final size:12
Alignment explanation
Indices: 100106--100202 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
100096 TTATTGGCGT
100106 GATATGGTGATG
1 GATATGGTGATG
100118 GAATATGGTGAT-
1 G-ATATGGTGATG
*
100130 GATATAGGCG-T-
1 GATAT-GGTGATG
100141 GATAATGGTGATG
1 GAT-ATGGTGATG
100154 GACTATGGTGAT-
1 GA-TATGGTGATG
*
100166 GATATAGGCG-T-
1 GATAT-GGTGATG
*
100177 GATAATGGAGATG
1 GAT-ATGGTGATG
100190 GATTATGGTGATG
1 GA-TATGGTGATG
100203 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:100161 original size:36 final size:36
Alignment explanation
Indices: 100091--100203 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
100081 AATGGAAGGA
* *
100091 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
100126 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
100162 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
100198 TGATGA
1 TGATGA
100204 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:100590 original size:19 final size:20
Alignment explanation
Indices: 100543--100593 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
100533 GAAACCCCTT
**
100543 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
100563 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
100582 TGAAGATACATG
1 TGAAAATACATG
100594 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:109178 original size:33 final size:33
Alignment explanation
Indices: 109136--109204 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
109126 GTTGATGAAT
*
109136 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
109169 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
109202 GAA
1 GAA
109205 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:109209 original size:13 final size:12
Alignment explanation
Indices: 109190--109286 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
109180 TTATTGGCGT
109190 GATATGGTGATG
1 GATATGGTGATG
109202 GAATATGGTGAT-
1 G-ATATGGTGATG
*
109214 GATATAGGCG-T-
1 GATAT-GGTGATG
109225 GATAATGGTGATG
1 GAT-ATGGTGATG
109238 GACTATGGTGAT-
1 GA-TATGGTGATG
*
109250 GATATAGGCG-T-
1 GATAT-GGTGATG
*
109261 GATAATGGAGATG
1 GAT-ATGGTGATG
109274 GATTATGGTGATG
1 GA-TATGGTGATG
109287 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:109245 original size:36 final size:36
Alignment explanation
Indices: 109175--109287 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
109165 AATGGAAGGA
* *
109175 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
109210 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
109246 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
109282 TGATGA
1 TGATGA
109288 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:112195 original size:35 final size:37
Alignment explanation
Indices: 112149--112227 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 37
112139 TTTGAGAATT
*
112149 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
112184 TGGTGATGATATAGGTGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
112221 TGGTGAT
1 TGGTGAT
112228 AAAAATAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:115461 original size:15 final size:16
Alignment explanation
Indices: 115410--115462 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
115400 AGATAGTGAA
115410 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
115427 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
115444 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
115459 ATAA
1 ATAA
115463 CTGACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:116123 original size:35 final size:37
Alignment explanation
Indices: 116077--116155 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
116067 TTTGAGAATT
*
116077 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
116112 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
116149 TGGTGAT
1 TGGTGAT
116156 TGAAATAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.32
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:119393 original size:15 final size:16
Alignment explanation
Indices: 119342--119394 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
119332 AGATAGTGAA
119342 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
119359 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
119376 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
119391 ATAA
1 ATAA
119395 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:120055 original size:35 final size:37
Alignment explanation
Indices: 120009--120087 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 37
119999 TTTGAGAATT
*
120009 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
120044 TGGTGATGATATAGGTGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
120081 TGGTGAT
1 TGGTGAT
120088 TGAAATAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:123324 original size:15 final size:16
Alignment explanation
Indices: 123273--123325 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
123263 AGATAGTGAA
123273 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
123290 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
123307 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
123322 ATAA
1 ATAA
123326 CTTACAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:123986 original size:35 final size:37
Alignment explanation
Indices: 123940--124019 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
123930 TTTGAGAATT
*
123940 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
123975 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
124012 TGGTGATG
1 TGGTGATG
124020 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:126816 original size:5 final size:5
Alignment explanation
Indices: 126808--126872 Score: 77
Period size: 5 Copynumber: 13.8 Consensus size: 5
126798 AATTTTTCTT
126808 TTTTC TTTTC TTTTC TTTTC --TTC TTTTC TTTTC TTTTC TTCTTC -TTT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC
*
126855 TTGTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTT
126873 TGTACTCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
3 3 0.06
4 8 0.15
5 38 0.73
6 3 0.06
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:126816 original size:13 final size:12
Alignment explanation
Indices: 126801--126867 Score: 79
Period size: 13 Copynumber: 5.7 Consensus size: 12
126791 CTTTTTGAAT
126801 TTTTCTTTTTTC
1 TTTTCTTTTTTC
126813 TTTTC--TTTTC
1 TTTTCTTTTTTC
126823 TTTTCTTCTTTTC
1 TTTTCTT-TTTTC
126836 TTTTC--TTTTC
1 TTTTCTTTTTTC
126846 TTCTTCTTTTTGTC
1 TT-TTCTTTTT-TC
126860 TTTTCTTT
1 TTTTCTTT
126868 CTTTTTGTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
10 17 0.35
11 3 0.06
12 5 0.10
13 19 0.40
14 4 0.08
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:126821 original size:18 final size:18
Alignment explanation
Indices: 126800--126873 Score: 77
Period size: 17 Copynumber: 4.3 Consensus size: 18
126790 TCTTTTTGAA
126800 TTTTTCTTTTTTCTTTTC
1 TTTTTCTTTTTTCTTTTC
126818 -TTTTCTTTTCTTCTTTTC
1 TTTTTCTTTT-TTCTTTTC
126836 -TTTTC--TTTTCTTCTTC
1 TTTTTCTTTTTTCTT-TTC
* *
126852 TTTTTGTCTTTTC-TTTC
1 TTTTTCTTTTTTCTTTTC
126869 TTTTT
1 TTTTT
126874 GTACTCCAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
15 5 0.10
16 5 0.10
17 21 0.42
18 14 0.28
19 5 0.10
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTTTCTTTTC
Found at i:126834 original size:23 final size:22
Alignment explanation
Indices: 126801--126872 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 22
126791 CTTTTTGAAT
126801 TTTTCTTTTTTCTTTTCTTTTC
1 TTTTCTTTTTTCTTTTCTTTTC
126823 TTTTCTTCTTTTCTTTTCTTTTC
1 TTTTCTT-TTTTCTTTTCTTTTC
126846 TTCTTCTTTTTGTCTTTTC-TTTC
1 TT-TTCTTTTT-TCTTTTCTTTTC
126869 TTTT
1 TTTT
126873 TGTACTCCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
22 9 0.19
23 26 0.55
24 12 0.26
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTTTCTTTTCTTTTC
Found at i:127146 original size:19 final size:18
Alignment explanation
Indices: 127124--127170 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
127114 AGTGAATTAT
127124 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
127143 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
127162 AATA-AAGAA
1 AATATAAGAA
127171 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:130061 original size:26 final size:26
Alignment explanation
Indices: 130025--130080 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
130015 GCCTTATTGG
*
130025 TGAATGAAGGGATGCTTGAATAATGA
1 TGAATGAAGGGATGCTTCAATAATGA
130051 TGAATGAAGGGATGCTTCAATAATGA
1 TGAATGAAGGGATGCTTCAATAATGA
130077 TGAA
1 TGAA
130081 AGGGTAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (26 bp):
TGAATGAAGGGATGCTTCAATAATGA
Found at i:133523 original size:95 final size:95
Alignment explanation
Indices: 133360--133559 Score: 262
Period size: 95 Copynumber: 2.1 Consensus size: 95
133350 TACTGATGGG
* ** *
133360 GTATCGATACTAAAAGGAAAGTATCGATACCATGGATTCCAGAATGCCAAAATGGTATCGATACT
1 GTATCGATACTAAAAGGAAAGTATCGATACCATGAATTAAAAAATGCCAAAATGGTATCGATACT
*
133425 GAAA-GGGAGTATCGGTACCATAGTATAGTA
66 GAAAGGGGA-TATCGGTACCATAGTATAGAA
* * *
133455 GTATCGATACTGAGA-GAAAGGTATCGATACCATGAATTAAAAAATG-TAGAAATGGTATCGATA
1 GTATCGATACTAAAAGGAAA-GTATCGATACCATGAATTAAAAAATGCCA-AAATGGTATCGATA
* *
133518 CTGAAAGGGGATATCGGTATCATAGTGTAGAA
64 CTGAAAGGGGATATCGGTACCATAGTATAGAA
133550 GTATCGATAC
1 GTATCGATAC
133560 CATGGTAGGA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
94 5 0.05
95 83 0.90
96 4 0.04
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (95 bp):
GTATCGATACTAAAAGGAAAGTATCGATACCATGAATTAAAAAATGCCAAAATGGTATCGATACT
GAAAGGGGATATCGGTACCATAGTATAGAA
Found at i:134056 original size:45 final size:45
Alignment explanation
Indices: 133935--134191 Score: 428
Period size: 45 Copynumber: 5.7 Consensus size: 45
133925 TGAAAAGGTT
* *
133935 ATTAAAGGCATGAAAGGATGTCATAAATGAAGTGCATAGA-GGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATA-ACGGTGC
133980 ATTAAAGGCATG-AAGGATGCCATAAATGAAATGCATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
134024 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
*
134069 ATTAAAGGCATGAAAAGGATGCCATAAATGAAATGCATAATGGTGC
1 ATTAAAGGCATG-AAAGGATGCCATAAATGAAATGCATAACGGTGC
* *
134115 ATTAAAGACATGAAAGGATGCCATAAATGAAATGTATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
*
134160 AATAAAGGCATGAAAGGATGCCATAAATGAAA
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAA
134192 ATAACGAATA
Statistics
Matches: 201, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
43 1 0.00
44 40 0.20
45 117 0.58
46 43 0.21
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.21
Consensus pattern (45 bp):
ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
Found at i:134132 original size:91 final size:90
Alignment explanation
Indices: 133935--134191 Score: 428
Period size: 91 Copynumber: 2.9 Consensus size: 90
133925 TGAAAAGGTT
* *
133935 ATTAAAGGCATGAAAGGATGTCATAAATGAAGTGCATAGA-GGTGCATTAAAGGCATG-AAGGAT
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATA-ACGGTGCATTAAAGGCATGAAAGGAT
133998 GCCATAAATGAAATGCATAACGGTGC
65 GCCATAAATGAAATGCATAACGGTGC
134024 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAAGGAT
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATG-AAAGGAT
*
134089 GCCATAAATGAAATGCATAATGGTGC
65 GCCATAAATGAAATGCATAACGGTGC
* * *
134115 ATTAAAGACATGAAAGGATGCCATAAATGAAATGTATAACGGTGCAATAAAGGCATGAAAGGATG
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
134180 CCATAAATGAAA
66 CCATAAATGAAA
134192 ATAACGAATA
Statistics
Matches: 159, Mismatches: 6, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
88 1 0.01
89 53 0.33
90 20 0.13
91 85 0.53
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.21
Consensus pattern (90 bp):
ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
CCATAAATGAAATGCATAACGGTGC
Found at i:134190 original size:136 final size:134
Alignment explanation
Indices: 133935--134191 Score: 435
Period size: 136 Copynumber: 1.9 Consensus size: 134
133925 TGAAAAGGTT
* * *
133935 ATTAAAGGCATGAAAGGATGTCATAAATGAAGTGCATAGAGGTGCATTAAAGGCATGAAGGATGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAGAGGTGCATTAAAGACATGAAGGATGC
*
134000 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACG
66 CATAAATGAAATGCATAACGGTGCAATAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACG
134065 GTGC
131 GTGC
134069 ATTAAAGGCATGAAAAGGATGCCATAAATGAAATGCATA-ATGGTGCATTAAAGACATGAAAGGA
1 ATTAAAGGCATG-AAAGGATGCCATAAATGAAATGCATAGA-GGTGCATTAAAGACATG-AAGGA
*
134133 TGCCATAAATGAAATGTATAACGGTGCAATAAAGGCATGAAAGGATGCCATAAATGAAA
63 TGCCATAAATGAAATGCATAACGGTGCAATAAAGGCATGAAAGGATGCCATAAATGAAA
134192 ATAACGAATA
Statistics
Matches: 115, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
134 13 0.11
135 40 0.35
136 62 0.54
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.21
Consensus pattern (134 bp):
ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAGAGGTGCATTAAAGACATGAAGGATGC
CATAAATGAAATGCATAACGGTGCAATAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACG
GTGC
Found at i:137217 original size:14 final size:15
Alignment explanation
Indices: 137188--137223 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
137178 TACAAAAAGA
137188 AAGAAAAGACAAAAAT
1 AAGAAAAGA-AAAAAT
137204 AAGAAAAG-AAAAAT
1 AAGAAAAGAAAAAAT
137218 AAGAAA
1 AAGAAA
137224 TTCAAAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.60
16 8 0.40
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.06
Consensus pattern (15 bp):
AAGAAAAGAAAAAAT
Found at i:139064 original size:19 final size:19
Alignment explanation
Indices: 139027--139065 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
139017 TATCTTTATT
*
139027 TCATTTTTTTCTATTTCCA
1 TCATTTTTATCTATTTCCA
139046 TCATTTTTAT-TATTATCCA
1 TCATTTTTATCTATT-TCCA
139065 T
1 T
139066 TTCTTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (19 bp):
TCATTTTTATCTATTTCCA
Found at i:144879 original size:18 final size:19
Alignment explanation
Indices: 144854--144902 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
144844 TTTTCTTTTC
144854 TTTT-CTTCTTTTCTG-AT
1 TTTTCCTTCTTTTCTGTAT
*
144871 TTTTCCTTCTTTTTTGTAT
1 TTTTCCTTCTTTTCTGTAT
*
144890 TTTTCTTTCTTTT
1 TTTTCCTTCTTTT
144903 TGCACTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.14
18 10 0.36
19 14 0.50
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTCCTTCTTTTCTGTAT
Found at i:144884 original size:19 final size:19
Alignment explanation
Indices: 144840--144903 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
144830 TTTTTTGAAT
* *
144840 TTCTTTTTCT-TTTCTTTTC
1 TTCTTTTTCTGATT-TTTCC
144859 TTC-TTTTCTGATTTTTCC
1 TTCTTTTTCTGATTTTTCC
*
144877 TTCTTTTT-TGTATTTTTCT
1 TTCTTTTTCTG-ATTTTTCC
144896 TTCTTTTT
1 TTCTTTTT
144904 GCACTCCAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 15 0.38
19 24 0.62
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (19 bp):
TTCTTTTTCTGATTTTTCC
Found at i:144903 original size:18 final size:16
Alignment explanation
Indices: 144854--144904 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 16
144844 TTTTCTTTTC
144854 TTTTCTTCTTTTCTGAT
1 TTTTCTTCTTTT-TGAT
144871 TTTTCCTTCTTTTTTGTAT
1 TTTT-CTTC-TTTTTG-AT
144890 TTTTCTTTCTTTTTG
1 TTTTC-TTCTTTTTG
144905 CACTCCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.13
18 13 0.43
19 13 0.43
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTTCTTCTTTTTGAT
Found at i:150079 original size:15 final size:16
Alignment explanation
Indices: 150039--150081 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
150029 AAAGTTTTAA
*
150039 TATAGTTATTTTCATC
1 TATAGTTATTATCATC
**
150055 TATAAATATTAT-ATC
1 TATAGTTATTATCATC
150070 TATAGTTATTAT
1 TATAGTTATTAT
150082 GATGATAACT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (16 bp):
TATAGTTATTATCATC
Found at i:152491 original size:5 final size:5
Alignment explanation
Indices: 152481--152521 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
152471 ACTCAAAAAG
152481 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
152522 GAAGTTGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:167213 original size:35 final size:35
Alignment explanation
Indices: 167137--167287 Score: 221
Period size: 35 Copynumber: 4.3 Consensus size: 35
167127 TACTATTTGT
* **
167137 TCATCACCATCTTCCTTCATAATTTTCACGCCTATA
1 TCATCACCATCTTCCATCACCA-TTTCACGCCTATA
* *
167173 ACATCACCATCTTCCATCACCATTGCACGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
* *
167208 TCATCATCATCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
*
167243 TCATCACCATCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
167278 TCATCACCAT
1 TCATCACCAT
167288 TCCCTTACCA
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
35 87 0.83
36 18 0.17
ACGTcount: A:0.26, C:0.36, G:0.03, T:0.34
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTTCACGCCTATA
Found at i:167700 original size:14 final size:14
Alignment explanation
Indices: 167662--167703 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
167652 CAACAAAAGT
*
167662 AACAAAAAGAGAAA
1 AACAAAAAGAAAAA
*
167676 AAGAAAGAAGAAAAA
1 AACAAA-AAGAAAAA
167691 AACAAAAAGAAAA
1 AACAAAAAGAAAA
167704 GACTCCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (14 bp):
AACAAAAAGAAAAA
Found at i:167925 original size:16 final size:16
Alignment explanation
Indices: 167904--167944 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
167894 ATTTTCTTAC
167904 TATTTCATTTCTTTAT
1 TATTTCATTTCTTTAT
* * *
167920 TCTTTCATTTTTTTCT
1 TATTTCATTTCTTTAT
167936 TATTTCATT
1 TATTTCATT
167945 ACCATATTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTCATTTCTTTAT
Found at i:177908 original size:35 final size:35
Alignment explanation
Indices: 177832--177982 Score: 167
Period size: 35 Copynumber: 4.3 Consensus size: 35
177822 TACTATCTGT
* ** *
177832 TCATCACCATCTTCCATCTCCATTTTCACGCCTATA
1 TCATCACCATCTTCTATAACCA-TTTCACACCTATA
* * * *
177868 ACATCACCTTCTTCTATTACCATTGCACACCTATA
1 TCATCACCATCTTCTATAACCATTTCACACCTATA
* * * **
177903 TCATCACCATCTTCGATCACTATTTCATGCCTATA
1 TCATCACCATCTTCTATAACCATTTCACACCTATA
*
177938 TCATCACCATCTTCTATAATCATTTCACACCTATA
1 TCATCACCATCTTCTATAACCATTTCACACCTATA
177973 TCATCACCAT
1 TCATCACCAT
177983 TCCCTTACCA
Statistics
Matches: 94, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 77 0.82
36 17 0.18
ACGTcount: A:0.27, C:0.34, G:0.03, T:0.36
Consensus pattern (35 bp):
TCATCACCATCTTCTATAACCATTTCACACCTATA
Found at i:177951 original size:70 final size:71
Alignment explanation
Indices: 177832--177982 Score: 214
Period size: 70 Copynumber: 2.1 Consensus size: 71
177822 TACTATCTGT
* * *
177832 TCATCACCATCTTCCATCTCCATTTTCACGCCTATAACATCACCTTCTTCTATTACCATTGCACA
1 TCATCACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCTATAACCATTGCACA
177897 CCTATA
66 CCTATA
* * * * * *
177903 TCATCACCATCTTCGATCACTA-TTTCATGCCTATATCATCACCATCTTCTATAATCATTTCACA
1 TCATCACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCTATAACCATTGCACA
177967 CCTATA
66 CCTATA
177973 TCATCACCAT
1 TCATCACCAT
177983 TCCCTTACCA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
70 52 0.73
71 19 0.27
ACGTcount: A:0.27, C:0.34, G:0.03, T:0.36
Consensus pattern (71 bp):
TCATCACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCTATAACCATTGCACA
CCTATA
Found at i:195248 original size:24 final size:24
Alignment explanation
Indices: 195199--195249 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
195189 TTTTCTTTTC
*
195199 TTTTCTTCTTTTTGACTGCTGGAA
1 TTTTCTTCTTTTTGACTGCTGCAA
* *
195223 TTTTCTTCTTTTTGAGTGCTTCAA
1 TTTTCTTCTTTTTGACTGCTGCAA
195247 TTT
1 TTT
195250 GTTTGTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.16, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTTCTTCTTTTTGACTGCTGCAA
Found at i:199078 original size:24 final size:22
Alignment explanation
Indices: 199051--199095 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
199041 TTGGCTCATT
* *
199051 CTTTGGAATTTCAAGAGGTACATC
1 CTTTGAAATGTCAA-AGG-ACATC
199075 CTTTGAAATGTCAAAGGACAT
1 CTTTGAAATGTCAAAGGACAT
199096 ATCTTGTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (22 bp):
CTTTGAAATGTCAAAGGACATC
Found at i:208916 original size:33 final size:33
Alignment explanation
Indices: 208874--208942 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
208864 GTTGATGAAT
*
208874 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGG-CATGAAATGGTAATG
* * *
208907 GAAGGATGATGTTATTGGCATGATATGGTGATG
1 GAAGGATGATGTTAATGGCATGAAATGGTAATG
208940 GAA
1 GAA
208943 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCATGAAATGGTAATG
Found at i:208947 original size:13 final size:12
Alignment explanation
Indices: 208928--209024 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
208918 TTATTGGCAT
208928 GATATGGTGATG
1 GATATGGTGATG
208940 GAATATGGTGAT-
1 G-ATATGGTGATG
*
208952 GATATAGGCG-T-
1 GATAT-GGTGATG
208963 GATAATGGTGATG
1 GAT-ATGGTGATG
208976 GACTATGGTGAT-
1 GA-TATGGTGATG
*
208988 GATATAGGCG-T-
1 GATAT-GGTGATG
*
208999 GATAATGGAGATG
1 GAT-ATGGTGATG
209012 GATTATGGTGATG
1 GA-TATGGTGATG
209025 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:208976 original size:36 final size:36
Alignment explanation
Indices: 208913--209025 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
208903 AATGGAAGGA
* * *
208913 TGATGTTATTGGCATGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
208948 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
208984 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
209020 TGATGA
1 TGATGA
209026 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 15 0.21
36 56 0.79
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:213472 original size:13 final size:12
Alignment explanation
Indices: 213453--213549 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
213443 TTATTGACGT
213453 GATATGGTGATG
1 GATATGGTGATG
213465 GAATATGGTGAT-
1 G-ATATGGTGATG
*
213477 GATATAGGCG-T-
1 GATAT-GGTGATG
213488 GATAATGGTGATG
1 GAT-ATGGTGATG
213501 GACTATGGTGAT-
1 GA-TATGGTGATG
*
213513 GATATAGGCG-T-
1 GATAT-GGTGATG
*
213524 GATAATGGAGATG
1 GAT-ATGGTGATG
213537 GATTATGGTGATG
1 GA-TATGGTGATG
213550 AAAATAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:213508 original size:36 final size:36
Alignment explanation
Indices: 213450--213550 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
213440 ATGTTATTGA
213450 CGTGAT-ATGGTGATGGAATATGGTGATGATATAGG
1 CGTGATAATGGTGATGGAATATGGTGATGATATAGG
*
213485 CGTGATAATGGTGATGGACTATGGTGATGATATAGG
1 CGTGATAATGGTGATGGAATATGGTGATGATATAGG
* *
213521 CGTGATAATGGAGATGGATTATGGTGATGA
1 CGTGATAATGGTGATGGAATATGGTGATGA
213551 AAATAATATC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 6 0.10
36 56 0.90
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.31
Consensus pattern (36 bp):
CGTGATAATGGTGATGGAATATGGTGATGATATAGG
Found at i:219057 original size:15 final size:16
Alignment explanation
Indices: 219017--219059 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
219007 AAAGTTTTAA
*
219017 TATAGTTATTTTCATC
1 TATAGTTATTATCATC
219033 TATA-TATATTAT-ATC
1 TATAGT-TATTATCATC
219048 TATAGTTATTAT
1 TATAGTTATTAT
219060 GATGATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (16 bp):
TATAGTTATTATCATC
Found at i:221775 original size:13 final size:13
Alignment explanation
Indices: 221754--221791 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
221744 CTGCGGAATT
221754 GATGGTATTGATG
1 GATGGTATTGATG
*
221767 GATGTTATTGATG
1 GATGGTATTGATG
*
221780 G-TGGTAATGATG
1 GATGGTATTGATG
221792 AAATGGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (13 bp):
GATGGTATTGATG
Found at i:222191 original size:19 final size:21
Alignment explanation
Indices: 222148--222199 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
222138 GAAACCCCTT
*
222148 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTGTAAA
222169 TGAAAATACATGA-TTGT-AA
1 TGAAAATACATGACTTGTAAA
*
222188 TGAAGATACATG
1 TGAAAATACATG
222200 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTTGTAAA
Found at i:225478 original size:8 final size:8
Alignment explanation
Indices: 225465--225489 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
225455 ACTTTTTCTT
225465 TTCTTTTC
1 TTCTTTTC
225473 TTCTTTTC
1 TTCTTTTC
225481 TTCTTTTC
1 TTCTTTTC
225489 T
1 T
225490 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:226263 original size:19 final size:21
Alignment explanation
Indices: 226220--226271 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
226210 GAAACCCCTT
226220 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
226241 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
226260 TGAAGATACATG
1 TGAAAATACATG
226272 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:233309 original size:30 final size:30
Alignment explanation
Indices: 233270--233345 Score: 143
Period size: 30 Copynumber: 2.5 Consensus size: 30
233260 GTCCAAAGCT
*
233270 CTCCCCCAGCTAAGTTCAGCTACATGCTAG
1 CTCCTCCAGCTAAGTTCAGCTACATGCTAG
233300 CTCCTCCAGCTAAGTTCAGCTACATGCTAG
1 CTCCTCCAGCTAAGTTCAGCTACATGCTAG
233330 CTCCTCCAGCTAAGTT
1 CTCCTCCAGCTAAGTT
233346 GAAGTTCTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (30 bp):
CTCCTCCAGCTAAGTTCAGCTACATGCTAG
Found at i:239663 original size:19 final size:21
Alignment explanation
Indices: 239620--239671 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
239610 GAAACCCCTT
*
239620 TGAAAATTCATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
239641 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
239660 TGAAGATACATG
1 TGAAAATACATG
239672 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:241438 original size:19 final size:21
Alignment explanation
Indices: 241414--241465 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
241404 CGGCCAAGAG
*
241414 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
241433 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
241454 CATGTATTTTCA
1 CATGTATTTTCA
241466 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:245497 original size:19 final size:21
Alignment explanation
Indices: 245473--245524 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
245463 CGGCCAAGAG
*
245473 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
245492 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
245513 CATGTATTTTCA
1 CATGTATTTTCA
245525 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:248246 original size:2 final size:2
Alignment explanation
Indices: 248239--248294 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
248229 AGTTATTTTC
*
248239 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
248281 AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT A
248295 GTTATTATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249522 original size:22 final size:21
Alignment explanation
Indices: 249485--249526 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
249475 CCATCTCCAT
249485 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
249506 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
249527 TTCTGCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:250881 original size:25 final size:27
Alignment explanation
Indices: 250831--250883 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
250821 CTAAAGGACC
250831 CAACAAGAGAGAATTGAGAGGAAAAAGG
1 CAACAAGAGAGAATTGAGA-GAAAAAGG
250859 CAAC-AGAGAG-ATTGAGA-ACAAAAGG
1 CAACAAGAGAGAATTGAGAGA-AAAAGG
250884 GGATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 1 0.04
25 6 0.25
26 7 0.29
27 6 0.25
28 4 0.17
ACGTcount: A:0.53, C:0.09, G:0.30, T:0.08
Consensus pattern (27 bp):
CAACAAGAGAGAATTGAGAGAAAAAGG
Found at i:256111 original size:11 final size:13
Alignment explanation
Indices: 256079--256108 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
256069 TGGCCAAAGA
256079 TGAAAAGGTATGT
1 TGAAAAGGTATGT
256092 TGAAAAGGTATG-
1 TGAAAAGGTATGT
256104 TGAAA
1 TGAAA
256109 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:261208 original size:36 final size:36
Alignment explanation
Indices: 261156--261255 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
261146 GATACTATTT
* *
261156 TCATGACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
261192 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
261228 TCATCACCATATTCCATCACCA-TATCAC
1 TCATCACCATAATCCATCACCATTATCAC
261256 CCAATAACAT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 6 0.10
36 54 0.90
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:261211 original size:13 final size:11
Alignment explanation
Indices: 261189--261254 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
261179 TATCACGCCT
261189 ATATCATCACC
1 ATATCATCACC
261200 ATAGTCCATCACC
1 ATA-T-CATCACC
*
261213 ATTATCA-CGCC
1 A-TATCATCACC
261224 TATATCATCACC
1 -ATATCATCACC
261236 ATATTCCATCACC
1 ATA-T-CATCACC
261249 ATATCA
1 ATATCA
261255 CCCAATAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:261282 original size:32 final size:33
Alignment explanation
Indices: 261239--261306 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
261229 CATCACCATA
261239 TTCCATCACCATATCA-C-CCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
261271 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
261304 TTC
1 TTC
261307 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 14 0.45
33 11 0.35
34 6 0.19
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:261674 original size:17 final size:17
Alignment explanation
Indices: 261654--261697 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
261644 CAAAAGCAAC
*
261654 AAAAAGAAA-AAAAAAG
1 AAAAAAAAAGAAAAAAG
*
261670 AAAAAAAAAGAAAGAAG
1 AAAAAAAAAGAAAAAAG
*
261687 AAAAGAAAAGA
1 AAAAAAAAAGA
261698 CTCCTACAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:261697 original size:10 final size:10
Alignment explanation
Indices: 261654--261695 Score: 66
Period size: 10 Copynumber: 4.0 Consensus size: 10
261644 CAAAAGCAAC
261654 AAAAAGAAAA
1 AAAAAGAAAA
261664 AAAAAGAAAA
1 AAAAAGAAAA
261674 AAAAAGAAAGA
1 AAAAAGAAA-A
261685 AGAAAAGAAAA
1 A-AAAAGAAAA
261696 GACTCCTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 19 0.63
11 3 0.10
12 8 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Done.