Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007873.1 Hibiscus syriacus cultivar Beakdansim tig00110248_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: 90306
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7887 original size:15 final size:16
Alignment explanation
Indices: 7864--7902 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
7854 AGATTATGAG
7864 TTTGAGGATTTAA-GAT
1 TTTG-GGATTTAACGAT
7880 TTTGGGATTTAACGAT
1 TTTGGGATTTAACGAT
*
7896 TTAGGGA
1 TTTGGGA
7903 GATTTAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (16 bp):
TTTGGGATTTAACGAT
Found at i:14636 original size:21 final size:21
Alignment explanation
Indices: 14594--14636 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
14584 TTTCTGGGCT
* *
14594 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
14615 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
14636 A
1 A
14637 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:14689 original size:20 final size:20
Alignment explanation
Indices: 14664--14701 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14654 GAATGCTAGA
*
14664 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
14684 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
14702 TAATGAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:18329 original size:105 final size:105
Alignment explanation
Indices: 18018--19312 Score: 2067
Period size: 105 Copynumber: 12.4 Consensus size: 105
18008 GTATTGTTCC
* * ** * * **
18018 GGAGCCCAATATCATTCACTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGTCGGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACA
** ****
18083 GTCAGCGGTCCCTTCGTC--GAAGTTGAACTTATACTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** *
18122 TGAGTCCAATATCCTTCGCGGTGAAGTTGAAATTGGCTCTGAAATTGAG-AATATTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
18186 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
18226 GGAGTCCAATATCCTTCATGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
18291 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* **
18331 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGAATCTG-AA-T--GAAAT-TTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
*
18391 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
18431 GGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACA
* * *
18496 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTGTTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
18537 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT-TGTTGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT-TTGTTGACA
18601 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
18642 -GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT-TGTTGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT-TTGTTGACA
**
18705 GGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
18746 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGAGAAATGTTTGGTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATGTTTGTTGACA
18810 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
18851 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
18916 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
18956 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGAGAAATGTTTGGTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATGTTTGTTGACA
19020 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
19061 GGAGTCCAATATCCTTCGTTGTGAAGCTTGAAATTGGCTCTGAACTTGAGAAATGTTTGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
19126 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
19167 GGAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTGAACTTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
19232 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
19272 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
19313 GGTAAAACCT
Statistics
Matches: 1116, Mismatches: 58, Indels: 33
0.92 0.05 0.03
Matches are distributed among these distances:
100 87 0.08
101 7 0.01
102 26 0.02
103 2 0.00
104 219 0.20
105 573 0.51
106 199 0.18
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:32682 original size:30 final size:30
Alignment explanation
Indices: 32648--32750 Score: 197
Period size: 30 Copynumber: 3.4 Consensus size: 30
32638 GGTTCTTCGG
*
32648 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32678 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32708 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32738 GACCTCTGGATAG
1 GACCTCTGGATAG
32751 GTCATTCGGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:33723 original size:3 final size:3
Alignment explanation
Indices: 33715--33740 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33705 AAATTTCAAT
33715 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
33741 GTTTTGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:36347 original size:18 final size:19
Alignment explanation
Indices: 36324--36361 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
36314 TTTGAAAAGG
36324 TATAA-TTAAAAAAATAAT
1 TATAATTTAAAAAAATAAT
36342 TATAATTTTAAAAAAATAAT
1 TATAA-TTTAAAAAAATAAT
36362 AAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATAATTTAAAAAAATAAT
Found at i:36366 original size:11 final size:11
Alignment explanation
Indices: 36350--36375 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
36340 ATTATAATTT
36350 TAAAAAAATAA
1 TAAAAAAATAA
36361 TAAAAAAATAA
1 TAAAAAAATAA
36372 TAAA
1 TAAA
36376 TATTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAAAAATAA
Found at i:36452 original size:4 final size:4
Alignment explanation
Indices: 36426--36473 Score: 62
Period size: 4 Copynumber: 12.0 Consensus size: 4
36416 AAGTATAATA
* *
36426 AAAT AAA- AATT AAAT AAAC AAAT AAAT AAAT AAAT AAAT AAACT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT
36474 TAGGATGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 2 0.05
4 32 0.84
5 4 0.11
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:43861 original size:31 final size:30
Alignment explanation
Indices: 43826--43891 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
43816 AGCAACGAGT
***
43826 CGAGTCAAGCAACAAGTTTTTTTAACGAATA
1 CGAGTCAAGCAA-AAAAATTTTTAACGAATA
*
43857 CGAGTCGAGCAAAAAAATTTTTAACGAATA
1 CGAGTCAAGCAAAAAAATTTTTAACGAATA
43887 CGAGT
1 CGAGT
43892 GGAACACTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (30 bp):
CGAGTCAAGCAAAAAAATTTTTAACGAATA
Found at i:47551 original size:14 final size:13
Alignment explanation
Indices: 47528--47557 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
47518 TTCTTGAAGT
47528 ATCGATATTGTTC
1 ATCGATATTGTTC
47541 ATCGAATATTGTTC
1 ATCG-ATATTGTTC
47555 ATC
1 ATC
47558 AAGTGATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (13 bp):
ATCGATATTGTTC
Found at i:49397 original size:27 final size:27
Alignment explanation
Indices: 49344--49398 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
49334 TTTAGATGAG
* **
49344 AAATTATGAAAATATTCTGATAGTGTA
1 AAATTACGAAAATACCCTGATAGTGTA
* *
49371 AAATTACGAAAATACCCTTATATTGTA
1 AAATTACGAAAATACCCTGATAGTGTA
49398 A
1 A
49399 GATGTCAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (27 bp):
AAATTACGAAAATACCCTGATAGTGTA
Found at i:51132 original size:24 final size:24
Alignment explanation
Indices: 51103--51214 Score: 138
Period size: 24 Copynumber: 4.7 Consensus size: 24
51093 ATTTGAATTA
*
51103 TGATCTGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
*
51127 AT-ATCTGATA-TCTGACATGGATTC
1 -TGATATGATACT-TGACATGGATTC
*
51151 TGATATGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTC
* *
51175 TGATATGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTC
*
51199 TGATATGATATTTGAC
1 TGATATGATACTTGAC
51215 CTGATTTATG
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
23 2 0.03
24 75 0.95
25 2 0.03
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:51435 original size:2 final size:2
Alignment explanation
Indices: 51428--51456 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51418 TGGATGGGGG
51428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51457 TTTTAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52055 original size:9 final size:9
Alignment explanation
Indices: 52033--52117 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
52023 ATACTTTATG
*
52033 TTTTTATATT
1 TTTTTATA-A
52043 TTTTTATAA
1 TTTTTATAA
* **
52052 TTTTCATTG
1 TTTTTATAA
*
52061 TTTTAAATAA
1 TTTT-TATAA
*
52071 TATGTTATAA
1 T-TTTTATAA
52081 TTTTTAT-A
1 TTTTTATAA
*
52089 -TTTTATGA
1 TTTTTATAA
*
52097 TTTCTATAA
1 TTTTTATAA
52106 -TTTTATAA
1 TTTTTATAA
52114 TTTT
1 TTTT
52118 CATAGCTTTA
Statistics
Matches: 57, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
7 6 0.11
8 9 0.16
9 24 0.42
10 16 0.28
11 2 0.04
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52094 original size:16 final size:16
Alignment explanation
Indices: 52070--52140 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
52060 GTTTTAAATA
*
52070 ATATGTTATAATTTTT
1 ATATTTTATAATTTTT
* *
52086 ATATTTTATGATTTCT
1 ATATTTTATAATTTTT
*
52102 ATAATTTTATAATTTTC
1 AT-ATTTTATAATTTTT
* *
52119 ATAGCTTTAACAATTTTT
1 ATA--TTTTATAATTTTT
52137 ATAT
1 ATAT
52141 AATTTTAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
16 17 0.40
17 13 0.30
18 13 0.30
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (16 bp):
ATATTTTATAATTTTT
Found at i:52099 original size:8 final size:8
Alignment explanation
Indices: 52075--52117 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
52065 AAATAATATG
52075 TTATAATT
1 TTATAATT
52083 TT-TATATT
1 TTATA-ATT
*
52091 TTATGATT
1 TTATAATT
52099 TCTATAATT
1 T-TATAATT
52108 TTATAATT
1 TTATAATT
52116 TT
1 TT
52118 CATAGCTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.07
8 20 0.67
9 8 0.27
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TTATAATT
Found at i:52147 original size:37 final size:35
Alignment explanation
Indices: 52101--52193 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 35
52091 TTATGATTTC
**
52101 TATAATTTTATAATTTTCATAGCTTTAACAATTTTT
1 TATAATTTTATAATTTT-ATAAATTTAACAATTTTT
* **
52137 ATATAATTTTAATACTTTTATAAATTTTCCAATTTTT
1 -TATAATTTT-ATAATTTTATAAATTTAACAATTTTT
*
52174 TAATAATTTTACAATTTTAT
1 T-ATAATTTTATAATTTTAT
52194 GCTATTATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
36 9 0.19
37 31 0.66
38 7 0.15
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (35 bp):
TATAATTTTATAATTTTATAAATTTAACAATTTTT
Found at i:52156 original size:29 final size:29
Alignment explanation
Indices: 52109--52164 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
52099 TCTATAATTT
*
52109 TATAATTTTCATAGCTTTA-ACAATTTTTA
1 TATAATTTTAATAGCTTTATA-AATTTTTA
52138 TATAATTTTAATA-CTTTTATAAATTTT
1 TATAATTTTAATAGC-TTTATAAATTTT
52165 CCAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.04
29 22 0.92
30 1 0.04
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (29 bp):
TATAATTTTAATAGCTTTATAAATTTTTA
Found at i:56178 original size:19 final size:18
Alignment explanation
Indices: 56137--56180 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
56127 ATGCACAATT
* *
56137 TATTTTTAAAATTATAAA
1 TATTTTAAAAAATATAAA
*
56155 TATTTTAAAAAATATATA
1 TATTTTAAAAAATATAAA
56173 TAATTTTA
1 T-ATTTTA
56181 TGAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTAAAAAATATAAA
Found at i:58286 original size:30 final size:27
Alignment explanation
Indices: 58230--58287 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
58220 CTTCTTTCTA
*
58230 TTTACTTTTTATAATCATTGCTAACAT
1 TTTACTTTATATAATCATTGCTAACAT
*
58257 TTTACTTTATACTAATACTATTTCTAACAT
1 TTTACTTTATA-TAAT-C-ATTGCTAACAT
58287 T
1 T
58288 GACGGGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 4 0.15
29 1 0.04
30 11 0.42
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTACTTTATATAATCATTGCTAACAT
Found at i:62892 original size:23 final size:23
Alignment explanation
Indices: 62866--62912 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
62856 GATCATCCGT
*
62866 ATGATGTTGATATATCACTATAA
1 ATGATGATGATATATCACTATAA
62889 ATGATGATGATATATCACTATAA
1 ATGATGATGATATATCACTATAA
62912 A
1 A
62913 GTACAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (23 bp):
ATGATGATGATATATCACTATAA
Found at i:70411 original size:30 final size:30
Alignment explanation
Indices: 70365--70447 Score: 118
Period size: 28 Copynumber: 2.9 Consensus size: 30
70355 AGGGAACAAT
*
70365 GGATGATGGG-GTTGGTGTTGAAAAAAATG
1 GGATGGTGGGTGTTGGTGTTGAAAAAAATG
70394 GGATGGTGGGTGTTGGTGTTG--AAAAATG
1 GGATGGTGGGTGTTGGTGTTGAAAAAAATG
* *
70422 GGGTGGTAGGTGTTGGTGTTGAAAAA
1 GGATGGTGGGTGTTGGTGTTGAAAAA
70448 TGGGATTTAC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 26 0.54
29 9 0.19
30 13 0.27
ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30
Consensus pattern (30 bp):
GGATGGTGGGTGTTGGTGTTGAAAAAAATG
Found at i:70448 original size:28 final size:28
Alignment explanation
Indices: 70375--70453 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
70365 GGATGATGGG
*
70375 GTTGGTGTTGAAAAAAATGGGATGGTGGGT
1 GTTGGTGTTG--AAAAATGGGATGGTAGGT
*
70405 GTTGGTGTTGAAAAATGGGGTGGTAGGT
1 GTTGGTGTTGAAAAATGGGATGGTAGGT
70433 GTTGGTGTTGAAAAATGGGAT
1 GTTGGTGTTGAAAAATGGGAT
70454 TTACAGATGC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 36 0.78
30 10 0.22
ACGTcount: A:0.25, C:0.00, G:0.43, T:0.32
Consensus pattern (28 bp):
GTTGGTGTTGAAAAATGGGATGGTAGGT
Found at i:71519 original size:267 final size:265
Alignment explanation
Indices: 70944--71693 Score: 986
Period size: 267 Copynumber: 2.8 Consensus size: 265
70934 AAAAATATCT
* * * * *
70944 ATCCATCTCCTTCTGTGATGGAATCGAATGAGATGTCGATGATGATCTTCCTCCTTCTGTAATAG
1 ATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATCTACCTCATTCTGTGATAG
* * *
71009 AATCGAGCAAAAATGACAATGTTGATGATGCTTATCCAACTCCTTCTACGATGGATTTGAGTG-A
66 AATCGAGC---AA--A-AA-GTTGA--AT-CTGATCCAACTCCTTCTGCGATGGATTTGAGCGAA
*
71073 AATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGCCGATGCTGATCTACCT
121 AATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCT
* * ** *
71138 CCTTTTGCGATAGAATCGAGCAAAATGTTGGTGATAATCCAACTCCTTCTGTGATGGATTTGAGC
186 CCTTCTGTGATAGAATCGAGCAAAATGTTGGACATAATCCAACTCCTTCTGCGATGGATTTGAGC
*
71203 AAAATAAAAATGTCG
251 AAAATAAAAAGGTCG
* * * *
71218 ATCCACCTCCTTTTGTGATGGAATCGAACGAGATGTCGATGTTGATCTACCTCATTCTATGATAT
1 ATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATCTACCTCATTCTGTGATAG
*
71283 AATCTAGCAAAAAGTTGAATCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG
66 AATCGAGCAAAAAGTTGAATCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG
* * * * **
71348 TCGATCCACCTCCTTCTATGATGGAAATCAAACGATATGTCGATAG-TGATCTATATCCTTCTGT
131 TCGATCCACCTCATTCTGTGATGG-AATCGAACGAGATGTCGAT-GCTGATCTACCTCCTTCTGT
* *
71412 GGTAGAATCGAGCTAAAA-GTT-GACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAT
194 GATAGAATCGAGC-AAAATGTTGGACA-TAATCCAACTCCTTCTGCGATGGATTTGAGC-AAAAT
71475 AAAAAGGTCG
256 AAAAAGGTCG
* * * *
71485 ATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCATTCTGTGATAG
1 ATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATCTACCTCATTCTGTGATAG
*** *
71550 AATCGAGCAAAAAGTTGCCGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAATG
66 AATCGAGCAAAAAGTTGAATCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG
* *
71615 TCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGA
131 TCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGA
*
71680 TAGAATCGACCAAA
196 TAGAATCGAGCAAA
71694 TAGTTGAACA
Statistics
Matches: 419, Mismatches: 50, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
264 30 0.07
265 41 0.10
266 116 0.28
267 164 0.39
268 2 0.00
269 1 0.00
271 2 0.00
274 63 0.15
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (265 bp):
ATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATCTACCTCATTCTGTGATAG
AATCGAGCAAAAAGTTGAATCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG
TCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGA
TAGAATCGAGCAAAATGTTGGACATAATCCAACTCCTTCTGCGATGGATTTGAGCAAAATAAAAA
GGTCG
Found at i:71555 original size:44 final size:44
Alignment explanation
Indices: 71085--71688 Score: 205
Period size: 44 Copynumber: 13.6 Consensus size: 44
71075 TAAAAATGTC
* * ** *
71085 GATCCACCTCATTCTGTGATGGAATCGAACGAGATGCCGATGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
* * * * * * *
71129 GATCTACCTCCTTTTGCGATAGAATCGAGCAAAATGTTGGTGAT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
* * * * * * *****
71173 AATCCAACTCCTTCTGTGATGGATTTGAGCAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
* * * * *
71216 CGATCCACCTCCTTTTGTGATGGAATCGAACGAGATGTCGATGTT
1 -GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
* * * ** * * * * *
71261 GATCTACCTCATTCTATGATATAATCTAGCAAAAAGTTGAAT-CT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTG-GTGCT
* * * * * *****
71305 GATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAATCGAACG-AAATGTTGGTGCT
* * * * *
71349 CGATCCACCTCCTTCTATGATGGAAATCAAACGATATGTCGATAG-T
1 -GATCCACCTCCTTCTGTGATGG-AATCGAACGAAATGTTGGT-GCT
* ** * * * * * ***
71395 GATCTATATCCTTCTGTGGTAGAATCGAGCTAAAAGTTGACACT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
* * * * * ***
71439 GATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAAGGT-C-
1 GATCCACCTCCTTCTGTGATGGAATCGAACG-AAAT--GTTGGTGCT
* *
71484 GATCCACCTCCTTCTATGATGGAATCGAACGAGATGTTGGTGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
* * * * * * **
71528 GATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGCCGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
* * * * *****
71572 GATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAATCGAACG-AAATGTTGGTGCT
* *
71616 CGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCT
1 -GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
* *
71661 GATCTACCTCCTTCTGTGATAGAATCGA
1 GATCCACCTCCTTCTGTGATGGAATCGA
71689 CCAAATAGTT
Statistics
Matches: 388, Mismatches: 155, Indels: 34
0.67 0.27 0.06
Matches are distributed among these distances:
42 3 0.01
43 2 0.01
44 269 0.69
45 105 0.27
46 8 0.02
47 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCT
Found at i:71602 original size:133 final size:133
Alignment explanation
Indices: 71042--71700 Score: 919
Period size: 133 Copynumber: 5.0 Consensus size: 133
71032 GATGATGCTT
* * *
71042 ATCCAACTCCTTCTACGATGGATTTGAGTG-AAATAAAAATGTCGATCCACCTCATTCTGTGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * * * **
71106 GAATCGAACGAGATGCCGATGCTGATCTACCTCCTTTTGCGATAGAATCGAGCAAAATGTTGGTG
66 GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACG
* *
71171 ATA
131 CTG
* *
71174 ATCCAACTCCTTCTGTGATGGATTTGAGC-AAAATAAAAATGTCGATCCACCTCCTTTTGTGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * * * * **
71238 GAATCGAACGAGATGTCGATGTTGATCTACCTCATTCTATGATATAATCTAGCAAAAAGTTGAAT
66 GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACG
71303 CTG
131 CTG
*
71306 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTATGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * ** * *
71371 GAAATCAAACGATATGTCGATAG-TGATCTATATCCTTCTGTGGTAGAATCGAGCTAAAAGTTGA
66 G-AATCGAACGAGATGTCGAT-GCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGA
*
71435 CACTG
129 CGCTG
* *
71440 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAAGGTCGATCCACCTCCTTCTATGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * * *
71505 GAATCGAACGAGATGTTGGTGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGCCG
66 GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACG
71570 CTG
131 CTG
* *
71573 ATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCATTCTGTGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * * *
71638 GAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGACCAAATAGTTGA
66 GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGA
71701 ACAATCTCTT
Statistics
Matches: 468, Mismatches: 54, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
132 141 0.30
133 208 0.44
134 118 0.25
135 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (133 bp):
ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACG
CTG
Found at i:72127 original size:36 final size:36
Alignment explanation
Indices: 72070--72431 Score: 226
Period size: 39 Copynumber: 9.9 Consensus size: 36
72060 CAAAGATTGA
*
72070 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAAT
* * *
72105 TCATTTTAAGGGAAACTGTCTCAAGAGAGACAAAACT
1 T-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAAT
* *
72142 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAAT
* * *
72178 TGTCTCAAGGGAAACTGTCTCAAGGGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-AT
* ***
72215 TGTTTCAAATGGG--AC-GTTTTC-A-A-AG---TTTA-
1 TGTTTC-AA-GGGAAACTG-TCTCAAGAGAGACAAAAAT
* * * *
72244 TGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-AT
* *
72281 TGTTTCAAGGGAAACTGTCTCAAGCGAGACAAAATCTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA---AT
* * *
72320 TGTTT-ATAGGGAAACTATCTCAAGCGAGACAAAATCTT
1 TGTTTCA-AGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * * *
72358 CTGTTTCTAGGGAAACTATCTCAAGCGAGACAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * * *
72397 CTGTTTCGAGGAAAACTATCTCAAGCGAGACAAAA
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
72432 TCTTTTGTTT
Statistics
Matches: 272, Mismatches: 33, Indels: 40
0.79 0.10 0.12
Matches are distributed among these distances:
27 2 0.01
28 2 0.01
29 10 0.04
30 2 0.01
32 2 0.01
34 2 0.01
35 1 0.00
36 92 0.34
37 48 0.18
38 5 0.02
39 106 0.39
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAAT
Found at i:72166 original size:15 final size:15
Alignment explanation
Indices: 72112--72204 Score: 69
Period size: 15 Copynumber: 5.4 Consensus size: 15
72102 AATTCATTTT
72112 AAGGGAAACTGTCTC
1 AAGGGAAACTGTCTC
*
72127 AAGAGAGACAAAACTTGTTTC
1 AAG-G-G---AAAC-TGTCTC
72148 AAGGGAAACTGTCTC
1 AAGGGAAACTGTCTC
72163 AAGGGAGACAAAACTTGTCTC
1 AA-GG-G---AAAC-TGTCTC
72184 AAGGGAAACTGTCTC
1 AAGGGAAACTGTCTC
72199 AAGGGA
1 AAGGGA
72205 GACAAAACTT
Statistics
Matches: 64, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
15 22 0.34
16 11 0.17
17 2 0.03
19 2 0.03
20 11 0.17
21 16 0.25
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (15 bp):
AAGGGAAACTGTCTC
Found at i:72332 original size:39 final size:39
Alignment explanation
Indices: 72261--72600 Score: 486
Period size: 39 Copynumber: 8.8 Consensus size: 39
72251 AGAGAAAATG
* * *
72261 TCTCAAGGGAGACAAAAT-TT-TGTTTCAAGGGAAACTG
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* **
72298 TCTCAAGCGAGACAAAATCTTTTGTTTATAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
72337 TCTCAAGCGAGACAAAATCTTCTGTTTCTAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
72376 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGAAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
72415 TCTCAAGCGAGACAAAATCTTTTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * *
72454 ACTCAAGCGAGATAAAATCTTCTGTTTCGAGAGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * * * *
72493 TCTAAAGTGAGATAAAATCTTATGTTTCGAGTGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
72532 TCTCAAGTGAGACAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* *
72571 TCTCAAGCGAGATAAAATCTTTTGTTTCGA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGA
72601 CAAAATCTTC
Statistics
Matches: 275, Mismatches: 26, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
37 17 0.06
38 2 0.01
39 256 0.93
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (39 bp):
TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
Found at i:72607 original size:18 final size:18
Alignment explanation
Indices: 72584--72618 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
72574 CAAGCGAGAT
*
72584 AAAATCTTTTGTTTCGAC
1 AAAATCTTCTGTTTCGAC
72602 AAAATCTTCTGTTTCGA
1 AAAATCTTCTGTTTCGA
72619 GGGAACCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
AAAATCTTCTGTTTCGAC
Found at i:72656 original size:39 final size:39
Alignment explanation
Indices: 72602--72844 Score: 364
Period size: 39 Copynumber: 6.3 Consensus size: 39
72592 TTGTTTCGAC
* * *
72602 AAAATCTTCTGTTTCGAGGGAACCTATCTCAAGCGAGAT
1 AAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
* *
72641 AAAATCTTTTATTTCGAGTGAATCTATCTCAAGCGAGAT
1 AAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
72680 AAAAAT-TTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
1 -AAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
* *
72719 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
* * *
72758 -AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCAAAAT
1 AAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
*
72796 AAAATCTTATATTTCGAGTGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
72835 AAAATCTTCT
1 AAAATCTTCT
72845 TTAAAAACAA
Statistics
Matches: 185, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
38 40 0.22
39 140 0.76
40 5 0.03
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (39 bp):
AAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
Found at i:72665 original size:57 final size:57
Alignment explanation
Indices: 72542--72657 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
72532 TCTCAAGTGA
*
72542 GACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTC
1 GACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTATTTC
*
72599 GACAAAATCTTCTGTTTCGAGGGAACCTATCTCAAGCGAGATAAAATCTTTTATTTC
1 GACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTATTTC
72656 GA
1 GA
72658 GTGAATCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (57 bp):
GACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTATTTC
Found at i:72670 original size:96 final size:96
Alignment explanation
Indices: 72506--72683 Score: 275
Period size: 96 Copynumber: 1.9 Consensus size: 96
72496 AAAGTGAGAT
* * *
72506 AAAATCTTATGTTTCGAGTGAAACTATCTCAAGTGAGACAAAATCTTCTGTTTCGAGGGAAACTA
1 AAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTCTATTTCGAGGGAAACTA
72571 TCTCAAGCGAGATAAAATCTTTTGTTTCGAC
66 TCTCAAGCGAGATAAAATCTTTTGTTTCGAC
* * * * * *
72602 AAAATCTTCTGTTTCGAGGGAACCTATCTCAAGCGAGATAAAATCTTTTATTTCGAGTGAATCTA
1 AAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTCTATTTCGAGGGAAACTA
72667 TCTCAAGCGAGATAAAA
66 TCTCAAGCGAGATAAAA
72684 ATTTCTATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (96 bp):
AAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTCTATTTCGAGGGAAACTA
TCTCAAGCGAGATAAAATCTTTTGTTTCGAC
Found at i:72709 original size:135 final size:135
Alignment explanation
Indices: 72467--72735 Score: 414
Period size: 135 Copynumber: 2.0 Consensus size: 135
72457 CAAGCGAGAT
* *
72467 AAAATCTTCTGTTTCGAGAGAAACTATCTAAAGTGAGATAAAATCTTATGTTTCGAGTGAAACTA
1 AAAATCTTCTGTTTCGAGAGAAACTATCTAAAGCGAGATAAAATCTTATATTTCGAGTGAAACTA
* * * *
72532 TCTCAAGTGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTT
66 TCTCAAGCGAGAAAAAATCTTCTATTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTT
72597 TCGAC
131 TCGAC
* * * * *
72602 AAAATCTTCTGTTTCGAGGGAACCTATCTCAAGCGAGATAAAATCTTTTATTTCGAGTGAATCTA
1 AAAATCTTCTGTTTCGAGAGAAACTATCTAAAGCGAGATAAAATCTTATATTTCGAGTGAAACTA
*
72667 TCTCAAGCGAGATAAAAAT-TTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
66 TCTCAAGCGAGA-AAAAATCTTCTATTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGT
72731 TTCGA
130 TTCGA
72736 GGGAAACTAT
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
135 116 0.96
136 5 0.04
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (135 bp):
AAAATCTTCTGTTTCGAGAGAAACTATCTAAAGCGAGATAAAATCTTATATTTCGAGTGAAACTA
TCTCAAGCGAGAAAAAATCTTCTATTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTT
TCGAC
Found at i:72725 original size:174 final size:173
Alignment explanation
Indices: 72425--72773 Score: 547
Period size: 174 Copynumber: 2.0 Consensus size: 173
72415 TCTCAAGCGA
* *
72425 GACAAAATCTTTTGTTTCGAGGGAAACTAACTCAAGCGAGATAAAATCTTCTGTTTCGAGAGAAA
1 GACAAAATCTTCTGTTTCGAGGGAAACTAACTCAAGCGAGATAAAATCTTCTATTTCGAGAGAAA
* * *
72490 CTATCTAAAGTGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAGTGAGACAAAATCTTCT
66 CTATCTAAAGCGAGATAAAATCTTATATTTCGAGTGAAACTATCTCAAGCGAGACAAAATCTTCT
*
72555 GTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTC
131 GTTTCGAGGGAAACTATCTCAAGCGAGAT-AAATCTTCTGTTTC
* * * * *
72599 GACAAAATCTTCTGTTTCGAGGGAACCTATCTCAAGCGAGATAAAATCTTTTATTTCGAGTGAAT
1 GACAAAATCTTCTGTTTCGAGGGAAACTAACTCAAGCGAGATAAAATCTTCTATTTCGAGAGAAA
* * *
72664 CTATCTCAAGCGAGATAAAAAT-TTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTC
66 CTATCTAAAGCGAGAT-AAAATCTTATATTTCGAGTGAAACTATCTCAAGCGAGACAAAATCTTC
72728 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAATCTTCTGTTTC
130 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAATCTTCTGTTTC
72772 GA
1 GA
72774 GTGAAACTAT
Statistics
Matches: 160, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
173 15 0.09
174 140 0.88
175 5 0.03
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (173 bp):
GACAAAATCTTCTGTTTCGAGGGAAACTAACTCAAGCGAGATAAAATCTTCTATTTCGAGAGAAA
CTATCTAAAGCGAGATAAAATCTTATATTTCGAGTGAAACTATCTCAAGCGAGACAAAATCTTCT
GTTTCGAGGGAAACTATCTCAAGCGAGATAAATCTTCTGTTTC
Found at i:72810 original size:116 final size:117
Alignment explanation
Indices: 72602--72844 Score: 400
Period size: 116 Copynumber: 2.1 Consensus size: 117
72592 TTGTTTCGAC
* * *
72602 AAAATCTTCTGTTTCGAGGGAACCTATCTCAAGCGAGATAAAATCTTTTATTTCGAGTGAATCTA
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
* * *
72667 TCTCAAGCGAGATAAAAATTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
66 TCTCAAGCAAAATAAAAATTTATATTTCGAGTGAAACTATCTCAAGCGAGAT
*
72719 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTA
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
72783 TCTCAAGCAAAAT-AAAATCTTATATTTCGAGTGAAACTATCTCAAGCGAGAT
66 TCTCAAGCAAAATAAAAAT-TTATATTTCGAGTGAAACTATCTCAAGCGAGAT
72835 AAAATCTTCT
1 AAAATCTTCT
72845 TTAAAAACAA
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
115 5 0.04
116 75 0.64
117 38 0.32
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (117 bp):
AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACTA
TCTCAAGCAAAATAAAAATTTATATTTCGAGTGAAACTATCTCAAGCGAGAT
Found at i:75188 original size:28 final size:28
Alignment explanation
Indices: 75138--75218 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
75128 ACACAGATGT
* * *
75138 ACATGCAAATGCAAAGATTCAAAAATGC
1 ACATGCAAATGCGAATATGCAAAAATGC
*
75166 ACATGCAAATGCGAATATGCAAACAAAATGG
1 ACATGCAAATGCGAATATGC--A-AAAATGC
75197 A-ATGCAAAATGCG-ATATGCAAA
1 ACATGC-AAATGCGAATATGCAAA
75219 TGCAACAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
27 2 0.04
28 18 0.40
30 11 0.24
31 14 0.31
ACGTcount: A:0.49, C:0.16, G:0.17, T:0.17
Consensus pattern (28 bp):
ACATGCAAATGCGAATATGCAAAAATGC
Found at i:75204 original size:30 final size:31
Alignment explanation
Indices: 75159--75218 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
75149 CAAAGATTCA
75159 AAAATGCACATGC-AAATGCGAATATGCAAAC
1 AAAATGCACATGCAAAATGCG-ATATGCAAAC
*
75190 AAAATGGA-ATGCAAAATGCGATATGCAAA
1 AAAATGCACATGCAAAATGCGATATGCAAA
75219 TGCAACAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (31 bp):
AAAATGCACATGCAAAATGCGATATGCAAAC
Found at i:78782 original size:29 final size:32
Alignment explanation
Indices: 78749--78807 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
78739 CGCATGAAAC
78749 AATAG-ATGAT-GG-GTTGGTGTTGAAAAAAA
1 AATAGAATGATGGGTGTTGGTGTTGAAAAAAA
78778 AATAGAATGATGGGTGTTGGTGTTGAAAAA
1 AATAGAATGATGGGTGTTGGTGTTGAAAAA
78808 TGAGGTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 5 0.19
30 5 0.19
31 2 0.07
32 15 0.56
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (32 bp):
AATAGAATGATGGGTGTTGGTGTTGAAAAAAA
Found at i:80449 original size:27 final size:27
Alignment explanation
Indices: 80411--80465 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
80401 TAACACTCAA
80411 ACTGTAAAAATAAATAAATGATTAAAT
1 ACTGTAAAAATAAATAAATGATTAAAT
*
80438 ACTGTAGAAATAAATAAATGATTAAAT
1 ACTGTAAAAATAAATAAATGATTAAAT
80465 A
1 A
80466 TACTGATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (27 bp):
ACTGTAAAAATAAATAAATGATTAAAT
Done.