Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008221.1 Hibiscus syriacus cultivar Beakdansim tig00110853_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: 87129
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2303 original size:33 final size:33
Alignment explanation
Indices: 2232--2305 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
2222 TAATACACTA
* *
2232 TTTT-TATATCACTTAACTAATAAAATATTATT
1 TTTTATATATAACTTAACTAATAAAATATAATT
* *
2264 TATTATATATAACTTAAACTAATAAACTA-AATT
1 TTTTATATATAACTT-AACTAATAAAATATAATT
2297 TTTTATATA
1 TTTTATATA
2306 ATATAAATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 3 0.09
33 20 0.57
34 12 0.34
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (33 bp):
TTTTATATATAACTTAACTAATAAAATATAATT
Found at i:2448 original size:22 final size:22
Alignment explanation
Indices: 2410--2465 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2400 TACTTATGTG
2410 TAATATAACTTAAACTAACAAAC
1 TAATATAAC-TAAACTAACAAAC
2433 TAATATAACTAAACTAACAAAC
1 TAATATAACTAAACTAACAAAC
2455 T-AT-TAACTAAA
1 TAATATAACTAAA
2466 ATTTTGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.24
21 2 0.06
22 14 0.42
23 9 0.27
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (22 bp):
TAATATAACTAAACTAACAAAC
Found at i:3150 original size:18 final size:18
Alignment explanation
Indices: 3127--3189 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
3117 GCACATATCC
3127 TCATTATCAACATCAATA
1 TCATTATCAACATCAATA
** **
3145 TCATTATCATGATCTCTA
1 TCATTATCAACATCAATA
*
3163 TCATTCTCAACATCAATA
1 TCATTATCAACATCAATA
3181 TCATTATCA
1 TCATTATCA
3190 TGTAATACAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (18 bp):
TCATTATCAACATCAATA
Found at i:3516 original size:37 final size:38
Alignment explanation
Indices: 3466--3542 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 38
3456 AGCATATAAA
* * *
3466 ATTATCCCGAAGGATTTCGTATATGTCCC-AAGGACCT
1 ATTATCCCGAAGGATGTCATATATGTCCCGAAGAACCT
*
3503 ATTATCCCGAAGGATGTCATATGTGTCCCGAAGAACCT
1 ATTATCCCGAAGGATGTCATATATGTCCCGAAGAACCT
3541 AT
1 AT
3543 AGAACCCTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
37 26 0.74
38 9 0.26
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (38 bp):
ATTATCCCGAAGGATGTCATATATGTCCCGAAGAACCT
Found at i:3887 original size:26 final size:26
Alignment explanation
Indices: 3849--3899 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3839 TATGTTCACA
* *
3849 TCAATCATGTCACATAAAATAACATG
1 TCAAACATATCACATAAAATAACATG
*
3875 TCAAACATATCACATATAATAACAT
1 TCAAACATATCACATAAAATAACAT
3900 ATGACACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (26 bp):
TCAAACATATCACATAAAATAACATG
Found at i:3908 original size:26 final size:26
Alignment explanation
Indices: 3848--3910 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
3838 ATATGTTCAC
* *
3848 ATCAATCATGTCACATAAAATAACAT
1 ATCAAACATATCACATAAAATAACAT
* *
3874 GTCAAACATATCACATATAATAACAT
1 ATCAAACATATCACATAAAATAACAT
* *
3900 ATGACACATAT
1 ATCAAACATAT
3911 ACCCATTTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (26 bp):
ATCAAACATATCACATAAAATAACAT
Found at i:4752 original size:29 final size:31
Alignment explanation
Indices: 4685--4752 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
4675 CAATCATTCA
*
4685 CAATTTTTCTAAAATTATCAAATTGGTCCCC
1 CAATTTTTCAAAAATTATCAAATTGGTCCCC
* *
4716 CAACTTTTCAAAAATTA-CAAA-TGGTCCCT
1 CAATTTTTCAAAAATTATCAAATTGGTCCCC
*
4745 GAATTTTT
1 CAATTTTT
4753 ATAAGGCCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
31 15 0.47
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (31 bp):
CAATTTTTCAAAAATTATCAAATTGGTCCCC
Found at i:6453 original size:18 final size:18
Alignment explanation
Indices: 6430--6467 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6420 GGCATTTTAA
6430 AAAATATATATATTA-ATT
1 AAAATAT-TATATTACATT
*
6448 AAAATATTTTATTACATT
1 AAAATATTATATTACATT
6466 AA
1 AA
6468 CTCAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATATTATATTACATT
Found at i:8149 original size:5 final size:5
Alignment explanation
Indices: 8139--8234 Score: 192
Period size: 5 Copynumber: 19.2 Consensus size: 5
8129 AATTGTTATT
8139 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
8189 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC A
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC A
8235 CATTAGACAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 91 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:13139 original size:23 final size:22
Alignment explanation
Indices: 13113--13181 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
13103 CACCACAGCT
*
13113 CGTATAAATGCACAGGAGTGCCA
1 CGTATAAATGCAC-GAAGTGCCA
* *
13136 CGTATAATTGCATCGAAGTGCCG
1 CGTATAAATGCA-CGAAGTGCCA
* *
13159 CGTAGAAATGCACTGTAGTGCCA
1 CGTATAAATGCAC-GAAGTGCCA
13182 TATAAGATGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (22 bp):
CGTATAAATGCACGAAGTGCCA
Found at i:13845 original size:2 final size:2
Alignment explanation
Indices: 13838--13874 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
13828 ACTTATAAAC
13838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13875 CTTATTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20281 original size:23 final size:23
Alignment explanation
Indices: 20255--20322 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
20245 ACCACAGCTC
*
20255 GTATAAATGCACCGGAGTGCCAA
1 GTATAAATGCACCGAAGTGCCAA
* * **
20278 GTATAATTGCATCGAAGTGCCGC
1 GTATAAATGCACCGAAGTGCCAA
* *
20301 GTAGAAATGCACCGTAGTGCCA
1 GTATAAATGCACCGAAGTGCCA
20323 TATAAGATGT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (23 bp):
GTATAAATGCACCGAAGTGCCAA
Found at i:20987 original size:2 final size:2
Alignment explanation
Indices: 20980--21013 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20970 ACTTATAAAC
20980 AT 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
21014 TACTTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27423 original size:23 final size:23
Alignment explanation
Indices: 27397--27464 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
27387 ACCACAGCTC
*
27397 GTATAAATGCACCGGAGTGCCAA
1 GTATAAATGCACCGAAGTGCCAA
* * **
27420 GTATAATTGCATCGAAGTGCCGC
1 GTATAAATGCACCGAAGTGCCAA
* *
27443 GTAGAAATGCACCGTAGTGCCA
1 GTATAAATGCACCGAAGTGCCA
27465 TATAAGATGT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (23 bp):
GTATAAATGCACCGAAGTGCCAA
Found at i:34545 original size:23 final size:23
Alignment explanation
Indices: 34519--34586 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
34509 ACCACAGCTC
*
34519 GTATAAATGCACCGGAGTGCCAA
1 GTATAAATGCACCGAAGTGCCAA
* * **
34542 GTATAATTGCATCGAAGTGCCGC
1 GTATAAATGCACCGAAGTGCCAA
* *
34565 GTAGAAATGCACCGTAGTGCCA
1 GTATAAATGCACCGAAGTGCCA
34587 TATAAGATGT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (23 bp):
GTATAAATGCACCGAAGTGCCAA
Found at i:39654 original size:45 final size:47
Alignment explanation
Indices: 39602--39690 Score: 146
Period size: 45 Copynumber: 1.9 Consensus size: 47
39592 CCGAATAAAT
*
39602 GCATGCGAACTAGATATCATGCGGTTATG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
*
39647 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
39691 TAACAAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 27 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:42173 original size:24 final size:24
Alignment explanation
Indices: 42146--42192 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42136 TTAATTTTTG
*
42146 CATTGCATTT-TATTCATTCATAAT
1 CATT-CATTTATATTCATTAATAAT
42170 CATTCATTTATATTCATTAATAA
1 CATTCATTTATATTCATTAATAA
42193 ATATCAGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (24 bp):
CATTCATTTATATTCATTAATAAT
Found at i:49362 original size:10 final size:10
Alignment explanation
Indices: 49332--49440 Score: 70
Period size: 10 Copynumber: 11.0 Consensus size: 10
49322 ATTTTGCTTG
*
49332 AAGAAGAAAT
1 AAGAAGAAAA
*
49342 AA-AAGAGAA
1 AAGAAGAAAA
49351 AAGAAGAAAA
1 AAGAAGAAAA
49361 AATG-AGAAAA
1 AA-GAAGAAAA
49371 AAG-A-AAAA
1 AAGAAGAAAA
* *
49379 ATGATGGAAAA
1 AAGA-AGAAAA
49390 AACGAAAAGAAAA
1 AA-G--AAGAAAA
*
49403 AA-AAGAGAA
1 AAGAAGAAAA
49412 AAGAAGAAAA
1 AAGAAGAAAA
49422 AATG-AGAAAA
1 AA-GAAGAAAA
49432 AAGAA-AAAA
1 AAGAAGAAAA
49441 TGATGGAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
8 6 0.08
9 22 0.28
10 35 0.44
11 7 0.09
12 1 0.01
13 7 0.09
14 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:49369 original size:18 final size:17
Alignment explanation
Indices: 49335--49513 Score: 110
Period size: 18 Copynumber: 9.5 Consensus size: 17
49325 TTGCTTGAAG
*
49335 AAGAAATAAAAGAGAAAA
1 AAGAAA-AAATGAGAAAA
49353 GAAGAAAAAATGAGAAAA
1 -AAGAAAAAATGAGAAAA
49371 AAGAAAAAATGATGGAAAAAACGAA
1 AAGAAAAAATGA--G----AA--AA
*
49396 AAGAAAAAAAAGAGAAAA
1 AAG-AAAAAATGAGAAAA
49414 GAAGAAAAAATGAGAAAA
1 -AAGAAAAAATGAGAAAA
49432 AAGAAAAAATGATGGAAAA
1 AAGAAAAAATGA--GAAAA
* *
49451 AACGAAAAGAA-AAAAAAA
1 AA-GAAAA-AATGAGAAAA
49469 GAGAGAAAAAATG-GAAAA
1 -A-AGAAAAAATGAGAAAA
* *
49487 ATGAATAAAAAGAGAAAA
1 AAGAA-AAAATGAGAAAA
*
49505 ATGAAAAAA
1 AAGAAAAAA
49514 GAAAAATAAA
Statistics
Matches: 132, Mismatches: 9, Indels: 40
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.02
17 34 0.26
18 45 0.34
19 23 0.17
20 9 0.07
21 2 0.02
23 2 0.02
24 1 0.01
25 5 0.04
26 8 0.06
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (17 bp):
AAGAAAAAATGAGAAAA
Found at i:49396 original size:27 final size:26
Alignment explanation
Indices: 49366--49435 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
49356 GAAAAAATGA
*
49366 GAAAAAAGAAAAAATGATGGAAAAAAC
1 GAAAAAAGAAAAAAAGA-GGAAAAAAC
*
49393 GAAAAGA-AAAAAAAGA-GAAAAGAA-
1 GAAAAAAGAAAAAAAGAGGAAAA-AAC
49417 GAAAAAATGAGAAAAAAGA
1 GAAAAAA-GA-AAAAAAGA
49436 AAAAATGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 11 0.31
25 2 0.06
26 9 0.25
27 14 0.39
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.04
Consensus pattern (26 bp):
GAAAAAAGAAAAAAAGAGGAAAAAAC
Found at i:49415 original size:41 final size:44
Alignment explanation
Indices: 49342--49438 Score: 123
Period size: 44 Copynumber: 2.2 Consensus size: 44
49332 AAGAAGAAAT
*
49342 AAAAGAGAAAAGAAGAAAAAATGAG-AAAA-AAGAAAAAATGATGG
1 AAAAAAGAAAAGAAGAAAAAATGAGAAAAAGAAGAAAAAATGA--G
49386 AAAAAACGAAAAGAA-AAAAAA-GAG-AAAAGAAGAAAAAATGAG
1 AAAAAA-GAAAAGAAGAAAAAATGAGAAAAAGAAGAAAAAATGAG
49428 AAAAAAGAAAA
1 AAAAAAGAAAA
49439 AATGATGGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
41 5 0.10
42 7 0.14
43 7 0.14
44 23 0.46
45 8 0.16
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.04
Consensus pattern (44 bp):
AAAAAAGAAAAGAAGAAAAAATGAGAAAAAGAAGAAAAAATGAG
Found at i:49430 original size:61 final size:61
Alignment explanation
Indices: 49335--49508 Score: 269
Period size: 61 Copynumber: 2.8 Consensus size: 61
49325 TTGCTTGAAG
*
49335 AAGAAATAAAAGAGAAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGATGGAAAAAACGAA
1 AAGAAAAAAAAGAGAAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGATGGAAAAAACGAA
49396 AAGAAAAAAAAGAGAAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGATGGAAAAAACGAA
1 AAGAAAAAAAAGAGAAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGATGGAAAAAACGAA
* *
49457 AAGAAAAAAAAAGAGAGAAAAAATGGAAAAATGA-ATAAAAAGAGAAAAATGA
1 AAG-AAAAAAAAGAGA-AAAGAA-GAAAAAATGAGA-AAAAAGA-AAAAATGA
49509 AAAAAGAAAA
Statistics
Matches: 105, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
61 63 0.60
62 12 0.11
63 6 0.06
64 16 0.15
65 8 0.08
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (61 bp):
AAGAAAAAAAAGAGAAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGATGGAAAAAACGAA
Found at i:49440 original size:27 final size:27
Alignment explanation
Indices: 49401--49519 Score: 115
Period size: 27 Copynumber: 4.4 Consensus size: 27
49391 ACGAAAAGAA
*
49401 AAAAAAGAGAAAAGA-AGAAAAAATGAG
1 AAAAAAGAAAAAAGAGAGAAAAAATG-G
*
49428 AAAAAAGAAAAAATGATG-GAAAAAA-CG
1 AAAAAAGAAAAAA-GA-GAGAAAAAATGG
*
49455 AAAAGAAAAAAAAAGAGAGAAAAAATGG
1 AAAA-AAGAAAAAAGAGAGAAAAAATGG
*
49483 AAAAATGAATAAAA-AGAG-AAAAAT-G
1 AAAAAAGAA-AAAAGAGAGAAAAAATGG
49508 AAAAAAGAAAAA
1 AAAAAAGAAAAA
49520 TAAAAGGAGG
Statistics
Matches: 78, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
24 3 0.04
25 9 0.12
26 7 0.09
27 33 0.42
28 19 0.24
29 7 0.09
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (27 bp):
AAAAAAGAAAAAAGAGAGAAAAAATGG
Found at i:49516 original size:14 final size:14
Alignment explanation
Indices: 49490--49524 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
49480 TGGAAAAATG
49490 AATAAAAAGAGAAA
1 AATAAAAAGAGAAA
49504 AATGAAAAA-AGAAA
1 AAT-AAAAAGAGAAA
49518 AATAAAA
1 AATAAAA
49525 GGAGGGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (14 bp):
AATAAAAAGAGAAA
Found at i:49524 original size:27 final size:28
Alignment explanation
Indices: 49349--49525 Score: 91
Period size: 29 Copynumber: 6.2 Consensus size: 28
49339 AATAAAAGAG
49349 AAAAGAAGAAAAAATGAGAAAAAAGAAAAA
1 AAAAG-AGAAAAAATG-GAAAAAAGAAAAA
* * * * *
49379 ATGATG-GAAAAAACGAAAAGAAAAAAAAGA
1 A-AAAGAGAAAAAATGGAAA-AAAGAAAA-A
*
49409 GAAAAGAAGAAAAAAT-GAGAAAAA-AGAAA
1 -AAAAG-AGAAAAAATGGA-AAAAAGAAAAA
* *
49438 AAATGATGGAAAAAA-CGAAAAGAA-AAAAA
1 AAAAGA--GAAAAAATGGAAAA-AAGAAAAA
* * *
49467 AAGAGAGAAAAAATGGAAAAATG-AATA
1 AAAAGAGAAAAAATGGAAAAAAGAAAAA
49494 AAAAGAG-AAAAAT-GAAAAAAGAAAAA
1 AAAAGAGAAAAAATGGAAAAAAGAAAAA
49520 TAAAAG
1 -AAAAG
49526 GAGGGTTCAA
Statistics
Matches: 112, Mismatches: 20, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
25 7 0.06
26 9 0.08
27 23 0.21
28 15 0.13
29 35 0.31
30 7 0.06
31 7 0.06
32 9 0.08
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (28 bp):
AAAAGAGAAAAAATGGAAAAAAGAAAAA
Found at i:50833 original size:153 final size:156
Alignment explanation
Indices: 50649--51290 Score: 607
Period size: 153 Copynumber: 4.0 Consensus size: 156
50639 AGTGAAGCAA
*
50649 ACAAGTTCGTTGAAGA-TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CAATTTTGTT
1 ACAAGTTCGTTGAAGATTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCAATTTTGTT
* *
50711 GAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAATATTGAGTCCT
66 GAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCCTTGAAGATTGAGTCCT
50776 ATACTCTCTGAATGAATAGGGAGCGG
131 ATACTCTCTGAATGAATAGGGAGCGG
* * * *
50802 ACAAGTTCGTTGAAGA-TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGA-CAAGTTCGTT
1 ACAAGTTCGTTGAAGATTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCAATTTTGTT
* * *
50864 GAAAATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAGTTCCTTGAAGATTGAGTCCT
66 GAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCCTTGAAGATTGAGTCCT
* *
50929 ATACTCCCTGAAAGAATAGGGAGCGG
131 ATACTCTCTGAATGAATAGGGAGCGG
** ** * * * *
50955 ACCTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACCCATTTTA
1 ACAAGTTCGTTGAAGA--TTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCAATTTTG
* * * * * *
51020 TTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTT-TTATGAAGATT
64 TTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCCT-TGAAGATT
* * *
51084 GTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAG
124 G----AGTCCTATACTCTCTGAATGAATAGGGAGCGG
** * * **
51121 ACCCGTTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 ACAAG-TTCGTTGAAGA-T-TTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCAATTTT
* * * * * ** *
51186 GTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGGATAGGGAGCGAACTCGTT-TTATGAAGAT
63 GTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCCT-TGAAGA-
* * *
51250 TGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAG
122 --TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGG
51288 ACA
1 ACA
51291 CGTTTGCCAA
Statistics
Matches: 411, Mismatches: 54, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
153 155 0.38
156 2 0.00
157 30 0.07
158 12 0.03
161 1 0.00
162 42 0.10
166 33 0.08
167 130 0.32
170 4 0.01
171 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (156 bp):
ACAAGTTCGTTGAAGATTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCAATTTTGTT
GAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCCTTGAAGATTGAGTCCT
ATACTCTCTGAATGAATAGGGAGCGG
Found at i:51083 original size:111 final size:105
Alignment explanation
Indices: 50667--51322 Score: 587
Period size: 102 Copynumber: 6.1 Consensus size: 105
50657 GTTGAAGATT
*
50667 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTTGTTGAAGATTGAGTCCTATACTCT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCATTTTGTTGAAGATTGAGTCCTATACTCT
* *
50732 CTGAATGAATAGGGAGCGGACAAGTTCGTTG-A-A-TATT-
66 CTGAATGAATAGGGAGCGGACACGTT-TTTGAAGATTATTC
* * * *
50769 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCATTTTGTTGAAGATTGAGTCCTATACTCT
* *
50834 CTGAATGAATAGGGAGCGGACAAGTTCGTTGAA-A--ATT-
66 CTGAATGAATAGGGAGCGGACACGTT-TTTGAAGATTATTC
* * ** *
50871 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAGTTCCTTGAAGATTGAGTCCTATACTCC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCATTTTGTTGAAGATTGAGTCCTATACTCT
* *
50936 CTGAAAGAATAGGGAGCGGAC-CTGTTTATTGAAGATTTTTC
66 CTGAATGAATAGGGAGCGGACAC-GTTT-TTGAAGATTATTC
* * * * * *
50977 GAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACCCATTTTATTAAAGATTGTTCAAGTCTTAT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CCATTTTGTTGAAGATTG----AGTCCTAT
* * *
51042 ACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTC
61 ACTCTCTGAATGAATAGGGAGCGGACACGTTTT-TGAAGATTATTC
* * * * * * *
51088 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CCATTTTGTTGAAGA---TT-GAGTCCTAT
* * * *
51153 ACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
61 ACTCTCTGAATGAATAGGGAGCGGACACG-TTT-TTGAAGATTATTC
* * * * * *
51200 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACTCGTTTT-ATGAAGATTGTTCGAGTCTTA
1 GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGAC-CATTTTGTTGAAGA---TT-GAGTCCTA
* * ***
51263 TACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCAAGGATTATTC
60 TACTCTCTGAATGAATAGGGAGCGGACACGTTTTTGAA-GATTATTC
*
51310 GAGTCTTATACTC
1 GAGTCCTATACTC
51323 CTTGAAAGAA
Statistics
Matches: 470, Mismatches: 61, Indels: 38
0.83 0.11 0.07
Matches are distributed among these distances:
102 185 0.39
103 3 0.01
105 2 0.00
106 31 0.07
107 13 0.03
109 2 0.00
110 22 0.05
111 161 0.34
112 46 0.10
113 2 0.00
114 2 0.00
115 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (105 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCATTTTGTTGAAGATTGAGTCCTATACTCT
CTGAATGAATAGGGAGCGGACACGTTTTTGAAGATTATTC
Found at i:51295 original size:55 final size:54
Alignment explanation
Indices: 50667--51360 Score: 522
Period size: 51 Copynumber: 12.9 Consensus size: 54
50657 GTTGAAGATT
* * **
50667 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTTGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTT-TTGAAGATTGTTC
* * * *
50718 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTG-A-A-TATT-
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTT-TTTGAAGATTGTTC
* * *
50769 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTT-TTTGAAGATTGTTC
* * * *
50820 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAA-A--ATT-
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTT-TTTGAAGATTGTTC
* * *
50871 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTA-GTTCCTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGAC-ACGTT-TTTGAAGATTGTTC
* * * *
50922 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-CTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAC-GTTT-TTGAAGATTGTTC
* * * * * *
50977 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCATTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAATGAATAGGGAGCGGACAC-GTTT-TTGAAGATTGTTC
* * *
51033 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTC
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTT-TGAAGATTGTTC
* * * *
51088 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACG-TTT-TTGAAGATTGTTC
* * *
51144 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAATGAATAGGGAGCGGACACG-TTT-TTGAAGATTGTTC
* * * * *
51200 GAGT-TCTATACTCCCTGAACGGATAGGGAGCGAACTCGTTTTATGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAATGAATAGGGAGCGGACACGTTTT-TGAAGATTGTTC
* * *** *
51255 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCAAGGATTATTC
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTTTGAA-GATTGTTC
* * * * *
51310 GAGTCTTATACTC-CTTGAAAGAAAAGGGACCAGACCCGTTATTTGAAGATT
1 GAGTCTTATACTCTC-TGAATGAATAGGGAGCGGACACGTT-TTTGAAGATT
51361 TTTCAAGTAT
Statistics
Matches: 566, Mismatches: 50, Indels: 50
0.85 0.08 0.08
Matches are distributed among these distances:
49 1 0.00
50 2 0.00
51 227 0.40
52 3 0.01
53 1 0.00
54 7 0.01
55 175 0.31
56 148 0.26
57 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (54 bp):
GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTTTGAAGATTGTTC
Found at i:58761 original size:15 final size:15
Alignment explanation
Indices: 58741--58773 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
58731 TGGAGTTGTT
58741 GACATTAAAAATACA
1 GACATTAAAAATACA
58756 GACATTAAAAATACA
1 GACATTAAAAATACA
58771 GAC
1 GAC
58774 GGGACGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.15, G:0.09, T:0.18
Consensus pattern (15 bp):
GACATTAAAAATACA
Found at i:60566 original size:24 final size:24
Alignment explanation
Indices: 60539--60591 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
60529 TGACCCGACT
*
60539 CCTGATCAGCACCGTTCTGAGACA
1 CCTGATCAGCACCGTTCTGACACA
* *
60563 CCTGATCCGCACCGTTCTGACACC
1 CCTGATCAGCACCGTTCTGACACA
60587 CCTGA
1 CCTGA
60592 ATATCCACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (24 bp):
CCTGATCAGCACCGTTCTGACACA
Found at i:66912 original size:2 final size:2
Alignment explanation
Indices: 66905--66945 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
66895 AGGAAAACAA
66905 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
66946 GTATATTACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:72700 original size:18 final size:18
Alignment explanation
Indices: 72677--72719 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
72667 AAAGCTAACT
72677 ATTCTTCAGCACATAGAG
1 ATTCTTCAGCACATAGAG
72695 ATTCTTCAGCACATAGAG
1 ATTCTTCAGCACATAGAG
72713 ATTCTTC
1 ATTCTTC
72720 TTAAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (18 bp):
ATTCTTCAGCACATAGAG
Found at i:73468 original size:24 final size:24
Alignment explanation
Indices: 73435--73484 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
73425 CTAATATCGT
73435 TTGGTCCGAACAAGAAGTTACGAC
1 TTGGTCCGAACAAGAAGTTACGAC
*
73459 TTGGTTCGAACAAGAAGTTACGAC
1 TTGGTCCGAACAAGAAGTTACGAC
73483 TT
1 TT
73485 TGAATAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (24 bp):
TTGGTCCGAACAAGAAGTTACGAC
Found at i:75795 original size:93 final size:93
Alignment explanation
Indices: 75636--76074 Score: 583
Period size: 93 Copynumber: 4.7 Consensus size: 93
75626 AGAAAACATT
* * * * * * **
75636 GTTGATTCTGATACAAGCCACAAGTTTGATGGTGATTCGGGAAGGGGTCCGGAACCGGTGGGAGA
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATCCCGAAAAAGGTCCGGAACCGGTGGGAGA
*
75701 AAACCAAGCTGATAAGAAACATTTGTCC
66 AAACAAAGCTGATAAGAAACATTTGTCC
* *
75729 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATCCCGAAAAAGGTCTGGAACCGATGGGAGA
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATCCCGAAAAAGGTCCGGAACCGGTGGGAGA
* *
75794 AAACCAAGCTGATAAGAAATATTTGTCC
66 AAACAAAGCTGATAAGAAACATTTGTCC
* * * *
75822 GTTGATTCTGAGTCAAGCTACAAGCTTGATGGTAATCCCGAAAAGGGTCCGGAACCGGTGGCAGA
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATCCCGAAAAAGGTCCGGAACCGGTGGGAGA
*
75887 AAACAAAGCTGATAATAAACATTTGTCC
66 AAACAAAGCTGATAAGAAACATTTGTCC
** * *
75915 GTTGATTCTGATTCAAGCTACAAGCTTGATATTGATTCCGAAAATGGTCCGGAACCGGTGGGAGA
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATCCCGAAAAAGGTCCGGAACCGGTGGGAGA
* * *
75980 AAACAAAGATGAAAAGAAATATTTGTCC
66 AAACAAAGCTGATAAGAAACATTTGTCC
* * * * * *
76008 GTTGCTTCTGATTTAAGCTACAAGCATGATGGTGATCCTG-AAAAGAGTCCGGAACAGATGGGAG
1 GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATCCCGAAAAAG-GTCCGGAACCGGTGGGAG
76072 AAA
65 AAA
76075 TTGCTTCTGG
Statistics
Matches: 304, Mismatches: 41, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
92 4 0.01
93 300 0.99
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (93 bp):
GTTGATTCTGATTCAAGCTACAAGCTTGATGGTGATCCCGAAAAAGGTCCGGAACCGGTGGGAGA
AAACAAAGCTGATAAGAAACATTTGTCC
Found at i:76117 original size:66 final size:66
Alignment explanation
Indices: 76009--76140 Score: 158
Period size: 66 Copynumber: 2.0 Consensus size: 66
75999 TATTTGTCCG
* * * *
76009 TTGCTTCTGATTTAAGCTACAAGCATGATGGTGATCCTGAAAAGAGTCCGGAACAGATGGGAGAA
1 TTGCTTCTGATTCAAGCTACAAGCATAATAGTGATCCTGAAAAGAGTCAGGAACAGATGGGAGAA
76074 A
66 A
* * * * * *
76075 TTGCTTCTGGTTCAAGCTACAAGCTTAATATTGATTCC-GAAAAGGGTCAGGAACCGGTGGGAGA
1 TTGCTTCTGATTCAAGCTACAAGCATAATAGTGA-TCCTGAAAAGAGTCAGGAACAGATGGGAGA
76139 AA
65 AA
76141 ACAAAGCTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 52 0.95
67 3 0.05
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (66 bp):
TTGCTTCTGATTCAAGCTACAAGCATAATAGTGATCCTGAAAAGAGTCAGGAACAGATGGGAGAA
A
Found at i:78280 original size:15 final size:15
Alignment explanation
Indices: 78260--78289 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
78250 TCTATTTTCC
78260 CGCACCTGCCCTTTA
1 CGCACCTGCCCTTTA
78275 CGCACCTGCCCTTTA
1 CGCACCTGCCCTTTA
78290 GGTGAACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.13, T:0.27
Consensus pattern (15 bp):
CGCACCTGCCCTTTA
Found at i:82498 original size:96 final size:96
Alignment explanation
Indices: 82381--82573 Score: 298
Period size: 96 Copynumber: 2.0 Consensus size: 96
82371 GTATAAACTA
* *
82381 TAAAATTAATGAATAAACTTTCTTCTTACTTTTATTCCGGTCATTGTATTTAAAAAAAT-TTCAA
1 TAAAATTAATGAATAAACTTTCTTCTTACTCTTATTCCGGTCATTATATTT-AAAAAATGTTCAA
82445 TTTAATAACTAAACTTTATACATTAAACTTTT
65 TTTAATAACTAAACTTTATACATTAAACTTTT
* * * *
82477 TAAAATTAATGACTGAACTTTCTTCTTACTCTTATTTCGGTCATTATATTTTAAAAATGTTCAAT
1 TAAAATTAATGAATAAACTTTCTTCTTACTCTTATTCCGGTCATTATATTTAAAAAATGTTCAAT
* *
82542 TTAATAACTAAAGTTTATACATTAGACTTTT
66 TTAATAACTAAACTTTATACATTAAACTTTT
82573 T
1 T
82574 GGGTCACTTC
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 6 0.07
96 82 0.93
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (96 bp):
TAAAATTAATGAATAAACTTTCTTCTTACTCTTATTCCGGTCATTATATTTAAAAAATGTTCAAT
TTAATAACTAAACTTTATACATTAAACTTTT
Found at i:83692 original size:15 final size:15
Alignment explanation
Indices: 83674--83712 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
83664 TAAATTAAAT
*
83674 AAAAATAAAGAAACG
1 AAAAATAAAGAAAAG
83689 AAAAGA-AAAGAAAAG
1 AAAA-ATAAAGAAAAG
83704 AAAAATAAA
1 AAAAATAAA
83713 TAAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (15 bp):
AAAAATAAAGAAAAG
Found at i:83715 original size:4 final size:4
Alignment explanation
Indices: 83706--83760 Score: 85
Period size: 4 Copynumber: 13.8 Consensus size: 4
83696 AAGAAAAGAA
*
83706 AAAT AAAT AAAT AAAT AAA- AAAT AAAAT ACAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
83754 AAAT AAA
1 AAAT AAA
83761 GTCCATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
3 3 0.06
4 40 0.85
5 4 0.09
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:83726 original size:24 final size:24
Alignment explanation
Indices: 83705--83788 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
83695 AAAGAAAAGA
83705 AAAATAAATAAATAAATAAAAAAT
1 AAAATAAATAAATAAATAAAAAAT
*
83729 AAAATACATAAATAAATAAATAAAT
1 AAAATAAATAAATAAATAAA-AAAT
** *
83754 -AAATAAAGTCCATAAA-AGAAAAT
1 AAAATAAA-TAAATAAATAAAAAAT
*
83777 GAAATAAATAAA
1 AAAATAAATAAA
83789 ATACTAGAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.12
24 34 0.68
25 10 0.20
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAATAAATAAATAAATAAAAAAT
Found at i:83740 original size:28 final size:29
Alignment explanation
Indices: 83708--83792 Score: 113
Period size: 28 Copynumber: 3.0 Consensus size: 29
83698 GAAAAGAAAA
83708 ATAAATAAATAAATAAA-AAATAAAATAC
1 ATAAATAAATAAATAAATAAATAAAATAC
* *
83736 ATAAATAAATAAATAAATAAATAAAGTCC
1 ATAAATAAATAAATAAATAAATAAAATAC
*
83765 ATAAA-AGA-AAATGAAATAAATAAAATAC
1 ATAAATAAATAAAT-AAATAAATAAAATAC
83793 TAGAAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 4 0.08
28 32 0.64
29 14 0.28
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.21
Consensus pattern (29 bp):
ATAAATAAATAAATAAATAAATAAAATAC
Found at i:83782 original size:36 final size:30
Alignment explanation
Indices: 83699--83788 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 30
83689 AAAAGAAAAG
83699 AAAAGAAAAATAAATAAATAAATAAAAAATA
1 AAAAG-AAAATAAATAAATAAATAAAAAATA
*
83730 AAATACATAAATAAATAAATAAATAAATAAAGTCCA
1 AAA-AGA-AAATAAATAAATAAATAAA-AAA-T--A
83766 TAAAAGAAAATGAAATAAATAAA
1 -AAAAGAAAAT-AAATAAATAAA
83789 ATACTAGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
31 4 0.08
32 20 0.41
33 3 0.06
34 1 0.02
35 4 0.08
36 14 0.29
37 3 0.06
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.19
Consensus pattern (30 bp):
AAAAGAAAATAAATAAATAAATAAAAAATA
Found at i:83884 original size:19 final size:20
Alignment explanation
Indices: 83860--83931 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 20
83850 GAGAAAAAAT
83860 ATAAAATAAAAT-TAAATAA
1 ATAAAATAAAATATAAATAA
*
83879 ATAAAAT-AGATATAAGATAA
1 ATAAAATAAAATATAA-ATAA
* * *
83899 ATGAAATGATAATATGTAAATAT
1 AT-AAA--ATAAAATATAAATAA
83922 ATAAAATAAA
1 ATAAAATAAA
83932 TAAAAACATA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.07
19 10 0.24
20 10 0.24
21 3 0.07
22 3 0.07
23 7 0.17
24 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
ATAAAATAAAATATAAATAA
Found at i:85238 original size:33 final size:34
Alignment explanation
Indices: 85166--85250 Score: 136
Period size: 36 Copynumber: 2.5 Consensus size: 34
85156 CGAGGGTTTG
*
85166 GTGTTCCAAGAGAAACAATTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGG--TTTTTTT
85202 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
85235 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
85251 TGTATTCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 22 0.46
36 26 0.54
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
Found at i:85317 original size:36 final size:36
Alignment explanation
Indices: 85268--85605 Score: 142
Period size: 36 Copynumber: 10.0 Consensus size: 36
85258 AAAGATTGAA
*
85268 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
85304 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
85338 CTTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
85374 GTTT-AACGTA-AAACATAT-TC-A-A-AG----ATTTT
1 GTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATTT
* *
85403 GTTTCAA-AGGAAACTGTTTTC-A-A-AG-----TTTAT
1 GTTTCAAGA-GAAACTG-TCTCAAGAGAGACAAAATT-T
* *
85433 GCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * *
85469 ATTTCAAGGGAAACTATCTCAAGAGTGACAAAATTC
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * *
85505 ATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTTAT
1 GTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT-T
*
85534 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTT
* *
85571 GTTTCAAGGGAACCTGTCTCAAGAGAGACAAAATT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
85606 CATTTTAAGG
Statistics
Matches: 229, Mismatches: 41, Indels: 64
0.69 0.12 0.19
Matches are distributed among these distances:
27 1 0.00
28 3 0.01
29 32 0.14
30 26 0.11
31 1 0.00
32 3 0.01
33 4 0.02
34 28 0.12
35 5 0.02
36 88 0.38
37 36 0.16
38 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:85350 original size:34 final size:35
Alignment explanation
Indices: 85277--85366 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 35
85267 AGTTTCAAGG
** * *
85277 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
85313 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
*
85347 GAAACTGTCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
85367 GAGATTTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 25 0.51
36 24 0.49
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:85427 original size:30 final size:30
Alignment explanation
Indices: 85391--85449 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
85381 GTAAAACATA
*
85391 TTCAAAGATTT-TGTTTCAA-AGGAAACTGTT
1 TTCAAAG-TTTATGCTTCAAGA-GAAACTGTT
85421 TTCAAAGTTTATGCTTCAAGAGAAACTGT
1 TTCAAAGTTTATGCTTCAAGAGAAACTGT
85450 CTCAAGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 22 0.85
31 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (30 bp):
TTCAAAGTTTATGCTTCAAGAGAAACTGTT
Found at i:85588 original size:37 final size:37
Alignment explanation
Indices: 85533--85605 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
85523 TCAATGTTTA
*
85533 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
85570 TGTTTCAAGGGAACCTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
85606 CATTTTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:85605 original size:102 final size:101
Alignment explanation
Indices: 85404--85786 Score: 453
Period size: 102 Copynumber: 3.8 Consensus size: 101
85394 AAAGATTTTG
* * * *
85404 TTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAA-TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
85469 ATTTCAAGGGAAACTATCTCAAGAGTGACAAAATTCA
65 ATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA
* * *
85506 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTT
* *
85571 GTTTCAAGGGAACCTGTCTCAAGAGAGACAAAATTCA
65 ATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA
* * * * *
85608 TTTTAAGGGAAATGTTTTTAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTA
1 TTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTA
* ** * * * **
85673 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTG
66 -TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA
** * * * *
85710 TTTCAAGGGAAACATATTCAAAGATTT-TATTTCAAGAGAAACTATCTTAAGAGAGACAAAATTC
1 TTTCAAGGGAAATGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
85774 ATTTCAAGGGAAA
65 ATTTCAAGGGAAA
85787 TGTTTTCAAT
Statistics
Matches: 241, Mismatches: 37, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
101 58 0.24
102 180 0.75
103 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTA
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA
Found at i:85764 original size:167 final size:166
Alignment explanation
Indices: 85562--85883 Score: 527
Period size: 167 Copynumber: 1.9 Consensus size: 166
85552 TCAAGGGAGA
* * * * * *
85562 CAAAATTTTGTTTCAAGGGAACCTGTCTCAAGAGAGACAAAATTCATTTTAAGGGAAATGTTTTT
1 CAAAATTTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
*
85627 AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTCT
66 AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACGTAGTTCCAAAAGAAAATGTCT
*
85692 CAAGGGAGACGAAATTTGTTTCAAGGGAAACATATT
131 CAAGGGAGACGAAATTTATTTCAAGGGAAACATATT
*
85728 CAAAGATTTTATTTCAAGAGAAACTATCTTAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * *
85793 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACGAAACGTAGTTCTAAAAGAAAATGTC
65 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACGTAGTTCCAAAAGAAAATGTC
85858 TCAAGGGAGACGAAATTTATTTCAAG
130 TCAAGGGAGACGAAATTTATTTCAAG
85884 AGAGACAAAA
Statistics
Matches: 143, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
166 4 0.03
167 139 0.97
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (166 bp):
CAAAATTTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACGTAGTTCCAAAAGAAAATGTCT
CAAGGGAGACGAAATTTATTTCAAGGGAAACATATT
Found at i:85785 original size:65 final size:65
Alignment explanation
Indices: 85689--85831 Score: 180
Period size: 65 Copynumber: 2.2 Consensus size: 65
85679 AAAGAAAATG
* * **
85689 TCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACATATTCAAAGATTT-TATTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAG-TTTATATTTCAAGAGAAACT
85753 A
65 A
* ** * * *
85754 TCTTAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATATTTCAAGAGAAACTA
85819 TCTCAAGAGAGAC
1 TCTCAAGAGAGAC
85832 GAAACGTAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
64 3 0.05
65 63 0.95
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATATTTCAAGAGAAACTA
Found at i:85886 original size:19 final size:21
Alignment explanation
Indices: 85858--85905 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
85848 AGAAAATGTC
* *
85858 TCAAGGGAGACGAAATTTATT
1 TCAAGAGAGACAAAATTTATT
*
85879 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTATT
85900 TCAAGA
1 TCAAGA
85906 AAAACAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTATT
Found at i:85912 original size:21 final size:21
Alignment explanation
Indices: 85870--85912 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
85860 AAGGGAGACG
* *
85870 AAATTTATTTCAAGAGAGACA
1 AAATTTATTTCAAGAAAAACA
*
85891 AAATTTGTTTCAAGAAAAACA
1 AAATTTATTTCAAGAAAAACA
85912 A
1 A
85913 TCTTGACTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (21 bp):
AAATTTATTTCAAGAAAAACA
Found at i:86139 original size:72 final size:72
Alignment explanation
Indices: 85879--86131 Score: 337
Period size: 72 Copynumber: 3.5 Consensus size: 72
85869 GAAATTTATT
* * * * *
85879 TCAAGAGAGACAAAATTTGTTTCAAGAAAAACAATCTTGACTGAAATAAATCTTTTTTCGAGTGA
1 TCAAGAGAGACAAAGTATGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGT-A
85944 AAACAGTC
65 AAACAGTC
* *
85952 CCAAGAGAGACAAA-TATGGTTTTAAGAAAAACAATCTTGAGTGGAATAAATCTTCTTTCGAGTA
1 TCAAGAGAGACAAAGTAT-GTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGTA
*
86016 AAATAGTC
65 AAACAGTC
* * * * *
86024 TCAAGTGAGACAAAGTTTGTTTTAAGCAAAGCAAACTTGAGTGAAATAAATCTTCTTTCGAGTAA
1 TCAAGAGAGACAAAGTATGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGTAA
*
86089 AACAATC
66 AACAGTC
* *
86096 TCAAGTGAGACAAAGTATGCTTTAAGAAAAACAATC
1 TCAAGAGAGACAAAGTATGTTTTAAGAAAAACAATC
86132 ACAAGTGAGA
Statistics
Matches: 157, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
72 101 0.64
73 56 0.36
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (72 bp):
TCAAGAGAGACAAAGTATGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGTAA
AACAGTC
Found at i:86182 original size:145 final size:145
Alignment explanation
Indices: 85879--86138 Score: 344
Period size: 145 Copynumber: 1.8 Consensus size: 145
85869 GAAATTTATT
* *
85879 TCAAGAGAGACAAAATTTGTTTCAAGAAAAACAATCTTGACTGAAATAAATCTTTTTTCGAGTGA
1 TCAAGAGAGACAAAATTTGTTTCAAGAAAAACAAACTTGACTGAAATAAATCTTCTTTCGAGTGA
* * ***
85944 AAACAGTCCCAAGAGAGACAAATATGGTTTTAAGAAAAACAATCTTGAGTGGAATAAATCTTCTT
66 AAACAATCCCAAGAGAGACAAATATGGCTTTAAGAAAAACAATCACAAGTGGAATAAATCTTCTT
**
86009 TCGAGTAAAATAGTC
131 TAAAGTAAAATAGTC
* * * * * *
86024 TCAAGTGAGACAAAGTTTGTTTTAAGCAAAGCAAACTTGAGTGAAATAAATCTTCTTTCGAGT-A
1 TCAAGAGAGACAAAATTTGTTTCAAGAAAAACAAACTTGACTGAAATAAATCTTCTTTCGAGTGA
* *
86088 AAACAATCTCAAGTGAGACAAAGTAT-GCTTTAAGAAAAACAATCACAAGTG
66 AAACAATCCCAAGAGAGACAAA-TATGGCTTTAAGAAAAACAATCACAAGTG
86139 AGATAATCAT
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
144 41 0.41
145 58 0.59
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (145 bp):
TCAAGAGAGACAAAATTTGTTTCAAGAAAAACAAACTTGACTGAAATAAATCTTCTTTCGAGTGA
AAACAATCCCAAGAGAGACAAATATGGCTTTAAGAAAAACAATCACAAGTGGAATAAATCTTCTT
TAAAGTAAAATAGTC
Done.