Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 95 of 276
Found at i:29923700 original size:29 final size:29
Alignment explanation
Indices: 29923658--29923714 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
29923648 TAAACACTCC
29923658 ACTAAACCGACTACTAACTCCATCACCCT
1 ACTAAACCGACTACTAACTCCATCACCCT
*
29923687 ACTAAACC-ATCTACTACCTCCATCACCC
1 ACTAAACCGA-CTACTAACTCCATCACCC
29923715 CCACACCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (29 bp):
ACTAAACCGACTACTAACTCCATCACCCT
Found at i:29923722 original size:37 final size:37
Alignment explanation
Indices: 29923681--29923755 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
29923671 CTAACTCCAT
*
29923681 CACCCTACTAAACCATCTACTACCTCCATCACCCCCA
1 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
29923718 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
1 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
29923755 C
1 C
29923756 TAACTCTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.17
Consensus pattern (37 bp):
CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
Found at i:29923757 original size:18 final size:18
Alignment explanation
Indices: 29923699--29923769 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
29923689 TAAACCATCT
29923699 ACTACCTCCATCACCCCC
1 ACTACCTCCATCACCCCC
* * *
29923717 AC-ACC-CTACTAAACCATCC
1 ACTACCTCCA-T-CACC-CCC
29923736 ACTACCTCCATCACCCCC
1 ACTACCTCCATCACCCCC
* *
29923754 ACTAACTCTATCACCC
1 ACTACCTCCATCACCC
29923770 TACTTGTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
16 2 0.05
17 4 0.10
18 21 0.52
19 7 0.17
20 4 0.10
21 2 0.05
ACGTcount: A:0.28, C:0.54, G:0.00, T:0.18
Consensus pattern (18 bp):
ACTACCTCCATCACCCCC
Found at i:29924180 original size:63 final size:63
Alignment explanation
Indices: 29924040--29924182 Score: 168
Period size: 63 Copynumber: 2.3 Consensus size: 63
29924030 TTTAACCCCT
* * *
29924040 TTTTTATTTTTGTTATTTTACTGTTAAATTAATTAATTTGAGCTTTATTCTCATTATTTTTATA
1 TTTTTATTTTTATTATTTTACTATTAAATTAATTAATTTGAGC-TTATTCTCATTATTATTATA
* *
29924104 TTTGTT-TTTTTATTATTTT-CTATTAATTTAATTAATTTGAG-TTATGTTTCA-TATTATTATA
1 TTT-TTATTTTTATTATTTTACTATTAAATTAATTAATTTGAGCTTAT-TCTCATTATTATTATA
29924165 TTATTTATTTATTATTAT
1 TT-TTTATTT-TTATTAT
29924183 ATATTTATTA
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
61 17 0.25
62 8 0.12
63 27 0.39
64 15 0.22
65 2 0.03
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (63 bp):
TTTTTATTTTTATTATTTTACTATTAAATTAATTAATTTGAGCTTATTCTCATTATTATTATA
Found at i:29924182 original size:14 final size:14
Alignment explanation
Indices: 29924163--29924201 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
29924153 CATATTATTA
*
29924163 TATTATTTATTTAT
1 TATTATATATTTAT
29924177 TATTATATATTTAT
1 TATTATATATTTAT
29924191 TATGTATATAT
1 TAT-TATATAT
29924202 ATATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
TATTATATATTTAT
Found at i:29924187 original size:21 final size:19
Alignment explanation
Indices: 29924154--29924212 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 19
29924144 GTTATGTTTC
*
29924154 ATATTATTATATTATTTATTT
1 ATATTA-TATATT-TTTATGT
29924175 ATTATTATATATTTATTATGT
1 A-TATTATATATTT-TTATGT
29924196 ATATATATATATTTTTA
1 ATAT-TATATATTTTTA
29924213 AGCGAAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATATTATATATTTTTATGT
Found at i:29926786 original size:21 final size:23
Alignment explanation
Indices: 29926749--29926794 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
29926739 TTTATTAATG
29926749 TTTTATAATATTATTTTTAAAAA
1 TTTTATAATATTATTTTTAAAAA
*
29926772 TTTTA-AATA-TATTTTTTAAAA
1 TTTTATAATATTATTTTTAAAAA
29926793 TT
1 TT
29926795 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 4 0.18
23 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTATAATATTATTTTTAAAAA
Found at i:29926796 original size:34 final size:34
Alignment explanation
Indices: 29926749--29926864 Score: 122
Period size: 34 Copynumber: 3.6 Consensus size: 34
29926739 TTTATTAATG
* *
29926749 TTTTATAATATTATTTTTAAAAATTTTAAATATA
1 TTTTTTAAAATTATTTTTAAAAATTTTAAATATA
*
29926783 TTTTTTAAAATTATTTTTTAAAA-TTTAAATATTA
1 TTTTTTAAAATTATTTTTAAAAATTTTAAATA-TA
29926817 TTTTTT--AA--A-TTTT--AAATTTTAAATATA
1 TTTTTTAAAATTATTTTTAAAAATTTTAAATATA
* *
29926844 GTTTTTGAAATTATTTTTAAA
1 TTTTTTAAAATTATTTTTAAA
29926865 TATATTCAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
27 10 0.14
28 8 0.12
29 6 0.09
30 1 0.01
31 1 0.01
32 6 0.09
33 8 0.12
34 29 0.42
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
TTTTTTAAAATTATTTTTAAAAATTTTAAATATA
Found at i:29926818 original size:21 final size:21
Alignment explanation
Indices: 29926786--29926833 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
29926776 AAATATATTT
29926786 TTTAAA-ATTATTTTTTAAAA
1 TTTAAATATTATTTTTTAAAA
*
29926806 TTTAAATATTATTTTTTAAAT
1 TTTAAATATTATTTTTTAAAA
29926827 TTTAAAT
1 TTTAAAT
29926834 TTTAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAAATATTATTTTTTAAAA
Found at i:29926825 original size:14 final size:14
Alignment explanation
Indices: 29926772--29926867 Score: 63
Period size: 13 Copynumber: 7.7 Consensus size: 14
29926762 TTTTTAAAAA
29926772 TTTTAAATA-TATT
1 TTTTAAATATTATT
29926785 TTTTAAA-ATTATT
1 TTTTAAATATTATT
29926798 TTTT-AA-A--A--
1 TTTTAAATATTATT
29926806 -TTTAAATATTATT
1 TTTTAAATATTATT
* **
29926819 TTTTAAATTTTAAA
1 TTTTAAATATTATT
*
29926833 TTTTAAATA-TAGT
1 TTTTAAATATTATT
*
29926846 TTTTGAA-ATTA-T
1 TTTTAAATATTATT
29926858 TTTTAAATAT
1 TTTTAAATAT
29926868 ATTCAAACTT
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
7 3 0.05
8 2 0.03
9 1 0.02
10 1 0.02
11 1 0.02
12 12 0.18
13 27 0.42
14 18 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TTTTAAATATTATT
Found at i:29926829 original size:7 final size:7
Alignment explanation
Indices: 29926798--29926840 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
29926788 TAAAATTATT
29926798 TTTTAAA
1 TTTTAAA
*
29926805 ATTTAAA
1 TTTTAAA
* **
29926812 TATTATT
1 TTTTAAA
29926819 TTTTAAA
1 TTTTAAA
29926826 TTTTAAA
1 TTTTAAA
29926833 TTTTAAA
1 TTTTAAA
29926840 T
1 T
29926841 ATAGTTTTTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTTAAA
Found at i:29926830 original size:28 final size:28
Alignment explanation
Indices: 29926798--29926855 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
29926788 TAAAATTATT
*
29926798 TTTTAAAATTTAAATATTA-TTTTTTAAA
1 TTTTAAAATTTAAATA-TAGTTTTTGAAA
*
29926826 TTTTAAATTTTAAATATAGTTTTTGAAA
1 TTTTAAAATTTAAATATAGTTTTTGAAA
29926854 TT
1 TT
29926856 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTTAAAATTTAAATATAGTTTTTGAAA
Found at i:29926860 original size:12 final size:12
Alignment explanation
Indices: 29926749--29926870 Score: 64
Period size: 14 Copynumber: 10.1 Consensus size: 12
29926739 TTTATTAATG
29926749 TTTTATAATATTAT
1 TTTTA-AATA-TAT
29926763 TTTTAAA-A-A-
1 TTTTAAATATAT
29926772 TTTTAAATATATT
1 TTTTAAATATA-T
29926785 TTTTAAA-ATTAT
1 TTTTAAATA-TAT
*
29926797 TTTTTAA-A-A-
1 TTTTAAATATAT
29926806 -TTTAAATATTATT
1 TTTTAAATA-TA-T
* *
29926819 TTTTAAATTTTAAA
1 TTTTAAA-TAT-AT
29926833 TTTTAAATATAGT
1 TTTTAAATATA-T
29926846 TTTTGAAAT-TAT
1 TTTT-AAATATAT
29926858 TTTTAAATATAT
1 TTTTAAATATAT
29926870 T
1 T
29926871 CAAACTTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 34
0.68 0.05 0.27
Matches are distributed among these distances:
8 5 0.06
9 8 0.09
10 3 0.03
11 6 0.07
12 20 0.23
13 19 0.22
14 23 0.27
15 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTTTAAATATAT
Found at i:29927069 original size:36 final size:36
Alignment explanation
Indices: 29927022--29927092 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
29927012 TATTTTATTT
29927022 TGGCTCCACCTCTTGATTCTCTAGCATATATAGAAA
1 TGGCTCCACCTCTTGATTCTCTAGCATATATAGAAA
*
29927058 TGGCTCCACCTCTTGATTCTCTAGTATATATAGAA
1 TGGCTCCACCTCTTGATTCTCTAGCATATATAGAA
29927093 TGGTGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (36 bp):
TGGCTCCACCTCTTGATTCTCTAGCATATATAGAAA
Found at i:29929822 original size:18 final size:19
Alignment explanation
Indices: 29929790--29929834 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
29929780 AAAGTCATAG
29929790 TTTTTTTAACAAATAAAT-
1 TTTTTTTAACAAATAAATC
*
29929808 TATTTTTTAA-TAATAAATC
1 T-TTTTTTAACAAATAAATC
29929827 TTTTTTTA
1 TTTTTTTA
29929835 TATTTTTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTTTAACAAATAAATC
Found at i:29930168 original size:23 final size:21
Alignment explanation
Indices: 29930138--29930187 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
29930128 AATAAAGGAC
*
29930138 AAAAAAATAAAATATTATTTTTA
1 AAAAAAATAAAATA-TA-ATTTA
*
29930161 AAAAAAATTAAATATAATTTA
1 AAAAAAATAAAATATAATTTA
29930182 AAAAAA
1 AAAAAA
29930188 TGTTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 13 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAAATAAAATATAATTTA
Found at i:29930234 original size:14 final size:15
Alignment explanation
Indices: 29930210--29930261 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
29930200 TTTAAAAATA
29930210 ATTTAAAAAATTTAT
1 ATTTAAAAAATTTAT
*
29930225 ATTT-AAAAATTTGT
1 ATTTAAAAAATTTAT
*
29930239 ATTTAAAAAATTTAA
1 ATTTAAAAAATTTAT
29930254 ATTTAAAA
1 ATTTAAAA
29930262 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATTTAAAAAATTTAT
Found at i:29930270 original size:22 final size:23
Alignment explanation
Indices: 29930245--29930314 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
29930235 TTGTATTTAA
* *
29930245 AAAATTTAA-ATTTAAAATTTTT
1 AAAATATAATATTTAAAAATTTT
*
29930267 AAAA-ATAATTTTTAAAAATTTT
1 AAAATATAATATTTAAAAATTTT
* *
29930289 AAAATATACAT-TTTAAATATTAT
1 AAAATATA-ATATTTAAAAATTTT
29930312 AAA
1 AAA
29930315 CCAAATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
22 19 0.47
23 16 0.40
24 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATATAATATTTAAAAATTTT
Found at i:29930276 original size:13 final size:13
Alignment explanation
Indices: 29930260--29930285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29930250 TTAAATTTAA
29930260 AATTTTTAAAAAT
1 AATTTTTAAAAAT
29930273 AATTTTTAAAAAT
1 AATTTTTAAAAAT
29930286 TTTAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:29930284 original size:23 final size:24
Alignment explanation
Indices: 29930255--29930302 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
29930245 AAAATTTAAA
*
29930255 TTTAAAATTTTTAAAA-ATA-ATT
1 TTTAAAAATTTTAAAATATACATT
29930277 TTTAAAAATTTTAAAATATACATT
1 TTTAAAAATTTTAAAATATACATT
29930301 TT
1 TT
29930303 AAATATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.65
23 3 0.13
24 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAAAAATTTTAAAATATACATT
Found at i:29930404 original size:20 final size:20
Alignment explanation
Indices: 29930381--29930480 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 20
29930371 ATAATATTAA
*
29930381 AAAATTATGTTTAAAAATTT
1 AAAATTATATTTAAAAATTT
*
29930401 AAAAATGATATTT--AAATTT
1 -AAAATTATATTTAAAAATTT
* *
29930420 TAAATATATATTTAAAATTTT
1 AAAAT-TATATTTAAAAATTT
*
29930441 AAAAAATAATATTATAAAAAATTT
1 --AAAATTATATT-T-AAAAATTT
*
29930465 AAAATATACATTTAAA
1 AAAAT-TATATTTAAA
29930481 TTATTATAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
18 4 0.07
19 12 0.20
21 18 0.30
22 11 0.18
23 9 0.15
24 7 0.11
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAATTATATTTAAAAATTT
Found at i:29930419 original size:19 final size:20
Alignment explanation
Indices: 29930380--29930480 Score: 87
Period size: 20 Copynumber: 4.8 Consensus size: 20
29930370 TATAATATTA
* *
29930380 AAAAATTATGTTTAAAAATTT
1 AAAAA-TATATTTAAAATTTT
29930401 AAAAATGATATTT-AAATTTT
1 AAAAAT-ATATTTAAAATTTT
*
29930421 AAATATATATTTAAAATTTT
1 AAAAATATATTTAAAATTTT
*
29930441 AAAAAATAATATTATAAAAAATTT
1 -AAAAAT-ATATT-T-AAAATTTT
*
29930465 AAAATATACATTTAAA
1 AAAA-ATATATTTAAA
29930481 TTATTATAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
19 6 0.09
20 19 0.28
21 18 0.27
22 6 0.09
23 9 0.13
24 9 0.13
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAATATATTTAAAATTTT
Found at i:29930502 original size:44 final size:45
Alignment explanation
Indices: 29930414--29930507 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 45
29930404 AATGATATTT
* * *
29930414 AAATTTTAAATATATATTTAAAATTTTAAAAAATAATATTATAAA-
1 AAATTTAAAATATACATTTAAAATTTTAAAAAACAATA-TATAAAC
*
29930459 AAATTTAAAATATACATTT-AAATTATTATAAAACCAATA-ATAAAC
1 AAATTTAAAATATACATTTAAAATT-TTA-AAAAACAATATATAAAC
29930504 AAAT
1 AAAT
29930508 AAAAAAGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
44 10 0.24
45 24 0.57
46 8 0.19
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (45 bp):
AAATTTAAAATATACATTTAAAATTTTAAAAAACAATATATAAAC
Found at i:29930518 original size:12 final size:11
Alignment explanation
Indices: 29930488--29930536 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
29930478 AAATTATTAT
*
29930488 AAAACCAATAA
1 AAAACAAATAA
*
29930499 TAAACAAATAA
1 AAAACAAATAA
29930510 AAAAGCAAATAA
1 AAAA-CAAATAA
**
29930522 AGGACAAATAA
1 AAAACAAATAA
29930533 AAAA
1 AAAA
29930537 ACTAAAATAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.73, C:0.10, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAACAAATAA
Found at i:29930543 original size:32 final size:34
Alignment explanation
Indices: 29930497--29930573 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 34
29930487 TAAAACCAAT
*
29930497 AATAAACAAATAAAAAAGCAAATAAAG-G-AC-A
1 AATAAAAAAATAAAAAAGCAAATAAAGAGAACAA
* *
29930528 AATAAAAAAACTAAAATAGTAAATAAAGAAGAACAA
1 AATAAAAAAA-TAAAAAAGCAAATAAAG-AGAACAA
29930564 AATAAAAAAA
1 AATAAAAAAA
29930574 AACGAAAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 9 0.24
32 15 0.39
34 1 0.03
35 2 0.05
36 11 0.29
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (34 bp):
AATAAAAAAATAAAAAAGCAAATAAAGAGAACAA
Found at i:29930551 original size:21 final size:22
Alignment explanation
Indices: 29930527--29930567 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29930517 AATAAAGGAC
29930527 AAATAAA-AA-AACTAAAATAGT
1 AAATAAAGAAGAAC-AAAATAGT
29930548 AAATAAAGAAGAACAAAATA
1 AAATAAAGAAGAACAAAATA
29930568 AAAAAAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 8 0.44
23 3 0.17
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATAAAGAAGAACAAAATAGT
Found at i:29932457 original size:12 final size:12
Alignment explanation
Indices: 29932440--29932464 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29932430 TTGTAAATTA
29932440 AACAAATAAAAT
1 AACAAATAAAAT
29932452 AACAAATAAAAT
1 AACAAATAAAAT
29932464 A
1 A
29932465 GTTTCTAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AACAAATAAAAT
Found at i:29933476 original size:101 final size:101
Alignment explanation
Indices: 29933299--29933660 Score: 433
Period size: 101 Copynumber: 3.6 Consensus size: 101
29933289 AATTGATGGA
*
29933299 TAAGACCTTGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGACATTTTAG
1 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGACATTTTAG
*
29933364 TGAAAAGACCATAATTGGGTTATGGCACCGTGAGCG
66 TGAAAAGACCATAACTGGGTTATGGCACCGTGAGCG
* *
29933400 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTAGGCTATGGCATTTTAG
1 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGACATTTTAG
*
29933465 TGAAAATACCATAACTGGGTTATGGCACCGTGAGCG
66 TGAAAAGACCATAACTGGGTTATGGCACCGTGAGCG
* * * * *
29933501 TAAGACCATGATTGGACCATGGTTGTATATATATAAGTGTGTAAGACCATAACTGGGCTATGACA
1 TAAGACCATGGTTGGACCAT-G--GCA-ATATTTAA--ATGTAAGACCATAGCTGGGCTATGACA
* * * * *** *
29933566 TCTGA-AGATAAGACCATAACTGGGTTATGGCACTACGAGTG
60 TTTTAGTGAAAAGACCATAACTGGGTTATGGCACCGTGAGCG
* * ** * *
29933607 TAAGACCATGGTAGGGCCATGGCAATA--TATGTGTAAGACCATAGTTGGACTATG
1 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATG
29933661 GCATCAAGAA
Statistics
Matches: 226, Mismatches: 29, Indels: 15
0.84 0.11 0.06
Matches are distributed among these distances:
98 21 0.09
100 2 0.01
101 115 0.51
102 4 0.02
103 2 0.01
104 2 0.01
105 8 0.04
106 46 0.20
107 26 0.12
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGACATTTTAG
TGAAAAGACCATAACTGGGTTATGGCACCGTGAGCG
Found at i:29940231 original size:12 final size:12
Alignment explanation
Indices: 29940214--29940238 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29940204 TTGTAAATTA
29940214 AACAAATAAAAT
1 AACAAATAAAAT
29940226 AACAAATAAAAT
1 AACAAATAAAAT
29940238 A
1 A
29940239 GTTTCTAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AACAAATAAAAT
Found at i:29942556 original size:24 final size:24
Alignment explanation
Indices: 29942498--29942547 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
29942488 GAATAAAGAA
29942498 TAATGATACATGAGTCAAAATATT
1 TAATGATACATGAGTCAAAATATT
*
29942522 TAATGATACATGAGTCAAGATATT
1 TAATGATACATGAGTCAAAATATT
29942546 TA
1 TA
29942548 GTGTAACATC
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:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (24 bp):
TAATGATACATGAGTCAAAATATT
Found at i:29944668 original size:82 final size:81
Alignment explanation
Indices: 29944565--29944731 Score: 316
Period size: 82 Copynumber: 2.0 Consensus size: 81
29944555 AAATTAAACT
29944565 ATTTAAACTTGTATTTATTTTATGTTTTTCATATTTTAACATACTTTTATTTCATTTATAAATTT
1 ATTTAAACTTGTATTTATTTTATGTTTTTCATATTTTAACATACTTTTATTTCATTTATAAATTT
*
29944630 AGTTTATAAATTGTTTA
66 AGTTTATAAATT-TTAA
29944647 ATTTAAACTTGTATTTATTTTATGTTTTTCATATTTTAACATACTTTTATTTCATTTATAAATTT
1 ATTTAAACTTGTATTTATTTTATGTTTTTCATATTTTAACATACTTTTATTTCATTTATAAATTT
29944712 AGTTTATAAATTTTAA
66 AGTTTATAAATTTTAA
29944728 ATTT
1 ATTT
29944732 CAACAATGTA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
81 7 0.08
82 77 0.92
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (81 bp):
ATTTAAACTTGTATTTATTTTATGTTTTTCATATTTTAACATACTTTTATTTCATTTATAAATTT
AGTTTATAAATTTTAA
Found at i:29947965 original size:21 final size:23
Alignment explanation
Indices: 29947930--29947972 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
29947920 CCAAAACAGT
*
29947930 ATAAATGATAGGAAAAC-TAAAG
1 ATAAATGACAGGAAAACATAAAG
29947952 ATAAAT-ACAGGAAAACATAAA
1 ATAAATGACAGGAAAACATAAA
29947973 AAACAGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.63, C:0.07, G:0.14, T:0.16
Consensus pattern (23 bp):
ATAAATGACAGGAAAACATAAAG
Found at i:29950809 original size:23 final size:21
Alignment explanation
Indices: 29950778--29950832 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
29950768 AGAGAGAATC
29950778 AAAAATAAAGAGTAA-ACAAAAG
1 AAAAATAAA-AG-AACACAAAAG
*
29950800 AAAAATTAAAAGAACATAAAAG
1 AAAAA-TAAAAGAACACAAAAG
29950822 AAAAAATAAAA
1 -AAAAATAAAA
29950833 TTGCTCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 2 0.07
22 18 0.62
23 9 0.31
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAAATAAAAGAACACAAAAG
Found at i:29951566 original size:39 final size:39
Alignment explanation
Indices: 29951523--29951608 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
29951513 GAGAAAAAAA
*
29951523 TAGGGTTTA-AGGTTTAAAAAGAATAAATAAA-TACGGGTT
1 TAGGGTTTAGAGGTTTAAAAA-AATAAATAAATTA-AGGTT
* **
29951562 TAGGGTTTAGAGTTTTTTAAAAATAAATAAATTAAGGTT
1 TAGGGTTTAGAGGTTTAAAAAAATAAATAAATTAAGGTT
29951601 TAGGGTTT
1 TAGGGTTT
29951609 TTAAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 31 0.76
40 10 0.24
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (39 bp):
TAGGGTTTAGAGGTTTAAAAAAATAAATAAATTAAGGTT
Found at i:29954261 original size:125 final size:125
Alignment explanation
Indices: 29954063--29954296 Score: 341
Period size: 125 Copynumber: 1.9 Consensus size: 125
29954053 AACTGGATGC
*
29954063 TTTTTTATTACAATTGATTTTGAAAAATAATTTTGAGAAGATGGTTCTAAAAAATAGGTTAAAAA
1 TTTTTTATTACAATTGATTCTGAAAAATAATTTTGAGAAGAT-GTTCTAAAAAATAGGTTAAAAA
29954128 ACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACT-AAAAAAGGCTCCTAGTTGGACGCT
65 ACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACTGAAAAAAGGCTCCTAGTTGGACGCT
*
29954188 TTTTTTTTGTACAATTGATTCTGAAAAAATAATTTTGAGATAG-T-TT-TGAAAAAATAGGTTAA
1 TTTTTTAT-TACAATTGATTCTG-AAAAATAATTTTGAGA-AGATGTTCT-AAAAAATAGGTTAA
* * * *
29954250 AAAACGCTTCAATCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAG
62 AAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACTGAAAAAAG
29954297 TTCCCAGCTG
Statistics
Matches: 98, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
124 1 0.01
125 58 0.59
126 20 0.20
127 17 0.17
128 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (125 bp):
TTTTTTATTACAATTGATTCTGAAAAATAATTTTGAGAAGATGTTCTAAAAAATAGGTTAAAAAA
CGCTTCAAGCAAGATACAATGTCAGCAAAAGTACTGAAAAAAGGCTCCTAGTTGGACGCT
Found at i:29954314 original size:125 final size:123
Alignment explanation
Indices: 29954041--29954317 Score: 339
Period size: 125 Copynumber: 2.2 Consensus size: 123
29954031 TAAATATACA
* * *
29954041 AAAAAAGCTT-CCAACTGGATGC-TTTTTTATTACAATTGATTTTGAAAAATAATTTTGAGAAGA
1 AAAAAAG-TTCCCAGCTGGAAGCTTTTTTTATTACAATTGATTCTGAAAAATAATTTTGAGAAGA
29954104 TGGTTCTAAAAAATAGGTTAAAAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACT
65 T-GTTCTAAAAAATAGGTTAAAAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACT
* * * * *
29954164 AAAAAAGGCTCCTAGTTGGACGCTTTTTTTTTGTACAATTGATTCTGAAAAAATAATTTTGAGAT
1 AAAAAA-GTTCCCAGCTGGAAGCTTTTTTTAT-TACAATTGATTCTG-AAAAATAATTTTGAGA-
* * * *
29954229 AG-T-TT-TGAAAAAATAGGTTAAAAAACGCTTCAATCAGGATGCACTGTCAGCAAAAGTACT
62 AGATGTTCT-AAAAAATAGGTTAAAAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACT
29954289 GAAAAAAGTTCCCAGCTGGAAGCTTTTTT
1 -AAAAAAGTTCCCAGCTGGAAGCTTTTTT
29954318 CAGTAGTGCT
Statistics
Matches: 131, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
123 7 0.05
124 10 0.08
125 76 0.58
126 19 0.15
127 17 0.13
128 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (123 bp):
AAAAAAGTTCCCAGCTGGAAGCTTTTTTTATTACAATTGATTCTGAAAAATAATTTTGAGAAGAT
GTTCTAAAAAATAGGTTAAAAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACT
Found at i:29957528 original size:59 final size:59
Alignment explanation
Indices: 29957425--29957591 Score: 172
Period size: 59 Copynumber: 2.8 Consensus size: 59
29957415 TAGTTCCTAA
* ****** * * *
29957425 TTTATTAAATGAAACTATATAAAAATAATTTGTATTGTCGTATTCAAAAGAACTTCTAT
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAACAACATATAT
* * *
29957484 TTTATTAAATGACACAATATAAAAATAATTTGTACAAAAATATTCAGAACAACATATTT
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAACAACATATAT
** * * *
29957543 TTTATTAAATGAAACAATATAAAAGCAGTTTGTACAAATATATTAAAAA
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAA
29957592 AATCAATGCA
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 88 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (59 bp):
TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAACAACATATAT
Found at i:29971623 original size:26 final size:26
Alignment explanation
Indices: 29971594--29971655 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 26
29971584 ATTTCATACT
29971594 TAAAACATTTATATAATTCACACAAA
1 TAAAACATTTATATAATTCACACAAA
29971620 TAAAAACATTTATATAATTCACACAAA
1 T-AAAACATTTATATAATTCACACAAA
*
29971647 TACAACATT
1 TAAAACATT
29971656 GAATTCAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 8 0.24
27 26 0.76
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAACATTTATATAATTCACACAAA
Found at i:29971626 original size:27 final size:27
Alignment explanation
Indices: 29971595--29971648 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
29971585 TTTCATACTT
29971595 AAAACATTTATATAATTCACACAAATA
1 AAAACATTTATATAATTCACACAAATA
29971622 AAAACATTTATATAATTCACACAAATA
1 AAAACATTTATATAATTCACACAAATA
29971649 CAACATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAACATTTATATAATTCACACAAATA
Found at i:29975914 original size:46 final size:44
Alignment explanation
Indices: 29975810--29975917 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
29975800 TGTCTTTGAC
** * * *
29975810 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
29975854 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
29975900 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
29975918 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:29980567 original size:17 final size:17
Alignment explanation
Indices: 29980545--29980577 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29980535 GAAATATATA
29980545 AGGGTTAGGATACACAT
1 AGGGTTAGGATACACAT
29980562 AGGGTTAGGATACACA
1 AGGGTTAGGATACACA
29980578 CCTGGCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (17 bp):
AGGGTTAGGATACACAT
Found at i:29988999 original size:20 final size:20
Alignment explanation
Indices: 29988960--29989000 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29988950 GACCATTTGC
* *
29988960 TAATTTCAAATAACACATAT
1 TAATTTCAAATAAAAAATAT
*
29988980 TAATTTCTAATAAAAAATAT
1 TAATTTCAAATAAAAAATAT
29989000 T
1 T
29989001 TTGCGAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTTCAAATAAAAAATAT
Found at i:29990974 original size:3 final size:3
Alignment explanation
Indices: 29990966--29991011 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
29990956 ATGGTTTGAA
* * *
29990966 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT GAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29991012 TTAACATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:29991187 original size:3 final size:3
Alignment explanation
Indices: 29991174--29991269 Score: 88
Period size: 3 Copynumber: 32.3 Consensus size: 3
29991164 TTAATTAGTT
*
29991174 TAA TAA T-A TAA TAA TAA TAA -AA TAAA GAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * * * * * * *
29991218 TAG TAA TAG TAA TAG TAA TAG TAA TAG TAG TAG TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29991266 TAA T
1 TAA T
29991270 TAATTTAATA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
2 4 0.05
3 70 0.92
4 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:29993849 original size:18 final size:18
Alignment explanation
Indices: 29993826--29993861 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29993816 TTCGATGTAA
29993826 GGCACATGGCCGTGTCCT
1 GGCACATGGCCGTGTCCT
*
29993844 GGCACATGGCTGTGTCCT
1 GGCACATGGCCGTGTCCT
29993862 AGCCCATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.31, G:0.33, T:0.25
Consensus pattern (18 bp):
GGCACATGGCCGTGTCCT
Found at i:29993869 original size:18 final size:18
Alignment explanation
Indices: 29993827--29993869 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29993817 TCGATGTAAG
*
29993827 GCACATGGCCGTGTCCTG
1 GCACATGGCCGTGTCCTA
*
29993845 GCACATGGCTGTGTCCTA
1 GCACATGGCCGTGTCCTA
*
29993863 GCCCATG
1 GCACATG
29993870 TCCTTACCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.33, G:0.30, T:0.23
Consensus pattern (18 bp):
GCACATGGCCGTGTCCTA
Found at i:29994608 original size:24 final size:23
Alignment explanation
Indices: 29994569--29994618 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
29994559 CGAGCACTAA
29994569 TAAAACAGAGAAAGAAAACCTAG
1 TAAAACAGAGAAAGAAAACCTAG
* *
29994592 TAAAACTGAGTAAAGAAAATCTAG
1 TAAAACAGAG-AAAGAAAACCTAG
29994616 TAA
1 TAA
29994619 GCATTTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.58, C:0.10, G:0.16, T:0.16
Consensus pattern (23 bp):
TAAAACAGAGAAAGAAAACCTAG
Found at i:29996855 original size:13 final size:13
Alignment explanation
Indices: 29996839--29996864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29996829 TTATTTACCG
29996839 AAATTATTATAAT
1 AAATTATTATAAT
29996852 AAATTATTATAAT
1 AAATTATTATAAT
29996865 TATGATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTATAAT
Found at i:30002085 original size:28 final size:27
Alignment explanation
Indices: 30002024--30002203 Score: 279
Period size: 28 Copynumber: 6.6 Consensus size: 27
30002014 ATATTAAGTC
* *
30002024 CGCACACTCAGTGCTATATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
30002051 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
30002079 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
30002106 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
30002134 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
* *
30002162 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
30002189 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30002204 GCACAATTTA
Statistics
Matches: 142, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
27 65 0.46
28 76 0.54
29 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:30002108 original size:55 final size:55
Alignment explanation
Indices: 30002024--30002203 Score: 308
Period size: 55 Copynumber: 3.3 Consensus size: 55
30002014 ATATTAAGTC
* *
30002024 CGCACACTCAGTGCTATATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
30002079 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
* *
30002134 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTCA-ATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAATCATACT
30002189 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30002204 GCACAATTTA
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
55 93 0.77
56 27 0.22
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
Found at i:30002145 original size:83 final size:82
Alignment explanation
Indices: 30002024--30002203 Score: 288
Period size: 83 Copynumber: 2.2 Consensus size: 82
30002014 ATATTAAGTC
* * * *
30002024 CGCACACTCAGTGCTATATAGTCAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
30002089 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
*
30002106 CGCACACTTAGTGCTACATAATCATACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
* *
30002171 AGTGCTACATATTCAATT
65 AGTGCTACATAGTCAACT
30002189 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30002204 GCACAATTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 21 0.23
83 69 0.77
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:30005257 original size:52 final size:52
Alignment explanation
Indices: 30005153--30005258 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 52
30005143 GGTGTAGGAT
* * * * * * *
30005153 TTGTGGCTTTAATCTGCTCTACTGCAACGTCAGGGAGATAAGATTGGTTATC
1 TTGTAGCTTTAATATGCTCTACTACAACGTCAGGGAAATAAAATTCGCTATC
* * *
30005205 TTGTAGCTTTAATATGTTCTACTATAACTTCAGGGAAATAAAATTCGCTATC
1 TTGTAGCTTTAATATGCTCTACTACAACGTCAGGGAAATAAAATTCGCTATC
30005257 TT
1 TT
30005259 TAATCTGCTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (52 bp):
TTGTAGCTTTAATATGCTCTACTACAACGTCAGGGAAATAAAATTCGCTATC
Found at i:30005409 original size:94 final size:94
Alignment explanation
Indices: 30005311--30005482 Score: 224
Period size: 94 Copynumber: 1.8 Consensus size: 94
30005301 GGCAAATTTG
* * * * *
30005311 ATCCGACCTACTGTAACTTC-AGAGGTAT-AGAAATTGTGACTTTAATCTACTCCATTACAACTT
1 ATCCGACCCACTGCAACTTCAAG-GGTATGAG-AATTGTAACTTCAATCTACTCCACTACAACTT
*
30005374 CAAG-GAGATGAGATTCGTCATAATAACTTTA
64 C-AGTGAGATAAGATTCGTCATAATAACTTTA
* *
30005405 ATCCGTCCCACTGCAACTTCAAGGGTATGAGATTTGTAACTTCAATCTACTCCACTACAACTTCA
1 ATCCGACCCACTGCAACTTCAAGGGTATGAGAATTGTAACTTCAATCTACTCCACTACAACTTCA
30005470 GTGAGATAAGATT
66 GTGAGATAAGATT
30005483 TGGTCTGTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
93 2 0.03
94 61 0.91
95 4 0.06
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (94 bp):
ATCCGACCCACTGCAACTTCAAGGGTATGAGAATTGTAACTTCAATCTACTCCACTACAACTTCA
GTGAGATAAGATTCGTCATAATAACTTTA
Found at i:30005482 original size:44 final size:44
Alignment explanation
Indices: 30005344--30005705 Score: 228
Period size: 44 Copynumber: 8.0 Consensus size: 44
30005334 GGTATAGAAA
* * * *
30005344 TTGTGACTTTAATCTACTCCATTACAACTTCAAGGAGATGAGATT
1 TTGTAACTTTAATCTACTCCACTACAACTTCAGGGAGATAAGA-T
* * * *
30005389 CGTCATAATAACTTTAATC--CGTCCCACTGCAACTTCAAGGG-TATGAGAT
1 --T--T-GTAACTTTAATCTAC-T-CCACTACAACTTC-AGGGAGATAAGAT
* *
30005438 TTGTAACTTCAATCTACTCCACTACAACTTCAGTGAGATAAGAT
1 TTGTAACTTTAATCTACTCCACTACAACTTCAGGGAGATAAGAT
*** * * *
30005482 TTGGTCTGTTTAATCTACTCCACTGCGACTTCAGGGAGATAAGAC
1 TT-GTAACTTTAATCTACTCCACTACAACTTCAGGGAGATAAGAT
* * * * * *
30005527 TTGTGACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGT
1 TTGTAACTTTAATCTACTCCACTACAACTTCAGGGAGATAAGAT
* * * * * *
30005571 TTATAGCTTTAATCTGCTCTAC-AGTAACTTCAGAGAGATAAGATT
1 TTGTAACTTTAATCTACTCCACTA-CAACTTCAGGGAGATAAGA-T
* ** * * * **
30005616 TTCTATTTTTAGTCTGCTCCACTGCAACTTCTTGGAGATAAGAT
1 TTGTAACTTTAATCTACTCCACTACAACTTCAGGGAGATAAGAT
* ** *
30005660 TTATGGCTTTAATCTACTCCACTACAACTTCAAGGAGATAAGAT
1 TTGTAACTTTAATCTACTCCACTACAACTTCAGGGAGATAAGAT
30005704 TT
1 TT
30005706 TCCATGATAA
Statistics
Matches: 244, Mismatches: 58, Indels: 29
0.74 0.18 0.09
Matches are distributed among these distances:
43 3 0.01
44 133 0.55
45 71 0.29
46 1 0.00
47 2 0.01
48 1 0.00
49 3 0.01
50 27 0.11
51 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
TTGTAACTTTAATCTACTCCACTACAACTTCAGGGAGATAAGAT
Found at i:30005633 original size:89 final size:89
Alignment explanation
Indices: 30005454--30005707 Score: 248
Period size: 89 Copynumber: 2.9 Consensus size: 89
30005444 CTTCAATCTA
* * * * * * *
30005454 CTCCACTACAACTTCAGTGAGATAAGATTTGGTCTG-TTTAATCTACTCCACTGCGACTTCAGGG
1 CTCCACTGCAACTTCAGGGAGATAAGATTT-AT-AGCTTTAATCTACTCCACTACAACTTCAAGG
* * * * **
30005518 AGATAAGACTTGT-GA-CTTCAACCTG
64 AGATAAGA-TTTTCTATTTTTAGTCTG
* * * *
30005543 CTCCACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTGCTCTAC-AGTAACTTC-AGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTACTCCACTA-CAACTTCAAG-G
30005606 AGATAAGATTTTCTATTTTTAGTCTG
64 AGATAAGATTTTCTATTTTTAGTCTG
** *
30005632 CTCCACTGCAACTTCTTGGAGATAAGATTTATGGCTTTAATCTACTCCACTACAACTTCAAGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTACTCCACTACAACTTCAAGGAG
30005697 ATAAGATTTTC
66 ATAAGATTTTC
30005708 CATGATAACT
Statistics
Matches: 134, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
87 5 0.04
88 29 0.22
89 97 0.72
90 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (89 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTACTCCACTACAACTTCAAGGAG
ATAAGATTTTCTATTTTTAGTCTG
Found at i:30005774 original size:94 final size:94
Alignment explanation
Indices: 30005654--30005853 Score: 240
Period size: 94 Copynumber: 2.1 Consensus size: 94
30005644 TTCTTGGAGA
* *
30005654 TAAGATTTATGGCTTTAATCTACTCCACTACAACT-TCAAGGAGATAAGATTTTCCATGATAACT
1 TAAGATTTATGGCTTCAATCTACTCCACTACAACTCT-AAGGAGATAAGATTTGCCATGATAACT
* **
30005718 TCGATCTGTCCCACTGTAATTTTAGGGGTG
65 TCAATCCATCCCACTGTAATTTTAGGGGTG
* * * * * * *
30005748 TAAGATTTGTGGCTTCAATTTGCTCCACTGCAACTCTAGGGAGATAAGATTTGGCATGATAGCTT
1 TAAGATTTATGGCTTCAATCTACTCCACTACAACTCTAAGGAGATAAGATTTGCCATGATAACTT
* *
30005813 CAATCCATCCCACTGTAATTTCAAGGGTG
66 CAATCCATCCCACTGTAATTTTAGGGGTG
* *
30005842 CAGGATTTATGG
1 TAAGATTTATGG
30005854 TTTTTTTGAT
Statistics
Matches: 88, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
94 87 0.99
95 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (94 bp):
TAAGATTTATGGCTTCAATCTACTCCACTACAACTCTAAGGAGATAAGATTTGCCATGATAACTT
CAATCCATCCCACTGTAATTTTAGGGGTG
Found at i:30007499 original size:62 final size:62
Alignment explanation
Indices: 30007402--30007525 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
30007392 ATGATATTTG
30007402 CATATGACGCATCTTTCACCCACTTAGTGAAATAATTGACGACCACAAAGATGAATCAATGC
1 CATATGACGCATCTTTCACCCACTTAGTGAAATAATTGACGACCACAAAGATGAATCAATGC
30007464 CATATGACGCATCTTTCACCCACTTAGTGAAATAATTGACGACCACAAAGATGAATCAATGC
1 CATATGACGCATCTTTCACCCACTTAGTGAAATAATTGACGACCACAAAGATGAATCAATGC
30007526 TTGCTAGAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (62 bp):
CATATGACGCATCTTTCACCCACTTAGTGAAATAATTGACGACCACAAAGATGAATCAATGC
Found at i:30009185 original size:247 final size:246
Alignment explanation
Indices: 30008744--30009237 Score: 862
Period size: 247 Copynumber: 2.0 Consensus size: 246
30008734 ATCTTGAAAG
30008744 GCCTTGATAGCTAGTGGTTACGGCCCCCGGCTAACCTACAATGACCGATTTAGAATACCCTTTAT
1 GCCTTGATAGCTAGTGGTTACGGCCCCCGGCTAACCTACAATGACCGATTTAGAATACCCTTTAT
* * *
30008809 TATATATGCTTAGGTTATTTACTTCATTTTCCTTATTCTTTGGGTTGATCTTTTGATGCTTTCTC
66 TATATATGCTCAGGTTATTTACTTCATTTTCCTTATTCTTCGGGTTGATCTTTTGATGCTTTCCC
30008874 CTGCATCTATCTTCCCACTTCTTATTGTGTTTTCAATCATCTCGCCAAACATTACTACATCTGAG
131 CTGCATCTATCTTCCCACTTCTTATTGTGTTTTCAATCATCTCGCCAAACATTACTACATCTGAG
* *
30008939 AAGCTTCTCGTAGCGCTTCCCAACATATGGGTAATGAATGGGGCTTTTAGA
196 AACCTCCTCGTAGCGCTTCCCAACATATGGGTAATGAATGGGGCTTTTAGA
* * * *
30008990 GCCTTGATAGCTAGTGGTTACGGCCCTCGGCTGACCTACAATGACTGATTTGGAATACCCTTTAT
1 GCCTTGATAGCTAGTGGTTACGGCCCCCGGCTAACCTACAATGACCGATTTAGAATACCCTTTAT
*
30009055 TATATATGCTCAGGTTATTTACTTCATTTTCCTTGTTCTTCGAGGTTGATCTTTTGATGCTTTCC
66 TATATATGCTCAGGTTATTTACTTCATTTTCCTTATTCTTCG-GGTTGATCTTTTGATGCTTTCC
* *
30009120 CCTGCATCTATCTTCCTACTTCTTATTGTGTTTTCAATCATCTCGCCAAACATTACTATATCTGA
130 CCTGCATCTATCTTCCCACTTCTTATTGTGTTTTCAATCATCTCGCCAAACATTACTACATCTGA
*
30009185 GAACCTCCTCGTAGCGCTTCCCAACATATGGTTAATGAATGGGGCTTTTAGA
195 GAACCTCCTCGTAGCGCTTCCCAACATATGGGTAATGAATGGGGCTTTTAGA
30009237 G
1 G
30009238 TGTTGATGAA
Statistics
Matches: 234, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
246 100 0.43
247 134 0.57
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (246 bp):
GCCTTGATAGCTAGTGGTTACGGCCCCCGGCTAACCTACAATGACCGATTTAGAATACCCTTTAT
TATATATGCTCAGGTTATTTACTTCATTTTCCTTATTCTTCGGGTTGATCTTTTGATGCTTTCCC
CTGCATCTATCTTCCCACTTCTTATTGTGTTTTCAATCATCTCGCCAAACATTACTACATCTGAG
AACCTCCTCGTAGCGCTTCCCAACATATGGGTAATGAATGGGGCTTTTAGA
Found at i:30010316 original size:19 final size:20
Alignment explanation
Indices: 30010285--30010338 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
30010275 GGTTTTTTTG
* *
30010285 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCAAATGCA
*
30010304 TGCAATGTAATGCAAATGCA
1 TGAAATGTAATGCAAATGCA
30010324 TGAAATG-AATGCAAA
1 TGAAATGTAATGCAAA
30010339 AAGAGGGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGCA
Found at i:30012312 original size:3 final size:3
Alignment explanation
Indices: 30012304--30012334 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30012294 ATGGTTTGAA
30012304 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
30012335 TTAACATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:30012469 original size:3 final size:3
Alignment explanation
Indices: 30012461--30012647 Score: 146
Period size: 3 Copynumber: 62.0 Consensus size: 3
30012451 AAAAATGATG
* *
30012461 TAA TAA TAA TGA TAA TAA -AA TAAA GAA TAA TAA TACA TTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA-A -TAA TAA TAA
* * * * * * *
30012508 TAG TAG TAG TAA -AGA CAA TAA T-A TAA TAA GAA TGA TGA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
30012552 TAC TAA TAC TAA TAA TAA TAG TAA TAA TAG TAA TAA TAG TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
30012600 TAA TAA TAA GAA TAA TAG TAA TAA TAA TAG TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30012648 AATTAATTAA
Statistics
Matches: 148, Mismatches: 29, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
2 5 0.03
3 136 0.92
4 5 0.03
5 2 0.01
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:30015682 original size:30 final size:30
Alignment explanation
Indices: 30015642--30015718 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
30015632 ATATGATCAT
*
30015642 GATCAGATCTTGGTATTTCAGTTAGGAAAG
1 GATCAGATCTTGGTATATCAGTTAGGAAAG
* *
30015672 GATCAAATCTTGGTAAATCAGTTAGGAAAG
1 GATCAGATCTTGGTATATCAGTTAGGAAAG
*
30015702 GATCTGATCTTGGTATA
1 GATCAGATCTTGGTATA
30015719 ACTATTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.32
Consensus pattern (30 bp):
GATCAGATCTTGGTATATCAGTTAGGAAAG
Found at i:30022389 original size:26 final size:26
Alignment explanation
Indices: 30022360--30022419 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
30022350 AAAGCTGCGG
30022360 AGAGCCATTAAACAGGAAGCTCACAA
1 AGAGCCATTAAACAGGAAGCTCACAA
* * * * *
30022386 AGAGCCTTTAATCGGGAAGCTTACGA
1 AGAGCCATTAAACAGGAAGCTCACAA
30022412 AGAGCCAT
1 AGAGCCAT
30022420 ATAATGGGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
AGAGCCATTAAACAGGAAGCTCACAA
Found at i:30022428 original size:26 final size:26
Alignment explanation
Indices: 30022374--30022434 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
30022364 CCATTAAACA
*
30022374 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCACAAAGAGCCTATAATCG
* *
30022400 GGAAGCTTACGAAGAGCCATATAAT-G
1 GGAAGCTCACAAAGAGCC-TATAATCG
*
30022426 GGATGCTCA
1 GGAAGCTCA
30022435 TAAGAGCTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTATAATCG
Found at i:30026595 original size:16 final size:16
Alignment explanation
Indices: 30026574--30026604 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30026564 TTCTCCGGAT
*
30026574 TCAGATTTTTTTGGGC
1 TCAGATTTTCTTGGGC
30026590 TCAGATTTTCTTGGG
1 TCAGATTTTCTTGGG
30026605 TTCATTCAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (16 bp):
TCAGATTTTCTTGGGC
Found at i:30039707 original size:40 final size:40
Alignment explanation
Indices: 30039659--30039921 Score: 324
Period size: 39 Copynumber: 6.7 Consensus size: 40
30039649 GCTCCTCGTT
* * *
30039659 CAAATGCCTTCGGGACATAGTCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * *
30039699 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
30039739 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
30039778 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
30039817 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
30039856 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
30039897 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
30039922 CATCATTCAA
Statistics
Matches: 202, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
38 2 0.01
39 113 0.56
40 74 0.37
41 13 0.06
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:30052008 original size:23 final size:23
Alignment explanation
Indices: 30051977--30052025 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
30051967 AATGATAGCC
*
30051977 AATCCATACCCAGAATAACATCA
1 AATCAATACCCAGAATAACATCA
30052000 AATCAATACCCAGAATAACATCA
1 AATCAATACCCAGAATAACATCA
30052023 AAT
1 AAT
30052026 TCCCAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.51, C:0.27, G:0.04, T:0.18
Consensus pattern (23 bp):
AATCAATACCCAGAATAACATCA
Found at i:30052381 original size:23 final size:23
Alignment explanation
Indices: 30052355--30052400 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
30052345 GAACAATAGT
30052355 GTATTTTGCTCTCGTACGAGTAA
1 GTATTTTGCTCTCGTACGAGTAA
*
30052378 GTATTTTGCTCTTGTACGAGTAA
1 GTATTTTGCTCTCGTACGAGTAA
30052401 TCCTTACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (23 bp):
GTATTTTGCTCTCGTACGAGTAA
Found at i:30057140 original size:29 final size:30
Alignment explanation
Indices: 30057098--30057171 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
30057088 ATGCTTCCAA
*
30057098 TCTTTATATCTTTTTACCT-TTAAAATTTAG
1 TCTTTATAT-TTTTTAACTCTTAAAATTTAG
* *
30057128 TCTTTCTA-TTTTTAATTCTTAAAATTTAG
1 TCTTTATATTTTTTAACTCTTAAAATTTAG
*
30057157 TCTTTTTAATTTTTT
1 TCTTTAT-ATTTTTT
30057172 TAATTTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.19
29 17 0.46
30 8 0.22
31 5 0.14
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.62
Consensus pattern (30 bp):
TCTTTATATTTTTTAACTCTTAAAATTTAG
Found at i:30065778 original size:14 final size:14
Alignment explanation
Indices: 30065759--30065794 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
30065749 TTGATAACAC
30065759 AAATTATTTAATTT
1 AAATTATTTAATTT
*
30065773 AAATTATTAAATTT
1 AAATTATTTAATTT
30065787 AAA-TATTT
1 AAATTATTT
30065795 TTCTACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATTATTTAATTT
Found at i:30066384 original size:3 final size:3
Alignment explanation
Indices: 30066376--30066410 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
30066366 AAATTAAGTT
30066376 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30066411 CTGTTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30071221 original size:22 final size:22
Alignment explanation
Indices: 30071193--30071234 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30071183 AATTGTAGAC
*
30071193 GACATAATAATCCTTCTAAGAT
1 GACATAATAATCCATCTAAGAT
*
30071215 GACATAATAATTCATCTAAG
1 GACATAATAATCCATCTAAG
30071235 TATTTGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (22 bp):
GACATAATAATCCATCTAAGAT
Found at i:30077618 original size:48 final size:46
Alignment explanation
Indices: 30077501--30077621 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
30077491 TTTACAGTGT
*
30077501 GCTAGTGTAAGACATGTCTGAGACATGCATCGGCCACATTATGAAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAAA
* * * * *
30077547 GCCAGTGTAAGATATGTCAGGGACATGTATCGGCCTCGATATAT-ACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AT-TATGA-AA
* *
30077595 GCTAGTGTAAGACCTGTTTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
30077622 GCGTCAGCTA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
46 31 0.51
47 3 0.05
48 27 0.44
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAAA
Found at i:30080373 original size:4 final size:4
Alignment explanation
Indices: 30080364--30080395 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
30080354 AATGAACTCT
*
30080364 TTTA TTTA TTTA TTTA TTTA TTTA TTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
30080396 AATACATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:30081268 original size:17 final size:17
Alignment explanation
Indices: 30081243--30081281 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
30081233 GTCCATTTGT
*
30081243 TTTTATTTTTATTTT-TA
1 TTTTGTTTTT-TTTTCTA
30081260 TTTTGTTTTTTTTTCTA
1 TTTTGTTTTTTTTTCTA
30081277 TTTTG
1 TTTTG
30081282 AACTGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTGTTTTTTTTTCTA
Found at i:30091876 original size:17 final size:17
Alignment explanation
Indices: 30091854--30091890 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
30091844 CCTAACTTTC
30091854 ATAAATTTTTATTTTGA
1 ATAAATTTTTATTTTGA
30091871 ATAAATTTTTATTTTGA
1 ATAAATTTTTATTTTGA
30091888 ATA
1 ATA
30091891 TTGTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
ATAAATTTTTATTTTGA
Found at i:30094467 original size:96 final size:97
Alignment explanation
Indices: 30094198--30094467 Score: 266
Period size: 96 Copynumber: 2.8 Consensus size: 97
30094188 TATGTGTGCC
* *
30094198 AGTGTAAGACCAT-TCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGTAAGACCATGTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCGCGATATGTGAGCCAGTGTAAGACCATGTTT
* * ** * *
30094262 GGAACGTGATATC-AGCGATGTTGTGAGAGCT
66 GGAACATGACATCGAGAAATGTAGTGAGAACT
* * * * * **
30094293 AGTGTAAAAGCACGTCTGGGACATGGCATCGG-TGTTGATATGT-ACGTTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCG-CGATATGTGA-GCCAGTGTAAGACCATGT
* **
30094356 CTGGGCCATGACATCGA-AAATG-AGACT-AGAACT
64 TTGGAACATGACATCGAGAAATGTAG--TGAGAACT
* *
30094389 AGTGTAAGACCATGTCTGAGACATGGCATCGGCCGCGACATGTGAGCCAGTGTAAGACCATGTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCGCGATATGTGAGCCAGTGTAAGACCATGTTT
*
30094454 GGAACATGGCATCG
66 GGAACATGACATCG
30094468 GTAATTCACC
Statistics
Matches: 136, Mismatches: 31, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
95 12 0.09
96 120 0.88
97 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (97 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCGCGATATGTGAGCCAGTGTAAGACCATGTTT
GGAACATGACATCGAGAAATGTAGTGAGAACT
Found at i:30112460 original size:49 final size:49
Alignment explanation
Indices: 30112399--30112527 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 49
30112389 ATCAAAGTTG
*
30112399 ATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG-GCCA
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCG-GTGCCA
* * * * * *
30112448 ATGCCGTGTCCCAAATAGGTCTTACACT-AGCTCTCATCTATCGGTGTCG
1 ATGCCATGTCCCAGACAGGTCTTACACTGA-CTCTCATATATCGGTGCCA
*
30112497 ATGCCATGTCCTAGACAGGTCTTACACTGAC
1 ATGCCATGTCCCAGACAGGTCTTACACTGAC
30112528 ACGCAACAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 2 0.03
49 63 0.95
50 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGTGCCA
Found at i:30112700 original size:48 final size:47
Alignment explanation
Indices: 30112540--30112701 Score: 155
Period size: 48 Copynumber: 3.4 Consensus size: 47
30112530 GCAACAAGCT
* * * *
30112540 GATGCCATGTCCTAGATAGGTCTTACACTAGCTTGTATATCTCGAGGCC
1 GATG-CATGTCCTAGACATGTCTTACACTGGC-TGTATATCTTGAGGCC
* * * * * ** * *
30112589 AAAGCATGTCCCAGACATGTCTTATACTGGCTCT-CGTCTTAATGCC
1 GATGCATGTCCTAGACATGTCTTACACTGGCTGTATATCTTGAGGCC
*
30112635 GATGCATGTCCTTGACATGTCTTACACTGGCTGGTATATCTTGAGGCC
1 GATGCATGTCCTAGACATGTCTTACACTGGCT-GTATATCTTGAGGCC
*
30112683 GATGCGTGTCCTAGACATG
1 GATGCATGTCCTAGACATG
30112702 ACTGTCTCTC
Statistics
Matches: 86, Mismatches: 25, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
46 34 0.40
47 3 0.03
48 47 0.55
49 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.31
Consensus pattern (47 bp):
GATGCATGTCCTAGACATGTCTTACACTGGCTGTATATCTTGAGGCC
Found at i:30119066 original size:13 final size:13
Alignment explanation
Indices: 30119045--30119080 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
30119035 CCTTGTTCTC
*
30119045 CACATGGCTGAGA
1 CACACGGCTGAGA
30119058 CACACGGCTGAGA
1 CACACGGCTGAGA
30119071 CACACGGCTG
1 CACACGGCTG
30119081 CGTCTCTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.31, T:0.11
Consensus pattern (13 bp):
CACACGGCTGAGA
Found at i:30120249 original size:49 final size:49
Alignment explanation
Indices: 30120137--30120250 Score: 140
Period size: 49 Copynumber: 2.3 Consensus size: 49
30120127 GCCATATTTT
* * *
30120137 AGACAGGTCTTACACTGACTTTCATATATCAAGGCCGATACCGTGTCCC
1 AGACAGGTCTTACATTGACTCTCATATATCAAGGCCGATACCATGTCCC
* * * * *
30120186 AGACAAGTCTTACATTGGCTCTCATCTATC-AGTGTCGATGCCATGTCCC
1 AGACAGGTCTTACATTGACTCTCATATATCAAG-GCCGATACCATGTCCC
30120235 AGACAGGTCTTACATT
1 AGACAGGTCTTACATT
30120251 AGCTTGTGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 2 0.04
49 53 0.96
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (49 bp):
AGACAGGTCTTACATTGACTCTCATATATCAAGGCCGATACCATGTCCC
Found at i:30120293 original size:48 final size:48
Alignment explanation
Indices: 30120221--30120392 Score: 185
Period size: 48 Copynumber: 3.6 Consensus size: 48
30120211 CTATCAGTGT
* *
30120221 CGATGCCATGTCCCAGACAGGTCTTACATTAGCTTGTGTATCTCGAGGC
1 CGATG-CATGTCCCAGACATGTCTTACACTAGCTTGTGTATCTCGAGGC
* * * * *
30120270 CAATGCGTGTCCCAGACATGTCTTATACTAGCTCTCGT-T-T-T-AATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCT-T-GTGTATCTCGAGGC
*
30120316 CGATGCATGTCCCAGACATGTCTTACACT-GGTTG-GTAAATCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTTGTGT--ATCTCGAGGC
30120364 CGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
30120393 GGCTCTAAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
43 2 0.02
44 1 0.01
45 2 0.02
46 30 0.29
47 2 0.02
48 57 0.56
49 6 0.06
50 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (48 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTTGTGTATCTCGAGGC
Found at i:30120358 original size:94 final size:94
Alignment explanation
Indices: 30120221--30120441 Score: 259
Period size: 94 Copynumber: 2.3 Consensus size: 94
30120211 CTATCAGTGT
* * *
30120221 CGATGCCATGTCCCAGACAGGTCTTACATTAGCTTGTGTATCTCGAGGCCAATGCGTGTCCCAGA
1 CGATG-CATGTCCCAGACATGTCTTACACTAGCTTGTGTATCTCGAGGCCAATGCATGTCCCAGA
* *** *
30120286 CATGTCTTATACTAGCTCTCGTTTTAAT-GC
65 CATGTCTTACACTAGCTCTAAATAT-ATGGC
* *
30120316 CGATGCATGTCCCAGACATGTCTTACACT-GGTTG-GTAAATCTCGAGGCCGATGCATGTCCCAG
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTTGTGT--ATCTCGAGGCCAATGCATGTCCCAG
*
30120379 ACATGTCTTACACTGGCTCTAAATATATGGC
64 ACATGTCTTACACTAGCTCTAAATATATGGC
* * *
30120410 CTATGCATGCCCCAGATATGTCTTACACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
30120442 ATACATATCA
Statistics
Matches: 107, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
92 2 0.02
93 6 0.06
94 93 0.87
95 6 0.06
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (94 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTTGTGTATCTCGAGGCCAATGCATGTCCCAGAC
ATGTCTTACACTAGCTCTAAATATATGGC
Found at i:30120433 original size:46 final size:47
Alignment explanation
Indices: 30120162--30120438 Score: 177
Period size: 46 Copynumber: 5.8 Consensus size: 47
30120152 TGACTTTCAT
* * * * *
30120162 ATATCAAGGCCGATACCGTGTCCCAGACAAGTCTTACATTGGCT-CTCAT
1 ATATC-AGGCCGAT-GCATGTCCCAGACATGTCTTACACTGGCTGCT-AA
* * * * * **
30120211 CTATCAGTGTCGATGCCATGTCCCAGACAGGTCTTACATTAGCTTG-TGT
1 ATATCAG-GCCGATG-CATGTCCCAGACATGTCTTACACTGGC-TGCTAA
* * * * * **
30120260 ATCTCGAGGCCAATGCGTGTCCCAGACATGTCTTATACTAGCT-CTCG
1 ATATC-AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTGCTAA
* * * * * *
30120307 TTTTAATGCCGATGCATGTCCCAGACATGTCTTACACTGGTTGGTAA
1 ATATCAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTGCTAA
*
30120354 ATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCT-CTAA
1 ATATC-AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTGCTAA
* * *
30120401 ATAT-ATGGCCTATGCATGCCCCAGATATGTCTTACACT
1 ATATCA-GGCCGATGCATGTCCCAGACATGTCTTACACT
30120439 AGCATACATA
Statistics
Matches: 180, Mismatches: 39, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
45 1 0.01
46 60 0.33
47 13 0.07
48 60 0.33
49 42 0.23
50 4 0.02
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (47 bp):
ATATCAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTGCTAA
Found at i:30121282 original size:37 final size:37
Alignment explanation
Indices: 30121227--30121298 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
30121217 ACCCCATTCT
* *
30121227 TGCTGAAATTTTCGGTGGAGGAGAAAGGAAAAATGCC
1 TGCTGAAAATTTCAGTGGAGGAGAAAGGAAAAATGCC
* *
30121264 TGCTGAAAATTTCAGTGGAGGATAAAGGGAAAATG
1 TGCTGAAAATTTCAGTGGAGGAGAAAGGAAAAATG
30121299 AAAAAAGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.22
Consensus pattern (37 bp):
TGCTGAAAATTTCAGTGGAGGAGAAAGGAAAAATGCC
Found at i:30122510 original size:42 final size:42
Alignment explanation
Indices: 30122451--30122532 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
30122441 CAAAGCATTT
30122451 AAGAACTGTTTTGAAGACATTACGAGATAAGCAACTATATAC
1 AAGAACTGTTTTGAAGACATTACGAGATAAGCAACTATATAC
30122493 AAGAACTGTTTTGAAGACATTACGAGATAAGCAACTATAT
1 AAGAACTGTTTTGAAGACATTACGAGATAAGCAACTATAT
30122533 GCTAAGTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (42 bp):
AAGAACTGTTTTGAAGACATTACGAGATAAGCAACTATATAC
Found at i:30122919 original size:13 final size:13
Alignment explanation
Indices: 30122901--30122929 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
30122891 AGTTGTTTAT
30122901 TAAACTAATTAAC
1 TAAACTAATTAAC
30122914 TAAACTAATTAAC
1 TAAACTAATTAAC
30122927 TAA
1 TAA
30122930 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:30127474 original size:48 final size:48
Alignment explanation
Indices: 30127403--30127830 Score: 369
Period size: 48 Copynumber: 8.9 Consensus size: 48
30127393 ACATTTAGGT
* *
30127403 GATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
* * * * * *
30127451 GATATGAGAGCCAATGTAAGACCATGT-TCAGAACATGGCATCGACGAT
1 GATATGAGAGCCAGTGTAAGACCATGTCT-GGGACATGGCATCGGCCAC
* * * ***
30127499 GTTGTGAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCGTT
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
* * * * * * *
30127547 GATATGTGCGCTAATGTAAGACCATGTCTGGGAGATAGCATCGACCAC
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
* ***
30127595 -ATCATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGTT
1 GAT-ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
*** * * *
30127643 GATATGCTCGCTAGTGTAAGACCATGTCTGGGAGATGGCATCGACCAC
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
* * ** *
30127691 -ATCATTAGAGCCAGTGTAAGACCATGTCTGGGACATGACATCGGTAAT
1 GAT-ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
* ** * * * * *
30127739 GAGAAAAGAGCTAGTGTAAGACCATGTCTAGGACATGGCGTCGGTCTC
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
* * * *
30127787 GACATGTGAGCCAGT-TAAGACCATGTTTGGAACATGGCATCGGC
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
30127831 AATTCACCCT
Statistics
Matches: 293, Mismatches: 81, Indels: 13
0.76 0.21 0.03
Matches are distributed among these distances:
47 29 0.10
48 260 0.89
49 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
Found at i:30127588 original size:96 final size:96
Alignment explanation
Indices: 30127412--30127830 Score: 441
Period size: 96 Copynumber: 4.4 Consensus size: 96
30127402 TGATATGTGT
*** * * *
30127412 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAATGTAAGACCATG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGCGCTAATGTAAGACCATG
* * * * ** **
30127477 T-TCAGAACATGGCATCGACGATGTTGTGAGA
66 TCT-GGGAGATGGCATCGACCACATCATGAGA
*
30127508 GCCAGTATAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGCGCTAATGTAAGACCATG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGCGCTAATGTAAGACCATG
*
30127573 TCTGGGAGATAGCATCGACCACATCATGAGA
66 TCTGGGAGATGGCATCGACCACATCATGAGA
* *
30127604 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGTTGATATGCT-CGCTAGTGTAAGACCAT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATG-TGCGCTAATGTAAGACCAT
*
30127668 GTCTGGGAGATGGCATCGACCACATCATTAGA
65 GTCTGGGAGATGGCATCGACCACATCATGAGA
* *** * *** * *
30127700 GCCAGTGTAAGACCATGTCTGGGACATGACATCGGTAATGAGAAAAGAGCTAGTGTAAGACCATG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGCGCTAATGTAAGACCATG
* * * ** * *
30127765 TCTAGGACATGGCGTCGGTCTCGA-CATGTGA
66 TCTGGGAGATGGCATCGACCAC-ATCATGAGA
* *
30127796 GCCAGT-TAAGACCATGTTTGGAACATGGCATCGGC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
30127831 AATTCACCCT
Statistics
Matches: 276, Mismatches: 43, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
95 25 0.09
96 248 0.90
97 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (96 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGCGCTAATGTAAGACCATG
TCTGGGAGATGGCATCGACCACATCATGAGA
Found at i:30130899 original size:30 final size:29
Alignment explanation
Indices: 30130863--30130931 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 29
30130853 TTCTGCCATT
30130863 AAGGCTCACATATAATTGAGA-ACAGCCACA
1 AAGGCTCACATATAA-T-AGATACAGCCACA
*
30130893 AAGGCTCACATATAATAGATTCAGCCACA
1 AAGGCTCACATATAATAGATACAGCCACA
30130922 AAGGCATCAC
1 AAGGC-TCAC
30130932 TTTTAGGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 3 0.08
29 14 0.39
30 19 0.53
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.17
Consensus pattern (29 bp):
AAGGCTCACATATAATAGATACAGCCACA
Found at i:30131272 original size:16 final size:16
Alignment explanation
Indices: 30131251--30131294 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
30131241 GCACATCCTC
* *
30131251 CTCATGTAGTGGCTTA
1 CTCATGTAGAGACTTA
*
30131267 CTCATGCAGAGACTTA
1 CTCATGTAGAGACTTA
*
30131283 TTCATGTAGAGA
1 CTCATGTAGAGA
30131295 ATCCATTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (16 bp):
CTCATGTAGAGACTTA
Found at i:30137801 original size:48 final size:48
Alignment explanation
Indices: 30137479--30137801 Score: 407
Period size: 48 Copynumber: 6.7 Consensus size: 48
30137469 TAAAGTACCA
* ** * * *
30137479 ATGCCATGTCCCAGACATGGTCTTACATGAATC-CACATATCATCACCA
1 ATGCCATGTCCCAGACATGGTCTTACA-CAGGCACATATATCATCGCCG
* * * *
30137527 ATGCCATGTCCCAAACATGGTTTTACA-ATGGCACATATATCATCGTCA
1 ATGCCATGTCCCAGACATGGTCTTACACA-GGCACATATATCATCGCCG
* * * * *
30137575 ATGCCATGTCCTAGACATGGTCCTACACAGACACATATATCATTGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
* *
30137623 ATGCCATGTCCTAGACATGGTCTTACACAGGTACATATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
* * *
30137671 ATGCCATGTCCTAGACATGGTCTTACACAGGCATATATATCATCGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
*
30137719 ATGCCATGTCCCAGACATGGTCTTACACATGCACATATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
* *
30137767 ATGCCATGTCCCAGACATGGGCTTACAAAGGCACA
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACA
30137802 CTTCTCGGAT
Statistics
Matches: 243, Mismatches: 29, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
46 1 0.00
47 1 0.00
48 240 0.99
49 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
Found at i:30140518 original size:18 final size:19
Alignment explanation
Indices: 30140485--30140524 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
30140475 GCAAGGTTAT
*
30140485 TATATTCATAGGGTTCGCA
1 TATAATCATAGGGTTCGCA
30140504 TATAATCAT-GGGTTCGCA
1 TATAATCATAGGGTTCGCA
30140522 TAT
1 TAT
30140525 CTTACTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (19 bp):
TATAATCATAGGGTTCGCA
Found at i:30143383 original size:44 final size:43
Alignment explanation
Indices: 30143230--30143396 Score: 122
Period size: 43 Copynumber: 3.9 Consensus size: 43
30143220 GGCTCGTACA
* * * * * * * *
30143230 ATGCTAACGTCTCAGATGTGGTCTTACATGTAATCACATATCA
1 ATGCCAACGTCCCAGATATAGTCTTACACGAAATCACAAATCG
* ** * * * *
30143273 ATGCC-ACAGTCCCAGACAGGGTCTTCCACGAACTCATATA-CG
1 ATGCCAAC-GTCCCAGATATAGTCTTACACGAAATCACAAATCG
* * *
30143315 ATGCCAATGTCCCAGATATGGTCTTACACATAAATCACAAATCG
1 ATGCCAACGTCCCAGATATAGTCTTACAC-GAAATCACAAATCG
* *
30143359 ATGCCAACGTCCTAGATGTAGTCTTACACGAAATCACA
1 ATGCCAACGTCCCAGATATAGTCTTACACGAAATCACA
30143397 TATCAGAATC
Statistics
Matches: 96, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
42 26 0.27
43 43 0.45
44 27 0.28
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGATATAGTCTTACACGAAATCACAAATCG
Found at i:30145155 original size:8 final size:8
Alignment explanation
Indices: 30145142--30145170 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
30145132 GCATACGATT
30145142 TCTGACGA
1 TCTGACGA
30145150 TCTGACGA
1 TCTGACGA
30145158 TCTGACGA
1 TCTGACGA
30145166 TCTGA
1 TCTGA
30145171 AACTATCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (8 bp):
TCTGACGA
Found at i:30151506 original size:43 final size:43
Alignment explanation
Indices: 30151459--30151610 Score: 139
Period size: 43 Copynumber: 3.5 Consensus size: 43
30151449 TCTCAAATGT
* * *
30151459 GGTCTTACATGTAATCACATATCGATGCCATTGTCCCAGATAG
1 GGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAG
* * *
30151502 GGTCTTACACG-AACTCATATAT-GATGCCAATGTCCTAGACAT
1 GGTCTTACACGTAA-TCACATATCGATGCCAATGTCCCAGACAG
* * * * *
30151544 GGTCTTACACATAAATCACAAATCGATGCCAACGCCCCAGGC-G
1 GGTCTTACACGT-AATCACATATCGATGCCAATGTCCCAGACAG
* *
30151587 CAGTCTTACACGAAATCACATATC
1 -GGTCTTACACGTAATCACATATC
30151611 AGAATCCTAT
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
42 28 0.33
43 33 0.38
44 25 0.29
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (43 bp):
GGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAG
Found at i:30151536 original size:42 final size:43
Alignment explanation
Indices: 30151440--30151610 Score: 134
Period size: 43 Copynumber: 4.0 Consensus size: 43
30151430 GGCTCGTACA
* * *
30151440 ATGCCAATGTCTCAAAT-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGATAG-GGTCTTACACGTAATCACATATCG
* *
30151483 ATGCCATTGTCCCAGATAGGGTCTTACACG-AACTCATATAT-G
1 ATGCCAATGTCCCAGATAGGGTCTTACACGTAA-TCACATATCG
* * * * *
30151525 ATGCCAATGTCCTAGACATGGTCTTACACATAAATCACAAATCG
1 ATGCCAATGTCCCAGATAGGGTCTTACACGT-AATCACATATCG
* * ** * *
30151569 ATGCCAACGCCCCAG-GCGCAGTCTTACACGAAATCACATATC
1 ATGCCAATGTCCCAGATAG-GGTCTTACACGTAATCACATATC
30151611 AGAATCCTAT
Statistics
Matches: 100, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
42 28 0.28
43 47 0.47
44 25 0.25
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATAGGGTCTTACACGTAATCACATATCG
Found at i:30161284 original size:43 final size:42
Alignment explanation
Indices: 30161235--30161325 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
30161225 TTATATGGGG
**
30161235 TCTCATA-TCGATACCAATAGCCCATCTATGGTCTTACACAAAA
1 TCTCATACT-GATACC-ATAGCCCAGATATGGTCTTACACAAAA
** * *
30161278 TCTCATACTGATGTCATATCTCAGATATGGTCTTACACAAAA
1 TCTCATACTGATACCATAGCCCAGATATGGTCTTACACAAAA
30161320 TCTCAT
1 TCTCAT
30161326 CTAACCCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 29 0.71
43 11 0.27
44 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (42 bp):
TCTCATACTGATACCATAGCCCAGATATGGTCTTACACAAAA
Found at i:30165392 original size:43 final size:43
Alignment explanation
Indices: 30165338--30165423 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
30165328 AACATAATGA
30165338 TAATTAGCTTTGAAATCGAAAGATATTTTGTTAACATTTATAT
1 TAATTAGCTTTGAAATCGAAAGATATTTTGTTAACATTTATAT
*
30165381 TAATTATCTTTGAAATCGAAAGATATTTTGTTAACATTTATAT
1 TAATTAGCTTTGAAATCGAAAGATATTTTGTTAACATTTATAT
30165424 ATGTGTATTC
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:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (43 bp):
TAATTAGCTTTGAAATCGAAAGATATTTTGTTAACATTTATAT
Found at i:30166915 original size:174 final size:174
Alignment explanation
Indices: 30166625--30166974 Score: 700
Period size: 174 Copynumber: 2.0 Consensus size: 174
30166615 GGTTAAATAC
30166625 ATAAAGATTTTAATGTTTAACGAAATTTATTTGATCATTTTGTGAAATTGATAATGTCACATATG
1 ATAAAGATTTTAATGTTTAACGAAATTTATTTGATCATTTTGTGAAATTGATAATGTCACATATG
30166690 CTAATGGACAAAATGCCATGTGATATGTTTTATTTGGTTAAACATGCGCATGTATAGTATTAAGA
66 CTAATGGACAAAATGCCATGTGATATGTTTTATTTGGTTAAACATGCGCATGTATAGTATTAAGA
30166755 AGTAAAATGTTTGACTTTTATTTAGGTATTTGATTATCATTAAA
131 AGTAAAATGTTTGACTTTTATTTAGGTATTTGATTATCATTAAA
30166799 ATAAAGATTTTAATGTTTAACGAAATTTATTTGATCATTTTGTGAAATTGATAATGTCACATATG
1 ATAAAGATTTTAATGTTTAACGAAATTTATTTGATCATTTTGTGAAATTGATAATGTCACATATG
30166864 CTAATGGACAAAATGCCATGTGATATGTTTTATTTGGTTAAACATGCGCATGTATAGTATTAAGA
66 CTAATGGACAAAATGCCATGTGATATGTTTTATTTGGTTAAACATGCGCATGTATAGTATTAAGA
30166929 AGTAAAATGTTTGACTTTTATTTAGGTATTTGATTATCATTAAA
131 AGTAAAATGTTTGACTTTTATTTAGGTATTTGATTATCATTAAA
30166973 AT
1 AT
30166975 GATGAACATA
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 176 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (174 bp):
ATAAAGATTTTAATGTTTAACGAAATTTATTTGATCATTTTGTGAAATTGATAATGTCACATATG
CTAATGGACAAAATGCCATGTGATATGTTTTATTTGGTTAAACATGCGCATGTATAGTATTAAGA
AGTAAAATGTTTGACTTTTATTTAGGTATTTGATTATCATTAAA
Found at i:30169950 original size:24 final size:24
Alignment explanation
Indices: 30169881--30169961 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
30169871 TATGAGCTCG
* *
30169881 TAAGAGCTTACTGTTTTCAGCTTA
1 TAAGAGCTTACTGTTTTCATCTCA
** *
30169905 TTGGAACTTACTG-TTTCATCTCA
1 TAAGAGCTTACTGTTTTCATCTCA
*
30169928 TAAGAGCTTACTGTTTTCATCTCG
1 TAAGAGCTTACTGTTTTCATCTCA
*
30169952 TTAGAGCTTA
1 TAAGAGCTTA
30169962 TCGATTCAGC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
23 18 0.39
24 28 0.61
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (24 bp):
TAAGAGCTTACTGTTTTCATCTCA
Found at i:30172093 original size:29 final size:28
Alignment explanation
Indices: 30172036--30172121 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
30172026 TACCTGTATC
*
30172036 TGGCCCATTTA-GCCCAATCATATTCATA
1 TGGCCCA-TTAGGCCCAATCACATTCATA
*
30172064 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTCATA
* * *
30172093 TGGCCCGTCAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
30172121 T
1 T
30172122 TCATGCTCAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.06
28 23 0.46
29 24 0.48
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:30173223 original size:260 final size:260
Alignment explanation
Indices: 30172762--30173281 Score: 988
Period size: 260 Copynumber: 2.0 Consensus size: 260
30172752 AGATCCAATA
* *
30172762 CTAATTCCCTACCACAGTTGATTAGAAAAAGTGAGGGACAATATTCGATACTTAGCAAAGAAAAT
1 CTAATTCCCTACCACAGTTGATTAGAAAAAGTGAGGGAAAATATTCGATACTTAGCAAAGAAAAC
30172827 TGATTGAAAGAGTAACGCTTACACTAGATTCGGTCAAAGAGTATTCGGCTCTAGAGATTTGAATG
66 TGATTGAAAGAGTAACGCTTACACTAGATTCGGTCAAAGAGTATTCGGCTCTAGAGATTTGAATG
30172892 GCAACAATTGCTTATTCGGCACCAAGGGAGAGAGGAAGAAGAATCGGCTAAACCCAAAAGTGAAA
131 GCAACAATTGCTTATTCGGCACCAAGGGAGAGAGGAAGAAGAATCGGCTAAACCCAAAAGTGAAA
30172957 CAAAGAAATCGGCACCAGGAAAATAAAAAGGAGAACAAGGGTTTTCGACTTTTGGAGAAATCAGT
196 CAAAGAAATCGGCACCAGGAAAATAAAAAGGAGAACAAGGGTTTTCGACTTTTGGAGAAATCAGT
*
30173022 CTAATTCCCTACCACAGTTGATTAGAAAGAGTGAGGGAAAATATTCGATACTTAGCAAAGAAAAC
1 CTAATTCCCTACCACAGTTGATTAGAAAAAGTGAGGGAAAATATTCGATACTTAGCAAAGAAAAC
*
30173087 TGATTGGAAA-AGTAACTCTTACACTAGATTCGGTCAAAGAGTATTCGGCTCTAGAGATTTGAAT
66 TGATT-GAAAGAGTAACGCTTACACTAGATTCGGTCAAAGAGTATTCGGCTCTAGAGATTTGAAT
30173151 GGCAACAATTGCTTATTCGGCACCAAGGGAGAGAGGAAGAAGAATCGGCTAAACCCAAAAGTGAA
130 GGCAACAATTGCTTATTCGGCACCAAGGGAGAGAGGAAGAAGAATCGGCTAAACCCAAAAGTGAA
30173216 ACAAAGAAATCGGCACCAGGAAAATAAAAAGGAGAACAAGGGTTTTCGACTTTTGGAGAAATCAG
195 ACAAAGAAATCGGCACCAGGAAAATAAAAAGGAGAACAAGGGTTTTCGACTTTTGGAGAAATCAG
30173281 T
260 T
30173282 AGAAAGAAAA
Statistics
Matches: 255, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
260 251 0.98
261 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (260 bp):
CTAATTCCCTACCACAGTTGATTAGAAAAAGTGAGGGAAAATATTCGATACTTAGCAAAGAAAAC
TGATTGAAAGAGTAACGCTTACACTAGATTCGGTCAAAGAGTATTCGGCTCTAGAGATTTGAATG
GCAACAATTGCTTATTCGGCACCAAGGGAGAGAGGAAGAAGAATCGGCTAAACCCAAAAGTGAAA
CAAAGAAATCGGCACCAGGAAAATAAAAAGGAGAACAAGGGTTTTCGACTTTTGGAGAAATCAGT
Found at i:30182151 original size:28 final size:29
Alignment explanation
Indices: 30182119--30182233 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
30182109 TACCTGTATC
* *
30182119 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
30182147 TGGCCCATTAGGCCCAAATCACCTAT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
* *
30182176 TGGCCCATTAGGCCCAAATCACATTTATT
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
30182205 TGGCCCGTTAGGCCC-AATCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
30182233 T
1 T
30182234 TCATGCTCAC
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 27 0.36
29 48 0.63
30 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:30182182 original size:57 final size:57
Alignment explanation
Indices: 30182110--30182225 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 57
30182100 AAATTCACAT
* * *
30182110 ACCTGTATCTGGCCCATTAAGCCC-AATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCC-AATC
* * * *
30182167 ACCTATATATGGCCCATTAGGCCCAAATCACATTTATTTGGCCCGTTAGGCCCAATC
1 ACCTATATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAATC
30182224 AC
1 AC
30182226 ATTCATATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 27 0.53
58 24 0.47
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27
Consensus pattern (57 bp):
ACCTATATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAATC
Found at i:30183965 original size:16 final size:17
Alignment explanation
Indices: 30183934--30183972 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
30183924 CACAAACATT
*
30183934 TCATAATCATCATATCA
1 TCATAGTCATCATATCA
30183951 TCATAGTCA-CATATCA
1 TCATAGTCATCATATCA
*
30183967 TTATAG
1 TCATAG
30183973 AGTCCCTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (17 bp):
TCATAGTCATCATATCA
Found at i:30185392 original size:42 final size:42
Alignment explanation
Indices: 30185305--30185453 Score: 156
Period size: 43 Copynumber: 3.5 Consensus size: 42
30185295 CCAACATCCT
* * * * *
30185305 AGACATGGTCTTACATGTAATCGAATATCGATGTCACTGCCCC
1 AGACATGGTCTTACATGAAATCAAATA-CGATGCCAATGTCCC
* *
30185348 AGACAGGGTCTTACTTGAAATCAAATACGATGCCAATGTCCC
1 AGACATGGTCTTACATGAAATCAAATACGATGCCAATGTCCC
* * *
30185390 AGACATGGTCTTACACGTAAATCATAAGT-CAATGCCAACGTCCC
1 AGACATGGTCTTACATG-AAATCA-AA-TACGATGCCAATGTCCC
*
30185434 AGACATGGTCTTACACGAAA
1 AGACATGGTCTTACATGAAA
30185454 ACACATATCG
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
42 26 0.29
43 32 0.35
44 32 0.35
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (42 bp):
AGACATGGTCTTACATGAAATCAAATACGATGCCAATGTCCC
Found at i:30186830 original size:66 final size:65
Alignment explanation
Indices: 30186715--30186850 Score: 157
Period size: 66 Copynumber: 2.1 Consensus size: 65
30186705 CACACACGGA
*
30186715 CGTGTGACCGGCCGTGTGGTACAAGTTAGTATACCCCCTGTTTGGCACACGGCCTAACACATGAG
1 CGTGTGACCGGCCGTGTGGTACAAGTCAGTATACCCCCTGTTTGGCACACGGCCTAACACATGAG
* * * * * * **
30186780 CGTGTGACTTGGCCGTGTTGTATAAGTCAGTATACTCTCTAGTTT-TCACACGGCCTGGCACATG
1 CGTGTGAC-CGGCCGTGTGGTACAAGTCAGTATACCCCCT-GTTTGGCACACGGCCTAACACATG
*
30186844 GG
64 AG
30186846 CGTGT
1 CGTGT
30186851 CTTCGGCCTG
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 8 0.14
66 47 0.80
67 4 0.07
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (65 bp):
CGTGTGACCGGCCGTGTGGTACAAGTCAGTATACCCCCTGTTTGGCACACGGCCTAACACATGAG
Found at i:30186871 original size:25 final size:24
Alignment explanation
Indices: 30186830--30186877 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
30186820 AGTTTTCACA
*
30186830 CGGCCTGGCACATGGGCGTGTCTT
1 CGGCCTGGCACACGGGCGTGTCTT
*
30186854 CGGCCTGTTCACACGGGCGTGTCT
1 CGGCCTG-GCACACGGGCGTGTCT
30186878 ACTAGCCGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.08, C:0.31, G:0.35, T:0.25
Consensus pattern (24 bp):
CGGCCTGGCACACGGGCGTGTCTT
Found at i:30192753 original size:41 final size:41
Alignment explanation
Indices: 30192685--30192861 Score: 239
Period size: 41 Copynumber: 4.3 Consensus size: 41
30192675 GCAGCGTTTT
* * * *
30192685 AAACGCCGCT-AAAAATAGAGCAATAGCGGCGTTTTTGGTA
1 AAACGCCGCTAAAAAACAGAGCATTAGCGGCGCTTTCGGTA
* * *
30192725 AAACGCCACTAAAAAATAGAGCATTAGCGGTGCTTTCGGTA
1 AAACGCCGCTAAAAAACAGAGCATTAGCGGCGCTTTCGGTA
* *
30192766 AAAAGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGTA
1 AAACGCCGCTAAAAAACAGAGCATTAGCGGCGCTTTCGGTA
* * *
30192807 AAACGTCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATA
1 AAACGCCGCTAAAAAACAGAGCATTAGCGGCGCTTTCGGTA
30192848 AAACGCCGCTAAAA
1 AAACGCCGCTAAAA
30192862 GTCATATAAC
Statistics
Matches: 122, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 9 0.07
41 113 0.93
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (41 bp):
AAACGCCGCTAAAAAACAGAGCATTAGCGGCGCTTTCGGTA
Found at i:30192973 original size:54 final size:55
Alignment explanation
Indices: 30192874--30192980 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 55
30192864 CATATAACCC
** *
30192874 CTAAAACCCTAAACCCCAAAAAAATCATAAACACTAATTTGTAACCCCTAAAATA
1 CTAAAACCCTAAACCCCAAAAAAATCATAAACACTAAACTATAACCCCTAAAATA
* * * *
30192929 CTAAAACCCTAAA-TCCTAAAAAATCCTAAACAGTAAACTATAACCCCTAAAA
1 CTAAAACCCTAAACCCCAAAAAAATCATAAACACTAAACTATAACCCCTAAAA
30192981 CCCTAAACCC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
54 32 0.71
55 13 0.29
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.20
Consensus pattern (55 bp):
CTAAAACCCTAAACCCCAAAAAAATCATAAACACTAAACTATAACCCCTAAAATA
Found at i:30193892 original size:9 final size:8
Alignment explanation
Indices: 30193874--30193947 Score: 62
Period size: 8 Copynumber: 8.9 Consensus size: 8
30193864 TTTATATGAT
30193874 AATTTAAA
1 AATTTAAA
30193882 AATTATAAA
1 AATT-TAAA
30193891 AATCTTCAAAA
1 AAT-TT--AAA
30193902 AATTTTAAA
1 AA-TTTAAA
30193911 AA-TTAAA
1 AATTTAAA
30193918 AA-TTAAA
1 AATTTAAA
*
30193925 AATTAAAA
1 AATTTAAA
*
30193933 AACTTAAA
1 AATTTAAA
*
30193941 TATTTAA
1 AATTTAA
30193948 TATTTAATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
7 14 0.25
8 19 0.35
9 13 0.24
10 1 0.02
11 7 0.13
12 1 0.02
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (8 bp):
AATTTAAA
Found at i:30193925 original size:6 final size:7
Alignment explanation
Indices: 30193906--30193933 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
30193896 TCAAAAAATT
30193906 TTAAAAA
1 TTAAAAA
30193913 TTAAAAA
1 TTAAAAA
30193920 TTAAAAA
1 TTAAAAA
30193927 TTAAAAA
1 TTAAAAA
30193934 ACTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:30194064 original size:8 final size:8
Alignment explanation
Indices: 30194053--30194101 Score: 98
Period size: 8 Copynumber: 6.1 Consensus size: 8
30194043 AAAAAAATAA
30194053 AAAATGAT
1 AAAATGAT
30194061 AAAATGAT
1 AAAATGAT
30194069 AAAATGAT
1 AAAATGAT
30194077 AAAATGAT
1 AAAATGAT
30194085 AAAATGAT
1 AAAATGAT
30194093 AAAATGAT
1 AAAATGAT
30194101 A
1 A
30194102 GTGTAATGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AAAATGAT
Found at i:30194111 original size:11 final size:11
Alignment explanation
Indices: 30194095--30194133 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
30194085 AAAATGATAA
30194095 AATGATAGTGT
1 AATGATAGTGT
30194106 AATGATAGTGT
1 AATGATAGTGT
30194117 AATGATAGTGT
1 AATGATAGTGT
30194128 AATGAT
1 AATGAT
30194134 TTTTGGCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (11 bp):
AATGATAGTGT
Found at i:30194530 original size:40 final size:40
Alignment explanation
Indices: 30194471--30194593 Score: 192
Period size: 40 Copynumber: 3.1 Consensus size: 40
30194461 GAGAATTGAG
* * ** *
30194471 AGTGATATATCCGGGCTAAGCCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCAGACTAAGTTCCGAAGAGCATTCGTGCT
30194511 AGTGATATATCCAGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCAGACTAAGTTCCGAAGAGCATTCGTGCT
*
30194551 AGTGATGTATCCAGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCAGACTAAGTTCCGAAGAGCATTCGTGCT
30194591 AGT
1 AGT
30194594 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCAGACTAAGTTCCGAAGAGCATTCGTGCT
Found at i:30197793 original size:37 final size:37
Alignment explanation
Indices: 30197737--30197815 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
30197727 CCGAGCTCTA
* * *
30197737 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
30197774 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
30197811 AAGAC
1 AAGAC
30197816 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:30200702 original size:96 final size:96
Alignment explanation
Indices: 30200536--30200729 Score: 307
Period size: 96 Copynumber: 2.0 Consensus size: 96
30200526 GTGTTCGAGG
** * * * *
30200536 AAGTCTGTTGTCGATGGGAATGATCGAGCAGATACGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATCGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
30200601 AAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
66 AAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
*
30200632 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATCGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
* *
30200697 TAAAGCCGAAGCCAAGAGGGCTAAGAGGAGC
66 AAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
30200728 AA
1 AA
30200730 AAAGAAGCGA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.35, C:0.18, G:0.35, T:0.12
Consensus pattern (96 bp):
AAGTCTGTCATCGAAGGGAACGATCGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
AAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
Found at i:30208462 original size:25 final size:25
Alignment explanation
Indices: 30208428--30208475 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
30208418 CCTCTAGGAG
30208428 AAGAAAATTCAATATGTCAAATTCA
1 AAGAAAATTCAATATGTCAAATTCA
* *
30208453 AAGAAAATTCACTATGTCGAATT
1 AAGAAAATTCAATATGTCAAATT
30208476 TGAATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (25 bp):
AAGAAAATTCAATATGTCAAATTCA
Found at i:30209222 original size:12 final size:12
Alignment explanation
Indices: 30209205--30209354 Score: 52
Period size: 12 Copynumber: 12.6 Consensus size: 12
30209195 ATTTAATCAT
30209205 TTTAATATTAAA
1 TTTAATATTAAA
30209217 TTTAAT-TTAATA
1 TTTAATATTAA-A
*
30209229 TTT-ATCTTGGTAAA
1 TTTAAT-AT--TAAA
30209243 TATT-ATATTAAA
1 T-TTAATATTAAA
30209255 TTTAATATTAAA
1 TTTAATATTAAA
*
30209267 --TATTATTAAA
1 TTTAATATTAAA
*
30209277 -TTAATA-CAATA
1 TTTAATATTAA-A
*
30209288 TTT-AT-CTACAA
1 TTTAATATTA-AA
* *
30209299 TATAAACATTAAA
1 T-TTAATATTAAA
30209312 TTTAAT-TTAATA
1 TTTAATATTAA-A
* * *
30209324 TTAAGATAATAAC
1 TTTA-ATATTAAA
30209337 TTTAATATTAAA
1 TTTAATATTAAA
30209349 -TTAATA
1 TTTAATA
30209355 AAATATTATT
Statistics
Matches: 104, Mismatches: 16, Indels: 37
0.66 0.10 0.24
Matches are distributed among these distances:
10 11 0.11
11 28 0.27
12 40 0.38
13 10 0.10
14 8 0.08
15 7 0.07
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (12 bp):
TTTAATATTAAA
Done.