Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003115.1 Hibiscus syriacus cultivar Beakdansim tig00006521_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: 55694
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Found at i:3459 original size:11 final size:12
Alignment explanation
Indices: 3428--3471 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
3418 TCAAAAATCA
3428 TAAAATAATTAT
1 TAAAATAATTAT
3440 T-AAAT--TTAT
1 TAAAATAATTAT
3449 TAAAAT-ATTA-
1 TAAAATAATTAT
3459 TAAAATAATTAT
1 TAAAATAATTAT
3471 T
1 T
3472 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:4851 original size:2 final size:2
Alignment explanation
Indices: 4846--4877 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4836 TCTCTCTCTC
4846 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4878 AGCTATAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5825 original size:27 final size:27
Alignment explanation
Indices: 5795--5851 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
5785 GACCTCTCAA
5795 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
*
5822 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
5849 TCC
1 TCC
5852 CCCTCCTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.11, C:0.54, G:0.11, T:0.25
Consensus pattern (27 bp):
TCCTAGTAACCGTCGTCCCCCTCCCCC
Found at i:6050 original size:42 final size:42
Alignment explanation
Indices: 6004--6413 Score: 319
Period size: 42 Copynumber: 10.5 Consensus size: 42
5994 ACACCTCCTA
*
6004 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* **
6046 CCCCTTCTCCTACTCCCCCTCCTCGTACACCTC-T-----TC
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* * * *
6082 CACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* ** *
6124 CCCCTGCTCCTACTCCCCCTCCTCGTACA-C-C-T---CCTA
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* *
6160 TCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTT-CCCCCTC
* *
6202 CTCCTGCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* * *
6244 CCCCTGCTCCTAC-CCCCCTCCT--CG-------TACACCT-
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* * *
6275 --CCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* ** *
6315 CCCCTGCTCCTACTCCCCCTCCTCGTACA-C-C-T---CCTA
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* *
6351 CCCCTCCACCTACT-CCCCTCCTAGCGCACCTCTTCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
*
6392 CCCCTGCTCCTACTCCCCCTCC
1 CCCCTCCTCCTACTCCCCCTCC
6414 ACGTACACCT
Statistics
Matches: 284, Mismatches: 50, Indels: 68
0.71 0.12 0.17
Matches are distributed among these distances:
29 9 0.03
30 8 0.03
32 7 0.02
35 11 0.04
36 72 0.25
37 3 0.01
38 2 0.01
39 9 0.03
40 2 0.01
41 27 0.10
42 132 0.46
43 2 0.01
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.24
Consensus pattern (42 bp):
CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
Found at i:6062 original size:21 final size:21
Alignment explanation
Indices: 5974--6145 Score: 85
Period size: 21 Copynumber: 8.5 Consensus size: 21
5964 AACACGCCTC
* *
5974 CTCCCCCTCCCCCTCCTCGTA
1 CTCCCCCTCCCCCTCCACCTA
* * *
5995 CACCTCCTACCCCTCCACCTA
1 CTCCCCCTCCCCCTCCACCTA
* *
6016 CTCCCCCTCCTCGC-GCACCT-
1 CTCCCCCTCC-CCCTCCACCTA
* *
6036 CTTCCCCCTCCCCCTTCTCCTA
1 C-TCCCCCTCCCCCTCCACCTA
* * *
6058 CTCCCCCTCCTCGTACACCT-
1 CTCCCCCTCCCCCTCCACCTA
*
6078 CT-----TCCACCTCCACCTA
1 CTCCCCCTCCCCCTCCACCTA
**
6094 CTCCCCCTCCTAGCT-CACCT-
1 CTCCCCCTCC-CCCTCCACCTA
* *
6114 CTTCCCCCTCCCCCTGCTCCTA
1 C-TCCCCCTCCCCCTCCACCTA
6136 CTCCCCCTCC
1 CTCCCCCTCC
6146 TCGTACACCT
Statistics
Matches: 113, Mismatches: 24, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
15 10 0.09
16 2 0.02
20 8 0.07
21 86 0.76
22 7 0.06
ACGTcount: A:0.09, C:0.63, G:0.03, T:0.24
Consensus pattern (21 bp):
CTCCCCCTCCCCCTCCACCTA
Found at i:6073 original size:78 final size:78
Alignment explanation
Indices: 5980--6253 Score: 408
Period size: 78 Copynumber: 3.5 Consensus size: 78
5970 CCTCCTCCCC
5980 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
*
6045 CCCCCTTCTCCTA
66 CCCCCTGCTCCTA
* * *
6058 CTCCCCCTCCTCGTACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
6122 TCCCCCTGCTCCTA
65 TCCCCCTGCTCCTA
*
6136 CTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCC
*
6200 TCCTCCTGCTCCTA
65 TCCCCCTGCTCCTA
** * * * *
6214 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
6254 TACCCCCCTC
Statistics
Matches: 177, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
77 6 0.03
78 168 0.95
79 3 0.02
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (78 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
CCCCCTGCTCCTA
Found at i:6242 original size:21 final size:21
Alignment explanation
Indices: 6173--6244 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 21
6163 CTCCACCTAC
6173 TCCCCCTCCTCGCGCACCT-T
1 TCCCCCTCCTCGCGCACCTCT
*
6193 TCCCCCCTCCTC-CTGCTCCTAC-
1 T-CCCCCTCCTCGC-GCACCT-CT
6215 TCCCCCTCCTCGCGCACCTCT
1 TCCCCCTCCTCGCGCACCTCT
6236 TCCCCCTCC
1 TCCCCCTCC
6245 CCCTGCTCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
20 3 0.07
21 39 0.89
22 2 0.05
ACGTcount: A:0.04, C:0.64, G:0.07, T:0.25
Consensus pattern (21 bp):
TCCCCCTCCTCGCGCACCTCT
Found at i:6261 original size:21 final size:21
Alignment explanation
Indices: 6194--6261 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
6184 GCGCACCTTT
*
6194 CCCCCCTCCTCCTGCTCCTAC
1 CCCCCCTCCCCCTGCTCCTAC
* * *
6215 TCCCCCTCCTCGC-GCACCT-C
1 CCCCCCTCC-CCCTGCTCCTAC
*
6235 TTCCCCCTCCCCCTGCTCCTAC
1 -CCCCCCTCCCCCTGCTCCTAC
6257 CCCCC
1 CCCCC
6262 TCCTCGTACA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
20 3 0.08
21 31 0.86
22 2 0.06
ACGTcount: A:0.04, C:0.68, G:0.06, T:0.22
Consensus pattern (21 bp):
CCCCCCTCCCCCTGCTCCTAC
Found at i:6453 original size:6 final size:6
Alignment explanation
Indices: 6430--6490 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
6420 ACCTCCTACC
* * *
6430 CCTCCA CCTACT CCTCCC CCTCC- CTCTCCA CCTCC- CCTCCA CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
6477 CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CC
6491 AGTTACCTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
5 6 0.12
6 41 0.85
7 1 0.02
ACGTcount: A:0.11, C:0.69, G:0.00, T:0.20
Consensus pattern (6 bp):
CCTCCA
Found at i:6464 original size:21 final size:21
Alignment explanation
Indices: 6377--6487 Score: 86
Period size: 21 Copynumber: 5.3 Consensus size: 21
6367 CCTCCTAGCG
* * *
6377 CACCTCTTCCCCCTCCCCCTG
1 CACCTCCTCCCCCTCCACCTC
* * * *
6398 CTCCTACTCCCCCTCCACGTA
1 CACCTCCTCCCCCTCCACCTC
*
6419 CACCTCCTACCCCTCCACCT-
1 CACCTCCTCCCCCTCCACCTC
6439 -A-CTCCTCCCCCTCC-CTCTC
1 CACCTCCTCCCCCTCCAC-CTC
*
6458 CACCTCCCCTCCACCTCCACCTC
1 CACCT--CCTCCCCCTCCACCTC
6481 CACCTCC
1 CACCTCC
6488 ACCAGTTACC
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
17 1 0.01
18 14 0.20
19 1 0.01
20 1 0.01
21 35 0.49
23 18 0.25
24 1 0.01
ACGTcount: A:0.11, C:0.66, G:0.02, T:0.22
Consensus pattern (21 bp):
CACCTCCTCCCCCTCCACCTC
Found at i:6469 original size:77 final size:78
Alignment explanation
Indices: 6210--6446 Score: 391
Period size: 77 Copynumber: 3.1 Consensus size: 78
6200 TCCTCCTGCT
* *
6210 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTAC-CCCCCTCCTCGTACA--
1 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
6272 -CCT---CCTCCA
66 TCCTACCCCTCCA
6281 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
6346 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
6359 CCTACTCC-CCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACC
1 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
6423 TCCTACCCCTCCA
66 TCCTACCCCTCCA
6436 CCTACTCCTCC
1 CCTACTCCTCC
6447 CCCTCCCTCT
Statistics
Matches: 155, Mismatches: 3, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
71 45 0.29
72 15 0.10
75 3 0.02
77 76 0.49
78 16 0.10
ACGTcount: A:0.10, C:0.62, G:0.05, T:0.23
Consensus pattern (78 bp):
CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCA
Found at i:10237 original size:20 final size:19
Alignment explanation
Indices: 10196--10269 Score: 91
Period size: 20 Copynumber: 4.0 Consensus size: 19
10186 TAGTCCAAAA
* * *
10196 AGTTTCGATACTTTTTAAG
1 AGTTTCGAAACTTCTCAAG
10215 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACT-TCTCAAG
10235 AGTTTCGAAACTTCT-AA-
1 AGTTTCGAAACTTCTCAAG
10252 AGTTTCG-AACTTCTCAAG
1 AGTTTCGAAACTTCTCAAG
10270 GCTTTCCAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
16 7 0.14
17 9 0.18
18 2 0.04
19 14 0.29
20 17 0.35
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (19 bp):
AGTTTCGAAACTTCTCAAG
Found at i:15012 original size:11 final size:12
Alignment explanation
Indices: 14981--15024 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
14971 TCAAAAATCA
14981 TAAAATAATTAT
1 TAAAATAATTAT
14993 T-AAAT--TTAT
1 TAAAATAATTAT
15002 TAAAAT-ATTA-
1 TAAAATAATTAT
15012 TAAAATAATTAT
1 TAAAATAATTAT
15024 T
1 T
15025 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:16423 original size:2 final size:2
Alignment explanation
Indices: 16418--16455 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
16408 TCTCTCTCTC
16418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16456 AGCTATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17404 original size:27 final size:27
Alignment explanation
Indices: 17374--17430 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
17364 GACCTCTCAA
17374 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
*
17401 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
17428 TCC
1 TCC
17431 CCTCCTCCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.11, C:0.54, G:0.11, T:0.25
Consensus pattern (27 bp):
TCCTAGTAACCGTCGTCCCCCTCCCCC
Found at i:17639 original size:21 final size:20
Alignment explanation
Indices: 17552--18038 Score: 98
Period size: 21 Copynumber: 24.6 Consensus size: 20
17542 AACACGCCTC
17552 CTCCCCCTCCCCCTC-CTCGTA
1 CTCCCCCTCCCCCTCAC-C-TA
* * *
17573 CACCTCCTACCCCTCACCTA
1 CTCCCCCTCCCCCTCACCTA
* *
17593 CTCCCCCTCCTCGCGCACCT-
1 CTCCCCCTCC-CCCTCACCTA
*
17613 CTTCCCCCTCCCCCTTCTCCTA
1 C-TCCCCCTCCCCC-TCACCTA
* *
17635 CTCCCCCTCCTCGTACACCT-
1 CTCCCCCTCCCCCT-CACCTA
*
17655 CT-----TCCACCTCCACCTA
1 CTCCCCCTCCCCCT-CACCTA
**
17671 CTCCCCCTCCTAGCTCACCT-
1 CTCCCCCTCC-CCCTCACCTA
*
17691 CTTCCCCCTCCCCCTGCTCCTA
1 C-TCCCCCTCCCCCT-CACCTA
*
17713 CTCCCCCT---CCT--CGTA
1 CTCCCCCTCCCCCTCACCTA
* * **
17728 CACCTCCTATCCCTCCACCTA
1 CTCCCCCTCCCCCT-CACCTA
* *
17749 CTCCCCCTCCTCGCGCACCT-
1 CTCCCCCTCC-CCCTCACCTA
* * *
17769 TTCCCCCCTCCTCCTGCTCCTA
1 CT-CCCCCTCCCCCT-CACCTA
* *
17791 CTCCCCCTCCTCGCGCACCT-
1 CTCCCCCTCC-CCCTCACCTA
*
17811 CTTCCCCCTCCCCCTGCTCCTA
1 C-TCCCCCTCCCCCT-CACCTA
*
17833 CTCCCCCT---CCT--CGTA
1 CTCCCCCTCCCCCTCACCTA
* * *
17848 CACCTCCTACCCCTCCACCTA
1 CTCCCCCTCCCCCT-CACCTA
* ** *
17869 CTCCTCCTCCTAGCGCACCT-
1 CTCCCCCTCC-CCCTCACCTA
*
17889 CTTCCCCCTCCCCCTGCTCCTA
1 C-TCCCCCTCCCCCT-CACCTA
*
17911 CTCCCCCT---CCT--CGTA
1 CTCCCCCTCCCCCTCACCTA
* * *
17926 CACCTCCTACCCCTCCACCTA
1 CTCCCCCTCCCCCT-CACCTA
** *
17947 CTCCCCCTCCTAGCGCACCT-
1 CTCCCCCTCC-CCCTCACCTA
*
17967 CTTCCCCCTCCCCCTGCTCCTA
1 C-TCCCCCTCCCCCT-CACCTA
* * *
17989 CTCCCCCTCCACGTACACCTC
1 CTCCCCCTCCCCCT-CACCTA
* * *
18010 CTACCCCTCCACCT-A-CTC
1 CTCCCCCTCCCCCTCACCTA
18028 CTCCCCCTCCC
1 CTCCCCCTCCC
18039 TCTCCACCTC
Statistics
Matches: 335, Mismatches: 81, Indels: 103
0.65 0.16 0.20
Matches are distributed among these distances:
15 37 0.11
16 2 0.01
18 30 0.09
19 1 0.00
20 27 0.08
21 223 0.67
22 15 0.04
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.24
Consensus pattern (20 bp):
CTCCCCCTCCCCCTCACCTA
Found at i:17804 original size:198 final size:198
Alignment explanation
Indices: 17589--17998 Score: 725
Period size: 198 Copynumber: 2.1 Consensus size: 198
17579 CTACCCCTCA
*
17589 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
* *
17654 T-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCTCCTACTCCC
66 TCCTACC-CCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCC
* * *
17718 CCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTC
130 CCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTT-CCCCCTCCCC
17782 CTGCT
194 CTGCT
17787 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
*
17852 TCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCC
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCC
17917 CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCT
131 CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCT
17982 GCT
196 GCT
17985 CCTACTCCCCCTCC
1 CCTACTCCCCCTCC
17999 ACGTACACCT
Statistics
Matches: 203, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
198 197 0.97
199 6 0.03
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.25
Consensus pattern (198 bp):
CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCC
CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCT
GCT
Found at i:17820 original size:78 final size:78
Alignment explanation
Indices: 17558--17830 Score: 399
Period size: 78 Copynumber: 3.5 Consensus size: 78
17548 CCTCCTCCCC
17558 CTCCCCCTCCTCGTACACCTCCTACCCCT-CACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
*
17622 CCCCCTTCTCCTA
66 CCCCCTGCTCCTA
* * *
17635 CTCCCCCTCCTCGTACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
17699 TCCCCCTGCTCCTA
65 TCCCCCTGCTCCTA
*
17713 CTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCC
*
17777 TCCTCCTGCTCCTA
65 TCCCCCTGCTCCTA
** * * * *
17791 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
17831 TACTCCCCCT
Statistics
Matches: 176, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
76 4 0.02
77 25 0.14
78 144 0.82
79 3 0.02
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (78 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
CCCCCTGCTCCTA
Found at i:17869 original size:78 final size:78
Alignment explanation
Indices: 17787--18028 Score: 457
Period size: 78 Copynumber: 3.1 Consensus size: 78
17777 TCCTCCTGCT
*
17787 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
17852 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
17865 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
17930 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
17943 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
18008 TCCTACCCCTCCA
66 TCCTACCCCTCCA
18021 CCTACTCC
1 CCTACTCC
18029 TCCCCCTCCC
Statistics
Matches: 160, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 160 1.00
ACGTcount: A:0.10, C:0.62, G:0.05, T:0.23
Consensus pattern (78 bp):
CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCA
Found at i:17922 original size:120 final size:120
Alignment explanation
Indices: 17667--17950 Score: 444
Period size: 120 Copynumber: 2.4 Consensus size: 120
17657 TCCACCTCCA
* *
17667 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
* * *
17732 TCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCTTTCCCCCCTCCTCCTGCT
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTTTCCCCCCTCCCCCTGCT
*
17787 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
*
17852 TCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTT-CCCCCTCCCCCTGCT
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCT-TTCCCCCCTCCCCCTGCT
* * * * *
17907 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCC
17951 CCCTCCTAGC
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
120 149 0.99
121 2 0.01
ACGTcount: A:0.09, C:0.61, G:0.05, T:0.25
Consensus pattern (120 bp):
CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTTTCCCCCCTCCCCCTGCT
Found at i:18008 original size:42 final size:42
Alignment explanation
Indices: 17589--18029 Score: 281
Period size: 42 Copynumber: 11.1 Consensus size: 42
17579 CTACCCCTCA
* * * * *
17589 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * * * *
17631 CCTACTCCCCCTCCT--CGTA-CACCT---CTTCCACCTCCA
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * * * *
17667 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* ** *
17709 CCTACTCCCCCTCCTCGTACACCTCCTATCCCT---CC-A--
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * *
17745 CCTACTCCCCCTCCTCGCGCACCTTTCC--CCCCTCCTCCTGCT
1 CCTACTCCCCCTCCTAGCGCACC--TCCTACCCCTCCACCTACT
* * * * *
17787 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* **
17829 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * * *
17871 -C--CT---CCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* **
17907 CCTACTCCCCCTCCTCGTACACCTCCTACCCCT---CC-A--
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * * *
17943 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
17985 CCTACTCCCCCTCC-A-CGTACACCTCCTACCCCTCCACCTACT
1 CCTACTCCCCCTCCTAGCG--CACCTCCTACCCCTCCACCTACT
18027 CCT
1 CCT
18030 CCCCCTCCCT
Statistics
Matches: 312, Mismatches: 57, Indels: 60
0.73 0.13 0.14
Matches are distributed among these distances:
36 102 0.33
37 1 0.00
38 5 0.02
39 18 0.06
40 7 0.02
41 2 0.01
42 177 0.57
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.24
Consensus pattern (42 bp):
CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
Found at i:18008 original size:120 final size:119
Alignment explanation
Indices: 17558--18029 Score: 382
Period size: 120 Copynumber: 4.0 Consensus size: 119
17548 CCTCCTCCCC
* *
17558 CTCCCCCTCCTCGTACACCTCCTACCCCT-CACCTACTCCCCCTCCTCGCGCACCTC-TTC-CC-
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCACTCC-C-C-CACCTCGTACACCT
* * * * * *
17619 CCTCCCCCTTCTCCTACTCCCCCTCCTCGTACACCTCTTCCACCT---C--CACCTA
63 CCTACCCCTCCACCTACTCCCCCTCCACGTACACCTCTTCCCCCTCCCCTGCTCCTA
* * * * * * *
17671 CTCCCCCTCCTAGCT-CACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTCC
1 CTCCCCCTCCTCG-TACACCTCCTACCCCTCCACCTACTCCCACTCCCCCACCTCGTACACCTCC
* * **
17735 TATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTGCTCCTA
65 TACCCCTCCACCTACTCCCCCTCCACGTACACCTCTT-CCCCCTCC-CCTGCTCCTA
** * * * * * *
17791 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTCCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCACTCCCCCACCTCGTACACCTCCT
*
17856 ACCCCTCCACCTACTCCTCCTCCTAGCG--CACCTCTTCCCCCTCCCCCTGCTCCTA
66 ACCCCTCCACCTACTCCCCCTCC-A-CGTACACCTCTTCCCCCT-CCCCTGCTCCTA
* * *
17911 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTC-TTC-CC-
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCACTCC---CCCACCTCGTACACCT
* * * * * *
17973 CCTCCCCCTGCTCCTACTCCCCCTCCACGTACACCTCCTACCCCTCCACCTACTCCT
63 CCTACCCCTCCACCTACTCCCCCTCCACGTACACCTCTTCCCCCTCC-CCTGCTCCT
18030 CCCCCTCCCT
Statistics
Matches: 296, Mismatches: 40, Indels: 39
0.79 0.11 0.10
Matches are distributed among these distances:
111 5 0.02
112 3 0.01
113 29 0.10
114 48 0.16
118 3 0.01
119 3 0.01
120 189 0.64
121 6 0.02
122 4 0.01
123 6 0.02
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.24
Consensus pattern (119 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCACTCCCCCACCTCGTACACCTCCT
ACCCCTCCACCTACTCCCCCTCCACGTACACCTCTTCCCCCTCCCCTGCTCCTA
Found at i:18028 original size:18 final size:18
Alignment explanation
Indices: 17929--18076 Score: 72
Period size: 18 Copynumber: 7.9 Consensus size: 18
17919 CCTCGTACAC
*
17929 CTCCTACCCCTCCACCTA
1 CTCCTCCCCCTCCACCTA
17947 CTCC-CCCTCCTAGCGCACCT-
1 CTCCTCCC-CCT--C-CACCTA
* *
17967 CT--TCCCCCTCCCCCTG
1 CTCCTCCCCCTCCACCTA
*
17983 CTCCTACTCCCCCTCCACGTACA
1 CT-C--CTCCCCCTCCACCT--A
*
18006 CCTCCTACCCCTCCACCTA
1 -CTCCTCCCCCTCCACCTA
*
18025 CTCCTCCCCCTCC-CTCTC
1 CTCCTCCCCCTCCAC-CTA
* *
18043 CACCTCCCCCTCCACCTC
1 CTCCTCCCCCTCCACCTA
* *
18061 CACCTCCACCTCCACC
1 CTCCTCCCCCTCCACC
18077 AGTTACCTGC
Statistics
Matches: 103, Mismatches: 11, Indels: 32
0.71 0.08 0.22
Matches are distributed among these distances:
15 4 0.04
16 3 0.03
17 3 0.03
18 54 0.52
19 5 0.05
20 3 0.03
21 28 0.27
23 1 0.01
24 2 0.02
ACGTcount: A:0.11, C:0.65, G:0.03, T:0.21
Consensus pattern (18 bp):
CTCCTCCCCCTCCACCTA
Found at i:18038 original size:6 final size:6
Alignment explanation
Indices: 18015--18076 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
18005 ACCTCCTACC
* * * *
18015 CCTCCA CCTACT CCTCCC CCTCC- CTCTCCA CCTCCC CCTCCA CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
18063 CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CC
18077 AGTTACCTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 1 0.02
6 46 0.96
7 1 0.02
ACGTcount: A:0.11, C:0.69, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCA
Found at i:18049 original size:21 final size:20
Alignment explanation
Indices: 17935--18067 Score: 71
Period size: 21 Copynumber: 6.7 Consensus size: 20
17925 ACACCTCCTA
*
17935 CCCCTCCACCTACTCCCCCT
1 CCCCTCCACCTCCTCCCCCT
*** *
17955 CCTAGCGCACCTCTTCCCCCT
1 CCCCTC-CACCTCCTCCCCCT
* * *
17976 CCCCCTGCTCCTACTCCCCCT
1 -CCCCTCCACCTCCTCCCCCT
* * *
17997 CCACGTACACCTCCTACCCCT
1 CC-CCTCCACCTCCTCCCCCT
18018 CCACCT--A-CTCCTCCCCCT
1 CC-CCTCCACCTCCTCCCCCT
18036 CCCTCTCCA---CCTCCCCCT
1 CCC-CTCCACCTCCTCCCCCT
18054 CCACCTCCACCTCC
1 CC-CCTCCACCTCC
18068 ACCTCCACCA
Statistics
Matches: 84, Mismatches: 19, Indels: 19
0.69 0.16 0.16
Matches are distributed among these distances:
17 1 0.01
18 30 0.36
19 2 0.02
20 6 0.07
21 43 0.51
22 2 0.02
ACGTcount: A:0.11, C:0.65, G:0.03, T:0.21
Consensus pattern (20 bp):
CCCCTCCACCTCCTCCCCCT
Found at i:21731 original size:20 final size:20
Alignment explanation
Indices: 21706--21780 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
21696 GATACTTTTT
21706 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
21726 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTC
21746 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
21766 AAAAGTTTCGAAACT
1 AAGAGTTTCGAAACT
21781 TTCCCTAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (20 bp):
AAGAGTTTCGAAACTATCTC
Found at i:21790 original size:20 final size:20
Alignment explanation
Indices: 21705--21796 Score: 102
Period size: 20 Copynumber: 4.6 Consensus size: 20
21695 CGATACTTTT
21705 TAAGAGTTTCGAAACTAT-C
1 TAAGAGTTTCGAAACTATCC
21724 TCAAGAGTTTCGAAACTAT-C
1 T-AAGAGTTTCGAAACTATCC
21744 TAAAGAGTTTCGAAACTAT-C
1 T-AAGAGTTTCGAAACTATCC
* *
21764 TCAAAAGTTTCGAAACTTTCCC
1 T-AAGAGTTTCGAAACTAT-CC
21786 TAA-AGTTTCGA
1 TAAGAGTTTCGA
21797 TACTTTGGCT
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 61 0.92
21 2 0.03
22 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (20 bp):
TAAGAGTTTCGAAACTATCC
Found at i:21793 original size:40 final size:39
Alignment explanation
Indices: 21687--21796 Score: 150
Period size: 40 Copynumber: 2.8 Consensus size: 39
21677 CAATAGTCCA
* *
21687 AAAAGTTTCGATACTTTTTAAGAGTTTCGAAACTATCTC
1 AAAAGTTTCGAAACTTTCTAAGAGTTTCGAAACTATCTC
* *
21726 AAGAGTTTCGAAACTATCTAAAGAGTTTCGAAACTATCTC
1 AAAAGTTTCGAAACTTTCT-AAGAGTTTCGAAACTATCTC
21766 AAAAGTTTCGAAACTTTCCCTAA-AGTTTCGA
1 AAAAGTTTCGAAACTTT--CTAAGAGTTTCGA
21797 TACTTTGGCT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
39 15 0.24
40 43 0.69
41 2 0.03
42 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (39 bp):
AAAAGTTTCGAAACTTTCTAAGAGTTTCGAAACTATCTC
Found at i:26474 original size:11 final size:12
Alignment explanation
Indices: 26443--26486 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
26433 TCAAAAATCA
26443 TAAAATAATTAT
1 TAAAATAATTAT
26455 T-AAAT--TTAT
1 TAAAATAATTAT
26464 TAAAAT-ATTA-
1 TAAAATAATTAT
26474 TAAAATAATTAT
1 TAAAATAATTAT
26486 T
1 T
26487 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:27368 original size:2 final size:2
Alignment explanation
Indices: 27361--27385 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27351 CTATTAAAAT
27361 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
27386 GGGAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27849 original size:2 final size:2
Alignment explanation
Indices: 27844--27885 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27834 TCTCTCTCTC
27844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27886 AGTATAATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28821 original size:27 final size:27
Alignment explanation
Indices: 28791--28847 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
28781 GACCTCTCAA
28791 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
*
28818 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
28845 TCC
1 TCC
28848 CCTCCTCCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.11, C:0.54, G:0.11, T:0.25
Consensus pattern (27 bp):
TCCTAGTAACCGTCGTCCCCCTCCCCC
Found at i:29056 original size:21 final size:20
Alignment explanation
Indices: 28969--29258 Score: 83
Period size: 21 Copynumber: 14.5 Consensus size: 20
28959 AACACGCCTC
28969 CTCCCCCTCCCCCTC-CTCGTA
1 CTCCCCCTCCCCCTCAC-C-TA
* * *
28990 CACCTCCTACCCCTCACCTA
1 CTCCCCCTCCCCCTCACCTA
* *
29010 CTCCCCCTCCTCGCGCACCT-
1 CTCCCCCTCC-CCCTCACCTA
*
29030 CTTCCCCCTCCCCCTTCTCCTA
1 C-TCCCCCTCCCCC-TCACCTA
* *
29052 CTCCCCCTCCTCGTACACCT-
1 CTCCCCCTCCCCCT-CACCTA
*
29072 CT-----TCCACCTCCACCTA
1 CTCCCCCTCCCCCT-CACCTA
**
29088 CTCCCCCTCCTAGCTCACCT-
1 CTCCCCCTCC-CCCTCACCTA
*
29108 CTTCCCCC-CCCCCTGCTCCTA
1 C-TCCCCCTCCCCCT-CACCTA
*
29129 CTCCCCCT---CCT--CGTA
1 CTCCCCCTCCCCCTCACCTA
* * **
29144 CACCTCCTATCCCTCCACCTA
1 CTCCCCCTCCCCCT-CACCTA
* *
29165 CTCCCCCTCCTCGCGCACCT-
1 CTCCCCCTCC-CCCTCACCTA
* * *
29185 TTCCCCCCTCCTCCTGCTCCTA
1 CT-CCCCCTCCCCCT-CACCTA
* *
29207 CTCCCCCTCCTCGCGCACCT-
1 CTCCCCCTCC-CCCTCACCTA
*
29227 CTTCCCCCTCCCCCTGCTCCTA
1 C-TCCCCCTCCCCCT-CACCTA
29249 CTCCCCCTCC
1 CTCCCCCTCC
29259 TCGTACACCT
Statistics
Matches: 194, Mismatches: 44, Indels: 62
0.65 0.15 0.21
Matches are distributed among these distances:
15 19 0.10
16 2 0.01
18 6 0.03
19 2 0.01
20 33 0.17
21 122 0.63
22 10 0.05
ACGTcount: A:0.08, C:0.63, G:0.04, T:0.24
Consensus pattern (20 bp):
CTCCCCCTCCCCCTCACCTA
Found at i:29060 original size:42 final size:42
Alignment explanation
Indices: 29006--29410 Score: 376
Period size: 42 Copynumber: 10.2 Consensus size: 42
28996 CTACCCCTCA
*
29006 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
** * *
29048 CCTACTCCCCCTCCTCGTACACCTCTTCCACCT----C--CA
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
* *
29084 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCC-CCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
** ** * *
29125 CCTACTCCCCCTCCTCGTACA-C-C-T---CCTATCCCTCCA
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
*
29161 CCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTT-CCCCCTCCCCCTGCT
29203 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
** * * *
29245 CCTACTCCCCCTCCTCGTACA-C-C-T---CCTACCCCTCCA
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
* *
29281 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
** * * *
29323 CCTACTCCCCCTCCTCGTACA-C-C-T---CCTACCCCTCCA
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
*
29359 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
29401 CCTACTCCCC
1 CCTACTCCCC
29411 TCCACGTACA
Statistics
Matches: 287, Mismatches: 49, Indels: 54
0.74 0.13 0.14
Matches are distributed among these distances:
35 2 0.01
36 106 0.37
37 3 0.01
38 5 0.02
39 6 0.02
40 3 0.01
41 21 0.07
42 139 0.48
43 2 0.01
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.24
Consensus pattern (42 bp):
CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
Found at i:29067 original size:77 final size:78
Alignment explanation
Indices: 28975--29246 Score: 390
Period size: 77 Copynumber: 3.5 Consensus size: 78
28965 CCTCCTCCCC
28975 CTCCCCCTCCTCGTACACCTCCTACCCCT-CACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
*
29039 CCCCCTTCTCCTA
66 CCCCCTGCTCCTA
* * *
29052 CTCCCCCTCCTCGTACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
29116 -CCCCCTGCTCCTA
65 TCCCCCTGCTCCTA
*
29129 CTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCC
*
29193 TCCTCCTGCTCCTA
65 TCCCCCTGCTCCTA
** * * * *
29207 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
29247 TACTCCCCCT
Statistics
Matches: 174, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
76 6 0.03
77 88 0.51
78 80 0.46
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (78 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
CCCCCTGCTCCTA
Found at i:29269 original size:120 final size:120
Alignment explanation
Indices: 29084--29366 Score: 435
Period size: 120 Copynumber: 2.4 Consensus size: 120
29074 TCCACCTCCA
* *
29084 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCC-CCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
* * *
29148 TCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTGCT
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTT-CCCCCTCCCCCTGCT
*
29203 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
*
29268 TCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
* * * * *
29323 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCC
29367 CCCTCCTAGC
Statistics
Matches: 150, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
119 30 0.20
120 118 0.79
121 2 0.01
ACGTcount: A:0.09, C:0.61, G:0.05, T:0.24
Consensus pattern (120 bp):
CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
Found at i:29285 original size:78 final size:78
Alignment explanation
Indices: 29203--29443 Score: 448
Period size: 78 Copynumber: 3.1 Consensus size: 78
29193 TCCTCCTGCT
*
29203 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
29268 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
29281 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
29346 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
29359 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACT-CCCCTCCACGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
29423 TCCTACCCCTCCA
66 TCCTACCCCTCCA
29436 CCTACTCC
1 CCTACTCC
29444 TCCCCCTCCC
Statistics
Matches: 159, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
77 36 0.23
78 123 0.77
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.23
Consensus pattern (78 bp):
CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCA
Found at i:29290 original size:21 final size:20
Alignment explanation
Indices: 29231--29474 Score: 86
Period size: 21 Copynumber: 12.6 Consensus size: 20
29221 GCACCTCTTC
* * *
29231 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* * *
29251 CCCCCTCCTCGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
29272 ACCCCTCCACCTACTCCTCCT
1 -CCCCTCCACCTACTCCTCCT
***
29293 CCTAGCGCACCT-CT--T-C-
1 CCCCTC-CACCTACTCCTCCT
* * *
29309 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* * *
29329 CCCCCTCCTCGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
*
29350 ACCCCTCCACCTACTCCCCCT
1 -CCCCTCCACCTACTCCTCCT
***
29371 CCTAGCGCACCT-CT--T-C-
1 CCCCTC-CACCTACTCCTCCT
* * *
29387 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* *
29407 CCCCTCCACGTACACCTCCT
1 CCCCTCCACCTACTCCTCCT
29427 ACCCCTCCACCTACTCCT-C-
1 -CCCCTCCACCTACTCCTCCT
*
29446 CCCCT-C-CCT-CTCCACCT
1 CCCCTCCACCTACTCCTCCT
29463 CCCCCTCCACCT
1 -CCCCTCCACCT
29475 CCACCTCCAC
Statistics
Matches: 162, Mismatches: 42, Indels: 39
0.67 0.17 0.16
Matches are distributed among these distances:
15 12 0.07
16 14 0.09
17 3 0.02
18 13 0.08
19 3 0.02
20 29 0.18
21 88 0.54
ACGTcount: A:0.10, C:0.63, G:0.04, T:0.23
Consensus pattern (20 bp):
CCCCTCCACCTACTCCTCCT
Found at i:29453 original size:6 final size:6
Alignment explanation
Indices: 29430--29491 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
29420 ACCTCCTACC
* * * *
29430 CCTCCA CCTACT CCTCCC CCTCC- CTCTCCA CCTCCC CCTCCA CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
29478 CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CC
29492 AGTTACCTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 1 0.02
6 46 0.96
7 1 0.02
ACGTcount: A:0.11, C:0.69, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCA
Found at i:29476 original size:18 final size:18
Alignment explanation
Indices: 29428--29491 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
29418 ACACCTCCTA
* *
29428 CCCCTCCACCTACTCCTC
1 CCCCTCCACCTCCACCTC
29446 CCCCTCC-CTCTCCACCTC
1 CCCCTCCAC-CTCCACCTC
29464 CCCCTCCACCTCCACCTC
1 CCCCTCCACCTCCACCTC
*
29482 CACCTCCACC
1 CCCCTCCACC
29492 AGTTACCTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
17 1 0.02
18 39 0.95
19 1 0.02
ACGTcount: A:0.11, C:0.70, G:0.00, T:0.19
Consensus pattern (18 bp):
CCCCTCCACCTCCACCTC
Found at i:36028 original size:11 final size:12
Alignment explanation
Indices: 35997--36040 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
35987 TCAAAAATCA
35997 TAAAATAATTAT
1 TAAAATAATTAT
36009 T-AAAT--TTAT
1 TAAAATAATTAT
36018 TAAAAT-ATTA-
1 TAAAATAATTAT
36028 TAAAATAATTAT
1 TAAAATAATTAT
36040 T
1 T
36041 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:36945 original size:2 final size:2
Alignment explanation
Indices: 36938--37016 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
36928 CTATTAAAAT
36938 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37017 GGGAATGATC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37490 original size:2 final size:2
Alignment explanation
Indices: 37485--37530 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
37475 TCTCTCTCTC
37485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37527 TA TA
1 TA TA
37531 AGCTATAATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37576 original size:16 final size:16
Alignment explanation
Indices: 37552--37582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37542 AATTACACAG
37552 TTTAAAACTTTTTAGT
1 TTTAAAACTTTTTAGT
*
37568 TTTATAACTTTTTAG
1 TTTAAAACTTTTTAG
37583 GATCGTTGGA
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:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTAAAACTTTTTAGT
Found at i:38494 original size:27 final size:27
Alignment explanation
Indices: 38464--38520 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
38454 GACCTCTCAA
38464 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
*
38491 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
38518 TCC
1 TCC
38521 CCCTCCTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.11, C:0.54, G:0.11, T:0.25
Consensus pattern (27 bp):
TCCTAGTAACCGTCGTCCCCCTCCCCC
Found at i:38744 original size:42 final size:42
Alignment explanation
Indices: 38680--39041 Score: 325
Period size: 42 Copynumber: 9.1 Consensus size: 42
38670 TACCCCTCCA
** *
38680 CCTACT-CCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCCTGCT
* *
38721 CCTACTCCCCCTCCTCGTACACCTCTTCCACCT----C--CA
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCCTGCT
*
38757 CCTACTCCCCCTCCTAGCT-CACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCG-TACACCTCTTCCCCCTCCCCCTGCT
** * *
38799 CCTACTCCCCCTCCTCGTACA-C-C-T---CCTATCCCTCCA
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCCTGCT
** *
38835 CCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTGCT
1 CCTACTCCCCCTCCTCGTACACCTCTT-CCCCCTCCCCCTGCT
**
38877 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCCTGCT
* * *
38919 CCTACTCCCCCTCCTCGTACA-C-C-T---CCTACCCCTCCA
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCCTGCT
* * **
38955 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCCTGCT
* * * *
38997 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCCTGCT
39039 CCT
1 CCT
39042 CCCCCTCCCT
Statistics
Matches: 258, Mismatches: 40, Indels: 45
0.75 0.12 0.13
Matches are distributed among these distances:
36 83 0.32
37 3 0.01
38 3 0.01
39 3 0.01
40 3 0.01
41 9 0.03
42 152 0.59
43 2 0.01
ACGTcount: A:0.09, C:0.61, G:0.05, T:0.25
Consensus pattern (42 bp):
CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCCTGCT
Found at i:38779 original size:21 final size:22
Alignment explanation
Indices: 38750--38933 Score: 73
Period size: 21 Copynumber: 9.0 Consensus size: 22
38740 CACCTCTTCC
*
38750 ACCTCCACCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
*
38772 AGCT-CACCT-CTTCCCCCTCC-
1 ACCTGCACCTAC-TCCCCCTCCT
* *
38792 CCCTGCTCCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
* * * **
38814 -CGTACACCTCCTATCCCTCC-
1 ACCTGCACCTACTCCCCCTCCT
38834 ACCT--A----CTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
*
38850 -CGC-GCACCTT-TCCCCCCTCCT
1 AC-CTGCACCTACT-CCCCCTCCT
*
38871 -CCTGCTCCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
38892 -CGC-GCACCT-CTTCCCCCTCC-
1 AC-CTGCACCTAC-TCCCCCTCCT
* *
38912 CCCTGCTCCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
38934 CGTACACCTC
Statistics
Matches: 123, Mismatches: 17, Indels: 44
0.67 0.09 0.24
Matches are distributed among these distances:
15 9 0.07
16 1 0.01
17 1 0.01
19 1 0.01
20 7 0.06
21 97 0.79
22 7 0.06
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (22 bp):
ACCTGCACCTACTCCCCCTCCT
Found at i:38910 original size:78 final size:78
Alignment explanation
Indices: 38648--38920 Score: 399
Period size: 78 Copynumber: 3.5 Consensus size: 78
38638 GCCTCCTCCC
38648 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACT-CCCCTCCTCGCGCACCTCTTCCCCCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
*
38712 CCCCCTTCTCCTA
66 CCCCCTGCTCCTA
* * *
38725 CTCCCCCTCCTCGTACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
38789 TCCCCCTGCTCCTA
65 TCCCCCTGCTCCTA
*
38803 CTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCC
*
38867 TCCTCCTGCTCCTA
65 TCCCCCTGCTCCTA
** * * * *
38881 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
38921 TACTCCCCCT
Statistics
Matches: 176, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
76 4 0.02
77 34 0.19
78 135 0.77
79 3 0.02
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (78 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
CCCCCTGCTCCTA
Found at i:38959 original size:78 final size:78
Alignment explanation
Indices: 38877--39048 Score: 310
Period size: 78 Copynumber: 2.2 Consensus size: 78
38867 TCCTCCTGCT
38877 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
38942 TCCTACCCCTCCA
66 TCCTACCCCTCCA
* *
38955 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
39020 TCCTACCCCTCCA
66 TCCTACCCCTCCA
39033 CCTACTCCTCCC-CCTC
1 CCTACTCC-CCCTCCTC
39049 CCTCTCCACC
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
78 87 0.98
79 2 0.02
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.24
Consensus pattern (78 bp):
CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCA
Found at i:38964 original size:21 final size:20
Alignment explanation
Indices: 38905--39095 Score: 69
Period size: 21 Copynumber: 9.6 Consensus size: 20
38895 GCACCTCTTC
* * *
38905 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* * *
38925 CCCCCTCCTCGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
38946 ACCCCTCCACCTACTCCTCCT
1 -CCCCTCCACCTACTCCTCCT
***
38967 CCTAGCGCACCT-CT--T-C-
1 CCCCTC-CACCTACTCCTCCT
* * *
38983 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* * *
39003 CCCCCTCCTCGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
39024 ACCCCTCCACCTACTCCT-C-
1 -CCCCTCCACCTACTCCTCCT
*
39043 CCCCT-C-CCT-CTCCACCT
1 CCCCTCCACCTACTCCTCCT
*
39060 CCCCCTCCACCTCCACCTCCACCT
1 -CCCCTCCACCT--A-CTCCTCCT
39084 CCACCTCCACCT
1 CC-CCTCCACCT
39096 CCACCTCCAC
Statistics
Matches: 127, Mismatches: 26, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.06
16 9 0.07
17 2 0.02
18 12 0.09
19 2 0.02
20 9 0.07
21 66 0.52
23 2 0.02
24 17 0.13
ACGTcount: A:0.10, C:0.64, G:0.03, T:0.23
Consensus pattern (20 bp):
CCCCTCCACCTACTCCTCCT
Found at i:39012 original size:120 final size:120
Alignment explanation
Indices: 38757--39041 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
38747 TCCACCTCCA
* *
38757 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
* * *
38822 TCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCTTTCCCCCCTCCTCCTGCT
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTTTCCCCCCTCCCCCTGCT
*
38877 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
*
38942 TCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTT-CCCCCTCCCCCTGCT
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCT-TTCCCCCCTCCCCCTGCT
* * * * *
38997 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCT
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCT
39042 CCCCCTCCCT
Statistics
Matches: 152, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
120 150 0.99
121 2 0.01
ACGTcount: A:0.09, C:0.61, G:0.05, T:0.25
Consensus pattern (120 bp):
CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTTTCCCCCCTCCCCCTGCT
Found at i:39050 original size:6 final size:6
Alignment explanation
Indices: 39027--39106 Score: 108
Period size: 6 Copynumber: 13.3 Consensus size: 6
39017 ACCTCCTACC
* * * *
39027 CCTCCA CCTACT CCTCCC CCTCC- CTCTCCA CCTCCC CCTCCA CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
39075 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
39107 AGTTACCTGC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
5 1 0.02
6 64 0.97
7 1 0.02
ACGTcount: A:0.12, C:0.69, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCA
Found at i:42848 original size:20 final size:20
Alignment explanation
Indices: 42823--42897 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
42813 GATACTTTTT
42823 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
42843 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTC
42863 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
42883 AAGAGTTTTGAAACT
1 AAGAGTTTCGAAACT
42898 TTCCCTAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
AAGAGTTTCGAAACTATCTC
Found at i:47659 original size:11 final size:12
Alignment explanation
Indices: 47628--47671 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
47618 TCAAAAATCA
47628 TAAAATAATTAT
1 TAAAATAATTAT
47640 T-AAAT--TTAT
1 TAAAATAATTAT
47649 TAAAAT-ATTA-
1 TAAAATAATTAT
47659 TAAAATAATTAT
1 TAAAATAATTAT
47671 T
1 T
47672 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:48584 original size:2 final size:2
Alignment explanation
Indices: 48577--48601 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48567 CTATTAAAAT
48577 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
48602 GGGAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49076 original size:2 final size:2
Alignment explanation
Indices: 49071--49116 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
49061 TCTCTCTCTC
49071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49113 TA TA
1 TA TA
49117 GCTATAATCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50059 original size:26 final size:26
Alignment explanation
Indices: 50030--50081 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
50020 GACCTCTCAA
50030 TCCTAGTAACCGTCGTCCCCCTCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCC
*
50056 TCCTAGTAACCGTCGTCCTCCTCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCC
50082 CTTCCCCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.25
Consensus pattern (26 bp):
TCCTAGTAACCGTCGTCCCCCTCCCC
Found at i:50307 original size:78 final size:78
Alignment explanation
Indices: 50214--50487 Score: 399
Period size: 78 Copynumber: 3.5 Consensus size: 78
50204 CCTCCTCCCC
*
50214 CTCCCCCTCCTCGTACACCTCCTACCCCTCAACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
*
50279 CCCCCTTCTCCTA
66 CCCCCTGCTCCTA
* * *
50292 CTCCCCCTCCTCGTACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
50356 TCCCCCTGCTCCTA
65 TCCCCCTGCTCCTA
*
50370 CTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCC
*
50434 TCCTCCTGCTCCTA
65 TCCCCCTGCTCCTA
** * * * *
50448 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
50488 TACTCCCCCT
Statistics
Matches: 176, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
77 6 0.03
78 167 0.95
79 3 0.02
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.25
Consensus pattern (78 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
CCCCCTGCTCCTA
Found at i:50389 original size:120 final size:118
Alignment explanation
Indices: 50246--50693 Score: 380
Period size: 120 Copynumber: 3.8 Consensus size: 118
50236 TACCCCTCAA
* * * * * *
50246 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCTCCTACTCC-CCCTCCTCGTACAC
1 CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCTCCCACCTC-TAC-C
* *
50310 CTCTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCT
64 CTCCTCC-CCTCCACCTACTCCCCCTCCTCGCTCACCTCTTCCCCCTCCCCCTGCT
* * ** *
50366 CCTACTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCC
1 CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCTC-C-CACCTCTACC
* * * *
50430 CCCCTCCTCCTGCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
64 CTCCTCC-CCTCCACCTACTCCCCCTCCTCGCTCACCTCTTCCCCCTCCCCCTGCT
* * * *
50486 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCC
1 CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCT--CCCACCTCTACC
* * * * *
50551 C-CCTCCCCCTGCTCCTACTCCCCCTCCTCG-T-ACAC-C-T---CCTACCCCTCCA
64 CTCCT-CCCCTCCACCTACTCCCCCTCCTCGCTCAC-CTCTTCCCCCTCCCCCTGCT
* * * * * * * *
50600 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCC-CCCTCCACGTACAC
1 CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCTCCCACCTC-TAC-C
50664 CTCCTACCCCTCCACCTACTCCTCCC-CCTC
64 CTCCT-CCCCTCCACCTACTCC-CCCTCCTC
50694 CCTCTCCACC
Statistics
Matches: 276, Mismatches: 40, Indels: 30
0.80 0.12 0.09
Matches are distributed among these distances:
111 5 0.02
112 2 0.01
113 2 0.01
114 72 0.26
115 3 0.01
117 1 0.00
118 3 0.01
119 1 0.00
120 171 0.62
121 10 0.04
122 2 0.01
123 4 0.01
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.24
Consensus pattern (118 bp):
CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCTCCCACCTCTACCCT
CCTCCCCTCCACCTACTCCCCCTCCTCGCTCACCTCTTCCCCCTCCCCCTGCT
Found at i:50450 original size:198 final size:198
Alignment explanation
Indices: 50246--50719 Score: 726
Period size: 198 Copynumber: 2.4 Consensus size: 198
50236 TACCCCTCAA
*
50246 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
* *
50311 T-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCTCCTACTCCC
66 TCCTACC-CCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCC
* * *
50375 CCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTC
130 CCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTT-CCCCCTCCCC
50439 CTGCT
194 CTGCT
50444 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
*
50509 TCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCC
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCC
50574 CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCT
131 CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCT
50639 GCT
196 GCT
* ** * * * * *
50642 CCTACTCCCCCTCCACGTACACCTCCTACCCCTCCACCTACT-C--CTCCCCCTCCCTC-TCCAC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCT-CCTCGTACAC
**
50703 CTCCCCCCCCTCCACCT
65 CTCCTACCCCTCCACCT
50720 CCACCCCACC
Statistics
Matches: 256, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
195 27 0.11
196 4 0.02
197 1 0.00
198 218 0.85
199 6 0.02
ACGTcount: A:0.09, C:0.62, G:0.04, T:0.24
Consensus pattern (198 bp):
CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCC
CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCT
GCT
Found at i:50518 original size:156 final size:156
Alignment explanation
Indices: 50214--50693 Score: 519
Period size: 156 Copynumber: 3.1 Consensus size: 156
50204 CCTCCTCCCC
*
50214 CTCCCCCTCCTCGTACACCTCCTACCCCTCAACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCC
* ** * * * ** *
50278 TCCCCCTTCTCCTACTCCCCCTCCTCGTACACCTCTTCCACCTCCACCTACTCCCCCTCCTAGCT
66 T-CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCC---CC
* * * * *
50343 CACCTC-TTC-CC-CCTCCCCCTGCTCCTA
127 CTCCTCGTACACCTCCTACCCCTCCACCTA
*
50370 CTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCC
*
50434 TCCTCCTGCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTC
66 TCC-CCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTC
50499 CTCGTACACCTCCTACCCCTCCACCTA
130 CTCGTACACCTCCTACCCCTCCACCTA
* * ** * * * * ** * * *
50526 CTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCC-C-C-CTCCTCGTACACCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTC-TTC-CCC
* *
50588 CCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCC
64 CCT-CCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCC
*
50653 TCCACGTACACCTCCTACCCCTCCACCTA
128 TCCTCGTACACCTCCTACCCCTCCACCTA
50682 CTCCTCCC-CCTC
1 CTCC-CCCTCCTC
50694 CCTCTCCACC
Statistics
Matches: 278, Mismatches: 36, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
153 10 0.04
154 3 0.01
155 9 0.03
156 252 0.91
157 4 0.01
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.24
Consensus pattern (156 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCC
TCCCCTCCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCC
TCGTACACCTCCTACCCCTCCACCTA
Found at i:50526 original size:78 final size:78
Alignment explanation
Indices: 50444--50685 Score: 457
Period size: 78 Copynumber: 3.1 Consensus size: 78
50434 TCCTCCTGCT
*
50444 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
50509 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
50522 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
50587 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
50600 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
50665 TCCTACCCCTCCA
66 TCCTACCCCTCCA
50678 CCTACTCC
1 CCTACTCC
50686 TCCCCCTCCC
Statistics
Matches: 160, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 160 1.00
ACGTcount: A:0.10, C:0.62, G:0.05, T:0.23
Consensus pattern (78 bp):
CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCA
Found at i:50665 original size:42 final size:42
Alignment explanation
Indices: 50246--50686 Score: 281
Period size: 42 Copynumber: 11.1 Consensus size: 42
50236 TACCCCTCAA
* * * * *
50246 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * * * *
50288 CCTACTCCCCCTCCT--CGTA-CACCT---CTTCCACCTCCA
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * * * *
50324 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* ** *
50366 CCTACTCCCCCTCCTCGTACACCTCCTATCCCT---CC-A--
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * *
50402 CCTACTCCCCCTCCTCGCGCACCTTTCC--CCCCTCCTCCTGCT
1 CCTACTCCCCCTCCTAGCGCACC--TCCTACCCCTCCACCTACT
* * * * *
50444 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* **
50486 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * * *
50528 -C--CT---CCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* **
50564 CCTACTCCCCCTCCTCGTACACCTCCTACCCCT---CC-A--
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
* * * *
50600 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
50642 CCTACTCCCCCTCC-A-CGTACACCTCCTACCCCTCCACCTACT
1 CCTACTCCCCCTCCTAGCG--CACCTCCTACCCCTCCACCTACT
50684 CCT
1 CCT
50687 CCCCCTCCCT
Statistics
Matches: 312, Mismatches: 57, Indels: 60
0.73 0.13 0.14
Matches are distributed among these distances:
36 102 0.33
37 1 0.00
38 5 0.02
39 18 0.06
40 7 0.02
41 2 0.01
42 177 0.57
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.24
Consensus pattern (42 bp):
CCTACTCCCCCTCCTAGCGCACCTCCTACCCCTCCACCTACT
Found at i:50706 original size:21 final size:21
Alignment explanation
Indices: 50314--50724 Score: 102
Period size: 21 Copynumber: 20.6 Consensus size: 21
50304 GTACACCTCT
*
50314 TCCACCTCCACCTACTCCCCC
1 TCCACCTCCACCTCCTCCCCC
* *
50335 TCCTAGCT-CACCTCTTCCCCC
1 TCC-ACCTCCACCTCCTCCCCC
* * * *
50356 TCCCCCTGCTCCTACTCCCCC
1 TCCACCTCCACCTCCTCCCCC
* * * **
50377 TCCTCGTACACCTCCTATCCC
1 TCCACCTCCACCTCCTCCCCC
50398 TCCACCT--A-CTCC-CCCTCC
1 TCCACCTCCACCTCCTCCC-CC
* * *
50416 T-C-GC-GCACCT-TTCCCCCC
1 TCCACCTCCACCTCCT-CCCCC
* * * *
50434 TCCTCCTGCTCCTACTCCCCC
1 TCCACCTCCACCTCCTCCCCC
* * *
50455 TCCTCGC-GCACCTCTTCCCCC
1 TCCAC-CTCCACCTCCTCCCCC
* * * *
50476 TCCCCCTGCTCCTACTCCCCC
1 TCCACCTCCACCTCCTCCCCC
* * * *
50497 TCCTCGTACACCTCCTACCCC
1 TCCACCTCCACCTCCTCCCCC
*
50518 TCCACCT--A-CTCCTCCTCC
1 TCCACCTCCACCTCCTCCCCC
* * *
50536 T--AGC-GCACCTCTTCCCCC
1 TCCACCTCCACCTCCTCCCCC
* * * *
50554 TCCCCCTGCTCCTACTCCCCC
1 TCCACCTCCACCTCCTCCCCC
* * * *
50575 TCCTCGTACACCTCCTACCCC
1 TCCACCTCCACCTCCTCCCCC
50596 TCCACCT--A----CTCCCCC
1 TCCACCTCCACCTCCTCCCCC
* * *
50611 TCCTAGC-GCACCTCTTCCCCC
1 TCC-ACCTCCACCTCCTCCCCC
* * * *
50632 TCCCCCTGCTCCTACTCCCCC
1 TCCACCTCCACCTCCTCCCCC
* * *
50653 TCCACGTACACCTCCTACCCC
1 TCCACCTCCACCTCCTCCCCC
50674 TCCACCT--A-CTCCTCCCCC
1 TCCACCTCCACCTCCTCCCCC
*
50692 TCC-CTCTCCACCTCCCCCCCC
1 TCCAC-CTCCACCTCCTCCCCC
50713 TCCACCTCCACC
1 TCCACCTCCACC
50725 CCACCTCCAC
Statistics
Matches: 283, Mismatches: 74, Indels: 66
0.67 0.17 0.16
Matches are distributed among these distances:
15 9 0.03
16 5 0.02
17 6 0.02
18 44 0.16
19 8 0.03
20 7 0.02
21 198 0.70
22 6 0.02
ACGTcount: A:0.10, C:0.63, G:0.04, T:0.23
Consensus pattern (21 bp):
TCCACCTCCACCTCCTCCCCC
Found at i:50715 original size:15 final size:17
Alignment explanation
Indices: 50697--50735 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
50687 CCCCCTCCCT
50697 CTCCACCTCC-CCCC-C
1 CTCCACCTCCACCCCAC
50712 CTCCACCTCCACCCCAC
1 CTCCACCTCCACCCCAC
50729 CTCCACC
1 CTCCACC
50736 AGTTACCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 10 0.45
16 4 0.18
17 8 0.36
ACGTcount: A:0.13, C:0.74, G:0.00, T:0.13
Consensus pattern (17 bp):
CTCCACCTCCACCCCAC
Found at i:50720 original size:6 final size:6
Alignment explanation
Indices: 50672--50735 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
50662 ACCTCCTACC
* * *
50672 CCTCCA CCTACT CCTCCC CCTCC- CTCTCCA CCTCC- CC-CC- CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
50717 CCTCCA CC-CCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CC
50736 AGTTACCTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.08
5 10 0.20
6 34 0.69
7 1 0.02
ACGTcount: A:0.11, C:0.72, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCCA
Found at i:50726 original size:17 final size:16
Alignment explanation
Indices: 50684--50735 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
50674 TCCACCTACT
50684 CCTCCCCCTCCCTCTCCA
1 CCTCCCCC-CCC-CTCCA
50702 CCT-CCCCCCCCTCCA
1 CCTCCCCCCCCCTCCA
*
50717 CCTCCACCCCACCTCCA
1 CCTCC-CCCCCCCTCCA
50734 CC
1 CC
50736 AGTTACCTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 8 0.26
16 4 0.13
17 16 0.52
18 3 0.10
ACGTcount: A:0.10, C:0.75, G:0.00, T:0.15
Consensus pattern (16 bp):
CCTCCCCCCCCCTCCA
Found at i:54386 original size:20 final size:20
Alignment explanation
Indices: 54361--54454 Score: 163
Period size: 20 Copynumber: 4.8 Consensus size: 20
54351 GATAATTTTT
*
54361 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTA
54381 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTA
54401 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTA
*
54421 AAGAG-TTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTA
54440 AAGAGTTTCGAAACT
1 AAGAGTTTCGAAACT
54455 TTCCCTAAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
19 18 0.25
20 53 0.75
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (20 bp):
AAGAGTTTCGAAACTATCTA
Found at i:54444 original size:39 final size:40
Alignment explanation
Indices: 54361--54454 Score: 163
Period size: 39 Copynumber: 2.4 Consensus size: 40
54351 GATAATTTTT
*
54361 AAGAGTTTCGAAACTATCTCAAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTAAAGAGTTTCGAAACTATCTA
*
54401 AAGAGTTTCGAAACTATCTAAAGAG-TTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTAAAGAGTTTCGAAACTATCTA
54440 AAGAGTTTCGAAACT
1 AAGAGTTTCGAAACT
54455 TTCCCTAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
39 28 0.54
40 24 0.46
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (40 bp):
AAGAGTTTCGAAACTATCTAAAGAGTTTCGAAACTATCTA
Found at i:54466 original size:20 final size:20
Alignment explanation
Indices: 54360--54470 Score: 126
Period size: 20 Copynumber: 5.6 Consensus size: 20
54350 CGATAATTTT
54360 TAAGAGTTTCGAAACTAT-C
1 TAAGAGTTTCGAAACTATCC
54379 TCAAGAGTTTCGAAACTAT-C
1 T-AAGAGTTTCGAAACTATCC
54399 TAAAGAGTTTCGAAACTAT-C
1 T-AAGAGTTTCGAAACTATCC
54419 TAAAGAG-TTCGAAACTAT-C
1 T-AAGAGTTTCGAAACTATCC
*
54438 TCAAGAGTTTCGAAACTTTCCC
1 T-AAGAGTTTCGAAACTAT-CC
54460 TAA-AGTTTCGA
1 TAAGAGTTTCGA
54471 TACTTTGGCT
Statistics
Matches: 85, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
19 19 0.22
20 62 0.73
21 2 0.02
22 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (20 bp):
TAAGAGTTTCGAAACTATCC
Done.