Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008995.1 Hibiscus syriacus cultivar Beakdansim tig00112371_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: 137607
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:17085 original size:22 final size:22
Alignment explanation
Indices: 17060--17102 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17050 ACTTTGCAAC
17060 TTTTTCACTTCTTTTTCTTTTA
1 TTTTTCACTTCTTTTTCTTTTA
**
17082 TTTTTTTCTTCTTTTTCTTTT
1 TTTTTCACTTCTTTTTCTTTT
17103 TTTCTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCACTTCTTTTTCTTTTA
Found at i:17098 original size:9 final size:8
Alignment explanation
Indices: 17077--17110 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
17067 CTTCTTTTTC
*
17077 TTTTATTT
1 TTTTCTTT
17085 TTTTCTTCT
1 TTTTCTT-T
17094 TTTTCTTT
1 TTTTCTTT
17102 TTTTCTTT
1 TTTTCTTT
17110 T
1 T
17111 GCACTCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTCTTT
Found at i:17110 original size:22 final size:22
Alignment explanation
Indices: 17067--17110 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17057 AACTTTTTCA
17067 CTTCTTTTTCTTTTATTTTTTT
1 CTTCTTTTTCTTTTATTTTTTT
17089 CTTCTTTTTCTTTT-TTTCTTTT
1 CTTCTTTTTCTTTTATTT-TTTT
17111 GCACTCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (22 bp):
CTTCTTTTTCTTTTATTTTTTT
Found at i:18275 original size:21 final size:21
Alignment explanation
Indices: 18251--18302 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18241 TTAAAGCTAG
18251 TGAGCTAATGTAAACATAACA
1 TGAGCTAATGTAAACATAACA
* *
18272 TGAGCTAGA-ATAAACATGACA
1 TGAGCTA-ATGTAAACATAACA
*
18293 TGAGTTAATG
1 TGAGCTAATG
18303 AATGAATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (21 bp):
TGAGCTAATGTAAACATAACA
Found at i:20079 original size:36 final size:35
Alignment explanation
Indices: 20029--20140 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
20019 TAAGATACTA
* *
20029 CCTATAACACCACCATCTTCCATCACCATTTTTACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* *
20065 CCTATAACATCACCATCTTTCATCACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * *
20100 CCTATATCATCACCAACTTCTATCACAATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
20135 CCTATA
1 CCTATA
20141 TAACCACCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 40 0.61
36 26 0.39
ACGTcount: A:0.29, C:0.37, G:0.04, T:0.30
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:22307 original size:21 final size:21
Alignment explanation
Indices: 22268--22307 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22258 TCTTCACTTA
*
22268 TTTTTCTTTGATTTTTTTTTC
1 TTTTTCTTTGATTTCTTTTTC
**
22289 TTTTTCTTTTCTTTCTTTT
1 TTTTTCTTTGATTTCTTTT
22308 GCACTCCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (21 bp):
TTTTTCTTTGATTTCTTTTTC
Found at i:22789 original size:14 final size:13
Alignment explanation
Indices: 22760--22797 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
22750 ATAGGCGTGA
*
22760 ATGGTGATGGAAG
1 ATGGTGATGAAAG
22773 ATGGTGATAGAAAG
1 ATGGTGAT-GAAAG
22787 ATGGTGATGAA
1 ATGGTGATGAA
22798 CAAATAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.39, T:0.24
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:25597 original size:12 final size:12
Alignment explanation
Indices: 25571--25608 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25561 TCTTCACTTC
*
25571 TTTTTCTTTGATT
1 TTTTTCTTT-CTT
25584 TTTTTC-TTCTT
1 TTTTTCTTTCTT
25595 TTTTTCTTTCTT
1 TTTTTCTTTCTT
25607 TT
1 TT
25609 GCACCCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 8 0.35
12 9 0.39
13 6 0.26
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:26087 original size:14 final size:13
Alignment explanation
Indices: 26054--26089 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
26044 ATAGGAGTGA
26054 ATGGTGATGGAAG
1 ATGGTGATGGAAG
*
26067 ATAGTGATGGAAAG
1 ATGGTGATGG-AAG
26081 ATGGTGATG
1 ATGGTGATG
26090 AACAAATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:29002 original size:20 final size:19
Alignment explanation
Indices: 28975--29014 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
28965 TGTAGGAGTC
*
28975 TTTTCTT-TTGCTTTTG-T
1 TTTTCTTCTTTCTTTTGCT
28992 TTTTCTTCTTTCTTTTGCT
1 TTTTCTTCTTTCTTTTGCT
29011 TTTT
1 TTTT
29015 GTTGCAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTCTTCTTTCTTTTGCT
Found at i:29816 original size:19 final size:20
Alignment explanation
Indices: 29775--29824 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
29765 GAAACCCCTT
*
29775 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
29795 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
29814 TGAAGATACAT
1 TGAAAATACAT
29825 TCTCTTGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:32261 original size:25 final size:25
Alignment explanation
Indices: 32214--32261 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
32204 ACTTTCTTCA
* *
32214 CTTCTTTTTCTTTGATTTTTTTTTT
1 CTTCTTGTTCTTTGATTTCTTTTTT
**
32239 CTTCTTGTTCTTTTCTTTCTTTT
1 CTTCTTGTTCTTTGATTTCTTTT
32262 GCACTCCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (25 bp):
CTTCTTGTTCTTTGATTTCTTTTTT
Found at i:32314 original size:13 final size:13
Alignment explanation
Indices: 32287--32327 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
32277 TGTAGGAGTC
32287 TTTTCTTTTGCTT
1 TTTTCTTTTGCTT
32300 TTTGT-TTTT-CTT
1 TTT-TCTTTTGCTT
32312 TTTTCTTTTGCTT
1 TTTTCTTTTGCTT
32325 TTT
1 TTT
32328 ATTGCAGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 10 0.40
13 13 0.52
14 1 0.04
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTGCTT
Found at i:32741 original size:14 final size:14
Alignment explanation
Indices: 32714--32763 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
32704 ATAGGCGTGA
32714 ATAGTGAT-GGAAG
1 ATAGTGATGGGAAG
32727 ATAGTGATGGGAAG
1 ATAGTGATGGGAAG
* * *
32741 ATGGTGATAGAAAG
1 ATAGTGATGGGAAG
*
32755 ATGGTGATG
1 ATAGTGATG
32764 AATAAATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
13 8 0.25
14 24 0.75
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (14 bp):
ATAGTGATGGGAAG
Found at i:33128 original size:19 final size:19
Alignment explanation
Indices: 33104--33153 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
33094 GAAATCCCTT
*
33104 TGAAAATACATGATTTTCA
1 TGAAAATACATGATTTTAA
33123 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
33142 TGAAGATACATG
1 TGAAAATACATG
33154 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:33472 original size:24 final size:24
Alignment explanation
Indices: 33444--33502 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
33434 TTCAATGGTA
*
33444 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAACT
33468 AGCTAGGTGAGTGTCTTGGTAACT
1 AGCTAGGTGAGTGTCTTGGTAACT
*
33492 AACTAGGTGAG
1 AGCTAGGTGAG
33503 CTATAGCTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.31
Consensus pattern (24 bp):
AGCTAGGTGAGTGTCTTGGTAACT
Found at i:33652 original size:30 final size:30
Alignment explanation
Indices: 33616--33691 Score: 152
Period size: 30 Copynumber: 2.5 Consensus size: 30
33606 GTCCAAAGTT
33616 CTCCTCCAGCTAAGTTCAGTTACATGCTAG
1 CTCCTCCAGCTAAGTTCAGTTACATGCTAG
33646 CTCCTCCAGCTAAGTTCAGTTACATGCTAG
1 CTCCTCCAGCTAAGTTCAGTTACATGCTAG
33676 CTCCTCCAGCTAAGTT
1 CTCCTCCAGCTAAGTT
33692 GAAGCTCTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (30 bp):
CTCCTCCAGCTAAGTTCAGTTACATGCTAG
Found at i:38880 original size:15 final size:15
Alignment explanation
Indices: 38857--38916 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
38847 TTGGCTCTTA
*
38857 TTTTGTTTTTTTGCC
1 TTTTTTTTTTTTGCC
38872 TTTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
**
38887 TTTTTTGTTTTTTGTT
1 TTTTTT-TTTTTTGCC
38903 TTTTTGTTTTTTTG
1 TTTTT-TTTTTTTG
38917 TTTTTTTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
15 20 0.50
16 19 0.47
17 1 0.03
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:38898 original size:8 final size:8
Alignment explanation
Indices: 38857--38924 Score: 86
Period size: 8 Copynumber: 8.6 Consensus size: 8
38847 TTGGCTCTTA
38857 TTTTGTTT
1 TTTTGTTT
**
38865 TTTTGCCT
1 TTTTGTTT
38873 TTTT-TTT
1 TTTTGTTT
*
38880 TTTTGCCTT
1 TTTTG-TTT
38889 TTTTG-TT
1 TTTTGTTT
38896 TTTTGTTT
1 TTTTGTTT
38904 TTTTGTTT
1 TTTTGTTT
38912 TTTTGTTT
1 TTTTGTTT
38920 TTTTG
1 TTTTG
38925 AAAAAAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
7 12 0.23
8 33 0.63
9 7 0.13
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (8 bp):
TTTTGTTT
Found at i:38922 original size:15 final size:17
Alignment explanation
Indices: 38843--38916 Score: 84
Period size: 16 Copynumber: 4.5 Consensus size: 17
38833 AAATTTTGGC
*
38843 TTTTTTGGCTCTTATTTTG
1 TTTTTTTGC-CTT-TTTTG
38862 TTTTTTTGCC-TTTTT-
1 TTTTTTTGCCTTTTTTG
38877 TTTTTTTGCCTTTTTTG
1 TTTTTTTGCCTTTTTTG
*
38894 -TTTTTTG-TTTTTTTG
1 TTTTTTTGCCTTTTTTG
38909 TTTTTTTG
1 TTTTTTTG
38917 TTTTTTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
15 17 0.34
16 23 0.46
17 1 0.02
18 1 0.02
19 8 0.16
ACGTcount: A:0.01, C:0.08, G:0.12, T:0.78
Consensus pattern (17 bp):
TTTTTTTGCCTTTTTTG
Found at i:41669 original size:6 final size:6
Alignment explanation
Indices: 41649--41689 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
41639 TGTAGGAGTC
* *
41649 TTTTCT TTTGCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
41690 ATTGCAGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:42107 original size:14 final size:14
Alignment explanation
Indices: 42079--42125 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
42069 GGCATGAATA
*
42079 GTGAT-GGAAGTTG
1 GTGATGGGAAGATG
42092 GTGATGGGAAGATG
1 GTGATGGGAAGATG
* *
42106 GTGATAGAAAGATG
1 GTGATGGGAAGATG
42120 GTGATG
1 GTGATG
42126 AATAAATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.26
Consensus pattern (14 bp):
GTGATGGGAAGATG
Found at i:42490 original size:19 final size:19
Alignment explanation
Indices: 42466--42515 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
42456 GAAATCCCTT
*
42466 TGAAAATACATGATTTTCA
1 TGAAAATACATGATTTTAA
*
42485 TGAAAATACATTATTTTAA
1 TGAAAATACATGATTTTAA
*
42504 TGAAGATACATG
1 TGAAAATACATG
42516 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:42834 original size:24 final size:24
Alignment explanation
Indices: 42806--42864 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
42796 TTCAATGGTA
42806 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
42830 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
*
42854 AACTAGGTGAG
1 AGCTAGGTGAG
42865 CTATAGCTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.37, T:0.31
Consensus pattern (24 bp):
AGCTAGGTGAGTGTCTTGGTAGCT
Found at i:44073 original size:24 final size:24
Alignment explanation
Indices: 44037--44090 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
44027 CTTTGAATGA
*
44037 TCATGTCCCTTGGCATC-CCAAAAT
1 TCATGTCCATTGG-ATCACCAAAAT
*
44061 TCATGTCCATTGGATCATGCAAAAT
1 TCATGTCCATTGGATCA-CCAAAAT
44086 TCATG
1 TCATG
44091 ATTCTATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.12
24 12 0.46
25 11 0.42
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (24 bp):
TCATGTCCATTGGATCACCAAAAT
Found at i:44420 original size:24 final size:24
Alignment explanation
Indices: 44374--44420 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
44364 ACGGACACAA
* * *
44374 CTCTTGGCACTTCAAGTGTCATTT
1 CTCTTGGAACTTCAAATGACATTT
44398 CTCTTGGAACTTCAAATGACATT
1 CTCTTGGAACTTCAAATGACATT
44421 ATCTTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (24 bp):
CTCTTGGAACTTCAAATGACATTT
Found at i:45728 original size:23 final size:23
Alignment explanation
Indices: 45684--45728 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
45674 CTTTCTTCAT
* *
45684 TTCTTTTTCTTTGATTTTTTTTC
1 TTCTTTTTCTTTGACTTCTTTTC
**
45707 TTCTTTTTCTTTTCCTTCTTTT
1 TTCTTTTTCTTTGACTTCTTTT
45729 GCACTCCAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (23 bp):
TTCTTTTTCTTTGACTTCTTTTC
Found at i:50824 original size:15 final size:15
Alignment explanation
Indices: 50804--50834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
50794 AAATTAAAAG
50804 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
50819 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
50834 G
1 G
50835 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:51006 original size:14 final size:14
Alignment explanation
Indices: 50979--51028 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
50969 ATGGGCGTGA
50979 ATGGTGAT-GAAAG
1 ATGGTGATGGAAAG
50992 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
*
51006 ATTGTGATGGAAAG
1 ATGGTGATGGAAAG
51020 ATGGTGATG
1 ATGGTGATG
51029 AACAAATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
13 8 0.24
14 26 0.76
ACGTcount: A:0.34, C:0.00, G:0.40, T:0.26
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:51999 original size:59 final size:59
Alignment explanation
Indices: 51907--52035 Score: 258
Period size: 59 Copynumber: 2.2 Consensus size: 59
51897 TGATTAAATG
51907 AGCTACCATAACATTCATGAGATACTCTGAGCTGATATGCTTGTACTTTTAGCTACCAA
1 AGCTACCATAACATTCATGAGATACTCTGAGCTGATATGCTTGTACTTTTAGCTACCAA
51966 AGCTACCATAACATTCATGAGATACTCTGAGCTGATATGCTTGTACTTTTAGCTACCAA
1 AGCTACCATAACATTCATGAGATACTCTGAGCTGATATGCTTGTACTTTTAGCTACCAA
52025 AGCTACCATAA
1 AGCTACCATAA
52036 TATGCCTTGC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 70 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (59 bp):
AGCTACCATAACATTCATGAGATACTCTGAGCTGATATGCTTGTACTTTTAGCTACCAA
Found at i:56083 original size:9 final size:9
Alignment explanation
Indices: 56069--56096 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56059 GGAGATAGTT
56069 AAAAATGAA
1 AAAAATGAA
56078 AAAAATGAA
1 AAAAATGAA
56087 AAAAATGAA
1 AAAAATGAA
56096 A
1 A
56097 GGATTGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAATGAA
Found at i:60008 original size:15 final size:15
Alignment explanation
Indices: 59980--60022 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
59970 CTTCACTTAT
* *
59980 TTTTCTTTGATTTTTT
1 TTTTCTTT-CTTTTTC
59996 TTTTC-TTCTTTTTC
1 TTTTCTTTCTTTTTC
60010 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
60023 GCACTCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.42
15 9 0.38
16 5 0.21
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:68929 original size:21 final size:21
Alignment explanation
Indices: 68877--68929 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
68867 TACTTTGCAA
68877 CTTTCTTTACTTCTTTTTCTTTG
1 CTTTCTTT--TTCTTTTTCTTTG
* * *
68900 ATTTTTTTTTCTTTTTCTTTT
1 CTTTCTTTTTCTTTTTCTTTG
68921 CTTTCTTTT
1 CTTTCTTTT
68930 GCACTTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 19 0.76
23 6 0.24
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (21 bp):
CTTTCTTTTTCTTTTTCTTTG
Found at i:69224 original size:15 final size:15
Alignment explanation
Indices: 69204--69234 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
69194 AAAGGAAATG
69204 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
69219 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
69234 G
1 G
69235 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:69419 original size:14 final size:13
Alignment explanation
Indices: 69391--69427 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
69381 TAGGCGTGAC
*
69391 TGGTGATGGAAGA
1 TGGTGATGAAAGA
69404 TGGTGATGTAAAGA
1 TGGTGATG-AAAGA
69418 TGGTGATGAA
1 TGGTGATGAA
69428 CAAATAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.27
Consensus pattern (13 bp):
TGGTGATGAAAGA
Found at i:72286 original size:22 final size:20
Alignment explanation
Indices: 72261--72300 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
72251 ATGTTTGTTT
72261 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
72283 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
72301 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:76552 original size:22 final size:20
Alignment explanation
Indices: 76527--76566 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
76517 ATGTTTGTTT
76527 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
76549 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
76567 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:76800 original size:15 final size:15
Alignment explanation
Indices: 76777--76812 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
76767 ACTAATATTC
* *
76777 TTATCATAATATATA
1 TTATAATAACATATA
76792 TTATAATAACATATA
1 TTATAATAACATATA
76807 TTATAA
1 TTATAA
76813 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:80825 original size:22 final size:20
Alignment explanation
Indices: 80800--80839 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
80790 ATGTTTGTTT
80800 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
80822 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
80840 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:81073 original size:15 final size:15
Alignment explanation
Indices: 81050--81085 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
81040 ACTAATATTC
* *
81050 TTATCATAATATATA
1 TTATAATAACATATA
81065 TTATAATAACATATA
1 TTATAATAACATATA
81080 TTATAA
1 TTATAA
81086 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:81233 original size:17 final size:20
Alignment explanation
Indices: 81211--81256 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 20
81201 TTTAAAAAAT
81211 GAAATGGTTA-GG-AT-ATA
1 GAAATGGTTATGGTATGATA
81228 GAAATGGTTATGGTATGATA
1 GAAATGGTTATGGTATGATA
81248 G-AATGGTTA
1 GAAATGGTTA
81257 AGCAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.38
18 2 0.08
19 10 0.38
20 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (20 bp):
GAAATGGTTATGGTATGATA
Found at i:81543 original size:12 final size:12
Alignment explanation
Indices: 81523--81563 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
81513 TGTAGGAGTC
81523 TTTTCTTTTGCT
1 TTTTCTTTTGCT
* *
81535 TTTTATTTTTCT
1 TTTTCTTTTGCT
81547 TCTTTCTTTTGCT
1 T-TTTCTTTTGCT
81560 TTTT
1 TTTT
81564 TGTTGCAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTGCT
Found at i:81795 original size:15 final size:15
Alignment explanation
Indices: 81775--81805 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
81765 AAAGGAAATG
81775 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
81790 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
81805 G
1 G
81806 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:81958 original size:13 final size:14
Alignment explanation
Indices: 81940--81975 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
81930 TGGTAAGTGA
81940 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
81953 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
81967 ATGGTGATG
1 ATGGTGATG
81976 AAAAAATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:81978 original size:13 final size:13
Alignment explanation
Indices: 81940--81978 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
81930 TGGTAAGTGA
*
81940 ATGGTGATGGAAG
1 ATGGTGATGAAAG
81953 ATGGTGATGGAAAG
1 ATGGTGAT-GAAAG
81967 ATGGTGATGAAA
1 ATGGTGATGAAA
81979 AAATAGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:85579 original size:20 final size:19
Alignment explanation
Indices: 85552--85591 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
85542 TGTAGGAGTC
*
85552 TTTTCTT-TTGCTTTTG-T
1 TTTTCTTCTTTCTTTTGCT
85569 TTTTCTTCTTTCTTTTGCT
1 TTTTCTTCTTTCTTTTGCT
85588 TTTT
1 TTTT
85592 GTTGCAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTCTTCTTTCTTTTGCT
Found at i:86413 original size:19 final size:20
Alignment explanation
Indices: 86366--86415 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
86356 GAAACCCCTT
*
86366 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
86386 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
* *
86405 TTAAGATACAT
1 TGAAAATACAT
86416 ACTCTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:89592 original size:14 final size:14
Alignment explanation
Indices: 89560--89601 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
89550 TCTTCAGTTC
**
89560 TTTTTCTTTGATTT
1 TTTTTCTTTCTTTT
89574 TTTTTC-TTCTTTT
1 TTTTTCTTTCTTTT
89587 TCTTTTCTTTCTTTT
1 T-TTTTCTTTCTTTT
89602 GCACTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.25
14 11 0.46
15 7 0.29
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTCTTTT
Found at i:89601 original size:23 final size:23
Alignment explanation
Indices: 89557--89601 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
89547 CTTTCTTCAG
*
89557 TTCTTTTTCTTTGATTTTTTTTC
1 TTCTTTTTCTTTGATTTCTTTTC
**
89580 TTCTTTTTCTTTTCTTTCTTTT
1 TTCTTTTTCTTTGATTTCTTTT
89602 GCACTTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (23 bp):
TTCTTTTTCTTTGATTTCTTTTC
Found at i:89654 original size:20 final size:19
Alignment explanation
Indices: 89627--89666 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
89617 TGTAGGAGTC
*
89627 TTTTCTT-TTACTTTTG-T
1 TTTTCTTCTTTCTTTTGCT
89644 TTTTCTTCTTTCTTTTGCT
1 TTTTCTTCTTTCTTTTGCT
89663 TTTT
1 TTTT
89667 GTTGCAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTCTTCTTTCTTTTGCT
Found at i:89898 original size:15 final size:15
Alignment explanation
Indices: 89878--89908 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
89868 AAAGGAAATG
89878 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
89893 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
89908 G
1 G
89909 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:90082 original size:13 final size:14
Alignment explanation
Indices: 90064--90099 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
90054 ATAGACGTGA
90064 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
*
90077 ATGGTGATGGAAAT
1 ATGGTGATGGAAAG
90091 ATGGTGATG
1 ATGGTGATG
90100 AACAAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.42, T:0.28
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:90474 original size:121 final size:121
Alignment explanation
Indices: 90246--90488 Score: 434
Period size: 121 Copynumber: 2.0 Consensus size: 121
90236 AATGAAGGGT
* *
90246 TTGACGCCACAAACTTTAGAAAGCTTGCTTTATCAAAATAGTTCTCAAAAGAACTTGAAGAGAGA
1 TTGACGCCACAAACTTTAGAAAGCTTGCTTAATCAAAATAGTTCTAAAAAGAACTTGAAGAGAGA
90311 ATAATCTCACAAGGATTTTTATATTATCAAAGGGTTGTCTTACAATGTAAATAGCC
66 ATAATCTCACAAGGATTTTTATATTATCAAAGGGTTGTCTTACAATGTAAATAGCC
* *
90367 TTGACGCCACAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAG
1 TTGACGCCACAAACTTTAG-AAAGCTTGCTTAATCAAAATAGTTCTAAAAAGAACTTGAAGAGAG
90432 AATAATCTCACAAGGA-TTTTATATTATCAAAGGGTTGTCTTACAATGTAAATAGCC
65 AATAATCTCACAAGGATTTTTATATTATCAAAGGGTTGTCTTACAATGTAAATAGCC
90488 T
1 T
90489 AGCCTATTTA
Statistics
Matches: 117, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
121 60 0.51
122 57 0.49
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (121 bp):
TTGACGCCACAAACTTTAGAAAGCTTGCTTAATCAAAATAGTTCTAAAAAGAACTTGAAGAGAGA
ATAATCTCACAAGGATTTTTATATTATCAAAGGGTTGTCTTACAATGTAAATAGCC
Found at i:90585 original size:19 final size:19
Alignment explanation
Indices: 90561--90602 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
90551 GAAACCCATT
*
90561 TGAAAATACATGATTTTCA
1 TGAAAATACATGATTTTAA
90580 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
90599 TGAA
1 TGAA
90603 GATATATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:93709 original size:10 final size:10
Alignment explanation
Indices: 93694--93728 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
93684 TCTTCACTTC
93694 TTTTTCTTTT
1 TTTTTCTTTT
93704 TTTTTCTTTT
1 TTTTTCTTTT
93714 TCTTTTCTTTCT
1 T-TTTTCTTT-T
93726 TTT
1 TTT
93729 GCGCTCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 11 0.48
11 10 0.43
12 2 0.09
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:93712 original size:16 final size:15
Alignment explanation
Indices: 93691--93728 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
93681 CTTTCTTCAC
*
93691 TTCTTTTTCTTTTTTT
1 TTCTTTTTC-TTTTCT
93707 TTCTTTTTCTTTTCT
1 TTCTTTTTCTTTTCT
93722 TTCTTTT
1 TTCTTTT
93729 GCGCTCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTTTTCTTTTCT
Found at i:94499 original size:19 final size:20
Alignment explanation
Indices: 94458--94500 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
94448 GAAACCTCTT
*
94458 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
94478 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
94497 TGAA
1 TGAA
94501 GATATATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:98045 original size:13 final size:14
Alignment explanation
Indices: 98027--98062 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
98017 ATAGGTGTGA
*
98027 ATGGTGATGG-ATG
1 ATGGTGATGGAAAG
98040 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
98054 ATGGTGATG
1 ATGGTGATG
98063 AACAAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:98426 original size:122 final size:122
Alignment explanation
Indices: 98209--98453 Score: 445
Period size: 122 Copynumber: 2.0 Consensus size: 122
98199 AAGGAAGGGA
*
98209 TTGACGCCACAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAG
1 TTGACACCACAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAG
* *
98274 AATAGTCTTACAAGGATTTTTATATTATCAAAGGGTTATCTTACAATGTAAATAGCC
66 AATAATCTCACAAGGATTTTTATATTATCAAAGGGTTATCTTACAATGTAAATAGCC
*
98331 TTGACACCACAAACTTTAGAAAAGCTTGCTTAATTGATATAGTTCTAAAAAGAACTTGAAGAGAG
1 TTGACACCACAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAG
*
98396 AATAATCTCACAAGGATTTTTATATTATCAAAGGGTTGTCTTACAATGTAAATAGCC
66 AATAATCTCACAAGGATTTTTATATTATCAAAGGGTTATCTTACAATGTAAATAGCC
98453 T
1 T
98454 AGCCTATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (122 bp):
TTGACACCACAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAG
AATAATCTCACAAGGATTTTTATATTATCAAAGGGTTATCTTACAATGTAAATAGCC
Found at i:107568 original size:23 final size:23
Alignment explanation
Indices: 107514--107568 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
107504 TACTTTGCAA
** *
107514 CTTTCTTCACTTCTTTTTCTTTG
1 CTTTCTTTTCTTCTTTTCCTTTG
* * *
107537 ATTTTTTTTCTTCTTTTCCTTTT
1 CTTTCTTTTCTTCTTTTCCTTTG
107560 CTTTCTTTT
1 CTTTCTTTT
107569 GCACTCCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (23 bp):
CTTTCTTTTCTTCTTTTCCTTTG
Found at i:107608 original size:11 final size:11
Alignment explanation
Indices: 107592--107651 Score: 59
Period size: 11 Copynumber: 5.1 Consensus size: 11
107582 ATTGTAGGAG
107592 TCTTTTCTTTT
1 TCTTTTCTTTT
*
107603 TCTTTTGTTTT
1 TCTTTTCTTTT
107614 TCTTCTTTCTTTT
1 TC-T-TTTCTTTT
107627 GT-TTTTCTTCTT
1 -TCTTTTCTT-TT
107639 TCTTTTGCTTTT
1 TCTTTT-CTTTT
107651 T
1 T
107652 GTTGCAGCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 19 0.46
12 11 0.27
13 10 0.24
14 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:107624 original size:7 final size:6
Alignment explanation
Indices: 107594--107651 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
107584 TGTAGGAGTC
* *
107594 TTTTCT TTTTC- TTTTGT TTTTCT TCTTTC- TTTTGT TTTTCT TCTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT T-TTTCT
*
107642 TTTGCT TTTT
1 TTTTCT TTTT
107652 GTTGCAGCAC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 7 0.17
6 25 0.60
7 10 0.24
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:107624 original size:18 final size:18
Alignment explanation
Indices: 107594--107651 Score: 100
Period size: 18 Copynumber: 3.2 Consensus size: 18
107584 TGTAGGAGTC
107594 TTTTCTT-TTTCTTTTGT
1 TTTTCTTCTTTCTTTTGT
107611 TTTTCTTCTTTCTTTTGT
1 TTTTCTTCTTTCTTTTGT
107629 TTTTCTTCTTTCTTTTGCT
1 TTTTCTTCTTTCTTTTG-T
107648 TTTT
1 TTTT
107652 GTTGCAGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.18
18 27 0.69
19 5 0.13
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTCTTCTTTCTTTTGT
Found at i:107883 original size:15 final size:15
Alignment explanation
Indices: 107863--107893 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
107853 AAAGGAAATA
107863 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
107878 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
107893 G
1 G
107894 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:108056 original size:13 final size:14
Alignment explanation
Indices: 108038--108073 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
108028 ATAGGCGTGA
108038 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
108051 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
*
108065 ATGATGATG
1 ATGGTGATG
108074 AACAAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:108454 original size:122 final size:122
Alignment explanation
Indices: 108223--108464 Score: 439
Period size: 122 Copynumber: 2.0 Consensus size: 122
108213 GAAGGGATTG
108223 ACGCCAAAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
1 ACGCCAAAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
108288 AATATCACAAGGATTTTTATATTATCAAAAGGTTATCTTACAATGTAAATAGCCTTA
66 AATATCACAAGGATTTTTATATTATCAAAAGGTTATCTTACAATGTAAATAGCCTTA
*
108345 ACGCCATAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
1 ACGCCAAAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
* * * *
108410 AATCTCACAAGGATTTTTATATTATCAAAGGGTTGTCTTGCAATGTAAATAGCCT
66 AATATCACAAGGATTTTTATATTATCAAAAGGTTATCTTACAATGTAAATAGCCT
108465 AGCCTATTTA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 115 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (122 bp):
ACGCCAAAAACTTTAGAAAAGCTTGCTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
AATATCACAAGGATTTTTATATTATCAAAAGGTTATCTTACAATGTAAATAGCCTTA
Found at i:108578 original size:19 final size:20
Alignment explanation
Indices: 108537--108587 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
108527 GAAACCCCTT
*
108537 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
108557 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
108576 TGAAGATACATG
1 TGAAAATACATG
108588 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:110386 original size:22 final size:20
Alignment explanation
Indices: 110361--110400 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
110351 ATGTTTGTTT
110361 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
110383 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
110401 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:111756 original size:13 final size:13
Alignment explanation
Indices: 111734--111763 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
111724 ACTAAACACC
111734 TTTC-ACATACCT
1 TTTCAACATACCT
111746 TTTCAACATACCT
1 TTTCAACATACCT
111759 TTTCA
1 TTTCA
111764 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:115934 original size:22 final size:20
Alignment explanation
Indices: 115909--115948 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
115899 ATGTTTGTTT
115909 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
115931 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
115949 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:118937 original size:23 final size:23
Alignment explanation
Indices: 118910--118962 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
118900 ACTTTGCAAC
118910 TTTC-TTCACTTCTTTTTCTTTGA
1 TTTCTTTCA-TTCTTTTTCTTTGA
* **
118933 TTTCTTTGATTCTTTTTCTTTTC
1 TTTCTTTCATTCTTTTTCTTTGA
118956 TTTCTTT
1 TTTCTTT
118963 TGCACTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTCTTTCATTCTTTTTCTTTGA
Found at i:119009 original size:12 final size:12
Alignment explanation
Indices: 118989--119029 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
118979 TGTAGGAGTC
118989 TTTTCTTTTGCT
1 TTTTCTTTTGCT
* *
119001 TTTTATTTTTCT
1 TTTTCTTTTGCT
119013 TCTTTCTTTTGCT
1 T-TTTCTTTTGCT
119026 TTTT
1 TTTT
119030 GTTGCAGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTGCT
Found at i:119403 original size:14 final size:14
Alignment explanation
Indices: 119374--119411 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
119364 ATAGGCGTGA
119374 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
119387 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
119401 ATGGTGATGGA
1 ATGGTGATGGA
119412 CAAATAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.24
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:119784 original size:19 final size:19
Alignment explanation
Indices: 119762--119798 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
119752 AAATAAACGG
*
119762 TTTTGATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
119781 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
119799 CTCTTGGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:120116 original size:24 final size:24
Alignment explanation
Indices: 120089--120171 Score: 148
Period size: 24 Copynumber: 3.5 Consensus size: 24
120079 TTCAACGGTA
*
120089 AGCTAGGTAAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
120113 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
120137 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
*
120161 AACTAGGTGAG
1 AGCTAGGTGAG
120172 CTATAGCTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.20, C:0.12, G:0.36, T:0.31
Consensus pattern (24 bp):
AGCTAGGTGAGTGTCTTGGTAGCT
Found at i:122942 original size:22 final size:23
Alignment explanation
Indices: 122916--122960 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
122906 ACTTTCTTCA
122916 CTTCTTTTTCTTTTATTT-TTTT
1 CTTCTTTTTCTTTTATTTCTTTT
*
122938 CTTCTTTTTCTTTTCTTTCTTTT
1 CTTCTTTTTCTTTTATTTCTTTT
122961 GCACTCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
CTTCTTTTTCTTTTATTTCTTTT
Found at i:123249 original size:15 final size:15
Alignment explanation
Indices: 123229--123259 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
123219 AAATTAAAAG
123229 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
123244 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
123259 G
1 G
123260 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:126215 original size:17 final size:16
Alignment explanation
Indices: 126193--126226 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
126183 TAAAAACAGT
126193 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
126210 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
126226 A
1 A
126227 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:131893 original size:19 final size:20
Alignment explanation
Indices: 131871--131914 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
131861 GAGAAAAGGT
131871 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
131890 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
131910 AAAAG
1 AAAAG
131915 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Done.