Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000878.1 Hibiscus syriacus cultivar Beakdansim tig00001710_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: 62986
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:42 original size:6 final size:6
Alignment explanation
Indices: 39--84 Score: 56
Period size: 6 Copynumber: 7.0 Consensus size: 6
29 ATTTTTTTTA
39 TTTTCT TTTTCT TTTTCT TTTTCT CTCTTTCTT TATTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT -T-TTTC-T T-TTTCT TTTTCT
85 CATTTTTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 23 0.64
7 3 0.08
8 9 0.25
9 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:53 original size:20 final size:19
Alignment explanation
Indices: 25--132 Score: 63
Period size: 20 Copynumber: 5.1 Consensus size: 19
15 TTGAACCCCC
*
25 TTTTATTTTTTTTATTTTCT
1 TTTTCTTTTTTTT-TTTTCT
*
45 TTTTCTTTTTCTTTTTCTCT
1 TTTTCTTTTT-TTTTTTTCT
*
65 CTTTCTTTATTTCTTTTTCTCAT
1 TTTTCTTT-TTT-TTTTT-TC-T
*
88 TTTTCATTTTTTCTCTTTTTAAT
1 TTTTC-TTTTTT-T-TTTTT-CT
*
111 TCTTTCTCTTTTTTTCTTTCT
1 T-TTTCT-TTTTTTTTTTTCT
132 T
1 T
133 CAGGCTAAGT
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
20 22 0.31
21 11 0.16
22 6 0.09
23 15 0.21
24 16 0.23
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTTTTTTTTTCT
Found at i:67 original size:16 final size:15
Alignment explanation
Indices: 44--129 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 15
34 TTTTATTTTC
44 TTTTTCTTTTTCT-T
1 TTTTTCTTTTTCTCT
* *
58 TTTCTCTCTTTCT-T
1 TTTTTCTTTTTCTCT
* *
72 TATTTCTTTTTCTCA
1 TTTTTCTTTTTCTCT
87 TTTTTCATTTTTTCTCT
1 TTTTTC--TTTTTCTCT
**
104 TTTTAATTCTTTCTCTT
1 TTTTTCTT-TTTCTC-T
121 TTTTTCTTT
1 TTTTTCTTT
130 CTTCAGGCTA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
14 22 0.40
15 7 0.13
16 7 0.13
17 19 0.35
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTTTTTCTCT
Found at i:67 original size:22 final size:22
Alignment explanation
Indices: 42--98 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
32 TTTTTTATTT
42 TCTTTTTCTTTTTCTTTTTCTC
1 TCTTTTTCTTTTTCTTTTTCTC
*
64 TCTTTCTT-TATTTCTTTTTCTC
1 TCTTT-TTCTTTTTCTTTTTCTC
*
86 -ATTTTTCATTTTT
1 TCTTTTTC-TTTTT
99 TCTCTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.07
21 3 0.10
22 22 0.76
23 2 0.07
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.75
Consensus pattern (22 bp):
TCTTTTTCTTTTTCTTTTTCTC
Found at i:83 original size:14 final size:13
Alignment explanation
Indices: 25--129 Score: 61
Period size: 14 Copynumber: 7.6 Consensus size: 13
15 TTGAACCCCC
* *
25 TTTTATTTTTTTT
1 TTTTCTTTTTCTT
38 ATTTTCTTTTTC-T
1 -TTTTCTTTTTCTT
51 TTTTCTTTTTCTCT
1 TTTTCTTTTTCT-T
*
65 CTTTCTTTATTTCTT
1 TTTTC-TT-TTTCTT
80 TTTCTCATTTTTCATT
1 TTT-TC-TTTTTC-TT
*
96 TTTTCTCTTT-TT
1 TTTTCTTTTTCTT
** *
108 AATTCTTTCTCTTT
1 TTTTCTTTTTC-TT
122 TTTTCTTT
1 TTTTCTTT
130 CTTCAGGCTA
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
12 19 0.27
13 1 0.01
14 26 0.37
15 11 0.15
16 14 0.20
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:106 original size:8 final size:8
Alignment explanation
Indices: 50--129 Score: 53
Period size: 8 Copynumber: 10.2 Consensus size: 8
40 TTTCTTTTTC
50 TTTT-TCT
1 TTTTCTCT
57 TTTTCTCT
1 TTTTCTCT
*
65 CTTTCT-T
1 TTTTCTCT
*
72 TATT-TCT
1 TTTTCTCT
79 TTTTCTCAT
1 TTTTCTC-T
88 TTTTCAT-T
1 TTTTC-TCT
96 TTTTCTCT
1 TTTTCTCT
*
104 TTTTAAT-T
1 TTTT-CTCT
*
112 CTTTCTCT
1 TTTTCTCT
*
120 TTTTTTCT
1 TTTTCTCT
128 TT
1 TT
130 CTTCAGGCTA
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
6 1 0.02
7 13 0.23
8 34 0.61
9 7 0.12
10 1 0.02
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTCTCT
Found at i:130 original size:14 final size:15
Alignment explanation
Indices: 47--131 Score: 68
Period size: 16 Copynumber: 5.5 Consensus size: 15
37 TATTTTCTTT
* *
47 TTCTTTTTCTTTTTC
1 TTCTTTCTCTTTTTA
*
62 TCTCTTTCT-TTATTTC
1 T-TCTTTCTCTT-TTTA
78 TT-TTTCTCATTTTTCA
1 TTCTTTCTC-TTTTT-A
*
94 TTTTTTCTCTTTTTAA
1 TTCTTTCTCTTTTT-A
110 TTCTTTCTCTTTTT-
1 TTCTTTCTCTTTTTA
124 TTCTTTCT
1 TTCTTTCT
132 TCAGGCTAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
14 13 0.22
15 7 0.12
16 34 0.57
17 6 0.10
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (15 bp):
TTCTTTCTCTTTTTA
Found at i:6462 original size:23 final size:23
Alignment explanation
Indices: 6436--6500 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
6426 CACCACAGCT
*
6436 CATATAAATGCACCGAAGTGCTA
1 CATAGAAATGCACCGAAGTGCTA
* *
6459 CATAGAATTGCACTGAAGTGCTA
1 CATAGAAATGCACCGAAGTGCTA
*
6482 CATAGAAATCCACCGAAGT
1 CATAGAAATGCACCGAAGT
6501 CCATATAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCTA
Found at i:6603 original size:21 final size:21
Alignment explanation
Indices: 6574--6635 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 21
6564 ACCATGTATG
*
6574 TGTCTCAAAGGACCTCATAAA
1 TGTCCCAAAGGACCTCATAAA
* * *
6595 TGTTCCAAAGTA--TACATATA
1 TGTCCCAAAGGACCT-CATAAA
*
6615 TGTCCCGAAGGACCTCATAAA
1 TGTCCCAAAGGACCTCATAAA
6636 CACTCTACTC
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.47
21 14 0.47
22 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (21 bp):
TGTCCCAAAGGACCTCATAAA
Found at i:7155 original size:24 final size:22
Alignment explanation
Indices: 7095--7155 Score: 52
Period size: 24 Copynumber: 2.7 Consensus size: 22
7085 ATTTTTCCCT
*
7095 TAAGTGGTATCGATACCCCTTTG
1 TAAG-GGTATCGATACCCCTTTA
* * *
7118 T-ACGGTACCAATACTTCCCTTTA
1 TAAGGGTATCGATAC--CCCTTTA
7141 TAAGGGTATCGATAC
1 TAAGGGTATCGATAC
7156 ACTACTTGGG
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
21 9 0.32
22 1 0.04
23 8 0.29
24 10 0.36
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (22 bp):
TAAGGGTATCGATACCCCTTTA
Found at i:10460 original size:85 final size:84
Alignment explanation
Indices: 10162--10470 Score: 399
Period size: 85 Copynumber: 3.6 Consensus size: 84
10152 TGACGCGCAA
* * * * * * *
10162 TTGTGTGTCATAAATCTATGACGCGCAT-TAATGACGTT-CTTTGAGTGTCATTGAAGCCCCCGA
1 TTGTGCGTCATAAATTTATGACACGCATGT-ATGAC-TTACATTGCGCGTCATTGAAGCCCCCGT
10225 CATAAATTAAGCTGACACACAT
64 CATAAATT-AGCTGACACACAT
10247 TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCA
1 TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCA
*
10312 TAAATTAAGATGACACACAT
66 TAAATT-AGCTGACACACAT
* * *
10332 TTGTGCGTCATAAATTTATGACACGTATGTATGACTCATATTGCGCGTCATTGAAGCCCCCGTCA
1 TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCA
*
10397 TAAATCT-GCTTGACATACAT
66 TAAAT-TAGC-TGACACACAT
* * **
10417 TTGTGTGTCATAAATTTATGACACGCATATATGACTTACATTGCATGTCATTGA
1 TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGA
10471 TGCATACGTC
Statistics
Matches: 200, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
84 3 0.01
85 195 0.98
86 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (84 bp):
TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCA
TAAATTAGCTGACACACAT
Found at i:11962 original size:12 final size:12
Alignment explanation
Indices: 11945--11975 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
11935 ATATATTCAT
11945 AATCAAATGAAA
1 AATCAAATGAAA
11957 AATCAAATGAAA
1 AATCAAATGAAA
*
11969 AAACAAA
1 AATCAAA
11976 CTCGGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:12559 original size:19 final size:20
Alignment explanation
Indices: 12535--12583 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
12525 TTCTTTCTCC
*
12535 TCTTCCTTTTTCCTTT-GCG
1 TCTTCCTTTTTCCTTTACCG
* * *
12554 TTTTCCCTTCTCCTTTACCG
1 TCTTCCTTTTTCCTTTACCG
12574 TCTTCCTTTT
1 TCTTCCTTTT
12584 CTTTCTCTTT
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.02, C:0.35, G:0.06, T:0.57
Consensus pattern (20 bp):
TCTTCCTTTTTCCTTTACCG
Found at i:23672 original size:23 final size:23
Alignment explanation
Indices: 23646--23701 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
23636 CATAAAAACA
*
23646 TTTCATAAGGGATTCAAATTGCT
1 TTTCATAACGGATTCAAATTGCT
23669 TTTCATAACGGATTCAAATTGCT
1 TTTCATAACGGATTCAAATTGCT
23692 TTTCATAACG
1 TTTCATAACG
23702 AGAATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (23 bp):
TTTCATAACGGATTCAAATTGCT
Found at i:23890 original size:23 final size:22
Alignment explanation
Indices: 23860--23944 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 22
23850 CATATTTGTC
23860 CCGAAGGACCACATAGTTTTAT
1 CCGAAGGACCACATAGTTTTAT
* *
23882 CACGAAGGATCACATAGTTTTTTT
1 C-CGAAGGACCACATAG-TTTTAT
* * * * *
23906 CTGAAGGACTACATAATATTGT
1 CCGAAGGACCACATAGTTTTAT
23928 CTCGAAGGACCACATAG
1 C-CGAAGGACCACATAG
23945 AACCCTCGAC
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
22 6 0.12
23 37 0.76
24 6 0.12
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (22 bp):
CCGAAGGACCACATAGTTTTAT
Found at i:34151 original size:27 final size:26
Alignment explanation
Indices: 34111--34161 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
34101 AATAATATAT
34111 ATATATATACATAAATATTTTCAAAAAC
1 ATATATATACAT-AA-ATTTTCAAAAAC
*
34139 ATATA-ATATATAAATTTTCAAAA
1 ATATATATACATAAATTTTCAAAA
34162 TGTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 2 0.09
27 5 0.23
28 5 0.23
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATATATACATAAATTTTCAAAAAC
Found at i:34180 original size:37 final size:37
Alignment explanation
Indices: 34123--34459 Score: 246
Period size: 37 Copynumber: 9.1 Consensus size: 37
34113 ATATATACAT
* * *
34123 AAATATTTTCAAAAAC-ATATAATATATAAATTTTCA
1 AAATGTTTTTAAAAACTATATAATATATAAGTTTTCA
** *
34159 AAATGTTTTTTTAAACTATATAATATACGAATGTTTTCA
1 AAATGTTTTTAAAAACTATATAATATA-TAA-GTTTTCA
* * * *
34198 ACATG-TTTTAAAAA-AAAATATTATATAAGTTTTCAA
1 AAATGTTTTTAAAAACTATATAATATATAAGTTTTC-A
*
34234 AAACG-TTTTAAAAACTATATAATATATAAATGTTTTCA
1 AAATGTTTTTAAAAACTATATAATATAT-AA-GTTTTCA
* *
34272 AAATG-TTTTCAAAAC--TATAATATATATGTTTTCAA
1 AAATGTTTTTAAAAACTATATAATATATAAGTTTTC-A
*
34307 AAATGTTTTCAAAAACTATAT-ATATATAAGTTTTCA
1 AAATGTTTTTAAAAACTATATAATATATAAGTTTTCA
* * * **
34343 AAATGATTTTAAAAAATTATATATTATATATTTTTTCTA
1 AAATG-TTTTTAAAAACTATATAATATATAAGTTTTC-A
*** *
34382 AAATGTTTTTTTTTAACTATATATTATAT-AGTTTT-A
1 AAATG-TTTTTAAAAACTATATAATATATAAGTTTTCA
** * * *
34418 AAA-ACTATTAAAAACTATATATTATATACGTAGTTTCA
1 AAATGTTTTTAAAAACTATATAATATATAAGT--TTTCA
34456 AAAT
1 AAAT
34460 ATGTATATAT
Statistics
Matches: 238, Mismatches: 44, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
34 24 0.10
35 15 0.06
36 55 0.23
37 57 0.24
38 47 0.20
39 40 0.17
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (37 bp):
AAATGTTTTTAAAAACTATATAATATATAAGTTTTCA
Found at i:34232 original size:74 final size:74
Alignment explanation
Indices: 34123--34391 Score: 278
Period size: 74 Copynumber: 3.6 Consensus size: 74
34113 ATATATACAT
* * * * **
34123 AAATATTTTCAAAAACATATAATATATAAATTTTC-AAAATGTTTTTTTAAACTATATAATATAC
1 AAATGTTTT-AAAAAAATATATTATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAATATA-
*
34187 GAATGTTTTCA
64 AAATGTTTTCA
* * *
34198 ACATGTTTTAAAAAAAAATATTATATAAGTTTTCAAAAACG-TTTTAAAAACTATATAATATATA
1 AAATGTTTTAAAAAAATATATTATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAATATA-A
34262 AATGTTTTCA
65 AATGTTTTCA
* * * * * *
34272 AAATGTTTT-CAAAACTATAATATATATGTTTTCAAAAATGTTTTCAAAAACTATAT-ATATATA
1 AAATGTTTTAAAAAAATATATTATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAATATAAA
34335 A-GTTTTCA
66 ATGTTTTCA
** *
34343 AAATGATTTTAAAAAATTATATATTATATATTTTTTCTAAAATGTTTTT
1 AAATG-TTTTAAAAAA--ATATATTATATAAGTTTTCAAAAATGTTTTT
34392 TTTTAACTAT
Statistics
Matches: 162, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
71 12 0.07
72 6 0.04
73 34 0.21
74 72 0.44
75 38 0.23
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (74 bp):
AAATGTTTTAAAAAAATATATTATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAATATAAA
ATGTTTTCA
Found at i:34277 original size:11 final size:11
Alignment explanation
Indices: 34261--34285 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34251 TATAATATAT
34261 AAATGTTTTCA
1 AAATGTTTTCA
34272 AAATGTTTTCA
1 AAATGTTTTCA
34283 AAA
1 AAA
34286 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:34314 original size:12 final size:12
Alignment explanation
Indices: 34297--34321 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34287 TATAATATAT
34297 ATGTTTTCAAAA
1 ATGTTTTCAAAA
34309 ATGTTTTCAAAA
1 ATGTTTTCAAAA
34321 A
1 A
34322 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:35275 original size:84 final size:82
Alignment explanation
Indices: 35087--36149 Score: 969
Period size: 84 Copynumber: 12.9 Consensus size: 82
35077 ACCTCGAAGT
* *** * * * * * *
35087 TGAGTGTAATCGAACGCGGGGGTCTTTG--GCAGGTAGCCCTTCTC-GACTTGAGCTATGATGTA
1 TGAGTGTAATCGAACTCAAAGGTCTTTGTTGCAGATAACCCTTC-CAGACTTAAGTTATGCTGCA
*
35149 AATGATGTGCCTTGGAGT
65 AATGATGTGCCTTGGAGC
* * *
35167 TGAGTGTAATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCCAGCCTTGAGTTATGCTGTA
1 TGAGTGTAATCGAACTCAAAGGTCTTTGTTG-CAGATAACCCTTCCAGACTTAAGTTATGCTGCA
* *
35232 AATGATATGCCCTTGAAGC
65 AATGATGTG-CCTTGGAGC
* * * * *
35251 TGAGTGTAATCGAACTTAAGGGTCTTTG--GCAGATAGCCCTTCTC-GACTTAAGCTATGCTACA
1 TGAGTGTAATCGAACTCAAAGGTCTTTGTTGCAGATAACCCTTC-CAGACTTAAGTTATGCTGCA
*
35313 AATGATATGCCTTGGAGC
65 AATGATGTGCCTTGGAGC
* * * *
35331 TGAGCGTAATCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
1 TGAGTGTAATCGAACTCAAAGGTC-TTTGTT-GCAGATAACCCTTCCAGACTTAAGTTATGCTGC
* *
35396 AAATGATGTGCCCTCGAAGC
64 AAATGATGTG-CCTTGGAGC
* * *
35416 TGAGTGTAATCGAACTCGAAGGTCTTTG--GCAGATAGCCCTTCTC-GACTTAAGCTATGCTGCA
1 TGAGTGTAATCGAACTCAAAGGTCTTTGTTGCAGATAACCCTTC-CAGACTTAAGTTATGCTGCA
35478 AATGATGTGCCTTGGAGC
65 AATGATGTGCCTTGGAGC
** * * * *
35496 TGAACGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTTA-ACTTAAGTTATGCTG
1 TGAGTGTAATCGAACTCAAAGGTCTTT-GTT-GCAGATAACCCTTC-CAGACTTAAGTTATGCTG
35560 CAAATGATGTGCCGTT-GAGC
63 CAAATGATGTGCC-TTGGAGC
* * * * *
35580 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
1 TGAGTGTAATCGAACTCAAAGGTC-TTTGTT-GCAGATAACCCTTCCAGACTTAAGTTATGCTGC
*
35645 AAATGATGTGACGTT-GAGC
64 AAATGATGTG-CCTTGGAGC
* * * * * * *
35664 TGAGCGTAGTCGAACTCAAAGGTCTTT-TGGTCATAGATAACTCTTCTAGCCTTGAGTTATGCTG
1 TGAGTGTAATCGAACTCAAAGGTCTTTGTTG-C--AGATAACCCTTCCAGACTTAAGTTATGCTG
* * * * *
35728 TAAATGATATGCCCTCGAAAC
63 CAAATGATGTG-CCTTGGAGC
*** * * * *
35749 TGAGTGTAATCGAACTCGGGGGTCTTTG--GCAGATAGCCC-TCCTCGACTTAAGTTATGCTACG
1 TGAGTGTAATCGAACTCAAAGGTCTTTGTTGCAGATAACCCTTCC-AGACTTAAGTTATGCTGCA
35811 AATGATGTGCCTTGGAGC
65 AATGATGTGCCTTGGAGC
* *
35829 TGAGCGTAGTCGAACTCAAAGGTCTTTGGTTAGCAGATAACCCTTCTC-GACTTAAGTTATGCTG
1 TGAGTGTAATCGAACTCAAAGGTCTTT-GTT-GCAGATAACCCTTC-CAGACTTAAGTTATGCTG
* *
35893 CAAATGATGTGCCCTCGAAGC
63 CAAATGATGTG-CCTTGGAGC
*** * * *
35914 TGAGTGTAATCGAACTCGGGGGTCTTTG--GCATATAGCCCTTTCTC-GACTTAAGCTATGCTGC
1 TGAGTGTAATCGAACTCAAAGGTCTTTGTTGCAGATAACCC-TTC-CAGACTTAAGTTATGCTGC
35976 AAATGATGTGCCTTGGAGC
64 AAATGATGTGCCTTGGAGC
* * * * *
35995 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCCAGCCTTGAGTTATGCTGC
1 TGAGTGTAATCGAACTCAAAGGTCTTT-GTT-GCAGATAACCCTTCCAGACTTAAGTTATGCTGC
*
36060 AAATGATATGCCTTGGAGC
64 AAATGATGTGCCTTGGAGC
* * * * * *
36079 TGAGTGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
1 TGAGTGTAATCGAACTCAAAGGTCTTTGTTG-CAGATAACCCTTCCAGACTTAAGTTATGCTGCA
36144 AATGAT
65 AATGAT
36150 TTGTTTTTTA
Statistics
Matches: 820, Mismatches: 121, Indels: 81
0.80 0.12 0.08
Matches are distributed among these distances:
80 114 0.14
81 145 0.18
82 39 0.05
83 80 0.10
84 342 0.42
85 99 0.12
86 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (82 bp):
TGAGTGTAATCGAACTCAAAGGTCTTTGTTGCAGATAACCCTTCCAGACTTAAGTTATGCTGCAA
ATGATGTGCCTTGGAGC
Found at i:35454 original size:165 final size:165
Alignment explanation
Indices: 35067--36149 Score: 1334
Period size: 165 Copynumber: 6.5 Consensus size: 165
35057 GCTATGTTGT
* * * ** *
35067 AAATGATATGACCTCGAAGTTGAGTGTAATCGAACGCGGGGGTCTTTGGCAGGTAGCCCTTCTCG
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG
* * * * * *
35132 ACTTGAGCTATGATGTAAATGATGTGCCTTGGAGTTGAGTGTAATCGAACTCAAAGGTCTTT-GT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
* * * * *
35196 TGACAGATAACCCTTCCAGCCTTGAGTTATGCTGT
131 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* *
35231 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTCTTTGGCAGATAGCCCTTCTC
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAA-GGTCTTTGGCAGATAGCCCTTCTC
* * * *
35295 GACTTAAGCTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTG
65 GACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* *
35360 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
130 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
*
35396 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG
* *
35461 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
*
35526 TGGTAGATAACCCTTCTTA-ACTTAAGTTATGCTGC
131 TGGCAGATAACCCTTC-TAGACTTAAGTTATGCTGC
* * * * * * * *
35561 AAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTT
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTT
* * * *
35625 CTAGACTTAAGTTGTGCTGCAAATGATGTGACGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCT
62 CTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-
*** * * * *
35689 TTTGG-TCATAGATAACTCTTCTAGCCTTGAGTTATGCTGT
125 TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* ** *
35729 AAATGATATGCCCTCGAAACTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTCCTCG
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG
* * *
35794 ACTTAAGTTATGCTACGAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
* *
35859 TAGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
131 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* ** *
35894 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCATATAGCCCTTTCTC
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCC-TTCTC
*
35959 GACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
65 GACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* * *
36024 TTGGCAGATAACCCTTCCAGCCTTGAGTTATGCTGC
130 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * * *
36060 AAATGATATG-CCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTC
1 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT-G-G-CAGATAGCCCTTC
* * * * *
36124 TAGCCTTGAGTTATGCTGTAAATGAT
63 TCGACTTAAGCTATGCTGCAAATGAT
36150 TTGTTTTTTA
Statistics
Matches: 796, Mismatches: 105, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
164 143 0.18
165 371 0.47
166 111 0.14
167 28 0.04
168 114 0.14
169 29 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (165 bp):
AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
Found at i:35542 original size:249 final size:247
Alignment explanation
Indices: 35123--36149 Score: 1158
Period size: 249 Copynumber: 4.1 Consensus size: 247
35113 TGGCAGGTAG
* * * * * * * *
35123 CCCTTCTCGACTTGAGCTATGATGTAAATGATGTG-CCTTGGAGTTGAGTGTAATCGAACTCAAA
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAA
* * * *
35187 GGTCTTTGTTGACAGATAACCCTTC-CAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGC
66 GGTCTTTG--GACAGATAACCCTTCTC-GACTTAAGCTATGCTGCAAATGATATGCCCTTGAAGC
* * * *
35251 TGAGTGTAATCGAACT-TAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAA
128 TGAGCGTAATCGAACTCGAA-GGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAA
*
35315 TGATATGCCTTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGTTGGCAGACAA
192 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
* *
35371 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAA
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAA
* * *
35436 GGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGA
66 GGTCTTTGGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTTGAAGCTGA
* * * ** *
35499 ACGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTTAACTTAAGTTATGCTGCAAA
131 GCGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAA
*
35564 TGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
192 TGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
* * * * * *
35620 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGACGTTG-AGCTGAGCGTAGTCGAACTCAAA
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAA
* * * * * * * * *
35684 GGTCTTTTGGTCATAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAAC
66 GGTC-TTTGG--ACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTTGAAGC
* ** * * *
35749 TGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTCCTCGACTTAAGTTATGCTACGAAT
128 TGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAAT
* * * *
35814 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTAGCAGATAA
193 GATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
* ***
35869 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAA
* * * *
35934 GGTCTTTGG-CATATAGCCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTG
66 GGTCTTTGGACAGATAACCC-TTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTTGAAGCTG
* * * *
35997 AGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC-CAGCCTTGAGTTATGCTGCA
130 AGCGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTC-GACTTAAGTTATGCTACA
* * * *
36061 AATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTC-TTTGGTGACAGATAA
190 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
* * *
36118 CCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGAT
36150 TTGTTTTTTA
Statistics
Matches: 653, Mismatches: 105, Indels: 41
0.82 0.13 0.05
Matches are distributed among these distances:
245 25 0.04
246 68 0.10
247 29 0.04
248 56 0.09
249 323 0.49
250 93 0.14
251 1 0.00
252 33 0.05
253 25 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (247 bp):
CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAA
GGTCTTTGGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTTGAAGCTGA
GCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGAT
ATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
Found at i:42488 original size:37 final size:36
Alignment explanation
Indices: 42431--42680 Score: 233
Period size: 37 Copynumber: 6.8 Consensus size: 36
42421 ATATATACAT
* *
42431 AAATATTTTCAAAAAC-ATATAATATATAAATTTTCA
1 AAATGTTTT-AAAAACTATATAATATATAAGTTTTCA
** *
42467 AAATGTTTTTTTAAACTATATAATATACGAATGTTTTCA
1 AAATG-TTTTAAAAACTATATAATATA-TAA-GTTTTCA
* * *
42506 ACATGTTTTCAAAAA--AAATATTATATAAGTTTTCAA
1 AAATGTTTT-AAAAACTATATAATATATAAGTTTTC-A
*
42542 AAACGTTTTAAAAACTATATAATATATAAATGTTTTCA
1 AAATGTTTTAAAAACTATATAATATAT-AA-GTTTTCA
* *
42580 AAATGTTTTCAAAAC--TATAATATATATGTTTTCAA
1 AAATGTTTTAAAAACTATATAATATATAAGTTTTC-A
42615 AAATGTTTTCAAAAACTATAT-ATATATAAGTTTTCA
1 AAATGTTTT-AAAAACTATATAATATATAAGTTTTCA
* *
42651 AAATGATTTTAAAAAATTATATATTATATA
1 AAATG-TTTT-AAAAACTATATAATATATA
42681 TATTTTCTAA
Statistics
Matches: 175, Mismatches: 23, Indels: 30
0.77 0.10 0.13
Matches are distributed among these distances:
34 6 0.03
35 22 0.13
36 39 0.22
37 58 0.33
38 31 0.18
39 19 0.11
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (36 bp):
AAATGTTTTAAAAACTATATAATATATAAGTTTTCA
Found at i:42540 original size:74 final size:74
Alignment explanation
Indices: 42431--42666 Score: 268
Period size: 74 Copynumber: 3.2 Consensus size: 74
42421 ATATATACAT
* * * **
42431 AAATATTTTCAAAAACATATAATATATAAATTTTC-AAAATGTTTTTTTAAACTATATAATATAC
1 AAATGTTTTCAAAAA-AAATAATATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAATATA-
*
42495 GAATGTTTTCA
64 AAATGTTTTCA
* * *
42506 ACATGTTTTCAAAAAAAATATTATATAAGTTTTCAAAAACG-TTTTAAAAACTATATAATATATA
1 AAATGTTTTCAAAAAAAATAATATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAATATA-A
42570 AATGTTTTCA
65 AATGTTTTCA
** * * *
42580 AAATGTTTTC-AAAACTATAATATATATGTTTTCAAAAATGTTTTCAAAAACTATAT-ATATATA
1 AAATGTTTTCAAAAAAAATAATATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAATATAAA
42643 A-GTTTTCA
66 ATGTTTTCA
42651 AAATGATTTT-AAAAAA
1 AAATG-TTTTCAAAAAA
42667 TTATATATTA
Statistics
Matches: 138, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
71 12 0.09
72 10 0.07
73 30 0.22
74 68 0.49
75 18 0.13
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (74 bp):
AAATGTTTTCAAAAAAAATAATATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAATATAAA
ATGTTTTCA
Found at i:42585 original size:11 final size:11
Alignment explanation
Indices: 42569--42593 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42559 TATAATATAT
42569 AAATGTTTTCA
1 AAATGTTTTCA
42580 AAATGTTTTCA
1 AAATGTTTTCA
42591 AAA
1 AAA
42594 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:42622 original size:12 final size:12
Alignment explanation
Indices: 42605--42629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42595 TATAATATAT
42605 ATGTTTTCAAAA
1 ATGTTTTCAAAA
42617 ATGTTTTCAAAA
1 ATGTTTTCAAAA
42629 A
1 A
42630 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:48085 original size:84 final size:85
Alignment explanation
Indices: 47872--48944 Score: 1145
Period size: 84 Copynumber: 12.8 Consensus size: 85
47862 TAAAGAAACT
* * * * * * *
47872 ATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
* * * *
47937 CTCAAC-TCAACGACACATC
66 CTCAGCTTCGAGGGCACATC
* * * * * *
47956 ATTTGCAGTATAGCTTAAGTCGAGAACGGCTATCTTCCAACCAAAGACCTTCGAGTTTGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
*
48021 CTCAGCTTCGAGGGCATATC
66 CTCAGCTTCGAGGGCACATC
* * * * * *
48041 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAA-CAAAGACCTTCAAGTTTGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
* * * *
48105 CTCAGCTTTGGGGGTATATC
66 CTCAGCTTCGAGGGCACATC
* *
48125 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
* *
48190 CTCAG-TTCCAAGGCACATC
66 CTCAGCTTCGAGGGCACATC
* * * * *
48209 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATG----CCAAAGACCCTCGAGTTAGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
48270 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCGAGGGCACATC
* * * * *
48290 ATTTACAGCATAACTCAAG-GGTAGAAGAGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGATTA
1 ATTTGCAGCATAACTTAAGTCG-AGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGATTA
48353 CACTCAGCTTCGAGGGCACATC
64 CACTCAGCTTCGAGGGCACATC
* ** * * * * *
48375 ATTTGTAGCATAACTTAAGTTTAGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCAACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
* * * *
48440 CTCAAC-TCAACGGTACATC
66 CTCAGCTTCGAGGGCACATC
* * * *
48459 ATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAACCAAAGACCTTCGAGTTTGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
48524 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCGAGGGCACATC
* * ** * *
48544 ATTTGCAGCATAACTCAAGGCTTGAAGGGTTATCTGCCAA-CAAAGACCTTCAAGTTTGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
* * *
48608 CTCAGTTTCGGGGGCATATC
66 CTCAGCTTCGAGGGCACATC
* *
48628 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
* ** *
48693 CTCAGC-TCCAAAGCACGTC
66 CTCAGCTTCGAGGGCACATC
* * * * * * *
48712 ATTTGCAACTTAGCTTAAGTCGAAAAGGGATATCTG----CCAAAGACCCTCGAGTTCGATTATA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
* * *
48773 CTCAGCTTCGGGGGAATATC
66 CTCAGCTTCGAGGGCACATC
* * * *
48793 ATTTGCAACATAACTTAATTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
* *
48858 CTCAGC-TCCAAGGCACATC
66 CTCAGCTTCGAGGGCACATC
* * * * * * *
48877 ATTTGTAGCATAGCTTAAGTCGAGAAAGGCTATCTGACAACCGAAGTCCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
48942 CTC
66 CTC
48945 CGCTCAGAGG
Statistics
Matches: 812, Mismatches: 160, Indels: 34
0.81 0.16 0.03
Matches are distributed among these distances:
80 55 0.07
81 76 0.09
84 421 0.52
85 257 0.32
86 3 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (85 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
CTCAGCTTCGAGGGCACATC
Found at i:48167 original size:169 final size:169
Alignment explanation
Indices: 47872--48944 Score: 1137
Period size: 169 Copynumber: 6.4 Consensus size: 169
47862 TAAAGAAACT
* * * *
47872 ATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGATTACA
* * * * * * * * *
47937 CTCAAC-TCAACGACACATCATTTGCAGTATAGCTTAAGTCGAGAACGGCTATCTTCCAACCAAA
65 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* * * * *
48001 GACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCATATC
130 GACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATC
* * *
48041 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAACAAAGACCTTCAAGTTTGATTACAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACAC
* * * * *
48106 TCAGCTTTGGGGGTATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAG
66 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
48171 ACCTTCGAGTTCGACTACACTCAG-TTCCAAGGCACATC
131 ACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATC
* * * * * * * *
48209 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATG-C--CAAAGACCCTCGAGTTAGATTACAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACAC
* * * * *
48271 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG-GGTAGAAGAGTTATCTGTC-ACCAAA
66 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCG-AGAAGGGTTATCTGCCAACC-AA
* * *
48334 AGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
129 AGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATC
* * ** * * * * *
48375 ATTTGTAGCATAACTTAAGTTTAGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCAACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGATTACA
* * * * * * *
48440 CTCAAC-TCAACGGTACATCATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAACCAAA
65 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* * * *
48504 GACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCACATC
130 GACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATC
* * *
48544 ATTTGCAGCATAACTCAAGGCTTGAAGGGTTATCTGCCAACAAAGACCTTCAAGTTTGATTACAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACAC
* * *
48609 TCAGTTTCGGGGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
66 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
* * *
48674 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAAGCACGTC
131 ACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATC
* * * * * * * * * *
48712 ATTTGCAACTTAGCTTAAGTCGAAAAGGGATATCTG-C--CAAAGACCCTCGAGTTCGATTATAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACAC
* * * * *
48774 TCAGCTTCGGGGGAATATCATTTGCAACATAACTTAATTCGAGAAGGGTTATCTGCCAACCAAAG
66 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
*
48839 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
131 ACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATC
* * * * * * * * * *
48877 ATTTGTAGCATAGCTTAAGTCGAGAAAGGCTATCTGACAACCGAAGTCCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGATTACA
48942 CTC
65 CTC
48945 CGCTCAGAGG
Statistics
Matches: 758, Mismatches: 131, Indels: 30
0.82 0.14 0.03
Matches are distributed among these distances:
164 4 0.01
165 242 0.32
166 43 0.06
167 3 0.00
168 122 0.16
169 317 0.42
170 27 0.04
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (169 bp):
ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACAC
TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
ACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATC
Found at i:48827 original size:503 final size:502
Alignment explanation
Indices: 47872--48934 Score: 1639
Period size: 503 Copynumber: 2.1 Consensus size: 502
47862 TAAAGAAACT
* * * *
47872 ATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGTAGCATAACTTAAGTCTAGAAGGGTTATCTGACAACCAAAGACCTTTGAGTTCAACTACG
* *
47937 CTCAACTCAACGACACATCATTTGCAGTATAGCTTAAGTCGAGAACGGCTATCTTCCAACCAAAG
66 CTCAACTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAACGGCTATCTGCCAACCAAAG
*
48002 ACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCATAACTCAAGGCTATAA
131 ACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCTATAA
*
48067 GGGTTATCTGCCAACAAAGACCTTCAAGTTTGATTACACTCAGCTTTGGGGGTATATCATTTGCA
196 GGGTTATCTGCCAACAAAGACCTTCAAGTTTGATTACACTCAGCTTTGGGGGCATATCATTTGCA
*
48132 GCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACACTCAGTT
261 GCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACACTCAGCT
* * * *
48197 CCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCTCGAGTT
326 CCAAAGCACATCATTTGCAACATAGCTTAAGTCGAAAAGGGATATATGCCAAAGACCCTCGAGTT
* * * *
48262 AGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGGTAGAAGAGTTATCTGT
391 AGATTACACTCAGCTTCGAGGGAACATCATTTACAACATAACTCAAGCGTAGAAGAGTTATCTGC
* * *
48327 C-ACCAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
456 CAACC-AAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATC
* *
48375 ATTTGTAGCATAACTTAAGTTTAGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCAACTACG
1 ATTTGTAGCATAACTTAAGTCTAGAAGGGTTATCTGACAACCAAAGACCTTTGAGTTCAACTACG
** *
48440 CTCAACTCAACGGTACATCATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAACCAAAG
66 CTCAACTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAACGGCTATCTGCCAACCAAAG
48505 ACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCT-TGA
131 ACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCTAT-A
48569 AGGGTTATCTGCCAACAAAGACCTTCAAGTTTGATTACACTCAG-TTTCGGGGGCATATCATTTG
195 AGGGTTATCTGCCAACAAAGACCTTCAAGTTTGATTACACTCAGCTTT-GGGGGCATATCATTTG
* *
48633 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
259 CAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACACTCAG
* * *
48698 CTCCAAAGCACGTCATTTGCAACTTAGCTTAAGTCGAAAAGGGATATCTGCCAAAGACCCTCGAG
324 CTCCAAAGCACATCATTTGCAACATAGCTTAAGTCGAAAAGGGATATATGCCAAAGACCCTCGAG
* * * * * * * *
48763 TTCGATTATACTCAGCTTCGGGGGAATATCATTTGCAACATAACTTAATTCG-AGAAGGGTTATC
389 TTAGATTACACTCAGCTTCGAGGGAACATCATTTACAACATAACTCAA-GCGTAGAAGAGTTATC
*
48827 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
453 TGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
* * * * * * *
48877 ATTTGTAGCATAGCTTAAGTCGAGAAAGGCTATCTGACAACCGAAGTCCTTCGAGTTC
1 ATTTGTAGCATAACTTAAGTCTAGAAGGGTTATCTGACAACCAAAGACCTTTGAGTTC
48935 GATTACACTC
Statistics
Matches: 509, Mismatches: 47, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
502 64 0.13
503 441 0.87
504 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (502 bp):
ATTTGTAGCATAACTTAAGTCTAGAAGGGTTATCTGACAACCAAAGACCTTTGAGTTCAACTACG
CTCAACTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAACGGCTATCTGCCAACCAAAG
ACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCTATAA
GGGTTATCTGCCAACAAAGACCTTCAAGTTTGATTACACTCAGCTTTGGGGGCATATCATTTGCA
GCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACACTCAGCT
CCAAAGCACATCATTTGCAACATAGCTTAAGTCGAAAAGGGATATATGCCAAAGACCCTCGAGTT
AGATTACACTCAGCTTCGAGGGAACATCATTTACAACATAACTCAAGCGTAGAAGAGTTATCTGC
CAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
Found at i:52682 original size:253 final size:257
Alignment explanation
Indices: 52110--52722 Score: 970
Period size: 253 Copynumber: 2.4 Consensus size: 257
52100 CTCCATCTGA
* *
52110 GACCCGACCCGATCAAAATAAAGTTTCACCCGATCCGACCCGAATATATGAATTAGAAACCCAAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAG--A---AAC
* *
52175 CCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTGATTGGAAAAATAT
61 CCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAAT
* *
52240 ATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATCATATATTTTTTG
126 ATATATATAGAGGGGTATTATTGTAATTATCCCTAAATATATAAGGTAAAATCATATATTATTT-
* *
52305 GTCGGGTTGGGTATTTTTCACCCTAAACCCGAACCCGACCCAACCCGAATATCACACTTAAAAAA
190 GTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCAGACCCAACCCGAATATCACACTTAAAAAA
52370 ACC
255 ACC
* * *
52373 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCAACCCGAATTTATGAATTAGAAATCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
*
52438 CCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATT-GAAAAAAAT-TAT
66 CCGAAATAAT-AAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAATATAT
*
52501 ATATAGAGGGGTATTATTGTAATTATCCCTAAATATATAAGGTAAAATTATATA-TATTT-TCGG
130 ATATAGAGGGGTATTATTGTAATTATCCCTAAATATATAAGGTAAAATCATATATTATTTGTCGG
* *
52564 GTCGGGTATTTTTCACCCTAAACCCGAACTCAG-CCCGACCCGAATATCACACTT-AAAAAACT
195 GTCGGGTATTTTTCACCCTAAACCCGAAC-CAGACCCAACCCGAATATCACACTTAAAAAAACC
52626 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
52691 CCGAAATAATAAAAAAA-TATTTTTATTCAATA
66 CCGAAATAATAAAAAAATTATTTTTATTCAATA
52723 TATGAATAAG
Statistics
Matches: 330, Mismatches: 18, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
251 15 0.05
252 7 0.02
253 79 0.24
254 52 0.16
255 2 0.01
256 4 0.01
257 55 0.17
258 25 0.08
259 38 0.12
261 1 0.00
263 52 0.16
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (257 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
CCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAATATATA
TATAGAGGGGTATTATTGTAATTATCCCTAAATATATAAGGTAAAATCATATATTATTTGTCGGG
TCGGGTATTTTTCACCCTAAACCCGAACCAGACCCAACCCGAATATCACACTTAAAAAAACC
Found at i:53237 original size:2 final size:2
Alignment explanation
Indices: 53230--53278 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
53220 CTACTACCTA
53230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53272 AT -T AT AT
1 AT AT AT AT
53279 TAGTACTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:56144 original size:34 final size:36
Alignment explanation
Indices: 56090--56184 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 36
56080 GTCCTACTAC
56090 GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTAG
1 GATTCAAACTCT-AAAAATAGGATAGAATTCTGCTAG
* *
56127 GATTC-AACTCT-AAAATAGGATAGAATTTTGCTAT
1 GATTCAAACTCTAAAAATAGGATAGAATTCTGCTAG
* * *
56161 GTTTTAAACTCCTAAAGATAGGAT
1 GATTCAAACT-CTAAAAATAGGAT
56185 CCACAAGCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
34 24 0.48
35 4 0.08
36 8 0.16
37 14 0.28
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
GATTCAAACTCTAAAAATAGGATAGAATTCTGCTAG
Found at i:56853 original size:16 final size:16
Alignment explanation
Indices: 56832--56865 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56822 CATGTATTTA
56832 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
56848 TATTATTTTACTTTAT
1 TATTATATTACATTAT
56864 TA
1 TA
56866 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:56870 original size:21 final size:21
Alignment explanation
Indices: 56845--56895 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
56835 TATATTACAT
*
56845 TATTATTATTTTACTTTATTAA
1 TATTATTATTTTACGTTA-TAA
* *
56867 -ATTATTTTTTTTCGTTATAA
1 TATTATTATTTTACGTTATAA
56887 TATTATTAT
1 TATTATTAT
56896 ATATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTATTATTTTACGTTATAA
Found at i:56870 original size:24 final size:22
Alignment explanation
Indices: 56837--56895 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
56827 ATTTATATTA
* *
56837 TATTACATTATTATTATTTTACTT
1 TATTAAATTATTATT-TTTT-CGT
56861 TATTAAATTATT-TTTTTTCGT
1 TATTAAATTATTATTTTTTCGT
56882 TA-TAATATTATTAT
1 TATTAA-ATTATTAT
56896 ATATATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 3 0.10
21 10 0.32
22 5 0.16
23 2 0.06
24 11 0.35
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTAAATTATTATTTTTTCGT
Found at i:60201 original size:10 final size:9
Alignment explanation
Indices: 60185--60237 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
60175 CAAAAAGGGC
60185 AAAAAGAAA
1 AAAAAGAAA
60194 AAAGAAGAAA
1 AAA-AAGAAA
*
60204 AAAAAAAAA
1 AAAAAGAAA
*
60213 AAACAAGAAC
1 AAA-AAGAAA
*
60223 AAAAATAAA
1 AAAAAGAAA
60232 AAAAAG
1 AAAAAG
60238 GGACAAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.85, C:0.04, G:0.09, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:60213 original size:19 final size:20
Alignment explanation
Indices: 60185--60237 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
60175 CAAAAAGGGC
*
60185 AAAAAGAAAAAAGAAGAA-A
1 AAAAAAAAAAAAGAAGAACA
*
60204 AAAAAAAAAAAACAAGAACA
1 AAAAAAAAAAAAGAAGAACA
60224 AAAATAAAAAAAAG
1 AAAA-AAAAAAAAG
60238 GGACAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.55
20 5 0.17
21 8 0.28
ACGTcount: A:0.85, C:0.04, G:0.09, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAGAAGAACA
Found at i:60220 original size:22 final size:21
Alignment explanation
Indices: 60185--60236 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
60175 CAAAAAGGGC
* *
60185 AAAAAGAAAAAAGAAGAAAAA
1 AAAAAAAAAAAAGAACAAAAA
60206 AAAAAAAAAACAAGAACAAAAA
1 AAAAAAAAAA-AAGAACAAAAA
*
60228 TAAAAAAAA
1 AAAAAAAAA
60237 GGGACAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.87, C:0.04, G:0.08, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAAAGAACAAAAA
Found at i:60243 original size:19 final size:19
Alignment explanation
Indices: 60176--60246 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
60166 CAATCAGAAC
60176 AAAAAGGG-CAAAAAGAAAA
1 AAAAAGGGACAAAAA-AAAA
* *
60195 AAGAA--GAAAAAAAAAAA
1 AAAAAGGGACAAAAAAAAA
* * *
60212 AAAACAAGAACAAAAATAAA
1 AAAA-AGGGACAAAAAAAAA
60232 AAAAAGGGACAAAAA
1 AAAAAGGGACAAAAA
60247 GCACATGCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
17 8 0.20
18 6 0.15
19 13 0.32
20 13 0.32
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (19 bp):
AAAAAGGGACAAAAAAAAA
Found at i:60865 original size:21 final size:21
Alignment explanation
Indices: 60839--60884 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
60829 ACCCATCAAT
60839 CCTTGAGCATCAAATACCAAA
1 CCTTGAGCATCAAATACCAAA
*
60860 CCTTGAGCATCAAATGCCAAA
1 CCTTGAGCATCAAATACCAAA
60881 CCTT
1 CCTT
60885 TGACCAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (21 bp):
CCTTGAGCATCAAATACCAAA
Found at i:61837 original size:38 final size:37
Alignment explanation
Indices: 61742--61852 Score: 161
Period size: 36 Copynumber: 3.0 Consensus size: 37
61732 GTGCTCACCA
61742 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
61778 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-CT
* * *
61816 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
61853 ATTGAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 31 0.46
37 3 0.04
38 30 0.45
39 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:61969 original size:102 final size:103
Alignment explanation
Indices: 61760--62012 Score: 400
Period size: 102 Copynumber: 2.5 Consensus size: 103
61750 CTTGAGACAG
** * * *** *
61760 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTTCTCCC
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTCCGTCTCCA
61825 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
61863 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAATTTCCCTTGAAACAAAA-TTCCGTCTCCA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTCCGTCTCCA
*
61927 TTGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
61965 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA
62013 TCTCTTGAAA
Statistics
Matches: 137, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
102 90 0.66
103 47 0.34
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (103 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTCCGTCTCCA
TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:62031 original size:75 final size:75
Alignment explanation
Indices: 61938--62082 Score: 281
Period size: 75 Copynumber: 1.9 Consensus size: 75
61928 TGAGACAGTT
*
61938 TCTCTTGAAACATAAACATTGGAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTT
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTT
62003 TCCCTTGAAA
66 TCCCTTGAAA
62013 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTT
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTT
62078 TCCCT
66 TCCCT
62083 CAAAAAAAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (75 bp):
TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTT
TCCCTTGAAA
Found at i:62046 original size:177 final size:167
Alignment explanation
Indices: 61819--62291 Score: 685
Period size: 177 Copynumber: 2.8 Consensus size: 167
61809 AAAATTTTTT
* * *
61819 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTTG
1 TCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
* ** *
61884 TCTCTCTTGAGATAATTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAAC
66 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
* **
61949 ATAAACATTGGAAACATTTCCCTTGAAATGAATTTTG
131 ATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
61986 TCTCTCTTGAGATAGTTTCCCTTGAAATCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAA
1 TCTCTCTTGAGATAG------TT----TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAA
** *
62051 ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCAAAAAAAAATTTTGTCTCCCTTGAGACAGTTT
56 ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTT
*
62116 CTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAATGAATTTCA
121 CTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
*
62163 TCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG
1 TCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
* * *
62228 TCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTTCTCTTGAA
66 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAC-AGTTTCTCTTGAA
62292 GCATCATCTT
Statistics
Matches: 274, Mismatches: 21, Indels: 21
0.87 0.07 0.07
Matches are distributed among these distances:
167 105 0.38
168 12 0.04
171 2 0.01
173 2 0.01
177 153 0.56
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (167 bp):
TCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
ATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
Found at i:62181 original size:65 final size:65
Alignment explanation
Indices: 62098--62256 Score: 282
Period size: 65 Copynumber: 2.4 Consensus size: 65
62088 AAAAATTTTG
* *
62098 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAATGAATTTCA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
* *
62163 TCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG
1 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
62228 TCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACA
62257 AAATTTTGTC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 89 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (65 bp):
TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
Found at i:62433 original size:37 final size:37
Alignment explanation
Indices: 62363--62434 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
62353 TGGAACTAAG
* * **
62363 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
62400 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
62435 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Done.