Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006138.1 Hibiscus syriacus cultivar Beakdansim tig00014564_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: 57028
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:8235 original size:23 final size:23
Alignment explanation
Indices: 8191--8236 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
8181 TTTATAAAAC
**
8191 CTTTTATATTATTTAATCAATTA
1 CTTTTATATTATAAAATCAATTA
8214 CTTTTATATTATAAACAT-AATTA
1 CTTTTATATTATAAA-ATCAATTA
8237 ATAATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
CTTTTATATTATAAAATCAATTA
Found at i:8603 original size:27 final size:28
Alignment explanation
Indices: 8573--8626 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
8563 ATATTAAAAA
*
8573 ATTA-TTATGTTAA-TTTTATATTATATC
1 ATTATTTAT-TTAATTTTTATATAATATC
8600 ATTATTTATTTAATTTTTATATAATAT
1 ATTATTTATTTAATTTTTATATAATAT
8627 AATATAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
ATTATTTATTTAATTTTTATATAATATC
Found at i:9681 original size:17 final size:17
Alignment explanation
Indices: 9666--9705 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
9656 GAGAAAAAAG
9666 AAGTAATGGAAAAAAATA
1 AAGTAA-GGAAAAAAATA
9684 AAGTAAGGAAAATAAAATA
1 AAGTAAGG-AAA-AAAATA
9703 AAG
1 AAG
9706 AAGATTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.10
18 9 0.45
19 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (17 bp):
AAGTAAGGAAAAAAATA
Found at i:9862 original size:31 final size:30
Alignment explanation
Indices: 9790--9862 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
9780 AAACAAAAAC
* * * *
9790 AAAAACGATAAATAATAAATAATAATAATA
1 AAAAACAAAAAATAATAAAAAATAAGAATA
* *
9820 ATAAAAGAAAAAATAATAAAAAATAAAGAATG
1 A-AAAACAAAAAATAATAAAAAAT-AAGAATA
9852 AAAAACAAAAA
1 AAAAACAAAAA
9863 TTAAAACCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 1 0.03
31 27 0.79
32 6 0.18
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (30 bp):
AAAAACAAAAAATAATAAAAAATAAGAATA
Found at i:10818 original size:7 final size:7
Alignment explanation
Indices: 10808--10845 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
10798 AAAGAAATGC
10808 ATAAATA
1 ATAAATA
10815 ATAAATA
1 ATAAATA
10822 ATAAATA
1 ATAAATA
10829 A-AAATA
1 ATAAATA
10835 ATAAA-A
1 ATAAATA
10841 ATAAA
1 ATAAA
10846 ATAAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
ATAAATA
Found at i:10835 original size:20 final size:20
Alignment explanation
Indices: 10810--10852 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
10800 AGAAATGCAT
10810 AAATAATAAATAAT-AAATAA
1 AAATAATAAA-AATAAAATAA
10830 AAATAATAAAAATAAAATAA
1 AAATAATAAAAATAAAATAA
10850 AAA
1 AAA
10853 AGAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAATAAAAATAAAATAA
Found at i:10846 original size:14 final size:14
Alignment explanation
Indices: 10808--10853 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
10798 AAAGAAATGC
10808 ATAAATAAT-AAATA
1 ATAAA-AATAAAATA
*
10822 ATAAATA-AAAATA
1 ATAAAAATAAAATA
10835 ATAAAAATAAAATA
1 ATAAAAATAAAATA
10849 A-AAAA
1 ATAAAA
10854 GAATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAAAAATAAAATA
Found at i:10851 original size:11 final size:10
Alignment explanation
Indices: 10810--10852 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
10800 AGAAATGCAT
10810 AAAT-AATAA
1 AAATAAATAA
10819 ATAATAAATAA
1 A-AATAAATAA
10830 AAAT-AATAA
1 AAATAAATAA
10839 AAATAAAATAA
1 AAAT-AAATAA
10850 AAA
1 AAA
10853 AGAATATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 10 0.33
10 6 0.20
11 14 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAATAA
Found at i:10968 original size:73 final size:71
Alignment explanation
Indices: 10874--11079 Score: 182
Period size: 73 Copynumber: 2.8 Consensus size: 71
10864 AAATCATATG
* *
10874 TTATATATATGTTTTTTAAAAATATTTTTAAAATCATATAATATATATTTTCAAATAACATTTTA
1 TTATATATATATATTTTAAAAATATTTTTAAAATCATATAATATATATTTTCAAATAACATTTTA
*
10939 AAACCAT
66 AAA-AAT
* * * * * **
10946 ATTATATATATATATTTTAAAAATGTTTTCAAAATTATATATTGTATAGTTTTC-AA-AATGTTT
1 -TTATATATATATATTTTAAAAATATTTTTAAAATCATATAATATATA-TTTTCAAATAACATTT
11009 TAAAAAAT
64 TAAAAAAT
** * *
11017 TATATATTATATATATTTTTCCAAATATTTTTTAAAAACCATATATTATATATATTTTTAAAT
1 T-TATA-TATATATA-TTTTAAAAATA-TTTTT-AAAATCATATA--ATATATATTTTCAAAT
11080 TGTTTTCGAA
Statistics
Matches: 104, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
70 1 0.01
71 6 0.06
72 18 0.17
73 50 0.48
74 9 0.09
75 9 0.09
76 4 0.04
77 7 0.07
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (71 bp):
TTATATATATATATTTTAAAAATATTTTTAAAATCATATAATATATATTTTCAAATAACATTTTA
AAAAAT
Found at i:11061 original size:39 final size:38
Alignment explanation
Indices: 10859--11274 Score: 206
Period size: 39 Copynumber: 10.9 Consensus size: 38
10849 AAAAAGAATA
* * * *
10859 TTTAAAAATCATATGTTATATATATGTTTTTTAAAAATATT
1 TTTAAAAACCATATATTATATATA--TTTTTCAAATAT-TT
* **
10900 TTT-AAAATCATATA--ATATATA-TTTTCAAATAACAT
1 TTTAAAAACCATATATTATATATATTTTTCAAAT-ATTT
* *
10935 TTT-AAAACCATAT-TATATATATATATTTT-AAAAATGT
1 TTTAAAAACCATATAT-TATATATAT-TTTTCAAATATTT
* ** * *
10972 TTTCAAAATTATATA-T-TGTATAGTTTTCAAA-ATGTT
1 TTTAAAAACCATATATTATATATATTTTTCAAATAT-TT
* **
11008 TTAAAAAATTATATATTATATATATTTTTCCAAATATTT
1 TTTAAAAACCATATATTATATATATTTTT-CAAATATTT
11047 TTTAAAAACCATATATTATATATATTTTT-AAAT-TGTT
1 TTTAAAAACCATATATTATATATATTTTTCAAATAT-TT
** *
11084 TTCGAAAA-C-TATATTATATATA--TTTCAAAATGTTTT
1 TTTAAAAACCATATATTATATATATTTTTC-AAAT-ATTT
** *
11120 TTTAAAAAAAACTATATAATATATATGTTTTCAAA-ATGTT
1 TTTAAAAACCA-TATATTATATATAT-TTTTCAAATAT-TT
* * * *
11160 TTCAAAAACTATATTATATATATATATATTTCCAAAATGTTTT
1 TTTAAAAACCATA-TAT-TATATATAT-TTTTC-AAAT-ATTT
*
11203 TTTAAAAA-C-TATATAATATATATGTTTTCAAA-ATGCTT
1 TTTAAAAACCATATATTATATATAT-TTTTCAAATAT--TT
* * *
11241 TTTAAAAAACTATATATTATATATCTATTTCAAA
1 TTT-AAAAACCATATATTATATATATTTTTCAAA
11275 AACCATTAGC
Statistics
Matches: 294, Mismatches: 45, Indels: 73
0.71 0.11 0.18
Matches are distributed among these distances:
33 3 0.01
35 43 0.15
36 34 0.12
37 27 0.09
38 35 0.12
39 68 0.23
40 35 0.12
41 32 0.11
42 7 0.02
43 9 0.03
44 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTAAAAACCATATATTATATATATTTTTCAAATATTT
Found at i:11292 original size:2 final size:2
Alignment explanation
Indices: 11285--11339 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
11275 AACCATTAGC
11285 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
11327 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
11340 AAATAAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11296 original size:80 final size:80
Alignment explanation
Indices: 11126--11306 Score: 206
Period size: 80 Copynumber: 2.2 Consensus size: 80
11116 TTTTTTTAAA
*
11126 AAAAACTATATAATATATATGTTTTCAAAATGTTTTCAAAAACTATATTATATATATATATATTT
1 AAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAAACTATATTATATATATATATATTT
* ** ****
11191 CCAAAATGTTTTTTT
66 CAAAAACATTAGCAT
*
11206 AAAAACTATATAATATATATGTTTTCAAAATGCTTTTTAAAAAACTATA-TAT-TATATATCTAT
1 AAAAACTATATAATATATATGTTTTCAAAATG--TTTTAAAAAACTATATTATATATATATATAT
11269 TTCAAAAACCATTAGCAT
64 TTCAAAAA-CATTAGCAT
* *
11287 ATATA-TATATATATATATAT
1 AAAAACTATATA-ATATATAT
11307 ATATATATAT
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
80 55 0.64
81 17 0.20
82 14 0.16
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (80 bp):
AAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAAACTATATTATATATATATATATTT
CAAAAACATTAGCAT
Found at i:12052 original size:84 final size:84
Alignment explanation
Indices: 11954--13163 Score: 1448
Period size: 84 Copynumber: 14.5 Consensus size: 84
11944 TCAAGGGGTT
* * * * * * * *
11954 TTTTTTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGTTACAAATAATGTGCCTTGGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
12019 GTAATCAAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * *
12038 TTTAGTTAGCAGATAGCCCTTCTTGCCTTGAGCTATTCTGCAAATGATGTGCCTTTGAGTTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
12103 GTAATCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* *
12122 TTTTGTTGACAGATAACCCTTCTAGCCTTTG-GTTATGCTGCAAATGATGTGCCTTGGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTTGCC-TTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* *
12186 CGTAGTGGAACTTGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * *
12206 TTTTGTTGGCAAATAACCCTTCTTTCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGTTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
12271 GTAGTTGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * *
12290 TTTGGTTGGAAGATAACCCTTCTAGTCTTGAGTTATGCTACAAATGATATGCCTTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
12355 GTAGTCGAACTCGAAGGTA
66 GTAGTCGAACTCGAAGGTC
* * *
12374 TTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
12439 GTAGCCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * *
12458 TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTT-----TGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
12518 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * **
12537 TTTCGTTGGCAAATAACTCTTCTTGCCTTGAGCTATATTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
12602 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * ** * * * * *
12621 TTTGGTTGGCAGATAAACTTTCTAACCTTGAGTTATACTGCAAATGATATGTCTTTGAGCTAAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
12686 GTAGTCAAACTCAAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * ** *
12705 TTTTGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATATTGCAAATGATGTGCCTTGGAGTTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
12770 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * *
12789 -TTTGATTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAG
1 TTTTG-TTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAG
12853 CGTAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * * *
12873 TTTTGTTGGTAAATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
12938 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * *
12957 TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGATGTGCCTTGGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
13022 GTAGTCGAACTTGAAGGT-
66 GTAGTCGAACTCGAAGGTC
* * * * * * *
13040 TTTTTTGTGGCAGATAGCTCTTTTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAG
1 TTTTGT-TGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* * *
13105 TGTAATCGAACTCGACGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * *
13125 -TTGGCTGACAGATAACCCTTCTCGCCTTGAGTTATGCTG
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTG
13164 TCTATAGTTT
Statistics
Matches: 959, Mismatches: 156, Indels: 23
0.84 0.14 0.02
Matches are distributed among these distances:
79 69 0.07
83 38 0.04
84 845 0.88
85 7 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTC
Found at i:12181 original size:168 final size:168
Alignment explanation
Indices: 11959--13163 Score: 1627
Period size: 168 Copynumber: 7.2 Consensus size: 168
11949 GGGTTTTTTT
* * * * * * * * *
11959 TTGGCAGATAGCCCTTCTCGCCTTGAGCTATGTTACAAATAATGTGCCTTGGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * *
12024 CAAACTCGAAGGTCTTTAGTTAGCAGATAGCCCTTCTTGCCTTGAGCTAT-TCTGCAAATGATGT
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATAT-TGCAAATGATGT
* * * * *
12088 GCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTG
130 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
12127 TTGACAGATAACCCTTCTAGCCTTTG-GTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTAGCC-TTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * * * * **
12191 TGGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTTTCCTTGAGTTATGCTGCAAATGATGT
65 TCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGCAAATGATGT
* *
12256 GCCTTGGAGTTGAGCGTAGTTGAACTCGAAGGTCTTTGG
130 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * *
12295 TTGGAAGATAACCCTTCTAGTCTTGAGTTATGCTACAAATGATATGCCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
12360 CGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGCAAATGATGTG
*
12425 CCTTGGAGCTGAGCGTAGCCGAACTCGAAGGTCTTTGG
131 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
*
12463 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTT-----TGAGTGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
12523 CGAACTCGAAGGTCTTTCGTTGGCAAATAACTCTTCTTGCCTTGAGCTATATTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGCAAATGATGTG
12588 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
131 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * * * *
12626 TTGGCAGATAAACTTTCTAACCTTGAGTTATACTGCAAATGATATGTCTTTGAGCTAAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
12691 CAAACTCAAAGGTCTTTTGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATATTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGCAAATGATGTG
* *
12756 CCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGA
131 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
12794 TTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
12859 CGAACTCGAAGGTCTTTTGTTGGTAAATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGCAAATGATGTG
12924 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
131 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * *
12962 TTGGCAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGATGTGCCTTGGAGCTGAGTGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * * * ** *
13027 CGAACTTGAAGGT-TTTTTTGTGGCAGATAGCTCTTTTTGCCTTGAGCTATGCTACAAATGATGT
66 CGAACTCGAAGGTCTTTTGT-TGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGCAAATGATGT
* * * *
13091 GCCTTTGAGCTGAGTGTAATCGAACTCGACGGTC-TTGG
130 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * *
13129 CTGACAGATAACCCTTCTCGCCTTGAGTTATGCTG
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTG
13164 TCTATAGTTT
Statistics
Matches: 926, Mismatches: 102, Indels: 19
0.88 0.10 0.02
Matches are distributed among these distances:
163 150 0.16
167 42 0.05
168 731 0.79
169 3 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (168 bp):
TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:14446 original size:88 final size:88
Alignment explanation
Indices: 14337--14516 Score: 279
Period size: 88 Copynumber: 2.0 Consensus size: 88
14327 ATTGTATAGA
* * * *
14337 TATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCATTTAACCAGTTT
1 TATTATAATCACCTTTATCAGGATAGCTGAATATTATCCATAAAGCTAGGGCATTTAACCAATTG
14402 CTCTAAAGGGACAACTCAAGCTT
66 CTCTAAAGGGACAACTCAAGCTT
* * *
14425 TATTATAATTACCTTTATCAGGATAGCTGAATCTTATCCATAAAGCTAGGGCGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGATAGCTGAATATTATCCATAAAGCTAGGGCATTTAACCAATTG
* *
14490 CTCTAGAGGGACATCTCAAGCTT
66 CTCTAAAGGGACAACTCAAGCTT
14513 TATT
1 TATT
14517 GTATATATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (88 bp):
TATTATAATCACCTTTATCAGGATAGCTGAATATTATCCATAAAGCTAGGGCATTTAACCAATTG
CTCTAAAGGGACAACTCAAGCTT
Found at i:18093 original size:14 final size:13
Alignment explanation
Indices: 18074--18173 Score: 52
Period size: 13 Copynumber: 7.9 Consensus size: 13
18064 TAATGGAAAT
* *
18074 AAATAAATTAAGG
1 AAATAAAATAAAG
18087 AAAATAAAATAAAG
1 -AAATAAAATAAAG
*
18101 AAAT-AAA-GAAG
1 AAATAAAATAAAG
* *
18112 -ATTAAGATAAAG
1 AAATAAAATAAAG
*
18124 AAAGT-AAATAAATA
1 AAA-TAAAATAAA-G
*
18138 AAATAAAA-AAGG
1 AAATAAAATAAAG
18150 ACAAT-AAATAAA-
1 A-AATAAAATAAAG
18162 AAATAAAATAAA
1 AAATAAAATAAA
18174 ATAAAGAGAA
Statistics
Matches: 65, Mismatches: 12, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
10 2 0.03
11 8 0.12
12 18 0.28
13 19 0.29
14 18 0.28
ACGTcount: A:0.72, C:0.01, G:0.10, T:0.17
Consensus pattern (13 bp):
AAATAAAATAAAG
Found at i:18104 original size:23 final size:21
Alignment explanation
Indices: 18070--18144 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 21
18060 AAAGTAATGG
*
18070 AAATAAATAAATTAAGGAAAATA
1 AAATAAAGAAA-TAA-GAAAATA
*
18093 AAATAAAGAAATAAAGAAGATTA
1 AAATAAAGAAAT-AAGAA-AATA
*
18116 AGATAAAGAAAGTAA-ATAAATA
1 AAATAAAGAAA-TAAGA-AAATA
18138 AAATAAA
1 AAATAAA
18145 AAAGGACAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 14 0.33
23 28 0.65
24 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.19
Consensus pattern (21 bp):
AAATAAAGAAATAAGAAAATA
Found at i:18116 original size:32 final size:31
Alignment explanation
Indices: 18069--18139 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
18059 AAAAGTAATG
* *
18069 GAAATAAATAAATTAAGGA-AAATAAAATAAA
1 GAAATAAAGAAATTAA-GATAAAGAAAATAAA
*
18100 GAAATAAAGAAGATTAAGATAAAGAAAGTAAA
1 GAAATAAAGAA-ATTAAGATAAAGAAAATAAA
*
18132 TAAATAAA
1 GAAATAAA
18140 ATAAAAAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (31 bp):
GAAATAAAGAAATTAAGATAAAGAAAATAAA
Found at i:18191 original size:29 final size:29
Alignment explanation
Indices: 18133--18205 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
18123 GAAAGTAAAT
* *
18133 AAATAAAATAAAAAAGGACAATAAATAAA
1 AAATAAAATAAAAAAAGACAATAAACAAA
*
18162 AAATAAAATAAAATAAAGAGAA-AAAC-AA
1 AAATAAAATAAAA-AAAGACAATAAACAAA
18190 AAATGATAAATAAAAA
1 AAAT-A-AAATAAAAA
18206 TAATAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.16
29 18 0.47
30 14 0.37
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.14
Consensus pattern (29 bp):
AAATAAAATAAAAAAAGACAATAAACAAA
Found at i:18228 original size:14 final size:14
Alignment explanation
Indices: 18188--18230 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
18178 AGAGAAAAAC
* *
18188 AAAAATGATAAA-T
1 AAAAATAATAAAGA
18201 AAAAATAATAAAAGA
1 AAAAATAAT-AAAGA
18216 AAAAATAATAAAGA
1 AAAAATAATAAAGA
18230 A
1 A
18231 TAAAGAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 8 0.31
14 9 0.35
15 9 0.35
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (14 bp):
AAAAATAATAAAGA
Found at i:18233 original size:31 final size:30
Alignment explanation
Indices: 18137--18299 Score: 82
Period size: 32 Copynumber: 5.1 Consensus size: 30
18127 GTAAATAAAT
* * *
18137 AAAATAA-AAAAGGACAATAAATAAAAAATA
1 AAAATAATAAAA-GAAAAAAAATAAAGAATA
* *
18167 AAATAAAATAAAGAGAAAAACAAA-AATGATAAATA
1 AAA-ATAATAAA-AGAAAAA-AAATAA--A-GAATA
18202 AAAATAATAAAAGAAAAAATAATAAAGAATA
1 AAAATAATAAAAGAAAAAA-AATAAAGAATA
* * *
18233 AAGAATGAA-AAATGAAAAACAAAAAAATAATA
1 AA-AAT-AATAAAAGAAAAA-AAATAAAGAATA
* * *
18265 ATAAT-ATAAAATGAATGAAAAATAAGGAATA
1 AAAATAATAAAA-GAA-AAAAAATAAAGAATA
18296 AAAA
1 AAAA
18300 ACAACAAATA
Statistics
Matches: 103, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
29 1 0.01
30 6 0.06
31 27 0.26
32 35 0.34
33 16 0.16
34 10 0.10
35 8 0.08
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (30 bp):
AAAATAATAAAAGAAAAAAAATAAAGAATA
Found at i:18234 original size:35 final size:37
Alignment explanation
Indices: 18118--18234 Score: 90
Period size: 34 Copynumber: 3.3 Consensus size: 37
18108 GAAGATTAAG
**
18118 ATAAAGAAAGTAAAT-AAATAAAATAAA-A-AAGGAC-A
1 ATAAAG-AA-TAAATAAAATAAAATAAAGAGAAAAACAA
* *
18153 ATAAATAAAAAATAAAATAAAATAAAGAGAAAAACAA
1 ATAAAGAATAAATAAAATAAAATAAAGAGAAAAACAA
* *
18190 A-AATG-ATAAATAAAA-ATAATAAA-AGAAAAA-ATA
1 ATAAAGAATAAATAAAATAAAATAAAGAGAAAAACA-A
18223 ATAAAGAATAAA
1 ATAAAGAATAAA
18235 GAATGAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
32 1 0.02
33 13 0.20
34 24 0.36
35 20 0.30
36 6 0.09
37 2 0.03
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (37 bp):
ATAAAGAATAAATAAAATAAAATAAAGAGAAAAACAA
Found at i:18299 original size:42 final size:42
Alignment explanation
Indices: 18207--18300 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
18197 AAATAAAAAT
18207 AATAAAAGAAAAAATAATAAAGAATAAAGAATGAAAAATGAAA
1 AATAAAA-AAAAAATAATAAAGAATAAAGAATGAAAAATGAAA
* * * * *
18250 AACAAAAAAATAATAATAATATAA-AATGAATGAAAAAT-AAGG
1 AATAAAAAAAAAATAATAA-AGAATAAAGAATGAAAAATGAA-A
18292 AATAAAAAA
1 AATAAAAAA
18301 CAACAAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 2 0.05
42 32 0.74
43 9 0.21
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (42 bp):
AATAAAAAAAAAATAATAAAGAATAAAGAATGAAAAATGAAA
Found at i:19553 original size:24 final size:27
Alignment explanation
Indices: 19510--19559 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 27
19500 CCATATATTA
19510 TATATATATATATAATGTTTTCAAAAT
1 TATATATATATATAATGTTTTCAAAAT
19537 TATATAT-TATAT-A-GTTTTCAAAA
1 TATATATATATATAATGTTTTCAAAA
19560 CGATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
26 5 0.22
27 7 0.30
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (27 bp):
TATATATATATATAATGTTTTCAAAAT
Found at i:19585 original size:37 final size:37
Alignment explanation
Indices: 19532--19737 Score: 204
Period size: 39 Copynumber: 5.5 Consensus size: 37
19522 TAATGTTTTC
* * * *
19532 AAAATTATATATTATATAGTTTTCAAAACGATTTAAA
1 AAAACTATATATTATATAGTTTTCAAAATGTTTTTAA
* * *
19569 AAAACTATATATTATATATATTTTTCCAAATGTTTTTTA
1 AAAACTATATA-T-TATATAGTTTTCAAAATGTTTTTAA
* * * **
19608 AAAACCATATATTATATATATTTTTAAAATG-TTTTCG
1 AAAACTATATATTATATA-GTTTTCAAAATGTTTTTAA
19645 AAAAC--TATATTATATA-TATTTCAAAATGTTTTTTAA
1 AAAACTATATATTATATAGT-TTTCAAAATG-TTTTTAA
*
19681 AAAACTATATAATATATATGTTTTCAAAATGCTTTTTAA
1 AAAACTATATATTATATA-GTTTTCAAAATG-TTTTTAA
19720 AAAACTATATATTATATA
1 AAAACTATATATTATATA
19738 TCTATTTCAA
Statistics
Matches: 140, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
33 1 0.01
34 9 0.06
35 11 0.08
36 9 0.06
37 25 0.18
38 21 0.15
39 63 0.45
40 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
AAAACTATATATTATATAGTTTTCAAAATGTTTTTAA
Found at i:19594 original size:39 final size:39
Alignment explanation
Indices: 19567--19749 Score: 220
Period size: 39 Copynumber: 4.8 Consensus size: 39
19557 AAACGATTTA
*
19567 AAAAAACTATATATTATATATATTTTTCCAAATGTTTTT
1 AAAAAACTATATATTATATATATTTTTCAAAATGTTTTT
* *
19606 TAAAAACCATATATTATATATATTTTT-AAAATG-TTTT
1 AAAAAACTATATATTATATATATTTTTCAAAATGTTTTT
**
19643 CGAAAAC--TATATTATATATA--TTTCAAAATGTTTTTT
1 AAAAAACTATATATTATATATATTTTTCAAAATG-TTTTT
19679 AAAAAACTATATA--ATATATATGTTTTCAAAATGCTTTTT
1 AAAAAACTATATATTATATATAT-TTTTCAAAATG-TTTTT
* *
19718 AAAAAACTATATATTATATATCTATTTCAAAA
1 AAAAAACTATATATTATATATATTTTTCAAAA
19750 ACCATTAGCA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
33 3 0.02
34 6 0.05
35 13 0.10
36 16 0.13
37 9 0.07
38 9 0.07
39 53 0.43
40 8 0.06
41 7 0.06
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (39 bp):
AAAAAACTATATATTATATATATTTTTCAAAATGTTTTT
Found at i:19617 original size:112 final size:112
Alignment explanation
Indices: 19497--19738 Score: 314
Period size: 112 Copynumber: 2.2 Consensus size: 112
19487 TAACATTTTT
*
19497 AAACCATATATTATATATATATATATAATGTTTTC-AAAATTATATATTATATAGT-TTTCAAAA
1 AAACCATATATTATATATATATATAAAATGTTTTCGAAAA--ATATATTATATA-TATTTCAAAA
* *
19560 CG-ATTTAAAAAAACTATATATTATATATAT-TTTTCCAAATG-TTTTTTAA
63 CGTATTTAAAAAAACTATATA--ATATATATGTTTTCAAAATGCTTTTTAAA
* * * *
19609 AAACCATATATTATATATATTTTTAAAATGTTTTCGAAAACTATATTATATATATTTCAAAATGT
1 AAACCATATATTATATATATATATAAAATGTTTTCGAAAAATATATTATATATATTTCAAAACGT
* *
19674 TTTTTAAAAAACTATATAATATATATGTTTTCAAAATGCTTTTTAAA
66 ATTTAAAAAAACTATATAATATATATGTTTTCAAAATGCTTTTTAAA
*
19721 AAACTATATATTATATAT
1 AAACCATATATTATATAT
19739 CTATTTCAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
110 9 0.08
111 30 0.26
112 72 0.63
113 4 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (112 bp):
AAACCATATATTATATATATATATAAAATGTTTTCGAAAAATATATTATATATATTTCAAAACGT
ATTTAAAAAAACTATATAATATATATGTTTTCAAAATGCTTTTTAAA
Found at i:20514 original size:84 final size:84
Alignment explanation
Indices: 20370--21589 Score: 1339
Period size: 84 Copynumber: 14.6 Consensus size: 84
20360 CTGAATGGAA
** * * * * * *
20370 TCGAACTC-AAGGGGTTTTTTTTGCAGATAGCCCTTCTCGCCTTG-GCTATGTTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
* * *
20433 GCCTTGGAGTTGAGTGTAA
66 GCCTTGGAGCTGAGCGTAG
* * * * *
20452 TCAAACTCGAAGGTCTTTAGTTAGCATATAACCCTTCTTGCCTTGAGCTATTCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
* * * *
20517 GCCTTTGAGTTGAGTGTAA
66 GCCTTGGAGCTGAGCGTAG
* * * *
20536 TCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTTG-GTTATGCTGCAAATGATG
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCC-TTGAGCTATGCTGCAAATGATG
*
20600 TGCCTTGGAGCTGAGCATAG
65 TGCCTTGGAGCTGAGCGTAG
* * * *
20620 TCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTTTCCTTGAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
*
20685 GCCTTGGAGCTGAGCATAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * * * *
20704 TTGAACTCAAAGGTCTTTGGTTGGAAGTTAACCCTTCTAGTCTTGAGTTATGCTACAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
* *
20769 GCCTTTGAGCTGAGTGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * **
20788 TCGAACTCGAAGGTATTTTATTGGCAAATAGCCCTTCTTGCCTTGAGCTATTTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
20853 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
20872 -CTGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATA
1 TC-GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
* *
20936 TGCCTT-----TGAGTGTAT
65 TGCCTTGGAGCTGAGCGTAG
* * * * *
20951 TCGAACTCGAAGGTCTTTCGTTGGCAAATAACTCTTCTTGCCTTGAGCTATGTTGCAAATGATTT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
*
21016 GCCTTGGATCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * ** * * * *
21035 TCGAACTCGAAGGTCTTTGGTTGGCAGATAAACTTTCTAACCTTGAGTTATACTGCAAATGGTAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
* * *
21100 GTCTTTGAGCTAAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * **
21119 TCAAACTCGAAGGTCTTTTGTTGGCAAATAGCCTTTCTTGCCTTGAGCTATATTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
21184 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * *
21203 TCGAACTCGAAGGTC-TTTGATTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATA
1 TCGAACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
* *
21267 TGCCTTTGAGCTGAGCATAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * *
21287 TCGAACTCGAAGGTCTTTTGTTGGTAAATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
21352 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
21371 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
21436 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * *
21455 TCGAACTTGAAGGT-TTTTTTGTGGCAGATAGCTCTTTTTGCCTTGAGCTATGCTACAAATGATG
1 TCGAACTCGAAGGTCTTTTGT-TGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
* * *
21519 TGCCTTTGAGCTGAGTGTAA
65 TGCCTTGGAGCTGAGCGTAG
* * * ** *
21539 TCGAACTCGAAGGTC-TTGGCTGACAGATAACCCTTCTCACCTTGAGTTATG
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
21590 TTGTCGATAG
Statistics
Matches: 956, Mismatches: 167, Indels: 29
0.83 0.14 0.03
Matches are distributed among these distances:
79 67 0.07
80 1 0.00
82 7 0.01
83 64 0.07
84 810 0.85
85 7 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:20719 original size:168 final size:168
Alignment explanation
Indices: 20392--21589 Score: 1565
Period size: 168 Copynumber: 7.2 Consensus size: 168
20382 GGTTTTTTTT
* * * * * * * * * * *
20392 GCAGATAGCCCTTCTCGCCTTG-GCTATGTTACAAATGATGTGCCTTGGAGTTGAGTGTAATCAA
1 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
* * * *
20456 ACTCGAAGGTCTTTAGTTAGCATATAACCCTTCTTGCCTTGAGCTAT-TCTGCAAATGATGTGCC
66 ACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGT-TGCAAATGATGTGCC
* * * * * *
20520 TTTGAGTTGAGTGTAATCAAACTCGAAGGTCTTTTGTTG
130 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
* * * *
20559 ACAGATAACCCTTCTAGCCTTTG-GTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCG
1 GCAGATAACCCTTCTAGCC-TTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCG
* * * * *
20623 AACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTTTCCTTGAGTTATGCTGCAAATGATGTGCC
65 AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCC
* * *
20688 TTGGAGCTGAGCATAGTTGAACTCAAAGGTCTTTGGTTG
130 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
* * * * *
20727 GAAGTTAACCCTTCTAGTCTTGAGTTATGCTACAAATGATATGCCTTTGAGCTGAGTGTAGTCGA
1 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
* * *
20792 ACTCGAAGGTATTTTATTGGCAAATAGCCCTTCTTGCCTTGAGCTATTTTGCAAATGATGTGCCT
66 ACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
*
20857 TGGAGCTGAGCGTAG-CTGAACTCGAAGGTATTTGGTTG
131 TGGAGCTGAGCGTAGTC-GAACTCGAAGGTCTTTGGTTG
*
20895 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAG-T----GTATTCGA
1 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
* * * *
20955 ACTCGAAGGTCTTTCGTTGGCAAATAACTCTTCTTGCCTTGAGCTATGTTGCAAATGATTTGCCT
66 ACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
*
21020 TGGATCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
* * * * * * * *
21058 GCAGATAAACTTTCTAACCTTGAGTTATACTGCAAATGGTATGTCTTTGAGCTAAGCGTAGTCAA
1 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
* *
21123 ACTCGAAGGTCTTTTGTTGGCAAATAGCCTTTCTTGCCTTGAGCTATATTGCAAATGATGTGCCT
66 ACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
*
21188 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGATTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
*
21226 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
* *
21291 ACTCGAAGGTCTTTTGTTGGTAAATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCT
66 ACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
21356 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
* * * *
21394 GCAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
* * * * * * *
21459 ACTTGAAGGT-TTTTTTGTGGCAGATAGCTCTTTTTGCCTTGAGCTATGCTACAAATGATGTGCC
66 ACTCGAAGGTCTTTTGT-TGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCC
* * * *
21523 TTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGCTG
130 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
*
21561 ACAGATAACCCTTCTCA-CCTTGAGTTATG
1 GCAGATAACCCTTCT-AGCCTTGAGTTATG
21590 TTGTCGATAG
Statistics
Matches: 909, Mismatches: 110, Indels: 24
0.87 0.11 0.02
Matches are distributed among these distances:
163 144 0.16
164 2 0.00
167 56 0.06
168 707 0.78
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (168 bp):
GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
Found at i:22891 original size:88 final size:88
Alignment explanation
Indices: 22782--22961 Score: 288
Period size: 88 Copynumber: 2.0 Consensus size: 88
22772 ATTGTATAGA
* * *
22782 TATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCATTTAACCAGTTG
1 TATTATAATCACCTTTATCAGGATAGCTGAATATTATCCATAAAGCTAGGGCATTTAACCAATTG
22847 CTCTAAAGGGACAACTCAAGCTT
66 CTCTAAAGGGACAACTCAAGCTT
* * *
22870 TATTATAATTACCTTTATCAGGATAGCTGAATCTTATCCATAAAGCTAGGGCGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGATAGCTGAATATTATCCATAAAGCTAGGGCATTTAACCAATTG
* *
22935 CTCTAGAGGGACATCTCAAGCTT
66 CTCTAAAGGGACAACTCAAGCTT
22958 TATT
1 TATT
22962 GTATATATAT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (88 bp):
TATTATAATCACCTTTATCAGGATAGCTGAATATTATCCATAAAGCTAGGGCATTTAACCAATTG
CTCTAAAGGGACAACTCAAGCTT
Found at i:26610 original size:7 final size:7
Alignment explanation
Indices: 26600--26714 Score: 54
Period size: 7 Copynumber: 15.6 Consensus size: 7
26590 AAAGGACAAT
26600 AAATAAA
1 AAATAAA
26607 AAATAAA
1 AAATAAA
*
26614 ATAA-AAT
1 A-AATAAA
*
26621 AAAGAGAA
1 AAATA-AA
*
26629 AAACAAA
1 AAATAAA
26636 AATGATAAA
1 AA--ATAAA
*
26645 TAA-AAA
1 AAATAAA
*
26651 TAATAAA
1 AAATAAA
26658 AGAATAAA
1 A-AATAAA
*
26666 TAATAAA
1 AAATAAA
*
26673 GAATAAA
1 AAATAAA
*
26680 GAATAAA
1 AAATAAA
*
26687 AACAAAAA
1 AA-ATAAA
26695 AAATAATA
1 AAATAA-A
*
26703 ATAATATA
1 A-AATAAA
26711 AAAT
1 AAAT
26715 GAATGAAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
6 8 0.09
7 46 0.53
8 23 0.27
9 9 0.10
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:26623 original size:21 final size:20
Alignment explanation
Indices: 26574--26713 Score: 72
Period size: 22 Copynumber: 6.6 Consensus size: 20
26564 ATAAATAAGT
26574 AAATAAATAAAATAA-AAAAGGA
1 AAATAAATAAAA-AATAAAA--A
*
26596 CAATAAATAAAAAATAAAATA
1 AAATAAATAAAAAATAAAA-A
* *
26617 AAATAAAGAGAAAAACAAAAA
1 AAATAAATA-AAAAATAAAAA
**
26638 TGATAAAT-AAAAATAATAAA
1 AAATAAATAAAAAATAA-AAA
* *
26658 AGAATAAATAATAAAGAATAAA
1 A-AATAAATAAAAAATAA-AAA
*
26680 GAATAAA-AACAAAA-AAAATA
1 AAATAAATAA-AAAATAAAA-A
26700 ATAATAATATAAAA
1 A-AATAA-ATAAAA
26714 TGAATGAAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
19 9 0.10
20 8 0.09
21 36 0.39
22 37 0.40
23 2 0.02
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (20 bp):
AAATAAATAAAAAATAAAAA
Found at i:26636 original size:29 final size:29
Alignment explanation
Indices: 26578--26650 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
26568 ATAAGTAAAT
* *
26578 AAATAAAATAAAAAAGGACAATAAATAAA
1 AAATAAAATAAAAAAAGACAATAAACAAA
*
26607 AAATAAAATAAAATAAAGAGAA-AAAC-AA
1 AAATAAAATAAAA-AAAGACAATAAACAAA
26635 AAATGATAAATAAAAA
1 AAAT-A-AAATAAAAA
26651 TAATAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.16
29 18 0.47
30 14 0.37
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.14
Consensus pattern (29 bp):
AAATAAAATAAAAAAAGACAATAAACAAA
Found at i:26651 original size:13 final size:13
Alignment explanation
Indices: 26566--26708 Score: 55
Period size: 13 Copynumber: 10.6 Consensus size: 13
26556 AGATTAAGAT
26566 AAATAAGTAAATAA
1 AAATAA-TAAATAA
26580 ATAA-AATAAA-AA
1 A-AATAATAAATAA
* *
26592 AGGACAATAAATAAA
1 A-AATAATAAAT-AA
26607 AAATAAAATAAAATAA
1 AAAT--AAT-AAATAA
* * *
26623 AGAGAA-AAACAA
1 AAATAATAAATAA
*
26635 AAATGATAAATAA
1 AAATAATAAATAA
*
26648 AAATAATAAAAGAA
1 AAATAAT-AAATAA
*
26662 TAAATAATAAAGAA
1 -AAATAATAAATAA
*
26676 TAAAGAATAAA-AA
1 -AAATAATAAATAA
26689 CAAA-AA-AAATAA
1 -AAATAATAAATAA
*
26701 TAATAATA
1 AAATAATA
26709 TAAAATGAAT
Statistics
Matches: 100, Mismatches: 16, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
11 5 0.05
12 18 0.18
13 27 0.27
14 27 0.27
15 12 0.12
16 7 0.07
17 4 0.04
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:26668 original size:15 final size:15
Alignment explanation
Indices: 26648--26687 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
26638 TGATAAATAA
26648 AAATAATAAAAGAAT
1 AAATAATAAAAGAAT
26663 AAATAAT-AAAGAAT
1 AAATAATAAAAGAAT
*
26677 AAAGAATAAAA
1 AAATAATAAAA
26688 ACAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATAATAAAAGAAT
Found at i:26675 original size:14 final size:14
Alignment explanation
Indices: 26635--26686 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
26625 AGAAAAACAA
* *
26635 AAATGATAAATAA-
1 AAATAATAAAGAAT
26648 AAATAATAAAAGAAT
1 AAATAAT-AAAGAAT
26663 AAATAATAAAGAAT
1 AAATAATAAAGAAT
*
26677 AAAGAATAAA
1 AAATAATAAA
26687 AACAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.18
14 21 0.62
15 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (14 bp):
AAATAATAAAGAAT
Found at i:26679 original size:35 final size:36
Alignment explanation
Indices: 26564--26679 Score: 93
Period size: 34 Copynumber: 3.3 Consensus size: 36
26554 GAAGATTAAG
* **
26564 ATAAATAAGTAAAT-AAATAAAATAAA-A-AAGGACA
1 ATAAAGAA-TAAATAAAATAAAATAAAGAGAAAAACA
* *
26598 ATAAATAAAAAATAAAATAAAATAAAGAGAAAAACA
1 ATAAAGAATAAATAAAATAAAATAAAGAGAAAAACA
* *
26634 A-AAATG-ATAAATAAAA-ATAATAAA-AGAATAAATA
1 ATAAA-GAATAAATAAAATAAAATAAAGAGAA-AAACA
26668 ATAAAGAATAAA
1 ATAAAGAATAAA
26680 GAATAAAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
33 8 0.12
34 33 0.49
35 21 0.31
36 6 0.09
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (36 bp):
ATAAAGAATAAATAAAATAAAATAAAGAGAAAAACA
Found at i:26703 original size:56 final size:56
Alignment explanation
Indices: 26611--26735 Score: 143
Period size: 56 Copynumber: 2.3 Consensus size: 56
26601 AATAAAAAAT
**
26611 AAAAT-AA-AATAAAGAGAAAAACAAAAATGATAAATAAAAATAATAAAA-GAAT-A
1 AAAATAAAGAATAAAGAGAAAAACAAAAAAAATAAATAAAAAT-ATAAAATGAATGA
* *
26664 AATAATAAAGAATAAAGAATAAAAACAAAAAAAAT-AATAATAATATAAAATGAATGA
1 AA-AATAAAGAATAAAG-AGAAAAACAAAAAAAATAAATAAAAATATAAAATGAATGA
*
26721 AAAATAAGGAATAAA
1 AAAATAAAGAATAAA
26736 AAACAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
53 2 0.03
54 3 0.05
55 8 0.13
56 31 0.51
57 17 0.28
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.17
Consensus pattern (56 bp):
AAAATAAAGAATAAAGAGAAAAACAAAAAAAATAAATAAAAATATAAAATGAATGA
Found at i:28034 original size:39 final size:39
Alignment explanation
Indices: 27991--28191 Score: 218
Period size: 39 Copynumber: 5.2 Consensus size: 39
27981 TATTATGTAG
* * *
27991 TTTTCAAAACGATTTAAAAAAACTATATATTATATATAT
1 TTTTCAAAATGTTTTTAAAAAACTATATATTATATATAT
* * *
28030 TTTTCCAAATGTTTTTTAAAAACCATATATTATATATAT
1 TTTTCAAAATGTTTTTAAAAAACTATATATTATATATAT
* **
28069 ATTTTTAAAATG-TTTTCGAAAAC--TATATTATATATA-
1 -TTTTCAAAATGTTTTTAAAAAACTATATATTATATATAT
28105 -TTTCAAAATGTGTTTTAAAAAACTATATA--ATATATAT
1 TTTTCAAAATGT-TTTTAAAAAACTATATATTATATATAT
*
28142 GTTTTCAAAATGCTTTTTAAAAAACTATATATTATATATCT
1 -TTTTCAAAATG-TTTTTAAAAAACTATATATTATATATAT
*
28183 ATTTCAAAA
1 TTTTCAAAA
28192 ACCATTAGCA
Statistics
Matches: 136, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
34 9 0.07
36 16 0.12
37 13 0.10
38 4 0.03
39 69 0.51
40 18 0.13
41 7 0.05
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (39 bp):
TTTTCAAAATGTTTTTAAAAAACTATATATTATATATAT
Found at i:28127 original size:114 final size:113
Alignment explanation
Indices: 27942--28186 Score: 300
Period size: 114 Copynumber: 2.2 Consensus size: 113
27932 TTTTAAAACC
* * * *
27942 ATATTATATATATATATATATAATGTTTTCAAAATTATATATTATGTAGTTTTCAAAACGATTTA
1 ATATTATATATATATTTATAAAATGTTTTCAAAACTATATATTATATAG-TTTCAAAACGATTTA
* *
28007 AAAAAACTATATATTATATATAT-TTTTCCAAATG-TTTTTTAAAAACCAT
65 AAAAAACTATATA--ATATATATGTTTTCAAAATGCTTTTTAAAAAACCAT
* * *
28056 ATATTATATATATATTTTTAAAATGTTTTCGAAAACTATAT-TATATATA-TTTCAAAATGTGTT
1 ATATTATATATATATTTATAAAATGTTTTC-AAAACTATATAT-TATATAGTTTCAAAACG-ATT
* *
28119 TTAAAAAACTATATAATATATATGTTTTCAAAATGCTTTTTAAAAAACTAT
63 TAAAAAAACTATATAATATATATGTTTTCAAAATGCTTTTTAAAAAACCAT
*
28170 ATATTATATATCTATTT
1 ATATTATATATATATTT
28187 CAAAAACCAT
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
112 8 0.07
113 19 0.17
114 73 0.64
115 14 0.12
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (113 bp):
ATATTATATATATATTTATAAAATGTTTTCAAAACTATATATTATATAGTTTCAAAACGATTTAA
AAAAACTATATAATATATATGTTTTCAAAATGCTTTTTAAAAAACCAT
Found at i:28210 original size:114 final size:111
Alignment explanation
Indices: 27977--28210 Score: 240
Period size: 114 Copynumber: 2.1 Consensus size: 111
27967 TTTTCAAAAT
* *
27977 TATATATTATGTAGTTTTCAAAACGATTTAAAAAAACTATATATTATATATATTTTTCCAAATGT
1 TATATATTATATAGTTTTCAAAACGATTTAAAAAAACTATATA-TATATATATTTTTCAAAATGT
* ** ** **
28042 TTTTTAAAAACCATATATTATATATATATTTTTAAAATGTTTTCGAA
65 TTTTAAAAAACCATATATTATATATATATTTCAAAAACATTAGCGAA
* * * *
28089 AACTATATTATATA-TATTTCAAAATGTGTTTTAAAAAACTATATA-ATATATATGTTTTCAAAA
1 TA-TATATTATATAGT-TTTCAAAACG-ATTTAAAAAAACTATATATATATATAT-TTTTCAAAA
* *
28152 TGCTTTTTAAAAAACTATATATTATATATCTATTTCAAAAACCATTAGC-ATA
62 TG-TTTTTAAAAAACCATATATTATATATATATTTCAAAAA-CATTAGCGA-A
28204 TATATAT
1 TATATAT
28211 AATAAATTTT
Statistics
Matches: 99, Mismatches: 16, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
112 10 0.10
113 29 0.29
114 55 0.56
115 5 0.05
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (111 bp):
TATATATTATATAGTTTTCAAAACGATTTAAAAAAACTATATATATATATATTTTTCAAAATGTT
TTTAAAAAACCATATATTATATATATATTTCAAAAACATTAGCGAA
Found at i:28933 original size:2 final size:2
Alignment explanation
Indices: 28926--28977 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
28916 AATTTATTTA
28926 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
28968 AT AT AT AT AT
1 AT AT AT AT AT
28978 TATCTAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30609 original size:2 final size:2
Alignment explanation
Indices: 30602--30666 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
30592 TTATTTAATT
30602 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30644 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
30667 CTAAATGTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32277 original size:2 final size:2
Alignment explanation
Indices: 32270--32311 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
32260 AAATTTATTA
32270 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
32312 CTAAAATGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35548 original size:2 final size:2
Alignment explanation
Indices: 35541--35582 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
35531 TTTAAATTTA
35541 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
35583 CTAAAATGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36648 original size:14 final size:15
Alignment explanation
Indices: 36629--36663 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
36619 GAGATTTGGT
*
36629 TTTTTTAAAA-ATTC
1 TTTTTTAAAATATTA
36643 TTTTTTAAAATATTA
1 TTTTTTAAAATATTA
36658 TTTTTT
1 TTTTTT
36664 GATTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTTAAAATATTA
Found at i:37903 original size:17 final size:19
Alignment explanation
Indices: 37881--37921 Score: 59
Period size: 17 Copynumber: 2.2 Consensus size: 19
37871 ATAAAAAATT
37881 AAAATTATT-TTAT-TTAA
1 AAAATTATTGTTATATTAA
37898 AAAATTATTGTTATAATTAA
1 AAAATTATTGTTAT-ATTAA
37918 AAAA
1 AAAA
37922 ATAACACCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 4 0.19
20 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAATTATTGTTATATTAA
Found at i:41544 original size:23 final size:23
Alignment explanation
Indices: 41493--41553 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
41483 GATAATCTTA
* *
41493 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
** *
41516 CAGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
41539 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
41554 TTTATACGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:41993 original size:2 final size:2
Alignment explanation
Indices: 41986--42026 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41976 TGTATAAATC
41986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42027 CGTATTTCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45232 original size:18 final size:18
Alignment explanation
Indices: 45209--45244 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
45199 CTGATGACTC
45209 AAAAAGAGCTTAATTTGA
1 AAAAAGAGCTTAATTTGA
45227 AAAAAGAGCTTAATTTGA
1 AAAAAGAGCTTAATTTGA
45245 GGCAACGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (18 bp):
AAAAAGAGCTTAATTTGA
Found at i:47713 original size:63 final size:63
Alignment explanation
Indices: 47642--47839 Score: 306
Period size: 63 Copynumber: 3.1 Consensus size: 63
47632 TTCAATGTGA
** * * * *
47642 ATCGATGCATCCTCAAGTAATTGAACATCGAATGTCGTCAGTGCATCGATGCATAAGGAGTGC
1 ATCGATGCATTTTCAATTAAATGAACATCGAATGACCTCAGTGCATCGATGCATAAGGAGTGC
*
47705 ATCGATGCATTTTCAATTAAATGAACATCGAATGCCCTCAGTGCATCGATGCATAAGGAGTGC
1 ATCGATGCATTTTCAATTAAATGAACATCGAATGACCTCAGTGCATCGATGCATAAGGAGTGC
* * *
47768 ATCGATGCATTTTCAATTAAATAAACATCGAATGACCTTAGTGCATCGATGAATAAGGAGTGC
1 ATCGATGCATTTTCAATTAAATGAACATCGAATGACCTCAGTGCATCGATGCATAAGGAGTGC
47831 ATCGATGCA
1 ATCGATGCA
47840 CATCCTTAAG
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 125 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (63 bp):
ATCGATGCATTTTCAATTAAATGAACATCGAATGACCTCAGTGCATCGATGCATAAGGAGTGC
Found at i:48593 original size:23 final size:23
Alignment explanation
Indices: 48525--48585 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
48515 TAATCTTATA
*
48525 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
48548 CGACACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
48571 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
48586 TTTATACGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:49234 original size:2 final size:2
Alignment explanation
Indices: 49227--49325 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
49217 TGTATAAACC
49227 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49311 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
49326 TATCGTATTT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.