Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 150 of 182
Found at i:46222747 original size:2 final size:2
Alignment explanation
Indices: 46222740--46222766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46222730 TTATACACAA
46222740 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
46222767 AAGGTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46223296 original size:3 final size:3
Alignment explanation
Indices: 46223282--46223316 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
46223272 AACTTGCTCT
*
46223282 ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
46223317 GTCATCACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:46229489 original size:19 final size:18
Alignment explanation
Indices: 46229444--46229481 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
46229434 AAAAAATCCT
46229444 AACCCTAACAAAATTAAA
1 AACCCTAACAAAATTAAA
*
46229462 AACCCTAACGAAATTAAA
1 AACCCTAACAAAATTAAA
46229480 AA
1 AA
46229482 ACCTTAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.21, G:0.03, T:0.16
Consensus pattern (18 bp):
AACCCTAACAAAATTAAA
Found at i:46229735 original size:21 final size:21
Alignment explanation
Indices: 46229688--46229725 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46229678 TTCATTTTCC
46229688 ATTTTTATTTATTTAGAATCA
1 ATTTTTATTTATTTAGAATCA
46229709 ATTTTTA-TTATTT-GAAT
1 ATTTTTATTTATTTAGAAT
46229726 TGATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 6 0.35
21 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTTTTATTTATTTAGAATCA
Found at i:46229861 original size:23 final size:25
Alignment explanation
Indices: 46229811--46229861 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 25
46229801 ATTTTTATCA
46229811 ATTTGATCCTTACATTTTTAATTTT
1 ATTTGATCCTTACATTTTTAATTTT
46229836 ATTTGATCC-TA-ATCTTTT-ATTTT
1 ATTTGATCCTTACAT-TTTTAATTTT
46229859 ATT
1 ATT
46229862 GACAAATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 10 0.40
24 6 0.24
25 9 0.36
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.61
Consensus pattern (25 bp):
ATTTGATCCTTACATTTTTAATTTT
Found at i:46230730 original size:19 final size:18
Alignment explanation
Indices: 46230703--46230747 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
46230693 AATATTTACA
*
46230703 TTAAAATAATATTATATAT
1 TTAATATAATATTAT-TAT
* *
46230722 TTAATATAATTTTATTTT
1 TTAATATAATATTATTAT
46230740 TTAATATA
1 TTAATATA
46230748 TTTTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATATAATATTATTAT
Found at i:46233961 original size:23 final size:23
Alignment explanation
Indices: 46233926--46233972 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
46233916 TATTTAACTA
* * *
46233926 AAAAATAATTTAAGGGTTTTTTT
1 AAAAAGAAATTAAGGGTTTATTT
46233949 AAAAAGAAATTAAGGGTTTATTT
1 AAAAAGAAATTAAGGGTTTATTT
46233972 A
1 A
46233973 GATATAACGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (23 bp):
AAAAAGAAATTAAGGGTTTATTT
Found at i:46237261 original size:14 final size:15
Alignment explanation
Indices: 46237242--46237270 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
46237232 CTTTGAGATT
46237242 TTTTGTA-AATGGAC
1 TTTTGTATAATGGAC
46237256 TTTTGTATAATGGAC
1 TTTTGTATAATGGAC
46237271 ATTAAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (15 bp):
TTTTGTATAATGGAC
Found at i:46237986 original size:49 final size:48
Alignment explanation
Indices: 46237933--46238478 Score: 399
Period size: 49 Copynumber: 11.2 Consensus size: 48
46237923 CGGTCGTAAC
*
46237933 CTTTCCCTCAATATCTTCGTGGTACTAGATTCACCGTTGCGGCTTAAAT
1 CTTTCCCTC-ATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * * * * *
46237982 CTTTCCCTTCATGT-TTCTGAGGTACAAGGTTCACCGTTGTGACTTAAAC
1 CTTTCCC-TCATATCTTC-GTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * ** *
46238031 CTTTCTCTCCATATCCTT-GTGGTATTGGATTCGCTATTGCAGCTTAAAT
1 CTTTCCCT-CATAT-CTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * *** * *
46238080 CTTTCCCTTCAT-GCTTCTGAGGTACAAGTTTCGTTATTGCGACTTAAAC
1 CTTTCCC-TCATATCTTC-GTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* *
46238129 CTTT-CCTCCATATCTTTGTGGTACTAGATTCGCCGTTGCGGCTTAAGT
1 CTTTCCCT-CATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * * * *
46238177 CTTTCCCTTCAT-GCTTTCGAGGTA-TAAGGTTTGCCATTGCGACTTAAAA
1 CTTTCCC-TCATATC-TTCGTGGTACT-AGATTCGCCGTTGCGGCTTAAAT
*
46238226 CTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGGGGCTTAAAT
1 CTTTCCCT-CATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * ** * *
46238275 CTTTCCCT-TTATGCTTCTGAGGTACAAGTTTTACCGTTGCGACTTAAAC
1 CTTTCCCTCATAT-CTTC-GTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* *
46238324 CTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCATTACGGCTTAAAT
1 CTTTCCCT-CATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * *
46238373 CTTTCCCTTCATGT-TTCTGAGGTA-TAAGGTTCGCCGTTGCGACTTAAAC
1 CTTTCCC-TCATATCTTC-GTGGTACT-AGATTCGCCGTTGCGGCTTAAAT
* *
46238422 CTTTCCCTCCATATCTTCGTGCTACTAGATTCACCGTTGCGGCTTAAAT
1 CTTTCCCT-CATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
46238471 CTTTCCCT
1 CTTTCCCT
46238479 TCATGTTTCC
Statistics
Matches: 377, Mismatches: 93, Indels: 54
0.72 0.18 0.10
Matches are distributed among these distances:
47 7 0.02
48 47 0.12
49 303 0.80
50 15 0.04
51 5 0.01
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (48 bp):
CTTTCCCTCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
Found at i:46238033 original size:98 final size:98
Alignment explanation
Indices: 46237881--46238487 Score: 799
Period size: 98 Copynumber: 6.2 Consensus size: 98
46237871 TCGTAGGTTC
* * * ** * * * *
46237881 AATCTTTCTCATCATGTTTCTAAGGTACTGGGTTCGCCATTGCGGTCGT-AACCTTTCCCTCAAT
1 AATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGC-GACTTAAACCTTTCCCTCCAT
*
46237945 ATCTTCGTGGTACTAGATTCACCGTTGCGGCTTA
65 ATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
* * *
46237979 AATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCTCTCCATA
1 AATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATA
* * ** *
46238044 TCCTT-GTGGTATTGGATTCGCTATTGCAGCTTA
66 T-CTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
* * ***
46238077 AATCTTTCCCTTCATGCTTCTGAGGTACAAGTTTCGTTATTGCGACTTAAACCTTT-CCTCCATA
1 AATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATA
*
46238141 TCTTTGTGGTACTAGATTCGCCGTTGCGGCTTA
66 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
* * * * *
46238174 AGTCTTTCCCTTCATGCTTTC-GAGGTATAAGGTTTGCCATTGCGACTTAAAACTTTCCCTCCAT
1 AATCTTTCCCTTCATG-TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
*
46238238 ATCTTCGTGGTACTAGATTCGCCGTTGGGGCTTA
65 ATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
* * * **
46238272 AATCTTTCCCTTTATGCTTCTGAGGTACAAGTTTTACCGTTGCGACTTAAACCTTTCCCTCCATA
1 AATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATA
* *
46238337 TCTTCGTGGTACTAGATTCGCCATTACGGCTTA
66 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
*
46238370 AATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATA
1 AATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATA
* *
46238435 TCTTCGTGCTACTAGATTCACCGTTGCGGCTTA
66 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
46238468 AATCTTTCCCTTCATGTTTC
1 AATCTTTCCCTTCATGTTTC
46238488 CGTGGTAATG
Statistics
Matches: 441, Mismatches: 62, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
96 3 0.01
97 81 0.18
98 354 0.80
99 3 0.01
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (98 bp):
AATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATA
TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
Found at i:46240297 original size:4 final size:4
Alignment explanation
Indices: 46240288--46240323 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
46240278 ATCTTGACTT
46240288 TTTC TTTC TTTC TTTC TTTC -TT- TTTC TTT- TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
46240324 TTTTTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 7 0.24
4 22 0.76
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:46240301 original size:8 final size:7
Alignment explanation
Indices: 46240286--46240330 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
46240276 TTATCTTGAC
46240286 TTTTTCT
1 TTTTTCT
46240293 TTCTTTCT
1 TT-TTTCT
46240301 TTCTTTC-
1 TT-TTTCT
46240308 TTTTTCT
1 TTTTTCT
46240315 TTTTTCT
1 TTTTTCT
46240322 TTTTT-T
1 TTTTTCT
46240328 TTT
1 TTT
46240331 GTTTTTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 8 0.22
7 16 0.44
8 12 0.33
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:46240303 original size:12 final size:12
Alignment explanation
Indices: 46240288--46240323 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
46240278 ATCTTGACTT
46240288 TTTCTTTCTTTC
1 TTTCTTTCTTTC
46240300 TTTCTTTC-TT-
1 TTTCTTTCTTTC
46240310 TTTCTTT-TTTC
1 TTTCTTTCTTTC
46240321 TTT
1 TTT
46240324 TTTTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.41
11 5 0.23
12 8 0.36
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTCTTTC
Found at i:46240322 original size:17 final size:17
Alignment explanation
Indices: 46240285--46240328 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
46240275 TTTATCTTGA
46240285 CTTTTTCTTTCTTTCTTT
1 CTTTTT-TTTCTTTCTTT
46240303 CTTTCTTTTTCTTT-TTT
1 CTTT-TTTTTCTTTCTTT
46240320 CTTTTTTTT
1 CTTTTTTTT
46240329 TTGTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.20
17 7 0.28
18 11 0.44
19 2 0.08
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
CTTTTTTTTCTTTCTTT
Found at i:46240336 original size:17 final size:17
Alignment explanation
Indices: 46240292--46240328 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
46240282 TGACTTTTTC
46240292 TTTCTTTCTTTCTTTCTT
1 TTTCTTT-TTTCTTTCTT
46240310 TTTCTTTTTTCTTT-TT
1 TTTCTTTTTTCTTTCTT
46240326 TTT
1 TTT
46240329 TTGTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 7 0.37
18 7 0.37
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTCTTTTTTCTTTCTT
Found at i:46246349 original size:11 final size:11
Alignment explanation
Indices: 46246313--46246349 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
46246303 GAGTCACGTG
46246313 GCTGACGTGGT
1 GCTGACGTGGT
*
46246324 ACTGACGTGGT
1 GCTGACGTGGT
*
46246335 GCTGACGTGGC
1 GCTGACGTGGT
46246346 GCTG
1 GCTG
46246350 TCATGGTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.11, C:0.22, G:0.43, T:0.24
Consensus pattern (11 bp):
GCTGACGTGGT
Found at i:46246356 original size:22 final size:22
Alignment explanation
Indices: 46246313--46246357 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
46246303 GAGTCACGTG
* *
46246313 GCTGACGTGGTACTGACGTGGT
1 GCTGACGTGGCACTGACATGGT
* *
46246335 GCTGACGTGGCGCTGTCATGGT
1 GCTGACGTGGCACTGACATGGT
46246357 G
1 G
46246358 TGTGCTGACG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.20, G:0.42, T:0.27
Consensus pattern (22 bp):
GCTGACGTGGCACTGACATGGT
Found at i:46248381 original size:30 final size:30
Alignment explanation
Indices: 46248347--46248411 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
46248337 AAATATTTTA
* *
46248347 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAAGCAT
46248377 TTGTTAATTTTGTTACTATTTTAGAAGCAT
1 TTGTTAATTTTGTTACTATTTTAGAAGCAT
46248407 TTGTT
1 TTGTT
46248412 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAAGCAT
Found at i:46249843 original size:6 final size:6
Alignment explanation
Indices: 46249834--46249858 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
46249824 TCTCAGTTTT
46249834 AATCTC AATCTC AATCTC AATCTC A
1 AATCTC AATCTC AATCTC AATCTC A
46249859 TGATATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
AATCTC
Found at i:46250566 original size:23 final size:23
Alignment explanation
Indices: 46250539--46250595 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
46250529 CAATGGTTGG
46250539 TCAAAGTCAATGATTCGGTTCGA
1 TCAAAGTCAATGATTCGGTTCGA
* * *
46250562 TCAAAGTTAACGGTTCGGTTCGA
1 TCAAAGTCAATGATTCGGTTCGA
46250585 TCAAAGTCAAT
1 TCAAAGTCAAT
46250596 AGGTCAAGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (23 bp):
TCAAAGTCAATGATTCGGTTCGA
Found at i:46252032 original size:13 final size:15
Alignment explanation
Indices: 46252006--46252042 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
46251996 AGAACTTTCG
46252006 TAATATATATTTATA
1 TAATATATATTTATA
46252021 TAATAT-TA-TTATA
1 TAATATATATTTATA
*
46252034 TATTATATA
1 TAATATATA
46252043 CAACACGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 10 0.50
14 4 0.20
15 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATATATATTTATA
Found at i:46254603 original size:16 final size:14
Alignment explanation
Indices: 46254582--46254621 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
46254572 AAACCTTCAA
* *
46254582 CCCCCCCTCCTCTC
1 CCCCCCCCCCCCTC
46254596 CCCCCCCCCCCCTC
1 CCCCCCCCCCCCTC
46254610 CCCCCCCCCCCC
1 CCCCCCCCCCCC
46254622 CAAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.00, C:0.90, G:0.00, T:0.10
Consensus pattern (14 bp):
CCCCCCCCCCCCTC
Found at i:46254606 original size:19 final size:17
Alignment explanation
Indices: 46254582--46254622 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 17
46254572 AAACCTTCAA
46254582 CCCCCCCTCCTCTCCCCCC
1 CCCCCCCTCC-C-CCCCCC
46254601 CCCCCCCTCCCCCCCCC
1 CCCCCCCTCCCCCCCCC
46254618 CCCCC
1 CCCCC
46254623 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 10 0.45
ACGTcount: A:0.00, C:0.90, G:0.00, T:0.10
Consensus pattern (17 bp):
CCCCCCCTCCCCCCCCC
Found at i:46254622 original size:16 final size:16
Alignment explanation
Indices: 46254582--46254622 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
46254572 AAACCTTCAA
* *
46254582 CCCCCCCTCCTCTCCC
1 CCCCCCCCCCTCCCCC
46254598 CCCCCCCCCCTCCCCC
1 CCCCCCCCCCTCCCCC
46254614 CCCCCCCCC
1 CCCCCCCCC
46254623 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.00, C:0.90, G:0.00, T:0.10
Consensus pattern (16 bp):
CCCCCCCCCCTCCCCC
Found at i:46255299 original size:35 final size:37
Alignment explanation
Indices: 46255259--46255332 Score: 121
Period size: 40 Copynumber: 1.9 Consensus size: 37
46255249 TATCTAGAAG
46255259 GCACAGCAAGACTGCAACTTTGGTTTATATAGAAGGCACA
1 GCACAGCAAGACTGCAACTTTGGTTTATATAGAAGG---A
46255299 GCACAGCAAGACTGCAACTTTGGTTTATATAGAA
1 GCACAGCAAGACTGCAACTTTGGTTTATATAGAA
46255333 ACCAGCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (37 bp):
GCACAGCAAGACTGCAACTTTGGTTTATATAGAAGGA
Found at i:46261630 original size:19 final size:19
Alignment explanation
Indices: 46261606--46261644 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
46261596 AAAGCTAATA
*
46261606 ACAAATTTTATTACGGTGG
1 ACAAATTTGATTACGGTGG
46261625 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
46261644 A
1 A
46261645 TGACAGTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:46266411 original size:18 final size:19
Alignment explanation
Indices: 46266390--46266425 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
46266380 TATTTTAAGT
*
46266390 TAAAATT-TATTATTAAAA
1 TAAAATTGTACTATTAAAA
46266408 TAAAATTGTACTATTAAA
1 TAAAATTGTACTATTAAA
46266426 TAATTTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATTGTACTATTAAAA
Found at i:46271262 original size:16 final size:16
Alignment explanation
Indices: 46271237--46271273 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
46271227 AATAGTTTTA
*
46271237 AATTTTGATCATTTCG
1 AATTTAGATCATTTCG
*
46271253 AATTTAGATCATTTTG
1 AATTTAGATCATTTCG
46271269 AATTT
1 AATTT
46271274 GAATTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (16 bp):
AATTTAGATCATTTCG
Found at i:46271804 original size:20 final size:18
Alignment explanation
Indices: 46271776--46271829 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 18
46271766 TATATTTTAA
46271776 AAAATATTTAAAAAAATTCT
1 AAAA-ATTTAAAAAAATT-T
*
46271796 AAAGAATTTATAAAGATATTT
1 AAA-AATTTA-AAA-AAATTT
46271817 AAAAATTTAAAAA
1 AAAAATTTAAAAA
46271830 TTTTCTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 14 0.47
21 8 0.27
22 4 0.13
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAAATTTAAAAAAATTT
Found at i:46273200 original size:2 final size:2
Alignment explanation
Indices: 46273195--46273231 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
46273185 AAATAGGACG
46273195 AT AT AT AT AT AT AT AT AT AT AT AT A- 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
46273232 CAAAATCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46275966 original size:19 final size:20
Alignment explanation
Indices: 46275934--46275971 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
46275924 AGACTGACCA
* *
46275934 ATTTTATTTGAAAA-AAATT
1 ATTTTATATAAAAATAAATT
46275953 ATTTTATATAAAAATAAAT
1 ATTTTATATAAAAATAAAT
46275972 GAGTTTTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTTATATAAAAATAAATT
Found at i:46276326 original size:31 final size:32
Alignment explanation
Indices: 46276265--46276334 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
46276255 TTTTTAGAGG
* * * *
46276265 TTGATTCATACAAATCTTTCAAGAAATTAAGA
1 TTGATTAATACAAACCCTTCAAAAAATTAAGA
46276297 TTGATTAATACAAACCCTT-AAAAAATTAAGA
1 TTGATTAATACAAACCCTTCAAAAAATTAAGA
46276328 TTGATTA
1 TTGATTA
46276335 GAAACTTAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.53
32 16 0.47
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (32 bp):
TTGATTAATACAAACCCTTCAAAAAATTAAGA
Found at i:46277279 original size:44 final size:44
Alignment explanation
Indices: 46277229--46277323 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
46277219 AGACCATGGG
*
46277229 TTCAAATATTGGATTATTTATTCCTTATACTATTACAACTGATA
1 TTCAAATATAGGATTATTTATTCCTTATACTATTACAACTGATA
46277273 TTCAAATATAGGATTATTTATTCCTTATACTATTACAACTGATA
1 TTCAAATATAGGATTATTTATTCCTTATACTATTACAACTGATA
46277317 TT-AAATA
1 TTCAAATA
46277324 AGTATTTATG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 5 0.10
44 45 0.90
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (44 bp):
TTCAAATATAGGATTATTTATTCCTTATACTATTACAACTGATA
Found at i:46281482 original size:30 final size:29
Alignment explanation
Indices: 46281447--46281752 Score: 231
Period size: 30 Copynumber: 10.1 Consensus size: 29
46281437 TAAGATTTTT
*
46281447 GGGGTTAAAATGTAATTTTGAGAAAGTTTA
1 GGGGTTAAAATGTGATTTT-AGAAAGTTTA
*
46281477 GGGGTTAAAATGTAATTTTAGGAAAGTTTA
1 GGGGTTAAAATGTGATTTTA-GAAAGTTTA
*
46281507 GGGGGTTAAAAATATGATTTTAGGAAAGTTT-
1 -GGGGTT-AAAATGTGATTTTA-GAAAGTTTA
* *
46281538 GAAGGTTAAAATGTGATTTTGGGAAAGTTTA
1 G-GGGTTAAAATGTGATTTT-AGAAAGTTTA
* *
46281569 AGGTTTAAAATGTGATTTTAGCAAAGTTTA
1 GGGGTTAAAATGTGATTTTAG-AAAGTTTA
* *
46281599 GAGGTTAAAATGTGATTTTAGGAAAGTTTG
1 GGGGTTAAAATGTGATTTTA-GAAAGTTTA
* * * * * *
46281629 GGGGTCAAAATATAATTTTGGGAAA-ATTC
1 GGGGTTAAAATGTGATTTT-AGAAAGTTTA
*
46281658 GAGGGTCAAAATGTGATTTTAGGAAAGTTTGA
1 G-GGGTTAAAATGTGATTTTA-GAAAGTTT-A
** * ** *
46281690 ATGGTCAAAATGCAATTTTGGTAAAGTTT-
1 GGGGTTAAAATGTGATTTTAG-AAAGTTTA
* *
46281719 GAGGGTTAAAATATGATTTTTAGAAAGTTCA
1 G-GGGTTAAAATGTGA-TTTTAGAAAGTTTA
46281750 GGG
1 GGG
46281753 ATCTTTTGAG
Statistics
Matches: 221, Mismatches: 38, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
29 5 0.02
30 154 0.70
31 41 0.19
32 21 0.10
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (29 bp):
GGGGTTAAAATGTGATTTTAGAAAGTTTA
Found at i:46281517 original size:61 final size:61
Alignment explanation
Indices: 46281447--46281752 Score: 297
Period size: 60 Copynumber: 5.0 Consensus size: 61
46281437 TAAGATTTTT
*
46281447 GGGGTTAAAATGTAATTTTGAGAAAGTTT-AGGGGTTAAAATGTAATTTTAGGAAAGTTTAG
1 GGGGTTAAAATGTAATTTTGAGAAAGTTTGA-GGGTTAAAATGTGATTTTAGGAAAGTTTAG
* * * *
46281508 GGGGTTAAAAATATGATTTT-AGGAAAGTTTGAAGGTTAAAATGTGATTTTGGGAAAGTTTA-
1 GGGGTT-AAAATGTAATTTTGA-GAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTAG
* * *
46281569 AGGTTTAAAATGTGATTTT-AGCAAAGTTT-AGAGGTTAAAATGTGATTTTAGGAAAGTTT-G
1 GGGGTTAAAATGTAATTTTGAG-AAAGTTTGAG-GGTTAAAATGTGATTTTAGGAAAGTTTAG
* * * * * *
46281629 GGGGTCAAAATATAATTTTGGGAAAATTCGAGGGTCAAAATGTGATTTTAGGAAAGTTT-G
1 GGGGTTAAAATGTAATTTTGAGAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTAG
** * * * *
46281689 AATGGTCAAAATGCAATTTTG-GTAAAGTTTGAGGGTTAAAATATGATTTTTA-GAAAGTTCAG
1 -GGGGTTAAAATGTAATTTTGAG-AAAGTTTGAGGGTTAAAATGTGA-TTTTAGGAAAGTTTAG
46281751 GG
1 GG
46281753 ATCTTTTGAG
Statistics
Matches: 203, Mismatches: 30, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
59 2 0.01
60 93 0.46
61 56 0.28
62 51 0.25
63 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (61 bp):
GGGGTTAAAATGTAATTTTGAGAAAGTTTGAGGGTTAAAATGTGATTTTAGGAAAGTTTAG
Found at i:46283500 original size:41 final size:41
Alignment explanation
Indices: 46283397--46284019 Score: 631
Period size: 41 Copynumber: 15.0 Consensus size: 41
46283387 AGGAAGATGG
* *
46283397 CTTCAATATGCCCCTATTGACTTAAGGGTAAAAGATTGGAAAGGT
1 CTTCAATCTGCCCCTCTTGA-TTAAGGGTAAAAGATTGG-AA--T
* *
46283442 CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGAAT
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* *
46283483 CTTCAATCTGTCGCTCTTGATT-AGGAGTAAAAGATTGGAAT
1 CTTCAATCTGCCCCTCTTGATTAAGG-GTAAAAGATTGGAAT
*
46283524 ATTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* * * *
46283565 GGCTTCAATCTGTCCCTCTTAATTAGGGGTAAAAGATTAGAAT
1 --CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* * * * **
46283608 CTTCAATTTGCCCCTCTTGACTAGGGGTAAAAAATTAAAAT
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* * * * * * *
46283649 ATTTAATCTACCCCTCTTGATTAGGGGTAAAAAACTAGAAT
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* * ** * * **
46283690 TTTTAATCTTTCCCTCTGTAATTTTAA-GGTAAAAGACTATAAT
1 CTTCAATCTGCCCCTCT-TGA--TTAAGGGTAAAAGATTGGAAT
* * *
46283733 CTTCAATTTGCCCCTCTTTTGATTAAGGGTAAAAGACTAGAAT
1 CTTCAATCTGCCCCTC--TTGATTAAGGGTAAAAGATTGGAAT
* *
46283776 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACTGGAAT
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* * *
46283817 ATTCAATCTGCCCCTCTTGATT-AGAGGTAAAAGATCGAAAT
1 CTTCAATCTGCCCCTCTTGATTAAG-GGTAAAAGATTGGAAT
* *
46283858 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACTGGAAT
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* * * * * *
46283899 CTTTAATCTGTCCCTCTTGATTAGGGGTAAAATACTAGAAT
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* *
46283940 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACTGGAAT
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
* **
46283981 CTTCAATCTGTCTTTCTTGATTAAGGGTAAAAGATTGGA
1 CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGA
46284020 TGATGATGTA
Statistics
Matches: 495, Mismatches: 71, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
40 4 0.01
41 348 0.70
42 11 0.02
43 92 0.19
44 22 0.04
45 18 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (41 bp):
CTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAAT
Found at i:46283650 original size:125 final size:123
Alignment explanation
Indices: 46283398--46284014 Score: 628
Period size: 125 Copynumber: 4.9 Consensus size: 123
46283388 GGAAGATGGC
* * * *
46283398 TTCAATATGCCCCTATTGACTTAAGGGTAAAAGATTGGAAAGGTCTTCAATCTACCCCTCTTGAT
1 TTCAATCTGCCCCTCTTGA-TTAAGGGTAAAAGACTGG-AA--TCTTCAATCTGCCCCTCTTGAT
* * * * * *
46283463 TAGGGGTAAAAGATTGGAATCTTCAATCTGTCGCTCTTGATT-AGGAGTAAAAGATTGGAATA
62 TAGGGGTAAAAGACTAGAATCTTCAATCTGCCCCTCTTGATTAAGG-GTAAAAGACTAGAATA
* * *
46283525 TTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAATGGCTTCAATCTGTCCCTCTTAATTA
1 TTCAATCTGCCCCTCTTGATTAAGGGTAAAAGACTGGAAT--CTTCAATCTGCCCCTCTTGATTA
* * * * * * *
46283590 GGGGTAAAAGATTAGAATCTTCAATTTGCCCCTCTTGACTAGGGGTAAAAAATTAAAATA
64 GGGGTAAAAGACTAGAATCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGACTAGAATA
* * * * * * * ** *
46283650 TTTAATCTACCCCTCTTGATTAGGGGTAAAAAACTAGAATTTTTAATCTTTCCCTCTGTAATTTT
1 TTCAATCTGCCCCTCTTGATTAAGGGTAAAAGACTGGAATCTTCAATCTGCCCCTCT-TGA--TT
* * * *
46283715 A-AGGTAAAAGACTATAATCTTCAATTTGCCCCTCTTTTGATTAAGGGTAAAAGACTAGAATC
63 AGGGGTAAAAGACTAGAATCTTCAATCTGCCCCTC--TTGATTAAGGGTAAAAGACTAGAATA
* * *
46283777 TTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACTGGAATATTCAATCTGCCCCTCTTGATTAGA
1 TTCAATCTGCCCCTCTTGATTAAGGGTAAAAGACTGGAATCTTCAATCTGCCCCTCTTGATTAGG
* * * *
46283842 GGTAAAAGA-TCGAAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACTGGAATC
66 GGTAAAAGACTAG-AATCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGACTAGAATA
* * * * * * *
46283900 TTTAATCTGTCCCTCTTGATTAGGGGTAAAATACTAGAATCTTCAATCTGCCCTTCTTGATTAAG
1 TTCAATCTGCCCCTCTTGATTAAGGGTAAAAGACTGGAATCTTCAATCTGCCCCTCTTGATTAGG
* * **
46283965 GGTAAAAGACTGGAATCTTCAATCTGTCTTTCTTGATTAAGGGTAAAAGA
66 GGTAAAAGACTAGAATCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGA
46284015 TTGGATGATG
Statistics
Matches: 418, Mismatches: 61, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
123 139 0.33
124 9 0.02
125 161 0.39
126 25 0.06
127 84 0.20
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (123 bp):
TTCAATCTGCCCCTCTTGATTAAGGGTAAAAGACTGGAATCTTCAATCTGCCCCTCTTGATTAGG
GGTAAAAGACTAGAATCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGACTAGAATA
Found at i:46284384 original size:49 final size:49
Alignment explanation
Indices: 46284323--46284457 Score: 146
Period size: 49 Copynumber: 2.8 Consensus size: 49
46284313 ACTAGGTTCG
* *
46284323 CCGTTGCAGCCTCAACCTTTCCCTTAAAATCTTCATGATACCAGGCTCA
1 CCGTTACAGCCTCAACCTTTCCCTTCAAATCTTCATGATACCAGGCTCA
** * * * * *
46284372 CCGTTATGGCCTCAACCTTTCCC-TCACATCTTCTAAGGTACCAGGTTCG
1 CCGTTACAGCCTCAACCTTTCCCTTCAAATCTTC-ATGATACCAGGCTCA
* * *
46284421 CCGTTGCAGCCTTAACCTTTCCCTTCAAATCCTCATG
1 CCGTTACAGCCTCAACCTTTCCCTTCAAATCTTCATG
46284458 GTATAGGGTT
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
48 8 0.12
49 52 0.76
50 8 0.12
ACGTcount: A:0.21, C:0.36, G:0.13, T:0.30
Consensus pattern (49 bp):
CCGTTACAGCCTCAACCTTTCCCTTCAAATCTTCATGATACCAGGCTCA
Found at i:46284481 original size:98 final size:98
Alignment explanation
Indices: 46284274--46284502 Score: 264
Period size: 98 Copynumber: 2.3 Consensus size: 98
46284264 TATAAGATTT
* * * * * *
46284274 ACCGTTGCGGCTTCAACTTTTTCATCATAT-TTCTAAGGTACTAGGTTCGCCGTTGCAGCCTCAA
1 ACCGTTGCGGCCTCAACCTTTCCCTCACATCTTCTAAGGTACCAGGTTCGCCGTTGCAGCCTCAA
*
46284338 CCTTTCCCTTAAAATCTTCATGATACCAGGCTC
66 CCTTTCCCTTAAAATCCTCATGATACCAGGCTC
** *
46284371 ACCGTTATGGCCTCAACCTTTCCCTCACATCTTCTAAGGTACCAGGTTCGCCGTTGCAGCCTTAA
1 ACCGTTGCGGCCTCAACCTTTCCCTCACATCTTCTAAGGTACCAGGTTCGCCGTTGCAGCCTCAA
* * * * *
46284436 CCTTTCCCTTCAAATCCTCATGGTA-TAGGGTTT
66 CCTTTCCCTTAAAATCCTCATGATACCA-GGCTC
** *
46284469 GTCGTTGCGGCCTCAACCTTTCCCATCGCATCTT
1 ACCGTTGCGGCCTCAACCTTTCCC-TCACATCTT
46284503 AATGTTTCCT
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
97 24 0.22
98 77 0.71
99 8 0.07
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.33
Consensus pattern (98 bp):
ACCGTTGCGGCCTCAACCTTTCCCTCACATCTTCTAAGGTACCAGGTTCGCCGTTGCAGCCTCAA
CCTTTCCCTTAAAATCCTCATGATACCAGGCTC
Found at i:46288247 original size:12 final size:12
Alignment explanation
Indices: 46288209--46288249 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
46288199 ACATTCTCGT
*
46288209 CATCTGCTCTTG
1 CATCTGTTCTTG
*
46288221 CAACTGTTCTTG
1 CATCTGTTCTTG
*
46288233 CATCTGTTCCTG
1 CATCTGTTCTTG
46288245 CATCT
1 CATCT
46288250 CTCTTTGGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.12, C:0.32, G:0.15, T:0.41
Consensus pattern (12 bp):
CATCTGTTCTTG
Found at i:46288561 original size:121 final size:121
Alignment explanation
Indices: 46288347--46288590 Score: 479
Period size: 121 Copynumber: 2.0 Consensus size: 121
46288337 TTACTGGTAT
46288347 AACTGTTAAAGTTTTAATTAGTTAGAATCCTCATGTTAAAATATGTAAAAATGCAATGCAAGTGA
1 AACTGTTAAAGTTTTAATTAGTTAGAATCCTCATGTTAAAATATGTAAAAATGCAATGCAAGTGA
*
46288412 ATGCATGTATGCAATGTAAGAAAAGGCATTGATTTTGAATTCAATCCTATTAGAAC
66 ACGCATGTATGCAATGTAAGAAAAGGCATTGATTTTGAATTCAATCCTATTAGAAC
46288468 AACTGTTAAAGTTTTAATTAGTTAGAATCCTCATGTTAAAATATGTAAAAATGCAATGCAAGTGA
1 AACTGTTAAAGTTTTAATTAGTTAGAATCCTCATGTTAAAATATGTAAAAATGCAATGCAAGTGA
46288533 ACGCATGTATGCAATGTAAGAAAAGGCATTGATTTTGAATTCAATCCTATTAGAAC
66 ACGCATGTATGCAATGTAAGAAAAGGCATTGATTTTGAATTCAATCCTATTAGAAC
46288589 AA
1 AA
46288591 TTTCTCTAGA
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (121 bp):
AACTGTTAAAGTTTTAATTAGTTAGAATCCTCATGTTAAAATATGTAAAAATGCAATGCAAGTGA
ACGCATGTATGCAATGTAAGAAAAGGCATTGATTTTGAATTCAATCCTATTAGAAC
Found at i:46290849 original size:30 final size:30
Alignment explanation
Indices: 46290791--46290997 Score: 217
Period size: 29 Copynumber: 7.0 Consensus size: 30
46290781 GAGAATTTTG
* * *
46290791 GGGTCAAAATGTAATTTTAGAAAAAGTTTAA
1 GGGTTAAAATGTGATTTTAG-GAAAGTTTAA
46290822 GGGTTAAAATGTGATTTTAGGAAAGTTTAA
1 GGGTTAAAATGTGATTTTAGGAAAGTTTAA
* *
46290852 GGGTTAAAATGTGATTTTTGGAAAATTT-A
1 GGGTTAAAATGTGATTTTAGGAAAGTTTAA
*
46290881 GGAG-TCAAATGTGATTTTAGGAAAGTTT-A
1 GG-GTTAAAATGTGATTTTAGGAAAGTTTAA
* *
46290910 GGGGTCAAATGTGATTTTAGGAAAGTTTAA
1 GGGTTAAAATGTGATTTTAGGAAAGTTTAA
* **
46290940 GGG-TCAAATGTGATTTT-GGAAAAGTTTGT
1 GGGTTAAAATGTGATTTTAGG-AAAGTTTAA
* * * *
46290969 GGGTCAAAATATGATTTTTGAAAAGTTTA
1 GGGTTAAAATGTGATTTTAGGAAAGTTTA
46290998 GGGACCTTTT
Statistics
Matches: 155, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
28 3 0.02
29 75 0.48
30 58 0.37
31 19 0.12
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (30 bp):
GGGTTAAAATGTGATTTTAGGAAAGTTTAA
Found at i:46294991 original size:26 final size:25
Alignment explanation
Indices: 46294962--46295053 Score: 71
Period size: 26 Copynumber: 3.5 Consensus size: 25
46294952 TTTTTTTTTA
*
46294962 AATACATATATTTAATTATAAAATTC
1 AATACATAT-TTTAATTATAAAATGC
46294988 AATATGCAT-TTTT-ATTATAAAGATGC
1 AATA--CATATTTTAATTATAAA-ATGC
**
46295014 AATACATAATTTTTAATTATTAAAATAT
1 AATACAT-A-TTTTAATTA-TAAAATGC
*
46295042 AACACATATTTT
1 AATACATATTTT
46295054 TTAAGCATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
24 3 0.06
25 8 0.15
26 18 0.33
27 6 0.11
28 15 0.28
29 4 0.07
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (25 bp):
AATACATATTTTAATTATAAAATGC
Found at i:46295236 original size:32 final size:32
Alignment explanation
Indices: 46295196--46295256 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
46295186 TTTTTGGTCC
46295196 AATTTGGTACTCAAACTTGACACTTTTTTTCT
1 AATTTGGTACTCAAACTTGACACTTTTTTTCT
*
46295228 AATTTGGTACTTAAACTTGACACTTTTTT
1 AATTTGGTACTCAAACTTGACACTTTTTT
46295257 AGGTTAGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (32 bp):
AATTTGGTACTCAAACTTGACACTTTTTTTCT
Found at i:46295267 original size:29 final size:31
Alignment explanation
Indices: 46295202--46295274 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
46295192 GTCCAATTTG
* * *
46295202 GTACTCAAACTTGACACTTTTTTTCTAATTTG
1 GTACTTAAACTTGACAC-TTTTTTCTAAGTTA
*
46295234 GTACTTAAACTTGACAC-TTTTT-TAGGTTA
1 GTACTTAAACTTGACACTTTTTTCTAAGTTA
46295263 GTACTTAAACTT
1 GTACTTAAACTT
46295275 TTTAGGGTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 16 0.43
30 5 0.14
32 16 0.43
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (31 bp):
GTACTTAAACTTGACACTTTTTTCTAAGTTA
Found at i:46295518 original size:32 final size:26
Alignment explanation
Indices: 46295438--46295520 Score: 69
Period size: 32 Copynumber: 2.9 Consensus size: 26
46295428 TAATAAATTT
46295438 AGGTACCAAATTGAATCTAAAAAAAGC
1 AGGTACCAAATTGAATC-AAAAAAAGC
* *
46295465 AGGTGCCAAATTAGAA-AAAAAATGCCAAGTTC
1 AGGTACCAAATT-GAATCAAAAA----AAG--C
46295497 AGGTACCAAATTGAATCAAAAAAA
1 AGGTACCAAATTGAATCAAAAAAA
46295521 TTAAATATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
26 5 0.11
27 11 0.25
28 5 0.11
30 3 0.07
31 3 0.07
32 17 0.39
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (26 bp):
AGGTACCAAATTGAATCAAAAAAAGC
Found at i:46295553 original size:57 final size:59
Alignment explanation
Indices: 46295438--46295566 Score: 145
Period size: 57 Copynumber: 2.2 Consensus size: 59
46295428 TAATAAATTT
** *
46295438 AGGTACCAAATTGAATCTAAAAAAAGCAGGTGCCAAATTAGAAAAAAAATGCCAAGTTC
1 AGGTACCAAATTGAATCTAAAAAAAGCAAATACCAAATTAGAAAAAAAATGCCAAGTTC
** * * * *
46295497 AGGTACCAAATTGAATC-AAAAAAATTAAATATCAAATTA-AGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTGAATCTAAAAAAAGCAAATACCAAATTAGAAAAAAAATGCCAAGTTC
* *
46295554 AAGTATCAAATTG
1 AGGTACCAAATTG
46295567 GGTCAAAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 26 0.44
58 16 0.27
59 17 0.29
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.22
Consensus pattern (59 bp):
AGGTACCAAATTGAATCTAAAAAAAGCAAATACCAAATTAGAAAAAAAATGCCAAGTTC
Found at i:46297994 original size:29 final size:29
Alignment explanation
Indices: 46297918--46297988 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
46297908 AACGATATCG
46297918 TAAGTGACTAAAACGTAATATTTCAAACA
1 TAAGTGACTAAAACGTAATATTTCAAACA
46297947 TAAGTGACTAAAACGTAATATTTCAAACA
1 TAAGTGACTAAAACGTAATATTTCAAACA
46297976 TAAGTGACTAAAA
1 TAAGTGACTAAAA
46297989 TATAATCTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (29 bp):
TAAGTGACTAAAACGTAATATTTCAAACA
Found at i:46298572 original size:18 final size:17
Alignment explanation
Indices: 46298542--46298606 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
46298532 TTGAATTATT
46298542 TTTTTATAGATTTTAATGA
1 TTTTTATA-ATTTTAAT-A
*
46298561 TTTTTATAATTTTCATCA
1 TTTTTATAATTTTAAT-A
* *
46298579 TTGTAATAAATTTTAATA
1 TTTTTAT-AATTTTAATA
*
46298597 TTTTTGTAAT
1 TTTTTATAAT
46298607 GATTTTTTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.08
18 18 0.49
19 16 0.43
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTTTATAATTTTAATA
Found at i:46307572 original size:17 final size:16
Alignment explanation
Indices: 46307537--46307576 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
46307527 TTGTGTCAAG
**
46307537 TCATTTTAAGTTTTGA
1 TCATTTTAAGTTTAAA
46307553 TCACTTTTAAGTTTAAA
1 TCA-TTTTAAGTTTAAA
46307570 TCATTTT
1 TCATTTT
46307577 GGATTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (16 bp):
TCATTTTAAGTTTAAA
Found at i:46311084 original size:5 final size:5
Alignment explanation
Indices: 46311074--46311098 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
46311064 CCCAGGGGAT
46311074 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
46311099 CTTGTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:46313387 original size:36 final size:35
Alignment explanation
Indices: 46313346--46313413 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
46313336 CCATTTTACG
*
46313346 ATTATATTATTAC-TATTTTATTATTAATGTTTGAAT
1 ATTATA-TAATACTTATTTTATTATTAAT-TTTGAAT
46313382 ATTATATAATACTTATTTTATTATTAATTTTG
1 ATTATATAATACTTATTTTATTATTAATTTTG
46313414 TTATTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 9 0.30
36 21 0.70
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (35 bp):
ATTATATAATACTTATTTTATTATTAATTTTGAAT
Found at i:46313417 original size:12 final size:11
Alignment explanation
Indices: 46313346--46313424 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
46313336 CCATTTTACG
*
46313346 ATTATATTATT
1 ATTATTTTATT
*
46313357 ACTATTTTATT
1 ATTATTTTATT
*
46313368 ATTAATGTTTGAAT
1 ATT-AT-TTT-ATT
* *
46313382 ATTA-TATAAT
1 ATTATTTTATT
46313392 ACTTATTTTATT
1 A-TTATTTTATT
*
46313404 ATTAATTTTGTT
1 ATT-ATTTTATT
46313416 ATTATTTTA
1 ATTATTTTA
46313425 AAAAAATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
10 4 0.08
11 23 0.43
12 17 0.32
13 4 0.08
14 5 0.09
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:46313677 original size:13 final size:13
Alignment explanation
Indices: 46313659--46313683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46313649 AGCCTTTGCT
46313659 AAAGCCCAACTTC
1 AAAGCCCAACTTC
46313672 AAAGCCCAACTT
1 AAAGCCCAACTT
46313684 GAACCCAGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAGCCCAACTTC
Found at i:46323806 original size:31 final size:31
Alignment explanation
Indices: 46323770--46323831 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
46323760 TTAATCACTT
*
46323770 AACTATTCAAAA-CTTTTTATTTAAGTTATTG
1 AACTATCCAAAAGC-TTTTATTTAAGTTATTG
*
46323801 AACTATCCAAAAGCTTTTGTTTAAGTTATTG
1 AACTATCCAAAAGCTTTTATTTAAGTTATTG
46323832 GGCTATTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (31 bp):
AACTATCCAAAAGCTTTTATTTAAGTTATTG
Found at i:46324809 original size:15 final size:15
Alignment explanation
Indices: 46324773--46324803 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46324763 AATATCACAT
*
46324773 AAGAAAATTTAATAA
1 AAGAAAATTTAAGAA
46324788 AAGAAAATTTAAGAA
1 AAGAAAATTTAAGAA
46324803 A
1 A
46324804 TAAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (15 bp):
AAGAAAATTTAAGAA
Found at i:46332614 original size:14 final size:14
Alignment explanation
Indices: 46332573--46332615 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
46332563 TAGATTAATG
*
46332573 ATTAAAATAAAAAAA
1 ATTAAAAT-AAAATA
* *
46332588 ATTAAACTTAAATA
1 ATTAAAATAAAATA
46332602 ATTAAAATAAAATA
1 ATTAAAATAAAATA
46332616 TGACTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
ATTAAAATAAAATA
Found at i:46335733 original size:17 final size:17
Alignment explanation
Indices: 46335694--46335733 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
46335684 TTCGAAATCG
* *
46335694 AATAATTAATCGAATTA
1 AATAATTAATCAAAATA
*
46335711 ACTAATTAATCAAAATA
1 AATAATTAATCAAAATA
46335728 AATAAT
1 AATAAT
46335734 ATAAATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (17 bp):
AATAATTAATCAAAATA
Found at i:46341173 original size:14 final size:14
Alignment explanation
Indices: 46341144--46341190 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
46341134 TGATTATATA
46341144 AAAATTTTCAATAAAT
1 AAAATTTT--ATAAAT
46341160 AAAATTTTATAAAT
1 AAAATTTTATAAAT
*
46341174 -AAATATTA-AAAT
1 AAAATTTTATAAAT
46341186 AAAAT
1 AAAAT
46341191 AGTATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.14
13 11 0.38
14 6 0.21
16 8 0.28
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTTTATAAAT
Found at i:46341190 original size:13 final size:14
Alignment explanation
Indices: 46341154--46341196 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
46341144 AAAATTTTCA
*
46341154 ATAAATAAAATTTT
1 ATAAATAAAATATT
46341168 ATAAAT-AAATATT
1 ATAAATAAAATATT
*
46341181 A-AAATAAAATAGT
1 ATAAATAAAATATT
46341194 ATA
1 ATA
46341197 TATATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 4 0.16
13 14 0.56
14 7 0.28
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAAATAAAATATT
Found at i:46345110 original size:14 final size:15
Alignment explanation
Indices: 46345093--46345123 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46345083 CCCATAGCTT
46345093 CTTGGTT-TCTTCTA
1 CTTGGTTCTCTTCTA
46345107 CTTGGTTCTCTTCTA
1 CTTGGTTCTCTTCTA
46345122 CT
1 CT
46345124 GTTTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.06, C:0.26, G:0.13, T:0.55
Consensus pattern (15 bp):
CTTGGTTCTCTTCTA
Found at i:46346709 original size:23 final size:20
Alignment explanation
Indices: 46346677--46346727 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
46346667 TTTAACTCGA
46346677 AATTAGTTATGAATTTTTTTATT
1 AATTA-TTATG-ATTTTTTT-TT
*
46346700 ATATTATTATGGTTTTTTTTT
1 A-ATTATTATGATTTTTTTTT
46346721 AATTATT
1 AATTATT
46346728 TAATGATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 3 0.12
22 7 0.27
23 6 0.23
24 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (20 bp):
AATTATTATGATTTTTTTTT
Found at i:46355073 original size:20 final size:20
Alignment explanation
Indices: 46355032--46355076 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
46355022 ATTTTTTTTG
*
46355032 AAAAATTCTAAAAATTTCAA
1 AAAAATTCTAAAAATATCAA
46355052 AAAAATTCTAAAAAATAT-AA
1 AAAAATTCT-AAAAATATCAA
46355072 AAAAA
1 AAAAA
46355077 AATTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATTCTAAAAATATCAA
Found at i:46356810 original size:6 final size:6
Alignment explanation
Indices: 46356799--46356830 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
46356789 ACGTTCATGC
46356799 CTGAAA CTGAAA CTGAAA CTGAAA CTGAAA CT
1 CTGAAA CTGAAA CTGAAA CTGAAA CTGAAA CT
46356831 TCGATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (6 bp):
CTGAAA
Found at i:46357478 original size:18 final size:19
Alignment explanation
Indices: 46357439--46357479 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
46357429 ATTATTTGGA
*
46357439 TATTGTATAATTCTTATTT
1 TATTGTATAATTCTTATAT
46357458 TATTGT-TAATT-TTACTAT
1 TATTGTATAATTCTTA-TAT
46357476 TATT
1 TATT
46357480 TTAGAGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 11 0.55
19 6 0.30
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTGTATAATTCTTATAT
Found at i:46360454 original size:39 final size:39
Alignment explanation
Indices: 46360388--46360521 Score: 126
Period size: 39 Copynumber: 3.4 Consensus size: 39
46360378 TACAGTATTA
* ** *
46360388 CAGTTTTTACAGTGTCGCCGTCAGTTCAGTATTAGATTG
1 CAGTGTTTACAGTGTCATCGTCAGTTCAATATTAGATTG
* * * * *
46360427 CAGTGTTTATAGTGTCATTGTCGGTTCAATA-TAGTGTTA
1 CAGTGTTTACAGTGTCATCGTCAGTTCAATATTAG-ATTG
* * * * *
46360466 CGGTGTTTACAATGTCATCGTCAATTCACTATTAAATTG
1 CAGTGTTTACAGTGTCATCGTCAGTTCAATATTAGATTG
46360505 CAGTGTTTACAGTGTCA
1 CAGTGTTTACAGTGTCA
46360522 CTGCTTGTTT
Statistics
Matches: 72, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
38 3 0.04
39 67 0.93
40 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (39 bp):
CAGTGTTTACAGTGTCATCGTCAGTTCAATATTAGATTG
Found at i:46360545 original size:78 final size:78
Alignment explanation
Indices: 46360350--46360524 Score: 197
Period size: 78 Copynumber: 2.2 Consensus size: 78
46360340 ATAGCTACAT
* * * * * * * * * *
46360350 AGTGTTTTCAGTGTCACTGCCAGCTCAGTACAGTATTACAGTTTTTACAGTGTCGCCGTCAGTTC
1 AGTGTTTACAGTGTCACTGTCGGTTCAATACAGTATTACGGTGTTTACAATGTCACCGTCAATTC
* *
46360415 AGTATTAGATTGC
66 ACTATTAAATTGC
* * * * *
46360428 AGTGTTTATAGTGTCATTGTCGGTTCAATATAGTGTTACGGTGTTTACAATGTCATCGTCAATTC
1 AGTGTTTACAGTGTCACTGTCGGTTCAATACAGTATTACGGTGTTTACAATGTCACCGTCAATTC
46360493 ACTATTAAATTGC
66 ACTATTAAATTGC
46360506 AGTGTTTACAGTGTCACTG
1 AGTGTTTACAGTGTCACTG
46360525 CTTGTTTGAT
Statistics
Matches: 78, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (78 bp):
AGTGTTTACAGTGTCACTGTCGGTTCAATACAGTATTACGGTGTTTACAATGTCACCGTCAATTC
ACTATTAAATTGC
Found at i:46360914 original size:64 final size:63
Alignment explanation
Indices: 46360813--46360949 Score: 186
Period size: 64 Copynumber: 2.2 Consensus size: 63
46360803 ATGGCTTAAC
* * *
46360813 ACACAAGCCCGTGTTCACAGATCGTGTAACTCACTGTTTATTGTTTATAGGGTACACGGTCTAG
1 ACACACGCCCGTGTTCACAGATCGTGTAACTCACTGTTTATTGTTTATAGGGCACACGG-CCAG
* * *
46360877 ACACACGCCCGTGTTCCCTA-ATCGTGTAACTCACTGTTTGTTGTTTATATGGCACACGGCCAG
1 ACACACGCCCGTGTTCAC-AGATCGTGTAACTCACTGTTTATTGTTTATAGGGCACACGGCCAG
*
46360940 ATACACGCCC
1 ACACACGCCC
46360950 ACATGTCCGC
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
63 12 0.18
64 52 0.80
65 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (63 bp):
ACACACGCCCGTGTTCACAGATCGTGTAACTCACTGTTTATTGTTTATAGGGCACACGGCCAG
Found at i:46366083 original size:29 final size:29
Alignment explanation
Indices: 46365825--46366085 Score: 174
Period size: 30 Copynumber: 8.9 Consensus size: 29
46365815 TATTTTATTT
*
46365825 AAAAGTTACATTTTGACCCT-AAACTTTCTT
1 AAAA-TTACATTTTGACCCTAAAACTTTC-C
** * * *
46365855 AAAATTGTATTTTGGCCCTTAAAAATTTTC
1 AAAATTACATTTTGACCC-TAAAACTTTCC
*
46365885 AAAATTACA-TTTGACCCTTAAACTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTCC
* * ** * *
46365913 AAAAATTAGATTTTAATCCCCCAAATTTTCT
1 -AAAATTACATTTTGA-CCCTAAAACTTTCC
* *
46365944 AAAATTGCAATTTGACCCCT-AAACTTTCC
1 AAAATTACATTTTGA-CCCTAAAACTTTCC
46365973 TAAAATTACATTTTGACTCC--AAACTTTCC
1 -AAAATTACATTTTGAC-CCTAAAACTTTCC
* ** *
46366002 AAAATTACA-TTTAACCCCCAAACTTTTCA
1 AAAATTACATTTTGACCCTAAAAC-TTTCC
* * *
46366031 AAAAATACATTTTAACCCCTAAAATTTTCC
1 AAAATTACATTTTGA-CCCTAAAACTTTCC
**
46366061 AAAATTGTATTTTGACCCTAAAACT
1 AAAATTACATTTTGACCCTAAAACT
46366086 CTTTTAAATT
Statistics
Matches: 179, Mismatches: 40, Indels: 25
0.73 0.16 0.10
Matches are distributed among these distances:
26 2 0.01
27 5 0.03
28 21 0.12
29 64 0.36
30 65 0.36
31 22 0.12
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTGACCCTAAAACTTTCC
Found at i:46366085 original size:117 final size:116
Alignment explanation
Indices: 46365833--46366082 Score: 297
Period size: 117 Copynumber: 2.1 Consensus size: 116
46365823 TTAAAAGTTA
* ** * * *
46365833 CATTTTGACCCTAAACTTTCTTAAAATTGTATTTTGGCCCTTAAAAATTTTCAAAATTACATTTG
1 CATTTTGACCCTAAACTTTCCTAAAATTACATTTTGACCC-T-AAAATTTCCAAAATTACATTTA
** * * * *
46365898 ACCCTTAAACTTTCCAAAAATTAGATTTTAATCCCCCAAATTTTCTAAAATTG
64 ACCCCCAAACTTTCCAAAAAATACATTTTAATCCCCAAAATTTTCCAAAATTG
* *
46365951 CAATTTGACCCCTAAACTTTCCTAAAATTACATTTTGACTCC-AAACTTTCCAAAATTACATTTA
1 CATTTTGA-CCCTAAACTTTCCTAAAATTACATTTTGAC-CCTAAAATTTCCAAAATTACATTTA
*
46366015 ACCCCCAAACTTTTCAAAAAATACATTTTAA-CCCCTAAAATTTTCCAAAATTG
64 ACCCCCAAACTTTCCAAAAAATACATTTTAATCCCC-AAAATTTTCCAAAATTG
*
46366068 TATTTTGACCCTAAA
1 CATTTTGACCCTAAA
46366083 ACTCTTTTAA
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
116 11 0.10
117 66 0.59
118 7 0.06
119 26 0.23
120 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.37
Consensus pattern (116 bp):
CATTTTGACCCTAAACTTTCCTAAAATTACATTTTGACCCTAAAATTTCCAAAATTACATTTAAC
CCCCAAACTTTCCAAAAAATACATTTTAATCCCCAAAATTTTCCAAAATTG
Found at i:46368908 original size:2 final size:2
Alignment explanation
Indices: 46368903--46368933 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46368893 ATATATATAT
46368903 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
46368934 GAGATGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:46369626 original size:20 final size:20
Alignment explanation
Indices: 46369584--46369661 Score: 54
Period size: 20 Copynumber: 3.9 Consensus size: 20
46369574 TGATTCAAGA
* *
46369584 TTTAAGGTTTATAGTTTGAG
1 TTTAAGATTTATAGGTTGAG
46369604 TTTAAGATTTAT-GGTTGAGG
1 TTTAAGATTTATAGGTTGA-G
* *
46369624 TTTGAAG-TTT-GAGATTTGAAG
1 TTT-AAGATTTATAG-GTTG-AG
*
46369645 TTTAAGATTTAGAGGTT
1 TTTAAGATTTATAGGTT
46369662 AAAATTCGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
19 5 0.11
20 22 0.48
21 15 0.33
22 4 0.09
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (20 bp):
TTTAAGATTTATAGGTTGAG
Found at i:46369641 original size:14 final size:14
Alignment explanation
Indices: 46369618--46369654 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
46369608 AGATTTATGG
*
46369618 TTGAGGTTTGAAGT
1 TTGAGATTTGAAGT
46369632 TTGAGATTTGAAGT
1 TTGAGATTTGAAGT
*
46369646 TTAAGATTT
1 TTGAGATTT
46369655 AGAGGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (14 bp):
TTGAGATTTGAAGT
Found at i:46374177 original size:36 final size:35
Alignment explanation
Indices: 46374115--46374229 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 35
46374105 ATTCTCTTAA
*
46374115 AATAAAAA-AAAA-T-TATTTAA-AATTTTAAAAT
1 AATAAAAATAAAATTATATTTAATCATTTTAAAAT
*
46374146 AATAAAAATAAAATTATATTTTAATCCTTTTAAAA-
1 AATAAAAATAAAATTATA-TTTAATCATTTTAAAAT
*
46374181 ATATAAAAAT----TTA-ATTTAATCATTTAAAAAT
1 A-ATAAAAATAAAATTATATTTAATCATTTTAAAAT
*
46374212 TATAAAAATATAAATTAT
1 AATAAAAATA-AAATTAT
46374230 TAAAATGATG
Statistics
Matches: 66, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
30 22 0.33
31 9 0.14
32 7 0.11
33 1 0.02
34 2 0.03
35 9 0.14
36 16 0.24
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (35 bp):
AATAAAAATAAAATTATATTTAATCATTTTAAAAT
Found at i:46374228 original size:15 final size:17
Alignment explanation
Indices: 46374208--46374246 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
46374198 AATCATTTAA
46374208 AAATTATAAAAAT-AT-
1 AAATTATAAAAATGATG
*
46374223 AAATTATTAAAATGATG
1 AAATTATAAAAATGATG
46374240 AAATTAT
1 AAATTAT
46374247 TTTTACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
AAATTATAAAAATGATG
Found at i:46375230 original size:37 final size:36
Alignment explanation
Indices: 46375154--46375230 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
46375144 AATTTTGAGA
* *
46375154 TTTAATCTTTTATTTTTAATTCCAATAATTTAACCAT
1 TTTAATCTTTTATTTATAATTCAAATAATTTAA-CAT
*
46375191 TTTACTCTTTTATTTAATAATTCAAATAATATTAA-AT
1 TTTAATCTTTTATTT-ATAATTCAAATAAT-TTAACAT
46375228 TTT
1 TTT
46375231 TTACCGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 19 0.54
38 12 0.34
39 4 0.11
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (36 bp):
TTTAATCTTTTATTTATAATTCAAATAATTTAACAT
Found at i:46381130 original size:20 final size:20
Alignment explanation
Indices: 46381105--46381146 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
46381095 TTCATTATAT
46381105 GAACGAAAATTAACCATGCA
1 GAACGAAAATTAACCATGCA
46381125 GAACGAAAATTAACCATGCA
1 GAACGAAAATTAACCATGCA
46381145 GA
1 GA
46381147 TTTACGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (20 bp):
GAACGAAAATTAACCATGCA
Found at i:46386105 original size:43 final size:43
Alignment explanation
Indices: 46386008--46386137 Score: 174
Period size: 43 Copynumber: 3.0 Consensus size: 43
46385998 TTATGAGGAA
* *
46386008 AAACGCCGCTATAGAACATGATCTTTAACGACGC-TTTCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCCCAC
* * *
46386050 AAACGCCACTAAAGAACATGATCTTTAGCGATGCTTTTCCTAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCCCAC
* *
46386093 AAATGCCGCTAAAGAACAT-AGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGA-TCTTTAGCGACGCTTTTCCCAC
46386136 AA
1 AA
46386138 TCACCCCTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
42 31 0.41
43 45 0.59
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCCCAC
Found at i:46392833 original size:41 final size:41
Alignment explanation
Indices: 46392764--46393079 Score: 305
Period size: 41 Copynumber: 7.7 Consensus size: 41
46392754 TTTAAATAAA
* * * *
46392764 TTAGCAGCGCTTTCCTATAAGCGTCGCTAATGCTTCGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTTCGACCT
* * *
46392805 TTAGTGACGCTTTCCCATAAACGCCGCTAATGCTCCGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTTCGACCT
** * * **
46392846 TTAGCGGCGCTTTCAAAGAAACGCCGCTAATGCTCCGATTT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTTCGACCT
* * * *
46392887 TTAGCGACGCTTTCTCAGAAACGCCGCTAATGCTTTGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTTCGACCT
* *
46392928 TTAGCGGCGCTTTCCCAAAAACGCCGCTAATGC-TCTAACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTTC-GACCT
* *
46392969 TTAGCGGCGCTTTCCCATAAATGCCGCTAATGC-TCTAACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTTC-GACCT
* * * * *
46393010 TTAGTGGTGCTTTCCCATAAATGCCACTAATG-ATCTGACCT
1 TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTTC-GACCT
* * * *
46393051 TTAGTGGCGTTTTTTCTATAAACGCCGCT
1 TTAGCGGCG-CTTTCCCATAAACGCCGCT
46393080 GTTGCTTTAC
Statistics
Matches: 234, Mismatches: 38, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.00
41 219 0.94
42 14 0.06
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (41 bp):
TTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTTCGACCT
Found at i:46393013 original size:123 final size:123
Alignment explanation
Indices: 46392788--46393059 Score: 337
Period size: 123 Copynumber: 2.2 Consensus size: 123
46392778 CTATAAGCGT
* * * *
46392788 CGCTAATGCTTCGACCTTTAGTGACGCTTTCCCATAAACGCCGCTAATGCTCCGACCTTTAGCGG
1 CGCTAATGCTTTGACCTTTAGTGGCGCTTTCCCAAAAACGCCGCTAATGCTCCAACCTTTAGCGG
* ** *
46392853 CGCTTTCAAAGAAACGCCGCTAATGCTCCGATTTTTAGCGACGCTTTCTCAGAAACGC
66 CGCTTTCAAAGAAACGCCGCTAATGCTCCAACCTTTAGCGACGCTTTCCCAGAAACGC
* *
46392911 CGCTAATGCTTTGACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAATGCTCTAACCTTTAGCGG
1 CGCTAATGCTTTGACCTTTAGTGGCGCTTTCCCAAAAACGCCGCTAATGCTCCAACCTTTAGCGG
** * * * * ** * *
46392976 CGCTTTCCCATAAATGCCGCTAATGCTCTAACCTTTAGTGGTGCTTTCCCATAAATGC
66 CGCTTTCAAAGAAACGCCGCTAATGCTCCAACCTTTAGCGACGCTTTCCCAGAAACGC
* * *
46393034 CACTAATGATCTGACCTTTAGTGGCG
1 CGCTAATGCTTTGACCTTTAGTGGCG
46393060 TTTTTTCTAT
Statistics
Matches: 125, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
123 125 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (123 bp):
CGCTAATGCTTTGACCTTTAGTGGCGCTTTCCCAAAAACGCCGCTAATGCTCCAACCTTTAGCGG
CGCTTTCAAAGAAACGCCGCTAATGCTCCAACCTTTAGCGACGCTTTCCCAGAAACGC
Found at i:46397906 original size:29 final size:29
Alignment explanation
Indices: 46397847--46397905 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
46397837 TTTAGTCTAA
* *
46397847 TGTGTAATTTTATACATATACTTTGATTT
1 TGTGCAATTTTATACATATAATTTGATTT
46397876 TGTGCAATTTTATACATGA-AATGTTGATTT
1 TGTGCAATTTTATACAT-ATAAT-TTGATTT
46397906 GATCAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.51
Consensus pattern (29 bp):
TGTGCAATTTTATACATATAATTTGATTT
Found at i:46398100 original size:29 final size:30
Alignment explanation
Indices: 46398048--46398104 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
46398038 GATTGAATCA
*
46398048 AAATTAAAGTTTCATATGTAAAATTGCATT
1 AAATTAAAGTTTCATATATAAAATTGCATT
*
46398078 AAATTAAAG-TTCATATATCAAATTGCA
1 AAATTAAAGTTTCATATATAAAATTGCA
46398105 CAATGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (30 bp):
AAATTAAAGTTTCATATATAAAATTGCATT
Found at i:46399488 original size:21 final size:22
Alignment explanation
Indices: 46399442--46399489 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
46399432 AATATGAGAT
*
46399442 TATG-TATATAGTATATGTATA
1 TATGATATATAGTATATATATA
*
46399463 TATGATATATATTAT-TATATA
1 TATGATATATAGTATATATATA
46399484 TATGAT
1 TATGAT
46399490 CTTAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
TATGATATATAGTATATATATA
Found at i:46400377 original size:85 final size:85
Alignment explanation
Indices: 46400223--46400395 Score: 301
Period size: 85 Copynumber: 2.0 Consensus size: 85
46400213 CGAACATGAT
* * *
46400223 TAAGGCCAATAAAACTTCAGTTAAAATTGATGATAAAGTTATGATTTAAGAATTTTCGTTTTCTC
1 TAAGACCAATAAAACTTCAGTTAAAATTGATGATAAAGTTACGATTTAAGAATTTTCGTTTTCTA
46400288 AGTTCAAATCCCACAATACA
66 AGTTCAAATCCCACAATACA
*
46400308 TAAGACCAATAAAACTTCAGTTAAAATTGATGATAAAGTTACGATTTAAGAATTTTCGTTTTTTA
1 TAAGACCAATAAAACTTCAGTTAAAATTGATGATAAAGTTACGATTTAAGAATTTTCGTTTTCTA
*
46400373 AGTTCAAATCCCACAATCCA
66 AGTTCAAATCCCACAATACA
46400393 TAA
1 TAA
46400396 ATACCTTGTA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (85 bp):
TAAGACCAATAAAACTTCAGTTAAAATTGATGATAAAGTTACGATTTAAGAATTTTCGTTTTCTA
AGTTCAAATCCCACAATACA
Found at i:46403445 original size:2 final size:2
Alignment explanation
Indices: 46403440--46403481 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
46403430 TTTTGTGTGC
46403440 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
46403482 TCATGAAATG
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:46408360 original size:5 final size:5
Alignment explanation
Indices: 46408350--46408384 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
46408340 TTTAAAAATA
46408350 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
46408385 TTTAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:46408412 original size:10 final size:10
Alignment explanation
Indices: 46408350--46408409 Score: 63
Period size: 10 Copynumber: 6.3 Consensus size: 10
46408340 TTTAAAAATA
*
46408350 ATTATATTAT
1 ATTATTTTAT
*
46408360 ATTATATTAT
1 ATTATTTTAT
*
46408370 ATTATATTAT
1 ATTATTTTAT
46408380 ATTATTTTA-
1 ATTATTTTAT
*
46408389 A-TATTTAAT
1 ATTATTTTAT
46408398 ATT-TTTTAT
1 ATTATTTTAT
46408407 ATT
1 ATT
46408410 TTTATTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
8 6 0.13
9 10 0.22
10 29 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:46408413 original size:18 final size:18
Alignment explanation
Indices: 46408378--46408410 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
46408368 ATATTATATT
46408378 ATATTATTTTAATATTTA
1 ATATTATTTTAATATTTA
46408396 ATATT-TTTT-ATATTT
1 ATATTATTTTAATATTT
46408411 TTATTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTATTTTAATATTTA
Found at i:46418035 original size:18 final size:18
Alignment explanation
Indices: 46418014--46418050 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
46418004 TTATATTTGA
*
46418014 TATTTGATTTATTCGAAT
1 TATTTGAATTATTCGAAT
46418032 TATTTGAATTATTCGAAT
1 TATTTGAATTATTCGAAT
46418050 T
1 T
46418051 CGAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (18 bp):
TATTTGAATTATTCGAAT
Found at i:46421518 original size:14 final size:14
Alignment explanation
Indices: 46421499--46421527 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46421489 CATTTTTCAC
46421499 TATTATATTGTTAT
1 TATTATATTGTTAT
46421513 TATTATATTGTTAT
1 TATTATATTGTTAT
46421527 T
1 T
46421528 GTTTAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (14 bp):
TATTATATTGTTAT
Found at i:46427822 original size:26 final size:26
Alignment explanation
Indices: 46427793--46427850 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
46427783 TTCACTCGAT
46427793 TCGACTCGAA-TTAAATTTCATTTCAC
1 TCGACTC-AACTTAAATTTCATTTCAC
* *
46427819 TCGACTCAACTTGAATTTTATTTCAC
1 TCGACTCAACTTAAATTTCATTTCAC
46427845 TCGACT
1 TCGACT
46427851 TGATTCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.40
Consensus pattern (26 bp):
TCGACTCAACTTAAATTTCATTTCAC
Found at i:46434873 original size:2 final size:2
Alignment explanation
Indices: 46434866--46434902 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46434856 TTATCTTTTC
46434866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46434903 ATGAGGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46436964 original size:18 final size:18
Alignment explanation
Indices: 46436938--46436972 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46436928 AAAGATATAT
* *
46436938 TAATTAATAATATTATTA
1 TAATAAATAATAATATTA
46436956 TAATAAATAATAATATT
1 TAATAAATAATAATATT
46436973 TTATTATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:46436985 original size:21 final size:21
Alignment explanation
Indices: 46436933--46436976 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46436923 TTTCAAAAGA
* *
46436933 TATATTAATTAATAATATTAT
1 TATAATAAATAATAATATTAT
46436954 TATAATAAATAATAATATT-T
1 TATAATAAATAATAATATTAT
46436974 TAT
1 TAT
46436977 TATTCAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATAATAAATAATAATATTAT
Found at i:46458990 original size:153 final size:153
Alignment explanation
Indices: 46458712--46459172 Score: 861
Period size: 153 Copynumber: 3.0 Consensus size: 153
46458702 GAAGCAATAA
46458712 CTGAAAGCTACTTGGAAATATTTGA-CTCACCTTGTCACATGAAGCAGTTCGAGAAAGAGAATTA
1 CTGAAAGCTACTTGGAAATATTTGACCT-ACCTTGTCACATGAAGCAGTTCGAGAAAGAGAATTA
* *
46458776 TCAGGGACCGATTCTTCCGTATCCATTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGTT
65 CCAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGTT
46458841 TACCTTTTCTTTTAAAGCAGAAAG
130 TACCTTTTCTTTTAAAGCAGAAAG
46458865 CTGAAAGCTACTTGGAAATATTTGACCTACCTTGTCACATGAAGCAGTTCGAGAAAGAGAATTAC
1 CTGAAAGCTACTTGGAAATATTTGACCTACCTTGTCACATGAAGCAGTTCGAGAAAGAGAATTAC
* *
46458930 CAGGGACCGATTCTTCTGTATCCTTTGAACTACTTTTAATCTGTCAGATAACCCAAACTAAGTTT
66 CAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGTTT
46458995 ACCTTTTCTTTTAAAGCAGAAAG
131 ACCTTTTCTTTTAAAGCAGAAAG
46459018 CTGAAAGCTACTTGGAAATATTTGACCTACCTTGTCACATGAAGCAGTTCGAGAAAGAGAATTAC
1 CTGAAAGCTACTTGGAAATATTTGACCTACCTTGTCACATGAAGCAGTTCGAGAAAGAGAATTAC
*
46459083 CAGGGACCGATTCTTCCGAATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGTTT
66 CAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGTTT
46459148 ACCTTTTCTTTTAAAGCAGAAAG
131 ACCTTTTCTTTTAAAGCAGAAAG
46459171 CT
1 CT
46459173 ACTAAGAGAA
Statistics
Matches: 300, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
153 298 0.99
154 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (153 bp):
CTGAAAGCTACTTGGAAATATTTGACCTACCTTGTCACATGAAGCAGTTCGAGAAAGAGAATTAC
CAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGTTT
ACCTTTTCTTTTAAAGCAGAAAG
Found at i:46460997 original size:25 final size:25
Alignment explanation
Indices: 46460940--46460997 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
46460930 ATCACATAAC
46460940 AAATTAAAAACAGGGCAGAACAAAA
1 AAATTAAAAACAGGGCAGAACAAAA
*
46460965 AAAATAAAAACAGGGCAGAACAAAA
1 AAATTAAAAACAGGGCAGAACAAAA
*
46460990 AATTTAAA
1 AAATTAAA
46460998 TCTTTACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.66, C:0.10, G:0.14, T:0.10
Consensus pattern (25 bp):
AAATTAAAAACAGGGCAGAACAAAA
Found at i:46464485 original size:1 final size:1
Alignment explanation
Indices: 46464479--46464514 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
46464469 CAACATAATT
46464479 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
46464515 CTATTGTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:46464903 original size:23 final size:23
Alignment explanation
Indices: 46464861--46464907 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
46464851 TTAAATTCTG
*
46464861 TTTATTTGTTTCAATTAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
* *
46464884 TTTATTTGTTTGAGTCAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
46464907 T
1 T
46464908 GTTAGTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (23 bp):
TTTATTTGTTTCAATCAAACTCT
Found at i:46466143 original size:45 final size:46
Alignment explanation
Indices: 46466060--46466154 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 46
46466050 CTAAAAGGAG
46466060 CCCCACAAAGAGGTTAAGATAAGAGTAAAAGGGGCCTATTTTAGAGC
1 CCCCACAAAGAGGTTAAGA-AAGAGTAAAAGGGGCCTATTTTAGAGC
46466107 CCCCACAAAGAGGTTAAG-AAGAGTAAAAGGGGCCTATTTTAGAGC
1 CCCCACAAAGAGGTTAAGAAAGAGTAAAAGGGGCCTATTTTAGAGC
46466152 CCC
1 CCC
46466155 AAAGCACCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 30 0.62
47 18 0.38
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (46 bp):
CCCCACAAAGAGGTTAAGAAAGAGTAAAAGGGGCCTATTTTAGAGC
Found at i:46469929 original size:21 final size:23
Alignment explanation
Indices: 46469885--46469928 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
46469875 GAATAATCTA
46469885 AAAAAAAAACAAATGGATTTTTT
1 AAAAAAAAACAAATGGATTTTTT
*
46469908 AAAAAAAAA-AATTGGATTTTT
1 AAAAAAAAACAAATGGATTTTT
46469929 ATGTTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (23 bp):
AAAAAAAAACAAATGGATTTTTT
Found at i:46479222 original size:24 final size:24
Alignment explanation
Indices: 46479195--46479240 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
46479185 AGTGCATCGG
*
46479195 ATGAAGAAGAGGAAGATGAAGATT
1 ATGAAGAAGAGGAAGAAGAAGATT
* **
46479219 ATGAGGTGGAGGAAGAAGAAGA
1 ATGAAGAAGAGGAAGAAGAAGA
46479241 AGATGACGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.39, T:0.13
Consensus pattern (24 bp):
ATGAAGAAGAGGAAGAAGAAGATT
Found at i:46479252 original size:39 final size:39
Alignment explanation
Indices: 46479197--46479298 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
46479187 TGCATCGGAT
* * * * *
46479197 GAAGAAGAGGAAGATGAAGATTATGAGGTGGAGGAAGAA
1 GAAGAAGATGACGATGAAGATGAAGAGGAGGAGGAAGAA
* * *
46479236 GAAGAAGATGACGATGATGATGAAGAGGAGGAGGAGGAG
1 GAAGAAGATGACGATGAAGATGAAGAGGAGGAGGAAGAA
* * *
46479275 GAGGAAGATGACGACGATGATGAA
1 GAAGAAGATGACGATGAAGATGAA
46479299 TTCACTCTAG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.43, C:0.03, G:0.42, T:0.12
Consensus pattern (39 bp):
GAAGAAGATGACGATGAAGATGAAGAGGAGGAGGAAGAA
Found at i:46479264 original size:33 final size:33
Alignment explanation
Indices: 46479197--46479264 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
46479187 TGCATCGGAT
* * **
46479197 GAAGAAGAGGAAGATGAAGATTATGAGGTGGAG
1 GAAGAAGAAGAAGATGAAGATGATGAGGAAGAG
* *
46479230 GAAGAAGAAGAAGATGACGATGATGATGAAGAG
1 GAAGAAGAAGAAGATGAAGATGATGAGGAAGAG
46479263 GA
1 GA
46479265 GGAGGAGGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.01, G:0.40, T:0.13
Consensus pattern (33 bp):
GAAGAAGAAGAAGATGAAGATGATGAGGAAGAG
Found at i:46482029 original size:46 final size:47
Alignment explanation
Indices: 46481958--46482048 Score: 114
Period size: 46 Copynumber: 1.9 Consensus size: 47
46481948 AAGGCGTCTG
* * *
46481958 AAGGTATAAAACTTTGATGGGCTATTTTCGT-TCACTGATTGCAATGGA
1 AAGGTAT-AAACTTCGATGGACTATTTTCGTAT-ACTAATTGCAATGGA
*
46482006 AAGGTAT-AACTTCGATGGACTATTTTGGTATACTAATTGCAAT
1 AAGGTATAAACTTCGATGGACTATTTTCGTATACTAATTGCAAT
46482049 TGTTATTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 30 0.79
47 1 0.03
48 7 0.18
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (47 bp):
AAGGTATAAACTTCGATGGACTATTTTCGTATACTAATTGCAATGGA
Found at i:46496581 original size:41 final size:41
Alignment explanation
Indices: 46496533--46496854 Score: 324
Period size: 41 Copynumber: 7.9 Consensus size: 41
46496523 TAAAAAGTTA
* * * *
46496533 AGCAATAGTGGCGCTTAAAGAAAAACGCCGCTAAAGATCAG
1 AGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAG
* **
46496574 AGCAATAGCGGTGCTTATAGGCAAGCGCCGCTAAAGGTCAG
1 AGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAG
* * * **
46496615 AGCAATAGCGGTGCTTATGGTAAAGCGGTGCTAAAGGTCAG
1 AGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAG
* *
46496656 AGCAATAGCGGCGCTTATGGTAAAGCGCCGCTAAAGGTCAG
1 AGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAG
* * * * *
46496697 AGAAATAGCGGAGCTTATAGGAAAGCGCCGTTAAAGGTTAG
1 AGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAG
* * **
46496738 AGCAATAGCGGCGCTTAT-GAAAAAGTGCCGTTAAATATCAG
1 AGCAATAGCGGCGCTTATAG-AAAAGCGCCGCTAAAGGTCAG
* * *
46496779 AGTAATAGCGACGCTTAT-GAGAAAGCGCCGCTAAAAGTCAG
1 AGCAATAGCGGCGCTTATAGA-AAAGCGCCGCTAAAGGTCAG
* * * * * *
46496820 AGAAATAGCAGCGCTTTTAAAAAAGCACCGTTAAA
1 AGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAA
46496855 AGTTGAGTTT
Statistics
Matches: 237, Mismatches: 41, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
40 2 0.01
41 234 0.99
42 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (41 bp):
AGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAG
Found at i:46496754 original size:123 final size:122
Alignment explanation
Indices: 46496533--46496828 Score: 367
Period size: 123 Copynumber: 2.4 Consensus size: 122
46496523 TAAAAAGTTA
* * * * * * * *
46496533 AGCAATAGTGGCGCTTAAAGAAAAACGCCGCTAAAGATCAGAGCAATAGCGGTGCTTATAGGCAA
1 AGCAATAGCGGCGCTT-ATGGAAAGCGCCGCTAAAGGTCAGAGAAATAGCGGAGCTTATAGGAAA
* ** ** *
46496598 GCGCCGCTAAAGGTCAGAGCAATAGCGGTGCTTATGGTAAAGCGGTGCTAAAGGTCAG
65 GCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAAAAAGCGCCGCTAAAGATCAG
46496656 AGCAATAGCGGCGCTTATGGTAAAGCGCCGCTAAAGGTCAGAGAAATAGCGGAGCTTATAGGAAA
1 AGCAATAGCGGCGCTTATGG-AAAGCGCCGCTAAAGGTCAGAGAAATAGCGGAGCTTATAGGAAA
* * * * *
46496721 GCGCCGTTAAAGGTTAGAGCAATAGCGGCGCTTATGAAAAAGTGCCGTTAAATATCAG
65 GCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAAAAAGCGCCGCTAAAGATCAG
* * *
46496779 AGTAATAGCGACGCTTATGAGAAAGCGCCGCTAAAAGTCAGAGAAATAGC
1 AGCAATAGCGGCGCTTATG-GAAAGCGCCGCTAAAGGTCAGAGAAATAGC
46496829 AGCGCTTTTA
Statistics
Matches: 149, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
122 2 0.01
123 146 0.98
124 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (122 bp):
AGCAATAGCGGCGCTTATGGAAAGCGCCGCTAAAGGTCAGAGAAATAGCGGAGCTTATAGGAAAG
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAAAAAGCGCCGCTAAAGATCAG
Found at i:46500858 original size:43 final size:43
Alignment explanation
Indices: 46500802--46501075 Score: 284
Period size: 43 Copynumber: 6.3 Consensus size: 43
46500792 TTTATTAATG
* * *
46500802 TTAGCGGCATTTGTGGGAAAAGTGCCGCTAAAGACTATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
*** *
46500845 TTAGCGGCGTTTGTATAAAAAGCGCCG-TAAAAAACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCT-AAAGACCATGTTCT
** *
46500888 TTAGCGGCGTTTGTATGAAAAGCGCAGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
46500931 TTAGCGGCGTTTATGGGGAAAAGCGCCGCTAAGCTAAAGACCATATTCT
1 TTAGCGGCGTTTGT-GGGAAAAGCG-C-C---GCTAAAGACCATGTTCT
* *
46500980 TTAGCGGCGTTTTTGGG-AAAGTGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * * *
46501022 TTAACGGTGTTTTTGGG-AAAGCGCCGTTAATGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
*
46501064 ATAGCGGCGTTT
1 TTAGCGGCGTTT
46501076 TTTCTAATAA
Statistics
Matches: 197, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
42 63 0.32
43 85 0.43
44 9 0.05
45 2 0.01
46 1 0.01
47 5 0.03
48 3 0.02
49 29 0.15
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:46500980 original size:49 final size:47
Alignment explanation
Indices: 46500913--46501047 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 47
46500903 TGAAAAGCGC
*
46500913 AGCTAAAGACCATGTTCTTTAGCGGCGTTTATGGGGAAAAGCGCCGCTA
1 AGCTAAAGACCATATTCTTTAGCGGCGTTT-TGGGG-AAAGCGCCGCTA
* *
46500962 AGCTAAAGACCATATTCTTTAGCGGCGTTTTTGGGAAAGTG-C-C--
1 AGCTAAAGACCATATTCTTTAGCGGCGTTTTGGGGAAAGCGCCGCTA
* * * *
46501005 -GCTAAAGACCATGTTCTTTAACGGTGTTTTTGGGAAAGCGCCG
1 AGCTAAAGACCATATTCTTTAGCGGCGTTTTGGGGAAAGCGCCG
46501048 TTAATGACCA
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
42 36 0.47
43 1 0.01
45 1 0.01
46 1 0.01
47 5 0.06
48 4 0.05
49 29 0.38
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (47 bp):
AGCTAAAGACCATATTCTTTAGCGGCGTTTTGGGGAAAGCGCCGCTA
Found at i:46507593 original size:24 final size:24
Alignment explanation
Indices: 46507532--46507594 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
46507522 TAGAGTAATA
* * *
46507532 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
46507556 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
46507580 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
46507595 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:46513369 original size:17 final size:18
Alignment explanation
Indices: 46513347--46513388 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
46513337 CCCAATAAGA
*
46513347 TAAATTTGGTTTTAAA-T
1 TAAATTTGATTTTAAATT
46513364 TAAATTT-ATTTTAAATT
1 TAAATTTGATTTTAAATT
46513381 TAAATTTG
1 TAAATTTG
46513389 CACAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TAAATTTGATTTTAAATT
Found at i:46513422 original size:17 final size:17
Alignment explanation
Indices: 46513359--46513422 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
46513349 AATTTGGTTT
*
46513359 TAAA-TTAAATTTATTT
1 TAAATTTAAATTTATTA
*
46513375 TAAATTTAAATTTGCA-CA
1 TAAATTTAAATTT--ATTA
*
46513393 -AAATTTAAGTTTATTA
1 TAAATTTAAATTTATTA
*
46513409 TAAATATAAATTTA
1 TAAATTTAAATTTA
46513423 AAATTAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 30 0.81
19 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTATTA
Found at i:46514253 original size:20 final size:21
Alignment explanation
Indices: 46514238--46514289 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
46514228 ATTAATATTT
* *
46514238 AATAATAATAACTAAT-AACA
1 AATATTAATAACTAATAAAAA
*
46514258 AATATTAATAA-TAATAAATA
1 AATATTAATAACTAATAAAAA
46514278 AATATTTAATAA
1 AATA-TTAATAA
46514290 AAAAAGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 17 0.61
21 7 0.25
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATTAATAACTAATAAAAA
Found at i:46515365 original size:29 final size:28
Alignment explanation
Indices: 46515322--46515408 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 28
46515312 GTAGGTCTCT
* *
46515322 AAACTGTCCAAAAATTACATTTTGACCTCG
1 AAACT-TCCAAAAATTACATTTTAACC-CC
46515352 AAACTTCCAAAAATTACTATTTTAACCCC
1 AAACTTCCAAAAATTAC-ATTTTAACCCC
*
46515381 AAACTTTCC-AAAATTCCATTTTTAACCC
1 AAAC-TTCCAAAAATTACA-TTTTAACCC
46515409 GATTTCACCA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.02
29 33 0.65
30 17 0.33
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTACATTTTAACCCC
Found at i:46515420 original size:58 final size:59
Alignment explanation
Indices: 46515358--46515643 Score: 314
Period size: 59 Copynumber: 4.8 Consensus size: 59
46515348 CTCGAAACTT
*
46515358 CCAAAAATTACTATTTTAACCC-CAAACTTTCCAAAATTCCATTTTTAACC-CGATTTCA
1 CCAAAAATTACTATTTT-ACCCTCAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
* *
46515416 CCAAAAATTACCATTTAACCCTTTAACCCCCAAACTTTCCAAAATCCCATTTTTAACCTCGATTT
1 CCAAAAATTA-C---T-A---TTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCTCGATTT
46515481 CA
58 CA
* * * *
46515483 CCAAAAATTGCCATTTTACCCTTAAACTTTCTAAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACTATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
* * *
46515542 CCAAAAATTACCATTTTACCCTCAAA-ATTCTAAAATCCCA-TTTTAACC-CTGATTTCA
1 CCAAAAATTACTATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCTC-GATTTCA
** *
46515599 CCAAAAATTA-TCATTTTACCCTTGAACTTTCCAAAATCCTATTTT
1 CCAAAAATTACT-ATTTTACCCTCAAACTTTCCAAAATCCCATTTT
46515644 ACCCCTAAAC
Statistics
Matches: 197, Mismatches: 17, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
56 1 0.01
57 37 0.19
58 34 0.17
59 70 0.36
62 2 0.01
63 1 0.01
65 4 0.02
66 31 0.16
67 17 0.09
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACTATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCA
Found at i:46515547 original size:29 final size:29
Alignment explanation
Indices: 46515454--46515547 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
46515444 CCCAAACTTT
46515454 CCAAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAATCCCATTTTTAACCTCGATTTCA
* * **
46515483 CCAAAAATTGCCA-TTTTACCCTTAAACTTT--
1 CC-AAAA-TCCCATTTTTAACC-TCGA-TTTCA
*
46515513 CTAAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAATCCCATTTTTAACCTCGATTTCA
46515542 CCAAAA
1 CCAAAA
46515548 ATTACCATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
27 3 0.06
28 6 0.12
29 18 0.38
30 12 0.25
31 6 0.12
32 3 0.06
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
CCAAAATCCCATTTTTAACCTCGATTTCA
Found at i:46515670 original size:28 final size:28
Alignment explanation
Indices: 46515602--46515737 Score: 105
Period size: 28 Copynumber: 4.6 Consensus size: 28
46515592 GATTTCACCA
* *
46515602 AAAATTATCATTTTACCCTTGAACTTTCC
1 AAAATT-TCATTTTACCCCTAAACTTTCC
*
46515631 AAAA-TCCTATTTTACCCCTAAACTTTCC
1 AAAATTTC-ATTTTACCCCTAAACTTTCC
* **
46515659 AAAATTTCATTTTAACCCTAATA-TCACC
1 AAAATTTCATTTTACCCCTAA-ACTTTCC
* *
46515687 AAAAATTATCATTTTACCCCAAAAACTTTCT
1 -AAAATT-TCATTTTACCCC-TAAACTTTCC
*
46515718 AAAATTCCATTCTTAACCCC
1 AAAATTTCATT-TT-ACCCC
46515738 GAATTTTCTC
Statistics
Matches: 85, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.01
28 38 0.45
29 17 0.20
30 20 0.24
31 9 0.11
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAATTTCATTTTACCCCTAAACTTTCC
Found at i:46533055 original size:13 final size:13
Alignment explanation
Indices: 46533037--46533062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46533027 AGTAAACGCA
46533037 GTAGCAGAGATTT
1 GTAGCAGAGATTT
46533050 GTAGCAGAGATTT
1 GTAGCAGAGATTT
46533063 CCCCTCCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
GTAGCAGAGATTT
Found at i:46533831 original size:19 final size:18
Alignment explanation
Indices: 46533809--46533852 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
46533799 TATTAAATAT
*
46533809 ATATTTAGAATTTTTATAA
1 ATATTTA-AATTTTTAAAA
*
46533828 ATATTTATATTTTTAAAA
1 ATATTTAAATTTTTAAAA
46533846 ATTATTT
1 A-TATTT
46533853 TTAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATATTTAAATTTTTAAAA
Found at i:46533860 original size:19 final size:18
Alignment explanation
Indices: 46533809--46533860 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
46533799 TATTAAATAT
* *
46533809 ATATTTAGAATTTTTATAA
1 ATATTTATAA-TTTTAAAA
*
46533828 ATATTTATATTTTTAAAA
1 ATATTTATAATTTTAAAA
*
46533846 ATTATTTTTAATTTT
1 A-TATTTATAATTTT
46533861 TTGTTGAGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATATTTATAATTTTAAAA
Found at i:46536026 original size:4 final size:4
Alignment explanation
Indices: 46536017--46536089 Score: 137
Period size: 4 Copynumber: 18.2 Consensus size: 4
46536007 CGTGGTCATG
*
46536017 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
46536065 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
46536090 ACACACTCAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TGTA
Done.