Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_698
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: 50469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6224 original size:27 final size:27
Alignment explanation
Indices: 6186--6262 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
6176 TAGTATTGGC
6186 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
6213 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
6240 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
6263 GCCGGGCCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:6497 original size:11 final size:11
Alignment explanation
Indices: 6483--6528 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
6473 TTTATTATTT
*
6483 ATTAGTAATAA
1 ATTACTAATAA
*
6494 ATTACTAA-AT
1 ATTACTAATAA
6504 ATTACTAATAA
1 ATTACTAATAA
*
6515 GTTACTAATAA
1 ATTACTAATAA
6526 ATT
1 ATT
6529 TATAACATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (11 bp):
ATTACTAATAA
Found at i:6506 original size:21 final size:21
Alignment explanation
Indices: 6482--6522 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6472 ATTTATTATT
*
6482 TATTAGTAATAAATTACTAAA
1 TATTACTAATAAATTACTAAA
*
6503 TATTACTAATAAGTTACTAA
1 TATTACTAATAAATTACTAA
6523 TAAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (21 bp):
TATTACTAATAAATTACTAAA
Found at i:6631 original size:48 final size:48
Alignment explanation
Indices: 6565--6736 Score: 240
Period size: 48 Copynumber: 3.5 Consensus size: 48
6555 AATTAATTAT
*
6565 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATT-ATAC
1 AAAA-AATTACAATATTCATAC--AAAATTATAATATTACAATATTCATAC
** *
6615 -CGACATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
*
6662 AAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
*
6710 AAAAAAATTACAATATTCATACTAAAT
1 -AAAAAATTACAATATTCATACAAAAT
6737 ATAGATAATT
Statistics
Matches: 109, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
46 21 0.19
47 4 0.04
48 59 0.54
49 25 0.23
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (48 bp):
AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
Found at i:6641 original size:19 final size:19
Alignment explanation
Indices: 6594--6696 Score: 64
Period size: 19 Copynumber: 5.9 Consensus size: 19
6584 TACAAAAAAT
*
6594 TACAATATTACAATATT-A
1 TACAAAATTACAATATTCA
* *
6612 TACCGACATTACAATATTCA
1 TA-CAAAATTACAATATTCA
*
6632 TACAAAATTATAATA-T--
1 TACAAAATTACAATATTCA
*
6648 TACAATATT-C-ATA--CA
1 TACAAAATTACAATATTCA
*
6663 -A-AAAATTGCAATATTCA
1 TACAAAATTACAATATTCA
*
6680 TACAAAATTATAATATT
1 TACAAAATTACAATATT
6697 ACAATATTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
13 5 0.08
14 5 0.08
15 3 0.05
16 8 0.12
17 2 0.03
18 4 0.06
19 35 0.54
20 3 0.05
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.35
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:6649 original size:27 final size:23
Alignment explanation
Indices: 6619--6737 Score: 127
Period size: 27 Copynumber: 4.9 Consensus size: 23
6609 TTATACCGAC
6619 ATTACAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC-AAA-TA-AA
6645 TATTACAATATTCATAC-AA-AAA
1 -ATTACAATATTCATACAAATAAA
*
6667 ATTGCAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC-AAA-TA-AA
6693 TATTACAATATTCATACAAA-AAA
1 -ATTACAATATTCATACAAATAAA
6716 ATTACAATATTCATACTAAATA
1 ATTACAATATTCATAC-AAATA
6738 TAGATAATTT
Statistics
Matches: 82, Mismatches: 2, Indels: 19
0.80 0.02 0.18
Matches are distributed among these distances:
21 15 0.18
22 18 0.22
23 8 0.10
24 2 0.02
25 3 0.04
26 5 0.06
27 31 0.38
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.34
Consensus pattern (23 bp):
ATTACAATATTCATACAAATAAA
Found at i:6650 original size:75 final size:69
Alignment explanation
Indices: 6565--6731 Score: 203
Period size: 75 Copynumber: 2.3 Consensus size: 69
6555 AATTAATTAT
* *
6565 AAAATAATTACAATATTCATACAAAAAATTACAATA-T-TACAATATTATACCGACATTACAATA
1 AAAAAAATTACAATATTCATACAAAAAATTACAATATTATACAAAATTATA---ACATTACAATA
6628 TTCATAC
63 TTCATAC
* *
6635 AAAATTATAATATTACAATATTCATACAAAAAATTGCAATATTCATACAAAATTATAATATTACA
1 -AAA--A-AA-ATTACAATATTCATACAAAAAATTACAATATT-ATACAAAATTATAACATTACA
6700 ATATTCATAC
60 ATATTCATAC
6710 AAAAAAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATAC
6732 TAAATATAGA
Statistics
Matches: 85, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
70 16 0.19
71 5 0.06
72 1 0.01
73 1 0.01
74 4 0.05
75 46 0.54
76 1 0.01
78 11 0.13
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (69 bp):
AAAAAAATTACAATATTCATACAAAAAATTACAATATTATACAAAATTATAACATTACAATATTC
ATAC
Found at i:6811 original size:27 final size:28
Alignment explanation
Indices: 6779--6851 Score: 114
Period size: 27 Copynumber: 2.6 Consensus size: 28
6769 AAAATATTGC
*
6779 AATTTTATATGAATATTGTAAT-TT-TGT
1 AATTTTGTATGAATATTGTAATATTAT-T
6806 AATTTTGTATGAATATTGTAATATTATT
1 AATTTTGTATGAATATTGTAATATTATT
6834 AATTTTGTATGAATATTG
1 AATTTTGTATGAATATTG
6852 AATGTCGGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
27 21 0.49
28 21 0.49
29 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (28 bp):
AATTTTGTATGAATATTGTAATATTATT
Found at i:7190 original size:22 final size:20
Alignment explanation
Indices: 7162--7206 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
7152 TATATTTTTA
7162 TTTTTTATTTTTAAAATACTTT
1 TTTTTTATTTTTAAAA-A-TTT
7184 TTTTTTATTTTTAAAAATTT
1 TTTTTTATTTTTAAAAATTT
7204 TTT
1 TTT
7207 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.26
21 1 0.04
22 16 0.70
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTATTTTTAAAAATTT
Found at i:8127 original size:22 final size:23
Alignment explanation
Indices: 8085--8130 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
8075 GCGGGTTAAA
8085 ATGGAAAAGAAATAAAATTTCAT
1 ATGGAAAAGAAATAAAATTTCAT
8108 ATGGAAAAGAAAT-AAATTTCAT
1 ATGGAAAAGAAATAAAATTTCAT
8130 A
1 A
8131 GGCAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (23 bp):
ATGGAAAAGAAATAAAATTTCAT
Found at i:9383 original size:14 final size:14
Alignment explanation
Indices: 9364--9390 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9354 TACTTACATC
9364 AAAGTGTACATAAT
1 AAAGTGTACATAAT
9378 AAAGTGTACATAA
1 AAAGTGTACATAA
9391 AAGATCGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (14 bp):
AAAGTGTACATAAT
Found at i:17124 original size:14 final size:14
Alignment explanation
Indices: 17105--17131 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17095 AAGCGATCTT
17105 TTATGTACACTTTA
1 TTATGTACACTTTA
17119 TTATGTACACTTT
1 TTATGTACACTTT
17132 GATGTAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (14 bp):
TTATGTACACTTTA
Found at i:18391 original size:23 final size:23
Alignment explanation
Indices: 18365--18411 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
18355 TTAATTTGCC
18365 TATGAAATTTTATTTCTTTTCCA
1 TATGAAATTTTATTTCTTTTCCA
18388 TATGAAATTTTATTTCTTTTCCA
1 TATGAAATTTTATTTCTTTTCCA
18411 T
1 T
18412 TTTAACCCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (23 bp):
TATGAAATTTTATTTCTTTTCCA
Found at i:19027 original size:23 final size:22
Alignment explanation
Indices: 19001--19043 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
18991 AATAATTTTT
19001 TTTTTGAATAAATATTTTTTATA
1 TTTTTGAAT-AATATTTTTTATA
* *
19024 TTTTTTAATAATTTTTTTTA
1 TTTTTGAATAATATTTTTTA
19044 AAAAATACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTGAATAATATTTTTTATA
Found at i:19309 original size:22 final size:22
Alignment explanation
Indices: 19284--19341 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
19274 AATAAACACC
19284 AAAAAAT-TTTTAAAAATAAAA
1 AAAAAATATTTTAAAAATAAAA
*
19305 AAAAAGTATTTTAAAAATAAAA
1 AAAAAATATTTTAAAAATAAAA
19327 ATAAAAATATATTTA
1 A-AAAAATAT-TTTA
19342 TTGTATTCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 6 0.19
22 15 0.47
23 7 0.22
24 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAATATTTTAAAAATAAAA
Found at i:19621 original size:8 final size:8
Alignment explanation
Indices: 19608--19696 Score: 54
Period size: 8 Copynumber: 10.4 Consensus size: 8
19598 CATACAAAAA
19608 ATTACAAT
1 ATTACAAT
19616 ATTACAAT
1 ATTACAAT
* *
19624 ATATACCGAC
1 AT-TA-CAAT
19634 ATT-CAAT
1 ATTACAAT
*
19641 ATCATACAAA
1 AT--TACAAT
*
19651 ATTATAAT
1 ATTACAAT
19659 ATTACAAT
1 ATTACAAT
*
19667 ATTCATACAAA
1 A-T--TACAAT
*
19678 ATTACAAA
1 ATTACAAT
19686 ATTACAAT
1 ATTACAAT
19694 ATT
1 ATT
19697 CATATAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
7 4 0.06
8 38 0.60
9 5 0.08
10 10 0.16
11 6 0.10
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.34
Consensus pattern (8 bp):
ATTACAAT
Found at i:19672 original size:27 final size:27
Alignment explanation
Indices: 19637--19707 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
19627 TACCGACATT
* *
19637 CAATA-TCATACAAAATTATAATATTA
1 CAATATTCATACAAAATTACAAAATTA
19663 CAATATTCATACAAAATTACAAAATTA
1 CAATATTCATACAAAATTACAAAATTA
*
19690 CAATATTCATATAAAATT
1 CAATATTCATACAAAATT
19708 GCAATATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 5 0.12
27 36 0.88
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.34
Consensus pattern (27 bp):
CAATATTCATACAAAATTACAAAATTA
Found at i:19779 original size:22 final size:24
Alignment explanation
Indices: 19746--19917 Score: 148
Period size: 27 Copynumber: 7.1 Consensus size: 24
19736 ATAAATTATC
*
19746 TATATTTAGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
19770 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
*
19794 TATAATTTTGTATGAATATTGCAAT
1 TAT-ATTTTGTATGAATATTGTAAT
19819 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
19843 TATAATTTTGTATGAATATTGTAATGT
1 TAT-ATTTTGTATGAATATTGTAA--T
*
19870 CGGTATATATTG--T-AATATTGTAA-
1 ---TATATTTTGTATGAATATTGTAAT
19893 T-T-TTTTGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
19915 TAT
1 TAT
19918 TTTATAATTA
Statistics
Matches: 123, Mismatches: 5, Indels: 41
0.73 0.03 0.24
Matches are distributed among these distances:
18 4 0.03
19 1 0.01
20 2 0.02
21 10 0.08
22 33 0.27
23 4 0.03
24 8 0.07
25 6 0.05
26 12 0.10
27 35 0.28
29 5 0.04
30 3 0.02
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (24 bp):
TATATTTTGTATGAATATTGTAAT
Found at i:19807 original size:49 final size:49
Alignment explanation
Indices: 19749--19920 Score: 235
Period size: 49 Copynumber: 3.6 Consensus size: 49
19739 AATTATCTAT
*
19749 ATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
19798 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
* ** *
19847 ATTTTGTATGAATATTGTAA--TGTCGGTAT--ATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
19892 ATTTTTTGTATGAATATTGTAATTATTTT
1 A--TTTTGTATGAATATTGTAATTTTTTT
19921 ATAATTAATT
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
45 16 0.15
47 25 0.23
49 67 0.62
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
Found at i:19985 original size:19 final size:19
Alignment explanation
Indices: 19963--20000 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19953 TATAAATTTA
*
19963 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
19982 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
20001 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:20257 original size:27 final size:28
Alignment explanation
Indices: 20219--20295 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
20209 CCGGCCCGGC
*
20219 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
20246 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
20273 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
20296 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:27090 original size:4 final size:4
Alignment explanation
Indices: 27081--27186 Score: 79
Period size: 4 Copynumber: 24.5 Consensus size: 4
27071 ATACAACAAC
* * ** *
27081 AAAT AAAT AAAT AAAT AAACT AAA- ACAT AAAA AAAT GGAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT
27129 AAAT AAAT AAAT AAAT GAACAT AAAGT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAT AAAT AAAT AAAT -AA-AT AAA-T -AAAT -AAAT -AAAT -AAAT -AAAT
27181 AAAT AA
1 AAAT AA
27187 TAATAACAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
3 2 0.02
4 50 0.57
5 30 0.34
6 5 0.06
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:27160 original size:44 final size:42
Alignment explanation
Indices: 27081--27186 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 42
27071 ATACAACAAC
* *
27081 AAATAAATAAATAAATAAACTAAAACATAAAAAAATGGATATA
1 AAATAAATAAATAAATAAACTAAAACATAAAAAAAT-AAAATA
*
27124 TAAATAAATAAATAAATAAA-T-GAACATAAAGTAAAATAAAATA
1 -AAATAAATAAATAAATAAACTAAAACATAAA--AAAATAAAATA
27167 AAATAAAATAAAATAAATAA
1 AAAT-AAAT-AAATAAATAA
27187 TAATAACAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
42 12 0.22
43 9 0.16
44 34 0.62
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.22
Consensus pattern (42 bp):
AAATAAATAAATAAATAAACTAAAACATAAAAAAATAAAATA
Found at i:27163 original size:5 final size:5
Alignment explanation
Indices: 27125--27199 Score: 70
Period size: 5 Copynumber: 15.4 Consensus size: 5
27115 ATGGATATAT
* *
27125 AAAT- AAAT- AAAT- AAAT- AAATGA ACATA AAGTA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAAT-A AAATA AAATA AAATA AAATA AAATA
27172 AAATA AAAT- AAATA ATAATA ACAATA AA
1 AAATA AAATA AAATA A-AATA A-AATA AA
27200 GGAAAATAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
4 20 0.32
5 29 0.47
6 13 0.21
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:27167 original size:15 final size:14
Alignment explanation
Indices: 27123--27199 Score: 79
Period size: 15 Copynumber: 5.4 Consensus size: 14
27113 AAATGGATAT
27123 ATAAAT-AAAT-AA
1 ATAAATAAAATAAA
*
27135 ATAAAT-AAATGAAC
1 ATAAATAAAAT-AAA
27149 ATAAAGTAAAATAAA
1 ATAAA-TAAAATAAA
27164 ATAAAATAAAATAAA
1 AT-AAATAAAATAAA
27179 ATAAATAATAATAACA
1 ATAAATAA-AATAA-A
27195 ATAAA
1 ATAAA
27200 GGAAAATAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
12 10 0.18
14 12 0.21
15 21 0.38
16 13 0.23
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (14 bp):
ATAAATAAAATAAA
Found at i:30068 original size:25 final size:25
Alignment explanation
Indices: 30036--30085 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
30026 CTTGGGGCGT
* *
30036 AAGATTCACTGTTGTAGCTTTAATC
1 AAGATTCACCGATGTAGCTTTAATC
*
30061 AAGATTCACCGATGTGGCTTTAATC
1 AAGATTCACCGATGTAGCTTTAATC
30086 TTTTCAACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (25 bp):
AAGATTCACCGATGTAGCTTTAATC
Found at i:30646 original size:50 final size:49
Alignment explanation
Indices: 30592--30887 Score: 382
Period size: 50 Copynumber: 5.9 Consensus size: 49
30582 AATCTTTTTA
*
30592 ACTGCAATG-TCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGCT-AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TTCC
* * **
30642 ACTGCAACGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTA
1 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TCC
* * *
30692 ATTGCAATG-TCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCC
1 ACTGCAATGCT-AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TTCC
**
30742 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTA
1 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TCC
* * *
30792 ATTGCAATG-TCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCC
1 ACTGCAATGCT-AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TTCC
30842 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
30888 CTTAATTGCA
Statistics
Matches: 212, Mismatches: 25, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
49 5 0.02
50 202 0.95
51 5 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (49 bp):
ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTCC
Found at i:30680 original size:125 final size:125
Alignment explanation
Indices: 29073--30602 Score: 2799
Period size: 125 Copynumber: 12.2 Consensus size: 125
29063 GATTCGTCAT
*
29073 TGTGGCTTTAATCTTTTTAACTGCAATGTCAGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
29138 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
29198 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTCAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
* * * *
29263 TTTCACTGCATTGCTTGGGGCGTAAGATTCGTTGTTGTAGTTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
29323 TGTGACTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
*
29388 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCATCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
29448 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTCAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
* * * *
29513 TTTCACTGCATTGCTTGGGGCGTAAGATTCGTTGTTGTAGTTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
29573 TGTGACTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
* *
29638 TTTCACTGCACCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
29698 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
29763 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
29823 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
*
29888 TTCCACTGCACCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
29948 TGTGGCTTTAATCTTTTTAACTGCAATGTCAGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
*
30013 TTCCACTGCATCGCTTGGGGCGTAAGATTCACTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
30073 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
30138 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
* *
30198 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATCTGGCTTTAATCTG
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
*
30263 TTCCACTGCATTGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
30323 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
* *
30388 TTCCACTGCATCGCTTAGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCAA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
30448 TGTGGCTTTAATCTTTTTAACTACAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
1 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
* *
30513 TTCCACTGCACCGCTTGGGGCGTAAGATTCGCTTTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
30573 TGTGGCTTTAATCTTTTTAACTGCAATGTC
1 TGTGGCTTTAATCTTTTTAACTGCAATGTC
30603 AGGGAAGTAA
Statistics
Matches: 1352, Mismatches: 53, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 1352 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (125 bp):
TGTGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTA
TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
Found at i:30920 original size:100 final size:100
Alignment explanation
Indices: 30577--30899 Score: 583
Period size: 100 Copynumber: 3.2 Consensus size: 100
30567 CACCGATGTG
* * * * *
30577 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCC
* *
30642 ACTGCAACGCTAAGAAAGTAAGATCCGCTGTTGTA
66 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTA
30677 GCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCC
1 GCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCC
30742 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTA
66 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTA
30777 GCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCC
1 GCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCC
30842 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTA
66 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTA
30877 GCTTCAATCTTCTTAATTGCAAT
1 GCTTCAATCTTCTTAATTGCAAT
30900 CTATGGTTTC
Statistics
Matches: 216, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 216 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (100 bp):
GCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTATTCC
ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTA
Found at i:33369 original size:13 final size:13
Alignment explanation
Indices: 33360--33390 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
33350 TGATTTTTTA
33360 TTTTTGTTTTTGT
1 TTTTTGTTTTTGT
33373 TTTTTGTTTTTGT
1 TTTTTGTTTTTGT
33386 TTTTT
1 TTTTT
33391 TTGAGTCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (13 bp):
TTTTTGTTTTTGT
Found at i:33390 original size:7 final size:6
Alignment explanation
Indices: 33354--33389 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
33344 TGACTTTGAT
*
33354 TTTTTA TTTTTG TTTTTG TTTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTT
33390 TTTGAGTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:33990 original size:273 final size:274
Alignment explanation
Indices: 33502--34049 Score: 866
Period size: 273 Copynumber: 2.0 Consensus size: 274
33492 TGTATGTGAG
* * **
33502 AAACCTTCTTTGGTACCAGATTTCTTTTATAGAGCCCTTTTGGGATGCAACTACGACAGAAAACT
1 AAACCTTCTTTGATACCAGATTTCTTTCATAGAGCCCTTTTGGGACACAACTACGACAGAAAACT
* * * *
33567 TTTGGATCTTCCTTTTTAATCCGGACAAAATCCAACAATATCTTGAAGGGATGGAAACTCAACTT
66 TTTAGATCTTCCTCTTTAATCAGGACAAAATCCAACAACATCTTGAAGGGATGGAAACTCAACTT
*
33632 CAAATGGGCAAAGCTATGCTGACTCAACGAGAGAGGCATTGCCCCGGCAAAGAATTGCATCGTTC
131 CAAATGGGCAAAGCTATGCTGACTCAACGAGAGAGGCATTGCCCCGGCAAAGAATTGCATCATTC
* * * **
33697 GCACTGTAAATTTCTGACATCGTGCTGTTGTGCAGGCTTTATTATAAGAATTGAGGCATACCCTG
196 GCACTGCAAATTTCTGACATCATGCTGTTGTGCAGACTTTATTATAAGAACCGAGGCATACCCTG
33762 GTATGATCATACAA
261 GTATGATCATACAA
*
33776 AAACCTTCTTTGATACCAGATTTCTTTCATAGAGCCCTTTTGGGACACAACTACGATAGAAAAC-
1 AAACCTTCTTTGATACCAGATTTCTTTCATAGAGCCCTTTTGGGACACAACTACGACAGAAAACT
* * * **
33840 TTTAGATCTTCCTCTTTAATTAGGATAAAATCCAGA-AACATCTTGAAGGGATGGGAACTTGACT
66 TTTAGATCTTCCTCTTTAATCAGGACAAAATCCA-ACAACATCTTGAAGGGATGGAAACTCAACT
33904 TCAAATGGGCAAAGCTATGCTGACTCAACGAGAGAGGCATTGCCCCGGCAAAGAATTGCATCATT
130 TCAAATGGGCAAAGCTATGCTGACTCAACGAGAGAGGCATTGCCCCGGCAAAGAATTGCATCATT
* * *
33969 CGCACTGCGAATTTCTGACATCATGCTGTTGTGTAGATTTTATTATAAGAACCGAGGCATACCCT
195 CGCACTGCAAATTTCTGACATCATGCTGTTGTGCAGACTTTATTATAAGAACCGAGGCATACCCT
34034 GGTATGATCATACAA
260 GGTATGATCATACAA
34049 A
1 A
34050 GACATCTTTG
Statistics
Matches: 250, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
273 190 0.76
274 60 0.24
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (274 bp):
AAACCTTCTTTGATACCAGATTTCTTTCATAGAGCCCTTTTGGGACACAACTACGACAGAAAACT
TTTAGATCTTCCTCTTTAATCAGGACAAAATCCAACAACATCTTGAAGGGATGGAAACTCAACTT
CAAATGGGCAAAGCTATGCTGACTCAACGAGAGAGGCATTGCCCCGGCAAAGAATTGCATCATTC
GCACTGCAAATTTCTGACATCATGCTGTTGTGCAGACTTTATTATAAGAACCGAGGCATACCCTG
GTATGATCATACAA
Found at i:35744 original size:19 final size:20
Alignment explanation
Indices: 35715--35763 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
35705 CACTTCGTGA
* *
35715 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
35734 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
35754 AAATG-AATGC
1 AAATGTAATGC
35764 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:37469 original size:4 final size:4
Alignment explanation
Indices: 37460--37561 Score: 71
Period size: 4 Copynumber: 23.5 Consensus size: 4
37450 ATACAACAAC
* * ** *
37460 AAAT AAAT AAAT AAAT AAACT AAA- ACAT AAAA AAAT GGAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT
37508 AAAT AAAT AAAT GAACAT AAAGT AAAAT AAAAT AAAAT AAAAT AAAAT AAAT
1 AAAT AAAT AAAT -AA-AT AAA-T -AAAT -AAAT -AAAT -AAAT -AAAT AAAT
37560 AA
1 AA
37562 TAACAATAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
3 2 0.02
4 46 0.55
5 30 0.36
6 5 0.06
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:37537 original size:10 final size:9
Alignment explanation
Indices: 37460--37561 Score: 70
Period size: 10 Copynumber: 11.1 Consensus size: 9
37450 ATACAACAAC
37460 AAATAAAT-
1 AAATAAATA
37468 AAATAAATA
1 AAATAAATA
*
37477 AACT-AA-A
1 AAATAAATA
*
37484 ACATAAA-A
1 AAATAAATA
*
37492 AAATGGATATA
1 AAAT--AAATA
37503 TAAATAAAT-
1 -AAATAAATA
37512 AAATAAATGA
1 AAATAAAT-A
*
37522 ACATAAAGTA
1 AAATAAA-TA
37532 AAATAAAATA
1 AAAT-AAATA
37542 AAATAAAATA
1 AAAT-AAATA
37552 AAATAAATA
1 AAATAAATA
37561 A
1 A
37562 TAACAATAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
7 3 0.04
8 24 0.32
9 9 0.12
10 31 0.41
11 5 0.07
12 4 0.05
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.22
Consensus pattern (9 bp):
AAATAAATA
Found at i:37538 original size:5 final size:5
Alignment explanation
Indices: 37504--37558 Score: 62
Period size: 5 Copynumber: 11.4 Consensus size: 5
37494 ATGGATATAT
* *
37504 AAAT- AAAT- AAAT- AAATGA ACATA AAGTA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA
37552 AAATA AA
1 AAATA AA
37559 TAATAACAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
4 12 0.27
5 30 0.67
6 3 0.07
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:37588 original size:43 final size:43
Alignment explanation
Indices: 37460--37579 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 43
37450 ATACAACAAC
* ** * *
37460 AAATAAATAAATAAATAAAC-TAAAACATAAA-AAAATGGATATA
1 AAATAAATAAATAAATGAACATAAAGGA-AAATAAAAT-AAAATA
*
37503 TAAATAAATAAATAAATGAACATAAAGTAAAATAAAATAAAATA
1 -AAATAAATAAATAAATGAACATAAAGGAAAATAAAATAAAATA
37547 AAATAAAATAAAT-AAT-AACAATAAAGGAAAATA
1 AAAT-AAATAAATAAATGAAC-ATAAAGGAAAATA
37580 GATAAAAATC
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
42 3 0.05
43 19 0.29
44 34 0.52
45 10 0.15
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (43 bp):
AAATAAATAAATAAATGAACATAAAGGAAAATAAAATAAAATA
Found at i:40632 original size:3 final size:3
Alignment explanation
Indices: 40615--40653 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
40605 TATCACATTG
*
40615 TTA TT- TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40654 CTTCACTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41591 original size:8 final size:8
Alignment explanation
Indices: 41578--41641 Score: 83
Period size: 8 Copynumber: 7.5 Consensus size: 8
41568 AGTAATCAAC
41578 TAAGACAT
1 TAAGACAT
41586 TAAGACAT
1 TAAGACAT
41594 TAAGACAT
1 TAAGACAT
*
41602 TAAGTAATCAAC
1 TAAG--A-C-AT
41614 TAAGACAT
1 TAAGACAT
41622 TAAGACAT
1 TAAGACAT
41630 TAAGACAT
1 TAAGACAT
41638 TAAG
1 TAAG
41642 TAATCAACTA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
8 41 0.82
9 1 0.02
10 2 0.04
11 1 0.02
12 5 0.10
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (8 bp):
TAAGACAT
Found at i:41615 original size:36 final size:36
Alignment explanation
Indices: 41568--41651 Score: 168
Period size: 36 Copynumber: 2.3 Consensus size: 36
41558 TAAAGTTTTC
41568 AGTAATCAACTAAGACATTAAGACATTAAGACATTA
1 AGTAATCAACTAAGACATTAAGACATTAAGACATTA
41604 AGTAATCAACTAAGACATTAAGACATTAAGACATTA
1 AGTAATCAACTAAGACATTAAGACATTAAGACATTA
41640 AGTAATCAACTA
1 AGTAATCAACTA
41652 GGTACCAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (36 bp):
AGTAATCAACTAAGACATTAAGACATTAAGACATTA
Found at i:49910 original size:27 final size:27
Alignment explanation
Indices: 49871--50048 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
49861 TTATTGAGCC
* * * * *
49871 CGCACACTCAGTGCTATATAATCGACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
49898 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
49925 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
49953 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
49980 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
50007 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
50034 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
50049 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:50010 original size:82 final size:81
Alignment explanation
Indices: 49897--50047 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
49887 TATAATCGAC
* *
49897 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
49962 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
49979 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
50043 AGTGC
65 AGTGC
50048 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Done.