Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 75 of 328
Found at i:20602595 original size:22 final size:22
Alignment explanation
Indices: 20602570--20602621 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
20602560 CATTTATATC
20602570 ATAATTTCTAAAATTTTAATTT
1 ATAATTTCTAAAATTTTAATTT
* * **
20602592 ATAAATCCTTGAATTTTAATTT
1 ATAATTTCTAAAATTTTAATTT
20602614 ATAATTTC
1 ATAATTTC
20602622 AATAATTAGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (22 bp):
ATAATTTCTAAAATTTTAATTT
Found at i:20602628 original size:22 final size:22
Alignment explanation
Indices: 20602570--20602628 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
20602560 CATTTATATC
20602570 ATAATTTCTAA-AATTTTAATTT
1 ATAATTTC-AATAATTTTAATTT
* **
20602592 ATAA-ATCCTTGAATTTTAATTT
1 ATAATTTCAAT-AATTTTAATTT
20602614 ATAATTTCAATAATT
1 ATAATTTCAATAATT
20602629 AGGCCACTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
21 2 0.07
22 23 0.82
23 3 0.11
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAATTTCAATAATTTTAATTT
Found at i:20603371 original size:2 final size:2
Alignment explanation
Indices: 20603364--20603397 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20603354 ACAAAAAGTT
20603364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20603398 AACAAACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20604614 original size:25 final size:25
Alignment explanation
Indices: 20604586--20604640 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
20604576 AAATATGAAT
20604586 AAAAATTGTAATAAAAAATTAATTAA
1 AAAAATT-TAATAAAAAATTAATTAA
* * **
20604612 AAAAACTTAATACAATTTTAATTAA
1 AAAAATTTAATAAAAAATTAATTAA
20604637 AAAA
1 AAAA
20604641 TGAGAGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAAATTTAATAAAAAATTAATTAA
Found at i:20611143 original size:19 final size:19
Alignment explanation
Indices: 20611107--20611143 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20611097 TAATTAGGCT
* *
20611107 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
20611126 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
20611144 GAAAAAGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:20611761 original size:2 final size:2
Alignment explanation
Indices: 20611754--20611782 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20611744 TTATTAACTA
20611754 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 A
20611783 AGATATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20611820 original size:14 final size:15
Alignment explanation
Indices: 20611803--20611831 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20611793 GAAATGAAAT
20611803 AAAGAAAGAA-AGCA
1 AAAGAAAGAATAGCA
20611817 AAAGAAAGAATAGCA
1 AAAGAAAGAATAGCA
20611832 TAAGCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.07, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAGAAAGAATAGCA
Found at i:20611868 original size:15 final size:16
Alignment explanation
Indices: 20611850--20611883 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20611840 TCGAAAACAA
*
20611850 GAAG-AAAGAAAAGGG
1 GAAGAAAAGAAAAAGG
20611865 GAAGAAAAGAAAAAGG
1 GAAGAAAAGAAAAAGG
20611881 GAA
1 GAA
20611884 AAATTAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
GAAGAAAAGAAAAAGG
Found at i:20612556 original size:70 final size:75
Alignment explanation
Indices: 20612473--20612648 Score: 202
Period size: 70 Copynumber: 2.3 Consensus size: 75
20612463 ATGTGAACAA
* *
20612473 ATTGGAAATTAAAAGTGATTTGAATT-AAGT-AATTGAATT-AT-G-AATTATGTGAATATTTGA
1 ATTGGAAACTAAAAGTGATTTGAATTGAA-TAAATTGAATTAATAGAAAATATGTGAATATTTGA
20612533 AA-GTATATTG
65 AATGTATATTG
*
20612543 ATTGGAAACTAAAAGTGATTTGAATTGAATCAAATTGAATTGAATGAAGAAAATATGTGAGTATT
1 ATTGGAAACTAAAAGTGATTTGAATTGAAT-AAATTGAATT-AAT--AGAAAATATGTGAATATT
20612608 TGAAATGTATATTG
62 TGAAATGTATATTG
* * *
20612622 ATTGAAAAGTAATTAGTGATTTGAATT
1 ATTGGAAACTAA-AAGTGATTTGAATT
20612649 TGATTGGAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
70 26 0.29
71 2 0.02
72 9 0.10
74 2 0.02
77 1 0.01
78 18 0.20
79 18 0.20
80 13 0.15
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38
Consensus pattern (75 bp):
ATTGGAAACTAAAAGTGATTTGAATTGAATAAATTGAATTAATAGAAAATATGTGAATATTTGAA
ATGTATATTG
Found at i:20612678 original size:13 final size:14
Alignment explanation
Indices: 20612656--20612696 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
20612646 ATTTGATTGG
20612656 AAAA-TGAATTAA-
1 AAAAGTGAATTAAT
*
20612668 AAATGTGAATTAAAT
1 AAAAGTGAATT-AAT
20612683 AAAAGTGAATTAAT
1 AAAAGTGAATTAAT
20612697 TTATGAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 3 0.12
13 6 0.25
14 5 0.21
15 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (14 bp):
AAAAGTGAATTAAT
Found at i:20612805 original size:27 final size:25
Alignment explanation
Indices: 20612756--20612805 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
20612746 GAATTGAACC
20612756 GAAATATGATTATATATGATTATCT
1 GAAATATGATTATATATGATTATCT
20612781 GAAATATGTATTGATAT-TGAATTAT
1 GAAATATG-ATT-ATATATG-ATTAT
20612806 TTATTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.36
26 5 0.23
27 9 0.41
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (25 bp):
GAAATATGATTATATATGATTATCT
Found at i:20613080 original size:23 final size:23
Alignment explanation
Indices: 20613050--20613157 Score: 127
Period size: 23 Copynumber: 4.9 Consensus size: 23
20613040 TTTTCTGATT
*
20613050 AGGCACTTTATGTGTCGTATATC
1 AGGCACCTTATGTGTCGTATATC
* *
20613073 AGGCACTTTATGTGTCGTATTTC
1 AGGCACCTTATGTGTCGTATATC
**
20613096 AGGCACCTCGTGTGTCG--TATC
1 AGGCACCTTATGTGTCGTATATC
*
20613117 AGGCACCTCATGTGTCGT-T-TC
1 AGGCACCTTATGTGTCGTATATC
20613138 AGGCA-CTTATGTGTCGTATA
1 AGGCACCTTATGTGTCGTATA
20613158 ATGATCAAGT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.15
21 27 0.36
22 1 0.01
23 36 0.48
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (23 bp):
AGGCACCTTATGTGTCGTATATC
Found at i:20613131 original size:44 final size:41
Alignment explanation
Indices: 20613050--20613156 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 41
20613040 TTTTCTGATT
* * *
20613050 AGGCACTTTATGTGTCGTATATCAGGCACTTTATGTGTCGTATTTC
1 AGGCAC-TCATGTGTCG--TATCAGGCACCTCATGTGTCG--TTTC
*
20613096 AGGCACCTCGTGTGTCGTATCAGGCACCTCATGTGTCGTTTC
1 AGGCA-CTCATGTGTCGTATCAGGCACCTCATGTGTCGTTTC
*
20613138 AGGCACTTATGTGTCGTAT
1 AGGCACTCATGTGTCGTAT
20613157 AATGATCAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
41 12 0.22
42 9 0.17
44 19 0.35
46 13 0.24
47 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (41 bp):
AGGCACTCATGTGTCGTATCAGGCACCTCATGTGTCGTTTC
Found at i:20613491 original size:16 final size:16
Alignment explanation
Indices: 20613472--20613514 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
20613462 ATTGAACTAT
*
20613472 TGAAAGTATGAGAAAG
1 TGAAATTATGAGAAAG
20613488 TGAAATTATGAGAAAG
1 TGAAATTATGAGAAAG
20613504 TGAAATTATGA
1 TGAAATTATGA
20613515 ATTGAAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (16 bp):
TGAAATTATGAGAAAG
Found at i:20616074 original size:15 final size:15
Alignment explanation
Indices: 20616054--20616090 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
20616044 AACTCGTATG
20616054 AAGCATTTTACTGAT
1 AAGCATTTTACTGAT
20616069 AAGCATTTTACTGAT
1 AAGCATTTTACTGAT
20616084 AAGCATT
1 AAGCATT
20616091 AGTTCGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
AAGCATTTTACTGAT
Found at i:20618615 original size:53 final size:50
Alignment explanation
Indices: 20618535--20618634 Score: 146
Period size: 53 Copynumber: 1.9 Consensus size: 50
20618525 GACATAGTTC
*
20618535 TTAAAAACATTATAGAAAATTGTTTAAAAATAATTAAAATCTATAAGAAATGA
1 TTAAAAACATTATAGAAAATTATTT--AAA-AATTAAAATCTATAAGAAATGA
* *
20618588 TTAAAAATATTATAGAAAATTATTTAAAAATTAAAATTTATAAGAAA
1 TTAAAAACATTATAGAAAATTATTTAAAAATTAAAATCTATAAGAAA
20618635 GTTTTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 18 0.41
51 3 0.07
53 23 0.52
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (50 bp):
TTAAAAACATTATAGAAAATTATTTAAAAATTAAAATCTATAAGAAATGA
Found at i:20618863 original size:22 final size:20
Alignment explanation
Indices: 20618836--20618877 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
20618826 AAAATTGGGC
20618836 TCAACTTAATTAACTAAAAATA
1 TCAACTTAATTAA--AAAAATA
*
20618858 TCAACTTCATTAAAAAAATA
1 TCAACTTAATTAAAAAAATA
20618878 CATATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (20 bp):
TCAACTTAATTAAAAAAATA
Found at i:20618984 original size:10 final size:9
Alignment explanation
Indices: 20618932--20619025 Score: 62
Period size: 10 Copynumber: 9.6 Consensus size: 9
20618922 TGGGTATACA
*
20618932 TATAGTTTT
1 TATAATTTT
*
20618941 TATAACTTT
1 TATAATTTT
*
20618950 TAAAATTTT
1 TATAATTTT
* *
20618959 CAATTATTATT
1 -TATAATT-TT
20618970 TATAATTTCT
1 TATAATTT-T
20618980 TATAATTTT
1 TATAATTTT
20618989 TCATAATTTT
1 T-ATAATTTT
*
20618999 TAAACAATTTTT
1 T--ATAA-TTTT
20619011 TATAATTTTT
1 TATAA-TTTT
20619021 TATAA
1 TATAA
20619026 CTATTTAAGA
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
9 17 0.25
10 40 0.60
11 5 0.07
12 5 0.07
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (9 bp):
TATAATTTT
Found at i:20619173 original size:21 final size:19
Alignment explanation
Indices: 20619121--20619174 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
20619111 TTTGGATGTC
*
20619121 ATTTTTAATAATTTTAAAT
1 ATTTTTAATAATTCTAAAT
* *
20619140 -TTTTTTATGATTCTAAAT
1 ATTTTTAATAATTCTAAAT
20619158 AATTTTTAAATAATTCT
1 -ATTTTT-AATAATTCT
20619175 CTTCTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 15 0.56
20 5 0.19
21 7 0.26
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTTAATAATTCTAAAT
Found at i:20620083 original size:20 final size:20
Alignment explanation
Indices: 20620042--20620095 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
20620032 AATTAAGTTT
* **
20620042 ATTTAAAATAAAAATATTAA
1 ATTTAAATTAAAAATAGAAA
20620062 ATTTAAATTAAAAATAGAAA
1 ATTTAAATTAAAAATAGAAA
20620082 ATTATAATATTAAA
1 ATT-TAA-ATTAAA
20620096 TATTTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 20 0.69
21 3 0.10
22 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTTAAATTAAAAATAGAAA
Found at i:20623604 original size:3 final size:3
Alignment explanation
Indices: 20623591--20623676 Score: 65
Period size: 3 Copynumber: 28.3 Consensus size: 3
20623581 GAGGGCATAT
20623591 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
20623635 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20623677 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 9 0.13
3 48 0.71
4 9 0.13
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:20623615 original size:12 final size:12
Alignment explanation
Indices: 20623591--20623673 Score: 73
Period size: 12 Copynumber: 6.8 Consensus size: 12
20623581 GAGGGCATAT
20623591 ATAATAT-AATA
1 ATAATATAAATA
20623602 ATAATATAAATA
1 ATAATATAAATA
20623614 ATAATATATACATGA
1 ATAATATA-A-AT-A
20623629 GA-AATA-ATAATA
1 -ATAATATA-AATA
20623641 ATAATATAAATA
1 ATAATATAAATA
* *
20623653 ATAGTAAAAATA
1 ATAATATAAATA
*
20623665 ATAAAATAA
1 ATAATATAA
20623674 TAAAACAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.13
12 37 0.62
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:20623635 original size:21 final size:18
Alignment explanation
Indices: 20623596--20623676 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
20623586 CATATATAAT
*
20623596 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
20623614 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
20623635 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
* *
20623653 ATAGTAAAAATA-ATAA-A
1 ATAATAATAATAGA-AATA
20623670 ATAATAA
1 ATAATAA
20623677 AACAAAGCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 8 0.15
18 24 0.44
19 5 0.09
20 5 0.09
21 12 0.22
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:20623664 original size:27 final size:27
Alignment explanation
Indices: 20623591--20623677 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
20623581 GAGGGCATAT
* *
20623591 ATAATAT-AATAATAATATAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
* *
20623617 AT-ATATACAT--GAG-AAATAATAATA
1 ATAATATAAATAATAGTAAA-AATAATA
20623641 ATAATATAAATAATAGTAAAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
20623668 A-AATAATAAA
1 ATAAT-ATAAA
20623678 ACAAAGCTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 11 0.23
26 7 0.15
27 15 0.31
28 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAATATAAATAATAGTAAAAATAATA
Found at i:20624034 original size:22 final size:23
Alignment explanation
Indices: 20624006--20624056 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
20623996 TAACCTTCTT
20624006 TCCAAAAAAACAAAAAAA-CACC
1 TCCAAAAAAACAAAAAAACCACC
*
20624028 TCC-AAAAAACAAAAAAACCTCC
1 TCCAAAAAAACAAAAAAACCACC
20624050 TCCAAAA
1 TCCAAAA
20624057 CAAAGAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.54
22 9 0.35
23 3 0.12
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.08
Consensus pattern (23 bp):
TCCAAAAAAACAAAAAAACCACC
Found at i:20624079 original size:23 final size:20
Alignment explanation
Indices: 20624012--20624079 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
20624002 TCTTTCCAAA
*
20624012 AAAACAAAAAAA-CACCTCC
1 AAAACAAAAAAACCTCCTCC
20624031 AAAAAACAAAAAAACCTCCTCC
1 --AAAACAAAAAAACCTCCTCC
*
20624053 AAAACAAAGAACAATCCTTCTCC
1 AAAACAAA-AA-AA-CCTCCTCC
20624076 AAAA
1 AAAA
20624080 AACCAAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.20
21 14 0.34
22 8 0.20
23 11 0.27
ACGTcount: A:0.59, C:0.29, G:0.01, T:0.10
Consensus pattern (20 bp):
AAAACAAAAAAACCTCCTCC
Found at i:20624649 original size:44 final size:44
Alignment explanation
Indices: 20624600--20625328 Score: 565
Period size: 44 Copynumber: 16.6 Consensus size: 44
20624590 TCTTCGATCC
* *
20624600 GTTCCCTATAAGCATAGGGATGCCAAATCTGATGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * *
20624644 GTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTCGA-TCT
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATTTTCAACT-T
* * * * * * * *
20624687 GCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTT-GATTT
1 G-TTCCCTATAAGCACAGGGATGCCAAATCTGATAT-TTTCAACTT
*
20624732 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * *
20624776 GTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGATC-T
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACTT
* * * * * * * * *
20624819 GCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTT
1 G-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* *
20624864 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * *
20624908 GTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGATC-T
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACTT
* * * * * * * * *
20624951 GCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATTT
1 G-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* *
20624996 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * * *
20625040 GTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTCGATTT
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATTTTCAACTT
* * * * * * * *
20625083 GCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGA-TCT
1 G-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT-T
* *
20625128 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * * *
20625172 GTTCCCTATAACCACAGGGATGCC--ATGCTGAAATCTTCGA-TCT
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATTTTCAACT-T
* * * * * * *
20625215 GCTTTACC-GTAAGCACAGGGATGCCAGATCTGCTATCTTCGATTT
1 G--TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* *
20625260 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
20625304 GTTCCCTATAAGCACAGGGATGCCA
1 GTTCCCTATAAGCACAGGGATGCCA
20625329 TGCTGAAATC
Statistics
Matches: 542, Mismatches: 109, Indels: 68
0.75 0.15 0.09
Matches are distributed among these distances:
42 12 0.02
43 52 0.10
44 410 0.76
45 54 0.10
46 14 0.03
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (44 bp):
GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
Found at i:20624781 original size:132 final size:132
Alignment explanation
Indices: 20624544--20625387 Score: 1517
Period size: 132 Copynumber: 6.4 Consensus size: 132
20624534 GATATCCGCT
* * **
20624544 ATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATTTGCTATCTTCGATCCGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
* *
20624609 AAGCATAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
66 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
20624674 AA
131 AA
* *
20624676 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTTGATTTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
*
20624741 AAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
66 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
20624806 AA
131 AA
*
20624808 ATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
20624873 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
66 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
20624938 AA
131 AA
* *
20624940 ATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATTTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
20625005 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
66 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
20625070 AA
131 AA
* *
20625072 ATCTTCGATTTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
*
20625137 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAACCACAGGGATGCCATGCTG
66 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
20625202 AA
131 AA
* * * *
20625204 ATCTTCGATCTGCTTTACCGTAAGCACAGGGATGCCAGATCTGCTATCTTCGATTTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
20625269 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
66 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
20625334 AA
131 AA
20625336 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
20625388 GTCTGCTCCT
Statistics
Matches: 684, Mismatches: 28, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 684 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (132 bp):
ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
AA
Found at i:20625522 original size:68 final size:68
Alignment explanation
Indices: 20625440--20625638 Score: 294
Period size: 68 Copynumber: 2.9 Consensus size: 68
20625430 TCTTCTTCCA
* * * * *
20625440 CTGAAACTTCAAGGAGGTCTGCTGTGGCTTTTAGCCTCTCCAATGCCATTTCTGGAAGAAGAGGT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGAT
*
20625505 -TT
66 CCT
* *
20625507 GCTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAAAAGA
1 -CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGA
20625572 TCCT
65 TCCT
*
20625576 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGGA-AAAAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGA
20625639 AATTTGTAAT
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
67 6 0.05
68 112 0.94
69 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGAT
CCT
Found at i:20625806 original size:44 final size:44
Alignment explanation
Indices: 20625710--20626597 Score: 393
Period size: 44 Copynumber: 20.4 Consensus size: 44
20625700 CTATTTCCCA
*
20625710 ACTGCTTAAGGGGTTAAGATCTGTAAA--TTCAACCTGTTACCCT
1 ACTGCTT-AGGGGTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
* *
20625753 ACTGGTTAGGGGTTAAGATTTGTAAATTTTCAGCCTGTTACCCT
1 ACTGCTTAGGGGTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
* * * * *
20625797 ACTACTTAGGGGTTTAAGGTTTGTAAA--TTCGGCTTGTTACCCT
1 ACTGCTTAGGGG-TTAAGATCTGTAAATTTTCAGCCTGTTACCCT
* ** * * * * *
20625840 ACTGCTTAGGGGGTTAA-AGCCCATCATTTTTTA-TCTGTTTCCCT
1 ACTGCTTA-GGGGTTAAGA-TCTGTAAATTTTCAGCCTGTTACCCT
* *
20625884 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCAGTTACCCT
1 ACTGCTTA-GGGGTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
* * *
20625929 ACTGCTTAGGGGTTTAAG-GCTTGTAAA--TTCGGCTTGTTACCCT
1 ACTGCTTAGGGG-TTAAGATC-TGTAAATTTTCAGCCTGTTACCCT
* ** * * * *
20625972 ACTGCTTAGGGGGTTAA-AGC-CCATCATCTTTGA-TCTGTTTCCCT
1 ACTGCTTA-GGGGTTAAGATCTGTA-AAT-TTTCAGCCTGTTACCCT
*
20626016 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCT
1 ACTGCTTA-GGGGTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
* * *
20626061 ACTGCTTAGGGGTTAAG-GCTTGTAAA-TTT-GGCTTGTTACCCT
1 ACTGCTTAGGGGTTAAGATC-TGTAAATTTTCAGCCTGTTACCCT
* ** * * * *
20626103 ACTGCTTAGGGGTTAA-AGC-CCATCATCTTC-GATCTGTTTCCCT
1 ACTGCTTAGGGGTTAAGATCTGTA-AATTTTCAG-CCTGTTACCCT
* * * *
20626146 ACTGCTTAGGGGGTTAAGATCT-T-CATCTTC-GATCTGTTTCCCT
1 ACTGCTTA-GGGGTTAAGATCTGTAAATTTTCAG-CCTGTTACCCT
* * * *
20626189 ACTGCTTAGGGAGATAAGATCTG-CAA--TTCGGTCTGTTACCCT
1 ACTGCTTAGGG-GTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
* * * ** * * *
20626231 ACCGATTAGGGGTTTAAGACCCT-T-CGTCTTC-GATCTGTTTCCCT
1 ACTGCTTAGGGG-TTAAGA-TCTGTAAATTTTCAG-CCTGTTACCCT
** *
20626275 ACTATTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCT
1 ACTGCTTA-GGGGTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
* * *
20626320 ACTGCTTAGGGGTTAAG-GCTTGTAAA-TTT-GGCTTGTTACCCT
1 ACTGCTTAGGGGTTAAGATC-TGTAAATTTTCAGCCTGTTACCCT
* ** * * * *
20626362 ACTGCTTAGGGGGTTAA-AGC-CCATCATCTTC-GATCTGTTTCCCT
1 ACTGCTTA-GGGGTTAAGATCTGTA-AATTTTCAG-CCTGTTACCCT
* * * *
20626406 ACTGCTTAGGGGGTTAAGATCT-T-CATCTTC-GATCTGTTTCCCT
1 ACTGCTTA-GGGGTTAAGATCTGTAAATTTTCAG-CCTGTTACCCT
* * * * *
20626449 ACTGCTTAGGGAGATGAGATCTG-CAA--TTCGGTCTGTTACCCT
1 ACTGCTTAGGG-GTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
* * * ** * * *
20626491 ACCGATTAGGGGTTTAAGACCCT-T-CGTCTTC-GATCTGTTTCCCT
1 ACTGCTTAGGGG-TTAAGA-TCTGTAAATTTTCAG-CCTGTTACCCT
* *
20626535 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCATGTTACCCT
1 ACTGCTTA-GGGGTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
*
20626580 ATTGCTTAGGGGCTTAAG
1 ACTGCTTAGGGG-TTAAG
20626598 GCTTGTGAAT
Statistics
Matches: 660, Mismatches: 118, Indels: 132
0.73 0.13 0.15
Matches are distributed among these distances:
40 1 0.00
41 5 0.01
42 130 0.20
43 180 0.27
44 218 0.33
45 123 0.19
46 3 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (44 bp):
ACTGCTTAGGGGTTAAGATCTGTAAATTTTCAGCCTGTTACCCT
Found at i:20625814 original size:87 final size:86
Alignment explanation
Indices: 20625710--20626597 Score: 431
Period size: 87 Copynumber: 10.2 Consensus size: 86
20625700 CTATTTCCCA
** * **
20625710 ACTGCTTAAGGGGTTAAGATCTGTAAATTCAACCTGTTACCCTACTGGTTAGGGGTTAAGATTTG
1 ACTGCTT-AGGGGTTAAGATCTGTAAATTCGGCCTGTTACCCTACTGCTTAGGGGTTAAGACCTG
20625775 TAAATTTTCAGCCTGTTACCCT
65 TAAATTTTCAGCCTGTTACCCT
* * * *
20625797 ACTACTTAGGGGTTTAAGGTTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAA-AGCC
1 ACTGCTTAGGGG-TTAAGATCTGTAAATTCGGCCTGTTACCCTACTGCTTA-GGGGTTAAGA-CC
** * * * * *
20625861 CATCATTTTTTA-TCTGTTTCCCT
63 TGTAAATTTTCAGCCTGTTACCCT
* * *
20625884 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCAGTTACCCTACTGCTTAGGGGTTTAAGGC
1 ACTGCTTA-GGGGTTAAGATCTGTAAA--TTCGGCCTGTTACCCTACTGCTTAGGGG-TTAAGAC
* * *
20625949 TTGTAAA--TTCGGCTTGTTACCCT
62 CTGTAAATTTTCAGCCTGTTACCCT
** * ** * ** * *
20625972 ACTGCTTAGGGGGTTAAAGCCCAT-CATCTTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGAT
1 ACTGCTTA-GGGGTT-AAGATC-TGTAAATTCGGCCTGTTACCCTACTGCTTA-GGGGTTAAGAC
*
20626036 CTGTAAATCTTCAGCCTGTTACCCT
62 CTGTAAATTTTCAGCCTGTTACCCT
* * * *
20626061 ACTGCTTAGGGGTTAAG-GCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGTTAA-AGCCC
1 ACTGCTTAGGGGTTAAGATC-TGTAAATTCGGCCTGTTACCCTACTGCTTAGGGGTTAAGA-CCT
* * * * *
20626124 AT-CATCTTC-GATCTGTTTCCCT
64 GTAAATTTTCAG-CCTGTTACCCT
** ** * * *
20626146 ACTGCTTAGGGGGTTAAGATCT-TCATCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATC
1 ACTGCTTA-GGGGTTAAGATCTGT-AAATTCGGCCTGTTACCCTACTGCTTAGGG-GTTAAGACC
* * *
20626210 TG-CAA--TTCGGTCTGTTACCCT
63 TGTAAATTTTCAGCCTGTTACCCT
* * * * ** * **
20626231 ACCGATTAGGGGTTTAAGACCCTTCGT--CTTCGATCTGTTTCCCTACTATTTAGGGGGTTAAGA
1 ACTGCTTAGGGG-TTAAGA-TC-T-GTAAATTCGGCCTGTTACCCTACTGCTTA-GGGGTTAAGA
* *
20626294 TCTGTAAATCTTCAGCCTGTTACCCT
61 CCTGTAAATTTTCAGCCTGTTACCCT
* * *
20626320 ACTGCTTAGGGGTTAAG-GCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAA-AGCC
1 ACTGCTTAGGGGTTAAGATC-TGTAAATTCGGCCTGTTACCCTACTGCTTA-GGGGTTAAGA-CC
** * * * *
20626383 CAT-CATCTTC-GATCTGTTTCCCT
63 TGTAAATTTTCAG-CCTGTTACCCT
** ** * * * *
20626406 ACTGCTTAGGGGGTTAAGATCT-TCATCTTCGATCTGTTTCCCTACTGCTTAGGGAGATGAGATC
1 ACTGCTTA-GGGGTTAAGATCTGT-AAATTCGGCCTGTTACCCTACTGCTTAGGG-GTTAAGACC
* * *
20626470 TG-CAA--TTCGGTCTGTTACCCT
63 TGTAAATTTTCAGCCTGTTACCCT
* * * * ** *
20626491 ACCGATTAGGGGTTTAAGACCCTTCGT--CTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGA
1 ACTGCTTAGGGG-TTAAGA-TC-T-GTAAATTCGGCCTGTTACCCTACTGCTTA-GGGGTTAAGA
* * *
20626554 TCTGTAAATCTTCAGCATGTTACCCT
61 CCTGTAAATTTTCAGCCTGTTACCCT
*
20626580 ATTGCTTAGGGGCTTAAG
1 ACTGCTTAGGGG-TTAAG
20626598 GCTTGTGAAT
Statistics
Matches: 616, Mismatches: 132, Indels: 104
0.72 0.15 0.12
Matches are distributed among these distances:
84 9 0.01
85 78 0.13
86 152 0.25
87 204 0.33
88 64 0.10
89 108 0.18
90 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (86 bp):
ACTGCTTAGGGGTTAAGATCTGTAAATTCGGCCTGTTACCCTACTGCTTAGGGGTTAAGACCTGT
AAATTTTCAGCCTGTTACCCT
Found at i:20625979 original size:132 final size:130
Alignment explanation
Indices: 20625743--20626609 Score: 1130
Period size: 132 Copynumber: 6.6 Consensus size: 130
20625733 TAAATTCAAC
* * * * *
20625743 CTGTTACCCTACTGGTTA-GGGGTTAAGATTTGTAAATTTTCAGCCTGTTACCCTACTACTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
* * **
20625807 GGTTTAAGGTTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTT
66 GG-TTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTA-GGGGTTAAAGCCCATCATCTTCG
20625872 AT
129 AT
*
20625874 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCAGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
20625939 GGTTTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTG
66 GG-TTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTA-GGGGTTAAAGCCCATCATCTTCG
20626004 AT
129 AT
20626006 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
20626071 GGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGTTAAAGCCCATCATCTTCGAT
66 GGTTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGTTAAAGCCCATCATCTTCGAT
* * *
20626136 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTC-GATCTGTTTCCCTACTGCTTAG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAG-CCTGTTACCCTACTGCTTAG
* * * * * * * *
20626198 GGAGATAA-GATCTG-CAATTCGG-TCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCT
65 GG-GTTAAGGCT-TGTAAATTCGGCT-TGTTACCCTACTGCTTAGGGGTTAAAG-CCCATCATCT
20626260 TCGAT
126 TCGAT
**
20626265 CTGTTTCCCTACTATTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
20626330 GGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGA
66 GGTTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTA-GGGGTTAAAGCCCATCATCTTCGA
20626395 T
130 T
* * *
20626396 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTC-GATCTGTTTCCCTACTGCTTAG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAG-CCTGTTACCCTACTGCTTAG
* * * * * * * * *
20626458 GGAGATGA-GATCTG-CAATTCGG-TCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCT
65 GG-GTTAAGGCT-TGTAAATTCGGCT-TGTTACCCTACTGCTTAGGGGTTAAAG-CCCATCATCT
20626520 TCGAT
126 TCGAT
* *
20626525 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCATGTTACCCTATTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
20626590 GGCTTAAGGCTTGTGAATTC
66 GG-TTAAGGCTTGTAAATTC
20626610 ACTGATTCTA
Statistics
Matches: 650, Mismatches: 62, Indels: 47
0.86 0.08 0.06
Matches are distributed among these distances:
127 2 0.00
128 69 0.11
129 144 0.22
130 71 0.11
131 173 0.27
132 191 0.29
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (130 bp):
CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
GGTTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGTTAAAGCCCATCATCTTCGAT
Found at i:20626436 original size:260 final size:261
Alignment explanation
Indices: 20625743--20626608 Score: 1327
Period size: 260 Copynumber: 3.3 Consensus size: 261
20625733 TAAATTCAAC
* * * * *
20625743 CTGTTACCCTACTGGTTA-GGGGTTAAGATTTGTAAATTTTCAGCCTGTTACCCTACTACTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
* * * * **
20625807 GGTTTAAGGTTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTT
66 GGCTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCG
* * * *
20625872 ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-AGCCAGTTACCCTACTGCTT
131 ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-TCTGTTTCCCTACTGCTT
* * * * * * *
20625936 AGGG-GTTTAAG-GCTTGTAAATTCGG-CTTGTTACCCTACTGCTTAGGGGGTTAA-AGCCCATC
193 AGGGAG-ATAAGATC-TG-CAATTCGGTC-TGTTACCCTACCGATTAGGGGTTTAAGA-CCCTTC
* *
20625997 ATCTTTGAT
253 GTCTTCGAT
20626006 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
20626071 GG-TTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTA-GGGGTTAAAGCCCATCATCTTCG
66 GGCTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCG
20626134 ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGG
131 ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGG
20626199 GAGATAAGATCTGCAATTCGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGA
196 GAGATAAGATCTGCAATTCGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGA
20626264 T
261 T
**
20626265 CTGTTTCCCTACTATTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
20626330 GG-TTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCG
66 GGCTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCG
20626394 ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGG
131 ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGG
*
20626459 GAGATGAGATCTGCAATTCGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGA
196 GAGATAAGATCTGCAATTCGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGA
20626524 T
261 T
* *
20626525 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCATGTTACCCTATTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
20626590 GGCTTAAGGCTTGTGAATT
66 GGCTTAAGGCTTGTAAATT
20626609 CACTGATTCT
Statistics
Matches: 564, Mismatches: 31, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
259 145 0.26
260 249 0.44
261 19 0.03
262 54 0.10
263 52 0.09
264 45 0.08
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (261 bp):
CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
GGCTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCG
ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGG
GAGATAAGATCTGCAATTCGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGA
T
Found at i:20626555 original size:86 final size:85
Alignment explanation
Indices: 20625873--20626597 Score: 517
Period size: 86 Copynumber: 8.3 Consensus size: 85
20625863 TCATTTTTTA
* * ** * * *
20625873 TCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-AGCCAGTTACCCTACTGCTTA
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGACCT-T-CGTCTTCGA-TCTGTTTCCCTACTGCTTA
* * *
20625937 GGGGTTTAAG-GCTTGTAAATTCGG
63 GGGGGTTAAGATC-TG-CAATTCGG
* * * *
20625961 -CTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAG
1 TC-TGTTACCCTACTGCTTAGGGGGTT-AAGACCTTCGTCTTCGATCTGTTTCCCTACTGCTTAG
* *
20626025 GGGGTTAAGATCTGTAAATCTTCAG
64 GGGGTTAAGATCTG-CAA--TTCGG
* * * * * *
20626050 CCTGTTACCCTACTGCTTA-GGGGTTAAG-GCTT-GTAAATTTG-GCTTGTTACCCTACTGCTTA
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGACCTTCGT--CTTCGATC-TGTTTCCCTACTGCTTA
** * *
20626111 -GGGGTTAAAGCCCAT-CATCTTCGA
63 GGGGGTT-AAGATC-TGCA-ATTCGG
* * *
20626135 TCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGG
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGACCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGG
* *
20626200 AGATAAGATCTGCAATTCGG
66 GGTTAAGATCTGCAATTCGG
* * * **
20626220 TCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTATTTAGG
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGA-CCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGG
* *
20626285 GGGTTAAGATCTGTAAATCTTCAG
65 GGGTTAAGATCTG-CAA--TTCGG
* * * * * *
20626309 CCTGTTACCCTACTGCTTA-GGGGTTAAG-GCTT-GTAAATTTG-GCTTGTTACCCTACTGCTTA
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGACCTTCGT--CTTCGATC-TGTTTCCCTACTGCTTA
** * *
20626370 GGGGGTTAAAGCCCAT-CATCTTCGA
63 GGGGGTT-AAGATC-TGCA-ATTCGG
* * *
20626395 TCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGG
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGACCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGG
* * *
20626460 AGATGAGATCTGCAATTCGG
66 GGTTAAGATCTGCAATTCGG
* * *
20626480 TCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGG
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGA-CCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGG
* *
20626545 GGGTTAAGATCTGTAAATCTTCAG
65 GGGTTAAGATCTG-CAA--TTCGG
* *
20626569 -CATGTTACCCTATTGCTTAGGGGCTTAAG
1 TC-TGTTACCCTACTGCTTAGGGGGTTAAG
20626598 GCTTGTGAAT
Statistics
Matches: 501, Mismatches: 97, Indels: 77
0.74 0.14 0.11
Matches are distributed among these distances:
85 85 0.17
86 156 0.31
87 134 0.27
88 51 0.10
89 74 0.15
90 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (85 bp):
TCTGTTACCCTACTGCTTAGGGGGTTAAGACCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGG
GGTTAAGATCTGCAATTCGG
Found at i:20626767 original size:66 final size:66
Alignment explanation
Indices: 20626661--20626787 Score: 218
Period size: 66 Copynumber: 1.9 Consensus size: 66
20626651 TCTATGCTTA
* * *
20626661 TGTCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
1 TGTCAAATAATTAGGATACTATGATCGAAATCAATCAAATGCTCCTAACTAGATGTGTTATGAAT
20626726 G
66 G
*
20626727 TGTCAAATAATTAGGATACTATGATTGAAATCAATCAAATGCTCCTAACTAGATGTGTTAT
1 TGTCAAATAATTAGGATACTATGATCGAAATCAATCAAATGCTCCTAACTAGATGTGTTAT
20626788 TATATGAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (66 bp):
TGTCAAATAATTAGGATACTATGATCGAAATCAATCAAATGCTCCTAACTAGATGTGTTATGAAT
G
Found at i:20627992 original size:6 final size:6
Alignment explanation
Indices: 20627983--20628030 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
20627973 TTTTTTTTTT
20627983 TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC
1 TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC
20628031 ATATAACTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.17, T:0.50
Consensus pattern (6 bp):
TTTGCC
Found at i:20631843 original size:2 final size:2
Alignment explanation
Indices: 20631790--20631823 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
20631780 ACAATAATAC
* *
20631790 TA TA TA TA AA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20631824 GAAATACACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:20631936 original size:12 final size:12
Alignment explanation
Indices: 20631914--20631956 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
20631904 AATAAAAAAC
20631914 AATACTATATATA
1 AATA-TATATATA
20631927 AATATATATATA
1 AATATATATATA
* * *
20631939 TATATACATAAA
1 AATATATATATA
20631951 AATATA
1 AATATA
20631957 CACTAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (12 bp):
AATATATATATA
Found at i:20632066 original size:3 final size:3
Alignment explanation
Indices: 20632058--20632153 Score: 54
Period size: 3 Copynumber: 31.0 Consensus size: 3
20632048 AATAGGGGTG
*
20632058 ATA ATA ATA ATA ATA ATA CA-A ACA ATA ATA CATA TATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA -ATA -ATA ATA ATA
* * * * * *
20632106 GTA GTA GA-A ATA AAA ATA ATA A-A AGTA ACA ATA ATG ATA GTA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
20632151 ATA
1 ATA
20632154 TAAATAAATA
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
2 4 0.05
3 57 0.77
4 13 0.18
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:20632191 original size:3 final size:3
Alignment explanation
Indices: 20632178--20632263 Score: 65
Period size: 3 Copynumber: 28.3 Consensus size: 3
20632168 GAGGGCATAT
20632178 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
20632222 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20632264 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 9 0.13
3 48 0.71
4 9 0.13
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:20632202 original size:12 final size:12
Alignment explanation
Indices: 20632178--20632260 Score: 73
Period size: 12 Copynumber: 6.8 Consensus size: 12
20632168 GAGGGCATAT
20632178 ATAATAT-AATA
1 ATAATATAAATA
20632189 ATAATATAAATA
1 ATAATATAAATA
20632201 ATAATATATACATGA
1 ATAATATA-A-AT-A
20632216 GA-AATA-ATAATA
1 -ATAATATA-AATA
20632228 ATAATATAAATA
1 ATAATATAAATA
* *
20632240 ATAGTAAAAATA
1 ATAATATAAATA
*
20632252 ATAAAATAA
1 ATAATATAA
20632261 TAAAACAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.13
12 37 0.62
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:20632222 original size:21 final size:18
Alignment explanation
Indices: 20632183--20632263 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
20632173 CATATATAAT
*
20632183 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
20632201 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
20632222 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
* *
20632240 ATAGTAAAAATA-ATAA-A
1 ATAATAATAATAGA-AATA
20632257 ATAATAA
1 ATAATAA
20632264 AACAAAGCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 8 0.15
18 24 0.44
19 5 0.09
20 5 0.09
21 12 0.22
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:20632251 original size:27 final size:27
Alignment explanation
Indices: 20632178--20632264 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
20632168 GAGGGCATAT
* *
20632178 ATAATAT-AATAATAATATAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
* *
20632204 AT-ATATACAT--GAG-AAATAATAATA
1 ATAATATAAATAATAGTAAA-AATAATA
20632228 ATAATATAAATAATAGTAAAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
20632255 A-AATAATAAA
1 ATAAT-ATAAA
20632265 ACAAAGCTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 11 0.23
26 7 0.15
27 15 0.31
28 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAATATAAATAATAGTAAAAATAATA
Found at i:20632618 original size:21 final size:22
Alignment explanation
Indices: 20632568--20632638 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 22
20632558 TAGCTTTTCC
* *
20632568 AAAAACAAAAATAACCTCTTTCCAA
1 AAAAACAAAAA-AACCAC-CTCC-A
20632593 AAAAACAAAAAAA-CACCTCCA
1 AAAAACAAAAAAACCACCTCCA
*
20632614 AAAAACAAAAAAACCTCCTCCA
1 AAAAACAAAAAAACCACCTCCA
20632636 AAA
1 AAA
20632639 CAAAGAACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 14 0.33
22 13 0.31
23 2 0.05
24 2 0.05
25 11 0.26
ACGTcount: A:0.62, C:0.27, G:0.00, T:0.11
Consensus pattern (22 bp):
AAAAACAAAAAAACCACCTCCA
Found at i:20632661 original size:23 final size:20
Alignment explanation
Indices: 20632594--20632688 Score: 68
Period size: 21 Copynumber: 4.4 Consensus size: 20
20632584 TCTTTCCAAA
*
20632594 AAAACAAAAAAA-CACCTCC
1 AAAACAAAAAAACCTCCTCC
20632613 AAAAAACAAAAAAACCTCCTCC
1 --AAAACAAAAAAACCTCCTCC
*
20632635 AAAACAAAGAACAATCCTTCTCC
1 AAAACAAA-AA-AA-CCTCCTCC
*
20632658 AAAA-AACCAAAAACCCCCTCCC
1 AAAACAA--AAAAACCTCCT-CC
20632680 TAAAACAAA
1 -AAAACAAA
20632689 GTCTTGAATG
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
20 8 0.13
21 18 0.30
22 15 0.25
23 17 0.28
24 3 0.05
ACGTcount: A:0.57, C:0.33, G:0.01, T:0.09
Consensus pattern (20 bp):
AAAACAAAAAAACCTCCTCC
Found at i:20635997 original size:15 final size:14
Alignment explanation
Indices: 20635957--20636012 Score: 85
Period size: 14 Copynumber: 3.9 Consensus size: 14
20635947 CATATATATT
20635957 ATATAATTCAATCA
1 ATATAATTCAATCA
20635971 ATATAATTCAATCA
1 ATATAATTCAATCA
*
20635985 AAATAATTTCAATCA
1 ATATAA-TTCAATCA
20636000 ATATAAATTCAAT
1 ATAT-AATTCAAT
20636013 AAATTCATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 19 0.50
15 17 0.45
16 2 0.05
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAATTCAATCA
Found at i:20642308 original size:15 final size:14
Alignment explanation
Indices: 20642282--20642323 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
20642272 CATATATATT
20642282 ATATAATTCAATCA
1 ATATAATTCAATCA
20642296 ATATAATTTCAATCA
1 ATATAA-TTCAATCA
20642311 ATATAAATTCAAT
1 ATAT-AATTCAAT
20642324 AAATTCATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.23
15 18 0.69
16 2 0.08
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAATTCAATCA
Found at i:20643597 original size:5 final size:5
Alignment explanation
Indices: 20643584--20643630 Score: 85
Period size: 5 Copynumber: 9.2 Consensus size: 5
20643574 TTCTTTAGTT
20643584 TATATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
20643631 TAAAACATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 37 0.90
6 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:20648882 original size:20 final size:20
Alignment explanation
Indices: 20648857--20648897 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20648847 GAAAAGATAA
20648857 CCATATAAAGCTCCTGCTTT
1 CCATATAAAGCTCCTGCTTT
20648877 CCATATAAAGCTCCTGCTTT
1 CCATATAAAGCTCCTGCTTT
20648897 C
1 C
20648898 ATGGTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (20 bp):
CCATATAAAGCTCCTGCTTT
Found at i:20651256 original size:26 final size:24
Alignment explanation
Indices: 20651207--20651256 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
20651197 CTTATTTCAT
* *
20651207 TAAATAAAAAATTTTAAAATATAA
1 TAAATAAAAAATTTAAAAACATAA
20651231 TAAATAAAATATATTTAAAAACATAA
1 TAAATAAAA-A-ATTTAAAAACATAA
20651257 AAACAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 1 0.05
26 12 0.55
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAATAAAAAATTTAAAAACATAA
Found at i:20651264 original size:23 final size:21
Alignment explanation
Indices: 20651230--20651271 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
20651220 TTAAAATATA
20651230 ATAAATAAAATATATTTAAAAAC
1 ATAAATAAAATA-A-TTAAAAAC
20651253 ATAAA-AACAATAATTAAAA
1 ATAAATAA-AATAATTAAAA
20651272 CAAGAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.33
22 3 0.17
23 9 0.50
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
ATAAATAAAATAATTAAAAAC
Found at i:20660495 original size:22 final size:22
Alignment explanation
Indices: 20660470--20660516 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
20660460 AATTGATGAA
20660470 TTAGGGGTCAAAATGAAAATGT
1 TTAGGGGTCAAAATGAAAATGT
20660492 TTAGGGGTCAAAATGAAAATGT
1 TTAGGGGTCAAAATGAAAATGT
20660514 TTA
1 TTA
20660517 AAAATATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (22 bp):
TTAGGGGTCAAAATGAAAATGT
Found at i:20664456 original size:42 final size:42
Alignment explanation
Indices: 20664396--20664483 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
20664386 TGGGTTTATA
* * *
20664396 CTTCGGCTTGTCTGATGATGCACTTATGTGCTAGTATATTTG
1 CTTCGACTTGGCTAATGATGCACTTATGTGCTAGTATATTTG
* *
20664438 CTTCGACTTGGCTAATGATGCACTTTTGTGCTGGTATATTTG
1 CTTCGACTTGGCTAATGATGCACTTATGTGCTAGTATATTTG
20664480 CTTC
1 CTTC
20664484 AGTTTATTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (42 bp):
CTTCGACTTGGCTAATGATGCACTTATGTGCTAGTATATTTG
Found at i:20675214 original size:17 final size:18
Alignment explanation
Indices: 20675192--20675229 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
20675182 AACCCAACTG
20675192 AAAATTAAAGGA-AATTT
1 AAAATTAAAGGACAATTT
**
20675209 AAAATTTTAGGACAATTT
1 AAAATTAAAGGACAATTT
20675227 AAA
1 AAA
20675230 TAGGGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (18 bp):
AAAATTAAAGGACAATTT
Found at i:20677030 original size:22 final size:22
Alignment explanation
Indices: 20676994--20677040 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
20676984 GAATGATAAG
20676994 TAAATAATCAAGCAAATAAATAT
1 TAAATAATCAAGCAAATAAAT-T
* *
20677017 TAAAT-ATTAAGCAAATTAATT
1 TAAATAATCAAGCAAATAAATT
20677038 TAA
1 TAA
20677041 TAGTATGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 13 0.59
23 5 0.23
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (22 bp):
TAAATAATCAAGCAAATAAATT
Found at i:20678128 original size:18 final size:18
Alignment explanation
Indices: 20678094--20678128 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20678084 GTTATTAGGG
*
20678094 TTTGGGTTTAAGTTTTAT
1 TTTGGGTTTAAGATTTAT
*
20678112 TTTGGGTTTTAGATTTA
1 TTTGGGTTTAAGATTTA
20678129 GGTTAAAAAC
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:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (18 bp):
TTTGGGTTTAAGATTTAT
Found at i:20687860 original size:21 final size:21
Alignment explanation
Indices: 20687836--20687883 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
20687826 ATAGTATTCT
20687836 TATGTTTGATTGAATGAAATA
1 TATGTTTGATTGAATGAAATA
20687857 TATGTTTGATTGAATGAAATA
1 TATGTTTGATTGAATGAAATA
20687878 TATGTT
1 TATGTT
20687884 GTAATAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (21 bp):
TATGTTTGATTGAATGAAATA
Found at i:20689916 original size:16 final size:16
Alignment explanation
Indices: 20689895--20689926 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20689885 AGACTCATAT
20689895 AGGTTCAAATAAAATA
1 AGGTTCAAATAAAATA
20689911 AGGTTCAAATAAAATA
1 AGGTTCAAATAAAATA
20689927 TGGAGCAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (16 bp):
AGGTTCAAATAAAATA
Found at i:20690026 original size:23 final size:24
Alignment explanation
Indices: 20689999--20690050 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
20689989 AAGTATTCCC
* *
20689999 CATCTAAGTTTTAATAACCTAAAA
1 CATCTAAGTTTTAAGAACCCAAAA
20690023 -ATCTAAGTTTTAAGAACCCAAAA
1 CATCTAAGTTTTAAGAACCCAAAA
20690046 CATCT
1 CATCT
20690051 TTCAATAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (24 bp):
CATCTAAGTTTTAAGAACCCAAAA
Found at i:20692185 original size:28 final size:28
Alignment explanation
Indices: 20692133--20692186 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
20692123 ATCCAACATA
*
20692133 AACCCAAATACCCAATCTAATATAAATT
1 AACCCAAATACCCAATCCAATATAAATT
*
20692161 AACCCAAGTACCCAA-CCAATCATAAA
1 AACCCAAATACCCAATCCAAT-ATAAA
20692187 AATTACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.19
Consensus pattern (28 bp):
AACCCAAATACCCAATCCAATATAAATT
Found at i:20692287 original size:9 final size:9
Alignment explanation
Indices: 20692269--20692354 Score: 127
Period size: 9 Copynumber: 9.6 Consensus size: 9
20692259 TTTATACAAA
20692269 TAATTCGGT
1 TAATTCGGT
*
20692278 TAATTTGGT
1 TAATTCGGT
*
20692287 TAATTAGGT
1 TAATTCGGT
* *
20692296 TAATTTGGG
1 TAATTCGGT
*
20692305 TAATTCGGG
1 TAATTCGGT
20692314 TAATTCGGT
1 TAATTCGGT
20692323 TAATTCGGT
1 TAATTCGGT
20692332 TAATTCGGT
1 TAATTCGGT
20692341 TAATTCGGT
1 TAATTCGGT
20692350 TAATT
1 TAATT
20692355 TTATACTTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 71 1.00
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.45
Consensus pattern (9 bp):
TAATTCGGT
Found at i:20694919 original size:2 final size:2
Alignment explanation
Indices: 20694914--20694950 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20694904 TCCTTAAAAA
20694914 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
20694951 CACATAAACA
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:20695001 original size:14 final size:16
Alignment explanation
Indices: 20694973--20695005 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
20694963 TTTAAGGGCA
20694973 AAAAATATATATACAT
1 AAAAATATATATACAT
20694989 AAAAATAT-T-TACAT
1 AAAAATATATATACAT
20695003 AAA
1 AAA
20695006 GCTATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATATATATACAT
Found at i:20697443 original size:17 final size:18
Alignment explanation
Indices: 20697423--20697459 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20697413 AAAAAATCTT
*
20697423 TTTTAAAA-ATAAAACAA
1 TTTTAAAATATAAAAAAA
20697440 TTTTAAAATATAAAAAAA
1 TTTTAAAATATAAAAAAA
20697458 TT
1 TT
20697460 GTTGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTTAAAATATAAAAAAA
Found at i:20697443 original size:18 final size:19
Alignment explanation
Indices: 20697422--20697469 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 19
20697412 AAAAAAATCT
*
20697422 TTTTTAAAA-ATAAAACAA
1 TTTTTAAAATATAAAAAAA
20697440 -TTTTAAAATATAAAAAAA
1 TTTTTAAAATATAAAAAAA
20697458 TTGTTGTAAAAT
1 TT-TT-TAAAAT
20697470 CGACACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.32
18 8 0.32
19 1 0.04
20 2 0.08
21 6 0.24
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
TTTTTAAAATATAAAAAAA
Found at i:20701257 original size:44 final size:43
Alignment explanation
Indices: 20701204--20701413 Score: 163
Period size: 44 Copynumber: 4.8 Consensus size: 43
20701194 CCATTGTAAT
* ** *
20701204 TTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGTTGGAAC
1 TTCAAGGAGAA-AGATTTGTAGCTTCGATCTACTCCAATGCAAC
* * * * * *
20701248 TTCAAGGAGATAAGAATTGTGGCTTCGAGCCACTCCAATGCCAT
1 TTCAAGGAGA-AAGATTTGTAGCTTCGATCTACTCCAATGCAAC
* * ** *
20701292 TTCAGGGAGAAAAATTTGTAGCTTCGATCTACTCCGCTGGAAC
1 TTCAAGGAGAAAGATTTGTAGCTTCGATCTACTCCAATGCAAC
* * * * * *
20701335 TTCAACGAGATAAGAATTG-CGACTTCGAGTC-GCTCCAATGCCAT
1 TTCAAGGAGA-AAGATTTGTAG-CTTCGA-TCTACTCCAATGCAAC
20701379 TTCAAGGAGAAGAGATTTGTAGCTTCGATCTACTC
1 TTCAAGGAGAA-AGATTTGTAGCTTCGATCTACTC
20701414 TGCCGAAACC
Statistics
Matches: 123, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
43 35 0.28
44 84 0.68
45 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
TTCAAGGAGAAAGATTTGTAGCTTCGATCTACTCCAATGCAAC
Found at i:20701333 original size:87 final size:86
Alignment explanation
Indices: 20701202--20701515 Score: 397
Period size: 87 Copynumber: 3.7 Consensus size: 86
20701192 TTCCATTGTA
* *
20701202 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGTTGGAACTTCAAGGAGATAAGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGAGATAAGAATTG
20701267 TGGCTTCGAGCCACTCCAATGCC
66 TGGCTTCGAG-C-CTCCAATGCC
* * *
20701290 ATTTCAGGGAGAA-AAATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAACGAGATAAGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGAGATAAGAATTG
* *
20701354 CGACTTCGAGTCGCTCCAATGCC
66 TGGCTTCGAG-C-CTCCAATGCC
* * * * *
20701377 ATTTCAAGGAGAAGAGATTTGTAGCTTCGATCTACTCTGCCGAAACCTCAAGGAGATACGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGAGATAAGAATTG
*
20701442 TGGCTTCGAGCC-GC--T-CC
66 TGGCTTCGAGCCTCCAATGCC
* * *
20701459 ATTCCAGGGAGAAGAGATTTGTAGCCTT-GATCTATTCCGTTGAAACTTCAAGGAGAT
1 ATTTCAGGGAGAAGAGATTTGTAG-CTTCGATCTACTCCGCTGAAACTTCAAGGAGAT
20701516 CTGCTGTTGA
Statistics
Matches: 199, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
82 48 0.24
83 4 0.02
85 1 0.01
86 1 0.01
87 80 0.40
88 65 0.33
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (86 bp):
ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGAGATAAGAATTG
TGGCTTCGAGCCTCCAATGCC
Found at i:20701846 original size:175 final size:174
Alignment explanation
Indices: 20701571--20702021 Score: 406
Period size: 175 Copynumber: 2.6 Consensus size: 174
20701561 ACTTGTAATT
* * ** * ** ** **
20701571 TTCAGCCTGTTACCCTATTGTTTAGGGGGTTAAGGTTCGCTGTCTTTTATCCGCTCAACTACTGC
1 TTCAGCCCGTTACCCTACTACTTAGGGGGTTAAGGCTAACTGTCTTCAATTTGCTCAACTACTGC
* * * * *
20701636 TTAGGGAGATAAGATCTGTAATTCAACATGTTACCCTACTGCTTAGAGGGTCGAGGCTCACCGTC
66 TTAGGGAGACAAGATCTATAATTCAACATGTTACCCTACTACTTAGAGGGTCAAGGCTCACCATC
* * *
20701701 TTTGATCTGTTCCACTACAACTTCT-GGGAGACAAGATCTGCAATC
131 TTCGATCTGCTCCACTAC-ACTT-TAGGGAGACAAGATCTACAATC
* * * ** * *
20701746 TTTAGCCCGTTACCTTACTACTTA-GGGGTTATGGCTTGCT-TCTTCAATTTGCTCCACTACTGT
1 TTCAGCCCGTTACCCTACTACTTAGGGGGTTAAGGCTAACTGTCTTCAATTTGCTCAACTACTGC
* * * * * *
20701809 TTAGGGAGGCAAGATCTATAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTACCA
66 TTAGGGAGACAAGATCTATAA--TTCAACATGTTACCCTACTACTTAGAGGGTCAAGGCTCACCA
* * ** *
20701874 TCTTCGATTTGCTCTACTACTGTTTAGGGAGACAAGGTCTACAATC
129 TCTTCGATCTGCTCCACTACACTTTAGGGAGACAAGATCTACAATC
* * * **
20701920 TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTAACTGTCTTCGATTTGCTTC-GCTACAA
1 TTCAGCCCGTTACCCTACTACTTAGGGGGTTAAGGCTAACTGTCTTCAATTTGC-TCAACTACTG
* *
20701984 CTTCAGGGAGACAAGATTTATGAATTCACCGATGTTAC
65 CTT-AGGGAGACAAGATCTAT-AATTCAAC-ATGTTAC
20702022 TACATTATAC
Statistics
Matches: 218, Mismatches: 49, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
173 36 0.17
174 54 0.25
175 81 0.37
176 22 0.10
177 23 0.11
178 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (174 bp):
TTCAGCCCGTTACCCTACTACTTAGGGGGTTAAGGCTAACTGTCTTCAATTTGCTCAACTACTGC
TTAGGGAGACAAGATCTATAATTCAACATGTTACCCTACTACTTAGAGGGTCAAGGCTCACCATC
TTCGATCTGCTCCACTACACTTTAGGGAGACAAGATCTACAATC
Found at i:20701857 original size:44 final size:43
Alignment explanation
Indices: 20701809--20701946 Score: 106
Period size: 44 Copynumber: 3.1 Consensus size: 43
20701799 CCACTACTGT
20701809 TTAGGGAGGCAAGATCTATAATCTTCAGCCTGTTACCCTACTAC
1 TTAGGGAGGCAAG-TCTATAATCTTCAGCCTGTTACCCTACTAC
* * * * *
20701853 TTAGGG-GGTTAAGGCT-TACCATCTTC-G-AT-TTGCTCTACTAC
1 TTAGGGAGG-CAAGTCTATA--ATCTTCAGCCTGTTACCCTACTAC
* *
20701894 TGTTTAGGGAGACAAGGTCTACAATCTTCAGCCTGTTACCCTACTAC
1 ---TTAGGGAGGCAA-GTCTATAATCTTCAGCCTGTTACCCTACTAC
20701941 TTAGGG
1 TTAGGG
20701947 GGTTAAGGCT
Statistics
Matches: 70, Mismatches: 12, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
41 10 0.14
42 3 0.04
43 5 0.07
44 35 0.50
45 5 0.07
46 2 0.03
47 10 0.14
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (43 bp):
TTAGGGAGGCAAGTCTATAATCTTCAGCCTGTTACCCTACTAC
Found at i:20701920 original size:88 final size:88
Alignment explanation
Indices: 20701571--20701974 Score: 354
Period size: 88 Copynumber: 4.6 Consensus size: 88
20701561 ACTTGTAATT
* ** * ** ** *
20701571 TTCAGCCTGTTACCCTATTGTTTAGGGGGTTAAGG-TT-CGCTGTCTTTTATCCGCTCAACTACT
1 TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTAC-C-ATCTTCGATTTGCTCCACTACT
* * **
20701634 GCTTAGGGAGATAAGATCTGTAA--
64 GTTTAGGGAGACAAGATCTACAATC
* * * * ** * * * * * **
20701657 TTCAACATGTTACCCTACTGCTTAGAGGGTCGAGGCTCACCGTCTTTGATCTGTTCCACTACAAC
1 TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTACCATCTTCGATTTGCTCCACTAC-TG
*
20701722 TTCT-GGGAGACAAGATCTGCAATC
65 TT-TAGGGAGACAAGATCTACAATC
* * * * * * *
20701746 TTTAGCCCGTTACCTTACTACTTA-GGGGTTATGGCTT-GCTTCTTCAATTTGCTCCACTACTGT
1 TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTACCATCTTCGATTTGCTCCACTACTGT
* *
20701809 TTAGGGAGGCAAGATCTATAATC
66 TTAGGGAGACAAGATCTACAATC
*
20701832 TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTACCATCTTCGATTTGCTCTACTACTGT
1 TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTACCATCTTCGATTTGCTCCACTACTGT
*
20701897 TTAGGGAGACAAGGTCTACAATC
66 TTAGGGAGACAAGATCTACAATC
* **
20701920 TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTAACTGTCTTCGATTTGCT
1 TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTACCATCTTCGATTTGCT
20701975 TCGCTACAAC
Statistics
Matches: 256, Mismatches: 53, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
85 1 0.00
86 85 0.33
87 48 0.19
88 104 0.41
89 18 0.07
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (88 bp):
TTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTACCATCTTCGATTTGCTCCACTACTGT
TTAGGGAGACAAGATCTACAATC
Found at i:20701966 original size:44 final size:43
Alignment explanation
Indices: 20701828--20701957 Score: 131
Period size: 44 Copynumber: 3.0 Consensus size: 43
20701818 CAAGATCTAT
20701828 AATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTAC
1 AATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGC-TAC
* * * * * **
20701872 CATCTTC-G-AT-TTGCTCTACTACTGTTTAGGGAGACAAGGTCTAC
1 AATCTTCAGCCTGTTACCCTACTAC---TTAGGGGGTTAAGG-CTAC
20701916 AATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTA
1 AATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTA
20701958 ACTGTCTTCG
Statistics
Matches: 65, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
41 10 0.15
42 1 0.02
43 4 0.06
44 37 0.57
45 2 0.03
46 1 0.02
47 10 0.15
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (43 bp):
AATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTAC
Found at i:20702172 original size:64 final size:64
Alignment explanation
Indices: 20702081--20702261 Score: 308
Period size: 64 Copynumber: 2.8 Consensus size: 64
20702071 TGCTTATACC
* * *
20702081 AAATAATTAGGATGTTATGATCAAAATGAATTAGATGCTCCTAACTAGATGTGATGCTTATGTT
1 AAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTGATGCTTATGTT
*
20702145 AAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTGATGCTTCTGTT
1 AAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTGATGCTTATGTT
* *
20702209 AAATAATTAGGATGCTATGATCGAAATGAATCAAATACTCCTAACTAGATGTG
1 AAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTG
20702262 TTATGAATGT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 111 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (64 bp):
AAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTGATGCTTATGTT
Found at i:20703185 original size:39 final size:39
Alignment explanation
Indices: 20703126--20703203 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
20703116 AAAACTAGGC
* *
20703126 GCCCCAGACATCGCAGCTTGAGCTTCTCTGTTCCAACTT
1 GCCCAAGACATCGCAGCTTGAGCTTCTCTGTACCAACTT
20703165 GCCCAAGACATCGCAGCTTGAGCTTCTCTGTACCAACTT
1 GCCCAAGACATCGCAGCTTGAGCTTCTCTGTACCAACTT
20703204 CTTGAGGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.27
Consensus pattern (39 bp):
GCCCAAGACATCGCAGCTTGAGCTTCTCTGTACCAACTT
Found at i:20705783 original size:46 final size:46
Alignment explanation
Indices: 20705724--20705991 Score: 358
Period size: 46 Copynumber: 5.8 Consensus size: 46
20705714 AGTGTGCTCT
* * *
20705724 CTGATGTGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
20705770 CTGATATGAAATGTGTAAGACCATGGTTGAAAAATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
20705816 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
20705862 CTAATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *
20705908 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
20705955 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
20705992 TATGACATCA
Statistics
Matches: 202, Mismatches: 19, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
46 160 0.79
47 42 0.21
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:20707405 original size:20 final size:19
Alignment explanation
Indices: 20707375--20707426 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
20707365 TCCCACGATC
20707375 CTTTTTGTTGTTTTTTCCCCT
1 CTTTTT-TTGTTTTTT-CCCT
* *
20707396 CTTTTTTTG-TGTTTCTCT
1 CTTTTTTTGTTTTTTCCCT
*
20707414 CTTTTTTTCTTTT
1 CTTTTTTTGTTTT
20707427 CTTTTTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 11 0.42
19 6 0.23
20 3 0.12
21 6 0.23
ACGTcount: A:0.00, C:0.19, G:0.08, T:0.73
Consensus pattern (19 bp):
CTTTTTTTGTTTTTTCCCT
Found at i:20712600 original size:11 final size:11
Alignment explanation
Indices: 20712584--20712611 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20712574 TATAAAAATA
20712584 TTAAATGTATT
1 TTAAATGTATT
20712595 TTAAATGTATT
1 TTAAATGTATT
20712606 TTAAAT
1 TTAAAT
20712612 TAGCAGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (11 bp):
TTAAATGTATT
Found at i:20714361 original size:18 final size:19
Alignment explanation
Indices: 20714327--20714363 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
20714317 TATAAATATA
20714327 ATATATAATTATTATTTAAC
1 ATATATAATTA-TATTTAAC
20714347 ATATATAATTA-ATTTAA
1 ATATATAATTATATTTAA
20714364 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATAATTATATTTAAC
Found at i:20716567 original size:13 final size:13
Alignment explanation
Indices: 20716549--20716574 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20716539 GCTATCAACA
20716549 CCGTGATTCCAGG
1 CCGTGATTCCAGG
20716562 CCGTGATTCCAGG
1 CCGTGATTCCAGG
20716575 TTTCGAATCA
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
CCGTGATTCCAGG
Found at i:20717553 original size:19 final size:19
Alignment explanation
Indices: 20717529--20717567 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20717519 CTTTATTCCT
20717529 TTTCGATTATTAT-TATATA
1 TTTCGA-TATTATGTATATA
*
20717548 TTTCGATATTTTGTATATA
1 TTTCGATATTATGTATATA
20717567 T
1 T
20717568 ATTTATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTCGATATTATGTATATA
Found at i:20723586 original size:2 final size:2
Alignment explanation
Indices: 20723579--20723605 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20723569 ATCCCACCTT
20723579 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20723606 TTAGTATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20727009 original size:27 final size:25
Alignment explanation
Indices: 20726976--20727039 Score: 94
Period size: 27 Copynumber: 2.5 Consensus size: 25
20726966 CCCTCCCTAA
20726976 AAAAAACCTAACCAAAAAAAGAAAAAG
1 AAAAAACCTAACC-AAAAAA-AAAAAG
*
20727003 AAAAAACCTAACCCAAAAAAAAAAG
1 AAAAAACCTAACCAAAAAAAAAAAG
20727028 -AAAAACCTAACC
1 AAAAAACCTAACC
20727040 CCCAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 12 0.33
25 6 0.17
26 5 0.14
27 13 0.36
ACGTcount: A:0.70, C:0.20, G:0.05, T:0.05
Consensus pattern (25 bp):
AAAAAACCTAACCAAAAAAAAAAAG
Found at i:20727040 original size:24 final size:25
Alignment explanation
Indices: 20726976--20727050 Score: 98
Period size: 24 Copynumber: 3.0 Consensus size: 25
20726966 CCCTCCCTAA
*
20726976 AAAAAACCTAACCAAAAAAAGAAAAAG
1 AAAAAACCTAACC-CAAAAA-AAAAAG
20727003 AAAAAACCTAACCCAAAAAAAAAAG
1 AAAAAACCTAACCCAAAAAAAAAAG
**
20727028 -AAAAACCTAACCCCCAAAAAAAA
1 AAAAAACCTAACCCAAAAAAAAAA
20727051 CTAAGAAACC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 21 0.47
25 6 0.13
26 5 0.11
27 13 0.29
ACGTcount: A:0.71, C:0.21, G:0.04, T:0.04
Consensus pattern (25 bp):
AAAAAACCTAACCCAAAAAAAAAAG
Found at i:20727047 original size:27 final size:26
Alignment explanation
Indices: 20726976--20727050 Score: 100
Period size: 25 Copynumber: 2.9 Consensus size: 26
20726966 CCCTCCCTAA
*
20726976 AAAAAACCTAACCAAAAAAAGAAAAAG
1 AAAAAACCTAACCCAAAAAA-AAAAAG
20727003 AAAAAACCTAACCC-AAAAAAAAAAG
1 AAAAAACCTAACCCAAAAAAAAAAAG
**
20727028 -AAAAACCTAACCCCCAAAAAAAA
1 AAAAAACCTAACCCAAAAAAAAAA
20727051 CTAAGAAACC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.29
25 14 0.31
26 5 0.11
27 13 0.29
ACGTcount: A:0.71, C:0.21, G:0.04, T:0.04
Consensus pattern (26 bp):
AAAAAACCTAACCCAAAAAAAAAAAG
Found at i:20727843 original size:37 final size:37
Alignment explanation
Indices: 20727801--20727902 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 37
20727791 CTAATATTTT
20727801 CTTTTATTGTAGATATTATTATTATTATTAT-TACATA
1 CTTTTATT-TAGATATTATTATTATTATTATGTACATA
*
20727838 CTTTTATTATATGCATATATATATATGTATTTTTATGTACATA
1 CTTTTATT-TA-G-ATAT-TAT-TAT-TATTATTATGTACATA
*
20727881 -TTATTATTT-TATATTATTATTA
1 CTT-TTATTTAGATATTATTATTA
20727903 CCAAATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 8 0.15
40 3 0.05
41 3 0.05
42 11 0.20
43 11 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (37 bp):
CTTTTATTTAGATATTATTATTATTATTATGTACATA
Found at i:20729546 original size:12 final size:12
Alignment explanation
Indices: 20729529--20729564 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
20729519 ATTCATTTGA
20729529 CATTCATGCATT
1 CATTCATGCATT
20729541 CATTCATGCATT
1 CATTCATGCATT
*
20729553 CATTCATACATT
1 CATTCATGCATT
20729565 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:20737406 original size:224 final size:221
Alignment explanation
Indices: 20737016--20737573 Score: 850
Period size: 224 Copynumber: 2.5 Consensus size: 221
20737006 TGATTAGTAC
*
20737016 AAAAAATCAACTCATATTGCGAGAAATAAGTTGAGCCTCAAGA-AGTGCTGAGGTATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA-TGCTGAGGTATTTTCAATT
*
20737080 TTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGT
65 TTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
* * ** * *
20737145 AAATTCGATTTCTGTTTTTAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATG
130 AAATTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
20737210 CTAAGGTAATTTCAATTTCTGTTGTCAAAA
195 CTAAGGTAATTTCAATTTCTGTTGTC---A
20737240 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTT
20737305 TTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
66 TTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
* *
20737370 ATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
131 AATTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGC
* * *
20737435 TGAGGTATTTTCAATTTCTGTTTTCA
196 TAAGGTAATTTCAATTTCTGTTGTCA
* ** * * *
20737461 AAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCATAGGCTAAGGTATTTTCAA
1 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACAT--GCTGAGGTATTTTCAA
* *
20737525 TTTCTGTCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGC
63 TTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
20737574 TTCAGATCAC
Statistics
Matches: 309, Mismatches: 21, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
220 1 0.00
221 40 0.13
223 62 0.20
224 205 0.66
225 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (221 bp):
AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTT
TTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
AATTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGC
TAAGGTAATTTCAATTTCTGTTGTCA
Found at i:20737598 original size:77 final size:74
Alignment explanation
Indices: 20737016--20737578 Score: 679
Period size: 72 Copynumber: 7.6 Consensus size: 74
20737006 TGATTAGTAC
** * * *
20737016 AAAAAATCAACTCATATTGCGAGAAATAAGTTGAGCCTCAAGA-AGTGCTGAGGTATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA-CGCTGAGGTATTTTCAATT
*
20737080 TTTGTCTTTCA
65 TCTGT-TTTCA
* * ** *
20737091 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGTAAATTCGATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
20737156 CTGTTTT--
66 CTGTTTTCA
* * * * *
20737163 TAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTAAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
20737228 CTGTTGTCAAAA
66 CTGTTTTC---A
** * *
20737240 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
20737305 TTGTCTTTCA
66 CTGT-TTTCA
* *
20737315 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
20737380 CTGTTTTC-
66 CTGTTTTCA
* ** * *
20737388 -AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
20737452 CTGTTTTCA
66 CTGTTTTCA
* * * *
20737461 AAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCATAGGCTAAGGTATTTTCAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAA
20737525 TTTCTGTCTTTCA
63 TTTCTGT-TTTCA
* *
20737538 AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTTCAG
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
20737579 ATCACACACT
Statistics
Matches: 423, Mismatches: 51, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
72 130 0.31
73 1 0.00
74 41 0.10
75 121 0.29
76 24 0.06
77 102 0.24
78 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (74 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
CTGTTTTCA
Found at i:20738498 original size:20 final size:20
Alignment explanation
Indices: 20738468--20738516 Score: 89
Period size: 20 Copynumber: 2.4 Consensus size: 20
20738458 CAAAAAAAGA
20738468 AAAAGAAAAAACCTAACCCCC
1 AAAA-AAAAAACCTAACCCCC
20738489 AAAAAAAAAACCTAACCCCC
1 AAAAAAAAAACCTAACCCCC
20738509 AAAAAAAA
1 AAAAAAAA
20738517 CCAAGAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.65, C:0.29, G:0.02, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAACCTAACCCCC
Found at i:20743405 original size:14 final size:14
Alignment explanation
Indices: 20743372--20743405 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20743362 ATAAAAGTAT
20743372 ATATATGTGTAATA
1 ATATATGTGTAATA
* *
20743386 AAATATGTGTACTA
1 ATATATGTGTAATA
20743400 ATATAT
1 ATATAT
20743406 AATAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (14 bp):
ATATATGTGTAATA
Found at i:20743637 original size:21 final size:21
Alignment explanation
Indices: 20743600--20743657 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
20743590 ATATAAATAT
*
20743600 ATATAAATA-ATAGTATTAGAA
1 ATATACATATATA-TATTAGAA
*
20743621 ATATACCATATA-ATATTAGAT
1 ATATA-CATATATATATTAGAA
20743642 ATATACATATATATAT
1 ATATACATATATATAT
20743658 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 6 0.19
21 21 0.66
22 4 0.12
23 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATATACATATATATATTAGAA
Found at i:20743653 original size:2 final size:2
Alignment explanation
Indices: 20743628--20743668 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
20743618 GAAATATACC
* *
20743628 AT AT A- AT AT -T AG AT AT AT AC 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
20743668 A
1 A
20743669 ATAGTATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:20743698 original size:64 final size:60
Alignment explanation
Indices: 20743590--20743734 Score: 145
Period size: 64 Copynumber: 2.4 Consensus size: 60
20743580 ACATACACAC
* * * *
20743590 ATATAAATATATATAAATAATAGTATTAGAAATATACCATATAATATT-AGATATATACAT
1 ATATATATATATATATATAATAGTATAAGAAATATACCATATAATATTAAAATATATA-AT
*
20743650 ATATATATATATATATATAATAGTATGAAAGAAAAATATAAC-TAATAATATTAAAAATATATAA
1 ATATATATATATATATATAATAGTAT--AAG--AAATATACCAT-ATAATATT-AAAATATATAA
20743714 T
60 T
*
20743715 A-ATATATATA-AAATATAATA
1 ATATATATATATATATATAATA
20743735 TTAAGGACTT
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
60 24 0.33
62 2 0.03
63 10 0.14
64 25 0.35
65 3 0.04
66 8 0.11
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (60 bp):
ATATATATATATATATATAATAGTATAAGAAATATACCATATAATATTAAAATATATAAT
Found at i:20743705 original size:21 final size:21
Alignment explanation
Indices: 20743681--20743734 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
20743671 AGTATGAAAG
20743681 AAAAATATAACTAATAATAT-T
1 AAAAATATAA-TAATAATATAT
20743702 AAAAATAT-ATAATAATATAT
1 AAAAATATAATAATAATATAT
20743722 ATAAAATATAATA
1 A-AAAATATAATA
20743735 TTAAGGACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.30
20 3 0.10
21 15 0.50
22 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATATAATAATAATATAT
Found at i:20743708 original size:9 final size:10
Alignment explanation
Indices: 20743681--20743731 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
20743671 AGTATGAAAG
20743681 AAAAATATAACT
1 AAAAATAT-A-T
*
20743693 AATAATAT-T
1 AAAAATATAT
20743702 AAAAATATAT
1 AAAAATATAT
*
20743712 AATAATATAT
1 AAAAATATAT
20743722 ATAAAATATA
1 A-AAAATATA
20743732 ATATTAAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 8 0.24
10 11 0.33
11 7 0.21
12 7 0.21
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATATAT
Found at i:20743949 original size:13 final size:14
Alignment explanation
Indices: 20743931--20743961 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
20743921 ATGTATGAAT
20743931 ATATACATATA-TA
1 ATATACATATATTA
20743944 ATATACATATATTA
1 ATATACATATATTA
20743958 ATAT
1 ATAT
20743962 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATACATATATTA
Found at i:20744557 original size:14 final size:14
Alignment explanation
Indices: 20744522--20744549 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20744512 AAAAAAAGAG
20744522 AAAAGGAGAGGGGA
1 AAAAGGAGAGGGGA
20744536 AAAAGGAGAGGGGA
1 AAAAGGAGAGGGGA
20744550 GAGGGGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (14 bp):
AAAAGGAGAGGGGA
Found at i:20746078 original size:74 final size:71
Alignment explanation
Indices: 20745933--20746181 Score: 254
Period size: 74 Copynumber: 3.5 Consensus size: 71
20745923 AATTAAAAGA
* * * * * *
20745933 CTCAACTCACCTCTCGTAATATGAATTGACTCTTTA-AGATA-GAATTTGAAAATACCTTAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGA-T-TTTAGAAACATGAA-TTGAAATTACCTCAGCGT
*
20745996 GCCGCAAGG
63 GCCCCAAGG
* *
20746005 CTCAACTCACCTCTCGCAATATGAGTCGATTTTAGATTTA-ATGGGAATTGAAATTACCTCAGCG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGA--AACAT--GAATTGAAATTACCTCAGCG
20746069 TGCCCCAAGG
62 TGCCCCAAGG
* * * * *
20746079 TTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATGAATTGAAATTACC-CAACGTGTC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAACATGAATTGAAATTACCTCAGCGTGCC
***
20746143 TTGAGG
66 CCAAGG
20746149 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
20746182 CTTGGAAACA
Statistics
Matches: 151, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
70 45 0.30
71 16 0.11
72 28 0.19
73 3 0.02
74 56 0.37
75 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (71 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAACATGAATTGAAATTACCTCAGCGTGCC
CCAAGG
Found at i:20746323 original size:71 final size:71
Alignment explanation
Indices: 20746207--20746573 Score: 272
Period size: 71 Copynumber: 4.9 Consensus size: 71
20746197 TAAAAAGCAG
* * *
20746207 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
20746272 AAACAT
66 AAACAT
* * *
20746278 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTCT
1 AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-TTT-T
20746343 TGGAAAACAT
64 T-G-AAACAT
* * ** * ** * * * * *
20746353 GAATTAAAAAGTAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATA
1 AAATTGAAAA-T---ACCTCAACGTGCC-CTGAG-G--CTCA-ACTC-A--C-C-TCTCGCAATA
* *
20746418 TGAGTTGATTTTT-ATTTA-AT
52 TGAGCTGATTTTTGA--AACAT
* * *
20746438 AGGAATTGAAATTACCTCAGA-GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGCTTT
1 A--AATTGAAAATACCTCA-ACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
20746502 TTGAAACAT
63 TTGAAACAT
* * *
20746511 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
20746574 CTTGGAAAAC
Statistics
Matches: 228, Mismatches: 42, Indels: 52
0.71 0.13 0.16
Matches are distributed among these distances:
70 1 0.00
71 109 0.48
72 4 0.02
73 26 0.11
74 3 0.01
75 14 0.06
76 1 0.00
77 1 0.00
78 3 0.01
79 9 0.04
80 2 0.01
81 2 0.01
82 3 0.01
83 9 0.04
84 5 0.02
85 3 0.01
86 2 0.01
87 10 0.04
88 4 0.02
89 17 0.07
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (71 bp):
AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
AAACAT
Found at i:20746403 original size:160 final size:159
Alignment explanation
Indices: 20746050--20746502 Score: 707
Period size: 160 Copynumber: 2.8 Consensus size: 159
20746040 ATTTAATGGG
* ** *
20746050 AATTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
* *
20746115 AACATGAATTGAAATTACC-CAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
20746179 TTTCTTGGAAACATGAACTAAAAAGCAGA
131 TTTCTTGGAAACATGAACTAAAAAGCAGA
20746208 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
20746273 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
* *
20746338 TTTCTTGGAAAACATGAATTAAAAAGTAGA
131 TTTCTTGG-AAACATGAACTAAAAAGCAGA
20746368 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-A
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
* * **
20746432 TTTA-ATAGGAATTGAAATTACCTCAGA-GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
66 --AACATA--AATTGAAATTACCTCA-ACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
*
20746495 CTGCTTTT
126 CTGATTTT
20746503 TGAAACATAA
Statistics
Matches: 275, Mismatches: 13, Indels: 10
0.92 0.04 0.03
Matches are distributed among these distances:
158 79 0.29
159 53 0.19
160 85 0.31
161 1 0.00
162 56 0.20
163 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (159 bp):
AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
TTTCTTGGAAACATGAACTAAAAAGCAGA
Found at i:20746487 original size:73 final size:71
Alignment explanation
Indices: 20746367--20746573 Score: 267
Period size: 73 Copynumber: 2.9 Consensus size: 71
20746357 TAAAAAGTAG
* * * *
20746367 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-
1 AAATTGAAATTACCTCAGAGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
*
20746431 ATTTA-AT
66 A--AACAT
* *
20746438 AGGAATTGAAATTACCTCAGAGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGCTTTT
1 A--AATTGAAATTACCTCAGAGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
20746503 TGAAACAT
64 TGAAACAT
* *
20746511 AAATTGAAATTACCTCA-ACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 AAATTGAAATTACCTCAGA-GTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
20746574 CTTGGAAAAC
Statistics
Matches: 120, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
70 1 0.01
71 57 0.47
72 1 0.01
73 60 0.50
74 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (71 bp):
AAATTGAAATTACCTCAGAGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
AAACAT
Found at i:20746487 original size:233 final size:233
Alignment explanation
Indices: 20746208--20746663 Score: 840
Period size: 233 Copynumber: 2.0 Consensus size: 233
20746198 AAAAAGCAGA
* * * *
20746208 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGAGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGA
20746273 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
*
20746338 TTTCTTGGAAAACATGAATTAAAAAGTAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
131 TTTCTTGGAAAACATGAATTAAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
20746403 TCACTTCTCGCAATATGAGTTGATTTTTATTTAATAGG
196 TCACTTCTCGCAATATGAGTTGATTTTTATTTAATAGG
* *
20746441 AATTGAAATTACCTCAGAGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGCTTTTTGA
1 AATTGAAAATACCTCAGAGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGA
20746506 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
*
20746571 TTTCTTGGAAAACATGAATTAAAAAGCAGAAATTGGAAATACCTCAGCGTGCCCTGAGGCTCAAC
131 TTTCTTGGAAAACATGAATTAAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
20746636 TCACTTCTCGCAATATGAGTTGATTTTT
196 TCACTTCTCGCAATATGAGTTGATTTTT
20746664 GGAAAAAACA
Statistics
Matches: 215, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
233 215 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (233 bp):
AATTGAAAATACCTCAGAGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGA
AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
TTTCTTGGAAAACATGAATTAAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
TCACTTCTCGCAATATGAGTTGATTTTTATTTAATAGG
Found at i:20753849 original size:13 final size:14
Alignment explanation
Indices: 20753831--20753864 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
20753821 TGTGTATTCT
20753831 TTATTTTATT-TTA
1 TTATTTTATTATTA
*
20753844 TTATTTTATTATTT
1 TTATTTTATTATTA
20753858 TTATTTT
1 TTATTTT
20753865 CACAAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTATTATTA
Found at i:20769550 original size:2 final size:2
Alignment explanation
Indices: 20769538--20769579 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
20769528 TCGAACTTTA
*
20769538 AT AT TT 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
20769580 CAGGATCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20771653 original size:42 final size:43
Alignment explanation
Indices: 20771531--20771705 Score: 139
Period size: 43 Copynumber: 4.1 Consensus size: 43
20771521 GGAACGTTGT
*
20771531 CATCGAT-CTGAGA-TATCATGTAAGACCGTGTCTGGGACA-CAGG
1 CATCGATACTGA-ATTA-CATGTAAGACCCTGTCTGGGACATC-GG
* * * * *
20771574 CCTCAAT-TTGAGATTTACATGTAAGACCATGTTTGGGACATCGG
1 CATCGATACTGA-A-TTACATGTAAGACCCTGTCTGGGACATCGG
* * **
20771618 CATCG-TATCTGAATT-CGTGTAAGACCCTGTCTGGGATAAAGG
1 CATCGATA-CTGAATTACATGTAAGACCCTGTCTGGGACATCGG
*
20771660 CATCGATACTGAATTACATGTAAGATCAC-GTCTGGGACATCGG
1 CATCGATACTGAATTACATGTAAGA-CCCTGTCTGGGACATCGG
20771703 CAT
1 CAT
20771706 TGTACCCGTT
Statistics
Matches: 105, Mismatches: 19, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
42 33 0.31
43 37 0.35
44 29 0.28
45 6 0.06
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (43 bp):
CATCGATACTGAATTACATGTAAGACCCTGTCTGGGACATCGG
Found at i:20771697 original size:85 final size:87
Alignment explanation
Indices: 20771531--20771705 Score: 214
Period size: 85 Copynumber: 2.0 Consensus size: 87
20771521 GGAACGTTGT
* * * *
20771531 CATCGATCTGAGATATCATGTAAGACCGTGTCTGGGACACAGGCCTCAATTTGAGATTTACATGT
1 CATCGATCTGAGATATCATGTAAGACCCTGTCTGGGACAAAGGCATCAATCTGAGATTTACATGT
* *
20771596 AAGACCATGTTTGGGACATCGG
66 AAGACCACGTCTGGGACATCGG
* * *
20771618 CATCGTATCTGA-AT-TCGTGTAAGACCCTGTCTGGGATAAAGGCATCGATACTGA-A-TTACAT
1 CATCG-ATCTGAGATATCATGTAAGACCCTGTCTGGGACAAAGGCATCAAT-CTGAGATTTACAT
*
20771679 GTAAGATCACGTCTGGGACATCGG
64 GTAAGACCACGTCTGGGACATCGG
20771703 CAT
1 CAT
20771706 TGTACCCGTT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
85 30 0.39
86 30 0.39
87 10 0.13
88 6 0.08
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (87 bp):
CATCGATCTGAGATATCATGTAAGACCCTGTCTGGGACAAAGGCATCAATCTGAGATTTACATGT
AAGACCACGTCTGGGACATCGG
Found at i:20771705 original size:43 final size:42
Alignment explanation
Indices: 20771588--20771705 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
20771578 AATTTGAGAT
* *
20771588 TTACATGTAAGACCATGTTTGGGACATCGGCATCGTATCTGAA
1 TTACATGTAAGA-CACGTCTGGGACATCGGCATCGTATCTGAA
* * * **
20771631 TT-CGTGTAAGACCCTGTCTGGGATAAAGGCATCG-ATACTGAA
1 TTACATGTAAGACAC-GTCTGGGACATCGGCATCGTAT-CTGAA
20771673 TTACATGTAAGATCACGTCTGGGACATCGGCAT
1 TTACATGTAAGA-CACGTCTGGGACATCGGCAT
20771706 TGTACCCGTT
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
41 3 0.05
42 30 0.51
43 24 0.41
44 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (42 bp):
TTACATGTAAGACACGTCTGGGACATCGGCATCGTATCTGAA
Found at i:20775205 original size:56 final size:56
Alignment explanation
Indices: 20775111--20775318 Score: 326
Period size: 56 Copynumber: 3.7 Consensus size: 56
20775101 GAAGTATATG
* * * *
20775111 TGGCATCAATATGTGACTCCGATATTTATGTGCGAGTAAGTCCACGTTTAATACGT
1 TGGCATCGATATGTGACTCCGATATATGTGTACGAGTAAGTCCACGTTTAATACGT
* * *
20775167 TGTCATCGATATGTGACTCTGATATATGTGTACGAGTAAGTCCACGTTTCATACGT
1 TGGCATCGATATGTGACTCCGATATATGTGTACGAGTAAGTCCACGTTTAATACGT
* *
20775223 TGGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCACGTTTAATACGT
1 TGGCATCGATATGTGACTCCGATATATGTGTACGAGTAAGTCCACGTTTAATACGT
*
20775279 TGGCATCGATATATGACTCCGATATATGTGTACGAGTAAG
1 TGGCATCGATATGTGACTCCGATATATGTGTACGAGTAAG
20775319 ACCCTGTCTG
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 138 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (56 bp):
TGGCATCGATATGTGACTCCGATATATGTGTACGAGTAAGTCCACGTTTAATACGT
Found at i:20777998 original size:2 final size:2
Alignment explanation
Indices: 20777991--20778018 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20777981 CATTTTATTC
20777991 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
20778019 CCCATGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20779720 original size:2 final size:2
Alignment explanation
Indices: 20779713--20779742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20779703 ATATAGAATA
20779713 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
20779743 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20781778 original size:301 final size:303
Alignment explanation
Indices: 20781428--20782019 Score: 759
Period size: 301 Copynumber: 1.9 Consensus size: 303
20781418 GTTTTTTTTT
* * * * *
20781428 AAAAAATGAGAAAGTTTATATTTTTAAAATTAAAAATTTGGTTTTAGTCATTTTAAAGGAAAGCT
1 AAAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAAATTT-GTTTTAGTCATTTTAAAGAAAAACT
* * *
20781493 TAAATTTTTAAAATAAAGTTTTGATTTTTTT-AACTATTTCGAAATAAAAGCTTTGATTTTTAAG
65 TAAATTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGCTTTAATATTTAAG
***** * *
20781557 AAAAGTAGT-TTTTTT-TTTTTAA-AGAAACTTTAGATTTTTAAAAATAAAAATATGTTTTTTTA
130 AAAAGTAGTATTTTTTAAAAAAAAGAGAAACTTTAGATTTTTAAAAATAAAAATACGTTGTTTTA
* * * *
20781619 GTCATTTTAAAGG-AAAGTTT-AAATTTTTAAAACAAATTTTTGATTTTTTTTTCAACTATTTCG
195 GTCATTTTAAAGGAAAAGTTTAAAAATTTTAAAACAAAGTTTTCA--TCTTTTTCAACTATTTCG
20781682 AAATAAAAGCTTT-AATCTTTAAGAAAAATAGTAATTTTTTTTCCTAA
258 AAAT-AAAGCTTTGAAT-TTTAAGAAAAATAGTAATTTTTTTTCCTAA
*
20781729 AAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAACATTT-TTTTAGTCATTTTAAAGAAAAAT
1 AAAAAAAGAGAAAGTTTAGATTTTT-AAAATAAAAA-ATTTGTTTTAGTCATTTTAAAGAAAAAC
* *
20781793 TTAACTTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGGAATAAAAGCTTTAATATTTAA
64 TTAAATTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGCTTTAATATTTAA
* * *
20781858 GAAAAGTAGTGATTTTTTAAAAGAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCCGTT
129 GAAAAGTAGT-ATTTTTT---A-AAAAAAAGAGAAACTTTAGATTTTTAAAAATAAAAATACGTT
* * *
20781923 GTTTTAGTCATTTTAAAGGAAAATTTTAAAAATTTTAAAATAAGGTTTTCATCTTTTTCAACTAT
189 GTTTTAGTCATTTTAAAGGAAAAGTTTAAAAATTTTAAAACAAAGTTTTCATCTTTTTCAACTAT
*
20781988 TTCGAAATAAAGTTTTGAATTTTAAGAAAAAT
254 TTCGAAATAAAGCTTTGAATTTTAAGAAAAAT
20782020 TGTGCATTTT
Statistics
Matches: 248, Mismatches: 29, Indels: 20
0.84 0.10 0.07
Matches are distributed among these distances:
301 73 0.29
302 48 0.19
303 4 0.02
304 6 0.02
309 21 0.08
310 72 0.29
311 6 0.02
312 18 0.07
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (303 bp):
AAAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAAATTTGTTTTAGTCATTTTAAAGAAAAACTT
AAATTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGCTTTAATATTTAAGA
AAAGTAGTATTTTTTAAAAAAAAGAGAAACTTTAGATTTTTAAAAATAAAAATACGTTGTTTTAG
TCATTTTAAAGGAAAAGTTTAAAAATTTTAAAACAAAGTTTTCATCTTTTTCAACTATTTCGAAA
TAAAGCTTTGAATTTTAAGAAAAATAGTAATTTTTTTTCCTAA
Found at i:20781861 original size:154 final size:151
Alignment explanation
Indices: 20781428--20782040 Score: 622
Period size: 156 Copynumber: 4.0 Consensus size: 151
20781418 GTTTTTTTTT
* * * * *
20781428 AAAAAATGAGAAAGTTTATATTTTT-AAAATTAAAA-ATTTGGTTTTAGTCATTTTAAAGGAAAG
1 AAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAACATTT--TTTTAGTCATTTTAAAGAAAAA
* * *
20781491 CTTAAATTTTTAAAATAAAGTTTTGATTTTTTT-AACTATTTCGAAATAAAAGCTTTGATTTTTA
64 TTTAAATTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGCTTT-AATTTTA
*
20781555 AGAAAAGTAGT--TTTTTT-----
128 AGAAAAATAGTAATTTTTTAAAAG
***** * * * *
20781572 TTTTTAA-AGAAACTTTAGATTTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAG
1 AAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAACA--TTTTTTTAGTCATTTTAAAGAAAAA
* *
20781636 TTTAAATTTTTAAAACAAATTTTTGATTTTTTTTTCAACTATTTCGAAATAAAAGCTTTAATCTT
64 TTTAAATTTTTAAAATAAAATTTTGA--TTTTTTTCAACTATTTCGAAATAAAAGCTTTAAT-TT
**
20781701 TAAGAAAAATAGTAATTTTTTTTCCTAA-
126 TAAGAAAAATAGTAA--TTTTTT-AAAAG
20781729 AAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAACATTTTTTTAGTCATTTTAAAGAAAAATT
1 AAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAACATTTTTTTAGTCATTTTAAAGAAAAATT
* *
20781794 TAACTTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGGAATAAAAGCTTTAATATTTAAG
66 TAAATTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGCTTTAAT-TTTAAG
* *
20781859 AAAAGTAGTGATTTTTTAAAAG
130 AAAAATAGTAATTTTTTAAAAG
* * *
20781881 AAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCCGTTGTTTTAGTCATTTTAAAGGAAAA
1 AAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAA--CATTTTTTTAGTCATTTTAAA-GAAAA
* * ** * * *
20781946 TTTTAAAAATTTTAAAATAAGGTTTTCATCTTTTTCAACTATTTCGAAAT-AAAGTTTTGAATTT
63 ATTT-AAATTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGCTTT-AATTT
* * *
20782010 TAAGAAAAATTGTGCATTTTTCAAAAG
126 TAAGAAAAATAGT-AATTTTTTAAAAG
20782037 AAAA
1 AAAA
20782041 CTTTGATTTT
Statistics
Matches: 396, Mismatches: 48, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
143 15 0.04
144 10 0.03
145 46 0.12
147 12 0.03
148 37 0.09
151 2 0.01
152 47 0.12
154 67 0.17
155 28 0.07
156 102 0.26
157 2 0.01
158 28 0.07
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (151 bp):
AAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAACATTTTTTTAGTCATTTTAAAGAAAAATT
TAAATTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGCTTTAATTTTAAGA
AAAATAGTAATTTTTTAAAAG
Found at i:20782055 original size:21 final size:23
Alignment explanation
Indices: 20782011--20782056 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
20782001 TTTGAATTTT
*
20782011 AAGAAAAATTGTGCATTTTTCAA
1 AAGAAAAATTGTGCATTTTGCAA
*
20782034 AAGAAAACTT-TG-ATTTTGCAA
1 AAGAAAAATTGTGCATTTTGCAA
20782055 AA
1 AA
20782057 AAATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 2 0.10
23 9 0.43
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (23 bp):
AAGAAAAATTGTGCATTTTGCAA
Found at i:20783856 original size:13 final size:13
Alignment explanation
Indices: 20783838--20783902 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 13
20783828 TAGATTTTTC
*
20783838 CTAAATATTATTA
1 CTAAATATTATCA
20783851 CTAAATA--ATCA
1 CTAAATATTATCA
20783862 -TAAATATTATCA
1 CTAAATATTATCA
*
20783874 CTAAATA--ATTA
1 CTAAATATTATCA
20783885 -TAAATATTATCA
1 CTAAATATTATCA
20783897 CTAAAT
1 CTAAAT
20783903 TTTAAAAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
10 12 0.28
11 6 0.14
12 7 0.16
13 18 0.42
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:20783869 original size:23 final size:23
Alignment explanation
Indices: 20783839--20783902 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
20783829 AGATTTTTCC
*
20783839 TAAATATTATTACTAAATAATCA
1 TAAATATTATCACTAAATAATCA
*
20783862 TAAATATTATCACTAAATAATTA
1 TAAATATTATCACTAAATAATCA
20783885 TAAATATTATCACTAAAT
1 TAAATATTATCACTAAAT
20783903 TTTAAAAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATCA
Found at i:20794908 original size:2 final size:2
Alignment explanation
Indices: 20794901--20794938 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20794891 TTCAAAGATA
20794901 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
20794939 TGTTAGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20795733 original size:20 final size:21
Alignment explanation
Indices: 20795691--20795735 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
20795681 TTTATCTAAG
* *
20795691 TAAAAAATTCAAAATTAATAT
1 TAAAAAATTAAAAATCAATAT
*
20795712 TAAAAACTTAAAAATCAA-AT
1 TAAAAAATTAAAAATCAATAT
20795732 TAAA
1 TAAA
20795736 GGGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAATTAAAAATCAATAT
Found at i:20796560 original size:20 final size:21
Alignment explanation
Indices: 20796516--20796561 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
20796506 TTAGTGTGCA
20796516 AGGGTTCAAGATTATGGTTTC
1 AGGGTTCAAGATTATGGTTTC
*
20796537 -GGGTTCTAAG-TTTTGG-TTC
1 AGGGTTC-AAGATTATGGTTTC
20796556 AGGGTT
1 AGGGTT
20796562 TGGGATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 16 0.73
21 3 0.14
ACGTcount: A:0.17, C:0.09, G:0.33, T:0.41
Consensus pattern (21 bp):
AGGGTTCAAGATTATGGTTTC
Found at i:20801058 original size:6 final size:6
Alignment explanation
Indices: 20800996--20801096 Score: 75
Period size: 6 Copynumber: 16.8 Consensus size: 6
20800986 TAATAGTAAA
* * * **
20800996 AGAAGA AGAAGA AGAAGA AGAATA AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* *
20801044 AGAAGG AGAATG AG-AGG A-AGAGG AGGAGG AGGAAGAGG AGAA-G AGAA-G
1 AGAAGG AGAAGG AGAAGG AGA-AGG AGAAGG A-G-A-AGG AGAAGG AGAAGG
20801092 AGAAG
1 AGAAG
20801097 AAATGGAGAT
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
5 13 0.16
6 61 0.75
7 2 0.02
8 1 0.01
9 4 0.05
ACGTcount: A:0.53, C:0.00, G:0.45, T:0.02
Consensus pattern (6 bp):
AGAAGG
Found at i:20808292 original size:30 final size:31
Alignment explanation
Indices: 20808258--20808359 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 31
20808248 ATTTTACATG
* * * *
20808258 TTATTTTATTGTCAGCTTGTGTGAGCAGT-C
1 TTATTATAATGTCAACTTGTGTGAGCAATAC
* *
20808288 TTATTATAATGCCAACTTGTGTGAACAATAC
1 TTATTATAATGTCAACTTGTGTGAGCAATAC
20808319 -TATTATAATGTCAACTTGTGTGAGCAA-AGC
1 TTATTATAATGTCAACTTGTGTGAGCAATA-C
20808349 -TATTATAATGT
1 TTATTATAATGT
20808360 TTCTATCATA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.02
30 60 0.97
31 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (31 bp):
TTATTATAATGTCAACTTGTGTGAGCAATAC
Found at i:20808397 original size:44 final size:44
Alignment explanation
Indices: 20808318--20808403 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
20808308 GTGAACAATA
* * *
20808318 CTATTATAATGTCAACTTGTGTGAGCAAAGCTATTATAATGTTT
1 CTATCATAACGTCAACTTGTGTGAGCAAACCTATTATAATGTTT
*
20808362 CTATCATAACGTCAGCTTGTGTGAG-AAACCTTATTATAATGT
1 CTATCATAACGTCAACTTGTGTGAGCAAACC-TATTATAATGT
20808404 CAACTTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (44 bp):
CTATCATAACGTCAACTTGTGTGAGCAAACCTATTATAATGTTT
Done.