Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 124 of 218
Found at i:37543579 original size:20 final size:19
Alignment explanation
Indices: 37543548--37543585 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
37543538 AGCTAGTAAC
*
37543548 GAGCTCAATGAGTTGAATT
1 GAGCTCAATGAGCTGAATT
37543567 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
37543586 AAAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:37548151 original size:20 final size:20
Alignment explanation
Indices: 37548128--37548165 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
37548118 TTGAGCTAAA
37548128 ATTGAGCTG-AGTTGAGCTCG
1 ATTGAGCTGTA-TTGAGCTCG
37548148 ATTGAGCTGTATTGAGCT
1 ATTGAGCTGTATTGAGCT
37548166 TTATTTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGAGCTGTATTGAGCTCG
Found at i:37551387 original size:21 final size:23
Alignment explanation
Indices: 37551342--37551388 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
37551332 TCACCTGCAA
* *
37551342 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
37551365 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
37551386 TAA
1 TAA
37551389 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:37556794 original size:11 final size:11
Alignment explanation
Indices: 37556778--37556810 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
37556768 GAAACCAAAT
37556778 TTTTTTTTGAA
1 TTTTTTTTGAA
37556789 TTTTTTTTGAA
1 TTTTTTTTGAA
37556800 TTTTTTTTGAA
1 TTTTTTTTGAA
37556811 GAAACTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:37557845 original size:21 final size:23
Alignment explanation
Indices: 37557800--37557846 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
37557790 TCACCTGCAA
* *
37557800 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
37557823 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
37557844 TAA
1 TAA
37557847 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:37560597 original size:20 final size:20
Alignment explanation
Indices: 37560572--37560626 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
37560562 TGTGGTTCAA
*
37560572 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
37560592 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
37560612 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
37560627 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:37563766 original size:39 final size:39
Alignment explanation
Indices: 37563682--37563792 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 39
37563672 AGATACTAAT
** *
37563682 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
37563722 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
37563762 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
37563793 GAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 25 0.42
40 35 0.58
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:37705098 original size:30 final size:30
Alignment explanation
Indices: 37705064--37705160 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
37705054 TAAACTAAAA
37705064 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
37705094 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
37705124 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
37705153 ATGAGCTA
1 -TGAGCTA
37705161 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:37715802 original size:15 final size:15
Alignment explanation
Indices: 37715782--37715832 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
37715772 ACTTTCATCA
*
37715782 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
* *
37715797 TTCTTTTCACTATTT
1 TTCTTTTCTCTCTTT
*
37715812 TT-GTTTCTCTCTTT
1 TTCTTTTCTCTCTTT
37715826 TTCTTTT
1 TTCTTTT
37715833 TCTTGCTCAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:37717049 original size:10 final size:10
Alignment explanation
Indices: 37717025--37717073 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
37717015 AGCTTGTTTC
*
37717025 CAGCTCACTT
1 CAGCTCAATT
* *
37717035 GAGCTCAAGT
1 CAGCTCAATT
37717045 CAGCTC-ATT
1 CAGCTCAATT
37717054 CGAGCTCAATT
1 C-AGCTCAATT
37717065 CAGCTCAAT
1 CAGCTCAAT
37717074 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:37717050 original size:20 final size:20
Alignment explanation
Indices: 37717025--37717071 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
37717015 AGCTTGTTTC
37717025 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
37717045 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
37717065 CAGCTCA
1 CAGCTCA
37717072 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:37719989 original size:10 final size:10
Alignment explanation
Indices: 37719974--37720022 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
37719964 TTGGGTTAAG
37719974 ATTGAGCTGA
1 ATTGAGCTGA
37719984 ATTGAGCTCGA
1 ATTGAGCT-GA
37719995 A-TGAGCTGA
1 ATTGAGCTGA
* *
37720004 CTTGAGCTCA
1 ATTGAGCTGA
*
37720014 AGTGAGCTG
1 ATTGAGCTG
37720023 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:37719999 original size:20 final size:20
Alignment explanation
Indices: 37719976--37720022 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
37719966 GGGTTAAGAT
37719976 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
37719996 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
37720016 TGAGCTG
1 TGAGCTG
37720023 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:37721927 original size:12 final size:12
Alignment explanation
Indices: 37721899--37721938 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
37721889 ACTCGATTTC
*
37721899 TTTTCAAGCTCT
1 TTTTCAATCTCT
* *
37721911 CTTTCAATTTCT
1 TTTTCAATCTCT
37721923 TTTTCAATCTCT
1 TTTTCAATCTCT
37721935 TTTT
1 TTTT
37721939 GCTTTTCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTTCAATCTCT
Found at i:37721991 original size:15 final size:15
Alignment explanation
Indices: 37721968--37722014 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
37721958 TTTTGAAATC
37721968 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
37721983 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
37721998 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
37722014 T
1 T
37722015 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:37722825 original size:45 final size:45
Alignment explanation
Indices: 37722776--37722961 Score: 300
Period size: 45 Copynumber: 4.1 Consensus size: 45
37722766 TCGGCCATGG
* * *
37722776 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
* * *
37722821 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
*
37722866 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
*
37722911 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
37722956 TGCTTC
1 TGCTTC
37722962 TTTGCCGTCC
Statistics
Matches: 131, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 131 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
Found at i:37729245 original size:13 final size:12
Alignment explanation
Indices: 37729215--37729270 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
37729205 AATGTGAAAC
*
37729215 AAAAAGAAATTG
1 AAAAAGAAGTTG
37729227 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
37729239 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
37729251 AAAATG-AGTTAG
1 AAAAAGAAGTT-G
37729263 AAAAAGAA
1 AAAAAGAA
37729271 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 22 0.63
13 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:37733021 original size:17 final size:16
Alignment explanation
Indices: 37732999--37733043 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
37732989 CACTTCTTTT
37732999 TTTTTTTTAATTTCGAA
1 TTTTTTTTAATTTC-AA
**
37733016 TTTTTTTTGAATTTCTC
1 TTTTTTTT-AATTTCAA
37733033 TTTTTTTTAAT
1 TTTTTTTTAAT
37733044 ACCGAATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.64
18 6 0.24
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTTTTAATTTCAA
Found at i:37733037 original size:18 final size:18
Alignment explanation
Indices: 37732992--37733040 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
37732982 TTTCAATCAC
* *
37732992 TTCTTTTTTTTTTTTAAT
1 TTCTATTTTTTTTTGAAT
* *
37733010 TTCGAATTTTTTTTGAAT
1 TTCTATTTTTTTTTGAAT
*
37733028 TTCTCTTTTTTTT
1 TTCTATTTTTTTT
37733041 AATACCGAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (18 bp):
TTCTATTTTTTTTTGAAT
Found at i:37733831 original size:45 final size:45
Alignment explanation
Indices: 37733782--37733967 Score: 309
Period size: 45 Copynumber: 4.1 Consensus size: 45
37733772 TCGGCCATGG
* * * *
37733782 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
* *
37733827 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
37733872 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
37733917 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
37733962 TGCTTC
1 TGCTTC
37733968 TTTGCCGTCC
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:37735284 original size:12 final size:12
Alignment explanation
Indices: 37735259--37735295 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
37735249 TTTGCTCACC
37735259 TTTTTTTTTC--
1 TTTTTTTTTCAA
37735269 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
37735281 TTTTTTTTTGAA
1 TTTTTTTTTCAA
37735293 TTT
1 TTT
37735296 CGATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:37736839 original size:10 final size:10
Alignment explanation
Indices: 37736824--37736872 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
37736814 TTGGGTTAAG
37736824 ATTGAGCTGA
1 ATTGAGCTGA
37736834 ATTGAGCTCGA
1 ATTGAGCT-GA
37736845 A-TGAGCTGA
1 ATTGAGCTGA
* *
37736854 CTTGAGCTCA
1 ATTGAGCTGA
*
37736864 AGTGAGCTG
1 ATTGAGCTG
37736873 GAAACAAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:37736849 original size:20 final size:20
Alignment explanation
Indices: 37736826--37736872 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
37736816 GGGTTAAGAT
37736826 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
37736846 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
37736866 TGAGCTG
1 TGAGCTG
37736873 GAAACAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:37738672 original size:15 final size:15
Alignment explanation
Indices: 37738647--37738693 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
37738637 AGAAAAGAAT
37738647 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
37738663 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
37738678 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
37738693 A
1 A
37738694 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:37738740 original size:12 final size:12
Alignment explanation
Indices: 37738723--37738798 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
37738713 AGTGAAAAGC
37738723 AAAAAGAGATTG
1 AAAAAGAGATTG
*
37738735 AAAAAGAAATTG
1 AAAAAGAGATTG
*
37738747 --AAAGAGA-AG
1 AAAAAGAGATTG
*
37738756 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
37738771 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
37738783 AAAGAGAGCTTG
1 AAAAAGAGATTG
37738795 AAAA
1 AAAA
37738799 GAAATCGAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 25 0.52
13 5 0.10
15 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:37738764 original size:15 final size:15
Alignment explanation
Indices: 37738746--37738779 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
37738736 AAAAGAAATT
37738746 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
37738761 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
37738776 GAAA
1 GAAA
37738780 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:37740391 original size:22 final size:22
Alignment explanation
Indices: 37740365--37740418 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
37740355 CCATTACCTA
*
37740365 TTCGTACCAAATACCATACTAT
1 TTCGTACCAAATACCATACCAT
* *
37740387 TTCGTACCAACTTCCATACCAT
1 TTCGTACCAAATACCATACCAT
37740409 TTCGTACCAA
1 TTCGTACCAA
37740419 TTCCTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31
Consensus pattern (22 bp):
TTCGTACCAAATACCATACCAT
Found at i:37740742 original size:12 final size:11
Alignment explanation
Indices: 37740725--37740756 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
37740715 TAGACTCGTG
37740725 AAAAAAAAATTT
1 AAAAAAAAA-TT
37740737 AAAAAAAAATT
1 AAAAAAAAATT
37740748 AAAAAAAAA
1 AAAAAAAAA
37740757 AGAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:37740757 original size:12 final size:12
Alignment explanation
Indices: 37740725--37740757 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
37740715 TAGACTCGTG
*
37740725 AAAAAAAAATTT
1 AAAAAAAAATTA
37740737 AAAAAAAAATTA
1 AAAAAAAAATTA
37740749 AAAAAAAAA
1 AAAAAAAAA
37740758 GAAAAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:37743047 original size:30 final size:30
Alignment explanation
Indices: 37743013--37743109 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
37743003 TAAACTAAAA
*
37743013 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
37743043 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
37743073 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
37743102 ATGAGCTA
1 -TGAGCTA
37743110 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:37745303 original size:12 final size:12
Alignment explanation
Indices: 37745288--37745318 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
37745278 TTCTTTTTGC
37745288 TTTTCAAAGGCT
1 TTTTCAAAGGCT
37745300 TTTTCAAAGGCT
1 TTTTCAAAGGCT
37745312 TTTTCAA
1 TTTTCAA
37745319 GTTCTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:37745395 original size:6 final size:6
Alignment explanation
Indices: 37745379--37745428 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
37745369 TTTCTTTTTA
*
37745379 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
37745428 T
1 T
37745429 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:37745411 original size:37 final size:37
Alignment explanation
Indices: 37745368--37745438 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
37745358 CTTGCCTCTC
37745368 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
37745405 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
37745439 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:37745439 original size:16 final size:16
Alignment explanation
Indices: 37745364--37745424 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
37745354 GCCTCTTGCC
*
37745364 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
37745380 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
37745396 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
37745412 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
37745425 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:37746366 original size:11 final size:11
Alignment explanation
Indices: 37746352--37746391 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
37746342 TTTAACTCGA
37746352 TTTTTTTAATT
1 TTTTTTTAATT
*
37746363 TTTTTTTCGA-T
1 TTTTTTT-AATT
37746374 TTTTTTTAATT
1 TTTTTTTAATT
37746385 TTTTTTT
1 TTTTTTT
37746392 CGAATTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 1 0.04
11 23 0.92
12 1 0.04
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTTTTAATT
Found at i:37746372 original size:21 final size:22
Alignment explanation
Indices: 37746348--37746394 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
37746338 TTTTTTTAAC
37746348 TCGA-TTTTTTTAATTTTTTTT
1 TCGATTTTTTTTAATTTTTTTT
37746369 TCGATTTTTTTTAATTTTTTTT
1 TCGATTTTTTTTAATTTTTTTT
37746391 TCGA
1 TCGA
37746395 ATTTCTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.72
Consensus pattern (22 bp):
TCGATTTTTTTTAATTTTTTTT
Found at i:37747117 original size:21 final size:21
Alignment explanation
Indices: 37747068--37747134 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
37747058 CCTCTTTGAA
* * *
37747068 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
37747091 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
37747112 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
37747133 CC
1 CC
37747135 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:37749074 original size:10 final size:10
Alignment explanation
Indices: 37749059--37749120 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
37749049 TTTGAACCAT
*
37749059 TACCAATTCG
1 TACCAATTCA
*
37749069 TACCAAATACCA
1 TACC-AAT-TCA
*
37749081 TACCATTTCA
1 TACCAATTCA
37749091 TACCAATTCCA
1 TACCAATT-CA
* *
37749102 TACCATTTCG
1 TACCAATTCA
37749112 TACCAATTC
1 TACCAATTC
37749121 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37749104 original size:21 final size:21
Alignment explanation
Indices: 37749059--37749121 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37749049 TTTGAACCAT
* *
37749059 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37749081 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37749102 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37749122 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37751753 original size:10 final size:11
Alignment explanation
Indices: 37751738--37751808 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 11
37751728 TTGGAGTAAC
37751738 AAAAAAATCAA
1 AAAAAAATCAA
37751749 AAAAAAATCGAA
1 AAAAAAATC-AA
* *
37751761 AAAAATTTGATTGAA
1 AAAAA----AATCAA
37751776 AAAAAAATTCAA
1 AAAAAAA-TCAA
*
37751788 AAAAAAAGTGAA
1 AAAAAAA-TCAA
37751800 AAAAAAATC
1 AAAAAAATC
37751809 GAGCAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
11 11 0.23
12 27 0.57
15 7 0.15
16 2 0.04
ACGTcount: A:0.72, C:0.06, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:37751815 original size:27 final size:26
Alignment explanation
Indices: 37751785--37751846 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
37751775 AAAAAAAATT
37751785 CAAAAAAAAAGTGAAAAAAAA-ATCGAG
1 CAAAAAAAAAG-GAAAAAAAAGAT-GAG
*
37751812 CAAAAAAAAAAGGAAAAAAAAGGTGAG
1 C-AAAAAAAAAGGAAAAAAAAGATGAG
37751839 CAAAAAAA
1 CAAAAAAA
37751847 TCATGTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 7 0.22
27 14 0.44
28 11 0.34
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.05
Consensus pattern (26 bp):
CAAAAAAAAAGGAAAAAAAAGATGAG
Found at i:37752913 original size:6 final size:6
Alignment explanation
Indices: 37752881--37752983 Score: 57
Period size: 6 Copynumber: 16.8 Consensus size: 6
37752871 AAAGAAATTG
* * ** *
37752881 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
37752928 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
37752979 AAAGA
1 AAAGA
37752984 GTTTGAAAAA
Statistics
Matches: 70, Mismatches: 22, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
5 4 0.06
6 54 0.77
7 8 0.11
8 4 0.06
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:37752942 original size:18 final size:18
Alignment explanation
Indices: 37752885--37752943 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
37752875 AAATTGAAAG
* *
37752885 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
37752903 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
*
37752921 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAATCGA
37752939 AAAAG
1 AAAAG
37752944 TGAGAGAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:37756109 original size:11 final size:10
Alignment explanation
Indices: 37756093--37756122 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
37756083 GTTCGTAACG
37756093 AAAAAAAAGTC
1 AAAAAAAA-TC
37756104 AAAAAAAATC
1 AAAAAAAATC
37756114 AAAAAAAAT
1 AAAAAAAAT
37756123 TTGAGTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:37756249 original size:26 final size:26
Alignment explanation
Indices: 37756218--37756280 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 26
37756208 AAAAAAAATT
*
37756218 CAAAAAAAAAGTGAAAAAAAAA-TCGAG
1 CAAAAAAAAA-AGAAAAAAAAAGT-GAG
37756245 CAAAAAAAAAAGAAAAAAAAAGGTGAG
1 CAAAAAAAAAAGAAAAAAAAA-GTGAG
37756272 CAAAAAAAA
1 CAAAAAAAA
37756281 TCATGTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 10 0.30
27 22 0.67
28 1 0.03
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.05
Consensus pattern (26 bp):
CAAAAAAAAAAGAAAAAAAAAGTGAG
Found at i:37757344 original size:6 final size:6
Alignment explanation
Indices: 37757312--37757414 Score: 57
Period size: 6 Copynumber: 16.8 Consensus size: 6
37757302 AAAGAAATTG
* * ** *
37757312 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
37757359 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
37757410 AAAGA
1 AAAGA
37757415 GTTTGAAAAA
Statistics
Matches: 70, Mismatches: 22, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
5 4 0.06
6 54 0.77
7 8 0.11
8 4 0.06
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:37757373 original size:18 final size:18
Alignment explanation
Indices: 37757316--37757374 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
37757306 AAATTGAAAG
* *
37757316 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
37757334 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
*
37757352 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAATCGA
37757370 AAAAG
1 AAAAG
37757375 TGAGAGAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:37760540 original size:11 final size:10
Alignment explanation
Indices: 37760524--37760553 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
37760514 GTTCGTAACG
37760524 AAAAAAAAGTC
1 AAAAAAAA-TC
37760535 AAAAAAAATC
1 AAAAAAAATC
37760545 AAAAAAAAT
1 AAAAAAAAT
37760554 TTGAGTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:37760622 original size:11 final size:10
Alignment explanation
Indices: 37760606--37760676 Score: 79
Period size: 10 Copynumber: 6.8 Consensus size: 10
37760596 GTATTGGAGT
37760606 AAAAAAAATC
1 AAAAAAAATC
37760616 AAAAAAAATC
1 AAAAAAAATC
* * *
37760626 GAAAAAATTA
1 AAAAAAAATC
37760636 AAAAAAAATTC
1 AAAAAAAA-TC
*
37760647 AAAAAAAATG
1 AAAAAAAATC
37760657 AAAAAAAATC
1 AAAAAAAATC
37760667 GAGAAAAAAA
1 -A-AAAAAAA
37760677 AAGAAAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
10 33 0.66
11 10 0.20
12 7 0.14
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:37760674 original size:24 final size:23
Alignment explanation
Indices: 37760647--37760700 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
37760637 AAAAAAATTC
*
37760647 AAAAAAAATGAAAAAAAA-TCGAG
1 AAAAAAAAAGAAAAAAAAGT-GAG
37760670 AAAAAAAAAGAAAAAAAAGTGAG
1 AAAAAAAAAGAAAAAAAAGTGAG
*
37760693 CAAAAAAA
1 AAAAAAAA
37760701 TCAGTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.78, C:0.04, G:0.13, T:0.06
Consensus pattern (23 bp):
AAAAAAAAAGAAAAAAAAGTGAG
Found at i:37760684 original size:41 final size:40
Alignment explanation
Indices: 37760606--37760685 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
37760596 GTATTGGAGT
37760606 AAAAAAAATCAAAAAAAATCGAAAAAATTAAAAAAAAATTC
1 AAAAAAAATCAAAAAAAATCGAAAAAA-TAAAAAAAAATTC
* *
37760647 AAAAAAAATGAAAAAAAATCGAGAAAAAAAAAGAAAAAA
1 AAAAAAAATCAAAAAAAATCGA-AAAAATAAA-AAAAAA
37760686 AAGTGAGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 24 0.69
42 11 0.31
ACGTcount: A:0.79, C:0.05, G:0.06, T:0.10
Consensus pattern (40 bp):
AAAAAAAATCAAAAAAAATCGAAAAAATAAAAAAAAATTC
Found at i:37760722 original size:12 final size:12
Alignment explanation
Indices: 37760647--37760722 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 12
37760637 AAAAAAATTC
37760647 AAAAAAAA-TGA
1 AAAAAAAAGTGA
* *
37760658 AAAAAAATCGAGA
1 AAAAAAA-AGTGA
37760671 AAAAAAAA--G-
1 AAAAAAAAGTGA
37760680 AAAAAAAAGTGA
1 AAAAAAAAGTGA
*
37760692 GCAAAAAAATCAGTTA
1 --AAAAAAA--AGTGA
37760708 AAAAAAAAGTGA
1 AAAAAAAAGTGA
37760720 AAA
1 AAA
37760723 GTCTTGCGAG
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
9 8 0.16
10 1 0.02
11 8 0.16
12 7 0.14
13 9 0.18
14 14 0.27
16 4 0.08
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (12 bp):
AAAAAAAAGTGA
Found at i:37761763 original size:6 final size:6
Alignment explanation
Indices: 37761731--37761833 Score: 57
Period size: 6 Copynumber: 16.8 Consensus size: 6
37761721 AAAGAAATTG
* * ** *
37761731 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
37761778 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
37761829 AAAGA
1 AAAGA
37761834 GTTTGAAAAA
Statistics
Matches: 70, Mismatches: 22, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
5 4 0.06
6 54 0.77
7 8 0.11
8 4 0.06
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:37761792 original size:18 final size:18
Alignment explanation
Indices: 37761735--37761793 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
37761725 AAATTGAAAG
* *
37761735 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
37761753 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
*
37761771 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAATCGA
37761789 AAAAG
1 AAAAG
37761794 TGAGAGAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:37765487 original size:20 final size:20
Alignment explanation
Indices: 37765462--37765516 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
37765452 GTGAAAATAC
*
37765462 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
37765482 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
*
37765501 AAAAGAGAATGAAAAA
1 AAAAGA-AAAGAAAAA
37765517 AAATGAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.59
20 5 0.17
21 7 0.24
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:37765527 original size:26 final size:26
Alignment explanation
Indices: 37765498--37765550 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
37765488 AAGAAAATTC
37765498 AAAA-AAAGAGAATGAAAAA-AAATGAG
1 AAAAGAAAGAG-ATGAAAAAGAAA-GAG
*
37765524 AAAAGCAAGAGATGAAAAAGAAAGAG
1 AAAAGAAAGAGATGAAAAAGAAAGAG
37765550 A
1 A
37765551 GAGTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.06
Consensus pattern (26 bp):
AAAAGAAAGAGATGAAAAAGAAAGAG
Found at i:37770788 original size:22 final size:22
Alignment explanation
Indices: 37770763--37770816 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
37770753 CCATTACCTA
37770763 TTCGTACCAAATACCATACCAT
1 TTCGTACCAAATACCATACCAT
* *
37770785 TTCGTACCAACTTCCATACCAT
1 TTCGTACCAAATACCATACCAT
37770807 TTCGTACCAA
1 TTCGTACCAA
37770817 TTCCTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.30
Consensus pattern (22 bp):
TTCGTACCAAATACCATACCAT
Found at i:37772408 original size:10 final size:10
Alignment explanation
Indices: 37772384--37772432 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
37772374 AGCTCGTTTC
*
37772384 CAGCTCACTT
1 CAGCTCAATT
* *
37772394 GAGCTCAAGT
1 CAGCTCAATT
37772404 CAGCTC-ATT
1 CAGCTCAATT
37772413 CGAGCTCAATT
1 C-AGCTCAATT
37772424 CAGCTCAAT
1 CAGCTCAAT
37772433 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:37772409 original size:20 final size:20
Alignment explanation
Indices: 37772384--37772430 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
37772374 AGCTCGTTTC
37772384 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
37772404 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
37772424 CAGCTCA
1 CAGCTCA
37772431 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:37778409 original size:20 final size:20
Alignment explanation
Indices: 37778386--37778432 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
37778376 AGGTTAAGAT
*
37778386 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
37778406 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
37778426 TGAGCTG
1 TGAGCTG
37778433 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:37780155 original size:48 final size:48
Alignment explanation
Indices: 37780100--37780205 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
37780090 TTGTCTTTTC
*
37780100 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
37780148 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
37780196 TTTCTTTTTC
1 TTTCTTTTTC
37780206 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:37780248 original size:18 final size:18
Alignment explanation
Indices: 37780181--37780248 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
37780171 TTTTCACATC
* *
37780181 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTCACTCT
* **
37780199 CTTTTTCCATGACACTCGTTT
1 CTTTTTCAATCTCACTC---T
37780220 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCACTCT
37780239 CTTTTTCAAT
1 CTTTTTCAAT
37780249 TTCTTGTTCC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 18 0.47
19 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.18, C:0.28, G:0.03, T:0.51
Consensus pattern (18 bp):
CTTTTTCAATCTCACTCT
Found at i:37781237 original size:22 final size:22
Alignment explanation
Indices: 37781207--37781251 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
37781197 CTCACAAGAC
* *
37781207 TTTTCACTTTTTTTTGTTCTTT
1 TTTTCACTTTATTTTCTTCTTT
*
37781229 TTTTTACTTTATTTTCTTCTTT
1 TTTTCACTTTATTTTCTTCTTT
37781251 T
1 T
37781252 GCTCACTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTCACTTTATTTTCTTCTTT
Found at i:37781259 original size:22 final size:22
Alignment explanation
Indices: 37781210--37781259 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
37781200 ACAAGACTTT
* * **
37781210 TCACTTTTTTTTGTTCTTTTTT
1 TCACTTTATTTTCTTCTTTTGC
*
37781232 TTACTTTATTTTCTTCTTTTGC
1 TCACTTTATTTTCTTCTTTTGC
37781254 TCACTT
1 TCACTT
37781260 CTTTTTTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.08, C:0.18, G:0.04, T:0.70
Consensus pattern (22 bp):
TCACTTTATTTTCTTCTTTTGC
Found at i:37782792 original size:20 final size:20
Alignment explanation
Indices: 37782769--37782815 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
37782759 AGGTTAAGAT
*
37782769 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
37782789 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
37782809 TGAGCTG
1 TGAGCTG
37782816 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:37786572 original size:18 final size:18
Alignment explanation
Indices: 37786551--37786585 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
37786541 TTTTTCTTTT
37786551 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
37786569 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
37786586 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:37787522 original size:13 final size:13
Alignment explanation
Indices: 37787480--37787515 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
37787470 ATATACTTCG
37787480 ATTTTTTTTTTGA
1 ATTTTTTTTTTGA
*
37787493 ATTTTTTTTTTGG
1 ATTTTTTTTTTGA
37787506 ATTTTTTTTT
1 ATTTTTTTTT
37787516 CAAATTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.81
Consensus pattern (13 bp):
ATTTTTTTTTTGA
Found at i:37788950 original size:30 final size:30
Alignment explanation
Indices: 37788893--37788951 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
37788883 CAAATTATTT
*
37788893 AAATAGGTGGAAAGAAGCTAAATTGAGCTC
1 AAATAGGTGGAAAGAAGCTAAAGTGAGCTC
* *
37788923 AAATAGGTGGAATTG-AGCTCAAGTGAGCT
1 AAATAGGTGGAA-AGAAGCTAAAGTGAGCT
37788952 GATTGAAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.22
Consensus pattern (30 bp):
AAATAGGTGGAAAGAAGCTAAAGTGAGCTC
Found at i:37803021 original size:12 final size:12
Alignment explanation
Indices: 37803004--37803047 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
37802994 CGTATGCAAT
37803004 TTTTTTTTCAAA
1 TTTTTTTTCAAA
*
37803016 TTTTTTTTTCAAT
1 -TTTTTTTTCAAA
*
37803029 TTTTTTTTC-GA
1 TTTTTTTTCAAA
37803040 TTTTTTTT
1 TTTTTTTT
37803048 TAATCTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 8 0.29
12 9 0.32
13 11 0.39
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:37803028 original size:25 final size:24
Alignment explanation
Indices: 37803000--37803048 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
37802990 AGACCGTATG
37803000 CAATTTTTTTTTCAAATTTTTTTTT
1 CAATTTTTTTTTC-AATTTTTTTTT
*
37803025 CAATTTTTTTTTCGATTTTTTTTT
1 CAATTTTTTTTTCAATTTTTTTTT
37803049 AATCTACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.73
Consensus pattern (24 bp):
CAATTTTTTTTTCAATTTTTTTTT
Found at i:37803048 original size:12 final size:12
Alignment explanation
Indices: 37803000--37803048 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
37802990 AGACCGTATG
37803000 CAATTTTTTTTT
1 CAATTTTTTTTT
37803012 CAAATTTTTTTTT
1 C-AATTTTTTTTT
37803025 CAATTTTTTTTT
1 CAATTTTTTTTT
*
37803037 CGATTTTTTTTT
1 CAATTTTTTTTT
37803049 AATCTACAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 23 0.66
13 12 0.34
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.73
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:37807651 original size:20 final size:20
Alignment explanation
Indices: 37807628--37807692 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
37807618 AAGCTCAAAC
37807628 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTAAGCTAAATT
37807648 GAGCTCAAACG-AA-CTAAATT
1 GAGCT-AAA-GTAAGCTAAATT
* * * * *
37807668 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGTAAGCTAAATT
37807688 GAGCT
1 GAGCT
37807693 GGGAAAAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 26 0.74
21 5 0.14
22 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (20 bp):
GAGCTAAAGTAAGCTAAATT
Found at i:37809335 original size:20 final size:20
Alignment explanation
Indices: 37809289--37809335 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
37809279 AGCTCGTTTC
*
37809289 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
37809309 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
37809329 CAGCTCA
1 CAGCTCA
37809336 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:37815014 original size:173 final size:172
Alignment explanation
Indices: 37814726--37815069 Score: 510
Period size: 173 Copynumber: 2.0 Consensus size: 172
37814716 GAAAATAAAT
* * * *
37814726 CTTGATTTTCTTTATCTTTTGTGTACACATCTAAGGCCCTGCTAACAAATTCTAAATGGTACCAT
1 CTTGATTTTCTTTATCCTTTGTATACACATCTAAGGCCCTGCTAACAAAGTCTAAATGATACCAT
* *
37814791 TTAGTTTTGAACGCATTTGTCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCA
66 TTAGTTTTCAACGCATTTGTCTAGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCA
* * **
37814856 TCATGTTCTTGAACTTGGGTTGGGCCTTTGTGACTCGTATCA
131 TCACGTCCTTGAACTTGAATTGGGCCTTTGTGACTCGTATCA
* * * ** *
37814898 CTTGATTTTCTTTTTCCTTTGTATACGCATCTAAGGCCTTGCTAATGAAGTCTTAAATGATTCCA
1 CTTGATTTTCTTTATCCTTTGTATACACATCTAAGGCCCTGCTAACAAAGTC-TAAATGATACCA
37814963 TTTAG-TTTCATACGCATTTGTCTAGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCC
65 TTTAGTTTTCA-ACGCATTTGTCTAGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCC
*
37815027 CATCACGTCCTTGAGCTTGAATTGGGCCTTTGTGACTCGTATC
129 CATCACGTCCTTGAACTTGAATTGGGCCTTTGTGACTCGTATC
37815070 GCTTAGCATG
Statistics
Matches: 153, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
172 48 0.31
173 105 0.69
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.40
Consensus pattern (172 bp):
CTTGATTTTCTTTATCCTTTGTATACACATCTAAGGCCCTGCTAACAAAGTCTAAATGATACCAT
TTAGTTTTCAACGCATTTGTCTAGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCA
TCACGTCCTTGAACTTGAATTGGGCCTTTGTGACTCGTATCA
Found at i:37817216 original size:22 final size:22
Alignment explanation
Indices: 37817191--37817235 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
37817181 TAGTAATTTC
37817191 TCAAAAAAACTC-AAAAAACAAT
1 TCAAAAAAACTCGAAAAAA-AAT
*
37817213 TCAAAAAAATTCGAAAAAAAAT
1 TCAAAAAAACTCGAAAAAAAAT
37817235 T
1 T
37817236 AGTTTCCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.18
Consensus pattern (22 bp):
TCAAAAAAACTCGAAAAAAAAT
Found at i:37817230 original size:12 final size:11
Alignment explanation
Indices: 37817193--37817235 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
37817183 GTAATTTCTC
*
37817193 AAAAAAACTCA
1 AAAAAAATTCA
37817204 AAAAACAATTC-
1 AAAAA-AATTCA
37817215 AAAAAAATTCGA
1 AAAAAAATTC-A
37817227 AAAAAAATT
1 AAAAAAATT
37817236 AGTTTCCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 5 0.18
11 10 0.36
12 13 0.46
ACGTcount: A:0.70, C:0.12, G:0.02, T:0.16
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:37817292 original size:14 final size:13
Alignment explanation
Indices: 37817271--37817311 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
37817261 GGATATCAAG
37817271 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
37817284 TTCGTGAAAAAAAAA
1 TT-GTG-AAAAAAAA
37817299 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
37817312 GCTAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.38
14 6 0.23
15 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:37817296 original size:15 final size:14
Alignment explanation
Indices: 37817271--37817311 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
37817261 GGATATCAAG
37817271 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
37817284 TTCGTGAAAAAAAAA
1 TT-GTGAAAAAAAAA
37817299 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
37817312 GCTAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.08
14 14 0.54
15 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:37822661 original size:28 final size:27
Alignment explanation
Indices: 37822600--37822663 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
37822590 TATTAATTCT
*
37822600 TGTAATAATTTAAAACATATTAAACAC
1 TGTAATAAATTAAAACATATTAAACAC
*
37822627 TCATAATAAATTAAAACATAATTAAA-AC
1 T-GTAATAAATTAAAACAT-ATTAAACAC
37822655 ATGTAATAA
1 -TGTAATAA
37822664 GCTGACAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.03
28 23 0.74
29 7 0.23
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (27 bp):
TGTAATAAATTAAAACATATTAAACAC
Found at i:37824411 original size:20 final size:20
Alignment explanation
Indices: 37824350--37824415 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
37824340 GAGCTCAATT
* * *
37824350 AGCTGAATTGAGCTTGTGGG
1 AGCTGACTTGAGCTTGAGTG
* * *
37824370 AGTTGACTTGAGCTTAAATG
1 AGCTGACTTGAGCTTGAGTG
*
37824390 AGCTGACTTGAGCTCGAGTG
1 AGCTGACTTGAGCTTGAGTG
37824410 AGCTGA
1 AGCTGA
37824416 ACCGCATGGA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (20 bp):
AGCTGACTTGAGCTTGAGTG
Found at i:37826068 original size:16 final size:14
Alignment explanation
Indices: 37826045--37826087 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
37826035 TTGTAAATTT
37826045 TCTTTCTTTTTCAC
1 TCTTTCTTTTTCAC
*
37826059 TCGATTTCTTTTCCCAC
1 TC--TTTCTTTT-TCAC
37826076 TCTTTCTTTTTC
1 TCTTTCTTTTTC
37826088 TTCTCTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 3 0.12
15 8 0.33
16 8 0.33
17 5 0.21
ACGTcount: A:0.07, C:0.30, G:0.02, T:0.60
Consensus pattern (14 bp):
TCTTTCTTTTTCAC
Found at i:37826125 original size:18 final size:18
Alignment explanation
Indices: 37826099--37826138 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
37826089 TCTCTTTCAA
* *
37826099 TTTCTTTTTCAATCTCTT
1 TTTCCTTTTCAATCACTT
*
37826117 TTTCCTTTTCACTCACTT
1 TTTCCTTTTCAATCACTT
37826135 TTTC
1 TTTC
37826139 AATTTCCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCCTTTTCAATCACTT
Found at i:37826153 original size:18 final size:18
Alignment explanation
Indices: 37826132--37826189 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
37826122 TTTTCACTCA
*
37826132 CTTTTTCAATTTCCTTTT
1 CTTTTTCAATTTCTTTTT
* *
37826150 CTTTTGCAGTTTCTTTTT
1 CTTTTTCAATTTCTTTTT
*
37826168 CTTTTTCAATGTCTTTTT
1 CTTTTTCAATTTCTTTTT
37826186 CTTT
1 CTTT
37826190 CATTTCTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.09, C:0.19, G:0.05, T:0.67
Consensus pattern (18 bp):
CTTTTTCAATTTCTTTTT
Found at i:37826166 original size:30 final size:30
Alignment explanation
Indices: 37826093--37826168 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
37826083 TTTTCTTCTC
* *
37826093 TTTCAATTTCTTTTTCAATCTCTTTTTCCT
1 TTTCACTTTCTTTTTCAATCTCCTTTTCCT
** *
37826123 TTTCACTCACTTTTTCAATTTCCTTTT-CT
1 TTTCACTTTCTTTTTCAATCTCCTTTTCCT
*
37826152 TTTGCAGTTTCTTTTTC
1 TTT-CACTTTCTTTTTC
37826169 TTTTTCAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.12, C:0.24, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTCACTTTCTTTTTCAATCTCCTTTTCCT
Found at i:37826241 original size:36 final size:36
Alignment explanation
Indices: 37826201--37826287 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
37826191 ATTTCTCCAA
* *
37826201 ACTCACCTTCTTTTTCAATTTCCTTTTCGTTCTCAC
1 ACTCATCTTCTTTTTCAATTTCCTTTTCGTCCTCAC
* *
37826237 ACTCATCTTCTTTTTCAATTTTCTTTTCGTCCTTAC
1 ACTCATCTTCTTTTTCAATTTCCTTTTCGTCCTCAC
37826273 ACTCATCTTCTTTTT
1 ACTCATCTTCTTTTT
37826288 ATTTCGTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.14, C:0.30, G:0.02, T:0.54
Consensus pattern (36 bp):
ACTCATCTTCTTTTTCAATTTCCTTTTCGTCCTCAC
Found at i:37827375 original size:10 final size:10
Alignment explanation
Indices: 37827360--37827396 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
37827350 AAATAAACTT
37827360 TTTTTTTGAA
1 TTTTTTTGAA
37827370 TTTTTTTTG-A
1 -TTTTTTTGAA
37827380 TTTTTTTGAA
1 TTTTTTTGAA
37827390 TTTTTTT
1 TTTTTTT
37827397 ACAATGACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.32
10 9 0.36
11 8 0.32
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:37827375 original size:11 final size:11
Alignment explanation
Indices: 37827359--37827396 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
37827349 AAAATAAACT
37827359 TTTTTTTTGAA
1 TTTTTTTTGAA
37827370 TTTTTTTTG-A
1 TTTTTTTTGAA
37827380 -TTTTTTTGAA
1 TTTTTTTTGAA
37827390 TTTTTTT
1 TTTTTTT
37827397 ACAATGACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.32
10 2 0.08
11 15 0.60
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:37831205 original size:28 final size:27
Alignment explanation
Indices: 37831144--37831207 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
37831134 TATTAATTCT
* *
37831144 TGTAATAATTTAAGACATATTAAACAC
1 TGTAATAAATTAAAACATATTAAACAC
*
37831171 TCATAATAAATTAAAACATAATTAAA-AC
1 T-GTAATAAATTAAAACAT-ATTAAACAC
37831199 ATGTAATAA
1 -TGTAATAA
37831208 GCTGACAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.03
28 22 0.73
29 7 0.23
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (27 bp):
TGTAATAAATTAAAACATATTAAACAC
Found at i:37831359 original size:20 final size:20
Alignment explanation
Indices: 37831336--37831380 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
37831326 GAGCTCGTGG
*
37831336 GAGCTCACTTGACCTCGAA-T
1 GAGCTAACTTGACCTC-AAGT
*
37831356 GAGCTAACTTGAGCTCAAGT
1 GAGCTAACTTGACCTCAAGT
37831376 GAGCT
1 GAGCT
37831381 GAACCACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
GAGCTAACTTGACCTCAAGT
Found at i:37838249 original size:6 final size:6
Alignment explanation
Indices: 37838238--37838263 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
37838228 AGTTGTAAAG
37838238 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
37838264 ATTTATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:37839721 original size:4 final size:4
Alignment explanation
Indices: 37839712--37839739 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
37839702 TATTTTTATT
37839712 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
37839740 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:37843577 original size:24 final size:25
Alignment explanation
Indices: 37843548--37843606 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
37843538 TGGTCTATTA
** *
37843548 CGTACCAAAATTTCCA-TACCATTT
1 CGTACCAAAATCCCCATTACCATAT
37843572 CGTACC-AAA-CCCCATTACCATAT
1 CGTACCAAAATCCCCATTACCATAT
37843595 CGTACCAAAATC
1 CGTACCAAAATC
37843607 AACATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.10
23 16 0.55
24 9 0.31
25 1 0.03
ACGTcount: A:0.36, C:0.34, G:0.05, T:0.25
Consensus pattern (25 bp):
CGTACCAAAATCCCCATTACCATAT
Found at i:37856503 original size:20 final size:19
Alignment explanation
Indices: 37856478--37856537 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
37856468 TCAAGTTCAT
37856478 TCAGCTCAATTTTAGCTCA
1 TCAGCTCAATTTTAGCTCA
* *
37856497 TCAAGCTCACTCTTAGCTCAA
1 TC-AGCTCAATTTTAGCTC-A
*
37856518 TCAGGTC-ATTTTAAGCTCA
1 TCAGCTCAATTTT-AGCTCA
37856537 T
1 T
37856538 TTGCGTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 7 0.21
20 23 0.70
21 3 0.09
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (19 bp):
TCAGCTCAATTTTAGCTCA
Found at i:37868793 original size:16 final size:18
Alignment explanation
Indices: 37868762--37868794 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
37868752 ACTCTTCAAT
37868762 CCATCATCCAAATCAAAG
1 CCATCATCCAAATCAAAG
37868780 CCATCA-CC-AATCAAA
1 CCATCATCCAAATCAAA
37868795 AATTGATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.45, C:0.36, G:0.03, T:0.15
Consensus pattern (18 bp):
CCATCATCCAAATCAAAG
Found at i:37869318 original size:15 final size:16
Alignment explanation
Indices: 37869293--37869324 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
37869283 TATCTCACAC
37869293 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
37869309 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
37869324 T
1 T
37869325 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:37870500 original size:19 final size:19
Alignment explanation
Indices: 37870478--37870515 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
37870468 AACTAGTCAA
37870478 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
37870497 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
37870516 TTCTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GGACAACTCAAGAGTCATT
Found at i:37870891 original size:46 final size:46
Alignment explanation
Indices: 37870840--37870933 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
37870830 ATAGTGTGGC
*
37870840 GTTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
37870886 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
37870932 GT
1 GT
37870934 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:37873950 original size:23 final size:22
Alignment explanation
Indices: 37873898--37873950 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
37873888 TCCACGTCTT
*
37873898 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
37873920 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
37873943 TTTCTTTT
1 TTTCTTTT
37873951 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:37876298 original size:12 final size:11
Alignment explanation
Indices: 37876276--37876308 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
37876266 TTAAACTAAG
37876276 TAAATAATAAA
1 TAAATAATAAA
37876287 TAAATAAATAAA
1 TAAAT-AATAAA
37876299 TAAA-AATAAA
1 TAAATAATAAA
37876309 ACTTTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 5 0.24
12 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:37876575 original size:25 final size:26
Alignment explanation
Indices: 37876536--37876595 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 26
37876526 TTTCAATCAC
*
37876536 TCTTTTTTTTCAATTTCG-ATTTTTCT
1 TCTTTTTTTTCAATTCCGAATTTTT-T
37876562 TCTTTTTTTT-AATTCCGAATTTTTT
1 TCTTTTTTTTCAATTCCGAATTTTTT
37876587 TCTTTTTTT
1 TCTTTTTTT
37876596 CTTCAATACT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.12, C:0.13, G:0.03, T:0.72
Consensus pattern (26 bp):
TCTTTTTTTTCAATTCCGAATTTTTT
Found at i:37877466 original size:11 final size:11
Alignment explanation
Indices: 37877450--37877493 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
37877440 AATTGTAGAT
37877450 TCAAAAAAAAA
1 TCAAAAAAAAA
37877461 TC-AAAAAAAA
1 TCAAAAAAAAA
* *
37877471 TCGAAAAAAAT
1 TCAAAAAAAAA
*
37877482 TGAAAAAAAAA
1 TCAAAAAAAAA
37877493 T
1 T
37877494 TGCATACGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.14
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:37877487 original size:9 final size:10
Alignment explanation
Indices: 37877454--37877490 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
37877444 GTAGATTCAA
*
37877454 AAAAAAATCA
1 AAAAAAATCG
37877464 AAAAAAATCG
1 AAAAAAATCG
*
37877474 AAAAAAATTG
1 AAAAAAATCG
37877484 AAAAAAA
1 AAAAAAA
37877491 AATTGCATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.11
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:37889161 original size:27 final size:27
Alignment explanation
Indices: 37889131--37889308 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
37889121 ATATTGAGTC
* * * *
37889131 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
37889158 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
37889185 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
37889213 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
37889240 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
* *
37889267 CGCACACTCAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
37889294 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
37889309 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:37889270 original size:82 final size:81
Alignment explanation
Indices: 37889152--37889307 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
37889142 TGCTATATAA
* * *
37889152 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTCAGTGCAACATAGTCAAA-TCGCA
37889217 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
37889234 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTCAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTCAGTGCAACATAGTCAAATCGCA
37889298 CACTTAGTGC
65 CACTTAGTGC
37889308 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTCAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:37891559 original size:20 final size:20
Alignment explanation
Indices: 37891513--37891559 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
37891503 AGCTCGTTTC
*
37891513 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
37891533 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
37891553 CAGCTCA
1 CAGCTCA
37891560 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:37893251 original size:26 final size:25
Alignment explanation
Indices: 37893220--37893280 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 25
37893210 TGTATGAGTT
37893220 TAAGACATTTAAGA-CACTAAACAAAG
1 TAAGACATTTAAGATCA--AAACAAAG
*
37893246 TAAGACATATTTAATATCAAAACAAAG
1 TAAGAC--ATTTAAGATCAAAACAAAG
37893273 TAAGACAT
1 TAAGACAT
37893281 ATTTAATATC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 2 0.06
26 6 0.19
27 14 0.45
28 7 0.23
29 2 0.06
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (25 bp):
TAAGACATTTAAGATCAAAACAAAG
Found at i:37893272 original size:27 final size:27
Alignment explanation
Indices: 37893238--37893291 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
37893228 TTAAGACACT
37893238 AAACAAAGTAAGACATATTTAATATCA
1 AAACAAAGTAAGACATATTTAATATCA
37893265 AAACAAAGTAAGACATATTTAATATCA
1 AAACAAAGTAAGACATATTTAATATCA
37893292 CTCAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (27 bp):
AAACAAAGTAAGACATATTTAATATCA
Found at i:37893452 original size:20 final size:20
Alignment explanation
Indices: 37893429--37893482 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
37893419 AACTAAGAAC
37893429 GAGCTGAATGAGCTAAGGTT
1 GAGCTGAATGAGCTAAGGTT
* *
37893449 GAGCTCAATGAGCTATGGTT
1 GAGCTGAATGAGCTAAGGTT
37893469 GAGCTGAATGAGCT
1 GAGCTGAATGAGCT
37893483 TGAAGTAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (20 bp):
GAGCTGAATGAGCTAAGGTT
Found at i:37900821 original size:4 final size:4
Alignment explanation
Indices: 37900783--37900814 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
37900773 TTAAACTAAG
37900783 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
37900815 AATAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:37903016 original size:30 final size:30
Alignment explanation
Indices: 37902982--37903078 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
37902972 AGCTCACTCC
37902982 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
37903012 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
37903042 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
37903072 TAGCTCA
1 TAGCTCA
37903079 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:37907204 original size:20 final size:20
Alignment explanation
Indices: 37907179--37907216 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
37907169 AAGGCTTGGC
37907179 CGGCCACACATTACATGATA
1 CGGCCACACATTACATGATA
37907199 CGGCCACACATTACATGA
1 CGGCCACACATTACATGA
37907217 CACAGCTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (20 bp):
CGGCCACACATTACATGATA
Found at i:37917390 original size:15 final size:15
Alignment explanation
Indices: 37917370--37917410 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
37917360 CGAGGCAAAA
37917370 AGAAAAAGAAATAAG
1 AGAAAAAGAAATAAG
37917385 AGAAAAAGAAATAAG
1 AGAAAAAGAAATAAG
37917400 A-AGAAAAGAAA
1 AGA-AAAAGAAA
37917411 GACAAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 1 0.04
15 24 0.96
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (15 bp):
AGAAAAAGAAATAAG
Found at i:37917409 original size:21 final size:21
Alignment explanation
Indices: 37917366--37917410 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
37917356 AAAGCGAGGC
* *
37917366 AAAAAGAAAAAGAAATAAGAG
1 AAAAAGAAAAAGAAAGAAAAG
37917387 AAAAAGAAATAAG-AAGAAAAG
1 AAAAAGAAA-AAGAAAGAAAAG
37917408 AAA
1 AAA
37917411 GACAAGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAGAAAAG
Found at i:37917531 original size:18 final size:18
Alignment explanation
Indices: 37917496--37917542 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
37917486 AGAACAAGAA
*
37917496 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGACAGTGAG
37917514 ATTGAAGAAAGACA-TGAG
1 ATTGAA-AAAGACAGTGAG
* *
37917532 AATGTAAAAGA
1 ATTGAAAAAGA
37917543 AACAAGTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 5 0.20
18 14 0.56
19 6 0.24
ACGTcount: A:0.53, C:0.02, G:0.28, T:0.17
Consensus pattern (18 bp):
ATTGAAAAAGACAGTGAG
Found at i:37918391 original size:20 final size:20
Alignment explanation
Indices: 37918366--37918412 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
37918356 AGCTCGTTTC
37918366 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
* *
37918386 CAGCTCATTCGAGTTCAATT
1 CAGCTCATTCGAGCTCAAGT
37918406 CAGCTCA
1 CAGCTCA
37918413 ATCTTAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:37919977 original size:30 final size:30
Alignment explanation
Indices: 37919945--37920000 Score: 98
Period size: 28 Copynumber: 1.9 Consensus size: 30
37919935 AAATTCTGAA
37919945 AAAAAAAAAG-AAAAAAA-AAGAAGTGAGC
1 AAAAAAAAAGTAAAAAAAGAAGAAGTGAGC
37919973 AAAAAAAAAGTAAAAAAAGAAGAAGTGA
1 AAAAAAAAAGTAAAAAAAGAAGAAGTGA
37920001 AAAGTCTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 10 0.38
29 7 0.27
30 9 0.35
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (30 bp):
AAAAAAAAAGTAAAAAAAGAAGAAGTGAGC
Found at i:37921941 original size:21 final size:21
Alignment explanation
Indices: 37921915--37921977 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
37921905 TTGGTATTTG
37921915 GGAATTGGCT-CGAAATGGTAT
1 GGAATTGG-TACGAAATGGTAT
37921936 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
37921957 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
37921978 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 21 0.55
22 16 0.42
ACGTcount: A:0.29, C:0.06, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:37923055 original size:46 final size:46
Alignment explanation
Indices: 37923002--37923095 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
37922992 CAAAGAAAAG
*
37923002 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
37923048 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
37923094 AC
1 AC
37923096 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:37924758 original size:20 final size:20
Alignment explanation
Indices: 37924733--37924787 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
37924723 TGTGGTTCAA
*
37924733 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
37924753 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
37924773 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
37924788 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:37926799 original size:12 final size:12
Alignment explanation
Indices: 37926784--37926824 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
37926774 TAAAAAAAAT
37926784 AAAAAAAACTT-G
1 AAAAAAAA-TTCG
37926796 AAAAAAAATTCG
1 AAAAAAAATTCG
37926808 -AAAAAAATTC-
1 AAAAAAAATTCG
37926818 AAAAAAA
1 AAAAAAA
37926825 GTTTGTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCG
Done.