Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 128 of 182
Found at i:39332557 original size:31 final size:31
Alignment explanation
Indices: 39332522--39332580 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
39332512 AGTCTTAAAC
*
39332522 ACCTTACACAACATTTTAAACAACTTAACAT
1 ACCTTACACAACATTATAAACAACTTAACAT
** *
39332553 ACCTTAGTCAACATTATAAATAACTTAA
1 ACCTTACACAACATTATAAACAACTTAA
39332581 AAACATGCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (31 bp):
ACCTTACACAACATTATAAACAACTTAACAT
Found at i:39338043 original size:64 final size:64
Alignment explanation
Indices: 39337942--39338133 Score: 240
Period size: 64 Copynumber: 3.0 Consensus size: 64
39337932 GAGCATCCCC
* * *
39337942 ATCGGTATTGATCATGCATGTATTGCGGACATACCGCAACTCTTTGTAAGCATCATGTTATATG
1 ATCGGTATTGATCCTGCATGTATTGCGGACATACCGCAGCTCTTTGTAAGCATCATGATATATG
* * * * *
39338006 ATCGGTATTGATCCTGCATGTGTTGTGGACATACCGCAGCTCTTTGTGAGCGTCCTGATATATG
1 ATCGGTATTGATCCTGCATGTATTGCGGACATACCGCAGCTCTTTGTAAGCATCATGATATATG
* * * * * * * *
39338070 ATTGGTATTGATCCTACATGTATTGCAGACATACCACAGCTCTTTATGAGCGTCTTGATATATG
1 ATCGGTATTGATCCTGCATGTATTGCGGACATACCGCAGCTCTTTGTAAGCATCATGATATATG
39338134 GCTCTTTATG
Statistics
Matches: 112, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 112 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (64 bp):
ATCGGTATTGATCCTGCATGTATTGCGGACATACCGCAGCTCTTTGTAAGCATCATGATATATG
Found at i:39341395 original size:26 final size:26
Alignment explanation
Indices: 39341366--39341472 Score: 144
Period size: 26 Copynumber: 4.1 Consensus size: 26
39341356 AACACACCAA
* *
39341366 TATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAACTGCCAGTAACAG
* *
39341392 TATCGCAACAAAACT-CTCAATAACAG
1 TATCGCAGCAAAACTGC-CAGTAACAG
39341418 TATCGCAGCAAAACTGCCAGTAACAG
1 TATCGCAGCAAAACTGCCAGTAACAG
* *
39341444 TATCGCAGCAAAGCTACCAGTAACAG
1 TATCGCAGCAAAACTGCCAGTAACAG
39341470 TAT
1 TAT
39341473 ACTTCCTCCA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
25 1 0.01
26 69 0.97
27 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (26 bp):
TATCGCAGCAAAACTGCCAGTAACAG
Found at i:39341654 original size:27 final size:26
Alignment explanation
Indices: 39341635--39341936 Score: 246
Period size: 27 Copynumber: 11.3 Consensus size: 26
39341625 GGGTATAATA
39341635 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * *
39341662 GTCATTTTACCTTATGAGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATT-TG
* * * **
39341689 ATCATTTTACCTTATAGGGGTATTCCA
1 GTCATTTTACCCTATGGGGGTATT-TG
* *
39341716 GTCATTTTACCTTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
*
39341743 GTCATTTTACCCTATGGGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATT-TG
* *
39341770 GTCATTTTACCCTGTAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* * ** *
39341797 ATCATTTTACCCTGTAAGGTTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * *
39341824 ATCATTTTACCTTGTGGGGGTAATTTG
1 GTCATTTTACCCTATGGGGGT-ATTTG
* * *
39341851 GTCATTTTACCCTGTGGGGATAATTCG
1 GTCATTTTACCCTATGGGGGT-ATTTG
* * *
39341878 GTTATTTTACCCTGT-GGGGTATTCG
1 GTCATTTTACCCTATGGGGGTATTTG
* *
39341903 GTCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATGGGGGT-ATTTG
39341930 GTCATTT
1 GTCATTT
39341937 ATTGACCTCT
Statistics
Matches: 235, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
25 19 0.08
26 12 0.05
27 198 0.84
28 6 0.03
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGGTATTTG
Found at i:39341694 original size:54 final size:52
Alignment explanation
Indices: 39341635--39341936 Score: 309
Period size: 54 Copynumber: 5.7 Consensus size: 52
39341625 GGGTATAATA
39341635 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTATGAGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTATG-GGGTATT-CG
* * * * *
39341689 ATCATTTTACCTTATAGGGGTATTCCAGTCATTTTACCTTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTATGG-GGTA-TTCG
* *
39341743 GTCATTTTACCCTATGGGGGTATTCCGGTCATTTTACCCTGTA-GGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTA-CCT-TATGGGGTA-TTCG
* * ** * * * *
39341797 ATCATTTTACCCTGTAAGGTTATTTCGATCATTTTACCTTGTGGGGGTAATTTG
1 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTAT-GGGGT-ATTCG
* * * * * *
39341851 GTCATTTTACCCTGTGGGGATAATTCGGTTATTTTACCCTGTGGGGTATTCG
1 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTATGGGGTATTCG
* *
39341903 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTT
1 GTCATTTTACCCTATGGGGGTATTTCGGTCATTT
39341937 ATTGACCTCT
Statistics
Matches: 212, Mismatches: 29, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
52 37 0.17
53 9 0.04
54 156 0.74
55 8 0.04
56 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (52 bp):
GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTATGGGGTATTCG
Found at i:39341744 original size:81 final size:80
Alignment explanation
Indices: 39341634--39341936 Score: 330
Period size: 81 Copynumber: 3.8 Consensus size: 80
39341624 GGGGTATAAT
* * *
39341634 AGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTATGAGGGTATTCCGATCATTTTAC
1 AGTCATTTTACCCTATGGAGGTATTTCGGTCATTTTACCTTATGGGGGTATTCCGGTCATTTTAC
* *
39341699 CTTATAGGGGTATTCC
66 CCTGTAGGGGTATT-C
* *
39341715 AGTCATTTTACCTTATGGAGGTATTTCGGTCATTTTACCCTATGGGGGTATTCCGGTCATTTTAC
1 AGTCATTTTACCCTATGGAGGTATTTCGGTCATTTTACCTTATGGGGGTATTCCGGTCATTTTAC
*
39341780 CCTGTAGGGGTATTT
66 CCTGTAGGGGTATTC
* * * * * *
39341795 TGATCATTTTACCCTGT-AAGGTTATTTCGATCATTTTACCTTGTGGGGGTAATT-TGGTCATTT
1 AG-TCATTTTACCCTATGGAGG-TATTTCGGTCATTTTACCTTATGGGGGT-ATTCCGGTCATTT
39341858 TACCCTGT-GGGGATAATTC
63 TACCCTGTAGGGG-T-ATTC
* * * * *
39341877 GGTTATTTTACCCTGTGG-GGTA-TTCGGTCATTTTACCCTGTGGGGGTAATT-CGGTCATTT
1 AGTCATTTTACCCTATGGAGGTATTTCGGTCATTTTACCTTATGGGGGT-ATTCCGGTCATTT
39341937 ATTGACCTCT
Statistics
Matches: 193, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
79 35 0.18
80 10 0.05
81 141 0.73
82 7 0.04
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (80 bp):
AGTCATTTTACCCTATGGAGGTATTTCGGTCATTTTACCTTATGGGGGTATTCCGGTCATTTTAC
CCTGTAGGGGTATTC
Found at i:39344075 original size:34 final size:34
Alignment explanation
Indices: 39344037--39344106 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
39344027 AGGGAATATG
39344037 CCAAAATCTTTAAATATCTTGTAACGCCCCAAAA
1 CCAAAATCTTTAAATATCTTGTAACGCCCCAAAA
*
39344071 CCAAAATCTTTAAATATCTTGTAACGCCTCAAAA
1 CCAAAATCTTTAAATATCTTGTAACGCCCCAAAA
39344105 CC
1 CC
39344107 CGGGCTAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.27, G:0.06, T:0.27
Consensus pattern (34 bp):
CCAAAATCTTTAAATATCTTGTAACGCCCCAAAA
Found at i:39345345 original size:20 final size:20
Alignment explanation
Indices: 39345322--39345381 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
39345312 GCTGTGTGGG
39345322 GGTCCACACGCCCATGTGAA
1 GGTCCACACGCCCATGTGAA
* *
39345342 GGTCGCACACACCCATGTGGA
1 GGTC-CACACGCCCATGTGAA
** *
39345363 GGGACACACGCCCGTGTGA
1 GGTCCACACGCCCATGTGA
39345382 GCAGCCTGTG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.13
Consensus pattern (20 bp):
GGTCCACACGCCCATGTGAA
Found at i:39345356 original size:21 final size:20
Alignment explanation
Indices: 39345322--39345360 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39345312 GCTGTGTGGG
*
39345322 GGTCCACACGCCCATGTGAA
1 GGTCCACACACCCATGTGAA
39345342 GGTCGCACACACCCATGTG
1 GGTC-CACACACCCATGTG
39345361 GAGGGACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (20 bp):
GGTCCACACACCCATGTGAA
Found at i:39347134 original size:37 final size:37
Alignment explanation
Indices: 39347067--39347144 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
39347057 GAAGATGGCT
* * ** *
39347067 AGATTGAAAGGGTGAAGATTTAAAGTTGGTTGGATTA
1 AGATTGAAAGGGTGAAAATTAAAAAATGGTTGGATAA
39347104 AGATTG-AAGGGTTGAAAATTAAAAAATGGTTGGATAA
1 AGATTGAAAGGG-TGAAAATTAAAAAATGGTTGGATAA
39347141 AGAT
1 AGAT
39347145 CAAACTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 5 0.14
37 30 0.86
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (37 bp):
AGATTGAAAGGGTGAAAATTAAAAAATGGTTGGATAA
Found at i:39357598 original size:19 final size:18
Alignment explanation
Indices: 39357576--39357615 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
39357566 CGCATGTAGT
*
39357576 GCCTCCGCGCCAAAGCCAC
1 GCCTCCGAGCC-AAGCCAC
*
39357595 GCCTCCGAGCCGAGCCAC
1 GCCTCCGAGCCAAGCCAC
39357613 GCC
1 GCC
39357616 GCCACCAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.17, C:0.53, G:0.25, T:0.05
Consensus pattern (18 bp):
GCCTCCGAGCCAAGCCAC
Found at i:39358638 original size:3 final size:3
Alignment explanation
Indices: 39358623--39358664 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
39358613 ATTGTTCAGT
39358623 TTA TTA TCT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39358665 GTAATAGTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 35 0.95
4 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39363863 original size:15 final size:15
Alignment explanation
Indices: 39363843--39363874 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39363833 CATTTCACTA
*
39363843 TTATATCTTTTGTAT
1 TTATATCTTTTATAT
39363858 TTATATCTTTTATAT
1 TTATATCTTTTATAT
39363873 TT
1 TT
39363875 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATATCTTTTATAT
Found at i:39372752 original size:22 final size:23
Alignment explanation
Indices: 39372726--39372888 Score: 99
Period size: 22 Copynumber: 7.0 Consensus size: 23
39372716 ATTTTCACAC
*
39372726 CAAAATTTGGACAGCATATATA-
1 CAAAATTTGGACAGCATATACAT
*
39372748 CAAAATTTGGACTGCATTTATACAT
1 CAAAATTTGGACAGCA--TATACAT
39372773 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* * * *
39372795 -ATATAA-TCGGACTGCATTTGTATAT
1 CA-A-AATTTGGACAGCA--TATACAT
39372820 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* * *
39372842 -ATATAA-TTGGACTGCTTTTGTACAT
1 CA-A-AATTTGGACAGC--ATATACAT
39372867 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
39372889 TCATTTACTC
Statistics
Matches: 107, Mismatches: 17, Indels: 34
0.68 0.11 0.22
Matches are distributed among these distances:
21 2 0.02
22 38 0.36
23 15 0.14
24 26 0.24
25 24 0.22
26 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (23 bp):
CAAAATTTGGACAGCATATACAT
Found at i:39372788 original size:24 final size:24
Alignment explanation
Indices: 39372713--39372882 Score: 99
Period size: 24 Copynumber: 7.2 Consensus size: 24
39372703 CAAACTAGAT
*
39372713 AGCATTT-TCACACCAAAATTTGGAC
1 AGCATTTAT-ACATCAAAATTT-GAC
*
39372738 AGCA--TATATA-CAAAATTTGGAC
1 AGCATTTATACATCAAAATTT-GAC
*
39372760 TGCATTTATACATCAAAATTTGAC
1 AGCATTTATACATCAAAATTTGAC
**
39372784 AGCA--TATACAT-ATATAATCGGAC
1 AGCATTTATACATCA-A-AATTTGAC
* * *
39372807 TGCATTTGTATATCAAAATTTGAC
1 AGCATTTATACATCAAAATTTGAC
*
39372831 AGCA--TATACAT-ATATAATTGGAC
1 AGCATTTATACATCA-A-AATTTGAC
* * *
39372854 TGCTTTTGTACATCAAAATTTGAC
1 AGCATTTATACATCAAAATTTGAC
39372878 AGCAT
1 AGCAT
39372883 ATACATTCAT
Statistics
Matches: 110, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
21 2 0.02
22 29 0.26
23 21 0.19
24 31 0.28
25 25 0.23
26 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (24 bp):
AGCATTTATACATCAAAATTTGAC
Found at i:39372886 original size:47 final size:47
Alignment explanation
Indices: 39372726--39372888 Score: 240
Period size: 47 Copynumber: 3.5 Consensus size: 47
39372716 ATTTTCACAC
* * *
39372726 CAAAATTTGGACAGCATAT--ATACAAAATTTGGACTGCATTTATACAT
1 CAAAATTT-GACAGCATATACATATATAA-TTGGACTGCATTTGTACAT
* *
39372773 CAAAATTTGACAGCATATACATATATAATCGGACTGCATTTGTATAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
*
39372820 CAAAATTTGACAGCATATACATATATAATTGGACTGCTTTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
39372867 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
39372889 TCATTTACTC
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
46 10 0.09
47 90 0.85
48 6 0.06
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (47 bp):
CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
Found at i:39373167 original size:14 final size:15
Alignment explanation
Indices: 39373127--39373172 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
39373117 CCATGCACAT
*
39373127 ATATATATACT-ACC
1 ATATAAATACTAACC
39373141 ATATAAATACTAACC
1 ATATAAATACTAACC
39373156 ATA-AAATACTAATCC
1 ATATAAATACTAA-CC
39373171 AT
1 AT
39373173 GATTAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATAAATACTAACC
Found at i:39373907 original size:43 final size:43
Alignment explanation
Indices: 39373819--39373942 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
39373809 AGCTAGTAAA
* *** * *
39373819 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-CCG
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA-AGTCG
* *
39373862 ATGCC-ACTGTCCCAGACAG-GGTGTTACACGAAAACACAAGTCG
1 ATGCCGAC-GTCCCAGAC-GTGGTCTTACACAAAAACACAAGTCG
39373905 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA
39373943 TATCGGAGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 4 0.06
43 62 0.90
44 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (43 bp):
ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACAAGTCG
Found at i:39380581 original size:11 final size:11
Alignment explanation
Indices: 39380567--39380592 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39380557 TTTTTTTAAA
39380567 TTTTAAAATAC
1 TTTTAAAATAC
39380578 TTTTAAAATAC
1 TTTTAAAATAC
39380589 TTTT
1 TTTT
39380593 TTTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:39380594 original size:41 final size:40
Alignment explanation
Indices: 39380546--39380652 Score: 144
Period size: 41 Copynumber: 2.6 Consensus size: 40
39380536 TAAATATTTT
39380546 TATTTTTTTT-ATTTTTTTAAATTTTAAAATACTTTTAAAA
1 TATTTTTTTTAATTTTTTT-AATTTTAAAATACTTTTAAAA
*
39380586 TACTTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAA
1 TA-TTTTTTTTAATTTTTTTAATTTTAAAATACTTTTAAAA
***
39380627 TATTTTTAAAATATTTTTTTAATTTT
1 TATTTTTTTTA-ATTTTTTTAATTTT
39380653 TTAATTTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
40 8 0.13
41 44 0.73
42 8 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (40 bp):
TATTTTTTTTAATTTTTTTAATTTTAAAATACTTTTAAAA
Found at i:39380603 original size:49 final size:50
Alignment explanation
Indices: 39380567--39380703 Score: 215
Period size: 49 Copynumber: 2.7 Consensus size: 50
39380557 TTTTTTTAAA
39380567 TTTTAAAATACTTTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTAAAATA-TTTTTTTTAA-TTTTTTAATTTTAAAATAT
*
39380619 TTTTAAAATATTTTTAAAATA-TTTTTTTAATTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTAAAATATTTTTTTTAATTTTTTAATTTTAAAATAT
*
39380668 TTTTAAAATACTTTTTAAAT-TTTTGTTTTAATTTTT
1 TTTTAAAATACTTTTAAAATATTTT-TTTTAATTTTT
39380704 AAAATATATT
Statistics
Matches: 80, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
49 40 0.50
50 20 0.25
52 20 0.25
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (50 bp):
TTTTAAAATACTTTTAAAATATTTTTTTTAATTTTTTAATTTTAAAATAT
Found at i:39380622 original size:11 final size:11
Alignment explanation
Indices: 39380608--39380686 Score: 89
Period size: 11 Copynumber: 7.6 Consensus size: 11
39380598 ATTTTTTTAA
39380608 TTTTAAAATAT
1 TTTTAAAATAT
39380619 TTTTAAAATAT
1 TTTTAAAATAT
39380630 TTTTAAAATAT
1 TTTTAAAATAT
**
39380641 TTTTTTAAT-T
1 TTTTAAAATAT
39380651 TTTT---A-A-
1 TTTTAAAATAT
39380657 TTTTAAAATAT
1 TTTTAAAATAT
39380668 TTTTAAAATACT
1 TTTTAAAATA-T
39380680 TTTTAAA
1 TTTTAAA
39380687 TTTTTGTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
6 4 0.07
7 1 0.02
9 1 0.02
10 6 0.10
11 39 0.66
12 8 0.14
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39380661 original size:38 final size:38
Alignment explanation
Indices: 39380619--39380691 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
39380609 TTTAAAATAT
* *
39380619 TTTTAAAATATTTTTAAAATATTTTTTTAATTTTTTAA
1 TTTTAAAATATTTTTAAAATACTTTTTAAATTTTTTAA
39380657 TTTTAAAATATTTTTAAAATACTTTTTAAATTTTT
1 TTTTAAAATATTTTTAAAATACTTTTTAAATTTTT
39380692 GTTTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTTAAAATATTTTTAAAATACTTTTTAAATTTTTTAA
Found at i:39382621 original size:18 final size:19
Alignment explanation
Indices: 39382598--39382635 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
39382588 TTTTATACTC
*
39382598 TTTTAACAAT-TTTTAATT
1 TTTTAAAAATATTTTAATT
*
39382616 TTTTAAAAATATTTTTATT
1 TTTTAAAAATATTTTAATT
39382635 T
1 T
39382636 ACATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAAAAATATTTTAATT
Found at i:39383139 original size:37 final size:35
Alignment explanation
Indices: 39383084--39383190 Score: 103
Period size: 37 Copynumber: 2.9 Consensus size: 35
39383074 AATTATAAAT
*
39383084 TAAT-AATAATTAAGAAAAAGAAAAATATTAAAA-A
1 TAATGAATATTTAA-AAAAAGAAAAATATTAAAAGA
*
39383118 TAAT-ACTTATTTTGAAAAAAAAGATAAAATATCTAAAAGA
1 TAATGA-ATA-TTT--AAAAAAAGA-AAAATAT-TAAAAGA
*
39383158 TAATGAATATTTAAAAAAAGATAAATATTAAAA
1 TAATGAATATTTAAAAAAAGAAAAATATTAAAA
39383191 TTATATATGA
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
34 5 0.08
35 7 0.11
36 8 0.13
37 16 0.26
38 9 0.15
39 8 0.13
40 7 0.11
41 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.28
Consensus pattern (35 bp):
TAATGAATATTTAAAAAAAGAAAAATATTAAAAGA
Found at i:39383184 original size:18 final size:18
Alignment explanation
Indices: 39383133--39383190 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
39383123 CTTATTTTGA
*
39383133 AAAAAAAGATAAAATATCT
1 AAAAAAAGAT-AAATATTT
* *
39383152 AAAAGATA-ATGAATATTT
1 AAAA-AAAGATAAATATTT
39383170 AAAAAAAGATAAATA-TT
1 AAAAAAAGATAAATATTT
39383187 AAAA
1 AAAA
39383191 TTATATATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 8 0.25
18 16 0.50
19 6 0.19
20 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (18 bp):
AAAAAAAGATAAATATTT
Found at i:39384124 original size:27 final size:27
Alignment explanation
Indices: 39384093--39384148 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
39384083 CAAAAAATCA
39384093 AAATTTTAATTAATT-TTTTATATTTTC
1 AAATTTTAATTAATTCTTTTA-ATTTTC
*
39384120 AAATTTTTATTAATTCTTTTAATTTTC
1 AAATTTTAATTAATTCTTTTAATTTTC
39384147 AA
1 AA
39384149 TTTAACTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (27 bp):
AAATTTTAATTAATTCTTTTAATTTTC
Found at i:39386394 original size:23 final size:24
Alignment explanation
Indices: 39386350--39386394 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
39386340 ATTTTCTGTT
39386350 TGAATTACGGTTTCTTTTTAATGA
1 TGAATTACGGTTTCTTTTTAATGA
* *
39386374 TGAATTAC-TTTTTTTTTTAAT
1 TGAATTACGGTTTCTTTTTAAT
39386395 TGTTAACGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.58
Consensus pattern (24 bp):
TGAATTACGGTTTCTTTTTAATGA
Found at i:39400661 original size:27 final size:27
Alignment explanation
Indices: 39400631--39400779 Score: 120
Period size: 27 Copynumber: 5.5 Consensus size: 27
39400621 AGGAAATCCT
* *
39400631 TTCAGA-TTATGCCACCGAGGTAGTTCA
1 TTCAGAGTT-TGCCACAGAGGCAGTTCA
*
39400658 TTCAGAGTTTTCCACAGAGGCAGTTCA
1 TTCAGAGTTTGCCACAGAGGCAGTTCA
* *
39400685 TTCAGAGTTTGCCACAAAGGCAGTTCT
1 TTCAGAGTTTGCCACAGAGGCAGTTCA
* *** * **
39400712 TTCCGAGTGCACCACAAAGGTTGTTCA
1 TTCAGAGTTTGCCACAGAGGCAGTTCA
* * * *
39400739 TTCAGAGCTTACCACAGAGGCAATTCT
1 TTCAGAGTTTGCCACAGAGGCAGTTCA
* *
39400766 TTTAGAGTGTGCCA
1 TTCAGAGTTTGCCA
39400780 TAAAGGCTAT
Statistics
Matches: 95, Mismatches: 26, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
27 93 0.98
28 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (27 bp):
TTCAGAGTTTGCCACAGAGGCAGTTCA
Found at i:39400785 original size:54 final size:54
Alignment explanation
Indices: 39400669--39400795 Score: 137
Period size: 54 Copynumber: 2.4 Consensus size: 54
39400659 TCAGAGTTTT
* * * * * *
39400669 CCACAGAGGCAGTTCATTCAGAGTTTGCCACAAAGGCAGTTCTTTCCGAGTGCA
1 CCACAAAGGCTGTTCATTCAGAGCTTACCACAAAGGCAATTCTTTCAGAGTGCA
* * * **
39400723 CCACAAAGGTTGTTCATTCAGAGCTTACCACAGAGGCAATTCTTTTAGAGTGTG
1 CCACAAAGGCTGTTCATTCAGAGCTTACCACAAAGGCAATTCTTTCAGAGTGCA
* *
39400777 CCATAAAGGCTATTCATTC
1 CCACAAAGGCTGTTCATTC
39400796 TTGTCGTGTT
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (54 bp):
CCACAAAGGCTGTTCATTCAGAGCTTACCACAAAGGCAATTCTTTCAGAGTGCA
Found at i:39401536 original size:22 final size:22
Alignment explanation
Indices: 39401507--39401565 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
39401497 TGCACTAATG
39401507 AACAGAGAGCACTGAA-GTGCT
1 AACAGAGAGCACTGAATGTGCT
*
39401528 ATACAGAGAGCAC-AAATGTGCT
1 A-ACAGAGAGCACTGAATGTGCT
39401550 AATCAGAGAGCACTGA
1 AA-CAGAGAGCACTGA
39401566 CGTACTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 4 0.12
22 27 0.84
23 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTGAATGTGCT
Found at i:39401583 original size:25 final size:25
Alignment explanation
Indices: 39401501--39401635 Score: 108
Period size: 25 Copynumber: 5.6 Consensus size: 25
39401491 TTATTATGCA
39401501 CTAATGAA-CAGAGAGCACTGAA-GTG
1 CTAAT-AATCAGAGAGCACT-AACGTG
* *
39401526 CT-AT-A-CAGAGAGCACAAATGTG
1 CTAATAATCAGAGAGCACTAACGTG
* *
39401548 C---TAATCAGAGAGCACTGACGTA
1 CTAATAATCAGAGAGCACTAACGTG
*
39401570 CTAGTAATCAGAGAGCA-TCAACGTG
1 CTAATAATCAGAGAGCACT-AACGTG
* *
39401595 CTAATAATCAGAGAACACCAACGTG
1 CTAATAATCAGAGAGCACTAACGTG
*
39401620 TTAATAATCAGAGAGC
1 CTAATAATCAGAGAGC
39401636 GTGCTAAAGT
Statistics
Matches: 90, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 29 0.32
24 3 0.03
25 54 0.60
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTAACGTG
Found at i:39401585 original size:47 final size:44
Alignment explanation
Indices: 39401509--39401599 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 44
39401499 CACTAATGAA
* *
39401509 CAGAGAGCACTGAAGTGCTATACAGAGAGCA-CAAATGTGCTAAT
1 CAGAGAGCACTGAAGTACTATACAGAGAGCATC-AACGTGCTAAT
*
39401553 CAGAGAGCACTGACGTACTAGTAATCAGAGAGCATCAACGTGCTAAT
1 CAGAGAGCACTGAAGTACTA-T-A-CAGAGAGCATCAACGTGCTAAT
39401600 AATCAGAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
44 18 0.45
45 1 0.03
46 1 0.03
47 19 0.47
48 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (44 bp):
CAGAGAGCACTGAAGTACTATACAGAGAGCATCAACGTGCTAAT
Found at i:39406490 original size:50 final size:50
Alignment explanation
Indices: 39406375--39406521 Score: 213
Period size: 50 Copynumber: 2.9 Consensus size: 50
39406365 GATAATAACA
**
39406375 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGG
* * ** *
39406426 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
39406476 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
39406522 ATCTCAATGA
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 51 0.61
51 33 0.39
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:39407969 original size:85 final size:85
Alignment explanation
Indices: 39407812--39408056 Score: 267
Period size: 85 Copynumber: 2.9 Consensus size: 85
39407802 ATGTGGTTTG
** * * * * *
39407812 ATCACGAACCAAGTGGTAGTTCGTTTAATATGCAAATATGTTGTGCACCCACAACAAGTGGCAGT
1 ATCACGAACCAAGTGACAGTTCATATAATCTACAAATATGTTGTGCACCCACAACAAGTGGCAAT
*
39407877 AATTGCAAATATG-TAGTTCA
66 AACTGCAAATATGCT-GTTCA
* ** * *
39407897 ATCATGAACCAAGTGACAGTTCATATAATCTTTAAATATGTTGTGCACCCACAATAAGTGACAAT
1 ATCACGAACCAAGTGACAGTTCATATAATCTACAAATATGTTGTGCACCCACAACAAGTGGCAAT
*
39407962 AACTGCAAATATGCTGTTCG
66 AACTGCAAATATGCTGTTCA
** * * ** * * *
39407982 ATCACGAACCAAGTGGTAGTTCGTTTGTTCTACAAATATGGTATGCACCTACAACAAGTGGCAAT
1 ATCACGAACCAAGTGACAGTTCATATAATCTACAAATATGTTGTGCACCCACAACAAGTGGCAAT
39408047 AACTGCAAAT
66 AACTGCAAAT
39408057 TATCAGTGGT
Statistics
Matches: 132, Mismatches: 27, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
85 131 0.99
86 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (85 bp):
ATCACGAACCAAGTGACAGTTCATATAATCTACAAATATGTTGTGCACCCACAACAAGTGGCAAT
AACTGCAAATATGCTGTTCA
Found at i:39408256 original size:14 final size:13
Alignment explanation
Indices: 39408227--39408265 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
39408217 TACAAGAAAA
*
39408227 TGTTTTTCTTAAT
1 TGTTTTTTTTAAT
39408240 TGTTTTTTTTAACT
1 TGTTTTTTTTAA-T
39408254 TGTGTTTTTTTA
1 TGT-TTTTTTTA
39408266 TTGGAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 4 0.17
15 8 0.35
ACGTcount: A:0.13, C:0.05, G:0.10, T:0.72
Consensus pattern (13 bp):
TGTTTTTTTTAAT
Found at i:39409091 original size:18 final size:18
Alignment explanation
Indices: 39409064--39409105 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
39409054 AAAATTGGGG
*
39409064 AATCAACTTTTGCAAAGC
1 AATCATCTTTTGCAAAGC
39409082 AATCATCTTTTGCAAAGC
1 AATCATCTTTTGCAAAGC
39409100 AATCAT
1 AATCAT
39409106 TGAAATTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (18 bp):
AATCATCTTTTGCAAAGC
Found at i:39412734 original size:6 final size:6
Alignment explanation
Indices: 39412719--39412790 Score: 63
Period size: 6 Copynumber: 11.5 Consensus size: 6
39412709 TATAAGTCTC
* * * * * *
39412719 AAAAAT AAAATAA AAACAACT AACAAT GAAAAT AATAGT ACAAAT AAAAAT
1 AAAAAT AAAA-AT AAA-AA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
39412770 AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAA
39412791 CAAAAACTAA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
6 41 0.80
7 7 0.14
8 3 0.06
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:39415734 original size:24 final size:24
Alignment explanation
Indices: 39415702--39415748 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
39415692 CTAAATTTAT
*
39415702 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
39415726 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
39415749 ATTTCCCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:39422304 original size:27 final size:28
Alignment explanation
Indices: 39422252--39422305 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
39422242 TAGGACATGA
39422252 AAAGACAAAATAGTTTTTTCCATTTTGG
1 AAAGACAAAATAGTTTTTTCCATTTTGG
*
39422280 AAAGACAAAATAG-TTTTTCTATTTTG
1 AAAGACAAAATAGTTTTTTCCATTTTG
39422306 AAATAGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (28 bp):
AAAGACAAAATAGTTTTTTCCATTTTGG
Found at i:39422479 original size:29 final size:31
Alignment explanation
Indices: 39422437--39422498 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
39422427 TAATAAAGGT
*
39422437 AAAATTACATTTTAACCC-CTAAAAATTATA
1 AAAATTACATTTTAACCCTCTAAAAACTATA
* * *
39422467 AAAATTTCA-TTTATCCCTTTAAAAACTATA
1 AAAATTACATTTTAACCCTCTAAAAACTATA
39422497 AA
1 AA
39422499 GATATAGGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATTACATTTTAACCCTCTAAAAACTATA
Found at i:39429807 original size:17 final size:16
Alignment explanation
Indices: 39429770--39429808 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39429760 TTCCTTAATT
39429770 AAAAATAACTAATAAC
1 AAAAATAACTAATAAC
* *
39429786 TAAAATAACTACTACAC
1 AAAAATAACTAATA-AC
39429803 AAAAAT
1 AAAAAT
39429809 GTCTAGTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATAACTAATAAC
Found at i:39440200 original size:25 final size:23
Alignment explanation
Indices: 39440161--39440206 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
39440151 AAGATAAAAG
39440161 CAATCGGAAAAGAAAAAAGAACC
1 CAATCGGAAAAGAAAAAAGAACC
39440184 CAATCGAGAAAAGGAAAAAAGAA
1 CAATCG-GAAAA-GAAAAAAGAA
39440207 AAACCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 5 0.24
25 10 0.48
ACGTcount: A:0.63, C:0.13, G:0.20, T:0.04
Consensus pattern (23 bp):
CAATCGGAAAAGAAAAAAGAACC
Found at i:39441791 original size:173 final size:173
Alignment explanation
Indices: 39441504--39441913 Score: 680
Period size: 173 Copynumber: 2.4 Consensus size: 173
39441494 CTTAGGAAGG
* *
39441504 CAAGATCTGCTATCTTTAACCAGCTCCACTGTAACCGATAGAGGCAAGGCTTTG-TTTCGATCTG
1 CAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
39441568 TTTCGCTATCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAG
65 CTTCGCTATCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAG
*
39441633 GCAAGGTTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGAAAGA
130 GCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGAAAGA
*
39441677 CAAGATCTGCTTCTTTAACTAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 CAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* * *
39441742 TTCGCTGTTAATGCAGGAAGGCAAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCGATGGAG
66 TTCGCTATCAATGCAGGAAGGC-AAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAG
* *
39441806 GCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGG
130 GCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGAAAGA
*
39441850 CAAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGTCTTTGTTTTCGATCT
1 C-AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
39441914 TCACGGGTCT
Statistics
Matches: 222, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
172 39 0.18
173 113 0.51
174 70 0.32
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (173 bp):
CAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
TTCGCTATCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGG
CAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGAAAGA
Found at i:39441810 original size:87 final size:86
Alignment explanation
Indices: 39441497--39441913 Score: 692
Period size: 87 Copynumber: 4.8 Consensus size: 86
39441487 GCTAGTGCTT
* *
39441497 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGTAACCGATAGAGGCAAGGCTTTG-TTT
1 AGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* * *
39441561 CGATCTGTTTCGCTATCAATGC
65 CGATCTGCTTCGCTGTTAATGC
* *
39441583 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGTTTTGTTTT
1 AGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
39441648 CGATCTGCTTCGCTGTTAATGC
65 CGATCTGCTTCGCTGTTAATGC
* * *
39441670 AGAAAGACAAGATCTGCTTCTTTAACTAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
1 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
39441735 GATCTGCTTCGCTGTTAATGC
66 GATCTGCTTCGCTGTTAATGC
39441756 AGGAAGGCAAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGC-AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
39441821 CGATCTGCTTCGCTGTTAATGC
65 CGATCTGCTTCGCTGTTAATGC
*
39441843 AGGAAGGCAAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGTCTTTGTTTT
1 AGGAAGGC-AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
39441908 CGATCT
65 CGATCT
39441914 TCACGGGTCT
Statistics
Matches: 313, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
86 128 0.41
87 185 0.59
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (86 bp):
AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
GATCTGCTTCGCTGTTAATGC
Found at i:39441852 original size:43 final size:43
Alignment explanation
Indices: 39441717--39441852 Score: 116
Period size: 43 Copynumber: 3.1 Consensus size: 43
39441707 CAACCGATGG
39441717 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
* * * ** * * * * * *
39441760 AGGCAAAGATCTGCTTCTTTAACCAGCTCCACTG-CAA-CCGATGG-
1 AGGCAAGGCTTTG-TT-TTCGATCTGCTTCGCTGTTAATGC-A-GGA
39441804 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
39441847 AGGCAA
1 AGGCAA
39441853 AGATCTGCTT
Statistics
Matches: 64, Mismatches: 22, Indels: 14
0.64 0.22 0.14
Matches are distributed among these distances:
42 13 0.20
43 22 0.34
44 16 0.25
45 13 0.20
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
Found at i:39443162 original size:21 final size:20
Alignment explanation
Indices: 39443138--39443205 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 20
39443128 TAGCCTCTCT
39443138 ATTTTTACTCTTTCATTTTTC
1 ATTTTT-CTCTTTCATTTTTC
39443159 ATTTTT-TCATTCTCATTTTTC
1 ATTTTTCTC-TT-TCATTTTTC
*
39443180 ATTTTCTCTTTTTC-TTTTTC
1 ATTTT-TCTCTTTCATTTTTC
39443200 ATTTTT
1 ATTTTT
39443206 TTTGAAATCC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
19 3 0.07
20 13 0.31
21 22 0.52
22 3 0.07
23 1 0.02
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTCTCTTTCATTTTTC
Found at i:39443184 original size:6 final size:7
Alignment explanation
Indices: 39443148--39443205 Score: 68
Period size: 7 Copynumber: 8.4 Consensus size: 7
39443138 ATTTTTACTC
39443148 TTTCATT
1 TTTCATT
39443155 TTTCATTT
1 TTTCA-TT
39443163 TTTCA-T
1 TTTCATT
*
39443169 TCTCATT
1 TTTCATT
39443176 TTTCATT
1 TTTCATT
39443183 TTCTC-TT
1 TT-TCATT
39443190 TTTC-TT
1 TTTCATT
39443196 TTTCATT
1 TTTCATT
39443203 TTT
1 TTT
39443206 TTTGAAATCC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
6 13 0.29
7 23 0.51
8 9 0.20
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCATT
Found at i:39443646 original size:34 final size:34
Alignment explanation
Indices: 39443608--39443673 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
39443598 TGATTTCTCT
* *
39443608 TTTTTGCTTTTGATTTTTTTCT-TTTCTTTTTTCG
1 TTTTTGATTTTGATTTTTCTCTCTTT-TTTTTTCG
*
39443642 TTTTTTATTTTGATTTTTCTCTCTTTTTTTTT
1 TTTTTGATTTTGATTTTTCTCTCTTTTTTTTT
39443674 GAATCTGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 25 0.89
35 3 0.11
ACGTcount: A:0.05, C:0.11, G:0.06, T:0.79
Consensus pattern (34 bp):
TTTTTGATTTTGATTTTTCTCTCTTTTTTTTTCG
Found at i:39444358 original size:4 final size:4
Alignment explanation
Indices: 39444351--39444375 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39444341 ACAATATGAT
39444351 AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG A
39444376 TGGTTTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:39463189 original size:29 final size:27
Alignment explanation
Indices: 39463132--39463199 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 27
39463122 TTTTTTATAC
*
39463132 TTTTAAAATAATTTTTATGATTTTTAA
1 TTTTAAAATAATTTTTATGATTTTAAA
*
39463159 TTTCTAAATATATTTTTTAT-ATTTTAAAA
1 TTT-TAAA-ATAATTTTTATGATTTT-AAA
39463188 TTTTAAAA-AATT
1 TTTTAAAATAATT
39463200 AATTAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 3 0.09
27 4 0.11
28 13 0.37
29 15 0.43
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTTAAAATAATTTTTATGATTTTAAA
Found at i:39471583 original size:18 final size:18
Alignment explanation
Indices: 39471557--39471595 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39471547 CCCGAGAAAC
*
39471557 TTTATATCCTTCTA-GGAT
1 TTTAAATCCTTC-AGGGAT
39471575 TTTAAATCCTTCAGGGAT
1 TTTAAATCCTTCAGGGAT
39471593 TTT
1 TTT
39471596 CATATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTAAATCCTTCAGGGAT
Found at i:39475523 original size:22 final size:21
Alignment explanation
Indices: 39475497--39475552 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
39475487 ATACGCATAT
39475497 TTATTTTTTTAATATAATGTAA
1 TTATTTTTTTAATAT-ATGTAA
*
39475519 TTATTTTTTTTATATATGTAA
1 TTATTTTTTTAATATATGTAA
*
39475540 TTATTTTTATAAT
1 TTATTTTTTTAAT
39475553 CTATATATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTATTTTTTTAATATATGTAA
Found at i:39475557 original size:25 final size:23
Alignment explanation
Indices: 39475501--39475572 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 23
39475491 GCATATTTAT
39475501 TTTTTTAA-TATA-ATGTAATTA
1 TTTTTTAATTATATATGTAATTA
39475522 TTTTTT--TTATATATGTAATTA
1 TTTTTTAATTATATATGTAATTA
39475543 TTTTTATAATCTATATATGTATATATA
1 TTTTT-TAAT-TATATATGTA-AT-TA
39475570 TTT
1 TTT
39475573 ATTCTTGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
20 4 0.09
21 20 0.47
22 1 0.02
24 1 0.02
25 10 0.23
26 2 0.05
27 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTTTTAATTATATATGTAATTA
Found at i:39475972 original size:17 final size:16
Alignment explanation
Indices: 39475946--39475979 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
39475936 ATATATGTTA
39475946 GTTTCATTATTTATAT
1 GTTTCATTATTTATAT
*
39475962 GTTTACATTATTTCTAT
1 GTTT-CATTATTTATAT
39475979 G
1 G
39475980 CCATTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (16 bp):
GTTTCATTATTTATAT
Found at i:39476022 original size:19 final size:20
Alignment explanation
Indices: 39475981--39476022 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
39475971 ATTTCTATGC
* *
39475981 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
39476001 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
39476020 CAT
1 CAT
39476023 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:39478143 original size:22 final size:22
Alignment explanation
Indices: 39478117--39478159 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
39478107 TTAAGCTCCT
*
39478117 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
39478139 TTACATTCAATCAATAAATGT
1 TTACATTCAATCAATAAATGT
39478160 GAATTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:39480219 original size:9 final size:9
Alignment explanation
Indices: 39480205--39480237 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
39480195 AACCCTAAGA
39480205 AATGTAGTT
1 AATGTAGTT
39480214 AATGTAGTT
1 AATGTAGTT
39480223 AAATGTAGTT
1 -AATGTAGTT
39480233 AATGT
1 AATGT
39480238 TGCCCCATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (9 bp):
AATGTAGTT
Found at i:39480229 original size:10 final size:10
Alignment explanation
Indices: 39480204--39480234 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
39480194 AAACCCTAAG
39480204 AAATGTAGTT
1 AAATGTAGTT
39480214 -AATGTAGTT
1 AAATGTAGTT
39480223 AAATGTAGTT
1 AAATGTAGTT
39480233 AA
1 AA
39480235 TGTTGCCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (10 bp):
AAATGTAGTT
Found at i:39481283 original size:18 final size:19
Alignment explanation
Indices: 39481262--39481305 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
39481252 ACCGTTTTAA
39481262 CACATATGTTTCAC-T-TTT
1 CACATAT-TTTCACATATTT
39481280 CACAT-TTTTCACATATTT
1 CACATATTTTCACATATTT
39481298 CACATATT
1 CACATATT
39481306 CATGCTCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 13 0.57
19 2 0.09
ACGTcount: A:0.27, C:0.23, G:0.02, T:0.48
Consensus pattern (19 bp):
CACATATTTTCACATATTT
Found at i:39484050 original size:38 final size:38
Alignment explanation
Indices: 39483999--39484222 Score: 160
Period size: 41 Copynumber: 5.7 Consensus size: 38
39483989 ATCAAGCTTA
* * **
39483999 CTAGGCTTTAAGCCTGAGTAACATTGGCACTAAGCCTG
1 CTAGGCATTAAGCCTGAATAACACCGGCACTAAGCCTG
39484037 CTAGGCATTAAGCCTGAATAACACCGGCACTAAGCCTG
1 CTAGGCATTAAGCCTGAATAACACCGGCACTAAGCCTG
* ** ** * *
39484075 CTAGACACAAAGTTTGAATCTATACACCGACACTAAGCTTG
1 CTAGGCATTAAGCCTGAA--TA-ACACCGGCACTAAGCCTG
* ** * * *
39484116 CTAAGCACGAAGCTTGAATCAATACACCGACACTAAGCTTG
1 CTAGGCATTAAGCCTGAAT--A-ACACCGGCACTAAGCCTG
* * *
39484157 CTAGGCATGAAGCCTGAATTAATACACCGACACTAAGCCTA
1 CTAGGCATTAAGCCTGAA-T-A-ACACCGGCACTAAGCCTG
* **
39484198 CTATGCACAAAGCCTGAATAACACC
1 CTAGGCATTAAGCCTGAATAACACC
39484223 CCATTTTAAT
Statistics
Matches: 157, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
38 52 0.33
39 2 0.01
40 3 0.02
41 99 0.63
42 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (38 bp):
CTAGGCATTAAGCCTGAATAACACCGGCACTAAGCCTG
Found at i:39484211 original size:41 final size:40
Alignment explanation
Indices: 39484026--39484216 Score: 197
Period size: 41 Copynumber: 4.8 Consensus size: 40
39484016 GTAACATTGG
** *
39484026 CACTAAGCCTGCTAGGCATTAAGCCTGAA-TA-ACACCGG
1 CACTAAGCCTGCTAGGCACAAAGCCTGAATTATACACCGA
* **
39484064 CACTAAGCCTGCTAGACACAAAGTTTGAATCTATACACCGA
1 CACTAAGCCTGCTAGGCACAAAGCCTGAAT-TATACACCGA
* * * * *
39484105 CACTAAGCTTGCTAAGCACGAAGCTTGAATCAATACACCGA
1 CACTAAGCCTGCTAGGCACAAAGCCTGAAT-TATACACCGA
* **
39484146 CACTAAGCTTGCTAGGCATGAAGCCTGAATTAATACACCGA
1 CACTAAGCCTGCTAGGCACAAAGCCTGAATT-ATACACCGA
* *
39484187 CACTAAGCCTACTATGCACAAAGCCTGAAT
1 CACTAAGCCTGCTAGGCACAAAGCCTGAAT
39484217 AACACCCCAT
Statistics
Matches: 128, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
38 24 0.19
40 2 0.02
41 102 0.80
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.20
Consensus pattern (40 bp):
CACTAAGCCTGCTAGGCACAAAGCCTGAATTATACACCGA
Found at i:39495976 original size:20 final size:20
Alignment explanation
Indices: 39495934--39495976 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
39495924 CTTGATTTGG
*
39495934 TTTGATTCCAATCAATTTAA
1 TTTGATTCCAATCAAATTAA
* * *
39495954 TTTGATTCTATTCAAATTGA
1 TTTGATTCCAATCAAATTAA
39495974 TTT
1 TTT
39495977 AAATGCTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (20 bp):
TTTGATTCCAATCAAATTAA
Found at i:39496718 original size:27 final size:26
Alignment explanation
Indices: 39496675--39496728 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
39496665 ATAAATTAAA
*
39496675 AAAAGGAAAAAAAATAAGAA-AAAAAT
1 AAAAGCAAAAAAAATAA-AATAAAAAT
*
39496701 AAAAGCAAAAAATTATAAAATAAAAAT
1 AAAAGCAAAAAA-AATAAAATAAAAAT
39496728 A
1 A
39496729 TATAGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (26 bp):
AAAAGCAAAAAAAATAAAATAAAAAT
Found at i:39496947 original size:21 final size:22
Alignment explanation
Indices: 39496915--39496961 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
39496905 AGAGAAAATA
39496915 AAAAATTGTCAAAAAAAATTAG
1 AAAAATTGTCAAAAAAAATTAG
* *
39496937 AAAAATT-TCAAAAAAATTTAT
1 AAAAATTGTCAAAAAAAATTAG
39496958 AAAA
1 AAAA
39496962 TCAGACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAAATTGTCAAAAAAAATTAG
Found at i:39496961 original size:11 final size:11
Alignment explanation
Indices: 39496914--39496955 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
39496904 AAGAGAAAAT
39496914 AAAAAATTGTCA
1 AAAAAATT-TCA
*
39496926 AAAAAAATT-A
1 AAAAAATTTCA
*
39496936 GAAAAATTTCA
1 AAAAAATTTCA
39496947 AAAAAATTT
1 AAAAAATTT
39496956 ATAAAATCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 10 0.40
12 7 0.28
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (11 bp):
AAAAAATTTCA
Found at i:39499232 original size:27 final size:27
Alignment explanation
Indices: 39499168--39499242 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
39499158 GTATAGGGGT
*
39499168 GTGGTGTCTATCTGATAGGCGGCACCA
1 GTGGTGTCTATCTGATAGGCGACACCA
**** **
39499195 GTGACCCCTATCTGATAGGCGACACTG
1 GTGGTGTCTATCTGATAGGCGACACCA
*
39499222 GTGGTGTCTATCTGAAAGGCG
1 GTGGTGTCTATCTGATAGGCG
39499243 GCATACCTAG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (27 bp):
GTGGTGTCTATCTGATAGGCGACACCA
Found at i:39502381 original size:14 final size:14
Alignment explanation
Indices: 39502362--39502392 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39502352 ATGTATTTAC
39502362 TTTATATAACAAAA
1 TTTATATAACAAAA
*
39502376 TTTATATTACAAAA
1 TTTATATAACAAAA
39502390 TTT
1 TTT
39502393 GTTACAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTATATAACAAAA
Found at i:39503001 original size:12 final size:12
Alignment explanation
Indices: 39502986--39503026 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
39502976 TGTGGCTTGG
*
39502986 GCTCAGGCTCGA
1 GCTCTGGCTCGA
*
39502998 GCTCTGGCTCTA
1 GCTCTGGCTCGA
39503010 GCTCTGGCTCGA
1 GCTCTGGCTCGA
*
39503022 CCTCT
1 GCTCT
39503027 ATATCTGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (12 bp):
GCTCTGGCTCGA
Found at i:39503680 original size:14 final size:14
Alignment explanation
Indices: 39503646--39503672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39503636 CAAATTACAT
39503646 GTTAGAATAGTATA
1 GTTAGAATAGTATA
39503660 GTTAGAATAGTAT
1 GTTAGAATAGTAT
39503673 CATTAGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (14 bp):
GTTAGAATAGTATA
Found at i:39507270 original size:90 final size:90
Alignment explanation
Indices: 39507202--39507398 Score: 261
Period size: 90 Copynumber: 2.2 Consensus size: 90
39507192 CTAGAATATG
* *
39507202 GGTGGATGAACCACTAGTGTTGCAGGTTAATACGCTCCCAGATGGTTGAT-AATGCACAACATAG
1 GGTGGATGAACCACCAGTGTTGCAGGTTAATACACTCCCAGATGGTTG-TGAATGCACAACATAG
39507266 TTGCAGATAAAAGCTACCAGAAAATA
65 TTGCAGATAAAAGCTACCAGAAAATA
* * * *
39507292 GGTGGATGAACCACCAGTGTTGCAGGTTAATACACTGCTAGATGGTTGTGAATGTACAAAATAGT
1 GGTGGATGAACCACCAGTGTTGCAGGTTAATACACTCCCAGATGGTTGTGAATGCACAACATAGT
** * * * *
39507357 TGTGGATAAAAGCTGCTAGATAATC
66 TGCAGATAAAAGCTACCAGAAAATA
*
39507382 TGTGGATGAACCACCAG
1 GGTGGATGAACCACCAG
39507399 AGTTTTGTAG
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
89 1 0.01
90 92 0.99
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (90 bp):
GGTGGATGAACCACCAGTGTTGCAGGTTAATACACTCCCAGATGGTTGTGAATGCACAACATAGT
TGCAGATAAAAGCTACCAGAAAATA
Found at i:39508995 original size:3 final size:3
Alignment explanation
Indices: 39508987--39509016 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39508977 ACGAGACTTG
39508987 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
39509017 ACCACCACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
TCC
Found at i:39509597 original size:62 final size:61
Alignment explanation
Indices: 39509501--39509624 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 61
39509491 CCCAAAAATC
* *
39509501 TATTTAATTTCTTCTCTTCTTTAAGAGTGAGTTTTCTAGGATTTGCTTCAAAGCTCGTTTT
1 TATTTAATTTCTTCTCTTCTTCAAGAGTGAGTTTTCTAGGATTTGCATCAAAGCTCGTTTT
* *
39509562 TATTTAATTTCTTATTCTTCTTCAAGAGTGAGTTTTCTAGGATTTGCATCAAAGCTTGTTTT
1 TATTTAATTTCTT-CTCTTCTTCAAGAGTGAGTTTTCTAGGATTTGCATCAAAGCTCGTTTT
39509624 T
1 T
39509625 CTTGCATTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
61 13 0.22
62 45 0.78
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.51
Consensus pattern (61 bp):
TATTTAATTTCTTCTCTTCTTCAAGAGTGAGTTTTCTAGGATTTGCATCAAAGCTCGTTTT
Found at i:39513648 original size:24 final size:24
Alignment explanation
Indices: 39513614--39513661 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
39513604 TGATCATGTC
*
39513614 AATGCAATGTTTTTAGAAAAAGGT
1 AATGCAATGTTTTCAGAAAAAGGT
*
39513638 AATGCAGTGTTTTCAGAAAAAGGT
1 AATGCAATGTTTTCAGAAAAAGGT
39513662 CCTATCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (24 bp):
AATGCAATGTTTTCAGAAAAAGGT
Found at i:39516238 original size:14 final size:15
Alignment explanation
Indices: 39516219--39516251 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
39516209 ACTAGAGAAA
39516219 TTTGCTTATATCTT-
1 TTTGCTTATATCTTG
39516233 TTTGCTTATATCTTG
1 TTTGCTTATATCTTG
39516248 TTTG
1 TTTG
39516252 ATGATCTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (15 bp):
TTTGCTTATATCTTG
Found at i:39518483 original size:43 final size:42
Alignment explanation
Indices: 39518430--39518526 Score: 142
Period size: 43 Copynumber: 2.2 Consensus size: 42
39518420 GAGGATGTTA
39518430 GGATATTATTATGGTATATTATC-CTTTAGCAATTTGATTCCTAAT
1 GGATATTA-TAT-G-ATATTATCTC-TTAGCAATTTGATTCCTAAT
39518475 GGAATATTATATGATATTATCTCTTAGCAATTTGATTCCTAAT
1 GG-ATATTATATGATATTATCTCTTAGCAATTTGATTCCTAAT
39518518 GGATATTAT
1 GGATATTAT
39518527 CTTTTAGGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
42 7 0.14
43 30 0.60
44 2 0.04
45 5 0.10
46 6 0.12
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (42 bp):
GGATATTATATGATATTATCTCTTAGCAATTTGATTCCTAAT
Found at i:39522733 original size:31 final size:32
Alignment explanation
Indices: 39522698--39522764 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 32
39522688 AACTCCCAAA
* *
39522698 CCTCTTTAC-TTTCCATTCAAAACTTTTACTC-
1 CCTCTTCACTTTTCC-TCCAAAACTTTTACTCT
*
39522729 CCTC-TCACTTTTCCTCCAAACCTTTTACTCT
1 CCTCTTCACTTTTCCTCCAAAACTTTTACTCT
39522760 CCTCT
1 CCTCT
39522765 CATCCCCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.18, C:0.39, G:0.00, T:0.43
Consensus pattern (32 bp):
CCTCTTCACTTTTCCTCCAAAACTTTTACTCT
Found at i:39523617 original size:13 final size:13
Alignment explanation
Indices: 39523599--39523627 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39523589 ACTTGATTAT
39523599 TAATGTAATAATA
1 TAATGTAATAATA
39523612 TAATGTAATAATA
1 TAATGTAATAATA
39523625 TAA
1 TAA
39523628 GAAAAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
TAATGTAATAATA
Found at i:39528102 original size:31 final size:31
Alignment explanation
Indices: 39528061--39528144 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
39528051 TTTTAATGAG
*
39528061 GAGTGGCTAAAACAAGAAATTTAAC-AAATA
1 GAGTGACTAAAACAAGAAATTTAACTAAATA
* * *
39528091 GAAGTGACTAAAACATGAAATTCAACTAACTA
1 G-AGTGACTAAAACAAGAAATTTAACTAAATA
* *
39528123 GAGTGACTAAAATAATAAATTT
1 GAGTGACTAAAACAAGAAATTT
39528145 TTAAAATGGG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 1 0.02
31 38 0.86
32 5 0.11
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (31 bp):
GAGTGACTAAAACAAGAAATTTAACTAAATA
Found at i:39528554 original size:20 final size:19
Alignment explanation
Indices: 39528503--39528559 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
39528493 TTGAATTTTA
*
39528503 TTAA-ATATTTTTATAAATT
1 TTAATATATTTTTA-AAACT
39528522 TTAATA-ATGTTTTAAAACT
1 TTAATATAT-TTTTAAAACT
39528541 TTATATATATTTTTTAAAA
1 TTA-ATATA-TTTTTAAAA
39528560 TAAATCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 13 0.41
20 9 0.28
21 9 0.28
22 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAATATATTTTTAAAACT
Found at i:39528557 original size:21 final size:19
Alignment explanation
Indices: 39528510--39528559 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
39528500 TTATTAAATA
*
39528510 TTTTTATAAATTTTAATAAT
1 TTTTTA-AAACTTTAATAAT
*
39528530 GTTTTAAAACTTTATATATAT
1 TTTTTAAAACTTTA-ATA-AT
39528551 TTTTTAAAA
1 TTTTTAAAA
39528560 TAAATCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 7 0.28
20 8 0.32
21 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTTAAAACTTTAATAAT
Found at i:39533663 original size:971 final size:971
Alignment explanation
Indices: 39532118--39534060 Score: 3886
Period size: 971 Copynumber: 2.0 Consensus size: 971
39532108 TTTTGTTGCA
39532118 TCCAGTGTTTGATTAAGTTAAAAGTAATTTTTTTTTGTTACATTGGAAATAAATCCTAAAATTTA
1 TCCAGTGTTTGATTAAGTTAAAAGTAATTTTTTTTTGTTACATTGGAAATAAATCCTAAAATTTA
39532183 TGGTTTAGAATTACTTTATTTGTTTGTTTGTATATCAATTAGAGATAAAACGAGGTAAATTTAGC
66 TGGTTTAGAATTACTTTATTTGTTTGTTTGTATATCAATTAGAGATAAAACGAGGTAAATTTAGC
39532248 TGAAGATAGTAAAATTTTCTTTGGGATACTATGGTTACTTGTAATGCATATGCTTGCATTCTTTT
131 TGAAGATAGTAAAATTTTCTTTGGGATACTATGGTTACTTGTAATGCATATGCTTGCATTCTTTT
39532313 CATACAGATTTTCAAAGAAGCCAAGGGTGGATGAGAGTGAGAACCTTACTCTCAACAGTATAAGA
196 CATACAGATTTTCAAAGAAGCCAAGGGTGGATGAGAGTGAGAACCTTACTCTCAACAGTATAAGA
39532378 CAGTCCTTAATTCGACAAGAAGATAGCATAATATTTAGCCTTTTGGAGAGAGCTCAGTACTGTTA
261 CAGTCCTTAATTCGACAAGAAGATAGCATAATATTTAGCCTTTTGGAGAGAGCTCAGTACTGTTA
39532443 TAACCCAGACACATATAAGCAAGATTCATTCTCCATGGATGGATTTCATGGGTCTTTGTCTTTGG
326 TAACCCAGACACATATAAGCAAGATTCATTCTCCATGGATGGATTTCATGGGTCTTTGTCTTTGG
39532508 TTGAGTTCATGGTTCGGGAAACCGAAAGGCTCCATGCTCAGGTAGTGTTCTCTATGTGGAGAAGA
391 TTGAGTTCATGGTTCGGGAAACCGAAAGGCTCCATGCTCAGGTAGTGTTCTCTATGTGGAGAAGA
39532573 TGTTAGGTAAACAGATTAAATCATGTATACAACATTCTGATGATTTTTCTATGTGAATAGGTTGG
456 TGTTAGGTAAACAGATTAAATCATGTATACAACATTCTGATGATTTTTCTATGTGAATAGGTTGG
39532638 CAGATATAAAAGTCCTGATGAACACCCTTTCTTCCCATCATATCTACCCGAGCCAATGCTTCCAC
521 CAGATATAAAAGTCCTGATGAACACCCTTTCTTCCCATCATATCTACCCGAGCCAATGCTTCCAC
39532703 CTTTGCAATATCCAAAGGTCAGACTTTTAGATGTTAACATATGAATAATTGGAAGTGACTCACGA
586 CTTTGCAATATCCAAAGGTCAGACTTTTAGATGTTAACATATGAATAATTGGAAGTGACTCACGA
39532768 TTTCTTAATCAGTAATGATCCTACTTTATAATACTTCCTACTTTTAAGGTGTGGGCATGCTTAAA
651 TTTCTTAATCAGTAATGATCCTACTTTATAATACTTCCTACTTTTAAGGTGTGGGCATGCTTAAA
39532833 GTATGTAAAACAACAAAAGAAAAAAAGCCAAAGTTTGATATTCCATGTTAGCCAACCATATGACT
716 GTATGTAAAACAACAAAAGAAAAAAAGCCAAAGTTTGATATTCCATGTTAGCCAACCATATGACT
39532898 TGAAGCTTTAGTTTGATAGGTTCATGTTAACACTAATATTTAACATATAATTAATTGGAAGCGAC
781 TGAAGCTTTAGTTTGATAGGTTCATGTTAACACTAATATTTAACATATAATTAATTGGAAGCGAC
39532963 TCTTGTTTCTTTTTCATCAATGATCTACTCTTAAGCTGTGGGTATGCTTAAAGTTATGTAAAACA
846 TCTTGTTTCTTTTTCATCAATGATCTACTCTTAAGCTGTGGGTATGCTTAAAGTTATGTAAAACA
39533028 ATAAACAAATGCCAAAGTTTGATATTCCATGATAGTCAACCATATGACCTAAAACTTTAGT
911 ATAAACAAATGCCAAAGTTTGATATTCCATGATAGTCAACCATATGACCTAAAACTTTAGT
39533089 TCCAGTGTTTGATTAAGTTAAAAGTAATTTTTTTTTGTTACATTGGAAATAAATCCTAAAATTTA
1 TCCAGTGTTTGATTAAGTTAAAAGTAATTTTTTTTTGTTACATTGGAAATAAATCCTAAAATTTA
39533154 TGGTTTAGAATTACTTTATTTGTTTGTTTGTATATCAATTAGAGATAAAACGAGGTAAATTTAGC
66 TGGTTTAGAATTACTTTATTTGTTTGTTTGTATATCAATTAGAGATAAAACGAGGTAAATTTAGC
39533219 TGAAGATAGTAAAATTTTCTTTGGGATACTATGGTTACTTGTAATGCATATGCTTGCATTCTTTT
131 TGAAGATAGTAAAATTTTCTTTGGGATACTATGGTTACTTGTAATGCATATGCTTGCATTCTTTT
39533284 CATACAGATTTTCAAAGAAGCCAAGGGTGGATGAGAGTGAGAACCTTACTCTCAACAGTATAAGA
196 CATACAGATTTTCAAAGAAGCCAAGGGTGGATGAGAGTGAGAACCTTACTCTCAACAGTATAAGA
39533349 CAGTCCTTAATTCGACAAGAAGATAGCATAATATTTAGCCTTTTGGAGAGAGCTCAGTACTGTTA
261 CAGTCCTTAATTCGACAAGAAGATAGCATAATATTTAGCCTTTTGGAGAGAGCTCAGTACTGTTA
39533414 TAACCCAGACACATATAAGCAAGATTCATTCTCCATGGATGGATTTCATGGGTCTTTGTCTTTGG
326 TAACCCAGACACATATAAGCAAGATTCATTCTCCATGGATGGATTTCATGGGTCTTTGTCTTTGG
39533479 TTGAGTTCATGGTTCGGGAAACCGAAAGGCTCCATGCTCAGGTAGTGTTCTCTATGTGGAGAAGA
391 TTGAGTTCATGGTTCGGGAAACCGAAAGGCTCCATGCTCAGGTAGTGTTCTCTATGTGGAGAAGA
39533544 TGTTAGGTAAACAGATTAAATCATGTATACAACATTCTGATGATTTTTCTATGTGAATAGGTTGG
456 TGTTAGGTAAACAGATTAAATCATGTATACAACATTCTGATGATTTTTCTATGTGAATAGGTTGG
39533609 CAGATATAAAAGTCCTGATGAACACCCTTTCTTCCCATCATATCTACCCGAGCCAATGCTTCCAC
521 CAGATATAAAAGTCCTGATGAACACCCTTTCTTCCCATCATATCTACCCGAGCCAATGCTTCCAC
39533674 CTTTGCAATATCCAAAGGTCAGACTTTTAGATGTTAACATATGAATAATTGGAAGTGACTCACGA
586 CTTTGCAATATCCAAAGGTCAGACTTTTAGATGTTAACATATGAATAATTGGAAGTGACTCACGA
39533739 TTTCTTAATCAGTAATGATCCTACTTTATAATACTTCCTACTTTTAAGGTGTGGGCATGCTTAAA
651 TTTCTTAATCAGTAATGATCCTACTTTATAATACTTCCTACTTTTAAGGTGTGGGCATGCTTAAA
39533804 GTATGTAAAACAACAAAAGAAAAAAAGCCAAAGTTTGATATTCCATGTTAGCCAACCATATGACT
716 GTATGTAAAACAACAAAAGAAAAAAAGCCAAAGTTTGATATTCCATGTTAGCCAACCATATGACT
39533869 TGAAGCTTTAGTTTGATAGGTTCATGTTAACACTAATATTTAACATATAATTAATTGGAAGCGAC
781 TGAAGCTTTAGTTTGATAGGTTCATGTTAACACTAATATTTAACATATAATTAATTGGAAGCGAC
39533934 TCTTGTTTCTTTTTCATCAATGATCTACTCTTAAGCTGTGGGTATGCTTAAAGTTATGTAAAACA
846 TCTTGTTTCTTTTTCATCAATGATCTACTCTTAAGCTGTGGGTATGCTTAAAGTTATGTAAAACA
39533999 ATAAACAAATGCCAAAGTTTGATATTCCATGATAGTCAACCATATGACCTAAAACTTTAGT
911 ATAAACAAATGCCAAAGTTTGATATTCCATGATAGTCAACCATATGACCTAAAACTTTAGT
39534060 T
1 T
39534061 TGATAGGTTC
Statistics
Matches: 972, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
971 972 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (971 bp):
TCCAGTGTTTGATTAAGTTAAAAGTAATTTTTTTTTGTTACATTGGAAATAAATCCTAAAATTTA
TGGTTTAGAATTACTTTATTTGTTTGTTTGTATATCAATTAGAGATAAAACGAGGTAAATTTAGC
TGAAGATAGTAAAATTTTCTTTGGGATACTATGGTTACTTGTAATGCATATGCTTGCATTCTTTT
CATACAGATTTTCAAAGAAGCCAAGGGTGGATGAGAGTGAGAACCTTACTCTCAACAGTATAAGA
CAGTCCTTAATTCGACAAGAAGATAGCATAATATTTAGCCTTTTGGAGAGAGCTCAGTACTGTTA
TAACCCAGACACATATAAGCAAGATTCATTCTCCATGGATGGATTTCATGGGTCTTTGTCTTTGG
TTGAGTTCATGGTTCGGGAAACCGAAAGGCTCCATGCTCAGGTAGTGTTCTCTATGTGGAGAAGA
TGTTAGGTAAACAGATTAAATCATGTATACAACATTCTGATGATTTTTCTATGTGAATAGGTTGG
CAGATATAAAAGTCCTGATGAACACCCTTTCTTCCCATCATATCTACCCGAGCCAATGCTTCCAC
CTTTGCAATATCCAAAGGTCAGACTTTTAGATGTTAACATATGAATAATTGGAAGTGACTCACGA
TTTCTTAATCAGTAATGATCCTACTTTATAATACTTCCTACTTTTAAGGTGTGGGCATGCTTAAA
GTATGTAAAACAACAAAAGAAAAAAAGCCAAAGTTTGATATTCCATGTTAGCCAACCATATGACT
TGAAGCTTTAGTTTGATAGGTTCATGTTAACACTAATATTTAACATATAATTAATTGGAAGCGAC
TCTTGTTTCTTTTTCATCAATGATCTACTCTTAAGCTGTGGGTATGCTTAAAGTTATGTAAAACA
ATAAACAAATGCCAAAGTTTGATATTCCATGATAGTCAACCATATGACCTAAAACTTTAGT
Found at i:39545584 original size:42 final size:42
Alignment explanation
Indices: 39545532--39545615 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
39545522 GTAGGAAAGT
* *
39545532 CACGATCGTGTGACTAAGCCACACACCCTTGTGGTTGAGAAA
1 CACGACCGTGTGACTAAGCCACACACCCGTGTGGTTGAGAAA
* ** *
39545574 CACGACCGTGTGACTGAGGTACACGCCCGTGTGGTTGAGAAA
1 CACGACCGTGTGACTAAGCCACACACCCGTGTGGTTGAGAAA
39545616 TACAGCCGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20
Consensus pattern (42 bp):
CACGACCGTGTGACTAAGCCACACACCCGTGTGGTTGAGAAA
Found at i:39545585 original size:21 final size:21
Alignment explanation
Indices: 39545561--39545615 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
39545551 CACACACCCT
39545561 TGTGGTTGAGAAACACGACCG
1 TGTGGTTGAGAAACACGACCG
** ** *
39545582 TGTGACTGAGGTACACGCCCG
1 TGTGGTTGAGAAACACGACCG
39545603 TGTGGTTGAGAAA
1 TGTGGTTGAGAAA
39545616 TACAGCCGTA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (21 bp):
TGTGGTTGAGAAACACGACCG
Found at i:39545636 original size:42 final size:42
Alignment explanation
Indices: 39545543--39545648 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
39545533 ACGATCGTGT
** * * **
39545543 GACTAAGCCACACACCCTTGTGGTTGAGAAACACGACCGTGT
1 GACTAAGGTACACGCCCGTGTGGTTGAGAAACACGACCGTAC
* *
39545585 GACTGAGGTACACGCCCGTGTGGTTGAGAAATAC-AGCCGTAC
1 GACTAAGGTACACGCCCGTGTGGTTGAGAAACACGA-CCGTAC
*
39545627 GACTAAGGTACACGCTCGTGTG
1 GACTAAGGTACACGCCCGTGTG
39545649 AAAAATGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.20
Consensus pattern (42 bp):
GACTAAGGTACACGCCCGTGTGGTTGAGAAACACGACCGTAC
Found at i:39547920 original size:9 final size:9
Alignment explanation
Indices: 39547908--39547958 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
39547898 GTTAGTTAAT
39547908 CGAATTACC
1 CGAATTACC
*
39547917 CGAATCACC
1 CGAATTACC
* *
39547926 TGAATTAAC
1 CGAATTACC
39547935 CGAATTACC
1 CGAATTACC
*
39547944 CGAATTAAC
1 CGAATTACC
39547953 CGAATT
1 CGAATT
39547959 GAATCACTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (9 bp):
CGAATTACC
Found at i:39547957 original size:27 final size:27
Alignment explanation
Indices: 39547903--39547958 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
39547893 ATTCGGTTAG
* *
39547903 TTAATCGAATTACCCGAATCACCTGAA
1 TTAACCGAATTACCCGAATAACCTGAA
39547930 TTAACCGAATTACCCGAATTAACC-GAA
1 TTAACCGAATTACCCGAA-TAACCTGAA
39547957 TT
1 TT
39547959 GAATCACTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.27
Consensus pattern (27 bp):
TTAACCGAATTACCCGAATAACCTGAA
Found at i:39547958 original size:18 final size:18
Alignment explanation
Indices: 39547908--39547958 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
39547898 GTTAGTTAAT
* *
39547908 CGAATTACCCGAATCACC
1 CGAATTAACCGAATTACC
*
39547926 TGAATTAACCGAATTACC
1 CGAATTAACCGAATTACC
39547944 CGAATTAACCGAATT
1 CGAATTAACCGAATT
39547959 GAATCACTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (18 bp):
CGAATTAACCGAATTACC
Found at i:39548033 original size:25 final size:25
Alignment explanation
Indices: 39547971--39548033 Score: 58
Period size: 26 Copynumber: 2.4 Consensus size: 25
39547961 ATCACTACAT
*
39547971 AATTAAAAGCATTACATAAGTCTTTG
1 AATTAACA-CATTACATAAGTCTTTG
*
39547997 AA-TCACTAACATTACATAAGTC-TTG
1 AATTAAC--ACATTACATAAGTCTTTG
39548022 AAATTAACACAT
1 -AATTAACACAT
39548034 AATTGAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
25 9 0.30
26 17 0.57
27 4 0.13
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (25 bp):
AATTAACACATTACATAAGTCTTTG
Found at i:39560556 original size:23 final size:23
Alignment explanation
Indices: 39560530--39560579 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
39560520 TGTAAACCTT
*
39560530 TCATTAA-AAACTAAAATATAAAA
1 TCATTAATAAAATAAAATA-AAAA
39560553 TCA-TAATAAAATAAAATAAAAA
1 TCATTAATAAAATAAAATAAAAA
39560575 T-ATTA
1 TCATTA
39560580 TGAATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 10 0.42
23 13 0.54
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (23 bp):
TCATTAATAAAATAAAATAAAAA
Found at i:39563428 original size:31 final size:30
Alignment explanation
Indices: 39563393--39563452 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
39563383 GGAGGTGGGA
*
39563393 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
39563424 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
39563453 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:39563680 original size:9 final size:9
Alignment explanation
Indices: 39563666--39563702 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
39563656 TATAGTTTGA
39563666 TATTCGAAT
1 TATTCGAAT
39563675 TATTCGAAT
1 TATTCGAAT
*
39563684 TATTCGAGT
1 TATTCGAAT
39563693 TATTCGAAT
1 TATTCGAAT
39563702 T
1 T
39563703 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:39564226 original size:27 final size:27
Alignment explanation
Indices: 39564196--39564290 Score: 138
Period size: 27 Copynumber: 3.6 Consensus size: 27
39564186 AACTGATATG
* *
39564196 AAATGACTGTTATGCCCCTACGTGGTA
1 AAATGACTGTTATGCCCCTATGTTGTA
39564223 AAATGACTGTTATGCCCCTATGTTGTA
1 AAATGACTGTTATGCCCCTATGTTGTA
* * *
39564250 AAATGATTGTTATGCCGCTATGTTATA
1 AAATGACTGTTATGCCCCTATGTTGTA
39564277 AAATGACTG-TATGC
1 AAATGACTGTTATGC
39564291 TTTATGTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
26 5 0.08
27 57 0.92
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (27 bp):
AAATGACTGTTATGCCCCTATGTTGTA
Found at i:39567220 original size:20 final size:20
Alignment explanation
Indices: 39567191--39567241 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
39567181 AAATCTCCAA
*
39567191 GTATCGATACTTGAATTATG
1 GTATCAATACTTGAATTATG
39567211 GTATCAATACTTGAATTATG
1 GTATCAATACTTGAATTATG
39567231 GTATCAATACT
1 GTATCAATACT
39567242 CCTTTACAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (20 bp):
GTATCAATACTTGAATTATG
Found at i:39568225 original size:22 final size:21
Alignment explanation
Indices: 39568197--39568248 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
39568187 ACACCACACT
*
39568197 AGAGAGCACCGTAGTGCTAAAC
1 AGAGAGCACCGAAG-GCTAAAC
** *
39568219 AGAGAGCATTGAAGGTTAAAC
1 AGAGAGCACCGAAGGCTAAAC
39568240 AGAGAGCAC
1 AGAGAGCAC
39568249 AAAAGTGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.13
Consensus pattern (21 bp):
AGAGAGCACCGAAGGCTAAAC
Found at i:39568240 original size:21 final size:22
Alignment explanation
Indices: 39568209--39568283 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
39568199 AGAGCACCGT
* **
39568209 AGTGCTAAACAGAGAGCATTGA
1 AGTGTTAAACAGAGAGCATAAA
*
39568231 AG-GTTAAACAGAGAGCACAAA
1 AGTGTTAAACAGAGAGCATAAA
*
39568252 AGTGTTGAACAGAGAGCATAAA
1 AGTGTTAAACAGAGAGCATAAA
*
39568274 AGTGCTAAAC
1 AGTGTTAAAC
39568284 CCGTACAAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 17 0.39
22 27 0.61
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.16
Consensus pattern (22 bp):
AGTGTTAAACAGAGAGCATAAA
Found at i:39576714 original size:71 final size:71
Alignment explanation
Indices: 39576598--39576776 Score: 358
Period size: 71 Copynumber: 2.5 Consensus size: 71
39576588 GTTTGCTTCC
39576598 ATTGAATTTCTATGATGTTGCAGCAAATATAGTTATAGAGTTTAAATAGGAAAATTGGAGTGATT
1 ATTGAATTTCTATGATGTTGCAGCAAATATAGTTATAGAGTTTAAATAGGAAAATTGGAGTGATT
39576663 TACGGT
66 TACGGT
39576669 ATTGAATTTCTATGATGTTGCAGCAAATATAGTTATAGAGTTTAAATAGGAAAATTGGAGTGATT
1 ATTGAATTTCTATGATGTTGCAGCAAATATAGTTATAGAGTTTAAATAGGAAAATTGGAGTGATT
39576734 TACGGT
66 TACGGT
39576740 ATTGAATTTCTATGATGTTGCAGCAAATATAGTTATA
1 ATTGAATTTCTATGATGTTGCAGCAAATATAGTTATA
39576777 ATATATTTAA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 108 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (71 bp):
ATTGAATTTCTATGATGTTGCAGCAAATATAGTTATAGAGTTTAAATAGGAAAATTGGAGTGATT
TACGGT
Found at i:39576883 original size:18 final size:17
Alignment explanation
Indices: 39576855--39576889 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39576845 ATTATTAAGA
*
39576855 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39576872 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39576890 TTATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39576889 original size:16 final size:17
Alignment explanation
Indices: 39576855--39576896 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
39576845 ATTATTAAGA
39576855 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
39576872 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAATATAT
39576888 ATTTATAAT
1 ATTT-TAAT
39576897 AATTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:39576955 original size:77 final size:77
Alignment explanation
Indices: 39576874--39577112 Score: 178
Period size: 77 Copynumber: 3.2 Consensus size: 77
39576864 AATTATATAT
*
39576874 TTTAATTAAAATATATTTATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTA
1 TTTAAATAAAATATATTTATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTA
39576939 ATCTTATTAAAA
66 ATCTTATTAAAA
* * ** * * * ** *
39576951 TTTAAATAAAATA-ATTTACCAA-AA-CA-AATT---TCTG-CT-AATTATTAAGAATT-TTATT
1 TTTAAATAAAATATATTTA-TAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATT
* * *
39577006 AA-ATTA-TATAT
65 AATCTTATTAAAA
* * *
39577017 TTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTATTTTTGATAAT
1 TTTAAATAAAATATATT-TATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGAT-AT
39577082 AAATAATCTTATTAAAA
64 ---TAATCTTATTAAAA
39577099 TTTAAATAACAATA
1 TTTAAATAA-AATA
39577113 ACAATAATCA
Statistics
Matches: 112, Mismatches: 31, Indels: 32
0.64 0.18 0.18
Matches are distributed among these distances:
66 15 0.13
67 8 0.07
68 9 0.08
69 12 0.11
70 3 0.03
71 3 0.03
73 3 0.03
74 3 0.03
75 11 0.10
76 8 0.07
77 16 0.14
80 3 0.03
81 3 0.03
82 11 0.10
83 4 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (77 bp):
TTTAAATAAAATATATTTATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTA
ATCTTATTAAAA
Found at i:39577002 original size:143 final size:147
Alignment explanation
Indices: 39576843--39577113 Score: 478
Period size: 143 Copynumber: 1.9 Consensus size: 147
39576833 ATAAGAATAT
*
39576843 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT-TATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
39576907 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
39576969 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
39576986 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
39577051 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
39577114 CAATAATCAT
Statistics
Matches: 120, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 48 0.40
144 42 0.35
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:39577026 original size:18 final size:17
Alignment explanation
Indices: 39576998--39577032 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39576988 ATTATTAAGA
*
39576998 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39577015 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39577033 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39577254 original size:44 final size:45
Alignment explanation
Indices: 39577191--39577288 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
39577181 CTATTACACC
* *
39577191 TCCATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTAT
** *
39577235 TCCATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTAT
1 TCCATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTAT
39577280 TCCATTACA
1 TCCATTACA
39577289 CCTCTAATCC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 21 0.44
45 27 0.56
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTAT
Found at i:39577288 original size:16 final size:16
Alignment explanation
Indices: 39577267--39577299 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39577257 TTGATTTGCT
*
39577267 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
39577283 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
39577299 A
1 A
39577300 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:39577309 original size:21 final size:21
Alignment explanation
Indices: 39577280--39577322 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
39577270 ACACCTCTAT
* *
39577280 TCCATTACACCTCTAATCCAA
1 TCCAATACACCGCTAATCCAA
39577301 TCCAATACACCGCTAATCCAA
1 TCCAATACACCGCTAATCCAA
39577322 T
1 T
39577323 ACAGCGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (21 bp):
TCCAATACACCGCTAATCCAA
Found at i:39577646 original size:61 final size:61
Alignment explanation
Indices: 39577527--39577643 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 61
39577517 TTATTAGCAT
* * * *
39577527 AATAAATTTAGTATTTAATATTTTACACATTCTGTCAATTTAGTCATAAATTTAAAATTTA
1 AATAAATTTAATATTCAATATTTTACAAATTCTATCAATTTAGTCATAAATTTAAAATTTA
* * * *
39577588 AATAAATTTAATCTTCAATA-TTTACAAATTCTATCAATTTGGTCTTAATTTTAAAA
1 AATAAATTTAATATTCAATATTTTACAAATTCTATCAATTTAGTCATAAATTTAAAA
39577644 ATTCAAAAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 31 0.65
61 17 0.35
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.45
Consensus pattern (61 bp):
AATAAATTTAATATTCAATATTTTACAAATTCTATCAATTTAGTCATAAATTTAAAATTTA
Found at i:39577699 original size:41 final size:41
Alignment explanation
Indices: 39577654--39577737 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 41
39577644 ATTCAAAAAC
39577654 ATAATTA-CAAAAATAAAAATTATTATAAAATAA-CTAAAATT
1 ATAATTATCAAAAATAAAAA-TA-TATAAAATAATCTAAAATT
* * *
39577695 ATAATTATTTAAAAATTAAAATATATAAAATAATTTAAAATT
1 ATAATTA-TCAAAAATAAAAATATATAAAATAATCTAAAATT
39577737 A
1 A
39577738 CCAAAATATC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 17 0.46
42 10 0.27
43 10 0.27
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (41 bp):
ATAATTATCAAAAATAAAAATATATAAAATAATCTAAAATT
Found at i:39577746 original size:26 final size:25
Alignment explanation
Indices: 39577656--39577751 Score: 81
Period size: 26 Copynumber: 3.7 Consensus size: 25
39577646 TCAAAAACAT
39577656 AATTACAAAA-ATAAAAATTATTATAA
1 AATTACAAAATAT-AAAATTATT-TAA
* *
39577682 AATAACTAAAAT-TATAATTATTTAAA
1 AATTAC-AAAATATAAAATTATTT-AA
*
39577708 AATTA-AAATATATAAAATAATTTAA
1 AATTACAAA-ATATAAAATTATTTAA
39577733 AATTACCAAAATATCAAAA
1 AATTA-CAAAATAT-AAAA
39577752 GAAATATTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
24 3 0.05
25 10 0.18
26 32 0.56
27 12 0.21
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AATTACAAAATATAAAATTATTTAA
Found at i:39579096 original size:24 final size:24
Alignment explanation
Indices: 39579069--39579133 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
39579059 TACTAGTACG
* * **
39579069 TTGTGGATAAACCATTGAAATGCA
1 TTGTGGATGAACCACTGAAAAACA
*
39579093 TTGTGGATGAACCACTGAAAAACG
1 TTGTGGATGAACCACTGAAAAACA
39579117 TTGTGGATGAACCACTG
1 TTGTGGATGAACCACTG
39579134 GTCATTGTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (24 bp):
TTGTGGATGAACCACTGAAAAACA
Found at i:39579277 original size:34 final size:34
Alignment explanation
Indices: 39579200--39579378 Score: 168
Period size: 34 Copynumber: 5.3 Consensus size: 34
39579190 ATGCAACATG
* * *
39579200 ACATACTTATAACAAATCAATACAGTAGTAA-TA
1 ACATGCTTATAACAAGTCAATACAGTAGCAATTA
* *
39579233 ACATGCTTATAACAAGTCAATACAATAACAATTA
1 ACATGCTTATAACAAGTCAATACAGTAGCAATTA
* * * *
39579267 TCATGCTTATAA-TAGATCATTACAGTAGCAATAA
1 ACATGCTTATAACAAG-TCAATACAGTAGCAATTA
* *
39579301 ACATGCTTATAACAA-ACTGATACAGTAGCAATTA
1 ACATGCTTATAACAAGTC-AATACAGTAGCAATTA
* * *
39579335 ACATGCTTATAAC-AGATCATTACGGTAGCAATAA
1 ACATGCTTATAACAAG-TCAATACAGTAGCAATTA
*
39579369 ACTTGCTTAT
1 ACATGCTTAT
39579379 CATACATTTG
Statistics
Matches: 117, Mismatches: 23, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
33 30 0.26
34 85 0.73
35 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (34 bp):
ACATGCTTATAACAAGTCAATACAGTAGCAATTA
Found at i:39579324 original size:68 final size:68
Alignment explanation
Indices: 39579200--39579378 Score: 227
Period size: 68 Copynumber: 2.6 Consensus size: 68
39579190 ATGCAACATG
* * * * *
39579200 ACATACTTATAACAAATCAATACAGTAGTAAT-AACATGCTTATAACAAGTCAATACAATAACAA
1 ACATGCTTATAACAGATCATTACAGTAGCAATAAACATGCTTATAACAACTCAATACAATAACAA
39579264 TTA
66 TTA
* * * * *
39579267 TCATGCTTATAATAGATCATTACAGTAGCAATAAACATGCTTATAACAAACT-GATACAGTAGCA
1 ACATGCTTATAACAGATCATTACAGTAGCAATAAACATGCTTATAAC-AACTCAATACAATAACA
39579331 ATTA
65 ATTA
* *
39579335 ACATGCTTATAACAGATCATTACGGTAGCAATAAACTTGCTTAT
1 ACATGCTTATAACAGATCATTACAGTAGCAATAAACATGCTTAT
39579379 CATACATTTG
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
67 26 0.27
68 67 0.70
69 3 0.03
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (68 bp):
ACATGCTTATAACAGATCATTACAGTAGCAATAAACATGCTTATAACAACTCAATACAATAACAA
TTA
Found at i:39595698 original size:374 final size:374
Alignment explanation
Indices: 39595009--39595756 Score: 1496
Period size: 374 Copynumber: 2.0 Consensus size: 374
39594999 AAATATTTAC
39595009 GAATATTTACGAGTGTCAATATGGTAGTGTTAAAGTTTCGTCAGAAAATTTTAACGTTTCGGCAG
1 GAATATTTACGAGTGTCAATATGGTAGTGTTAAAGTTTCGTCAGAAAATTTTAACGTTTCGGCAG
39595074 TCAATTAATTAAAAAGGACTAAATTGAAAAGATACAAAACTTGCTAAAGTGATTAAATAGCTTAA
66 TCAATTAATTAAAAAGGACTAAATTGAAAAGATACAAAACTTGCTAAAGTGATTAAATAGCTTAA
39595139 AAATTAAATAAGAAAGGACTAAAAGAGTAAATGGACCAACTTAAGTTGTAGAGACGGCATACCTT
131 AAATTAAATAAGAAAGGACTAAAAGAGTAAATGGACCAACTTAAGTTGTAGAGACGGCATACCTT
39595204 TAAAAAAAATCAAAGATTTTTTTATGTATTTAAGGACAAAATTGGAATTACAATAAAGTTTATGT
196 TAAAAAAAATCAAAGATTTTTTTATGTATTTAAGGACAAAATTGGAATTACAATAAAGTTTATGT
39595269 GGCCAAAATTTATTTTAAGGATTTCAAGACCATTTCTTCTTGAAATTTTTGTGGGAAATAGTCAT
261 GGCCAAAATTTATTTTAAGGATTTCAAGACCATTTCTTCTTGAAATTTTTGTGGGAAATAGTCAT
39595334 GGAAGAGGGTTTAGAGCTGGTCTTCCATATTTTAGCTTCAAGTAAGTGT
326 GGAAGAGGGTTTAGAGCTGGTCTTCCATATTTTAGCTTCAAGTAAGTGT
39595383 GAATATTTACGAGTGTCAATATGGTAGTGTTAAAGTTTCGTCAGAAAATTTTAACGTTTCGGCAG
1 GAATATTTACGAGTGTCAATATGGTAGTGTTAAAGTTTCGTCAGAAAATTTTAACGTTTCGGCAG
39595448 TCAATTAATTAAAAAGGACTAAATTGAAAAGATACAAAACTTGCTAAAGTGATTAAATAGCTTAA
66 TCAATTAATTAAAAAGGACTAAATTGAAAAGATACAAAACTTGCTAAAGTGATTAAATAGCTTAA
39595513 AAATTAAATAAGAAAGGACTAAAAGAGTAAATGGACCAACTTAAGTTGTAGAGACGGCATACCTT
131 AAATTAAATAAGAAAGGACTAAAAGAGTAAATGGACCAACTTAAGTTGTAGAGACGGCATACCTT
39595578 TAAAAAAAATCAAAGATTTTTTTATGTATTTAAGGACAAAATTGGAATTACAATAAAGTTTATGT
196 TAAAAAAAATCAAAGATTTTTTTATGTATTTAAGGACAAAATTGGAATTACAATAAAGTTTATGT
39595643 GGCCAAAATTTATTTTAAGGATTTCAAGACCATTTCTTCTTGAAATTTTTGTGGGAAATAGTCAT
261 GGCCAAAATTTATTTTAAGGATTTCAAGACCATTTCTTCTTGAAATTTTTGTGGGAAATAGTCAT
39595708 GGAAGAGGGTTTAGAGCTGGTCTTCCATATTTTAGCTTCAAGTAAGTGT
326 GGAAGAGGGTTTAGAGCTGGTCTTCCATATTTTAGCTTCAAGTAAGTGT
39595757 AATTCTTACT
Statistics
Matches: 374, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
374 374 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (374 bp):
GAATATTTACGAGTGTCAATATGGTAGTGTTAAAGTTTCGTCAGAAAATTTTAACGTTTCGGCAG
TCAATTAATTAAAAAGGACTAAATTGAAAAGATACAAAACTTGCTAAAGTGATTAAATAGCTTAA
AAATTAAATAAGAAAGGACTAAAAGAGTAAATGGACCAACTTAAGTTGTAGAGACGGCATACCTT
TAAAAAAAATCAAAGATTTTTTTATGTATTTAAGGACAAAATTGGAATTACAATAAAGTTTATGT
GGCCAAAATTTATTTTAAGGATTTCAAGACCATTTCTTCTTGAAATTTTTGTGGGAAATAGTCAT
GGAAGAGGGTTTAGAGCTGGTCTTCCATATTTTAGCTTCAAGTAAGTGT
Found at i:39601172 original size:5 final size:5
Alignment explanation
Indices: 39601162--39601199 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
39601152 TGCATTCTCT
39601162 TTTTC TTTTC -TTTC -TTTC TTTTC TTTTC -TTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
39601200 AGTTTGCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 12 0.39
5 19 0.61
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:39601177 original size:9 final size:9
Alignment explanation
Indices: 39601163--39601199 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
39601153 GCATTCTCTT
39601163 TTTCTTTTC
1 TTTCTTTTC
39601172 TTTC-TTTC
1 TTTCTTTTC
39601180 TTTTCTTTTC
1 -TTTCTTTTC
39601190 TTTCTTTTC
1 TTTCTTTTC
39601199 T
1 T
39601200 AGTTTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 4 0.15
9 18 0.69
10 4 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:39601185 original size:18 final size:18
Alignment explanation
Indices: 39601162--39601196 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39601152 TGCATTCTCT
39601162 TTTTCTTTTCTTTCTTTC
1 TTTTCTTTTCTTTCTTTC
39601180 TTTTCTTTTCTTTCTTT
1 TTTTCTTTTCTTTCTTT
39601197 TCTAGTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTCTTTCTTTC
Found at i:39601273 original size:26 final size:26
Alignment explanation
Indices: 39601223--39601275 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
39601213 TCCTCTTTCC
*
39601223 ATTTTCTTTATTATTTCTTTAATTAT
1 ATTTTCATTATTATTTCTTTAATTAT
*
39601249 ATTTTCATT-TTATTTCTTATTATTAT
1 ATTTTCATTATTATTTCTT-TAATTAT
39601275 A
1 A
39601276 ACATATATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.68
Consensus pattern (26 bp):
ATTTTCATTATTATTTCTTTAATTAT
Found at i:39613104 original size:23 final size:22
Alignment explanation
Indices: 39613057--39613105 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
39613047 TCAAATAATG
39613057 TAAATTTATAAATATTAAAAGT
1 TAAATTTATAAATATTAAAAGT
*
39613079 TAAATTTACTAAATTTTTAAAA-T
1 TAAATTTA-TAAA-TATTAAAAGT
39613102 TAAA
1 TAAA
39613106 ATCAAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
23 9 0.38
24 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATTTATAAATATTAAAAGT
Found at i:39614958 original size:21 final size:22
Alignment explanation
Indices: 39614923--39614967 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
39614913 TTCTAAAAAA
*
39614923 TTCAAACAAATATATAAATATT
1 TTCAAACAAAAATATAAATATT
39614945 TTCAAA-AAAAATATAAATATT
1 TTCAAACAAAAATATAAATATT
39614966 TT
1 TT
39614968 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
TTCAAACAAAAATATAAATATT
Found at i:39615001 original size:17 final size:18
Alignment explanation
Indices: 39614961--39615001 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
39614951 AAAAATATAA
*
39614961 ATATTTTAATATATTTTT
1 ATATTTTAATATATTATT
*
39614979 AAATTTT-ATATATTATT
1 ATATTTTAATATATTATT
39614996 ATATTT
1 ATATTT
39615002 GTCAACATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTTTAATATATTATT
Found at i:39621420 original size:171 final size:171
Alignment explanation
Indices: 39621131--39621461 Score: 518
Period size: 171 Copynumber: 1.9 Consensus size: 171
39621121 TGAAATCACC
* * **
39621131 CCAGGCCATATAACTTTCGAACAAGGGACACACGACCGTGTCCCAGCCTGTGTCGTCACTCGTGT
1 CCAGGCCATATAACTTTCAAACAAGGGACACACGACCGTGTCCCAGCCTATGTCCACACTCGTGT
* * * *
39621196 AACTTACTGAGTAGCCCCACACGCCCGTGTGCCGGGCCATATGCTAAGCTGTGTAACTCTCTGAC
66 AACTCACTGAGTAGCCCCACACCCCCGTATGCCAGGCCATATGCTAAGCTGTGTAACTCTCTGAC
*
39621261 TTGTATACTAAGAAACTCACAAATGACACATGGCTGTGTCG
131 TTGTACACTAAGAAACTCACAAATGACACATGGCTGTGTCG
* * * *
39621302 CCAGGCCGTGTAACTTTCAAACAAGGGACATACGACCGTGTCCCAGCTTATGTCCACACTCGTGT
1 CCAGGCCATATAACTTTCAAACAAGGGACACACGACCGTGTCCCAGCCTATGTCCACACTCGTGT
* * *
39621367 AACTCACTGAGTAGCCCTACACCCCCGTATGCCAGGCCATGTGCTAGGCTGTGTAACTCTCTGAC
66 AACTCACTGAGTAGCCCCACACCCCCGTATGCCAGGCCATATGCTAAGCTGTGTAACTCTCTGAC
39621432 TTGTACACTAAGAAACTCACAAATGACACA
131 TTGTACACTAAGAAACTCACAAATGACACA
39621462 CGACCATGTC
Statistics
Matches: 144, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
171 144 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (171 bp):
CCAGGCCATATAACTTTCAAACAAGGGACACACGACCGTGTCCCAGCCTATGTCCACACTCGTGT
AACTCACTGAGTAGCCCCACACCCCCGTATGCCAGGCCATATGCTAAGCTGTGTAACTCTCTGAC
TTGTACACTAAGAAACTCACAAATGACACATGGCTGTGTCG
Done.