Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008136.1 Hibiscus syriacus cultivar Beakdansim tig00110691_pilon, whole genome shotgun sequence
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: 1585607
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:124784 original size:6 final size:6
Alignment explanation
Indices: 124769--124800 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
124759 CAGGTTTGAA
124769 TTTGGG -TTGGG TTTGGG TTTGGG TTTGGG TTT
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTT
124801 AATTAGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (6 bp):
TTTGGG
Found at i:124876 original size:12 final size:12
Alignment explanation
Indices: 124769--124913 Score: 55
Period size: 12 Copynumber: 12.2 Consensus size: 12
124759 CAGGTTTGAA
*
124769 TTTGGG-TTGGG
1 TTTGGGTTTAGG
*
124780 TTTGGGTTTGGG
1 TTTGGGTTTAGG
*
124792 TTTGGGTTTA-A
1 TTTGGGTTTAGG
* * *
124803 TTAGGGGTTGGG
1 TTTGGGTTTAGG
* *
124815 TCTGAGTTTAGG
1 TTTGGGTTTAGG
* *
124827 TTTTAGGTTTAAG
1 -TTTGGGTTTAGG
* * *
124840 TTAGGGTTCAGC
1 TTTGGGTTTAGG
*
124852 TATGGG-TTAGG
1 TTTGGGTTTAGG
* *
124863 TTTAGGTTTGGG
1 TTTGGGTTTAGG
* * *
124875 TTTGAGTTCAAG
1 TTTGGGTTTAGG
**
124887 TTCAGG-TTAGG
1 TTTGGGTTTAGG
124898 TTTAGGGTTTAGG
1 TTT-GGGTTTAGG
124911 TTT
1 TTT
124914 AAGTTAGGGT
Statistics
Matches: 89, Mismatches: 39, Indels: 10
0.64 0.28 0.07
Matches are distributed among these distances:
11 25 0.28
12 48 0.54
13 16 0.18
ACGTcount: A:0.14, C:0.03, G:0.38, T:0.45
Consensus pattern (12 bp):
TTTGGGTTTAGG
Found at i:125644 original size:16 final size:15
Alignment explanation
Indices: 125604--125671 Score: 74
Period size: 15 Copynumber: 4.7 Consensus size: 15
125594 TAATTTTTTA
125604 AATTAACTATT-T-AT
1 AATTAA-TATTATAAT
125618 AATTAATATTATAAT
1 AATTAATATTATAAT
*
125633 AATT-ATA-TATTAT
1 AATTAATATTATAAT
125646 AATTAATATTA-ATAT
1 AATTAATATTATA-AT
125661 AATTAATATTA
1 AATTAATATTA
125672 ATATTAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
13 13 0.28
14 13 0.28
15 21 0.45
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTAATATTATAAT
Found at i:125650 original size:28 final size:28
Alignment explanation
Indices: 125604--125685 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 28
125594 TAATTTTTTA
125604 AATTAACTATTTATAATTAATATTATA-AT
1 AATTAA-TA-TTATAATTAATATTATATAT
125633 AATTATATATTATAATTAATATTA-ATAT
1 AATTA-ATATTATAATTAATATTATATAT
125661 AATTAATATTA-ATATTAA-ATTATAT
1 AATTAATATTATA-ATTAATATTATAT
125686 TAGTAAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
26 5 0.10
27 14 0.29
28 22 0.45
29 7 0.14
30 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
AATTAATATTATAATTAATATTATATAT
Found at i:125656 original size:6 final size:6
Alignment explanation
Indices: 125601--125756 Score: 58
Period size: 6 Copynumber: 25.2 Consensus size: 6
125591 ATATAATTTT
*
125601 TTAA-A TTAACTA TTTATAA TTAATA TTATAATAA TTATATA TT-ATAA
1 TTAATA TTAA-TA TTAAT-A TTAATA -T-TAAT-A TTA-ATA TTAAT-A
*
125648 TTAATA TTAATA -T-A-A TTAATA TTAATA TTAA-A TT-ATA TTAGTA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
** * * * * *
125691 AAATATA GTTTATAA TTTATAA TTAATA TTAATA -TAAAA TATAGTA TATAACA
1 TTA-ATA -TTAAT-A TTAAT-A TTAATA TTAATA TTAATA T-TAATA T-TAATA
125744 TTAATA TTAATA T
1 TTAATA TTAATA T
125757 AAACTATATG
Statistics
Matches: 116, Mismatches: 16, Indels: 37
0.69 0.09 0.22
Matches are distributed among these distances:
3 1 0.01
4 3 0.03
5 18 0.16
6 44 0.38
7 41 0.35
8 8 0.07
9 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (6 bp):
TTAATA
Found at i:125686 original size:31 final size:30
Alignment explanation
Indices: 125615--125896 Score: 132
Period size: 31 Copynumber: 8.9 Consensus size: 30
125605 ATTAACTATT
*
125615 TATAATTAATATT-ATA-ATAATTATA-TAT
1 TATAATTAATATTAATATA-AATTATATTAA
125643 TATAATTAATATTAATAT-AATTAATATTAA
1 TATAATTAATATTAATATAAATT-ATATTAA
* *
125673 TATTAAATT-ATATTAGTA-AAATATAGTTTATAA
1 TA-T-AATTAATATTAATATAAAT-TA-TAT-TAA
* *
125706 TTTATAATTAATATTAATATAAAATATAGT-A
1 --TATAATTAATATTAATATAAATTATATTAA
* *
125737 TATAACATTAATATTAATATAAACTATATGTTA
1 TAT-A-ATTAATATTAATATAAATTATAT-TAA
* *
125770 TA-AATTATATACTATAGTTTATAAACTATAGTTAA
1 TATAATTA-ATA-T-TA--ATATAAATTATA-TTAA
* *
125805 TATAATTAATATTAATATAATATAGTTTATAAA
1 TATAATTAATATTAATATAA-AT--TATATTAA
* *
125838 CTATATACT-ATATTAATATAAATTATAGTGAA
1 -TATA-ATTAATATTAATATAAATTATA-TTAA
* * * *
125870 GATAATTAACATAAATATAAACTATAT
1 TATAATTAATATTAATATAAATTATAT
125897 AGTACATTAA
Statistics
Matches: 199, Mismatches: 23, Indels: 62
0.70 0.08 0.22
Matches are distributed among these distances:
28 17 0.09
29 9 0.05
30 12 0.06
31 65 0.33
32 14 0.07
33 20 0.10
34 31 0.16
35 25 0.13
36 6 0.03
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (30 bp):
TATAATTAATATTAATATAAATTATATTAA
Found at i:125783 original size:21 final size:21
Alignment explanation
Indices: 125754--125960 Score: 63
Period size: 21 Copynumber: 9.6 Consensus size: 21
125744 TTAATATTAA
*
125754 TATAAACTATATGTTATAAAT
1 TATATACTATATGTTATAAAT
*
125775 TATATACTATA-GTTTATAAAC
1 TATATACTATATG-TTATAAAT
* * *
125796 TATAGTTAATATA-ATTA-ATAT
1 TATA--TACTATATGTTATAAAT
* *
125817 TAATATAATATA-GTTTATAAAC
1 T-ATATACTATATG-TTATAAAT
125839 TATATACTATAT-TAATATAAAT
1 TATATACTATATGT--TATAAAT
** *
125861 TATAGTGAAGATAAT-TAACATAAA-
1 TATA-T-ACTAT-ATGT--TATAAAT
* * *
125885 TATAAACTATATAGTACATTAA-
1 TATATACTATAT-GT-TATAAAT
*
125907 TATAAACTATA-GTTTATAAAT
1 TATATACTATATG-TTATAAAT
* *
125928 TATATACCATAGGTTATAAAT
1 TATATACTATATGTTATAAAT
*
125949 TATAAACTATAT
1 TATATACTATAT
125961 AGTACACTAA
Statistics
Matches: 144, Mismatches: 25, Indels: 34
0.71 0.12 0.17
Matches are distributed among these distances:
20 14 0.10
21 65 0.45
22 40 0.28
23 8 0.06
24 7 0.05
25 10 0.07
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (21 bp):
TATATACTATATGTTATAAAT
Found at i:125800 original size:14 final size:14
Alignment explanation
Indices: 125774--125842 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
125764 ATGTTATAAA
*
125774 TTATATACTATAGT
1 TTATAAACTATAGT
125788 TTATAAACTATAGT
1 TTATAAACTATAGT
* *
125802 TAATATAATTAATA-T
1 TTATA-AACT-ATAGT
*
125817 TAATATAA-TATAGT
1 TTATA-AACTATAGT
125831 TTATAAACTATA
1 TTATAAACTATA
125843 TACTATATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
13 5 0.11
14 27 0.57
15 12 0.26
16 3 0.06
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (14 bp):
TTATAAACTATAGT
Found at i:125827 original size:131 final size:133
Alignment explanation
Indices: 125669--125931 Score: 315
Period size: 131 Copynumber: 2.0 Consensus size: 133
125659 ATAATTAATA
* ** *
125669 TTAATATTAAATTATATTAGTAAAATATAGTTTATAATTTATA-ATTAATATTAATATAAAATAT
1 TTAATATTAAATTATATTAATAAAATATAGTTTATAAACTATATACT-ATATTAATATAAAATAT
* * * * *
125733 AGT--ATATAACATTAATATTAATATAAACTATAT-GT-TATAAATTATATACTATAGTTTATAA
65 AGTGAAGAT-A-ATTAACATAAATATAAACTATATAGTACATAAA-TATAAACTATAGTTTATAA
125794 ACTATAG
127 ACTATAG
* *
125801 TTAATA-T-AATTAATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAATTAT
1 TTAATATTAAATT-ATATTAATAAAATATAGTTTATAAACTATATACTATATTAATATAAAATAT
* *
125864 AGTGAAGATAATTAACATAAATATAAACTATATAGTACATTAATATAAACTATAGTTTATAAATT
65 AGTGAAGATAATTAACATAAATATAAACTATATAGTACATAAATATAAACTATAGTTTATAAACT
125929 ATA
130 ATA
125932 TACCATAGGT
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
130 4 0.04
131 67 0.60
132 34 0.30
133 7 0.06
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (133 bp):
TTAATATTAAATTATATTAATAAAATATAGTTTATAAACTATATACTATATTAATATAAAATATA
GTGAAGATAATTAACATAAATATAAACTATATAGTACATAAATATAAACTATAGTTTATAAACTA
TAG
Found at i:125919 original size:20 final size:21
Alignment explanation
Indices: 125878--125977 Score: 64
Period size: 22 Copynumber: 4.7 Consensus size: 21
125868 AAGATAATTA
125878 ACATAAATATAAACTATATAGT
1 ACATAAATATAAAC-ATATAGT
*
125900 ACATTAATATAAAC-TATAGT
1 ACATAAATATAAACATATAGT
** * *
125920 TTATAAATTATATACCATA-GGT
1 ACATAAA-TATA-AACATATAGT
*
125942 -TATAAATTATAAACTATATAGT
1 ACATAAA-TATAAAC-ATATAGT
125964 ACACT-AATATAAAC
1 ACA-TAAATATAAAC
125978 TATTGAATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
20 12 0.19
21 18 0.29
22 26 0.42
23 5 0.08
24 1 0.02
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
ACATAAATATAAACATATAGT
Found at i:126029 original size:20 final size:22
Alignment explanation
Indices: 125999--126090 Score: 77
Period size: 24 Copynumber: 4.2 Consensus size: 22
125989 AACTATAGGT
125999 TACATAT--ATAGTT-TATATA
1 TACATATAAATAGTTATATATA
*
126018 -ACATATAAATAGATTGTATATA
1 TACATATAAATAG-TTATATATA
*
126040 TACATATACTATAGGTTATATATA
1 TACATATA-AATA-GTTATATATA
* *
126064 TACACTATACATAGTT-TATACA
1 TACA-TATAAATAGTTATATATA
126086 TACAT
1 TACAT
126091 GATACATGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
18 6 0.10
20 4 0.07
21 3 0.05
22 15 0.25
23 10 0.16
24 18 0.30
25 5 0.08
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (22 bp):
TACATATAAATAGTTATATATA
Found at i:126059 original size:22 final size:23
Alignment explanation
Indices: 126012--126097 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 23
126002 ATATATAGTT
* * *
126012 TATATA-ACATATAAATAGATTG
1 TATATATACATATACATAGGTTA
126034 TATATATACATATACTATAGGTTA
1 TATATATACATATAC-ATAGGTTA
126058 TATATATACACTATACATA-GTT-
1 TATATATACA-TATACATAGGTTA
*
126080 TATACATACATGATACAT
1 TATATATACAT-ATACAT
126098 GTACTATAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.02
22 21 0.38
23 10 0.18
24 19 0.34
25 5 0.09
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (23 bp):
TATATATACATATACATAGGTTA
Found at i:126157 original size:21 final size:22
Alignment explanation
Indices: 126109--126161 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
126099 TACTATAAGT
*
126109 TATATA-TATAGTTTACATGTA
1 TATATATTATAGGTTACATGTA
126130 TACATATATTATAGGTTACAT-TA
1 T--ATATATTATAGGTTACATGTA
126153 TATATATTA
1 TATATATTA
126162 ACTATTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 9 0.32
23 8 0.29
24 11 0.39
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (22 bp):
TATATATTATAGGTTACATGTA
Found at i:126183 original size:7 final size:7
Alignment explanation
Indices: 126174--126260 Score: 95
Period size: 7 Copynumber: 12.6 Consensus size: 7
126164 TATTGTTTAT
*
126174 GTTTAGT
1 GTTTAGG
*
126181 GTTTAGT
1 GTTTAGG
*
126188 GTTTAGA
1 GTTTAGG
126195 GTTTAGG
1 GTTTAGG
126202 G-TTAGG
1 GTTTAGG
*
126208 TTTTAGG
1 GTTTAGG
126215 GTTTAGG
1 GTTTAGG
126222 GTTTAGG
1 GTTTAGG
* **
126229 ATTTAAA
1 GTTTAGG
*
126236 GTTTAGA
1 GTTTAGG
126243 GTTTAGG
1 GTTTAGG
126250 GTTTAGG
1 GTTTAGG
126257 GTTT
1 GTTT
126261 TTATAAACTA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
6 5 0.07
7 64 0.93
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:126339 original size:49 final size:48
Alignment explanation
Indices: 126257--126352 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 48
126247 AGGGTTTAGG
* ** * *
126257 GTTTTTATAAACTATATACTTTATTAATTTATAT-AGTTTATGTATATT
1 GTTTCTATAAACTATATAAGTAATTAATTTATATGA-TTTATATATATT
*
126305 GTTTCTATAAACTATATAAGTAATTTACTTTATATGATTTATATATAT
1 GTTTCTATAAACTATATAAGTAA-TTAATTTATATGATTTATATATAT
126353 ATATATACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 19 0.47
49 20 0.50
50 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.53
Consensus pattern (48 bp):
GTTTCTATAAACTATATAAGTAATTAATTTATATGATTTATATATATT
Found at i:126406 original size:35 final size:36
Alignment explanation
Indices: 126366--126439 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
126356 TATACTATAC
*
126366 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
126401 ATAGTTTACATGTATACATATACTATAAGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
126438 AT
1 AT
126440 TAACTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.21
37 27 0.79
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:126660 original size:2 final size:2
Alignment explanation
Indices: 126653--126797 Score: 56
Period size: 2 Copynumber: 74.0 Consensus size: 2
126643 TGTTTCTTTA
*
126653 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT -T ACT -T AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
126693 GT -T AT AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * *
126732 A- AC AT AT AA ACT AT AT AT -T TT AT AT AGT TT AT AC AT AT AT AGT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T
* * *
126775 TT TT AT AT AT AT AC AT ACT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT
126798 TAATATAAAT
Statistics
Matches: 108, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
1 9 0.08
2 91 0.84
3 8 0.07
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:126691 original size:9 final size:9
Alignment explanation
Indices: 126654--126683 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
126644 GTTTCTTTAA
126654 TATATATAT
1 TATATATAT
126663 ATATATATAT
1 -TATATATAT
126673 TATATATAT
1 TATATATAT
126682 TA
1 TA
126684 CTTATATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TATATATAT
Found at i:126835 original size:18 final size:18
Alignment explanation
Indices: 126812--126854 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
126802 ATAAATAATA
126812 TTTTATAAACTATATACT
1 TTTTATAAACTATATACT
***
126830 TTTTATAGTTTATATACT
1 TTTTATAAACTATATACT
126848 TTTTATA
1 TTTTATA
126855 GTTTATACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTATAAACTATATACT
Found at i:126855 original size:18 final size:18
Alignment explanation
Indices: 126822--126861 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
126812 TTTTATAAAC
126822 TATATACTTTTTATAGTT
1 TATATACTTTTTATAGTT
126840 TATATACTTTTTATAGTT
1 TATATACTTTTTATAGTT
126858 TATA
1 TATA
126862 CATATATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATACTTTTTATAGTT
Found at i:126974 original size:83 final size:83
Alignment explanation
Indices: 126882--127036 Score: 238
Period size: 83 Copynumber: 1.9 Consensus size: 83
126872 TTATATGTAT
* *
126882 AGTTCACATAAACATAATTTTTATATATAGCTTATAATAATTATATAGTTTGTAATATAAATATA
1 AGTTCACATAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTATAATATAAATATA
*
126947 TTTTATAATTTTATATAC
66 GTTTATAATTTTATATAC
* * * * *
126965 AGTTGACATAAATATAATTTATATATATAGTTTATACTAATTATATAGTTTATAATATAATTATA
1 AGTTCACATAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTATAATATAAATATA
127030 GTTTATA
66 GTTTATA
127037 TATAATTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 64 1.00
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.47
Consensus pattern (83 bp):
AGTTCACATAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTATAATATAAATATA
GTTTATAATTTTATATAC
Found at i:127011 original size:18 final size:17
Alignment explanation
Indices: 126988--127065 Score: 68
Period size: 18 Copynumber: 4.3 Consensus size: 17
126978 ATAATTTATA
*
126988 TATATAGTTTATACTAAT
1 TATATAGTTTATAAT-AT
127006 TATATAGTTTATAATAT
1 TATATAGTTTATAATAT
*
127023 AATTATAGTTTATATATAAT
1 TA-TATAGTTTATA-AT-AT
*
127043 TTTATA-TTATATATATAT
1 TATATAGTT-TATA-ATAT
127061 TATAT
1 TATAT
127066 TTTTTCAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.06
18 33 0.65
19 13 0.25
20 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TATATAGTTTATAATAT
Found at i:128097 original size:18 final size:18
Alignment explanation
Indices: 128065--128104 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
128055 TTATTAAGAA
*
128065 ATGTTTTTATTAAAATTT
1 ATGTTTTTATTAAAAGTT
128083 ATGTTTTT-TTAAAAAGTT
1 ATGTTTTTATT-AAAAGTT
128101 ATGT
1 ATGT
128105 ACTTTGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (18 bp):
ATGTTTTTATTAAAAGTT
Found at i:129438 original size:52 final size:52
Alignment explanation
Indices: 129376--129474 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 52
129366 TAATGAACAC
129376 TTAGATTTTTAGGGCTTTATTTGAAAAGCAGACAACACAATTAGGTTGTTTA
1 TTAGATTTTTAGGGCTTTATTTGAAAAGCAGACAACACAATTAGGTTGTTTA
* * * * *
129428 TTAGATTTTTAGGGTTTTATTTGGAAAGCATATAACACATTTAGGTT
1 TTAGATTTTTAGGGCTTTATTTGAAAAGCAGACAACACAATTAGGTT
129475 TAGATGGATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.41
Consensus pattern (52 bp):
TTAGATTTTTAGGGCTTTATTTGAAAAGCAGACAACACAATTAGGTTGTTTA
Found at i:131116 original size:21 final size:21
Alignment explanation
Indices: 131090--131132 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
131080 TCAATCCATC
**
131090 ACATGCATGAAATATGCAACT
1 ACATGCAACAAATATGCAACT
*
131111 ACATGCAACTAATATGCAACT
1 ACATGCAACAAATATGCAACT
131132 A
1 A
131133 AATGAGCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (21 bp):
ACATGCAACAAATATGCAACT
Found at i:131129 original size:11 final size:11
Alignment explanation
Indices: 131100--131133 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
131090 ACATGCATGA
131100 AATATGCAACT
1 AATATGCAACT
*
131111 -ACATGCAACT
1 AATATGCAACT
131121 AATATGCAACT
1 AATATGCAACT
131132 AA
1 AA
131134 ATGAGCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.24
Consensus pattern (11 bp):
AATATGCAACT
Found at i:147087 original size:7 final size:7
Alignment explanation
Indices: 147071--147102 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
147061 ATATAATATA
147071 TTTAAGAT
1 TTTAA-AT
147079 TTTAAAT
1 TTTAAAT
147086 TTTAAAT
1 TTTAAAT
147093 TTTAAAT
1 TTTAAAT
147100 TTT
1 TTT
147103 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (7 bp):
TTTAAAT
Found at i:147188 original size:23 final size:22
Alignment explanation
Indices: 147084--147232 Score: 89
Period size: 21 Copynumber: 6.9 Consensus size: 22
147074 AAGATTTTAA
* * *
147084 ATTTTAA-ATTTTAAATTTTTT
1 ATTTTAATATTTAAAATATATT
*
147105 ATTTTTATAATGTTAAAATATATT
1 ATTTTAAT-AT-TTAAAATATATT
* *
147129 A-TTTAATTATTAAAAATATAGT
1 ATTTTAA-TATTTAAAATATATT
** *
147151 AAATT-AT-TATAAAATATATT
1 ATTTTAATATTTAAAATATATT
147171 ATTTTAATACTTT-AAA-ATATT
1 ATTTTAATA-TTTAAAATATATT
* *
147192 A--TAAATAATTATAAATATATT
1 ATTTTAATATTTA-AAATATATT
147213 ATTTTAATTATTTAAAATAT
1 ATTTTAA-TATTTAAAATAT
147233 CGATATATTC
Statistics
Matches: 96, Mismatches: 18, Indels: 26
0.69 0.13 0.19
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 16 0.17
21 21 0.22
22 15 0.16
23 21 0.22
24 16 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (22 bp):
ATTTTAATATTTAAAATATATT
Found at i:147197 original size:43 final size:44
Alignment explanation
Indices: 147118--147232 Score: 168
Period size: 42 Copynumber: 2.7 Consensus size: 44
147108 TTTATAATGT
* *
147118 TAAAATATATTA-TTTAATTATTAAAAATA-TAGTAAATTATTA
1 TAAAATATATTATTTTAATTATTTAAAATATTAGTAAATAATTA
147160 TAAAATATATTATTTTAA-TACTTTAAAATATTA-TAAATAATTA
1 TAAAATATATTATTTTAATTA-TTTAAAATATTAGTAAATAATTA
147203 T-AAATATATTATTTTAATTATTTAAAATAT
1 TAAAATATATTATTTTAATTATTTAAAATAT
147233 CGATATATTC
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
42 40 0.60
43 25 0.37
44 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (44 bp):
TAAAATATATTATTTTAATTATTTAAAATATTAGTAAATAATTA
Found at i:148199 original size:23 final size:23
Alignment explanation
Indices: 148171--148234 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
148161 TAGTTGACCC
*
148171 TTGACTTTGACTATTGATCATCG
1 TTGACTTTAACTATTGATCATCG
148194 TTGACTTTAACTATTGATCATCG
1 TTGACTTTAACTATTGATCATCG
148217 TTGACTTTAACTATTGAT
1 TTGACTTTAACTATTGAT
148235 TGGACCATTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (23 bp):
TTGACTTTAACTATTGATCATCG
Found at i:153706 original size:21 final size:20
Alignment explanation
Indices: 153682--153738 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 20
153672 TGCAATCTTA
153682 TCTTCTTCTGTTAATTCT-G
1 TCTTCTTCTGTTAATTCTGG
153701 -CTTCTTCTGTTAATTCTGGG
1 TCTTCTTCTGTTAATTCT-GG
* *
153721 TTTTTTTCTGTTAATTCT
1 TCTTCTTCTGTTAATTCT
153739 TGATCTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 17 0.52
20 1 0.03
21 15 0.45
ACGTcount: A:0.11, C:0.18, G:0.12, T:0.60
Consensus pattern (20 bp):
TCTTCTTCTGTTAATTCTGG
Found at i:173891 original size:14 final size:14
Alignment explanation
Indices: 173872--173908 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
173862 TGTCTATTAT
173872 ACTTTTGGAGAATA
1 ACTTTTGGAGAATA
173886 ACTTTTGGAGAATA
1 ACTTTTGGAGAATA
173900 ACTTTTGGA
1 ACTTTTGGA
173909 AATTATTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (14 bp):
ACTTTTGGAGAATA
Found at i:183784 original size:16 final size:16
Alignment explanation
Indices: 183736--183784 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
183726 GTTTATGAGA
183736 GAATTAGAATATATGAAC
1 GAATTA-AA-ATATGAAC
* *
183754 GAATTAGAATATGAAG
1 GAATTAAAATATGAAC
*
183770 GAATTAAAATCTGAA
1 GAATTAAAATATGAA
183785 TCTGAAACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 20 0.74
17 1 0.04
18 6 0.22
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (16 bp):
GAATTAAAATATGAAC
Found at i:184441 original size:30 final size:31
Alignment explanation
Indices: 184384--184449 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
184374 AACCGAACCT
184384 GACCCGAACCCGAAATTATTTAAAAAAATCC
1 GACCCGAACCCGAAATTATTTAAAAAAATCC
* *
184415 GACCCGATCCC-AAATTTTTTTTAAAAAAATCC
1 GACCCGAACCCGAAA--TTATTTAAAAAAATCC
184447 GAC
1 GAC
184450 ATGAATACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 3 0.10
31 10 0.32
32 18 0.58
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (31 bp):
GACCCGAACCCGAAATTATTTAAAAAAATCC
Found at i:184441 original size:31 final size:32
Alignment explanation
Indices: 184384--184449 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
184374 AACCGAACCT
184384 GACCCGAACCCGAAATTATTT-AAAAAAATCC
1 GACCCGAACCCGAAATTATTTAAAAAAAATCC
* * *
184415 GACCCGATCCC-AAATTTTTTTTAAAAAAATCC
1 GACCCGAACCCGAAA-TTATTTAAAAAAAATCC
184447 GAC
1 GAC
184450 ATGAATACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 3 0.10
31 15 0.48
32 13 0.42
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (32 bp):
GACCCGAACCCGAAATTATTTAAAAAAAATCC
Found at i:185000 original size:23 final size:21
Alignment explanation
Indices: 184962--185004 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
184952 ATAATTATTT
184962 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
184983 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
185004 A
1 A
185005 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:186785 original size:37 final size:38
Alignment explanation
Indices: 186706--186792 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 38
186696 TTATCAAAAC
**
186706 ATATA-ATAGTTTTGAAAACACATTTTTAAAAATGTAT
1 ATATATATAGTTTTGAAAACACATTTTTAAAAATAAAT
*
186743 A-ATATATAGTTTTGAAAACACA-TTTTAAATATAAAT
1 ATATATATAGTTTTGAAAACACATTTTTAAAAATAAAT
*
186779 ATATATATACTTTT
1 ATATATATAGTTTT
186793 TTAAAATGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 15 0.34
37 29 0.66
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (38 bp):
ATATATATAGTTTTGAAAACACATTTTTAAAAATAAAT
Found at i:186923 original size:5 final size:5
Alignment explanation
Indices: 186891--186922 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
186881 GTTTTTATTA
*
186891 TATAT TATAT TATAT TATAT TATAT TAGAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TA
186923 GGTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:189059 original size:43 final size:43
Alignment explanation
Indices: 188998--189092 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
188988 CCTCCAACCG
*
188998 AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
*
189041 AACACACCATAATGTGTAGGTTCCCCAGAATCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
189084 AACACACCA
1 AACACACCA
189093 AGTAAGGCCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.37, C:0.36, G:0.11, T:0.17
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
Found at i:189238 original size:24 final size:24
Alignment explanation
Indices: 189211--189326 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
189201 CATAATTTAT
* *
189211 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
189235 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
189259 GTCAAGTATCAGATCATAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
189283 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
189307 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
189327 TCAAATCGAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:189342 original size:72 final size:72
Alignment explanation
Indices: 189209--189344 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
189199 AACATAATTT
* * * *
189209 ATGTCAAGTATCATATCAAAATCCAAGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGATC
1 ATGTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGATC
189274 ATAATCC
66 ATAATCC
* * *
189281 ATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATCGAA-AATCAGA
1 ATGTCAAG-TATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATC-AAGAATCAGA
189344 T
64 T
189345 AAAATATTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 2 0.04
72 51 0.93
73 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (72 bp):
ATGTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGATC
ATAATCC
Found at i:191902 original size:13 final size:13
Alignment explanation
Indices: 191881--191910 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
191871 CAACAATCAA
*
191881 CGGGTCAACGGGT
1 CGGGACAACGGGT
191894 CGGGACAACGGGT
1 CGGGACAACGGGT
191907 CGGG
1 CGGG
191911 TCGGGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.50, T:0.10
Consensus pattern (13 bp):
CGGGACAACGGGT
Found at i:194098 original size:43 final size:43
Alignment explanation
Indices: 194035--194129 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
194025 CCTCCAACCG
*
194035 AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
* *
194078 ATCACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACT
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
194121 AACACACCA
1 AACACACCA
194130 AGTAAGGCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.18
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
Found at i:194258 original size:24 final size:24
Alignment explanation
Indices: 194245--194363 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
194235 AAACATAATT
*
194245 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
194269 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* *
194293 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
194317 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
194341 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
194364 TCAAATCAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.02
24 82 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:194362 original size:72 final size:72
Alignment explanation
Indices: 194224--194381 Score: 201
Period size: 72 Copynumber: 2.2 Consensus size: 72
194214 AAACGGATAT
* * * * *
194224 ATCAAAAATCAAAACATAATTCATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAG
1 ATCAAAAATCAGATCAGAATCCATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAG
194289 AATCCAA
66 AATCCAA
* ** * *
194296 GTCAAGTATCAGATCAGAATCCATGTC-AGATATCATATCAGAATCCATGTCAAGTATCAGATCA
1 ATCAAAAATCAGATCAGAATCCATGTCAAG-TATCATATCAAAATCCAGGTCAAGTATCAGATCA
*
194360 GAATTCAA
65 GAATCCAA
194368 ATCAAAAATCAGAT
1 ATCAAAAATCAGAT
194382 AAAATATTCA
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
71 2 0.03
72 69 0.97
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (72 bp):
ATCAAAAATCAGATCAGAATCCATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAG
AATCCAA
Found at i:194372 original size:24 final size:24
Alignment explanation
Indices: 194248--194381 Score: 153
Period size: 24 Copynumber: 5.6 Consensus size: 24
194238 CATAATTCAT
* * *
194248 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
*
194272 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
194296 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
194320 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
*
194344 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCAA
* **
194368 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
194382 AAAATATTCA
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 2 0.02
24 93 0.96
25 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:196949 original size:13 final size:13
Alignment explanation
Indices: 196931--196960 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
196921 ACGGTTGACA
*
196931 GGTCAACGGGTCG
1 GGTCAACAGGTCG
196944 GGTCAACAGGTCG
1 GGTCAACAGGTCG
196957 GGTC
1 GGTC
196961 GGGTTAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:196960 original size:18 final size:18
Alignment explanation
Indices: 196937--196983 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
196927 GACAGGTCAA
196937 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
* *
196955 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACAGGT
*
196973 CGGATCGGGTC
1 CGGGTCGGGTC
196984 GGGTTATGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.21, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:200447 original size:21 final size:21
Alignment explanation
Indices: 200421--200465 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
200411 GATTTCTGGG
* *
200421 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
200442 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
200463 CAA
1 CAA
200466 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:201801 original size:30 final size:30
Alignment explanation
Indices: 201754--201996 Score: 434
Period size: 30 Copynumber: 8.1 Consensus size: 30
201744 CGGGACCTAG
201754 GGACAGTTTACCGAGGATCTTTATGACCTCT
1 GGACAG-TTACCGAGGATCTTTATGACCTCT
*
201785 GGACAGTTACCAAGGATCTTTATGACCTCT
1 GGACAGTTACCGAGGATCTTTATGACCTCT
201815 GGACAGTTACCGAGGATCTTTATGACCTCT
1 GGACAGTTACCGAGGATCTTTATGACCTCT
201845 GGACAGTTACCGAGGATCTTTATGACCTCT
1 GGACAGTTACCGAGGATCTTTATGACCTCT
201875 GGACAGTTACCGAGGATCTTTATGACCTCT
1 GGACAGTTACCGAGGATCTTTATGACCTCT
201905 GGACAGTTACCGAGGATCTTTATGACCTCT
1 GGACAGTTACCGAGGATCTTTATGACCTCT
201935 GGACAGTTACCGAGGATCTTTATGACCTCT
1 GGACAGTTACCGAGGATCTTTATGACCTCT
* * *
201965 GGATAGTTACCG-GGGTCTTTGTGACCTCT
1 GGACAGTTACCGAGGATCTTTATGACCTCT
201994 GGA
1 GGA
201997 TAGGTCCTTC
Statistics
Matches: 207, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
29 18 0.09
30 183 0.88
31 6 0.03
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (30 bp):
GGACAGTTACCGAGGATCTTTATGACCTCT
Found at i:204327 original size:21 final size:23
Alignment explanation
Indices: 204303--204362 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
204293 TATCTACTAC
204303 AAAAGCACAAGCTTCA-T-CTGT
1 AAAAGCACAAGCTTCATTGCTGT
*
204324 AAAAGCACAAACTTCATTGGCTGT
1 AAAAGCACAAGCTTCATT-GCTGT
*
204348 AAAAGAACAAGCTTC
1 AAAAGCACAAGCTTC
204363 TGTAACTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.45
22 1 0.03
24 17 0.52
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (23 bp):
AAAAGCACAAGCTTCATTGCTGT
Found at i:210367 original size:18 final size:18
Alignment explanation
Indices: 210340--210374 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
210330 ACTGTATATT
*
210340 TGTCCCGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
*
210358 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
210375 CCTTAAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:214658 original size:21 final size:21
Alignment explanation
Indices: 214633--214672 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
214623 TTCATGCACC
214633 ACTTATCTA-ATATCCTTTTAT
1 ACTTATCTATATA-CCTTTTAT
214654 ACTTATCTATATACCTTTT
1 ACTTATCTATATACCTTTT
214673 CCTTGAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.53
Consensus pattern (21 bp):
ACTTATCTATATACCTTTTAT
Found at i:215106 original size:21 final size:20
Alignment explanation
Indices: 215056--215113 Score: 75
Period size: 18 Copynumber: 3.0 Consensus size: 20
215046 GGGCACTGTA
215056 TATTTGTCCCGAAGGACCAC
1 TATTTGTCCCGAAGGACCAC
215076 TA--TGTCCCGAAGGACCAC
1 TATTTGTCCCGAAGGACCAC
* *
215094 TGATTTATCCCGAAAGACCA
1 T-ATTTGTCCCGAAGGACCA
215114 TTCCTTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (20 bp):
TATTTGTCCCGAAGGACCAC
Found at i:215936 original size:19 final size:19
Alignment explanation
Indices: 215908--215959 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
215898 CTTAAGGAGG
215908 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
* *
215927 TGCATTGATGCACTCTTTA
1 TGCATCGATGCACTCCTTA
*
215946 CGCATCGATGCACT
1 TGCATCGATGCACT
215960 AATTGCATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:219640 original size:21 final size:21
Alignment explanation
Indices: 219601--219640 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
219591 TTCATACACC
*
219601 ACTTATCTAATATCCTTTTAT
1 ACTTATCTAATATCATTTTAT
219622 ACTTATCT-ATATACATTTT
1 ACTTATCTAATAT-CATTTT
219641 CCTTGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (21 bp):
ACTTATCTAATATCATTTTAT
Found at i:224967 original size:18 final size:18
Alignment explanation
Indices: 224944--224978 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
224934 ACTGTATATT
224944 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
*
224962 TGTCCCTAAGGACCACT
1 TGTCCCAAAGGACCACT
224979 CCTTAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:228806 original size:16 final size:16
Alignment explanation
Indices: 228785--228818 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
228775 AGCTCTAATA
228785 CCATTAAATGTAACAC
1 CCATTAAATGTAACAC
228801 CCATTAAATGTAACAC
1 CCATTAAATGTAACAC
228817 CC
1 CC
228819 CAACCCGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (16 bp):
CCATTAAATGTAACAC
Found at i:231093 original size:37 final size:38
Alignment explanation
Indices: 230989--231126 Score: 147
Period size: 37 Copynumber: 3.6 Consensus size: 38
230979 ACATATATAA
**
230989 TTTTGAAAACATATA-ATATATAGTTTTTTTAAAAATTCAGT
1 TTTTGAAAACATATATATATATAG---TTTTAAAAACACA-T
* * * *
231030 TTTGGAAAACATATAT-GATATGGTTTTGAAAACACAT
1 TTTTGAAAACATATATATATATAGTTTTAAAAACACAT
* *
231067 TTTTGAAAGCGTATA-ATATATAGTTTTAAAAACACAT
1 TTTTGAAAACATATATATATATAGTTTTAAAAACACAT
231104 TTTTGAAAACATATATATATATA
1 TTTTGAAAACATATATATATATA
231127 TATATATATA
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
37 44 0.55
38 17 0.21
41 19 0.24
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (38 bp):
TTTTGAAAACATATATATATATAGTTTTAAAAACACAT
Found at i:231121 original size:2 final size:2
Alignment explanation
Indices: 231114--231140 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
231104 TTTTGAAAAC
231114 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
231141 GTTTTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:231210 original size:22 final size:22
Alignment explanation
Indices: 231176--231226 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
231166 CTTATGTAAT
* *
231176 ATATATAATTTTTTTAAAACATA
1 ATATAT-AGTTTTTGAAAACATA
* *
231199 TTATATAGTTTTTGAAAATATA
1 ATATATAGTTTTTGAAAACATA
231221 ATATAT
1 ATATAT
231227 GTTATATAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATATAGTTTTTGAAAACATA
Found at i:231219 original size:20 final size:21
Alignment explanation
Indices: 231186--231225 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
231176 ATATATAATT
*
231186 TTTTTAAAACATATTATATAG
1 TTTTTAAAACATATAATATAG
*
231207 TTTTTGAAA-ATATAATATA
1 TTTTTAAAACATATAATATA
231226 TGTTATATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTTTAAAACATATAATATAG
Found at i:231250 original size:5 final size:5
Alignment explanation
Indices: 231241--231280 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
231231 TATAGTTTTT
* * *
231241 ATTAT ATTAT ATTAA ATTAC ATTAC ATTAC ATTAC ATTAC
1 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC
231281 TTATTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (5 bp):
ATTAC
Found at i:232166 original size:21 final size:21
Alignment explanation
Indices: 232122--232166 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
232112 GATTTCTGGG
* * *
232122 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
232143 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
232164 CAA
1 CAA
232167 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:232239 original size:23 final size:22
Alignment explanation
Indices: 232191--232239 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
232181 ACAGAATGTC
232191 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* * *
232212 CAGGAGGGAACTGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
232235 AAGGA
1 AAGGA
232240 AAAATGTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:233338 original size:62 final size:62
Alignment explanation
Indices: 233218--233342 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
233208 AGGGTCGAGG
* * * *
233218 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
233280 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAA-CATATGGACT
233342 G
1 G
233343 GTCCTTCGAG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 57 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
Found at i:233342 original size:31 final size:31
Alignment explanation
Indices: 233218--233327 Score: 202
Period size: 31 Copynumber: 3.5 Consensus size: 31
233208 AGGGTCGAGG
233218 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
233249 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
233280 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
233311 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
233328 AGAATCTATG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:235912 original size:23 final size:23
Alignment explanation
Indices: 235886--235978 Score: 64
Period size: 23 Copynumber: 4.0 Consensus size: 23
235876 CACCGAATTG
*
235886 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATATCCCGAAGGA
* * * * *
235909 CCACATAGTATTGTCCTGAACGA
1 CCACATAGAAATATCCCGAAGGA
* *
235932 -CAGCGTA-AAATTATCCCGAATGA
1 CCA-CATAGAAA-TATCCCGAAGGA
* *
235955 CCACGTAGAATTATCCCGAAGGA
1 CCACATAGAAATATCCCGAAGGA
235978 C
1 C
235979 TGCGTAGAAC
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
22 3 0.06
23 47 0.87
24 4 0.07
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (23 bp):
CCACATAGAAATATCCCGAAGGA
Found at i:235984 original size:23 final size:23
Alignment explanation
Indices: 235899--235987 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 23
235889 CATAGAAATG
* * * *
235899 TCCCGAAGGACCACATAGTATTG
1 TCCCGAAGGACCGCGTAGAATTA
* * * *
235922 TCCTGAACGACAGCGTAAAATTA
1 TCCCGAAGGACCGCGTAGAATTA
* *
235945 TCCCGAATGACCACGTAGAATTA
1 TCCCGAAGGACCGCGTAGAATTA
*
235968 TCCCGAAGGACTGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
235988 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (23 bp):
TCCCGAAGGACCGCGTAGAATTA
Found at i:236083 original size:14 final size:15
Alignment explanation
Indices: 236064--236105 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
236054 TTTTAACAGT
*
236064 TCACATAACTTA-TA
1 TCACATAACTCATTA
*
236078 TCACATAGCTCATTA
1 TCACATAACTCATTA
*
236093 TCACATAGCTCAT
1 TCACATAACTCAT
236106 GTCACATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (15 bp):
TCACATAACTCATTA
Found at i:236096 original size:15 final size:15
Alignment explanation
Indices: 236076--236105 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
236066 ACATAACTTA
236076 TATCACATAGCTCAT
1 TATCACATAGCTCAT
236091 TATCACATAGCTCAT
1 TATCACATAGCTCAT
236106 GTCACATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
TATCACATAGCTCAT
Found at i:236112 original size:14 final size:14
Alignment explanation
Indices: 236064--236112 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
236054 TTTTAACAGT
* *
236064 TCACATAACTTATA
1 TCACATAGCTCATA
236078 TCACATAGCTCATTA
1 TCACATAGCTCA-TA
*
236093 TCACATAGCTCATG
1 TCACATAGCTCATA
236107 TCACAT
1 TCACAT
236113 TTTCTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.33
Consensus pattern (14 bp):
TCACATAGCTCATA
Found at i:239989 original size:41 final size:41
Alignment explanation
Indices: 239930--240007 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
239920 TGTGTATCGG
* * *
239930 TACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGA
1 TACACTAAAGAGTATATCGATACCCTCAAAACATCGAATGA
239971 TACACTAAAGAGTATATCGATACCCTCAAAACATCGA
1 TACACTAAAGAGTATATCGATACCCTCAAAACATCGA
240008 GTGCTATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (41 bp):
TACACTAAAGAGTATATCGATACCCTCAAAACATCGAATGA
Found at i:240796 original size:21 final size:21
Alignment explanation
Indices: 240770--240904 Score: 107
Period size: 21 Copynumber: 6.4 Consensus size: 21
240760 AGTCGAGGGT
240770 TTATGTGGTCATTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
* * *
240791 TTATGTGGTCCTTCGAGATAA
1 TTATGTGGTCATTCGGGACAA
*
240812 TTATGTGGTCCTTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
* *
240833 TT-TTTGGT-ATTTCAGGACAA
1 TTATGTGGTCA-TTCGGGACAA
*
240853 ATATGTGG-CATTTCGGTG-CAAA
1 TTATGTGGTCA-TTCGG-GAC-AA
* * *
240875 CCTATGTGGTCCTTTGGGACAA
1 -TTATGTGGTCATTCGGGACAA
240897 TTATGTGG
1 TTATGTGG
240905 CACTTCGATG
Statistics
Matches: 91, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
20 15 0.16
21 57 0.63
22 6 0.07
23 12 0.13
24 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:242574 original size:13 final size:13
Alignment explanation
Indices: 242556--242580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242546 TGATAGTTGA
242556 GGAAAAATAAGTC
1 GGAAAAATAAGTC
242569 GGAAAAATAAGT
1 GGAAAAATAAGT
242581 GCAGTGTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.24, T:0.16
Consensus pattern (13 bp):
GGAAAAATAAGTC
Found at i:244935 original size:4 final size:4
Alignment explanation
Indices: 244926--244950 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
244916 CTGGAAGCTC
244926 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
244951 CTTCTTGCCT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:245554 original size:55 final size:55
Alignment explanation
Indices: 245482--245628 Score: 204
Period size: 55 Copynumber: 2.7 Consensus size: 55
245472 TTTGTATGAG
* * *
245482 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTTAAAACATCGAATGCTCTT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATACTATT
* * * * *
245537 TTTGTATCGGTATACTGAAGAGTGTATCGATACTCTCAAAACATCGAGTACTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATACTATT
*
245592 TGTGTATCTGTACACTGAGGAGTGTATCGATATCCCT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATA-CCCT
245629 AAGTATGAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
55 75 0.96
56 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATACTATT
Found at i:246373 original size:21 final size:21
Alignment explanation
Indices: 246347--246435 Score: 99
Period size: 21 Copynumber: 4.1 Consensus size: 21
246337 GTCGATGGTC
246347 TATGTGGTCATTCGGGACAAT
1 TATGTGGTCATTCGGGACAAT
* *
246368 TATGTGGTCATTCGGAACAAA
1 TATGTGGTCATTCGGGACAAT
* *
246389 TATGTGG-CACTTCGGTACAAACC
1 TATGTGGTCA-TTCGGGAC-AA-T
*
246412 TATGTGGTCATTTGGGACAAT
1 TATGTGGTCATTCGGGACAAT
246433 TAT
1 TAT
246436 ATGGCACTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
20 2 0.04
21 36 0.63
22 4 0.07
23 13 0.23
24 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACAAT
Found at i:246423 original size:44 final size:44
Alignment explanation
Indices: 246368--246453 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
246358 TCGGGACAAT
*
246368 TATGTGGTCATTCGGAACAAATATGTGGCACTTCGGTACAAACC
1 TATGTGGTCATTCGGAACAAATATATGGCACTTCGGTACAAACC
* * * *
246412 TATGTGGTCATTTGGGACAATTATATGGCACTTCGGTGCAAA
1 TATGTGGTCATTCGGAACAAATATATGGCACTTCGGTACAAA
246454 TTACGAGCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (44 bp):
TATGTGGTCATTCGGAACAAATATATGGCACTTCGGTACAAACC
Found at i:249503 original size:31 final size:31
Alignment explanation
Indices: 249441--249504 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
249431 ATGTACAAAA
* * *
249441 AACATCATATATTTAATCAACAAGAATATAT
1 AACATCATACATTTAACCAACAAGAACATAT
* * *
249472 AACATCATGCATTTAACCAATAGGAACATAT
1 AACATCATACATTTAACCAACAAGAACATAT
249503 AA
1 AA
249505 TATTTTGCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (31 bp):
AACATCATACATTTAACCAACAAGAACATAT
Found at i:249705 original size:23 final size:23
Alignment explanation
Indices: 249653--249705 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
249643 AGAAATTGCA
*
249653 CCGAAGTGCCACATAGAAATGTC
1 CCGAAGGGCCACATAGAAATGTC
* * *
249676 CCAAAGGGCCACATAGTATTGTC
1 CCGAAGGGCCACATAGAAATGTC
*
249699 CTGAAGG
1 CCGAAGG
249706 ACTGCGTAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CCGAAGGGCCACATAGAAATGTC
Found at i:249722 original size:24 final size:23
Alignment explanation
Indices: 249693--249760 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
249683 GCCACATAGT
*
249693 ATTGTCCTGAAGGACTGCGTAGAA
1 ATTGTCCCGAAGGACTGCGTA-AA
* ***
249717 ATTGTCCCGAATGACCATGTAAA
1 ATTGTCCCGAAGGACTGCGTAAA
*
249740 ATTGTCCCGAAGGATTGCGTA
1 ATTGTCCCGAAGGACTGCGTA
249761 TAACCCTCGA
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (23 bp):
ATTGTCCCGAAGGACTGCGTAAA
Found at i:249859 original size:14 final size:16
Alignment explanation
Indices: 249840--249877 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
249830 TTTTAGCAGT
249840 TCACATA-ACTTAT-A
1 TCACATAGACTTATAA
*
249854 TCACATAGACTTGTAA
1 TCACATAGACTTATAA
249870 TCACATAG
1 TCACATAG
249878 CTCATTTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 5 0.24
16 9 0.43
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (16 bp):
TCACATAGACTTATAA
Found at i:254194 original size:16 final size:16
Alignment explanation
Indices: 254173--254203 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
254163 ATTTGTGTTT
254173 TTTTTTTTAAATTTAA
1 TTTTTTTTAAATTTAA
*
254189 TTTTTTTTAATTTTA
1 TTTTTTTTAAATTTA
254204 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTTAAATTTAA
Found at i:254550 original size:18 final size:18
Alignment explanation
Indices: 254527--254594 Score: 136
Period size: 18 Copynumber: 3.8 Consensus size: 18
254517 CCCTTCATGG
254527 ACTCCAAGAACCCACCAA
1 ACTCCAAGAACCCACCAA
254545 ACTCCAAGAACCCACCAA
1 ACTCCAAGAACCCACCAA
254563 ACTCCAAGAACCCACCAA
1 ACTCCAAGAACCCACCAA
254581 ACTCCAAGAACCCA
1 ACTCCAAGAACCCA
254595 TACCTGTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.44, C:0.44, G:0.06, T:0.06
Consensus pattern (18 bp):
ACTCCAAGAACCCACCAA
Found at i:261098 original size:31 final size:31
Alignment explanation
Indices: 261060--261215 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
261050 AGGGTCGAGG
261060 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
261091 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
261122 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
261153 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * *
261184 GATTACTTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
261215 G
1 G
261216 GTCCTTCGGG
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:262825 original size:30 final size:30
Alignment explanation
Indices: 262726--262828 Score: 104
Period size: 30 Copynumber: 3.4 Consensus size: 30
262716 GAAAGCAAAC
* *
262726 CAAAGAAAGAAGAAACCCATCACAAC-AAAC
1 CAAAGAAACAA-AAACCCATCACAACAAAAA
*
262756 CAAAGAAAACAAAAACCC-TCACAGCAGAAGAA
1 CAAAG-AAACAAAAACCCATCACAACA-AA-AA
* *
262788 -AAGGAAACAAAAGCCCATCACAACAAAAA
1 CAAAGAAACAAAAACCCATCACAACAAAAA
262817 CAAAGAAACAAA
1 CAAAGAAACAAA
262829 TATAGGGGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
29 8 0.13
30 34 0.57
31 17 0.28
32 1 0.02
ACGTcount: A:0.62, C:0.24, G:0.11, T:0.03
Consensus pattern (30 bp):
CAAAGAAACAAAAACCCATCACAACAAAAA
Found at i:268110 original size:21 final size:21
Alignment explanation
Indices: 268085--268132 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
268075 GATCCGGATC
*
268085 ATCCGGATCGGTTTTTATCCG
1 ATCCGGATCGGTTTTTATACG
268106 ATCCGGATCGGTTTTTATACG
1 ATCCGGATCGGTTTTTATACG
268127 ATCCGG
1 ATCCGG
268133 TTTTTTCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (21 bp):
ATCCGGATCGGTTTTTATACG
Found at i:268256 original size:17 final size:17
Alignment explanation
Indices: 268231--268266 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
268221 TCGGTTTCGG
*
268231 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGATT
*
268248 TTTTTAAAAAACCGATT
1 TTTTAAAAAAACCGATT
268265 TT
1 TT
268267 AATATTCCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (17 bp):
TTTTAAAAAAACCGATT
Found at i:268489 original size:21 final size:21
Alignment explanation
Indices: 268437--268477 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
268427 ACACTTAGGG
268437 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
268458 AACCGATTCCCTATGAGAGG
1 AACCGATTCCCTATGAGAGG
268478 GTATCGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:268706 original size:13 final size:13
Alignment explanation
Indices: 268685--268739 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
268675 AAGTTCGATA
*
268685 AATTCAAATACTT
1 AATTGAAATACTT
268698 AATTGAAATACTT
1 AATTGAAATACTT
* *
268711 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
268725 AATTGAAATACTT
1 AATTGAAATACTT
268738 AA
1 AA
268740 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:268821 original size:32 final size:33
Alignment explanation
Indices: 268725--268823 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
268715 AACTCAACAT
* * *
268725 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
268758 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
268791 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
268823 A
1 A
268824 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:268842 original size:21 final size:21
Alignment explanation
Indices: 268818--268857 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
268808 ACTTCAAGTT
268818 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
268839 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
268858 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:271046 original size:23 final size:24
Alignment explanation
Indices: 271020--271067 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
271010 CCATACCGAT
* *
271020 TTTTTTTTCCGG-ATAAAAACCGG
1 TTTTTTATCCGGTAAAAAAACCGG
271043 TTTTTTATCCGGTAAAAAAACCGG
1 TTTTTTATCCGGTAAAAAAACCGG
271067 T
1 T
271068 CTAGGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TTTTTTATCCGGTAAAAAAACCGG
Found at i:286239 original size:8 final size:8
Alignment explanation
Indices: 286226--286251 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
286216 TAGACTTGGA
286226 AAAAAAAT
1 AAAAAAAT
286234 AAAAAAAT
1 AAAAAAAT
286242 AAAAAAAT
1 AAAAAAAT
286250 AA
1 AA
286252 TGTGCCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:294603 original size:14 final size:14
Alignment explanation
Indices: 294584--294614 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
294574 TTAGAGATTA
294584 TTTCCTTTTTATTC
1 TTTCCTTTTTATTC
294598 TTTCCTTTTTATTC
1 TTTCCTTTTTATTC
294612 TTT
1 TTT
294615 TTCTGCTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCCTTTTTATTC
Found at i:301522 original size:15 final size:16
Alignment explanation
Indices: 301504--301548 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 16
301494 GTATGTTAGT
301504 AAAATATTTTGTTAAA
1 AAAATATTTTGTTAAA
301520 AAAA-A-TTTGTTAAA
1 AAAATATTTTGTTAAA
301534 AGAAATATTGTTGTT
1 A-AAATATT-TTGTT
301549 TTTAGAGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.40
15 4 0.16
16 5 0.20
17 1 0.04
18 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (16 bp):
AAAATATTTTGTTAAA
Found at i:302691 original size:15 final size:15
Alignment explanation
Indices: 302667--302717 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
302657 ATATTTAGCT
*
302667 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
*
302682 GGGCGAGCGGATGCG
1 GGGCGGGCGGATGCG
302697 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
302712 GGGCGG
1 GGGCGG
302718 ATAATGTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.18, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:304498 original size:16 final size:16
Alignment explanation
Indices: 304477--304523 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
304467 ATTCATTCAG
304477 AGCATTTGAATCATTC
1 AGCATTTGAATCATTC
304493 AGCATTTGAATCATTC
1 AGCATTTGAATCATTC
*
304509 AGCACTT-AATCATTC
1 AGCATTTGAATCATTC
304524 TAAAATAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (16 bp):
AGCATTTGAATCATTC
Found at i:311027 original size:2 final size:2
Alignment explanation
Indices: 311020--311057 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
311010 ATTTTAACCC
311020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
311058 TTCTGACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322343 original size:68 final size:67
Alignment explanation
Indices: 322269--322451 Score: 321
Period size: 68 Copynumber: 2.7 Consensus size: 67
322259 GATAATTAAT
*
322269 TGATTTTTCATTTAAAAAAAACTACTGATCACGAAATTTTGTTTATTATAATTATTAATCAATAT
1 TGATTTTTCATTT-AAAAAAACTACTGATCACGAAATTTTGTTTACTATAATTATTAATCAATAT
322334 GAC
65 GAC
322337 TGATTTTTCATTTTAAAAAAACTACTGATCACGAAATTTTGTTTACTATAATTATTAATCAATAT
1 TGATTTTTCA-TTTAAAAAAACTACTGATCACGAAATTTTGTTTACTATAATTATTAATCAATAT
322402 GAC
65 GAC
* *
322405 TGATCTTTCATTTTAAAAAACTACTGATCACGAAATTTTGTTTACTA
1 TGATTTTTCATTTAAAAAAACTACTGATCACGAAATTTTGTTTACTA
322452 ATTAATTTAA
Statistics
Matches: 111, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
67 36 0.32
68 72 0.65
69 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.43
Consensus pattern (67 bp):
TGATTTTTCATTTAAAAAAACTACTGATCACGAAATTTTGTTTACTATAATTATTAATCAATATG
AC
Found at i:322740 original size:34 final size:36
Alignment explanation
Indices: 322675--322749 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 36
322665 AACGTAATCC
*
322675 TCAATTTCATTATAAACCCCAAATTTCAAAATA-AT
1 TCAATTACATTATAAACCCCAAATTTCAAAATACAT
* * *
322710 TCAATTACATTTTAAA-CCCTAATTTTAAAATACAT
1 TCAATTACATTATAAACCCCAAATTTCAAAATACAT
322745 T-AATT
1 TCAATT
322750 TAGGGTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (36 bp):
TCAATTACATTATAAACCCCAAATTTCAAAATACAT
Found at i:322772 original size:33 final size:34
Alignment explanation
Indices: 322734--322803 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 34
322724 AACCCTAATT
322734 TTAAAATACATT-AATTTAGGGTTTAGAATATAA
1 TTAAAATACATTAAATTTAGGGTTTAGAATATAA
** * *
322767 TTAAAATATTTTAGAATTTGGGGTTTAGAATGTAA
1 TTAAAATACATTA-AATTTAGGGTTTAGAATATAA
322802 TT
1 TT
322804 GAAGTGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 10 0.32
35 21 0.68
ACGTcount: A:0.40, C:0.01, G:0.16, T:0.43
Consensus pattern (34 bp):
TTAAAATACATTAAATTTAGGGTTTAGAATATAA
Found at i:323750 original size:18 final size:18
Alignment explanation
Indices: 323727--323778 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
323717 TTAAAATTTA
*
323727 TCCCGAATGACCACTTTG
1 TCCCGAAGGACCACTTTG
*
323745 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTTTG
323763 TCCCGAAGGACCACTT
1 TCCCGAAGGACCACTT
323779 ATAACCCTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (18 bp):
TCCCGAAGGACCACTTTG
Found at i:330610 original size:17 final size:17
Alignment explanation
Indices: 330588--330641 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
330578 GCACTTAAAA
*
330588 TTTGTCCGAATGACCAC
1 TTTGTCCGAAAGACCAC
*
330605 TTTGTCTGAAAGACCA-
1 TTTGTCCGAAAGACCAC
*
330621 TTATGTCCCGAAGGACCAC
1 TT-TGT-CCGAAAGACCAC
330640 TT
1 TT
330642 ATAACCCTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 17 0.57
18 9 0.30
19 2 0.07
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (17 bp):
TTTGTCCGAAAGACCAC
Found at i:334896 original size:15 final size:15
Alignment explanation
Indices: 334862--334896 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
334852 TAATGAAATG
* *
334862 ATGTCTAATTTTAAT
1 ATGTTTAATTTTAAA
334877 ATGTTTAATTTTAAA
1 ATGTTTAATTTTAAA
334892 ATGTT
1 ATGTT
334897 GGATGAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (15 bp):
ATGTTTAATTTTAAA
Found at i:349203 original size:16 final size:15
Alignment explanation
Indices: 349182--349212 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
349172 TAAAATTAGA
349182 AATTTTAATTATTTAT
1 AATTTTAATT-TTTAT
349198 AATTTTAATTTTTAT
1 AATTTTAATTTTTAT
349213 CATTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTTTAATTTTTAT
Found at i:358877 original size:23 final size:22
Alignment explanation
Indices: 358836--358906 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 22
358826 GCTATGTATT
* *
358836 GATACACT-ATGAATATGTACC
1 GATACACTCCTGAATGTGTACC
* *
358857 GATACATTCCTTGAATGTGTATC
1 GATACACTCC-TGAATGTGTACC
*
358880 GATACACTCCT--AGGTGTACC
1 GATACACTCCTGAATGTGTACC
358900 GATACAC
1 GATACAC
358907 CCGTCGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
20 14 0.34
21 7 0.17
22 1 0.02
23 19 0.46
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (22 bp):
GATACACTCCTGAATGTGTACC
Found at i:359378 original size:13 final size:13
Alignment explanation
Indices: 359347--359384 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
359337 ACGTTTTATG
359347 ATTTTTCAAACATA
1 ATTTTTCAAA-ATA
359361 ATTTTTCAAAAT-
1 ATTTTTCAAAATA
*
359373 AGTTTTCAAAAT
1 ATTTTTCAAAAT
359385 TTTGCCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 2 0.09
14 10 0.43
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTTTTCAAAATA
Found at i:361147 original size:13 final size:13
Alignment explanation
Indices: 361118--361149 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
361108 GGGGAGTAAT
361118 TTTTCAAAAATGA
1 TTTTCAAAAATGA
361131 -TTTCAAAAATGA
1 TTTTCAAAAATGA
361143 TTTTCAA
1 TTTTCAA
361150 GAAGAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:363300 original size:16 final size:16
Alignment explanation
Indices: 363275--363306 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
363265 CCGATGTGTC
363275 ACATTGACTTTTAAAA
1 ACATTGACTTTTAAAA
*
363291 ACATTTACTTTTAAAA
1 ACATTGACTTTTAAAA
363307 GATAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (16 bp):
ACATTGACTTTTAAAA
Found at i:363914 original size:25 final size:25
Alignment explanation
Indices: 363867--363916 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
363857 TCTGTATAAA
* * **
363867 TTGCACCGAAGTGTCGCGTAGAAAT
1 TTGCACCGAAGTGCCACAAAGAAAT
363892 TTGCACCGAAGTGCCACAAAGAAAT
1 TTGCACCGAAGTGCCACAAAGAAAT
363917 GTTCCAAAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (25 bp):
TTGCACCGAAGTGCCACAAAGAAAT
Found at i:365253 original size:27 final size:27
Alignment explanation
Indices: 365230--365285 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
365220 TTCAAGAATC
365230 AACACCAACTTAAAAAATGAAAGAAAT
1 AACACCAACTTAAAAAATGAAAGAAAT
* *
365257 AACACCATCTTAAAAAATGAAAGGAAT
1 AACACCAACTTAAAAAATGAAAGAAAT
365284 AA
1 AA
365286 TCAATAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.61, C:0.14, G:0.09, T:0.16
Consensus pattern (27 bp):
AACACCAACTTAAAAAATGAAAGAAAT
Found at i:370979 original size:24 final size:24
Alignment explanation
Indices: 370952--371009 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
370942 CACCACAGCT
*
370952 CGTATAAATTGCACCGAAGTGCCG
1 CGTATAAATTGCACCGAAGTGCCA
* **
370976 CGTAGAAATTTGCATTGAAGTGCCA
1 CGTATAAA-TTGCACCGAAGTGCCA
*
371001 CATATAAAT
1 CGTATAAAT
371010 GTCCCGAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (24 bp):
CGTATAAATTGCACCGAAGTGCCA
Found at i:371024 original size:23 final size:23
Alignment explanation
Indices: 370998--371045 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
370988 CATTGAAGTG
370998 CCACATA-TAAATGTCCCGAAGGA
1 CCACATAGT-AATGTCCCGAAGGA
*
371021 CCACATAGTATTGTCCCGAAGGA
1 CCACATAGTAATGTCCCGAAGGA
371044 CC
1 CC
371046 TCGTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (23 bp):
CCACATAGTAATGTCCCGAAGGA
Found at i:371060 original size:23 final size:23
Alignment explanation
Indices: 371011--371065 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
371001 CATATAAATG
* *
371011 TCCCGAAGGACCACATAGTATTG
1 TCCCGAAGGACCACATAGAATTA
* *
371034 TCCCGAAGGACCTCGTAGAATTA
1 TCCCGAAGGACCACATAGAATTA
*
371057 TCCCAAAGG
1 TCCCGAAGG
371066 GCCGTGTAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGAATTA
Found at i:372486 original size:54 final size:54
Alignment explanation
Indices: 372283--372604 Score: 494
Period size: 54 Copynumber: 6.1 Consensus size: 54
372273 TTGCATCCGT
372283 AGTG-CAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTG--CACAC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* *
372334 AGTACCAATACGAAATTTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
*
372388 AGTGCCAATACGGAAA-TCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* * * *
372441 AATGCCAATATGAAAATTCATAAACTTATTATGAATTTATTAAGTTGCACACAT
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* *
372495 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGTACACAC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* * *
372549 AGTGCTAATATGAAAATTCATAAAC-T-TTATGAATTTCTTAAGTTGCACACAT
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
372601 AGTG
1 AGTG
372605 TAACACCCCA
Statistics
Matches: 246, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
51 3 0.01
52 69 0.28
53 51 0.21
54 123 0.50
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.34
Consensus pattern (54 bp):
AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
Found at i:373533 original size:22 final size:22
Alignment explanation
Indices: 373508--373562 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
373498 ACTGAAGTGG
*
373508 GTATCAGTATTATAGAAGAGAA
1 GTATCAGTACTATAGAAGAGAA
373530 GTATCAGTACTATAGAAGAGAA
1 GTATCAGTACTATAGAAGAGAA
*
373552 GTATCGGTACT
1 GTATCAGTACT
373563 GTAGGCAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (22 bp):
GTATCAGTACTATAGAAGAGAA
Found at i:375043 original size:54 final size:54
Alignment explanation
Indices: 374985--375425 Score: 715
Period size: 54 Copynumber: 8.2 Consensus size: 54
374975 AGGGGTGTTG
*
374985 CACATAGTGACAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
1 CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
* * * *
375039 CACATAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTATAAAGTTGCA
1 CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
* *
375093 CACATAGTGCCAATACGAAAATTCATAAACATATTATAAATTTCTTAAGTTGCA
1 CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
* * * * *
375147 CACACAATGCTAATAAGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
1 CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
*
375201 CAC-TAGTGCCAATAAGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
1 CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
375254 CACA-AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
1 CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
*
375307 CACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
1 CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
* * *
375361 CACATAGTGTCAATTCAAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
1 CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
375415 CACATAGTGCC
1 CACATAGTGCC
375426 CATTTGGTAA
Statistics
Matches: 357, Mismatches: 28, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
53 101 0.28
54 256 0.72
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (54 bp):
CACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
Found at i:383224 original size:17 final size:17
Alignment explanation
Indices: 383202--383245 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
383192 CTCCCCCAAA
383202 ATCTTTCTTTTGTTCTT
1 ATCTTTCTTTTGTTCTT
383219 ATCTTTCTTTTGTTCTT
1 ATCTTTCTTTTGTTCTT
383236 ATCTTTCTTT
1 ATCTTTCTTT
383246 CCTTTCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.07, C:0.18, G:0.05, T:0.70
Consensus pattern (17 bp):
ATCTTTCTTTTGTTCTT
Done.