Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011115.1 Kokia drynarioides strain JFW-HI SEQ_126088, 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: 224211
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:1037 original size:43 final size:42
Alignment explanation
Indices: 955--1047 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 42
945 ACTAACATGT
* * *
955 TAAATTATATTACTTGACTCATGTTAATGTGGTTGCATGTTA
1 TAAATTATATTACTTGACTCATATTAATATGCTTGCATGTTA
* *
997 CTAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 -TAAATTATATTACTTGACTCATATTAATATGCTTG-CATGTTA
*
1040 TTAATTAT
1 TAAATTAT
1048 GCAGTTCATC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 10 0.23
43 33 0.77
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (42 bp):
TAAATTATATTACTTGACTCATATTAATATGCTTGCATGTTA
Found at i:1680 original size:45 final size:45
Alignment explanation
Indices: 1614--1743 Score: 181
Period size: 45 Copynumber: 2.9 Consensus size: 45
1604 TCATCAAGCC
*
1614 AAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAA-ACT
1 AAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGA-G
* * *
1659 AAGGATATCAGCCTCAATTTGACGAGCCACTGTAATACTCAAGAG
1 AAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGAG
* * *
1704 AAGGATATCAGGCTGAGTTTGACGAGCCACCGCGATACTC
1 AAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTC
1744 TATTCCTCCC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 73 0.99
46 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (45 bp):
AAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGAG
Found at i:2098 original size:28 final size:28
Alignment explanation
Indices: 2016--2101 Score: 109
Period size: 28 Copynumber: 3.1 Consensus size: 28
2006 TTGTAAACCT
* * * *
2016 TAAACTTAAAATCCTAAATCATAAATAC
1 TAAACTTGAAACCCTAAACCATAAACAC
2044 TAAACTTGAAACCCTAAACCATAAACAC
1 TAAACTTGAAACCCTAAACCATAAACAC
* * *
2072 TAGACTTGAAACTCTAAACCGTAAACAC
1 TAAACTTGAAACCCTAAACCATAAACAC
2100 TA
1 TA
2102 TATTGATTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (28 bp):
TAAACTTGAAACCCTAAACCATAAACAC
Found at i:5176 original size:4 final size:4
Alignment explanation
Indices: 5157--5221 Score: 60
Period size: 4 Copynumber: 16.0 Consensus size: 4
5147 ACACATTACG
* * * *
5157 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
*
5205 TTTTC TTTC TTTT TTTC
1 -TTTC TTTC TTTC TTTC
5222 CCGTTTATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.06
4 39 0.80
5 7 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:5190 original size:17 final size:15
Alignment explanation
Indices: 5157--5216 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 15
5147 ACACATTACG
5157 TTTCTTTCCTTCTTC
1 TTTCTTTCCTTCTTC
5172 TTTCTTTCC-TC-TC
1 TTTCTTTCCTTCTTC
*
5185 CTTC-TTCC-T-TTC
1 TTTCTTTCCTTCTTC
5197 TTTCTTT-CTT-TTC
1 TTTCTTTCCTTCTTC
5210 TTTCTTT
1 TTTCTTT
5217 TTTTCCCGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 11 0.28
13 18 0.45
14 2 0.05
15 9 0.22
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTCTTTCCTTCTTC
Found at i:5214 original size:25 final size:23
Alignment explanation
Indices: 5157--5215 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
5147 ACACATTACG
5157 TTTCTTTCCTTCTTCTTTCTTTCC
1 TTTCTTT-CTTCTTCTTTCTTTCC
* * *
5181 TCTCCTTCTTCCTTTCTTTCTTTCT
1 TTTCTTTCTT-C-TTCTTTCTTTCC
5206 TTTCTTTCTT
1 TTTCTTTCTT
5216 TTTTTCCCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.11
24 6 0.21
25 19 0.68
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTCTTTCTTCTTCTTTCTTTCC
Found at i:30320 original size:27 final size:27
Alignment explanation
Indices: 30290--30390 Score: 121
Period size: 27 Copynumber: 3.7 Consensus size: 27
30280 TACAGAAATG
* * *
30290 TAGCTCATTCGAGCCTAGAACAGAGTT
1 TAGCTCATTCGAGCCCATAAAAGAGTT
* *
30317 TAGCTCATTCGAACCCATAAAAGATTT
1 TAGCTCATTCGAGCCCATAAAAGAGTT
* *
30344 TAGCTCATTTGAGCCCATAATAGAGTT
1 TAGCTCATTCGAGCCCATAAAAGAGTT
* *
30371 CAGCTCATTCGAGCGCATAA
1 TAGCTCATTCGAGCCCATAA
30391 CAGAATAATG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (27 bp):
TAGCTCATTCGAGCCCATAAAAGAGTT
Found at i:37105 original size:27 final size:27
Alignment explanation
Indices: 37075--37233 Score: 203
Period size: 27 Copynumber: 5.9 Consensus size: 27
37065 TACAAGAATG
*
37075 TAGCTCATTCGAGCCTAGAACAGAGTT
1 TAGCTCATTCGAGCCCAGAACAGAGTT
*
37102 TAGCTCATTCGAGCCCAGAATAGAGTT
1 TAGCTCATTCGAGCCCAGAACAGAGTT
* *
37129 TAGCTCATTCGAGCCTAAAACAGAGTT
1 TAGCTCATTCGAGCCCAGAACAGAGTT
* *
37156 TAGCTCATTTC-AACCTAGAACAGAGTT
1 TAGCTCA-TTCGAGCCCAGAACAGAGTT
* *
37183 GAGCTCATTCGAGCCCATAACAGAGTT
1 TAGCTCATTCGAGCCCAGAACAGAGTT
* * *
37210 CAACTCATTCAAGCCCAGAACAGA
1 TAGCTCATTCGAGCCCAGAACAGA
37234 ATAACGCTCT
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.03
27 109 0.95
28 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (27 bp):
TAGCTCATTCGAGCCCAGAACAGAGTT
Found at i:37248 original size:54 final size:54
Alignment explanation
Indices: 37076--37251 Score: 212
Period size: 54 Copynumber: 3.3 Consensus size: 54
37066 ACAAGAATGT
* * * *
37076 AGCTCATTCGAGCCTAGAACAGAGTTTAGCTCATTCGAGCCCAGAATAGAGTTT
1 AGCTCATTCGAGCCTAAAACAGAGTTTAGCTCATTCAAGCCCAGAACAGAGTTA
* *
37130 AGCTCATTCGAGCCTAAAACAGAGTTTAGCTCATTTCAA-CCTAGAACAGAGTTG
1 AGCTCATTCGAGCCTAAAACAGAGTTTAGCTCA-TTCAAGCCCAGAACAGAGTTA
* * * * *
37184 AGCTCATTCGAGCCCATAACAGAGTTCAACTCATTCAAGCCCAGAACAGA-ATA
1 AGCTCATTCGAGCCTAAAACAGAGTTTAGCTCATTCAAGCCCAGAACAGAGTTA
*
37237 ACGCTCTTTCGAGCC
1 A-GCTCATTCGAGCC
37252 AAAGTCCAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 7 0.07
54 95 0.90
55 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (54 bp):
AGCTCATTCGAGCCTAAAACAGAGTTTAGCTCATTCAAGCCCAGAACAGAGTTA
Found at i:44741 original size:51 final size:51
Alignment explanation
Indices: 44686--44870 Score: 266
Period size: 51 Copynumber: 3.6 Consensus size: 51
44676 TAGGAATTCA
** * *
44686 TACTCACGATGACACAGAGTCATCGGACCATTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAATGGATTCATT
* * *
44737 TACTCACGATGACACTTAGTCATTGGACTTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAATGGATTCATT
*
44788 TACTCACGATGACACTTAGTCATCGGACTTTTAAT-CAGTAAAT-GATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCA-T-AATGGATTCATT
44839 TACTCACGATGACACTTAGTCATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
44871 TCGTTTATAG
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
50 2 0.02
51 118 0.97
52 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAATGGATTCATT
Found at i:44811 original size:102 final size:103
Alignment explanation
Indices: 44643--44871 Score: 281
Period size: 102 Copynumber: 2.2 Consensus size: 103
44633 AATACTCATA
* ** * *
44643 ATGACA-TATAGTCATCGGACCTCTTGTTCCGTATAGGAATTCA--TACTCACGATGACACAGAG
1 ATGACACT-TAGTCATCGGACCTTTTAATCCATAAAGG-ATTCATTTACTCACGATGACACAGAG
*
44705 TCATCGGACCATTAATCCA-T-CATGGATTCATTTACTCACG
64 TCATCGGACCATTAAT-CAGTAAAT-GATTCATTTACTCACG
* **
44745 ATGACACTTAGTCATTGGA-CTTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTC
1 ATGACACTTAGTCATCGGACCTTTTAATCCATAAAGGATTCATTTACTCACGATGACACAGAGTC
**
44809 ATCGGACTTTTAATCAGTAAATGATTCATTTACTCACG
66 ATCGGACCATTAATCAGTAAATGATTCATTTACTCACG
44847 ATGACACTTAGTCATCGGACCTTTT
1 ATGACACTTAGTCATCGGACCTTTT
44872 CGTTTATAGC
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
100 5 0.05
101 14 0.13
102 82 0.75
103 8 0.07
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (103 bp):
ATGACACTTAGTCATCGGACCTTTTAATCCATAAAGGATTCATTTACTCACGATGACACAGAGTC
ATCGGACCATTAATCAGTAAATGATTCATTTACTCACG
Found at i:53253 original size:36 final size:36
Alignment explanation
Indices: 53177--53246 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
53167 ATATAATCAG
*
53177 TCACATAGTATGAAAAACATACCCACATATTTACCA
1 TCACATAGTATGAAAAACATACCCACATATTCACCA
* * *
53213 TCACAT-GTCATGAATAACATGCCCTCATATTCAC
1 TCACATAGT-ATGAAAAACATACCCACATATTCAC
53247 TTTCACAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (36 bp):
TCACATAGTATGAAAAACATACCCACATATTCACCA
Found at i:58967 original size:18 final size:18
Alignment explanation
Indices: 58944--58994 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
58934 CACATCATGA
58944 TCAGATACAGTCACACAC
1 TCAGATACAGTCACACAC
* **
58962 TCAGATATAGTCACATGC
1 TCAGATACAGTCACACAC
*
58980 TCATATACAGTCACA
1 TCAGATACAGTCACA
58995 GCAGGCTGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (18 bp):
TCAGATACAGTCACACAC
Found at i:75486 original size:30 final size:30
Alignment explanation
Indices: 75452--75508 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
75442 ATTAAGGACT
*
75452 AAATT-ATGATTTTAGGGAAATTTAGGGATA
1 AAATTGATAATTTT-GGGAAATTTAGGGATA
* *
75482 AAATTGGTAATTTTGTGAAATTTAGGG
1 AAATTGATAATTTTGGGAAATTTAGGG
75509 TTTAATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 17 0.74
31 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.25, T:0.39
Consensus pattern (30 bp):
AAATTGATAATTTTGGGAAATTTAGGGATA
Found at i:82814 original size:37 final size:39
Alignment explanation
Indices: 82767--82880 Score: 133
Period size: 37 Copynumber: 2.9 Consensus size: 39
82757 TCAGATAAGC
*
82767 CTAAGGAAATATACTGGCACATGTAGTGCATCATCGG-A
1 CTAAGAAAATATACTGGCACATGTAGTGCATCATCGGAA
** *
82805 -TAAGAAAATATACTGGCACACCTAGTCCATCATCGGATAAA
1 CTAAGAAAATATACTGGCACATGTAGTGCATCATCGG---AA
*
82846 CTGAAGAAAATATACTTGCACATGTAGTGCATCAT
1 CT-AAGAAAATATACTGGCACATGTAGTGCATCAT
82881 TAGATAAACC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
37 32 0.52
41 1 0.02
42 1 0.02
43 28 0.45
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (39 bp):
CTAAGAAAATATACTGGCACATGTAGTGCATCATCGGAA
Found at i:82867 original size:43 final size:42
Alignment explanation
Indices: 82806--82980 Score: 156
Period size: 43 Copynumber: 4.1 Consensus size: 42
82796 ATCATCGGAT
* * *
82806 AAGAAAATATACTGGCACACCTAGTCCATCATCGGATAAACTG
1 AAGAAAATATA-TTGCACACCTAGTGCATCATCGGATAAACTA
** ** *
82849 AAGAAAATATACTTGCACATGTAGTGCATCATTAGATAAACCA
1 AAGAAAATATA-TTGCACACCTAGTGCATCATCGGATAAACTA
* * *
82892 AAGAAAATATATTGGCACACATAATGCATCATCGAATTAAAC-A
1 AAGAAAATATATT-GCACACCTAGTGCATCATCGGA-TAAACTA
* * *
82935 AAGTAATTATATTG-ACACCTATAGTGCATCATTGGATAAACTA
1 AAGAAAATATATTGCACACC--TAGTGCATCATCGGATAAACTA
82978 AAG
1 AAG
82981 TATGACCTGT
Statistics
Matches: 107, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
41 4 0.04
42 8 0.07
43 90 0.84
44 5 0.05
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (42 bp):
AAGAAAATATATTGCACACCTAGTGCATCATCGGATAAACTA
Found at i:82960 original size:86 final size:86
Alignment explanation
Indices: 82806--82980 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 86
82796 ATCATCGGAT
* * * * *
82806 AAGAAAATATACTGGCACACCTAGTCCATCATCGGATAAACTGAAGAAAATATACTTGCACATGT
1 AAGAAAATATACTGGCACACATAATCCATCATCGAATAAACTAAAGAAAATATACTTGCACATAT
82871 AGTGCATCATTAGATAAACCA
66 AGTGCATCATTAGATAAACCA
* * * * *
82892 AAGAAAATATATTGGCACACATAATGCATCATCGAATTAAAC-AAAGTAATTATA-TTGACACCT
1 AAGAAAATATACTGGCACACATAATCCATCATCGAA-TAAACTAAAGAAAATATACTTG-CACAT
* *
82955 ATAGTGCATCATTGGATAAACTA
64 ATAGTGCATCATTAGATAAACCA
82978 AAG
1 AAG
82981 TATGACCTGT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
85 3 0.04
86 67 0.89
87 5 0.07
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (86 bp):
AAGAAAATATACTGGCACACATAATCCATCATCGAATAAACTAAAGAAAATATACTTGCACATAT
AGTGCATCATTAGATAAACCA
Found at i:84897 original size:16 final size:16
Alignment explanation
Indices: 84876--84906 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
84866 GAAATTTTTG
*
84876 TGTTAAAGGACTAAAA
1 TGTTAAAGGAATAAAA
84892 TGTTAAAGGAATAAA
1 TGTTAAAGGAATAAA
84907 TTTGTAAGAA
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:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (16 bp):
TGTTAAAGGAATAAAA
Found at i:87093 original size:53 final size:53
Alignment explanation
Indices: 87013--87205 Score: 262
Period size: 53 Copynumber: 3.6 Consensus size: 53
87003 ATAAATTCAA
* *
87013 AAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
1 AAAGGTCCGATGACTCTTTGTCATCGTGAGTTATATGAATCCTATTACAGATT
* * **
87066 AAAGGTCCGATGACTCTTTGTCATCGTGGGTTATATGAATTCTATTATGGATT
1 AAAGGTCCGATGACTCTTTGTCATCGTGAGTTATATGAATCCTATTACAGATT
* * * *
87119 AAAGGTTCGATGACT-TTATATCATCGTGAGTTATATGGATCCTATTACAAATT
1 AAAGGTCCGATGACTCTT-TGTCATCGTGAGTTATATGAATCCTATTACAGATT
**
87172 AAAGGTCCGATGACTCCATGTCATCGTGAGTTAT
1 AAAGGTCCGATGACTCTTTGTCATCGTGAGTTAT
87206 CAAAGGTGAT
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
52 2 0.02
53 118 0.98
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (53 bp):
AAAGGTCCGATGACTCTTTGTCATCGTGAGTTATATGAATCCTATTACAGATT
Found at i:91964 original size:53 final size:53
Alignment explanation
Indices: 91877--92069 Score: 269
Period size: 53 Copynumber: 3.6 Consensus size: 53
91867 TAAATGCAAA
* *
91877 AAAGGTCTGATGACTCTGTGTTATCATGAGTTATATGAATCCTATTACGGATT
1 AAAGGTCTGATGACTCTATGTCATCATGAGTTATATGAATCCTATTACGGATT
* * * **
91930 AAACGTTTGATGACTCTATGTCATCATGGGTTATATGAATCCTATTGTGGATT
1 AAAGGTCTGATGACTCTATGTCATCATGAGTTATATGAATCCTATTACGGATT
* * *
91983 AAAGGTCTAATGACTCTATGTCATCGTGAGTTATGTGAATCCTATTACGGATT
1 AAAGGTCTGATGACTCTATGTCATCATGAGTTATATGAATCCTATTACGGATT
* **
92036 AAAGGTCCGATGACTCCGTGTCATCATGAGTTAT
1 AAAGGTCTGATGACTCTATGTCATCATGAGTTAT
92070 TAAAGGTGAA
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 120 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (53 bp):
AAAGGTCTGATGACTCTATGTCATCATGAGTTATATGAATCCTATTACGGATT
Found at i:92802 original size:21 final size:21
Alignment explanation
Indices: 92778--92835 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
92768 CTAGAAGAGA
92778 CACTTGTATCGGTAGATTTAT
1 CACTTGTATCGGTAGATTTAT
92799 CACTTGTATCGGTAGATTTAT
1 CACTTGTATCGGTAGATTTAT
92820 CACTTGTATCGGTAGA
1 CACTTGTATCGGTAGA
92836 ATCGATATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (21 bp):
CACTTGTATCGGTAGATTTAT
Found at i:96325 original size:16 final size:16
Alignment explanation
Indices: 96304--96334 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
96294 GAAATTTTTG
*
96304 TGTTAAAGGACTAAAA
1 TGTTAAAGGAATAAAA
96320 TGTTAAAGGAATAAA
1 TGTTAAAGGAATAAA
96335 TTTGTAAGAT
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:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (16 bp):
TGTTAAAGGAATAAAA
Found at i:96881 original size:53 final size:53
Alignment explanation
Indices: 96798--96937 Score: 172
Period size: 53 Copynumber: 2.6 Consensus size: 53
96788 ATAAATGCAA
* * * *
96798 AAAGGTTCGATGACTCTATGTCATCATGAGTTATATGAATCCTGTTGCAGATT
1 AAAGGTCCAATGACTCTATGTCATCATGAGTTATATGAATCCTATTACAGATT
* * ** * *
96851 AAAGGTCTAATGACTCTGTGTCATTGTGAGTTATGTGAATCCTATTACGGATT
1 AAAGGTCCAATGACTCTATGTCATCATGAGTTATATGAATCCTATTACAGATT
* *
96904 AAAGGTCCGATGACTCCATGTCATCATGAGTTAT
1 AAAGGTCCAATGACTCTATGTCATCATGAGTTAT
96938 CAAAGGTGAA
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 71 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (53 bp):
AAAGGTCCAATGACTCTATGTCATCATGAGTTATATGAATCCTATTACAGATT
Found at i:104051 original size:7 final size:7
Alignment explanation
Indices: 104005--104050 Score: 74
Period size: 7 Copynumber: 6.4 Consensus size: 7
103995 CAAGTGACCC
104005 GACCTGTT
1 GACC-GTT
104013 GACCGTT
1 GACCGTT
104020 GACCGTT
1 GACCGTT
104027 GACCGTT
1 GACCGTT
104034 GACCGTT
1 GACCGTT
*
104041 GACTGTT
1 GACCGTT
104048 GAC
1 GAC
104051 TTTGATCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
7 33 0.89
8 4 0.11
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (7 bp):
GACCGTT
Found at i:105068 original size:19 final size:19
Alignment explanation
Indices: 105046--105102 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
105036 TTTAATTTCA
*
105046 TTTTATTTTATTATTTTAC
1 TTTTATTTTATTATTATAC
*
105065 TTTTGAGTTT-TTATTATAC
1 TTTT-ATTTTATTATTATAC
*
105084 TTTGTTTTTTATTATTATA
1 TTT-TATTTTATTATTATA
105103 TTTAGGTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.21, C:0.04, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTTATTATTATAC
Found at i:109774 original size:24 final size:24
Alignment explanation
Indices: 109747--109792 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
109737 ACAATCAATT
109747 CATTTTATATTACAGTTGCACTGA
1 CATTTTATATTACAGTTGCACTGA
*
109771 CATTTTATATTACATTTGCACT
1 CATTTTATATTACAGTTGCACT
109793 AATAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (24 bp):
CATTTTATATTACAGTTGCACTGA
Found at i:122067 original size:103 final size:103
Alignment explanation
Indices: 121887--122083 Score: 331
Period size: 103 Copynumber: 1.9 Consensus size: 103
121877 CGAGCTATCG
* *
121887 AGAATATGCACTTATGCATAAATCCCAACCATCGTAGGGCCTGTAATCCATTTTAGGATTCATAT
1 AGAATATGCACTTATGCATAAATCCCAACCATCGCAGGGCCTGTAATCCAATTTAGGATTCATAT
* *
121952 CTCTTTCCCGACTCATGATGCTGCTCACAGAATTGTCA
66 CTCTTTCCCGACTCACGATGCTACTCACAGAATTGTCA
* *
121990 AGAATATGCACTTATGCATAAATCCTAGCCATCGCAGGGCCTGTAATCCAATTTAGGATTCATAT
1 AGAATATGCACTTATGCATAAATCCCAACCATCGCAGGGCCTGTAATCCAATTTAGGATTCATAT
*
122055 CTCTTTCTCGACTCACGATGCTACTCACA
66 CTCTTTCCCGACTCACGATGCTACTCACA
122084 CGAGCTATCG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 87 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (103 bp):
AGAATATGCACTTATGCATAAATCCCAACCATCGCAGGGCCTGTAATCCAATTTAGGATTCATAT
CTCTTTCCCGACTCACGATGCTACTCACAGAATTGTCA
Found at i:125566 original size:194 final size:194
Alignment explanation
Indices: 125223--125607 Score: 526
Period size: 194 Copynumber: 2.0 Consensus size: 194
125213 ACTGTGAGTC
* *
125223 AGTCTAGCTTTGTTTAGACAAAATGGAGATTGATTTTGATTTGTAGTCTAAAATATATTAATTTT
1 AGTCTAGCTTTGTTTAGACAAAATGGAGATTGATTTTGATTTGTAGTCTAAAATATATGAATATT
* * * * *
125288 TCAGTTTTGAAAGGTCATAAAAATCTAGCAACATAATTCTTATGAAACAAATTTAGCAGTGACTT
66 TCAATGTTGAAAGGTCATAAAAATCTAGCAACATAATTCTTATAAAACAAATCTAGCAATGACTT
* * *
125353 TGACAAATCACAAAAAAATTGCATAAGATAAAA-TAGGAAGTGAGCCTTATATCCATATAATGGA
131 TGAAAAATCACAAAAAAATTGCACAAGATAAAATTA-GAAATGAGCCTTATATCCATATAATGGA
* *
125417 AGTCTAG-TTTCGTTTAGA-ATAAATGGAGATTGATTTTGATTTGTAGTTTAAAATATCTGAATA
1 AGTCTAGCTTT-GTTTAGACA-AAATGGAGATTGATTTTGATTTGTAGTCTAAAATATATGAATA
* * *** *
125480 TTTGAATGTTGAAAGGTCATAAAAATCTGGCAGTGTAATTCTTATAAAACAGATCTAGCAATGAC
64 TTTCAATGTTGAAAGGTCATAAAAATCTAGCAACATAATTCTTATAAAACAAATCTAGCAATGAC
* *
125545 TTTGAAAAAATCAC-CAAAAATTGCACAAGATAAAATTAGAAATGAGCCTTATATCCCTATAAT
129 TTTG-AAAAATCACAAAAAAATTGCACAAGATAAAATTAGAAATGAGCCTTATATCCATATAAT
125608 TGTATGGAAG
Statistics
Matches: 167, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
193 4 0.02
194 153 0.92
195 10 0.06
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (194 bp):
AGTCTAGCTTTGTTTAGACAAAATGGAGATTGATTTTGATTTGTAGTCTAAAATATATGAATATT
TCAATGTTGAAAGGTCATAAAAATCTAGCAACATAATTCTTATAAAACAAATCTAGCAATGACTT
TGAAAAATCACAAAAAAATTGCACAAGATAAAATTAGAAATGAGCCTTATATCCATATAATGGA
Found at i:128953 original size:25 final size:25
Alignment explanation
Indices: 128900--128954 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
128890 CAGAGTGTTT
* *
128900 CTCTTACGAGCCAGATAAAATAACG
1 CTCTTACGAGCCAGACAAAATAACA
* *
128925 CTCTTACGAGCTAGACAAAATATCA
1 CTCTTACGAGCCAGACAAAATAACA
128950 CTCTT
1 CTCTT
128955 TTGAGCCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (25 bp):
CTCTTACGAGCCAGACAAAATAACA
Found at i:152326 original size:29 final size:29
Alignment explanation
Indices: 152297--152359 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
152287 GAAAATCAAC
*
152297 AAAAG-AAAGATAAATAGATTAGTAAAAACA
1 AAAAGTAAAGAAAAATA-ATT-GTAAAAACA
**
152327 AAAAGTAAAGAAAAATAATTGTAACTACA
1 AAAAGTAAAGAAAAATAATTGTAAAAACA
152356 AAAA
1 AAAA
152360 TGAGCATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 11 0.38
30 8 0.28
31 10 0.34
ACGTcount: A:0.67, C:0.05, G:0.11, T:0.17
Consensus pattern (29 bp):
AAAAGTAAAGAAAAATAATTGTAAAAACA
Found at i:163134 original size:24 final size:23
Alignment explanation
Indices: 163102--163169 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 23
163092 TGAGGGTATT
*
163102 AAAGCAAAAGAAGAAGAGAAGAG
1 AAAGAAAAAGAAGAAGAGAAGAG
*
163125 AAAAGAAAAATAA-AA-AGAAGAG
1 -AAAGAAAAAGAAGAAGAGAAGAG
*
163147 AAAGAAAAGGAAGAAGAAGAAGA
1 AAAGAAAAAGAAGAAG-AGAAGA
163170 AGACGTTGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 10 0.27
22 9 0.24
23 2 0.05
24 16 0.43
ACGTcount: A:0.71, C:0.01, G:0.26, T:0.01
Consensus pattern (23 bp):
AAAGAAAAAGAAGAAGAGAAGAG
Found at i:163163 original size:21 final size:22
Alignment explanation
Indices: 163102--163166 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
163092 TGAGGGTATT
*
163102 AAAGCAAAAGAAGAAGAGAAGAGA
1 AAAGAAAAAGAAG-A-AGAAGAGA
* *
163126 AAAGAAAAATAAAAAGAAGAG-
1 AAAGAAAAAGAAGAAGAAGAGA
*
163147 AAAGAAAAGGAAGAAGAAGA
1 AAAGAAAAAGAAGAAGAAGA
163167 AGAAGACGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 17 0.49
22 7 0.20
23 1 0.03
24 10 0.29
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAGAAGAAGAAGAGA
Found at i:163169 original size:27 final size:27
Alignment explanation
Indices: 163109--163172 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
163099 ATTAAAGCAA
*
163109 AAGAAGAAGAGAAGAGAAAAGAAAAAT
1 AAGAAGAAGAGAAGAGAAAAGAAAAAG
* *
163136 AAAAAGAAGAGAA-AGAAAAGGAAGAAG
1 AAGAAGAAGAGAAGAGAAAA-GAAAAAG
163163 AAGAAGAAGA
1 AAGAAGAAGA
163173 CGTTGCCTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.19
27 26 0.81
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (27 bp):
AAGAAGAAGAGAAGAGAAAAGAAAAAG
Found at i:175285 original size:25 final size:26
Alignment explanation
Indices: 175257--175307 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
175247 TAGCTCAAAT
*
175257 GAGCCTAGAAAGAGT-TAGCTCTTAC
1 GAGCCCAGAAAGAGTATAGCTCTTAC
* *
175282 GAGCCCAGATAGAGTATCGCTCTTAC
1 GAGCCCAGAAAGAGTATAGCTCTTAC
175308 AAACCAGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (26 bp):
GAGCCCAGAAAGAGTATAGCTCTTAC
Found at i:175459 original size:78 final size:75
Alignment explanation
Indices: 175352--175515 Score: 195
Period size: 78 Copynumber: 2.1 Consensus size: 75
175342 AGAATAAAGG
* * * *
175352 CTCTTACGAGCCAGACAGAACATCACTCTTTCGAGCCAGACAGAATATCACTCTTTCAAGCCAGA
1 CTCTTACAAGCCAGACAAAACAACACTCTTACGAGCCAGACAGAATATCACTCTTTCAAGCCA-A
*
175417 ATCCA-AAGTGTTA
65 AT--AGAA-TATTA
* * * * *
175430 CTCTTACAAGCCAGACAAAATAACGCTCTTACGAGCCAGATAGAATATCGCTCTTTCGAGCCAAA
1 CTCTTACAAGCCAGACAAAACAACACTCTTACGAGCCAGACAGAATATCACTCTTTCAAGCCAAA
175495 TAGAATATTA
66 TAGAATATTA
175505 CTCTTACAAGC
1 CTCTTACAAGC
175516 TAAAATGCTA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
75 16 0.21
76 2 0.03
77 3 0.04
78 54 0.72
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (75 bp):
CTCTTACAAGCCAGACAAAACAACACTCTTACGAGCCAGACAGAATATCACTCTTTCAAGCCAAA
TAGAATATTA
Found at i:175484 original size:103 final size:104
Alignment explanation
Indices: 175327--175515 Score: 281
Period size: 103 Copynumber: 1.8 Consensus size: 104
175317 AGAATAACGT
* * * *
175327 TCTTACAAGCTAGACAGAATAAAGGCTCTTACGAGCCAGACAGAACATCACTCTTTCGAGCCAGA
1 TCTTACAAGCCAGACAAAATAAACGCTCTTACGAGCCAGACAGAACATCACTCTTTCGAGCCAAA
*
175392 CAGAATATCACTCTTTCAAGCCAGAATCCAAAGTGTTAC
66 CAGAATATCACTCTTACAAGCCAGAATCCAAAGTGTTAC
* * *
175431 TCTTACAAGCCAGACAAAAT-AACGCTCTTACGAGCCAGATAGAATATCGCTCTTTCGAGCCAAA
1 TCTTACAAGCCAGACAAAATAAACGCTCTTACGAGCCAGACAGAACATCACTCTTTCGAGCCAAA
* *
175495 TAGAATATTACTCTTACAAGC
66 CAGAATATCACTCTTACAAGC
175516 TAAAATGCTA
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
103 57 0.76
104 18 0.24
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.23
Consensus pattern (104 bp):
TCTTACAAGCCAGACAAAATAAACGCTCTTACGAGCCAGACAGAACATCACTCTTTCGAGCCAAA
CAGAATATCACTCTTACAAGCCAGAATCCAAAGTGTTAC
Found at i:175489 original size:25 final size:25
Alignment explanation
Indices: 175274--175511 Score: 163
Period size: 25 Copynumber: 9.3 Consensus size: 25
175264 GAAAGAGTTA
* *
175274 GCTCTTACGAGCCCAGATAGAGTATC
1 GCTCTTACGAG-CCAGACAGAATATC
* * *
175300 GCTCTTACAAACCAGACAGAATAAC
1 GCTCTTACGAGCCAGACAGAATATC
* * * **
175325 GTTCTTACAAGCTAGACAGAATAAAG
1 GCTCTTACGAGCCAGACAGAAT-ATC
*
175351 GCTCTTACGAGCCAGACAGAACATC
1 GCTCTTACGAGCCAGACAGAATATC
* *
175376 ACTCTTTCGAGCCAGACAGAATATC
1 GCTCTTACGAGCCAGACAGAATATC
* * * * *
175401 ACTCTTTCAAGCCAGAATCCA-AAGTGTT
1 GCTCTTACGAGCCAG-A--CAGAA-TATC
* * * *
175429 ACTCTTACAAGCCAGACAAAATAAC
1 GCTCTTACGAGCCAGACAGAATATC
*
175454 GCTCTTACGAGCCAGATAGAATATC
1 GCTCTTACGAGCCAGACAGAATATC
* * * *
175479 GCTCTTTCGAGCCAAATAGAATATT
1 GCTCTTACGAGCCAGACAGAATATC
*
175504 ACTCTTAC
1 GCTCTTAC
175512 AAGCTAAAAT
Statistics
Matches: 171, Mismatches: 35, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
25 118 0.69
26 32 0.19
27 3 0.02
28 18 0.11
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (25 bp):
GCTCTTACGAGCCAGACAGAATATC
Found at i:177610 original size:21 final size:21
Alignment explanation
Indices: 177565--177617 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
177555 GAATTGAGAT
*** *
177565 TTCTATCGATACAACTTTGAG
1 TTCTATCGATACAACCCGGAC
177586 TTCTATCGATACAACCCGGAC
1 TTCTATCGATACAACCCGGAC
177607 TTCTATCGATA
1 TTCTATCGATA
177618 GAACAAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (21 bp):
TTCTATCGATACAACCCGGAC
Found at i:184684 original size:6 final size:6
Alignment explanation
Indices: 184653--184747 Score: 74
Period size: 6 Copynumber: 16.3 Consensus size: 6
184643 AGTGCATAAG
* *
184653 AAAAT- AAAAT- AAAATA AAAACT- -AAATA GAAATA AAAATA AAACTA
1 AAAATA AAAATA AAAATA AAAA-TA AAAATA AAAATA AAAATA AAAATA
* * * **
184698 AAAATA AAAATGA AAAA-C AAAATG AAAATG AAGCTA AAAATA AAAATA
1 AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
184746 AA
1 AA
184748 TGTACTAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
4 1 0.01
5 17 0.23
6 50 0.68
7 6 0.08
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:184686 original size:22 final size:21
Alignment explanation
Indices: 184654--184699 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
184644 GTGCATAAGA
184654 AAATAAAAT-AAAATAAAAACT
1 AAATAAAATAAAAAT-AAAACT
184675 AAATAGAAATAAAAATAAAACT
1 AAATA-AAATAAAAATAAAACT
184697 AAA
1 AAA
184700 AATAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
22 13 0.57
23 5 0.22
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.17
Consensus pattern (21 bp):
AAATAAAATAAAAATAAAACT
Found at i:184702 original size:18 final size:17
Alignment explanation
Indices: 184653--184747 Score: 88
Period size: 18 Copynumber: 5.5 Consensus size: 17
184643 AGTGCATAAG
184653 AAAATAAAAT-AAAATA
1 AAAATAAAATAAAAATA
*
184669 AAAACT-AAATAGAAATA
1 AAAA-TAAAATAAAAATA
184686 AAAATAAAACTAAAAATA
1 AAAATAAAA-TAAAAATA
*
184704 AAAATGAAAA-ACAAAATG
1 AAAAT-AAAATA-AAAATA
**
184722 AAAATGAAGCTAAAAATA
1 AAAAT-AAAATAAAAATA
184740 AAAATAAA
1 AAAATAAA
184748 TGTACTAATT
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
16 9 0.14
17 16 0.25
18 35 0.54
19 5 0.08
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:184767 original size:10 final size:10
Alignment explanation
Indices: 184754--184787 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
184744 TAAATGTACT
184754 AATTTTTTTG
1 AATTTTTTTG
184764 AA--TTTTTG
1 AATTTTTTTG
184772 AATTTTTTTG
1 AATTTTTTTG
184782 AATTTT
1 AATTTT
184788 CTAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (10 bp):
AATTTTTTTG
Found at i:187407 original size:14 final size:14
Alignment explanation
Indices: 187381--187413 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
187371 TAAAAAGGAA
187381 AAAAAATTAAAATAT
1 AAAAAATTAAAAT-T
187396 AAAAAATT-AAATT
1 AAAAAATTAAAATT
187409 AAAAA
1 AAAAA
187414 TGCAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAAATTAAAATT
Found at i:188414 original size:25 final size:23
Alignment explanation
Indices: 188386--188431 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
188376 GTTGGATCCA
188386 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
188411 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
188432 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:191900 original size:78 final size:78
Alignment explanation
Indices: 191771--191929 Score: 318
Period size: 78 Copynumber: 2.0 Consensus size: 78
191761 ACTTTATGTA
191771 AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
1 AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
191836 TAATAACAAAAAC
66 TAATAACAAAAAC
191849 AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
1 AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
191914 TAATAACAAAAAC
66 TAATAACAAAAAC
191927 AAT
1 AAT
191930 GAATGAATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (78 bp):
AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
TAATAACAAAAAC
Found at i:193468 original size:28 final size:29
Alignment explanation
Indices: 193361--193502 Score: 162
Period size: 29 Copynumber: 4.9 Consensus size: 29
193351 TAATTTTTTT
* * * *
193361 GAAAAATAGTGGCGAAATTGTAAAATTTG
1 GAAAACTAGTGGCAAAATTGTAAAATCTA
* *
193390 GAAAACAAGTGGCAAAATTGTAAACTCTA
1 GAAAACTAGTGGCAAAATTGTAAAATCTA
*
193419 AAAAACTAGTGGCAAAATTGTAAAATCTA
1 GAAAACTAGTGGCAAAATTGTAAAATCTA
* *
193448 GAAAA-TAGTGGCAAAACTGTAAAAAT-TT
1 GAAAACTAGTGGCAAAATTGT-AAAATCTA
*
193476 GAAAAATTAGTGGCAAAATTGTAAAAT
1 G-AAAACTAGTGGCAAAATTGTAAAAT
193503 AGTTGCAGTT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
28 16 0.16
29 67 0.69
30 14 0.14
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (29 bp):
GAAAACTAGTGGCAAAATTGTAAAATCTA
Found at i:194150 original size:3 final size:3
Alignment explanation
Indices: 194144--194181 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
194134 AATAAAACAA
*
194144 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
194182 GTATATTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:201553 original size:376 final size:384
Alignment explanation
Indices: 200849--201629 Score: 1256
Period size: 376 Copynumber: 2.0 Consensus size: 384
200839 AGGAAAGATC
*
200849 ATATACCGCTAGTAAAAGTCTTATGGAGAAATCATGGAATTAAGGAAGCTACTTGGGAACCAAAA
1 ATATACCGCTAGTAAAAGTCTTATGGAGAAATCATGGAATTAAAGAAGCTACTTGGGAACCAAAA
200914 GACTTGATACATCGACAATATCCCCATCTATTATGATCAGGTTATGATCAGGTAAATTTTGAGGA
66 GACTTGATACATCGACAATATCCCCATCTATTATGATC-------GA-CAGGTAAATTTTGAGGA
* *
200979 TGAAATTTATTTTTTTAGGAGGGTAGAGTTGTCACGCCATATAATTTATTTTATTTCCATTAGCT
123 TGAAATTTATTTTTTTAGGAGGGTAGAATTGTCACGCCACATAATTTATTTTATTTCCATTAGCT
201044 TTTGAACAAGTAAAGTAGTCTAGTGGTTAAAAGCTTAAATAATTTCCTTAAGGTCTTATGTTCAA
188 TTTGAACAAGTAAAGTAGTCTAGTGGTTAAAAGCTTAAATAATTTCCTTAAGGTCTTATGTTCAA
* * *
201109 TCCCCACATTTTAATACCCTAAACCTATAACTGTTTCCCAGTTAGGGTCTAGAAGTACTACCTTA
253 TCCCCACATTGTAATACCCTAAACCTATAACTATTTCCCAATTAGGGTCTAGAAGTACTACCTTA
201174 AC-A-AT-A-C-ATGACTCATAATTAAACTTACAAATTCTTACAAAAATATAAATAGAGAAAAAC
318 ACAACATGACCAATGACTCATAATTAAACTTACAAATTCTTACAAAAATATAAATAGAGAAAAAC
201234 AT
383 AT
* *
201236 ATATACCGCTAGTAAAAGTCTTATGGAGAAATCATGTAATTAAAGAAGCTACTTGGGAACTAAAA
1 ATATACCGCTAGTAAAAGTCTTATGGAGAAATCATGGAATTAAAGAAGCTACTTGGGAACCAAAA
*
201301 GACTTGATACGTCGACAATATCCCCATCTATTATGATC-A-A-GTAAATTTTGAGGATGAAATTT
66 GACTTGATACATCGACAATATCCCCATCTATTATGATCGACAGGTAAATTTTGAGGATGAAATTT
201363 ATTTTTTTAGGAGGGTAGAATTGTCACGCCACATAATTTATTTTATTTCCATTAGCTTTTGAACA
131 ATTTTTTTAGGAGGGTAGAATTGTCACGCCACATAATTTATTTTATTTCCATTAGCTTTTGAACA
201428 AGTAAAGTAGTCTAGTGGTTAAAAGCTTAAATAATTTCCTTAAGGTCTTATGTTCAATCCCCAC-
196 AGTAAAGTAGTCTAGTGGTTAAAAGCTTAAATAATTTCCTTAAGGTCTTATGTTCAATCCCCACA
*
201492 TCTGTAATACCTTAAACCTATAACTATTTCCCAATTAGGGTCTAGAAGTACTACCTTAACAATAC
261 T-TGTAATACCCTAAACCTATAACTATTTCCCAATTAGGGTCTAGAAGTACTACCTTAAC-A-AC
201557 ATGACTCATAATTATGACTCATAATTAAACTTACAAATTCTTACAAAAATATAAATAGAGAAAAA
323 ATGAC-C---A--ATGACTCATAATTAAACTTACAAATTCTTACAAAAATATAAATAGAGAAAAA
201622 CAT
382 CAT
201625 ATATA
1 ATATA
201630 TATAAATCAA
Statistics
Matches: 370, Mismatches: 10, Indels: 26
0.91 0.02 0.06
Matches are distributed among these distances:
375 1 0.00
376 203 0.55
377 1 0.00
379 2 0.01
380 2 0.01
381 1 0.00
383 1 0.00
387 99 0.27
389 60 0.16
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (384 bp):
ATATACCGCTAGTAAAAGTCTTATGGAGAAATCATGGAATTAAAGAAGCTACTTGGGAACCAAAA
GACTTGATACATCGACAATATCCCCATCTATTATGATCGACAGGTAAATTTTGAGGATGAAATTT
ATTTTTTTAGGAGGGTAGAATTGTCACGCCACATAATTTATTTTATTTCCATTAGCTTTTGAACA
AGTAAAGTAGTCTAGTGGTTAAAAGCTTAAATAATTTCCTTAAGGTCTTATGTTCAATCCCCACA
TTGTAATACCCTAAACCTATAACTATTTCCCAATTAGGGTCTAGAAGTACTACCTTAACAACATG
ACCAATGACTCATAATTAAACTTACAAATTCTTACAAAAATATAAATAGAGAAAAACAT
Found at i:201575 original size:13 final size:13
Alignment explanation
Indices: 201557--201583 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
201547 TTAACAATAC
201557 ATGACTCATAATT
1 ATGACTCATAATT
201570 ATGACTCATAATT
1 ATGACTCATAATT
201583 A
1 A
201584 AACTTACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (13 bp):
ATGACTCATAATT
Found at i:202846 original size:38 final size:38
Alignment explanation
Indices: 202762--202948 Score: 166
Period size: 37 Copynumber: 5.0 Consensus size: 38
202752 AATTCGTTAA
* *
202762 ACACCGGCACAAAGGCCTGCTAGGCATAAAGCTCGA-T
1 ACACCGGCACAAAGGCCTGCTAGGCACATAGCTCGATT
* * *
202799 ATCATCGGCACAAAGGCTTGCTAGGCACATAGCCCGATT
1 A-CACCGGCACAAAGGCCTGCTAGGCACATAGCTCGATT
* ** *
202838 ACACCGGCAC-GAGGCCTATTAGGCACATAGCCCGATT
1 ACACCGGCACAAAGGCCTGCTAGGCACATAGCTCGATT
* * ** *
202875 ACACTGACATGAA-GCCTGCTAGGCACATAGCTCAATT
1 ACACCGGCACAAAGGCCTGCTAGGCACATAGCTCGATT
* ** * *
202912 ACACCAGCATGAA-GCTTGCAAGGCACATAGCTCGATT
1 ACACCGGCACAAAGGCCTGCTAGGCACATAGCTCGATT
202949 CCTTTCAAAT
Statistics
Matches: 123, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
37 82 0.67
38 39 0.32
39 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.18
Consensus pattern (38 bp):
ACACCGGCACAAAGGCCTGCTAGGCACATAGCTCGATT
Found at i:219030 original size:37 final size:37
Alignment explanation
Indices: 218987--219082 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
218977 GCGCAAAGGC
* * * * *
218987 CTGCTAGGAACATAGCCTGATTACACTGGCATGAATA
1 CTGCTAGGCACATAGCCTGATTACACCGACACGAAGA
*
219024 CTGCTAGGCACATAG-CTCGATTACACCGACACGAAGC
1 CTGCTAGGCACATAGCCT-GATTACACCGACACGAAGA
219061 CTGCTAGGCACATAGCCTGATT
1 CTGCTAGGCACATAGCCTGATT
219083 CCTTTCATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
36 2 0.04
37 47 0.92
38 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (37 bp):
CTGCTAGGCACATAGCCTGATTACACCGACACGAAGA
Found at i:222380 original size:96 final size:96
Alignment explanation
Indices: 222199--222386 Score: 224
Period size: 96 Copynumber: 2.0 Consensus size: 96
222189 ATTTTTGCAA
**
222199 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAATATTTCA
* * *
222264 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAATCGAAGATAAAGAAACATTACCTCGATT
* * *
222295 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTG-AGCCTAGTGAGTTAAGGCACG-AAT-TT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCA-CCTAGTAAGTTAAGG--CGTAATATT
222357 TCAAAACTCGAA-ATAAA-AGAACATTACCTC
63 TCAAAA-TCGAAGATAAAGA-AACATTACCTC
222387 AATTTTTAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
95 2 0.03
96 67 0.85
97 8 0.10
98 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAATATTTCA
AAATCGAAGATAAAGAAACATTACCTCGATT
Found at i:222776 original size:30 final size:29
Alignment explanation
Indices: 222711--223113 Score: 271
Period size: 30 Copynumber: 13.7 Consensus size: 29
222701 TTCGGATATC
* * *
222711 CGAGAGTAAAATGGTAATTTTTGAAAGTTT
1 CGAGGGTAAAATGGGAATTTTTGGAAG-TT
222741 C-AGGGTCAAAAATGGGAATTTTT-GAAGTT
1 CGAGGGT--AAAATGGGAATTTTTGGAAGTT
* *
222770 CGAGGGTAAAATGGTAA-TTTTGGAAATT
1 CGAGGGTAAAATGGGAATTTTTGGAAGTT
** *
222798 TTAGGATCAAAAATGGG-ATTTTTGGAAGTT
1 CGAGGGT--AAAATGGGAATTTTTGGAAGTT
* * *
222828 TGAAGGTAAAATGGTAATTTTTGGAAGTTT
1 CGAGGGTAAAATGGGAATTTTTGGAAG-TT
*
222858 TG-GGGTCAAAAATGGG-ATTTTTGGAA-TT
1 CGAGGGT--AAAATGGGAATTTTTGGAAGTT
**
222886 CG-GGGTTAAAATGATAATTTTTGGAAGTTT
1 CGAGGG-TAAAATGGGAATTTTTGGAAG-TT
222916 CGA-GGTCAAAAT-GGAATTTTTGGAAGTT
1 CGAGGGT-AAAATGGGAATTTTTGGAAGTT
* *
222944 -AAGGGGTAAAATGGTAATTTTTGGAAGTTT
1 CGA-GGGTAAAATGGGAATTTTTGGAAG-TT
*
222974 TG-GGGTCAAAAATGGG-ATTTTTGGAAGTT
1 CGAGGGT--AAAATGGGAATTTTTGGAAGTT
* * *
223003 CGAGGGTGAAATGGTAATTTTTGAAAGTTT
1 CGAGGGTAAAATGGGAATTTTTGGAAG-TT
* **
223033 TG-GGGTAAAAAATAAG-ATTTTTGGAAGTT
1 CGAGGGT--AAAATGGGAATTTTTGGAAGTT
* *
223062 CGAGGGTCAAAAATGAG-ATTTTTAGAAGTT
1 CGAGGGT--AAAATGGGAATTTTTGGAAGTT
*
223092 CGAGGGGTAAAATGGTAATTTT
1 CGA-GGGTAAAATGGGAATTTT
223114 CAGACTGTTT
Statistics
Matches: 300, Mismatches: 41, Indels: 64
0.74 0.10 0.16
Matches are distributed among these distances:
27 11 0.04
28 54 0.18
29 82 0.27
30 117 0.39
31 36 0.12
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
CGAGGGTAAAATGGGAATTTTTGGAAGTT
Found at i:222779 original size:59 final size:59
Alignment explanation
Indices: 222711--223073 Score: 468
Period size: 59 Copynumber: 6.2 Consensus size: 59
222701 TTCGGATATC
* **
222711 CGAGAGTAAAATGGTAATTTTTGAAAGTTTCAGGGTCAAAAATGGGAATTTTT-GAAGTT
1 CGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGG-ATTTTTGGAAGTT
* * *
222770 CGAGGGTAAAATGGTAATTTTGGAAA-TTTTAGGATCAAAAATGGGATTTTTGGAAGTT
1 CGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
222828 TGAAGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAA-TT
1 CGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * * *
222886 CG-GGGTTAAAATGATAATTTTTGGAAGTTTCGAGGTC-AAAATGGAATTTTTGGAAGTT
1 CGAGGG-TAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
* *
222944 -AAGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGA-GGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
* * **
223003 CGAGGGTGAAATGGTAATTTTTGAAAGTTTTGGGGTAAAAAATAAGATTTTTGGAAGTT
1 CGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
223062 CGAGGGTCAAAA
1 CGAGGGT-AAAA
223074 ATGAGATTTT
Statistics
Matches: 267, Mismatches: 28, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
57 25 0.09
58 106 0.40
59 132 0.49
60 4 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:222959 original size:116 final size:118
Alignment explanation
Indices: 222716--223032 Score: 452
Period size: 116 Copynumber: 2.7 Consensus size: 118
222706 ATATCCGAGA
* **
222716 GTAAAATGGTAATTTTTGAAAGTTTCAGGGTCAAAAATGGGAATTTTT-GAAGTTCGAGGGTAAA
1 GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGG-ATTTTTGGAAGTTCGAGGGTAAA
* * *
222780 ATGGTAA-TTTTGGAAATTTTAGGATCAAAAATGGGATTTTTGGAAGTTTGAAG
65 ATGGTAATTTTTGGAAGTTTGAGGATCAAAAATGGAATTTTTGGAAGTTTGAAG
222833 GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAA-TTCG-GGGTTAAA
1 GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAA
*
222896 ATGATAATTTTTGGAAGTTTCGAGG-TC-AAAATGGAATTTTTGGAAG-TT-AAGGG
65 ATGGTAATTTTTGGAAGTTT-GAGGATCAAAAATGGAATTTTTGGAAGTTTGAA--G
*
222949 GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTGAAA
1 GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAA
*
223014 TGGTAATTTTTGAAAGTTT
66 TGGTAATTTTTGGAAGTTT
223033 TGGGGTAAAA
Statistics
Matches: 182, Mismatches: 10, Indels: 16
0.88 0.05 0.08
Matches are distributed among these distances:
114 2 0.01
115 5 0.03
116 90 0.49
117 79 0.43
118 6 0.03
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (118 bp):
GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAA
TGGTAATTTTTGGAAGTTTGAGGATCAAAAATGGAATTTTTGGAAGTTTGAAG
Found at i:224144 original size:15 final size:15
Alignment explanation
Indices: 224126--224164 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
224116 TATTATTGAT
224126 ATTATTATTAAT-GTC
1 ATTATTATT-ATCGTC
224141 ATTATTATTATCGTC
1 ATTATTATTATCGTC
*
224156 ATTAATATT
1 ATTATTATT
224165 GTTAATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (15 bp):
ATTATTATTATCGTC
Done.