Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007426.1 Hibiscus syriacus cultivar Beakdansim tig00020128_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: 276956
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4159 original size:19 final size:20
Alignment explanation
Indices: 4135--4182 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
4125 TCGCCAAGAG
4135 CATGTATCTTCA-TTAAAA-T
1 CATGTAT-TTCATTTAAAAGT
4154 CATGTATTTCATTTAAAAGT
1 CATGTATTTCATTTAAAAGT
4174 CATGTATTT
1 CATGTATTT
4183 TCAAAGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 13 0.48
20 10 0.37
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAGT
Found at i:10235 original size:19 final size:20
Alignment explanation
Indices: 10211--10250 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
10201 ATCTTTTTAT
10211 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
10230 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
10250 T
1 T
10251 ATTATTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:10753 original size:24 final size:25
Alignment explanation
Indices: 10703--10755 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
10693 TTGATGTTTC
*
10703 AAAGATAATGCCGTTTGAAGTTACA
1 AAAGATAATGCCGTTTGAAGTGACA
* *
10728 AAAGA-AATGTCGTTTGAAGTGCCA
1 AAAGATAATGCCGTTTGAAGTGACA
10752 AAAG
1 AAAG
10756 TTTTGTCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (25 bp):
AAAGATAATGCCGTTTGAAGTGACA
Found at i:15496 original size:19 final size:20
Alignment explanation
Indices: 15468--15507 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
15458 GGATAATAAT
15468 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
15488 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
15507 A
1 A
15508 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:15963 original size:19 final size:21
Alignment explanation
Indices: 15920--15971 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
15910 GAAACCCCTT
15920 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
15941 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
15960 TGAAGATACATG
1 TGAAAATACATG
15972 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:18802 original size:34 final size:31
Alignment explanation
Indices: 18745--18816 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
18735 CTTAGCTTGC
*
18745 TTTCTTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTGAATTTCTTCTTCTTTT-TGTCT
18776 TTTCATTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTC-TTTT-TGAA-TTTCTTCTTCTTTTTGTCT
18810 TTTCTTT
1 TTTCTTT
18817 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 8 0.22
34 20 0.56
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (31 bp):
TTTCTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:19109 original size:19 final size:20
Alignment explanation
Indices: 19077--19120 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
19067 AGGGGATAAT
19077 AAAT-ATAAGTAATGAAAAG
1 AAATAATAAGTAATGAAAAG
*
19096 AAATAATAAG-AATGAAATG
1 AAATAATAAGTAATGAAAAG
19115 AAATAA
1 AAATAA
19121 GGATGGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (20 bp):
AAATAATAAGTAATGAAAAG
Found at i:19575 original size:19 final size:21
Alignment explanation
Indices: 19532--19583 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
19522 GAAACCCCTT
*
19532 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGAATTTTAAA
19553 TGAAAATACAT-AATTTT-AA
1 TGAAAATACATGAATTTTAAA
*
19572 TGAAGATACATG
1 TGAAAATACATG
19584 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGAATTTTAAA
Found at i:24757 original size:2 final size:2
Alignment explanation
Indices: 24750--24799 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
24740 AGTTATTTTC
24750 AT AT 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 AT AT
24792 AT AT -T AT A
1 AT AT AT AT A
24800 CCTATAGTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32320 original size:21 final size:21
Alignment explanation
Indices: 32288--32346 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
32278 CCTTGGCTTG
*
32288 CTTTCTCTTTTTCTTT-TCTT
1 CTTTGTCTTTTTCTTTCTCTT
32308 CTTT-TCTAATTTT-TTTCTCTT
1 CTTTGTCT--TTTTCTTTCTCTT
32329 CTTTGTCTTTTTCTTTCT
1 CTTTGTCTTTTTCTTTCT
32347 TTTGCACTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 17 0.50
22 3 0.09
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.73
Consensus pattern (21 bp):
CTTTGTCTTTTTCTTTCTCTT
Found at i:33087 original size:19 final size:20
Alignment explanation
Indices: 33050--33097 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
33040 AACCCCTTTG
*
33050 AAATACATGTTTTTAAATGA
1 AAATACATGATTTTAAATGA
33070 AAATACATGATTTT-AATGA
1 AAATACATGATTTTAAATGA
*
33089 AGATACATG
1 AAATACATG
33098 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
AAATACATGATTTTAAATGA
Found at i:34822 original size:82 final size:79
Alignment explanation
Indices: 34655--34863 Score: 175
Period size: 79 Copynumber: 2.6 Consensus size: 79
34645 ATCATCATGT
* * * *
34655 AGCACATCTTGCACTCATATTAAACAAAACATCATGTTTATCCTTTATTTTAATTAACTCATGTG
1 AGCACGTCTTGCACTCATATTAAACAAAACAACATGTTTATCATTTATTATAATTAACTCATGTG
* * *
34720 TATTCCCATTGTTA
66 CATTCACATTGATA
* * * ** * *
34734 AACACGTCTTGCACTCTTATTCAACATGACAACATGTTTTTCATTTAATTATAATTACCATTCAT
1 AGCACGTCTTGCACTCATATTAAACAAAACAACATGTTTATCATTT-ATTATAATTA--ACTCAT
*
34799 GTGCATTCATATTGATA
63 GTGCATTCACATTGATA
* * * * * * *
34816 AGCACGTTTTTTGCATTTATATTCAACATAACAGCATGTTTATAATTT
1 AGCACG--TCTTGCACTCATATTAAACAAAACAACATGTTTATCATTT
34864 GTTTTGTTAA
Statistics
Matches: 101, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
79 37 0.37
80 9 0.09
82 23 0.23
84 32 0.32
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.41
Consensus pattern (79 bp):
AGCACGTCTTGCACTCATATTAAACAAAACAACATGTTTATCATTTATTATAATTAACTCATGTG
CATTCACATTGATA
Found at i:34935 original size:28 final size:28
Alignment explanation
Indices: 34895--34948 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
34885 CTCACATTCT
34895 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
34923 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
34949 AGTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:36523 original size:21 final size:22
Alignment explanation
Indices: 36497--36545 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
36487 ATTCATCCTG
36497 AAAAAA-AAATTCCGAAAATTA
1 AAAAAACAAATTCCGAAAATTA
*
36518 AAAAAACAAATTCGGAAAATTA
1 AAAAAACAAATTCCGAAAATTA
36540 AAAAAA
1 AAAAAA
36546 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAAAACAAATTCCGAAAATTA
Found at i:39309 original size:28 final size:28
Alignment explanation
Indices: 39269--39322 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
39259 CTCACATTCA
39269 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
39297 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
39323 AGTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:59183 original size:24 final size:24
Alignment explanation
Indices: 59156--59210 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
59146 CCAACTTTTC
59156 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
59179 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
59203 CTTCTTTT
1 TTTCTTTT
59211 CTGATTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:64852 original size:36 final size:35
Alignment explanation
Indices: 64779--64882 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 35
64769 ATTTATAAGT
* * *
64779 TGGTGATAATATAAGCGTGATATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
**
64814 TGGTGATGATATAGGCGTGATGATGGTGATGGTCTA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAATA
64850 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGA
64883 CAGATTGTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 19 0.31
36 42 0.69
ACGTcount: A:0.27, C:0.04, G:0.38, T:0.32
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAATA
Found at i:66316 original size:10 final size:10
Alignment explanation
Indices: 66297--66337 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
66287 AGTGCTTCAA
66297 CTTTCTTTTT
1 CTTTCTTTTT
66307 CTTTTCTTTTT
1 C-TTTCTTTTT
66318 CTTTCTTTTT
1 CTTTCTTTTT
66328 CTTTCTTTTT
1 CTTTCTTTTT
66338 GAGTGCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:66323 original size:21 final size:20
Alignment explanation
Indices: 66297--66337 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
66287 AGTGCTTCAA
66297 CTTTCTTTTTCTTTTCTTTTT
1 CTTTCTTTTTC-TTTCTTTTT
66318 CTTTCTTTTTCTTTCTTTTT
1 CTTTCTTTTTCTTTCTTTTT
66338 GAGTGCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
CTTTCTTTTTCTTTCTTTTT
Found at i:66364 original size:23 final size:24
Alignment explanation
Indices: 66325--66378 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
66315 TTTCTTTCTT
*
66325 TTTCTTTCTTTTTGAGTGCTTTCAA
1 TTTC-TTCTTTTTGAGTACTTTCAA
* *
66350 TTTCTTC-TTTTGAGTACTTTGAT
1 TTTCTTCTTTTTGAGTACTTTCAA
66373 TTTCTT
1 TTTCTT
66379 TGCTGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 19 0.73
24 3 0.12
25 4 0.15
ACGTcount: A:0.11, C:0.15, G:0.11, T:0.63
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTACTTTCAA
Found at i:71163 original size:23 final size:25
Alignment explanation
Indices: 71115--71165 Score: 88
Period size: 23 Copynumber: 2.1 Consensus size: 25
71105 CTTTTATTTT
71115 TTTTCTTCTTTTTGAGTGCTTGCAA
1 TTTTCTTCTTTTTGAGTGCTTGCAA
71140 TTTTCTTC-TTTTGAGT-CTTGCAA
1 TTTTCTTCTTTTTGAGTGCTTGCAA
71163 TTT
1 TTT
71166 CTTTGCTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 10 0.38
24 8 0.31
25 8 0.31
ACGTcount: A:0.12, C:0.16, G:0.14, T:0.59
Consensus pattern (25 bp):
TTTTCTTCTTTTTGAGTGCTTGCAA
Found at i:74617 original size:19 final size:20
Alignment explanation
Indices: 74593--74635 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
74583 AGCATTTATC
*
74593 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
74612 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
74632 TTCA
1 TTCA
74636 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:77262 original size:24 final size:20
Alignment explanation
Indices: 77209--77266 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
77199 TTTCCCTTGA
*
77209 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
77229 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
77252 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
77267 CCATCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:87785 original size:19 final size:20
Alignment explanation
Indices: 87744--87794 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
87734 GAAACCCCTT
*
87744 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
87764 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
87783 TGAAGATACATG
1 TGAAAATACATG
87795 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:88739 original size:30 final size:31
Alignment explanation
Indices: 88699--88758 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
88689 ACATGCTGCC
**
88699 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
88730 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
88759 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:90985 original size:27 final size:27
Alignment explanation
Indices: 90955--91023 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
90945 TGAACTTCTC
*
90955 TTTTTATTTTCTTTTCTTCTTTTCTGA
1 TTTTTCTTTTCTTTTCTTCTTTTCTGA
*
90982 TTTTTCTGTTCTTTTCTTCTTTTCTGA
1 TTTTTCTTTTCTTTTCTTCTTTTCTGA
91009 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCTTTT
91024 TGCACTCTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTTCTTTTCTTTTCTTCTTTTCTGA
Found at i:90988 original size:9 final size:10
Alignment explanation
Indices: 90964--91015 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 10
90954 CTTTTTATTT
90964 TCTTTTCT--
1 TCTTTTCTGA
90972 TCTTTTCTGA
1 TCTTTTCTGA
*
90982 T-TTTTCTGT
1 TCTTTTCTGA
90991 TCTTTTCT--
1 TCTTTTCTGA
90999 TCTTTTCTGA
1 TCTTTTCTGA
91009 T-TTTTCT
1 TCTTTTCT
91016 TTTCTTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
8 16 0.42
9 14 0.37
10 8 0.21
ACGTcount: A:0.04, C:0.19, G:0.06, T:0.71
Consensus pattern (10 bp):
TCTTTTCTGA
Found at i:90993 original size:14 final size:14
Alignment explanation
Indices: 90971--91020 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
90961 TTTTCTTTTC
90971 TTCTTTTCTGATTT
1 TTCTTTTCTGATTT
*
90985 TTCTGTTCT--TTT
1 TTCTTTTCTGATTT
90997 CTTCTTTTCTGATTT
1 -TTCTTTTCTGATTT
91012 TTCTTTTCT
1 TTCTTTTCT
91021 TTTTGCACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 3 0.10
13 8 0.26
14 17 0.55
15 3 0.10
ACGTcount: A:0.04, C:0.18, G:0.06, T:0.72
Consensus pattern (14 bp):
TTCTTTTCTGATTT
Found at i:91402 original size:20 final size:21
Alignment explanation
Indices: 91365--91403 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
91355 GATGGTCTTG
*
91365 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
91386 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
91404 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:91782 original size:19 final size:20
Alignment explanation
Indices: 91741--91791 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
91731 GAAACCCCTT
*
91741 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
91761 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
91780 TGAAGATACATG
1 TGAAAATACATG
91792 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:102719 original size:20 final size:19
Alignment explanation
Indices: 102690--102729 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
102680 AAACCATTTC
* *
102690 ATTAGTTCATATGCATTCAT
1 ATTAGCTCATAAGC-TTCAT
102710 ATTAGCTCATAAGCTTCAT
1 ATTAGCTCATAAGCTTCAT
102729 A
1 A
102730 CATTATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (19 bp):
ATTAGCTCATAAGCTTCAT
Found at i:105556 original size:2 final size:2
Alignment explanation
Indices: 105549--105656 Score: 209
Period size: 2 Copynumber: 54.5 Consensus size: 2
105539 TGGCAGCGGA
105549 AT AT 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 AT AT
105591 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
105632 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 A
105657 AGTTTGATGT
Statistics
Matches: 105, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 104 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:106170 original size:165 final size:165
Alignment explanation
Indices: 105898--106225 Score: 620
Period size: 165 Copynumber: 2.0 Consensus size: 165
105888 GAACCAATGT
*
105898 GAGAGCAAAGACCCAGACTTTATATTGCTTCTTTAAGGGATGGTAATAAGGACTTGAACCCACTA
1 GAGAGCAAAGACCCAGACTTTATATTACTTCTTTAAGGGATGGTAATAAGGACTTGAACCCACTA
105963 TCTATATAGAGATAGGAACCACAAGTATCAAGGGGAAGGGGTTGACACCACAAGTATTAAAATAC
66 TCTATATAGAGATAGGAACCACAAGTATCAAGGGGAAGGGGTTGACACCACAAGTATTAAAATAC
106028 TTGATAAGTCGATAAAAGTCACAAGGACTTAAGAA
131 TTGATAAGTCGATAAAAGTCACAAGGACTTAAGAA
*
106063 GAGAGCAAAGACCCAGACTTTATATTACTTCTTTAAGGGATGGTAATAAGGACTTGGACCCACTA
1 GAGAGCAAAGACCCAGACTTTATATTACTTCTTTAAGGGATGGTAATAAGGACTTGAACCCACTA
* *
106128 TCTATATGGAGATAGGAACCACAAGTATCAAGGGGAAGGGGTTGACGCCACAAGTATTAAAATAC
66 TCTATATAGAGATAGGAACCACAAGTATCAAGGGGAAGGGGTTGACACCACAAGTATTAAAATAC
106193 TTGATAAGTCGATAAAAGTCACAAGGACTTAAG
131 TTGATAAGTCGATAAAAGTCACAAGGACTTAAG
106226 CAAAGAGAAT
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 159 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (165 bp):
GAGAGCAAAGACCCAGACTTTATATTACTTCTTTAAGGGATGGTAATAAGGACTTGAACCCACTA
TCTATATAGAGATAGGAACCACAAGTATCAAGGGGAAGGGGTTGACACCACAAGTATTAAAATAC
TTGATAAGTCGATAAAAGTCACAAGGACTTAAGAA
Found at i:110214 original size:14 final size:14
Alignment explanation
Indices: 110195--110227 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
110185 AGTGCTTCAA
110195 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
110209 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
110223 CTTTT
1 CTTTT
110228 TTGAGTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:110288 original size:22 final size:23
Alignment explanation
Indices: 110221--110292 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
110211 TTTCTTTTTC
110221 TTCTT-TTTTGAGTGCTTTCAAT
1 TTCTTCTTTTGAGTGCTTTCAAT
*
110243 TTTTTCTTTTGAGTGCTTTCAAT
1 TTCTTCTTTTGAGTGCTTTCAAT
110266 TTCTTCTTTTGAGTGC-TTCAAT
1 TTCTTCTTTTGAGTGCTTTCAAT
110288 TTCTT
1 TTCTT
110293 TGCTGATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.32
23 32 0.68
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.60
Consensus pattern (23 bp):
TTCTTCTTTTGAGTGCTTTCAAT
Found at i:111619 original size:157 final size:157
Alignment explanation
Indices: 111328--111643 Score: 550
Period size: 158 Copynumber: 2.0 Consensus size: 157
111318 TGATGGCGAT
111328 GAAACAAAAAAAAGGATGGTTGTGATGATAGTATCTTGAAGATGCTCAAAGAAGAACCATGCTAT
1 GAAACAAAAAAAAGGATGGTTGTGATGATAGTATCTTGAAGATGCTCAAAGAAGAACCATGCTAT
111393 AGAGAGCAAAGAACAATCTTTTATTGTTTCTTCAAGGGTGGTGTTAAGTACTTTGAACCACTAGT
66 AGAGAGCAAAGAACAATCTTTTA-T-TTTCTTCAAGGGTGGTGTTAAGTACTTTGAACCACTAGT
111458 TATATGAA-TAGGAACTAGAAGTATCAAG
129 TATATGAACTAGGAACTAGAAGTATCAAG
111486 GAAACAAAAAAAAGGATGGTTGTGATGATAGTATCTTGAAGAATGCTCAAAGAAGAACCAATGCT
1 GAAACAAAAAAAAGGATGGTTGTGATGATAGTATCTTGAAG-ATGCTCAAAGAAGAACC-ATGCT
111551 ATAGAGAGC-AAGAACCAATC-TTTA-TTTCTTCAAGGGGTGGTGTTAAGTACTTTGAACCACTA
64 ATAGAGAGCAAAGAA-CAATCTTTTATTTTCTTCAA-GGGTGGTGTTAAGTACTTTGAACCACTA
111613 GTTATATGAACTAGGAACTAGAAGTATCAAG
127 GTTATATGAACTAGGAACTAGAAGTATCAAG
111644 ATGAAAGAAG
Statistics
Matches: 153, Mismatches: 0, Indels: 10
0.94 0.00 0.06
Matches are distributed among these distances:
156 9 0.06
157 38 0.25
158 61 0.40
159 26 0.17
160 19 0.12
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (157 bp):
GAAACAAAAAAAAGGATGGTTGTGATGATAGTATCTTGAAGATGCTCAAAGAAGAACCATGCTAT
AGAGAGCAAAGAACAATCTTTTATTTTCTTCAAGGGTGGTGTTAAGTACTTTGAACCACTAGTTA
TATGAACTAGGAACTAGAAGTATCAAG
Found at i:113926 original size:13 final size:13
Alignment explanation
Indices: 113904--113933 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
113894 ACTAAACACC
113904 TTTC-ACATACCT
1 TTTCAACATACCT
113916 TTTCAACATACCT
1 TTTCAACATACCT
113929 TTTCA
1 TTTCA
113934 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:114743 original size:28 final size:28
Alignment explanation
Indices: 114703--114761 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
114693 TTGACAAGTA
114703 CTGATGTCCTCGAATTTATAAGTTTGGG
1 CTGATGTCCTCGAATTTATAAGTTTGGG
114731 CTGATGTCCTCGAATTTATAAGTTTGGG
1 CTGATGTCCTCGAATTTATAAGTTTGGG
114759 CTG
1 CTG
114762 CAAATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.39
Consensus pattern (28 bp):
CTGATGTCCTCGAATTTATAAGTTTGGG
Found at i:119030 original size:10 final size:9
Alignment explanation
Indices: 119016--119062 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 9
119006 TTTTGAATTC
119016 TTTTTCTTT
1 TTTTTCTTT
119025 TCTTTTCTTT
1 T-TTTTCTTT
119035 TTTTTC--T
1 TTTTTCTTT
*
119042 TTTGTCTTT
1 TTTTTCTTT
119051 TTCTTTCTTT
1 TT-TTTCTTT
119061 TT
1 TT
119063 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
7 6 0.19
9 9 0.28
10 17 0.53
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:119062 original size:26 final size:25
Alignment explanation
Indices: 119013--119062 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
119003 CTTTTTTGAA
119013 TTCTTTTTCTTTTCTTTTCTTTTTT
1 TTCTTTTTCTTTTCTTTTCTTTTTT
119038 TTCTTTTGTCTTTT-TCTTTCTTTTT
1 TTCTTTT-TCTTTTCT-TTTCTTTTT
119063 GCACTCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (25 bp):
TTCTTTTTCTTTTCTTTTCTTTTTT
Found at i:119249 original size:21 final size:22
Alignment explanation
Indices: 119225--119275 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
119215 TTAATAAGGG
* *
119225 TAATAATATAA-GTAATGAATA
1 TAATAATAGAATGAAATGAATA
119246 TAATAATAGAATGAAATGAATA
1 TAATAATAGAATGAAATGAATA
119268 -AA-AATAGA
1 TAATAATAGA
119276 GAGGGCTGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 12 0.44
22 9 0.33
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (22 bp):
TAATAATAGAATGAAATGAATA
Found at i:122821 original size:23 final size:25
Alignment explanation
Indices: 122769--122823 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
122759 TTCTTTTCTT
*
122769 TTTTCTTCCTCTTTGAGTGTTTTCA
1 TTTTCTTCCTCTTTGAGTGCTTTCA
* *
122794 ATTTCTT-CT-TTTGAGTGCTTTGA
1 TTTTCTTCCTCTTTGAGTGCTTTCA
122817 TTTTCTT
1 TTTTCTT
122824 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 2 0.08
25 6 0.23
ACGTcount: A:0.09, C:0.16, G:0.13, T:0.62
Consensus pattern (25 bp):
TTTTCTTCCTCTTTGAGTGCTTTCA
Found at i:126576 original size:24 final size:23
Alignment explanation
Indices: 126549--126594 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
126539 ATAGGCGTGA
* *
126549 TATAGTAATGGAATATGGTGATGT
1 TATAGGAAT-GAAAATGGTGATGT
*
126573 TATAGGCATGAAAATGGTGATG
1 TATAGGAATGAAAATGGTGATG
126595 GAAGGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (23 bp):
TATAGGAATGAAAATGGTGATGT
Found at i:133598 original size:48 final size:49
Alignment explanation
Indices: 133510--133614 Score: 167
Period size: 48 Copynumber: 2.2 Consensus size: 49
133500 CTATCTGTTC
*
133510 ATCACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCC
1 ATCACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCA
* * *
133559 ATTACCATCTTCTATCACCA-TTTCACGCCTATATCATCACCATCTTCA
1 ATCACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCA
133607 ATCACCAT
1 ATCACCAT
133615 TTCACACCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 33 0.65
49 18 0.35
ACGTcount: A:0.28, C:0.38, G:0.02, T:0.32
Consensus pattern (49 bp):
ATCACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCA
Found at i:133601 original size:35 final size:35
Alignment explanation
Indices: 133562--133636 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
133552 ATCTTCCATT
* *
133562 ACCATCTTCTATCACCATTTCACGCCTATATCATC
1 ACCATCTTCAATCACCATTTCACACCTATATCATC
133597 ACCATCTTCAATCACCATTTCACACCTATATCATC
1 ACCATCTTCAATCACCATTTCACACCTATATCATC
133632 ACCAT
1 ACCAT
133637 TACCTTACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.37, G:0.01, T:0.32
Consensus pattern (35 bp):
ACCATCTTCAATCACCATTTCACACCTATATCATC
Found at i:133612 original size:13 final size:11
Alignment explanation
Indices: 133507--133637 Score: 70
Period size: 13 Copynumber: 11.1 Consensus size: 11
133497 ATACTATCTG
133507 TTCATCACCAT
1 TTCATCACCAT
133518 CTTCCATCACCATT
1 -TT-CATCACCA-T
*
133532 TTCA-CGCCTAT
1 TTCATCACC-AT
**
133543 AACATCACCAT
1 TTCATCACCAT
*
133554 CTTCCATTACCAT
1 -TT-CATCACCAT
133567 CTTCTATCACCAT
1 -TTC-ATCACCAT
*
133580 TTCA-CGCCTAT
1 TTCATCACC-AT
*
133591 ATCATCACCAT
1 TTCATCACCAT
133602 CTTCAATCACCAT
1 -TTC-ATCACCAT
133615 TTCA-CACCTAT
1 TTCATCACC-AT
*
133626 ATCATCACCAT
1 TTCATCACCAT
133637 T
1 T
133638 ACCTTACAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
10 7 0.08
11 24 0.26
12 24 0.26
13 36 0.39
14 1 0.01
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.34
Consensus pattern (11 bp):
TTCATCACCAT
Found at i:134038 original size:21 final size:21
Alignment explanation
Indices: 134014--134054 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
134004 TAAAAACAAC
134014 AAAAAGAGAAAA-AGAAAGAAT
1 AAAAAGA-AAAAGAGAAAGAAT
134035 AAAAAGAAAAAGAGAAAGAA
1 AAAAAGAAAAAGAGAAAGAA
134055 AAGACTCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAAAGAAAAAGAGAAAGAAT
Found at i:134303 original size:15 final size:16
Alignment explanation
Indices: 134265--134304 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
134255 ATTTTCCTAC
134265 TATTTCATTTCTTTAT
1 TATTTCATTTCTTTAT
* *
134281 TCTTTCATTT-TTTCT
1 TATTTCATTTCTTTAT
134296 TATTTCATT
1 TATTTCATT
134305 ACCATATCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTCATTTCTTTAT
Found at i:137980 original size:13 final size:13
Alignment explanation
Indices: 137962--138032 Score: 67
Period size: 13 Copynumber: 5.7 Consensus size: 13
137952 ACTATCTGTT
137962 CATCACCATCTTC
1 CATCACCATCTTC
*
137975 CATCACCAT-TTT
1 CATCACCATCTTC
* * **
137987 CA-CGCC-TATAA
1 CATCACCATCTTC
137998 CATCACCATCTTC
1 CATCACCATCTTC
138011 CATCACCATCTTC
1 CATCACCATCTTC
*
138024 TATCACCAT
1 CATCACCAT
138033 TTCACGCCTA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.13
12 7 0.15
13 32 0.70
ACGTcount: A:0.27, C:0.41, G:0.01, T:0.31
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:138057 original size:35 final size:35
Alignment explanation
Indices: 138011--138089 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
138001 CACCATCTTC
*
138011 CATCACCATCTTCTATCACCATTTCACGCCTATAT
1 CATCACCATCTTCTATCACCATTTCACACCTATAT
*
138046 CATCACTATCTTCTATCACCATTTCACACCTATAT
1 CATCACCATCTTCTATCACCATTTCACACCTATAT
138081 CATCACCAT
1 CATCACCAT
138090 TACCTTACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.28, C:0.37, G:0.01, T:0.34
Consensus pattern (35 bp):
CATCACCATCTTCTATCACCATTTCACACCTATAT
Found at i:138057 original size:48 final size:49
Alignment explanation
Indices: 137944--138067 Score: 171
Period size: 48 Copynumber: 2.6 Consensus size: 49
137934 TTCTTATTTT
* *
137944 TATAAGAT-ACTATCTGTTCATCACCATCTTCCATCACCATTTTCACGCC
1 TATAACATCACTATCT-TCCATCACCATCTTCCATCACCATTTTCACGCC
* *
137993 TATAACATCACCATCTTCCATCACCATCTTCTATCACCA-TTTCACGCC
1 TATAACATCACTATCTTCCATCACCATCTTCCATCACCATTTTCACGCC
* *
138041 TATATCATCACTATCTTCTATCACCAT
1 TATAACATCACTATCTTCCATCACCAT
138068 TTCACACCTA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
48 33 0.49
49 28 0.42
50 6 0.09
ACGTcount: A:0.27, C:0.35, G:0.03, T:0.35
Consensus pattern (49 bp):
TATAACATCACTATCTTCCATCACCATCTTCCATCACCATTTTCACGCC
Found at i:143462 original size:19 final size:20
Alignment explanation
Indices: 143438--143488 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
143428 CGGCCAAGAG
* *
143438 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
143457 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
143477 CATGTATTTTCA
1 CATGTATTTTCA
143489 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:144241 original size:5 final size:5
Alignment explanation
Indices: 144214--144280 Score: 70
Period size: 5 Copynumber: 13.8 Consensus size: 5
144204 AGAAAAAGAC
* *
144214 AAAAG AAGAG AAAA- AAATCAG AAAAG --AAG AAAAG AAAAG AAAAG GAAA-
1 AAAAG AAAAG AAAAG AAA--AG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
144262 AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAA
144281 AGAGAAAGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.06
4 6 0.12
5 39 0.75
6 1 0.02
7 3 0.06
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:144244 original size:19 final size:16
Alignment explanation
Indices: 144219--144288 Score: 65
Period size: 14 Copynumber: 4.2 Consensus size: 16
144209 AAGACAAAAG
144219 AAGAGAAAAAAATCAGAA
1 AAGAGAAAAAAA--AGAA
144237 AAGAAGAAAAGAAAAGAA
1 AAG-AGAAAA-AAAAGAA
144255 AAG-G-AAAAAAAGAA
1 AAGAGAAAAAAAAGAA
144269 AAGA-AAAGAAAAAGAGA
1 AAGAGAAA-AAAAAGA-A
144286 AAG
1 AAG
144289 CAAGCTAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
14 10 0.22
15 5 0.11
16 8 0.17
17 4 0.09
18 10 0.22
19 6 0.13
20 3 0.07
ACGTcount: A:0.76, C:0.01, G:0.21, T:0.01
Consensus pattern (16 bp):
AAGAGAAAAAAAAGAA
Found at i:144249 original size:24 final size:24
Alignment explanation
Indices: 144197--144280 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
144187 TTGGAGTGCA
* *
144197 AAAAG-AAAGAAAAAG-ACAAAAG
1 AAAAGAAAAGAAAAGGAAAAAAAG
* *
144219 AAGAGAAAA-AAATCA-GAAAAGAAG
1 AAAAGAAAAGAAA--AGGAAAAAAAG
144243 AAAAGAAAAGAAAAGGAAAAAAAG
1 AAAAGAAAAGAAAAGGAAAAAAAG
144267 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
144281 AGAGAAAGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
22 7 0.14
23 5 0.10
24 36 0.71
25 3 0.06
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.01
Consensus pattern (24 bp):
AAAAGAAAAGAAAAGGAAAAAAAG
Found at i:144267 original size:14 final size:13
Alignment explanation
Indices: 144197--144287 Score: 55
Period size: 13 Copynumber: 6.8 Consensus size: 13
144187 TTGGAGTGCA
144197 AAAAGAAAGAAAAAG
1 AAAA-AAAG-AAAAG
144212 ACAAAAGAAGAGAAA-
1 A-AAAA-AAGA-AAAG
**
144227 AAAATCAGAAAAG
1 AAAAAAAGAAAAG
*
144240 AAGAAAAGAAAAG
1 AAAAAAAGAAAAG
*
144253 --AAAAGGAAAA-
1 AAAAAAAGAAAAG
144263 AAAGAAAAGAAAAG
1 AAA-AAAAGAAAAG
*
144277 AAAAAGAGAAA
1 AAAAAAAGAAA
144288 GCAAGCTAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
11 8 0.14
12 4 0.07
13 28 0.47
14 6 0.10
15 4 0.07
16 9 0.15
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.01
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:144286 original size:18 final size:17
Alignment explanation
Indices: 144197--144287 Score: 87
Period size: 18 Copynumber: 5.2 Consensus size: 17
144187 TTGGAGTGCA
*
144197 AAAAG-AAAGAAAAAGAC
1 AAAAGAAAAGAAAAA-AG
*
144214 AAAAGAAGAGAAAAAA-
1 AAAAGAAAAGAAAAAAG
**
144230 ATCAGAAAAGAAGAAAAG
1 AAAAGAAAAGAA-AAAAG
144248 AAAAGAAAAGGAAAAAAAG
1 AAAAGAAAA-G-AAAAAAG
144267 AAAAGAAAAGAAAAAGAG
1 AAAAGAAAAGAAAAA-AG
144285 AAA
1 AAA
144288 GCAAGCTAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
16 9 0.15
17 15 0.24
18 21 0.34
19 15 0.24
20 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.01
Consensus pattern (17 bp):
AAAAGAAAAGAAAAAAG
Found at i:146521 original size:23 final size:23
Alignment explanation
Indices: 146476--146521 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
146466 TTATACCTAT
*
146476 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
146499 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
146522 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:149127 original size:19 final size:21
Alignment explanation
Indices: 149103--149154 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
149093 CGGCCAAGAG
*
149103 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
149122 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
149143 CATGTATTTTCA
1 CATGTATTTTCA
149155 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:149920 original size:21 final size:22
Alignment explanation
Indices: 149863--149921 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
149853 GAGTGCAAAA
*
149863 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAGAAAAAGAGAAAAGAAG
**
149885 AGAAA-AAAATCAGAAAAGAAG
1 AGAAAGAAAAAGAGAAAAGAAG
149906 A-AAAGAAAAAGAGAAA
1 AGAAAGAAAAAGAGAAA
149922 GCAAGCCAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.10
21 23 0.74
22 5 0.16
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (22 bp):
AGAAAGAAAAAGAGAAAAGAAG
Found at i:153157 original size:19 final size:20
Alignment explanation
Indices: 153133--153183 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
153123 CGTCCAAGAG
* *
153133 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
153152 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
153172 CATGTATTTTCA
1 CATGTATTTTCA
153184 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:153925 original size:29 final size:29
Alignment explanation
Indices: 153892--153965 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
153882 ATTGGAGTGC
* *
153892 AAAAAGAAAGAAAAAG-ACAAAAGAAGAG
1 AAAAAAAAAGAAAAAGAACAAAAGAAAAG
*
153920 AAAAAAATAAG-AAAAGAAGAAAAGAAAAG
1 AAAAAAA-AAGAAAAAGAACAAAAGAAAAG
*
153949 AAAAGAAAAAGAGAAAG
1 AAAA-AAAAAGAAAAAG
153966 CAAGCCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 11 0.29
29 20 0.53
30 7 0.18
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (29 bp):
AAAAAAAAAGAAAAAGAACAAAAGAAAAG
Found at i:153926 original size:13 final size:13
Alignment explanation
Indices: 153893--153952 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
153883 TTGGAGTGCA
153893 AAAAGAAAGAAAAAG
1 AAAA-AAAG-AAAAG
153908 ACAAAAGAAGAGAAA-
1 A-AAAA-AAGA-AAAG
*
153923 AAAATAAGAAAAG
1 AAAAAAAGAAAAG
*
153936 AAGAAAAGAAAAG
1 AAAAAAAGAAAAG
153949 AAAA
1 AAAA
153953 GAAAAAGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
12 3 0.08
13 18 0.49
14 3 0.08
15 4 0.11
16 9 0.24
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:153936 original size:5 final size:5
Alignment explanation
Indices: 153910--153957 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
153900 AGAAAAAGAC
* *
153910 AAAAG AAGAG AAAAA AATAAG AAAAG --AAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
153958 AGAGAAAGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
5 29 0.81
6 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:153963 original size:18 final size:17
Alignment explanation
Indices: 153893--153964 Score: 76
Period size: 18 Copynumber: 4.2 Consensus size: 17
153883 TTGGAGTGCA
*
153893 AAAAG-AAAGAAAAAGAC
1 AAAAGAAAAGAAAAA-AG
*
153910 AAAAGAAGAGAAAAAA-
1 AAAAGAAAAGAAAAAAG
*
153926 ATAAGAAAAGAAGAAAAG
1 AAAAGAAAAGAA-AAAAG
153944 AAAAGAAAAGAAAAAGAG
1 AAAAGAAAAGAAAAA-AG
153962 AAA
1 AAA
153965 GCAAGCCAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
16 10 0.21
17 13 0.28
18 24 0.51
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (17 bp):
AAAAGAAAAGAAAAAAG
Found at i:156533 original size:23 final size:22
Alignment explanation
Indices: 156500--156542 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
156490 TTAGTACTGG
*
156500 AAACAATATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
156523 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
156543 AAAGGAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:158491 original size:11 final size:12
Alignment explanation
Indices: 158461--158506 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
158451 TTGGTGCTGG
158461 AAACAAGATAAA
1 AAACAAGATAAA
* *
158473 AAATAAGAT-TA
1 AAACAAGATAAA
158484 AAACAAGATAAA
1 AAACAAGATAAA
*
158496 TAA-AAGATAAA
1 AAACAAGATAAA
158507 GGAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:158491 original size:23 final size:22
Alignment explanation
Indices: 158461--158503 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
158451 TTGGTGCTGG
158461 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
158484 AAACAAGATAAATAAAAGAT
1 AAACAAGATAAAAAAAAGAT
158504 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:166944 original size:24 final size:25
Alignment explanation
Indices: 166909--166963 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
166899 ACTTGGAGCC
*
166909 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
166933 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
166957 TCAAGTG
1 TCAAGTG
166964 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:168325 original size:23 final size:24
Alignment explanation
Indices: 168276--168328 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
168266 TTCTTTGCTT
* *
168276 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
168299 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
168322 TTTCTTT
1 TTTCTTT
168329 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:170847 original size:19 final size:21
Alignment explanation
Indices: 170804--170855 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
170794 GAAACCCCTT
170804 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
170825 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
170844 TGAAGATACATG
1 TGAAAATACATG
170856 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:179866 original size:36 final size:35
Alignment explanation
Indices: 179826--179904 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
179816 ACTATCTATT
* *
179826 CATCACCACCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCACATTCCATCACCA-TATCACGCCTATAA
* * * *
179862 CATCACCATATTCCATTACTATATCACGCCTATAT
1 CATCACCACATTCCATCACCATATCACGCCTATAA
179897 CATCACCA
1 CATCACCA
179905 ACTTATAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 20 0.54
36 17 0.46
ACGTcount: A:0.30, C:0.38, G:0.03, T:0.29
Consensus pattern (35 bp):
CATCACCACATTCCATCACCATATCACGCCTATAA
Found at i:182869 original size:33 final size:32
Alignment explanation
Indices: 182805--182869 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
182795 CTTGTTGATG
*
182805 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
182837 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
182870 GATGGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:186824 original size:33 final size:32
Alignment explanation
Indices: 186760--186824 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
186750 CTTGTTGATG
*
186760 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
186792 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
186825 GATGGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:186879 original size:36 final size:35
Alignment explanation
Indices: 186802--186882 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
186792 AATGAAAGGA
* * **
186802 TGATGTTATTGGCGTGATATGGTGATGGATTATGG
1 TGATCTTATAGGCGTGATATGGTGATGGAAGATGG
*
186837 TGATCTTATAGGCGTGATAATGGTGATGGACAGATTG
1 TGATCTTATAGGCGTGAT-ATGGTGATGGA-AGATGG
186874 T-ATCTTATA
1 TGATCTTATA
186883 AAACTAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 16 0.41
36 19 0.49
37 4 0.10
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (35 bp):
TGATCTTATAGGCGTGATATGGTGATGGAAGATGG
Found at i:190794 original size:33 final size:32
Alignment explanation
Indices: 190730--190794 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
190720 CTTGTTGATG
*
190730 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
190762 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
190795 GATGGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:194759 original size:33 final size:32
Alignment explanation
Indices: 194695--194759 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
194685 CTTGTTGATG
*
194695 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
194727 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
194760 GATGGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:200180 original size:11 final size:10
Alignment explanation
Indices: 200148--200173 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
200138 TTTTTTTTTC
200148 AAAAAAACAA
1 AAAAAAACAA
200158 AAAAAAACAA
1 AAAAAAACAA
200168 AAAAAA
1 AAAAAA
200174 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:205486 original size:14 final size:13
Alignment explanation
Indices: 205469--205518 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
205459 GTGCAAAAAG
205469 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
205483 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
205496 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
205507 AAAGAAAAAGAA
1 AAAGAAAAAGAA
205519 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:205515 original size:19 final size:18
Alignment explanation
Indices: 205463--205518 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
205453 ATTGGAGTGC
205463 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
205480 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
205499 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
205518 A
1 A
205519 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:205516 original size:11 final size:11
Alignment explanation
Indices: 205463--205518 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
205453 ATTGGAGTGC
205463 AAAAAG-AAAG
1 AAAAAGAAAAG
205473 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
205487 AAGAAGAAAAG
1 AAAAAGAAAAG
205498 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
205511 AAAAAGAA
1 AAAAAGAA
205519 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:211264 original size:13 final size:12
Alignment explanation
Indices: 211229--211269 Score: 73
Period size: 12 Copynumber: 3.3 Consensus size: 12
211219 TTATATATTG
211229 GAAATAAGAAAT
1 GAAATAAGAAAT
211241 GAAATAAGAAAT
1 GAAATAAGAAAT
211253 GAAATAAAGAAAT
1 GAAAT-AAGAAAT
211266 GAAA
1 GAAA
211270 GGATAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (12 bp):
GAAATAAGAAAT
Found at i:211285 original size:28 final size:24
Alignment explanation
Indices: 211230--211285 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 24
211220 TATATATTGG
*
211230 AAATAAGAAATGAAATAAGAAATG
1 AAATAAGAAATGAAATAAGAAATA
211254 AAATAAAGAAATGAAAGGATAAGAAATA
1 AAAT-AAGAAATG-AA--ATAAGAAATA
211282 AAAT
1 AAAT
211286 GGATAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 4 0.15
25 8 0.30
26 2 0.07
28 13 0.48
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (24 bp):
AAATAAGAAATGAAATAAGAAATA
Found at i:211858 original size:19 final size:20
Alignment explanation
Indices: 211816--211858 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
211806 GAAACCCCTT
*
211816 TGAAAACACATGATTTTCAA
1 TGAAAACACATAATTTTCAA
*
211836 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTCAA
211855 TGAA
1 TGAA
211859 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTCAA
Found at i:215065 original size:18 final size:18
Alignment explanation
Indices: 215042--215081 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
215032 TGTAAGAGTC
215042 TTTTCTT-TTGCTTTTTGT
1 TTTTCTTCTTGC-TTTTGT
*
215060 TTTTCTTCTTTCTTTTGT
1 TTTTCTTCTTGCTTTTGT
215078 TTTT
1 TTTT
215082 GTTGTAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTCTTCTTGCTTTTGT
Found at i:215280 original size:12 final size:13
Alignment explanation
Indices: 215263--215291 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
215253 TTATATATTG
215263 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
215275 GAAATAAAGAAAT
1 GAAATAAAGAAAT
215288 GAAA
1 GAAA
215292 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:215879 original size:19 final size:20
Alignment explanation
Indices: 215837--215879 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
215827 GAAACCCCTT
*
215837 TGAAAACACATGATTTTCAA
1 TGAAAACACATAATTTTCAA
*
215857 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTCAA
215876 TGAA
1 TGAA
215880 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTCAA
Found at i:218561 original size:24 final size:23
Alignment explanation
Indices: 218521--218568 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
218511 GAACGTTCGA
218521 TTATGTTCTTCGGTTATATTCAT
1 TTATGTTCTTCGGTTATATTCAT
* * *
218544 TTATGTTTGTTCGTTTATGTTCAT
1 TTATG-TTCTTCGGTTATATTCAT
218568 T
1 T
218569 CATTTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.60
Consensus pattern (23 bp):
TTATGTTCTTCGGTTATATTCAT
Found at i:218562 original size:14 final size:14
Alignment explanation
Indices: 218537--218580 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
218527 TCTTCGGTTA
218537 TATTCATTTATGTT
1 TATTCATTTATGTT
* *
218551 TGTTCGTTTATGTT
1 TATTCATTTATGTT
*
218565 CATTCATTTATGTT
1 TATTCATTTATGTT
218579 TA
1 TA
218581 ACTCAATCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.61
Consensus pattern (14 bp):
TATTCATTTATGTT
Found at i:219352 original size:16 final size:16
Alignment explanation
Indices: 219331--219387 Score: 105
Period size: 16 Copynumber: 3.6 Consensus size: 16
219321 GTGTCCAACG
219331 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
219347 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
219363 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
219379 TTTATGTTC
1 TTTATGTTC
219388 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:219484 original size:16 final size:16
Alignment explanation
Indices: 219459--219491 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
219449 AAAAACAATT
219459 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
219475 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
219491 T
1 T
219492 TTATTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:233952 original size:26 final size:26
Alignment explanation
Indices: 233921--233983 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
233911 CTTGGCTTGC
233921 TTTTCTCTTTTTC-GAAATCTTT-TTCT
1 TTTTCTCTTTTTCTG-AAT-TTTCTTCT
233947 TTTTCT-TATTTTCTGAATTTTCTTCT
1 TTTTCTCT-TTTTCTGAATTTTCTTCT
*
233973 TTTTGTCTTTT
1 TTTTCTCTTTT
233984 CTTTCTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
25 4 0.12
26 26 0.81
27 2 0.06
ACGTcount: A:0.10, C:0.16, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTTCTCTTTTTCTGAATTTTCTTCT
Found at i:235197 original size:33 final size:33
Alignment explanation
Indices: 235155--235223 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
235145 GTTGATGAAT
*
235155 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
235188 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
235221 GAA
1 GAA
235224 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:235228 original size:13 final size:12
Alignment explanation
Indices: 235209--235273 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
235199 TTATTGGCGT
235209 GATATGGTGATG
1 GATATGGTGATG
235221 GAATATGGTGAT-
1 G-ATATGGTGATG
*
235233 GATATAGGCG-T-
1 GATAT-GGTGATG
235244 GATAATGGTGATG
1 GAT-ATGGTGATG
235257 GACTATGGTGAT-
1 GA-TATGGTGATG
235269 GATAT
1 GATAT
235274 AGGCATGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:235264 original size:36 final size:36
Alignment explanation
Indices: 235194--235295 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
235184 AATGGAAGGA
* * *
235194 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
235229 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
* *
235265 TGATGATATAGGCATGATAATGGTAATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
235296 AGATTGTATC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 16 0.26
36 45 0.74
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:239041 original size:22 final size:24
Alignment explanation
Indices: 238999--239046 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
238989 AGAGGTTAAG
*
238999 AAAGATGATAAGGTAATGAAA-GA
1 AAAGATGATAAGATAATGAAATGA
239022 AAAGATGA-AAGAATAA-GAAATGA
1 AAAGATGATAAG-ATAATGAAATGA
239045 AA
1 AA
239047 TAGTAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (24 bp):
AAAGATGATAAGATAATGAAATGA
Found at i:239046 original size:15 final size:15
Alignment explanation
Indices: 239013--239061 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
239003 ATGATAAGGT
239013 AATGAAAGAA-AAG-
1 AATGAAAGAATAAGA
239026 -ATGAAAGAATAAGA
1 AATGAAAGAATAAGA
* *
239040 AATGAAATAGTAAGA
1 AATGAAAGAATAAGA
239055 AAGTGAA
1 AA-TGAA
239062 GATAACTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 9 0.30
13 3 0.10
15 14 0.47
16 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.14
Consensus pattern (15 bp):
AATGAAAGAATAAGA
Found at i:239279 original size:17 final size:17
Alignment explanation
Indices: 239257--239289 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
239247 GTAGGAGTAT
239257 TTTTCTT-TTCTCTTTTG
1 TTTTCTTATT-TCTTTTG
239274 TTTTCTTATTTCTTTT
1 TTTTCTTATTTCTTTT
239290 TGCTTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTCTTATTTCTTTTG
Found at i:239680 original size:33 final size:33
Alignment explanation
Indices: 239630--239706 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
239620 TATGCCTTGT
*
239630 TGGTGAAT-GAAGGATGAT-TTAATGGTGATGAAA
1 TGGT-AATGGAAGGATGATGTTAATGGCG-TGAAA
* *
239663 TGGTAATGGAAGGATGATGTTATTGGCGTGATA
1 TGGTAATGGAAGGATGATGTTAATGGCGTGAAA
*
239696 TGGTGATGGAA
1 TGGTAATGGAA
239707 TATGGTGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.08
33 28 0.74
34 7 0.18
ACGTcount: A:0.31, C:0.01, G:0.36, T:0.31
Consensus pattern (33 bp):
TGGTAATGGAAGGATGATGTTAATGGCGTGAAA
Found at i:239711 original size:13 final size:12
Alignment explanation
Indices: 239692--239777 Score: 67
Period size: 11 Copynumber: 7.2 Consensus size: 12
239682 TTATTGGCGT
239692 GATATGGTGATG
1 GATATGGTGATG
239704 GAATATGGTGAT-
1 G-ATATGGTGATG
239716 GATATAGGTG-T-
1 GATAT-GGTGATG
239727 GATAATGGTGATG
1 GAT-ATGGTGATG
239740 GACTATGGTGAT-
1 GA-TATGGTGATG
*
239752 GATATAGGCG-T-
1 GATAT-GGTGATG
239763 GATAATGGTGATG
1 GAT-ATGGTGATG
239776 GA
1 GA
239778 AAGATTGTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 22 0.35
12 17 0.27
13 22 0.35
14 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:239741 original size:36 final size:36
Alignment explanation
Indices: 239677--239778 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
239667 AATGGAAGGA
* *
239677 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
239712 TGATGATATAGGTGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
239748 TGATGATATAGGCGTGATAATGGTGATGGAA
1 TGATGATATAGGCGTGATAATGGTGATGGAA
239779 AGATTGTATC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 15 0.25
36 45 0.75
ACGTcount: A:0.27, C:0.03, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:248363 original size:14 final size:15
Alignment explanation
Indices: 248344--248376 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
248334 AATGGATTAA
248344 GAAATAG-AAGTAAT
1 GAAATAGAAAGTAAT
*
248358 GAAATAGAAAGTATT
1 GAAATAGAAAGTAAT
248373 GAAA
1 GAAA
248377 GAGATGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (15 bp):
GAAATAGAAAGTAAT
Found at i:251028 original size:30 final size:30
Alignment explanation
Indices: 250992--251058 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
250982 ACATCAAATA
250992 CAGCTCACAAACAGCTCACAAGGAACATGG
1 CAGCTCACAAACAGCTCACAAGGAACATGG
*
251022 CAGCTCACAAACAGCTCAGAAGGAACATGG
1 CAGCTCACAAACAGCTCACAAGGAACATGG
251052 CAGCTCA
1 CAGCTCA
251059 TGGAACACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.39, C:0.30, G:0.21, T:0.10
Consensus pattern (30 bp):
CAGCTCACAAACAGCTCACAAGGAACATGG
Found at i:257481 original size:19 final size:21
Alignment explanation
Indices: 257457--257508 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
257447 CGGCCAAGAG
*
257457 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
257476 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
257497 CATGTATTTTCA
1 CATGTATTTTCA
257509 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:262248 original size:19 final size:21
Alignment explanation
Indices: 262224--262275 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
262214 CGGCCAAGAG
*
262224 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
262243 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
262264 CATGTATTTTCA
1 CATGTATTTTCA
262276 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:266130 original size:19 final size:20
Alignment explanation
Indices: 266106--266143 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
266096 TGGCCAAGAG
266106 CATGTATCTTCA-TTAAAAT
1 CATGTATCTTCATTTAAAAT
*
266125 CATGTATTTTCATTTAAAA
1 CATGTATCTTCATTTAAAA
266144 GTTGTGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (20 bp):
CATGTATCTTCATTTAAAAT
Found at i:269192 original size:907 final size:909
Alignment explanation
Indices: 267438--269257 Score: 3599
Period size: 907 Copynumber: 2.0 Consensus size: 909
267428 ATGAATGAAT
267438 AAGTCCTTTACGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCTAAGG
1 AAGTCCTTTACGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCTAAGG
267503 ATGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCCCCCTTT
66 ATGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCCCCCTTT
267568 GGCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAAAGGCTCTCATGTGTATGGCATGTGA
131 GGCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAAAGGCTCTCATGTGTATGGCATGTGA
267633 TGTGGCCGAATAGGCATGGAGCCTCTAGCTCATGTTTCTTGATGATTTAAGCATCCAATAGGCGT
196 TGTGGCCGAATAGGCATGGAGCCTCTAGCTCATGTTTCTTGATGATTTAAGCATCCAATAGGCGT
267698 GATCTCTTCACCGATGTGTTCCTTGTTGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGG
261 GATCTCTTCACCGATGTGTTCCTTGTTGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGG
267763 TCACAATGTTTGAGAAAGGTACCCCTTCATGTTTGAGCTACTTCGGGTGTGAATGAGCTGGTGGT
326 TCACAATGTTTGAGAAAGGTACCCCTTCATGTTTGAGCTACTTCGGGTGTGAATGAGCTGGTGGT
267828 GAGCTGACCTTAGATGACTTGTAACATGATGAACGTTTGGGCAGCTCCTTGTGAAGAGGTACCTC
391 GAGCTGACCTTAGATGACTTGTAACATGATGAACGTTTGGGCAGCTCCTTGTGAAGAGGTACCTC
267893 TTGAGATGGCAACTATTCGCGAAAAGGTACGATTTCACAAATTTTGATGTAGGACATATTTGAAG
456 TTGAGATGGCAACTATTCGCGAAAAGGTACGATTTCACAAATTTTGATGTAGGACATATTTGAAG
267958 TGTCCTAAGTGGTGATGATGATGGTGCAACTCCCCAGCTGAAATGAGTTCATCTTGTAGCTCAAA
521 TGTCCTAAGTGGTGATGATGATGGTGCAACTCCCCAGCTGAAATGAGTTCATCTTGTAGCTCAAA
268023 TCTTCAGCTCAATCCAGCTATGAGCTCGCAGCCTCAAAACAACTTTTCACCAAATTGCTCCTTAA
586 TCTTCAGCTCAATCCAGCTATGAGCTCGCAGCCTCAAAACAACTTTTCACCAAATTGCTCCTTAA
268088 GCTCCCCTGATCGTTCCCATGTAAGTATCCTTGCTTTTGCATGCTCCATTTAGCTCCAATGTAGC
651 GCTCCCCTGATCGTTCCCATGTAAGTATCCTTGCTTTTGCATGCTCCATTTAGCTCCAATGTAGC
268153 TCCCAAGTATTGGCCGAATGTGCCTACACGCATAATATAAAGAAATAAACTAAGTAAATGAACTT
716 TCCCAAGTATTGGCCGAATGTGCCTACACGCATAATATAAAGAAATAAACTAAGTAAATGAACTT
268218 TATACAATGTATTATATAATAATGTGGACTATAGGTTATTTAATATTCAATATGTAATATATTAA
781 TATACAATGTATTATATAATAATGTGGACTATAGGTTATTTAATATTCAATATGTAATATATTAA
268283 ACAACCTA-TATCTGATGGTTCTTTCTCATTAAAAGATTTAAAAACATTAAGGCACTTATGAGA
846 ACAACCTATTATCTGATGGTTCTTTCTCATTAAAAGATTTAAAAACATTAAGGCACTTATGAGA
**
268346 AAGTCCTTTGGGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCTAAGG
1 AAGTCCTTTACGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCTAAGG
268411 ATGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCCCCCTTT
66 ATGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCCCCCTTT
268476 GGCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAAAGGCTCTCATGTGTATGGCATGTGA
131 GGCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAAAGGCTCTCATGTGTATGGCATGTGA
268541 TGTGGCCGAATAGGCATGGAGCCTCTAGCTCATG-TTCTTGATGATTTAAGCATCCAATAGGCGT
196 TGTGGCCGAATAGGCATGGAGCCTCTAGCTCATGTTTCTTGATGATTTAAGCATCCAATAGGCGT
268605 GATCTCTTCACCGATGTGTTCCTTGTTGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGG
261 GATCTCTTCACCGATGTGTTCCTTGTTGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGG
268670 TCACAATGTTTGAGAAAGGTACCCCTTCATGTTTGAGCTACTTCGGGTGTGAATGAGCTGGTGGT
326 TCACAATGTTTGAGAAAGGTACCCCTTCATGTTTGAGCTACTTCGGGTGTGAATGAGCTGGTGGT
268735 GAGCTGACCTTAGATGACTTGTAACATGATGAACGTTTGGGCAGCTCCTTGTGAAGAGGTACCTC
391 GAGCTGACCTTAGATGACTTGTAACATGATGAACGTTTGGGCAGCTCCTTGTGAAGAGGTACCTC
268800 TTGAGATGGCAACTATTCGCGAAAAGGTACGATTTCACAAATTTTGATGTAGGACATATTTGAAG
456 TTGAGATGGCAACTATTCGCGAAAAGGTACGATTTCACAAATTTTGATGTAGGACATATTTGAAG
268865 TGTCCTAAGTGGTGATGATGATGGTGCAACTCCCCAGCTGAAATGAGTTCATCTTGTAGCTCAAA
521 TGTCCTAAGTGGTGATGATGATGGTGCAACTCCCCAGCTGAAATGAGTTCATCTTGTAGCTCAAA
*
268930 TCTTCAGCTCAATCCAGCTATGAGCTCGCAGCCTCAAAACGACTTTTCACCAAATTGCTCCTTAA
586 TCTTCAGCTCAATCCAGCTATGAGCTCGCAGCCTCAAAACAACTTTTCACCAAATTGCTCCTTAA
268995 GCTCCCCTGATCGTTCCCATGTAAGTATCCTTGCTTTTGCATGCTCCATTTAGCTCCAATGTAGC
651 GCTCCCCTGATCGTTCCCATGTAAGTATCCTTGCTTTTGCATGCTCCATTTAGCTCCAATGTAGC
269060 TCCCAAGTATTGGCCGAATGTGCCTACACGCATAATATAAAGAAATAAACTAAGTAAATGAACTT
716 TCCCAAGTATTGGCCGAATGTGCCTACACGCATAATATAAAGAAATAAACTAAGTAAATGAACTT
269125 TATACAATGTATTATATAATAATGTGGACTATAGGTTATTTAATATTCAATATGTAATATATTAA
781 TATACAATGTATTATATAATAATGTGGACTATAGGTTATTTAATATTCAATATGTAATATATTAA
269190 ACAACCTATTATCTGATGGTTCTTTCTCATTAAAAGATTTAAAAACATTAAGGCACTTATGAGA
846 ACAACCTATTATCTGATGGTTCTTTCTCATTAAAAGATTTAAAAACATTAAGGCACTTATGAGA
269254 AAGT
1 AAGT
269258 ACTTCCCTGA
Statistics
Matches: 908, Mismatches: 3, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
907 622 0.69
908 286 0.31
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (909 bp):
AAGTCCTTTACGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCTAAGG
ATGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCCCCCTTT
GGCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAAAGGCTCTCATGTGTATGGCATGTGA
TGTGGCCGAATAGGCATGGAGCCTCTAGCTCATGTTTCTTGATGATTTAAGCATCCAATAGGCGT
GATCTCTTCACCGATGTGTTCCTTGTTGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGG
TCACAATGTTTGAGAAAGGTACCCCTTCATGTTTGAGCTACTTCGGGTGTGAATGAGCTGGTGGT
GAGCTGACCTTAGATGACTTGTAACATGATGAACGTTTGGGCAGCTCCTTGTGAAGAGGTACCTC
TTGAGATGGCAACTATTCGCGAAAAGGTACGATTTCACAAATTTTGATGTAGGACATATTTGAAG
TGTCCTAAGTGGTGATGATGATGGTGCAACTCCCCAGCTGAAATGAGTTCATCTTGTAGCTCAAA
TCTTCAGCTCAATCCAGCTATGAGCTCGCAGCCTCAAAACAACTTTTCACCAAATTGCTCCTTAA
GCTCCCCTGATCGTTCCCATGTAAGTATCCTTGCTTTTGCATGCTCCATTTAGCTCCAATGTAGC
TCCCAAGTATTGGCCGAATGTGCCTACACGCATAATATAAAGAAATAAACTAAGTAAATGAACTT
TATACAATGTATTATATAATAATGTGGACTATAGGTTATTTAATATTCAATATGTAATATATTAA
ACAACCTATTATCTGATGGTTCTTTCTCATTAAAAGATTTAAAAACATTAAGGCACTTATGAGA
Found at i:269424 original size:7 final size:6
Alignment explanation
Indices: 269407--269465 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
269397 ATTGGAGTAC
* *
269407 AAAAAG AAAAAG ACAAAAAG AAGAA- AAGAAG AAAAAG -AAAAG AAGAAAAG
1 AAAAAG AAAAAG --AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG
269457 AAAAAG AAA
1 AAAAAG AAA
269466 TTCAAAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
5 10 0.22
6 23 0.51
7 1 0.02
8 11 0.24
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:269433 original size:8 final size:8
Alignment explanation
Indices: 269422--269458 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
269412 GAAAAAGACA
269422 AAAAGAAG
1 AAAAGAAG
269430 AAAAGAAG
1 AAAAGAAG
269438 -AAA-AAG
1 AAAAGAAG
269444 AAAAGAAG
1 AAAAGAAG
269452 AAAAGAA
1 AAAAGAA
269459 AAAGAAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.11
7 6 0.22
8 18 0.67
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:269433 original size:22 final size:22
Alignment explanation
Indices: 269408--269464 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
269398 TTGGAGTACA
269408 AAAAGAAAAAGACA-AAAAGAAG
1 AAAAGAAAAAGA-AGAAAAGAAG
269430 AAAAGAAGAAA-AAGAAAAGAAG
1 AAAAGAA-AAAGAAGAAAAGAAG
269452 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
269465 ATTCAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.12
22 25 0.78
23 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAGAAGAAAAGAAG
Found at i:269441 original size:25 final size:24
Alignment explanation
Indices: 269410--269476 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 24
269400 GGAGTACAAA
269410 AAGAAAAAGACAAAAAGAAGAAAAG
1 AAGAAAAAG-CAAAAAGAAGAAAAG
269435 AAGAAAAAG--AAAAGAAGAAAAG
1 AAGAAAAAGCAAAAAGAAGAAAAG
* *
269457 AAAAAGAAATTCAAAAAGAA
1 AAGAA-AAA-GCAAAAAGAA
269477 AGCAAGCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
22 17 0.47
23 3 0.08
25 9 0.25
26 7 0.19
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (24 bp):
AAGAAAAAGCAAAAAGAAGAAAAG
Found at i:269449 original size:19 final size:19
Alignment explanation
Indices: 269414--269465 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
269404 TACAAAAAGA
*
269414 AAAAGACAAAA-AGAAGAA-
1 AAAAGA-AAAAGAAAAGAAG
269432 AAGAAGAAAAAGAAAAGAAG
1 AA-AAGAAAAAGAAAAGAAG
269452 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
269466 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.20
19 22 0.73
20 2 0.07
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAGAAAAGAAG
Found at i:269464 original size:14 final size:15
Alignment explanation
Indices: 269408--269464 Score: 68
Period size: 14 Copynumber: 3.9 Consensus size: 15
269398 TTGGAGTACA
269408 AAAAGA-AAAAGACA-
1 AAAAGAGAAAAGA-AG
269422 AAAAGAAGAAAAGAAG
1 AAAAG-AGAAAAGAAG
269438 AAAA-AGAAAAGAAG
1 AAAAGAGAAAAGAAG
269452 AAAAGA-AAAAGAA
1 AAAAGAGAAAAGAA
269465 ATTCAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 26 0.67
15 3 0.08
16 10 0.26
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAAGAAG
Found at i:269691 original size:17 final size:18
Alignment explanation
Indices: 269669--269703 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
269659 ACCTTTAAAT
*
269669 CATTTCTTTTA-TCTTTC
1 CATTTCTTATATTCTTTC
269686 CATTTCTTATATTCTTTC
1 CATTTCTTATATTCTTTC
269704 TACCCTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (18 bp):
CATTTCTTATATTCTTTC
Found at i:273155 original size:22 final size:20
Alignment explanation
Indices: 273130--273169 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
273120 ATGTTTGTTT
273130 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
273152 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
273170 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Done.