Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015120.1 Kokia drynarioides strain JFW-HI SEQ_130164, 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: 618428
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 267 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:3643 original size:29 final size:30
Alignment explanation
Indices: 3554--3709 Score: 124
Period size: 30 Copynumber: 5.3 Consensus size: 30
3544 AAAATTCAAA
* * * *
3554 TTTAACCCCCAAACTTCCCAAAAACTA-AT
1 TTTAACCCTCAAACTTTCTAAAAATTACAT
* * * * ** *
3583 TTTGACTCTCGAACTTTCCAAAAAAAAGAT
1 TTTAACCCTCAAACTTTCTAAAAATTACAT
*
3613 TTTAACCCTCAAAATTTCT-AAAATTACA-
1 TTTAACCCTCAAACTTTCTAAAAATTACAT
3641 TTTAGATCCCT-AAACTTTCTAAAAATTACAT
1 TTTA-A-CCCTCAAACTTTCTAAAAATTACAT
*
3672 GTTAACCC-CTAAACTTTCTAAAAATTACAT
1 TTTAACCCTC-AAACTTTCTAAAAATTACAT
*
3702 TTTGACCC
1 TTTAACCC
3710 CTTTTCCTTA
Statistics
Matches: 101, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.04
29 38 0.38
30 56 0.55
31 3 0.03
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (30 bp):
TTTAACCCTCAAACTTTCTAAAAATTACAT
Found at i:3710 original size:30 final size:30
Alignment explanation
Indices: 3618--3711 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
3608 AAGATTTTAA
* * *
3618 CCCTCAAAATTTCT-AAAATTACATTTAGAT
1 CCCT-AAACTTTCTAAAAATTACATTTTGAC
* *
3648 CCCTAAACTTTCTAAAAATTACATGTTAAC
1 CCCTAAACTTTCTAAAAATTACATTTTGAC
3678 CCCTAAACTTTCTAAAAATTACATTTTGAC
1 CCCTAAACTTTCTAAAAATTACATTTTGAC
3708 CCCT
1 CCCT
3712 TTTCCTTATT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 8 0.14
30 48 0.86
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTAAACTTTCTAAAAATTACATTTTGAC
Found at i:5670 original size:18 final size:18
Alignment explanation
Indices: 5627--5671 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5617 TTTAAAAAAA
5627 TATATAAATA-AATATTT
1 TATATAAATATAATATTT
*
5644 TTTA-AAATATAATATTT
1 TATATAAATATAATATTT
*
5661 TATATTAATAT
1 TATATAAATAT
5672 TTATAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATAAATATAATATTT
Found at i:5998 original size:18 final size:20
Alignment explanation
Indices: 5963--5999 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
5953 TTTATTTTAT
5963 TTAATATTAATATAAATATC
1 TTAATATTAATATAAATATC
5983 TTAAT-TTAAT-TAAATAT
1 TTAATATTAATATAAATAT
6000 TAATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATATTAATATAAATATC
Found at i:12893 original size:40 final size:38
Alignment explanation
Indices: 12801--12893 Score: 89
Period size: 40 Copynumber: 2.3 Consensus size: 38
12791 GATTACGATA
**
12801 TTGATTTTTATTTTTGATTTAGGGTTTTTTTATAGTGATT
1 TTGATTTTTA-TTTTGATTTAGGGTTTTTAAATAGTGA-T
* *
12841 TTCATTTTTTATTTTGATTTAGGGTTATTTAAATATTTG-T
1 TTGA-TTTTTATTTTGATTTAGGGTT-TTTAAATA-GTGAT
12881 TTGATTTGTTATT
1 TTGATTT-TTATT
12894 CACATATTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
39 3 0.07
40 27 0.61
41 12 0.27
42 2 0.05
ACGTcount: A:0.19, C:0.01, G:0.15, T:0.65
Consensus pattern (38 bp):
TTGATTTTTATTTTGATTTAGGGTTTTTAAATAGTGAT
Found at i:13022 original size:29 final size:29
Alignment explanation
Indices: 12978--13039 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
12968 ATCTATTAAC
12978 ATTTGTTTGATCTGTTAACACTGTGTGGG
1 ATTTGTTTGATCTGTTAACACTGTGTGGG
* * *
13007 ATTTGTTTGATTTGTTAATACTGTTTGGG
1 ATTTGTTTGATCTGTTAACACTGTGTGGG
13036 ATTT
1 ATTT
13040 AAGGTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.52
Consensus pattern (29 bp):
ATTTGTTTGATCTGTTAACACTGTGTGGG
Found at i:15175 original size:21 final size:21
Alignment explanation
Indices: 15149--15190 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
15139 TTTTTTAATA
*
15149 TTATTTTGCATATTATTTTTT
1 TTATTTTGCATACTATTTTTT
*
15170 TTATTTTGTATACTATTTTTT
1 TTATTTTGCATACTATTTTTT
15191 AATACCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (21 bp):
TTATTTTGCATACTATTTTTT
Found at i:15268 original size:11 final size:11
Alignment explanation
Indices: 15228--15283 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
15218 TGATGTGTTT
15228 TGTTGGCTTTA
1 TGTTGGCTTTA
* *
15239 TGATGACTTTA
1 TGTTGGCTTTA
15250 T-TCT-GCTTTA
1 TGT-TGGCTTTA
15260 TGTTGGCTTTAA
1 TGTTGGCTTT-A
15272 TGTTGGCTTTA
1 TGTTGGCTTTA
15283 T
1 T
15284 ATTGAATGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 7 0.19
11 19 0.51
12 11 0.30
ACGTcount: A:0.14, C:0.11, G:0.21, T:0.54
Consensus pattern (11 bp):
TGTTGGCTTTA
Found at i:15276 original size:12 final size:12
Alignment explanation
Indices: 15254--15282 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
15244 ACTTTATTCT
15254 GCTTT-ATGTTG
1 GCTTTAATGTTG
15265 GCTTTAATGTTG
1 GCTTTAATGTTG
15277 GCTTTA
1 GCTTTA
15283 TATTGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (12 bp):
GCTTTAATGTTG
Found at i:16717 original size:20 final size:20
Alignment explanation
Indices: 16650--16718 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
16640 TACTTTCAAG
16650 CAACAAAATTACAACCAAAC
1 CAACAAAATTACAACCAAAC
* * *
16670 CAGCCCCAAAGTTACAACCAAAG
1 CA---ACAAAATTACAACCAAAC
*
16693 TAACAAAATTACAACCAAAC
1 CAACAAAATTACAACCAAAC
16713 CAACAA
1 CAACAA
16719 CCATGAGAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 22 0.58
23 16 0.42
ACGTcount: A:0.55, C:0.30, G:0.04, T:0.10
Consensus pattern (20 bp):
CAACAAAATTACAACCAAAC
Found at i:16738 original size:16 final size:16
Alignment explanation
Indices: 16714--16753 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
16704 CAACCAAACC
16714 AACAACCATGAGAAGT
1 AACAACCATGAGAAGT
*
16730 AACAGCCATGAGAAGT
1 AACAACCATGAGAAGT
16746 AACAACCA
1 AACAACCA
16754 ACAAAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (16 bp):
AACAACCATGAGAAGT
Found at i:17105 original size:9 final size:9
Alignment explanation
Indices: 17082--17121 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
17072 GGAATCTCTA
17082 TTTTCTTCT
1 TTTTCTTCT
* *
17091 TCTTCTTTT
1 TTTTCTTCT
17100 TTTTCTTCT
1 TTTTCTTCT
17109 TTTTCTTCT
1 TTTTCTTCT
17118 TTTT
1 TTTT
17122 ATGCCCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:17107 original size:12 final size:12
Alignment explanation
Indices: 17087--17118 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17077 CTCTATTTTC
17087 TTCTTCTTCTTT
1 TTCTTCTTCTTT
*
17099 TTTTTCTTCTTT
1 TTCTTCTTCTTT
17111 TTCTTCTT
1 TTCTTCTT
17119 TTTATGCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:26751 original size:79 final size:79
Alignment explanation
Indices: 26620--26776 Score: 296
Period size: 79 Copynumber: 2.0 Consensus size: 79
26610 TTTCTAAAAG
*
26620 TTAAAAAGGAAAAACTAAAATATAAAAATTCACCAAGTAATGGCTGATCTCATTGTTGATTTTCA
1 TTAAAAAAGAAAAACTAAAATATAAAAATTCACCAAGTAATGGCTGATCTCATTGTTGATTTTCA
26685 TTGATATTGAACCA
66 TTGATATTGAACCA
26699 TTAAAAAAGAAAAACTAAAATATAAAAATTCACCAAGTAATGGCTGATCTCATTGTTGATTTTCA
1 TTAAAAAAGAAAAACTAAAATATAAAAATTCACCAAGTAATGGCTGATCTCATTGTTGATTTTCA
*
26764 TTGATATTTAACC
66 TTGATATTGAACC
26777 GTGAGAAATA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (79 bp):
TTAAAAAAGAAAAACTAAAATATAAAAATTCACCAAGTAATGGCTGATCTCATTGTTGATTTTCA
TTGATATTGAACCA
Found at i:28247 original size:19 final size:20
Alignment explanation
Indices: 28225--28272 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
28215 GGTATAATCC
*
28225 ATAAATTTTTTTAAAA-ATA
1 ATAAATTATTTTAAAATATA
* *
28244 ATAAAAATATTTTAAAATTTA
1 AT-AAATTATTTTAAAATATA
28265 ATAAATTA
1 ATAAATTA
28273 AAAAAATCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 17 0.74
21 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATTATTTTAAAATATA
Found at i:29586 original size:5 final size:5
Alignment explanation
Indices: 29576--29601 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29566 TTGTATATAT
29576 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
29602 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:31788 original size:41 final size:41
Alignment explanation
Indices: 31704--31795 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
31694 TATTACAACC
*
31704 GTAAATTCATATATAAATATTAATAAATTAGAATTCCTCAT
1 GTAAAATCATATATAAATATTAATAAATTAGAATTCCTCAT
** *
31745 GTAAAATCATATATAAATATTAATAAATTAGAATTTTTTAT
1 GTAAAATCATATATAAATATTAATAAATTAGAATTCCTCAT
31786 GTAAAATCAT
1 GTAAAATCAT
31796 TAAAAAGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (41 bp):
GTAAAATCATATATAAATATTAATAAATTAGAATTCCTCAT
Found at i:42957 original size:17 final size:18
Alignment explanation
Indices: 42916--42957 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
42906 TTAATAAAAA
42916 ATTTTAATCATTAAATAT
1 ATTTTAATCATTAAATAT
*
42934 ATATTAAT-A-TAAATAAT
1 ATTTTAATCATTAAAT-AT
42951 ATTTTAA
1 ATTTTAA
42958 ATTCGTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTTAATCATTAAATAT
Found at i:57696 original size:20 final size:20
Alignment explanation
Indices: 57671--57712 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
57661 GCCATCTTCA
57671 ACAAAATATAAAAGTATTTC
1 ACAAAATATAAAAGTATTTC
57691 ACAAAATATAAAAGTATTTC
1 ACAAAATATAAAAGTATTTC
57711 AC
1 AC
57713 CCTTTTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.29
Consensus pattern (20 bp):
ACAAAATATAAAAGTATTTC
Found at i:68068 original size:11 final size:11
Alignment explanation
Indices: 68052--68084 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
68042 AGGCCGCCTA
68052 ATTGAATTTCT
1 ATTGAATTTCT
68063 ATTGAATTTCT
1 ATTGAATTTCT
*
68074 ATTTAATTTCT
1 ATTGAATTTCT
68085 TTTATTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (11 bp):
ATTGAATTTCT
Found at i:68093 original size:10 final size:11
Alignment explanation
Indices: 68056--68093 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
68046 CGCCTAATTG
*
68056 AATTTCTATTG
1 AATTTCTATTT
68067 AATTTCTATTT
1 AATTTCTATTT
68078 AATTTCT-TTT
1 AATTTCTATTT
*
68088 ATTTTC
1 AATTTC
68094 ACTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.63
Consensus pattern (11 bp):
AATTTCTATTT
Found at i:74559 original size:16 final size:16
Alignment explanation
Indices: 74538--74572 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
74528 TGGGTGAAAT
74538 AAAATATTTTATATTA
1 AAAATATTTTATATTA
*
74554 AAAATATTTTATTTTA
1 AAAATATTTTATATTA
74570 AAA
1 AAA
74573 TTTATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATATTTTATATTA
Found at i:77353 original size:14 final size:13
Alignment explanation
Indices: 77331--77365 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
77321 CAATTCCCCA
77331 TTTTCTCTCTCTC
1 TTTTCTCTCTCTC
77344 -TTTCTCTCTCTC
1 TTTTCTCTCTCTC
77356 TTTTCT-TCTC
1 TTTTCTCTCTC
77366 CTATTCTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTCTCTCTCTC
Found at i:77831 original size:15 final size:15
Alignment explanation
Indices: 77811--77843 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
77801 ATCAATGAAC
77811 CATATTAAGTTATCT
1 CATATTAAGTTATCT
77826 CATATTAAGTTATCT
1 CATATTAAGTTATCT
77841 CAT
1 CAT
77844 CAATACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (15 bp):
CATATTAAGTTATCT
Found at i:82029 original size:9 final size:9
Alignment explanation
Indices: 82015--82039 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
82005 TCAAATTTGA
82015 CAGCAAAGG
1 CAGCAAAGG
82024 CAGCAAAGG
1 CAGCAAAGG
82033 CAGCAAA
1 CAGCAAA
82040 AGAAGCACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.28, T:0.00
Consensus pattern (9 bp):
CAGCAAAGG
Found at i:90671 original size:31 final size:31
Alignment explanation
Indices: 90636--90706 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
90626 ATAAAATTGT
90636 TCAAATAAGGGTCAAACATTTTCGAAAA-TGC
1 TCAAATAAGGGTCAAACATTTTC-AAAAGTGC
*
90667 TCAAATAAGGGTCAATCATTTTCAAAAGTGC
1 TCAAATAAGGGTCAAACATTTTCAAAAGTGC
90698 TCAAATAAG
1 TCAAATAAG
90707 ATTTTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (31 bp):
TCAAATAAGGGTCAAACATTTTCAAAAGTGC
Found at i:93301 original size:43 final size:43
Alignment explanation
Indices: 93253--93357 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
93243 CAAAATATTG
* * * *
93253 AACACCATCGACATCTTAATGCTTTAAATGTACGAAAGCCTCA
1 AACACCATCAACATCTTAATGCTTTAAATATACGAAAACATCA
* * * ** *
93296 AACACCATCAATACCCTAATGCTTTGGATATACGAAAACATTA
1 AACACCATCAACATCTTAATGCTTTAAATATACGAAAACATCA
93339 AACACCATCAACATCTTAA
1 AACACCATCAACATCTTAA
93358 ATATGCAAGA
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.25
Consensus pattern (43 bp):
AACACCATCAACATCTTAATGCTTTAAATATACGAAAACATCA
Found at i:94923 original size:10 final size:10
Alignment explanation
Indices: 94884--94951 Score: 56
Period size: 10 Copynumber: 7.3 Consensus size: 10
94874 ACTGAAATGT
*
94884 AAATATTATA
1 AAATATAATA
94894 AAATATAA-A
1 AAATATAATA
**
94903 AAACCTAATA
1 AAATATAATA
*
94913 AACTATAATA
1 AAATATAATA
*
94923 AATTATAA-A
1 AAATATAATA
94932 AAA-AT-ATA
1 AAATATAATA
94940 AAAT-TAATA
1 AAATATAATA
94949 AAA
1 AAA
94952 CCTATTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
7 1 0.02
8 7 0.15
9 16 0.35
10 22 0.48
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATATAATA
Found at i:95005 original size:18 final size:17
Alignment explanation
Indices: 94983--95024 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
94973 ATTAAAATTC
94983 TTAAAAATAATAAAAAA
1 TTAAAAATAATAAAAAA
* *
95000 TGTAAAAGTTATAAAAAA
1 T-TAAAAATAATAAAAAA
95018 TTAAAAA
1 TTAAAAA
95025 AATTAACATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
TTAAAAATAATAAAAAA
Found at i:95305 original size:12 final size:12
Alignment explanation
Indices: 95268--95306 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
95258 CGTCCAGTTC
95268 AATTAAATAAAA
1 AATTAAATAAAA
* *
95280 TATTAAAAATAAA
1 AATTAAATA-AAA
95293 AATTAAATAAAA
1 AATTAAATAAAA
95305 AA
1 AA
95307 ATGTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AATTAAATAAAA
Found at i:95488 original size:10 final size:10
Alignment explanation
Indices: 95475--95589 Score: 58
Period size: 10 Copynumber: 11.5 Consensus size: 10
95465 TACTTTTAAT
95475 ATTTTTTATA
1 ATTTTTTATA
95485 A-TTTTTATA
1 ATTTTTTATA
***
95494 AAAATTTATA
1 ATTTTTTATA
*
95504 TATTTTTTACA
1 -ATTTTTTATA
* *
95515 ATTTATTA-G
1 ATTTTTTATA
*
95524 ATTTTAATATA
1 ATTTT-TTATA
*
95535 TTTTTTTAT-
1 ATTTTTTATA
95544 ATATTTTTATA
1 AT-TTTTTATA
*
95555 A-TATTTATA
1 ATTTTTTATA
*
95564 ATTCTTTATA
1 ATTTTTTATA
* *
95574 AGTTTATATCA
1 ATTTTTTAT-A
95585 ATTTT
1 ATTTT
95590 CATATTTAGT
Statistics
Matches: 77, Mismatches: 20, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
9 22 0.29
10 39 0.51
11 16 0.21
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:95563 original size:19 final size:18
Alignment explanation
Indices: 95479--95574 Score: 61
Period size: 19 Copynumber: 4.9 Consensus size: 18
95469 TTTAATATTT
*
95479 TTTATAATTTTTATAAAAA
1 TTTATAATTTTTAT-AATA
95498 TTTATATATTTTT-TACA-A
1 TTTATA-ATTTTTATA-ATA
* *
95516 TTTATTAGATTTTAATATATTTT
1 TTTA-TA-ATTTT--TATA-ATA
95539 TTTATATATTTTTATAATA
1 TTTATA-ATTTTTATAATA
95558 TTTATAATTCTTTATAA
1 TTTATAATT-TTTATAA
95575 GTTTATATCA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
18 9 0.15
19 29 0.47
20 10 0.16
21 1 0.02
22 9 0.15
23 4 0.06
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (18 bp):
TTTATAATTTTTATAATA
Found at i:95563 original size:29 final size:28
Alignment explanation
Indices: 95476--95596 Score: 84
Period size: 30 Copynumber: 4.1 Consensus size: 28
95466 ACTTTTAATA
*
95476 TTTTTTATAATTTTTATAAAAATTTATAT
1 TTTTTTATAATTTTTAT-AATATTTATAT
* * *
95505 ATTTTTTACAATTTATTA-GATTTTAATATAT
1 -TTTTTTATAATTT-TTATAATATT--TATAT
*
95536 TTTTTTATATATTTTTATAATATTTATAA
1 TTTTTTATA-ATTTTTATAATATTTATAT
* *
95565 TTCTTTATAAGTTTATATCAAT-TTTCATAT
1 TTTTTTATAA-TTTTTAT-AATATTT-ATAT
95595 TT
1 TT
95597 AGTAATTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
28 1 0.01
29 24 0.33
30 31 0.43
31 16 0.22
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTTTATAATTTTTATAATATTTATAT
Found at i:104674 original size:18 final size:18
Alignment explanation
Indices: 104648--104687 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
104638 ATAAAACCAC
* *
104648 CCTCTTCATCACCATCTT
1 CCTCATCATCACCATCAT
*
104666 CCTCATCATCAGCATCAT
1 CCTCATCATCACCATCAT
104684 CCTC
1 CCTC
104688 CAACACTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.45, G:0.03, T:0.33
Consensus pattern (18 bp):
CCTCATCATCACCATCAT
Found at i:116001 original size:17 final size:17
Alignment explanation
Indices: 115979--116018 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
115969 TTTAATATAT
115979 CATAATAAAAGGAGGTC
1 CATAATAAAAGGAGGTC
115996 CATAATAAAAGGAGGTC
1 CATAATAAAAGGAGGTC
116013 CATAAT
1 CATAAT
116019 TAATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.20
Consensus pattern (17 bp):
CATAATAAAAGGAGGTC
Found at i:118060 original size:17 final size:17
Alignment explanation
Indices: 118034--118067 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
118024 CCACCCACCA
118034 CATACACAGATCGCGAC
1 CATACACAGATCGCGAC
*
118051 CATACGCAGATCGCGAC
1 CATACACAGATCGCGAC
118068 GGACAACCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.35, G:0.21, T:0.12
Consensus pattern (17 bp):
CATACACAGATCGCGAC
Found at i:118180 original size:17 final size:18
Alignment explanation
Indices: 118129--118180 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
118119 AAAAAGTTTT
*
118129 GAAGAAAAAAATATAACAA
1 GAAGATAAAAA-ATAACAA
* *
118148 TAAAATAAATAAATAAC-A
1 GAAGATAAA-AAATAACAA
118166 GAAGATAAAAAATAA
1 GAAGATAAAAAATAA
118181 TAATATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 11 0.41
20 2 0.07
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (18 bp):
GAAGATAAAAAATAACAA
Found at i:123746 original size:26 final size:26
Alignment explanation
Indices: 123711--123780 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
123701 GAGCTCAATG
123711 AAAATGCCGTAAGTGATTTAACCACA
1 AAAATGCCGTAAGTGATTTAACCACA
123737 AAAATGCCGTAAGTGATTTAACCACA
1 AAAATGCCGTAAGTGATTTAACCACA
*
123763 AAAATGCCGCAAGTGATT
1 AAAATGCCGTAAGTGATT
123781 GCGAAACAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (26 bp):
AAAATGCCGTAAGTGATTTAACCACA
Found at i:142380 original size:17 final size:17
Alignment explanation
Indices: 142347--142381 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
142337 CAGTTACGTC
**
142347 AAATTTTAATATGAATG
1 AAATTTTAATACAAATG
142364 AAATTTTAATACAAATG
1 AAATTTTAATACAAATG
142381 A
1 A
142382 TCAATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (17 bp):
AAATTTTAATACAAATG
Found at i:144380 original size:7 final size:7
Alignment explanation
Indices: 144376--144409 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
144366 ATTTTTTTAT
*
144376 TTTTTTA
1 TTTTCTA
144383 TTTTCTA
1 TTTTCTA
144390 TTTTCTA
1 TTTTCTA
144397 TTTTCTA
1 TTTTCTA
144404 TTTTCT
1 TTTTCT
144410 TTTCACTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCTA
Found at i:152906 original size:21 final size:20
Alignment explanation
Indices: 152854--152906 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
152844 TAATACATAA
* *
152854 AAAATAAATAAAAACAACTC
1 AAAATAAAAAAAAAAAACTC
*
152874 AAAACAAAAAAAAAAAAACTC
1 AAAA-TAAAAAAAAAAAACTC
*
152895 AAAATAACAAAA
1 AAAATAAAAAAA
152907 TAACCACGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.09
Consensus pattern (20 bp):
AAAATAAAAAAAAAAAACTC
Found at i:160390 original size:9 final size:9
Alignment explanation
Indices: 160360--160401 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
160350 ATCTTTACTA
160360 ATTTAAAA-
1 ATTTAAAAG
* *
160368 TTTTAAAAT
1 ATTTAAAAG
*
160377 TTTTAAAAG
1 ATTTAAAAG
160386 ATTTAAAAG
1 ATTTAAAAG
160395 ATTTAAA
1 ATTTAAA
160402 TGAAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (9 bp):
ATTTAAAAG
Found at i:162279 original size:24 final size:23
Alignment explanation
Indices: 162229--162291 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
162219 AAAAAAATAT
* *
162229 AAAAGCTACATTTTTTTGTTTACA
1 AAAAGCTACATTTTTTTG-TGAAA
162253 AAAA-CTACATTTTTTGTGTGAAA
1 AAAAGCTACATTTTTT-TGTGAAA
*
162276 AAAAGCTACACTTTTT
1 AAAAGCTACATTTTTT
162292 AAAACAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (23 bp):
AAAAGCTACATTTTTTTGTGAAA
Found at i:172899 original size:11 final size:12
Alignment explanation
Indices: 172869--172909 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
172859 TTTATTAACC
172869 ATATTATTTTAAT
1 ATATTA-TTTAAT
*
172882 TTATTATTTAA-
1 ATATTATTTAAT
172893 ATATTATTTAAT
1 ATATTATTTAAT
172905 ATATT
1 ATATT
172910 TACGTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.40
12 10 0.40
13 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTATTTAAT
Found at i:173632 original size:89 final size:89
Alignment explanation
Indices: 173504--173708 Score: 299
Period size: 89 Copynumber: 2.3 Consensus size: 89
173494 ATTTTTATAT
* * *
173504 AATT-TTAAACAATTTACATTT-AAT-ATTAAAACTTTTAATAATTTGATTTAATATCTATGCAA
1 AATTATTAAAAAATTT-TATTTAAATCATTAAAACTTTTAATAATTTGATTTAATATATATGCAA
*
173566 TGCACAATTTACAATTTTGTCATTG
65 TGCACAATTTACAATTTTATCATTG
*
173591 AATTATTAAAAAATTTTATTTAAATCATTAAAACTTTTAATAATTTGATTTAATATATGTGCAAT
1 AATTATTAAAAAATTTTATTTAAATCATTAAAACTTTTAATAATTTGATTTAATATATATGCAAT
*
173656 GCACAATTTACAATTTTATCATTT
66 GCACAATTTACAATTTTATCATTG
* * *
173680 AACTATTAAAAAGTTTTATTTAAGTCATT
1 AATTATTAAAAAATTTTATTTAAATCATT
173709 GGATTGTTAA
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
87 8 0.08
88 13 0.12
89 85 0.80
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (89 bp):
AATTATTAAAAAATTTTATTTAAATCATTAAAACTTTTAATAATTTGATTTAATATATATGCAAT
GCACAATTTACAATTTTATCATTG
Found at i:175139 original size:20 final size:20
Alignment explanation
Indices: 175114--175155 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
175104 AATTTCATGA
175114 TTGAAAATTTACGGATTAGT
1 TTGAAAATTTACGGATTAGT
175134 TTGAAAATTTACGGATTAGT
1 TTGAAAATTTACGGATTAGT
175154 TT
1 TT
175156 AACCGTGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (20 bp):
TTGAAAATTTACGGATTAGT
Found at i:180221 original size:15 final size:16
Alignment explanation
Indices: 180203--180232 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
180193 TAAATATTAA
180203 AAATTTA-AATTAATT
1 AAATTTACAATTAATT
180218 AAATTTACAATTAAT
1 AAATTTACAATTAAT
180233 AACATTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTTACAATTAATT
Found at i:183227 original size:22 final size:23
Alignment explanation
Indices: 183202--183253 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
183192 ATAATCATTT
*
183202 TCAAATTAGATTGGT-GGTCAAA
1 TCAAATTAGATTCGTCGGTCAAA
*
183224 TCAATATT-GATTCGTCGGTCCAA
1 TCAA-ATTAGATTCGTCGGTCAAA
183247 T-AAATTA
1 TCAAATTA
183254 AACTAGTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 12 0.48
23 10 0.40
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (23 bp):
TCAAATTAGATTCGTCGGTCAAA
Found at i:183529 original size:57 final size:57
Alignment explanation
Indices: 183441--183553 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
183431 ATCCAATTCA
183441 AATATCTTTATGTAAAGTTAAAAAACTCCATTGGTAGTTGACAAAATAATAACAATT
1 AATATCTTTATGTAAAGTTAAAAAACTCCATTGGTAGTTGACAAAATAATAACAATT
183498 AATATCTTTATGTAAAGTTAAAAAACTCCATTGGTAGTTGACAAAATAATAACAAT
1 AATATCTTTATGTAAAGTTAAAAAACTCCATTGGTAGTTGACAAAATAATAACAAT
183554 AGCTTTAGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (57 bp):
AATATCTTTATGTAAAGTTAAAAAACTCCATTGGTAGTTGACAAAATAATAACAATT
Found at i:192456 original size:32 final size:32
Alignment explanation
Indices: 192415--192477 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
192405 AAGCTTTATC
* *
192415 GTCTAAGAAACACATCCTGTTTACTGAAATTT
1 GTCTAAGAAACAAATCCCGTTTACTGAAATTT
192447 GTCTAAGAAACAAATCCCGTTTACTGAAATT
1 GTCTAAGAAACAAATCCCGTTTACTGAAATT
192478 ATGCTCCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
GTCTAAGAAACAAATCCCGTTTACTGAAATTT
Found at i:199155 original size:29 final size:28
Alignment explanation
Indices: 199101--199171 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
199091 TATTTAAAAA
199101 TATTAAAATATTTTTATTTATATTAAAT
1 TATTAAAATATTTTTATTTATATTAAAT
* * *
199129 TATTTAAATATTGTTTA-TTATTTTTAAT
1 TATTAAAATATT-TTTATTTATATTAAAT
*
199157 TTTATAAAATATTTT
1 TAT-TAAAATATTTT
199172 ATGTTTCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 24 0.67
29 12 0.33
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (28 bp):
TATTAAAATATTTTTATTTATATTAAAT
Found at i:200543 original size:30 final size:30
Alignment explanation
Indices: 200507--200609 Score: 83
Period size: 30 Copynumber: 3.5 Consensus size: 30
200497 TAAATATTTC
200507 TTAAATTTTTTATTTTTTATATATTTAAAT
1 TTAAATTTTTTATTTTTTATATATTTAAAT
* ** *
200537 TTAAA-TTTTCATATTTTTAT-TATCAAAAAA
1 TTAAATTTTTTAT-TTTTTATATAT-TTAAAT
200567 TT-AATTTTTTA-TTTTTA-A-ATTTAAAAT
1 TTAAATTTTTTATTTTTTATATATTT-AAAT
200594 TTAAAATTTATTTATT
1 TT-AAATTT-TTTATT
200610 AACGTTATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
27 7 0.12
28 6 0.11
29 16 0.29
30 26 0.46
31 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (30 bp):
TTAAATTTTTTATTTTTTATATATTTAAAT
Found at i:213224 original size:21 final size:22
Alignment explanation
Indices: 213190--213234 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
213180 ATATATATAT
*
213190 ATATATAACTGATTATTCAATCA
1 ATATATAAC-GATTATTAAATCA
213213 ATATATAA-GATTATTAAATCA
1 ATATATAACGATTATTAAATCA
213234 A
1 A
213235 CCAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
23 8 0.38
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (22 bp):
ATATATAACGATTATTAAATCA
Found at i:215651 original size:16 final size:16
Alignment explanation
Indices: 215627--215657 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
215617 AAAGGAAATG
*
215627 AAAGGAAAGAAAAAAA
1 AAAGAAAAGAAAAAAA
215643 AAAGAAAAGAAAAAA
1 AAAGAAAAGAAAAAA
215658 GTGGAAGGTT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAAAAAAA
Found at i:222517 original size:49 final size:49
Alignment explanation
Indices: 222444--222542 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
222434 GTATGTCATC
*
222444 AGGGGGAATTCAGTCATGATACTATAGAGGAATGACTTCGTAACTAAAT
1 AGGGGGAATTCAGTCATGAAACTATAGAGGAATGACTTCGTAACTAAAT
*
222493 AGGGGGAATTCAGTCATGAAACTATAGAGGAATGACTTCGTAACTCAAT
1 AGGGGGAATTCAGTCATGAAACTATAGAGGAATGACTTCGTAACTAAAT
222542 A
1 A
222543 AGTTTATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (49 bp):
AGGGGGAATTCAGTCATGAAACTATAGAGGAATGACTTCGTAACTAAAT
Found at i:228432 original size:21 final size:21
Alignment explanation
Indices: 228402--228447 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
228392 TAAATTATAT
* *
228402 ATTTAATTTA-TGTTTTCAAA
1 ATTTAATTTATTGTATTAAAA
228422 ATTTATATTTATTGTATTAAAA
1 ATTTA-ATTTATTGTATTAAAA
228444 ATTT
1 ATTT
228448 TAAAAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTAATTTATTGTATTAAAA
Found at i:229929 original size:22 final size:22
Alignment explanation
Indices: 229904--229950 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
229894 TGCAACAATA
229904 ATGAATTTAAACCCATTTAAAT
1 ATGAATTTAAACCCATTTAAAT
229926 ATGAATTTAAACCCATTTAAAT
1 ATGAATTTAAACCCATTTAAAT
229948 ATG
1 ATG
229951 TATTATCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (22 bp):
ATGAATTTAAACCCATTTAAAT
Found at i:235149 original size:23 final size:22
Alignment explanation
Indices: 235123--235166 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
235113 ATTCAAAAAA
235123 TTTGATAATTAAGTTTTTTTCAT
1 TTTGATAATTAA-TTTTTTTCAT
*
235146 TTTGATATTTAATTTTTTTCA
1 TTTGATAATTAATTTTTTTCA
235167 GTTAAGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTGATAATTAATTTTTTTCAT
Found at i:236341 original size:2 final size:2
Alignment explanation
Indices: 236334--236358 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
236324 CAAATTACTT
236334 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
236359 TAAGTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:237055 original size:19 final size:18
Alignment explanation
Indices: 237025--237062 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
237015 TTTCATTGTA
237025 ATTTATTTTTAAATATAT
1 ATTTATTTTTAAATATAT
*
237043 ATTTATATTTTAAATTTAT
1 ATTTAT-TTTTAAATATAT
237062 A
1 A
237063 ATTTCTACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTATTTTTAAATATAT
Found at i:242004 original size:139 final size:138
Alignment explanation
Indices: 241728--242004 Score: 378
Period size: 138 Copynumber: 2.0 Consensus size: 138
241718 GTTTGATTTA
*
241728 TCTCCTACTCATATTTGTAATTTTGATTTCATGTTGCTTCAAATTTTTTAAATTTTTAATTAATT
1 TCTCCTACTCATATTTGTAATTTTGATTTCATGTTGCTTCAAACTTTTTAAATTTTTAATTAATT
* *** *
241793 TTTTAAACATATTAGTTCTTTGGTTAGATAGTTAGACAGTTGCAATTATATCTTTAAGTCTCGAG
66 TTTTAAACATATTAATTCTTCCATTAGATAGTTAGACAGTTGCAATTACATCTTTAAGTCTCGAG
*
241858 TTTAATTC
131 TTCAATTC
* * *
241866 TCTCCTACTCATATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAATTAATG
1 TCTCCTACTCATATTTGTAATTTTGATTTCATGTTGCTTCAAACTTTTTAAATTTTTAATTAAT-
* * * * *
241931 TTTTTTAACATATTAATT-TTCCCATTAGATGGTTAGATAGTTGTAATTACATCTTTGAA-TCTT
65 TTTTTAAACATATTAATTCTT-CCATTAGATAGTTAGACAGTTGCAATTACATCTTT-AAGTCTC
241994 GAGTTCAATTC
128 GAGTTCAATTC
242005 CTCTACAAAG
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
138 62 0.51
139 57 0.47
140 2 0.02
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (138 bp):
TCTCCTACTCATATTTGTAATTTTGATTTCATGTTGCTTCAAACTTTTTAAATTTTTAATTAATT
TTTTAAACATATTAATTCTTCCATTAGATAGTTAGACAGTTGCAATTACATCTTTAAGTCTCGAG
TTCAATTC
Found at i:242230 original size:16 final size:16
Alignment explanation
Indices: 242209--242241 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
242199 TTGATGATAT
242209 TTTTTAATTATTTTTA
1 TTTTTAATTATTTTTA
242225 TTTTTAATTATTTTTA
1 TTTTTAATTATTTTTA
242241 T
1 T
242242 AAGCATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTAATTATTTTTA
Found at i:253488 original size:2 final size:2
Alignment explanation
Indices: 253483--253508 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
253473 TGTATATATT
253483 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
253509 TTGAGATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:257554 original size:15 final size:15
Alignment explanation
Indices: 257536--257564 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
257526 TTCGACTCTT
257536 TGGTTTTAAGAATGC
1 TGGTTTTAAGAATGC
257551 TGGTTTTAAGAATG
1 TGGTTTTAAGAATG
257565 AGTGATTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (15 bp):
TGGTTTTAAGAATGC
Found at i:260889 original size:22 final size:22
Alignment explanation
Indices: 260861--260902 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
260851 TTTGATTTTT
*
260861 CATAATTGAGTGACAAAAAAAA
1 CATAATTAAGTGACAAAAAAAA
*
260883 CATAATTAAGTGACTAAAAA
1 CATAATTAAGTGACAAAAAA
260903 TGTCATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (22 bp):
CATAATTAAGTGACAAAAAAAA
Found at i:272893 original size:26 final size:26
Alignment explanation
Indices: 272862--272915 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
272852 GACATACTAC
272862 ATTTGACATATGAAAAACAAAAGATG
1 ATTTGACATATGAAAAACAAAAGATG
*
272888 ATTTGATATATGAAAAACAAAAGATG
1 ATTTGACATATGAAAAACAAAAGATG
272914 AT
1 AT
272916 AGATTAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.26
Consensus pattern (26 bp):
ATTTGACATATGAAAAACAAAAGATG
Found at i:272933 original size:24 final size:26
Alignment explanation
Indices: 272873--272935 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
272863 TTTGACATAT
* *
272873 GAAAAACAAAAGATGATTTGATATAT
1 GAAAAACAAAAGATGATTAGATATAG
272899 GAAAAACAAAAGATGA-TAGAT-TAG
1 GAAAAACAAAAGATGATTAGATATAG
*
272923 GTAAAACAAAAGA
1 GAAAAACAAAAGA
272936 GTTGGACATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 14 0.41
25 4 0.12
26 16 0.47
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.19
Consensus pattern (26 bp):
GAAAAACAAAAGATGATTAGATATAG
Found at i:278697 original size:7 final size:6
Alignment explanation
Indices: 278666--278695 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
278656 TGACTAAATC
278666 TTTTCT TTTTCT TTTTCT TTTTCAT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTC
278696 ATGATATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:287217 original size:16 final size:16
Alignment explanation
Indices: 287198--287250 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
287188 AGATGAAGTC
287198 AAAAAAAGAAAAAAGA
1 AAAAAAAGAAAAAAGA
287214 AAAAAAAGAGAAAATA-A
1 AAAAAAAGA-AAAA-AGA
*
287231 AAAAAAACAAAAAAGA
1 AAAAAAAGAAAAAAGA
287247 AAAA
1 AAAA
287251 GAGGTACAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.03
16 18 0.55
17 13 0.39
18 1 0.03
ACGTcount: A:0.87, C:0.02, G:0.09, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAAAAGA
Found at i:289527 original size:6 final size:6
Alignment explanation
Indices: 289506--289567 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
289496 TTTAATTTAT
*
289506 TTTAAA TTT-TA TTTAAA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
289552 GTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
289568 CTTCAAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
4 2 0.04
5 10 0.21
6 32 0.68
7 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:289534 original size:23 final size:23
Alignment explanation
Indices: 289518--289561 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
289508 TAAATTTTAT
289518 TTAAATTTAAATTTAAATTAATC
1 TTAAATTTAAATTTAAATTAATC
* *
289541 TTAAATTTAAAGTTAATTTAA
1 TTAAATTTAAATTTAAATTAA
289562 ATTTAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTAATC
Found at i:289538 original size:17 final size:16
Alignment explanation
Indices: 289496--289567 Score: 81
Period size: 17 Copynumber: 4.3 Consensus size: 16
289486 CTGGGCCCTT
* *
289496 TTTAATTTATTTTAAA
1 TTTAAATTAATTTAAA
* *
289512 TTTTATTTAAATTTAAA
1 TTTAAATT-AATTTAAA
289529 TTTAAATTAATCTTAAA
1 TTTAAATTAAT-TTAAA
289546 TTTAAAGTTAATTTAAA
1 TTTAAA-TTAATTTAAA
289563 TTTAA
1 TTTAA
289568 CTTCAAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
16 10 0.20
17 34 0.69
18 5 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:289567 original size:11 final size:11
Alignment explanation
Indices: 289499--289550 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
289489 GGCCCTTTTT
*
289499 AATTTATTTTA
1 AATTTAATTTA
*
289510 AATTTTATTTA
1 AATTTAATTTA
289521 AATTTAAATTTA
1 AATTT-AATTTA
289533 AA-TTAATCTTA
1 AATTTAAT-TTA
289544 AATTTAA
1 AATTTAA
289551 AGTTAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 3 0.09
11 21 0.60
12 11 0.31
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:289567 original size:23 final size:22
Alignment explanation
Indices: 289507--289567 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
289497 TTAATTTATT
* *
289507 TTAAATTTTATTTAAATTTAAAT
1 TTAAA-TTAATTTAAATTTAAAG
289530 TTAAATTAATCTTAAATTTAAAG
1 TTAAATTAAT-TTAAATTTAAAG
*
289553 TTAATTTAAATTTAA
1 TTAAATT-AATTTAA
289568 CTTCAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 4 0.12
23 26 0.79
24 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTAATTTAAATTTAAAG
Found at i:290574 original size:17 final size:17
Alignment explanation
Indices: 290552--290584 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
290542 ACGTTGTTTT
290552 AAAAAAAGAAAAAAAGA
1 AAAAAAAGAAAAAAAGA
*
290569 AAAAAAAGAAAGAAAG
1 AAAAAAAGAAAAAAAG
290585 GAGAGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAGA
Found at i:291441 original size:29 final size:30
Alignment explanation
Indices: 291363--291566 Score: 183
Period size: 29 Copynumber: 7.0 Consensus size: 30
291353 GAAGGTCCGT
* *
291363 AAACTATCCGAAAATTACCA-TTTACCCCCG
1 AAACT-TCCAAAAATTACCATTTTAACCCCG
** * *
291393 -AACTTCTTAAAA-TCCCATTTTAACCTCG
1 AAACTTCCAAAAATTACCATTTTAACCCCG
* *
291421 AAACTT-CAAAAATTACTATTTT-ACCCCC
1 AAACTTCCAAAAATTACCATTTTAACCCCG
* *
291449 AAACTTCCAAAAA-TCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACCA-TTTTAACCCCG
*
291479 AAACTTCCAAAAATTACCATTTTACCCCCG
1 AAACTTCCAAAAATTACCATTTTAACCCCG
*
291509 -AACTTCCAAAAA-T-CTCATTTTTGACCCCG
1 AAACTTCCAAAAATTAC-CA-TTTTAACCCCG
* *
291538 AAACTTCCACAAATTACCATTTTTACCCC
1 AAACTTCCAAAAATTACCATTTTAACCCC
291567 CGGATGTCCG
Statistics
Matches: 141, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
27 5 0.04
28 34 0.24
29 47 0.33
30 47 0.33
31 7 0.05
32 1 0.01
ACGTcount: A:0.36, C:0.32, G:0.03, T:0.29
Consensus pattern (30 bp):
AAACTTCCAAAAATTACCATTTTAACCCCG
Found at i:291505 original size:59 final size:59
Alignment explanation
Indices: 291363--291568 Score: 283
Period size: 59 Copynumber: 3.5 Consensus size: 59
291353 GAAGGTCCGT
* ** *
291363 AAACTATCCGAAAATTACCA-TTTACCCCCGAACTTCTTAAAATCCCA-TTTTAACCTCG
1 AAACT-TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * *
291421 AAACTT-CAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG
* *
291479 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG
*
291538 AAACTTCCACAAATTACCATTTTTACCCCCG
1 AAACTTCCAAAAATTACCA-TTTTACCCCCG
291569 GATGTCCGAA
Statistics
Matches: 131, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
56 10 0.08
57 25 0.19
58 20 0.15
59 65 0.50
60 11 0.08
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG
Found at i:303691 original size:204 final size:204
Alignment explanation
Indices: 303341--304557 Score: 1977
Period size: 204 Copynumber: 6.0 Consensus size: 204
303331 CACAAACCAC
* * * * *
303341 GTGATCATCTTCCCGATGAGACACTGAGAAGAAGACTCAGATGAGGCTCAAAACGAGTAATATCT
1 GTGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
* *
303406 TCAAACCCCAGCTTTCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGTTTCCTG
66 TCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
* *
303471 ATGAGATACTGAGAAGTGAACCAAATTCATCTTCATGATGAGGTACAGAGGAGCGAATTGAAACA
131 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
303536 AACAGCGAT
196 AACAGCGAT
*
303545 GTGATCATCTTCCTGATGAGACATTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
1 GTGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
* * *
303610 TCAAACCCCAGCTTCCTGATGAGACATTGAGAAGCAAGTCGAAGCAATAAAATGTTAGCTTCCTG
66 TCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
*
303675 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCGAATTGAAACA
131 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
303740 AACAGCGAT
196 AACAGCGAT
* *
303749 GTGATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAGACGAGGCTCAAAACGAGTAAAATCT
1 GTGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
*
303814 TCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATATAAGGTTAGCTTCCTG
66 TCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
303879 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
131 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
303944 AACAGCGAT
196 AACAGCGAT
* * * *
303953 ATGATCATCTTCTTGATGGGACACTGAGAAGAAAACCCAGACGAGGCTCAAAACGAGCAAAATCT
1 GTGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
*
304018 TCAAACCTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
66 TCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
*
304083 ATGAGATACTGAGAAGTGAACCAAATTCGTCGTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
131 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
*
304148 AATAGCGAT
196 AACAGCGAT
* *
304157 GTGATCATCTTCTTGATGGGACACTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
1 GTGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
* *
304222 TCAAACCTCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
66 TCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
* * *
304287 ATGAGATACTGAGAAGTAAACCAAATTCGTCTTCTTGACGAGATACAGAGGAGCGAATTGAAACA
131 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
*
304352 AACAGCGAC
196 AACAGCGAT
* * * *
304361 GTAATCATCTTCCTGATAAGACACTGAGAAGAAGACCCAAACGAAGCTC-AAACGAGCAAAATCT
1 GTGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
* * * * * **
304425 TCGAACCCAAGCTCCCTGATGTGACATTGAGAAGTGGGTCGAAGCAATAAAAGGTTAGCTTCCTG
66 TCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
* * * * * * *
304490 ATGAGATACTGAGAAGTGAACCAAACTCGTCTTCCTGATGAGATATAGAGAAGCGAATCGAAATA
131 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
304555 AAC
196 AAC
304558 GATGCAGTAA
Statistics
Matches: 950, Mismatches: 63, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
203 131 0.14
204 819 0.86
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (204 bp):
GTGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAGACGAGGCTCAAAACGAGCAAAATCT
TCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGGTACAGAGGAGCGAATTGAAACA
AACAGCGAT
Found at i:304872 original size:17 final size:17
Alignment explanation
Indices: 304840--304873 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
304830 TTTAATTTAT
* *
304840 TTTAAATTTTATTTAAA
1 TTTAAATTTAACTTAAA
304857 TTTAAATTTAACTTAAA
1 TTTAAATTTAACTTAAA
304874 AATTAAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAACTTAAA
Found at i:306723 original size:29 final size:29
Alignment explanation
Indices: 306688--306945 Score: 202
Period size: 30 Copynumber: 8.7 Consensus size: 29
306678 CTAAACTGTT
*
306688 CAAAAATTATCATTTTACCCCCAAACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTC
* * * *
306717 TAAAAA-TCCCATTTTTAACCCCGAAACATC
1 CAAAAATTACCA-TTTT-ACCCCCAAACTTC
* * *
306747 CAAAAATTACCATTTTACCCTCGAACTGC
1 CAAAAATTACCATTTTACCCCCAAACTTC
* * *
306776 CAAAAA-TCCCATTTTTGACCTCAAAACTTC
1 CAAAAATTACCA-TTTT-ACCCCCAAACTTC
*
306806 TAAAAATTACCATTTTACCCCCAAACTTC
1 CAAAAATTACCATTTTACCCCCAAACTTC
* * * *
306835 CAAAAA-TCCCATTTTCGACCTCAAAATTTC
1 CAAAAATTACCATTTT--ACCCCCAAACTTC
*
306865 CAAAAATTACCATTTTACCCCCGAAC-TC
1 CAAAAATTACCATTTTACCCCCAAACTTC
* ***
306893 CTAAAAA-TCCCATTTTTAACCTTGAAACTTC
1 C-AAAAATTACCA-TTTT-ACCCCCAAACTTC
306924 CAAAAATTACCATTCTTACCCC
1 CAAAAATTACCATT-TTACCCC
306946 GGATGTCCGA
Statistics
Matches: 174, Mismatches: 40, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
28 22 0.13
29 58 0.33
30 69 0.40
31 25 0.14
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.29
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCAAACTTC
Found at i:306781 original size:59 final size:59
Alignment explanation
Indices: 306688--306980 Score: 342
Period size: 59 Copynumber: 5.0 Consensus size: 59
306678 CTAAACTGTT
* * * * * *
306688 CAAAAATTATCATTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCGAAACATC
1 CAAAAATTACCATTTTACCCCCGAACTGCCAAAAATCCCATTTTTAACCTCGAAACTTC
* * *
306747 CAAAAATTACCATTTTACCCTCGAACTGCCAAAAATCCCATTTTTGACCTCAAAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTGCCAAAAATCCCATTTTTAACCTCGAAACTTC
* * * ** * *
306806 TAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTCGACCTCAAAATTTC
1 CAAAAATTACCATTTTACCCCCGAACTGCCAAAAATCCCATTTTTAACCTCGAAACTTC
*
306865 CAAAAATTACCATTTTACCCCCGAACT-CCTAAAAATCCCATTTTTAACCTTGAAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTGCC-AAAAATCCCATTTTTAACCTCGAAACTTC
* * *
306924 CAAAAATTACCATTCTTA-CCCCGGA-TGTCCGAAGA-CTCCATTTTTAACCTCGAAACT
1 CAAAAATTACCATT-TTACCCCCGAACTG-CCAAAAATC-CCATTTTTAACCTCGAAACT
306981 CTTAAAGTTA
Statistics
Matches: 203, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
58 4 0.02
59 194 0.96
60 5 0.02
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.29
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAACTGCCAAAAATCCCATTTTTAACCTCGAAACTTC
Found at i:309828 original size:52 final size:52
Alignment explanation
Indices: 309771--309872 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
309761 CACTTTTTTC
309771 CAACTAAAACATTTTTTTAATGCTAAACTATTTCCATGAATTAGATACATCA
1 CAACTAAAACATTTTTTTAATGCTAAACTATTTCCATGAATTAGATACATCA
**
309823 CAACTAAAACATTTTTTTAATGCTAAACTATTTCCATGGGTTAGATACAT
1 CAACTAAAACATTTTTTTAATGCTAAACTATTTCCATGAATTAGATACAT
309873 TACGGATGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (52 bp):
CAACTAAAACATTTTTTTAATGCTAAACTATTTCCATGAATTAGATACATCA
Found at i:318539 original size:66 final size:64
Alignment explanation
Indices: 318413--318539 Score: 164
Period size: 66 Copynumber: 2.0 Consensus size: 64
318403 GTGTTTGGTA
* * * * *
318413 TAGCATACCTGTTACAAGTTCTATTTTGGAATTTTTCTCCTTCAATCTATTTTCATGTTTGGCG
1 TAGCATACCTGTTACAAGTTCTATTATGGAATTTGTCTCCTTCAATATATTTCCAAGTTTGGCG
* * *
318477 TAGCATACCTGTTACAAGTTTTTGATTATGGAATTTGTCTCCTTGAATATGTTTCCAAGTTTG
1 TAGCATACCTGTTACAAG-TTCT-ATTATGGAATTTGTCTCCTTCAATATATTTCCAAGTTTG
318540 TTTTCTTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 18 0.34
65 3 0.06
66 32 0.60
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.46
Consensus pattern (64 bp):
TAGCATACCTGTTACAAGTTCTATTATGGAATTTGTCTCCTTCAATATATTTCCAAGTTTGGCG
Found at i:320811 original size:22 final size:20
Alignment explanation
Indices: 320776--320818 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
320766 CAAAAAATGA
**
320776 AGAAGAAAGCAGAAGAAGCAAG
1 AGAAGAAAAAAGAA-AAG-AAG
320798 AGAAGAAAAAAGAAAAGAAG
1 AGAAGAAAAAAGAAAAGAAG
320818 A
1 A
320819 AAAAAACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 12 0.63
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAAGAAAAGAAG
Found at i:325108 original size:69 final size:69
Alignment explanation
Indices: 324997--325145 Score: 280
Period size: 69 Copynumber: 2.2 Consensus size: 69
324987 CAAATCCACT
324997 TTGTAAGATATTGTTTAGAGTTTGTCTGCTTATATCCCTCTCCTTCTATAAAAAGGGAGATAGTA
1 TTGTAAGATATTGTTTAGAGTTTGTCTGCTTATATCCCTCTCCTTCTATAAAAAGGGAGATAGTA
325062 TCAG
66 TCAG
* *
325066 TTGTACGATATTGTTTAGAGTTTGTCTGCTTATATTCCTCTCCTTCTATAAAAAGGGAGATAGTA
1 TTGTAAGATATTGTTTAGAGTTTGTCTGCTTATATCCCTCTCCTTCTATAAAAAGGGAGATAGTA
325131 TCAG
66 TCAG
325135 TTGTAAGATAT
1 TTGTAAGATAT
325146 CAAGTTTTCA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 77 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (69 bp):
TTGTAAGATATTGTTTAGAGTTTGTCTGCTTATATCCCTCTCCTTCTATAAAAAGGGAGATAGTA
TCAG
Found at i:331188 original size:24 final size:23
Alignment explanation
Indices: 331135--331188 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
331125 TTATAACTTT
*
331135 TATTATAATATATATTACAATAA
1 TATTATAATATATAATACAATAA
*
331158 TAGTTAT-ATATAATAATACATTATA
1 TA-TTATAATAT-ATAATACAATA-A
331183 TATTAT
1 TATTAT
331189 TATTTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.23
24 17 0.65
25 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATAATATATAATACAATAA
Found at i:333716 original size:17 final size:17
Alignment explanation
Indices: 333694--333774 Score: 92
Period size: 17 Copynumber: 4.8 Consensus size: 17
333684 GTGTCCAAAT
*
333694 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
333711 TTTT-AAGTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
333727 TTTCAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
* *
333744 TTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
333761 TTTTAAATTAAAAT
1 TTTTAAATTTAAAT
333775 GAGTTAAAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
16 13 0.25
17 38 0.75
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:333736 original size:33 final size:34
Alignment explanation
Indices: 333698--333769 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
333688 CCAAATTTTT
*
333698 AAATTTTAATTTATTTTAAG-TTAAATTTATTTC
1 AAATTTGAATTTATTTTAAGTTTAAATTTATTTC
* *
333731 AAATTTGAATTTATTTTGAGTTTAAATTTATTTT
1 AAATTTGAATTTATTTTAAGTTTAAATTTATTTC
333765 AAATT
1 AAATT
333770 AAAATGAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 18 0.51
34 17 0.49
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (34 bp):
AAATTTGAATTTATTTTAAGTTTAAATTTATTTC
Found at i:335839 original size:29 final size:29
Alignment explanation
Indices: 335758--336208 Score: 230
Period size: 29 Copynumber: 15.5 Consensus size: 29
335748 TCCTTGAACT
** *
335758 AAAATTACATTTTGACCCTTAAA-ATTCCTA
1 AAAATTACATTTT-ACCCCCAAACTTTCC-A
* * * *
335788 AAATTTAAATTTTTGCCCTCAAACTTTCCA
1 AAAATTACA-TTTTACCCCCAAACTTTCCA
*
335818 AAAATTACATTTTACCCCCAAAC-TTCCT
1 AAAATTACATTTTACCCCCAAACTTTCCA
* **
335846 AAAATTACCATTTT-GCCCTGAA-TTTCCCA
1 AAAATTA-CATTTTACCCCCAAACTTT-CCA
* ** *
335875 AAAATCACACTTTTAGACCCGAAC-TTCCA
1 AAAATTACA-TTTTACCCCCAAACTTTCCA
* *
335904 AAAATTACCATTTTACCCTCAAAC-TTCAA
1 AAAATTA-CATTTTACCCCCAAACTTTCCA
* ***
335933 AAAATTACATTTTTTCCCTTGAACTTT-CA
1 AAAATTACA-TTTTACCCCCAAACTTTCCA
* **
335962 AAAATTCCATTTTGA--CCCAAACTTTTTA
1 AAAATTACATTTT-ACCCCCAAACTTTCCA
*** *
335990 AAAATTACCATTTTACCCTTGAA-TTTTCA
1 AAAATTA-CATTTTACCCCCAAACTTTCCA
* *
336019 AAAATTTCATTTTAACCCCAAACTTTCCA
1 AAAATTACATTTTACCCCCAAACTTTCCA
* *
336048 AAAATTACCATTTTACCCCTAAA-TTTCAA
1 AAAATTA-CATTTTACCCCCAAACTTTCCA
* * * *
336077 AAAAATCCATTTTGA-CCTCAAACTTCCCA
1 AAAATTACATTTT-ACCCCCAAACTTTCCA
* * *
336106 AAAATTACCAATTTACCACTAAA-TTTCCA
1 AAAATTA-CATTTTACCCCCAAACTTTCCA
** * * *
336135 AAAATTTTATTTTTA-CACCTAAGTTTCCA
1 AAAATTACA-TTTTACCCCCAAACTTTCCA
* * *
336164 AAAATTACCGTTTTACCCCCGAAC-CTCCA
1 AAAATTA-CATTTTACCCCCAAACTTTCCA
336193 AAAATTACCATTTTAC
1 AAAATTA-CATTTTAC
336209 TCCTCGGGCA
Statistics
Matches: 321, Mismatches: 74, Indels: 53
0.72 0.17 0.12
Matches are distributed among these distances:
27 7 0.02
28 62 0.19
29 180 0.56
30 64 0.20
31 8 0.02
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTACCCCCAAACTTTCCA
Found at i:336196 original size:116 final size:115
Alignment explanation
Indices: 335758--336206 Score: 324
Period size: 116 Copynumber: 3.9 Consensus size: 115
335748 TCCTTGAACT
* * * * ** *
335758 AAAATTA-CATTTTGACCCTTAAAATTCCTAAAATTTAAATTTTTGCCCTCAAACTTTCCAAAAA
1 AAAATTACCAATTT-ACCCTTAAATTTCCAAAAATTT-CATTTTAACAC-CAAACTTTCCAAAAA
* * * *
335822 TTA-CATTTTACCCCCAAACTTCCTAAAATTACCATTTTG-CCCTGAATTTCCCA
63 TTACCATTTTACCCCCAAACCTCCAAAAATT-CCATTTTGACCC-AAACTTCCCA
* * * * * * *
335875 AAAATCA-CACTTTTAGACCC--GAACTTCCAAAAATTACCATTTT-ACCCTCAAAC-TTCAAAA
1 AAAATTACCA-ATTT--ACCCTTAAATTTCCAAAAATT-TCATTTTAACAC-CAAACTTTCCAAA
* *** * * ***
335935 AATTA-CATTTTTTCCCTTGAACTTTCAAAAATTCCATTTTGACCCAAACTTTTTA
61 AATTACCA-TTTTACCCCCAAACCTCCAAAAATTCCATTTTGACCCAAACTTCCCA
* * * *
335990 AAAATTACCATTTTACCCTTGAATTTTCAAAAATTTCATTTTAACCCCAAACTTTCCAAAAATTA
1 AAAATTACCAATTTACCCTTAAATTTCCAAAAATTTCATTTTAACACCAAACTTTCCAAAAATTA
* ** * *
336055 CCATTTTACCCCTAAATTTCAAAAAAATCCATTTTGACCTCAAACTTCCCA
66 CCATTTTACCCCCAAACCTCCAAAAATTCCATTTTGACC-CAAACTTCCCA
* * * *
336106 AAAATTACCAATTTACCAC-TAAATTTCCAAAAATTTTATTTTTACACCTAAGTTTCCAAAAATT
1 AAAATTACCAATTTACC-CTTAAATTTCCAAAAATTTCATTTTAACACCAAACTTTCCAAAAATT
* *
336170 ACCGTTTTACCCCCGAACCTCCAAAAATTACCATTTT
65 ACCATTTTACCCCCAAACCTCCAAAAATT-CCATTTT
336207 ACTCCTCGGG
Statistics
Matches: 269, Mismatches: 49, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
113 4 0.01
114 11 0.04
115 93 0.35
116 119 0.44
117 33 0.12
118 4 0.01
119 5 0.02
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (115 bp):
AAAATTACCAATTTACCCTTAAATTTCCAAAAATTTCATTTTAACACCAAACTTTCCAAAAATTA
CCATTTTACCCCCAAACCTCCAAAAATTCCATTTTGACCCAAACTTCCCA
Found at i:336207 original size:58 final size:56
Alignment explanation
Indices: 335807--336208 Score: 312
Period size: 58 Copynumber: 7.0 Consensus size: 56
335797 TTTTTGCCCT
** * *
335807 CAAACTTTCCAAAAATTA-CATTTTACCCCCAAACTTCCTAAAATTACCATTTTGCC
1 CAAACTTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATT-CCATTTTACC
* * *
335863 CTGAA-TTTCCCAAAAATCA-CACTTTTAGACCC-GAACTTCCAAAAATTACCATTTTACCC
1 C-AAACTTT-CCAAAAATTACCA-TTTTA-CCCCTGAACTTCCAAAAATT-CCATTTTA-CC
* * * *
335922 TCAAAC-TTCAAAAAATTA-CATTTTTTCCCTTGAACTTTCAAAAATTCCATTTTGACC
1 -CAAACTTTCCAAAAATTACCA-TTTTACCCCTGAACTTCCAAAAATTCCATTTT-ACC
** * * * *
335979 CAAACTTTTTAAAAATTACCATTTTACCCTTGAATTTTCAAAAATTTCATTTTAACCC
1 CAAACTTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTT-A-CC
* * * *
336037 CAAACTTTCCAAAAATTACCATTTTACCCCTAAATTTCAAAAAAATCCATTTTGACC
1 CAAACTTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTT-ACC
* * * * * **
336094 TCAAACTTCCCAAAAATTACCAATTTACCACTAAATTTCCAAAAATTTTATTTTTACAC
1 -CAAACTTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCA-TTTTAC-C
* * * * *
336153 CTAAGTTTCCAAAAATTACCGTTTTACCCCCGAACCTCCAAAAATTACCATTTTAC
1 CAAACTTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATT-CCATTTTAC
336209 TCCTCGGGCA
Statistics
Matches: 282, Mismatches: 48, Indels: 30
0.78 0.13 0.08
Matches are distributed among these distances:
56 9 0.03
57 66 0.23
58 191 0.68
59 15 0.05
60 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (56 bp):
CAAACTTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTACC
Found at i:345440 original size:32 final size:32
Alignment explanation
Indices: 345399--345462 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
345389 AATAAAGGAA
*
345399 AATTCAAACTCAAA-ATTCT-AAATTTAAAATCT
1 AATTCAAACT-AAAGA-TCTAAAATCTAAAATCT
*
345431 AATTGAAACTAAAGATCTAAAATCTAAAATCT
1 AATTCAAACTAAAGATCTAAAATCTAAAATCT
345463 TCGAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (32 bp):
AATTCAAACTAAAGATCTAAAATCTAAAATCT
Found at i:348353 original size:19 final size:19
Alignment explanation
Indices: 348317--348356 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
348307 CAAAATTAAC
348317 TTGTCTAATCAGAATGAGA
1 TTGTCTAATCAGAATGAGA
*
348336 TTGTCGTAATCA-ATTGAGA
1 TTGTC-TAATCAGAATGAGA
348355 TT
1 TT
348357 AAATTATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (19 bp):
TTGTCTAATCAGAATGAGA
Found at i:350830 original size:29 final size:29
Alignment explanation
Indices: 350798--350860 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
350788 TAAAAATACG
* *
350798 ATTTTTGGATATTCGAGGGTAAAATGGTA
1 ATTTTTGAAGATTCGAGGGTAAAATGGTA
*
350827 ATTTTTGAAGGTTCGAGGGTAAAATGGTA
1 ATTTTTGAAGATTCGAGGGTAAAATGGTA
350856 ATTTT
1 ATTTT
350861 GGACACTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.40
Consensus pattern (29 bp):
ATTTTTGAAGATTCGAGGGTAAAATGGTA
Found at i:351004 original size:58 final size:58
Alignment explanation
Indices: 350932--351154 Score: 209
Period size: 59 Copynumber: 3.8 Consensus size: 58
350922 GAAGTTCAAA
* *
350932 GGTAAAATGGTAATTTTTGAAAAATTCGAGATCAAAAATGTAATTTTTGGACATCTGG
1 GGTAAAATGGTAATTTTTGAAAAATTCGAGGTCAAAAATGGAATTTTTGGACATCTGG
* * ** * * * *
350990 GCTAAAATGATAATTTTTGAAATTTTTGAGGTCAAAAATGGAAATTTAGAACATCTGAG
1 GGTAAAATGGTAATTTTTGAAAAATTCGAGGTCAAAAATGGAATTTTTGGACATCTG-G
* * * *
351049 GGTAAAATGGT-ATTTTTTAGAAAGTTCGAGGTCAAAAAGGGAATTTTTGGA-AGTTTAGG
1 GGTAAAATGGTAATTTTTGA-AAAATTCGAGGTCAAAAATGGAATTTTTGGACA-TCT-GG
* ** * *
351108 GGTGAAAAT-GTAATTTTTGAGAAATTTAAGGACAAAAATGCAATTTT
1 GGT-AAAATGGTAATTTTTGAAAAATTCGAGGTCAAAAATGGAATTTT
351155 AGAAAGTTCA
Statistics
Matches: 130, Mismatches: 29, Indels: 11
0.76 0.17 0.06
Matches are distributed among these distances:
58 55 0.42
59 62 0.48
60 13 0.10
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTTGAAAAATTCGAGGTCAAAAATGGAATTTTTGGACATCTGG
Found at i:351153 original size:30 final size:31
Alignment explanation
Indices: 351052--351279 Score: 122
Period size: 30 Copynumber: 7.6 Consensus size: 31
351042 ATCTGAGGGT
* * *
351052 AAAATGGT-ATTTTTTAGAAAGTTCGAGGTCA
1 AAAAT-GTAATTTTTGAGAAAGTTCAAGGACA
* * * * ***
351083 AAAAGGGAATTTTTG-G-AAGTTTAGGGGTG
1 AAAATGTAATTTTTGAGAAAGTTCAAGGACA
*
351112 AAAATGTAATTTTTGAGAAA-TTTAAGGACA
1 AAAATGTAATTTTTGAGAAAGTTCAAGGACA
* *
351142 AAAATGCAA-TTTT-AGAAAGTTCAAGGGCA
1 AAAATGTAATTTTTGAGAAAGTTCAAGGACA
*** *
351171 AAAATGTAATTTTTG-GAAAGCTTGGTGGTC-
1 AAAATGTAATTTTTGAGAAAG-TTCAAGGACA
* * *
351201 AAAATATAATTTTT--GAAAGTTTAGGGATC-
1 AAAATGTAATTTTTGAGAAAGTTCAAGGA-CA
* * *
351230 AAAATGTAATTTTTG-GAAAGTTTATGGGGC-
1 AAAATGTAATTTTTGAGAAAGTTCA-AGGACA
351260 AAAATGTAATTTTTGAGAAA
1 AAAATGTAATTTTTGAGAAA
351280 TTCGAGGGCC
Statistics
Matches: 156, Mismatches: 30, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
28 9 0.06
29 59 0.38
30 64 0.41
31 24 0.15
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (31 bp):
AAAATGTAATTTTTGAGAAAGTTCAAGGACA
Found at i:351162 original size:59 final size:58
Alignment explanation
Indices: 351048--351275 Score: 176
Period size: 59 Copynumber: 3.9 Consensus size: 58
351038 GAACATCTGA
* * ** * * *
351048 GGGT-AAAATGGTATTTTTTAGAAAGTTCGAGGTCAAAAAGGGAATTTTTGGAAGTTTAG
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTTAAGGACAAAAA-TGAATTTTTGAAAGTTTAG
* * * *
351107 GGGTGAAAATGTAATTTTTGAGAAA-TTTAAGGACAAAAATGCAATTTTAGAAAGTTCAA
1 GGGTAAAAATGTAATTTTTG-GAAAGTTTAAGGACAAAAATG-AATTTTTGAAAGTTTAG
* *** *
351166 GGGCAAAAATGTAATTTTTGGAAAGCTTGGTGGTCAAAATAT-AATTTTTGAAAGTTTAG
1 GGGTAAAAATGTAATTTTTGGAAAG-TTTAAGGACAAAA-ATGAATTTTTGAAAGTTTAG
* * * *
351225 GGATCAAAATGTAATTTTTGGAAAGTTTATGGGGC-AAAATGTAATTTTTGA
1 GGGTAAAAATGTAATTTTTGGAAAGTTTA-AGGACAAAAATG-AATTTTTGA
351276 GAAATTCGAG
Statistics
Matches: 134, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
57 2 0.01
58 10 0.07
59 102 0.76
60 18 0.13
61 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAAGTTTAAGGACAAAAATGAATTTTTGAAAGTTTAG
Found at i:351316 original size:29 final size:29
Alignment explanation
Indices: 351090--351316 Score: 151
Period size: 30 Copynumber: 7.7 Consensus size: 29
351080 TCAAAAAGGG
** *
351090 AATTTTTGG-AAGTTTAGGGGTGAAAATGT
1 AATTTTTGGAAAGTTTA-GGGCCAAAATAT
* *
351119 AATTTTTGAGAAA-TTTAAGGACAAAA-AT
1 AATTTTTG-GAAAGTTTAGGGCCAAAATAT
* * * *
351147 GCAA-TTTTAGAAAGTTCAAGGGCAAAAATGT
1 --AATTTTTGGAAAGTT-TAGGGCCAAAATAT
* * *
351178 AATTTTTGGAAAGCTTGGTGGTCAAAATAT
1 AATTTTTGGAAAGTTTAG-GGCCAAAATAT
* *
351208 AATTTTT-GAAAGTTTAGGGATCAAAATGT
1 AATTTTTGGAAAGTTTAGGG-CCAAAATAT
* *
351237 AATTTTTGGAAAGTTTATGGGGCAAAATGT
1 AATTTTTGGAAAGTTTA-GGGCCAAAATAT
*
351267 AATTTTTGAGAAA-TTCGAGGGCCAAAATAT
1 AATTTTTG-GAAAGTT-TAGGGCCAAAATAT
* *
351297 GATTTTTGGATAGTTTAGGG
1 AATTTTTGGAAAGTTTAGGG
351317 ACCTTTTAGG
Statistics
Matches: 156, Mismatches: 27, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
28 7 0.04
29 53 0.34
30 85 0.54
31 11 0.07
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.35
Consensus pattern (29 bp):
AATTTTTGGAAAGTTTAGGGCCAAAATAT
Found at i:352407 original size:18 final size:18
Alignment explanation
Indices: 352378--352422 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
352368 TGTTTATTAA
352378 TATTATTTAATATGAATA-T
1 TATTA-TTAATA-GAATATT
*
352397 TATTATTAATAGCATATT
1 TATTATTAATAGAATATT
352415 TATTATTA
1 TATTATTA
352423 TCATTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (18 bp):
TATTATTAATAGAATATT
Found at i:352432 original size:15 final size:15
Alignment explanation
Indices: 352395--352436 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
352385 TAATATGAAT
*
352395 ATTATTATTAATAGC
1 ATTATTATTATTAGC
*
352410 A-TATTTATTATTATC
1 ATTA-TTATTATTAGC
352425 ATTATTATTATT
1 ATTATTATTATT
352437 GTTTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 19 0.83
16 2 0.09
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTATTATTATTAGC
Found at i:353167 original size:17 final size:16
Alignment explanation
Indices: 353145--353224 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 16
353135 ATTTTGGACT
*
353145 TTTTAAATTTAATTTAA
1 TTTTAAATTTAA-ATAA
*
353162 TTTTAAGTTTAAA-ACCA
1 TTTTAAATTTAAATA--A
*
353179 TTTTAAATTTAACTAA
1 TTTTAAATTTAAATAA
* *
353195 ATTTAAATTTAAAACAA
1 TTTTAAATTT-AAATAA
*
353212 ATTTAAATTTAAA
1 TTTTAAATTTAAA
353225 ACAAATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
15 1 0.02
16 13 0.25
17 37 0.71
18 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (16 bp):
TTTTAAATTTAAATAA
Found at i:353206 original size:33 final size:34
Alignment explanation
Indices: 353145--353223 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 34
353135 ATTTTGGACT
* * * *
353145 TTTTAAATTTAATTTAATTTTAAGTTTAAAACCA
1 TTTTAAATTTAATCTAAATTTAAATTTAAAACAA
353179 TTTTAAATTTAA-CTAAATTTAAATTTAAAACAA
1 TTTTAAATTTAATCTAAATTTAAATTTAAAACAA
*
353212 ATTTAAATTTAA
1 TTTTAAATTTAA
353224 AACAAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 28 0.70
34 12 0.30
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (34 bp):
TTTTAAATTTAATCTAAATTTAAATTTAAAACAA
Found at i:353225 original size:17 final size:17
Alignment explanation
Indices: 353163--353231 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
353153 TTAATTTAAT
* * *
353163 TTTAAGTTTAAAACCAT
1 TTTAAATTTAAAACAAA
353180 TTTAAATTT--AACTAAA
1 TTTAAATTTAAAAC-AAA
353196 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAACAAA
353213 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAACAAA
353230 TT
1 TT
353232 AAAACCAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 3 0.07
16 10 0.22
17 30 0.65
18 3 0.07
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAACAAA
Found at i:353233 original size:27 final size:28
Alignment explanation
Indices: 353199--353268 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
353189 AACTAAATTT
*
353199 AAATTTAAAACAAATTTAAATTTAAAAC
1 AAATTTAAAACAAATTTAAACTTAAAAC
* * *
353227 AAA-TTAAAACCAATTTAAACTTAATAT
1 AAATTTAAAACAAATTTAAACTTAAAAC
353254 AAATTTAAAATCAAA
1 AAATTTAAAA-CAAA
353269 AGTTTGATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 23 0.66
28 9 0.26
29 3 0.09
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATTTAAAACAAATTTAAACTTAAAAC
Found at i:354246 original size:208 final size:209
Alignment explanation
Indices: 353629--354416 Score: 1121
Period size: 209 Copynumber: 3.8 Consensus size: 209
353619 ATCACTTGTT
* * * * * *
353629 TTTGATTCACTTCTCTGTATCTCATCTGGAAGGTAACCATTTTATTGCTTTGACCTACTTCTCAG
1 TTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAG
* * * **
353694 TATCTTATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCTTGGTTTCATTGATTTGGTC
66 TATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACTTTGAGCTTGACTTCATTGATTTGGTC
* * * *
353759 TTCTTCTTAGTATCTCATCTGGAAGATGACCGCATCGCTTGTTTCAATTCGCTTCTCTGTATCTC
131 TACTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
* *
353824 ATCAGCAAGGCGAA
196 ATCAGGAAGACGAA
* * * * * * * *
353838 TTTGGTCCATTTCTTAGTATCTCATCAGGAAGCTAGCTATTTTATTGCTTTGACTTGCTTCTCAA
1 TTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAG
* * * *
353903 TATCTCATCAGGAAGTTGAGGTTCGAAGAATTGCTCACATTGAGCTTGACTTCATTGATTTGATC
66 TATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACTTTGAGCTTGACTTCATTGATTTGGTC
* *
353968 TACTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
131 TACTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
*
354033 ATCAGGAAGACGAC
196 ATCAGGAAGACGAA
*
354047 TTTGGTTCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAG
1 TTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAG
* * *
354112 TATCTCATTAGGAAGTTAAGGTTCGAAGATTTGCTCACTTTGAG-TCTG-CTTCATTGATTTGGT
66 TATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACTTTGAGCT-TGACTTCATTGATTTGGT
* *
354175 CTACTTCTTTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCT
130 CTACTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCT
354240 CATCAGGAAGACGAA
195 CATCAGGAAGACGAA
* *
354255 TTTGGTTCACTTCTCAGTATCTCATCAGGAAGATAACCATTTTATTGCTTCAACCTGCTTCTCAG
1 TTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAG
* * * * *
354320 TATCTAATCAGGAAGCTGAGGTTCAAAGATTTGCTCACTTTTAGCCTGATTTCATTGATTTGGTC
66 TATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACTTTGAGCTTGACTTCATTGATTTGGTC
** *
354385 TACTTCTTTTTATCTCATCAAGAAGATGACCG
131 TACTTCTTAGTATCTCATCAGGAAGATGACCG
354417 ACTCGTTGTT
Statistics
Matches: 514, Mismatches: 62, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
208 192 0.37
209 322 0.63
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (209 bp):
TTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAG
TATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACTTTGAGCTTGACTTCATTGATTTGGTC
TACTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
ATCAGGAAGACGAA
Found at i:354316 original size:417 final size:418
Alignment explanation
Indices: 353629--354416 Score: 1148
Period size: 417 Copynumber: 1.9 Consensus size: 418
353619 ATCACTTGTT
** * * *
353629 TTTGATTCACTTCTCTGTATCTCATCTGGAAGGTAACCATTTTATTGCTTTGACCTACTTCTCAG
1 TTTGATTCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAG
* ** *
353694 TATCTTATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCTTGGTTTCATTGATTTGGTC
66 TATCTCATCAAGAAGCTAAGGTTCGAAGATTTGCTCACTTTGAGCTTGGCTTCATTGATTTGGTC
* * * * *
353759 TTCTTCTTAGTATCTCATCTGGAAGATGACCGCATCGCTTGTTTCAATTCGCTTCTCTGTATCTC
131 TACTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCTC
* * * * * * *
353824 ATCAGCAAGGCGAATTTGGTCCATTTCTTAGTATCTCATCAGGAAGCTAGCTATTTTATTGCTTT
196 ATCAGCAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACCATTTTATTGCTTC
* * * * * *
353889 GACTTGCTTCTCAATATCTCATCAGGAAGTTGAGGTTCGAAGAATTGCTCACATTGAGCTTGACT
261 AACCTGCTTCTCAATATCTAATCAGGAAGCTGAGGTTCAAAGAATTGCTCACATTGAGCCTGACT
*
353954 TCATTGATTTGATCTACTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
326 TCATTGATTTGATCTACTTCTCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCG
354019 CTTCTCTGTATCTCATCAGGAAGACGAC
391 CTTCTCTGTATCTCATCAGGAAGACGAC
* *
354047 TTTGGTTCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAG
1 TTTGATTCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAG
* * *
354112 TATCTCATTAGGAAGTTAAGGTTCGAAGATTTGCTCACTTTGAG-TCT-GCTTCATTGATTTGGT
66 TATCTCATCAAGAAGCTAAGGTTCGAAGATTTGCTCACTTTGAGCT-TGGCTTCATTGATTTGGT
*
354175 CTACTTCTTTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCT
130 CTACTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCT
* *
354240 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGATAACCATTTTATTGCTT
195 CATCAGCAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACCATTTTATTGCTT
* * * * *
354305 CAACCTGCTTCTCAGTATCTAATCAGGAAGCTGAGGTTCAAAGATTTGCTCACTTTTAGCCTGAT
260 CAACCTGCTTCTCAATATCTAATCAGGAAGCTGAGGTTCAAAGAATTGCTCACATTGAGCCTGAC
* ***
354370 TTCATTGATTTGGTCTACTTCTTTTTATCTCATCAAGAAGATGACCG
325 TTCATTGATTTGATCTACTTCTCAATATCTCATCAAGAAGATGACCG
354417 ACTCGTTGTT
Statistics
Matches: 324, Mismatches: 45, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
417 227 0.70
418 97 0.30
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (418 bp):
TTTGATTCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAG
TATCTCATCAAGAAGCTAAGGTTCGAAGATTTGCTCACTTTGAGCTTGGCTTCATTGATTTGGTC
TACTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCTC
ATCAGCAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACCATTTTATTGCTTC
AACCTGCTTCTCAATATCTAATCAGGAAGCTGAGGTTCAAAGAATTGCTCACATTGAGCCTGACT
TCATTGATTTGATCTACTTCTCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCG
CTTCTCTGTATCTCATCAGGAAGACGAC
Found at i:366429 original size:30 final size:29
Alignment explanation
Indices: 366367--366435 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
366357 TAAAAATATG
* ***
366367 ATTTTTGGATACCCGAGGGTAAAATGGTA
1 ATTTTTGGATACCCGAGGATAAAATAAAA
*
366396 ATTTTTGGATACTCGAGGATGAAAATAAAA
1 ATTTTTGGATACCCGAGGAT-AAAATAAAA
*
366426 ATTTTCGGAT
1 ATTTTTGGAT
366436 GTTCAGGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (29 bp):
ATTTTTGGATACCCGAGGATAAAATAAAA
Found at i:366546 original size:29 final size:30
Alignment explanation
Indices: 366380--366988 Score: 102
Period size: 29 Copynumber: 20.4 Consensus size: 30
366370 TTTGGATACC
*
366380 CGAGGGT-AAAATGGTAATTTTTGGATA-CT
1 CGAGGGTAAAAATGGTAATTTTTGGA-AGTT
* * *** * *
366409 CGAGGATGAAAATAAAAATTTTCGGATGTT
1 CGAGGGTAAAAATGGTAATTTTTGGAAGTT
* *
366439 C-AGGGGT-AAAATAGTAA-TTTTGGACACTT
1 CGA-GGGTAAAAATGGTAATTTTTGGA-AGTT
* * * * * *
366468 CGAGGG-CAAAACGATAATCTTTAGAAATTT
1 CGAGGGTAAAAATGGTAAT-TTTTGGAAGTT
* *
366498 CGA-GATAAAAAATGAT-ATTTTTGGAAGTT
1 CGAGGGT-AAAAATGGTAATTTTTGGAAGTT
** *
366527 CGAGGGT-AAAATGGTAATTTTTAAAAATT
1 CGAGGGTAAAAATGGTAATTTTTGGAAGTT
** * ** *
366556 TTAGGGTCAAAAATAG-AA-TTTTCAAACTTT
1 CGAGGGT-AAAAATGGTAATTTTTGGAA-GTT
* *
366586 CGAGTGT-AAAATAGTAATTTTTGGAAAGTT
1 CGAGGGTAAAAATGGTAATTTTTGG-AAGTT
* *
366616 CG-GGGTCAAAAA-GG-ATTTTTTTTGAAGTT
1 CGAGGGT-AAAAATGGTA-ATTTTTGGAAGTT
** * *
366645 TAAGGGTGAAAAT-GTAATCTTTGAGAA-TT
1 CGAGGGTAAAAATGGTAATTTTTG-GAAGTT
*** * *
366674 TTTGGGTCAAAATGGGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGTAATTTTTGGAAGTT
*
366704 C-ATGGGTGAAAAT-GTAATTTTTGAGAAATTTGAGTGT
1 CGA-GGGTAAAAATGGTAATTTTTG-G--A----AGT-T
** *
366741 TTAGAGGTAAAAAT-GTAATTTTTGAGAAATT
1 CGAG-GGTAAAAATGGTAATTTTTG-GAAGTT
* * *
366772 C-AAGGTCAAAAA-GGGAATTTTTTGAAGTT
1 CGAGGGT-AAAAATGGTAATTTTTGGAAGTT
* *
366801 -TAGGGGTAAAAAT-GTAATTTTTGAGAAATT
1 CGA-GGGTAAAAATGGTAATTTTTG-GAAGTT
* * *
366831 TGA-GGTCAAAGAT-GTAA-TTTGGGAAAGTT
1 CGAGGGT-AAAAATGGTAATTTTTGG-AAGTT
* * *
366860 CGAGGGAAAAAAT-ATAA-TTTTAGAAGTT
1 CGAGGGTAAAAATGGTAATTTTTGGAAGTT
** *
366888 TAAGGGTTAAAATATGG---TTTTTGAAAAGTT
1 CGAGGG-TAAAA-ATGGTAATTTTTG-GAAGTT
* * *
366918 -TAGGGGTTAAAAT-GTAATTTTTAGAAAGTT
1 CGA-GGGTAAAAATGGTAATTTTT-GGAAGTT
366948 CGAGGGT-AAAAT-GTAATTTTTGAGAAGTT
1 CGAGGGTAAAAATGGTAATTTTTG-GAAGTT
*
366977 CGGGGGCTAAAA
1 CGAGGG-TAAAA
366989 TATGATTTTT
Statistics
Matches: 425, Mismatches: 93, Indels: 122
0.66 0.15 0.19
Matches are distributed among these distances:
27 1 0.00
28 33 0.08
29 190 0.45
30 140 0.33
31 31 0.07
32 3 0.01
36 4 0.01
37 2 0.00
38 21 0.05
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (30 bp):
CGAGGGTAAAAATGGTAATTTTTGGAAGTT
Found at i:366568 original size:59 final size:59
Alignment explanation
Indices: 366505--366734 Score: 168
Period size: 59 Copynumber: 3.9 Consensus size: 59
366495 TTTCGAGATA
366505 AAAAAT-GATATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTAAAAATTTTAGGGTC
1 AAAAATGGA-ATTTTTGGAAGTTCGAGGGTGAAAAT-GTAATTTTTAAAAATTTTAGGGTC
* ** * * ** * **
366564 AAAAATAGAA-TTTTCAAACTTTCGAGTGT-AAAATAGTAATTTTTGGAAAGTTCGGGGTC
1 AAAAATGGAATTTTTGGAA-GTTCGAGGGTGAAAAT-GTAATTTTTAAAAATTTTAGGGTC
* * ** * * * *
366623 AAAAA-GGATTTTTTTTGAAGTTTAAGGGTGAAAATGTAATCTTTGAGAATTTTTGGGTC
1 AAAAATGGA-ATTTTTGGAAGTTCGAGGGTGAAAATGTAATTTTTAAAAATTTTAGGGTC
*
366682 -AAAATGGGAATTTTTGGAAGTTC-ATGGGTGAAAATGTAATTTTTGAGAAATTT
1 AAAAAT-GGAATTTTTGGAAGTTCGA-GGGTGAAAATGTAATTTTT-AAAAATTT
366735 GAGTGTTTAG
Statistics
Matches: 131, Mismatches: 31, Indels: 17
0.73 0.17 0.09
Matches are distributed among these distances:
58 13 0.10
59 97 0.74
60 21 0.16
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTGAAAATGTAATTTTTAAAAATTTTAGGGTC
Found at i:366716 original size:30 final size:29
Alignment explanation
Indices: 366633--366976 Score: 103
Period size: 29 Copynumber: 11.4 Consensus size: 29
366623 AAAAAGGATT
* *
366633 TTTTTTGAAGTTTAAGGGTGAAAATGTAA
1 TTTTTGGAAGTTTATGGGTGAAAATGTAA
* * * *
366662 TCTTTGAGAA-TTTTTGGGTCAAAATGGGAA
1 TTTTTG-GAAGTTTATGGGTGAAAAT-GTAA
*
366692 TTTTTGGAAGTTCATGGGTGAAAATGTAA
1 TTTTTGGAAGTTTATGGGTGAAAATGTAA
* *
366721 TTTTTGAGAAATTTGAGTGTTTAGAGGTAAAAATGTAA
1 TTTTTG-GAAGTTT-A-----T-G-GGTGAAAATGTAA
* * * * * *
366759 TTTTTGAGAAATTCA-AGGTCAAAAAGGGAA
1 TTTTTG-GAAGTTTATGGGT-GAAAATGTAA
* * *
366789 TTTTTTGAAGTTTAGGGGTAAAAATGTAA
1 TTTTTGGAAGTTTATGGGTGAAAATGTAA
* *
366818 TTTTTGAGAA-ATT-TGAGGTCAAAGATGTAA
1 TTTTTG-GAAGTTTATG-GGTGAAA-ATGTAA
* * ** *
366848 -TTTGGGAAAGTTCGA-GGGAAAAAATATAA
1 TTTTTGG-AAGTT-TATGGGTGAAAATGTAA
* * * * **
366877 -TTTTAGAAGTTTAAGGGTTAAAATATGG
1 TTTTTGGAAGTTTATGGGTGAAAATGTAA
* * *
366905 TTTTTGAAAAGTTTAGGGGTTAAAATGTAA
1 TTTTTG-GAAGTTTATGGGTGAAAATGTAA
* *
366935 TTTTTAGAAAGTTCGA-GGGT-AAAATGTAA
1 TTTTT-GGAAGTT-TATGGGTGAAAATGTAA
366964 TTTTTGAGAAGTT
1 TTTTTG-GAAGTT
366977 CGGGGGCTAA
Statistics
Matches: 239, Mismatches: 49, Indels: 54
0.70 0.14 0.16
Matches are distributed among these distances:
27 1 0.00
28 18 0.08
29 96 0.40
30 92 0.38
31 4 0.02
36 1 0.00
37 2 0.01
38 25 0.10
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTTTGGAAGTTTATGGGTGAAAATGTAA
Found at i:366758 original size:97 final size:97
Alignment explanation
Indices: 366653--366834 Score: 274
Period size: 97 Copynumber: 1.9 Consensus size: 97
366643 TTTAAGGGTG
* *** * * *
366653 AAAATGTAATCTTTGAGAATTTTTGGGTCAAAATGGGAATTTTTGGAAGTTCATGGGTGAAAATG
1 AAAATGTAATCTTTGAGAAATTCAAGGTCAAAAAGGGAATTTTTGGAAGTTCAGGGGTAAAAATG
366718 TAATTTTTGAGAAATTTGAGTGTTTAGAGGTA
66 TAATTTTTGAGAAATTTGAGTGTTTAGAGGTA
* * *
366750 AAAATGTAATTTTTGAGAAATTCAAGGTCAAAAAGGGAATTTTTTGAAGTTTAGGGGTAAAAATG
1 AAAATGTAATCTTTGAGAAATTCAAGGTCAAAAAGGGAATTTTTGGAAGTTCAGGGGTAAAAATG
366815 TAATTTTTGAGAAATTTGAG
66 TAATTTTTGAGAAATTTGAG
366835 GTCAAAGATG
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 75 1.00
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (97 bp):
AAAATGTAATCTTTGAGAAATTCAAGGTCAAAAAGGGAATTTTTGGAAGTTCAGGGGTAAAAATG
TAATTTTTGAGAAATTTGAGTGTTTAGAGGTA
Found at i:366878 original size:156 final size:157
Alignment explanation
Indices: 366593--366880 Score: 365
Period size: 156 Copynumber: 1.8 Consensus size: 157
366583 TTTCGAGTGT
** * *
366593 AAAATAGTAATTTTTGGAAAGTTCGGGGTCAAAAAGGATTTTTTTTGAAGTTTAAGGGTGAAAAT
1 AAAATAGTAATTTTTGGAAAGTTCAAGGTCAAAAAGGATATTTTTTGAAGTTTAAGGGTAAAAAT
* * ** *
366658 GTAATCTTTGAGAATTTTTGGGTCAAAATGGGAATTTTTGGAAGTTCATGGGTGAAAATGTAATT
66 GTAATCTTTGAGAATATTTGGGTCAAAATGGGAATTTTGGGAAGTTCATGGGAAAAAATATAATT
366723 TTTGAGAAATTTGAGTGTTTAGAGGTA
131 TTTGAGAAATTTGAGTGTTTAGAGGTA
*
366750 AAAAT-GTAATTTTTGAGAAA-TTCAAGGTCAAAAAGGGA-ATTTTTTGAAGTTTAGGGGTAAAA
1 AAAATAGTAATTTTTG-GAAAGTTCAAGGTCAAAAA-GGATATTTTTTGAAGTTTAAGGGTAAAA
* *
366812 ATGTAATTTTTGAGAA-ATTTGAGGTCAAAGAT-GTAA-TTTGGGAAAGTTCGA-GGGAAAAAAT
64 ATGTAATCTTTGAGAATATTTG-GGTCAAA-ATGGGAATTTTGGG-AAGTTC-ATGGGAAAAAAT
366873 ATAATTTT
125 ATAATTTT
366881 AGAAGTTTAA
Statistics
Matches: 113, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
155 9 0.08
156 89 0.79
157 15 0.13
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (157 bp):
AAAATAGTAATTTTTGGAAAGTTCAAGGTCAAAAAGGATATTTTTTGAAGTTTAAGGGTAAAAAT
GTAATCTTTGAGAATATTTGGGTCAAAATGGGAATTTTGGGAAGTTCATGGGAAAAAATATAATT
TTTGAGAAATTTGAGTGTTTAGAGGTA
Found at i:366988 original size:30 final size:30
Alignment explanation
Indices: 366750--366999 Score: 129
Period size: 30 Copynumber: 8.5 Consensus size: 30
366740 TTTAGAGGTA
* * *
366750 AAAATGTAATTTTTGAGAAATTCAAGGTCA
1 AAAATGTAATTTTTGAGAAGTTCAAGGGCT
* * * * *
366780 AAAAGGGAATTTTT-TGAAGTT-TAGGGGT
1 AAAATGTAATTTTTGAGAAGTTCAAGGGCT
* ** *
366808 AAAAATGTAATTTTTGAGAAATTTGAGGTC-
1 -AAAATGTAATTTTTGAGAAGTTCAAGGGCT
** * **
366838 AAAGATGTAATTTGGGA-AAGTTCGAGGGAA
1 AAA-ATGTAATTTTTGAGAAGTTCAAGGGCT
* * *
366868 AAAATATAA-TTTT-AGAAGTTTAAGGGTT
1 AAAATGTAATTTTTGAGAAGTTCAAGGGCT
* ** * * * *
366896 AAAATATGGTTTTTGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTTGAGAAGTTCAAGGGCT
*
366926 AAAATGTAATTTTT-AGAAAGTTCGAGGG-T
1 AAAATGTAATTTTTGAG-AAGTTCAAGGGCT
**
366955 AAAATGTAATTTTTGAGAAGTTCGGGGGCT
1 AAAATGTAATTTTTGAGAAGTTCAAGGGCT
* *
366985 AAAATATGATTTTTG
1 AAAATGTAATTTTTG
367000 GACAATTTAG
Statistics
Matches: 167, Mismatches: 42, Indels: 22
0.72 0.18 0.10
Matches are distributed among these distances:
27 1 0.01
28 21 0.13
29 63 0.38
30 79 0.47
31 3 0.02
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTCAAGGGCT
Found at i:366988 original size:59 final size:59
Alignment explanation
Indices: 366750--366999 Score: 174
Period size: 59 Copynumber: 4.3 Consensus size: 59
366740 TTTAGAGGTA
* * * * *
366750 AAAATGTAATTTTTGAGAAATTC-AAGGTCAAAAAGGGAATTTTT-TGAAGTTTAGGGGT
1 AAAATGTAATTTTTGAGAAATTCGAGGGTC-AAAATGTAATTTTTGAGAAGTTCAGGGGT
* ** **
366808 AAAAATGTAATTTTTGAGAAATTTGA-GGTCAAAGATGTAATTTGGGA-AAGTTCGAGGGAA
1 -AAAATGTAATTTTTGAGAAATTCGAGGGTCAAA-ATGTAATTTTTGAGAAGTTC-AGGGGT
* * ** * * ** * *
366868 AAAATATAA-TTTT-AGAAGTTTAAGGGTTAAAATATGGTTTTTGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTTGAGAAATTCGAGGGTCAAAATGTAATTTTTGAGAAGTTCAGGGG-T
*
366926 AAAATGTAATTTTT-AGAAAGTTCGAGGGT-AAAATGTAATTTTTGAGAAGTTCGGGGGCT
1 AAAATGTAATTTTTGAGAAA-TTCGAGGGTCAAAATGTAATTTTTGAGAAGTTCAGGGG-T
* *
366985 AAAATATGATTTTTG
1 AAAATGTAATTTTTG
367000 GACAATTTAG
Statistics
Matches: 147, Mismatches: 34, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
57 20 0.14
58 26 0.18
59 89 0.61
60 12 0.08
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (59 bp):
AAAATGTAATTTTTGAGAAATTCGAGGGTCAAAATGTAATTTTTGAGAAGTTCAGGGGT
Found at i:368304 original size:34 final size:33
Alignment explanation
Indices: 368266--368386 Score: 115
Period size: 33 Copynumber: 3.7 Consensus size: 33
368256 ATTTTGGACT
* *
368266 TTTTAAATTTAATTTAATTTTAAATTTAAAACCA
1 TTTTAAATTTAA-CTAAATTTAAATTTAAAACCA
**
368300 TTTTAAATTTAACTAAATTTAAATTTAAAAATA
1 TTTTAAATTTAACTAAATTTAAATTTAAAACCA
**
368333 TATTTAAA-TTAA--AAA-ACAAATTTAAAACCA
1 T-TTTAAATTTAACTAAATTTAAATTTAAAACCA
* *
368363 ATTTAAATTTAATATAAATTTAAA
1 TTTTAAATTTAA-CTAAATTTAAA
368387 ATCAAAAGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
29 6 0.09
30 15 0.21
31 3 0.04
33 25 0.36
34 21 0.30
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (33 bp):
TTTTAAATTTAACTAAATTTAAATTTAAAACCA
Found at i:368339 original size:18 final size:18
Alignment explanation
Indices: 368284--368358 Score: 68
Period size: 18 Copynumber: 4.3 Consensus size: 18
368274 TTAATTTAAT
* *
368284 TTTAAATTT-AAAACCAT
1 TTTAAATTTAAAAACAAA
368301 TTTAAATTT---AACTAAA
1 TTTAAATTTAAAAAC-AAA
* *
368317 TTTAAATTTAAAAATATA
1 TTTAAATTTAAAAACAAA
*
368335 TTTAAATTAAAAAACAAA
1 TTTAAATTTAAAAACAAA
368353 TTTAAA
1 TTTAAA
368359 ACCAATTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
15 3 0.06
16 10 0.21
17 9 0.19
18 23 0.49
19 2 0.04
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAATTTAAAAACAAA
Found at i:368382 original size:17 final size:17
Alignment explanation
Indices: 368267--368386 Score: 81
Period size: 17 Copynumber: 7.4 Consensus size: 17
368257 TTTTGGACTT
** *
368267 TTTAAATTTAATTTAAT
1 TTTAAATTTAAAATAAA
** *
368284 TTTAAATTTAAAACCAT
1 TTTAAATTTAAAATAAA
*
368301 TTTAAATTT-AACTAAA
1 TTTAAATTTAAAATAAA
*
368317 TTTAAATTTAAAAATATA
1 TTTAAATTT-AAAATAAA
368335 TTTAAA-TT-AAA-AAA
1 TTTAAATTTAAAATAAA
* **
368349 --CAAATTTAAAACCAA
1 TTTAAATTTAAAATAAA
*
368364 TTTAAATTTAATATAAA
1 TTTAAATTTAAAATAAA
368381 TTTAAA
1 TTTAAA
368387 ATCAAAAGTT
Statistics
Matches: 79, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
12 3 0.04
13 2 0.03
14 5 0.06
15 5 0.06
16 12 0.15
17 41 0.52
18 11 0.14
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:377043 original size:17 final size:18
Alignment explanation
Indices: 377010--377044 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
377000 TAATAAAATG
*
377010 TGTATAATAAATTTAAAA
1 TGTATAATAAATATAAAA
377028 TGTATAA-AAATATAAAA
1 TGTATAATAAATATAAAA
377045 ATAAAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TGTATAATAAATATAAAA
Found at i:379707 original size:18 final size:18
Alignment explanation
Indices: 379667--379709 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
379657 GTTCAAGGTG
379667 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
379685 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
379703 TAATTAA
1 TAATTAA
379710 AAACCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:388209 original size:2 final size:2
Alignment explanation
Indices: 388202--388231 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
388192 AGCACCATCA
388202 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
388232 GCTTCCTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.