Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012530.1 Kokia drynarioides strain JFW-HI SEQ_127537, 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: 532565
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 13 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:9502 original size:15 final size:15
Alignment explanation
Indices: 9482--9517 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
9472 CTAACTTATT
9482 AAAAATCATTTTTTA
1 AAAAATCATTTTTTA
9497 AAAAATCATTTTTTA
1 AAAAATCATTTTTTA
9512 AAAAAT
1 AAAAAT
9518 AAGGCTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAAATCATTTTTTA
Found at i:10198 original size:29 final size:30
Alignment explanation
Indices: 10120--10248 Score: 136
Period size: 30 Copynumber: 4.4 Consensus size: 30
10110 AAAAATTTGA
* * * *
10120 ATTTAAACCCC-AAACTTTCCAAGAATTAT
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
*
10149 GTTTTAACCCCTAAACTTTTCAAAAATTAC
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
* * * *
10179 ATTTT-AGCCCTAAACATTTCCAAAATTAT
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
* *
10208 ATTTTAACCCCTAAATTTTTCTAAAATTAC
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
*
10238 ATTTTGACCCC
1 ATTTTAACCCC
10249 AAAAATTATC
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
29 34 0.41
30 48 0.59
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ATTTTAACCCCTAAACTTTTCAAAAATTAC
Found at i:10228 original size:59 final size:59
Alignment explanation
Indices: 10131--10242 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
10121 TTTAAACCCC
*
10131 AAACTTTCCAAGAATTATGTTTTAACCCCTAAACTTTTCAAAAATTACATTTTAGCCCT
1 AAACTTTCCAAGAATTATATTTTAACCCCTAAACTTTTCAAAAATTACATTTTAGCCCT
* *
10190 AAACATTTCCAA-AATTATATTTTAACCCCTAAATTTTTCTAAAATTACATTTT
1 AAAC-TTTCCAAGAATTATATTTTAACCCCTAAACTTTTCAAAAATTACATTTT
10243 GACCCCAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
59 42 0.86
60 7 0.14
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (59 bp):
AAACTTTCCAAGAATTATATTTTAACCCCTAAACTTTTCAAAAATTACATTTTAGCCCT
Found at i:10287 original size:59 final size:58
Alignment explanation
Indices: 10127--10280 Score: 161
Period size: 59 Copynumber: 2.6 Consensus size: 58
10117 TGAATTTAAA
* * *
10127 CCCC-AAACTTTCCAAGAATTATGTTTTAACCCCTAAACTTTTCAAAAATTACATTTTAG
1 CCCCAAAAATTTCCAA-AATTATATTTTAACCCCT-AATTTTTCAAAAATTACATTTTAG
* * *
10186 CCCTAAACATTTCCAAAATTATATTTTAACCCCTAAATTTTTCTAAAATTACATTTT-G
1 CCCCAAAAATTTCCAAAATTATATTTTAACCCCT-AATTTTTCAAAAATTACATTTTAG
*
10244 ACCCCAAAAATTATCCAAAACTTCAT-TTTTGACCCCT
1 -CCCCAAAAATT-TCCAAAA-TT-ATATTTTAACCCCT
10281 TTTTTTCCTC
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
58 1 0.01
59 50 0.62
60 16 0.20
61 12 0.15
62 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (58 bp):
CCCCAAAAATTTCCAAAATTATATTTTAACCCCTAATTTTTCAAAAATTACATTTTAG
Found at i:14366 original size:24 final size:21
Alignment explanation
Indices: 14334--14383 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 21
14324 CATGATGTCA
14334 AAAAAAGAGAAAAAGGAAAGCAAG
1 AAAAAAGAGAAAAA-GAAA--AAG
14358 AAAAAAGAGAAAAAGAAAAAG
1 AAAAAAGAGAAAAAGAAAAAG
14379 AAAAA
1 AAAAA
14384 GGGACGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.31
23 4 0.15
24 14 0.54
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAAGAGAAAAAGAAAAAG
Found at i:14373 original size:15 final size:14
Alignment explanation
Indices: 14335--14377 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 14
14325 ATGATGTCAA
14335 AAAAAGAGAAAAAGG
1 AAAAAGA-AAAAAGG
14350 AAAGCAAGAAAAAAGAG
1 AAA--AAGAAAAAAG-G
14367 AAAAAGAAAAA
1 AAAAAGAAAAA
14378 GAAAAAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.44
16 6 0.24
17 8 0.32
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGG
Found at i:14382 original size:12 final size:13
Alignment explanation
Indices: 14336--14384 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 13
14326 TGATGTCAAA
14336 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
* * *
14349 GAAAG-CAAGAA-
1 AAAAGAGAAAAAG
14360 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
14373 AAAA-AGAAAAAG
1 AAAAGAGAAAAAG
14385 GGACGAGATG
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
11 4 0.14
12 16 0.57
13 8 0.29
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:16544 original size:48 final size:48
Alignment explanation
Indices: 16469--16560 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
16459 CTTCACACCC
* **
16469 CATCTTCCTGATGAGATACAGAGAAGTAGGTCAAAACAATGAAGTGAT
1 CATCTTCCTGATGAGATACAGAAAAGTAGACCAAAACAATGAAGTGAT
*
16517 CATCTTCTTGATGAGATACAGAAAAGTAGACCAAAACAATGAAG
1 CATCTTCCTGATGAGATACAGAAAAGTAGACCAAAACAATGAAG
16561 CGAAGCTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAGAAAAGTAGACCAAAACAATGAAGTGAT
Found at i:16658 original size:124 final size:122
Alignment explanation
Indices: 16392--16758 Score: 452
Period size: 124 Copynumber: 3.0 Consensus size: 122
16382 TAATTAAGTG
* *
16392 GTCATCTTCCTGATGAGATACAGAGATA-TAGACCAAAATAATAAAGTGAAGCTCAATG-AGAGT
1 GTCATCTTCCTGATGAGATACAGA-AAAGTAGACCAAAATAATGAAGTGAAGCTCAATGTA-AGT
* *
16455 GAAACTTCACACCCCATCTTCCTGATGAGATACAGAGAAGTAGGTCAAAACAATGAAGT
64 GAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTAGGTCAAAACAATGAAGA
* * *
16514 GATCATCTTCTTGATGAGATACAGAAAAGTAGACCAAAACAATGAAGCGAAGCTCAATGTAAGTG
1 G-TCATCTTCCTGATGAGATACAGAAAAGTAGACCAAAATAATGAAGTGAAGCTCAATGTAAGTG
* * * *
16579 AAACTTCAAACCCCCATCTTCCTGATAAGATACAGAGAAGT-GGATGAAAATAGTGAAGCA
65 AAACTTCAAA-CCCCATCTTCCTGATGAGATACAGAGAAGTAGG-TCAAAACAATGAAG-A
* * * * * * *
16639 GTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAATTAATGAAGTGGAGATCAATGTGAGTGA
1 GTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAAATAATGAAGTGAAGCTCAATGTAAGTGA
* * ***
16704 AACTTCAAACCCCATCTTTCTGATGAGATACAGAAAAGTAAACCAAAACAATGAA
66 AACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTAGGTCAAAACAATGAA
16759 CCGAGGCTCA
Statistics
Matches: 208, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
122 3 0.01
123 100 0.48
124 104 0.50
125 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (122 bp):
GTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAAATAATGAAGTGAAGCTCAATGTAAGTGA
AACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTAGGTCAAAACAATGAAGA
Found at i:16684 original size:48 final size:48
Alignment explanation
Indices: 16593--16684 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
16583 TTCAAACCCC
** *
16593 CATCTTCCTGATAAGATACAGAGAAGTGGATGAAAATAGTGAAGCAGT
1 CATCTTCCTGATAAGATACAGAGAAGTGGACCAAAATAATGAAGCAGT
* * *
16641 CATCTTCCTGATGAGATATAGAGAAGTGGACCAAATTAATGAAG
1 CATCTTCCTGATAAGATACAGAGAAGTGGACCAAAATAATGAAG
16685 TGGAGATCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (48 bp):
CATCTTCCTGATAAGATACAGAGAAGTGGACCAAAATAATGAAGCAGT
Found at i:16751 original size:199 final size:198
Alignment explanation
Indices: 16517--17129 Score: 861
Period size: 199 Copynumber: 3.1 Consensus size: 198
16507 ATGAAGTGAT
* * * *
16517 CATCTTCTTGATGAGATACAGAAAAGTAGACCAAAACAATGAAGCGAAGCTCAATGTAAGTGAAA
1 CATCTTCCTGATGAGATACAGAAAAGTAAACCAAAACAATGAACCGAGGCTCAATGTAAGTGAAA
* * *
16582 CTTCAAACCCCCATCTTCCTGATAAGATACAGAGAAGTGGATGAAAATAGTGAAGCAGTCATCTT
66 CTTCAAA-CCCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCAGTCATCTT
* *
16647 CCTGATGAGATATAGAGAAGTGGACCAAATTAATGAAGTGGAGATCAATGTGAGTGAAACTTCAA
130 CCTGATGAGATACAGAGAAGTGGACCAAATTAATGAAGTGGAGCTCAATGTGAGTGAAACTTCAA
16712 ACCC
195 ACCC
*
16716 CATCTTTCTGATGAGATACAGAAAAGTAAACCAAAACAATGAACCGAGGCTCAATG-AGAGTGAA
1 CATCTTCCTGATGAGATACAGAAAAGTAAACCAAAACAATGAACCGAGGCTCAATGTA-AGTGAA
* * *
16780 ACTTCAAATCCCCATCTTCCTGATGAGGTACAGAGAAGTGGATTAAAACAATGAAGTAGTCATCT
65 ACTTCAAA-CCCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCAGTCATCT
* * * * * * *
16845 TCCTGATAAGATACAAAGAACTAGACCAAAATAATGAA-TCGAGGCTCAATGCGAGTGAAACTTC
129 TCCTGATGAGATACAGAGAAGTGGACCAAATTAATGAAGTGGA-GCTCAATGTGAGTGAAACTTC
16909 AAACCC
193 AAACCC
* * * * * **
16915 CATCTTCCTGATGAGATATAGAGAAGTAAACAAAAACAATGAACCGAGGCTTAATGTGAGCAAAA
1 CATCTTCCTGATGAGATACAGAAAAGTAAACCAAAACAATGAACCGAGGCTCAATGTAAGTGAAA
* * *
16980 CTTCAAACCCTATCTTCTTGATGAGATACAGAGAAGTGGGTTAAAATAATGAAGCAGTCATCTTC
66 CTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCAGTCATCTTC
* *
17045 CTGATGAGATACAGAGAAGTGGACCAAATCAACGAAGTGGAGCTCAATGTGAGTGAAACTTCAAA
131 CTGATGAGATACAGAGAAGTGGACCAAATTAATGAAGTGGAGCTCAATGTGAGTGAAACTTCAAA
**
17110 TAC
196 CCC
*
17113 CATCTTCCTAATGAGAT
1 CATCTTCCTGATGAGAT
17130 CATCTTCTTT
Statistics
Matches: 363, Mismatches: 47, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
198 125 0.34
199 238 0.66
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (198 bp):
CATCTTCCTGATGAGATACAGAAAAGTAAACCAAAACAATGAACCGAGGCTCAATGTAAGTGAAA
CTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCAGTCATCTTC
CTGATGAGATACAGAGAAGTGGACCAAATTAATGAAGTGGAGCTCAATGTGAGTGAAACTTCAAA
CCC
Found at i:16828 original size:76 final size:75
Alignment explanation
Indices: 16641--16834 Score: 237
Period size: 75 Copynumber: 2.6 Consensus size: 75
16631 GTGAAGCAGT
* ** ** *
16641 CATCTTCCTGATGAGATATAGAGAAGTGGACCAAATTAATGAAGTGGAGATCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAACCGGAGATCAATGAGAGTGAAA
16706 CTTCAAACCC
66 CTTCAAACCC
* * ** *
16716 CATCTTTCTGATGAGATACAGAAAAGTAAACCAAAACAATGAACC-GAGGCTCAATGAGAGTGAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAACCGGA-GATCAATGAGAGTGAA
16780 ACTTCAAATCCC
65 ACTTCAAA-CCC
* **
16792 CATCTTCCTGATGAGGTACAGAGAAGTGGATTAAAACAATGAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAA
16835 GTAGTCATCT
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
74 2 0.02
75 58 0.59
76 39 0.39
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (75 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAACCGGAGATCAATGAGAGTGAAA
CTTCAAACCC
Found at i:17032 original size:75 final size:75
Alignment explanation
Indices: 16840--17016 Score: 228
Period size: 75 Copynumber: 2.4 Consensus size: 75
16830 ATGAAGTAGT
* * * * * * **
16840 CATCTTCCTGATAAGATACAAAGAACTAGACCAAAATAATGAATCGAGGCTCAATGCGAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTAAACAAAAATAATGAACCGAGGCTCAATGCGAGCAAAA
16905 CTTCAAACCC
66 CTTCAAACCC
* * * *
16915 CATCTTCCTGATGAGATATAGAGAAGTAAACAAAAACAATGAACCGAGGCTTAATGTGAGCAAAA
1 CATCTTCCTGATGAGATACAGAGAAGTAAACAAAAATAATGAACCGAGGCTCAATGCGAGCAAAA
16980 CTTCAAACCC
66 CTTCAAACCC
* *
16990 TATCTTCTTGATGAGATACAGAGAAGT
1 CATCTTCCTGATGAGATACAGAGAAGT
17017 GGGTTAAAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 87 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (75 bp):
CATCTTCCTGATGAGATACAGAGAAGTAAACAAAAATAATGAACCGAGGCTCAATGCGAGCAAAA
CTTCAAACCC
Found at i:17135 original size:17 final size:17
Alignment explanation
Indices: 17113--17146 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17103 CTTCAAATAC
17113 CATCTTCCTAATGAGAT
1 CATCTTCCTAATGAGAT
* *
17130 CATCTTCTTTATGAGAT
1 CATCTTCCTAATGAGAT
17147 ACAAAGAAGT
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:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (17 bp):
CATCTTCCTAATGAGAT
Found at i:17194 original size:92 final size:92
Alignment explanation
Indices: 17037--17221 Score: 228
Period size: 92 Copynumber: 2.0 Consensus size: 92
17027 AATGAAGCAG
* * *** **
17037 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAACGAAGTGGAGCTCAATGTGAGTGAA
1 TCATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAACGAAGCAAAGCTCAATGCAAGTGAA
*
17102 ACTTCAAATACCATCTTCCTAATGAGA
66 ACTTCAAACACCATCTTCCTAATGAGA
* * * *
17129 TCATCTTCTTTATGAGATACAAAGAAGTAGACCAAAAT-AATGAAGCAAATCTCAATGCAAGTGA
1 TCATCTTCCTGATGAGATACAAAGAAGTAGACC-AAATCAACGAAGCAAAGCTCAATGCAAGTGA
* *
17193 AACTTCAAACCCCATCTTCCTGATGAGA
65 AACTTCAAACACCATCTTCCTAATGAGA
17221 T
1 T
17222 ATAGAGAAGT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 74 0.95
93 4 0.05
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (92 bp):
TCATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAACGAAGCAAAGCTCAATGCAAGTGAA
ACTTCAAACACCATCTTCCTAATGAGA
Found at i:17398 original size:45 final size:45
Alignment explanation
Indices: 17302--17414 Score: 118
Period size: 45 Copynumber: 2.5 Consensus size: 45
17292 CATCATCATT
* * * ** * *
17302 CAATCTTGTAACCCTAAGTCAAGAGGGGCAAATTGAAGCCATTGTT
1 CAATCTT-TTACCCTAAGTCAAGAAGGACAAATTGAAAACATTATC
* *
17348 TAATCTTTTACCCTAAGTCAAGAAGGACAGATTGAAAACATTATC
1 CAATCTTTTACCCTAAGTCAAGAAGGACAAATTGAAAACATTATC
*
17393 CAATCTCTTACCCTTAAGTCAA
1 CAATCTTTTACCC-TAAGTCAA
17415 AAAGAGCATA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 41 0.75
46 14 0.25
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (45 bp):
CAATCTTTTACCCTAAGTCAAGAAGGACAAATTGAAAACATTATC
Found at i:19121 original size:30 final size:29
Alignment explanation
Indices: 19048--19172 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 29
19038 TTTTATTTAG
* *
19048 AAATTATGTTTTGACCCCTAAA-TTATCCAAA
1 AAATTATATTTTAACCCCTAAACTT-TCC--A
*
19079 AAATTA-AATTTAACCCCTAAACTTTCCA
1 AAATTATATTTTAACCCCTAAACTTTCCA
* *
19107 AGAATTATGTTTTAACCCTTAAACTTTTCCA
1 A-AATTATATTTTAACCCCTAAAC-TTTCCA
* * *
19138 AAATTACATTTT-ACACCTAAACTTTTACA
1 AAATTATATTTTAACCCCTAAAC-TTTCCA
19167 AAATTA
1 AAATTA
19173 GGTTTTGATC
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.03
29 25 0.32
30 37 0.47
31 15 0.19
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (29 bp):
AAATTATATTTTAACCCCTAAACTTTCCA
Found at i:19157 original size:59 final size:59
Alignment explanation
Indices: 19049--19197 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 59
19039 TTTATTTAGA
* *
19049 AATTATGTTTTGACCCCTAAATTATCCAAAAAATTAAATTTAACCCCTAAACTTTCCAAG
1 AATTATGTTTTAACCCCTAAATTATCC-AAAAATTAAATTTAACACCTAAACTTTCCAAG
* * * * *
19109 AATTATGTTTTAACCCTTAAACTTTTCC-AAAATTACATTTTACACCTAAACTTTTACAA-
1 AATTATGTTTTAACCCCTAAA-TTATCCAAAAATTAAATTTAACACCTAAAC-TTTCCAAG
* * * * *
19168 AATTAGGTTTTGATCCCAAAATTCTCCAAA
1 AATTATGTTTTAACCCCTAAATTATCCAAA
19198 CCTTCATTGT
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
58 5 0.07
59 38 0.52
60 25 0.34
61 5 0.07
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (59 bp):
AATTATGTTTTAACCCCTAAATTATCCAAAAATTAAATTTAACACCTAAACTTTCCAAG
Found at i:19178 original size:29 final size:29
Alignment explanation
Indices: 19087--19178 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
19077 AAAAATTAAA
*
19087 TTTAACCCCTAAAC-TTTCCAAGAATTATGT
1 TTTAA-CCCTAAACTTTTCCAA-AATTACGT
*
19117 TTTAACCCTTAAACTTTTCCAAAATTACAT
1 TTTAACCC-TAAACTTTTCCAAAATTACGT
* *
19147 TTT-ACACCTAAACTTTTACAAAATTAGGT
1 TTTAAC-CCTAAACTTTTCCAAAATTACGT
19176 TTT
1 TTT
19179 GATCCCAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
29 26 0.48
30 21 0.39
31 7 0.13
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (29 bp):
TTTAACCCTAAACTTTTCCAAAATTACGT
Found at i:52261 original size:24 final size:23
Alignment explanation
Indices: 52226--52272 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
52216 AAGAGTTAAT
52226 TTGTCAACGCAAATATAAAATAAA
1 TTGTCAACGCAAAT-TAAAATAAA
*
52250 TTGTCAGA-GCAAATTAAGATAAA
1 TTGTCA-ACGCAAATTAAAATAAA
52273 AATGAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.26
Consensus pattern (23 bp):
TTGTCAACGCAAATTAAAATAAA
Found at i:56000 original size:21 final size:21
Alignment explanation
Indices: 55976--56024 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
55966 GAAGCATGAT
*
55976 TTGTTTCGGTAGAAG-CTTCA
1 TTGTTTCGGTAGAAGTCTGCA
55996 CTTGTATT-GGTAGAAGTCTGCA
1 -TTGT-TTCGGTAGAAGTCTGCA
56018 TTGTTTC
1 TTGTTTC
56025 ATGAATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.43
Consensus pattern (21 bp):
TTGTTTCGGTAGAAGTCTGCA
Found at i:63188 original size:26 final size:26
Alignment explanation
Indices: 63145--63202 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
63135 AAAGGAAAGA
*
63145 AAATCAAATCTCCGAAAATG-GATTGT
1 AAATCAAATCTCC-AAAAAGAGATTGT
*
63171 AAATCAAATCTGCAAAAAGAAGATTGT
1 AAATCAAATCTCCAAAAAG-AGATTGT
63198 AAATC
1 AAATC
63203 TCGTGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.18
26 12 0.43
27 11 0.39
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (26 bp):
AAATCAAATCTCCAAAAAGAGATTGT
Found at i:64135 original size:49 final size:49
Alignment explanation
Indices: 63908--64261 Score: 208
Period size: 49 Copynumber: 7.2 Consensus size: 49
63898 ATGGATACTT
* * * ** ** * *
63908 ACACCTTAAATTTGAAAAGGGATAGGTTGAAGCCACAACGGCAAACCTA
1 ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGATAGATCTA
* * * * ** * *
63957 ACACCCTAAAATCGAAGACGGATAGATTGGAGCCAAAATGGTAGATCTA
1 ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGATAGATCTA
* * * ** * ** * * * *
64006 ACACCTTAAAATCGAAGAGGGAAATATTAAAGTTGCAATGGT-GAATCTT
1 ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGATAG-ATCTA
** * * * ** * * *
64055 ACAATCTAAAATCGAAGAGGAAAAGACTGAAGTCGTAACGATGGATCTT
1 ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGATAGATCTA
** * * * *
64104 ACACTTTAAAATTGAAGAGGGATAGGTTGAAGCCATAATGACAGACCTA
1 ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGATAGATCTA
*
64153 ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGATAGAACTA
1 ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGATAGATCTA
* * * * *
64202 ACACCCTAAAATTGAATAGAGATAGGTTAAAGTCGAAAC-ATTAGATCTA
1 ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGA-TAGATCTA
*
64251 AAACCCTAAAA
1 ACACCCTAAAA
64262 CCAAAGAGAA
Statistics
Matches: 241, Mismatches: 61, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
48 2 0.01
49 238 0.99
50 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (49 bp):
ACACCCTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGATAGATCTA
Found at i:64369 original size:45 final size:45
Alignment explanation
Indices: 64319--64932 Score: 636
Period size: 45 Copynumber: 13.8 Consensus size: 45
64309 AAAACCTAAA
* * ** *
64319 CAGATTGAAGCTATCATCCAATCTTTTACTTCTAATCCAGAGGGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
** *
64364 CAGATTGAAGCCACCATCCAATCTTTTACTTCTAATCCAGAGGGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* *
64409 CAGATTGAAGCCACCATTCAATCTTTTACCCCTAATCTAGAGTGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* * *
64454 CAGATTGAAGTCACCATCTAGTCTTTTACCCCTAATCTAGAGGGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* *
64499 TAGATT---G--A--A-CCAATCTTTTACCCCTAATCTGGAGGGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* * * * * **
64536 TAGATTGAAGCAACAATCCAATCTTTTACCCC-AATTCCAAAGAAG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAA-TCTAGAGGGG
* ** **
64581 CAGATTGAAGCCACCATCCAGTCTTTTACCTTTAATCTAGACAGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* * * * *
64626 CAGATTGAAGCAATCATTCAGTCTTTTACCACTAATCTAGAGGGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* *
64671 CAGATTGAAACCACCATCCAATCTTTTACCCCTAATCTAGAGGTG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* * * *** *
64716 CAAATTGAAGCAACCGTCTGGTCTTTTACCCCTAATCTATAGGGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* * * *
64761 TAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCCAGAGAGA
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* * *
64806 CAGATTAAAGCCATCATCCAATCTTTTACCCCAAATCTAGCA-GGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAG-AGGGG
* **
64851 CAGATTGAAGCAACCATCCAATCTTTTATACCTAATCTAGAGGGG
1 CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
* * *
64896 CAGATTGAAGTCACCAAATCTAATCTTTTATCCCTAA
1 CAGATTGAAGCCACC--ATCCAATCTTTTACCCCTAA
64933 ATACAAAAGG
Statistics
Matches: 473, Mismatches: 82, Indels: 26
0.81 0.14 0.04
Matches are distributed among these distances:
37 31 0.07
38 1 0.00
40 2 0.00
42 2 0.00
44 4 0.01
45 412 0.87
46 3 0.01
47 18 0.04
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (45 bp):
CAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCTAGAGGGG
Found at i:65662 original size:38 final size:38
Alignment explanation
Indices: 65604--65682 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
65594 TTCATCAGAG
*
65604 TTAATCTTATTATTTATATTTAGTTGTTTATTTTGACAT
1 TTAATCTTATTATTTATATTTAGTTATTTA-TTTGACAT
* *
65643 TTAAT-TTATTGATTT-TATTTATTTATTTATTTGTCAT
1 TTAATCTTATT-ATTTATATTTAGTTATTTATTTGACAT
65680 TTA
1 TTA
65683 TTTTCATGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 10 0.28
38 17 0.47
39 9 0.25
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (38 bp):
TTAATCTTATTATTTATATTTAGTTATTTATTTGACAT
Found at i:65805 original size:100 final size:98
Alignment explanation
Indices: 65610--65790 Score: 251
Period size: 100 Copynumber: 1.8 Consensus size: 98
65600 AGAGTTAATC
* *
65610 TTATTATTTATATTTAGTTGTTTATTTTGACATTTAATTTATTGATTTTATTTATTTATTTATTT
1 TTATTATTTATATTTAGTTGCTTATTTTGACATTTAATTTATTGATTTTATTTATTTATTTAGTT
65675 GTCATTTATTTTCATGCCCAATCCCAATTATTT
66 GTCATTTATTTTCATGCCCAATCCCAATTATTT
* *
65708 TTATTGTTTATATTT-GTTTGCTTATTTT-AGCATTTAATTTTTATTTATTTTATTTATTTATCT
1 TTATTATTTATATTTAG-TTGCTTATTTTGA-CATTTAA--TTTATTGATTTTATTTATTTAT-T
*
65771 T-GTTGTTATTTATTTTCATG
61 TAGTTGTCATTTATTTTCATG
65791 TCATTTTATT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
97 2 0.03
98 31 0.42
100 38 0.52
101 2 0.03
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (98 bp):
TTATTATTTATATTTAGTTGCTTATTTTGACATTTAATTTATTGATTTTATTTATTTATTTAGTT
GTCATTTATTTTCATGCCCAATCCCAATTATTT
Found at i:65983 original size:15 final size:15
Alignment explanation
Indices: 65963--65997 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
65953 GCACTTCATA
**
65963 TATTTATTGTTTATT
1 TATTTATTAATTATT
65978 TATTTATTAATTATT
1 TATTTATTAATTATT
65993 TATTT
1 TATTT
65998 GTTATTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTATTAATTATT
Found at i:66048 original size:22 final size:21
Alignment explanation
Indices: 66023--66068 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
66013 TGTTATTTAC
*
66023 ATTC-TTGCTTTTATTTAATTTT
1 ATTCATTG-TTTTATGT-ATTTT
66045 ATTCATTGTTTTATGTATTTT
1 ATTCATTGTTTTATGTATTTT
66066 ATT
1 ATT
66069 TTTTTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 11 0.50
23 3 0.14
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (21 bp):
ATTCATTGTTTTATGTATTTT
Found at i:66140 original size:23 final size:23
Alignment explanation
Indices: 66114--66158 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
66104 TTAATTTAAT
*
66114 TTTATTTATCAT-TGATATTTTTA
1 TTTATTTAT-ATGTCATATTTTTA
66137 TTTATTTATATGTCATATTTTT
1 TTTATTTATATGTCATATTTTT
66159 TGTGCATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTATTTATATGTCATATTTTTA
Found at i:66329 original size:23 final size:23
Alignment explanation
Indices: 66302--66354 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
66292 TTTAATACAA
*
66302 TAATTATATCTTTATTGTGTTA-T
1 TAATTATAT-TTGATTGTGTTATT
*
66325 TAATTATATTTGATTGTTTTATT
1 TAATTATATTTGATTGTGTTATT
66348 TAATTAT
1 TAATTAT
66355 TTATATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (23 bp):
TAATTATATTTGATTGTGTTATT
Found at i:70933 original size:10 final size:10
Alignment explanation
Indices: 70918--70942 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
70908 TATGAAATAT
70918 TAATTTTAAA
1 TAATTTTAAA
70928 TAATTTTAAA
1 TAATTTTAAA
70938 TAATT
1 TAATT
70943 AATATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTTTAAA
Found at i:71081 original size:14 final size:15
Alignment explanation
Indices: 71046--71082 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
71036 ATAGTTGTAT
71046 TATTTTAAATATATA
1 TATTTTAAATATATA
71061 TATTTTAAAT-TA-A
1 TATTTTAAATATATA
71074 TGATTTTAA
1 T-ATTTTAA
71083 CACATTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 9 0.43
15 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TATTTTAAATATATA
Found at i:81898 original size:18 final size:17
Alignment explanation
Indices: 81873--81906 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
81863 TATTCCTTTT
81873 CTAACTTTTATTGATTG
1 CTAACTTTTATTGATTG
81890 CTAATCTTTTATTGATT
1 CTAA-CTTTTATTGATT
81907 TCCTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTG
Found at i:83206 original size:18 final size:18
Alignment explanation
Indices: 83183--83230 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
83173 GCCTGATTAA
*
83183 ATGCAGTCACATACTCAG
1 ATGCAGTCACATAATCAG
*
83201 ATGCAGTCATATAATCAG
1 ATGCAGTCACATAATCAG
* *
83219 TTGCAATCACAT
1 ATGCAGTCACAT
83231 GTTTGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (18 bp):
ATGCAGTCACATAATCAG
Found at i:89624 original size:2 final size:2
Alignment explanation
Indices: 89617--89649 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
89607 TGATAAAAAG
*
89617 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89650 TATTATACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93053 original size:13 final size:12
Alignment explanation
Indices: 93026--93058 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
93016 GCCAATTGAG
93026 TTAG-TTTTATT
1 TTAGTTTTTATT
93037 TTAGTTTTTAGTT
1 TTAGTTTTTA-TT
93050 TTAGTTTTT
1 TTAGTTTTT
93059 CATTCATACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 5 0.25
13 11 0.55
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (12 bp):
TTAGTTTTTATT
Found at i:93156 original size:17 final size:17
Alignment explanation
Indices: 93134--93178 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
93124 GTTACATCTA
*
93134 ATTGTCATTGCATTTGC
1 ATTGTCATTGCATTTCC
*
93151 ATTGTCATTTCATTTCC
1 ATTGTCATTGCATTTCC
93168 ATTTGTCATTG
1 A-TTGTCATTG
93179 TAACTTAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (17 bp):
ATTGTCATTGCATTTCC
Found at i:94239 original size:26 final size:26
Alignment explanation
Indices: 94203--94265 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
94193 TTGCGCCATG
*
94203 AATTGTCGCTGTAAGAACTTGTTCAA
1 AATTGTCGCTGCAAGAACTTGTTCAA
* *
94229 AATTGTGGCTGCAGGAACTTGTTCAA
1 AATTGTCGCTGCAAGAACTTGTTCAA
*
94255 AATTATCGCTG
1 AATTGTCGCTG
94266 TGAGAATGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (26 bp):
AATTGTCGCTGCAAGAACTTGTTCAA
Found at i:104414 original size:22 final size:21
Alignment explanation
Indices: 104384--104425 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
104374 AGCATTATTA
*
104384 TTATATATTTTTTTTTTCTTTT
1 TTATATA-TTTTTCTTTCTTTT
*
104406 TTATCTATTTTTCTTTCTTT
1 TTATATATTTTTCTTTCTTT
104426 CTTTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (21 bp):
TTATATATTTTTCTTTCTTTT
Found at i:115623 original size:18 final size:18
Alignment explanation
Indices: 115600--115643 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
115590 TATTAAAAAA
115600 AAAGAAGAAAAAG-AAAGC
1 AAAGAA-AAAAAGAAAAGC
*
115618 AAAGAAAAAGAGAAAAGC
1 AAAGAAAAAAAGAAAAGC
115636 AAA-AAAAA
1 AAAGAAAAA
115644 TATATATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAGAAAAGC
Found at i:121338 original size:6 final size:6
Alignment explanation
Indices: 121327--121372 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
121317 TAGCAATTTA
*
121327 TTCTTT TTCTTT TTCTTT CTTCTTT TTCTCTT TT-TTT TTGTTT TTC
1 TTCTTT TTCTTT TTCTTT -TTCTTT TTCT-TT TTCTTT TTCTTT TTC
121373 AAGTGACTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 4 0.11
6 22 0.61
7 10 0.28
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:121351 original size:19 final size:18
Alignment explanation
Indices: 121327--121372 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
121317 TAGCAATTTA
121327 TTCTTTTTCT-TTTTCTTT
1 TTCTTTTTCTCTTTT-TTT
121345 CTTCTTTTTCTCTTTTTTT
1 -TTCTTTTTCTCTTTTTTT
*
121364 TTGTTTTTC
1 TTCTTTTTC
121373 AAGTGACTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 13 0.52
20 4 0.16
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (18 bp):
TTCTTTTTCTCTTTTTTT
Found at i:121977 original size:17 final size:17
Alignment explanation
Indices: 121955--121992 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
121945 AACTAAAATG
*
121955 AATGCA-ACGACAATTAA
1 AATGCAGAC-ACAATAAA
121972 AATGCAGACACAATAAA
1 AATGCAGACACAATAAA
121989 AATG
1 AATG
121993 TATGAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (17 bp):
AATGCAGACACAATAAA
Found at i:128946 original size:17 final size:17
Alignment explanation
Indices: 128908--128987 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
128898 TTGTTAGTAA
* *
128908 GCATTGTCATCACATTC
1 GCATTGTCATTACATTT
* *
128925 CCATTATCATTACATTT
1 GCATTGTCATTACATTT
*
128942 GCATTGTCACTACATTT
1 GCATTGTCATTACATTT
*
128959 GCATTGTCATTGCATTT
1 GCATTGTCATTACATTT
*
128976 CCATTTGTCATT
1 GCA-TTGTCATT
128988 GTAATTTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
17 44 0.85
18 8 0.15
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.44
Consensus pattern (17 bp):
GCATTGTCATTACATTT
Found at i:140941 original size:16 final size:16
Alignment explanation
Indices: 140917--140948 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
140907 TCCTTACAAA
*
140917 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
140933 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
140949 AAAAATTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:171772 original size:18 final size:18
Alignment explanation
Indices: 171748--171799 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
171738 AACAGTTTGG
*
171748 CAAATTAATACAGTTCAT
1 CAAATTAATACAGTTCAC
* * *
171766 CATATTAATATAGATCAC
1 CAAATTAATACAGTTCAC
*
171784 CAAATTAACACAGTTC
1 CAAATTAATACAGTTC
171800 TCCATAATAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (18 bp):
CAAATTAATACAGTTCAC
Found at i:172329 original size:3 final size:3
Alignment explanation
Indices: 172315--172359 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
172305 CCCACAAGTT
*
172315 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
172360 TTCCACTACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:176329 original size:19 final size:19
Alignment explanation
Indices: 176305--176466 Score: 71
Period size: 19 Copynumber: 8.1 Consensus size: 19
176295 TGGTCAAAGA
*
176305 AAAGTCAACAGTCAAATTC
1 AAAGTCAACAGTCAAAGTC
** *
176324 AAAGTCAATGGTTAAAGTC
1 AAAGTCAACAGTCAAAGTC
176343 AAAGTCAACTA-TCAAAGTC
1 AAAGTCAAC-AGTCAAAGTC
* *
176362 AACAAATCAATAGGTCAAAGTC
1 -A-AAGTCAACA-GTCAAAGTC
* * *
176384 AATGGGTC-A-GGTTAATAGGTC
1 AA--AGTCAACAGTCAA-A-GTC
** *
176405 AAAGTCAATGGTTAAAGTC
1 AAAGTCAACAGTCAAAGTC
176424 AAAGTCAACTA-TCAAAGTC
1 AAAGTCAAC-AGTCAAAGTC
*
176443 AACAGATCAACGGGTCAAAGTC
1 AA-AG-TCAAC-AGTCAAAGTC
176465 AA
1 AA
176467 TGGGTCAAGT
Statistics
Matches: 109, Mismatches: 19, Indels: 27
0.70 0.12 0.17
Matches are distributed among these distances:
19 57 0.52
20 8 0.07
21 24 0.22
22 20 0.18
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.22
Consensus pattern (19 bp):
AAAGTCAACAGTCAAAGTC
Found at i:176380 original size:13 final size:14
Alignment explanation
Indices: 176364--176507 Score: 81
Period size: 14 Copynumber: 10.6 Consensus size: 14
176354 TCAAAGTCAA
176364 CAAA-TCAATAGGT
1 CAAAGTCAATAGGT
*
176377 CAAAGTCAATGGGT
1 CAAAGTCAATAGGT
* *
176391 C-AGGTTAATAGGT
1 CAAAGTCAATAGGT
176404 CAAAGTCAAT-GGT
1 CAAAGTCAATAGGT
*
176417 TAAAGTCAA-A-GT
1 CAAAGTCAATAGGT
176429 CAACTA-TCAA-A-GT
1 CAA--AGTCAATAGGT
**
176442 CAACAGATCAACGGGT
1 CAA-AG-TCAATAGGT
*
176458 CAAAGTCAATGGGT
1 CAAAGTCAATAGGT
* *
176472 C-AAGTCAACAAGT
1 CAAAGTCAATAGGT
* **
176485 CAAAGACAACGGGT
1 CAAAGTCAATAGGT
176499 CAAAGTCAA
1 CAAAGTCAA
176508 CGGGTCGGGA
Statistics
Matches: 103, Mismatches: 18, Indels: 19
0.74 0.13 0.14
Matches are distributed among these distances:
12 5 0.05
13 45 0.44
14 46 0.45
15 2 0.02
16 5 0.05
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (14 bp):
CAAAGTCAATAGGT
Found at i:176410 original size:81 final size:81
Alignment explanation
Indices: 176322--176473 Score: 277
Period size: 81 Copynumber: 1.9 Consensus size: 81
176312 ACAGTCAAAT
*
176322 TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAAATCAATAGGTCAAAGTCAAT
1 TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAAATCAACAGGTCAAAGTCAAT
176387 GGGTCAGGTTAATAGG
66 GGGTCAGGTTAATAGG
* *
176403 TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAGATCAACGGGTCAAAGTCAAT
1 TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAAATCAACAGGTCAAAGTCAAT
176468 GGGTCA
66 GGGTCA
176474 AGTCAACAAG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (81 bp):
TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAAATCAACAGGTCAAAGTCAAT
GGGTCAGGTTAATAGG
Found at i:176480 original size:27 final size:28
Alignment explanation
Indices: 176440--176513 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
176430 AACTATCAAA
* *
176440 GTCAACAGATCAACGGGTCAAAGTCAATGG
1 GTCAA-AG-TCAACGGGTCAAAGACAACGG
**
176470 GTC-AAGTCAACAAGTCAAAGACAACGG
1 GTCAAAGTCAACGGGTCAAAGACAACGG
176497 GTCAAAGTCAACGGGTC
1 GTCAAAGTCAACGGGTC
176514 GGGACAACGG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
27 20 0.54
28 13 0.35
29 1 0.03
30 3 0.08
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.15
Consensus pattern (28 bp):
GTCAAAGTCAACGGGTCAAAGACAACGG
Found at i:176487 original size:81 final size:81
Alignment explanation
Indices: 176322--176507 Score: 273
Period size: 81 Copynumber: 2.3 Consensus size: 81
176312 ACAGTCAAAT
*
176322 TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAAATCAATAGGTCAAAGTCAAT
1 TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAAATCAACAGGTCAAAGTCAAT
* * * *
176387 GGGTCAGGTTAATAGG
66 GGGTCAAGTCAACAAG
* *
176403 TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAGATCAACGGGTCAAAGTCAAT
1 TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAAATCAACAGGTCAAAGTCAAT
176468 GGGTCAAGTCAACAAG
66 GGGTCAAGTCAACAAG
* * *
176484 TCAAAGACAACGGGTCAAAGTCAA
1 TCAAAGTCAA-TGGTTAAAGTCAA
176508 CGGGTCGGGA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
81 83 0.88
82 11 0.12
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (81 bp):
TCAAAGTCAATGGTTAAAGTCAAAGTCAACTATCAAAGTCAACAAATCAACAGGTCAAAGTCAAT
GGGTCAAGTCAACAAG
Found at i:176508 original size:14 final size:14
Alignment explanation
Indices: 176449--176513 Score: 87
Period size: 14 Copynumber: 4.7 Consensus size: 14
176439 AGTCAACAGA
176449 TCAACGGGTCAAAG
1 TCAACGGGTCAAAG
*
176463 TCAATGGGTC-AAG
1 TCAACGGGTCAAAG
**
176476 TCAACAAGTCAAAG
1 TCAACGGGTCAAAG
*
176490 ACAACGGGTCAAAG
1 TCAACGGGTCAAAG
176504 TCAACGGGTC
1 TCAACGGGTC
176514 GGGACAACGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.24
14 32 0.76
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TCAACGGGTCAAAG
Found at i:177641 original size:17 final size:18
Alignment explanation
Indices: 177609--177645 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
177599 AAATATCTTG
*
177609 AAAATATAATATAAATAA
1 AAAATATAATAAAAATAA
177627 AAAATATAA-AAAAATAA
1 AAAATATAATAAAAATAA
177644 AA
1 AA
177646 GAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAATATAATAAAAATAA
Found at i:190430 original size:21 final size:23
Alignment explanation
Indices: 190396--190437 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
190386 TTAAAACACA
*
190396 GATCTGAGTCTAGATC-GAAATC
1 GATCTGAGCCTAGATCTGAAATC
190418 GATCT-AGCCTAGATCTGAAA
1 GATCTGAGCCTAGATCTGAAA
190438 AAAAAGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (23 bp):
GATCTGAGCCTAGATCTGAAATC
Found at i:190671 original size:2 final size:2
Alignment explanation
Indices: 190664--190689 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
190654 AATGGGCAAT
190664 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
190690 AAAGATAGAT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:191651 original size:40 final size:39
Alignment explanation
Indices: 191596--191694 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 39
191586 GTTGTGACTT
* * *
191596 CATGATCTAGGTAAGAGATCGAATGGTTTTCAATTTGCCC
1 CATGATC-AGGTAAGAGATCGAATGATTTTCAATCTACCC
191636 CATGATCGAGGTAAGAGATCGAATGATTTTCAATCTACCC
1 CATGATC-AGGTAAGAGATCGAATGATTTTCAATCTACCC
*
191676 CATCATCAGGGTAAGAGAT
1 CATGATCA-GGTAAGAGAT
191695 TGGCTGATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 1 0.02
40 52 0.98
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (39 bp):
CATGATCAGGTAAGAGATCGAATGATTTTCAATCTACCC
Found at i:191769 original size:78 final size:78
Alignment explanation
Indices: 191684--192161 Score: 511
Period size: 78 Copynumber: 6.1 Consensus size: 78
191674 CCCATCATCA
* *
191684 GGGTAAGAGATTGGCTGATGATGATCTGCCCTAAGCTCGAGGTAAAAGATCAGATGACTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGAGGTAAAAGATCGGATGACTGCAATC
*
191749 TACCCCAAGCTCG
66 TGCCCCAAGCTCG
* * * * *
191762 AGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGTTCGAGGTAAAAGAACGGAT-AGCTACAAT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGAGGTAAAAGATCGGATGA-CTGCAAT
**
191826 CTGCCCCAAGCTTT
65 CTGCCCCAAGCTCG
* * * * *
191840 AGGTAAGAGATTAGCTGATGGTGATCTGCCCCAGGCTC-AGGGTAAAAGATCGAAT-AGCTGCAA
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGA-GGTAAAAGATCGGATGA-CTGCAA
* **
191903 TTTGCCTTAAGCTCG
64 TCTGCCCCAAGCTCG
* * * *
191918 GGGTAAGAGATTGGTTGATGGTGATCTG-CCTCAAGCTAGAGGTAAAAGATCGGATGGCTACAAT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCT-AAGCTCGAGGTAAAAGATCGGATGACTGCAAT
* *
191982 TTGCCCCAGGCTCG
65 CTGCCCCAAGCTCG
* * ** * *
191996 GGGTAAGAGATTGGTTTATGGTGATCTGTTCT-AGCCTCG-GGGAAAAGATCGGATGGCTGCAAT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAG-CTCGAGGTAAAAGATCGGATGACTGCAAT
*
192059 CTGCCCTAAGCTCG
65 CTGCCCCAAGCTCG
* * * * **
192073 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGA-TAGTGAT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGAGGTAAAAGATCGGATGACT-GCAAT
192137 CTGCCCCAAGCTCG
65 CTGCCCCAAGCTCG
*
192151 GGGTAAAAGAT
1 GGGTAAGAGAT
192162 CGGATGGCTG
Statistics
Matches: 336, Mismatches: 54, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
77 71 0.21
78 262 0.78
79 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (78 bp):
GGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGAGGTAAAAGATCGGATGACTGCAATC
TGCCCCAAGCTCG
Found at i:191802 original size:39 final size:39
Alignment explanation
Indices: 191685--192242 Score: 238
Period size: 39 Copynumber: 14.3 Consensus size: 39
191675 CCATCATCAG
*
191685 GGTAAGAGATTGGCTGATGATGATCTGCCCTAAGCTCGA
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGA
* ** * ** * *
191724 GGTAAAAGATCAGATGACT-GCAATCTACCCCAAGCTCGA
1 GGTAAGAGATTGGCTGA-TGGTGATCTGCCCTAAGCTCGA
* *
191763 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGTTCGA
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGA
* ** * * * * **
191802 GGTAAAAGAACGGAT-A-GCTACAATCTGCCCCAAGCTTTA
1 GGTAAGAGATTGGCTGATGGT--GATCTGCCCTAAGCTCGA
* * *
191841 GGTAAGAGATTAGCTGATGGTGATCTGCCCCAGGCTC-A
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGA
* * ** * * * *
191879 GGGTAAAAGATCGAAT-A-GCTGCAATTTGCCTTAAGCTCGG
1 -GGTAAGAGATTGGCTGATGGTG--ATCTGCCCTAAGCTCGA
* *
191919 GGTAAGAGATTGGTTGATGGTGATCTG-CCTCAAGCTAGA
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCT-AAGCTCGA
* * * * * * *
191958 GGTAAAAGA-T--CGGATGGCTACAATTTGCCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGG-T--GATCTGCCCTAAGCTCGA
* * **
191997 GGTAAGAGATTGGTTTATGGTGATCTGTTCT-AGCCTCG-
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAAG-CTCGA
* * * *
192035 GGGAAAAGA-T--CGGATGGCTGCAATCTGCCCTAAGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCTAAGCTCGA
* *
192074 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGA
* * * *
192113 GGTAAAAGATTGGCTGATAGTGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGA
* * * * *
192152 GGTAAAAGA-T--CGGATGGCTGCAATCTGCCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCTAAGCTCGA
* * *
192191 GGTAAGGGATTGGCTTATGGTGA-CTTG-CCTCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATC-TGCCCT-AAGCTCGA
*
192230 GGTAAAAGATTGG
1 GGTAAGAGATTGG
192243 ATGGCTGCAA
Statistics
Matches: 380, Mismatches: 102, Indels: 74
0.68 0.18 0.13
Matches are distributed among these distances:
35 4 0.01
36 12 0.03
37 9 0.02
38 30 0.08
39 292 0.77
40 8 0.02
41 10 0.03
42 15 0.04
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (39 bp):
GGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGA
Found at i:191872 original size:117 final size:117
Alignment explanation
Indices: 191746--192242 Score: 429
Period size: 117 Copynumber: 4.3 Consensus size: 117
191736 GATGACTGCA
* * * * * *
191746 ATCTACCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGTTCGAGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGA
* * ** *
191811 ACGGATAGCTACAATCTGCCCCAAGCTTTAGGTAAGAGATTAGCTGATGGTG
66 TCGGATAGCTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTG
* * * ** * * * *
191863 ATCTGCCCCAGGCTCAGGGTAAAAGATCGAAT-A-GCTGCAATTTGCCTTAAGCTCGGGGTAAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG--ATCTGCCCTAAGCTCGGGGTAAAA
* * * * * * * *
191926 GATTGGTTGATGGTG--ATCTGCCTCAAGCTAGAGGTAAAAGA-T--CGGATGGCTACA
64 GATCGGAT-A-GCTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGGCTGATGG-T--G
* * * * * **
191980 ATTTGCCCCAGGCTCGGGGTAAGAGATTGGTTTATGGTGATCTGTTCT-AGCCTCGGGG-AAAAG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCTAAG-CTCGGGGTAAAAG
* * *
192043 ATCGGATGGCTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTGGCTGATGGTG
65 ATCGGATAGCTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTG
* *
192096 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGA
* * * * *
192161 TCGGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGGGATTGGCTTATGGTG
66 TCGGATAGCTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTG
*
192213 A-CTTGCCTCAAGCTCGGGGTAAAAGATTGG
1 ATC-TGCCCCAAGCTCGGGGTAAAAGATTGG
192243 ATGGCTGCAA
Statistics
Matches: 299, Mismatches: 63, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
114 9 0.03
115 4 0.01
116 81 0.27
117 191 0.64
118 3 0.01
119 11 0.04
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (117 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGA
TCGGATAGCTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTG
Found at i:192276 original size:42 final size:41
Alignment explanation
Indices: 192229--192360 Score: 185
Period size: 41 Copynumber: 3.2 Consensus size: 41
192219 CTCAAGCTCG
*
192229 GGGTAAAAGATTGG-ATGGCTGCAATATGCCCTTCTTGATTAA
1 GGGTAAAAGATTGGAAT--CTTCAATATGCCCTTCTTGATTAA
* * *
192271 GGGTAAAAGACTGGAATCTTCAATCTGTCCTTCTTGATTAA
1 GGGTAAAAGATTGGAATCTTCAATATGCCCTTCTTGATTAA
* *
192312 GGGTAAAATATTGGAATCTTCAATTTGCCCTTCTTGATTAA
1 GGGTAAAAGATTGGAATCTTCAATATGCCCTTCTTGATTAA
192353 GGGTAAAA
1 GGGTAAAA
192361 AAAACTGGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
41 66 0.81
42 13 0.16
43 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (41 bp):
GGGTAAAAGATTGGAATCTTCAATATGCCCTTCTTGATTAA
Found at i:220827 original size:27 final size:28
Alignment explanation
Indices: 220796--220874 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 28
220786 GCAAAAAATG
*
220796 GAGTATTGCTTC-TTCGAGCTAGAAACA
1 GAGTATTGCTTCTTTCGAGCCAGAAACA
* ** *
220823 TAGTATCAC-TCTTTTGAGCCAGAAACA
1 GAGTATTGCTTCTTTCGAGCCAGAAACA
*
220850 GAGTATTGC-TCTTTTGAGCCAGAAA
1 GAGTATTGCTTCTTTCGAGCCAGAAA
220875 TAGAAACAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.05
27 41 0.95
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (28 bp):
GAGTATTGCTTCTTTCGAGCCAGAAACA
Found at i:221385 original size:22 final size:22
Alignment explanation
Indices: 221343--221385 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
221333 GTGGGGTTAT
**
221343 TAAAATATAATTAAATTAAAAA
1 TAAAATATAATTAAAACAAAAA
*
221365 TAAAATATATTTAAAACAAAA
1 TAAAATATAATTAAAACAAAA
221386 GTTAAAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATATAATTAAAACAAAAA
Found at i:223365 original size:25 final size:26
Alignment explanation
Indices: 223319--223383 Score: 114
Period size: 25 Copynumber: 2.5 Consensus size: 26
223309 CTCGACCCAC
*
223319 AGCTCGTGTCAGCAGGACCATTTCAT
1 AGCTCGTGTGAGCAGGACCATTTCAT
223345 AGCTCGTGTGAG-AGGACCATTTCAT
1 AGCTCGTGTGAGCAGGACCATTTCAT
223370 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
223384 TATATGGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
25 25 0.68
26 12 0.32
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGGACCATTTCAT
Found at i:226610 original size:43 final size:43
Alignment explanation
Indices: 226549--226755 Score: 234
Period size: 43 Copynumber: 4.8 Consensus size: 43
226539 GTGAATTCTT
* * *
226549 AATGGAAAACTTATGTCTCGGTTAGAGCATAAGATTGCTTATA
1 AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTACTTATA
** * *
226592 AATGGAAGACTTATGTCTCGATTAGAGCATAAAATTGCTTATA
1 AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTACTTATA
* * *
226635 AATGGAAGACTTATGTCTTGGCTAGAGCATAAGATTATTTGTA
1 AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTACTTATA
** * *
226678 AATGGAAGAACTTATGTCTCAACTAGAGCATAAGATTATTTGTA
1 AATGGAAG-ACTTATGTCTCGGCTAGAGCATAAGATTACTTATA
* * * *
226722 AACGGAAGAACTTATGACTTGGATAGAGCATAAG
1 AATGGAAG-ACTTATGTCTCGGCTAGAGCATAAG
226756 GTTAACTCAG
Statistics
Matches: 144, Mismatches: 19, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
43 84 0.58
44 60 0.42
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (43 bp):
AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTACTTATA
Found at i:232487 original size:158 final size:158
Alignment explanation
Indices: 232203--232506 Score: 365
Period size: 158 Copynumber: 1.9 Consensus size: 158
232193 ATAGCTAGTG
* ** * * * * * **
232203 TGAGCGTTAAAGGTTATATGTTTGTTGGTCTTGGATGTCTTATTGATGGTTGAGGTCCTGCATTG
1 TGAGCATTAAAGGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGATTGAGGTCCAACATTG
* * ** * *
232268 GTTGCAGATTCTCCACAGCTTGTGTTAGCAGCATCGTATAACCTAACATCTCGACCCACAACTCG
66 ATTGCAGAATCTCCACAGCTCATGTGAGCAGCATCGTATAACCCAACATCTCGACCCACAACTCG
232333 TGTGAGCAGACCCATTTCATAGCTTCTA
131 TGTGAGCAGACCCATTTCATAGCTTCTA
* *
232361 TGAGCATTATAGGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGATTGAGGTCCAACATTT
1 TGAGCATTAAAGGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGATTGAGGTCCAACATTG
* * * * * * * *
232426 ATTGCGGAATCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCCCACGTCTTGATCTACAACTCG
66 ATTGCAGAATCTCCACAGCTCATGTGAGCAGCATCGTATAACCCAACATCTCGACCCACAACTCG
*
232491 TGTGAGCAGGCCCATT
131 TGTGAGCAGACCCATT
232507 CCACAACTCG
Statistics
Matches: 119, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
158 119 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (158 bp):
TGAGCATTAAAGGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGATTGAGGTCCAACATTG
ATTGCAGAATCTCCACAGCTCATGTGAGCAGCATCGTATAACCCAACATCTCGACCCACAACTCG
TGTGAGCAGACCCATTTCATAGCTTCTA
Found at i:233864 original size:27 final size:27
Alignment explanation
Indices: 233787--233917 Score: 102
Period size: 27 Copynumber: 4.9 Consensus size: 27
233777 GTGTTACATG
* *
233787 TAGAGTATCACTCTTTTGAGTCAGAAA
1 TAGAGTATCGCTCTTTTGAGCCAGAAA
* * * * *
233814 CAAAGCATCGCTCTATCT-ACCCAGAAA
1 TAGAGTATCGCTCT-TTTGAGCCAGAAA
233841 TAGAGTATCGCTCTTTTGAGCCAGAAA
1 TAGAGTATCGCTCTTTTGAGCCAGAAA
* * ** **
233868 CAGAGTATTGCTCTTTCAAGCTTGAAA
1 TAGAGTATCGCTCTTTTGAGCCAGAAA
* * *
233895 TAGAATATTGCTCTTTCGAGCCA
1 TAGAGTATCGCTCTTTTGAGCCA
233918 TAAACAAAGT
Statistics
Matches: 79, Mismatches: 23, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
26 2 0.03
27 75 0.95
28 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (27 bp):
TAGAGTATCGCTCTTTTGAGCCAGAAA
Found at i:233869 original size:54 final size:54
Alignment explanation
Indices: 233787--233926 Score: 154
Period size: 54 Copynumber: 2.6 Consensus size: 54
233777 GTGTTACATG
* * *
233787 TAGAGTATCACTCTTTTGAGTCAGAAACAAAGCATCGCTCTATCTACCCAGAAA
1 TAGAGTATCGCTCTTTTGAGCCAGAAACAAAGCATCGCTCTATCAACCCAGAAA
* * * * * **
233841 TAGAGTATCGCTCTTTTGAGCCAGAAACAGAGTATTGCTCTTTCAAGCTTGAAA
1 TAGAGTATCGCTCTTTTGAGCCAGAAACAAAGCATCGCTCTATCAACCCAGAAA
* * * *
233895 TAGAATATTGCTCTTTCGAGCCATAAACAAAG
1 TAGAGTATCGCTCTTTTGAGCCAGAAACAAAG
233927 TATTTATTAT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
TAGAGTATCGCTCTTTTGAGCCAGAAACAAAGCATCGCTCTATCAACCCAGAAA
Found at i:233930 original size:27 final size:27
Alignment explanation
Indices: 233844--233930 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
233834 CCAGAAATAG
* * * *
233844 AGTATCGCTCTTTTGAGCCAGAAACAG
1 AGTATTGCTCTTTCGAGCCATAAACAA
* * *
233871 AGTATTGCTCTTTCAAG-CTTGAAATAGA
1 AGTATTGCTCTTTCGAGCCAT-AAACA-A
233899 A-TATTGCTCTTTCGAGCCATAAACAA
1 AGTATTGCTCTTTCGAGCCATAAACAA
233925 AGTATT
1 AGTATT
233931 TATTATTGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
26 3 0.07
27 40 0.87
28 3 0.07
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (27 bp):
AGTATTGCTCTTTCGAGCCATAAACAA
Found at i:240956 original size:136 final size:138
Alignment explanation
Indices: 240581--240984 Score: 568
Period size: 137 Copynumber: 2.9 Consensus size: 138
240571 AAGAATTATA
* * ** * *
240581 TTCCAATAGAATATTAATTTTCATGCCTTTTATATTTCG-ACTAAAATTAATTAATATAACTGTT
1 TTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGAAC-GAAATTAATTAATATAACTGTT
* * * * *
240645 TATATTAATAAATTCAATAATATATATA-ATATTAATA-TTTCTATGATTCAAATTCATCTATTA
65 TATATTAATAAATTCAGTAAAATATATACA-ATTAATATTTTGTATGAATCAAATTCATATATTA
240708 ATTATATTCT
129 ATTATATTCT
* *
240718 TTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGAACGAAATTAATTAATATAATTATTT
1 TTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGAACGAAATTAATTAATATAACTGTTT
*
240783 ATATTAATAAA-TCTAGTAAAATATATACACTTAATATTTTGTATGAATCAAATTCATATATTAA
66 ATATTAATAAATTC-AGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAA
240847 TTATATTCT
130 TTATATTCT
* * * *
240856 TTCCAAAAGATTATTAATTT-CATCTCTTTTGTATTTT-ATCGAAATTAATTAATATAACTGTTT
1 TTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGAACGAAATTAATTAATATAACTGTTT
*
240919 ATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
66 ATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
240984 T
131 T
240985 TTATCTATGT
Statistics
Matches: 240, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
136 86 0.36
137 99 0.41
138 55 0.23
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (138 bp):
TTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGAACGAAATTAATTAATATAACTGTTT
ATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
TATATTCT
Found at i:242143 original size:25 final size:26
Alignment explanation
Indices: 242090--242143 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
242080 AAATATTTCA
* *
242090 TTAATAATTTAGATTTATTTAATTAT
1 TTAATAATTAAGATTAATTTAATTAT
* *
242116 TTAATAATTAAG-TTAATTTTATTCT
1 TTAATAATTAAGATTAATTTAATTAT
242141 TTA
1 TTA
242144 GTCTCTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (26 bp):
TTAATAATTAAGATTAATTTAATTAT
Found at i:247489 original size:21 final size:21
Alignment explanation
Indices: 247443--247490 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
247433 TAGGTTTTAA
*
247443 AATT-TTTTAAGTTTCATTTT
1 AATTGTTTTAAGTTTAATTTT
** *
247463 TGTTGTTTTAATTTTAATTTT
1 AATTGTTTTAAGTTTAATTTT
247484 AATTGTT
1 AATTGTT
247491 ATGTTAATAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.67
Consensus pattern (21 bp):
AATTGTTTTAAGTTTAATTTT
Found at i:249023 original size:20 final size:21
Alignment explanation
Indices: 248989--249028 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
248979 TGAACCAAAT
248989 GTTGAGCCAAAAGATAAACCA
1 GTTGAGCCAAAAGATAAACCA
*
249010 GTTGAGCC-AAAGATGAACC
1 GTTGAGCCAAAAGATAAACC
249029 TAAATTCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (21 bp):
GTTGAGCCAAAAGATAAACCA
Found at i:251935 original size:15 final size:16
Alignment explanation
Indices: 251899--251936 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
251889 CTCTTCCTTC
251899 TCTTCTTCAGGGTCCT
1 TCTTCTTCAGGGTCCT
*
251915 TC-TCTTTA-GGTCCT
1 TCTTCTTCAGGGTCCT
251929 TCTTCTTC
1 TCTTCTTC
251937 TCTTTCATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 8 0.42
15 9 0.47
16 2 0.11
ACGTcount: A:0.05, C:0.32, G:0.13, T:0.50
Consensus pattern (16 bp):
TCTTCTTCAGGGTCCT
Found at i:255677 original size:30 final size:30
Alignment explanation
Indices: 255605--255754 Score: 189
Period size: 30 Copynumber: 5.0 Consensus size: 30
255595 GAAAGTTGGG
* **
255605 GGTTAAAATTTAATTTTTGGAAAAAATTA-A
1 GGTTAAAATATAATTTTT-GAAAAGTTTAGA
255635 GGGTTAAAATATAATTTTT-AGAAAGTTTAGA
1 -GGTTAAAATATAATTTTTGA-AAAGTTTAGA
* *
255666 GGTTAAGATATAATTTTTGAAAAGTTTAGG
1 GGTTAAAATATAATTTTTGAAAAGTTTAGA
*
255696 GGTCAAAATATAATTTTTGAAAAGTTT-GA
1 GGTTAAAATATAATTTTTGAAAAGTTTAGA
255725 GGGTTAAAATATAATTTTTGAAAAGTTTAG
1 -GGTTAAAATATAATTTTTGAAAAGTTTAG
255755 CTTAAGGACT
Statistics
Matches: 105, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
29 2 0.02
30 83 0.79
31 20 0.19
ACGTcount: A:0.41, C:0.01, G:0.19, T:0.39
Consensus pattern (30 bp):
GGTTAAAATATAATTTTTGAAAAGTTTAGA
Found at i:255749 original size:60 final size:60
Alignment explanation
Indices: 255591--255754 Score: 208
Period size: 60 Copynumber: 2.7 Consensus size: 60
255581 AAAATGTAAA
* * * ** * *
255591 TTTGGAAAG-TTGGGGGTTAAAATTTAATTTTTGGAAAAAATTAAGGGTTAAAATATAATT
1 TTTGAAAAGTTTGAGGGTTAAAATATAATTTTT-GAAAAGTTTAGGGGTCAAAATATAATT
*
255651 TTT-AGAAAGTTT-AGAGGTTAAGATATAATTTTTGAAAAGTTTAGGGGTCAAAATATAATT
1 TTTGA-AAAGTTTGAG-GGTTAAAATATAATTTTTGAAAAGTTTAGGGGTCAAAATATAATT
255711 TTTGAAAAGTTTGAGGGTTAAAATATAATTTTTGAAAAGTTTAG
1 TTTGAAAAGTTTGAGGGTTAAAATATAATTTTTGAAAAGTTTAG
255755 CTTAAGGACT
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
60 69 0.77
61 21 0.23
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.39
Consensus pattern (60 bp):
TTTGAAAAGTTTGAGGGTTAAAATATAATTTTTGAAAAGTTTAGGGGTCAAAATATAATT
Found at i:258015 original size:50 final size:50
Alignment explanation
Indices: 257790--258230 Score: 233
Period size: 49 Copynumber: 8.9 Consensus size: 50
257780 GCGATAACAA
* * * * * *
257790 TATCTTCTTGGTATTAGATTCGCCATTGCGGCTTAAATCTTTCCCTCCAT
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
* * * * * ** *
257840 TCT-TTTGAGGTA-T-AACGTTCGTCGTTATGACTTAAACCTTTCCCT--TT
1 TATCTTCGTGGTACTGGA--TTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
* * * *
257887 GTATCTTCGTGGTACTAGATTCGCCGTTGC-AGCTTAAATCTGTCCCTTCA-
1 -TATCTTCGTGGTACTGGATTCGCCGTTGCGA-CTTAAACCTTTCCCTCCAT
** * * * * **
257937 -CGCTTCTGAGGTACAAGG-TTTGCAGTTGCGACTTAAACCTTTTTCTCCAT
1 TATCTTC-GTGGTAC-TGGATTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
* * * *
257987 TATCTTCGTGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
** * * * * * *
258037 GCT-TTTGAGGTACAAGG-TTCACAGTTGCGACTTAAACCTTTCCCTCCAG
1 TATCTTCGTGGTAC-TGGATTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
* * * * *
258086 TATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTACAT
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
* * * * ** * *
258136 TCT-TTTGAGATAAAAGG-TTCGTCGTTGCGACTTAAACCTTTCCCTCAAT
1 TATCTTCGTGGT-ACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
* * *
258185 TATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCT
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAACCTTTCCCT
258231 TCGTGCTTCG
Statistics
Matches: 276, Mismatches: 94, Indels: 42
0.67 0.23 0.10
Matches are distributed among these distances:
47 2 0.01
48 8 0.03
49 157 0.57
50 104 0.38
51 5 0.02
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (50 bp):
TATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
Found at i:258024 original size:99 final size:99
Alignment explanation
Indices: 257790--258238 Score: 573
Period size: 99 Copynumber: 4.5 Consensus size: 99
257780 GCGATAACAA
* * * * * *
257790 TATCTTCTTGGTATTAGATTCGCCATTGCGGCTTAAATCTTTCCCTCCATTCTTTTGAGGTATAA
1 TATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAA
* ** *
257855 CGTTCGTC-GTTATGACTTAAACCTTTCCCT--TT
66 GGTTCG-CAGTTGCGACTTAAACCTTTCCCTCCAT
* * * *
257887 GTATCTTCGTGGTACTAGATTCGCCGTTGCAGCTTAAATCTGTCCCTTCACGCTTCTGAGGTACA
1 -TATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACA
* **
257952 AGGTTTGCAGTTGCGACTTAAACCTTTTTCTCCAT
65 AGGTTCGCAGTTGCGACTTAAACCTTTCCCTCCAT
* *
257987 TATCTTCGTGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAA
1 TATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAA
* *
258052 GGTTCACAGTTGCGACTTAAACCTTTCCCTCCAG
66 GGTTCGCAGTTGCGACTTAAACCTTTCCCTCCAT
* * * * *
258086 TATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTACATTCTTTTGAGATAAAA
1 TATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAA
*
258151 GGTTCGTC-GTTGCGACTTAAACCTTTCCCTCAAT
66 GGTTCG-CAGTTGCGACTTAAACCTTTCCCTCCAT
* * *
258185 TATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCGTGCTT
1 TATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
258239 CGTGGTAATG
Statistics
Matches: 303, Mismatches: 44, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
97 1 0.00
98 77 0.25
99 223 0.74
100 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (99 bp):
TATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAA
GGTTCGCAGTTGCGACTTAAACCTTTCCCTCCAT
Found at i:269790 original size:115 final size:115
Alignment explanation
Indices: 269600--269830 Score: 428
Period size: 115 Copynumber: 2.0 Consensus size: 115
269590 AAAAGGGGAC
269600 TAATTTTGAATTTAAAATAAAATTTGAGAAAAAAATGTGAAAATAAGAAAGTCAGGATTAAAAAC
1 TAATTTTGAATTTAAAATAAAATTTGAGAAAAAAATGTGAAAATAAGAAAGTCAGGATTAAAAAC
269665 GTAAATTTGGAAAGTTGGGGATCAAAATTTATTTTTTGGAAAATTTAAGGG
66 GTAAATTTGGAAAGTTGGGG-TCAAAATTTATTTTTTGGAAAATTTAAGGG
* *
269716 TAATTTTGAATTTAAAATAAAATTTGAGTAAAAAA-GTGAAAATAAGAAAGTCGGGATTAAAAAC
1 TAATTTTGAATTTAAAATAAAATTTGAGAAAAAAATGTGAAAATAAGAAAGTCAGGATTAAAAAC
269780 GTAAATTTGGAAAGTTGGGGTCAAAATTTATTTTTTGGAAAATTTAAGGG
66 GTAAATTTGGAAAGTTGGGGTCAAAATTTATTTTTTGGAAAATTTAAGGG
269830 T
1 T
269831 TAAAATATAA
Statistics
Matches: 113, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
114 31 0.27
115 48 0.42
116 34 0.30
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (115 bp):
TAATTTTGAATTTAAAATAAAATTTGAGAAAAAAATGTGAAAATAAGAAAGTCAGGATTAAAAAC
GTAAATTTGGAAAGTTGGGGTCAAAATTTATTTTTTGGAAAATTTAAGGG
Found at i:269845 original size:30 final size:30
Alignment explanation
Indices: 269797--269968 Score: 206
Period size: 30 Copynumber: 5.7 Consensus size: 30
269787 TGGAAAGTTG
* * *
269797 GGGTCAAAATTTATTTTTTGGAAAA-TTTAA
1 GGGTTAAAATATAATTTTT-GAAAAGTTTAA
* *
269827 GGGTTAAAATATAATTTTTTAAAAGTTTAG
1 GGGTTAAAATATAATTTTTGAAAAGTTTAA
* * *
269857 GGGTCAAAATATAATTTTTAAAAAGTTCAA
1 GGGTTAAAATATAATTTTTGAAAAGTTTAA
269887 GGGTTAAAATATAATTTTTGAAAAGTTT-A
1 GGGTTAAAATATAATTTTTGAAAAGTTTAA
* *
269916 GGTGTTAAAATATAATTTTTGAATAGTTCATA
1 GG-GTTAAAATATAATTTTTGAAAAGTTTA-A
269948 -GGTTAAAATATAATTTTTGAA
1 GGGTTAAAATATAATTTTTGAA
269969 CAAAACAGGG
Statistics
Matches: 124, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
29 7 0.06
30 115 0.93
31 1 0.01
32 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (30 bp):
GGGTTAAAATATAATTTTTGAAAAGTTTAA
Found at i:269875 original size:60 final size:59
Alignment explanation
Indices: 269796--269968 Score: 231
Period size: 60 Copynumber: 2.9 Consensus size: 59
269786 TTGGAAAGTT
* * * *
269796 GGGGTCAAAATTTATTTTTTGGAAAATTTAAGGGTTAAAATATAATTTTTTAAAAGTTTA
1 GGGGTCAAAATATAATTTTT-GAAAATTCAAGGGTTAAAATATAATTTTTGAAAAGTTTA
*
269856 GGGGTCAAAATATAATTTTTAAAAAGTTCAAGGGTTAAAATATAATTTTTGAAAAGTTTA
1 GGGGTCAAAATATAATTTTTGAAAA-TTCAAGGGTTAAAATATAATTTTTGAAAAGTTTA
* * *
269916 GGTGTTAAAATATAATTTTTGAATAGTTCATA-GGTTAAAATATAATTTTTGAA
1 GGGGTCAAAATATAATTTTTGAA-AATTCA-AGGGTTAAAATATAATTTTTGAA
269969 CAAAACAGGG
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.04
60 95 0.94
61 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.41
Consensus pattern (59 bp):
GGGGTCAAAATATAATTTTTGAAAATTCAAGGGTTAAAATATAATTTTTGAAAAGTTTA
Found at i:271387 original size:14 final size:14
Alignment explanation
Indices: 271368--271434 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
271358 TTGACATGGA
271368 TGCTGACGTGGCAG
1 TGCTGACGTGGCAG
*
271382 TGCTGA--T-GCGG
1 TGCTGACGTGGCAG
* *
271393 TGTTGACATGG-A-
1 TGCTGACGTGGCAG
271405 TGCTGACGTGGCAG
1 TGCTGACGTGGCAG
*
271419 TGCTGATGTGGCAG
1 TGCTGACGTGGCAG
271433 TG
1 TG
271435 GCGGTTGGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
11 8 0.19
12 10 0.24
13 2 0.05
14 22 0.52
ACGTcount: A:0.15, C:0.16, G:0.42, T:0.27
Consensus pattern (14 bp):
TGCTGACGTGGCAG
Found at i:271404 original size:37 final size:37
Alignment explanation
Indices: 271354--271426 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
271344 TGGCTAATGT
271354 GGTGTTGACATGGATGCTGACGTGGCAGTGCTGATGC
1 GGTGTTGACATGGATGCTGACGTGGCAGTGCTGATGC
271391 GGTGTTGACATGGATGCTGACGTGGCAGTGCTGATG
1 GGTGTTGACATGGATGCTGACGTGGCAGTGCTGATG
271427 TGGCAGTGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.16, C:0.15, G:0.41, T:0.27
Consensus pattern (37 bp):
GGTGTTGACATGGATGCTGACGTGGCAGTGCTGATGC
Found at i:282654 original size:15 final size:15
Alignment explanation
Indices: 282630--282671 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
282620 TATAGCAATA
* *
282630 TTTCTTTTTTTTTCT
1 TTTCTCTTTTTCTCT
282645 TTTCTC-TTTTCTCT
1 TTTCTCTTTTTCTCT
282659 TTT-TCTTTTTCTC
1 TTTCTCTTTTTCTC
282672 ATTCACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 17 0.71
15 5 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTCTTTTTCTCT
Found at i:282659 original size:14 final size:13
Alignment explanation
Indices: 282638--282670 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
282628 TATTTCTTTT
282638 TTTTTCTTTTCTC
1 TTTTTCTTTTCTC
282651 TTTTCTCTTTT-TC
1 TTTT-TCTTTTCTC
282664 TTTTTCT
1 TTTTTCT
282671 CATTCACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 10 0.53
14 6 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:282665 original size:6 final size:6
Alignment explanation
Indices: 282630--282670 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
282620 TATAGCAATA
282630 TTTC-T TTT-TT TTTCTT TTCTCTT TTCTCTT TTTCTT TTTCT
1 TTTCTT TTTCTT TTTCTT TT-TCTT TT-TCTT TTTCTT TTTCT
282671 CATTCACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 7 0.21
6 13 0.39
7 13 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:282671 original size:14 final size:15
Alignment explanation
Indices: 282630--282671 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
282620 TATAGCAATA
* *
282630 TTTCTTTTTTTTTCT
1 TTTCTTTTTCTCTCT
282645 TTTCTCTTTTCTCT-T
1 TTTCT-TTTTCTCTCT
282660 TTTCTTTTTCTC
1 TTTCTTTTTCTC
282672 ATTCACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 11 0.46
16 6 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTCTCTCT
Found at i:283502 original size:3 final size:3
Alignment explanation
Indices: 283494--283525 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
283484 CCATCATATT
283494 TTC TTC TTC TTC TTC TTC TTC TTC TTCC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC T
283526 CTTGGCCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:289885 original size:15 final size:16
Alignment explanation
Indices: 289865--289896 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
289855 ATTGTTATGG
289865 TAACTCCCTTGA-CTA
1 TAACTCCCTTGAGCTA
289880 TAACTCCCTTGAGCTA
1 TAACTCCCTTGAGCTA
289896 T
1 T
289897 TTTTCAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.34
Consensus pattern (16 bp):
TAACTCCCTTGAGCTA
Found at i:304586 original size:20 final size:20
Alignment explanation
Indices: 304561--304603 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
304551 AAAAAAAATC
*
304561 CATGTCAAATTTTCATTTGT
1 CATGTCAAATTTTAATTTGT
* *
304581 CATGTCATATTTTAATTTTT
1 CATGTCAAATTTTAATTTGT
304601 CAT
1 CAT
304604 TTTAACGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (20 bp):
CATGTCAAATTTTAATTTGT
Found at i:310753 original size:29 final size:29
Alignment explanation
Indices: 310705--310760 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
310695 ATCAACATAC
*
310705 GATAACACAACCCAAGATAAAATCACACA
1 GATAACACAACACAAGATAAAATCACACA
*
310734 GATAACACAACAC-AGAATAATATCACA
1 GATAACACAACACAAG-ATAAAATCACA
310761 TAAGGTGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.55, C:0.25, G:0.07, T:0.12
Consensus pattern (29 bp):
GATAACACAACACAAGATAAAATCACACA
Found at i:316203 original size:39 final size:38
Alignment explanation
Indices: 316108--316208 Score: 121
Period size: 39 Copynumber: 2.6 Consensus size: 38
316098 AACGAAATCT
* * *
316108 TTGTTATAATTATAGTAATTATAATTTATGATCGAATA
1 TTGTTATAATTATAGTAATTGTAATTTATGATCAAACA
* * * *
316146 TTATTATAATTATTGTAATTGTAATTTTTCGGTCAAACA
1 TTGTTATAATTATAGTAATTGTAATTTAT-GATCAAACA
*
316185 TTGTTATAATTATGGTAATTGTAA
1 TTGTTATAATTATAGTAATTGTAA
316209 CTATTATATT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 25 0.47
39 28 0.53
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.49
Consensus pattern (38 bp):
TTGTTATAATTATAGTAATTGTAATTTATGATCAAACA
Found at i:333816 original size:48 final size:48
Alignment explanation
Indices: 333745--333836 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
333735 CTTCAAACCC
* * *
333745 CATCTTCTTAATGAGATATAGAGAAGTGAATCAAAACAATGAAGCGGT
1 CATCTTCCTAATGAGATACAGAGAAGTGAACCAAAACAATGAAGCGGT
* *
333793 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAG
1 CATCTTCCTAATGAGATACAGAGAAGTGAACCAAAACAATGAAG
333837 AGAAGCTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (48 bp):
CATCTTCCTAATGAGATACAGAGAAGTGAACCAAAACAATGAAGCGGT
Found at i:333901 original size:123 final size:123
Alignment explanation
Indices: 333671--333912 Score: 301
Period size: 123 Copynumber: 2.0 Consensus size: 123
333661 ATCAAACCCT
* * *
333671 ATCTTTCTAATGAGATATAAAGAAGTGGAGAAAAACAATGAAACAAAGCTCAATATGAGTGAAAC
1 ATCTTCCTAATGAGATACAAAGAAGTGGACAAAAACAATGAAACAAAGCTCAATATGAGTGAAAC
* * * **
333736 TTCAAACCCCATCTTCTTAATGAGATATAGAGAAGTGAATCAAAACAATGAAGCGGTC
66 TTCAAACCCCATCTTCTGAATGAGACAAAGAGAAAAGAATCAAAACAATGAAGCGGTC
* * * * *
333794 ATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGA-GAAGCTCAATGTGAGTGAAA
1 ATCTTCCTAATGAGATACAAAGAAGTGGACAAAAACAATGAA-ACAAAGCTCAATATGAGTGAAA
* *
333858 CTTCAAACCCCATCTTCCTGATATGATACAAAGA-AAAAG-ATCAAAACATTGAAGC
65 CTTCAAACCCCATCTT-CTGA-ATGAGACAAAGAGAAAAGAATCAAAACAATGAAGC
333913 AAAGCTCAAC
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
123 85 0.84
124 7 0.07
125 9 0.09
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.21
Consensus pattern (123 bp):
ATCTTCCTAATGAGATACAAAGAAGTGGACAAAAACAATGAAACAAAGCTCAATATGAGTGAAAC
TTCAAACCCCATCTTCTGAATGAGACAAAGAGAAAAGAATCAAAACAATGAAGCGGTC
Found at i:334034 original size:48 final size:48
Alignment explanation
Indices: 333963--334055 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
333953 CTTAAAACCC
* *
333963 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGAT
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAAAGAAGCGAT
334011 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAAAGAAGC
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAAAGAAGC
334056 AAAGCTCAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (48 bp):
CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAAAGAAGCGAT
Found at i:334120 original size:218 final size:217
Alignment explanation
Indices: 333728--334129 Score: 628
Period size: 218 Copynumber: 1.8 Consensus size: 217
333718 GCTCAATATG
* * *
333728 AGTGAAACTTCAAACCCCATCTTCTTAATGAGATATAGAGAAGTGAATCAAAACAATGAAGCGGT
1 AGTGAAACTTAAAACCCCATCTTCTTAATGAGATACAGAGAAGTGAATCAAAACAATGAAGCGAT
* *
333793 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGAGAAGCTCAATGTGAGTGAAA
66 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAAAGAAGAGAAGCTCAATATGAGTGAAA
*
333858 CTTCAAACCCCATCTTCCTGATATGATACAAAGAAAAAGATCAAAACATTGAAGCAAAGCTCAAC
131 CTTCAAACCCCATCTTCCTGATATGATACAAAGAAAAAGATC-AAACAATGAAGCAAAGCTCAAC
333923 ATCCCAAAGGTTACATGGAGTAA
195 ATCCCAAAGGTTACATGGAGTAA
* * *
333946 AGTGAAACTTAAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGAT
1 AGTGAAACTTAAAACCCCATCTTCTTAATGAGATACAGAGAAGTGAATCAAAACAATGAAGCGAT
* *
334011 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAAAGAAGCA-AAGCTCAATATGAGTGAA
66 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAAAGAAG-AGAAGCTCAATATGAGTGAA
* * **
334075 ACTTCAAACCCCATCTTCTTGATGA-GATACAGAGAAATGGATCAAACAATGAAGC
130 ACTTCAAACCCCATCTTCCTGAT-ATGATACAAAGAAAAAGATCAAACAATGAAGC
334130 GATCATCTTC
Statistics
Matches: 167, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
217 11 0.07
218 154 0.92
219 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (217 bp):
AGTGAAACTTAAAACCCCATCTTCTTAATGAGATACAGAGAAGTGAATCAAAACAATGAAGCGAT
CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAAAGAAGAGAAGCTCAATATGAGTGAAA
CTTCAAACCCCATCTTCCTGATATGATACAAAGAAAAAGATCAAACAATGAAGCAAAGCTCAACA
TCCCAAAGGTTACATGGAGTAA
Found at i:334249 original size:122 final size:121
Alignment explanation
Indices: 333946--334251 Score: 461
Period size: 122 Copynumber: 2.5 Consensus size: 121
333936 CATGGAGTAA
*
333946 AGTGAAACTTAAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGAT
1 AGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATC-AAA-AATGAAGCGAT
* *
334011 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAAAGAAGCAAAGCTCAATATG
64 CATCTTCTTGATGAGATACAAAGAAGTGGACCAAAACAAAGAAGCAAAGCTCAATATG
*
334069 AGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAATGGATCAAACAATGAAGCGATC
1 AGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAA-AATGAAGCGATC
* **
334134 ATCTTCTTGATGAGATACAAAGAAGTGGACCAAAACAATGAAGCGGAGCTCAATGA-G
65 ATCTTCTTGATGAGATACAAAGAAGTGGACCAAAACAAAGAAGCAAAGCTCAAT-ATG
* * * *
334191 AGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGTACCAAAAGATGAAGC
1 AGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAA-ATGAAGC
334252 TACAACACCA
Statistics
Matches: 168, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
121 1 0.01
122 119 0.71
123 48 0.29
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (121 bp):
AGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAAATGAAGCGATCA
TCTTCTTGATGAGATACAAAGAAGTGGACCAAAACAAAGAAGCAAAGCTCAATATG
Found at i:343649 original size:16 final size:15
Alignment explanation
Indices: 343616--343658 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
343606 CTAAAGTATT
*
343616 CTAAACTAAATTAAA
1 CTAAATTAAATTAAA
*
343631 CTAAGTTAAATTAAAA
1 CTAAATTAAATT-AAA
343647 CTAAATTAAATT
1 CTAAATTAAATT
343659 CCTATGCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (15 bp):
CTAAATTAAATTAAA
Found at i:350110 original size:27 final size:27
Alignment explanation
Indices: 350072--350159 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
350062 ATCAAACTCG
* *
350072 TTGACTTCGACTCCTTGACCTGACCTA
1 TTGACTTTGACTCCTTGACCTGACCCA
350099 TTGACTTTGACTCCTTGACCTGACCCA
1 TTGACTTTGACTCCTTGACCTGACCCA
* * * * *
350126 TTAACTTTGAC-CATTGACCTTAACCG
1 TTGACTTTGACTCCTTGACCTGACCCA
350152 TTGACTTT
1 TTGACTTT
350160 TTTGACCAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 18 0.34
27 35 0.66
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (27 bp):
TTGACTTTGACTCCTTGACCTGACCCA
Found at i:352036 original size:26 final size:26
Alignment explanation
Indices: 352007--352068 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
351997 CAGGAACTTG
352007 TCCAAAATTATCACTGCATGAACATA
1 TCCAAAATTATCACTGCATGAACATA
* * * * *
352033 TCCATAGTTGTCGCTGCATGAGCATA
1 TCCAAAATTATCACTGCATGAACATA
352059 TCCAAAATTA
1 TCCAAAATTA
352069 CGCCTAAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (26 bp):
TCCAAAATTATCACTGCATGAACATA
Found at i:354396 original size:17 final size:17
Alignment explanation
Indices: 354374--354407 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
354364 TGTTAGTAAG
*
354374 CATTGTCATTGTATTTT
1 CATTGTCATTGCATTTT
354391 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTT
354408 AGTGTTAATT
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:0.18, C:0.15, G:0.12, T:0.56
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:355586 original size:26 final size:26
Alignment explanation
Indices: 355524--355591 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
355514 TTGCACCCAA
* * *
355524 AATTGTCACTGCAGGAACTTGTCTAG
1 AATTGTCGCTGCATGAACATGTCTAG
*
355550 AATT-ACTGCTGCATGAACATGTCTAG
1 AATTGTC-GCTGCATGAACATGTCTAG
* *
355576 AGTTGTCGCTGTATGA
1 AATTGTCGCTGCATGA
355592 GCATATCCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
25 1 0.03
26 31 0.94
27 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (26 bp):
AATTGTCGCTGCATGAACATGTCTAG
Found at i:359029 original size:51 final size:51
Alignment explanation
Indices: 358968--359152 Score: 235
Period size: 51 Copynumber: 3.6 Consensus size: 51
358958 GAATCTATAA
* * * *
358968 ACTCATGATGACAATTAGTTATCGAACCTTTAATCCATACAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGAACCTTTAATCCATACAAGATTCATTT
* * * * *
359019 ACTCACGATGACACTTAGTCATCAAACCATTAATCCATAAAATATTCATTC
1 ACTCACGATGACACTTAGTCATCGAACCTTTAATCCATACAAGATTCATTT
* * *
359070 ACTCGCGATGACACTTAGTCATCGGACTTTTAATCCATACAAGATTCATTT
1 ACTCACGATGACACTTAGTCATCGAACCTTTAATCCATACAAGATTCATTT
* *
359121 ACTCATGATGACACTTAGTCATCAGACCCTTT
1 ACTCACGATGACACTTAGTCATC-GAACCTTT
359153 CGTCTATAAC
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
51 106 0.95
52 5 0.05
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGAACCTTTAATCCATACAAGATTCATTT
Found at i:359937 original size:50 final size:50
Alignment explanation
Indices: 359858--359958 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
359848 AATTGAATGT
*
359858 GTAAACCCTAATTCCTCCCTCTTTAGCCGTGAGAAGAAGATGTAAAGAAA
1 GTAAACCCTAATTCCTCCCTCTTTAGCCGTGAGAAGAAGATGAAAAGAAA
*
359908 GTAAACCCTAATTCCTCCCTCTTTGGCCGTGAGAAGAAGATGAAAAGAAA
1 GTAAACCCTAATTCCTCCCTCTTTAGCCGTGAGAAGAAGATGAAAAGAAA
359958 G
1 G
359959 AAAATATGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (50 bp):
GTAAACCCTAATTCCTCCCTCTTTAGCCGTGAGAAGAAGATGAAAAGAAA
Found at i:360432 original size:29 final size:30
Alignment explanation
Indices: 360400--360460 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
360390 TGAAGGGTTA
*
360400 AATTAG-AATTTTTGTGAAATTTAGGGACT
1 AATTAGTAATTTTAGTGAAATTTAGGGACT
* * * *
360429 AATTTGTTATTTTAGTGGAATTTCGGGACT
1 AATTAGTAATTTTAGTGAAATTTAGGGACT
360459 AA
1 AA
360461 ATTGAGCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (30 bp):
AATTAGTAATTTTAGTGAAATTTAGGGACT
Found at i:363064 original size:25 final size:26
Alignment explanation
Indices: 363026--363082 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
363016 ATTGCGCCCT
* *
363026 AAATTGTCATTGTAGGA-TATGTCCA
1 AAATTGTCACTGTAGAAGTATGTCCA
* *
363051 GAATTGTCACTGTATAAGTATGTCCA
1 AAATTGTCACTGTAGAAGTATGTCCA
363077 AAATTG
1 AAATTG
363083 CGCCTAGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (26 bp):
AAATTGTCACTGTAGAAGTATGTCCA
Found at i:366092 original size:35 final size:35
Alignment explanation
Indices: 366053--366127 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
366043 AAGCAACACT
366053 TCCCACTTCAGAACAAGTGATAAAATCTCTTCTAA
1 TCCCACTTCAGAACAAGTGATAAAATCTCTTCTAA
*
366088 TCCCACTTCAGAACAAGTGATAGAATCTCTTCTAA
1 TCCCACTTCAGAACAAGTGATAAAATCTCTTCTAA
366123 TCCCA
1 TCCCA
366128 AGCAGCTCTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (35 bp):
TCCCACTTCAGAACAAGTGATAAAATCTCTTCTAA
Found at i:370334 original size:17 final size:17
Alignment explanation
Indices: 370312--370345 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
370302 TTTAAAATTC
*
370312 TTCATCAAAATTTTAAA
1 TTCATCAAAATTCTAAA
370329 TTCATCAAAATTCTAAA
1 TTCATCAAAATTCTAAA
370346 ATAATATATC
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:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
TTCATCAAAATTCTAAA
Found at i:371445 original size:50 final size:50
Alignment explanation
Indices: 371362--371484 Score: 124
Period size: 50 Copynumber: 2.4 Consensus size: 50
371352 AAATCACTAC
* * * **
371362 TTTACTTAAAAATCTAAA-TTTTTATTTCGAAATAGTTAAAAAATCAAAAT
1 TTTATTTAAAAATATAAACTTTTTATTTCAAAATAACTAAAAAAT-AAAAT
* * * *
371412 TTTATTTAAAAATTTAAACTTTTTCTTT-AAAATAACTAAAAAATAGATT
1 TTTATTTAAAAATATAAACTTTTTATTTCAAAATAACTAAAAAATAAAAT
371461 TTTATTTTTAAAAATATAAACTTT
1 TTTA--TTTAAAAATATAAACTTT
371485 CTTTCTTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
49 7 0.11
50 29 0.48
51 25 0.41
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (50 bp):
TTTATTTAAAAATATAAACTTTTTATTTCAAAATAACTAAAAAATAAAAT
Found at i:371505 original size:152 final size:149
Alignment explanation
Indices: 371219--371738 Score: 645
Period size: 152 Copynumber: 3.4 Consensus size: 149
371209 TTTTAAAAAT
* *
371219 AAATCAAAACTTTTATTTCAAAATAATTTAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTT
1 AAATCTAAACTTTTATTTCAAAAT-AGTTAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTT
* * * * * *
371284 CACATTAAAATCACTAAAAAAATAGATTTTTATTTTTTTAAAATTTGAA-CTTTCTTTTTTTTTA
65 -TCTTTAAAATAACT-AAAAAATAGATTTTTA-TTTTTAAAAATATAAATCTTTCTTTTTTTTTA
371348 ATGAAAATCACTACTTTACTTAA
127 ATGAAAATCACTACTTTACTTAA
* * *
371371 AAATCTAAATTTTTATTTCGAAATAGTTAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTT
1 AAATCTAAACTTTTATTTCAAAATAGTTAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTTT
371436 CTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATAAACTTTCTTTCTTTTTTTTTAA
66 CTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATAAA---TCTTTCTTTTTTTTTAA
*
371501 TGAAAATCACTAATTTACTTAA
128 TGAAAATCACTACTTTACTTAA
* * * ** **
371523 AAATCCAATCTTTTATTTCAAAATAGCTAAAAAAAAATCAAAA-TTT-TGTTAAATTTTTAATTT
1 AAATCTAAACTTTTATTTCAAAATAG-T--TAAAAAATCAAAACTTTAT-TTAAAAATTTAA-AC
* **
371586 TTTTTCTTTAAAATAACTAAAACATAGATTTTTATTTTTAAAAATATAAAT-TTTCTCCTTTTTT
61 TTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATAAATCTTTCTTTTTTTTT
371650 AATGAAAATCACTACTTT-CTTAA
126 AATGAAAATCACTACTTTACTTAA
* * * *
371673 AAATCTAAACTTTTATTTCAAAATAGTTAAAAAAAATTAAAACTTTGTTTAAAATTTTGAACTTT
1 AAATCTAAACTTTTATTTCAAAATAGTT--AAAAAATCAAAACTTTATTTAAAAATTTAAACTTT
371738 T
64 T
371739 CTAAAAAATA
Statistics
Matches: 322, Mismatches: 33, Indels: 29
0.84 0.09 0.08
Matches are distributed among these distances:
148 13 0.04
149 32 0.10
150 53 0.16
151 67 0.21
152 81 0.25
153 2 0.01
154 13 0.04
155 61 0.19
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (149 bp):
AAATCTAAACTTTTATTTCAAAATAGTTAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTTT
CTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATAAATCTTTCTTTTTTTTTAATGA
AAATCACTACTTTACTTAA
Found at i:372269 original size:3 final size:3
Alignment explanation
Indices: 372261--372310 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
372251 CAGAAAACCC
372261 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
372309 TA
1 TA
372311 GTAGTAGTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:372315 original size:3 final size:3
Alignment explanation
Indices: 372309--372343 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
372299 ATAATAATAA
372309 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
372344 ATGATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:378679 original size:72 final size:71
Alignment explanation
Indices: 378589--378732 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 71
378579 CTAACCCACT
*
378589 CAACCCATAACCCTAAACTATTGACCTTCACCCATTGACCCGGCCCGTTGACCTTGACACGTTGG
1 CAACCCATAACCCTAAACTATTGACCTTCACCCATTGACCCGACCCGTTGACCTTGACACGTTGG
378654 CTTGAC
66 CTTGAC
378660 NCAACCCATAACCCTAAACTATTGACCTTCACCCATTGACCCGACCCGTTGACCTTGACACGTTG
1 -CAACCCATAACCCTAAACTATTGACCTTCACCCATTGACCCGACCCGTTGACCTTGACACGTTG
378725 GCTTGAC
65 GCTTGAC
378732 C
1 C
378733 CATTAACCCT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 1 0.01
72 70 0.99
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (71 bp):
CAACCCATAACCCTAAACTATTGACCTTCACCCATTGACCCGACCCGTTGACCTTGACACGTTGG
CTTGAC
Found at i:386117 original size:21 final size:21
Alignment explanation
Indices: 386087--386126 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
386077 CCTACCCTAT
* *
386087 ACTTCTACCGATACAAGTAGA
1 ACTTCCACCGAAACAAGTAGA
386108 ACTTCCACCGAAACAAGTA
1 ACTTCCACCGAAACAAGTA
386127 AGCAAAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (21 bp):
ACTTCCACCGAAACAAGTAGA
Found at i:387705 original size:15 final size:15
Alignment explanation
Indices: 387685--387713 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
387675 GGGAATCAGA
387685 TATGCATGATGATAT
1 TATGCATGATGATAT
387700 TATGCATGATGATA
1 TATGCATGATGATA
387714 GATATGGAAA
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:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (15 bp):
TATGCATGATGATAT
Found at i:388022 original size:2 final size:2
Alignment explanation
Indices: 388017--388048 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
388007 TATAAAATGC
388017 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
388049 TGAGGATGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:394838 original size:21 final size:21
Alignment explanation
Indices: 394814--394855 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
394804 TAGTGCAGAC
*
394814 TTCTATAGATACTTAGGAAAA
1 TTCTACAGATACTTAGGAAAA
* *
394835 TTCTACCGATACTTATGAAAA
1 TTCTACAGATACTTAGGAAAA
394856 CTTTACCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (21 bp):
TTCTACAGATACTTAGGAAAA
Found at i:394862 original size:21 final size:21
Alignment explanation
Indices: 394821--394864 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
394811 GACTTCTATA
394821 GATACTTAGGAAAATTCTACC
1 GATACTTAGGAAAATTCTACC
*
394842 GATACTTATGAAAACTT-TACC
1 GATACTTAGGAAAA-TTCTACC
394863 GA
1 GA
394865 AACATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (21 bp):
GATACTTAGGAAAATTCTACC
Found at i:411020 original size:17 final size:18
Alignment explanation
Indices: 410980--411023 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
410970 GTAGTGTTTT
410980 TTAAAAGTATTTTTGACA
1 TTAAAAGTATTTTTGACA
*
410998 TAAAAAGTACTTTTT-A-A
1 TTAAAAGTA-TTTTTGACA
411015 TTAAAAGTA
1 TTAAAAGTA
411024 ATGTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 9 0.39
19 5 0.22
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (18 bp):
TTAAAAGTATTTTTGACA
Found at i:411235 original size:31 final size:31
Alignment explanation
Indices: 411198--411262 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
411188 TGCTGAGATT
411198 GATTCTACTATAAACAGAGCTTTCTACACTA
1 GATTCTACTATAAACAGAGCTTTCTACACTA
411229 GATTCTACTATAAACAGAGCTTTCTACACTA
1 GATTCTACTATAAACAGAGCTTTCTACACTA
411260 GAT
1 GAT
411263 CGTGTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (31 bp):
GATTCTACTATAAACAGAGCTTTCTACACTA
Done.