Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold326.1
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: 1283098
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 31207 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:287445 original size:13 final size:13
Alignment explanation
Indices: 287427--287452 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
287417 GACTTTATCG
287427 TTATTTAAAAATC
1 TTATTTAAAAATC
287440 TTATTTAAAAATC
1 TTATTTAAAAATC
287453 AATTTATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTATTTAAAAATC
Found at i:291868 original size:20 final size:21
Alignment explanation
Indices: 291843--291882 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
291833 AAATCATTGA
291843 TAAATCCAA-CCAACTTTTCT
1 TAAATCCAAGCCAACTTTTCT
*
291863 TAAATCCAAGCCATCTTTTC
1 TAAATCCAAGCCAACTTTTC
291883 ATAGGCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAATCCAAGCCAACTTTTCT
Found at i:293481 original size:17 final size:17
Alignment explanation
Indices: 293459--293494 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
293449 CTTCATTCTA
293459 TTCACTGATAGTGATCG
1 TTCACTGATAGTGATCG
*
293476 TTCACTGATATTGATCG
1 TTCACTGATAGTGATCG
293493 TT
1 TT
293495 GATACTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (17 bp):
TTCACTGATAGTGATCG
Found at i:293861 original size:107 final size:107
Alignment explanation
Indices: 293669--293874 Score: 333
Period size: 107 Copynumber: 1.9 Consensus size: 107
293659 CAAAAATTTA
* *
293669 ATTCAATTTTTTTCAATTGGCAGGTCTAAGTTAATTAGAATTTTAAAAGTTTTGAGTCAGATTTT
1 ATTCAATTTTTTTCAATTGACAGGTCTAAGTTAATTAGAATTATAAAAGTTTTGAGTCAGATTTT
*
293734 GTTTAGTCAAAGAATTTTATTCAATC-AAATTTTAAATTTTC
66 GTTTAGTCAAAGAATTTTATTCAACCAAAATTTTAAATTTTC
* *
293775 ATTCAATTTTTTTTCAATTGATAGGTCTAAGTTAATTAGAATTATAAAAGTTTTGAGTTAGATTT
1 ATTCAA-TTTTTTTCAATTGACAGGTCTAAGTTAATTAGAATTATAAAAGTTTTGAGTCAGATTT
* *
293840 TGTTTAGTGATAGAATTTTATTCAACCAAAATTTT
65 TGTTTAGTCAAAGAATTTTATTCAACCAAAATTTT
293875 TTTAAGTCCA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
106 6 0.07
107 78 0.86
108 7 0.08
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (107 bp):
ATTCAATTTTTTTCAATTGACAGGTCTAAGTTAATTAGAATTATAAAAGTTTTGAGTCAGATTTT
GTTTAGTCAAAGAATTTTATTCAACCAAAATTTTAAATTTTC
Found at i:293922 original size:20 final size:20
Alignment explanation
Indices: 293893--293938 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
293883 CAAGTCTATA
*
293893 TTAAAAAATATATTTTAAAT
1 TTAAATAATATATTTTAAAT
* **
293913 TTAAATAATATTTTTTTTAT
1 TTAAATAATATATTTTAAAT
293933 TTAAAT
1 TTAAAT
293939 TGATGTTGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAATAATATATTTTAAAT
Found at i:295854 original size:8 final size:8
Alignment explanation
Indices: 295837--295866 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
295827 CTATATAATT
295837 TGAT-ATC
1 TGATGATC
295844 TGATGATC
1 TGATGATC
295852 TGATGATC
1 TGATGATC
295860 TGATGAT
1 TGATGAT
295867 GAATAACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.18
8 18 0.82
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (8 bp):
TGATGATC
Found at i:296595 original size:25 final size:25
Alignment explanation
Indices: 296560--296632 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
296550 TTTGTAGCTC
* * **
296560 TGTCCTATTCTGTTATATTCTGGTT
1 TGTCCTGTTCTGATATATTCTGCCT
*
296585 TGTCCTGTTCTGATATGTTCTGCCT
1 TGTCCTGTTCTGATATATTCTGCCT
* *
296610 TGTCCTGTTCTAATATGTTCTGC
1 TGTCCTGTTCTGATATATTCTGC
296633 TCTGTTCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.51
Consensus pattern (25 bp):
TGTCCTGTTCTGATATATTCTGCCT
Found at i:297081 original size:7 final size:7
Alignment explanation
Indices: 297071--297096 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
297061 ATATTAATAA
297071 TTAAAAT
1 TTAAAAT
297078 TTAAAAT
1 TTAAAAT
297085 TTAAAAT
1 TTAAAAT
297092 TTAAA
1 TTAAA
297097 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAAAT
Found at i:298173 original size:21 final size:21
Alignment explanation
Indices: 298149--298262 Score: 54
Period size: 21 Copynumber: 5.4 Consensus size: 21
298139 TTAGGGTTTG
298149 GGTTTTGGGTTTTGGGTTCAA
1 GGTTTTGGGTTTTGGGTTCAA
* * *
298170 GGTTTAAGGG-TTTGGATTTAA
1 GGTTT-TGGGTTTTGGGTTCAA
* ** *
298191 AGTTTAAGGTTTTGGGGTT-AT
1 GGTTTTGGGTTTT-GGGTTCAA
* * ** *
298212 GTGTTATGAGTTCGGGGTTCAC
1 G-GTTTTGGGTTTTGGGTTCAA
*
298234 GG-TTTGGGTTTTGGATTCAA
1 GGTTTTGGGTTTTGGGTTCAA
*
298254 GGGTTTGGG
1 GGTTTTGGG
298263 GTTATGAGCT
Statistics
Matches: 66, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
20 17 0.26
21 34 0.52
22 15 0.23
ACGTcount: A:0.15, C:0.04, G:0.38, T:0.43
Consensus pattern (21 bp):
GGTTTTGGGTTTTGGGTTCAA
Found at i:298999 original size:16 final size:16
Alignment explanation
Indices: 298959--298992 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
298949 GGGTTTTTAA
298959 TTAAATTT-GAATTATT
1 TTAAATTTAG-ATTATT
298975 TTAAATTTAGATTATT
1 TTAAATTTAGATTATT
298991 TT
1 TT
298993 CGATTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TTAAATTTAGATTATT
Found at i:303558 original size:21 final size:21
Alignment explanation
Indices: 303532--303594 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
303522 GATTCTCCAA
303532 GTGTTTACGAAACATAGTCA-
1 GTGTTTACGAAACATAGTCAG
303552 GTGGTTTACGAAACATAGTCAG
1 GT-GTTTACGAAACATAGTCAG
* *
303574 GTGTTTACGAATCATACTCAG
1 GTGTTTACGAAACATAGTCAG
303595 AACAAAGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
20 2 0.05
21 35 0.90
22 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (21 bp):
GTGTTTACGAAACATAGTCAG
Found at i:303881 original size:24 final size:25
Alignment explanation
Indices: 303834--303881 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
303824 TAATATTTGA
*
303834 TTTTTCAGTGCAATAGCATCATTTCT
1 TTTTTCAGTGCAATA-CATAATTTCT
*
303860 TTTTTCAGTGCCAT-CATAATTT
1 TTTTTCAGTGCAATACATAATTT
303882 ACTAAATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
26 13 0.65
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (25 bp):
TTTTTCAGTGCAATACATAATTTCT
Found at i:311640 original size:15 final size:18
Alignment explanation
Indices: 311606--311639 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
311596 CAAGTTCTTC
311606 TCTTCTTTCTTCACATTT
1 TCTTCTTTCTTCACATTT
311624 TCTTCTTT-TTCA-ATTT
1 TCTTCTTTCTTCACATTT
311640 CCTTTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTTCTTTCTTCACATTT
Found at i:312479 original size:25 final size:25
Alignment explanation
Indices: 312451--312545 Score: 93
Period size: 25 Copynumber: 3.7 Consensus size: 25
312441 TATCTGATTA
312451 TGATTATGATTCTATGTTTTTTATC
1 TGATTATGATTCTATGTTTTTTATC
* * *
312476 TGATTATGATTCTATGTATTGTGTC
1 TGATTATGATTCTATGTTTTTTATC
* * *
312501 TG-TTTTCGTACTGTGTTTGTTTTTTATC
1 TGATTAT-G-A-T-TCTATGTTTTTTATC
312529 TGATTATGATTCTATGT
1 TGATTATGATTCTATGT
312546 GTTCTGACCC
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
24 3 0.06
25 30 0.57
26 2 0.04
27 2 0.04
28 13 0.25
29 3 0.06
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (25 bp):
TGATTATGATTCTATGTTTTTTATC
Found at i:314192 original size:30 final size:30
Alignment explanation
Indices: 314158--314219 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
314148 ACTTACTTTA
*
314158 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTCTGTTATTATTTTAAAGGCAT
* *
314188 TTGTTAATTCTGTTATTATTTTAGAGGTAT
1 TTGTTAATTCTGTTATTATTTTAAAGGCAT
314218 TT
1 TT
314220 ACTTATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTCTGTTATTATTTTAAAGGCAT
Found at i:314357 original size:13 final size:13
Alignment explanation
Indices: 314341--314376 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
314331 ATATATATTT
*
314341 AAAAATTATATAA
1 AAAAATAATATAA
314354 AAAAATAATATAA
1 AAAAATAATATAA
*
314367 AAAATTAATA
1 AAAAATAATA
314377 CGGGCAGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATAATATAA
Found at i:315198 original size:29 final size:30
Alignment explanation
Indices: 315156--315217 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
315146 ACTTAACAAG
315156 CAAATGTCTCTAAAATAATAA-AAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
* *
315185 CAAATGTCTTTAAAATAATAACAAATTTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
315215 CAA
1 CAA
315218 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:315813 original size:27 final size:26
Alignment explanation
Indices: 315772--315900 Score: 78
Period size: 27 Copynumber: 4.7 Consensus size: 26
315762 TTGTTATTTA
**
315772 ATTTTAATAGGATTATAATTTAATCAT
1 ATTTTAATAAAATTATAATTTAAT-AT
* *
315799 ATTTTAATAAAATTATTATTAAATAT
1 ATTTTAATAAAATTATAATTTAATAT
* *
315825 AATTTAAAATAATAATATATAATTTAATAAC
1 -ATTT-TAATAA-AAT-TATAATTTAAT-AT
* * *
315856 ATTCTTAATATAATAATTATTTAAATAT
1 ATT-TTAATAAAATTATAATTT-AATAT
** *
315884 AAATTAATAAAAATATA
1 ATTTTAATAAAATTATA
315901 TAATATTAGA
Statistics
Matches: 76, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
26 2 0.03
27 34 0.45
28 13 0.17
29 9 0.12
30 16 0.21
31 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTTTAATAAAATTATAATTTAATAT
Found at i:315852 original size:57 final size:57
Alignment explanation
Indices: 315785--315904 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 57
315775 TTAATAGGAT
* * * * *
315785 TATAATTTAATCATATT-TTAATAAAATTATTA-TTAAATATAATTTAAAATAATAATA
1 TATAATTTAATAACATTCTTAATAAAATAATTATTTAAATATAAATT--AATAAAAATA
*
315842 TATAATTTAATAACATTCTTAATATAATAATTATTTAAATATAAATTAATAAAAATA
1 TATAATTTAATAACATTCTTAATAAAATAATTATTTAAATATAAATTAATAAAAATA
315899 TATAAT
1 TATAAT
315905 ATTAGAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
57 30 0.55
58 13 0.24
59 12 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (57 bp):
TATAATTTAATAACATTCTTAATAAAATAATTATTTAAATATAAATTAATAAAAATA
Found at i:315903 original size:18 final size:21
Alignment explanation
Indices: 315880--315924 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
315870 AATTATTTAA
*
315880 ATATAA-ATTA-ATAAA-AAT
1 ATATAATATTAGAAAAATAAT
315898 ATATAATATTAGAAAAATAAT
1 ATATAATATTAGAAAAATAAT
315919 ATATAA
1 ATATAA
315925 CCTACTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 4 0.17
21 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATAATATTAGAAAAATAAT
Found at i:320168 original size:21 final size:21
Alignment explanation
Indices: 320125--320168 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
320115 GTTTTGATGA
* *
320125 TTTATGATAGATTATGAATTT
1 TTTATGATAGATTATCAAATT
320146 TTTATGATAG-TTATACAAATT
1 TTTATGATAGATTAT-CAAATT
320167 TT
1 TT
320169 GTTAAGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (21 bp):
TTTATGATAGATTATCAAATT
Found at i:323547 original size:44 final size:44
Alignment explanation
Indices: 323437--323595 Score: 193
Period size: 44 Copynumber: 3.6 Consensus size: 44
323427 AGCTCGTACA
*
323437 ATGCCAACATCCCAGACGTGGTCTTACATGT--A-ATCAAACATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGTAAATATC-AA-ATCG
* *
323480 ATGCC-ACTGTCCCAAACAG-GGTCTTACACGTAAATATCAAATCG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACGTAAATATCAAATCG
* *
323524 ATGCCAACGTCTCAGACGTGGTCTTACACGTAAATATCAAATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGTAAATATCAAATCG
*
323568 ATTCCAACATCCCAGACGTGGTCTTACA
1 ATGCCAACATCCCAGACGTGGTCTTACA
323596 TGATTACTCA
Statistics
Matches: 101, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
42 2 0.02
43 24 0.24
44 67 0.66
45 5 0.05
46 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (44 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGTAAATATCAAATCG
Found at i:325167 original size:49 final size:49
Alignment explanation
Indices: 325089--325190 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
325079 ATGATTCATG
* *
325089 TTATACAATGCTAAACTTGGTATTTCACTGTCTAAACTCTTATCACTAT
1 TTATACAATGCTAAACTTAGTATTCCACTGTCTAAACTCTTATCACTAT
* * *
325138 TTATACATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTAT
1 TTATACAATGCTAAACTTAGTATTCCACTGTCTAAACTCTTATCACTAT
325187 TTAT
1 TTAT
325191 CCCTTCTTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (49 bp):
TTATACAATGCTAAACTTAGTATTCCACTGTCTAAACTCTTATCACTAT
Found at i:325697 original size:30 final size:30
Alignment explanation
Indices: 325652--325718 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
325642 TGACTTGGGT
*
325652 CACACGCCTATGTGTGTTGCCCGTGTGTGA
1 CACACGCCCATGTGTGTTGCCCGTGTGTGA
*
325682 CACATGCCCATGTGTGTTGCCCGTGTGTGA
1 CACACGCCCATGTGTGTTGCCCGTGTGTGA
325712 CACACGC
1 CACACGC
325719 TCGTGTGGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (30 bp):
CACACGCCCATGTGTGTTGCCCGTGTGTGA
Found at i:332331 original size:22 final size:22
Alignment explanation
Indices: 332305--332347 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
332295 TAAGCTTGAA
332305 TTTCATTAAATTACTTTCAAAT
1 TTTCATTAAATTACTTTCAAAT
332327 TTTCATTAAATTACTTTCAAA
1 TTTCATTAAATTACTTTCAAA
332348 GTTAAGGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTCATTAAATTACTTTCAAAT
Found at i:334221 original size:63 final size:63
Alignment explanation
Indices: 334122--334248 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
334112 TGTAGATTGC
*
334122 TGAATCTAATGTTTATTAAATCCAACAAGTCCAAAGCAAGTACATACATAATCTAAACAAGGT
1 TGAATCTAATATTTATTAAATCCAACAAGTCCAAAGCAAGTACATACATAATCTAAACAAGGT
* *
334185 TGAATCTAATATTTATTAAATCCAACAAGTGCAAAGCAAGTATATACATAATCTAAACAAGGT
1 TGAATCTAATATTTATTAAATCCAACAAGTCCAAAGCAAGTACATACATAATCTAAACAAGGT
334248 T
1 T
334249 TATCTAGATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (63 bp):
TGAATCTAATATTTATTAAATCCAACAAGTCCAAAGCAAGTACATACATAATCTAAACAAGGT
Found at i:334930 original size:51 final size:51
Alignment explanation
Indices: 334865--335067 Score: 397
Period size: 51 Copynumber: 4.0 Consensus size: 51
334855 CATTCCTTTT
*
334865 TCTTTGTAGGCTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTTG
1 TCTTTGTAGACTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTTG
334916 TCTTTGTAGACTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTTG
1 TCTTTGTAGACTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTTG
334967 TCTTTGTAGACTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTTG
1 TCTTTGTAGACTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTTG
335018 TCTTTGTAGACTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTT
1 TCTTTGTAGACTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTT
335068 TATAATCTTG
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 151 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (51 bp):
TCTTTGTAGACTCATATTGTATATTTGTTCTACTTCACCAATTAAAAGTTG
Found at i:336281 original size:16 final size:16
Alignment explanation
Indices: 336260--336311 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
336250 TTTGGTTCGC
336260 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
336276 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
** *
336292 TGTATAAGAATAGAGG
1 TGTATTGGATTAGAGG
336308 TGTA
1 TGTA
336312 ATAGCAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:336569 original size:18 final size:17
Alignment explanation
Indices: 336548--336582 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
336538 TTATTATTTA
*
336548 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
336566 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
336583 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:336576 original size:28 final size:27
Alignment explanation
Indices: 336506--336578 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
336496 TTTATTATCA
*
336506 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
336534 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
336561 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
336579 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:336751 original size:47 final size:46
Alignment explanation
Indices: 336685--336851 Score: 146
Period size: 47 Copynumber: 3.6 Consensus size: 46
336675 TTAATTAAAA
*
336685 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTATCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTATCT
* * * * * *
336732 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
* * * *
336777 TA-AT-AATAATATATAATTTCATAA-AATTCTTAATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTATCT
*
336823 TATATGAATTTATACAATTTAAAATAATT
1 TATATGAATTTATATAATTTAAAATAATT
336852 CGGATCAATC
Statistics
Matches: 92, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
43 3 0.03
44 15 0.16
45 14 0.15
46 13 0.14
47 40 0.43
48 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
Found at i:336773 original size:26 final size:28
Alignment explanation
Indices: 336744--336815 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
336734 TATGAATTTG
*
336744 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
336770 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
336798 TAAAATTCTTAATAATAA
1 TATAA-T-TTAATAATAA
336816 ATTTTCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 12 0.31
29 1 0.03
30 10 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:337011 original size:22 final size:22
Alignment explanation
Indices: 336983--337027 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
336973 ACTAAGCTTG
336983 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
337005 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
337027 A
1 A
337028 GTTAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTCATTAAATTACTTTCAA
Found at i:348469 original size:3 final size:3
Alignment explanation
Indices: 348461--348492 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
348451 TATAAAAGGG
348461 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
348493 GACTAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:349717 original size:40 final size:40
Alignment explanation
Indices: 349668--349751 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
349658 TCATATCTAA
349668 AAACCCTAAATTAAATTAAACTATTTCAATTGAATCGAAC
1 AAACCCTAAATTAAATTAAACTATTTCAATTGAATCGAAC
349708 AAACCCTAAATTAAATTAAACTATTTCAATTGAATCGAAC
1 AAACCCTAAATTAAATTAAACTATTTCAATTGAATCGAAC
349748 AAAC
1 AAAC
349752 AAATTGGACC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.29
Consensus pattern (40 bp):
AAACCCTAAATTAAATTAAACTATTTCAATTGAATCGAAC
Found at i:357446 original size:2 final size:2
Alignment explanation
Indices: 357439--357465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
357429 TGAATCCATG
357439 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
357466 TTGGGAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:370438 original size:28 final size:28
Alignment explanation
Indices: 370407--370955 Score: 682
Period size: 28 Copynumber: 20.4 Consensus size: 28
370397 TAGGGTTTTT
*
370407 AATTAAGTTAAGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370435 AATTAATTTAGGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370463 AATTAAATTAGGTTAGGGTTTTTAATT-
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370490 AA-T---TTAAGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370514 AATTAAATTAGGTTAGGG--TTT--TT-
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370537 AATTAAGTTAAGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370565 AATTAAATTAGGTTAGGG-TTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
370592 AATTAAGTTAGGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370620 AATTAGGTTATGGTTAGGGTTTTTAATTA
1 AATTAAGTTA-GGTTAGGGTTTTTAATTA
*
370649 AATTAAGTTAGGTTAGTGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
* *
370677 AATTAGGTTAGGGTTAGAGTTTTTAATTA
1 AATTAAGTTA-GGTTAGGGTTTTTAATTA
* *
370706 AAATAAGTTAGGGTTAGGGTTTTTAACT-
1 AATTAAGTTA-GGTTAGGGTTTTTAATTA
*
370734 -A--AA-TTAGGTTAGGGATTTTAATT-
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370757 -A--AA-TTAGGTTAGGGATTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370781 AATTAAATTAGGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
* *
370809 AATTAAATTAGGTTAGGGATTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370837 AATTAAATTAGGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370865 AATTAAATTAGGTTAGGG--TTT--TT-
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370888 AATTAAGTTAAGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370916 AATTAAATTAGGTTAGGGTTTTTAATTA
1 AATTAAGTTAGGTTAGGGTTTTTAATTA
*
370944 AGTTAAGTTAGG
1 AATTAAGTTAGG
370956 GTTGTTCTTC
Statistics
Matches: 468, Mismatches: 30, Indels: 46
0.86 0.06 0.08
Matches are distributed among these distances:
23 89 0.19
24 9 0.02
25 10 0.02
26 7 0.01
27 35 0.07
28 250 0.53
29 68 0.15
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (28 bp):
AATTAAGTTAGGTTAGGGTTTTTAATTA
Found at i:370474 original size:51 final size:51
Alignment explanation
Indices: 370391--370958 Score: 548
Period size: 51 Copynumber: 10.7 Consensus size: 51
370381 ATGTGCTCGA
* *
370391 TTAGGTTAGGGTTTTTAATTAAGTTAAGTTAGGGTTTTTAATTAAATTAAT
1 TTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAATTAAATTAAG
*
370442 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAATTTAAG
1 TTAGGTTAGGGTTTTTAATTAAATT--A--A-GTTAGGGTTTTTAATTAAATTAAG
* *
370498 TTAGGGTT----TTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAGTTAAG
1 TTA-GGTTAGGGTTT--TT-AATTAAATTAAGTTAGGGTTTTTAATTAAATTAAG
*
370549 TTAGGGTT----TTTAATTAAATTAAATTAGGTTAGGG-TTTTAATTAAATTAAG
1 TTA-GGTTAGGGTTT--TT-AATTAAATTAAGTTAGGGTTTTTAATTAAATTAAG
370599 TTAGGTTAGGGTTTTTAATTAAATTAGGTTATGGTTAGGGTTTTTAATTAAATTAAG
1 TTAGGTTAGGGTTTTTAATTAAATTA----A--GTTAGGGTTTTTAATTAAATTAAG
* * *
370656 TTAGGTTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAAATAAG
1 TTAGGTTAGGGTTTTTAATTAAATTA----A--GTTAGGGTTTTTAATTAAATTAAG
* * * *
370713 TTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGGATTTTAATTAAATTAGG
1 TTA-GGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAATTAAATTAAG
** * *
370765 TTAGG---GATTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGTTAGGGTTT--TT-AATTAAATTAAGTTAGGGTTTTTAATTAAATTAAG
* *
370816 TTAGGTTAGGGATTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGTTAGGG--TTT--TT-AATTAAATTAAGTTAGGGTTTTTAATTAAATTAAG
* *
370872 TTAGGTTAGGGTTTTTAATTAAGTTAAGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAATTAAATTAAG
*
370923 TTAGGTTAGGGTTTTTAATTAAGTTAAGTTAGGGTT
1 TTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTT
370959 GTTCTTCCTC
Statistics
Matches: 460, Mismatches: 28, Indels: 58
0.84 0.05 0.11
Matches are distributed among these distances:
48 4 0.01
49 4 0.01
50 30 0.07
51 190 0.41
52 25 0.05
53 7 0.02
54 5 0.01
55 3 0.01
56 95 0.21
57 76 0.17
58 21 0.05
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.46
Consensus pattern (51 bp):
TTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAATTAAATTAAG
Found at i:370756 original size:18 final size:21
Alignment explanation
Indices: 370733--370785 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 21
370723 GGTTTTTAAC
370733 TAAATTAGGTTAGGGATTTTAAT
1 TAAATTAGGTTAGGGA-TTT-AT
370756 TAAATTAGGTTAGGGATTTTAAT
1 TAAATTAGGTTAGGGA-TTT-AT
370779 TAAATTA
1 TAAATTA
370786 AATTAGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
TAAATTAGGTTAGGGATTTAT
Found at i:372936 original size:14 final size:15
Alignment explanation
Indices: 372919--372952 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
372909 AATAAATATC
372919 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
372933 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
372948 TAAAA
1 TAAAA
372953 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:373180 original size:22 final size:22
Alignment explanation
Indices: 373150--373191 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
373140 ATTTGGAGAT
*
373150 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
373172 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
373192 TTTGAGAGAA
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:373199 original size:30 final size:30
Alignment explanation
Indices: 373163--373221 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
373153 TTGAAGGAAA
* *
373163 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
373193 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
373222 AATTTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:373212 original size:52 final size:51
Alignment explanation
Indices: 373141--373243 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
373131 TTAATATGGA
* * *
373141 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAA-TTGAGAG
*
373192 TTTGAGAGAATTTTGGAAGGAAATTGAGAGAATTTTTGAACGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
373244 AATTTTTGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 38 0.83
53 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
Found at i:373218 original size:22 final size:22
Alignment explanation
Indices: 373193--373262 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
373183 ATTTGAGAGT
*
373193 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
373215 TTGAGAGAATTTTTGAACGG-AA
1 TTGAGAGAATTTTTGAA-GGAAA
373237 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
373259 TTGA
1 TTGA
373263 TATTGAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.29, T:0.31
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:375547 original size:16 final size:16
Alignment explanation
Indices: 375528--375570 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
375518 TTCTTTTTTC
375528 ATTCTTTGTTCGATTT
1 ATTCTTTGTTCGATTT
375544 ATTCTTTGTTCGATTT
1 ATTCTTTGTTCGATTT
375560 ATTCTTTGTTC
1 ATTCTTTGTTC
375571 TCAGATCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.63
Consensus pattern (16 bp):
ATTCTTTGTTCGATTT
Found at i:385410 original size:213 final size:213
Alignment explanation
Indices: 385157--387408 Score: 3591
Period size: 213 Copynumber: 10.6 Consensus size: 213
385147 TGTTTTAAAT
385157 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
* * *
385222 GAACAACTGTAAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTTACGACAT
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
** * * *
385287 TCCGTCTTCATGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGGAGTGGTTG
131 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGTGGTTG
385352 TACGAACTTGATTTAAGC
196 TACGAACTTGATTTAAGC
* * *
385370 GGAACAGCTTTGAAGGAAATACCATCCTCAATTGGCAATCTTATTGGTCTTATGCG-TTTGAATA
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAG-GATTTGAATA
* * *
385434 TGAACAACTGTAAAAACCTTGTTTGCCTTCCTGACAGCTTTTGTAAATTGAAATCTCTCTCGAGA
65 TGAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGA
* * * *
385499 TTTTATCTTCAAGGTTGCTCGAGATTGGAGATTTTCCCAGAAATCATGGACACCATGGAGTGGTT
130 TTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGTGGTT
* *
385564 GTATGAACTTGATTTAAGT
195 GTACGAACTTGATTTAAGC
*
385583 GGAACGGCTTTGAAGGAATTACCATCCTCGATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
* *
385648 GAACAACTGTAAAAACTTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAGGAGAT
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
* *
385713 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCGTGAAGAGGTTG
131 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGTGGTTG
* *
385778 TATGAACTTGATTTAAGT
196 TACGAACTTGATTTAAGC
*
385796 GGAACAGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
* * * * *
385861 GAACAACTGTAAAAACTTTGTTTTCCTTCCTGACAGCTTTTGTAAATTGAAATCTCTTACAACAT
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
** * * * * *
385926 TCCGTCTTCATGGTTGCTTGAGATTGGAGATTTTCCCGGAAATCATGGACACCGTGAAGAGGTTG
131 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGTGGTTG
* *
385991 TATGAACTTGATTTAAGT
196 TACGAACTTGATTTAAGC
*
386009 GGAACAGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
* * * *
386074 GAACAACTGTAAAAGCCTTGTTTTCCTTCCTGACAGCTTTTGTAAATTGAAATCCCTGGA-GAGA
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCT-CACGAGA
386138 TTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGAT-GT
130 TTCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAG-TGGT
386202 TGTACGAACTTGATTTAAGC
194 TGTACGAACTTGATTTAAGC
*
386222 GAAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
*
386287 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGAT
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
*
386352 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCAGAAATCATGGACACCATGAAGAT-GTT
131 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAG-TGGTT
386416 GTACGAACTTGATTTAAGC
195 GTACGAACTTGATTTAAGC
*
386435 GGAACGGCTTTGAAGGAATTACCATCCCCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
* *
386500 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAACTTTTATAAATTGAAATCTCTCAAGAGAT
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
*
386565 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCAGAAATCATGGACACCATGAAGAT-GTT
131 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAG-TGGTT
386629 GTACGAACTTGATTTAAGC
195 GTACGAACTTGATTTAAGC
*
386648 GGAACGGCTTTGAAGGAATTACCATCCCCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
* *
386713 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGGCAGCTTTTATAAATTGAAATCTCTCAAGAGAT
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
386778 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGAT-GTT
131 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAG-TGGTT
386842 GTACGAACTTGATTTAAGC
195 GTACGAACTTGATTTAAGC
*
386861 GGAACAGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
* *
386926 GAACAACTGTAAAAGCCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAGGAGAT
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
* *
386991 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTGGACACCATGAAGAGGTTG
131 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGTGGTTG
*
387056 TATGAACTTGATTTAAGC
196 TACGAACTTGATTTAAGC
*
387074 GGAACAGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
* * * * *
387139 GAACAACTGTAAAAACCTTGTTTGCCTTCCTGACAGCTTTTGTAAATTGAAATCTCTTACAACAT
66 GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
** * * * * * *
387204 TCCGTCTTCATGGTTGCTTGAGATTGGAGATTTTCCCGGAAATCATAGACACCATGGAGAGGTTG
131 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGTGGTTG
*
387269 TATGAACTTGATTTAAGC
196 TACGAACTTGATTTAAGC
* * * *
387287 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGACAATCTTGTTGGTCTTAAGTATTTGAGCT-
1 GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGA-ATA
* * * * * * *
387351 TGAACGACTGTGAAAACTTTGTTTGCTTTCTTGACAGCTTTTTTAAATTGAAATCTCT
65 TGAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCT
387409 TTTGTGTCTT
Statistics
Matches: 1929, Mismatches: 103, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
212 2 0.00
213 1924 1.00
214 3 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (213 bp):
GGAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAATAT
GAACAACTGTAAAAACCTTGTTTTCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCACGAGAT
TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGTGGTTG
TACGAACTTGATTTAAGC
Found at i:394825 original size:213 final size:212
Alignment explanation
Indices: 394496--395068 Score: 736
Period size: 213 Copynumber: 2.7 Consensus size: 212
394486 GTATAGTTTT
* *
394496 CCAGAAATCATGGACACCATGGAGAGTTTGAGGCATCTTTATTT-AAGCGGAACGGCTTTGAAGG
1 CCAGAAATCATGGACACCATGGAGAG-TTGAGGGATCTTGATTTAAAG-GGAACGGCTTTGAAGG
* * * ** * * *
394560 AATTACCATCCTCAATTGAAAACCTTATCGGTCTTAAGCAATTGAGATTGAAAAACTATAAAAAG
64 AATTACCATCCTCAATTGATAATCTTATTGGTCTTGTGAAATTGAGATTGAAAAACTGTAAAAAC
* *
394625 CTTGTTTGTCTTTCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTCTATCTTAAAGGTTG
129 CTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTCTATCTTAAAGGTTG
394690 CTCGAGATTGGAGACTTTC
194 CTCGAGATTGGAGACTTTC
* * * * * *
394709 CCAGAAATCATAGACAACATGGAGATGTTGAGGGAACTTGATTTAAAGGGATCAGATTTGAAGGA
1 CCAGAAATCATGGACACCATGGAGA-GTTGAGGGATCTTGATTTAAAGGGAACGGCTTTGAAGGA
* * * *
394774 ATTACCATCCTCAATTGATAATCTTATTAGTCTTGTGGATTTGAAATTGAAAAACTGTAAAAACC
65 ATTACCATCCTCAATTGATAATCTTATTGGTCTTGTGAAATTGAGATTGAAAAACTGTAAAAACC
* * * * * *
394839 TTATTTGCCTTCCTGATAGCTTTTATAAATTGAAATCTCTCAAGATATTTTGTCTTGAAGGTTGC
130 TTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTCTATCTTAAAGGTTGC
394904 TCGAGATTGGAGACTTTC
195 TCGAGATTGGAGACTTTC
* *** *
394922 CCAGAAATCATGGACACCATGGAGAGGTTGAGGCG-TCTTGATTTAGATCCAACGGCTTCGAAGG
1 CCAGAAATCATGGACACCATGGAGA-GTTGAGG-GATCTTGATTTAAAGGGAACGGCTTTGAAGG
* * * * * *
394986 ACTTACCATCCTCAATCGATAATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAAC
64 AATTACCATCCTCAATTGATAATCTTATTGGTCTTGTGAAATTGAGATTGAAAAACTGTAAAAAC
395051 CTTGTTTGCCTTCCTGAC
129 CTTGTTTGCCTTCCTGAC
395069 GAATTACCAC
Statistics
Matches: 307, Mismatches: 50, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
213 302 0.98
214 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (212 bp):
CCAGAAATCATGGACACCATGGAGAGTTGAGGGATCTTGATTTAAAGGGAACGGCTTTGAAGGAA
TTACCATCCTCAATTGATAATCTTATTGGTCTTGTGAAATTGAGATTGAAAAACTGTAAAAACCT
TGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTCTATCTTAAAGGTTGCT
CGAGATTGGAGACTTTC
Found at i:395129 original size:84 final size:84
Alignment explanation
Indices: 395006--397326 Score: 4633
Period size: 84 Copynumber: 27.6 Consensus size: 84
394996 CTCAATCGAT
395006 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395071 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395090 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395155 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395174 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395239 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395258 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395323 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395342 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395407 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395426 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395491 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395510 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395575 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395594 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395659 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395678 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395743 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395762 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395827 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395846 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395911 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
395930 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
395995 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396014 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396079 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396098 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396163 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396182 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396247 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396266 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396331 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396350 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396415 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396434 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396499 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396518 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396583 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396602 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396667 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396686 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396751 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396770 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396835 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396854 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
396919 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
396938 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
397003 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
397022 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
397087 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
397106 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
397171 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
397190 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
397255 ATTACCACCATTAATTGGC
66 ATTACCACCATTAATTGGC
*
397274 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTATTTG
1 AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTG
397327 TATTCTTGAC
Statistics
Matches: 2236, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 2236 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (84 bp):
AATCTTATTGGTCTTGTGAAGTTGAGTTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACGA
ATTACCACCATTAATTGGC
Found at i:397620 original size:213 final size:213
Alignment explanation
Indices: 397274--397786 Score: 825
Period size: 213 Copynumber: 2.4 Consensus size: 213
397264 ATTAATTGGC
* * ** *
397274 AATCTTATTGGTCTTG-TGAAGTTGAGTTTGAACAACTGTGAAAACCTTATTTGTATTCTTGACA
1 AATCTTATTGGTCTTGAGGAA-TTGAGTTTGAACAATTGTGAAAACCTTATTTGCCTTCCTGACA
*
397338 GCTTTTATAAATTGAAATCTCTTGAGAGAGTAACACGTCAAGGTTGCTCGAGATTGGAGATTTTT
65 GCTTTTATAAATTGAAATCTCTTAAGAGAGTAACACGTCAAGGTTGCTCGAGATTGGAGATTTTT
* **
397403 CCAGAAATCTTAGAGACCATGGAGAGATTGAGGGATCTTGATTTAAGTGGAACGGCTTTGAAGGA
130 CCAGAAATCTTAGAGACCATGGAGAGATTGAGGGATCTTGATTTAAGCGGAACAACTTTGAAGGA
397468 ATTACCATCCTCAATAGAA
195 ATTACCATCCTCAATAGAA
* *
397487 AATCTTATTGGTCTTGAGGAATTG-GTAGTGAACAATTGTGAAAACCTTCTTTGCCTTCCTGACA
1 AATCTTATTGGTCTTGAGGAATTGAGT-TTGAACAATTGTGAAAACCTTATTTGCCTTCCTGACA
* * *
397551 ACTTTTATAAATTGAAATCTCTTAAGAGATTAACACTTCAAGGTTGCTCGAGATTGGAGATTTTT
65 GCTTTTATAAATTGAAATCTCTTAAGAGAGTAACACGTCAAGGTTGCTCGAGATTGGAGATTTTT
*
397616 CCAGAAATCTTAGAGACCATGGAGAGTTTGAGGGATCTTGATTTAAGCGGAACAACTTTGAAGGA
130 CCAGAAATCTTAGAGACCATGGAGAGATTGAGGGATCTTGATTTAAGCGGAACAACTTTGAAGGA
397681 ATTACCATCCTCAATAGAA
195 ATTACCATCCTCAATAGAA
* *
397700 AATCTTATTGGTCTT-ATGGAGTTGAGTTTGAACAATTGTGAAAACCTTGTTTGCCTTCCTGACA
1 AATCTTATTGGTCTTGA-GGAATTGAGTTTGAACAATTGTGAAAACCTTATTTGCCTTCCTGACA
397764 GCTTTTATAAATTGAAATCTCTT
65 GCTTTTATAAATTGAAATCTCTT
397787 GAAATAGTTG
Statistics
Matches: 277, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
212 3 0.01
213 269 0.97
214 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (213 bp):
AATCTTATTGGTCTTGAGGAATTGAGTTTGAACAATTGTGAAAACCTTATTTGCCTTCCTGACAG
CTTTTATAAATTGAAATCTCTTAAGAGAGTAACACGTCAAGGTTGCTCGAGATTGGAGATTTTTC
CAGAAATCTTAGAGACCATGGAGAGATTGAGGGATCTTGATTTAAGCGGAACAACTTTGAAGGAA
TTACCATCCTCAATAGAA
Found at i:401065 original size:16 final size:15
Alignment explanation
Indices: 401038--401069 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
401028 AAATGTCAAG
401038 TTTTTTATATTATTA
1 TTTTTTATATTATTA
401053 TTTTTTATAATTATTA
1 TTTTTTAT-ATTATTA
401069 T
1 T
401070 ATATTTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTATATTATTA
Found at i:401742 original size:3 final size:3
Alignment explanation
Indices: 401734--401760 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
401724 TGCTTCAACA
401734 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
401761 GCTGCTGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:405523 original size:25 final size:23
Alignment explanation
Indices: 405469--405514 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
405459 AGATTGATGT
405469 AAGCA-TTTTTTGAACTAATTCC
1 AAGCATTTTTTTGAACTAATTCC
405491 AAGCATTTTTTTGAACTAATTCC
1 AAGCATTTTTTTGAACTAATTCC
405514 A
1 A
405515 TTGTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (23 bp):
AAGCATTTTTTTGAACTAATTCC
Found at i:422627 original size:18 final size:16
Alignment explanation
Indices: 422600--422638 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
422590 ACATAAATTC
422600 AAATAACAAAACACCTAA
1 AAATAAC-AAACA-CTAA
*
422618 AAATATCAAACACTAA
1 AAATAACAAACACTAA
422634 AAATA
1 AAATA
422639 GTAGCCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATAACAAACACTAA
Found at i:424715 original size:17 final size:17
Alignment explanation
Indices: 424693--424725 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
424683 TAACTTCGAA
*
424693 CATCTTCTGTCTTATAG
1 CATCTTCTGTCATATAG
424710 CATCTTCTGTCATATA
1 CATCTTCTGTCATATA
424726 TGCCTTTTCC
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:0.21, C:0.24, G:0.09, T:0.45
Consensus pattern (17 bp):
CATCTTCTGTCATATAG
Found at i:426202 original size:16 final size:16
Alignment explanation
Indices: 426181--426218 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
426171 CAAAACACCT
426181 AAAATAACAAA-TATTA
1 AAAATAACAAACT-TTA
426197 AAAATAACAAACTTTA
1 AAAATAACAAACTTTA
426213 AAAATA
1 AAAATA
426219 GCAGTCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAACAAACTTTA
Found at i:430455 original size:3 final size:3
Alignment explanation
Indices: 430449--430510 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
430439 ATCAGGTCAA
430449 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
430497 CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CT
430511 ATATATATAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:431175 original size:15 final size:15
Alignment explanation
Indices: 431152--431187 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
431142 CAAACCCTAA
* *
431152 ATATGTTGTTAATAT
1 ATATTTTGTTAATAC
431167 ATATTTTGTTAATAC
1 ATATTTTGTTAATAC
431182 ATATTT
1 ATATTT
431188 ATCATAGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (15 bp):
ATATTTTGTTAATAC
Found at i:431977 original size:23 final size:23
Alignment explanation
Indices: 431951--431996 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
431941 ATAGGAAAGT
*
431951 TTAAAGAACATAAAAGAAAAAAA
1 TTAAAGAACATAAAACAAAAAAA
** *
431974 TTAAATTACTTAAAACAAAAAAA
1 TTAAAGAACATAAAACAAAAAAA
431997 ATGGGGATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (23 bp):
TTAAAGAACATAAAACAAAAAAA
Found at i:434738 original size:16 final size:17
Alignment explanation
Indices: 434705--434738 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
434695 TAGAATTTTA
434705 TTATTTTGATTGTATTT
1 TTATTTTGATTGTATTT
*
434722 TTATTTT-ATTTTATTT
1 TTATTTTGATTGTATTT
434738 T
1 T
434739 ATCTCTGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
TTATTTTGATTGTATTT
Found at i:435721 original size:21 final size:21
Alignment explanation
Indices: 435695--435738 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
435685 TTCATGTGTT
435695 ATTATT-TATAATTTA-TCATTA
1 ATTATTCTA-AATTTACT-ATTA
435716 ATTATTCTAAATTTACTATTA
1 ATTATTCTAAATTTACTATTA
435737 AT
1 AT
435739 CTTATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTCTAAATTTACTATTA
Found at i:438339 original size:6 final size:6
Alignment explanation
Indices: 438330--438411 Score: 146
Period size: 6 Copynumber: 13.7 Consensus size: 6
438320 AAATAACCCT
*
438330 AAATCA AAATCA AAATCT AAATCA AAATCA AAATCA AAATCA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
*
438378 AAATCA AAATCA AAATCA AAATCA AAATCG AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
438412 AACCCAAAAG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.65, C:0.16, G:0.01, T:0.18
Consensus pattern (6 bp):
AAATCA
Found at i:449663 original size:28 final size:28
Alignment explanation
Indices: 449610--449700 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 28
449600 ATTTTAATTT
*
449610 TTAAAATTTTTATAAATATGTAAAATATTA
1 TTAAAATTTATA-AAATAT-TAAAATATTA
**
449640 TTAAAATTTATAAAAGTATT-AAATAAAA
1 TTAAAATTTATAAAA-TATTAAAATATTA
*
449668 TTTAAAATGTTA-AAAAAATTAAAATATTA
1 -TTAAAAT-TTATAAAATATTAAAATATTA
449697 TTAA
1 TTAA
449701 GAATGATATC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
28 13 0.25
29 21 0.41
30 17 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (28 bp):
TTAAAATTTATAAAATATTAAAATATTA
Found at i:449689 original size:17 final size:19
Alignment explanation
Indices: 449658--449692 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
449648 TATAAAAGTA
449658 TTAAATAAAATTTAAAATG
1 TTAAATAAAATTTAAAATG
449677 TTAAA-AAAA-TTAAAAT
1 TTAAATAAAATTTAAAAT
449693 ATTATTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
TTAAATAAAATTTAAAATG
Found at i:451932 original size:17 final size:17
Alignment explanation
Indices: 451887--451932 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
451877 ACATAACTTA
*
451887 TTAACATTTATATATAT
1 TTAAAATTTATATATAT
* *
451904 TTATAATATATATATAT
1 TTAAAATTTATATATAT
451921 TTAAAATTTATA
1 TTAAAATTTATA
451933 ACTTACATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAATTTATATATAT
Found at i:451944 original size:9 final size:9
Alignment explanation
Indices: 451930--452150 Score: 222
Period size: 9 Copynumber: 26.2 Consensus size: 9
451920 TTTAAAATTT
451930 ATAACTTAC
1 ATAACTTAC
451939 ATAACTTAC
1 ATAACTTAC
* *
451948 AT-ACATAA
1 ATAACTTAC
451956 ATAA--TAC
1 ATAACTTAC
451963 ATAA--TAC
1 ATAACTTAC
*
451970 ATAACTTAT
1 ATAACTTAC
451979 ATAACTTAC
1 ATAACTTAC
451988 ATAACTTAC
1 ATAACTTAC
451997 ATAA--TAC
1 ATAACTTAC
452004 ATAACTTAC
1 ATAACTTAC
452013 ATAACTTAC
1 ATAACTTAC
452022 ATAA--TAC
1 ATAACTTAC
*
452029 AGAACTTAC
1 ATAACTTAC
452038 ATAACTTAC
1 ATAACTTAC
452047 ATAA--TAC
1 ATAACTTAC
*
452054 ATAACTTAT
1 ATAACTTAC
*
452063 ATAA-TGCAC
1 ATAACT-TAC
**
452072 ATAACGCAC
1 ATAACTTAC
452081 ATAACTTAC
1 ATAACTTAC
452090 ATAACTTAC
1 ATAACTTAC
452099 ATAACTTAC
1 ATAACTTAC
452108 ATAA--TAC
1 ATAACTTAC
*
452115 AGAACTTAC
1 ATAACTTAC
*
452124 AGAACTTAC
1 ATAACTTAC
452133 ATAA--TAC
1 ATAACTTAC
*
452140 ATAGCTTAC
1 ATAACTTAC
452149 AT
1 AT
452151 TGTAGAAGCC
Statistics
Matches: 181, Mismatches: 16, Indels: 30
0.80 0.07 0.13
Matches are distributed among these distances:
7 45 0.25
8 7 0.04
9 129 0.71
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (9 bp):
ATAACTTAC
Found at i:451988 original size:18 final size:18
Alignment explanation
Indices: 451930--452150 Score: 222
Period size: 16 Copynumber: 13.1 Consensus size: 18
451920 TTTAAAATTT
451930 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
* *
451948 AT-ACATAAATAA--TAC
1 ATAACTTACATAACTTAC
*
451963 ATAA--TACATAACTTAT
1 ATAACTTACATAACTTAC
451979 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
451997 ATAA--TACATAACTTAC
1 ATAACTTACATAACTTAC
452013 ATAACTTACATAA--TAC
1 ATAACTTACATAACTTAC
*
452029 AGAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
*
452047 ATAA--TACATAACTTAT
1 ATAACTTACATAACTTAC
* **
452063 ATAA-TGCACATAACGCAC
1 ATAACT-TACATAACTTAC
452081 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
452099 ATAACTTACATAA--TAC
1 ATAACTTACATAACTTAC
* *
452115 AGAACTTACAGAACTTAC
1 ATAACTTACATAACTTAC
*
452133 ATAA--TACATAGCTTAC
1 ATAACTTACATAACTTAC
452149 AT
1 AT
452151 TGTAGAAGCC
Statistics
Matches: 169, Mismatches: 20, Indels: 30
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.04
15 5 0.03
16 79 0.47
17 8 0.05
18 70 0.41
19 1 0.01
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:451990 original size:25 final size:25
Alignment explanation
Indices: 451930--452136 Score: 164
Period size: 25 Copynumber: 8.2 Consensus size: 25
451920 TTTAAAATTT
*
451930 ATAACTTACATAACTTACAT-ACATAA
1 ATAACTTACATAAC-TACATAAC-TAC
*
451956 ATAA--TACATAA-TACATAACTTAT
1 ATAACTTACATAACTACATAAC-TAC
451979 ATAACTTACATAACTTACATAA-TAC
1 ATAACTTACATAAC-TACATAACTAC
452004 ATAACTTACATAACTTACATAA-TAC
1 ATAACTTACATAAC-TACATAACTAC
*
452029 AGAACTTACATAACTTACATAA-TAC
1 ATAACTTACATAAC-TACATAACTAC
* *
452054 ATAACTTATATAA-TGCACATAACGCAC
1 ATAACTTACATAACT--ACATAAC-TAC
452081 ATAACTTACATAACTTACATAACTTAC
1 ATAACTTACATAAC-TACATAAC-TAC
* *
452108 ATAA--TACAGAACTTACAGAACTTAC
1 ATAACTTACATAAC-TACATAAC-TAC
452133 ATAA
1 ATAA
452137 TACATAGCTT
Statistics
Matches: 158, Mismatches: 12, Indels: 23
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.03
23 9 0.06
24 7 0.04
25 98 0.62
26 4 0.03
27 34 0.22
29 1 0.01
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.30
Consensus pattern (25 bp):
ATAACTTACATAACTACATAACTAC
Found at i:452003 original size:34 final size:34
Alignment explanation
Indices: 451936--452150 Score: 223
Period size: 34 Copynumber: 6.4 Consensus size: 34
451926 ATTTATAACT
* *
451936 TACATAACTTACAT-ACATAAATAA--TACATAA
1 TACATAACTTACATAACTTACATAACTTACATAA
*
451967 TACATAACTTATATAACTTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAACTTACATAA
*
452001 TACATAACTTACATAACTTACATAA--TACAGAA
1 TACATAACTTACATAACTTACATAACTTACATAA
*
452033 CTTACATAACTTACATAA--TACATAACTTATATAA
1 --TACATAACTTACATAACTTACATAACTTACATAA
**
452067 TGCACATAACGCACATAACTTACATAACTTACATAA
1 T--ACATAACTTACATAACTTACATAACTTACATAA
* *
452103 CTTACATAA--TACAGAACTTACAGAACTTACATAA
1 --TACATAACTTACATAACTTACATAACTTACATAA
*
452137 TACATAGCTTACAT
1 TACATAACTTACAT
452151 TGTAGAAGCC
Statistics
Matches: 154, Mismatches: 15, Indels: 27
0.79 0.08 0.14
Matches are distributed among these distances:
31 13 0.08
32 28 0.18
34 91 0.59
36 21 0.14
38 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (34 bp):
TACATAACTTACATAACTTACATAACTTACATAA
Found at i:452303 original size:8 final size:8
Alignment explanation
Indices: 452292--452316 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
452282 CCACCTACCC
452292 CCCACTTG
1 CCCACTTG
452300 CCCACTTG
1 CCCACTTG
452308 CCCACTTG
1 CCCACTTG
452316 C
1 C
452317 GCCGAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.24
Consensus pattern (8 bp):
CCCACTTG
Found at i:452821 original size:11 final size:11
Alignment explanation
Indices: 452805--452839 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
452795 CCCTTTCCCC
452805 CTCCCTTCTCT
1 CTCCCTTCTCT
452816 CTCCCTTCTCT
1 CTCCCTTCTCT
452827 CTTCCC-TCTCT
1 C-TCCCTTCTCT
452838 CT
1 CT
452840 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:453329 original size:3 final size:3
Alignment explanation
Indices: 453305--453375 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
453295 AATATCCTTG
* * * *
453305 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
453352 TGTA TTA GTA TATA TTT TTA TTA T
1 T-TA TTA TTA T-TA TTA TTA TTA T
453376 GTACGTGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:453372 original size:23 final size:22
Alignment explanation
Indices: 453317--453378 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
453307 ATTTTTATAT
*
453317 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
453338 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
453360 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
453379 CGTGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:453385 original size:23 final size:23
Alignment explanation
Indices: 453312--453386 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
453302 TTGTTATTTT
* *
453312 TATATTATTAGTATTAT-TAGTAT
1 TATA-TATTATTATTATGTAGTAG
*
453335 TACTATTATTATTATTATGTATTAG
1 TA-TA-TATTATTATTATGTAGTAG
*
453360 TATATATTTTTATTATGTACGT-G
1 TATATATTATTATTATGTA-GTAG
453383 TATA
1 TATA
453387 CATATATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 21 0.48
24 17 0.39
25 6 0.14
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (23 bp):
TATATATTATTATTATGTAGTAG
Found at i:454386 original size:25 final size:25
Alignment explanation
Indices: 454357--454464 Score: 153
Period size: 25 Copynumber: 4.3 Consensus size: 25
454347 TGGTGTCAAC
*
454357 ATACATAACTCACATAACTTACATA
1 ATACATAACTTACATAACTTACATA
* *
454382 ATACACAATTTACATAACTTACATA
1 ATACATAACTTACATAACTTACATA
*
454407 ATACACAACTTACATAACTTACATA
1 ATACATAACTTACATAACTTACATA
* * *
454432 TTACATAAGTTACATAATTTACATA
1 ATACATAACTTACATAACTTACATA
454457 ATACATAA
1 ATACATAA
454465 ATATATAAAC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.31
Consensus pattern (25 bp):
ATACATAACTTACATAACTTACATA
Found at i:454458 original size:9 final size:9
Alignment explanation
Indices: 454358--454457 Score: 104
Period size: 9 Copynumber: 11.8 Consensus size: 9
454348 GGTGTCAACA
454358 TACATAACT
1 TACATAACT
*
454367 CACATAACT
1 TACATAACT
454376 TACATAA--
1 TACATAACT
* *
454383 TACACAATT
1 TACATAACT
454392 TACATAACT
1 TACATAACT
454401 TACATAA--
1 TACATAACT
*
454408 TACACAACT
1 TACATAACT
454417 TACATAACT
1 TACATAACT
454426 TACAT-A-T
1 TACATAACT
*
454433 TACATAAGT
1 TACATAACT
*
454442 TACATAATT
1 TACATAACT
454451 TACATAA
1 TACATAA
454458 TACATAAATA
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
7 18 0.23
8 2 0.03
9 57 0.74
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:455126 original size:17 final size:18
Alignment explanation
Indices: 455096--455141 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
455086 ATTTAAATTG
455096 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
455114 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
455130 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
455142 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:461441 original size:25 final size:24
Alignment explanation
Indices: 461388--461567 Score: 97
Period size: 25 Copynumber: 7.2 Consensus size: 24
461378 TTTATAGCTT
*
461388 ACATAACTTACATACATAAATAA-T
1 ACATAACTTACATA-ATACATAACT
*
461412 ACATAA--TACATAACTTATATAACTT
1 ACATAACTTACATAA--TACATAAC-T
**
461437 ACATAACGCACATAATTTACATAA-T
1 ACATAACTTACATAA--TACATAACT
461462 ACATAACTTACATAACTTACATAA-T
1 ACATAACTTACATAA--TACATAACT
* *
461487 ACACAACTTACATAACTTACGTAA-T
1 ACATAACTTACATAA--TACATAACT
* *
461512 ACACAACTTTCATAACTTACATAA-T
1 ACATAACTTACATAA--TACATAACT
*
461537 ACATAAGTTACATAATTTACATAA-T
1 ACATAACTTACATAA--TACATAACT
461562 ACATAA
1 ACATAA
461568 ATATATAAAC
Statistics
Matches: 135, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.01
22 6 0.04
23 6 0.04
24 6 0.04
25 103 0.76
27 13 0.10
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (24 bp):
ACATAACTTACATAATACATAACT
Found at i:461500 original size:50 final size:50
Alignment explanation
Indices: 461387--461567 Score: 217
Period size: 50 Copynumber: 3.6 Consensus size: 50
461377 ATTTATAGCT
* *
461387 TACATAACTTACATACA--TAAATAATACATAA--TACATAACTTATATAA
1 TACATAACTTACATA-ATTTACATAATACATAACTTACATAACTTACATAA
**
461434 CTTACATAACGCACATAATTTACATAATACATAACTTACATAACTTACATAA
1 --TACATAACTTACATAATTTACATAATACATAACTTACATAACTTACATAA
* * * * *
461486 TACACAACTTACATAACTTACGTAATACACAACTTTCATAACTTACATAA
1 TACATAACTTACATAATTTACATAATACATAACTTACATAACTTACATAA
*
461536 TACATAAGTTACATAATTTACATAATACATAA
1 TACATAACTTACATAATTTACATAATACATAA
461568 ATATATAAAC
Statistics
Matches: 112, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.01
49 13 0.12
50 83 0.74
52 15 0.13
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (50 bp):
TACATAACTTACATAATTTACATAATACATAACTTACATAACTTACATAA
Found at i:461561 original size:9 final size:9
Alignment explanation
Indices: 461385--461560 Score: 153
Period size: 9 Copynumber: 21.0 Consensus size: 9
461375 AAATTTATAG
461385 CTTACATAA
1 CTTACATAA
461394 CTTACAT-A
1 CTTACATAA
* *
461402 CATAAATAA
1 CTTACATAA
461411 --TACATAA
1 CTTACATAA
461418 --TACATAA
1 CTTACATAA
*
461425 CTTATATAA
1 CTTACATAA
461434 CTTACATAA
1 CTTACATAA
**
461443 CGCACATAA
1 CTTACATAA
*
461452 TTTACATAA
1 CTTACATAA
461461 --TACATAA
1 CTTACATAA
461468 CTTACATAA
1 CTTACATAA
461477 CTTACATAA
1 CTTACATAA
*
461486 --TACACAA
1 CTTACATAA
461493 CTTACATAA
1 CTTACATAA
*
461502 CTTACGTAA
1 CTTACATAA
*
461511 --TACACAA
1 CTTACATAA
*
461518 CTTTCATAA
1 CTTACATAA
461527 CTTACATAA
1 CTTACATAA
461536 --TACATAA
1 CTTACATAA
*
461543 GTTACATAA
1 CTTACATAA
*
461552 TTTACATAA
1 CTTACATAA
461561 TACATAAATA
Statistics
Matches: 137, Mismatches: 19, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
7 38 0.28
8 6 0.04
9 93 0.68
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (9 bp):
CTTACATAA
Found at i:462155 original size:20 final size:20
Alignment explanation
Indices: 462130--462187 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 20
462120 CGTGTAATTA
462130 GCAGTAGGGTTAGTTAGGCT
1 GCAGTAGGGTTAGTTAGGCT
462150 GCAGTAGGGTTAGTTAGTTAGGCT
1 GCAGTA-GG---GTTAGTTAGGCT
462174 GCAGTAGGGTTAGT
1 GCAGTAGGGTTAGT
462188 GACAGTCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 12 0.35
21 2 0.06
23 2 0.06
24 18 0.53
ACGTcount: A:0.21, C:0.09, G:0.40, T:0.31
Consensus pattern (20 bp):
GCAGTAGGGTTAGTTAGGCT
Found at i:462165 original size:24 final size:24
Alignment explanation
Indices: 462138--462187 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
462128 TAGCAGTAGG
462138 GTTAGTTAGGCTGCAGTAGGGTTA
1 GTTAGTTAGGCTGCAGTAGGGTTA
462162 GTTAGTTAGGCTGCAGTAGGGTTA
1 GTTAGTTAGGCTGCAGTAGGGTTA
462186 GT
1 GT
462188 GACAGTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.08, G:0.38, T:0.34
Consensus pattern (24 bp):
GTTAGTTAGGCTGCAGTAGGGTTA
Found at i:478769 original size:6 final size:6
Alignment explanation
Indices: 478758--478791 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
478748 AAACTTAGGC
478758 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAG
478792 AGAGATATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:481549 original size:20 final size:19
Alignment explanation
Indices: 481526--481585 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
481516 TATTTTTTTT
*
481526 ATAATTTGTATACTTTTTAA
1 ATAATTT-TATAATTTTTAA
*
481546 ATAATTTTA-ATTTTTTCAA
1 ATAATTTTATAATTTTT-AA
481565 ATAATTTTTATAATTTTTAA
1 ATAA-TTTTATAATTTTTAA
481585 A
1 A
481586 ATTAATTGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.17
19 8 0.23
20 15 0.43
21 6 0.17
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (19 bp):
ATAATTTTATAATTTTTAA
Found at i:497734 original size:213 final size:211
Alignment explanation
Indices: 497428--499092 Score: 2338
Period size: 213 Copynumber: 7.8 Consensus size: 211
497418 ATCTGTGTAG
* * * * * * * *
497428 TTTT-CCAGAAATCGTGGGCACCATGGAGAGTTTG-AGGCATCTTGTTTTAAGTGGAATGGCTTT
1 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATG-AACTTGATTTAAGCGGAACGGCTTT
*
497491 GAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTGAGAATTTGCATATGAACAACTGTG
65 GAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTT-AGCATTTGCAT-TGAACAACTGTG
* **
497556 AAAACCTTGTTTGCCTTCCTGGCAGCTTTTGCAAATTGAAATCTCTCGAGAGATTCTATCTTAAA
128 AAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCTATCTTAAA
*
497621 GGTTGCTTGAGATTGGAGA
193 GGTTGCTCGAGATTGGAGA
* *
497640 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTCAGTGGAACGGCTTTG
1 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
* * * * *
497705 AAGGAATTGCCATCCTCAATTGCCAATCTTATTGGTCTTGTGTATTTG-AGCTTGAACGACTGTG
66 AAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTT-AGCATTTGCA--TTGAACAACTGTG
* * * ** *
497769 AAAACCTTGTTTGCCTTCCTGACAGCTTTTGTAAATTGAAATCTCT-TACGACATTCCGTCTTCA
128 AAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA-GAGATTCTATCTTAA
*
497833 TGGTTGCTCGAGATTGGAGA
192 AGGTTGCTCGAGATTGGAGA
*
497853 TTTTCCCGGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
1 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
* * * *
497918 AAGGAATTACCATCCTCAATTGTCAATCTTATTGGTCTTGTGTATTTG-AGCTTGAACGACTGTG
66 AAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTT-AGCATTTGCA--TTGAACAACTGTG
* *
497982 AAAACCTTGTTTGCCTTCCTGACAGCTTTTGTAAATTGAAATCTCTTGAGAGATTCTATCTTAAA
128 AAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCTATCTTAAA
498047 GGTTGCTCGAGATTGGAGA
193 GGTTGCTCGAGATTGGAGA
498066 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
1 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
* *
498131 AAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTACGCGTTT-CAATATGAACAACTGTA
66 AAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTA-GCATTTGC-AT-TGAACAACTGTG
* * * * *
498195 AAAACCTTGTTTGCTTTCGTGACAGCTTTTATAAATTGAAATCTCTTGAGATATTCAATCTTAAA
128 AAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCTATCTTAAA
*
498260 GGTTGTTCGAGATTGGAGA
193 GGTTGCTCGAGATTGGAGA
* **
498279 TTTTCCCAGAAATCATGGACACCAGGGAGAGGTTGTATGAACTTGATTTAAGCGGAATAGCTTTG
1 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
* * * *
498344 AAGGAATTACCATCCTCAATTGGAAATCTTATTGGTCTTACGCGTTTGAATATGAACAACTGTAA
66 AAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTA-GCATTTGCAT-TGAACAACTGTGA
* * *
498409 AAACCTTGTTTGCCTTCCTGGCAGCTTTTGTAAATTGAAATCTCTCGAGAGATTCTATCTTACAG
129 AAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCTATCTTAAAG
*
498474 GTTGCTTGAGATTGGAGA
194 GTTGCTCGAGATTGGAGA
*
498492 TTTTCCCGGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
1 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
* * * *
498557 AAGGAATTACCATCCTCAATTGCCAATCTTATTGGTCTTAAGTATTTGGGATTGAACAATTGTGA
66 AAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTT-AGCATTT-GCATTGAACAACTGTGA
* * *
498622 AAACCTTATTTGCCTTCCTGACAGTTTTTATAAATTGAAATCTCTCGGGAGATTCTATCTTAAAG
129 AAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCTATCTTAAAG
498687 GTTGCTCGAGATTGGAGA
194 GTTGCTCGAGATTGGAGA
* *
498705 TTTTCCC-GAAAATCATGGACACCATGGAGAGGTTGTTTGAACTTGATTTAAGCGGAACAGCTTT
1 TTTTCCCAG-AAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTT
* *
498769 GAAGGAATTACCATCCTCGATTGGCAATCTTATTGGTCTTCAGGATTTGACATTGCAA-AACTGT
65 GAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTT-AGCATTTG-CATTG-AACAACTGT
* * ** *
498833 GAAAATCTTGTTTGCCTTCCTAACAGCTTTTATAAATTGAAATCTCTCTCGAGATTCTATCTTAC
127 GAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCTATCTTAA
498898 AGGTTGCTCGAGATTGGAGA
192 AGGTTGCTCGAGATTGGAGA
* * * * * * * *
498918 TTTTTCCGGAAGTCATGGACACCATGGAGTGGTTGAAGGATCTTGATTTAAGTGGAACGGCTTTG
1 TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
* * *
498983 AAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTACGCATTTGAATATGAACAACTGTAA
66 AAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTA-GCATTTGCAT-TGAACAACTGTGA
499048 AAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCT
129 AAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCT
499093 TTTGTGTCTT
Statistics
Matches: 1323, Mismatches: 110, Indels: 39
0.90 0.07 0.03
Matches are distributed among these distances:
212 14 0.01
213 1297 0.98
214 12 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (211 bp):
TTTTCCCAGAAATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTG
AAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAGCATTTGCATTGAACAACTGTGAAA
ACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCTATCTTAAAGGT
TGCTCGAGATTGGAGA
Found at i:504033 original size:219 final size:219
Alignment explanation
Indices: 503654--504075 Score: 817
Period size: 219 Copynumber: 1.9 Consensus size: 219
503644 AGACGAATCC
503654 CTGGAGACCAATTGGTTGGGTGGGATCACTTATTTCTGTGATGACAATGCTGAAGTTAGTCGGTT
1 CTGGAGACCAATTGGTTGGGTGGGATCACTTATTTCTGTGATGACAATGCTGAAGTTAGTCGGTT
*
503719 TGTGGAAACCCAGGCATCCAACAAACGAGGCCTGGTTTGGTTTAAATTCTACCCTCTTGTTTGCA
66 TGTGGAAACCCAGGCATCAAACAAACGAGGCCTGGTTTGGTTTAAATTCTACCCTCTTGTTTGCA
503784 AGGGGGATTGGTCTCACTGCATTTGTTGTGAGGTAAAGCATTGCGGAGTTCATGTATCATTTGCA
131 AGGGGGATTGGTCTCACTGCATTTGTTGTGAGGTAAAGCATTGCGGAGTTCATGTATCATTTGCA
503849 AAGGACGAATCCCTGGAGACAATG
196 AAGGACGAATCCCTGGAGACAATG
503873 CTGGAGACCAATTGGTTGGGTGGGATCACTTATTTCTGTGATGACAATGCTGAAGTTAGTCGGTT
1 CTGGAGACCAATTGGTTGGGTGGGATCACTTATTTCTGTGATGACAATGCTGAAGTTAGTCGGTT
* *
503938 TGTGGAAACTCAGGCATCAAACAAATGAGGCCTGGTTTGGTTTAAATTCTACCCTCTTGTTTGCA
66 TGTGGAAACCCAGGCATCAAACAAACGAGGCCTGGTTTGGTTTAAATTCTACCCTCTTGTTTGCA
504003 AGGGGGATTGGTCTCACTGCATTTGTTGTGAGGTAAAGCATTGCGGAGTTCATGTATCATTTGCA
131 AGGGGGATTGGTCTCACTGCATTTGTTGTGAGGTAAAGCATTGCGGAGTTCATGTATCATTTGCA
504068 AAGGACGA
196 AAGGACGA
504076 GGCAGAGGTA
Statistics
Matches: 200, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
219 200 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (219 bp):
CTGGAGACCAATTGGTTGGGTGGGATCACTTATTTCTGTGATGACAATGCTGAAGTTAGTCGGTT
TGTGGAAACCCAGGCATCAAACAAACGAGGCCTGGTTTGGTTTAAATTCTACCCTCTTGTTTGCA
AGGGGGATTGGTCTCACTGCATTTGTTGTGAGGTAAAGCATTGCGGAGTTCATGTATCATTTGCA
AAGGACGAATCCCTGGAGACAATG
Found at i:504316 original size:18 final size:19
Alignment explanation
Indices: 504286--504321 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
504276 AAAAATATTT
*
504286 AAAAATATATAAATTTATA
1 AAAAATATATAAAATTATA
504305 AAAAATAT-TAAAATTAT
1 AAAAATATATAAAATTAT
504322 TTAACATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATATATAAAATTATA
Found at i:504483 original size:16 final size:15
Alignment explanation
Indices: 504456--504487 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
504446 AAATGTCAAG
504456 TTTTTTATATTATTA
1 TTTTTTATATTATTA
504471 TTTTTTATAATTATTA
1 TTTTTTAT-ATTATTA
504487 T
1 T
504488 ATATTTGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTATATTATTA
Found at i:506259 original size:17 final size:19
Alignment explanation
Indices: 506239--506273 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
506229 AATAATAGAT
506239 TTATTAAA-CT-AATTAAA
1 TTATTAAATCTAAATTAAA
506256 TTATTAAATCTAAATTAA
1 TTATTAAATCTAAATTAA
506274 CCTAATCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATTAAATCTAAATTAAA
Found at i:506577 original size:25 final size:25
Alignment explanation
Indices: 506549--506599 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
506539 CTATACCAAC
506549 TAACCCTATTATGAATCTTTATTAT
1 TAACCCTATTATGAATCTTTATTAT
*
506574 TAACCCTGTTATGAATCTTTATTAT
1 TAACCCTATTATGAATCTTTATTAT
506599 T
1 T
506600 TTGTTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (25 bp):
TAACCCTATTATGAATCTTTATTAT
Found at i:508392 original size:24 final size:24
Alignment explanation
Indices: 508360--508406 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
508350 TAGTAAGTCA
*
508360 AATAAATTATGCTAATAAATACTT
1 AATAAATTATACTAATAAATACTT
* *
508384 AATATATTATATTAATAAATACT
1 AATAAATTATACTAATAAATACT
508407 AAATCTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
AATAAATTATACTAATAAATACTT
Found at i:512244 original size:13 final size:13
Alignment explanation
Indices: 512226--512250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
512216 TAGGTCATTC
512226 TTTATTTTAAATA
1 TTTATTTTAAATA
512239 TTTATTTTAAAT
1 TTTATTTTAAAT
512251 TTGAGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTTTAAATA
Found at i:513765 original size:3 final size:3
Alignment explanation
Indices: 513759--513783 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
513749 ATCAGGTCAG
513759 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
513784 ATATATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:524432 original size:20 final size:18
Alignment explanation
Indices: 524407--524461 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 18
524397 AAATTTACTT
524407 ATAATTTGTATATTTTTTAA
1 ATAATTT-TA-ATTTTTTAA
524427 ATAATTTTAATTTTTTAA
1 ATAATTTTAATTTTTTAA
*
524445 AT--TTTTAATATTTTAA
1 ATAATTTTAATTTTTTAA
524461 A
1 A
524462 AAGTTAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 14 0.41
18 11 0.32
19 2 0.06
20 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATAATTTTAATTTTTTAA
Found at i:525977 original size:18 final size:19
Alignment explanation
Indices: 525954--526001 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
525944 CTAGCGAATA
525954 AAATATATAAATAT-AAAT
1 AAATATATAAATATAAAAT
* *
525972 AAATATTTATATATAAAAT
1 AAATATATAAATATAAAAT
525991 AAA-ATATAAAT
1 AAATATATAAAT
526002 CAAATAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATATAAATATAAAAT
Found at i:525998 original size:30 final size:32
Alignment explanation
Indices: 525962--526020 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
525952 TAAAATATAT
525962 AAATATAAAT-AAAT-ATTTATATATAAAATA
1 AAATATAAATCAAATAATTTATATATAAAATA
*
525992 AAATATAAATCAAATAATTTATATTTAAA
1 AAATATAAATCAAATAATTTATATATAAA
526021 TTGTCAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 10 0.38
31 4 0.15
32 12 0.46
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (32 bp):
AAATATAAATCAAATAATTTATATATAAAATA
Found at i:531164 original size:17 final size:17
Alignment explanation
Indices: 531118--531164 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
531108 TTACTCTTCG
531118 TTTTTTTCTATTTATTTA
1 TTTTTTTCT-TTTATTTA
* *
531136 TTTGTTTGTTTTATTCT-
1 TTTTTTTCTTTTATT-TA
531153 TTTTTTTCTTTT
1 TTTTTTTCTTTT
531165 CTTTTGCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (17 bp):
TTTTTTTCTTTTATTTA
Found at i:540192 original size:21 final size:21
Alignment explanation
Indices: 540166--540206 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
540156 ATCTGCTCAA
* *
540166 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
540187 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
540207 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:544972 original size:21 final size:21
Alignment explanation
Indices: 544946--544986 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
544936 ATCTGCTCAA
* *
544946 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
544967 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
544987 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:549450 original size:3 final size:3
Alignment explanation
Indices: 549444--549470 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
549434 TCTTCTTCTT
549444 CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG
549471 ATATGATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:549980 original size:22 final size:23
Alignment explanation
Indices: 549927--549982 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
549917 TTTAATTAAA
* * *
549927 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
549950 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
549972 ATTAAAATTAA
1 ATTAAAATTAA
549983 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:549995 original size:16 final size:16
Alignment explanation
Indices: 549958--549997 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
549948 TTAATAAAAT
* *
549958 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
549974 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
549990 TAAAATTA
1 TAAAATTA
549998 TCAAATTATT
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:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:550067 original size:66 final size:67
Alignment explanation
Indices: 549986--550128 Score: 243
Period size: 68 Copynumber: 2.1 Consensus size: 67
549976 AAATTAATTG
*
549986 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
*
550050 TA
66 GA
*
550052 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
550117 TGA
65 TGA
550120 TTAGTAAAA
1 TTAGTAAAA
550129 CAAACTTGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 26 0.37
68 45 0.63
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:550082 original size:9 final size:9
Alignment explanation
Indices: 550070--550097 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
550060 TTTATCAAAT
550070 TATTAATTG
1 TATTAATTG
550079 TATTAATTG
1 TATTAATTG
550088 TATTAATTG
1 TATTAATTG
550097 T
1 T
550098 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:555040 original size:213 final size:211
Alignment explanation
Indices: 554566--555748 Score: 1852
Period size: 213 Copynumber: 5.6 Consensus size: 211
554556 GTTTTAAGTT
* *
554566 GAACGGCTTTGAAGGAATTACCATCCTCAATGGGCAATCTTATTGGTCTTAAGTATTTGAGCT-T
1 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAG-ATTTGA-ATAT
* * * * *
554630 GAGCGATTGCGAAAACTTTGTTTGCCTTCCTGACAGCATTTATAAATTGAAATCTCTCGAGAGAT
64 GAAC-ACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGAT
* * * *
554695 TCTATCTTAAAGGTTGCTCAAGATTGGAGA-TTTCCCGGAAATCATGGACACCATGGAGTGGTTG
128 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTGGACACCATGAAGAGGTTG
*
554759 TATGAACTTGATTTAAGCG
193 TACGAACTTGATTTAAGCG
* *
554778 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTATGCGTTTGAATATG
1 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAG-ATTTGAATATG
*
554843 AACAACTGTAAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTC-AGGAGAT
65 AAC-ACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGA-GAGAT
*
554907 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTAGACACCATGAAGAGGTTG
128 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTGGACACCATGAAGAGGTTG
554972 TACGAACTTGATTTAAGCG
193 TACGAACTTGATTTAAGCG
** *
554991 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTGTGCATTTGAGCT-T
1 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAG-ATTTGA-ATAT
** *
555055 GGATGACTGTGAAAACCTTGTTCGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGAT
64 -GAACACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGAT
* * *
555120 TCTATCTTAAAGGTTGCTTGAGATTGGAGATTTTCCCGGAAATCATGGACACCATGAAGATGTTG
128 TCTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTGGACACCATGAAGAGGTTG
555185 TACGAACTTGATTTAAGCG
193 TACGAACTTGATTTAAGCG
*
555204 GAACGACTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAATGATTTGAATATG
1 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAA-GATTTGAATATG
* * * *
555269 AACAGCTGTAAAAACCTTGTTTTCCTTCCTGACAACTTTTATAAATTGAAATCTCTGGAGAGATT
65 AACA-CTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATT
* *
555334 CTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCAGAAATCTTGGACACCATGAAGATGTTGT
129 CTATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTGGACACCATGAAGAGGTTGT
555399 ACGAACTTGATTTAAGCG
194 ACGAACTTGATTTAAGCG
* *
555417 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAAGATA
1 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAA-GATTTGAATATG
*
555482 AACACTGTGAAAACCTTGTTCGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTC
65 AACACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTC
* *
555547 TATTTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTAGACACCATGAAGAGGTTGTA
130 TATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTGGACACCATGAAGAGGTTGTA
*
555612 TGAACTTGATTTAAGCG
195 CGAACTTGATTTAAGCG
* * *
555629 GAACCGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGGATTTGAAGATA
1 GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAA-GATTTGAATATG
555694 AACACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCT
65 AACACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCT
555749 TTGGTGTCTT
Statistics
Matches: 903, Mismatches: 59, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
211 2 0.00
212 397 0.44
213 499 0.55
214 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (211 bp):
GAACGGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTGGTCTTAAGATTTGAATATGA
ACACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCT
ATCTTAAAGGTTGCTCGAGATTGGAGATTTTCCCGGAAATCTTGGACACCATGAAGAGGTTGTAC
GAACTTGATTTAAGCG
Found at i:563632 original size:27 final size:27
Alignment explanation
Indices: 563594--563645 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
563584 ATGGTTATGT
563594 GAAATGATTATAAG-AATTGGTTATACA
1 GAAATGATTATAAGTAA-TGGTTATACA
*
563621 GAAATAGA-TATATGTAATGGTTATA
1 GAAAT-GATTATAAGTAATGGTTATA
563646 TGAATCAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (27 bp):
GAAATGATTATAAGTAATGGTTATACA
Found at i:563685 original size:40 final size:40
Alignment explanation
Indices: 563594--563698 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
563584 ATGGTTATGT
* ** * *
563594 GAAATGATTATAAGAATTGGTTATACAGAAATAGATATAT
1 GAAATGATTATATGAATCAGTTATACAGAAATAGATAAAC
* *
563634 GTAATGGTTATATGAATCAGTTATACAGAAATAGATAAAC
1 GAAATGATTATATGAATCAGTTATACAGAAATAGATAAAC
* *
563674 GAAATAATTATATGAATCAATTATA
1 GAAATGATTATATGAATCAGTTATA
563699 TGGAAATAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (40 bp):
GAAATGATTATATGAATCAGTTATACAGAAATAGATAAAC
Found at i:563695 original size:13 final size:12
Alignment explanation
Indices: 563676--563716 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
563666 AGATAAACGA
563676 AATAATTATATG
1 AATAATTATATG
563688 AATCAATTATATGG
1 AAT-AATTATAT-G
563702 AAATAATTATATG
1 -AATAATTATATG
563715 AA
1 AA
563717 GTGTTATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 9 0.35
15 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (12 bp):
AATAATTATATG
Found at i:563711 original size:14 final size:14
Alignment explanation
Indices: 563674--563714 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
563664 ATAGATAAAC
563674 GAAATAATTATAT-
1 GAAATAATTATATG
563687 G-AATCAATTATATG
1 GAAAT-AATTATATG
563701 GAAATAATTATATG
1 GAAATAATTATATG
563715 AAGTGTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 9 0.36
14 10 0.40
15 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (14 bp):
GAAATAATTATATG
Found at i:569163 original size:45 final size:45
Alignment explanation
Indices: 569099--569186 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
569089 TGAATCTTTG
*
569099 CAGCTTTTCTGTCAACGTGCCTTCAAAAGCAATTATCCCACGGGT
1 CAGCTCTTCTGTCAACGTGCCTTCAAAAGCAATTATCCCACGGGT
*
569144 CAGCTCTTCTGTCAACGTGCCTTCAGAAGCAATTATCCCACGG
1 CAGCTCTTCTGTCAACGTGCCTTCAAAAGCAATTATCCCACGG
569187 CATATCGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (45 bp):
CAGCTCTTCTGTCAACGTGCCTTCAAAAGCAATTATCCCACGGGT
Found at i:582035 original size:9 final size:9
Alignment explanation
Indices: 582021--582049 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
582011 TTATTAATTT
582021 AAAATTTTA
1 AAAATTTTA
582030 AAAATTTTA
1 AAAATTTTA
582039 AAAATTTTA
1 AAAATTTTA
582048 AA
1 AA
582050 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:585416 original size:2 final size:2
Alignment explanation
Indices: 585409--585459 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
585399 TCCTTTGTTT
*
585409 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
585451 AG AG AG AG A
1 AG AG AG AG A
585460 ACACGAGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:585509 original size:2 final size:2
Alignment explanation
Indices: 585502--585539 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
585492 TTCCTTTGTT
585502 GA GA GA GA GA GA 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 GA GA GA GA GA GA
585540 ACACGAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:586703 original size:4 final size:4
Alignment explanation
Indices: 586688--586739 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
586678 ACAAAGGAAT
* *
586688 AATA AGTA AATA AATA AATA AAT- AATAA AATAA AATG AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AAT-A AAT-A AATA AATA AATA AATA
586737 AAT
1 AAT
586740 GCTCGATGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 3 0.07
4 31 0.74
5 8 0.19
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:588946 original size:18 final size:17
Alignment explanation
Indices: 588920--588953 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
588910 CAAGATGATT
*
588920 TTTATAAATTATATAAAG
1 TTTAAAAATTA-ATAAAG
588938 TTTAAAAATTAATAAA
1 TTTAAAAATTAATAAA
588954 AATTAATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTAAAAATTAATAAAG
Found at i:593039 original size:351 final size:351
Alignment explanation
Indices: 592396--593099 Score: 1408
Period size: 351 Copynumber: 2.0 Consensus size: 351
592386 TTTTTAATTA
592396 TGAAATTAAATTTTTTATACAATAAAATCTCAAATTCACATACTTATTTAAATTATTAATTTGAA
1 TGAAATTAAATTTTTTATACAATAAAATCTCAAATTCACATACTTATTTAAATTATTAATTTGAA
592461 AGTAAGGTTAACCCAATTTCCTTACCCACTGAGTGCAGTAACTTTGCTTTTAGGATCAAATTTTC
66 AGTAAGGTTAACCCAATTTCCTTACCCACTGAGTGCAGTAACTTTGCTTTTAGGATCAAATTTTC
592526 CACAAAAGAAAAAGAAAGCAATAATTGCTATTGTCTCTTTCATGACATCTACTTATCTAATTTAC
131 CACAAAAGAAAAAGAAAGCAATAATTGCTATTGTCTCTTTCATGACATCTACTTATCTAATTTAC
592591 AAAGGATAATATATAATATTGACCCCAAGTCAAGTGCAGATTTTGCTTTCACCAAAAAGCAACCA
196 AAAGGATAATATATAATATTGACCCCAAGTCAAGTGCAGATTTTGCTTTCACCAAAAAGCAACCA
592656 AAGATTATAAATTTAGAAAGTGATGCCCTCACTTCATTGATGTCATTTATGCTACCATCATCTTA
261 AAGATTATAAATTTAGAAAGTGATGCCCTCACTTCATTGATGTCATTTATGCTACCATCATCTTA
592721 CTTTTTTCTCTTTTACATGTTTCACG
326 CTTTTTTCTCTTTTACATGTTTCACG
592747 TGAAATTAAATTTTTTATACAATAAAATCTCAAATTCACATACTTATTTAAATTATTAATTTGAA
1 TGAAATTAAATTTTTTATACAATAAAATCTCAAATTCACATACTTATTTAAATTATTAATTTGAA
592812 AGTAAGGTTAACCCAATTTCCTTACCCACTGAGTGCAGTAACTTTGCTTTTAGGATCAAATTTTC
66 AGTAAGGTTAACCCAATTTCCTTACCCACTGAGTGCAGTAACTTTGCTTTTAGGATCAAATTTTC
592877 CACAAAAGAAAAAGAAAGCAATAATTGCTATTGTCTCTTTCATGACATCTACTTATCTAATTTAC
131 CACAAAAGAAAAAGAAAGCAATAATTGCTATTGTCTCTTTCATGACATCTACTTATCTAATTTAC
592942 AAAGGATAATATATAATATTGACCCCAAGTCAAGTGCAGATTTTGCTTTCACCAAAAAGCAACCA
196 AAAGGATAATATATAATATTGACCCCAAGTCAAGTGCAGATTTTGCTTTCACCAAAAAGCAACCA
593007 AAGATTATAAATTTAGAAAGTGATGCCCTCACTTCATTGATGTCATTTATGCTACCATCATCTTA
261 AAGATTATAAATTTAGAAAGTGATGCCCTCACTTCATTGATGTCATTTATGCTACCATCATCTTA
593072 CTTTTTTCTCTTTTACATGTTTCACG
326 CTTTTTTCTCTTTTACATGTTTCACG
593098 TG
1 TG
593100 GATTCTATTT
Statistics
Matches: 353, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
351 353 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (351 bp):
TGAAATTAAATTTTTTATACAATAAAATCTCAAATTCACATACTTATTTAAATTATTAATTTGAA
AGTAAGGTTAACCCAATTTCCTTACCCACTGAGTGCAGTAACTTTGCTTTTAGGATCAAATTTTC
CACAAAAGAAAAAGAAAGCAATAATTGCTATTGTCTCTTTCATGACATCTACTTATCTAATTTAC
AAAGGATAATATATAATATTGACCCCAAGTCAAGTGCAGATTTTGCTTTCACCAAAAAGCAACCA
AAGATTATAAATTTAGAAAGTGATGCCCTCACTTCATTGATGTCATTTATGCTACCATCATCTTA
CTTTTTTCTCTTTTACATGTTTCACG
Found at i:599139 original size:8 final size:8
Alignment explanation
Indices: 599122--599151 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
599112 AATAGTTACA
*
599122 ATTTAGTT
1 ATTTAATT
599130 ATTTAATT
1 ATTTAATT
599138 ATTTAATT
1 ATTTAATT
599146 ATTTAA
1 ATTTAA
599152 AAATTTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (8 bp):
ATTTAATT
Found at i:601213 original size:20 final size:20
Alignment explanation
Indices: 601183--601221 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
601173 TGGAGTATTA
601183 GATTTTTTAGT-AATGGGAG
1 GATTTTTTAGTCAATGGGAG
601202 GATTTGTTTAGTCAATGGGA
1 GATTT-TTTAGTCAATGGGA
601222 TTAGTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.26, C:0.03, G:0.31, T:0.41
Consensus pattern (20 bp):
GATTTTTTAGTCAATGGGAG
Found at i:614397 original size:209 final size:206
Alignment explanation
Indices: 614072--614471 Score: 534
Period size: 209 Copynumber: 1.9 Consensus size: 206
614062 TAGAATGATT
* * * *
614072 GCAAAGTAATAAGAAAAAAAAAATAAGAACAAATAAATTTTACGTGGAAACCCTTTCGAGAAAAA
1 GCAAAGCAATAAG-AAAAAAAAATAAGAACAAACAAATTTTACATAGAAACCCTTTCGAGAAAAA
* * * * * **
614137 CTACGGGTAGAGAAGAAGAAAATTCACTATTGTCGAATTCAAATTATACAAGAGGAGTTTCGGCT
65 CCACGAGTAGAGAAGAAGAAAATTCACTAATGTCGAATTCAAATGATACAAGAGGAGCTTCAACT
*
614202 AAATCTATATTTATATATTGAAAACCCTTATTCTAATCAATATCAAATAGAAGCA-ATGTAGTAA
130 AAATC--TATTTATAGATTGAAAA-CCTTATTCTAATCAATATCAAATAGAAGCAGA-GTAGTAA
614266 GCAGCATAAAACGATC
191 GCAGCATAAAACGATC
* * *
614282 GCAAAGCAATAAG-AAAAAAAATAAGAACACACAGATTTTACATAGAAACCCTTTCGGGAAAAAA
1 GCAAAGCAATAAGAAAAAAAAATAAGAACAAACAAATTTTACATAGAAACCCTTTCGAG-AAAAA
* *
614346 CCACGAGTAGAGGAGAAGAAAATTCACTAATGTCGAATTCGAATGATACAAGAGGAGCTTCAACT
65 CCACGAGTAGAGAAGAAGAAAATTCACTAATGTCGAATTCAAATGATACAAGAGGAGCTTCAACT
* * * * *
614411 ACATCTATTTATAGGTTGAAAACCTTATTCTAATTAATGTCAAGTAGAAGCAGAGTAGTAA
130 AAATCTATTTATAGATTGAAAACCTTATTCTAATCAATATCAAATAGAAGCAGAGTAGTAA
614472 CCTTATTCTA
Statistics
Matches: 166, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
206 34 0.20
207 16 0.10
208 39 0.23
209 65 0.39
210 12 0.07
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (206 bp):
GCAAAGCAATAAGAAAAAAAAATAAGAACAAACAAATTTTACATAGAAACCCTTTCGAGAAAAAC
CACGAGTAGAGAAGAAGAAAATTCACTAATGTCGAATTCAAATGATACAAGAGGAGCTTCAACTA
AATCTATTTATAGATTGAAAACCTTATTCTAATCAATATCAAATAGAAGCAGAGTAGTAAGCAGC
ATAAAACGATC
Found at i:614986 original size:10 final size:9
Alignment explanation
Indices: 614970--615017 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 9
614960 ACATAACATA
614970 AAATAAAAG
1 AAATAAAAG
614979 AAAGTAAAAG
1 AAA-TAAAAG
614989 AAATAAAAG
1 AAATAAAAG
614998 -AA-AAAAG
1 AAATAAAAG
*
615005 AAAAAGAAAG
1 AAATA-AAAG
615015 AAA
1 AAA
615018 GAACAGAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 5 0.14
8 4 0.11
9 10 0.29
10 16 0.46
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (9 bp):
AAATAAAAG
Found at i:615361 original size:18 final size:18
Alignment explanation
Indices: 615321--615364 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
615311 ATTGGAATAG
*
615321 ATTGAAATTGTATATTGA
1 ATTGAAATTGAATATTGA
*
615339 TTTGAAATTGAAT-TATGA
1 ATTGAAATTGAATAT-TGA
615357 ATTGAAAT
1 ATTGAAAT
615365 ACCCTATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (18 bp):
ATTGAAATTGAATATTGA
Done.