Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 2 of 27
Found at i:127893 original size:22 final size:22
Alignment explanation
Indices: 127839--127883 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
127829 ACTTATCAAC
* *
127839 ATAAAAAAATAAAAAAATTAAA
1 ATAAAAAATTACAAAAATTAAA
127861 ATAAAAAATTACAAAAATTAAA
1 ATAAAAAATTACAAAAATTAAA
127883 A
1 A
127884 AATTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (22 bp):
ATAAAAAATTACAAAAATTAAA
Found at i:128279 original size:17 final size:17
Alignment explanation
Indices: 128257--128315 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
128247 ATTTAATAAC
128257 TATATTTTTTATTTTAT
1 TATATTTTTTATTTTAT
* *
128274 TATATTTATTT-TTTAAA
1 TATATTT-TTTATTTTAT
* *
128291 TATATTTTATATTTTTT
1 TATATTTTTTATTTTAT
128308 TA-ATTTTT
1 TATATTTTT
128316 ATAAAAGTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 7 0.21
17 23 0.70
18 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TATATTTTTTATTTTAT
Found at i:128426 original size:18 final size:17
Alignment explanation
Indices: 128378--128427 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
128368 ATAAAATAAT
128378 ATAAATTATTATTTATTA
1 ATAAA-TATTATTTATTA
*
128396 ATAAAAATATATTTATTAA
1 ATAAATAT-TATTTATT-A
*
128415 ATTAATATTATTT
1 ATAAATATTATTT
128428 TATATGGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 2 0.07
18 18 0.67
19 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAAATATTATTTATTA
Found at i:128464 original size:32 final size:32
Alignment explanation
Indices: 128409--128473 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
128399 AAAATATATT
**
128409 TATTAAATTAATATTATTTTATATGGATTAAA
1 TATTAAATTAATATTATTTTATATAAATTAAA
128441 TATTAAATT-AT-TTATTTAATATATAAATTAAA
1 TATTAAATTAATATTATTT--TATATAAATTAAA
128473 T
1 T
128474 TTTTTCACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.21
31 2 0.07
32 21 0.72
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
TATTAAATTAATATTATTTTATATAAATTAAA
Found at i:129068 original size:16 final size:17
Alignment explanation
Indices: 129041--129072 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
129031 ATTAAATATT
129041 ATTAAAATTATAAAAAA
1 ATTAAAATTATAAAAAA
129058 ATTAAAA-TATAAAAA
1 ATTAAAATTATAAAAA
129073 GTTACCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATTAAAATTATAAAAAA
Found at i:130703 original size:18 final size:20
Alignment explanation
Indices: 130674--130710 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
130664 TTAATTAAAA
130674 TAGTTCTTGAAAC-GTTTCC
1 TAGTTCTTGAAACTGTTTCC
130693 TAGTT-TTGAAACTGTTTC
1 TAGTTCTTGAAACTGTTTC
130711 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (20 bp):
TAGTTCTTGAAACTGTTTCC
Found at i:131220 original size:2 final size:2
Alignment explanation
Indices: 131213--131243 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
131203 TTTTGCAGTA
131213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
131244 CATACAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:131966 original size:13 final size:13
Alignment explanation
Indices: 131948--131972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
131938 CTTGTAAACA
131948 AGATTAAAAGTTG
1 AGATTAAAAGTTG
131961 AGATTAAAAGTT
1 AGATTAAAAGTT
131973 AATCCTGTTA
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
AGATTAAAAGTTG
Found at i:136696 original size:18 final size:20
Alignment explanation
Indices: 136667--136703 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
136657 TTAATTCAAA
136667 TAGTTCTTGAAACT-TTTCT
1 TAGTTCTTGAAACTGTTTCT
136686 TAGTT-TTGAAACTGTTTC
1 TAGTTCTTGAAACTGTTTC
136704 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (20 bp):
TAGTTCTTGAAACTGTTTCT
Found at i:138066 original size:10 final size:9
Alignment explanation
Indices: 138041--138065 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
138031 GACATAAAGC
138041 TTTTTTTGG
1 TTTTTTTGG
138050 TTTTTTTGG
1 TTTTTTTGG
138059 TTTTTTT
1 TTTTTTT
138066 TTTTTCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTTTTTTGG
Found at i:139466 original size:2 final size:2
Alignment explanation
Indices: 139459--139486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
139449 ACATGTTAAG
139459 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
139487 CCCTCCTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:141795 original size:29 final size:28
Alignment explanation
Indices: 141763--141980 Score: 114
Period size: 29 Copynumber: 7.5 Consensus size: 28
141753 TTTATATTTA
141763 TTAATTTATTTTTAAATATAAATATAATT
1 TTAA-TTATTTTTAAATATAAATATAATT
* *
141792 TTAA-TAGTTTTTAATTATTATTTAATATAAAT
1 TTAATTA-TTTTTAA--A-TA-TAAATATAATT
*
141824 ATAATTTTAATTATTT-AATATAAATAT-ATAT
1 TTAA--TT-ATT-TTTAAATATAAATATAAT-T
*
141855 TT--TTATTTTT-AATAAAAATA-AATTT
1 TTAATTATTTTTAAATATAAATATAA-TT
*
141880 TTAATTATTATTTAACATA-AAATATATTT
1 TTAATTATT-TTTAA-ATATAAATATAATT
* *
141909 TTAATT-TGTCTGTT-ATTGTAAATATAATT
1 TTAATTAT-T-T-TTAAATATAAATATAATT
* *
141938 TTAATAATTCTTTTAATATAAATATAATT
1 TTAATTATT-TTTAAATATAAATATAATT
*
141967 TTAATAATTTTTAA
1 TTAATTATTTTTAA
141981 TTATTATTTA
Statistics
Matches: 149, Mismatches: 16, Indels: 49
0.70 0.07 0.23
Matches are distributed among these distances:
25 16 0.11
26 4 0.03
27 9 0.06
28 18 0.12
29 60 0.40
30 9 0.06
31 10 0.07
32 14 0.09
33 1 0.01
35 4 0.03
36 4 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (28 bp):
TTAATTATTTTTAAATATAAATATAATT
Found at i:141842 original size:25 final size:25
Alignment explanation
Indices: 141808--141976 Score: 117
Period size: 25 Copynumber: 6.3 Consensus size: 25
141798 GTTTTTAATT
141808 ATTATTTAATATAAATATAATTTTA
1 ATTATTTAATATAAATATAATTTTA
*
141833 ATTATTTAATATAAATATATATTTTT
1 ATTATTTAATATAAATATA-ATTTTA
*
141859 ATT-TTTAATAAAAATA-AATTTTTAA
1 ATTATTTAATATAAATATAA-TTTT-A
* *
141884 TTATTATTTAACATAAAATATATTTTTA
1 --ATTATTTAATAT-AAATATAATTTTA
* * *
141912 ATTTGTCTGTTATTGTAAATATAATTTTAATA
1 A--T-TAT-TTAATATAAATATAA-TTT--TA
*
141944 ATTCTTTTAATATAAATATAATTTTA
1 ATT-ATTTAATATAAATATAATTTTA
*
141970 ATAATTT
1 ATTATTT
141977 TTAATTATTA
Statistics
Matches: 112, Mismatches: 16, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
23 1 0.01
24 5 0.04
25 34 0.30
26 13 0.12
27 3 0.03
28 11 0.10
29 32 0.29
30 10 0.09
32 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
ATTATTTAATATAAATATAATTTTA
Found at i:141866 original size:50 final size:52
Alignment explanation
Indices: 141806--141911 Score: 139
Period size: 50 Copynumber: 2.1 Consensus size: 52
141796 TAGTTTTTAA
* *
141806 TTATTATTTAATATAAATATAA-TTTT-A-ATTATTTAATATAAATATATATTT
1 TTATTATTTAATAAAAATA-AATTTTTAATATTATTTAACATAAA-ATATATTT
141857 TTATT-TTTAATAAAAATAAATTTTTAATTATTATTTAACATAAAATATATTT
1 TTATTATTTAATAAAAATAAATTTTTAA-TATTATTTAACATAAAATATATTT
141909 TTA
1 TTA
141912 ATTTGTCTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
49 2 0.04
50 16 0.33
51 6 0.12
52 11 0.22
53 14 0.29
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (52 bp):
TTATTATTTAATAAAAATAAATTTTTAATATTATTTAACATAAAATATATTT
Found at i:142023 original size:38 final size:38
Alignment explanation
Indices: 141932--142007 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
141922 TATTGTAAAT
* * * *
141932 ATAA-TTTTAATAATTCTTTTAATATAAATATAATTTTA
1 ATAATTTTTAATTATT-ATTTAACATAAATATAATCTTA
141970 ATAATTTTTAATTATTATTTAACATAAATATAATCTTA
1 ATAATTTTTAATTATTATTTAACATAAATATAATCTTA
142008 TTTATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 23 0.70
39 10 0.30
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (38 bp):
ATAATTTTTAATTATTATTTAACATAAATATAATCTTA
Found at i:142032 original size:35 final size:37
Alignment explanation
Indices: 141949--142055 Score: 101
Period size: 38 Copynumber: 2.9 Consensus size: 37
141939 TAATAATTCT
* *
141949 TTTAATATAAATATAATTTTAATAATTTTTAATTATTA
1 TTTAATATAAATATAATCTTAATAATTATT-ATTATTA
* * *
141987 TTTAACATAAATATAATCTTATTTA-TATT-TTATTA
1 TTTAATATAAATATAATCTTAATAATTATTATTATTA
* * *
142022 TTTAATATAAAAATAAATTTTAATTATTTATTAT
1 TTTAATATAAATAT-AATCTTAA-TAATTATTAT
142056 ATGCATATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
35 18 0.33
36 6 0.11
37 4 0.07
38 25 0.46
39 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (37 bp):
TTTAATATAAATATAATCTTAATAATTATTATTATTA
Found at i:142487 original size:22 final size:22
Alignment explanation
Indices: 142461--142503 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
142451 CATATATTAT
142461 TGTAATCAATTATAATAAATAA
1 TGTAATCAATTATAATAAATAA
142483 TGTAATCAATTATAATAAATA
1 TGTAATCAATTATAATAAATA
142504 TTGATAACGA
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:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (22 bp):
TGTAATCAATTATAATAAATAA
Found at i:144696 original size:20 final size:20
Alignment explanation
Indices: 144660--144712 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
144650 AAAAGTAATT
144660 ATTA-TAATAATAAAATTAAAA
1 ATTATTAATAA-AAAATT-AAA
144681 ATT-TTAATAAAAAATTAAA
1 ATTATTAATAAAAAATTAAA
144700 ATTATTAATAAAA
1 ATTATTAATAAAA
144713 TATATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.20
20 15 0.50
21 9 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTATTAATAAAAAATTAAA
Found at i:144832 original size:42 final size:42
Alignment explanation
Indices: 144693--144832 Score: 94
Period size: 39 Copynumber: 3.3 Consensus size: 42
144683 TTTAATAAAA
* * *
144693 AATT-AAAATTATTAATAAAATATATATATTTAAATATAATAATAAAA
1 AATTAAAAATTAATAATTAAA-AT-TATATTTAAAT-T-A-AAT-AAT
* * * *
144740 AAATAAAAAATAATTATTAAAA--ATA-TTATATT-AA-AAT
1 AATTAAAAATTAATAATTAAAATTATATTTAAATTAAATAAT
*
144777 ATTTATAATAATTAATAATTAAAATTATATTTAAATTAAATAAT
1 AATTA-AA-AATTAATAATTAAAATTATATTTAAATTAAATAAT
144821 AATTAAAAATTA
1 AATTAAAAATTA
144833 TGTTTATATT
Statistics
Matches: 72, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
37 5 0.07
38 2 0.03
39 15 0.21
41 3 0.04
42 12 0.17
43 9 0.12
44 10 0.14
47 4 0.06
48 12 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (42 bp):
AATTAAAAATTAATAATTAAAATTATATTTAAATTAAATAAT
Found at i:144838 original size:29 final size:29
Alignment explanation
Indices: 144775--144860 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
144765 TTATATTAAA
*
144775 ATATTTATAA-TAATTAATAATT-AAAATT
1 ATATTTA-AATTAAATAATAATTAAAAATT
144803 ATATTTAAATTAAATAATAATTAAAAATT
1 ATATTTAAATTAAATAATAATTAAAAATT
* * *
144832 ATGTTTATATTAAAAAATAAATATAAAAA
1 ATATTTAAATTAAATAAT-AAT-TAAAAA
144861 ATTTTAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
27 2 0.04
28 18 0.36
29 21 0.42
30 3 0.06
31 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (29 bp):
ATATTTAAATTAAATAATAATTAAAAATT
Found at i:145178 original size:16 final size:16
Alignment explanation
Indices: 145157--145201 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
145147 AAACTAAAAT
145157 TATTAATAAATATAAA
1 TATTAATAAATATAAA
*
145173 TATTAATATATA-AAA
1 TATTAATAAATATAAA
*
145188 AATTAATATAATAT
1 TATTAATA-AATAT
145202 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATTAATAAATATAAA
Found at i:145194 original size:15 final size:16
Alignment explanation
Indices: 145158--145197 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
145148 AACTAAAATT
* *
145158 ATTAATAAATATAAAT
1 ATTAATATATATAAAA
145174 ATTAATATATA-AAAA
1 ATTAATATATATAAAA
145189 ATTAATATA
1 ATTAATATA
145198 ATATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTAATATATATAAAA
Found at i:145982 original size:40 final size:40
Alignment explanation
Indices: 145925--146011 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 40
145915 TGAAATATTC
* *
145925 TAGAATATCGTGGAAGGCTCTGAAAAATTCTAGAATGTTT
1 TAGAATATCATGAAAGGCTCTGAAAAATTCTAGAATGTTT
*
145965 TAGAATATCATGAAAGGCTCTGAAAGATTCTAGAATGTTT
1 TAGAATATCATGAAAGGCTCTGAAAAATTCTAGAATGTTT
146005 TAGAATA
1 TAGAATA
146012 ATGTAGAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (40 bp):
TAGAATATCATGAAAGGCTCTGAAAAATTCTAGAATGTTT
Found at i:151145 original size:15 final size:15
Alignment explanation
Indices: 151127--151181 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 15
151117 ATAAATAAAA
151127 AAAATATTATTTAAT
1 AAAATATTATTTAAT
*
151142 AAAATATT-TTTTAT
1 AAAATATTATTTAAT
* *
151156 TAAA-ATTATTTGAT
1 AAAATATTATTTAAT
151170 -AAAT-TTATTTAA
1 AAAATATTATTTAA
151182 CTATTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 13 0.38
14 13 0.38
15 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AAAATATTATTTAAT
Found at i:151328 original size:26 final size:25
Alignment explanation
Indices: 151283--151333 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
151273 AGAACACATG
151283 ACACAAGAAATAAAATAAAA-AATA
1 ACACAAGAAATAAAATAAAATAATA
151307 ACACAAGCACAATATAAA-AAAATAATA
1 ACACAAG-A-AATA-AAATAAAATAATA
151334 TGAACACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.30
25 1 0.04
26 8 0.35
27 7 0.30
ACGTcount: A:0.71, C:0.12, G:0.04, T:0.14
Consensus pattern (25 bp):
ACACAAGAAATAAAATAAAATAATA
Found at i:151587 original size:24 final size:24
Alignment explanation
Indices: 151560--151616 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
151550 TTGAAAAGAT
*
151560 TAATATGAACATGATATAAAAAAA
1 TAATATGAACATAATATAAAAAAA
* * *
151584 TAATACGAATATAATATTAAAAAA
1 TAATATGAACATAATATAAAAAAA
*
151608 TTATATGAA
1 TAATATGAA
151617 AAAAATCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.30
Consensus pattern (24 bp):
TAATATGAACATAATATAAAAAAA
Found at i:151757 original size:17 final size:15
Alignment explanation
Indices: 151735--151769 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
151725 ATGTACTAAA
151735 AATTTTACAATATTTAT
1 AATTTTA-AATATTT-T
151752 AATTTTAAATATTTT
1 AATTTTAAATATTTT
151767 AAT
1 AAT
151770 AATTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 7 0.39
17 7 0.39
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTTAAATATTTT
Found at i:151775 original size:16 final size:16
Alignment explanation
Indices: 151743--151799 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 16
151733 AAAATTTTAC
*
151743 AATATTTATAAT-TTTA
1 AATATTT-TAATAATTA
151759 AATATTTTAATAATTAAATA
1 AATATTTTAATAA-T---TA
151779 AATATTTTAATAATTA
1 AATATTTTAATAATTA
151795 AATAT
1 AATAT
151800 ATTCGTGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 4 0.11
16 14 0.40
17 1 0.03
19 1 0.03
20 15 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATTTTAATAATTA
Found at i:151782 original size:20 final size:20
Alignment explanation
Indices: 151757--151798 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
151747 TTTATAATTT
151757 TAAATATTTTAATAATTAAA
1 TAAATATTTTAATAATTAAA
151777 TAAATATTTTAATAATTAAA
1 TAAATATTTTAATAATTAAA
151797 TA
1 TA
151799 TATTCGTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATATTTTAATAATTAAA
Found at i:152397 original size:12 final size:12
Alignment explanation
Indices: 152363--152402 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
152353 TCGTAACCCC
*
152363 CTCTCTGTCTGT
1 CTCTCTGTCTCT
*
152375 CTGTCTGTCTCT
1 CTCTCTGTCTCT
*
152387 CTCTCTCTCTCT
1 CTCTCTGTCTCT
152399 CTCT
1 CTCT
152403 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.40, G:0.10, T:0.50
Consensus pattern (12 bp):
CTCTCTGTCTCT
Found at i:157137 original size:124 final size:124
Alignment explanation
Indices: 156943--157171 Score: 320
Period size: 124 Copynumber: 1.8 Consensus size: 124
156933 CTTGAAAACA
* * *
156943 AATTAAAATCAAAATTATTTCAGTAATTATTTTTATTTTAATTTTAAATAATTTATTTACAGAAA
1 AATTAAAATCAAAATTATTTCAGTAATTATTTTTATTTTAATTTAAAATAATATATTTACAAAAA
* *
157008 TTAATTTATATATTAACTCATAAATAAATTTAAGATTTATATCCAAATTGGACGATGAAT
66 TTAATTTATATAATAACT-ATAAATAAATTTAAAATTTATATCCAAATTGGACGATGAAT
* * *
157068 AATTAAAAAT-AAATTTATTTTATTAATTATTTTTATTTT-ATTTAAAATAATATATTTA-AAAT
1 AATT-AAAATCAAAATTATTTCAGTAATTATTTTTATTTTAATTTAAAATAATATATTTACAAA-
* *
157130 AATTAATTTATATAATAACTATAGATTAATTTAAAATTTATA
64 AATTAATTTATATAATAACTATAAATAAATTTAAAATTTATA
157172 CTTAATTCTA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
123 21 0.23
124 36 0.39
125 30 0.33
126 5 0.05
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (124 bp):
AATTAAAATCAAAATTATTTCAGTAATTATTTTTATTTTAATTTAAAATAATATATTTACAAAAA
TTAATTTATATAATAACTATAAATAAATTTAAAATTTATATCCAAATTGGACGATGAAT
Found at i:157139 original size:14 final size:14
Alignment explanation
Indices: 157106--157132 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
157096 ATTTTTATTT
157106 TATTTAAAATAATA
1 TATTTAAAATAATA
157120 TATTTAAAATAAT
1 TATTTAAAATAAT
157133 TAATTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTTAAAATAATA
Found at i:157624 original size:19 final size:19
Alignment explanation
Indices: 157568--157624 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
157558 AATATTGTAT
*
157568 TTTATATATACTTTGATATG
1 TTTATAT-TATTTTGATATG
*
157588 TTTGTA-TATTTGTGATATG
1 TTTATATTATTT-TGATATG
*
157607 TTTATATTATTTTTATAT
1 TTTATATTATTTTGATAT
157625 TATGTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 4 0.13
19 17 0.55
20 10 0.32
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (19 bp):
TTTATATTATTTTGATATG
Found at i:158945 original size:21 final size:20
Alignment explanation
Indices: 158919--158962 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
158909 ATCAAGTTTC
*
158919 AAAATTACAAATTATAATGCA
1 AAAATT-CAAATTACAATGCA
* *
158940 AAAATTCCAATTCCAATGCA
1 AAAATTCAAATTACAATGCA
158960 AAA
1 AAA
158963 TCAATCCCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAATTCAAATTACAATGCA
Found at i:161158 original size:24 final size:24
Alignment explanation
Indices: 161130--161175 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
161120 AATTAAAATT
*
161130 AGCCATCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
*
161154 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
161176 AAATAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:161194 original size:50 final size:54
Alignment explanation
Indices: 161140--161254 Score: 134
Period size: 56 Copynumber: 2.2 Consensus size: 54
161130 AGCCATCAAT
*
161140 TTTGACAAAC-AA-CAAGCCACCA-ATTTTTAC-AA-ACAAAA-ATAACCACCATA
1 TTTGACAAACAAAGCAAGCCACCATA-TTTGACAAATACAAAAGA-AACCACCATA
*
161190 TTTGACAAATACAAAGGAAGCCACCATATTTGACAAATACAAAAGAAACCACCATA
1 TTTGAC-AA-ACAAAGCAAGCCACCATATTTGACAAATACAAAAGAAACCACCATA
161246 TTTGACAAA
1 TTTGACAAA
161255 TACAAAAGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
50 6 0.11
51 2 0.04
52 2 0.04
53 2 0.04
54 15 0.27
55 5 0.09
56 22 0.40
57 1 0.02
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.20
Consensus pattern (54 bp):
TTTGACAAACAAAGCAAGCCACCATATTTGACAAATACAAAAGAAACCACCATA
Found at i:161262 original size:28 final size:28
Alignment explanation
Indices: 161172--161262 Score: 148
Period size: 28 Copynumber: 3.2 Consensus size: 28
161162 ATTTTTACAA
161172 ACAAAA-ATAACCACCATATTTGACAAAT
1 ACAAAAGA-AACCACCATATTTGACAAAT
* *
161200 ACAAAGGAAGCCACCATATTTGACAAAT
1 ACAAAAGAAACCACCATATTTGACAAAT
161228 ACAAAAGAAACCACCATATTTGACAAAT
1 ACAAAAGAAACCACCATATTTGACAAAT
161256 ACAAAAG
1 ACAAAAG
161263 GTGGCATTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 57 0.98
29 1 0.02
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (28 bp):
ACAAAAGAAACCACCATATTTGACAAAT
Found at i:165913 original size:19 final size:19
Alignment explanation
Indices: 165889--165956 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
165879 AATTCAACAA
165889 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
165908 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
165923 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
165940 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
165957 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:165928 original size:13 final size:13
Alignment explanation
Indices: 165910--165934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
165900 ACATAAGTTT
165910 TGTATCGATACAA
1 TGTATCGATACAA
165923 TGTATCGATACA
1 TGTATCGATACA
165935 TAAGTATTGT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:165932 original size:32 final size:32
Alignment explanation
Indices: 165891--165953 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
165881 TTCAACAATT
*
165891 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
165923 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
165954 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:166014 original size:13 final size:13
Alignment explanation
Indices: 165996--166021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
165986 CATTTTTCTG
165996 TGTATCGATACAT
1 TGTATCGATACAT
166009 TGTATCGATACAT
1 TGTATCGATACAT
166022 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:166018 original size:33 final size:33
Alignment explanation
Indices: 165976--166042 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
165966 GCCAAGGAAA
***
165976 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
166009 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
166042 T
1 T
166043 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:166067 original size:31 final size:31
Alignment explanation
Indices: 166029--166105 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
166019 CATGGATCTT
*
166029 TGTATCGATACATTTGGAAATTTTACCCAGA
1 TGTATCGATACATTTGGAAATTTTAACCAGA
166060 TGTATCGATACATTTGGAAATTTTAACCAGA
1 TGTATCGATACATTTGGAAATTTTAACCAGA
166091 TGTATCGATACATTT
1 TGTATCGATACATTT
166106 TACAATGTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (31 bp):
TGTATCGATACATTTGGAAATTTTAACCAGA
Found at i:168473 original size:51 final size:53
Alignment explanation
Indices: 168409--168539 Score: 169
Period size: 51 Copynumber: 2.5 Consensus size: 53
168399 AGTTTCTCAA
* * * *
168409 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
168460 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
168514 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
168540 CCCGTTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 33 0.49
53 9 0.13
54 20 0.30
55 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:168548 original size:51 final size:49
Alignment explanation
Indices: 168406--168551 Score: 143
Period size: 51 Copynumber: 2.9 Consensus size: 49
168396 TTGAGTTTCT
* * *
168406 CAATTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCG--TTTATTTCCAAAACAC
* * *
168457 TAATT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACTCCG--TTTATTTCC--AAAACAC
*
168510 CAATTTCTTCACAATCGGGGATACTCCAACCCCG-TTATTTCC
1 CAA-TTCTTCACAATCGGGGATACTCCAACTCCGTTTATTTCC
168552 GAGGGGATAC
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
50 2 0.03
51 43 0.54
53 9 0.11
54 23 0.29
55 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (49 bp):
CAATTCTTCACAATCGGGGATACTCCAACTCCGTTTATTTCCAAAACAC
Found at i:168638 original size:52 final size:51
Alignment explanation
Indices: 168554--168724 Score: 168
Period size: 52 Copynumber: 3.3 Consensus size: 51
168544 TTATTTCCGA
** *
168554 GGGGATACTCCAACCTCGGTTTTATCACTAAAACACTAATTTTTTCACAATC
1 GGGGATACTCCAACC-CGGTTTTATTTCTAAAACACCAATTTTTTCACAATC
* * *
168606 GGGGATACTCCAATCCCGGTTTTATTTTTAAAACGCCAATTTTCCTT--TAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTCTAAAACACCAATTTT--TTCACAATC
* * * *
168658 GGGGATACTTCAACTCCGATTTTATTTCCAAAAATACCAA-TTTTTCACAATC
1 GGGGATACTCCAAC-CCGGTTTTATTT-CTAAAACACCAATTTTTTCACAATC
*
168710 GAGGATACTCCAACC
1 GGGGATACTCCAACC
168725 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
50 2 0.02
51 2 0.02
52 81 0.84
53 10 0.10
54 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCGGTTTTATTTCTAAAACACCAATTTTTTCACAATC
Found at i:168739 original size:28 final size:28
Alignment explanation
Indices: 168707--168783 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
168697 ATTTTTCACA
* *
168707 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTACTTC
168735 ATCGAGGATACTCCAACCCCGTTACTTC
1 ATCGAGGATACTCCAACCCCGTTACTTC
168763 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
168784 GCTTTATTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.07
28 42 0.93
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTACTTC
Found at i:168746 original size:184 final size:184
Alignment explanation
Indices: 168414--168752 Score: 508
Period size: 185 Copynumber: 1.8 Consensus size: 184
168404 CTCAATTCTC
* *
168414 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
*
168479 CTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCG
66 CTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
168544 TTATTTCCGAGGGGATACTCCAACCTCGGTTTTATCACTAAAACACTAATTTTTT
131 TTATTTCCGA-GGGATACTCCAACCTCGGTTTTATCACTAAAACACTAATTTTTT
* * * *
168599 CACAATCGGGGATACTCCAA-TCCCGGTTTTATTTTTAAAACGCCAATTTTCCTTTAATCGGGGA
1 CACAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGA
*
168663 TACT-TCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACC
64 TACTCT-AACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
*
168725 TCGTTATTTCATCGA-GGATACTCCAACC
128 CCGTTATTTC--CGAGGGATACTCCAACC
168753 CCGTTACTTC
Statistics
Matches: 140, Mismatches: 9, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
184 46 0.33
185 57 0.41
186 37 0.26
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (184 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
CTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
TTATTTCCGAGGGATACTCCAACCTCGGTTTTATCACTAAAACACTAATTTTTT
Found at i:170058 original size:23 final size:24
Alignment explanation
Indices: 170032--170091 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
170022 CTCCCCCATT
* *
170032 TTTTAATAAA-AATTAGCCACCAA
1 TTTTAACAAACAATAAGCCACCAA
*
170055 TTTTGACAAACAATAAGCCACCAA
1 TTTTAACAAACAATAAGCCACCAA
*
170079 TTTTTACAAACAA
1 TTTTAACAAACAA
170092 AAATAACTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 8 0.25
24 24 0.75
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (24 bp):
TTTTAACAAACAATAAGCCACCAA
Found at i:170089 original size:24 final size:24
Alignment explanation
Indices: 170046--170091 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
170036 AATAAAAATT
170046 AGCCACCAATTTTGACAAACAATA
1 AGCCACCAATTTTGACAAACAATA
*
170070 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
170092 AAATAACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAATA
Found at i:170119 original size:28 final size:28
Alignment explanation
Indices: 170088--170148 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
170078 ATTTTTACAA
170088 ACAAA-AATAACTACCATATTTGACAAAT
1 ACAAAGAA-AACTACCATATTTGACAAAT
* *
170116 ACAAAGAAAATTATCATATTTGACAAAT
1 ACAAAGAAAACTACCATATTTGACAAAT
170144 ACAAA
1 ACAAA
170149 TGGTGACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.25
Consensus pattern (28 bp):
ACAAAGAAAACTACCATATTTGACAAAT
Found at i:172584 original size:23 final size:24
Alignment explanation
Indices: 172521--172585 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
172511 TATCTTACTG
* *
172521 AATT-TAATAATAATTTTTATATA
1 AATTATAATATTAAATTTTATATA
*
172544 AATAATAA-ATTTATAATTTTATA-A
1 AATTATAATA-TTA-AATTTTATATA
172568 AATTATAATATTAAATTT
1 AATTATAATATTAAATTT
172586 AATTTTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 9 0.26
24 16 0.47
25 9 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTATAATATTAAATTTTATATA
Found at i:172788 original size:22 final size:21
Alignment explanation
Indices: 172763--172810 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
172753 TAAAATTAAC
*
172763 ATAATAATTTAATT-TATTAAT
1 ATAATAATATAATTATA-TAAT
*
172784 AATAAAAATATAATTATATAAT
1 -ATAATAATATAATTATATAAT
172806 ATAAT
1 ATAAT
172811 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.18
22 16 0.73
23 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATAATATAATTATATAAT
Found at i:172817 original size:19 final size:19
Alignment explanation
Indices: 172738--172838 Score: 59
Period size: 19 Copynumber: 5.5 Consensus size: 19
172728 TTAATTTTTT
* *
172738 ATTAAAATTATTTAATAAA
1 ATTAAAATTATATAATATA
* *
172757 ATTAACA-TA-ATAATTTA
1 ATTAAAATTATATAATATA
* *
172774 ATT--TATTA-ATAATAAA
1 ATTAAAATTATATAATATA
* *
172790 AATATAATTATATAATATA
1 ATTAAAATTATATAATATA
* *
172809 ATTAAAATTTTATAATTTA
1 ATTAAAATTATATAATATA
*
172828 TATAAAAATTA
1 -ATTAAAATTA
172839 ACAAAAAAAT
Statistics
Matches: 61, Mismatches: 16, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
15 1 0.02
16 10 0.16
17 8 0.13
18 6 0.10
19 28 0.46
20 8 0.13
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAAAATTATATAATATA
Found at i:176532 original size:20 final size:20
Alignment explanation
Indices: 176499--176538 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
176489 TATCAACATA
176499 AATTATTCATTTTAAATAAAT
1 AATTATTCATTTTAAA-AAAT
176520 AATTATT-ATTTTAAAAAAT
1 AATTATTCATTTTAAAAAAT
176539 TATACATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTATTCATTTTAAAAAAT
Found at i:177404 original size:19 final size:19
Alignment explanation
Indices: 177368--177406 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
177358 ACGCATAATT
*
177368 TAAATAAATCATTATTAAA
1 TAAATAAATAATTATTAAA
177387 TAAATAAATAAATT-TTAAA
1 TAAATAAAT-AATTATTAAA
177406 T
1 T
177407 TATCTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATAAATAATTATTAAA
Found at i:184352 original size:288 final size:287
Alignment explanation
Indices: 183819--184399 Score: 783
Period size: 288 Copynumber: 2.0 Consensus size: 287
183809 TAGCAAATAG
* *
183819 AAATGGTAAGTGAATAGGTTTGAGCAAGTCGAGATCAAATCATTTTATGTTCAGATTATTTTAGC
1 AAATGGTAAGTGAACAGGTTTGAGCAAGTCGAGATCAAATCATTTTATGTTCAGATTATTTCAGC
* * * * *
183884 TTTAAGTTATTTTAGGTTCGGACCTATTCAGGTTCGAGTTTATTCTGGTTTAAGCTTATTTGAGT
66 TTTAACTTATTTCAGGTTCGGACCTATTCAGGTTCAAGTTTACTCGGGTTTAAGCTTATTTGAGT
* * * *
183949 TTGGTCTTTTTGAGGCTCGGGCCTATTTGGATTCAATCTTTTTAGAATTTGAACCTTTTCGAGTT
131 TTAGTCTTTTTGAGGCTCGGGCCTACTTAGATTCAAACTTTTTAGAATTTGAACCTTTTCGAGTT
* * * * * *
184014 CGGACTTTTTTGAGTTTAAACTTTTCTGGTTTGGGTTGAGTTCGAGTCGATTTTGGGTTTGAGTA
196 CGAACCTTTTCGAGTTTAAACTTTTCT-GTTTGGATTAAGTTCAAGTCGATTTTGGGTTTGAGTA
**
184079 GGTTTTAAATCATTTTTTATTTTATATT
260 GAATTTAAATCATTTTTTATTTTATATT
*
184107 AAATGGTAAGTGAACAGGTTTGAGCAAGTTGAGATCAAATCATTTTATGTTCAGATTATTTCATG
1 AAATGGTAAGTGAACAGGTTTGAGCAAGTCGAGATCAAATCATTTTATGTTCAGATTATTTCA-G
* * * *
184172 -TTTGACTTATTTCAGGTTCGGACCTATTCAGGTTCAAGTTTACTCGGGTTTAGGCTTCTTTGGG
65 CTTTAACTTATTTCAGGTTCGGACCTATTCAGGTTCAAGTTTACTCGGGTTTAAGCTTATTTGAG
* * * * *
184236 TTTAGTATTTTTTTAGGCTCGGGCCTACTTAGATTCAAACTTTTTAGAATTTGAGCTTTTTTG-G
130 TTTAGT-CTTTTTGAGGCTCGGGCCTACTTAGATTCAAACTTTTTAGAATTTGAACCTTTTCGAG
** *
184300 CTTCGAACCTTTTCGAGTTTAGGCTTTT-T-TTTGTTGATTAAGTTTAAGTCGATTTTGGGTTTG
194 -TTCGAACCTTTTCGAGTTTAAACTTTTCTGTTTG--GATTAAGTTCAAGTCGATTTTGGGTTTG
*
184363 AGTATAATTTAAATCATTTTTTATTTTATATT
256 AGTAGAATTTAAATCATTTTTTATTTTATATT
184395 AAATG
1 AAATG
184400 TAATCATTTT
Statistics
Matches: 255, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
286 4 0.02
288 180 0.71
289 71 0.28
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.46
Consensus pattern (287 bp):
AAATGGTAAGTGAACAGGTTTGAGCAAGTCGAGATCAAATCATTTTATGTTCAGATTATTTCAGC
TTTAACTTATTTCAGGTTCGGACCTATTCAGGTTCAAGTTTACTCGGGTTTAAGCTTATTTGAGT
TTAGTCTTTTTGAGGCTCGGGCCTACTTAGATTCAAACTTTTTAGAATTTGAACCTTTTCGAGTT
CGAACCTTTTCGAGTTTAAACTTTTCTGTTTGGATTAAGTTCAAGTCGATTTTGGGTTTGAGTAG
AATTTAAATCATTTTTTATTTTATATT
Found at i:184490 original size:31 final size:30
Alignment explanation
Indices: 184442--184528 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 30
184432 AAAAGCAAGT
184442 TATT-AAATTATTATTTTTGAATAAATTT-T-
1 TATTAAAATT-TTATTTTT-AATAAATTTATG
*
184471 TATTATAATATTTTATTTTTAATATATTTATG
1 TATTA-AA-ATTTTATTTTTAATAAATTTATG
184503 TATTAAAATTTATATTTTTATATAAA
1 TATTAAAATTT-TATTTTTA-ATAAA
184529 ATCAATTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
29 4 0.08
30 12 0.24
31 21 0.43
32 12 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
TATTAAAATTTTATTTTTAATAAATTTATG
Found at i:184508 original size:16 final size:14
Alignment explanation
Indices: 184468--184518 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 14
184458 TTGAATAAAT
184468 TTTTATTA-TAATA
1 TTTTATTATTAATA
*
184481 TTTTATTTTTAATA
1 TTTTATTATTAATA
*
184495 TATTTATGTATTAAAA
1 T-TTTAT-TATTAATA
184511 TTTATATT
1 TTT-TATT
184519 TTTATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 7 0.23
14 6 0.19
15 8 0.26
16 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTTATTATTAATA
Found at i:185108 original size:29 final size:29
Alignment explanation
Indices: 185054--185109 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
185044 TTTACTTTTG
** *
185054 ATAAATTACTATTTTATCATATATAAAAT
1 ATAAATTAAAATTTTATCATAAATAAAAT
185083 ATAAATTAAAATTTTAAT-ATAAATAAA
1 ATAAATTAAAATTTT-ATCATAAATAAA
185110 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAAATTAAAATTTTATCATAAATAAAAT
Found at i:185264 original size:16 final size:15
Alignment explanation
Indices: 185243--185309 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 15
185233 GTTCGAATTC
*
185243 TTTTAATTTTAAACTA
1 TTTTAAATTTAAA-TA
* *
185259 TTTTAAGTTTGAACTA
1 TTTTAAATTT-AAATA
* *
185275 TTTCAAATTTAAATT
1 TTTTAAATTTAAATA
185290 TTTTAAATTTAAAT-
1 TTTTAAATTTAAATA
185304 TTTTAA
1 TTTTAA
185310 CTTTTTAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
14 6 0.14
15 16 0.37
16 19 0.44
17 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTAAATTTAAATA
Found at i:185729 original size:14 final size:14
Alignment explanation
Indices: 185679--185729 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
185669 ATAATAAAAA
185679 AATATTTTTAATTT
1 AATATTTTTAATTT
* *
185693 TATATTATTAAATTT
1 AATATT-TTTAATTT
185708 AATA-TTTTAATTT
1 AATATTTTTAATTT
185721 AATATTTTT
1 AATATTTTT
185730 TAAATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.35
14 10 0.32
15 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATATTTTTAATTT
Found at i:186962 original size:2 final size:2
Alignment explanation
Indices: 186957--186982 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
186947 ATATATATAT
186957 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
186983 GATAGGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:187719 original size:18 final size:19
Alignment explanation
Indices: 187696--187738 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
187686 AAATTGTATA
*
187696 TTTTAAAATGTA-AAATTT
1 TTTTAAAATGTATAAATAT
*
187714 TTTTAAAGTGTATAAATAT
1 TTTTAAAATGTATAAATAT
187733 TTTTAA
1 TTTTAA
187739 TTTGATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTTAAAATGTATAAATAT
Found at i:187923 original size:23 final size:22
Alignment explanation
Indices: 187868--187929 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
187858 ATAGCTTTTG
* *
187868 TAAAAATAAATATTTTAAAAGA
1 TAAAAATAATTATTTAAAAAGA
*
187890 -AAAAATAAATTAATTTAAAAATA
1 TAAAAAT-AATT-ATTTAAAAAGA
187913 TAAAAATAATT-TTTAAA
1 TAAAAATAATTATTTAAA
187930 TAAATAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 12 0.35
22 3 0.09
23 13 0.38
24 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TAAAAATAATTATTTAAAAAGA
Found at i:187929 original size:21 final size:22
Alignment explanation
Indices: 187868--187929 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
187858 ATAGCTTTTG
187868 TAAAAATAAATATTTT-AAAAGA
1 TAAAAATAAAT-TTTTAAAAAGA
*
187890 -AAAAATAAATTAATTTAAAAATA
1 TAAAAATAAATT--TTTAAAAAGA
187913 TAAAAAT-AATTTTTAAA
1 TAAAAATAAATTTTTAAA
187930 TAAATAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 1 0.03
21 16 0.46
22 3 0.09
23 9 0.26
24 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TAAAAATAAATTTTTAAAAAGA
Found at i:187930 original size:19 final size:18
Alignment explanation
Indices: 187908--187946 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
187898 ATTAATTTAA
187908 AAATATAAAAATAATTTTT
1 AAATA-AAAAATAATTTTT
* *
187927 AAATAAATAATTATTTTT
1 AAATAAAAAATAATTTTT
187945 AA
1 AA
187947 TGGGTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATAAAAAATAATTTTT
Found at i:187944 original size:18 final size:17
Alignment explanation
Indices: 187912--187946 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
187902 ATTTAAAAAT
187912 ATAAAAATAATTTTTAA
1 ATAAAAATAATTTTTAA
*
187929 ATAAATAATTATTTTTAA
1 ATAAA-AATAATTTTTAA
187947 TGGGTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAAAATAATTTTTAA
Found at i:190492 original size:45 final size:45
Alignment explanation
Indices: 190402--190511 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 45
190392 AATATATAAA
*
190402 ATTTTAAAATTTAAT-AT-TTAAAATTTATTTTTATTACATATATT
1 ATTTTAAAATTTAATAATATT-AAATTTATTTTTATTACAAATATT
190446 ATTTTAAAATTTAATAATATT-AATTTAATTTTT-TTAACAAATATT
1 ATTTTAAAATTTAATAATATTAAATTT-ATTTTTATT-ACAAATATT
* * * *
190491 ATTATAATATATAATATTATT
1 ATTTTAAAATTTAATAATATT
190512 TATATTAACA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
44 22 0.39
45 33 0.58
46 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (45 bp):
ATTTTAAAATTTAATAATATTAAATTTATTTTTATTACAAATATT
Found at i:190635 original size:30 final size:31
Alignment explanation
Indices: 190601--190665 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
190591 ATTTTATTGA
* *
190601 TAAAAATATTATGT-TAAT-ACTATTAAAATT
1 TAAAAATAATATGTATAATAAATA-TAAAATT
*
190631 TAAAATTAATATGTATAATAAATATAAAATT
1 TAAAAATAATATGTATAATAAATATAAAATT
190662 TAAA
1 TAAA
190666 TATTAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 12 0.40
31 15 0.50
32 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (31 bp):
TAAAAATAATATGTATAATAAATATAAAATT
Found at i:193835 original size:19 final size:20
Alignment explanation
Indices: 193791--193837 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
193781 CTGTCAGTTT
**
193791 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
193811 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
193830 CATGTATC
1 CATGTATC
193838 CATGCAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:196468 original size:50 final size:50
Alignment explanation
Indices: 196400--196509 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
196390 TACATCTGGG
* **
196400 TTTTCCAGATGTATCGATATATCCTTCAATGTATCGATACATTTTGAAAAA
1 TTTT-CAGAAGTATCGATATATCCTTCAATGTATCGATACATTCAGAAAAA
* * *
196451 TTTTTAGAAGTATCGATATATTCTTCAATGTATTGATACATTCAGAAAAA
1 TTTTCAGAAGTATCGATATATCCTTCAATGTATCGATACATTCAGAAAAA
196501 TTTTCAGAA
1 TTTTCAGAA
196510 AAAAGTGACA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
50 48 0.92
51 4 0.08
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (50 bp):
TTTTCAGAAGTATCGATATATCCTTCAATGTATCGATACATTCAGAAAAA
Found at i:198608 original size:11 final size:12
Alignment explanation
Indices: 198568--198606 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
198558 ATGCTTATTC
*
198568 TAAATTTTCTTCA
1 TAAA-TTTCTACA
198581 TAAATTTCTA-A
1 TAAATTTCTACA
198592 TAAATTTCTACA
1 TAAATTTCTACA
198604 TAA
1 TAA
198607 TTGTTAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 11 0.46
12 9 0.38
13 4 0.17
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (12 bp):
TAAATTTCTACA
Found at i:202723 original size:13 final size:13
Alignment explanation
Indices: 202705--202729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202695 CAATTGTCCA
202705 TGTATCGATACAT
1 TGTATCGATACAT
202718 TGTATCGATACA
1 TGTATCGATACA
202730 AAGTATAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:203758 original size:17 final size:17
Alignment explanation
Indices: 203736--203774 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
203726 ATTGCCTATG
203736 CCCTTTTGTATCTTTAA
1 CCCTTTTGTATCTTTAA
203753 CCC-TTTGTATCTTTAA
1 CCCTTTTGTATCTTTAA
203769 CCCTTT
1 CCCTTT
203775 GATTGCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.15, C:0.28, G:0.05, T:0.51
Consensus pattern (17 bp):
CCCTTTTGTATCTTTAA
Found at i:203761 original size:16 final size:16
Alignment explanation
Indices: 203740--203775 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
203730 CCTATGCCCT
203740 TTTGTATCTTTAACCC
1 TTTGTATCTTTAACCC
203756 TTTGTATCTTTAACCC
1 TTTGTATCTTTAACCC
203772 TTTG
1 TTTG
203776 ATTGCTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.08, T:0.53
Consensus pattern (16 bp):
TTTGTATCTTTAACCC
Found at i:207079 original size:13 final size:13
Alignment explanation
Indices: 207061--207085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
207051 CTTGAAATAG
207061 TGAATAATTATAA
1 TGAATAATTATAA
207074 TGAATAATTATA
1 TGAATAATTATA
207086 TATGCATTTA
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
TGAATAATTATAA
Found at i:208617 original size:17 final size:17
Alignment explanation
Indices: 208595--208636 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
208585 TTTACATATG
208595 CATCTATGACCCTCAGC
1 CATCTATGACCCTCAGC
208612 CATCTATGACCCTCAGC
1 CATCTATGACCCTCAGC
*
208629 CAGCTATG
1 CATCTATG
208637 CTCACTGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (17 bp):
CATCTATGACCCTCAGC
Found at i:208945 original size:24 final size:23
Alignment explanation
Indices: 208912--208957 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
208902 AAATATATCT
208912 ATTAAATTAAGTTATTAAATTTA
1 ATTAAATTAAGTTATTAAATTTA
* *
208935 ATTAATATTAATTTATTATATTT
1 ATTAA-ATTAAGTTATTAAATTT
208958 TTAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTAAATTAAGTTATTAAATTTA
Found at i:210107 original size:21 final size:22
Alignment explanation
Indices: 210058--210117 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
210048 AATTATTTAA
*
210058 AATTAAAATATTAAATACTTTT
1 AATTAAAATTTTAAATACTTTT
* *
210080 ATTTTAAAATTTTAAAT-TTTTT
1 A-ATTAAAATTTTAAATACTTTT
210102 AATTAAAA-TTTAAATA
1 AATTAAAATTTTAAATA
210118 ATACAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.22
21 6 0.19
22 6 0.19
23 13 0.41
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAAATTTTAAATACTTTT
Found at i:213612 original size:14 final size:14
Alignment explanation
Indices: 213593--213631 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
213583 TTTATCAATG
213593 AAAAATTTTAATAA
1 AAAAATTTTAATAA
*
213607 AAAAATATTT-TTAA
1 AAAAAT-TTTAATAA
213621 AAAAATTTTAA
1 AAAAATTTTAA
213632 ATTAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 3 0.14
14 15 0.71
15 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAAATTTTAATAA
Found at i:215660 original size:43 final size:43
Alignment explanation
Indices: 215610--215699 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
215600 CCCCTTCAGG
215610 CTCTAACTCCTTCACGCAAACTGCAACATCCGCTTCATACTTA
1 CTCTAACTCCTTCACGCAAACTGCAACATCCGCTTCATACTTA
215653 CTCTAACTCCTTCACGCAAACTGCAACATCCGCTTCATACTTA
1 CTCTAACTCCTTCACGCAAACTGCAACATCCGCTTCATACTTA
215696 CTCT
1 CTCT
215700 GTAACTTACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.27, C:0.38, G:0.07, T:0.29
Consensus pattern (43 bp):
CTCTAACTCCTTCACGCAAACTGCAACATCCGCTTCATACTTA
Found at i:219721 original size:2 final size:2
Alignment explanation
Indices: 219714--219751 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
219704 AGGTCTAATG
219714 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
219752 ATATGTGTGT
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:220869 original size:8 final size:9
Alignment explanation
Indices: 220813--220878 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
220803 TTAATATGAC
*
220813 ATATTTAAT
1 ATATTTATT
*
220822 GTATTTATT
1 ATATTTATT
220831 ATATTTA-T
1 ATATTTATT
220839 AT-TTTA--
1 ATATTTATT
*
220845 A-ATTTGAAT
1 ATATTT-ATT
220854 ATATTTATT
1 ATATTTATT
220863 A-ATTTATT
1 ATATTTATT
220871 ATATTTAT
1 ATATTTAT
220879 GTTTACATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
6 4 0.09
7 5 0.11
8 11 0.23
9 23 0.49
10 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
ATATTTATT
Found at i:220873 original size:17 final size:16
Alignment explanation
Indices: 220823--220878 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
220813 ATATTTAATG
220823 TATTTATTATATTTATA
1 TATTTATTA-ATTTATA
220840 T-TTTA--AATTTGAATA
1 TATTTATTAATTT--ATA
220855 TATTTATTAATTTATTA
1 TATTTATTAATTTA-TA
220872 TATTTAT
1 TATTTAT
220879 GTTTACATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 4 0.12
14 1 0.03
15 4 0.12
16 9 0.27
17 10 0.30
18 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTTATTAATTTATA
Found at i:221321 original size:5 final size:5
Alignment explanation
Indices: 221311--221335 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
221301 ATAAGTATAA
221311 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
221336 GTTAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:221342 original size:30 final size:30
Alignment explanation
Indices: 221286--221343 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
221276 ATATGATTGA
* *
221286 AATATAATGTATTTAATAAGTATAAAATAT
1 AATATAATATATATAATAAGTATAAAATAT
*
221316 AATATAATATAATATAATATGT-TAAAAT
1 AATATAATAT-ATATAATAAGTATAAAAT
221344 TTGTTTAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (30 bp):
AATATAATATATATAATAAGTATAAAATAT
Found at i:221403 original size:17 final size:19
Alignment explanation
Indices: 221381--221424 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
221371 ATATTAAATT
221381 TATATTTAA-A-ATTTTAA
1 TATATTTAATATATTTTAA
*
221398 TATATTTAATATATTTTAT
1 TATATTTAATATATTTTAA
221417 TATATTTA
1 TATATTTA
221425 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 1 0.04
19 14 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTTAATATATTTTAA
Found at i:221415 original size:10 final size:10
Alignment explanation
Indices: 221391--221423 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
221381 TATATTTAAA
221391 ATTTTAATAT
1 ATTTTAATAT
221401 A-TTTAATAT
1 ATTTTAATAT
*
221410 ATTTTATTAT
1 ATTTTAATAT
221420 ATTT
1 ATTT
221424 ATAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:221425 original size:9 final size:9
Alignment explanation
Indices: 221381--221424 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
221371 ATATTAAATT
221381 TATATTTAA
1 TATATTTAA
*
221390 AAT-TTTAA
1 TATATTTAA
221398 TATATTTAA
1 TATATTTAA
*
221407 TATATTTTAT
1 TATA-TTTAA
221417 TATATTTA
1 TATATTTA
221425 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATTTAA
Found at i:225645 original size:19 final size:19
Alignment explanation
Indices: 225600--225655 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
225590 AATAATATGT
**
225600 TATTTAAT-AAATTAAAAA
1 TATTTAATAAAATTATTAA
* *
225618 TAATAAATAAAATTATTAA
1 TATTTAATAAAATTATTAA
225637 TATTTAATATAATATTATT
1 TATTTAATA-AA-ATTATT
225656 GTAAATATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 6 0.21
19 15 0.52
20 2 0.07
21 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTTAATAAAATTATTAA
Found at i:226519 original size:23 final size:24
Alignment explanation
Indices: 226462--226520 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
226452 AAAAATTACG
* * *
226462 TATAAAAATAA-ATTTATATTTGA
1 TATATAAATAATATATAAATTTGA
* *
226485 TATATTATTAATATATAAATTT-A
1 TATATAAATAATATATAAATTTGA
226508 TATATAAATAATA
1 TATATAAATAATA
226521 AATATTAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TATATAAATAATATATAAATTTGA
Found at i:228800 original size:2 final size:2
Alignment explanation
Indices: 228788--228830 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
228778 GGAGGAGGGC
*
228788 GA GA AA 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 GA GA
228830 G
1 G
228831 GGGTACTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:237594 original size:22 final size:24
Alignment explanation
Indices: 237547--237607 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
237537 GGTATGGTTA
* *
237547 ATTTTAT-ATTATATATATATATT
1 ATTTTATAATTATATATATAAAAT
237570 ATTTTATAATTATAT-T-TAAAAT
1 ATTTTATAATTATATATATAAAAT
*
237592 ATTTTATATTTATATA
1 ATTTTATAATTATATA
237608 AATTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 18 0.55
23 8 0.24
24 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTATAATTATATATATAAAAT
Found at i:238429 original size:2 final size:2
Alignment explanation
Indices: 238424--238448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
238414 TGGGGGGAGG
238424 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 G
238449 GAAAAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:240159 original size:13 final size:13
Alignment explanation
Indices: 240125--240163 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
240115 TGAATTTTAA
*
240125 TATATTTATATATT
1 TATATTT-TATTTT
240139 TATATTTTATTTT
1 TATATTTTATTTT
*
240152 TATTTTTTATTT
1 TATATTTTATTT
240164 GTGTAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATATTTTATTTT
Found at i:240794 original size:17 final size:17
Alignment explanation
Indices: 240772--240812 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
240762 TTAATAGTAT
* *
240772 AAATATTAACTATATTA
1 AAATATTAAATATAATA
240789 AAATATTAAATATAATA
1 AAATATTAAATATAATA
*
240806 TAATATT
1 AAATATT
240813 TATATTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTAAATATAATA
Found at i:242780 original size:18 final size:18
Alignment explanation
Indices: 242757--242794 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
242747 GATTATAAAT
242757 GTTGCCTGGGTGGATAAG
1 GTTGCCTGGGTGGATAAG
242775 GTTGCCTGGGTGGATAAG
1 GTTGCCTGGGTGGATAAG
242793 GT
1 GT
242795 GGACAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.45, T:0.29
Consensus pattern (18 bp):
GTTGCCTGGGTGGATAAG
Found at i:243157 original size:25 final size:25
Alignment explanation
Indices: 243125--243178 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
243115 TGTTAATTTA
243125 TTATTTT-TTATAAAATAATAATTTTT
1 TTATTTTGTTAT-AAA-AATAATTTTT
*
243151 TTATTTTGTTATAAACATAATTTTT
1 TTATTTTGTTATAAAAATAATTTTT
243176 TTA
1 TTA
243179 AATAAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.46
26 10 0.38
27 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTTTGTTATAAAAATAATTTTT
Found at i:247878 original size:5 final size:5
Alignment explanation
Indices: 247845--247897 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
247835 TTCTTTTTCC
* * * * *
247845 TTCTG TTCTT TTCCT TTCTT TTCCT TTCTT TTCTG TTCTT TGCTT TTGCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT-CTT
247896 TT
1 TT
247898 AGGCACCAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
5 33 0.87
6 5 0.13
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.70
Consensus pattern (5 bp):
TTCTT
Found at i:249533 original size:27 final size:28
Alignment explanation
Indices: 249467--249533 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
249457 CAAATGATTA
*
249467 TTATTAATAAATTTTAAAATATTTAATT
1 TTATTAATAAATATTAAAATATTTAATT
* * * *
249495 ATATAAAAAAATATT-AAATTTTTAATT
1 TTATTAATAAATATTAAAATATTTAATT
*
249522 TTATTATTAAAT
1 TTATTAATAAAT
249534 TATAAAAAAT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATTAATAAATATTAAAATATTTAATT
Found at i:253839 original size:2 final size:2
Alignment explanation
Indices: 253832--253870 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
253822 TTCACCAAGA
* * *
253832 AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
253871 CCGGAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
AT
Found at i:256292 original size:21 final size:21
Alignment explanation
Indices: 256267--256329 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
256257 AAAAAAATTA
256267 AATTTAAATATTATAATATTT
1 AATTTAAATATTATAATATTT
256288 AATTTAAATTATTTATAA-ATTT
1 AATTTAAA-TA-TTATAATATTT
* * *
256310 AA-ATAAATATTTTATTATTT
1 AATTTAAATATTATAATATTT
256330 TTAATTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
19 4 0.11
20 6 0.17
21 12 0.33
22 8 0.22
23 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTAAATATTATAATATTT
Found at i:256300 original size:22 final size:21
Alignment explanation
Indices: 256261--256321 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
256251 ATTATGAAAA
*
256261 AAATTAAATTTAAATA-TTAT
1 AAATTTAATTTAAATATTTAT
256281 AATATTTAATTTAAATTATTTAT
1 AA-ATTTAATTTAAA-TATTTAT
*
256304 AAATTTAA-ATAAATATTT
1 AAATTTAATTTAAATATTT
256322 TATTATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 7 0.19
21 15 0.42
22 8 0.22
23 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTTAATTTAAATATTTAT
Found at i:257713 original size:13 final size:13
Alignment explanation
Indices: 257691--257724 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
257681 TATATCAGGC
*
257691 TTTTTATGTTTTT
1 TTTTTTTGTTTTT
257704 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
*
257717 TTGTTTTG
1 TTTTTTTG
257725 GCTATACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (13 bp):
TTTTTTTGTTTTT
Found at i:261900 original size:18 final size:17
Alignment explanation
Indices: 261847--261923 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
261837 AAATATAAAT
*
261847 AAAATTACATTTTTATTA
1 AAAATTA-ATTTATATTA
* * *
261865 AACATTAATTAAAAATTA
1 AAAATTAATT-TATATTA
261883 AAAATTAGATTTATATTA
1 AAAATTA-ATTTATATTA
* *
261901 AATAATAAAATATATATTA
1 AA-AAT-TAATTTATATTA
261920 AAAA
1 AAAA
261924 AATTAAAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
17 3 0.07
18 25 0.54
19 17 0.37
20 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (17 bp):
AAAATTAATTTATATTA
Found at i:261932 original size:21 final size:18
Alignment explanation
Indices: 261879--261936 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
261869 TTAATTAAAA
* * *
261879 ATTAAAAATTAGATTTAT
1 ATTAAAAAATAAAATTAT
*
261897 ATTAAATAATAAAATATAT
1 ATTAAAAAATAAAAT-TAT
261916 ATTAAAAAAATTAAAATTAT
1 ATT-AAAAAA-TAAAATTAT
261936 A
1 A
261937 CTTATATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 11 0.34
19 6 0.19
20 9 0.28
21 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTAAAAAATAAAATTAT
Found at i:261953 original size:71 final size:70
Alignment explanation
Indices: 261803--261977 Score: 169
Period size: 71 Copynumber: 2.5 Consensus size: 70
261793 GATAAATAAT
* * * ***
261803 TTAAATTATT-AAAATATATTTATATTAAATAATAAAATATAAATAAAATTACATTTTTATTAAA
1 TTAAATAATTAAAAATAGATTTATATTAAATAATAAAATATAAATAAAA-TAAATTAAAATTAAA
261867 CATTAA
65 CATTAA
* *
261873 TTAAA-AATTAAAAATTAGATTTATATTAAATAATAAAATATATATTAAAA-AAATTAAAATTAT
1 TTAAATAATTAAAAA-TAGATTTATATTAAATAATAAAATATA-AATAAAATAAATTAAAATTAA
261936 AC-TTATA
64 ACATTA-A
* *
261943 TTAAATAATTATTAAATATTATTTATATTTAAATA
1 TTAAATAATTA-AAAATA-GATTTATA-TTAAATA
261978 TAATTTAATA
Statistics
Matches: 87, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
69 6 0.07
70 25 0.29
71 33 0.38
72 16 0.18
73 7 0.08
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (70 bp):
TTAAATAATTAAAAATAGATTTATATTAAATAATAAAATATAAATAAAATAAATTAAAATTAAAC
ATTAA
Found at i:261956 original size:28 final size:26
Alignment explanation
Indices: 261913--261987 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
261903 TAATAAAATA
261913 TATATTAAA-AAAATTAAA-ATTATACT
1 TATATTAAATAAAATTAAATATTAT--T
*
261939 TATATTAAATAATTATTAAATATTATT
1 TATATTAAATAA-AATTAAATATTATT
* *
261966 TATATTTAAATATAATTTAATA
1 TATA-TTAAATAAAATTAAATA
261988 AAAAAAGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 9 0.22
27 14 0.34
28 13 0.32
29 5 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATTAAATAAAATTAAATATTATT
Found at i:262520 original size:20 final size:19
Alignment explanation
Indices: 262482--262520 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
262472 CTTAAAAAAA
* *
262482 ATTCGTAAAATTAATATTT
1 ATTCGTAAAAATAAAATTT
262501 ATTCGTCAAAAATAAAATTT
1 ATTCGT-AAAAATAAAATTT
262521 TCATTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTCGTAAAAATAAAATTT
Found at i:263001 original size:16 final size:16
Alignment explanation
Indices: 262938--263013 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 16
262928 ATTATAATAA
* *
262938 AATTAATATATAATTA
1 AATTAAAATATAATTT
262954 AATTAAAA-ATAAATTTT
1 AATTAAAATAT-AA-TTT
**
262971 AAATATTTAATATATATTT
1 -AAT-TAAAATATA-ATTT
262990 GAATTAAAATATAATTT
1 -AATTAAAATATAATTT
263007 AATTAAA
1 AATTAAA
263014 TCTTAATTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
15 2 0.04
16 16 0.34
17 6 0.13
18 10 0.21
19 10 0.21
20 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (16 bp):
AATTAAAATATAATTT
Found at i:263588 original size:28 final size:25
Alignment explanation
Indices: 263520--263583 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 25
263510 TATTAAATTT
263520 ATATAAATATAAAATTTTAAACATA
1 ATATAAATATAAAATTTTAAACATA
*
263545 TTAATATAATAATAAAATTTATAAACATA
1 AT-ATA-AAT-ATAAAATTT-TAAACATA
263574 ATATAAATAT
1 ATATAAATAT
263584 TTAAATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 6 0.18
28 12 0.36
29 9 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATAAATATAAAATTTTAAACATA
Found at i:264046 original size:15 final size:14
Alignment explanation
Indices: 263997--264050 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 14
263987 AAAAAATTTT
263997 AAAAATTATTTATA
1 AAAAATTATTTATA
* *
264011 AATATTTA-TTA-A
1 AAAAATTATTTATA
*
264023 ATAAA-TATTTATA
1 AAAAATTATTTATA
264036 AAAAATTTATTTATA
1 AAAAA-TTATTTATA
264051 TCGATATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
11 2 0.07
12 6 0.20
13 8 0.27
14 6 0.20
15 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAAAATTATTTATA
Found at i:264992 original size:21 final size:20
Alignment explanation
Indices: 264942--264998 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
264932 CATTTTTATT
*
264942 TATTATA-ATTATATTTAAAA
1 TATTATATATT-TATATAAAA
264962 TATTATATATTTATATAAAA
1 TATTATATATTTATATAAAA
*
264982 TTTTAATATATTTATAT
1 TATT-ATATATTTATAT
264999 CATATTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATATATTTATATAAAA
Found at i:265034 original size:11 final size:10
Alignment explanation
Indices: 264965--265070 Score: 64
Period size: 11 Copynumber: 10.3 Consensus size: 10
264955 TTTAAAATAT
264965 TATATATTTA
1 TATATATTTA
*
264975 TATAAAATTT-
1 TAT-ATATTTA
264985 TAATATATTTA
1 T-ATATATTTA
264996 TATCATATTTA
1 TAT-ATATTTA
265007 TAT-TATTT-
1 TATATATTTA
265015 T-TATA-TTA
1 TATATATTTA
265023 TATCATATTTA
1 TAT-ATATTTA
265034 TTATCATATTT-
1 -TAT-ATATTTA
265045 TAT-TAATTTTAA
1 TATAT-A-TTT-A
265057 TATGATATTTA
1 TAT-ATATTTA
265068 TAT
1 TAT
265071 TGTATAATTA
Statistics
Matches: 78, Mismatches: 2, Indels: 31
0.70 0.02 0.28
Matches are distributed among these distances:
7 3 0.04
8 5 0.06
9 7 0.09
10 20 0.26
11 25 0.32
12 16 0.21
13 1 0.01
14 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (10 bp):
TATATATTTA
Found at i:265039 original size:39 final size:38
Alignment explanation
Indices: 264989--265064 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
264979 AAATTTTAAT
* *
264989 ATATTTATATCATATTTATATT-ATTTTTATATTATATC
1 ATATTTATATCATATTT-TATTAATTTTAATATGATATC
265027 ATATTTATTATCATATTTTATTAATTTTAATATGATAT
1 ATATTTA-TATCATATTTTATTAATTTTAATATGATAT
265065 TTATATTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 11 0.32
39 23 0.68
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (38 bp):
ATATTTATATCATATTTTATTAATTTTAATATGATATC
Found at i:265040 original size:12 final size:13
Alignment explanation
Indices: 264987--265049 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
264977 TAAAATTTTA
264987 ATATATTTA-TATC
1 ATAT-TTTATTATC
*
265000 ATATTTATATTATTT
1 ATATTT-TATTA-TC
* *
265015 TTATATTA-TATC
1 ATATTTTATTATC
265027 ATA-TTTATTATC
1 ATATTTTATTATC
265039 ATATTTTATTA
1 ATATTTTATTA
265050 ATTTTAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
11 3 0.08
12 12 0.31
13 15 0.38
14 4 0.10
15 5 0.13
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTTTATTATC
Found at i:265048 original size:27 final size:27
Alignment explanation
Indices: 264988--265049 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
264978 AAAATTTTAA
* *
264988 TATATTTATATCATATTTATATTATTTT
1 TATA-TTATATCATATTTATATCATATT
265016 TATATTATATCATATTTATTATCATATT
1 TATATTATATCATATTTA-TATCATATT
265044 T-TATTA
1 TATATTA
265050 ATTTTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (27 bp):
TATATTATATCATATTTATATCATATT
Found at i:265247 original size:24 final size:23
Alignment explanation
Indices: 265208--265252 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
265198 AAGTAGGTCA
* *
265208 TTTTTAAAAAAGTTATTATTATT
1 TTTTTAAAAAAATTATAATTATT
265231 TTTTTAAATAAAATTATAATTA
1 TTTTTAAA-AAAATTATAATTA
265253 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTTAAAAAAATTATAATTATT
Found at i:265402 original size:27 final size:26
Alignment explanation
Indices: 265316--265400 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 26
265306 ATTTTTTATC
*
265316 AATTTAATAA-ATAAATTGATATTACTT
1 AATTTAATAATATAAATT-ATA-TATTT
*
265343 AATTTAATGATATCAAATTCA-ATATTT
1 AATTTAATAATAT-AAATT-ATATATTT
** *
265370 TTTTATAATAATATAAATTTTATATTT
1 AATT-TAATAATATAAATTATATATTT
265397 AATT
1 AATT
265401 ATTTATTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
27 28 0.62
28 11 0.24
29 6 0.13
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (26 bp):
AATTTAATAATATAAATTATATATTT
Done.