Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003844.1 Hibiscus syriacus cultivar Beakdansim tig00008242_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 412420
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1088 original size:2 final size:2
Alignment explanation
Indices: 1081--1107 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1071 TCAATCTACA
1081 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 A
1108 ATTTACGACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1197 original size:13 final size:13
Alignment explanation
Indices: 1179--1208 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1169 AATGACACAC
*
1179 AATGTAAGTCGTA
1 AATGTAAGTCATA
1192 AATGTAAGTCATA
1 AATGTAAGTCATA
1205 AATG
1 AATG
1209 CGTGTCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:1266 original size:98 final size:95
Alignment explanation
Indices: 1135--1368 Score: 238
Period size: 98 Copynumber: 2.4 Consensus size: 95
1125 ACGACACACG
* * * * * *
1135 AATGTGTGTCATCTTTTTTAACGACGTGTGCTTCAATGACACACAATGTAAGTCGTAAATGTAAG
1 AATGTGTGTCATCTTATTT-ATGACGGGGGCTTCAATGACACACAATGTAAGTCATAAATGCAAG
**
1200 TCATAAATGCGTGTCATAAATTTATGACAAACA-
65 TCAT-AATGCACGTCATAAATTTATGAC--ACAT
* * ** **
1233 AATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACGCGCAATGTGCGTCATAAATGCGTG
1 AATGTGTGTCATCTT-ATTTATGACGGGGGCTTCAATGACACACAATGTAAGTCATAAATGCAAG
*
1298 TCATAATGCACGTCATAGATTTATGACACAT
65 TCATAATGCACGTCATAAATTTATGACACAT
* *
1329 AAT-TGTGTCATCTGAGATTTATGACGGTGGCTTCAATGAC
1 AATGTGTGTCATCT--TATTTATGACGGGGGCTTCAATGAC
1369 GCTCATTTGT
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
95 13 0.11
96 26 0.23
97 20 0.17
98 53 0.46
99 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (95 bp):
AATGTGTGTCATCTTATTTATGACGGGGGCTTCAATGACACACAATGTAAGTCATAAATGCAAGT
CATAATGCACGTCATAAATTTATGACACAT
Found at i:3875 original size:44 final size:44
Alignment explanation
Indices: 3825--3909 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
3815 AAATGAATGA
* * *
3825 ATAAATGAAAATGCATAACGGTGTATTATTGACATAAAGGTTCC
1 ATAAATGAAAATGCAAAACGGTGCATTATTGACAGAAAGGTTCC
* *
3869 ATAAATGAAAATGCAAAATGGTGCATTATTGGCAGAAAGGT
1 ATAAATGAAAATGCAAAACGGTGCATTATTGACAGAAAGGT
3910 GCATGTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.27
Consensus pattern (44 bp):
ATAAATGAAAATGCAAAACGGTGCATTATTGACAGAAAGGTTCC
Found at i:18122 original size:13 final size:13
Alignment explanation
Indices: 18104--18137 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
18094 AATAGTGAAT
18104 AGTGAACAATAAC
1 AGTGAACAATAAC
*
18117 AGTGAACAATACC
1 AGTGAACAATAAC
*
18130 CGTGAACA
1 AGTGAACA
18138 GACGACATTT
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:0.47, C:0.21, G:0.18, T:0.15
Consensus pattern (13 bp):
AGTGAACAATAAC
Found at i:28220 original size:47 final size:49
Alignment explanation
Indices: 28096--28226 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 49
28086 ATATAAATTT
* *
28096 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* ** *
28142 CTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATTTTTTTTTCAATATA
1 CTTACCATTT--AATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* *
28193 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
28227 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
46 6 0.08
47 26 0.37
49 20 0.28
50 2 0.03
51 17 0.24
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
Found at i:36931 original size:29 final size:29
Alignment explanation
Indices: 36889--36992 Score: 199
Period size: 29 Copynumber: 3.6 Consensus size: 29
36879 AATTCGACAG
36889 TGGCATCCGAGCGACCTTGGAGGTCGCCA
1 TGGCATCCGAGCGACCTTGGAGGTCGCCA
36918 TGGCATCCGAGCGACCTTGGAGGTCGCCA
1 TGGCATCCGAGCGACCTTGGAGGTCGCCA
*
36947 TGGCATCCGGGCGACCTTGGAGGTCGCCA
1 TGGCATCCGAGCGACCTTGGAGGTCGCCA
36976 TGGCATCCGAGCGACCT
1 TGGCATCCGAGCGACCT
36993 GTGTGGTGTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.17
Consensus pattern (29 bp):
TGGCATCCGAGCGACCTTGGAGGTCGCCA
Found at i:37657 original size:21 final size:21
Alignment explanation
Indices: 37632--37675 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
37622 AATTTAGTTA
37632 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
37653 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
37674 AT
1 AT
37676 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:37685 original size:28 final size:30
Alignment explanation
Indices: 37652--37714 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
37642 TAGTATAAAT
*
37652 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
37680 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
37710 TATTA
1 TATTA
37715 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:38264 original size:20 final size:21
Alignment explanation
Indices: 38220--38264 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
38210 AAATATTGTG
**
38220 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
38241 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
38261 TTTA
1 TTTA
38265 CATTGTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:38470 original size:20 final size:20
Alignment explanation
Indices: 38434--38477 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
38424 AATCATTATT
* *
38434 ATTAGTATAATTACTAAATG
1 ATTAGTATAAATACTAAATC
38454 ATTAGTATCAAAT-CTAAATC
1 ATTAGTAT-AAATACTAAATC
38474 ATTA
1 ATTA
38478 AATATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (20 bp):
ATTAGTATAAATACTAAATC
Found at i:38553 original size:26 final size:25
Alignment explanation
Indices: 38524--38582 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
38514 AAATCATATT
*
38524 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
38550 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
38576 ATTATTA
1 ATTATTA
38583 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:41464 original size:35 final size:35
Alignment explanation
Indices: 41425--41591 Score: 113
Period size: 35 Copynumber: 4.4 Consensus size: 35
41415 TATAAAAATT
*
41425 ATTTAATAATGATTTAAATATTTAATGATTTGATG
1 ATTTAATAATGATTTAAATATTTAATGATTTAATG
* * *
41460 ATTTAGTAATGATTTGATAATAATCATTATATTTGATAATAATC
1 ATTTAATAATGATTT-A-AAT-AT--TTA-A--TGAT-TTAATG
* * *
41504 ATTATAATAATGATTT-AGTA-ATAATCATTATAAAAATG
1 ATT-TAATAATGATTTAAATATTTAATGATT-T---AATG
*
41542 ATTTAATAATGATTTAAATATTTAATGATTTGATG
1 ATTTAATAATGATTTAAATATTTAATGATTTAATG
*
41577 ATTTAGTAATGATTT
1 ATTTAATAATGATTT
41592 GATAATAATC
Statistics
Matches: 101, Mismatches: 15, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
35 35 0.35
36 1 0.01
37 16 0.16
38 14 0.14
39 7 0.07
40 3 0.03
41 2 0.02
42 2 0.02
43 4 0.04
44 6 0.06
45 11 0.11
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (35 bp):
ATTTAATAATGATTTAAATATTTAATGATTTAATG
Found at i:41493 original size:19 final size:19
Alignment explanation
Indices: 41471--41509 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
41461 TTTAGTAATG
41471 ATTTGATAATAATCATTAT
1 ATTTGATAATAATCATTAT
41490 ATTTGATAATAATCATTAT
1 ATTTGATAATAATCATTAT
41509 A
1 A
41510 ATAATGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTTGATAATAATCATTAT
Found at i:41572 original size:98 final size:98
Alignment explanation
Indices: 41466--41649 Score: 266
Period size: 98 Copynumber: 1.9 Consensus size: 98
41456 GATGATTTAG
*
41466 TAATGATTTGATAATAATCA-TTAT-ATTTGATAATAATCATTATAATAATGATTT-AGTAATAA
1 TAATGATTTGATAAT--TCAGTAATGATTTGATAATAATCATTATAATAATGATTTGA-TAATAA
41528 TCATTATAAAAATGATTTAATAATGATTTAAATATT
63 TCATTATAAAAATGATTTAATAATGATTTAAATATT
* * *
41564 TAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCA
1 TAATGATTTGATAATTCAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCA
* *
41629 TTATAATAATGATTTAGTAAT
66 TTATAAAAATGATTTAATAAT
41650 AATCATTATA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
96 2 0.03
97 3 0.04
98 71 0.92
99 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (98 bp):
TAATGATTTGATAATTCAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCA
TTATAAAAATGATTTAATAATGATTTAAATATT
Found at i:41679 original size:124 final size:124
Alignment explanation
Indices: 41408--42042 Score: 1110
Period size: 124 Copynumber: 5.2 Consensus size: 124
41398 ATGTATTTAT
*
41408 TAATCATTATAAAAATTATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
41473 TTGATAATAATC---AT--T-AT-ATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
41525 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
41590 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
41649 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
41714 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
41773 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTAATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
41838 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
41897 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
41962 TTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
42020 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
42043 CTAATGATTT
Statistics
Matches: 500, Mismatches: 11, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
117 76 0.15
120 2 0.00
121 18 0.04
122 1 0.00
123 19 0.04
124 384 0.77
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:41752 original size:150 final size:146
Alignment explanation
Indices: 41580--41923 Score: 421
Period size: 150 Copynumber: 2.3 Consensus size: 146
41570 TTTGATGATT
* *
41580 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGATTTA
* * * *
41645 GTAATAATCATTATAA-A-AATGATTTAATAATGATTTA-AAT-ATTTAATGATTTGATGATT-T
65 ATAATAAT--TTA-AATATAATGA-TT--TAATGATTTAGAATGATTTAAT-A-ATAATCATTAT
41705 AGTAATGATTTGATAATAATCATTA
122 AGTAATGATTTGATAATAATCATTA
41730 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTA
* *
41795 ATAATGATTTAAATATTTAATGATTTAATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
65 ATAATAATTTAAATA--TAATGATTTAATGATTTAG-AATGATTTAATAATAATCATTATAGTAA
41860 TGATTTGATAATAATCATTA
127 TGATTTGATAATAATCATTA
* *
41880 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAAT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTT-ATAAT
41924 GATTTAAATA
Statistics
Matches: 173, Mismatches: 10, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
147 2 0.01
148 14 0.08
149 8 0.05
150 137 0.79
151 12 0.07
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (146 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAA
TAATAATTTAAATATAATGATTTAATGATTTAGAATGATTTAATAATAATCATTATAGTAATGAT
TTGATAATAATCATTA
Found at i:41820 original size:8 final size:8
Alignment explanation
Indices: 41796--41829 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
41786 AATGATTTAA
41796 TAATGATT
1 TAATGATT
41804 TAAAT-ATT
1 T-AATGATT
41812 TAATGATT
1 TAATGATT
41820 TAATGATT
1 TAATGATT
41828 TA
1 TA
41830 GTAATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 3 0.12
8 18 0.75
9 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (8 bp):
TAATGATT
Found at i:41984 original size:26 final size:26
Alignment explanation
Indices: 41490--42056 Score: 399
Period size: 26 Copynumber: 22.9 Consensus size: 26
41480 TAATCATTAT
41490 ATTTGATAATAATCATTATAATAATG
1 ATTTGATAATAATCATTATAATAATG
*
41516 ATTT-AGTAATAATCATTATAAAAATG
1 ATTTGA-TAATAATCATTATAATAATG
* * * *
41542 ATTTAATAATGAT--TTA-AATATTT
1 ATTTGATAATAATCATTATAATAATG
* * * * *
41565 A-ATGAT-TTGATGATT-TAGTAATG
1 ATTTGATAATAATCATTATAATAATG
*
41588 ATTTGATAATAATCATTATAGTAATG
1 ATTTGATAATAATCATTATAATAATG
41614 ATTTGATAATAATCATTATAATAATG
1 ATTTGATAATAATCATTATAATAATG
*
41640 ATTT-AGTAATAATCATTATAAAAATG
1 ATTTGA-TAATAATCATTATAATAATG
* * * *
41666 ATTTAATAATGAT--TTA-AATATTT
1 ATTTGATAATAATCATTATAATAATG
* * * * *
41689 A-ATGAT-TTGATGATT-TAGTAATG
1 ATTTGATAATAATCATTATAATAATG
*
41712 ATTTGATAATAATCATTATAGTAATG
1 ATTTGATAATAATCATTATAATAATG
41738 ATTTGATAATAATCATTATAATAATG
1 ATTTGATAATAATCATTATAATAATG
*
41764 ATTT-AGTAATAATCATTATAAAAATG
1 ATTTGA-TAATAATCATTATAATAATG
* * * *
41790 ATTTAATAATGAT--TTA-AATATTT
1 ATTTGATAATAATCATTATAATAATG
* * * *
41813 A-ATGAT-TTAATGATT-TAGTAATG
1 ATTTGATAATAATCATTATAATAATG
*
41836 ATTTGATAATAATCATTATAGTAATG
1 ATTTGATAATAATCATTATAATAATG
41862 ATTTGATAATAATCATTATAATAATG
1 ATTTGATAATAATCATTATAATAATG
*
41888 ATTT-AGTAATAATCATTATAAAAATG
1 ATTTGA-TAATAATCATTATAATAATG
* * * *
41914 ATTTAATAATGAT--TTA-AATATTT
1 ATTTGATAATAATCATTATAATAATG
* * * * *
41937 A-ATGAT-TTGATGATT-TAGTAATG
1 ATTTGATAATAATCATTATAATAATG
41960 ATTTGATAATAATCATTATAATAATG
1 ATTTGATAATAATCATTATAATAATG
* * * * *
41986 ATTTTATAATAATTATT-TAGTTATT
1 ATTTGATAATAATCATTATAATAATG
*
42011 ATTT-AGTAATTAT--TTATAATAATG
1 ATTTGA-TAATAATCATTATAATAATG
* * *
42035 ATTTAATACTAATGATT-TAATA
1 ATTTGATAATAATCATTATAATA
42057 TTATTACTAA
Statistics
Matches: 429, Mismatches: 75, Indels: 75
0.74 0.13 0.13
Matches are distributed among these distances:
21 15 0.03
22 12 0.03
23 50 0.12
24 43 0.10
25 50 0.12
26 255 0.59
27 4 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
ATTTGATAATAATCATTATAATAATG
Found at i:42049 original size:14 final size:14
Alignment explanation
Indices: 41490--42056 Score: 185
Period size: 12 Copynumber: 41.6 Consensus size: 14
41480 TAATCATTAT
* *
41490 ATTTGATAATAATC
1 ATTTAATAATAATG
41504 A-TT-ATAATAATG
1 ATTTAATAATAATG
* *
41516 ATTTAGTAATAATC
1 ATTTAATAATAATG
*
41530 A-TT-ATAAAAATG
1 ATTTAATAATAATG
41542 A-TT--TAATAATG
1 ATTTAATAATAATG
*
41553 ATTTAAATATTTAATG
1 ATTT-AATA-ATAATG
*
41569 ATTTGATGATTTAGTAATG
1 ATTT-A--A--TAATAATG
* *
41588 ATTTGATAATAATC
1 ATTTAATAATAATG
*
41602 A-TT-ATAGTAATG
1 ATTTAATAATAATG
* *
41614 ATTTGATAATAATC
1 ATTTAATAATAATG
41628 A-TT-ATAATAATG
1 ATTTAATAATAATG
* *
41640 ATTTAGTAATAATC
1 ATTTAATAATAATG
*
41654 A-TT-ATAAAAATG
1 ATTTAATAATAATG
41666 A-TT--TAATAATG
1 ATTTAATAATAATG
*
41677 ATTTAAATATTTAATG
1 ATTT-AATA-ATAATG
*
41693 ATTTGATGATTTAGTAATG
1 ATTT-A--A--TAATAATG
* *
41712 ATTTGATAATAATC
1 ATTTAATAATAATG
*
41726 A-TT-ATAGTAATG
1 ATTTAATAATAATG
* *
41738 ATTTGATAATAATC
1 ATTTAATAATAATG
41752 A-TT-ATAATAATG
1 ATTTAATAATAATG
* *
41764 ATTTAGTAATAATC
1 ATTTAATAATAATG
*
41778 A-TT-ATAAAAATG
1 ATTTAATAATAATG
41790 A-TT--TAATAATG
1 ATTTAATAATAATG
*
41801 ATTTAAATATTTAATG
1 ATTT-AATA-ATAATG
41817 ATTTAATGATTTAGTAATG
1 ATTTAAT-A---A-TAATG
* *
41836 ATTTGATAATAATC
1 ATTTAATAATAATG
*
41850 A-TT-ATAGTAATG
1 ATTTAATAATAATG
* *
41862 ATTTGATAATAATC
1 ATTTAATAATAATG
41876 A-TT-ATAATAATG
1 ATTTAATAATAATG
* *
41888 ATTTAGTAATAATC
1 ATTTAATAATAATG
*
41902 A-TT-ATAAAAATG
1 ATTTAATAATAATG
41914 A-TT--TAATAATG
1 ATTTAATAATAATG
*
41925 ATTTAAATATTTAATG
1 ATTT-AATA-ATAATG
*
41941 ATTTGATGATTTAGTAATG
1 ATTT-A--A--TAATAATG
* *
41960 ATTTGATAATAATC
1 ATTTAATAATAATG
41974 A-TT-ATAATAATG
1 ATTTAATAATAATG
* *
41986 ATTTTATAATAATT
1 ATTTAATAATAATG
* *
42000 ATTTAGT--T-ATT
1 ATTTAATAATAATG
*
42011 ATTTAGTAAT--T-
1 ATTTAATAATAATG
42022 ATTT-ATAATAATG
1 ATTTAATAATAATG
*
42035 ATTTAATACTAATG
1 ATTTAATAATAATG
42049 ATTTAATA
1 ATTTAATA
42057 TTATTACTAA
Statistics
Matches: 427, Mismatches: 68, Indels: 116
0.70 0.11 0.19
Matches are distributed among these distances:
10 4 0.01
11 46 0.11
12 116 0.27
13 45 0.11
14 112 0.26
15 12 0.03
16 43 0.10
18 5 0.01
19 38 0.09
20 6 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (14 bp):
ATTTAATAATAATG
Found at i:42290 original size:17 final size:17
Alignment explanation
Indices: 42265--42297 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42255 ACTAAATATT
*
42265 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
42282 TAATGATTTGATACTA
1 TAATGATTTGATACTA
42298 AAAATCATTG
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:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:42290 original size:25 final size:23
Alignment explanation
Indices: 42211--42290 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
42201 GATTTATTGT
42211 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
42232 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
42259 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
42281 GTAATGATTT
1 -TAAT-ATTT
42291 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:44458 original size:15 final size:14
Alignment explanation
Indices: 44435--44465 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
44425 TACAACACTA
44435 AACTTTAATATAAT
1 AACTTTAATATAAT
44449 AACTTATAATATAAT
1 AACTT-TAATATAAT
44464 AA
1 AA
44466 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:44473 original size:16 final size:16
Alignment explanation
Indices: 44440--44486 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
44430 CACTAAACTT
*
44440 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
44455 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
44471 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
44487 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:44607 original size:32 final size:34
Alignment explanation
Indices: 44527--44608 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
44517 CTAAACCCTT
*
44527 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
44560 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
44593 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
44609 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:44725 original size:45 final size:45
Alignment explanation
Indices: 44648--44780 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
44638 TCAACAAACA
*
44648 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
44696 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
44740 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
44781 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:44808 original size:41 final size:40
Alignment explanation
Indices: 44720--44808 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
44710 TTAACAAAAC
* *
44720 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
44761 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
44802 AAACTAA
1 AAACTAA
44809 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:45347 original size:29 final size:29
Alignment explanation
Indices: 45314--45417 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
45304 TCGTGAGCTA
**
45314 GGACTACATGGCGACCTACTTGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
*
45343 GGACTACATGGCAACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
*
45372 GGACTACATGGCGACCTACAAGGTCGCCC
1 GGACTACATGGCGACCTACAAGGTCGCCG
* *
45401 AGACTGCATGGCGACCT
1 GGACTACATGGCGACCT
45418 CTCCATTGGC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.23, C:0.32, G:0.29, T:0.16
Consensus pattern (29 bp):
GGACTACATGGCGACCTACAAGGTCGCCG
Found at i:45438 original size:9 final size:9
Alignment explanation
Indices: 45424--45462 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
45414 ACCTCTCCAT
45424 TGGCTCGTA
1 TGGCTCGTA
45433 TGGCTCGTATA
1 TGGCTCG--TA
*
45444 TGGCTTGTA
1 TGGCTCGTA
45453 TGGCTCGTA
1 TGGCTCGTA
45462 T
1 T
45463 TCGTATGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:45453 original size:20 final size:20
Alignment explanation
Indices: 45424--45462 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
45414 ACCTCTCCAT
45424 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
*
45444 TGGCTTGTATGGCTCGTAT
1 TGGCTCGTATGGCTCGTAT
45463 TCGTATGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:47149 original size:22 final size:22
Alignment explanation
Indices: 47124--47175 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
47114 AAAGCGATAA
47124 AATTATATGGTAAACAATGTGT
1 AATTATATGGTAAACAATGTGT
*
47146 AATTATATGGTACACAATGTGT
1 AATTATATGGTAAACAATGTGT
47168 AATTATAT
1 AATTATAT
47176 TTTAGTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (22 bp):
AATTATATGGTAAACAATGTGT
Found at i:51463 original size:19 final size:18
Alignment explanation
Indices: 51435--51475 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
51425 TATTATAGAA
51435 ATAAGAATTATTGTTAAG
1 ATAAGAATTATTGTTAAG
*
51453 ATAATGAATTATTGTTAGG
1 ATAA-GAATTATTGTTAAG
51472 ATAA
1 ATAA
51476 ATCTCAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (18 bp):
ATAAGAATTATTGTTAAG
Found at i:58771 original size:20 final size:20
Alignment explanation
Indices: 58746--58793 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
58736 ATGGTGATTT
58746 TTAAACTTATTGTTTAGAGC
1 TTAAACTTATTGTTTAGAGC
58766 TTAAACTTATTGTTTAGAGC
1 TTAAACTTATTGTTTAGAGC
58786 TTAAACTT
1 TTAAACTT
58794 CTAGGCGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.46
Consensus pattern (20 bp):
TTAAACTTATTGTTTAGAGC
Found at i:66963 original size:30 final size:30
Alignment explanation
Indices: 66929--67005 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
66919 TTTATCCTTA
66929 AACTTTCAAAACTTTATACTTTGGCCACTC
1 AACTTTCAAAACTTTATACTTTGGCCACTC
66959 AACTTTCAAAACTTTATACTTTGGCCACTC
1 AACTTTCAAAACTTTATACTTTGGCCACTC
66989 AACTTTCAAAA-TTTATA
1 AACTTTCAAAACTTTATA
67006 TTTTAGTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 6 0.13
30 41 0.87
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTCAAAACTTTATACTTTGGCCACTC
Found at i:67393 original size:23 final size:22
Alignment explanation
Indices: 67367--67415 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
67357 CTCTTAAATC
*
67367 TTCTTC-TTAATCTTATTTTAATT
1 TTCTTCTTTAATCTT-CTTT-ATT
67390 TTC-TCTTTAATCTTCTTTATT
1 TTCTTCTTTAATCTTCTTTATT
67411 TTCTT
1 TTCTT
67416 GTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 6 0.26
22 6 0.26
23 11 0.48
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCTTCTTTAATCTTCTTTATT
Found at i:73676 original size:27 final size:27
Alignment explanation
Indices: 73645--73697 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
73635 CACTCAAGAA
73645 TCGTCGTCTTTCATATCATCTTCATCT
1 TCGTCGTCTTTCATATCATCTTCATCT
73672 TCGTCGTCTTTCATATCATCTTCATC
1 TCGTCGTCTTTCATATCATCTTCATC
73698 GCTAGTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.08, T:0.47
Consensus pattern (27 bp):
TCGTCGTCTTTCATATCATCTTCATCT
Found at i:77958 original size:21 final size:22
Alignment explanation
Indices: 77906--77958 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
77896 CCATATTCAA
77906 TTTA-TTTCTATTCAATCTTCT
1 TTTATTTTCTATTCAATCTTCT
* *
77927 TTTACTTTTCTCTTTAATCTTC-
1 TTTA-TTTTCTATTCAATCTTCT
77949 TTTATTTTCT
1 TTTATTTTCT
77959 TGTTTCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.36
22 4 0.14
23 14 0.50
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATTTTCTATTCAATCTTCT
Found at i:87368 original size:13 final size:13
Alignment explanation
Indices: 87350--87385 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
87340 ATATTTATTT
87350 ATTTTCATTTCTA
1 ATTTTCATTTCTA
87363 ATTTTCATTTCTA
1 ATTTTCATTTCTA
87376 ATTTTC-TTTC
1 ATTTTCATTTC
87386 GTTTTCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTCATTTCTA
Found at i:88852 original size:34 final size:34
Alignment explanation
Indices: 88809--88885 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
88799 TAAGTGTGAA
* * *
88809 TATGTGTGGAAGAGTGGAGTTATTTCGTTTTCCT
1 TATGTGTGGAAGAGTGGAGTTATCTCGCTTCCCT
*
88843 TATGTGTGGACGAGTGGAGTTATCTCGCTTCCCT
1 TATGTGTGGAAGAGTGGAGTTATCTCGCTTCCCT
88877 TATGTGTGG
1 TATGTGTGG
88886 TTGATCGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.16, C:0.13, G:0.31, T:0.40
Consensus pattern (34 bp):
TATGTGTGGAAGAGTGGAGTTATCTCGCTTCCCT
Found at i:90215 original size:22 final size:21
Alignment explanation
Indices: 90182--90246 Score: 103
Period size: 21 Copynumber: 3.0 Consensus size: 21
90172 GCATTTTTTG
*
90182 TGAAAAAAGATCGATCCCTTT
1 TGAAAAAAGATCCATCCCTTT
90203 TGAAAAAAGGATCCATCCCTTT
1 TGAAAAAA-GATCCATCCCTTT
*
90225 TGAAAAATGATCCATCCCTTT
1 TGAAAAAAGATCCATCCCTTT
90246 T
1 T
90247 AAGTGTTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 22 0.54
22 19 0.46
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (21 bp):
TGAAAAAAGATCCATCCCTTT
Found at i:106683 original size:20 final size:20
Alignment explanation
Indices: 106645--106683 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
106635 GATGGAATTG
*
106645 AATGTTAGAATGTTGATTTT
1 AATGTTAGAATGTTAATTTT
106665 AATGTTAGAA-GTTTAATTT
1 AATGTTAGAATG-TTAATTT
106684 GGATCGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (20 bp):
AATGTTAGAATGTTAATTTT
Found at i:114622 original size:42 final size:41
Alignment explanation
Indices: 114549--114697 Score: 145
Period size: 42 Copynumber: 3.5 Consensus size: 41
114539 AGAACAGAAG
* * *
114549 GAAGCATAGCACTATCGATTCTCGTCTAAAGTATAACGAAAG
1 GAAGCATA-CACTTTCAATTCTCGTCTAAAGTATAACGAAAT
* * * * *
114591 GAGGCATCACACTTTCAATTTTCGTTTAAAGTAGAACGGAAT
1 GAAGCAT-ACACTTTCAATTCTCGTCTAAAGTATAACGAAAT
* ** *
114633 CAAGCATATCACTTTTGATTCTCGTCTAAAGTATAATGAAAT
1 GAAGCATA-CACTTTCAATTCTCGTCTAAAGTATAACGAAAT
*
114675 GAAGCATAACACTTTCGATTCTC
1 GAAGCAT-ACACTTTCAATTCTC
114698 AATGAATCAT
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
41 1 0.01
42 82 0.96
43 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (41 bp):
GAAGCATACACTTTCAATTCTCGTCTAAAGTATAACGAAAT
Found at i:117343 original size:5 final size:5
Alignment explanation
Indices: 117333--117373 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
117323 CATACTACCC
* *
117333 GTTCG GTTCG GTTCG GTTCG GTTCG GTTTG GATCG GTTCG G
1 GTTCG GTTCG GTTCG GTTCG GTTCG GTTCG GTTCG GTTCG G
117374 ATTTCCAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.02, C:0.17, G:0.41, T:0.39
Consensus pattern (5 bp):
GTTCG
Found at i:118561 original size:50 final size:50
Alignment explanation
Indices: 118458--118554 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
118448 CCTTGCACAT
*
118458 GATGACTTTGGCACCAAGATGAACAAGCACATCACCATTCGACCAAGGTA
1 GATGACTTTGGCACCAAAATGAACAAGCACATCACCATTCGACCAAGGTA
* * *
118508 GATGACTTTGGCACCAAAATGAATAAGCATATCACCATTCGTCCAAG
1 GATGACTTTGGCACCAAAATGAACAAGCACATCACCATTCGACCAAG
118555 AGAGATGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (50 bp):
GATGACTTTGGCACCAAAATGAACAAGCACATCACCATTCGACCAAGGTA
Found at i:121965 original size:16 final size:16
Alignment explanation
Indices: 121927--121958 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
121917 TCAAAGCAAT
121927 ATGTCTTCAATGGAAA
1 ATGTCTTCAATGGAAA
121943 ATGTCTTCAATGGAAA
1 ATGTCTTCAATGGAAA
121959 TGATCTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTCTTCAATGGAAA
Found at i:123104 original size:50 final size:50
Alignment explanation
Indices: 123045--123148 Score: 163
Period size: 50 Copynumber: 2.1 Consensus size: 50
123035 CCTTGTACAC
*
123045 GATGACTTTGGCACCAAGATGAACAAGAACATCACCATTCGACCAAGGGA
1 GATGACTTTGGCACCAAGATGAACAAGAACATCACCATTCGACCAAGAGA
* * * *
123095 GATGACTTTGGCGCCAAGATGAACAAGCATATCACCATTCGGCCAAGAGA
1 GATGACTTTGGCACCAAGATGAACAAGAACATCACCATTCGACCAAGAGA
123145 GATG
1 GATG
123149 TATCTTCATC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (50 bp):
GATGACTTTGGCACCAAGATGAACAAGAACATCACCATTCGACCAAGAGA
Found at i:123621 original size:23 final size:23
Alignment explanation
Indices: 123590--123653 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
123580 GAGATACACT
*
123590 TTCATCACCATCAACCATTCAAC
1 TTCAACACCATCAACCATTCAAC
123613 TTCAACACCATCAACCATTCAAC
1 TTCAACACCATCAACCATTCAAC
* *
123636 TTTAATACCATCAACCAT
1 TTCAACACCATCAACCAT
123654 CTGCCATAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.27
Consensus pattern (23 bp):
TTCAACACCATCAACCATTCAAC
Found at i:126933 original size:2 final size:2
Alignment explanation
Indices: 126926--126983 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
126916 TAGCTATATT
126926 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
126968 CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA
126984 TATATATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:129463 original size:64 final size:64
Alignment explanation
Indices: 129395--129517 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
129385 AATTGTTCAA
* * * * *
129395 AGTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGACATC
1 AGTGTATCGATCCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATC
* * * * *
129459 AGTGTATCTATCCATAAGTAGTGCATCGATGTACCCCCTTAAAATACAAACATCGAATG
1 AGTGTATCGATCCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATG
129518 GGATTTATGT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (64 bp):
AGTGTATCGATCCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATC
Found at i:130258 original size:23 final size:23
Alignment explanation
Indices: 130201--130260 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
130191 AATCTTATAT
* *
130201 GGCACTACGGTACAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
130224 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
130247 GGCACTTTGGTGCA
1 GGCACTTCGGTGCA
130261 TTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:130268 original size:23 final size:23
Alignment explanation
Indices: 130201--130268 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
130191 AATCTTATAT
* * *
130201 GGCACTACGGTACAATTCTACGC
1 GGCACTTCGGTGCAATTATACGC
* *
130224 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTATACGC
* *
130247 GGCACTTTGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
130269 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:139414 original size:64 final size:64
Alignment explanation
Indices: 139273--139395 Score: 192
Period size: 64 Copynumber: 1.9 Consensus size: 64
139263 AAATTGTTCA
* * * *
139273 AGTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATC
1 AGTGTATCGATGCACAAGTAGTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATC
* *
139337 AGTGTATCGATGCACAAGTAGTGTATCAATGCACCCCCTTAAAATACAAACATCGAATG
1 AGTGTATCGATGCACAAGTAGTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATG
139396 GGATTTATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (64 bp):
AGTGTATCGATGCACAAGTAGTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATC
Found at i:139423 original size:64 final size:64
Alignment explanation
Indices: 139273--139436 Score: 190
Period size: 64 Copynumber: 2.6 Consensus size: 64
139263 AAATTGTTCA
* *
139273 AGTGTATCGATGCACATGA-AGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATC
1 AGTGTATCGATGCACA-GATAGTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATC
* * **
139337 AGTGTATCGATGCACA-AGTAGTGTATCAATGCACCCCCTTAAAATACAAACATCGAATGGGATT
1 AGTGTATCGATGCACAGA-TAGTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCA-T
*
139401 T
64 C
* * *
139402 A-TGTACCGATGCATAGATAGTGCATCGATGCACCC
1 AGTGTATCGATGCACAGATAGTGTATCGATGCACCC
139437 GTCAAGGGAT
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
62 1 0.01
64 81 0.95
65 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (64 bp):
AGTGTATCGATGCACAGATAGTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATC
Found at i:140114 original size:23 final size:23
Alignment explanation
Indices: 140078--140131 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
140068 AATCTTATAT
* *
140078 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGATGCAATTCTACGC
*
140101 GGCACTTCGATGCAATTCTACGT
1 GGCACTTCGATGCAATTCTACGC
140124 GGCACTTC
1 GGCACTTC
140132 AGTGCATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (23 bp):
GGCACTTCGATGCAATTCTACGC
Found at i:140145 original size:23 final size:22
Alignment explanation
Indices: 140077--140137 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 22
140067 TAATCTTATA
*
140077 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTC-GTGCAATTCTACG
*
140100 CGGCACTTCGATGCAATTCTACG
1 TGGCACTTCG-TGCAATTCTACG
140123 TGGCACTTCAGTGCA
1 TGGCACTTC-GTGCA
140138 TTTATACGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (22 bp):
TGGCACTTCGTGCAATTCTACG
Found at i:149137 original size:20 final size:20
Alignment explanation
Indices: 149114--149180 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
149104 GTTTTTTTTT
149114 AAAAAAATAGATTTTTATTA
1 AAAAAAATAGATTTTTATTA
*
149134 AAAAAATTAGATTTTTATTA
1 AAAAAAATAGATTTTTATTA
149154 AAAAAAATAGATTTTTATTA
1 AAAAAAATAGATTTTTATTA
149174 AAAAAAA
1 AAAAAAA
149181 ATAAGGTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AAAAAAATAGATTTTTATTA
Found at i:150363 original size:31 final size:31
Alignment explanation
Indices: 150328--150403 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
150318 GTTTTAAAAG
* **
150328 TAACAAACTAGTCGTTAACGTTATCGATTTA
1 TAACAAAATAGTCACTAACGTTATCGATTTA
* * *
150359 TAACAAAATGGTCACTAATGTTATCGATTTG
1 TAACAAAATAGTCACTAACGTTATCGATTTA
*
150390 TAACAAAATGGTCA
1 TAACAAAATAGTCA
150404 TTCCATCGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (31 bp):
TAACAAAATAGTCACTAACGTTATCGATTTA
Found at i:151500 original size:21 final size:22
Alignment explanation
Indices: 151475--151530 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
151465 TTCAATTTTC
*
151475 AAATTTATTTTTATACATATT-
1 AAATTTATTTTTATAAATATTA
*
151496 AAATTTAATTTTA-AAATATTA
1 AAATTTATTTTTATAAATATTA
*
151517 AAATTTATTATTAT
1 AAATTTATTTTTAT
151531 TGTAAACCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATTTATTTTTATAAATATTA
Found at i:155256 original size:31 final size:31
Alignment explanation
Indices: 155219--155281 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
155209 ATTTATCTAG
155219 TTAATTTTTTTAAACACTCCACCACCACAAT
1 TTAATTTTTTTAAACACTCCACCACCACAAT
155250 TTAATTTTTTTAAACACTCCACCACCACAAT
1 TTAATTTTTTTAAACACTCCACCACCACAAT
155281 T
1 T
155282 ATATTCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (31 bp):
TTAATTTTTTTAAACACTCCACCACCACAAT
Found at i:162456 original size:17 final size:17
Alignment explanation
Indices: 162421--162466 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
162411 TATAAAATGT
*
162421 TTAAATTTAAAATTATA
1 TTAAAATTAAAATTATA
162438 TTAAAATTATAAATT-TA
1 TTAAAATTA-AAATTATA
*
162455 TTAATATTAAAA
1 TTAAAATTAAAA
162467 ATATTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 18 0.69
18 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAAATTAAAATTATA
Found at i:162468 original size:17 final size:17
Alignment explanation
Indices: 162429--162489 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
162419 GTTTAAATTT
*
162429 AAAATTATATTAAAATTA
1 AAAATT-TATTAATATTA
*
162447 TAAATTTATTAATATTA
1 AAAATTTATTAATATTA
*
162464 AAAATAT-TTAAGTAGTTA
1 AAAATTTATTAA-TA-TTA
162482 AAAATTTA
1 AAAATTTA
162490 CAAAATTTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.11
17 17 0.49
18 14 0.40
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAAATTTATTAATATTA
Found at i:163290 original size:42 final size:42
Alignment explanation
Indices: 163225--163332 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 42
163215 TGTGATTGAC
**
163225 CGATCTCACATGGC-ATCAAGCATGAATTAAAAAGGAGAATAT
1 CGATCTCACATAACAATCAAGCATGAATTAAAAAGGAGAA-AT
*
163267 -GATCTCACATAACAATCAAGCATGAATTATAAAGGAGAAAT
1 CGATCTCACATAACAATCAAGCATGAATTAAAAAGGAGAAAT
*
163308 CGATCTCAC--AACAATCAAACATGAA
1 CGATCTCACATAACAATCAAGCATGAA
163333 GGAGAACTCG
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
40 15 0.25
41 13 0.22
42 32 0.53
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (42 bp):
CGATCTCACATAACAATCAAGCATGAATTAAAAAGGAGAAAT
Found at i:165801 original size:131 final size:131
Alignment explanation
Indices: 165448--165805 Score: 448
Period size: 131 Copynumber: 2.7 Consensus size: 131
165438 CGATATTGAG
* * * * *
165448 AATAGTAATATCTTTTCATTTTGGTTGGAGCAATAAATGTTTGTTTTAAGGCATGAAAGGTCATT
1 AATAGTAATATCTCTTCATTTCGATTGGAGCAATAAATGATTGTTTTAAGGTATGAAAGGTCATT
* * * * * * * *
165513 TGTTCTCAATTGGAAATAATTCA-ATACTACCGTTTTCTCTCGAATCAATATTGATTTTTAAGAC
66 TATTCTCGATTAGAAATAA-TCAGATATTATCGTTTTCACTAGAATCAATATTGAATTTTAAGAC
165577 AA
130 AA
* * * * *
165579 AATAGTGATATCTCTTCATTTCGATTGGAGGAATAAATGACTGCTTTAAGGTATGAGAGGTCATT
1 AATAGTAATATCTCTTCATTTCGATTGGAGCAATAAATGATTGTTTTAAGGTATGAAAGGTCATT
* * * * ** *
165644 CATTATCGATTAGAAATCATTAGATATTATCGTTTTCACTAGAATTGATATTGAATTTTAAGACG
66 TATTCTCGATTAGAAATAATCAGATATTATCGTTTTCACTAGAATCAATATTGAATTTTAAGACA
165709 A
131 A
* *
165710 AATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGTATGAAAAGTCATT
1 AATAGTAATATCTCTTCATTTCGATTGGAGCAATAAATGATTGTTTTAAGGTATGAAAGGTCATT
*
165775 TATTCTCGATTTGAAATAATCAGATATTATC
66 TATTCTCGATTAGAAATAATCAGATATTATC
165806 ATTCTCTCTT
Statistics
Matches: 190, Mismatches: 36, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
130 2 0.01
131 188 0.99
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (131 bp):
AATAGTAATATCTCTTCATTTCGATTGGAGCAATAAATGATTGTTTTAAGGTATGAAAGGTCATT
TATTCTCGATTAGAAATAATCAGATATTATCGTTTTCACTAGAATCAATATTGAATTTTAAGACA
A
Found at i:168054 original size:13 final size:13
Alignment explanation
Indices: 168038--168063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
168028 TCAAGTTTTG
168038 AAATTAGAAATTA
1 AAATTAGAAATTA
168051 AAATTAGAAATTA
1 AAATTAGAAATTA
168064 CTCCCCCTTA
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:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AAATTAGAAATTA
Found at i:170384 original size:23 final size:21
Alignment explanation
Indices: 170358--170416 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
170348 TTCCCCTGTG
170358 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
170381 GGGGGAATCGGTT-CCCTCAG
1 GGGGGAATCGGTTCCCCTCAA
*
170401 GGGGGAATCGATTCCC
1 GGGGGAATCGGTTCCC
170417 TCTGCACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.39
21 4 0.12
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.25, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:170418 original size:20 final size:21
Alignment explanation
Indices: 170334--170416 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
170324 AGCAGAACCC
*
170334 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATTCCCCT
** *
170355 GTGGGGGGAATCGGTTCCCCTT
1 CAGGGGGGAATCGATTCCCC-T
* *
170377 CAAAGGGGGAATCGGTT-CCCT
1 C-AGGGGGGAATCGATTCCCCT
170398 CAGGGGGGAATCGATTCCC
1 CAGGGGGGAATCGATTCCC
170417 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 13 0.26
21 20 0.40
22 4 0.08
23 13 0.26
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.22
Consensus pattern (21 bp):
CAGGGGGGAATCGATTCCCCT
Found at i:182818 original size:14 final size:14
Alignment explanation
Indices: 182799--182859 Score: 104
Period size: 14 Copynumber: 4.4 Consensus size: 14
182789 ATGGTTATGC
182799 AAGATGGTGATGGA
1 AAGATGGTGATGGA
182813 AAGATGGTGATGGA
1 AAGATGGTGATGGA
* *
182827 AAGATGATGATGCA
1 AAGATGGTGATGGA
182841 AAGATGGTGATGGA
1 AAGATGGTGATGGA
182855 AAGAT
1 AAGAT
182860 AGTATCTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.38, T:0.21
Consensus pattern (14 bp):
AAGATGGTGATGGA
Found at i:183211 original size:20 final size:21
Alignment explanation
Indices: 183172--183215 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
183162 ATTCGGCTAG
**
183172 ATACATGTCTTTTTAATGAAA
1 ATACATGTCTTTAAAATGAAA
183193 ATACATGTC-TTAAAATGAAA
1 ATACATGTCTTTAAAATGAAA
183213 ATA
1 ATA
183216 GATGATGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
ATACATGTCTTTAAAATGAAA
Found at i:187319 original size:14 final size:14
Alignment explanation
Indices: 187300--187332 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
187290 ATGGTTATGG
187300 AAGATGGTGATGAA
1 AAGATGGTGATGAA
*
187314 AAGATGGTGATGGA
1 AAGATGGTGATGAA
187328 AAGAT
1 AAGAT
187333 AGTATCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.21
Consensus pattern (14 bp):
AAGATGGTGATGAA
Found at i:187617 original size:20 final size:21
Alignment explanation
Indices: 187578--187621 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
187568 ATTCGGCTAG
**
187578 ATACATGTCTTTCTAATGAAA
1 ATACATGTCTTTAAAATGAAA
187599 ATACATGTC-TTAAAATGAAA
1 ATACATGTCTTTAAAATGAAA
187619 ATA
1 ATA
187622 GATGATACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
ATACATGTCTTTAAAATGAAA
Found at i:197504 original size:21 final size:20
Alignment explanation
Indices: 197474--197516 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
197464 TAAAGCTATG
*
197474 ATATGTTAAAGTCATGTAAT
1 ATATGTTAAAGTCATGAAAT
197494 ATATGCTTAAAGTCATGAAAT
1 ATATG-TTAAAGTCATGAAAT
197515 AT
1 AT
197517 TTAATTATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (20 bp):
ATATGTTAAAGTCATGAAAT
Found at i:201193 original size:16 final size:16
Alignment explanation
Indices: 201163--201205 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
201153 TACCCTTGTT
201163 TTCTT-GTTTTAATTC
1 TTCTTAGTTTTAATTC
*
201178 TTCTTAGTTTTCATTC
1 TTCTTAGTTTTAATTC
*
201194 TTCTTATTTTTA
1 TTCTTAGTTTTA
201206 TTGTCTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (16 bp):
TTCTTAGTTTTAATTC
Found at i:209306 original size:89 final size:89
Alignment explanation
Indices: 209155--209321 Score: 298
Period size: 89 Copynumber: 1.9 Consensus size: 89
209145 CCTAACACAC
*
209155 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
209220 ATTTAATTAATTGGATTTAATAAT
66 ATTTAATCAATTGGATTTAATAAT
* *
209244 CCTTTTATATCCAAGTTACCCTGATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
209309 ATTTAATCAATTG
66 ATTTAATCAATTG
209322 AAATTAAATA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 74 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.46
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATCAATTGGATTTAATAAT
Found at i:213358 original size:41 final size:41
Alignment explanation
Indices: 213301--213413 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 41
213291 TTTCGAGTAG
* *
213301 TATCGATAC-CTATTCAAGTAGTATCGGTACTTCATGAACAA
1 TATCGATACTC-ATTCAAGTAGTATCGATACTGCATGAACAA
* * * *
213342 TATCGATACTCATTCAAGTAGTAACGATACTGGATGGACAG
1 TATCGATACTCATTCAAGTAGTATCGATACTGCATGAACAA
* * *
213383 TATCGATGCTAATTCTAGTAGTATCGATACT
1 TATCGATACTCATTCAAGTAGTATCGATACT
213414 ATGCTAGTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 60 0.98
42 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (41 bp):
TATCGATACTCATTCAAGTAGTATCGATACTGCATGAACAA
Found at i:213422 original size:20 final size:20
Alignment explanation
Indices: 213381--213474 Score: 93
Period size: 20 Copynumber: 4.5 Consensus size: 20
213371 CTGGATGGAC
* *
213381 AGTATCGATGCTAATTCTAGT
1 AGTATCGATACT-ATGCTAGT
213402 AGTATCGATACTATGCTAGT
1 AGTATCGATACTATGCTAGT
* *
213422 AGTTTCGATATCTA-GCAAGAGT
1 AGTATCGATA-CTATGC--TAGT
213444 AGTATCGATACTATG-TAAGT
1 AGTATCGATACTATGCT-AGT
213464 AGTATCGATAC
1 AGTATCGATAC
213475 CAAGTACACA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
20 32 0.52
21 17 0.27
22 13 0.21
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTATGCTAGT
Found at i:213869 original size:15 final size:15
Alignment explanation
Indices: 213840--213879 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
213830 TGCAAAGTAT
* *
213840 ATACATATTCTAGAA
1 ATACATCTTCCAGAA
*
213855 CTACATCTTCCAGAA
1 ATACATCTTCCAGAA
213870 ATACATCTTC
1 ATACATCTTC
213880 TTTTGTGACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (15 bp):
ATACATCTTCCAGAA
Found at i:217229 original size:33 final size:33
Alignment explanation
Indices: 217187--217255 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
217177 GTTGATGAAT
*
217187 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
217220 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
217253 GAA
1 GAA
217256 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:217296 original size:36 final size:36
Alignment explanation
Indices: 217226--217338 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
217216 AATGGAAGGA
* * *
217226 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
217261 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
217297 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
217333 TGATGA
1 TGATGA
217339 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:221637 original size:33 final size:33
Alignment explanation
Indices: 221595--221663 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
221585 GTTGATGAAT
*
221595 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
221628 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
221661 GAA
1 GAA
221664 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:221704 original size:36 final size:36
Alignment explanation
Indices: 221634--221746 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
221624 AATGGAAGGA
* * *
221634 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
221669 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
221705 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
221741 TGATGA
1 TGATGA
221747 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:226591 original size:17 final size:17
Alignment explanation
Indices: 226566--226601 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
226556 TTGCGTCGGC
226566 TATAAAAATGGTTAGGG
1 TATAAAAATGGTTAGGG
* *
226583 TATAGAAATGGTTATGG
1 TATAAAAATGGTTAGGG
226600 TA
1 TA
226602 GAGGTAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (17 bp):
TATAAAAATGGTTAGGG
Found at i:232298 original size:26 final size:26
Alignment explanation
Indices: 232258--232329 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
232248 CATATGGTGT
232258 GCACGACCTTATGTGTATTATAGTGA
1 GCACGACCTTATGTGTATTATAGTGA
* * * *
232284 GCATGACCTTATGTGTATGATGGTGG
1 GCACGACCTTATGTGTATTATAGTGA
* *
232310 GTACAACCTTATGTGTATTA
1 GCACGACCTTATGTGTATTA
232330 GCACTTCGGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (26 bp):
GCACGACCTTATGTGTATTATAGTGA
Found at i:236641 original size:2 final size:2
Alignment explanation
Indices: 236636--236668 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
236626 GAAAAAAATG
*
236636 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
236669 CAAAACAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:244797 original size:77 final size:79
Alignment explanation
Indices: 244714--244866 Score: 195
Period size: 77 Copynumber: 2.0 Consensus size: 79
244704 GAATTAAATA
* **
244714 AAAATCTTATTTAATTAATTCAAATTAGATAT-ACATT-AAAGACTTATAATCTGAATTACAATC
1 AAAATCTTATTTAATTAATTCAAATTAAATATCA-ATTAAAAGACTTATAATCAAAATTACAATC
244777 -TTTAATGTTTATTT
65 ATTTAATGTTTATTT
* ** * * *
244791 AAAATCTTATTTAATTATTTTGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTCA
1 AAAATCTTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCA
244856 TTTAATGTTTA
66 TTTAATGTTTA
244867 CTTTCTATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 31 0.48
78 22 0.34
79 11 0.17
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (79 bp):
AAAATCTTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCA
TTTAATGTTTATTT
Found at i:246612 original size:31 final size:31
Alignment explanation
Indices: 246574--246641 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
246564 ACCTATGGCC
246574 AGCTCACCTCCAGCTCATTCACCTATGAACT
1 AGCTCACCTCCAGCTCATTCACCTATGAACT
246605 AGCTCACCTCCAGCTCATTCACCTATGAACT
1 AGCTCACCTCCAGCTCATTCACCTATGAACT
246636 AGCTCA
1 AGCTCA
246642 ATCTTAAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.38, G:0.10, T:0.25
Consensus pattern (31 bp):
AGCTCACCTCCAGCTCATTCACCTATGAACT
Found at i:247322 original size:16 final size:16
Alignment explanation
Indices: 247277--247330 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
247267 AAATTATTTA
247277 ATTTATTTTTAATAATT
1 ATTTATTTTTAAT-ATT
**
247294 ATTTAAATTTAATATT
1 ATTTATTTTTAATATT
247310 CA-TTATTTTTAATAGTT
1 -ATTTATTTTTAATA-TT
247327 ATTT
1 ATTT
247331 TAAATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTTATTTTTAATATT
Found at i:247353 original size:20 final size:20
Alignment explanation
Indices: 247252--247365 Score: 70
Period size: 22 Copynumber: 5.3 Consensus size: 20
247242 TACATATAAA
247252 TAAATATATTTATCTAAATTATT
1 TAAAT-TATTT-T-TAAATTATT
*
247275 TAATTTATTTTTAATAATTATT
1 TAAATTATTTTT-A-AATTATT
* * *
247297 TAAATTTAATATT-CATTATTTT
1 TAAA-TTATTTTTAAATTA--TT
247319 TAATAGTTA-TTTTAAATTATT
1 TAA-A-TTATTTTTAAATTATT
* *
247340 TAAATTATTTTTAATTTATC
1 TAAATTATTTTTAAATTATT
247360 TAAATT
1 TAAATT
247366 TTCTGTTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
19 3 0.04
20 22 0.30
21 7 0.10
22 23 0.32
23 18 0.25
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.58
Consensus pattern (20 bp):
TAAATTATTTTTAAATTATT
Found at i:247790 original size:21 final size:20
Alignment explanation
Indices: 247744--247793 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
247734 TGCATGTAAT
* * *
247744 TGTTTTTTTTCTTTTAAATT
1 TGTTTTTTTGCTGTTAAATA
*
247764 TATTTTCTTTGCTGTTAAATA
1 TGTTTT-TTTGCTGTTAAATA
247785 TGTTTTTTT
1 TGTTTTTTT
247794 CGATATTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.16, C:0.06, G:0.08, T:0.70
Consensus pattern (20 bp):
TGTTTTTTTGCTGTTAAATA
Found at i:253580 original size:35 final size:36
Alignment explanation
Indices: 253529--253602 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 36
253519 ATAAGATACT
*
253529 ATCTGTCCATCACCATTTCATGCCTATATCATCACC
1 ATCTGTCCATCACCATTTCACGCCTATATCATCACC
253565 ATCT-TCCATCACCATTTCACGCCTATATCATCACC
1 ATCTGTCCATCACCATTTCACGCCTATATCATCACC
253600 ATC
1 ATC
253603 CCTTAACCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 33 0.89
36 4 0.11
ACGTcount: A:0.26, C:0.38, G:0.04, T:0.32
Consensus pattern (36 bp):
ATCTGTCCATCACCATTTCACGCCTATATCATCACC
Found at i:253994 original size:20 final size:20
Alignment explanation
Indices: 253953--253993 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
253943 CAAGTGGTGC
*
253953 AACAAGAAGAAAATGAAAAA
1 AACAAAAAGAAAATGAAAAA
253973 AACAAAAAGAAAA-GAAAAA
1 AACAAAAAGAAAATGAAAAA
253992 AA
1 AA
253994 AAGAATCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.02
Consensus pattern (20 bp):
AACAAAAAGAAAATGAAAAA
Found at i:254041 original size:15 final size:15
Alignment explanation
Indices: 254021--254079 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
254011 TTTGTAGTGC
254021 AAAAGAAAGAAAATA
1 AAAAGAAAGAAAATA
*
254036 AAAAG-AAGAAAAATT
1 AAAAGAAAG-AAAATA
* *
254051 CAAAGAAA-AAAAGA
1 AAAAGAAAGAAAATA
*
254065 AAAAGTGAAGAAAAT
1 AAAAG-AAAGAAAAT
254080 TGCAAAGTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
14 11 0.33
15 16 0.48
16 6 0.18
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (15 bp):
AAAAGAAAGAAAATA
Found at i:254078 original size:31 final size:30
Alignment explanation
Indices: 254022--254086 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 30
254012 TTGTAGTGCA
*
254022 AAAGAAAGAAAATAAAAAGAAGAAAAATT-C
1 AAAGAAAGAAAAGAAAAAGAAG-AAAATTGC
254052 AAAGAAA-AAAAGAAAAAGTGAAGAAAATTGC
1 AAAGAAAGAAAAGAAAAA--GAAGAAAATTGC
254083 AAAG
1 AAAG
254087 TACAAAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 9 0.29
30 13 0.42
31 9 0.29
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.09
Consensus pattern (30 bp):
AAAGAAAGAAAAGAAAAAGAAGAAAATTGC
Found at i:258039 original size:13 final size:12
Alignment explanation
Indices: 258021--258083 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
258011 ATACTATATG
258021 TCCATCACCATCT
1 TCCATCACCAT-T
258034 TCCATCACCATT
1 TCCATCACCATT
* *
258046 T-CA-CGCCTATA
1 TCCATCACC-ATT
258057 T-CATCACCATCT
1 TCCATCACCAT-T
258069 TCCATCACCATT
1 TCCATCACCATT
258081 TCC
1 TCC
258084 CGGCTATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
10 3 0.07
11 9 0.21
12 10 0.24
13 20 0.48
ACGTcount: A:0.24, C:0.43, G:0.02, T:0.32
Consensus pattern (12 bp):
TCCATCACCATT
Found at i:258063 original size:35 final size:35
Alignment explanation
Indices: 258023--258102 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
258013 ACTATATGTC
258023 CATCACCATCTTCCATCACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
* *
258058 CATCACCATCTTCCATCACCATTTCCCGGCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
258093 CATCACCATC
1 CATCACCATC
258103 CCTTAACCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.25, C:0.41, G:0.04, T:0.30
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAT
Found at i:268627 original size:36 final size:36
Alignment explanation
Indices: 268550--268654 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
268540 ATTTATAAGT
* * * *
268550 TGGTGATAATATAGGCGTGAT-TTAGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
268585 TAGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
268621 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
268655 AGATTGTATC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:276167 original size:43 final size:47
Alignment explanation
Indices: 276114--276214 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 47
276104 ACTAAAGAAT
*
276114 AAATATTAATAAACT-AAACA-TGTTTTAA-C-CC-TAATTCCTAATA
1 AAATAATAAT-AACTAAAACATTGTTTTAACCACCTTAATTCCTAATA
*
276157 AAATAATAATAACTAAAATATTGTTTTAACCCAACCTTAATTCCTAATA
1 AAATAATAATAACTAAAACATTGTTTTAA-CC-ACCTTAATTCCTAATA
276206 AAATAATAA
1 AAATAATAA
276215 ATCTGATCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
42 4 0.08
43 13 0.27
44 8 0.16
46 1 0.02
48 2 0.04
49 21 0.43
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.34
Consensus pattern (47 bp):
AAATAATAATAACTAAAACATTGTTTTAACCACCTTAATTCCTAATA
Found at i:280054 original size:12 final size:12
Alignment explanation
Indices: 280035--280068 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
280025 TTTTTTGTTT
280035 TTTTTTTTTGCC
1 TTTTTTTTTGCC
*
280047 TTTTTTTTTACC
1 TTTTTTTTTGCC
280059 TTTTTTTTTG
1 TTTTTTTTTG
280069 TTTTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGCC
Found at i:280074 original size:12 final size:12
Alignment explanation
Indices: 280024--280091 Score: 57
Period size: 12 Copynumber: 5.7 Consensus size: 12
280014 TTTTTGGCTC
280024 TTTTTTTGTTTTT
1 TTTTTTTG-TTTT
**
280037 TTTTTTTGCCTT
1 TTTTTTTGTTTT
***
280049 TTTTTTTACCTT
1 TTTTTTTGTTTT
280061 TTTTTTTGTTTT
1 TTTTTTTGTTTT
* *
280073 TTGTTTT-TTTG
1 TTTTTTTGTTTT
280084 TTTTTTTG
1 TTTTTTTG
280092 AAAAAAAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
11 9 0.20
12 28 0.62
13 8 0.18
ACGTcount: A:0.01, C:0.06, G:0.09, T:0.84
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:280079 original size:15 final size:15
Alignment explanation
Indices: 280061--280089 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
280051 TTTTTACCTT
280061 TTTTTTTGTTTTTTG
1 TTTTTTTGTTTTTTG
280076 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
280090 TGAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTTTTGTTTTTTG
Found at i:282650 original size:8 final size:8
Alignment explanation
Indices: 282639--282700 Score: 65
Period size: 8 Copynumber: 8.0 Consensus size: 8
282629 TTTTTGGCTC
282639 TTTTTTTG
1 TTTTTTTG
282647 TTTTTTTG
1 TTTTTTTG
**
282655 CCTTTTT-
1 TTTTTTTG
***
282662 TTTTTGCC
1 TTTTTTTG
282670 TTTTTTTG
1 TTTTTTTG
282678 -TTTTTTG
1 TTTTTTTG
282685 TTTTTTTG
1 TTTTTTTG
282693 TTTTTTTG
1 TTTTTTTG
282701 AAAAAAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
7 10 0.23
8 33 0.77
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:282650 original size:19 final size:18
Alignment explanation
Indices: 282628--282698 Score: 68
Period size: 15 Copynumber: 4.3 Consensus size: 18
282618 AAATTTTGGC
282628 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
282647 TTTTTTTGCC---TTTT-
1 TTTTTTGGCCTTTTTTTG
282661 TTTTTT-GCCTTTTTTTG
1 TTTTTTGGCCTTTTTTTG
282678 TTTTTT-G--TTTTTTTG
1 TTTTTTGGCCTTTTTTTG
282693 TTTTTT
1 TTTTTT
282699 TGAAAAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
13 3 0.06
14 6 0.13
15 18 0.38
16 4 0.09
17 7 0.15
18 1 0.02
19 8 0.17
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.80
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:282663 original size:13 final size:13
Alignment explanation
Indices: 282647--282676 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
282637 TCTTTTTTTG
282647 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
282660 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
282673 TTTT
1 TTTT
282677 GTTTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:282665 original size:20 final size:20
Alignment explanation
Indices: 282628--282664 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
282618 AAATTTTGGC
*
282628 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
282648 TTTTTTGCCT-TTTTTTT
1 TTTTTTGCCTCTTTTTTT
282665 TTGCCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:282684 original size:30 final size:30
Alignment explanation
Indices: 282628--282691 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
282618 AAATTTTGGC
282628 TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTTT
1 TTTTTTGGCTCTTTTTTTGTTTTTTTG--TTT
*
282660 TTTTTTTGC-CTTTTTTTG-TTTTTTGTTT
1 TTTTTTGGCTCTTTTTTTGTTTTTTTGTTT
282688 TTTT
1 TTTT
282692 GTTTTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.23
30 7 0.23
31 9 0.29
32 8 0.26
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (30 bp):
TTTTTTGGCTCTTTTTTTGTTTTTTTGTTT
Found at i:304115 original size:19 final size:19
Alignment explanation
Indices: 304077--304115 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
304067 GTTCAAAGAC
**
304077 AAAAAGAAGAAAAATTAGA
1 AAAAAGAAGAAAAAAGAGA
*
304096 AAAAAGATGAAAAAAGAGA
1 AAAAAGAAGAAAAAAGAGA
304115 A
1 A
304116 TTTCAACAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (19 bp):
AAAAAGAAGAAAAAAGAGA
Found at i:319927 original size:1 final size:1
Alignment explanation
Indices: 319923--319975 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
319913 TTTTTGGCTC
* *** * *
319923 TTTTTTTTTTGTTTTTTTTTTTGCCTTTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
319976 GGAAAAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:319938 original size:12 final size:12
Alignment explanation
Indices: 319923--319975 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
319913 TTTTTGGCTC
319923 TTTTTTTTTTGT
1 TTTTTTTTTTGT
*
319935 TTTTTTTTTTGC
1 TTTTTTTTTTGT
*
319947 CTTTTTTTTTG-
1 TTTTTTTTTTGT
319958 -TTTTTTTTTGT
1 TTTTTTTTTTGT
319969 TTTTTTT
1 TTTTTTT
319976 GGAAAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 10 0.27
12 27 0.73
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:319939 original size:24 final size:23
Alignment explanation
Indices: 319912--319967 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
319902 AAATTTTGGC
319912 TTTTTTGGCTCTTTTTTTTTTGTTTT
1 TTTTTTGGC-C-TTTTTTTTTG-TTT
*
319938 TTTTTTTGCCTTTTTTTTTGTTT
1 TTTTTTGGCCTTTTTTTTTGTTT
319961 TTTTTTG
1 TTTTTTG
319968 TTTTTTTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.32
24 10 0.36
25 1 0.04
26 8 0.29
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (23 bp):
TTTTTTGGCCTTTTTTTTTGTTT
Found at i:325679 original size:11 final size:11
Alignment explanation
Indices: 325657--325713 Score: 64
Period size: 11 Copynumber: 5.0 Consensus size: 11
325647 TTTGAGAATT
325657 TGGTGATGATA
1 TGGTGATGATA
325668 TAGGTG-TGATA
1 T-GGTGATGATA
325679 TGGTGATGGACTA
1 TGGTGAT-GA-TA
325692 TGGTGATGATA
1 TGGTGATGATA
325703 TAGGTG-TGATA
1 T-GGTGATGATA
325714 ATGGAAGATG
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.10
11 16 0.39
12 12 0.29
13 9 0.22
ACGTcount: A:0.26, C:0.02, G:0.37, T:0.35
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:325685 original size:22 final size:22
Alignment explanation
Indices: 325657--325713 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
325647 TTTGAGAATT
325657 TGGTGATGATATAGGTG-TGATA
1 TGGTGATGATAT-GGTGATGATA
325679 TGGTGATGGACTATGGTGATGATA
1 TGGTGAT-GA-TATGGTGATGATA
325703 TAGGTG-TGATA
1 T-GGTGATGATA
325714 ATGGAAGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 9 0.29
23 8 0.26
24 10 0.32
25 4 0.13
ACGTcount: A:0.26, C:0.02, G:0.37, T:0.35
Consensus pattern (22 bp):
TGGTGATGATATGGTGATGATA
Found at i:325703 original size:35 final size:37
Alignment explanation
Indices: 325657--325736 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
325647 TTTGAGAATT
*
325657 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
*
325692 TGGTGATGATATAGGTGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
*
325729 CGGTGATG
1 TGGTGATG
325737 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
Found at i:330190 original size:35 final size:37
Alignment explanation
Indices: 330142--330221 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
330132 TTTGAGAATT
*
330142 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
330177 TGGTGATGCTATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
330214 TGGTGATG
1 TGGTGATG
330222 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.26, C:0.05, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:333465 original size:22 final size:22
Alignment explanation
Indices: 333437--333480 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
333427 TTTGAGAATT
333437 TGGTGATGATATAGGCGTGATA
1 TGGTGATGATATAGGCGTGATA
*
333459 TGGTGATGGTATAGGCGTGATA
1 TGGTGATGATATAGGCGTGATA
333481 ATGGAAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.39, T:0.32
Consensus pattern (22 bp):
TGGTGATGATATAGGCGTGATA
Found at i:338248 original size:2 final size:2
Alignment explanation
Indices: 338241--338278 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
338231 ACTATAGATA
338241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
338279 GAAAATAACT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344036 original size:12 final size:12
Alignment explanation
Indices: 344006--344041 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
343996 TTACCATTGC
344006 AAAG-AAAAG-A
1 AAAGTAAAAGAA
344016 AAA-TAAAAGAA
1 AAAGTAAAAGAA
344027 AAAGTAAAAGAA
1 AAAGTAAAAGAA
344039 AAA
1 AAA
344042 TTCAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.35
11 4 0.17
12 11 0.48
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (12 bp):
AAAGTAAAAGAA
Found at i:345642 original size:17 final size:19
Alignment explanation
Indices: 345620--345657 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
345610 ACCAATAGTT
345620 CACATC-TTA-ATAATATG
1 CACATCATTATATAATATG
*
345637 CACATCATTATATTATATG
1 CACATCATTATATAATATG
345656 CA
1 CA
345658 TTATATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (19 bp):
CACATCATTATATAATATG
Found at i:348721 original size:22 final size:22
Alignment explanation
Indices: 348676--348734 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
348666 TTGGAGTGCA
348676 AAAAGAAAGAAAAAGACAAAAAG
1 AAAAGAAA-AAAAAGACAAAAAG
* *
348699 AAGAGAAAAATAAGA-AAAGAAG
1 AAAAGAAAAAAAAGACAAA-AAG
348721 AAAAGAAAAGAAAA
1 AAAAGAAAA-AAAA
348735 AGAATTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 17 0.57
23 10 0.33
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (22 bp):
AAAAGAAAAAAAAGACAAAAAG
Found at i:348735 original size:19 final size:20
Alignment explanation
Indices: 348675--348738 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
348665 ATTGGAGTGC
* *
348675 AAAAAGAA-AGAAAAA-GAC
1 AAAAAGAAGAGAAAAATAAG
348693 AAAAAGAAGAGAAAAATAAG
1 AAAAAGAAGAGAAAAATAAG
348713 -AAAAGAAGA-AAAGAA-AAG
1 AAAAAGAAGAGAAA-AATAAG
348731 AAAAAGAA
1 AAAAAGAA
348739 TTCAAAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 14 0.35
19 25 0.62
20 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAAAGAAGAGAAAAATAAG
Found at i:348737 original size:11 final size:11
Alignment explanation
Indices: 348675--348738 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
348665 ATTGGAGTGC
348675 AAAAAG-AAAG
1 AAAAAGAAAAG
348685 AAAAAGACAAA-
1 AAAAAGA-AAAG
*
348696 AAGAAGAGAAA-
1 AAAAAGA-AAAG
*
348707 AATAAGAAAAG
1 AAAAAGAAAAG
348718 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
348731 AAAAAGAA
1 AAAAAGAA
348739 TTCAAAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
10 9 0.20
11 22 0.49
12 5 0.11
13 9 0.20
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:355067 original size:24 final size:25
Alignment explanation
Indices: 355032--355086 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
355022 ACTTGGAGCC
*
355032 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
355056 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
355080 TCAAGTG
1 TCAAGTG
355087 GCATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Done.