Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007985.1 Hibiscus syriacus cultivar Beakdansim tig00110430_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: 2235968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:2735 original size:17 final size:17
Alignment explanation
Indices: 2709--2743 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2699 ACACGAAAAC
2709 TATATAAAT-AAACAAA
1 TATATAAATAAAACAAA
2725 TATATTAAATAAAACAAA
1 TATA-TAAATAAAACAAA
2743 T
1 T
2744 GAATAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
TATATAAATAAAACAAA
Found at i:11072 original size:39 final size:39
Alignment explanation
Indices: 10968--11073 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
10958 CATAATTCTC
* ** * *
10968 AAATTATTTCACTATAACATTCTAAAATCCTAATTTTTT
1 AAATTATTTCACAATAATGTTCTAAATTCCTAATTTATT
* * *
11007 AAATT-TTGACACCATAATGTTCTAAATTCTTAATTTATT
1 AAATTATT-TCACAATAATGTTCTAAATTCCTAATTTATT
11046 AAATTATTTCACAATAATGTTCTAAATT
1 AAATTATTTCACAATAATGTTCTAAATT
11074 GTTTTTTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.04
39 52 0.93
40 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (39 bp):
AAATTATTTCACAATAATGTTCTAAATTCCTAATTTATT
Found at i:11397 original size:26 final size:23
Alignment explanation
Indices: 11320--11401 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 23
11310 ATATAATATA
*
11320 ATTTTATATATATTAAATTAAAAAT
1 ATTTTAT-TAAATT-AATTAAAAAT
*
11345 ATTTATATTAAATT-ATTAAATAT
1 ATTT-TATTAAATTAATTAAAAAT
*
11368 ATTTTATTATGAACTTAATTAAAAAC
1 ATTTTATTA--AA-TTAATTAAAAAT
11394 ATTTTATT
1 ATTTTATT
11402 TTTATTTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
22 5 0.10
23 12 0.25
24 2 0.04
25 11 0.23
26 18 0.38
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTTTATTAAATTAATTAAAAAT
Found at i:11583 original size:31 final size:31
Alignment explanation
Indices: 11540--11615 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
11530 GTTAACTCGG
* *
11540 GTGATCAAATCTTACTTAAATAAAAATGAAA
1 GTGATCATATCTTAATTAAATAAAAATGAAA
*
11571 TTGATCATATCTTAATTAAATAAAAATGAAA
1 GTGATCATATCTTAATTAAATAAAAATGAAA
11602 GTGA-CAATATCTTA
1 GTGATC-ATATCTTA
11616 TATTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.03
31 39 0.98
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (31 bp):
GTGATCATATCTTAATTAAATAAAAATGAAA
Found at i:14653 original size:172 final size:172
Alignment explanation
Indices: 14339--14662 Score: 381
Period size: 172 Copynumber: 1.9 Consensus size: 172
14329 CAATGCAACA
* *
14339 TGGTGCTAGAGGTGGAGGGAATCAAGCTAGACAAGAAAAAACATATTCCATGCTCGTCATCGGGA
1 TGGTGCTAGAGGTGGAGGGAATCAAGCTAGACAAGAAAAAACACATTCCAAGCTCGTCATCGGGA
* * * * *
14404 ATGACACCAGTGCCGACACAATCAAAAGTAGAGCATCAGACACCGGTGTCTTCACCTATACTCAT
66 ATAACACCAGTGCCGACACAATCAAAAGTAGAGCATCAGACACCAGTGCCCTCACCTACACTCAT
*
14469 CTACTCGACTCAGTCAATATTTAAGCGTATATCGATGTAACG
131 CTACTCGACTCAGTCAACATTTAAGCGTATATCGATGTAACG
* *
14511 TGGTGCTAGAGGTGGAGGGAATCAAGAC-AGATAAGAAGAAACACACTT-CAAGCTCGTCATCGG
1 TGGTGCTAGAGGTGGAGGGAATCAAG-CTAGACAAGAAAAAACACA-TTCCAAGCTCGTCATCGG
* * * ** *
14574 GAATAACA-CTGTCGTCTG-CACAGTCAACTGTAGAGCATCAGACACCAGTGCCACT-ACCTGCA
64 GAATAACACCAGT-G-CCGACACAATCAAAAGTAGAGCATCAGACACCAGTGCC-CTCACCTACA
* * *
14636 TTTA-CTCACTTGACTCAGTCAACATTT
126 CTCATCT-ACTCGACTCAGTCAACATTT
14663 TAGCATATGT
Statistics
Matches: 127, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
171 5 0.04
172 116 0.91
173 6 0.05
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (172 bp):
TGGTGCTAGAGGTGGAGGGAATCAAGCTAGACAAGAAAAAACACATTCCAAGCTCGTCATCGGGA
ATAACACCAGTGCCGACACAATCAAAAGTAGAGCATCAGACACCAGTGCCCTCACCTACACTCAT
CTACTCGACTCAGTCAACATTTAAGCGTATATCGATGTAACG
Found at i:14970 original size:12 final size:12
Alignment explanation
Indices: 14955--14997 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
14945 AGGTGATGAC
*
14955 AATGGTGGTGAT
1 AATGATGGTGAT
14967 AATGATGGTGAT
1 AATGATGGTGAT
**
14979 GGTGATGGTGAT
1 AATGATGGTGAT
14991 AATGATG
1 AATGATG
14998 AAAAAGATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.33
Consensus pattern (12 bp):
AATGATGGTGAT
Found at i:15122 original size:20 final size:20
Alignment explanation
Indices: 15094--15133 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
15084 TTTTAATCCG
*
15094 AAAAATTA-TGTAATGTTTT
1 AAAAATTATTGTAATATTTT
15113 AAAAATTTATTGTAATATTTT
1 AAAAA-TTATTGTAATATTTT
15134 TTTGAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
AAAAATTATTGTAATATTTT
Found at i:21305 original size:32 final size:31
Alignment explanation
Indices: 21256--21324 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
21246 AAATATAATT
*
21256 TTTTATTAAATTAATATCATTTAGTTTATTA
1 TTTTATTAAATTAATATCAATTAGTTTATTA
* * *
21287 TTTTGTTAATATTGATATCAATTAGTTTA-TC
1 TTTTATTAA-ATTAATATCAATTAGTTTATTA
21318 TTTTATT
1 TTTTATT
21325 TAAAACTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.59
Consensus pattern (31 bp):
TTTTATTAAATTAATATCAATTAGTTTATTA
Found at i:29990 original size:22 final size:22
Alignment explanation
Indices: 29965--30019 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
29955 TAATATAACA
29965 ATAA-AAAAATAGATAAATAAAG
1 ATAATAAAAATAGA-AAATAAAG
*
29987 ATAATAAAAA-AGAAAAGATAA-
1 ATAATAAAAATAGAAAATA-AAG
30008 ATAATAAAAATA
1 ATAATAAAAATA
30020 AAACAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 14 0.48
22 10 0.34
23 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (22 bp):
ATAATAAAAATAGAAAATAAAG
Found at i:30037 original size:21 final size:20
Alignment explanation
Indices: 29967--30089 Score: 67
Period size: 20 Copynumber: 5.9 Consensus size: 20
29957 ATATAACAAT
* *
29967 AAAAAAATAGATAAATAAAG
1 AAAAAAATAAAAAAATAAAG
*
29987 ATAATAAAA-AAGAAAAGATAAAT
1 A-AA-AAAATAA-AAAA-ATAAAG
30010 AATAAAAATAAAACAAATAAAG
1 AA-AAAAATAAAA-AAATAAAG
30032 -AAAAAATAAAATAAA-ATAA-
1 AAAAAAATAAAA-AAATA-AAG
* * *
30051 AAAATAGTAAATAAAA-AACG
1 AAAAAAATAAA-AAAATAAAG
30071 AAAAAAATGAAAAAAATAA
1 AAAAAAAT-AAAAAAATAA
30090 TAATAACAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 25
0.70 0.09 0.22
Matches are distributed among these distances:
19 2 0.03
20 38 0.47
21 10 0.12
22 19 0.24
23 11 0.14
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAAAAATAAAAAAATAAAG
Found at i:30049 original size:39 final size:40
Alignment explanation
Indices: 29964--30092 Score: 99
Period size: 39 Copynumber: 3.2 Consensus size: 40
29954 TTAATATAAC
* * * *
29964 AATAAAAAAATAGATAAATAAAGATAATAAAAAAGA-AAAGATA
1 AATAATAAAATAG-TAAATAAA-AAAAGAAAAAA-ATAAA-AAA
30007 AATAATAAAA-A-TAAA-ACAAATAAAG-AAAAAATAAAATAA
1 AATAATAAAATAGTAAATA-AAA-AAAGAAAAAAATAAAA-AA
* *
30046 AATAA-AAAATAGTAAATAAAAAACGAAAAAAATGAAAAA
1 AATAATAAAATAGTAAATAAAAAAAGAAAAAAATAAAAAA
30085 AATAATAA
1 AATAATAA
30093 TAACAAAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
38 6 0.08
39 27 0.38
40 27 0.38
41 1 0.01
42 1 0.01
43 9 0.13
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.16
Consensus pattern (40 bp):
AATAATAAAATAGTAAATAAAAAAAGAAAAAAATAAAAAA
Found at i:30067 original size:25 final size:24
Alignment explanation
Indices: 30010--30100 Score: 62
Period size: 25 Copynumber: 3.8 Consensus size: 24
30000 AAAGATAAAT
*
30010 AATAAAAATAAAACAAATAAAGAA
1 AATAAAAATAAAACAAAAAAAGAA
* * *
30034 AAAATAAAATAAAATAAAAAATAGTA
1 AATA-AAAATAAAACAAAAAA-AGAA
** *
30060 AATAAAAA-ACGA-AAAAAATGAA
1 AATAAAAATAAAACAAAAAAAGAA
30082 AA-AAATAATAATAACAAAA
1 AATAAA-AATAA-AACAAAA
30101 GTTAAATTCT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
21 3 0.06
22 6 0.12
23 7 0.14
24 6 0.12
25 22 0.44
26 6 0.12
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.14
Consensus pattern (24 bp):
AATAAAAATAAAACAAAAAAAGAA
Found at i:30086 original size:50 final size:54
Alignment explanation
Indices: 29979--30100 Score: 121
Period size: 49 Copynumber: 2.3 Consensus size: 54
29969 AAAAATAGAT
*
29979 AAATAAAGATAATAAAAAAGAAAAGATAAATAATAAAAATAAAACAAATAAAGAAA
1 AAATAAA-ATAATAAAAAAGAAAAGATAAATAATAAAAAGAAAACAAAT-AAGAAA
* * *
30035 AAATAAAATAA-AATAAAA-AATAG-TAAATAA-AAAACGAAAA-AAATGA-AAA
1 AAATAAAATAATAA-AAAAGAAAAGATAAATAATAAAAAGAAAACAAATAAGAAA
*
30084 AAATAATAATAACAAAA
1 AAATAA-AATAATAAAA
30101 GTTAAATTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
49 9 0.15
50 8 0.14
51 6 0.10
52 8 0.14
53 7 0.12
54 6 0.10
55 8 0.14
56 7 0.12
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (54 bp):
AAATAAAATAATAAAAAAGAAAAGATAAATAATAAAAAGAAAACAAATAAGAAA
Found at i:31672 original size:3 final size:3
Alignment explanation
Indices: 31643--31700 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
31633 AAAAATGATT
* *
31643 ATA ATA TATA A-A TTA ATA A-A TTA ATA ATA ATA A-A ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31686 ATA AT- ATA AT- ATA AT
1 ATA ATA ATA ATA ATA AT
31701 GTCTTTGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
2 8 0.18
3 34 0.76
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:31673 original size:14 final size:14
Alignment explanation
Indices: 31656--31700 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
31646 ATATATAAAT
*
31656 TAATAAATTAATAA
1 TAATAAAATAATAA
31670 TAATAAAATAATAA
1 TAATAAAATAATAA
*
31684 TAATAATATAAT-A
1 TAATAAAATAATAA
31697 TAAT
1 TAAT
31701 GTCTTTGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAAAATAATAA
Found at i:32469 original size:124 final size:124
Alignment explanation
Indices: 32310--32648 Score: 495
Period size: 124 Copynumber: 2.7 Consensus size: 124
32300 CACTCCTTAT
* * *
32310 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATTTTGCTTGTGTGCA
1 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATTTTGCTTGTGTGCA
* *
32375 CGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAATTTGAGCC
66 CGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGAC
* * *
32434 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTAGTGAGCA
1 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATTTTGCTTGTGTGCA
* *
32499 CGAT-TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGAC
66 CGATAT-CCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGAC
* * * *
32558 TTGAATTAGATATCTTTCGTCGTAAAGTTGAAATCCAATCTAAAGATGAATTTTGCTTCGAGT-C
1 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATTTTGCTT-GTGTGC
* *
32622 -CAATATCCTTCGCCGTGAAGTTGAAAT
65 ACGATATCCTTCGTCGTGAAGTTGAAAT
32649 TGGCTCTGAA
Statistics
Matches: 192, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
123 23 0.12
124 167 0.87
125 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (124 bp):
TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATTTTGCTTGTGTGCA
CGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGAC
Found at i:34242 original size:95 final size:94
Alignment explanation
Indices: 34070--34265 Score: 295
Period size: 95 Copynumber: 2.1 Consensus size: 94
34060 GGATAACTCA
* * * * * *
34070 ATATGTAAACACCTTTATCAGGTTAGTTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATTG
1 ATATATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG
*
34135 CCTTAGAGGGACAACTCAAGCTTTATCGT
66 CCTTAAAGGGACAACTCAAGCTTTATCGT
34164 ATAGTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATA-TATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
*
34229 G-CTCTAAAGGGACAACTCAAGCTTTATTGT
65 GCCT-TAAAGGGACAACTCAAGCTTTATCGT
34259 ATATATA
1 ATATATA
34266 TAATTATAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 9 0.10
95 83 0.90
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (94 bp):
ATATATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG
CCTTAAAGGGACAACTCAAGCTTTATCGT
Found at i:36906 original size:15 final size:15
Alignment explanation
Indices: 36888--36929 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
36878 AAAGAAAATT
36888 AATAAAAATAAAACA
1 AATAAAAATAAAACA
*
36903 AATAAAGA-AAAACA
1 AATAAAAATAAAACA
36917 AA-ATAAAATAAAA
1 AATA-AAAATAAAA
36930 AATAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.04
14 11 0.48
15 11 0.48
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (15 bp):
AATAAAAATAAAACA
Found at i:37164 original size:13 final size:13
Alignment explanation
Indices: 37146--37170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37136 AAACATGCAT
37146 AAAATTGAAAATC
1 AAAATTGAAAATC
37159 AAAATTGAAAAT
1 AAAATTGAAAAT
37171 AATGAAAACA
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:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAATTGAAAATC
Found at i:38710 original size:23 final size:24
Alignment explanation
Indices: 38667--38715 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
38657 TTCATTATGG
38667 ATTTTATATGAATATTATTTTTTAA
1 ATTTTATATGAATA-TATTTTTTAA
*
38692 ATTTT-TA-GAATATTTTTTTTAA
1 ATTTTATATGAATATATTTTTTAA
38714 AT
1 AT
38716 ATACATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 5 0.22
24 2 0.09
25 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTTATATGAATATATTTTTTAA
Found at i:45421 original size:6 final size:6
Alignment explanation
Indices: 45410--45436 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45400 CACATACTTA
45410 CATTTG CATTTG CATTTG CATTTG CAT
1 CATTTG CATTTG CATTTG CATTTG CAT
45437 GTCTAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
CATTTG
Found at i:45923 original size:18 final size:19
Alignment explanation
Indices: 45888--45924 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
45878 CACGGAATGT
45888 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
45908 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
45925 GATTACTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:49381 original size:14 final size:15
Alignment explanation
Indices: 49357--49385 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
49347 ATAAACATAA
49357 TAAAGTATTAAAAAT
1 TAAAGTATTAAAAAT
49372 TAAA-TATTAAAAAT
1 TAAAGTATTAAAAAT
49386 ATTGTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TAAAGTATTAAAAAT
Found at i:49422 original size:29 final size:29
Alignment explanation
Indices: 49365--49422 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
49355 AATAAAGTAT
* *
49365 TAAAAATTAAATATTAAAAATATTGTAAA
1 TAAAAATTAAATATTAAAAAAAATGTAAA
49394 TAAAAATT-AA-ATTACAAAAAAATGCTAAA
1 TAAAAATTAAATATTA-AAAAAAATG-TAAA
49423 AATACTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 4 0.16
28 9 0.36
29 12 0.48
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (29 bp):
TAAAAATTAAATATTAAAAAAAATGTAAA
Found at i:49501 original size:17 final size:19
Alignment explanation
Indices: 49468--49510 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
49458 CAAGCTATAA
49468 ATTAAAAAATTATAAAT-T
1 ATTAAAAAATTATAAATGT
49486 ATTAAAAAATTA-AAATGT
1 ATTAAAAAATTATAAATGT
49504 -TTAAAAA
1 ATTAAAAA
49511 TATATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTAAAAAATTATAAATGT
Found at i:52414 original size:32 final size:31
Alignment explanation
Indices: 52373--52450 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
52363 ATGGTATATA
*
52373 TTATGGTTTAAGGTTTAGAGTTTAGAAACGGT
1 TTATGGTTTAAGGTTTA-AGTTTAGAAACGGC
*
52405 TTATGGTTTAAGATTTAAGTTTAGAAACGGC
1 TTATGGTTTAAGGTTTAAGTTTAGAAACGGC
*
52436 CTATGGTTTAAGGTT
1 TTATGGTTTAAGGTT
52451 CAGGTTCAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 26 0.62
32 16 0.38
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (31 bp):
TTATGGTTTAAGGTTTAAGTTTAGAAACGGC
Found at i:53920 original size:3 final size:3
Alignment explanation
Indices: 53914--53968 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
53904 TATCTTTCGG
53914 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53962 ATT ATT A
1 ATT ATT A
53969 CATGTGAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:57957 original size:14 final size:15
Alignment explanation
Indices: 57938--57971 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
57928 ATATTAAATT
57938 ATTAAGTTCTTTTA-
1 ATTAAGTTCTTTTAC
57952 ATTAAGTTCTTTTAC
1 ATTAAGTTCTTTTAC
57967 ATTAA
1 ATTAA
57972 AAAATTCGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (15 bp):
ATTAAGTTCTTTTAC
Found at i:57997 original size:19 final size:20
Alignment explanation
Indices: 57973--58021 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
57963 TTACATTAAA
* *
57973 AAATTCGCAATTCGATCTC-
1 AAATTCGCAATGCGAACTCT
*
57992 AAATTCGTAATGCGAACTCT
1 AAATTCGCAATGCGAACTCT
*
58012 AATTTCGCAA
1 AAATTCGCAA
58022 CTCAGTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (20 bp):
AAATTCGCAATGCGAACTCT
Found at i:58068 original size:20 final size:20
Alignment explanation
Indices: 58043--58082 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
58033 ATTTCGCAAT
58043 GCGAATCTGTAAATCGTAAC
1 GCGAATCTGTAAATCGTAAC
*
58063 GCGAATTTGTAAATCGTAAC
1 GCGAATCTGTAAATCGTAAC
58083 ACATAAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (20 bp):
GCGAATCTGTAAATCGTAAC
Found at i:58114 original size:21 final size:20
Alignment explanation
Indices: 58090--58162 Score: 76
Period size: 19 Copynumber: 3.6 Consensus size: 20
58080 AACACATAAG
*
58090 TCAAATTCGCAACGCGGCATT
1 TCAAATTCGCAAC-CGGAATT
*
58111 TCAAATTCGCAA-CTGAATT
1 TCAAATTCGCAACCGGAATT
** *
58130 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACCGGAATT
*
58150 TCGAATTCGCAAC
1 TCAAATTCGCAAC
58163 AGGTTTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.38
20 16 0.36
21 12 0.27
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (20 bp):
TCAAATTCGCAACCGGAATT
Found at i:58132 original size:19 final size:20
Alignment explanation
Indices: 58108--58162 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
58098 GCAACGCGGC
58108 ATTTCAAATTCGCAACT-GA
1 ATTTCAAATTCGCAACTAGA
58127 ATTTCAAATTCGCAACTAGA
1 ATTTCAAATTCGCAACTAGA
* *
58147 TTTTCGAATTCGCAAC
1 ATTTCAAATTCGCAAC
58163 AGGTTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (20 bp):
ATTTCAAATTCGCAACTAGA
Found at i:61329 original size:18 final size:18
Alignment explanation
Indices: 61306--61341 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61296 AAGCAAAAGG
61306 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
61324 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
61342 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:61876 original size:66 final size:65
Alignment explanation
Indices: 61794--61967 Score: 212
Period size: 66 Copynumber: 2.6 Consensus size: 65
61784 AATTTAAAAC
61794 AACAAATCAACTTTTACAAATTAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATTAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
61859 A
65 A
* * * *
61860 AACAAATCAACTTTTACAAATCAATTAAAC-A--AAAAAAATAATTCTTATTTCCTCATCAGTTA
1 AACAAATCAACTTTTACAAATTAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
*
61922 AATAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAATT-AATTAAACAAGCAAAAAAA
61968 GTGTACCACA
Statistics
Matches: 93, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
62 14 0.15
63 26 0.28
65 1 0.01
66 34 0.37
67 10 0.11
68 1 0.01
70 7 0.08
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATTAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:63351 original size:21 final size:21
Alignment explanation
Indices: 63290--63352 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
63280 GTGAATCGGG
* * *
63290 CTCTTGAACGGCGGACGGGAC
1 CTCTTGAACGGTGGAAGGGGC
*
63311 CTCTTGAACGAT-GACAGGGGC
1 CTCTTGAACGGTGGA-AGGGGC
63332 CTCTTGAACGGTGGAAGGGGC
1 CTCTTGAACGGTGGAAGGGGC
63353 TTTTTCGATG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.17
Consensus pattern (21 bp):
CTCTTGAACGGTGGAAGGGGC
Found at i:63386 original size:21 final size:21
Alignment explanation
Indices: 63310--63402 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
63300 GCGGACGGGA
* *
63310 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATAAGAGGGG
* *
63331 CCTCTTGAACGGT-GGAAGGGG
1 CCTCTTGAACGATAAG-AGGGG
* * *
63352 CTTTTTCG-ATGATAAGAGGGG
1 CCTCTT-GAACGATAAGAGGGG
* **
63373 CCTCTTGAACGATAGGAGACG
1 CCTCTTGAACGATAAGAGGGG
63394 CCTCTTGAA
1 CCTCTTGAA
63403 TGATGATAGG
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
20 1 0.02
21 51 0.94
22 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATAAGAGGGG
Found at i:63481 original size:38 final size:39
Alignment explanation
Indices: 63407--63483 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
63397 CTTGAATGAT
63407 GATAGGTGCATCGGGCTTCTTCTTACGGAGTATTGGCAC
1 GATAGGTGCATCGGGCTTCTTCTTACGGAGTATTGGCAC
*
63446 GATAGGTGCATCGGGCTTCTT-TTACGGAGTCTTGGCAC
1 GATAGGTGCATCGGGCTTCTTCTTACGGAGTATTGGCAC
63484 TAGTGGGGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 16 0.43
39 21 0.57
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (39 bp):
GATAGGTGCATCGGGCTTCTTCTTACGGAGTATTGGCAC
Found at i:63884 original size:21 final size:21
Alignment explanation
Indices: 63854--63896 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
63844 ATCATTATCT
*
63854 TAACGTAAAGCACCGACCTCA
1 TAACGCAAAGCACCGACCTCA
63875 TAACGCAAAGCACCGACCTCA
1 TAACGCAAAGCACCGACCTCA
63896 T
1 T
63897 CACGTAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.35, G:0.14, T:0.14
Consensus pattern (21 bp):
TAACGCAAAGCACCGACCTCA
Found at i:65649 original size:19 final size:19
Alignment explanation
Indices: 65597--65651 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
65587 GAGTAGTTTC
*
65597 TGAAACTTAAATTCGCAAAG
1 TGAAAC-TAAAATCGCAAAG
* * *
65617 CGAAAATGAAAATCGCAACG
1 TGAAACT-AAAATCGCAAAG
65637 TGAAACTAAAATCGC
1 TGAAACTAAAATCGC
65652 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (19 bp):
TGAAACTAAAATCGCAAAG
Found at i:66197 original size:20 final size:20
Alignment explanation
Indices: 66172--66282 Score: 125
Period size: 20 Copynumber: 5.5 Consensus size: 20
66162 TTTCGTGTTA
66172 CGAATTTGACTATCGCGTTG
1 CGAATTTGACTATCGCGTTG
*
66192 CGAATTTGACTATCGTGTTG
1 CGAATTTGACTATCGCGTTG
* *
66212 CGAATTTGGCTATCGCATTG
1 CGAATTTGACTATCGCGTTG
* * *
66232 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTATCGCGTTG
* * *
66252 CGATTTATAAAT-TCGCGTTG
1 CGAATT-TGACTATCGCGTTG
66272 CGAATTTGACT
1 CGAATTTGACT
66283 TTTGTGTTAC
Statistics
Matches: 73, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
19 3 0.04
20 67 0.92
21 3 0.04
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (20 bp):
CGAATTTGACTATCGCGTTG
Found at i:66208 original size:40 final size:40
Alignment explanation
Indices: 66162--66294 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
66152 TAATATTGTG
66162 TTTCGTGTTACGAATTTGACTATCGCGTTGCGAATTTGAC
1 TTTCGTGTTACGAATTTGACTATCGCGTTGCGAATTTGAC
* * * *
66202 TATCGTGTTGCGAATTTGGCTATCGCATTGCGAATTTGAC
1 TTTCGTGTTACGAATTTGACTATCGCGTTGCGAATTTGAC
* * * * *
66242 TTTTGTGTTGCGATTTATAAAT-TCGCGTTGCGAATTTGAC
1 TTTCGTGTTACGAATT-TGACTATCGCGTTGCGAATTTGAC
*
66282 TTTTGTGTTACGA
1 TTTCGTGTTACGA
66295 TTTAAAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 78 0.98
41 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (40 bp):
TTTCGTGTTACGAATTTGACTATCGCGTTGCGAATTTGAC
Found at i:66296 original size:40 final size:40
Alignment explanation
Indices: 66184--66314 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 40
66174 AATTTGACTA
* * * ***
66184 TCGCGTTGCGAATTTGACTATCGTGTTGCGAATT-TGGCT
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTATAAAT
*
66223 ATCGCATTGCGAATTTGACTTTTGTGTTGCGATTTATAAAT
1 -TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTATAAAT
* *
66264 TCGCGTTGCGAATTTGACTTTTGTGTTACGATTTAAAAAT
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTATAAAT
66304 TCGCGTTGCGA
1 TCGCGTTGCGA
66315 TTTACATATT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 78 0.98
41 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTATAAAT
Found at i:66317 original size:20 final size:20
Alignment explanation
Indices: 66248--66334 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
66238 TGACTTTTGT
*
66248 GTTGCGATTTATAAATTCGC
1 GTTGCGATTTAAAAATTCGC
* ** * *
66268 GTTGCGAATTT-GACTTTTGT
1 GTTGCG-ATTTAAAAATTCGC
*
66288 GTTACGATTTAAAAATTCGC
1 GTTGCGATTTAAAAATTCGC
* *
66308 GTTGCGATTTACATATTCGC
1 GTTGCGATTTAAAAATTCGC
66328 GTTGCGA
1 GTTGCGA
66335 AATTAGAAAC
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 4 0.08
20 43 0.84
21 4 0.08
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTAAAAATTCGC
Found at i:77287 original size:25 final size:25
Alignment explanation
Indices: 77252--77302 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
77242 TAAACCGACG
77252 ATATATCAATTAATTTT-TAAAATT
1 ATATATCAATTAATTTTATAAAATT
*
77276 ATATCATCAATTAGTTTTCATAAAATT
1 ATAT-ATCAATTAATTTT-ATAAAATT
77303 TTGTGTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
27 7 0.30
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (25 bp):
ATATATCAATTAATTTTATAAAATT
Found at i:82024 original size:39 final size:38
Alignment explanation
Indices: 81950--82024 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 38
81940 ACTTTAATAA
*
81950 TTTTATTGATAATTGATTTAATTTAAAATATAAATTTC
1 TTTTATTGATAATTGATTTAAATTAAAATATAAATTTC
*
81988 TTTTGATTGATAATAT-ATTTATAATTAAATTA-AAATT
1 TTTT-ATTGATAAT-TGATTTA-AATTAAAATATAAATT
82025 GAATAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 4 0.12
39 19 0.59
40 9 0.28
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (38 bp):
TTTTATTGATAATTGATTTAAATTAAAATATAAATTTC
Found at i:82339 original size:13 final size:14
Alignment explanation
Indices: 82314--82342 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
82304 AATTTTTTAA
82314 CGGTTCGGGTTTTT
1 CGGTTCGGGTTTTT
82328 CGGTTC-GGTTTTT
1 CGGTTCGGGTTTTT
82341 CG
1 CG
82343 ATAAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.17, G:0.34, T:0.48
Consensus pattern (14 bp):
CGGTTCGGGTTTTT
Found at i:83370 original size:25 final size:24
Alignment explanation
Indices: 83342--83393 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
83332 AAAAAAATGC
*
83342 CACAAAGACAGAGATAAACGTACAA
1 CACAAA-ACAAAGATAAACGTACAA
*
83367 CAC-AAACAAAGATAAACGTGCAA
1 CACAAAACAAAGATAAACGTACAA
83390 CACA
1 CACA
83394 TAGAGATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 19 0.79
24 2 0.08
25 3 0.12
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (24 bp):
CACAAAACAAAGATAAACGTACAA
Found at i:83402 original size:21 final size:22
Alignment explanation
Indices: 83349--83414 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
83339 TGCCACAAAG
83349 ACAGAGATAAACGTACAACACAA
1 ACAGAGATAAACGTACAACAC-A
* *
83372 ACAAAGATAAACGTGCAACAC-
1 ACAGAGATAAACGTACAACACA
*
83393 ATAGAGAT-AACGT-CTAACACA
1 ACAGAGATAAACGTAC-AACACA
83414 A
1 A
83415 ACAAAATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 10 0.27
21 7 0.19
23 19 0.51
ACGTcount: A:0.53, C:0.21, G:0.14, T:0.12
Consensus pattern (22 bp):
ACAGAGATAAACGTACAACACA
Found at i:87081 original size:12 final size:12
Alignment explanation
Indices: 87044--87073 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
87034 TGGTATTTTT
87044 TACTTTTTTCTA
1 TACTTTTTTCTA
87056 TACTTTTTTCTA
1 TACTTTTTTCTA
87068 TACTTT
1 TACTTT
87074 ATTATATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (12 bp):
TACTTTTTTCTA
Found at i:89555 original size:12 final size:12
Alignment explanation
Indices: 89540--89589 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
89530 AAAACTAAAA
89540 CTAAAACCCAAC
1 CTAAAACCCAAC
89552 CTAAAACCCAA-
1 CTAAAACCCAAC
**
89563 C-AAGCCCCAAC
1 CTAAAACCCAAC
*
89574 C-AAAGCCCAAC
1 CTAAAACCCAAC
89585 CTAAA
1 CTAAA
89590 TATCCAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 7 0.22
11 11 0.34
12 14 0.44
ACGTcount: A:0.48, C:0.42, G:0.04, T:0.06
Consensus pattern (12 bp):
CTAAAACCCAAC
Found at i:90777 original size:108 final size:109
Alignment explanation
Indices: 90558--90770 Score: 268
Period size: 108 Copynumber: 2.0 Consensus size: 109
90548 TAGTTATCTA
* * * * *
90558 TAGGGTTTAAAACTATTATTTTCCTTTTTCTTTGCATGCTTTATAATTTTTGGGTTATTCACCGT
1 TAGGGTTTAAAACTATTATTTTCCCTTTTATTTGAATACTTTATAATTTTTGGGTTATTCACCAT
* *
90623 TTAATCCCTCTAACTTTAGTGCATTTTTGCATTATGGTCACCTG
66 TTAATCCCTCTAACTTTAGCGCATTTTTACATTATGGTCACCTG
* * *
90667 TAGGGTTT-AAACTGTTATTTTCCCTTTTATTTGAATACTTTGTAATTTTTGGGTTATTCACTAT
1 TAGGGTTTAAAACTATTATTTTCCCTTTTATTTGAATACTTTATAATTTTTGGGTTATTCACCAT
** * **
90731 TTGGTCCCTCTAAGTTTAGCGTGTTTTTACACTT-TGGTCA
66 TTAATCCCTCTAACTTTAGCGCATTTTTACA-TTATGGTCA
90771 TGTGTAGTGA
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
108 78 0.89
109 10 0.11
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (109 bp):
TAGGGTTTAAAACTATTATTTTCCCTTTTATTTGAATACTTTATAATTTTTGGGTTATTCACCAT
TTAATCCCTCTAACTTTAGCGCATTTTTACATTATGGTCACCTG
Found at i:91361 original size:55 final size:55
Alignment explanation
Indices: 91277--91386 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
91267 TTACTCAAGT
91277 CAATTGCTCAACTTTTAAAATTTGTTAATCATCCATATTTTCTTTAAAAAAACAC
1 CAATTGCTCAACTTTTAAAATTTGTTAATCATCCATATTTTCTTTAAAAAAACAC
91332 CAATTGCTCAACTTTTAAAATTTGTTAATCATCCATATTTTCTTTAAAAAAACAC
1 CAATTGCTCAACTTTTAAAATTTGTTAATCATCCATATTTTCTTTAAAAAAACAC
91387 TCTTTTAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (55 bp):
CAATTGCTCAACTTTTAAAATTTGTTAATCATCCATATTTTCTTTAAAAAAACAC
Found at i:93216 original size:16 final size:14
Alignment explanation
Indices: 93166--93218 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
93156 AAATGATTTC
93166 TAAAAAAT-AAAAA
1 TAAAAAATGAAAAA
93179 TAAAAAAGTGAAAATA
1 TAAAAAA-TGAAAA-A
*
93195 TGAAAATATGAAAACA
1 T-AAAAAATGAAAA-A
93211 TAAAAAAT
1 TAAAAAAT
93219 ATGTTTTCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.21
14 1 0.03
15 10 0.30
16 10 0.30
17 5 0.15
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.19
Consensus pattern (14 bp):
TAAAAAATGAAAAA
Found at i:94450 original size:21 final size:21
Alignment explanation
Indices: 94412--94451 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
94402 CTATTCGTTT
*
94412 AATTATATTTTAAGTTTATAA
1 AATTATATATTAAGTTTATAA
94433 AATTGATATATTAA-TTTAT
1 AATT-ATATATTAAGTTTAT
94452 TTTGTTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTATATATTAAGTTTATAA
Found at i:96625 original size:3 final size:3
Alignment explanation
Indices: 96619--96653 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
96609 TGACAAGGAG
96619 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
96654 GAAATTGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:98349 original size:21 final size:21
Alignment explanation
Indices: 98325--98367 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
98315 CTGGCGTGAT
*
98325 AGTTTATAATGTTAACATAAC
1 AGTTTATAATATTAACATAAC
*
98346 AGTTTATAATATTGACATAAC
1 AGTTTATAATATTAACATAAC
98367 A
1 A
98368 ATCTATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (21 bp):
AGTTTATAATATTAACATAAC
Found at i:98655 original size:25 final size:28
Alignment explanation
Indices: 98595--98656 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
98585 TATAATTTTT
*
98595 TTAAAAAATAATATATATATATAATATG
1 TTAAAAAATAATATATATATATAATATA
*
98623 TTATAAAATAAT-TACT-TATA-AAT-TA
1 TTAAAAAATAATATA-TATATATAATATA
98648 TTAAAAAAT
1 TTAAAAAAT
98657 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 9 0.30
26 3 0.10
27 6 0.20
28 12 0.40
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
TTAAAAAATAATATATATATATAATATA
Found at i:99169 original size:21 final size:20
Alignment explanation
Indices: 99145--99188 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
99135 TTAATATGTA
99145 TATTCAATTTTTTAGTAATTT
1 TATTCAA-TTTTTAGTAATTT
**
99166 TATTTTATTTTTAGTAATTT
1 TATTCAATTTTTAGTAATTT
99186 TAT
1 TAT
99189 AATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTCAATTTTTAGTAATTT
Found at i:99178 original size:20 final size:21
Alignment explanation
Indices: 99153--99198 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
99143 TATATTCAAT
*
99153 TTTTTAGTAATTTTAT-TTTA
1 TTTTTAGTAATTTTATAATTA
99173 TTTTTAGTAATTTTATAATTA
1 TTTTTAGTAATTTTATAATTA
99194 TTTTT
1 TTTTT
99199 TGAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTAGTAATTTTATAATTA
Found at i:99208 original size:21 final size:20
Alignment explanation
Indices: 99153--99212 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
99143 TATATTCAAT
**
99153 TTTTTAGTAATTTTATTTTA
1 TTTTTAGTAATTTTAAATTA
99173 TTTTTAGTAATTTTATAATTA
1 TTTTTAGTAATTTTA-AATTA
*
99194 TTTTTTG-AATATTTAAATT
1 TTTTTAGTAAT-TTTAAATT
99213 TTAAAATAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTTAGTAATTTTAAATTA
Found at i:103287 original size:3 final size:3
Alignment explanation
Indices: 103279--103314 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
103269 ATTTTTTACG
* *
103279 TAT TAT TAT TGT TAT TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
103315 GAGTAACCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:106333 original size:27 final size:27
Alignment explanation
Indices: 106297--106352 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
106287 TATTGTAAAC
* *
106297 TAAAATATATGGTTA-ATCATTTAAATT
1 TAAAAGATATGATTATAT-ATTTAAATT
*
106324 TAAAAGATATTATTATATATTTAAATT
1 TAAAAGATATGATTATATATTTAAATT
106351 TA
1 TA
106353 GATATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (27 bp):
TAAAAGATATGATTATATATTTAAATT
Found at i:111806 original size:83 final size:83
Alignment explanation
Indices: 111714--111877 Score: 240
Period size: 83 Copynumber: 2.0 Consensus size: 83
111704 GTATATATTT
* * * *
111714 GTTTAATATTTTAATTTTAAAATATATTATTATCTATTTAAATTTA-TATATTAAAAGATATCTG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGT-TATTAAAAGAGATCTA
* *
111778 GTTGGAGTAAATCTCTCAG
65 GTTGGAGAAAAACTCTCAG
* *
111797 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGTTATTAAAAGAGATTTAG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGTTATTAAAAGAGATCTAG
111862 TTGGAGAAAAACTCTC
66 TTGGAGAAAAACTCTC
111878 TCGAAATTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
83 71 0.99
84 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (83 bp):
GTTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGTTATTAAAAGAGATCTAG
TTGGAGAAAAACTCTCAG
Found at i:114381 original size:146 final size:146
Alignment explanation
Indices: 114117--114414 Score: 587
Period size: 146 Copynumber: 2.0 Consensus size: 146
114107 TCATGCTTTC
114117 ACGTAAAAAATAAATCATAATATTATTATATCGTTCATGATTTAATGATTGAGGGACAAAATCAA
1 ACGTAAAAAATAAATCATAATATTATTATATCGTTCATGATTTAATGATTGAGGGACAAAATCAA
114182 AACAGTATAAAAGTTAAATAATCAAATTGGCAAAGTATAGTAACCAAAAAGTTAAATAATCATAA
66 AACAGTATAAAAGTTAAATAATCAAATTGGCAAAGTATAGTAACCAAAAAGTTAAATAATCATAA
114247 TAAAGACTTAATTTTT
131 TAAAGACTTAATTTTT
*
114263 ACGTAAAAAATAAATCATAATATTATTATATCGTTCATGATTTAATGATTGAGGGACAAAATCGA
1 ACGTAAAAAATAAATCATAATATTATTATATCGTTCATGATTTAATGATTGAGGGACAAAATCAA
114328 AACAGTATAAAAGTTAAATAATCAAATTGGCAAAGTATAGTAACCAAAAAGTTAAATAATCATAA
66 AACAGTATAAAAGTTAAATAATCAAATTGGCAAAGTATAGTAACCAAAAAGTTAAATAATCATAA
114393 TAAAGACTTAATTTTT
131 TAAAGACTTAATTTTT
114409 ACGTAA
1 ACGTAA
114415 CACCGTACCA
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 151 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (146 bp):
ACGTAAAAAATAAATCATAATATTATTATATCGTTCATGATTTAATGATTGAGGGACAAAATCAA
AACAGTATAAAAGTTAAATAATCAAATTGGCAAAGTATAGTAACCAAAAAGTTAAATAATCATAA
TAAAGACTTAATTTTT
Found at i:115460 original size:13 final size:13
Alignment explanation
Indices: 115444--115471 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
115434 CAGTTCTTTA
115444 TGTGAGTTTTCTC
1 TGTGAGTTTTCTC
115457 TGTGAGTTTTCTC
1 TGTGAGTTTTCTC
115470 TG
1 TG
115472 AGTGTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.25, T:0.54
Consensus pattern (13 bp):
TGTGAGTTTTCTC
Found at i:121225 original size:30 final size:30
Alignment explanation
Indices: 121166--121284 Score: 195
Period size: 30 Copynumber: 4.0 Consensus size: 30
121156 CCCGAAGGAC
* *
121166 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
121195 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
121225 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
121255 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
121285 ACTGTCCATA
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 19 0.22
30 67 0.78
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:122857 original size:21 final size:21
Alignment explanation
Indices: 122833--122873 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
122823 TGTTGTTCGT
* *
122833 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
122854 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
122874 TTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:126392 original size:28 final size:27
Alignment explanation
Indices: 126360--126417 Score: 93
Period size: 25 Copynumber: 2.2 Consensus size: 27
126350 ACACATTTGT
126360 TGGACTACCAAGCTACCACCGGCAACAA
1 TGGAC-ACCAAGCTACCACCGGCAACAA
126388 TGG--ACCAAGCTACCACCGGCAACAA
1 TGGACACCAAGCTACCACCGGCAACAA
126413 TGGAC
1 TGGAC
126418 CCATTTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 25 0.89
28 3 0.11
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.10
Consensus pattern (27 bp):
TGGACACCAAGCTACCACCGGCAACAA
Found at i:126395 original size:25 final size:25
Alignment explanation
Indices: 126366--126418 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
126356 TTGTTGGACT
126366 ACCAAGCTACCACCGGCAACAATGG
1 ACCAAGCTACCACCGGCAACAATGG
126391 ACCAAGCTACCACCGGCAACAATGG
1 ACCAAGCTACCACCGGCAACAATGG
126416 ACC
1 ACC
126419 CATTTTCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.38, G:0.19, T:0.08
Consensus pattern (25 bp):
ACCAAGCTACCACCGGCAACAATGG
Found at i:129042 original size:4 final size:4
Alignment explanation
Indices: 129033--129071 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
129023 GGCTCTCATC
129033 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
129072 CCAAATCCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:130500 original size:15 final size:15
Alignment explanation
Indices: 130459--130503 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
130449 TAATTTATAA
*
130459 TTATATATTAAATATT
1 TTATAAATTAAAT-TT
* *
130475 TTAGAATTTAAATTT
1 TTATAAATTAAATTT
130490 TTATAAATTAAATT
1 TTATAAATTAAATT
130504 AATGATATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TTATAAATTAAATTT
Found at i:134255 original size:74 final size:74
Alignment explanation
Indices: 134133--134273 Score: 239
Period size: 74 Copynumber: 1.9 Consensus size: 74
134123 AATCTGTTGC
* * *
134133 AAAGTTATACAAGCTGGTCATTCACCCAGAAACAGTTACTAAAGCTCTTAAC-TTGGCTGAATAT
1 AAAGTTATACAAGCTGGACATTCACCCAGAAACAGCTACTAAAACTCTTAACATT-GCTGAATAT
134197 ATCTGCTACG
65 ATCTGCTACG
134207 AAAGTTATACAAGCTGGACATTCACCCAGAAACAGCTACTAAAACTCTTAACATTGCTGAATATA
1 AAAGTTATACAAGCTGGACATTCACCCAGAAACAGCTACTAAAACTCTTAACATTGCTGAATATA
134272 TC
66 TC
134274 CCATCTTGTC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 61 0.97
75 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (74 bp):
AAAGTTATACAAGCTGGACATTCACCCAGAAACAGCTACTAAAACTCTTAACATTGCTGAATATA
TCTGCTACG
Found at i:144969 original size:51 final size:50
Alignment explanation
Indices: 144912--145069 Score: 183
Period size: 51 Copynumber: 3.1 Consensus size: 50
144902 CTTATATTGG
* *
144912 TGTAAGTGAATAAAATAAACAAGTGTATCACTTAATAAATACTTACACCGA
1 TGTAAGTGAATAAAATAAA-AAGTGTAACACTTAACAAATACTTACACCGA
* * ** * *
144963 TATAAGTGAATAAAACAAAAAAGTGTAACACTTAACGCATAC-TACATCGG
1 TGTAAGTGAATAAAA-TAAAAAGTGTAACACTTAACAAATACTTACACCGA
* * * *
145013 TGTAAGTAAATAAAATAAAAAGTGTAGCACTTAACATATACTTATACCGA
1 TGTAAGTGAATAAAATAAAAAGTGTAACACTTAACAAATACTTACACCGA
145063 TGTAAGT
1 TGTAAGT
145070 ATACACATCT
Statistics
Matches: 88, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
49 22 0.25
50 31 0.35
51 32 0.36
52 3 0.03
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (50 bp):
TGTAAGTGAATAAAATAAAAAGTGTAACACTTAACAAATACTTACACCGA
Found at i:145046 original size:49 final size:50
Alignment explanation
Indices: 144886--145056 Score: 182
Period size: 51 Copynumber: 3.4 Consensus size: 50
144876 CAAAAAAATA
* * * *
144886 TAGCACTTAACTCAAACTTATATTGGTGTAAGTGAATAAAATAAACAAGTG
1 TAGCACTTAACACATACTTACATCGGTGTAAGTGAATAAAATAAA-AAGTG
* * * * * * *
144937 TATCACTTAATAAATACTTACACCGATATAAGTGAATAAAACAAAAAAGTG
1 TAGCACTTAACACATACTTACATCGGTGTAAGTGAATAAAA-TAAAAAGTG
* * *
144988 TAACACTTAACGCATAC-TACATCGGTGTAAGTAAATAAAATAAAAAGTG
1 TAGCACTTAACACATACTTACATCGGTGTAAGTGAATAAAATAAAAAGTG
*
145037 TAGCACTTAACATATACTTA
1 TAGCACTTAACACATACTTA
145057 TACCGATGTA
Statistics
Matches: 95, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
49 22 0.23
50 21 0.22
51 49 0.52
52 3 0.03
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (50 bp):
TAGCACTTAACACATACTTACATCGGTGTAAGTGAATAAAATAAAAAGTG
Found at i:150444 original size:71 final size:71
Alignment explanation
Indices: 150309--150444 Score: 184
Period size: 71 Copynumber: 1.9 Consensus size: 71
150299 GTTTAACAAG
* * * *
150309 TAACTAGTTTAATGAGCTACGAGTCGAGTTGAGCAACAAGTTTTTTAACGAGCACGAATTGAGCA
1 TAACGAGTTTAACGAGCTACGAGTCGAGTTGAGCAACAACTTTTTTAACGAGCACGAATCGAGCA
150374 AAATTT
66 AAATTT
* * * *
150380 TAACGAGTTTAACGA-CTAACGATTCGAGTTGAGCAATAACTTTTTTAACGAGCATGCATCGAGC
1 TAACGAGTTTAACGAGCT-ACGAGTCGAGTTGAGCAACAACTTTTTTAACGAGCACGAATCGAGC
150444 A
65 A
150445 CTGCACAACT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 2 0.04
71 54 0.96
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (71 bp):
TAACGAGTTTAACGAGCTACGAGTCGAGTTGAGCAACAACTTTTTTAACGAGCACGAATCGAGCA
AAATTT
Found at i:150893 original size:22 final size:22
Alignment explanation
Indices: 150865--150918 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
150855 ATTGTTGATA
150865 AAAATAAAAACATTCTAAAATT
1 AAAATAAAAACATTCTAAAATT
150887 AAAATAAAAACATTCTAAAATT
1 AAAATAAAAACATTCTAAAATT
150909 AAAATAAAAA
1 AAAATAAAAA
150919 TATAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATAAAAACATTCTAAAATT
Found at i:150930 original size:28 final size:28
Alignment explanation
Indices: 150862--150933 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 28
150852 TAAATTGTTG
150862 ATAAAAATAAAAACATTCTAAAA-T---
1 ATAAAAATAAAAACATTCTAAAATTAAA
150886 -T-AAAATAAAAACATTCTAAAATTAAA
1 ATAAAAATAAAAACATTCTAAAATTAAA
*
150912 ATAAAAATATAAAA-TTTCTAAA
1 ATAAAAATA-AAAACATTCTAAA
150934 GATACCACCT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 20 0.50
23 2 0.05
27 1 0.03
28 13 0.32
29 4 0.10
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAAAAATAAAAACATTCTAAAATTAAA
Found at i:151166 original size:13 final size:13
Alignment explanation
Indices: 151148--151173 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
151138 TTTTTGACTA
151148 CAAGAAATACTTT
1 CAAGAAATACTTT
151161 CAAGAAATACTTT
1 CAAGAAATACTTT
151174 AAGTACCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
CAAGAAATACTTT
Found at i:153193 original size:65 final size:65
Alignment explanation
Indices: 153068--153225 Score: 239
Period size: 65 Copynumber: 2.5 Consensus size: 65
153058 TTGATTCTTG
* * * * *
153068 AGTTAGGCATATATTTGCTATACAC--AAAAAACATATATTATTGCTGTAAGGTATATCATATGA
1 AGTTAGGCAGATATTTGCCATACACAAAAAAAACATATATTACTACTGCAAGGTATATCATATGA
*
153131 AGTTAGGCAGATATTTGCCATACACAAAAAAAACATATATTACTATTGCAAGGTATATCATATGA
1 AGTTAGGCAGATATTTGCCATACACAAAAAAAACATATATTACTACTGCAAGGTATATCATATGA
*
153196 AGTTAGGCAGATATTTTCCATACACAAAAA
1 AGTTAGGCAGATATTTGCCATACACAAAAA
153226 GAAGCTCAAC
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 23 0.27
65 63 0.73
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (65 bp):
AGTTAGGCAGATATTTGCCATACACAAAAAAAACATATATTACTACTGCAAGGTATATCATATGA
Found at i:155993 original size:12 final size:12
Alignment explanation
Indices: 155975--156007 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
155965 ACAATCAACA
155975 ACACCCTCAGTT
1 ACACCCTCAGTT
*
155987 GCACCCTCAGTT
1 ACACCCTCAGTT
155999 ACACCCTCA
1 ACACCCTCA
156008 CCAGCACCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.45, G:0.09, T:0.21
Consensus pattern (12 bp):
ACACCCTCAGTT
Found at i:158930 original size:20 final size:20
Alignment explanation
Indices: 158905--159010 Score: 108
Period size: 21 Copynumber: 5.3 Consensus size: 20
158895 TTTTCCCAAT
*
158905 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
158925 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
158946 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
158966 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
158987 TCGCAATGCG-ATAA-AAAA
1 TCGCAATGCGAATAAGAAAA
159005 TCGCAA
1 TCGCAA
159011 CGAGATACTT
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
18 10 0.14
19 1 0.01
20 28 0.41
21 30 0.43
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:158950 original size:41 final size:41
Alignment explanation
Indices: 158905--159012 Score: 193
Period size: 41 Copynumber: 2.7 Consensus size: 41
158895 TTTTCCCAAT
158905 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
158946 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
158987 TCGCAATGCG-ATAA-AAAATCGCAACG
1 TCGCAATGCGAATAAGTAAATCGCAACG
159013 AGATACTTAC
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
39 11 0.17
40 4 0.06
41 51 0.77
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:159017 original size:18 final size:18
Alignment explanation
Indices: 158983--159017 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
158973 GCGAATTGGG
* *
158983 AAAATCGCAATGCGATAA
1 AAAATCGCAACGAGATAA
159001 AAAATCGCAACGAGATA
1 AAAATCGCAACGAGATA
159018 CTTACTTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.14
Consensus pattern (18 bp):
AAAATCGCAACGAGATAA
Found at i:159030 original size:20 final size:20
Alignment explanation
Indices: 159005--159057 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
158995 CGATAAAAAA
* *
159005 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
159025 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
159045 TCGCAACGCGATA
1 TCGCAACGCGATA
159058 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:159273 original size:22 final size:22
Alignment explanation
Indices: 159245--159288 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
159235 CACTCTCTCA
159245 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
159267 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
159289 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:159578 original size:20 final size:20
Alignment explanation
Indices: 159553--159590 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
159543 CGATTCTCTC
159553 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
159573 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
159591 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:160931 original size:18 final size:18
Alignment explanation
Indices: 160910--160954 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
160900 TCCACTTCGG
*
160910 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
160928 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
160946 GAGCCATCA
1 GAGCCATCA
160955 TTTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:161490 original size:19 final size:20
Alignment explanation
Indices: 161436--161491 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
161426 TAGTTTACTT
* *
161436 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
161456 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
161476 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
161492 AAATCGCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:161497 original size:19 final size:19
Alignment explanation
Indices: 161475--161570 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
161465 GGAAATGGCT
161475 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
161494 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
161508 ATCGCAACGTGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
161526 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
161540 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
161559 ATCGCAATGCGA
1 ATCGCAATGCGA
161571 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 20 0.34
15 1 0.02
16 4 0.07
17 1 0.02
18 11 0.19
19 22 0.37
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:161538 original size:32 final size:33
Alignment explanation
Indices: 161475--161565 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
161465 GGAAATGGCT
* *
161475 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
161508 ATCGCAACGTGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
161540 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
161566 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:161547 original size:14 final size:14
Alignment explanation
Indices: 161491--161548 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
161481 ATGCGAAATG
*
161491 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
161505 AAAATCGCAACGTGAA
1 AAAATCGCAAC--GAC
161521 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
161537 AAAATCGCAACG
1 AAAATCGCAACG
161549 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 6 0.16
18 10 0.27
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:161601 original size:14 final size:14
Alignment explanation
Indices: 161582--161639 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
161572 TTGTGTTTCG
161582 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
161596 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
161612 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
161628 CATTGCGATTTT
1 CGTTGCGATTTT
161640 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:161616 original size:32 final size:33
Alignment explanation
Indices: 161577--161655 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
161567 GCGATTTGTG
*
161577 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
161609 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
*
161642 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
161656 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
Found at i:161652 original size:19 final size:19
Alignment explanation
Indices: 161628--161694 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
161618 GCGATTTTGT
**
161628 CATTGCGATTTTCATTTCG
1 CATTGCGATAGTCATTTCG
*
161647 CATTGCGATAGCCATTTCCG
1 CATTGCGATAGTCATTT-CG
*
161667 CGTTGCGATAGTCATTTCG
1 CATTGCGATAGTCATTTCG
*
161686 CGTTGCGAT
1 CATTGCGAT
161695 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 25 0.60
20 17 0.40
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (19 bp):
CATTGCGATAGTCATTTCG
Found at i:161674 original size:20 final size:19
Alignment explanation
Indices: 161640--161694 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
161630 TTGCGATTTT
*
161640 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
161659 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
161679 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
161695 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:163579 original size:14 final size:14
Alignment explanation
Indices: 163560--163595 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
163550 ATTGTTTAAT
163560 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
163574 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
163588 TGATTTGT
1 TGATTTGT
163596 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:163728 original size:33 final size:36
Alignment explanation
Indices: 163683--163777 Score: 115
Period size: 38 Copynumber: 2.7 Consensus size: 36
163673 AAAACAGACT
* ***
163683 ATCGCAACGCGAAATGGTTATCGCAA-CG-A-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
163716 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
163754 ATCGCAATGCGAAATGAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGC
163778 TTCTCGTTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
33 22 0.42
35 2 0.04
37 1 0.02
38 28 0.53
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:163734 original size:19 final size:19
Alignment explanation
Indices: 163712--163777 Score: 132
Period size: 19 Copynumber: 3.5 Consensus size: 19
163702 ATCGCAACGA
163712 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
163731 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
163750 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
163769 GAAAATCGC
1 GAAAATCGC
163778 TTCTCGTTGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:163832 original size:20 final size:20
Alignment explanation
Indices: 163782--163832 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
163772 AATCGCTTCT
* *
163782 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
*
163802 CGTTGTGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
163822 CGTTGCGATAG
1 CGTTGCGATAG
163833 TCAAATGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:164921 original size:24 final size:24
Alignment explanation
Indices: 164894--164947 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
164884 GTATTCGAAA
* *
164894 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
164918 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
164942 TTTGAT
1 TTTGAT
164948 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:165138 original size:12 final size:12
Alignment explanation
Indices: 165121--165145 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
165111 ATATAATCCT
165121 GAAGAAGAAAAA
1 GAAGAAGAAAAA
165133 GAAGAAGAAAAA
1 GAAGAAGAAAAA
165145 G
1 G
165146 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:167459 original size:19 final size:19
Alignment explanation
Indices: 167437--167495 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
167427 GGAAATTACT
167437 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
167456 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
167470 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
167489 ATCGCAA
1 ATCGCAA
167496 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:167641 original size:14 final size:14
Alignment explanation
Indices: 167622--167658 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
167612 CATCAATTAA
167622 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
167636 ACAAATCACCTTTT
1 ACAAATCAACTTTT
167650 ACAAATCAA
1 ACAAATCAA
167659 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:171221 original size:33 final size:33
Alignment explanation
Indices: 171164--171262 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
171154 ACGAGATAAT
*
171164 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
171198 GAGAATCGCAACGCGAAATGACTATCGCAACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * * **
171231 GACAATTGCAACGCGACATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
171263 GCGAAATGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:171226 original size:19 final size:19
Alignment explanation
Indices: 171139--171304 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
171129 TCTTTTGGTT
*
171139 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
171158 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
171178 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
171196 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
171212 GAAATGACTATCGCAAC-C
1 GAAATGAAAATCGCAACGC
* *
171230 ---A-GACAATTGCAACGC
1 GAAATGAAAATCGCAACGC
*
171245 GACATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
171265 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
171284 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
171303 GA
1 GA
171305 TTTTGGTTTC
Statistics
Matches: 120, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 44 0.37
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:171333 original size:19 final size:19
Alignment explanation
Indices: 171300--171366 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
171290 AAAATCGCAA
**
171300 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
171319 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
171338 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
171358 TGCGATTTT
1 TGCGATTTT
171367 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:171908 original size:20 final size:20
Alignment explanation
Indices: 171883--171935 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
171873 GCGCTATGTA
171883 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
171903 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
171923 TATCTCGTTGCGA
1 AATCGCGTTGCGA
171936 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:171969 original size:20 final size:20
Alignment explanation
Indices: 171944--171997 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
171934 GATTTTGTAT
171944 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
171964 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
171984 TATCGCATTGCGAT
1 TATCGCATTGCGAT
171998 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:171982 original size:61 final size:61
Alignment explanation
Indices: 171884--172000 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
171874 CGCTATGTAA
* * * * *
171884 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
171945 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
172001 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:172016 original size:61 final size:61
Alignment explanation
Indices: 171884--172018 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
171874 CGCTATGTAA
* * * * * ** *
171884 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
171945 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
172007 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
172019 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:172108 original size:21 final size:21
Alignment explanation
Indices: 172068--172108 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
172058 ATTGTATACC
**
172068 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
172089 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
172109 ACGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:173152 original size:59 final size:58
Alignment explanation
Indices: 173083--173236 Score: 175
Period size: 59 Copynumber: 2.6 Consensus size: 58
173073 GTTGGATGGA
** * *
173083 TTTGAGGATGAAATTGGAATATTCAAAAGTTTGGGTACTAATTTAGAAAGAGGGTCATAG
1 TTTGAGGATGAAATT--AATATTCAAAAGTTTAAGAACTAATTTAGAAAGAGAGTCATAG
* *
173143 TTT-AGGATGAAATTAAAATGTCAAAAAGTTTAAGAACTAATTTAGAATGAGAGTCATAG
1 TTTGAGGATGAAATTAATAT-TC-AAAAGTTTAAGAACTAATTTAGAAAGAGAGTCATAG
* *
173202 TTTGGGGATGAAATTATAATATTTAAAAGTTTAAG
1 TTTGAGGATGAAA-T-TAATATTCAAAAGTTTAAG
173237 GATCAATTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
57 4 0.05
58 2 0.03
59 45 0.56
60 22 0.28
61 2 0.03
62 5 0.06
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (58 bp):
TTTGAGGATGAAATTAATATTCAAAAGTTTAAGAACTAATTTAGAAAGAGAGTCATAG
Found at i:173236 original size:60 final size:60
Alignment explanation
Indices: 173083--173265 Score: 190
Period size: 60 Copynumber: 3.1 Consensus size: 60
173073 GTTGGATGGA
** * ** * * *
173083 TTTGAGGATGAAATTGGAATATTCAAAAGTTTGGGTACTAATTTAGAAAGAGGGTCATAG
1 TTTGAGGATGAAATTAAAATATTAAAAAGTTTAAGAACTAATTTAGAATGAGAGTCATAG
* *
173143 TTT-AGGATGAAATTAAAATGTCAAAAAGTTTAAGAACTAATTTAGAATGAGAGTCATAG
1 TTTGAGGATGAAATTAAAATATTAAAAAGTTTAAGAACTAATTTAGAATGAGAGTCATAG
* * * * * * *
173202 TTTGGGGATGAAATTATAATATTTAAAAGTTTAAGGA-TCAATTTAAAATGAGAATTATAG
1 TTTGAGGATGAAATTAAAATATTAAAAAGTTTAAGAACT-AATTTAGAATGAGAGTCATAG
173262 TTTG
1 TTTG
173266 GGGGCATATG
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 50 0.49
60 52 0.51
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (60 bp):
TTTGAGGATGAAATTAAAATATTAAAAAGTTTAAGAACTAATTTAGAATGAGAGTCATAG
Found at i:173745 original size:13 final size:13
Alignment explanation
Indices: 173729--173755 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
173719 AAAAAATAGT
173729 ATTATTTTTATAA
1 ATTATTTTTATAA
173742 ATTATTTTTATAA
1 ATTATTTTTATAA
173755 A
1 A
173756 AACACTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTATTTTTATAA
Found at i:185563 original size:42 final size:42
Alignment explanation
Indices: 185511--185626 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
185501 TAATTTTAAC
*
185511 AATATAATATAATATTTTATTTTTATAATTATATTATTA-TAA
1 AATATAATATAATATTTTATTTTTATAA-TAAATTATTAGTAA
* *
185553 TATATAATATAATATTTTTATTTTAATAATAAATTATTAGTAA
1 AATATAATATAATA-TTTTATTTTTATAATAAATTATTAGTAA
* *
185596 AAT-TAATATTAT-TTATTAATTTTATAA-AAAT
1 AATATAATATAATATT-TTATTTTTATAATAAAT
185627 AATATTATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
40 6 0.09
41 10 0.16
42 30 0.47
43 18 0.28
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.53
Consensus pattern (42 bp):
AATATAATATAATATTTTATTTTTATAATAAATTATTAGTAA
Found at i:185701 original size:8 final size:8
Alignment explanation
Indices: 185685--185717 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
185675 TATAGTATTT
185685 TATTTTAA
1 TATTTTAA
*
185693 TATTATAA
1 TATTTTAA
185701 T-TTTTAA
1 TATTTTAA
185708 TATTTTAA
1 TATTTTAA
185716 TA
1 TA
185718 AATAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTTAA
Found at i:185707 original size:15 final size:15
Alignment explanation
Indices: 185687--185716 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
185677 TAGTATTTTA
185687 TTTTAATATTATAAT
1 TTTTAATATTATAAT
*
185702 TTTTAATATTTTAAT
1 TTTTAATATTATAAT
185717 AAATAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAATATTATAAT
Found at i:185777 original size:21 final size:20
Alignment explanation
Indices: 185703--185777 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 20
185693 TATTATAATT
185703 TTTAATAT-TTTAATAAATA
1 TTTAATATATTTAATAAATA
* *
185722 ATTAATATAATTAA-AAATA
1 TTTAATATATTTAATAAATA
** *
185741 TATTTTTCTCATTTTAATAAATA
1 T-TTAATAT-A-TTTAATAAATA
185764 TTTAATATAGTTTA
1 TTTAATATA-TTTA
185778 TAATAATTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
19 12 0.30
20 8 0.20
21 6 0.15
22 8 0.20
23 6 0.15
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (20 bp):
TTTAATATATTTAATAAATA
Found at i:185822 original size:14 final size:13
Alignment explanation
Indices: 185751--185893 Score: 66
Period size: 14 Copynumber: 10.8 Consensus size: 13
185741 TATTTTTCTC
185751 ATTTTAATA-AAT
1 ATTTTAATATAAT
*
185763 A-TTTAATATAGT
1 ATTTTAATATAAT
* **
185775 -TTATAATAATTTT
1 ATTTTAAT-ATAAT
*
185788 ATTTTAATAAAAT
1 ATTTTAATATAAT
**
185801 ATAATAATCATAAT
1 ATTTTAAT-ATAAT
*
185815 ATTTTAATTTATAAA
1 ATTTTAA--TATAAT
*
185830 ATTGTAGATATAAT
1 ATTTTA-ATATAAT
185844 ATTTTAATAATAAT
1 ATTTTAAT-ATAAT
185858 ATTGATATAA-ATAAT
1 ATT--T-TAATATAAT
185873 A--TTAA-ATAATT
1 ATTTTAATATAA-T
185884 ATTTTAATAT
1 ATTTTAATAT
185894 TTTATAAATA
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
10 7 0.07
11 10 0.10
12 8 0.08
13 17 0.17
14 35 0.36
15 15 0.15
16 3 0.03
17 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (13 bp):
ATTTTAATATAAT
Found at i:185871 original size:29 final size:29
Alignment explanation
Indices: 185787--185875 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
185777 ATAATAATTT
185787 TATTTTAATAA-AATA-T-A-ATAATCATAA
1 TATTTTAATAATAATATTGATATAA--ATAA
* * * *
185814 TATTTTAATTTATAAAATTG-TAGATATAA
1 TATTTTAA-TAATAATATTGATATAAATAA
185843 TATTTTAATAATAATATTGATATAAATAA
1 TATTTTAATAATAATATTGATATAAATAA
185872 TATT
1 TATT
185876 AAATAATTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
27 8 0.17
28 11 0.23
29 26 0.54
30 1 0.02
31 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (29 bp):
TATTTTAATAATAATATTGATATAAATAA
Done.