Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004529.1 Hibiscus syriacus cultivar Beakdansim tig00010001_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: 93917
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:27 original size:12 final size:12
Alignment explanation
Indices: 10--70 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
1 TACCTGCAG
10 GACAATGACGAT
1 GACAATGACGAT
22 GACAATGACGAT
1 GACAATGACGAT
*
34 GACGATG--G-T
1 GACAATGACGAT
* *
43 GACGACGACGAT
1 GACAATGACGAT
* *
55 AACAATGATGAT
1 GACAATGACGAT
67 GACA
1 GACA
71 GCGAGGAGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 7 0.18
10 1 0.03
11 1 0.03
12 30 0.77
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.16
Consensus pattern (12 bp):
GACAATGACGAT
Found at i:4001 original size:15 final size:15
Alignment explanation
Indices: 3978--4007 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3968 TAGCATATAA
3978 ATATAATATTAATAT
1 ATATAATATTAATAT
*
3993 ATATTATATTAATAT
1 ATATAATATTAATAT
4008 TTTTATTTTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATAATATTAATAT
Found at i:10531 original size:18 final size:18
Alignment explanation
Indices: 10508--10560 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
10498 AGGGATTATC
10508 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
10526 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
10544 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
10561 AATAGTCAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:17204 original size:18 final size:18
Alignment explanation
Indices: 17181--17233 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
17171 AGGAATTATC
17181 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
17199 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
17217 AATAGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
17234 AATAGTCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:17239 original size:17 final size:18
Alignment explanation
Indices: 17185--17240 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
17175 ATTATCAGTG
* *
17185 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAATA
17203 GTCCTTCGGGACATAATA
1 GTCCTTCGGGACATAATA
17221 GTCCTTCGGGACA-AATA
1 GTCCTTCGGGACATAATA
17238 GTC
1 GTC
17241 AGTTCCCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 7 0.19
18 29 0.81
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (18 bp):
GTCCTTCGGGACATAATA
Found at i:17945 original size:21 final size:21
Alignment explanation
Indices: 17919--17960 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17909 CCAGAATGGG
*
17919 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
17940 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
17961 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:18187 original size:30 final size:31
Alignment explanation
Indices: 18140--18230 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
18130 AAATTTTGAA
18140 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
18169 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
18200 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
18231 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:19052 original size:30 final size:30
Alignment explanation
Indices: 18947--19052 Score: 98
Period size: 29 Copynumber: 3.7 Consensus size: 30
18937 GCATTGGATT
18947 GTTTTTA--TTTGCTA-TTTAGTCCCTT-A
1 GTTTTTATTTTTGCTATTTTAGTCCCTTAA
* * * **
18973 GATTTCTATTTTTGCCATTTTAATCATTTAA
1 G-TTTTTATTTTTGCTATTTTAGTCCCTTAA
19004 G--TTTATGTTTTGCTATTTTAGTCCCTTAA
1 GTTTTTAT-TTTTGCTATTTTAGTCCCTTAA
*
19033 GTTTTTATTTTTTCTATTTT
1 GTTTTTATTTTTGCTATTTT
19053 GGACCTTTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
26 1 0.02
27 5 0.08
28 4 0.07
29 25 0.41
30 19 0.31
31 7 0.11
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.60
Consensus pattern (30 bp):
GTTTTTATTTTTGCTATTTTAGTCCCTTAA
Found at i:19062 original size:59 final size:59
Alignment explanation
Indices: 18954--19128 Score: 151
Period size: 59 Copynumber: 2.9 Consensus size: 59
18944 ATTGTTTTTA
* * * *
18954 TTTGCTA-TTTAGTCCCTT-AGATTTCTATTTTTGCCATTTT-AATCATTTAAGTT-TATGT
1 TTTGCTATTTTAGTCCCTTAAG-TTTATATTTTTTCCATTTTGGA-CCTTTAAGTTCTAT-T
* * *
19012 TTTGCTATTTTAGTCCCTTAAGTTTTTATTTTTTCTATTTTGGACCTTTAAATTCCTATT
1 TTTGCTATTTTAGTCCCTTAAGTTTATATTTTTTCCATTTTGGACCTTTAAGTT-CTATT
* * * * * *
19072 TGTACTATTTTGGTCCTTTAAGTTTATGTTTTTCTCCATTTTGGTCCTTGTAAGTTC
1 TTTGCTATTTTAGTCCCTTAAGTTTATATTTTT-TCCATTTTGGACCTT-TAAGTTC
19129 AATTACTTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
58 7 0.07
59 35 0.37
60 31 0.33
61 17 0.18
62 5 0.05
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (59 bp):
TTTGCTATTTTAGTCCCTTAAGTTTATATTTTTTCCATTTTGGACCTTTAAGTTCTATT
Found at i:19115 original size:31 final size:29
Alignment explanation
Indices: 18999--19127 Score: 118
Period size: 30 Copynumber: 4.3 Consensus size: 29
18989 ATTTTAATCA
* *
18999 TTTAAGTTTATGTTTTGCTATTTTAGTCC
1 TTTAAGTTTATGTTTTTCTATTTTGGTCC
* *
19028 CTTAAGTTTTTAT-TTTTTCTATTTTGGACC
1 TTTAAG--TTTATGTTTTTCTATTTTGGTCC
* * *
19058 TTTAAATTCCTAT-TTGTACTATTTTGGTCC
1 TTTAAGTT--TATGTTTTTCTATTTTGGTCC
19088 TTTAAGTTTATGTTTTTCTCCATTTTGGTCC
1 TTTAAGTTTATGTTTTTCT--ATTTTGGTCC
19119 TTGTAAGTT
1 TT-TAAGTT
19128 CAATTACTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
28 5 0.06
29 10 0.12
30 42 0.52
31 17 0.21
32 6 0.08
ACGTcount: A:0.17, C:0.13, G:0.12, T:0.57
Consensus pattern (29 bp):
TTTAAGTTTATGTTTTTCTATTTTGGTCC
Found at i:21591 original size:18 final size:18
Alignment explanation
Indices: 21568--21605 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
21558 TCATGACATG
21568 TATATAAGAACAATTATT
1 TATATAAGAACAATTATT
21586 TATATAAGAACAATTATT
1 TATATAAGAACAATTATT
21604 TA
1 TA
21606 GAACAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (18 bp):
TATATAAGAACAATTATT
Found at i:24022 original size:14 final size:14
Alignment explanation
Indices: 24003--24042 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
23993 AGACTTGTCT
24003 GTTTTCTACAGTCA
1 GTTTTCTACAGTCA
*
24017 GTTTTCTACACAGTCT
1 GTTTTCT--ACAGTCA
24033 GTTTTCTACA
1 GTTTTCTACA
24043 TGGTATTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.43
16 13 0.57
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (14 bp):
GTTTTCTACAGTCA
Found at i:24031 original size:16 final size:16
Alignment explanation
Indices: 24010--24042 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
24000 TCTGTTTTCT
24010 ACAGTCAGTTTTCTAC
1 ACAGTCAGTTTTCTAC
*
24026 ACAGTCTGTTTTCTAC
1 ACAGTCAGTTTTCTAC
24042 A
1 A
24043 TGGTATTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (16 bp):
ACAGTCAGTTTTCTAC
Found at i:34130 original size:2 final size:2
Alignment explanation
Indices: 34123--34172 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
34113 TGGATAATTA
34123 AT AT 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 AT AT
34165 AT AT AT AT
1 AT AT AT AT
34173 CAAGCTTTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38594 original size:44 final size:45
Alignment explanation
Indices: 38505--38606 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 45
38495 ATTATAACAT
**
38505 CTTTTCTGTTGATAATGCACCCATATGTATTTCAACACTAATATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACACTAATATA
* * *
38550 CTTTTTTGTTGATAATGTA-CCATATACATTTCAAC-CATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACAC-TAATATA
38594 CTTTTCTGTTGAT
1 CTTTTCTGTTGAT
38607 TGAATGATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.02
44 32 0.64
45 17 0.34
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATACATTTCAACACTAATATA
Found at i:38849 original size:18 final size:18
Alignment explanation
Indices: 38809--38843 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38799 GTTAGCTTGT
* *
38809 AAATGTTGTATGTGAATA
1 AAATTTTGTACGTGAATA
38827 AAATTTTGTACGTGAAT
1 AAATTTTGTACGTGAAT
38844 GGAATTATGT
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:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (18 bp):
AAATTTTGTACGTGAATA
Found at i:38901 original size:49 final size:48
Alignment explanation
Indices: 38827--38969 Score: 214
Period size: 49 Copynumber: 2.9 Consensus size: 48
38817 TATGTGAATA
* *
38827 AAATTTTGTACGTGAATGGAATTATGTATATGATTACCAAAGTTACAAC
1 AAATTTTGTATGTGAAT-GAATTATGTATGTGATTACCAAAGTTACAAC
38876 AAATTTTGTATGTGAATGAAGTTATGTATGTGATTACCAAAGTTACAAC
1 AAATTTTGTATGTGAATGAA-TTATGTATGTGATTACCAAAGTTACAAC
* * *
38925 AAGTTTTGTATGTGAATGAAATTTTGTATGTGATTAGCAAAGTTA
1 AAATTTTGTATGTGAATG-AATTATGTATGTGATTACCAAAGTTA
38970 GCAAATATTA
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
48 3 0.03
49 82 0.94
50 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (48 bp):
AAATTTTGTATGTGAATGAATTATGTATGTGATTACCAAAGTTACAAC
Found at i:41791 original size:146 final size:146
Alignment explanation
Indices: 41527--41852 Score: 460
Period size: 146 Copynumber: 2.2 Consensus size: 146
41517 GTTAGGACAT
*
41527 ATTATTAAAGTATCAATATTTATAATTTCGAAACAATGTATGCAAAGTATGAAAATGTCCAAGTA
1 ATTATTAAAGTATCGATATTTATAATTTCGAAACAATGTATGCAAAGTATGAAAATGTCCAAGTA
* * * * * *
41592 TTGATACTTATTATGCCGGTATGAATACTTTTACTCCAGTATGTTTGTCAAACAATTT-ACACGC
66 TCGATACTTATGATGCCGGTATGAACACTTTTACTCCAATATGATTCTCAAACAATTTGA-ACGC
* *
41656 CAAATGTATCAATACAC
130 AAAATGTATCAATAAAC
*
41673 ATTATTAAAGTATCGATATTTATAATTTTGAAACAATGTATGCAAAGTATGAAAATGTCCACA-T
1 ATTATTAAAGTATCGATATTTATAATTTCGAAACAATGTATGCAAAGTATGAAAATGTCCA-AGT
* * *
41737 ATCGATACTTCTGATGCCGGTATGGACACTTTTATTCCAATATGATTCTCAAACAATTTGAACGC
65 ATCGATACTTATGATGCCGGTATGAACACTTTTACTCCAATATGATTCTCAAACAATTTGAACGC
41802 AAAATGTATCAATAAAC
130 AAAATGTATCAATAAAC
* **
41819 ATGT-TTAAAGTATCGATACTTGGAATTTCGAAAC
1 AT-TATTAAAGTATCGATATTTATAATTTCGAAAC
41853 CTATTACTTT
Statistics
Matches: 160, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
146 157 0.98
147 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (146 bp):
ATTATTAAAGTATCGATATTTATAATTTCGAAACAATGTATGCAAAGTATGAAAATGTCCAAGTA
TCGATACTTATGATGCCGGTATGAACACTTTTACTCCAATATGATTCTCAAACAATTTGAACGCA
AAATGTATCAATAAAC
Found at i:43118 original size:199 final size:196
Alignment explanation
Indices: 42723--43575 Score: 1088
Period size: 199 Copynumber: 4.3 Consensus size: 196
42713 AAATGTTCAA
* * *
42723 GTATCGATACTTTTATTCCAGTATGCTTCCCAAACAATTTGCACAC-AAATATATTGATACACAT
1 GTAT-GATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACACAAAATGTATCGATACACAT
* * * *
42787 GTATAAAGTATCGATACTTGGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAAT
65 CTACAAAGTATCGATACTT-TAATTT-TAAACCTATTACTTTAAAGTAATAGGTAAATTAACAAT
* * *
42852 GTAAATAGTAAAAGTCTACCGGTATATTGATAATAGGCATAAATACCAAGTATCGATACTTTTAT
128 GTAAACAGTAAAAGTCTACCAGTATATTGATAATAGGCGTAAATACCAAGTATCGATACTTTTAT
42917 ATAG
193 ATAG
* * *
42921 GTATGTATTCTTTTATTCCATTATGCTTCTCAAACAATTTGCACGCAAAATGTATCGATACACAT
1 GTATG-ATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACACAAAATGTATCGATACACAT
* *
42986 CTACAAAGTATCGATACTTTCAATTTTAAAACCTATTACTTTAATGTAACAGGTAAATTAACAAT
65 CTACAAAGTATCGATACTTT-AATTTT-AAACCTATTACTTTAAAGTAATAGGTAAATTAACAAT
* *
43051 GTAAACTGTAAAAGTCTACCAATATATTGATAATAGGCGTAAATACCAAGTATCGATACTTTTAT
128 GTAAACAGTAAAAGTCTACCAGTATATTGATAATAGGCGTAAATACCAAGTATCGATACTTTTAT
43116 ATAG
193 ATAG
* * * * *
43120 GTACCGATACTTTTATTCCAGTGTTCTTTTCAAACAATTTGCACATAAAATGTATCGATACACAT
1 GTA-TGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACACAAAATGTATCGATACACAT
* * ** *
43185 ATATAAAGTATCGATACCAATAATTTTGAA---A-TACTTTAAAGTAATAGGTAAATTAACAATG
65 CTACAAAGTATCGATA-CTTTAATTTTAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATG
* * * * * * *
43246 TACAGAGTAAACATTTCTACCAGTGTAATGAAAATAGGCGTAAATGTCCAAGTATCGATACTTTT
129 TAAACAGTAAA-A-GTCTACCAGTATATTGATAATAGGCGTAAAT-ACCAAGTATCGATACTTTT
*
43311 ATATAA
191 ATATAG
* * * * *
43317 GTATCAATACTTTTATTCCAGTATGGTTCTCAAATAATATGCACACAAAATGTATTGATACACAT
1 GTAT-GATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACACAAAATGTATCGATACACAT
* *
43382 CT-CTAAAGTATCGATACTTTAAATTTCTAAACCTATTACTTTAAAGTAATAGTTAAAATAACAA
65 CTAC-AAAGTATCGATACTTT-AATTT-TAAACCTATTACTTTAAAGTAATAGGTAAATTAACAA
* ***
43446 TGTAAACAGTAAAAGTCTACCGGTATATTGATAATAAATGTAAATACCAAGTATCGATACTTTTA
127 TGTAAACAGTAAAAGTCTACCAGTATATTGATAATAGGCGTAAATACCAAGTATCGATACTTTTA
43511 TATAG
192 TATAG
**
43516 GTATCGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACACAAAATAAATCGATA
1 GTAT-GATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACACAAAATGTATCGATA
43576 TTAATAATTT
Statistics
Matches: 560, Mismatches: 78, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
194 36 0.06
195 2 0.00
196 28 0.05
197 96 0.17
198 45 0.08
199 288 0.51
200 26 0.05
201 2 0.00
202 37 0.07
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (196 bp):
GTATGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACACAAAATGTATCGATACACATC
TACAAAGTATCGATACTTTAATTTTAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTA
AACAGTAAAAGTCTACCAGTATATTGATAATAGGCGTAAATACCAAGTATCGATACTTTTATATA
G
Found at i:43340 original size:20 final size:20
Alignment explanation
Indices: 43295--43332 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43285 GTAAATGTCC
*
43295 AAGTATCGATACTTTTATAT
1 AAGTATCAATACTTTTATAT
43315 AAGTATCAATACTTTTAT
1 AAGTATCAATACTTTTAT
43333 TCCAGTATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (20 bp):
AAGTATCAATACTTTTATAT
Found at i:43486 original size:768 final size:764
Alignment explanation
Indices: 41955--43511 Score: 1752
Period size: 768 Copynumber: 2.0 Consensus size: 764
41945 TTTTATATAG
* * *
41955 GTATCTATACTTTTATTCCAGTATGTATATCAAACGATTTGCACACAAAATATATCTATACACAA
1 GTATCGATACTTTTATTCCAGTATGTATACCAAACAATTTGCACACAAAATATATCTATACACAA
* * * ** *
42020 CTATAAAGTATTGATACTTTCAAATTTGACATTTAATACTTTAAAGTTATAGGTAAATTAACAAT
66 CTATAAAGTATCGATACTTTCAAATTTAAAACCTAATACTTTAAAGTAATAGGTAAATTAACAAT
** *
42085 GTAAACAATAAAATCTATTGGTATATTGATAATAGACGTAAATACCAAATATCGATACTTTTATA
131 GTAAACAATAAAATCTACCGGTATATTGATAATAGACATAAATACCAAATATCGATACTTTTATA
* * * *
42150 TCGGTACCGATACTTTTATTTCAGTATTCTTCTCAAACAATTTGCACGCAAAATATATCGATAGA
196 TAGGTACCGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATATATCGATACA
* * *
42215 CATATATAAAGTATCAATACTAATAATTTCGAAACATATTACTTTAAAGTAATAGGTAAATTAAC
261 CATATACAAAGTATCAATACTAATAATTTCAAAACATATTACTTTAAAGTAACAGGTAAATTAAC
* * ** * *
42280 AATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATATGGTAAATGTCCAAGTATCAATACT
326 AATGTAAACGGTAAAAG-TTCTACCAATATAATGAAAATAGGGTAAATGACCAAGTATCAATACT
** * * **
42345 TTTATATAAGTATTGATACTTTTACTCCATTATGCTTATAAAATAATCTGCATGCAAAATGTATC
390 TTTATATAAGTACCGATACTTTTACTCCAGTATGCTTATAAAACAATCTGCACACAAAATGTATC
* **
42410 AATACACATCTATAAAGTATCGATACTTTATATTTCAAAACCTATTACTTTAAAGTAATAGGTAA
455 AATACACATATATAAAGTATCGATACAATATATTTCAAAA-C-ATTACTTTAAAGTAATAGGTAA
* ** * *
42475 ATTAACAATGTAAACAGTAAAATTCTGCTGGTATATTGATAATAGGCGTAAATACCAAGTATCAA
518 ATTAACAATGTAAACAGTAAAATTCTACCAGTATAATGAAAATAGGCGTAAATACCAAGTATCAA
* * *
42540 TCCTTTTATACTTTTATTCCAGTATGTTTCTCAAATAATTTGCACACAAAATGAATCAATACACA
583 TCATTTTATACTTTTATTCCAGTATGGTTCTCAAATAATATGCACACAAAATGAATCAATACACA
* * *
42605 TATAAAAAGTATCGATACTAATAATTTCAAATCCTATTACTTTGAGGTAATAGGTAAATTAACAA
648 TATAAAAAGTATCGATACTAATAATTTCAAATCCTATTACTTTAAAGTAATAGGTAAAATAACAA
**** * *
42670 TGTACTTGGTAAATATTTCTATCGATATAATGAAAATAGATGTAAATGT-T-CAA
713 TGTAAACAGTAAATATGTCTACCGATATAATG--AATAGA-GTAAATGTATACAA
*
42723 GTATCGATACTTTTATTCCAGTATGCT-TCCCAAACAATTTGCACAC-AAATATAT-TGATACAC
1 GTATCGATACTTTTATTCCAGTATG-TATACCAAACAATTTGCACACAAAATATATCT-ATACAC
** ** *
42785 ATGTATAAAGTATCGATAC-TTGGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAAC
64 AACTATAAAGTATCGATACTTTCAAATTT-AAAACCTAATACTTTAAAGTAATAGGTAAATTAAC
* * * *
42849 AATGTAAATAGTAAAAGTCTACCGGTATATTGATAATAGGCATAAATACCAAGTATCGATACTTT
128 AATGTAAACAATAAAA-TCTACCGGTATATTGATAATAGACATAAATACCAAATATCGATACTTT
* * * *
42914 TATATAGGTA-TGTATTCTTTTATTCCATTATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
192 TATATAGGTACCG-ATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATATATCG
* * * * * *
42978 ATACACATCTACAAAGTATCGATACT-TTCAATTTTAAAACCTATTACTTTAATGTAACAGGTAA
256 ATACACATATACAAAGTATCAATACTAAT-AATTTCAAAACATATTACTTTAAAGTAACAGGTAA
* * *
43042 ATTAACAATGTAAACTGTAAAAG-TCTACCAATATATTGATAATAGGCGTAAAT-ACCAAGTATC
320 ATTAACAATGTAAACGGTAAAAGTTCTACCAATATAATGAAAATAGG-GTAAATGACCAAGTATC
* * * * * * * * *
43105 GATACTTTTATATAGGTACCGATACTTTTATTCCAGTGTTCTTTTCAAACAATTTGCACATAAAA
384 AATACTTTTATATAAGTACCGATACTTTTACTCCAGTATGCTTATAAAACAATCTGCACACAAAA
* **
43170 TGTATCGATACACATATATAAAGTATCGATACCAATA-ATTT-TGAA-A-TACTTTAAAGTAATA
449 TGTATCAATACACATATATAAAGTATCGATA-CAATATATTTCAAAACATTACTTTAAAGTAATA
* * * *
43231 GGTAAATTAACAATGTACAGAGTAAACATTTCTACCAGTGTAATGAAAATAGGCGTAAATGTCCA
513 GGTAAATTAACAATGTAAACAGTAAA-A-TTCTACCAGTATAATGAAAATAGGCGTAAAT-ACCA
*
43296 AGTATCGATACTTTTATATAAGTATCAATACTTTTATTCCAGTATGGTTCTCAAATAATATGCAC
575 AGTATC-A-A---TCAT-T---T-T--ATACTTTTATTCCAGTATGGTTCTCAAATAATATGCAC
* ** * ** *
43361 ACAAAATGTATTGATACACATCTCTAAAGTATCGATACT-TTAAATTTCTAAA-CCTATTACTTT
628 ACAAAATGAATCAATACACATATAAAAAGTATCGATACTAAT-AATTTC-AAATCCTATTACTTT
* * *
43424 AAAGTAATAGTTAAAATAACAATGTAAACAGTAAA-A-GTCTACCGGTATATTG-ATA-A-TAAA
691 AAAGTAATAGGTAAAATAACAATGTAAACAGTAAATATGTCTACCGATATAATGAATAGAGTAAA
43484 TGTAAATACCAA
756 TGT--ATA-CAA
43496 GTATCGATACTTTTAT
1 GTATCGATACTTTTAT
43512 ATAGGTATCG
Statistics
Matches: 658, Mismatches: 101, Indels: 55
0.81 0.12 0.07
Matches are distributed among these distances:
761 39 0.06
762 2 0.00
763 25 0.04
764 9 0.01
765 3 0.00
766 119 0.18
767 84 0.13
768 217 0.33
769 3 0.00
770 2 0.00
771 4 0.01
773 20 0.03
774 13 0.02
775 2 0.00
776 113 0.17
777 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (764 bp):
GTATCGATACTTTTATTCCAGTATGTATACCAAACAATTTGCACACAAAATATATCTATACACAA
CTATAAAGTATCGATACTTTCAAATTTAAAACCTAATACTTTAAAGTAATAGGTAAATTAACAAT
GTAAACAATAAAATCTACCGGTATATTGATAATAGACATAAATACCAAATATCGATACTTTTATA
TAGGTACCGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATATATCGATACA
CATATACAAAGTATCAATACTAATAATTTCAAAACATATTACTTTAAAGTAACAGGTAAATTAAC
AATGTAAACGGTAAAAGTTCTACCAATATAATGAAAATAGGGTAAATGACCAAGTATCAATACTT
TTATATAAGTACCGATACTTTTACTCCAGTATGCTTATAAAACAATCTGCACACAAAATGTATCA
ATACACATATATAAAGTATCGATACAATATATTTCAAAACATTACTTTAAAGTAATAGGTAAATT
AACAATGTAAACAGTAAAATTCTACCAGTATAATGAAAATAGGCGTAAATACCAAGTATCAATCA
TTTTATACTTTTATTCCAGTATGGTTCTCAAATAATATGCACACAAAATGAATCAATACACATAT
AAAAAGTATCGATACTAATAATTTCAAATCCTATTACTTTAAAGTAATAGGTAAAATAACAATGT
AAACAGTAAATATGTCTACCGATATAATGAATAGAGTAAATGTATACAA
Found at i:43856 original size:81 final size:81
Alignment explanation
Indices: 43754--44282 Score: 783
Period size: 81 Copynumber: 6.6 Consensus size: 81
43744 ATAAAGTATC
*
43754 GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTGTTTAACCTTTCA
1 GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA
*
43819 TCTAACTGGTATAATT
66 TCTAACTGGCATAATT
*
43835 GACACCTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA
1 GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA
43900 TCTAACTGGCATAATT
66 TCTAACTGGCATAATT
* *** * * *
43916 GACACATTTCTTTAAAATACACAGCTAGACCATTAATATTTTACTCAAAGGTATTTAACCTTTCA
1 GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA
*
43981 TCTAACTGGCATAACT
66 TCTAACTGGCATAATT
* * * *
43997 GACACATTTCTGCCAAATACACAACTAGGCCATTAATCTTTTACTCAAATGTATTTAACCTTTCA
1 GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA
44062 TCTAACTGGCATAATT
66 TCTAACTGGCATAATT
* * * *
44078 GACACCTTTCTGCCAAATGCACAGTTAGGCCATTAATCTTTTACTTAAAGGTTTTTAATCTTTCA
1 GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA
* *
44143 TATAACTAGCATAATT
66 TCTAACTGGCATAATT
* * *
44159 GACACC-TTCTGCCAAATGCACAACTAGGCCATTAATATTTTACTCAAAGGTATTTAATCTTTCA
1 GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA
44223 TCTAACTGGCAT-ATT
66 TCTAACTGGCATAATT
* * * * *
44238 GACACTTTTTTACCAAATGAACAGCTAGGCTATTAATCTTTTACT
1 GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
44283 TTGGAATAAT
Statistics
Matches: 403, Mismatches: 44, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
79 8 0.02
80 95 0.24
81 300 0.74
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (81 bp):
GACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA
TCTAACTGGCATAATT
Found at i:44474 original size:55 final size:55
Alignment explanation
Indices: 44414--44530 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 55
44404 TATGTAGGTG
* * * ** * *
44414 GCACACACATTACCAATATC-GAAATTCATAAACTTCTTATGAATTTATTATTTTT
1 GCACACAAAGTACCAATA-CGGAAATTCATAAACTTATTAACAATTTATGAGTTTT
* *
44469 GCACACAAAGTGCCCATACGGAAATTCATAAACTTATTAACAATTTATGAGTTTT
1 GCACACAAAGTACCAATACGGAAATTCATAAACTTATTAACAATTTATGAGTTTT
44524 GCACACA
1 GCACACA
44531 TAGTGCCATT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 1 0.02
55 51 0.98
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (55 bp):
GCACACAAAGTACCAATACGGAAATTCATAAACTTATTAACAATTTATGAGTTTT
Found at i:44536 original size:55 final size:55
Alignment explanation
Indices: 44434--44537 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 55
44424 TACCAATATC
* ** * *
44434 GAAATTCATAAACTTCTTATGAATTTATTATTTTTGCACACAAAGTGCCCATACG
1 GAAATTCATAAACTTATTAACAATTTATGAGTTTTGCACACAAAGTGCCCATACG
*
44489 GAAATTCATAAACTTATTAACAATTTATGAGTTTTGCACACATAGTGCC
1 GAAATTCATAAACTTATTAACAATTTATGAGTTTTGCACACAAAGTGCC
44538 ATTTGGAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (55 bp):
GAAATTCATAAACTTATTAACAATTTATGAGTTTTGCACACAAAGTGCCCATACG
Found at i:50698 original size:37 final size:37
Alignment explanation
Indices: 50646--50809 Score: 123
Period size: 37 Copynumber: 4.6 Consensus size: 37
50636 TATATTTTTG
* * * *
50646 AAATCATATAGTATATAAATATTTCT-GAATGTTTTCTA
1 AAAT-ATATATTATATATATATTTCTAAAACGTTTTC-A
50684 AAATATATATTATATATAT-TTTCTAAAACGTTTTCA
1 AAATATATATTATATATATATTTCTAAAACGTTTTCA
* * *
50720 ATAT-TATATTATATATATATTTTTAAAAATGTTTT--
1 AAATATATATTATATATATATTTCT-AAAACGTTTTCA
* *
50755 AAA-A-CTA-TATATATA-CTTTC-AGAAACGTTTTCA
1 AAATATATATTATATATATATTTCTA-AAACGTTTTCA
*
50788 AAACTATGTATTATATATATAT
1 AAA-TATATATTATATATATAT
50810 ATATTTCAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 24
0.72 0.10 0.17
Matches are distributed among these distances:
30 1 0.01
31 8 0.08
32 3 0.03
33 11 0.11
34 2 0.02
35 17 0.17
36 15 0.15
37 38 0.38
38 5 0.05
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (37 bp):
AAATATATATTATATATATATTTCTAAAACGTTTTCA
Found at i:50767 original size:31 final size:32
Alignment explanation
Indices: 50694--50803 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 32
50684 AAATATATAT
* *
50694 TATATATATTTTCTAAAACGTTTTCAATATTATATTA
1 TATATATATTTTCAAAAACGTTTTC-A-A--A-ACTA
* *
50731 TATATATATTTTTAAAAATGTTTT-AAAACTA
1 TATATATATTTTCAAAAACGTTTTCAAAACTA
* *
50762 TATATATACTTTCAGAAACGTTTTCAAAACTA
1 TATATATATTTTCAAAAACGTTTTCAAAACTA
*
50794 TGTATTATAT
1 TATA-TATAT
50804 ATATATATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 23 0.38
32 11 0.18
33 4 0.07
34 1 0.02
35 1 0.02
37 21 0.34
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (32 bp):
TATATATATTTTCAAAAACGTTTTCAAAACTA
Found at i:50853 original size:43 final size:42
Alignment explanation
Indices: 50760--50857 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 42
50750 GTTTTAAAAC
* * *
50760 TATATATATACTTTCAGAAACGTTTTCAAAACTATGTATTATA
1 TATATATATA-TTTCAAAAACATTTTCAAAACTATCTATTATA
*
50803 TATATATATATTTCAAAAATATTTTCAAAAACTATTCTA-TATTA
1 TATATATATATTTCAAAAACATTTTC-AAAACTA-TCTATTA-TA
50847 TCATATATATA
1 T-ATATATATA
50858 CTAAATAAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
42 13 0.28
43 19 0.40
44 6 0.13
45 9 0.19
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (42 bp):
TATATATATATTTCAAAAACATTTTCAAAACTATCTATTATA
Found at i:51551 original size:201 final size:201
Alignment explanation
Indices: 51206--51586 Score: 525
Period size: 201 Copynumber: 1.9 Consensus size: 201
51196 AAGTGGCTTC
* * * * * *
51206 TTGTTGCCAAATCGTAGTCAACCTAGGTCTTCTTCTTGGCTTAAAGACCCTGGTTTAAAATTTAA
1 TTGTTGCCAAATCGTAGCCAACCCAGGTCTTCTTCTTGACTTAAAGACCCTAGTATAAAATTCAA
*** * *
51271 CCTAAAAGTAGTTCATCGATGCTACCATGTGGTTTATATGCTCTTGAGCTGAATGGAATCGAACT
66 CCTAAAAGTAGTTCATCGATGCTACCATCCAGTTAATATGCTCTCGAGCTGAATGGAATCGAACT
* * *
51336 TGAAGATTTTTGTTGACAGATAGCCCTTCTTGCCTTGAGTTATGTTGTAAATTTAACTAGGATAT
131 CGAAGATTTTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTAACTAGGATAT
51401 AGTTCA
196 AGTTCA
* * *
51407 TTGTTGCTAAATCGTAGCCAACCCAGGTCTTCTTCTTGACTTAAAGACCTTAGTATAAGATTCAA
1 TTGTTGCCAAATCGTAGCCAACCCAGGTCTTCTTCTTGACTTAAAGACCCTAGTATAAAATTCAA
* * * *
51472 -CTGGAAAGTAGTTCCTCGTTGCTACTATCCAGTTAATATG-TCATCGAGCTGAATGGAATCGAA
66 CCT-AAAAGTAGTTCATCGATGCTACCATCCAGTTAATATGCTC-TCGAGCTGAATGGAATCGAA
51535 CTCGAA-AGTTTTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAA
129 CTCGAAGA-TTTTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAA
51587 TAGGCTGGGA
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
200 5 0.03
201 151 0.97
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (201 bp):
TTGTTGCCAAATCGTAGCCAACCCAGGTCTTCTTCTTGACTTAAAGACCCTAGTATAAAATTCAA
CCTAAAAGTAGTTCATCGATGCTACCATCCAGTTAATATGCTCTCGAGCTGAATGGAATCGAACT
CGAAGATTTTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTAACTAGGATAT
AGTTCA
Found at i:53179 original size:98 final size:98
Alignment explanation
Indices: 53003--53190 Score: 216
Period size: 98 Copynumber: 1.9 Consensus size: 98
52993 TTGTGATTTC
* *** * * *
53003 CCTTTATCAGCTAGCTAAATCTTATCCATAAAGCCAAGGTGTTTAACTAATTTCTCTAAAGGGAC
1 CCTTTATCAGCTAGCTAAATCTTATACATAAAGCCAAGGCCATTAACCAATTGCTCTAAAGGAAC
* * * *
53068 AGCCCAAGCTTTATTGTATATATATTATAATCA
66 AACCCAAGATTTATTATATACATATTATAATCA
* * * *
53101 CCTTTATCAGGCTAGCTAAATCTTATATATAAAGTC-GGGCCATTAACCAATTGCTCTAGAGGAA
1 CCTTTATCA-GCTAGCTAAATCTTATACATAAAGCCAAGGCCATTAACCAATTGCTCTAAAGGAA
*
53165 CAACTCAAGATTTATTATATACATAT
65 CAACCCAAGATTTATTATATACATAT
53191 AATATTATAA
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
98 50 0.68
99 23 0.32
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (98 bp):
CCTTTATCAGCTAGCTAAATCTTATACATAAAGCCAAGGCCATTAACCAATTGCTCTAAAGGAAC
AACCCAAGATTTATTATATACATATTATAATCA
Found at i:58508 original size:38 final size:40
Alignment explanation
Indices: 58445--58519 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
58435 TTTTTAAAAC
58445 TATATATATACTTTCAAAAACATTTTC-AAAACTATAGAT
1 TATATATATACTTTCAAAAACATTTTCAAAAACTATAGAT
*
58484 TATATATATA-TTTCAAAAATATTTTCAAAAACTATA
1 TATATATATACTTTCAAAAACATTTTCAAAAACTATA
58520 TTATATTATC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 15 0.44
39 19 0.56
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (40 bp):
TATATATATACTTTCAAAAACATTTTCAAAAACTATAGAT
Found at i:58511 original size:12 final size:13
Alignment explanation
Indices: 58450--58521 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 13
58440 AAAACTATAT
58450 ATATACTTTCAAAA
1 ATATA-TTTCAAAA
*
58464 ACAT-TTTCAAAA
1 ATATATTTCAAAA
* * * *
58476 CTATAGATT-ATAT
1 ATATA-TTTCAAAA
58489 ATATATTTCAAAA
1 ATATATTTCAAAA
58502 ATAT-TTTCAAAA
1 ATATATTTCAAAA
58514 ACTATATT
1 A-TATATT
58522 ATATTATCAT
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
12 21 0.49
13 15 0.35
14 7 0.16
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.40
Consensus pattern (13 bp):
ATATATTTCAAAA
Found at i:66556 original size:34 final size:31
Alignment explanation
Indices: 66518--66608 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 31
66508 AATAATATCA
66518 TTTAATTTGAAATATTCAAAAGATATATACATGT
1 TTTAATTTGAAATATTCAAAAG-TATAT--ATGT
* * *
66552 TTTAATCATCAAA-CTT-AAATAG-ATAT-TGT
1 TTTAAT-TTGAAATATTCAAA-AGTATATATGT
66581 TTTAATTTGAAATATTCAAAAGTATATA
1 TTTAATTTGAAATATTCAAAAGTATATA
66609 ATTATCATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
28 4 0.09
29 13 0.29
30 7 0.16
32 4 0.09
33 3 0.07
34 10 0.22
35 4 0.09
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTAATTTGAAATATTCAAAAGTATATATGT
Found at i:72737 original size:14 final size:13
Alignment explanation
Indices: 72716--72754 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
72706 ATATAAATAA
72716 TTTTAAATTTTAT
1 TTTTAAATTTTAT
72729 TTATTAAATTTTTTAT
1 TT-TTAAA--TTTTAT
72745 TTTTAAATTT
1 TTTTAAATTT
72755 AAATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.22
14 5 0.22
15 5 0.22
16 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAT
Found at i:72750 original size:15 final size:16
Alignment explanation
Indices: 72723--72754 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
72713 TAATTTTAAA
72723 TTTTATTTATTAAATT
1 TTTTATTTATTAAATT
72739 TTTTATTT-TTAAATT
1 TTTTATTTATTAAATT
72754 T
1 T
72755 AAATATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTTATTAAATT
Found at i:72920 original size:24 final size:23
Alignment explanation
Indices: 72874--72920 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
72864 TATCATGAAC
*
72874 TTAATTTTTAAAATAAATTAATA
1 TTAATTTTTAAAATAAATAAATA
*
72897 TTAATTTTATAAAATATATAAATA
1 TTAATTTT-TAAAATAAATAAATA
72921 AATATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAATTTTTAAAATAAATAAATA
Found at i:72945 original size:28 final size:27
Alignment explanation
Indices: 72884--72963 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 27
72874 TTAATTTTTA
*
72884 AAATAAATTAATA-TTAATTTTATAAAAT
1 AAATAAATAAATATTTAA-TTT-TAAAAT
* *
72912 ATATAAATAAATATTTAATTTTAAATT
1 AAATAAATAAATATTTAATTTTAAAAT
**
72939 GAAATAAGA-ATTTATTTAATTTTAA
1 -AAATAA-ATAAATATTTAATTTTAA
72964 TTAATATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 5 0.12
28 33 0.77
29 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (27 bp):
AAATAAATAAATATTTAATTTTAAAAT
Found at i:73331 original size:14 final size:15
Alignment explanation
Indices: 73312--73343 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
73302 TCAACACTAT
73312 ATTAGTTAAATAA-A
1 ATTAGTTAAATAATA
73326 ATTAGTTAAATAATA
1 ATTAGTTAAATAATA
73341 ATT
1 ATT
73344 TAAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
ATTAGTTAAATAATA
Found at i:73954 original size:12 final size:10
Alignment explanation
Indices: 73914--73955 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
73904 TTTATCACAC
73914 CAAATTCTCT
1 CAAATTCTCT
73924 CAAATTCTCT
1 CAAATTCTCT
73934 -AAATTTCTCT
1 CAAA-TTCTCT
*
73944 CAAATACTCT
1 CAAATTCTCT
73954 CA
1 CA
73956 CTTTTTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.10
10 23 0.79
11 3 0.10
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.38
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:74031 original size:17 final size:18
Alignment explanation
Indices: 74001--74034 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
73991 ATGTATATAA
74001 TTTATTTAAGTATTTTAC
1 TTTATTTAAGTATTTTAC
74019 TTTATTTAA-TATTTTA
1 TTTATTTAAGTATTTTA
74035 TTAATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTATTTAAGTATTTTAC
Found at i:74292 original size:111 final size:111
Alignment explanation
Indices: 74098--74430 Score: 603
Period size: 111 Copynumber: 3.0 Consensus size: 111
74088 TGGAAATCAT
* ** *
74098 ATATCTCTACACTTTGCTGATACGGTAACATTACAACTTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
74163 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
74209 ATATCTCAACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
74274 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
74320 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
74385 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
74431 TTTTTGTAAT
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 214 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:76307 original size:9 final size:9
Alignment explanation
Indices: 76292--76357 Score: 60
Period size: 9 Copynumber: 7.3 Consensus size: 9
76282 TCAGGATGAC
*
76292 GACGACGAC
1 GACGACGAT
*
76301 GATGACGAT
1 GACGACGAT
* *
76310 AATGACGAT
1 GACGACGAT
*
76319 GACGATGAT
1 GACGACGAT
*
76328 GATGACGAT
1 GACGACGAT
*
76337 GACGACGAC
1 GACGACGAT
*
76346 GACGATGAT
1 GACGACGAT
76355 GAC
1 GAC
76358 AGCGAGGAGT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.15
Consensus pattern (9 bp):
GACGACGAT
Found at i:79805 original size:51 final size:50
Alignment explanation
Indices: 79702--79813 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 50
79692 CCCCTACGTG
* * *
79702 GCGTATAGCGCGGAGCATGGGGCTCGATATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGAGCAGGGGGCGCGATATACCCCACGTG-AACCCAATCA
* *
79753 GCGTATAGCGCGGTA-CAGGGGGCGCGCTATACTCCACGTG-ACGCCAAATCA
1 GCGTATAGCGCGG-AGCAGGGGGCGCGATATACCCCACGTGAAC-CC-AATCA
*
79804 GCATATAGCG
1 GCGTATAGCG
79814 TTGTTCAGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
49 2 0.04
50 2 0.04
51 47 0.90
52 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.30, T:0.17
Consensus pattern (50 bp):
GCGTATAGCGCGGAGCAGGGGGCGCGATATACCCCACGTGAACCCAATCA
Found at i:81876 original size:96 final size:96
Alignment explanation
Indices: 81709--81898 Score: 256
Period size: 96 Copynumber: 2.0 Consensus size: 96
81699 TAGTAACCAA
* * * * * *
81709 TAGATTTCATGATCCATAAATCAGAAACAATCATATTTTCTAGTGAAAACATGAAACCATATAAC
1 TAGATTCCATGATCCATAAAACAGAAACAATAATATTTTATAGTGAAAACATGAAACCAGAGAAC
*
81774 ACATTTCAGGTAACCATAGTTCATAAACCTG
66 ACATTTCAGGCAACCATAGTTCATAAACCTG
* * * *
81805 TAGATTCCATGATCTATAAAACA-AGAACGATAATATTTTATAGTGAAAACATGTAACCAGGGAA
1 TAGATTCCATGATCCATAAAACAGA-AACAATAATATTTTATAGTGAAAACATGAAACCAGAGAA
*
81869 CATATTTCAGGCAACCATAGTTCATAAACC
65 CACATTTCAGGCAACCATAGTTCATAAACC
81899 AGTAAATTAG
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
95 1 0.01
96 80 0.99
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (96 bp):
TAGATTCCATGATCCATAAAACAGAAACAATAATATTTTATAGTGAAAACATGAAACCAGAGAAC
ACATTTCAGGCAACCATAGTTCATAAACCTG
Found at i:85719 original size:138 final size:140
Alignment explanation
Indices: 85554--85831 Score: 542
Period size: 138 Copynumber: 2.0 Consensus size: 140
85544 GGTTTCTAGT
85554 TATCTTTAATCTTTTTTATATACTATTTAGTATTTGTATGGATTTACTTAACTTTGCAAATGTTG
1 TATCTTTAATCTTTTTTATATACTATTTAGTATTTGTATGGATTTACTTAACTTTGCAAATGTTG
85619 -AAGGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGAC-T
66 AAAGGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTT
85682 TGAATTTCCA
131 TGAATTTCCA
85692 TATCTTTAATCTTTTTTATATACTATTTAGTATTTGTATGGATTTACTTAACTTTGCAAATGTTG
1 TATCTTTAATCTTTTTTATATACTATTTAGTATTTGTATGGATTTACTTAACTTTGCAAATGTTG
85757 AAAGGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTT
66 AAAGGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTT
85822 TGAATTTCCA
131 TGAATTTCCA
85832 GAGAGAGATT
Statistics
Matches: 138, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
138 65 0.47
139 62 0.45
140 11 0.08
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (140 bp):
TATCTTTAATCTTTTTTATATACTATTTAGTATTTGTATGGATTTACTTAACTTTGCAAATGTTG
AAAGGGGATATGAACCATTGTTTAAAATTCAACTTAACTTCCTTGATTAAAAAAAACCTTGACTT
TGAATTTCCA
Found at i:88483 original size:2 final size:2
Alignment explanation
Indices: 88476--88511 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
88466 AGTTCATAAC
88476 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
88512 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.