Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007404.1 Hibiscus syriacus cultivar Beakdansim tig00020006_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: 64739
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:7933 original size:5 final size:5
Alignment explanation
Indices: 7923--8118 Score: 356
Period size: 5 Copynumber: 38.4 Consensus size: 5
7913 GGTACACTAC
7923 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
7973 TAATA TAATAA TATATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAAT-A TA-ATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
8025 TAATATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 T-A-ATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
8077 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
8119 TAGTCTAAGA
Statistics
Matches: 187, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
5 173 0.93
6 8 0.04
7 6 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:9946 original size:23 final size:23
Alignment explanation
Indices: 9920--9967 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
9910 ATAAAGTACA
*
9920 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
9943 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
9966 AT
1 AT
9968 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:10373 original size:21 final size:20
Alignment explanation
Indices: 10343--10396 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
10333 GATAGACACT
*
10343 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
10364 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
10387 TTACATTATA
1 TTACATTATA
10397 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:10384 original size:23 final size:23
Alignment explanation
Indices: 10358--10420 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
10348 ATATAACCAT
10358 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
10381 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
10404 TACCTATTACATCATAT
1 TACCTATTACATTATAT
10421 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:13402 original size:183 final size:184
Alignment explanation
Indices: 12973--13633 Score: 1261
Period size: 184 Copynumber: 3.6 Consensus size: 184
12963 TTTTAAATGG
** *
12973 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATACCGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
13038 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
13103 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
13157 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
13222 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
13287 GATGTGTAAAATGTCGACAC-TTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
13340 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
13405 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
13470 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
13524 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
13589 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATT
13634 TTATATAATA
Statistics
Matches: 470, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
183 181 0.39
184 289 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
Found at i:15014 original size:3 final size:3
Alignment explanation
Indices: 15006--15056 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
14996 ACTTGTTTGG
* * * *
15006 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
15054 ATC
1 ATC
15057 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:15023 original size:12 final size:12
Alignment explanation
Indices: 15006--15068 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
14996 ACTTGTTTGG
15006 ATCATCATCTTC
1 ATCATCATCTTC
*
15018 ATCATCATCGTC
1 ATCATCATCTTC
*
15030 ATCATCATCATC
1 ATCATCATCTTC
*
15042 ATCGTCATCTTC
1 ATCATCATCTTC
* *
15054 ATCGTCAGCTTC
1 ATCATCATCTTC
15066 ATC
1 ATC
15069 TTCTGCGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:15067 original size:18 final size:18
Alignment explanation
Indices: 15010--15071 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
15000 GTTTGGATCA
15010 TCATCTTCATCATCATCG
1 TCATCTTCATCATCATCG
*
15028 TCATCATCATCATCATCG
1 TCATCTTCATCATCATCG
* * *
15046 TCATCTTCATCGTCAGCT
1 TCATCTTCATCATCATCG
15064 TCATCTTC
1 TCATCTTC
15072 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCATCATCG
Found at i:15071 original size:6 final size:6
Alignment explanation
Indices: 15010--15071 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
15000 GTTTGGATCA
* * * * * *
15010 TCATCT TCATCA TCATCG TCATCA TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
15058 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
15072 TGCGACCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:17020 original size:198 final size:199
Alignment explanation
Indices: 16534--18675 Score: 3781
Period size: 198 Copynumber: 10.8 Consensus size: 199
16524 TTTAAATTAG
* *
16534 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
16599 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
16664 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
16729 AAAA
196 AAAA
16733 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
16798 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * ***
16863 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
16927 AAAA
196 AAAA
16931 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
16996 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
17061 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
*
17126 TAAAA
195 AAAAA
17131 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
17195 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * ***
17259 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
17323 AAAA
196 AAAA
* *
17327 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
17392 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAA
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
17457 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-GA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
17521 AAAAA
195 AAAAA
17526 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
17591 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * ***
17656 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
17720 AAAA
196 AAAA
17724 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
17789 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
17854 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
17918 AAAA
196 AAAA
17922 TATCG--ACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
17985 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * ***
18050 CGACACTTTTTTATATATAGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
18114 AAAAAA
194 AAAAAA
18120 TATCGACACAAACTATATTAGTGTCG--ACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
18183 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
18247 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-GAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
18311 AAAA
196 AAAA
18315 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
18380 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
18445 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
18510 AAAAA
195 AAAAA
18515 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
18580 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
18645 CGACACTTTTTTATATATGGATCGACACTTT
131 CGACAC-TTTTTATATATGGATCGACACTTT
18676 TTTAATGTGT
Statistics
Matches: 1852, Mismatches: 72, Indels: 37
0.94 0.04 0.02
Matches are distributed among these distances:
195 32 0.02
196 233 0.13
197 283 0.15
198 534 0.29
199 500 0.27
200 270 0.15
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAA
Found at i:17326 original size:397 final size:396
Alignment explanation
Indices: 16534--18675 Score: 4012
Period size: 397 Copynumber: 5.4 Consensus size: 396
16524 TTTAAATTAG
* *
16534 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
16599 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
16664 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
16729 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
16794 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
16859 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
325 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
16924 AAAAAAA
390 AAAAAAA
16931 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
16996 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
17061 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
17126 TAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCG
195 -AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
17190 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTT
259 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
17254 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG
324 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG
17319 AAAAAAAA
389 AAAAAAAA
* *
17327 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
17392 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAA
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
17457 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
17522 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
17587 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
17652 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
325 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
17717 AAAAAAA
390 AAAAAAA
17724 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
17789 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
17854 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA-
17918 AAAATATCG--ACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
17981 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
18046 GGATCGACACTTTTTTATATATAGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG
325 GGATCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG
18111 AAAAAAAAA
389 -AAAAAAAA
18120 TATCGACACAAACTATATTAGTGTCG--ACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
18183 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
18247 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
18312 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
*
18377 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
* * ***
18442 GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
326 GATCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGG
*
18507 GAAAAAAA
389 AAAAAAAA
18515 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
18580 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
18645 CGACACTTTTTTATATATGGATCGACACTTT
131 CGACAC-TTTTTATATATGGATCGACACTTT
18676 TTTAATGTGT
Statistics
Matches: 1712, Mismatches: 18, Indels: 28
0.97 0.01 0.02
Matches are distributed among these distances:
393 28 0.02
394 274 0.16
395 359 0.21
396 396 0.23
397 504 0.29
398 127 0.07
399 24 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (396 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAA
AAAAAA
Found at i:18118 original size:793 final size:791
Alignment explanation
Indices: 16534--18675 Score: 4053
Period size: 793 Copynumber: 2.7 Consensus size: 791
16524 TTTAAATTAG
16534 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
16599 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
16664 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
16729 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
16794 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
16859 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
325 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
16924 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
390 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
16989 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
455 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
17054 TTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATT
520 TTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATT
17119 CTGGGAATAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT
585 CTGGGAATAAAATATCGA-ACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT
17184 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGAT
649 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGAT
*
17249 GATTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCAT
714 GATTTGGGATCGACACTTTTTATATATAGATCGACACTTTATTGATGCACCTTGTAAAAATTCAT
17314 TCTGGAAAAAAAA
779 TCTGGAAAAAAAA
17327 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
17392 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAA
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
17457 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
17522 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
17587 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
17652 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
325 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
17717 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
390 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
17782 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
455 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
17847 TTGGGATCGACAC-TTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATT
520 TTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATT
17910 CTGGGAATAAAATATCG-ACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATA
585 CTGGGAATAAAATATCGAACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-
17974 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGAT
649 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGAT
18039 GATTTTGGGATCGACACTTTTTTATATATAGATCGACACTTTATTGATGCACCTTGTAAAAATTC
714 GA-TTTGGGATCGACAC-TTTTTATATATAGATCGACACTTTATTGATGCACCTTGTAAAAATTC
18104 ATTCTGGAAAAAAAAA
777 ATTCTGG-AAAAAAAA
* *
18120 TATCGACACAAACTATATTAGTGTCG--ACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
18183 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
18247 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
18312 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
*
18377 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
* * ***
18442 GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
326 GATCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGG
*
18507 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
389 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
*
18572 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
454 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
18637 TTTGGGATCGACACTTTTTTATATATGGATCGACACTTT
519 TTTGGGATCGACACTTTTTTATATATGGATCGACACTTT
18676 TTTAATGTGT
Statistics
Matches: 1327, Mismatches: 13, Indels: 18
0.98 0.01 0.01
Matches are distributed among these distances:
789 243 0.18
790 116 0.09
791 323 0.24
792 63 0.05
793 526 0.40
794 56 0.04
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (791 bp):
TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAA
AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
TGGGAATAAAATATCGAACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAA
ACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
TTTGGGATCGACACTTTTTATATATAGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTC
TGGAAAAAAAA
Found at i:18777 original size:37 final size:38
Alignment explanation
Indices: 18736--18815 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
18726 TCTCATTCAT
*
18736 AATTAT-ATTCACATAAAAAAATATAAATCGTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
** * * *
18773 AATTATAAATCGTATACAAAATTATAAATCTTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
18811 AATTA
1 AATTA
18816 ACTCGACATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 6 0.17
38 30 0.83
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (38 bp):
AATTATAAATCACATAAAAAAATATAAATCGTATACAA
Found at i:18779 original size:19 final size:19
Alignment explanation
Indices: 18752--18815 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
18742 ATTCACATAA
*
18752 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
18771 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
18790 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
18809 AAAATTA
1 AAAATTA
18816 ACTCGACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:20647 original size:33 final size:33
Alignment explanation
Indices: 20610--20675 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
20600 CATCTTAATA
*
20610 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
20643 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
20676 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:22818 original size:24 final size:24
Alignment explanation
Indices: 22781--22833 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
22771 CCGTTCTATC
22781 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
22805 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
22829 TATTT
1 TATTT
22834 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:23024 original size:20 final size:19
Alignment explanation
Indices: 22978--23024 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
22968 TCCGGTATCA
*
22978 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
22997 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
23018 TTTTACC
1 TTTTACC
23025 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:23172 original size:20 final size:20
Alignment explanation
Indices: 23145--23191 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
23135 ACACTTTTAA
23145 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
23164 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
23185 TTTTACC
1 TTTTACC
23192 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:28363 original size:15 final size:15
Alignment explanation
Indices: 28339--28368 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28329 TAATTCGATA
28339 GCTATCTGGTCTACT
1 GCTATCTGGTCTACT
*
28354 GCTATTTGGTCTACT
1 GCTATCTGGTCTACT
28369 AGTCTATTAT
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:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (15 bp):
GCTATCTGGTCTACT
Found at i:34827 original size:25 final size:23
Alignment explanation
Indices: 34781--34836 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 23
34771 CGAAAATTCG
*
34781 ATTTGATTTAAAAAATTGATTTA
1 ATTTGATTAAAAAAATTGATTTA
34804 ATTTGATGTAAAAGAAATTGATTTA
1 ATTTGAT-TAAAA-AAATTGATTTA
34829 ATTTGATT
1 ATTTGATT
34837 TAATCTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.23
24 5 0.17
25 18 0.60
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (23 bp):
ATTTGATTAAAAAAATTGATTTA
Found at i:43143 original size:230 final size:223
Alignment explanation
Indices: 42796--43234 Score: 585
Period size: 230 Copynumber: 1.9 Consensus size: 223
42786 TATCGGATCT
* * * * *
42796 ATCCTAACCCATATAGGGACATGATTTGTTTAAACACAGTGTAAAACTAAAAGTCTTACATCTTT
1 ATCCTAACCCACACAAGGACATGATCTGTTTAAACACAATGTAAAACTAAAAGTCTTACATCTTT
** * *
42861 TTAGGATTATTCAATGAGAGAAATCAATGGTTGAGATTAATAGTAAGAAATGAGAATATATTCAT
66 TTAGGACCACTCAATGAGAGAAATCAATGGTTGAGATTAACAGTAAGAAATGAGAATATATTCAT
*
42926 TGGGAAAACAAACAAAGACTTAATCTCAGCCTTTGATTTCCCCCAATCCAATGGTCCTAAAAAGG
131 T--G--AAC-AA-AAAGACTTAATCTCAGCCATTGATTTCCCCCAATCCAATGGTCC-AAAAAGG
42991 TGTAAAACTCTTAATTTTACATTGGGTCTATCTGG
189 TGTAAAACTCTTAATTTTACATTGGGTCTATCTGG
* * * * *
43026 ATCCTAACCCACACAAGGACATGATCTGTTTACACCCAATGTAAAATTAAGAGTTTTACATCTTT
1 ATCCTAACCCACACAAGGACATGATCTGTTTAAACACAATGTAAAACTAAAAGTCTTACATCTTT
**
43091 TTAGGACCACT-AGATGAGAGAAATCAAAT-GTTGAGATTAACAGTTGGAAATGAGAATATATTC
66 TTAGGACCACTCA-ATGAGAGAAATC-AATGGTTGAGATTAACAGTAAGAAATGAGAATATATTC
* * * * *
43154 ATTGAACAAGATGAGTTAATCTCAGTCATTGATTTCCCTCAATCCAATGGTCCAAAAAGGTGTAA
129 ATTGAACAAAAAGACTTAATCTCAGCCATTGATTTCCCCCAATCCAATGGTCCAAAAAGGTGTAA
43219 AACTCTTAATTTTACA
194 AACTCTTAATTTTACA
43235 CTGATGTAAG
Statistics
Matches: 185, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
223 28 0.15
224 38 0.21
225 2 0.01
226 3 0.02
228 1 0.01
229 1 0.01
230 109 0.59
231 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (223 bp):
ATCCTAACCCACACAAGGACATGATCTGTTTAAACACAATGTAAAACTAAAAGTCTTACATCTTT
TTAGGACCACTCAATGAGAGAAATCAATGGTTGAGATTAACAGTAAGAAATGAGAATATATTCAT
TGAACAAAAAGACTTAATCTCAGCCATTGATTTCCCCCAATCCAATGGTCCAAAAAGGTGTAAAA
CTCTTAATTTTACATTGGGTCTATCTGG
Found at i:44254 original size:556 final size:558
Alignment explanation
Indices: 42875--44469 Score: 2341
Period size: 558 Copynumber: 2.9 Consensus size: 558
42865 GATTATTCAA
* * * *
42875 TGAGAGAAATCAATGGTTGAGATTAATAGTAAGAAATGAGAATATATTCATTGGGAAAACAAACA
1 TGAGGGAAATCAAAGGTTGAGATTAATAGTAGGAAATGAGAATATATTCACT--G-AAA-AAACA
* * * *
42940 AAGACTTAATCTCAGCCTTTGATTTCCCCCAATCCAATGGTCCTAAAAAGGTGTAAAACTCTTAA
62 AGGAGTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCTAAAAAGGTATAAAACTCTTAA
* ***
43005 TTTTACATTGGGTCTATCTGGATCCTAACCCACACAAGGACATGATCTGTTTACACCCAATGTAA
127 TTTTACATTGGGTCTAACTGGATCCTAACCCACATGGGGACATGATCTGTTTACACCCAATGTAA
* *
43070 AATTAAGAGTTTTACATCTTTTTAGGACCACTAGATGAGAGAAATCAAATGTTGAGATTAACAGT
192 AACTAAGAGTTTTACATCTTTTTAGGACCACTTGATGAGAGAAATCAAATGTTGAGATTAACAGT
* * * * * *
43135 TGGAAATGAGAATATATTCATTGAACAAGATGAGTTAATCTCAGTCATTGATTTCCCTCAATCCA
257 AGGAAATGAGAAGATATTCACTGAACAAAATGAGTTAATCTCAGCCTTTGATTTCCCTCAATCCA
* * *
43200 ATGGTCC-AAAAAGGTGTAAAACTCTTAATTTTACACTGATGTAAGTGGAATCTAACCTATATAG
322 ATGGTCCAAAAAAGGTGTAAAACTCTTAATTTTACATTG-TGTAAGTGGATTCTAACCCATATAG
* **
43264 GGGTAGGATCCATTTACACCTAGTGTAAAACTAAGAGTTTTACATCTTTTTAGGATAATTGGATT
386 GGGTATGATCCATTTACACCTAGTGTAAAACTAAGAGTTTTACATCTTTTTAGGACCATTGGATT
* * * * * * * *
43329 GAGAAAAATCAAATATTAAAATTAACTCTTTGTTTTTTTATATAGGGAGAGGATCCGTTTACACC
451 AAGGAAAATCAAATGTTGAGATTAACTCATTGTTTTTTTATACAGGGAGAGGATCCATTTACACC
43394 CAATGTAAAACTCTTGTTATACACCTTTTTAGGACAATTAGAT
516 CAATGTAAAACTCTTGTTATACACCTTTTTAGGACAATTAGAT
* * * * ** * *
43437 TTAGGAAAATCAAAGGCTAAGATTAATAGTAGGAAATGAGAAGGTATTCACTAAAAAAACATGGA
1 TGAGGGAAATCAAAGGTTGAGATTAATAGTAGGAAATGAGAATATATTCACTGAAAAAACAAGGA
* * * *
43502 GTTAATATCAACCTTTGATTTCCCTCAATCCAATGGTTCTAAAAATGTATAAAACTCTTAATTTT
66 GTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCTAAAAAGGTATAAAACTCTTAATTTT
* * *
43567 ACATTGGGTCTAAATGAATCCTAACCCACATGGGGATATGATCTGTTTACACCCAATGTAAAACT
131 ACATTGGGTCTAACTGGATCCTAACCCACATGGGGACATGATCTGTTTACACCCAATGTAAAACT
* * *
43632 AAGAGTTTTACATTTTTTTAGGACCACATGATGAGAGAAATCAAATGTTGAGATTAACAATAGGA
196 AAGAGTTTTACATCTTTTTAGGACCACTTGATGAGAGAAATCAAATGTTGAGATTAACAGTAGGA
43697 AATGAGAAGATATTCACTGAACAAAATGAGTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGG
261 AATGAGAAGATATTCACTGAACAAAATGAGTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGG
* * * *
43762 TCCAAAAAAGGTGTAAAACCCTTAATTTTATATTGTGTTAGTGGATTCTAACCCATATAGGGGCA
326 TCCAAAAAAGGTGTAAAACTCTTAATTTTACATTGTGTAAGTGGATTCTAACCCATATAGGGGTA
* *
43827 TGATCCATTTACACCTAGTGTAAAACTAAGAGTTTTACATCTTTTTAAGACCATTGGATTCAGGA
391 TGATCCATTTACACCTAGTGTAAAACTAAGAGTTTTACATCTTTTTAGGACCATTGGATTAAGGA
* * * * *
43892 AAATCAAATGTTGAGATTAACTCATTGTTTTTTTATACATGGATA-TATCCATTTACATCCAGTG
456 AAATCAAATGTTGAGATTAACTCATTGTTTTTTTATACAGGGAGAGGATCCATTTACACCCAATG
* * *
43956 TAAAACTCTTGTTTTACACCTTTTTAGGACCATTGGAT
521 TAAAACTCTTGTTATACACCTTTTTAGGACAATTAGAT
* * * *
43994 TGAGGGAAATCAAAGGTTGTGATTAACAATTGGAAATGAGAATATATTCACT-AAAAAACAAGGA
1 TGAGGGAAATCAAAGGTTGAGATTAATAGTAGGAAATGAGAATATATTCACTGAAAAAACAAGGA
*
44058 GTTAATCTCAGCCTTTAATTTCCCTCAATCCAATGGTCCTAAAAAGGTATAAAACTCTTAATTTT
66 GTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCTAAAAAGGTATAAAACTCTTAATTTT
* * * *
44123 ACACTGGGTCTAACTGGATCCTAATCCACATGGGGGCATGATCTATTTACACCCAATGTAAAACT
131 ACATTGGGTCTAACTGGATCCTAACCCACATGGGGACATGATCTGTTTACACCCAATGTAAAACT
* *
44188 AAGAGTTTTACATCTTTTTAGGACCACTTGATGAGAGAAATCAAAGGTTGAGACTAACAGTAGGA
196 AAGAGTTTTACATCTTTTTAGGACCACTTGATGAGAGAAATCAAATGTTGAGATTAACAGTAGGA
*
44253 AATGAGAAGATATTCACTGAACAAAATGAGTTAATCTCAACCTTTGATTTCCCTCAATCCAATGG
261 AATGAGAAGATATTCACTGAACAAAATGAGTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGG
* * **
44318 TCCAAAAAAGGTGTAAAACTCTTAATTTTACACTGGTGTAAGTGGATCCTAACCCATATAGCAGT
326 TCCAAAAAAGGTGTAAAACTCTTAATTTTACA-TTGTGTAAGTGGATTCTAACCCATATAGGGGT
* * *
44383 ATGATACATATACACCTAGTGTAAAACTAAGAGTTTTACATCTTCTTAGGACCATTGGATTAAGG
390 ATGATCCATTTACACCTAGTGTAAAACTAAGAGTTTTACATCTTTTTAGGACCATTGGATTAAGG
44448 AAAAATCAAATGTTGAGATTAA
455 -AAAATCAAATGTTGAGATTAA
44470 ATCCTTTTTC
Statistics
Matches: 923, Mismatches: 107, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
556 283 0.31
557 178 0.19
558 389 0.42
559 31 0.03
562 42 0.05
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (558 bp):
TGAGGGAAATCAAAGGTTGAGATTAATAGTAGGAAATGAGAATATATTCACTGAAAAAACAAGGA
GTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCTAAAAAGGTATAAAACTCTTAATTTT
ACATTGGGTCTAACTGGATCCTAACCCACATGGGGACATGATCTGTTTACACCCAATGTAAAACT
AAGAGTTTTACATCTTTTTAGGACCACTTGATGAGAGAAATCAAATGTTGAGATTAACAGTAGGA
AATGAGAAGATATTCACTGAACAAAATGAGTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGG
TCCAAAAAAGGTGTAAAACTCTTAATTTTACATTGTGTAAGTGGATTCTAACCCATATAGGGGTA
TGATCCATTTACACCTAGTGTAAAACTAAGAGTTTTACATCTTTTTAGGACCATTGGATTAAGGA
AAATCAAATGTTGAGATTAACTCATTGTTTTTTTATACAGGGAGAGGATCCATTTACACCCAATG
TAAAACTCTTGTTATACACCTTTTTAGGACAATTAGAT
Found at i:44338 original size:224 final size:225
Alignment explanation
Indices: 43966--44465 Score: 675
Period size: 223 Copynumber: 2.2 Consensus size: 225
43956 TAAAACTCTT
* * * * *
43966 GTTTTACACCTTTTTAGGACCATTGGATTGAGGGAAATCAAAGGTTGTGATTAACAATTGGAAAT
1 GTTTTACATCTTTTTAGGACCATTGGATTGAGAGAAATCAAAGGTTGAGACTAACAATAGGAAAT
* *
44031 GAGAATATATTCACTAAAAAACAAGGAGTTAATCTCAGCCTTTAATTTCCCTCAATCCAATGGTC
66 GAGAAGATATTCACTAAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGTC
* * * **
44096 CTAAAAAGGTATAAAACTCTTAATTTTACACTGGGTCTAACTGGATCCTAATCCACATGGGGGCA
131 CAAAAAAGGTATAAAACTCTTAATTTTACACT-GGTCTAACTGGATCCTAACCCACATAGCAGCA
*
44161 TGAT-CTATTTACACCCAATGTAAAACTAAGA
195 TGATAC-ATATACACCCAATGTAAAACTAAGA
*
44192 GTTTTACATCTTTTTAGGACCACTT-GA-TGAGAGAAATCAAAGGTTGAGACTAACAGTAGGAAA
1 GTTTTACATCTTTTTAGGACCA-TTGGATTGAGAGAAATCAAAGGTTGAGACTAACAATAGGAAA
* * * *
44255 TGAGAAGATATTCACTGAACAA-AATGAGTTAATCTCAACCTTTGATTTCCCTCAATCCAATGGT
65 TGAGAAGATATTCACTAAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGT
* * * * *
44319 CCAAAAAAGGTGTAAAACTCTTAATTTTACACTGGTGTAAGTGGATCCTAACCCATATAGCAGTA
130 CCAAAAAAGGTATAAAACTCTTAATTTTACACTGGTCTAACTGGATCCTAACCCACATAGCAGCA
* *
44384 TGATACATATACACCTAGTGTAAAACTAAGA
195 TGATACATATACACCCAATGTAAAACTAAGA
* * * *
44415 GTTTTACATCTTCTTAGGACCATTGGATTAAGGAAAAATCAAATGTTGAGA
1 GTTTTACATCTTTTTAGGACCATTGGATTGA-GAGAAATCAAAGGTTGAGA
44466 TTAAATCCTT
Statistics
Matches: 240, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
222 2 0.01
223 73 0.30
224 73 0.30
225 67 0.28
226 23 0.10
227 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (225 bp):
GTTTTACATCTTTTTAGGACCATTGGATTGAGAGAAATCAAAGGTTGAGACTAACAATAGGAAAT
GAGAAGATATTCACTAAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGTC
CAAAAAAGGTATAAAACTCTTAATTTTACACTGGTCTAACTGGATCCTAACCCACATAGCAGCAT
GATACATATACACCCAATGTAAAACTAAGA
Found at i:50480 original size:11 final size:13
Alignment explanation
Indices: 50455--50492 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
50445 AAGTTATGAT
50455 AATTTGTGAATAAA
1 AATTTGTGAA-AAA
50469 AATTT-TGAAAAA
1 AATTTGTGAAAAA
50481 AATTTGTGAAAA
1 AATTTGTGAAAA
50493 CAAAAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 10 0.43
14 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (13 bp):
AATTTGTGAAAAA
Found at i:50482 original size:13 final size:14
Alignment explanation
Indices: 50455--50497 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 14
50445 AAGTTATGAT
*
50455 AATTTGTGAATAAA
1 AATTTGTGAAAAAA
50469 AATTT-TG-AAAAA
1 AATTTGTGAAAAAA
50481 AATTTGTGAAAACAA
1 AATTTGTGAAAA-AA
50496 AA
1 AA
50498 GATTATAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 9 0.36
13 4 0.16
14 8 0.32
15 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (14 bp):
AATTTGTGAAAAAA
Found at i:51245 original size:20 final size:20
Alignment explanation
Indices: 51209--51246 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51199 ATCCTATTCC
**
51209 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
51229 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
51247 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:53047 original size:2 final size:2
Alignment explanation
Indices: 53040--53081 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
53030 TTAGACAGGT
53040 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
53082 TCAAATGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58333 original size:25 final size:24
Alignment explanation
Indices: 58269--58336 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
58259 TCAATCAAAT
*
58269 TTAATATT-TTAAATTTTAAAATA
1 TTAATATTATTAAATTTTATAATA
* *
58292 -TATATATAATT-AGTTTTATAATA
1 TTA-ATATTATTAAATTTTATAATA
58315 TTAATATTATTAACATTTTATA
1 TTAATATTATTAA-ATTTTATA
58337 CTTGTGATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
22 2 0.06
23 21 0.60
24 5 0.14
25 7 0.20
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (24 bp):
TTAATATTATTAAATTTTATAATA
Found at i:59503 original size:18 final size:17
Alignment explanation
Indices: 59480--59521 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
59470 ATATATTTTA
59480 TAAATT-ATAAAATCGATT
1 TAAATTAATAAAAT--ATT
59498 TAAATTAAATAAAATATT
1 TAAATT-AATAAAATATT
59516 TAAATT
1 TAAATT
59522 TTTATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.68
20 7 0.32
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTAATAAAATATT
Found at i:61406 original size:19 final size:20
Alignment explanation
Indices: 61382--61421 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
61372 TATCATTTCT
61382 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
61401 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
61421 T
1 T
61422 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:61424 original size:19 final size:18
Alignment explanation
Indices: 61378--61424 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
61368 TCTCTATCAT
61378 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
61395 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
61414 TTACTTATATT
1 TT-CTTATATT
61425 ATTATTCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Done.