Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009113.1 Hibiscus syriacus cultivar Beakdansim tig00112595_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: 55179
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3310 original size:182 final size:185
Alignment explanation
Indices: 2682--3530 Score: 1524
Period size: 184 Copynumber: 4.6 Consensus size: 185
2672 TTTTAAATGG
* *
2682 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATAT-GGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2746 TAAAACCGGTATATTTATACCGGTTTATATTAC-AAATTATCTATTACATTATAATTATGGGTTT
66 TAAGACCGGTATATTTATACCGG-TTATATTACAAAATTATCTATTACATTATAATTATGGGTTT
2810 CCGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
130 CCGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2866 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
2931 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG-TTC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTTC
2995 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
3050 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATT--CGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
3113 TAAGACCGGTATATTTATACCGGTTATATTAC-AAATTATCTATTAC-TTATAATTATGGG-TTC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTTC
*
3175 CGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
* *
3230 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
3295 TAAAACCGGTATATTTATA-CGGTTATA-TACAAAATTATCTATTACATTATAATTATGGGTTTC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTTC
3358 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
3413 TAT-GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
3477 TAAGACC-GTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
3531 ATGTTGAAAG
Statistics
Matches: 644, Mismatches: 12, Indels: 19
0.95 0.02 0.03
Matches are distributed among these distances:
180 132 0.20
181 47 0.07
182 143 0.22
183 84 0.13
184 168 0.26
185 70 0.11
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (185 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTTC
CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:3479 original size:364 final size:368
Alignment explanation
Indices: 2682--3530 Score: 1527
Period size: 364 Copynumber: 2.3 Consensus size: 368
2672 TTTTAAATGG
* *
2682 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATAT-GGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2746 TAAAACCGGTATATTTATACCGGTTTATATTACAAATTATCTATTACATTATAATTATGGGTTTC
66 TAAGACCGGTATATTTATACCGG-TTATATTACAAATTATCTATTACATTATAATTATGGGTTTC
2811 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATA
130 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATA
*
2876 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGT
195 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGT
2941 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAA
260 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAA
3006 ATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
325 ATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
3050 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATT--CGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
3113 TAAGACCGGTATATTTATACCGGTTATATTACAAATTATCTATTAC-TTATAATTATGGG-TTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAATTATCTATTACATTATAATTATGGGTTTCC
*
3176 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
* *
3241 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCATAAAACCGGTA
196 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTA
3306 TATTTATA-CGGTTATA-TACAAAATTATCTATTACATTATAATTATGGGTTTCCGATGTGTAAA
261 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG-TTCCGATGTGTAAA
3369 ATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
325 ATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
3413 TAT-GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
3477 TAAGACC-GTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTAC-AAATTATCTATTACATTATAAT
3531 ATGTTGAAAG
Statistics
Matches: 466, Mismatches: 9, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
362 87 0.19
363 93 0.20
364 161 0.35
365 20 0.04
366 23 0.05
367 25 0.05
368 42 0.09
369 15 0.03
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (368 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAATTATCTATTACATTATAATTATGGGTTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTA
TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAA
TGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:4996 original size:3 final size:3
Alignment explanation
Indices: 4988--5074 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
4978 ACTTGTTTGG
* * * **
4988 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
5036 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
5075 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:5011 original size:18 final size:18
Alignment explanation
Indices: 4988--5089 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
4978 ACTTGTTTGG
4988 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
5006 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
5024 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
5042 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
5060 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
5078 AGCTTCATCTTC
1 ATCATCATCTTC
5090 TGCGACCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:5055 original size:42 final size:42
Alignment explanation
Indices: 4996--5086 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
4986 GGATCATCAT
*
4996 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
5038 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
5080 CTTCATC
1 CTTCATC
5087 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:7078 original size:199 final size:199
Alignment explanation
Indices: 6538--8557 Score: 3801
Period size: 199 Copynumber: 10.1 Consensus size: 199
6528 TTTAAATTAG
* *
6538 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
6603 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6668 CGACACTTTTTAAATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
6732 AAAA
196 AAAA
6736 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
6801 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6866 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAA
6931 AAAAA
195 AAAAA
6936 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
7001 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
7066 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
7131 AAAA
196 AAAA
7135 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
7200 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
7265 CGACACTTTTTAAATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
7330 AAAA
196 AAAA
7334 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
7399 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
7464 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
7529 AAAAA
195 AAAAA
7534 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
7599 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
7664 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAA
7729 AAAAA
195 AAAAA
7734 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
7799 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
7864 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
7929 AAAA
196 AAAA
7933 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
7998 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
8063 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
8128 AAAA
196 AAAA
*
8132 TATCGACACAAACTATATTAGTATCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
8197 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGTTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
8262 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
8326 AAAA
196 AAAA
*
8330 TATCCACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
8395 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
8460 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
8525 AAAA
196 AAAA
*
8529 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
8558 TGACCCTTAA
Statistics
Matches: 1787, Mismatches: 30, Indels: 9
0.98 0.02 0.00
Matches are distributed among these distances:
198 324 0.18
199 981 0.55
200 426 0.24
201 56 0.03
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAA
Found at i:8072 original size:798 final size:797
Alignment explanation
Indices: 6538--8557 Score: 3830
Period size: 798 Copynumber: 2.5 Consensus size: 797
6528 TTTAAATTAG
* *
6538 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
6603 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6668 CGACACTTTTTAAATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
6732 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
6797 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
6862 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
6927 GGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAA
391 GGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAA
6992 ACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
456 ACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
7057 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCAT
521 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCAT
*
7122 TCTGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCA
586 TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCA
*
7187 TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCG
651 TAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCG
*
7252 ATGATTTTGGGATCGACACTTTTTAAATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAAT
716 ATGATTTTGGGATCGACACTTTTTAAATATGGATCGACACTTTATTGATGCACCTTGTTTTTAAT
*
7317 TCATTCTGGGAAAAAAA
781 TCATTCTGGAAAAAAAA
7334 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
7399 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
7464 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
7529 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
*
7594 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
7659 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
325 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
7724 GGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAA
390 GGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAA
7789 AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG
455 AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG
*
7854 ATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCA
520 ATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCA
7919 TTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTC
585 TTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTC
7984 ATAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTC
650 ATAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTC
*
8049 GATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAA
715 GATGATTTTGGGATCGACACTTTTTAAATATGGATCGACACTTTATTGATGCACCTTGTTTTTAA
8114 TTCATTCTGGAAAAAAAA
780 TTCATTCTGGAAAAAAAA
*
8132 TATCGACACAAACTATATTAGTATCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
8197 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGTTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
8262 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
*
8326 AAAATATCCACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
8391 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
8456 GGATCGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
* *
8520 GAAAAAAAATATCGACACAAACTATATTAGTATCGACA
391 GGAAAAAAATATCGACACAAACTATATTAGTGTCGACA
8558 TGACCCTTAA
Statistics
Matches: 1199, Mismatches: 23, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
795 89 0.07
796 328 0.27
797 2 0.00
798 780 0.65
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (797 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
GGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAA
ACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCAT
TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCA
TAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCG
ATGATTTTGGGATCGACACTTTTTAAATATGGATCGACACTTTATTGATGCACCTTGTTTTTAAT
TCATTCTGGAAAAAAAA
Found at i:10506 original size:33 final size:33
Alignment explanation
Indices: 10469--10534 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
10459 CATCTTAATA
*
10469 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
10502 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
10535 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:12673 original size:24 final size:24
Alignment explanation
Indices: 12636--12688 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
12626 CCGTTCTATC
12636 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
12660 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
12684 TATTT
1 TATTT
12689 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:12879 original size:20 final size:19
Alignment explanation
Indices: 12833--12879 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
12823 TCCGGTATCA
*
12833 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
12852 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
12873 TTTTACC
1 TTTTACC
12880 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:13027 original size:20 final size:20
Alignment explanation
Indices: 13001--13046 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
12991 CACTTTTAAA
13001 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
*
13020 TGTTACCGGTTTTGTCATATT
1 T-TTACCGGTTTTATCATATT
13041 TTTACC
1 TTTACC
13047 TGGTATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.15, C:0.17, G:0.13, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:35868 original size:32 final size:32
Alignment explanation
Indices: 35832--35919 Score: 167
Period size: 32 Copynumber: 2.8 Consensus size: 32
35822 GGAGGTCAAT
35832 AAATGTAATTGTATGAAATGGAAAGTATTAGC
1 AAATGTAATTGTATGAAATGGAAAGTATTAGC
35864 AAATGTAATTGTATGAAATGGAAAGTATTAGC
1 AAATGTAATTGTATGAAATGGAAAGTATTAGC
*
35896 AAATGTAATTGTATGAAACGGAAA
1 AAATGTAATTGTATGAAATGGAAA
35920 CCACGTGGAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (32 bp):
AAATGTAATTGTATGAAATGGAAAGTATTAGC
Found at i:38703 original size:30 final size:30
Alignment explanation
Indices: 38667--38726 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
38657 GCTATGTTTC
*
38667 TCTTTGGATTTTCCATCGGCTTTTCATCGA
1 TCTTTGGATTTTCCATCAGCTTTTCATCGA
*
38697 TCTTTGGATTTTGCATCAGCTTTTCATCGA
1 TCTTTGGATTTTCCATCAGCTTTTCATCGA
38727 AGCATGCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (30 bp):
TCTTTGGATTTTCCATCAGCTTTTCATCGA
Found at i:39039 original size:27 final size:27
Alignment explanation
Indices: 39001--39069 Score: 103
Period size: 22 Copynumber: 2.7 Consensus size: 27
38991 GAACAACGTA
39001 TATTGAAATTAACTATTAAAAAAAGTT
1 TATTGAAATTAACTATTAAAAAAAGTT
39028 TATTGAAATTAAC---T--AAAAAGTT
1 TATTGAAATTAACTATTAAAAAAAGTT
39050 TATTGAAATTAACTATTAAA
1 TATTGAAATTAACTATTAAA
39070 GTATATTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
22 21 0.57
24 1 0.03
25 1 0.03
27 14 0.38
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (27 bp):
TATTGAAATTAACTATTAAAAAAAGTT
Found at i:39046 original size:22 final size:22
Alignment explanation
Indices: 39020--39084 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
39010 TAACTATTAA
39020 AAAAAGTTTATTGAAATTAACT
1 AAAAAGTTTATTGAAATTAACT
39042 AAAAAGTTTATTGAAATTAACT
1 AAAAAGTTTATTGAAATTAACT
* *
39064 ATTAAAGTATATTGAAATTAA
1 A-AAAAGTTTATTGAAATTAA
39085 AGAGGCATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 23 0.57
23 17 0.43
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (22 bp):
AAAAAGTTTATTGAAATTAACT
Found at i:39046 original size:23 final size:23
Alignment explanation
Indices: 39001--39084 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 23
38991 GAACAACGTA
39001 TATTGAAATTAACTATTAAAAAAAGTT
1 TATTGAAATTAAC---T-AAAAAAGTT
39028 TATTGAAATTAACT-AAAAAGTT
1 TATTGAAATTAACTAAAAAAGTT
** *
39050 TATTGAAATTAACTATTAAAGTA
1 TATTGAAATTAACTAAAAAAGTT
39073 TATTGAAATTAA
1 TATTGAAATTAA
39085 AGAGGCATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 22 0.42
23 17 0.32
24 1 0.02
27 13 0.25
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (23 bp):
TATTGAAATTAACTAAAAAAGTT
Found at i:42133 original size:21 final size:21
Alignment explanation
Indices: 42101--42148 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
42091 TAATTTTCAA
*
42101 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
*
42122 ATATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
42143 ACATTG
1 ACATTG
42149 CAATATTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:46774 original size:21 final size:21
Alignment explanation
Indices: 46744--46791 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
46734 TAATTTTCAA
*
46744 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
46765 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
46786 ACATTG
1 ACATTG
46792 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Done.