Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005923.1 Hibiscus syriacus cultivar Beakdansim tig00013902_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: 73669
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3177 original size:18 final size:18
Alignment explanation
Indices: 3150--3216 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
3140 TTAAGGAGTA
*
3150 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
3168 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
**
3190 GTCCTTTGGGACATAGTG
1 GTCCTACGGGACATAGTG
3208 GTCCTACGG
1 GTCCTACGG
3217 ACGAATACTG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 22 0.55
20 4 0.10
22 14 0.35
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.27
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:4139 original size:13 final size:14
Alignment explanation
Indices: 4109--4148 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
4099 TTTACCGGAT
4109 AAAAAACCGGTTTGA
1 AAAAAACCGG-TTGA
*
4124 AAAAAATCGGTT-A
1 AAAAAACCGGTTGA
4137 AAAAAACCGGTT
1 AAAAAACCGGTT
4149 TTTATCCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 2 0.09
15 9 0.39
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.20
Consensus pattern (14 bp):
AAAAAACCGGTTGA
Found at i:6461 original size:21 final size:21
Alignment explanation
Indices: 6437--6476 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6427 TTTATTTTAT
6437 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
6458 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
6477 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:6524 original size:33 final size:33
Alignment explanation
Indices: 6471--6569 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
6461 TTTGTTTCAA
6471 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
6503 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
6536 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
6569 T
1 T
6570 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:6598 original size:13 final size:13
Alignment explanation
Indices: 6555--6609 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
6545 TTGGAAGTAT
6555 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
6568 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
6582 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
6595 TTAAGTATTTGAA
1 TTAAGTATTTCAA
6608 TT
1 TT
6610 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:6831 original size:21 final size:21
Alignment explanation
Indices: 6805--6861 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
6795 TGGAGCGTGG
*
6805 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
6826 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
6847 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
6862 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:9641 original size:21 final size:22
Alignment explanation
Indices: 9616--9667 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
9606 ACACTTTACA
*
9616 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
9639 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
9662 ATATAA
1 ATATAA
9668 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:9652 original size:23 final size:23
Alignment explanation
Indices: 9626--9688 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
9616 ATATAACCAC
9626 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
9649 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
9672 TACCTATTACATCATAT
1 TACCTATTACATTATAT
9689 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:10146 original size:39 final size:39
Alignment explanation
Indices: 10092--10178 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
10082 TCAAGTTGTA
*
10092 GATTTTGATTTCCTTTTGCTTGGCATCATATGAAATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAAATTTG
**
10131 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAAATTTG
10170 GATTTTGAT
1 GATTTTGAT
10179 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAAATTTG
Found at i:10460 original size:18 final size:18
Alignment explanation
Indices: 10437--10473 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10427 CGAAATATAT
10437 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
10455 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
10473 A
1 A
10474 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:10750 original size:25 final size:25
Alignment explanation
Indices: 10722--10772 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
10712 TTAATCCAAA
*
10722 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
10747 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
10772 T
1 T
10773 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:11100 original size:23 final size:22
Alignment explanation
Indices: 11038--11109 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
11028 ACACTTTACA
*
11038 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
11061 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
* *
11083 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
11106 ATAT
1 ATAT
11110 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 20 0.47
23 23 0.53
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:13635 original size:3 final size:3
Alignment explanation
Indices: 13627--13713 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
13617 ACTTGTTTGG
* * * **
13627 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
* * * * *
13675 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
13714 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:13650 original size:18 final size:18
Alignment explanation
Indices: 13627--13728 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
13617 ACTTGTTTGG
13627 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
13645 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
13663 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
13681 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
13699 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
13717 AGCTTCATCTTC
1 ATCATCATCTTC
13729 TGCGACCGCT
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:13694 original size:42 final size:42
Alignment explanation
Indices: 13635--13725 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
13625 GGATCATCAT
*
13635 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
13677 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
13719 CTTCATC
1 CTTCATC
13726 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:16041 original size:399 final size:399
Alignment explanation
Indices: 15186--16558 Score: 2610
Period size: 399 Copynumber: 3.4 Consensus size: 399
15176 TTTAAATTAG
15186 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
15251 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTTGGTTCTATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
** *
15316 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTAATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
15381 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
15446 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTT
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTT
15511 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
15576 G-AAAAAAA
391 GAAAAAAAA
15584 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
15649 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGATTTTGGGA
15714 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
15778 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
15843 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTT
260 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTT
15908 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
325 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
15973 GGAAAAAAAA
390 GGAAAAAAAA
15983 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
16048 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGATTTTGGGA
16113 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
*
16178 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
16243 GTATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGG-TTCGATGATTT
260 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTT
16306 TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
325 TGGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
16371 TGGAAAAAAAA
389 TGGAAAAAAAA
16382 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
16447 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
16512 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
16559 GGCCATATTG
Statistics
Matches: 962, Mismatches: 8, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
398 357 0.37
399 517 0.54
400 88 0.09
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (399 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTT
GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
GAAAAAAAA
Found at i:16119 original size:200 final size:200
Alignment explanation
Indices: 15186--16558 Score: 2614
Period size: 199 Copynumber: 6.9 Consensus size: 200
15176 TTTAAATTAG
15186 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
15251 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTTGG-TTCTATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
** *
15315 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTAATTCTGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
15380 AAAAA
196 AAAAA
15385 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
15450 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
15515 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
15579 AAAAA
196 AAAAA
15584 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
15649 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
15714 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
15778 AAAAA
196 AAAAA
15783 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
15848 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
15913 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
15978 AAAAA
196 AAAAA
15983 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
16048 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
16113 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
16178 AAAAA
196 AAAAA
*
16183 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
16248 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGG-TTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
16311 TCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAA
131 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAA
16376 AAAAAA
195 AAAAAA
16382 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
16447 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGG-TTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
*
16511 TCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
16559 GGCCATATTG
Statistics
Matches: 1162, Mismatches: 8, Indels: 7
0.99 0.01 0.01
Matches are distributed among these distances:
198 23 0.02
199 684 0.59
200 455 0.39
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (200 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
AAAAA
Found at i:16723 original size:19 final size:19
Alignment explanation
Indices: 16677--16725 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
16667 TTATATTCAC
*
16677 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
16696 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
16715 ATACAAAATTA
1 ATACAAAATTA
16726 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:18552 original size:33 final size:33
Alignment explanation
Indices: 18515--18580 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
18505 CATCTTAATA
*
18515 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
18548 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
18581 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:20931 original size:20 final size:19
Alignment explanation
Indices: 20885--20931 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
20875 TCCGGTATCA
*
20885 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
20904 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
20925 TTTTACC
1 TTTTACC
20932 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:21079 original size:20 final size:20
Alignment explanation
Indices: 21053--21098 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
21043 CACTTTTAAA
21053 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
21072 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
21093 TTTACC
1 TTTACC
21099 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:26724 original size:22 final size:21
Alignment explanation
Indices: 26689--26730 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
26679 ATGCTCAAAT
26689 TTTTTAATAATTTAGAATAATG
1 TTTTTAATAATTTA-AATAATG
**
26711 TTTTTAATTTTTTAAATAAT
1 TTTTTAATAATTTAAATAAT
26731 TGATAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTTAATAATTTAAATAATG
Found at i:35224 original size:28 final size:28
Alignment explanation
Indices: 35193--35284 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
35183 AGACTCGAAA
35193 AAAAAATTCTAAGTCAACTCCGAGTTGT
1 AAAAAATTCTAAGTCAACTCCGAGTTGT
*** * * *
35221 AAAATAGGACT-CGTCAACT-CGAATTACTCGA
1 AAAA-AATTCTAAGTCAACTCCG-AGT--T-GT
35252 AAAAAATTCTAAGTCAACTCCGAGTTGT
1 AAAAAATTCTAAGTCAACTCCGAGTTGT
35280 AAAAA
1 AAAAA
35285 TTCAATTGGA
Statistics
Matches: 45, Mismatches: 12, Indels: 14
0.63 0.17 0.20
Matches are distributed among these distances:
27 2 0.04
28 19 0.42
29 4 0.09
30 4 0.09
31 14 0.31
32 2 0.04
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (28 bp):
AAAAAATTCTAAGTCAACTCCGAGTTGT
Found at i:35465 original size:31 final size:31
Alignment explanation
Indices: 35428--35491 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
35418 GATCACATCA
35428 TAATTAAATAAAAACGAAAGTGACTATATCT
1 TAATTAAATAAAAACGAAAGTGACTATATCT
*
35459 TAATTAAATAAAAACGAAAGTGGCTATATCT
1 TAATTAAATAAAAACGAAAGTGACTATATCT
35490 TA
1 TA
35492 TGTTTTTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (31 bp):
TAATTAAATAAAAACGAAAGTGACTATATCT
Found at i:37094 original size:6 final size:6
Alignment explanation
Indices: 37083--37132 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
37073 TCAAAATTTA
*
37083 AACTCG AACTCG AACTCG AACTCG AACTCG AACTCA AACTCG AACTCG
1 AACTCG AACTCG AACTCG AACTCG AACTCG AACTCG AACTCG AACTCG
37131 AA
1 AA
37133 AACCGAATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (6 bp):
AACTCG
Found at i:38107 original size:43 final size:40
Alignment explanation
Indices: 38050--38129 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
38040 CGGGAAGTTC
*
38050 TTTTATGTGCGTTTATTTATTAAATGAACGAACATGAACAAGA
1 TTTTATGTGCGTTTA---ATTAAATGAACAAACATGAACAAGA
* * *
38093 TTTTGTGTTCGTTTAATTAAATGAACAAATATGAACA
1 TTTTATGTGCGTTTAATTAAATGAACAAACATGAACA
38130 TAGGTCTCGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 20 0.61
43 13 0.39
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (40 bp):
TTTTATGTGCGTTTAATTAAATGAACAAACATGAACAAGA
Found at i:39303 original size:16 final size:16
Alignment explanation
Indices: 39284--39342 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
39274 CCAACATTTA
39284 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
39300 TGTTCATTTATGTTGG
1 TGTTCGTTTATGTTCG
*
39316 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCG
39332 TGTTCGTTTAT
1 TGTTCGTTTAT
39343 TTATTAAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.10, C:0.10, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:39392 original size:31 final size:31
Alignment explanation
Indices: 39357--39429 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
39347 TAAATGAACG
39357 AACATGAACAAGTTATATTCCTTAATAAACA
1 AACATGAACAAGTTATATTCCTTAATAAACA
*
39388 AACATGAACAAGTTATATTCCTTAATAAACG
1 AACATGAACAAGTTATATTCCTTAATAAACA
39419 AACATGAACAA
1 AACATGAACAA
39430 AAAAATTTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.26
Consensus pattern (31 bp):
AACATGAACAAGTTATATTCCTTAATAAACA
Found at i:43312 original size:2 final size:2
Alignment explanation
Indices: 43305--43329 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43295 TAGCTGGTAA
43305 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
43330 GTGGGGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:49386 original size:16 final size:15
Alignment explanation
Indices: 49354--49387 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
49344 TTTTGACCAT
*
49354 AAATTAAAATGTTAA
1 AAATTAAAATCTTAA
49369 AAATTAAAATACTTAA
1 AAATTAAAAT-CTTAA
49385 AAA
1 AAA
49388 AATAGAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (15 bp):
AAATTAAAATCTTAA
Found at i:54330 original size:24 final size:20
Alignment explanation
Indices: 54273--54313 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54263 TTCCCATTGA
*
54273 AGTGCATCGGTGCATTCTTT
1 AGTGCATCGATGCATTCTTT
54293 AGTGCATCGATGCATTCTTT
1 AGTGCATCGATGCATTCTTT
54313 A
1 A
54314 ACATGTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTT
Found at i:68980 original size:87 final size:87
Alignment explanation
Indices: 68808--69055 Score: 371
Period size: 87 Copynumber: 2.9 Consensus size: 87
68798 GTAAGCATGC
*
68808 AAATAAGCTTAC--GCTTATGGAATAATGACAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATGGAATAATG-TAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
68871 GAATAAATGGTAAGTATATTGGTA
65 GAA-AAATGGTAAGTATATTGGTA
68895 AAATAAGCTTACGAGCTTATGGAATAATAGTAAGTATATTGGTAAAATAAGC-TACGAGCTTATG
1 AAATAAGCTTACGAGCTTATGGAATAAT-GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
68959 GAAAAATGGTAAGTATATTGGTA
65 GAAAAATGGTAAGTATATTGGTA
* *
68982 AAATAAGC-TACGAGCTTATGGAATAAATGGTAAGTATTTTGGT-AAATAAGCTTACAAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAAT-AAT-GTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
* *
69045 GGGATAATGGT
64 GGAAAAATGGT
69056 GAGAAATTTT
Statistics
Matches: 150, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
86 24 0.16
87 75 0.50
88 15 0.10
89 35 0.23
90 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (87 bp):
AAATAAGCTTACGAGCTTATGGAATAATGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
AAAAATGGTAAGTATATTGGTA
Found at i:69065 original size:44 final size:44
Alignment explanation
Indices: 68808--69055 Score: 380
Period size: 43 Copynumber: 5.7 Consensus size: 44
68798 GTAAGCATGC
**
68808 AAATAAGCTTAC--GCTTATGGAATAATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
68850 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGTA
*
68895 AAATAAGCTTACGAGCTTATGGAATAATAGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
*
68939 AAATAAGC-TACGAGCTTATGGAAAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
*
68982 AAATAAGC-TACGAGCTTATGGAATAAATGGTAAGTATTTTGGT-
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGTA
* *
69025 AAATAAGCTTACAAGCTTATGGGATAATGGT
1 AAATAAGCTTACGAGCTTATGGAATAATGGT
69056 GAGAAATTTT
Statistics
Matches: 192, Mismatches: 9, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
42 12 0.06
43 70 0.36
44 68 0.35
45 42 0.22
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
Done.