Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004792.1 Hibiscus syriacus cultivar Beakdansim tig00010802_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: 85150
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2845 original size:2 final size:2
Alignment explanation
Indices: 2840--2868 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2830 AAGCAATATA
2840 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2869 AAAGCTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4890 original size:22 final size:22
Alignment explanation
Indices: 4860--4902 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4850 ATGACACGTC
*
4860 ACAAATAAAATCAATTAAATTA
1 ACAAATAAAATAAATTAAATTA
* *
4882 ACAATTAAATTAAATTAAATT
1 ACAAATAAAATAAATTAAATT
4903 TATCAATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
ACAAATAAAATAAATTAAATTA
Found at i:7372 original size:21 final size:21
Alignment explanation
Indices: 7348--7400 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
7338 TATGGTATTG
7348 ATGTGACGGTCTACGATGCTA
1 ATGTGACGGTCTACGATGCTA
* * *
7369 ATGTGATGATCTACGGTGCTA
1 ATGTGACGGTCTACGATGCTA
*
7390 ACGTGACGGTC
1 ATGTGACGGTC
7401 CATGGTGGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (21 bp):
ATGTGACGGTCTACGATGCTA
Found at i:7539 original size:178 final size:178
Alignment explanation
Indices: 7240--7598 Score: 691
Period size: 178 Copynumber: 2.0 Consensus size: 178
7230 TGTAACTCAG
*
7240 TGGATCTGGTCGTAACGCATAGGCATGTCTAGGGGGTTACAATGTGGCCCTTTAATCAACGATTT
1 TGGATCTGGTCGTAACGCACAGGCATGTCTAGGGGGTTACAATGTGGCCCTTTAATCAACGATTT
*
7305 TTCGTTGATCATTACGATGTTGATATGACATTTTATGGTATTGATGTGACGGTCTACGATGCTAA
66 TTCGTTGATCATTACGATGTTGATATGACATTTTATGGTACTGATGTGACGGTCTACGATGCTAA
7370 TGTGATGATCTACGGTGCTAACGTGACGGTCCATGGTGGATAATGACA
131 TGTGATGATCTACGGTGCTAACGTGACGGTCCATGGTGGATAATGACA
7418 TGGATCTGGTCGTAACGCACAGGCATGTCTAGGGGGTTACAATGTGGCCCTTTAATCAACGATTT
1 TGGATCTGGTCGTAACGCACAGGCATGTCTAGGGGGTTACAATGTGGCCCTTTAATCAACGATTT
7483 TTCGTTGATCATTACGATGTTGATATGACATTTTATGGTACTGATGTGACGGTCTACGATGCTAA
66 TTCGTTGATCATTACGATGTTGATATGACATTTTATGGTACTGATGTGACGGTCTACGATGCTAA
*
7548 TGTGATGATCTACGGTGCTAACGTGACGGTCTATGGTGGATAATGACA
131 TGTGATGATCTACGGTGCTAACGTGACGGTCCATGGTGGATAATGACA
7596 TGG
1 TGG
7599 TTTATAGGCT
Statistics
Matches: 178, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 178 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (178 bp):
TGGATCTGGTCGTAACGCACAGGCATGTCTAGGGGGTTACAATGTGGCCCTTTAATCAACGATTT
TTCGTTGATCATTACGATGTTGATATGACATTTTATGGTACTGATGTGACGGTCTACGATGCTAA
TGTGATGATCTACGGTGCTAACGTGACGGTCCATGGTGGATAATGACA
Found at i:7550 original size:21 final size:21
Alignment explanation
Indices: 7526--7580 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
7516 TATGGTACTG
7526 ATGTGACGGTCTACGATGCTA
1 ATGTGACGGTCTACGATGCTA
* * *
7547 ATGTGATGATCTACGGTGCTA
1 ATGTGACGGTCTACGATGCTA
*
7568 ACGTGACGGTCTA
1 ATGTGACGGTCTA
7581 TGGTGGATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (21 bp):
ATGTGACGGTCTACGATGCTA
Found at i:11576 original size:18 final size:19
Alignment explanation
Indices: 11524--11582 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
11514 TTTTTATATG
*
11524 AATAAAATATAAATAAAATT
1 AATAAAA-ATAAATATAATT
*
11544 --TTAAAATAAATATAATT
1 AATAAAAATAAATATAATT
11561 AATAAAAATAAA-ATAATT
1 AATAAAAATAAATATAATT
11579 AATA
1 AATA
11583 GAAGAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 11 0.32
18 14 0.41
19 9 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAAAATAAATATAATT
Found at i:18272 original size:14 final size:13
Alignment explanation
Indices: 18254--18300 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
18244 TGAACGTTTG
18254 GTTATGTTCGTTC
1 GTTATGTTCGTTC
18267 GATTATGTTCG-T-
1 G-TTATGTTCGTTC
18279 -TTATGTTCGTTC
1 GTTATGTTCGTTC
18291 GTTTATGTTC
1 G-TTATGTTC
18301 ATTCATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 9 0.31
11 1 0.03
13 2 0.07
14 17 0.59
ACGTcount: A:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (13 bp):
GTTATGTTCGTTC
Found at i:18282 original size:24 final size:24
Alignment explanation
Indices: 18255--18300 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
18245 GAACGTTTGG
18255 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTCGT
*
18279 TTATGTTCGTTCGTTTATGTTC
1 TTATGTTCGTTCGATTATGTTC
18301 ATTCATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.13, G:0.20, T:0.57
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTCGT
Found at i:19187 original size:12 final size:12
Alignment explanation
Indices: 19170--19212 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
19160 TGTCGAGCTT
19170 GAATCGAGCTCA
1 GAATCGAGCTCA
19182 GAATCGAGCTCA
1 GAATCGAGCTCA
*
19194 GAATCGAGCT-T
1 GAATCGAGCTCA
19205 GAATCGAG
1 GAATCGAG
19213 TTCGAGTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.19
Consensus pattern (12 bp):
GAATCGAGCTCA
Found at i:19472 original size:16 final size:16
Alignment explanation
Indices: 19449--19503 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
19439 CGTTTATGTC
19449 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
* *
19465 CATTTATGTTCGTATT
1 CGTTTATGTTCGTGTT
*
19481 TGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
19497 CGTTTAT
1 CGTTTAT
19504 TTATTAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.58
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:19589 original size:16 final size:16
Alignment explanation
Indices: 19568--19600 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19558 AAAAAAAATT
19568 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
19584 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
19600 T
1 T
19601 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:20334 original size:19 final size:20
Alignment explanation
Indices: 20312--20349 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
20302 TTTTGTAACA
20312 ATTTGATAA-ATTTAAAATT
1 ATTTGATAATATTTAAAATT
* *
20331 ATTTTATAATGTTTAAAAT
1 ATTTGATAATATTTAAAAT
20350 GTTAATGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTTGATAATATTTAAAATT
Found at i:21705 original size:21 final size:21
Alignment explanation
Indices: 21681--21727 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21671 GAGGGAACAT
21681 ATTCCTCCCCAAGGGGTATCG
1 ATTCCTCCCCAAGGGGTATCG
*
21702 ATTCCTCCCCAGGGGGTATCG
1 ATTCCTCCCCAAGGGGTATCG
21723 ATTCC
1 ATTCC
21728 CCGGGAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.34, G:0.23, T:0.26
Consensus pattern (21 bp):
ATTCCTCCCCAAGGGGTATCG
Found at i:21756 original size:34 final size:35
Alignment explanation
Indices: 21702--21779 Score: 122
Period size: 34 Copynumber: 2.2 Consensus size: 35
21692 AGGGGTATCG
21702 ATTCCTCCCCAGGGGGTATCGATTCCCCGGGAACAA
1 ATTCC-CCCCAGGGGGTATCGATTCCCCGGGAACAA
* *
21738 ATTCCCCCCA-GGGGTATCGATTCCCCGGGTACAG
1 ATTCCCCCCAGGGGGTATCGATTCCCCGGGAACAA
21772 ATTCCCCC
1 ATTCCCCC
21780 TGCATGGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 30 0.75
35 5 0.12
36 5 0.12
ACGTcount: A:0.19, C:0.37, G:0.23, T:0.21
Consensus pattern (35 bp):
ATTCCCCCCAGGGGGTATCGATTCCCCGGGAACAA
Found at i:21918 original size:21 final size:21
Alignment explanation
Indices: 21892--21933 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21882 ATTTGAATAT
*
21892 TATGAAGGGGTATCAATTCCC
1 TATGAAGGGGTACCAATTCCC
*
21913 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCAATTCCC
21934 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCAATTCCC
Found at i:23169 original size:19 final size:20
Alignment explanation
Indices: 23145--23192 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
23135 AACGATTTCC
*
23145 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
23164 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
23184 TTTTGAAAA
1 TTTTGAAAA
23193 AGGATTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:24637 original size:33 final size:35
Alignment explanation
Indices: 24574--24638 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
24564 TGCCCAGAGG
24574 GAACAGATTCCCCCCAGGGGGTATCGATTCCCCAA
1 GAACAGATTCCCCCCAGGGGGTATCGATTCCCCAA
*
24609 GAACAGATT-CCCCCA-GGGGTATCTATTCCC
1 GAACAGATTCCCCCCAGGGGGTATCGATTCCC
24639 TGGGTACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 14 0.48
34 6 0.21
35 9 0.31
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.20
Consensus pattern (35 bp):
GAACAGATTCCCCCCAGGGGGTATCGATTCCCCAA
Found at i:24794 original size:21 final size:21
Alignment explanation
Indices: 24768--24810 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
24758 ATTTGAATAT
*
24768 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
24789 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
24810 T
1 T
24811 CCATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:24871 original size:21 final size:21
Alignment explanation
Indices: 24838--24877 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
24828 TTTTTGCAGA
*
24838 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
24860 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
24878 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:41565 original size:14 final size:15
Alignment explanation
Indices: 41546--41579 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
41536 GTTTTTTAAG
*
41546 ATAAATAAA-TGAGC
1 ATAAATAAAGTGAAC
41560 ATAAATAAAGTGAAC
1 ATAAATAAAGTGAAC
41575 ATAAA
1 ATAAA
41580 CGAACACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (15 bp):
ATAAATAAAGTGAAC
Found at i:41658 original size:24 final size:22
Alignment explanation
Indices: 41606--41658 Score: 52
Period size: 24 Copynumber: 2.3 Consensus size: 22
41596 TGTTTCCGGT
*
41606 TCATTTATGTTCACGAACAAGC
1 TCATTTATGTTCACGAACAAAC
* * *
41628 TCGTTTATAAGTTCATGAGCAAAC
1 TCATTTAT--GTTCACGAACAAAC
41652 TCATTTA
1 TCATTTA
41659 ATTTTTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 7 0.29
24 17 0.71
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATTTATGTTCACGAACAAAC
Found at i:42581 original size:23 final size:23
Alignment explanation
Indices: 42551--42606 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
42541 TTGTGAACGC
*
42551 TAAACGAATATATTCG-AGAATGT
1 TAAACGAACATATTCGCA-AATGT
*
42574 TAAACGAACATGTTCGCAAATGT
1 TAAACGAACATATTCGCAAATGT
*
42597 TAAATGAACA
1 TAAACGAACA
42607 AACACAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (23 bp):
TAAACGAACATATTCGCAAATGT
Found at i:43588 original size:22 final size:22
Alignment explanation
Indices: 43560--43602 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43550 TCTAGTAATT
* *
43560 TTAAAAATATTATTTAAAAAAC
1 TTAAAAAGATAATTTAAAAAAC
43582 TTAAAAAGATAATTTAAAAAA
1 TTAAAAAGATAATTTAAAAAA
43603 ACCCTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAAAGATAATTTAAAAAAC
Found at i:44461 original size:14 final size:15
Alignment explanation
Indices: 44426--44454 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44416 ATAAAAATCC
44426 AAAA-TTCATTTTTA
1 AAAATTTCATTTTTA
44440 AAAATTTCATTTTTA
1 AAAATTTCATTTTTA
44455 TAATTTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAATTTCATTTTTA
Found at i:47351 original size:43 final size:43
Alignment explanation
Indices: 47290--47375 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
47280 GAGTTTTGAC
*
47290 GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCTACCTCAG
1 GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
47333 GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
1 GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
47376 CACTTTATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.24
Consensus pattern (43 bp):
GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
Found at i:51572 original size:106 final size:106
Alignment explanation
Indices: 51387--52332 Score: 1601
Period size: 106 Copynumber: 8.9 Consensus size: 106
51377 TTGCTCGAGT
51387 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
51452 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
51493 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * * *
51558 AGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
*
51599 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
51664 AGGGACCGCTGGTTGTCAACGAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
51705 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
51770 AGGGACCGCTGGTTGTCAACAAATAATTTC-CTAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTC-AATATCAGA
* *
51811 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
51876 AGGGGCCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
* *
51917 G-CAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACAACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
51981 AGGGACCGCTGGTTTTCAACAAACAATTTCCCAATATTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATA-TCAGA
* * *
52023 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACAACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
52088 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
*
52129 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
52194 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
* * * * *
52235 GCCAAGTTCAACTTCATAGCAAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
52300 AGGGACCGCTGGTTGTCAATAAACAACTT-TCAA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
52333 CTTCATGACG
Statistics
Matches: 793, Mismatches: 43, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
105 96 0.12
106 601 0.76
107 96 0.12
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
Found at i:55117 original size:43 final size:43
Alignment explanation
Indices: 55056--55141 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
55046 GAGTTTTGAC
55056 GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
1 GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
55099 GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
1 GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
55142 CACTTTATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (43 bp):
GCTTTCCAATGACCGGAATCTTCAAGCACGTGGTCCACCTCAG
Found at i:57274 original size:22 final size:20
Alignment explanation
Indices: 57246--57286 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
57236 CGAACCGAAA
57246 AACCCGAACCGTTAAAAAACCC
1 AACCCGAACCG--AAAAAACCC
57268 AACCCGAACCGAAAAAACC
1 AACCCGAACCGAAAAAACC
57287 GGTTTCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.49, C:0.37, G:0.10, T:0.05
Consensus pattern (20 bp):
AACCCGAACCGAAAAAACCC
Found at i:64247 original size:20 final size:20
Alignment explanation
Indices: 64191--64261 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
64181 GCGATTTTCC
*
64191 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
64211 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
64231 GACTATCGCAATGCGATTTT
1 GACTATCGCAATGCGATTAT
*
64251 GACTGTCGCAA
1 GACTATCGCAA
64262 CACTGAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:65134 original size:24 final size:24
Alignment explanation
Indices: 65083--65136 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
65073 GTATTCGAAA
*
65083 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
65107 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
65131 TTTGAT
1 TTTGAT
65137 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:67756 original size:140 final size:140
Alignment explanation
Indices: 67495--67764 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
67485 AAACGTTGTA
*
67495 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATAAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATAAGTAACTTAAGTTTGAACATTGCTA
* *
67560 TGATCTGTTCAGTTGTTATCACTTATTACATATTCATTTGAATATCGCAACACGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
67625 TATGTGTATT
131 TATGTGTATT
*
67635 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATAAGTAACTTAAGTTTGAACATTGCTA
* *
67700 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGTAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
67765 CGCAACGCGA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATAAGTAACTTAAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
TATGTGTATT
Found at i:67760 original size:20 final size:20
Alignment explanation
Indices: 67735--67960 Score: 163
Period size: 20 Copynumber: 11.8 Consensus size: 20
67725 TTACACATTC
*
67735 ATTTGAATATCGTAACGCGA
1 ATTTGAATATCGCAACGCGA
*
67755 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
67775 ATTTGATTATCGCAA--CTA
1 ATTTGAATATCGCAACGCGA
* *
67793 A---AAAAATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
67810 ATTT-AACTATCGTAACACGA
1 ATTTGAA-TATCGCAACGCGA
* *
67830 ATATGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
67849 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
67864 ATTTGACTATCGCAACG-GTT
1 ATTTGAATATCGCAACGCG-A
*
67884 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
67904 ATTTGAGTATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
* * * *
67924 ATTTGATTATCTCAACGGGT
1 ATTTGAATATCGCAACGCGA
*
67944 ATTTGACTATCGCAACG
1 ATTTGAATATCGCAACG
67961 AGAAAATCGC
Statistics
Matches: 163, Mismatches: 28, Indels: 30
0.74 0.13 0.14
Matches are distributed among these distances:
14 10 0.06
15 11 0.07
17 3 0.02
18 3 0.02
19 6 0.04
20 128 0.79
21 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:67841 original size:55 final size:54
Alignment explanation
Indices: 67743--67879 Score: 193
Period size: 55 Copynumber: 2.5 Consensus size: 54
67733 TCATTTGAAT
* * * *
67743 ATCGTAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTAAAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAAC-AAAAAA
* * **
67798 ATCGCAACGCGAATTTAACTATCGTAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACAAAAAA
67852 ATCGCAACGCGAATTTGACTATCGCAAC
1 ATCGCAACGCGAATTTGACTATCGCAAC
67880 GGTTATTTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
54 30 0.42
55 42 0.58
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACAAAAAA
Found at i:68028 original size:20 final size:20
Alignment explanation
Indices: 67999--68056 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
67989 GCAACGTGAA
*
67999 TTGACTTTCGCGTTGCGCTT
1 TTGACTTTCGCGTTGCGATT
* *
68019 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
68039 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
68057 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:69709 original size:42 final size:42
Alignment explanation
Indices: 69611--69722 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
69601 TCTAGAATGT
* * * *
69611 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAAGGATGACAGGGGCCTCTTGAACGA
* *
69653 TGGGAGGGGACTCTTGAGGGATGACAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAAGGATGACAGGGGCCTCTTGAACGA
* *
69695 TAGGG-GAGGCCTCTTGAATGATGACAGG
1 T-GGGAGAGGACTCTTGAAGGATGACAGG
69723 TGAGTCGGGC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 53 0.90
43 6 0.10
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAAGGATGACAGGGGCCTCTTGAACGA
Found at i:70268 original size:20 final size:18
Alignment explanation
Indices: 70210--70274 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 18
70200 GAAACTTAAA
*
70210 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
* *
70228 ATCGCAGCGCGAAAATAACT
1 ATCGCAACGCG--AATGACT
70248 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
70268 ATCGCAA
1 ATCGCAA
70275 TGAGAGAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.29
20 27 0.71
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:70519 original size:18 final size:18
Alignment explanation
Indices: 70495--70544 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
70485 TTTACTAAGC
70495 AATCTAAGTGAAAT-GAT
1 AATCTAAGTGAAATGGAT
*
70512 ACATCTAAGTGAAATGGTT
1 A-ATCTAAGTGAAATGGAT
70531 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
70545 TACGAGTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 1 0.03
18 26 0.87
19 3 0.10
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (18 bp):
AATCTAAGTGAAATGGAT
Found at i:72281 original size:20 final size:20
Alignment explanation
Indices: 72258--72331 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
72248 GAAACTTAAA
72258 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
72278 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
72298 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
72318 ATCGCAACGCGAAA
1 ATCGCAACACGAAA
72332 CTAAAATCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:72770 original size:22 final size:22
Alignment explanation
Indices: 72715--72771 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
72705 GATGGAGATA
*
72715 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
* *
72737 GGCTGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
72759 GACGGATGTCGTC
1 GACGGATTTCGTC
72772 TTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.16, C:0.18, G:0.44, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:73045 original size:20 final size:20
Alignment explanation
Indices: 72935--73033 Score: 144
Period size: 20 Copynumber: 5.0 Consensus size: 20
72925 GTGCTTTGAA
* *
72935 AATCGCATTGCGATAGTTAG
1 AATCGCGTTGCGATAGTCAG
* *
72955 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
72975 AATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
72995 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
73015 AATCTCGTTGCGATAGTCA
1 AATCGCGTTGCGATAGTCA
73034 TACTCGCATT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Done.