Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003111.1 Hibiscus syriacus cultivar Beakdansim tig00006503_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: 57890
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2327 original size:76 final size:72
Alignment explanation
Indices: 2220--2430 Score: 275
Period size: 76 Copynumber: 2.9 Consensus size: 72
2210 ATTTTAAACA
*
2220 TTATACTTTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
1 TTATA-TTTAT-TTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTA
2285 GGATATTATTT
63 GGATATTA-TT
*
2296 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATA-TTTAT-TTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTA
2361 GGATATTATT
63 GGATATTATT
* * * *
2371 TTA-A-ATATTTTTTTTTAGGTATTTTAGTTTAAATAGTTTTAAGT-GTTTAATTAGGATTTA
1 TTATATTTATTTTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAAGATTTA
2431 AGATGTTTTA
Statistics
Matches: 126, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
70 20 0.16
71 29 0.23
72 3 0.02
74 1 0.01
75 5 0.04
76 68 0.54
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (72 bp):
TTATATTTATTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGATTTAGGA
TATTATT
Found at i:2403 original size:28 final size:27
Alignment explanation
Indices: 2357--2410 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2347 TTAATTAGGA
* *
2357 TTTAGGATATTATTTTAAATATTTTTT
1 TTTAGGATATTAGTTTAAATAGTTTTT
*
2384 TTTAGGTATTTTAGTTTAAATAGTTTT
1 TTTAGG-ATATTAGTTTAAATAGTTTT
2411 AAGTGTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (27 bp):
TTTAGGATATTAGTTTAAATAGTTTTT
Found at i:3649 original size:51 final size:51
Alignment explanation
Indices: 3569--3682 Score: 149
Period size: 51 Copynumber: 2.2 Consensus size: 51
3559 GCAATTACTA
* * * **
3569 AATAAAATAATAATAAATTAAAGAAAATATTTTGATTATATCCTAATTTCT
1 AATAAAATAATAATAAATTAAAGAAAATATTTTAACTATATCATAATACCT
* *
3620 AATAAAATAATAATAAGA-TAAAGATAATATTTTAACTCTATCATAATACCT
1 AATAAAATAATAATAA-ATTAAAGAAAATATTTTAACTATATCATAATACCT
3671 AATAAAATAATA
1 AATAAAATAATA
3683 TATCTAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 54 0.98
52 1 0.02
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (51 bp):
AATAAAATAATAATAAATTAAAGAAAATATTTTAACTATATCATAATACCT
Found at i:4258 original size:27 final size:27
Alignment explanation
Indices: 4228--4289 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
4218 TTAGTCCAAA
4228 GAAGCATGCATTATCATTTTGGAATCT
1 GAAGCATGCATTATCATTTTGGAATCT
*
4255 GAAGCATGCATTATCATTTTGGACTCT
1 GAAGCATGCATTATCATTTTGGAATCT
4282 GAAGCATG
1 GAAGCATG
4290 TATCATTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (27 bp):
GAAGCATGCATTATCATTTTGGAATCT
Found at i:6663 original size:21 final size:21
Alignment explanation
Indices: 6638--6678 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
6628 ATTTGGCATT
*
6638 ATTTAATAATTAAAA-AATAA
1 ATTTTATAATTAAAATAATAA
6658 ATTTTATAATTAAAATAATAA
1 ATTTTATAATTAAAATAATAA
6679 TAAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTTATAATTAAAATAATAA
Found at i:7835 original size:15 final size:15
Alignment explanation
Indices: 7815--7844 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7805 TCGATTGCAT
*
7815 GGGAAGAGAGTGAAG
1 GGGAAGAGAGGGAAG
7830 GGGAAGAGAGGGAAG
1 GGGAAGAGAGGGAAG
7845 AGGAGAGAAA
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:0.40, C:0.00, G:0.57, T:0.03
Consensus pattern (15 bp):
GGGAAGAGAGGGAAG
Found at i:9657 original size:24 final size:24
Alignment explanation
Indices: 9603--9696 Score: 71
Period size: 24 Copynumber: 3.9 Consensus size: 24
9593 ATAGTAAAAC
* *
9603 TGTGCACTCTTGTATTAGTGCAAA
1 TGTGCACTCCTGCATTAGTGCAAA
** *
9627 TACGCACTCCTGCATTAGTGCAAT
1 TGTGCACTCCTGCATTAGTGCAAA
*** * *
9651 TGTGCACTCCCATATTAGTACCAA
1 TGTGCACTCCTGCATTAGTGCAAA
* * *
9675 TGGGTACTCCTGTATTAGTGCA
1 TGTGCACTCCTGCATTAGTGCA
9697 TCCGTGCACT
Statistics
Matches: 51, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (24 bp):
TGTGCACTCCTGCATTAGTGCAAA
Found at i:15627 original size:4 final size:4
Alignment explanation
Indices: 15602--15645 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
15592 ATATTAAAAT
* *
15602 TAAA TATA TATA T-AA TATAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAAA TAAA TAAA TAAA
15646 AAGGATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
4 30 0.83
5 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (4 bp):
TAAA
Found at i:16979 original size:84 final size:83
Alignment explanation
Indices: 16755--17174 Score: 370
Period size: 84 Copynumber: 5.1 Consensus size: 83
16745 GAGTTGAAAA
* * * * * *
16755 TTTGGTGACAGATAACCCTTCTAG-CATTGAGTTATGCTGTAAATAATGTGCCCTTGAAGCTGAG
1 TTTGTTGACAGATAACCCTTCTAGAC-TTAAGTTATACTGCAAATGATATGCCCTTG-AGCTGAG
* * *
16819 TGTAATCGAACTCGAGGGTC
64 CGTAATCGAACTCAAAGGTC
* * * * * * *
16839 TTTG--G-CAGATAGCCCTCCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCG
1 TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTTGAGCTGAGCG
*
16901 TAGTCGAACTCAAAGGTC
66 TAATCGAACTCAAAGGTC
* * *
16919 TTTTGTTGACAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATG-CCTGGGAGCTGAG
1 -TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCT-TGAGCTGAG
* *
16983 CGTAATCAAACTCGAAGGTC
64 CGTAATCGAACTCAAAGGTC
* * * * * * *
17003 TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATATGCCCTCGAGGCTGAGT
1 TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTTGA-GCTGAGC
***
17068 GTAATCGAACTCGGGGGTC
65 GTAATCGAACTCAAAGGTC
* * * * * * *
17087 TTTG--G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCTGAGCG
1 TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTTGAGCTGAGCG
*
17149 TAGTCGAACTCAAAGGTC
66 TAATCGAACTCAAAGGTC
17167 TTTTGTTG
1 -TTTGTTG
17175 GCGGACACTC
Statistics
Matches: 271, Mismatches: 54, Indels: 23
0.78 0.16 0.07
Matches are distributed among these distances:
80 44 0.16
81 83 0.31
82 3 0.01
83 49 0.18
84 92 0.34
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTTGAGCTGAGCG
TAATCGAACTCAAAGGTC
Found at i:17555 original size:106 final size:106
Alignment explanation
Indices: 17370--18785 Score: 2409
Period size: 106 Copynumber: 13.4 Consensus size: 106
17360 TATTGTTCCA
* * * * * * *
17370 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
17435 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
17476 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
17541 CAGCGGTCCCTTCGTCGTGAAGTCGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
17582 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
17647 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
17688 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
17753 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
17794 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
17859 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
17900 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
17965 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
18006 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
18071 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
18112 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
18177 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
18218 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
18283 CAGCGGTCCCTTCGCCGTGATGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
18324 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
18389 CAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
18430 AGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
18495 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
18536 AGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
18601 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
18642 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
18707 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
18748 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
18786 CGAGAAAAAT
Statistics
Matches: 1247, Mismatches: 63, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 1247 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:22591 original size:33 final size:34
Alignment explanation
Indices: 22540--22604 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
22530 CTAAAAGGTA
** *
22540 AAAAAAAGTTAGATAAAAA-AGATTAAATAAATCG
1 AAAAAAAGAAAGATAAAAATA-AATAAATAAATCG
22574 AAAAAAAGAAAGA-AAAAATAAATAAATAAAT
1 AAAAAAAGAAAGATAAAAATAAATAAATAAAT
22605 AAATTGAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (34 bp):
AAAAAAAGAAAGATAAAAATAAATAAATAAATCG
Found at i:22765 original size:4 final size:4
Alignment explanation
Indices: 22740--22791 Score: 70
Period size: 4 Copynumber: 13.0 Consensus size: 4
22730 ATATTAAAAT
* *
22740 TAAA TATA TATA TATAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TA-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
22788 TAAA
1 TAAA
22792 AAGGATTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 3 0.07
4 39 0.89
5 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
TAAA
Found at i:22841 original size:30 final size:30
Alignment explanation
Indices: 22790--22846 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
22780 TAAATAAATA
* * *
22790 AAAAGGATTAAAATAGCAAAAACAAAAGGT
1 AAAAGGACTAAAATAGAAAAAAAAAAAGGT
*
22820 AAAAGGACTAAAATGGAAAAAAAAAAA
1 AAAAGGACTAAAATAGAAAAAAAAAAA
22847 CTAAAGTCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (30 bp):
AAAAGGACTAAAATAGAAAAAAAAAAAGGT
Found at i:22851 original size:29 final size:30
Alignment explanation
Indices: 22790--22851 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
22780 TAAATAAATA
* * **
22790 AAAAGGATTAAAATAGCAAAAACAAAAGGT
1 AAAAGGACTAAAATAGCAAAAAAAAAAACT
*
22820 AAAAGGACTAAAAT-GGAAAAAAAAAAACT
1 AAAAGGACTAAAATAGCAAAAAAAAAAACT
22849 AAA
1 AAA
22852 GTCCCAAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.11
Consensus pattern (30 bp):
AAAAGGACTAAAATAGCAAAAAAAAAAACT
Found at i:23969 original size:102 final size:102
Alignment explanation
Indices: 23857--24153 Score: 301
Period size: 102 Copynumber: 2.9 Consensus size: 102
23847 TCTATAAAAG
* * * *
23857 ACCTATTTAAATTAAAATTAATTCTTATTTTTGTTTAATATATCATAATTTAGTATAATATTATA
1 ACCTATTTAAATCAAAATTAATTCATATTTTTGTTTAATATATCATAATTTAGTCTAATATTATT
* *
23922 AATATTATAATATTTGGGTTACATTTGAAC-GTGAAA
66 AATATTATAATATTTGAGTTACATTTGAACTCTGAAA
** * * * *
23958 GATTTATTTAAACCAAAATTAATCGCA-ATTTTTGTTTAATATATCATAATTTAGTCTGATATTG
1 -ACCTATTTAAATCAAAATTAAT-TCATATTTTTGTTTAATATATCATAATTTAGTCTAATATTA
* * ** * **
24022 TTAATATCAAAATATTTTTGTTACATCTGGTCTCTGAAA
64 TTAATATTATAATATTTGAGTTACATTTGAACTCTGAAA
* * * ** *
24061 ACCTATTTAGATCAAAGTTAATCCATATTTTTGTTTAATACCTCATAATATAGTCTAATATTATT
1 ACCTATTTAAATCAAAATTAATTCATATTTTTGTTTAATATATCATAATTTAGTCTAATATTATT
* * * *
24126 AAGACTGTAATATTTGAGTTGCATTTGA
66 AATATTATAATATTTGAGTTACATTTGA
24154 TCCGTTAAAG
Statistics
Matches: 153, Mismatches: 39, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
101 2 0.01
102 145 0.95
103 6 0.04
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (102 bp):
ACCTATTTAAATCAAAATTAATTCATATTTTTGTTTAATATATCATAATTTAGTCTAATATTATT
AATATTATAATATTTGAGTTACATTTGAACTCTGAAA
Found at i:24429 original size:28 final size:28
Alignment explanation
Indices: 24397--24485 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
24387 TAAAAATATG
24397 AATAACCCAAATATTTCATTCAGTTAGA
1 AATAACCCAAATATTTCATTCAGTTAGA
** ** **
24425 AATAA-AAAAAT-TTATCAATAAAAATATG-
1 AATAACCCAAATATT-TC-ATTCAGTTA-GA
24453 AATAACCCAAATATTTCATTCAGTTAGA
1 AATAACCCAAATATTTCATTCAGTTAGA
24481 AATAA
1 AATAA
24486 AAAATTATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
26 2 0.05
27 7 0.16
28 25 0.58
29 7 0.16
30 2 0.05
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (28 bp):
AATAACCCAAATATTTCATTCAGTTAGA
Found at i:24447 original size:56 final size:56
Alignment explanation
Indices: 24380--24489 Score: 220
Period size: 56 Copynumber: 2.0 Consensus size: 56
24370 TCACCCATAA
24380 TTATCAATAAAAATATGAATAACCCAAATATTTCATTCAGTTAGAAATAAAAAAAT
1 TTATCAATAAAAATATGAATAACCCAAATATTTCATTCAGTTAGAAATAAAAAAAT
24436 TTATCAATAAAAATATGAATAACCCAAATATTTCATTCAGTTAGAAATAAAAAA
1 TTATCAATAAAAATATGAATAACCCAAATATTTCATTCAGTTAGAAATAAAAAA
24490 TTATTTGCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (56 bp):
TTATCAATAAAAATATGAATAACCCAAATATTTCATTCAGTTAGAAATAAAAAAAT
Found at i:28948 original size:25 final size:25
Alignment explanation
Indices: 28914--28979 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
28904 ACGTTTAAAC
28914 TTGTTTTCTCGACATATGCCTGCTA
1 TTGTTTTCTCGACATATGCCTGCTA
28939 TTGTTTTCTCGACATATGCCTGCTA
1 TTGTTTTCTCGACATATGCCTGCTA
*
28964 TTGTTTTCTCAACATA
1 TTGTTTTCTCGACATA
28980 AACAAATGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45
Consensus pattern (25 bp):
TTGTTTTCTCGACATATGCCTGCTA
Found at i:33825 original size:21 final size:21
Alignment explanation
Indices: 33791--33834 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33781 TATTCTAATT
*
33791 ATATTTTTTAATATAATTTCA
1 ATATTTTTTAATATAATTACA
*
33812 ATATTTTTCT-ATATGATTACA
1 ATATTTTT-TAATATAATTACA
33833 AT
1 AT
33835 TACACACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
ATATTTTTTAATATAATTACA
Found at i:33857 original size:2 final size:2
Alignment explanation
Indices: 33852--33881 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33842 ATACACATCA
33852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33882 TAATTAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46810 original size:18 final size:16
Alignment explanation
Indices: 46776--46813 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
46766 TAATTAACCA
46776 AAAT-TATTAATTATT
1 AAATATATTAATTATT
46791 AAATATATTATATATATT
1 AAATATATTA-AT-TATT
46809 AAATA
1 AAATA
46814 CACACTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 2 0.10
18 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATATTAATTATT
Found at i:46962 original size:10 final size:10
Alignment explanation
Indices: 46947--46975 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
46937 TTAATCTAAT
46947 TAAAAAATTA
1 TAAAAAATTA
46957 TAAAAAATTA
1 TAAAAAATTA
46967 TAAAAAATT
1 TAAAAAATT
46976 GGTTAATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:49949 original size:21 final size:21
Alignment explanation
Indices: 49923--49967 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
49913 GAATTATGCA
*
49923 TTTAGTACTTAAACTATTAGT
1 TTTAGTACTTAAACTATTAAT
* *
49944 TTTAGTATTTAAACTTTTAAT
1 TTTAGTACTTAAACTATTAAT
49965 TTT
1 TTT
49968 TTCAAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTAGTACTTAAACTATTAAT
Found at i:50157 original size:16 final size:17
Alignment explanation
Indices: 50136--50187 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 17
50126 TTTTTAATTT
50136 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
50152 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
50167 AATTACTCTAACTTTCA
1 AATTACTCTAACTTTCA
50184 AATT
1 AATT
50188 TACTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 4 0.13
15 10 0.32
16 7 0.23
17 7 0.23
18 3 0.10
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:50172 original size:15 final size:14
Alignment explanation
Indices: 50130--50177 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
50120 TTAATTTTTT
50130 TAATTTAATTACT-
1 TAATTTAATTACTC
50143 TAACTTTCAAATTACTCC
1 TAA-TTT--AATTACT-C
50161 TAATTTAATTACTC
1 TAATTTAATTACTC
50175 TAA
1 TAA
50178 CTTTCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 7 0.23
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATTTAATTACTC
Found at i:53814 original size:20 final size:20
Alignment explanation
Indices: 53789--53874 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
53779 TTTCTAGATG
53789 AGAGTATCGATACTTTCCCA
1 AGAGTATCGATACTTTCCCA
*
53809 AGAGTAT--ATATTTTCCACA
1 AGAGTATCGATACTTTCC-CA
*
53828 AGATTATCGATACTTTCCCA
1 AGAGTATCGATACTTTCCCA
* *
53848 AGAGTATCAATACTTTCCCT
1 AGAGTATCGATACTTTCCCA
53868 AGAGTAT
1 AGAGTAT
53875 GTATACTGAG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.14
19 8 0.14
20 33 0.58
21 8 0.14
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
AGAGTATCGATACTTTCCCA
Found at i:54687 original size:22 final size:22
Alignment explanation
Indices: 54618--54687 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
54608 GTTCTATGGC
*
54618 ACTTTAGTATCAGTGCTAATGA
1 ACTTTAGTATCAGTGCTAAGGA
* * * *
54640 ACTTCTA-TATTAGTGTTGAGGC
1 ACTT-TAGTATCAGTGCTAAGGA
* *
54662 ACTTTAGTACCAGTGCTAAGGT
1 ACTTTAGTATCAGTGCTAAGGA
54684 ACTT
1 ACTT
54688 CCGTTAACAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (22 bp):
ACTTTAGTATCAGTGCTAAGGA
Found at i:54722 original size:4 final size:4
Alignment explanation
Indices: 54713--54775 Score: 117
Period size: 4 Copynumber: 15.8 Consensus size: 4
54703 AATGCCACCA
*
54713 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
54761 TATG TATG TATG TAT
1 TATG TATG TATG TAT
54776 ATTCAATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Done.