Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001083.1 Hibiscus syriacus cultivar Beakdansim tig00002144_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: 79325
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2468 original size:63 final size:64
Alignment explanation
Indices: 2401--2554 Score: 165
Period size: 63 Copynumber: 2.5 Consensus size: 64
2391 TAATGAAGGT
* * *
2401 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATAATGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATTATAAAGAG
* * * * * *
2464 ATGCATCGGTGCA-TGCCTTAT-CATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAGAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTATAAAGAG
*
2527 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
2555 ACACCTTCAA
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
62 36 0.49
63 37 0.51
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTATAAAGAG
Found at i:4009 original size:34 final size:34
Alignment explanation
Indices: 3953--4018 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
3943 TCAATCACAT
* * *
3953 CATTTAATACTTTGAACTAAATAAAACCTCAAAA
1 CATTTAATACTTTAAACAAAATAAAACATCAAAA
*
3987 CATTTAATATTTTAAACAAAATAAAACATCAA
1 CATTTAATACTTTAAACAAAATAAAACATCAA
4019 GATCGAACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.30
Consensus pattern (34 bp):
CATTTAATACTTTAAACAAAATAAAACATCAAAA
Found at i:10811 original size:20 final size:20
Alignment explanation
Indices: 10786--10823 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10776 TTTGGTTCAC
10786 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
10806 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
10824 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:11051 original size:36 final size:36
Alignment explanation
Indices: 10978--11051 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
10968 CAAGTTGGAA
**
10978 AATATTTATATATTTTCTTTAAAAATTTAAATTTAT
1 AATATTTATATATTTTCTTTAAAAATTTAAAAATAT
11014 AATATTTATATAATTTT-TTTACAAAA-TTAAAAATAT
1 AATATTTATAT-ATTTTCTTTA-AAAATTTAAAAATAT
11050 AA
1 AA
11052 AAAAAGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 25 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAATTTAAAAATAT
Found at i:15119 original size:416 final size:414
Alignment explanation
Indices: 14304--15130 Score: 1467
Period size: 416 Copynumber: 2.0 Consensus size: 414
14294 ACCCAACAAA
*
14304 ATAAGTCTAGATTCATTGTTTTCACCCACTTGATTCTCATGTTTAAACAATTTTTAGGGGCTAAA
1 ATAAGTCTAGATTCATTGTTTTCACCCACTTGATTCTCATGTTTAAACAATTTTTAAGGGCTAAA
* *
14369 CAAACATAGGTTTAGCTTTTAAAATCCCAGGTTCGTCAGTTTTGTAAGTAAATATGGATTTATTA
66 CAAACATAGGTTTAGCTTTTAAAATCCCAGGTTCATCAGTTTTGTAAGTAAATATGGATTTATCA
* * *
14434 TTCACTACAGTAACCAAAACAAGGTTCTTCCCTTCATTTTTAAAGGTATTAGGAGTTTGTACCTG
131 TTCACTACAATAACCAAAACAAGGTTCTTCCATTCATTTTTAAAGGTATTAGGAGTTTGTACATG
14499 TTCACCAGCAGAATTTTCTTGCTCACCATTTCTGTCTGTTAAGATCTTTAACAGCTCCACAACAT
196 TTCACCAGCAGAATTTTCTTGCTCACCATTTCTGTCTGTTAAGATCTTTAACAGCTCCACAACAT
* * *
14564 AACCTTGATTAGTAGACATGCTTGATTCCAATGCAGTAATTTGATTTTCTTAAGTTTCCCACCAT
261 AACCTTGATTAGTAGACATCCTTGATTCCAATGCAGTAATTTCATTTTCTTAAATTTCCCACCAT
14629 TTAGGTGGATTAGTTTTTCTTGGCCTTGTTTCACCAACGCAACTAAATCTTCAATATGTTTTTGT
326 TTAGGTGGATTAGTTTTTCTTGGCCTTGTTTCACCAACGCAACTAAATCTTCAATATGTTTTTGT
14694 AGCGCAGAGAAATCAGCTTCAACC
391 AGCGCAGAGAAATCAGCTTCAACC
*
14718 ATAAGTCTAGATTCATTGTTTTCACCCATTTGATTCTCATGTTTATAACAATTTTTAAGGGCTAA
1 ATAAGTCTAGATTCATTGTTTTCACCCACTTGATTCTCATGTTTA-AACAATTTTTAAGGGCTAA
*
14783 ACAAACATCAGGTTTAGCTTTTAAAATCCCAGGTTCATCAGTTTTGTAAGTAAATATGGATTTGT
65 ACAAACAT-AGGTTTAGCTTTTAAAATCCCAGGTTCATCAGTTTTGTAAGTAAATATGGATTTAT
* * * *
14848 CATTCATTACAATAACCAAAACAGGGTTCTTCTATTCATTTTTAGAGGTATTAGGAGTTTGTACA
129 CATTCACTACAATAACCAAAACAAGGTTCTTCCATTCATTTTTAAAGGTATTAGGAGTTTGTACA
*
14913 TGTTCACCAGCAGAATTTTCTTGCTCACCATTTCTGTCTGTTAAGATCTTTAACAGCTCCTCAAC
194 TGTTCACCAGCAGAATTTTCTTGCTCACCATTTCTGTCTGTTAAGATCTTTAACAGCTCCACAAC
14978 ATAACCTTGATTAGTAGACATCCTTGATTCCAATGCAGTAA-TTCATTTTCTTAAATTTCCCACC
259 ATAACCTTGATTAGTAGACATCCTTGATTCCAATGCAGTAATTTCATTTTCTTAAATTTCCCACC
*
15042 ATTTAGGTGGATTAGTTTTTTCTTGGCCTTGTTTCACCAACGCAACTAAATCTTCAATCTGTTTT
324 ATTTAGGTGGATTAG-TTTTTCTTGGCCTTGTTTCACCAACGCAACTAAATCTTCAATATGTTTT
15107 TGTAGCGCAGAGAAATCAGCTTCA
388 TGTAGCGCAGAGAAATCAGCTTCA
15131 GTCATATTCT
Statistics
Matches: 393, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
414 44 0.11
415 62 0.16
416 287 0.73
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (414 bp):
ATAAGTCTAGATTCATTGTTTTCACCCACTTGATTCTCATGTTTAAACAATTTTTAAGGGCTAAA
CAAACATAGGTTTAGCTTTTAAAATCCCAGGTTCATCAGTTTTGTAAGTAAATATGGATTTATCA
TTCACTACAATAACCAAAACAAGGTTCTTCCATTCATTTTTAAAGGTATTAGGAGTTTGTACATG
TTCACCAGCAGAATTTTCTTGCTCACCATTTCTGTCTGTTAAGATCTTTAACAGCTCCACAACAT
AACCTTGATTAGTAGACATCCTTGATTCCAATGCAGTAATTTCATTTTCTTAAATTTCCCACCAT
TTAGGTGGATTAGTTTTTCTTGGCCTTGTTTCACCAACGCAACTAAATCTTCAATATGTTTTTGT
AGCGCAGAGAAATCAGCTTCAACC
Found at i:18318 original size:16 final size:16
Alignment explanation
Indices: 18299--18424 Score: 65
Period size: 16 Copynumber: 7.8 Consensus size: 16
18289 AACCATAACT
18299 AAAATTAACCCGAACC
1 AAAATTAACCCGAACC
** * *
18315 AAAAGCAACCTGAATC
1 AAAATTAACCCGAACC
* *
18331 GAAATTAAACCGAACC
1 AAAATTAACCCGAACC
* **
18347 GAAAA-CAATTCGAACC
1 -AAAATTAACCCGAACC
* *
18363 GAAATTAACCCGAATCG
1 AAAATTAACCCGAA-CC
** * *
18380 AATTTTAACCCGATCT
1 AAAATTAACCCGAACC
*
18396 AAAAGTAACCCGAACC
1 AAAATTAACCCGAACC
* *
18412 GAATTTAACCCGA
1 AAAATTAACCCGA
18425 CCCGAAAGCA
Statistics
Matches: 75, Mismatches: 32, Indels: 6
0.66 0.28 0.05
Matches are distributed among these distances:
15 3 0.04
16 58 0.77
17 14 0.19
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.17
Consensus pattern (16 bp):
AAAATTAACCCGAACC
Found at i:18336 original size:32 final size:32
Alignment explanation
Indices: 18300--18381 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
18290 ACCATAACTA
*
18300 AAATTAACCCGAACC-AAAAGCAAC-CTGAATCG
1 AAATTAACCCGAACCGAAAA-CAACTC-GAACCG
* *
18332 AAATTAAACCGAACCGAAAACAATTCGAACCG
1 AAATTAACCCGAACCGAAAACAACTCGAACCG
*
18364 AAATTAACCCGAATCGAA
1 AAATTAACCCGAACCGAA
18382 TTTTAACCCG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
32 38 0.88
33 5 0.12
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.13
Consensus pattern (32 bp):
AAATTAACCCGAACCGAAAACAACTCGAACCG
Found at i:18650 original size:19 final size:19
Alignment explanation
Indices: 18626--18662 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18616 TTTACTTATC
*
18626 TTATAAAAAAATATTAGAT
1 TTATAAAAAAATAATAGAT
*
18645 TTATAATAAAATAATAGA
1 TTATAAAAAAATAATAGA
18663 AAACAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TTATAAAAAAATAATAGAT
Found at i:24418 original size:32 final size:32
Alignment explanation
Indices: 24382--24460 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
24372 ATGTCCAATT
24382 ACTTCACTTT-AGAAACTTTTCAGTGAGATATC
1 ACTTCA-TTTCAGAAACTTTTCAGTGAGATATC
*
24414 ACTTCATTTCAGAAACTTTTCAGTGATATATC
1 ACTTCATTTCAGAAACTTTTCAGTGAGATATC
* *
24446 ACTTTATTTAAGAAA
1 ACTTCATTTCAGAAA
24461 AACATCATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 3 0.07
32 40 0.93
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (32 bp):
ACTTCATTTCAGAAACTTTTCAGTGAGATATC
Found at i:25862 original size:45 final size:45
Alignment explanation
Indices: 25806--26056 Score: 157
Period size: 45 Copynumber: 6.2 Consensus size: 45
25796 ATAAAAGAAT
*
25806 AATGCATATGGGTGCATTATTAACATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
* *
25851 AATGTATATGGGTGCATTATCGACAT-AAA--A-G--A-A--T--
1 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
*
25885 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
* *
25930 AATGCAGT-TGAGTGCATTATCGACAT-AAA--A-G--A-A--T--
1 AATGCA-TATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
* * *
25964 AATGCATATGGATGCATTATTG-----AAAGGATGTCAAAGCTGA
1 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
* * *
26004 AATGCATATGGGTGCATTATCGACAT-AGAAGTATGCTATA-CTTGA
1 AATGCATATGGGTGCATTATTGACATGA-AAGGATGCCATAGC-TGA
26049 AATGCATA
1 AATGCATA
26057 ATGGTGTATT
Statistics
Matches: 159, Mismatches: 18, Indels: 58
0.68 0.08 0.25
Matches are distributed among these distances:
30 3 0.02
32 1 0.01
33 2 0.01
34 40 0.25
35 4 0.03
36 3 0.02
37 1 0.01
38 4 0.03
39 2 0.01
40 21 0.13
41 3 0.02
42 2 0.01
43 1 0.01
44 8 0.05
45 63 0.40
46 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
Found at i:25899 original size:34 final size:34
Alignment explanation
Indices: 25851--25983 Score: 104
Period size: 34 Copynumber: 3.6 Consensus size: 34
25841 CCATAGCTGA
*
25851 AATGTATATGGGTGCATTATCGACATAAAAGAAT
1 AATGCATATGGGTGCATTATCGACATAAAAGAAT
* *
25885 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGACAT-AAA--A-G--A-A--T
** *
25928 GAAATGCAGTTGAGTGCATTATCGACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGACATAAAAGAAT
*
25964 AATGCATATGGATGCATTAT
1 AATGCATATGGGTGCATTAT
25984 TGAAAGGATG
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
34 39 0.51
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.03
39 1 0.01
40 1 0.01
41 2 0.03
42 1 0.01
43 1 0.01
44 3 0.04
45 21 0.28
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGACATAAAAGAAT
Found at i:25927 original size:79 final size:77
Alignment explanation
Indices: 25796--26030 Score: 352
Period size: 79 Copynumber: 3.0 Consensus size: 77
25786 GAATGAATGA
*
25796 ATAAAAGAATAATGCATATGGGTGCATTATTAACATGAAAGGATGCCATAGCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATT--CATGAAAGGATGCCATAGCTGAAATGCATATG
25861 GGTGCATTATCGAC
64 GGTGCATTATCGAC
25875 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCAGT-T
1 ATAAAAGAATAATGCATATGGGTGCATTATT--CATGAAAGGATGCCATAGCTGAAATGCA-TAT
*
25939 GAGTGCATTATCGAC
63 GGGTGCATTATCGAC
* * *
25954 ATAAAAGAATAATGCATATGGATGCATTA-T--TGAAAGGATGTCAAAGCTGAAATGCATATGGG
1 ATAAAAGAATAATGCATATGGGTGCATTATTCATGAAAGGATGCCATAGCTGAAATGCATATGGG
26016 TGCATTATCGAC
66 TGCATTATCGAC
26028 ATA
1 ATA
26031 GAAGTATGCT
Statistics
Matches: 146, Mismatches: 8, Indels: 9
0.90 0.05 0.06
Matches are distributed among these distances:
73 1 0.01
74 42 0.29
78 1 0.01
79 101 0.69
80 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.27
Consensus pattern (77 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTCATGAAAGGATGCCATAGCTGAAATGCATATGGG
TGCATTATCGAC
Found at i:33924 original size:21 final size:20
Alignment explanation
Indices: 33873--33943 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
33863 ATGCAAAACT
*
33873 GGTATCGATACCAT-G-AGAA
1 GGTATCGATACCATAGTAG-G
*
33892 GGTATCTG-TACCCTAGTATGG
1 GGTATC-GATACCATAGTA-GG
* *
33913 TGTATCGATACCATGGTAGG
1 GGTATCGATACCATAGTAGG
33933 GGTATCGATAC
1 GGTATCGATAC
33944 TGTGGAACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
19 11 0.27
20 15 0.37
21 14 0.34
22 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGG
Found at i:34485 original size:79 final size:79
Alignment explanation
Indices: 34350--34592 Score: 378
Period size: 79 Copynumber: 3.1 Consensus size: 79
34340 TAACGAATGA
* * * **
34350 ATAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATTACATAGCTGAAATGTATACA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGAATATG
*
34415 GGTGCATTATCGGC
66 GGTGCATTATCGAC
* * *
34429 ATATAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGAATATG
34494 GGTGCATTATCGAC
66 GGTGCATTATCGAC
* * *
34508 ATAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATGGCTGAAATGAATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGAATATG
34573 GGTGCATTATCGAC
66 GGTGCATTATCGAC
34587 ATAAAA
1 ATAAAA
34593 ATATGCTATA
Statistics
Matches: 150, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 150 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGAATATG
GGTGCATTATCGAC
Found at i:34503 original size:45 final size:44
Alignment explanation
Indices: 34439--34582 Score: 155
Period size: 45 Copynumber: 3.5 Consensus size: 44
34429 ATATAAGAAT
34439 AATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAG-TGA
* *
34484 AATGCATATGGGTGCATTATCGACAT-AAA--A-T--A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGTGA
* *
34518 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATGGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAG-TGA
*
34563 AATGAATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
34583 CGACATAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
34 24 0.30
35 3 0.04
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 3 0.04
45 43 0.53
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGTGA
Found at i:43193 original size:24 final size:24
Alignment explanation
Indices: 43166--43212 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
43156 AAAATTTATT
*
43166 TAAATA-CCAAAATAAATAAATAAA
1 TAAATAGCAAAAATAAA-AAATAAA
*
43190 TAAATAGTAAAAATAAAAAATAA
1 TAAATAGCAAAAATAAAAAATAA
43213 TATTAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (24 bp):
TAAATAGCAAAAATAAAAAATAAA
Found at i:43665 original size:8 final size:9
Alignment explanation
Indices: 43652--43778 Score: 54
Period size: 9 Copynumber: 14.1 Consensus size: 9
43642 TTTTAATTAC
43652 TATATTTA-
1 TATATTTAT
43660 TATA-TTAT
1 TATATTTAT
43668 TATATTT-T
1 TATATTTAT
*
43676 AATTATTTAT
1 TA-TATTTAT
43686 TATATTTA-
1 TATATTTAT
* *
43694 -ATAATTAG
1 TATATTTAT
*
43702 TATTATTAAT
1 TA-TATTTAT
*
43712 TCATA-TCAT
1 T-ATATTTAT
*
43721 TATATTTAA
1 TATATTTAT
43730 TA-ATTAATAT
1 TATATT--TAT
* *
43740 TATTAATTAA
1 TA-TATTTAT
43750 TATCATTATAT
1 TAT-ATT-TAT
43761 T-TATTTAT
1 TATATTTAT
43769 TATATTTAT
1 TATATTTAT
43778 T
1 T
43779 TAATATCTAC
Statistics
Matches: 89, Mismatches: 14, Indels: 31
0.66 0.10 0.23
Matches are distributed among these distances:
7 9 0.10
8 20 0.22
9 34 0.38
10 20 0.22
11 4 0.04
12 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (9 bp):
TATATTTAT
Found at i:43671 original size:16 final size:16
Alignment explanation
Indices: 43647--43784 Score: 59
Period size: 16 Copynumber: 8.1 Consensus size: 16
43637 ATCTATTTTA
*
43647 ATTACTATATTTATAT
1 ATTATTATATTTATAT
43663 ATTATTATATTT-TAATT
1 ATTATTATATTTAT-A-T
43680 ATTTATTATATTTA-AT
1 A-TTATTATATTTATAT
* *
43696 AATTAGTATTATTAATTCAT
1 -ATTATTA-TATTTA-T-AT
*
43716 ATCATTATATTTA-AT
1 ATTATTATATTTATAT
* *
43731 AATTAATATTATTAATTAAT
1 -ATTATTA-TATTTA-T-AT
* *
43751 ATCATTATATTTATTT
1 ATTATTATATTTATAT
*
43767 ATTATATTTATTTA-AT
1 ATTAT-TATATTTATAT
43783 AT
1 AT
43785 CTACGTTTCA
Statistics
Matches: 91, Mismatches: 16, Indels: 30
0.66 0.12 0.22
Matches are distributed among these distances:
15 3 0.03
16 31 0.34
17 22 0.24
18 21 0.23
19 10 0.11
20 4 0.04
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:43722 original size:22 final size:22
Alignment explanation
Indices: 43708--43751 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
43698 TTAGTATTAT
*
43708 TAATTCATATCATTATATTTAA
1 TAATTAATATCATTATATTTAA
*
43730 TAATTAATATTATTA-A-TTAA
1 TAATTAATATCATTATATTTAA
43750 TA
1 TA
43752 TCATTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTAATATCATTATATTTAA
Found at i:43726 original size:35 final size:33
Alignment explanation
Indices: 43652--43774 Score: 142
Period size: 35 Copynumber: 3.6 Consensus size: 33
43642 TTTTAATTAC
*
43652 TATATTTATATATTATTATATT-TTAATTAT-TTAT
1 TATATTTA-ATA--ATTATATTATTAATTATATCAT
43686 TATATTTAATAATTAGTATTATTAATTCATATCAT
1 TATATTTAATAATTA-TATTATTAATT-ATATCAT
43721 TATATTTAATAATTAATATTATTAATTAATATCAT
1 TATATTTAATAATT-ATATTATTAATT-ATATCAT
* *
43756 TATATTTATTTATTATATT
1 TATATTTAATAATTATATT
43775 TATTTAATAT
Statistics
Matches: 80, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
31 4 0.05
32 4 0.05
33 9 0.11
34 15 0.19
35 47 0.59
36 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (33 bp):
TATATTTAATAATTATATTATTAATTATATCAT
Found at i:43777 original size:13 final size:13
Alignment explanation
Indices: 43654--43780 Score: 57
Period size: 13 Copynumber: 9.5 Consensus size: 13
43644 TTAATTACTA
43654 TATTTA-TATA-T
1 TATTTATTATATT
* *
43665 TATTATATTTTAAT
1 TATT-TATTATATT
43679 TATTTATTATATT
1 TATTTATTATATT
* *
43692 TAATAATTAGTA-T
1 TATTTATTA-TATT
*
43705 TATTAATTCATATCAT
1 TATTTATT-ATAT--T
*
43721 TATATT-TAATAATT
1 TAT-TTATTAT-ATT
*
43735 AATATTATTA-ATT
1 TAT-TTATTATATT
* *
43748 AATATCATTATATT
1 TAT-TTATTATATT
43762 TATTTATTATATT
1 TATTTATTATATT
43775 TATTTA
1 TATTTA
43781 ATATCTACGT
Statistics
Matches: 91, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
11 4 0.04
12 2 0.02
13 54 0.59
14 19 0.21
15 4 0.04
16 7 0.08
17 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (13 bp):
TATTTATTATATT
Found at i:47236 original size:11 final size:12
Alignment explanation
Indices: 47207--47254 Score: 62
Period size: 11 Copynumber: 3.9 Consensus size: 12
47197 CTTAAAAGTT
47207 ATATATTATTAAA
1 ATATATT-TTAAA
47220 ATATATTTTAAA
1 ATATATTTTAAA
47232 A-ATATTTTAAA
1 ATATATTTTAAA
*
47243 ATTTATTATTAA
1 ATATATT-TTAA
47255 TTCGAGCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 11 0.34
12 10 0.31
13 11 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATTTTAAA
Found at i:58165 original size:20 final size:20
Alignment explanation
Indices: 58140--58184 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
58130 GTGAGTATCG
*
58140 ATACTTCATAGGTGGTAACA
1 ATACTTCACAGGTGGTAACA
*
58160 ATACTTCACAGGTGGTATCA
1 ATACTTCACAGGTGGTAACA
58180 ATACT
1 ATACT
58185 CGAGGCCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (20 bp):
ATACTTCACAGGTGGTAACA
Found at i:58972 original size:151 final size:151
Alignment explanation
Indices: 58698--59001 Score: 581
Period size: 151 Copynumber: 2.0 Consensus size: 151
58688 TTTTACACGG
*
58698 GATTAGCTAGAACCTTTCCCTTTTATAAAATGATAAAAGAAGTAAACAAGAAAACCTCTCTAAGG
1 GATTAGCTAGAACATTTCCCTTTTATAAAATGATAAAAGAAGTAAACAAGAAAACCTCTCTAAGG
* *
58763 TAGGTGTTTACAAGATTGAGCTCACAAGAACAAAATATTTACAAGATAAAGATGAAATAAGAATG
66 TAGGTGTTTACAAGACTGAGCTCACAAGAACAAAATATTTACAAGAGAAAGATGAAATAAGAATG
58828 AAAAACTCTTCTCTTGTGTTT
131 AAAAACTCTTCTCTTGTGTTT
58849 GATTAGCTAGAACATTTCCCTTTTATAAAATGATAAAAGAAGTAAACAAGAAAACCTCTCTAAGG
1 GATTAGCTAGAACATTTCCCTTTTATAAAATGATAAAAGAAGTAAACAAGAAAACCTCTCTAAGG
58914 TAGGTGTTTACAAGACTGAGCTCACAAGAACAAAATATTTACAAGAGAAAGATGAAATAAGAATG
66 TAGGTGTTTACAAGACTGAGCTCACAAGAACAAAATATTTACAAGAGAAAGATGAAATAAGAATG
58979 AAAAACTCTTCTCTTGTGTTT
131 AAAAACTCTTCTCTTGTGTTT
59000 GA
1 GA
59002 ATACTTGGAT
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (151 bp):
GATTAGCTAGAACATTTCCCTTTTATAAAATGATAAAAGAAGTAAACAAGAAAACCTCTCTAAGG
TAGGTGTTTACAAGACTGAGCTCACAAGAACAAAATATTTACAAGAGAAAGATGAAATAAGAATG
AAAAACTCTTCTCTTGTGTTT
Found at i:59108 original size:20 final size:22
Alignment explanation
Indices: 59083--59122 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
59073 TGTTGTATAT
59083 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
59103 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
59123 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:59264 original size:20 final size:20
Alignment explanation
Indices: 59235--59308 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
59225 GCAGCCTTCG
*
59235 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* **
59255 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-AGCAGGA
*
59276 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
*
59296 TGCATCTATGCAC
1 TGCATCGATGCAC
59309 TAATTGCATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:59398 original size:21 final size:21
Alignment explanation
Indices: 59329--59469 Score: 203
Period size: 21 Copynumber: 6.7 Consensus size: 21
59319 CGGTGTTTAA
*
59329 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* * **
59349 GTGCATCGATGCACTAGTACAG
1 GTGCATGGATGCACT-GCAGGG
*
59371 GTGCATGGATGCACTACAGGG
1 GTGCATGGATGCACTGCAGGG
*
59392 ATGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
59413 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
59434 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
59455 GTGCATGGATGCACT
1 GTGCATGGATGCACT
59470 TTGACACCCT
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
20 14 0.13
21 79 0.73
22 15 0.14
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:59570 original size:29 final size:29
Alignment explanation
Indices: 59549--59606 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
59539 AAACTTTGAA
59549 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
59578 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
59607 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:59596 original size:30 final size:30
Alignment explanation
Indices: 59549--59608 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
59539 AAACTTTGAA
59549 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
59578 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
59609 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:60890 original size:19 final size:20
Alignment explanation
Indices: 60847--60894 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
60837 TCTAAATCCT
*
60847 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
60867 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
60886 TTTTCAAAA
1 TTTTCAAAA
60895 GAAAATTATT
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:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:62057 original size:20 final size:22
Alignment explanation
Indices: 62032--62071 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
62022 TATTGTATAT
62032 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
62052 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
62072 TCTACTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:62199 original size:21 final size:21
Alignment explanation
Indices: 62175--62281 Score: 146
Period size: 21 Copynumber: 5.1 Consensus size: 21
62165 CTAGCCGTTG
*
62175 CAGCCTTCG-TGCATGGATGCA
1 CAGCCTT-GATGCATCGATGCA
**
62196 CAG-CAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
*
62216 CAACCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
*
62237 CAACCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
62258 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
62279 CAG
1 CAG
62282 AAGGATGCAT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
19 1 0.01
20 14 0.18
21 62 0.81
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.21
Consensus pattern (21 bp):
CAGCCTTGATGCATCGATGCA
Found at i:62367 original size:22 final size:23
Alignment explanation
Indices: 62334--62376 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
62324 ATGGATGCAC
62334 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
62357 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
62377 GCAGGGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:62392 original size:21 final size:20
Alignment explanation
Indices: 62320--62439 Score: 143
Period size: 21 Copynumber: 5.8 Consensus size: 20
62310 CGGTGTTTGA
*
62320 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
62340 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
62362 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
62382 GATGTATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGCAGG
62403 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
*
62425 GTACATGGATGCACT
1 GTGCATGGATGCACT
62440 ATGACACCCT
Statistics
Matches: 89, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.04
20 15 0.17
21 49 0.55
22 17 0.19
23 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:62540 original size:29 final size:29
Alignment explanation
Indices: 62519--62576 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
62509 AAACTTTGAA
62519 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
62548 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
62577 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:62566 original size:30 final size:30
Alignment explanation
Indices: 62519--62578 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
62509 AAACTTTGAA
62519 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
62548 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
62579 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:64807 original size:12 final size:12
Alignment explanation
Indices: 64790--64820 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
64780 TTTCCACTTT
64790 CATATTCATTTA
1 CATATTCATTTA
*
64802 CATATTCATTTT
1 CATATTCATTTA
64814 CATATTC
1 CATATTC
64821 CATGTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (12 bp):
CATATTCATTTA
Found at i:64944 original size:19 final size:19
Alignment explanation
Indices: 64873--64947 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
64863 TGAATCAGAA
*
64873 CTTA-TTTCTAGATTCATAA
1 CTTATTTTC-AGATTCATAG
*
64892 CTTATTTTCAGAGTCATAG
1 CTTATTTTCAGATTCATAG
* *
64911 CTTACTGTCAGATTCATAG
1 CTTATTTTCAGATTCATAG
*
64930 CTTATTTTCAAATTCATA
1 CTTATTTTCAGATTCATA
64948 TCCCAATGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 43 0.91
20 4 0.09
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.44
Consensus pattern (19 bp):
CTTATTTTCAGATTCATAG
Found at i:71190 original size:23 final size:23
Alignment explanation
Indices: 71164--71224 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
71154 CACCACAGCT
*
71164 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
71187 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
71210 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
71225 TAGTTCCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:72175 original size:2 final size:2
Alignment explanation
Indices: 72168--72243 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
72158 ATATCTCCTA
72168 AT AT AT AT AT AT 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 AT AT AT AT AT AT
72210 AT AT 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 AT AT
72244 TAATCTCATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.