Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002486.1 Hibiscus syriacus cultivar Beakdansim tig00005072_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: 79928
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:316 original size:144 final size:144
Alignment explanation
Indices: 56--353 Score: 560
Period size: 144 Copynumber: 2.1 Consensus size: 144
46 GAACTGATAA
56 CTGATAACTGAACATTGATACACGAATGTACCAAAGATGAACTGGTAAGTACTCCTCAATAGCAT
1 CTGATAACTGAACATTGATACACGAATGTACCAAAGATGAACTGGTAAGTACTCCTCAATAGCAT
*
121 GCCAAATGTACCTACGACTCTCAATGCAACATACAATGGACTTATAATTATCATCGTAAAATCAT
66 GCCAAATGTACATACGACTCTCAATGCAACATACAATGGACTTATAATTATCATCGTAAAATCAT
186 TTATTAATCTGTAT
131 TTATTAATCTGTAT
200 CTGATAACTGAACATTGATACACGAATGTACCAAAGATGAACTGGTAAGTACTCCTCAATAGCAT
1 CTGATAACTGAACATTGATACACGAATGTACCAAAGATGAACTGGTAAGTACTCCTCAATAGCAT
* *
265 GCCAAATGTACATACGACTCTCAATGCAACATACAATGGGCTTATATTTATCATCGTAAAATCAT
66 GCCAAATGTACATACGACTCTCAATGCAACATACAATGGACTTATAATTATCATCGTAAAATCAT
*
330 TTATTAATTTGTAT
131 TTATTAATCTGTAT
344 CTGATAACTG
1 CTGATAACTG
354 TAAAATATAT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 150 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (144 bp):
CTGATAACTGAACATTGATACACGAATGTACCAAAGATGAACTGGTAAGTACTCCTCAATAGCAT
GCCAAATGTACATACGACTCTCAATGCAACATACAATGGACTTATAATTATCATCGTAAAATCAT
TTATTAATCTGTAT
Found at i:386 original size:35 final size:37
Alignment explanation
Indices: 341--428 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 37
331 TATTAATTTG
* *
341 TATCTGATAACTGTAAAAT-ATATGATATTTG-TAAT
1 TATCTGATAACTGTAAAATCATATGATAATTGAAAAT
* *
376 TATCTAATAACTGT-AAATCATCTGATAATTGAAAAT
1 TATCTGATAACTGTAAAATCATATGATAATTGAAAAT
*
412 CATCTGATAACTGTAAA
1 TATCTGATAACTGTAAA
429 TGTTTAGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
34 4 0.09
35 23 0.52
36 15 0.34
37 2 0.05
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (37 bp):
TATCTGATAACTGTAAAATCATATGATAATTGAAAAT
Found at i:403 original size:18 final size:18
Alignment explanation
Indices: 342--429 Score: 90
Period size: 18 Copynumber: 4.9 Consensus size: 18
332 ATTAATTTGT
342 ATCTGATAACTGTAAAAT-
1 ATCTGATAACTGT-AAATC
* ** *
360 ATATGATATTTGT-AATT
1 ATCTGATAACTGTAAATC
*
377 ATCTAATAACTGTAAATC
1 ATCTGATAACTGTAAATC
* *
395 ATCTGATAATTGAAAATC
1 ATCTGATAACTGTAAATC
413 ATCTGATAACTGTAAAT
1 ATCTGATAACTGTAAAT
430 GTTTAGAATT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
16 3 0.05
17 9 0.16
18 43 0.78
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (18 bp):
ATCTGATAACTGTAAATC
Found at i:646 original size:11 final size:11
Alignment explanation
Indices: 630--654 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
620 TTAAACACTT
630 TATTATTATTA
1 TATTATTATTA
641 TATTATTATTA
1 TATTATTATTA
652 TAT
1 TAT
655 CAAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATTATTA
Found at i:5899 original size:77 final size:75
Alignment explanation
Indices: 5744--6040 Score: 347
Period size: 77 Copynumber: 4.0 Consensus size: 75
5734 AAATATCGAA
* * * * * * ** *
5744 TTTTTTGAATGTTGGTAATAATATAAACGGT-AAAAAAAATAGACGGTATATATTACATTAAAGT
1 TTTTTTGAAGGTTGTTAATAATGTAAACGGTAAAAAAAAACAGGCGCTACCTATTACATTAAAAT
5808 ACCTACCGAT
66 ACCTACCGAT
* * *
5818 TTTTTTGAATGTTGCTAATAATGTAAACAGTAAAAAAAAAAACAGGCGCTACCTATTACATTAAA
1 TTTTTTGAAGGTTGTTAATAATGTAAACGGT--AAAAAAAAACAGGCGCTACCTATTACATTAAA
5883 ATACCTACCGAT
64 ATACCTACCGAT
* * *
5895 TTTTTTGAAGGTTGTTAATAATGTAAAC----AAAAAAAA-AGGTGCTACCTATTACAATAAACT
1 TTTTTTGAAGGTTGTTAATAATGTAAACGGTAAAAAAAAACAGGCGCTACCTATTACATTAAAAT
5955 ACCTACCGA-
66 ACCTACCGAT
* * *
5964 TTTTTTGAAGGTTGTTAATAATGTAAACGGTAAAAAAAAATAGCCGCTACTTATTACATTAAAAT
1 TTTTTTGAAGGTTGTTAATAATGTAAACGGTAAAAAAAAACAGGCGCTACCTATTACATTAAAAT
* *
6029 ACGTATCGAT
66 ACCTACCGAT
6039 TT
1 TT
6041 CATTATAATA
Statistics
Matches: 193, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
69 28 0.15
70 30 0.16
71 8 0.04
73 8 0.04
74 54 0.28
75 2 0.01
77 63 0.33
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (75 bp):
TTTTTTGAAGGTTGTTAATAATGTAAACGGTAAAAAAAAACAGGCGCTACCTATTACATTAAAAT
ACCTACCGAT
Found at i:5939 original size:70 final size:71
Alignment explanation
Indices: 5847--6040 Score: 259
Period size: 70 Copynumber: 2.7 Consensus size: 71
5837 AATGTAAACA
5847 GTAAA-AAAAAAAACAGGCGCTACCTATTACATTAAAATACCTACCGATTTTTTTGAAGGTTGTT
1 GTAAACAAAAAAAACAGGCGCTACCTATTACATTAAAATACCTACCGATTTTTTTGAAGGTTGTT
5911 AATAAT
66 AATAAT
* * *
5917 GTAAACAAAAAAAA-AGGTGCTACCTATTACAATAAACTACCTACCGA-TTTTTTGAAGGTTGTT
1 GTAAACAAAAAAAACAGGCGCTACCTATTACATTAAAATACCTACCGATTTTTTTGAAGGTTGTT
5980 AATAAT
66 AATAAT
* * * * *
5986 GTAAACGGTAAAAAAAAATAGCCGCTACTTATTACATTAAAATACGTATCGATTT
1 GTAAAC----AAAAAAAACAGGCGCTACCTATTACATTAAAATACCTACCGATTT
6041 CATTATAATA
Statistics
Matches: 107, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
69 28 0.26
70 35 0.33
71 8 0.07
73 8 0.07
74 26 0.24
75 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (71 bp):
GTAAACAAAAAAAACAGGCGCTACCTATTACATTAAAATACCTACCGATTTTTTTGAAGGTTGTT
AATAAT
Found at i:6358 original size:182 final size:183
Alignment explanation
Indices: 6050--6477 Score: 617
Period size: 182 Copynumber: 2.3 Consensus size: 183
6040 TCATTATAAT
* *
6050 AGTAATAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATATAACATG
1 AGTAATAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATAAATAACAATATAACAGG
** * * **
6115 TAAAAATATGACAAAATTGGTTTCATTATGACAAAACCTGTAAAGTTCTACCGGATATGTTGAAA
66 TAAAAATATGACAAAACCGGTTTCATTATAACAAAACCGGTAAAGCGCTACCGGATATGTTGAAA
* *
6180 GTATCGATT-TCATTTAAATAAATATCGACACTTTTAGAATTTAAAAGAAAAAC
131 GTATCGATTCT-ATTCAAATAAATATCAACACTTTTAGAATTTAAAAGAAAAAC
** *
6233 AGTAATAATTCCTATAAAGTATCGATACTTTA-AAAAATGTATCGATAAATAACAATATAATAGG
1 AGTAATAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATAAATAACAATATAACAGG
* *
6297 TAAAAATATGATAAAACCGGTTTCATTATAACAAAACCGGTAAAGCGCTACTGGATATGTTGAAA
66 TAAAAATATGACAAAACCGGTTTCATTATAACAAAACCGGTAAAGCGCTACCGGATATGTTGAAA
* * * **
6362 GTATCGATTCTATTCAAATAAGTATCAATACTTTTGGAATTTAAAAGAAAAGT
131 GTATCGATTCTATTCAAATAAATATCAACACTTTTAGAATTTAAAAGAAAAAC
* * * *
6415 AGTAATAGCGCTTATAAAATATCGATACTTTATAAAAATGTATCGATATATAACAATATAACA
1 AGTAATAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATAAATAACAATATAACA
6478 TGACAATATT
Statistics
Matches: 216, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
182 157 0.73
183 59 0.27
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (183 bp):
AGTAATAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATAAATAACAATATAACAGG
TAAAAATATGACAAAACCGGTTTCATTATAACAAAACCGGTAAAGCGCTACCGGATATGTTGAAA
GTATCGATTCTATTCAAATAAATATCAACACTTTTAGAATTTAAAAGAAAAAC
Found at i:7173 original size:18 final size:18
Alignment explanation
Indices: 7152--7191 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7142 TCTTTAAAAA
7152 TTTAAAATTTTCATATAT
1 TTTAAAATTTTCATATAT
* * *
7170 TTTAAATTTTTTATATTT
1 TTTAAAATTTTCATATAT
7188 TTTA
1 TTTA
7192 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTAAAATTTTCATATAT
Found at i:7186 original size:16 final size:17
Alignment explanation
Indices: 7151--7188 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
7141 TTCTTTAAAA
*
7151 ATTTAAAATTTTCATAT
1 ATTTTAAATTTTCATAT
*
7168 ATTTTAAATTTT-TTAT
1 ATTTTAAATTTTCATAT
7184 ATTTT
1 ATTTT
7189 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTAAATTTTCATAT
Found at i:9977 original size:70 final size:70
Alignment explanation
Indices: 9857--10058 Score: 316
Period size: 70 Copynumber: 2.9 Consensus size: 70
9847 AAGAGCATAG
* ** *
9857 AAGAGCAAAAATAGGAGAACAAAA-AATTTCACATGGCTAAGAAACATAGAAGAACATCCCAAAA
1 AAGAGTAAAAATAGGAGAACAAAACAATCACACATGGCTAAGAAACATAGAAGAGCATCCCAAAA
9921 GTCTA
66 GTCTA
* *
9926 AAGAGTAAAAATGGGAGAACAAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAA
1 AAGAGTAAAAATAGGAGAACAAAACAATCACACATGGCTAAGAAACATAGAAGAGCATCCCAAAA
*
9991 GTGTA
66 GTCTA
* *
9996 AAGAGTAAAAATATGAGAACAAAACAATCACACATGACTAAGAAACATAGAAGAGCATCCCAA
1 AAGAGTAAAAATAGGAGAACAAAACAATCACACATGGCTAAGAAACATAGAAGAGCATCCCAA
10059 TTGACTTCTA
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
69 22 0.18
70 100 0.82
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.13
Consensus pattern (70 bp):
AAGAGTAAAAATAGGAGAACAAAACAATCACACATGGCTAAGAAACATAGAAGAGCATCCCAAAA
GTCTA
Found at i:10825 original size:53 final size:53
Alignment explanation
Indices: 10765--10872 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
10755 TTAAAATTTT
10765 ATAAAAACTCTAATCACCATCTTTTGGAGTTGCCCTTCCGGATATGGTTATTA
1 ATAAAAACTCTAATCACCATCTTTTGGAGTTGCCCTTCCGGATATGGTTATTA
10818 ATAAAAACTCTAATCACCATCTTTTGGAGTTGCCCTTCCGGATATGGTTATTA
1 ATAAAAACTCTAATCACCATCTTTTGGAGTTGCCCTTCCGGATATGGTTATTA
10871 AT
1 AT
10873 TGCATTAATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (53 bp):
ATAAAAACTCTAATCACCATCTTTTGGAGTTGCCCTTCCGGATATGGTTATTA
Found at i:13689 original size:17 final size:17
Alignment explanation
Indices: 13667--13700 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13657 TTCAATATTC
* *
13667 TTTTAATTCTTTTTTTA
1 TTTTAAGTCTATTTTTA
13684 TTTTAAGTCTATTTTTA
1 TTTTAAGTCTATTTTTA
13701 ACCAAATGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTAAGTCTATTTTTA
Found at i:22905 original size:16 final size:17
Alignment explanation
Indices: 22880--22912 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22870 GTTTAGGGAC
*
22880 TAAAATTATA-ATTTTA
1 TAAAAATATATATTTTA
22896 TAAAAATATATATTTTA
1 TAAAAATATATATTTTA
22913 GCACGTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAAATATATATTTTA
Found at i:32760 original size:14 final size:14
Alignment explanation
Indices: 32718--32760 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
32708 GCCCTCTGTT
*
32718 CGAACATAAATAAA
1 CGAACATAAATGAA
*
32732 TGAACATAAATGAA
1 CGAACATAAATGAA
*
32746 CGAACATAAACGAA
1 CGAACATAAATGAA
32760 C
1 C
32761 ATATAATCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:39067 original size:20 final size:20
Alignment explanation
Indices: 39042--39080 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39032 CAATTATAAA
39042 ATTTTTTA-GTTCATATTTTT
1 ATTTTTTATG-TCATATTTTT
39062 ATTTTTTATGTCATATTTT
1 ATTTTTTATGTCATATTTT
39081 AGAGATAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (20 bp):
ATTTTTTATGTCATATTTTT
Found at i:57825 original size:192 final size:192
Alignment explanation
Indices: 57493--58027 Score: 944
Period size: 192 Copynumber: 2.8 Consensus size: 192
57483 TGATTTTCGG
* * * * * * * * *
57493 TTGGCTCATGCCTCTTAACTATATGGCTTCAATCTTGTACTACTATTGAAACAGATTTCAACATC
1 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
*
57558 TTTGTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
66 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
57623 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
131 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
57685 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
1 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
57750 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
66 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
57815 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
131 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
57877 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
1 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
* * *
57942 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGGCATAGAAACACCAAAACCTGTAG
66 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
*
58007 CAGAAATGTTGGGAAACTTCT
131 CAGAAATGTTGGGAAAGTTCT
58028 GGGAAAGTTA
Statistics
Matches: 329, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
192 329 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (192 bp):
TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
Found at i:63918 original size:50 final size:50
Alignment explanation
Indices: 63843--63944 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
63833 ATATAGCTTA
*
63843 TTTATGATTTATGTATGTTTTTGTCGTATTCAAACAAATTAACTCTAAAG
1 TTTATGATTTATATATGTTTTTGTCGTATTCAAACAAATTAACTCTAAAG
*
63893 TTTATGATTTATATATGTTTTTGTCGTATTGAAACAAATTAACTCTAAAG
1 TTTATGATTTATATATGTTTTTGTCGTATTCAAACAAATTAACTCTAAAG
63943 TT
1 TT
63945 GCAGGTTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (50 bp):
TTTATGATTTATATATGTTTTTGTCGTATTCAAACAAATTAACTCTAAAG
Found at i:66838 original size:19 final size:18
Alignment explanation
Indices: 66814--66865 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
66804 CCCTTGCATG
*
66814 CCCCATGCAACTGCTGCCA
1 CCCCATGC-ACTACTGCCA
*
66833 CCCCATGCGCTACTGCCA
1 CCCCATGCACTACTGCCA
*
66851 CCCCATGCGCTACTG
1 CCCCATGCACTACTG
66866 TCATGTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.17
Consensus pattern (18 bp):
CCCCATGCACTACTGCCA
Found at i:66850 original size:18 final size:18
Alignment explanation
Indices: 66827--66865 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
66817 CATGCAACTG
66827 CTGCCACCCCATGCGCTA
1 CTGCCACCCCATGCGCTA
66845 CTGCCACCCCATGCGCTA
1 CTGCCACCCCATGCGCTA
66863 CTG
1 CTG
66866 TCATGTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.49, G:0.18, T:0.18
Consensus pattern (18 bp):
CTGCCACCCCATGCGCTA
Found at i:67070 original size:2 final size:2
Alignment explanation
Indices: 67063--67087 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67053 GGTTTAAATC
67063 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
67088 GGGGTGTAGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67169 original size:16 final size:16
Alignment explanation
Indices: 67120--67169 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
67110 CACCGGGAGT
67120 GAAAGAAAGAAGGAGAGA
1 GAAAGAAAGAA-GA-AGA
67138 GAAAGAAGAGAA-AAGA
1 GAAAGAA-AGAAGAAGA
*
67154 GAAAGAAACAAGAAGA
1 GAAAGAAAGAAGAAGA
67170 AGAGAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 3 0.10
16 14 0.48
17 1 0.03
18 7 0.24
19 4 0.14
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAGAAGA
Found at i:68888 original size:14 final size:14
Alignment explanation
Indices: 68864--68914 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
68854 TATAAATAAT
68864 ATTTAATTTAATTTA
1 ATTT-ATTTAATTTA
*
68879 ATTTATTTAAATTA
1 ATTTATTTAATTTA
*
68893 AGTTATTT-ATTTA
1 ATTTATTTAATTTA
68906 TATTTATTT
1 -ATTTATTT
68915 CTTTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 23 0.74
15 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
ATTTATTTAATTTA
Found at i:68912 original size:10 final size:9
Alignment explanation
Indices: 68863--68914 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
68853 ATATAAATAA
68863 TATTTAATT
1 TATTTAATT
68872 TAATTTAATT
1 T-ATTTAATT
68882 TATTTAAATT
1 TATTT-AATT
* *
68892 AAGTT-ATT
1 TATTTAATT
68900 TATTTATATT
1 TATTTA-ATT
68910 TATTT
1 TATTT
68915 CTTTTTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 6 0.17
9 5 0.14
10 24 0.69
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:70023 original size:21 final size:23
Alignment explanation
Indices: 69975--70020 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
69965 TTGACAAACT
*
69975 TAAAAAAACATAAATTATTATAC
1 TAAAAAAACATAAATGATTATAC
69998 TAAAAAATACATAAATGATTATA
1 TAAAAAA-ACATAAATGATTATA
70021 AAATAAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAAAAAACATAAATGATTATAC
Found at i:70042 original size:34 final size:34
Alignment explanation
Indices: 70004--70069 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
69994 ATACTAAAAA
70004 ATACATAAATGATTATAAAATAAAGTTAATTATT
1 ATACATAAATGATTATAAAATAAAGTTAATTATT
* *
70038 ATACATAAATTATTATAAAATCAAGTTAATTA
1 ATACATAAATGATTATAAAATAAAGTTAATTA
70070 AGTTAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (34 bp):
ATACATAAATGATTATAAAATAAAGTTAATTATT
Found at i:70932 original size:21 final size:20
Alignment explanation
Indices: 70901--70968 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 20
70891 TATGATAATA
*
70901 AATAGTAAAAATGATATTATAC
1 AATA-TAAAAATAATATTA-AC
70923 AATATAAAAATAATATTAAC
1 AATATAAAAATAATATTAAC
70943 ATATATTTATAAAAATAATATTAAC
1 --A-A--TATAAAAATAATATTAAC
70968 A
1 A
70969 TAATAATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 2 0.05
21 13 0.32
22 5 0.12
23 2 0.05
25 18 0.45
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (20 bp):
AATATAAAAATAATATTAAC
Found at i:71569 original size:141 final size:141
Alignment explanation
Indices: 71306--71570 Score: 408
Period size: 141 Copynumber: 1.9 Consensus size: 141
71296 GGATAGAGGT
71306 ATGGGTTAAACTTTTATCATTCGAATGCCAGCTACCAACTGTACCTACGTGAATGGCATGCCATG
1 ATGGGTTAAACTTTTATCATTCGAATGCCAGCTACCAACTGTACCTACGTGAATGGCATGCCATG
* * *
71371 CGACTTTTCCAGCCATGCGAGAGGACCCCGAGGAGACGCATGCGGCCGCTTGCAACCCAGCCGCC
66 CGACTTTTCCAGCCACGCGAGAGGACCCCGAGGAGACGCATGCGACCACTTGCAACCCAGCCGCC
71436 TTAGGAGACGC
131 TTAGGAGACGC
* * *
71447 ATGGGTTTAACTTTTATCATTTGAATGCCAGCTA-CATACTGTACCTACGTGAGTGGCATGCCAT
1 ATGGGTTAAACTTTTATCATTCGAATGCCAGCTACCA-ACTGTACCTACGTGAATGGCATGCCAT
* * * *
71511 GCGA-TTTTGCCGGCCACGCGAGGGGACCCTGAGGAGACGCATGCGACCACTTGTAACCCA
65 GCGACTTTT-CCAGCCACGCGAGAGGACCCCGAGGAGACGCATGCGACCACTTGCAACCCA
71571 ACCCAGGAGA
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
140 6 0.05
141 106 0.95
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.23
Consensus pattern (141 bp):
ATGGGTTAAACTTTTATCATTCGAATGCCAGCTACCAACTGTACCTACGTGAATGGCATGCCATG
CGACTTTTCCAGCCACGCGAGAGGACCCCGAGGAGACGCATGCGACCACTTGCAACCCAGCCGCC
TTAGGAGACGC
Found at i:72404 original size:32 final size:32
Alignment explanation
Indices: 72363--72441 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
72353 GTGTCGCATG
72363 GTTCTATGCGACTTAGGTGGGTATTGCATTGT
1 GTTCTATGCGACTTAGGTGGGTATTGCATTGT
72395 GTTCTATGCGACTTAGGTGGGTATTGCATTGT
1 GTTCTATGCGACTTAGGTGGGTATTGCATTGT
*
72427 GTTCCATGCGACTTA
1 GTTCTATGCGACTTA
72442 AGGTTCACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.39
Consensus pattern (32 bp):
GTTCTATGCGACTTAGGTGGGTATTGCATTGT
Done.