Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006681.1 Hibiscus syriacus cultivar Beakdansim tig00016576_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: 66641
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3815 original size:23 final size:22
Alignment explanation
Indices: 3782--3866 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
3772 TTTAGTGCAG
*
3782 AGGGAATCGATACCCCCCTTGA
1 AGGGAACCGATACCCCCCTTGA
* *
3804 AGGGGAACCGATTCCCCCTTTGA
1 A-GGGAACCGATACCCCCCTTGA
* * *
3827 ATGGGAACCGATTCCCTCATTG-
1 A-GGGAACCGATACCCCCCTTGA
*
3849 AGGGAATCGATACCCCCC
1 AGGGAACCGATACCCCCC
3867 ACAGGTTCTG
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 13 0.25
22 2 0.04
23 37 0.71
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATACCCCCCTTGA
Found at i:3820 original size:22 final size:23
Alignment explanation
Indices: 3783--3842 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
3773 TTAGTGCAGA
* * *
3783 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
3806 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAG
3829 GGGAACCGATTCCC
1 GGGAACCGATTCCC
3843 TCATTGAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:8194 original size:125 final size:125
Alignment explanation
Indices: 7972--8221 Score: 500
Period size: 125 Copynumber: 2.0 Consensus size: 125
7962 TTCACGTAAT
7972 TGCATTGGCATATGCTTATTATATATATCAATGATATTCTCAAACGGTCGTAAATTCGAGTGACG
1 TGCATTGGCATATGCTTATTATATATATCAATGATATTCTCAAACGGTCGTAAATTCGAGTGACG
8037 AGTCAACACTTAACCTGGTTTAGGTTAATAAGAATAAGTACTGTCATTGTGAAGATGAAG
66 AGTCAACACTTAACCTGGTTTAGGTTAATAAGAATAAGTACTGTCATTGTGAAGATGAAG
8097 TGCATTGGCATATGCTTATTATATATATCAATGATATTCTCAAACGGTCGTAAATTCGAGTGACG
1 TGCATTGGCATATGCTTATTATATATATCAATGATATTCTCAAACGGTCGTAAATTCGAGTGACG
8162 AGTCAACACTTAACCTGGTTTAGGTTAATAAGAATAAGTACTGTCATTGTGAAGATGAAG
66 AGTCAACACTTAACCTGGTTTAGGTTAATAAGAATAAGTACTGTCATTGTGAAGATGAAG
8222 CTAGAGGCTG
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (125 bp):
TGCATTGGCATATGCTTATTATATATATCAATGATATTCTCAAACGGTCGTAAATTCGAGTGACG
AGTCAACACTTAACCTGGTTTAGGTTAATAAGAATAAGTACTGTCATTGTGAAGATGAAG
Found at i:8675 original size:75 final size:75
Alignment explanation
Indices: 8531--8725 Score: 257
Period size: 75 Copynumber: 2.6 Consensus size: 75
8521 CGACGTTTAA
* * * * *
8531 TATTTTTCTATACTTAATATTATGGTTTCAGTCTTAAGATTTGACACTTTAATATTATGGTTTGA
1 TATTGTTCTAAACTTAATATTATGGTTTGAGTCTTGAGATTTGACACTTTAATATTATGATTTGA
8596 TTATGGATTT
66 TTATGGATTT
* * * * *
8606 TATTGTTTTAGAA-TTAATATTGTGGTTTGAATCTTGAGATTTGACATTTTAATATTGTGATTTG
1 TATTGTTCTA-AACTTAATATTATGGTTTGAGTCTTGAGATTTGACACTTTAATATTATGATTTG
* *
8670 TTTATGTATTT
65 ATTATGGATTT
*
8681 TATTGTTCTAAACTTAATATTATGGTTTGAGTCTTGATATTTGAC
1 TATTGTTCTAAACTTAATATTATGGTTTGAGTCTTGAGATTTGAC
8726 TTTATTATAA
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
74 2 0.02
75 99 0.97
76 1 0.01
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.52
Consensus pattern (75 bp):
TATTGTTCTAAACTTAATATTATGGTTTGAGTCTTGAGATTTGACACTTTAATATTATGATTTGA
TTATGGATTT
Found at i:10358 original size:4 final size:4
Alignment explanation
Indices: 10349--10375 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10339 TGCTAAGAGA
10349 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
10376 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:15740 original size:20 final size:20
Alignment explanation
Indices: 15690--15750 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
15680 AATCGAGTTG
* * *
15690 AATATATTTGTTTAAATTTA
1 AATATAATTATTTAAATATA
15710 AATACTAATTATTTAAATATA
1 AATA-TAATTATTTAAATATA
15731 AATATAATTATTTATAATAT
1 AATATAATTATTTA-AATAT
15751 TATTTACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATAATTATTTAAATATA
Found at i:17474 original size:44 final size:44
Alignment explanation
Indices: 17420--17555 Score: 123
Period size: 44 Copynumber: 3.1 Consensus size: 44
17410 TTAGCGACGT
* * * *
17420 TTTTTTGGATACAAACGCCGC-AACAGGTATGGTATATAGAGGCG
1 TTTTTCGGATACAAACGCCGCAAAAAGTTA-GGTATATAGAGGCA
* ** * *
17464 TTTTTCGGATACAAATGCTACAAAAAGTTAGGTATATAGCGTCA
1 TTTTTCGGATACAAACGCCGCAAAAAGTTAGGTATATAGAGGCA
* * * *
17508 TTTTTCGGATACAAACGCCGTAAAATGTCTA-GTATATAGCGACA
1 TTTTTCGGATACAAACGCCGCAAAAAGT-TAGGTATATAGAGGCA
17552 TTTT
1 TTTT
17556 ATGTTACAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
44 67 0.89
45 8 0.11
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (44 bp):
TTTTTCGGATACAAACGCCGCAAAAAGTTAGGTATATAGAGGCA
Found at i:23444 original size:16 final size:16
Alignment explanation
Indices: 23423--23456 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
23413 TAATCACTCC
23423 TAAATT-ATAAAACTTT
1 TAAATTGATAAAA-TTT
23439 TAAATTGATAAAATTT
1 TAAATTGATAAAATTT
23455 TA
1 TA
23457 TGGGAGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAATTGATAAAATTT
Found at i:25551 original size:16 final size:16
Alignment explanation
Indices: 25530--25561 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25520 GAATTCAACC
25530 GGCTGCCATCTAGAAT
1 GGCTGCCATCTAGAAT
25546 GGCTGCCATCTAGAAT
1 GGCTGCCATCTAGAAT
25562 TTCAACAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (16 bp):
GGCTGCCATCTAGAAT
Found at i:31580 original size:41 final size:40
Alignment explanation
Indices: 31535--31761 Score: 138
Period size: 41 Copynumber: 5.5 Consensus size: 40
31525 ACTACTGTCT
*
31535 AACTCTATAGCGGCGTTTGTACAAAAATGCCTCTATAGTTC
1 AACTCTATAGCGGCGTTTGTA-AAAAACGCCTCTATAGTTC
** * * * *
31576 AACTCTATCA-CATCGTCTATCTATAAAACGCCACTA-ATGTCC
1 AACTCTAT-AGCGGCGT-T-TGTAAAAAACGCCTCTATA-GTTC
* * ** *
31618 AACTCTATAGCGACATTTGTTTGAAAATGCCTCTATAGTGT-
1 AACTCTATAGCGGCGTTTG-TAAAAAACGCCTCTATAGT-TC
* * * *** *
31659 AACTCTATCGCGGCGTTTACTAAAAAACGGCAGAACT-GTCC
1 AACTCTATAGCGGCGTTT-GTAAAAAACGCCTCTA-TAGTTC
*
31700 AACTCTATAGCGGCATTTGTACAAAAAGCGCCTCTATAGTTC
1 AACTCTATAGCGGCGTTTGTA-AAAAA-CGCCTCTATAGTTC
*
31742 AACTCTATCGCGGCGTTTGT
1 AACTCTATAGCGGCGTTTGT
31762 GTTTAAAAAC
Statistics
Matches: 134, Mismatches: 38, Indels: 27
0.67 0.19 0.14
Matches are distributed among these distances:
40 3 0.02
41 75 0.56
42 53 0.40
43 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (40 bp):
AACTCTATAGCGGCGTTTGTAAAAAACGCCTCTATAGTTC
Found at i:31610 original size:83 final size:82
Alignment explanation
Indices: 31461--31750 Score: 282
Period size: 83 Copynumber: 3.5 Consensus size: 82
31451 ATATAAGTTT
* * * * * **
31461 GCGGCGTTTGTA-AAATAATGCCTCTATAGTGCTAA-TATATCGC-GACGTTTACTTAAAAAATA
1 GCGGCATTTGTACAAA-AATGCCTCTATAGTTC-AACTCTATCACAG-CGTCTAC-TAAAAAACG
*
31523 CCACTACTGTCTAACTCTATA
62 CCACTACTGTCCAACTCTATA
* * *
31544 GCGGCGTTTGTACAAAAATGCCTCTATAGTTCAACTCTATCACATCGTCTATCTATAAAACGCCA
1 GCGGCATTTGTACAAAAATGCCTCTATAGTTCAACTCTATCACAGCGTCTA-CTAAAAAACGCCA
*
31609 CTAATGTCCAACTCTATA
65 CTACTGTCCAACTCTATA
* *** * * * *
31627 GCGACATTTGTTTGAAAATGCCTCTATAGTGT-AACTCTATCGCGGCGTTTACTAAAAAACGGCA
1 GCGGCATTTGTACAAAAATGCCTCTATAGT-TCAACTCTATCACAGCGTCTACTAAAAAACGCCA
**
31691 GAACTGTCCAACTCTATA
65 CTACTGTCCAACTCTATA
*
31709 GCGGCATTTGTACAAAAAGCGCCTCTATAGTTCAACTCTATC
1 GCGGCATTTGTACAAAAA-TGCCTCTATAGTTCAACTCTATC
31751 GCGGCGTTTG
Statistics
Matches: 171, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
82 43 0.25
83 123 0.72
84 5 0.03
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (82 bp):
GCGGCATTTGTACAAAAATGCCTCTATAGTTCAACTCTATCACAGCGTCTACTAAAAAACGCCAC
TACTGTCCAACTCTATA
Found at i:33074 original size:64 final size:64
Alignment explanation
Indices: 33001--33163 Score: 152
Period size: 64 Copynumber: 2.5 Consensus size: 64
32991 ATTGTTTGAA
* *** *
33001 GGTGTATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCATC-CCAGTAAT-AAACAAACATCGAATGCAAT
33064 T
64 T
* * * *
33065 GGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAAACAAACATCGAATGTATTT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATGCAATT
** * * *
33129 TTTGCACCGATGCACAAGTAGTGCATCGATTCATC
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCATC
33164 GTTAGGGAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 8
0.77 0.16 0.08
Matches are distributed among these distances:
63 5 0.06
64 69 0.87
65 5 0.06
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (64 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATGCAATT
Found at i:34130 original size:103 final size:103
Alignment explanation
Indices: 33946--34157 Score: 379
Period size: 103 Copynumber: 2.1 Consensus size: 103
33936 GTCGAGGGTC
*
33946 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
34011 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
34049 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
34114 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
34152 TATGTG
1 TATGTG
34158 TCATTATGGA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:39968 original size:103 final size:103
Alignment explanation
Indices: 39743--39956 Score: 374
Period size: 103 Copynumber: 2.1 Consensus size: 103
39733 GTCGAGGGTC
*
39743 TATGTGGTACTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTACTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
39808 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
*
39846 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTACTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
39911 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
39949 TATGTGGT
1 TATGTGGT
39957 CCTTATGGAC
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTACTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
Found at i:45689 original size:27 final size:27
Alignment explanation
Indices: 45659--45751 Score: 82
Period size: 27 Copynumber: 3.3 Consensus size: 27
45649 TTGAATAAAG
45659 CTATGTGAAATATTATGCATATATGTT
1 CTATGTGAAATATTATGCATATATGTT
* ** *
45686 CTATGTGAATAAACATTAATTTAAATAATG--
1 CTATGTG---AAATATT-ATGCATAT-ATGTT
*
45716 CTATGTGAAATATTATGCATATATATT
1 CTATGTGAAATATTATGCATATATGTT
45743 CTATGTGAA
1 CTATGTGAA
45752 TAAACGTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
25 2 0.04
26 5 0.10
27 22 0.44
30 13 0.26
31 5 0.10
32 3 0.06
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.41
Consensus pattern (27 bp):
CTATGTGAAATATTATGCATATATGTT
Found at i:45689 original size:57 final size:57
Alignment explanation
Indices: 45621--45838 Score: 337
Period size: 57 Copynumber: 3.8 Consensus size: 57
45611 TTGCTATGTG
* *
45621 TATATGTTCTATGTGAATAAATGTTAATTTGAATAAAGCTATGTGAAATATTATGCA
1 TATATGTTCTATGTGAATAAACGTTAATTTGAATAATGCTATGTGAAATATTATGCA
* *
45678 TATATGTTCTATGTGAATAAACATTAATTTAAATAATGCTATGTGAAATATTATGCA
1 TATATGTTCTATGTGAATAAACGTTAATTTGAATAATGCTATGTGAAATATTATGCA
* ***
45735 TATATATTCTATGTGAATAAACGTTAATTTGAATAATGCTATGTGAAATATTATATG
1 TATATGTTCTATGTGAATAAACGTTAATTTGAATAATGCTATGTGAAATATTATGCA
* **
45792 TATATGTTCTATGTGAATAAATGACAATTTGAATAATGCTATGTGAA
1 TATATGTTCTATGTGAATAAACGTTAATTTGAATAATGCTATGTGAA
45839 TACTTATATG
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 147 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (57 bp):
TATATGTTCTATGTGAATAAACGTTAATTTGAATAATGCTATGTGAAATATTATGCA
Found at i:45722 original size:30 final size:30
Alignment explanation
Indices: 45686--45781 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
45676 CATATATGTT
45686 CTATGTGAATAAACATTAATTTAAATAATG
1 CTATGTGAATAAACATTAATTTAAATAATG
* ** * *
45716 CTATGTG---AAATATT-ATGCATATATATT
1 CTATGTGAATAAACATTAATTTAAATA-ATG
* *
45743 CTATGTGAATAAACGTTAATTTGAATAATG
1 CTATGTGAATAAACATTAATTTAAATAATG
45773 CTATGTGAA
1 CTATGTGAA
45782 ATATTATATG
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
26 6 0.12
27 15 0.31
30 23 0.47
31 5 0.10
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (30 bp):
CTATGTGAATAAACATTAATTTAAATAATG
Found at i:45958 original size:23 final size:23
Alignment explanation
Indices: 45918--45961 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
45908 CTACGCGGTC
* * *
45918 CTTCGGGATAATTCTATGTGGTT
1 CTTCGGGACAAATATATGTGGTT
45941 CTTCGGGACAAATATATGTGG
1 CTTCGGGACAAATATATGTGG
45962 CACTTTGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (23 bp):
CTTCGGGACAAATATATGTGGTT
Found at i:45985 original size:24 final size:24
Alignment explanation
Indices: 45958--46006 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
45948 ACAAATATAT
* *
45958 GTGGCACTTTGATGCATATTCTAC
1 GTGGCACTTCGATGCAAATTCTAC
* *
45982 GTGGTACTTCGGTGCAAATTCTAC
1 GTGGCACTTCGATGCAAATTCTAC
46006 G
1 G
46007 CGACAGTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (24 bp):
GTGGCACTTCGATGCAAATTCTAC
Found at i:51895 original size:11 final size:11
Alignment explanation
Indices: 51881--51905 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
51871 AATAATGATT
51881 TGGGTTTTAAA
1 TGGGTTTTAAA
51892 TGGGTTTTAAA
1 TGGGTTTTAAA
51903 TGG
1 TGG
51906 ATTGGACCGG
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:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGGTTTTAAA
Found at i:53775 original size:30 final size:29
Alignment explanation
Indices: 53739--53834 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 29
53729 CATATATGTT
53739 CTATGTGAATAAAGGTTAATTTGAATAATC
1 CTATGTGAATAAA-GTTAATTTGAATAATC
* * * * *
53769 CTATGTGAA-ATA-TT-ATGTGTATATGTT
1 CTATGTGAATAAAGTTAATTTGAATA-ATC
*
53796 CTATGTGAATAAACGTTAATTTGAATAATG
1 CTATGTGAATAAA-GTTAATTTGAATAATC
53826 CTATGTGAA
1 CTATGTGAA
53835 ATATTATGCT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
26 7 0.14
27 12 0.24
28 2 0.04
29 2 0.04
30 21 0.41
31 7 0.14
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (29 bp):
CTATGTGAATAAAGTTAATTTGAATAATC
Found at i:53800 original size:57 final size:57
Alignment explanation
Indices: 53731--53948 Score: 348
Period size: 57 Copynumber: 3.8 Consensus size: 57
53721 TTACTATGCA
* *
53731 TATATGTTCTATGTGAATAAAGGTTAATTTGAATAATCCTATGTGAAATATTATGTG
1 TATATGTTCTATGTGAATAAAAGTTAATTTGAATAATGCTATGTGAAATATTATGTG
*
53788 TATATGTTCTATGTGAATAAACGTTAATTTGAATAATGCTATGTGAAATATTATGCT-
1 TATATGTTCTATGTGAATAAAAGTTAATTTGAATAATGCTATGTGAAATATTATG-TG
* *
53845 TATATGTTCTATGTGAATAAAAGTTCATTTGAATAATGATATGTGAAATATTATGTG
1 TATATGTTCTATGTGAATAAAAGTTAATTTGAATAATGCTATGTGAAATATTATGTG
* **
53902 TATATGTTCTATGTGAATAAATGACAATTTGAATAATGCTATGTGAA
1 TATATGTTCTATGTGAATAAAAGTTAATTTGAATAATGCTATGTGAA
53949 CACTTGTATA
Statistics
Matches: 149, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
56 1 0.01
57 147 0.99
58 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (57 bp):
TATATGTTCTATGTGAATAAAAGTTAATTTGAATAATGCTATGTGAAATATTATGTG
Found at i:53804 original size:27 final size:27
Alignment explanation
Indices: 53769--53918 Score: 103
Period size: 27 Copynumber: 5.3 Consensus size: 27
53759 TTGAATAATC
53769 CTATGTGAAATATTATGTGTATATGTT
1 CTATGTGAAATATTATGTGTATATGTT
* * *
53796 CTATGTGAATAAACGTTAATTTGAATAATG--
1 CTATGTGAA-ATA--TT-ATGTGTAT-ATGTT
53826 CTATGTGAAATATTATGCT-TATATGTT
1 CTATGTGAAATATTATG-TGTATATGTT
* * *
53853 CTATGTGAATAAAAGTTCATTTGAATAATG--
1 CTATGTG-A-AATA-TT-ATGTGTAT-ATGTT
*
53883 ATATGTGAAATATTATGTGTATATGTT
1 CTATGTGAAATATTATGTGTATATGTT
53910 CTATGTGAA
1 CTATGTGAA
53919 TAAATGACAA
Statistics
Matches: 93, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
25 6 0.06
26 10 0.11
27 29 0.31
28 6 0.06
29 6 0.06
30 20 0.22
31 10 0.11
32 6 0.06
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (27 bp):
CTATGTGAAATATTATGTGTATATGTT
Found at i:54078 original size:23 final size:22
Alignment explanation
Indices: 54022--54094 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
54012 GAGTCGAGGG
54022 TTCTACGCGGTCCTTCGGACAA
1 TTCTACGCGGTCCTTCGGACAA
* * *
54044 TTCTATGTGGTCCTTTGGGACAA
1 TTCTACGCGGTCC-TTCGGACAA
*
54067 TTCTACGCGGTCTTTCTGGACAA
1 TTCTACGCGGTCCTTC-GGACAA
*
54090 ATCTA
1 TTCTA
54095 TACGGAACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 13 0.32
23 28 0.68
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (22 bp):
TTCTACGCGGTCCTTCGGACAA
Found at i:59226 original size:507 final size:507
Alignment explanation
Indices: 58273--59279 Score: 2014
Period size: 507 Copynumber: 2.0 Consensus size: 507
58263 GCTATGAGGA
58273 AGCTAGCCTACTGCTCCTCGAATTAAAAGTCATTAGGCTCTTCGGCCTTTAAGTCTTCAAATAGC
1 AGCTAGCCTACTGCTCCTCGAATTAAAAGTCATTAGGCTCTTCGGCCTTTAAGTCTTCAAATAGC
58338 CTCTTATAAGTTTCTAATTGAATGAAATTGCCATGGTAAAATTGATATGCTTCTCCTTCTATAAA
66 CTCTTATAAGTTTCTAATTGAATGAAATTGCCATGGTAAAATTGATATGCTTCTCCTTCTATAAA
58403 TGAATCCACTTCTAAAATGCTCTAGCATTCTTCAGAATCATCTATGTATTTGAGAGAATGGAAGA
131 TGAATCCACTTCTAAAATGCTCTAGCATTCTTCAGAATCATCTATGTATTTGAGAGAATGGAAGA
58468 CATTCACTATGACACATTGGTCGGCCACCCTCATGGTCAGGTCACCCTTCTCGCAGTTGATAAGA
196 CATTCACTATGACACATTGGTCGGCCACCCTCATGGTCAGGTCACCCTTCTCGCAGTTGATAAGA
58533 ATGCGACCGGTAGCTAGGAATGGTCTCCCCAAAATTATGGGTATTGTGGTATCAACCTCACAGTC
261 ATGCGACCGGTAGCTAGGAATGGTCTCCCCAAAATTATGGGTATTGTGGTATCAACCTCACAGTC
58598 CAGAATAAGAAAATATACTGGAAATATGAACTTGTCAACCCATACAATGACATCCTCGATTCGCC
326 CAGAATAAGAAAATATACTGGAAATATGAACTTGTCAACCCATACAATGACATCCTCGATTCGCC
58663 CTTCAGGACGAATATGTGAACGATCAGCTAATTGCAAGATAACAGATGTGGGTCTCGTATTTCCT
391 CTTCAGGACGAATATGTGAACGATCAGCTAATTGCAAGATAACAGATGTGGGTCTCGTATTTCCT
58728 ATTCCAAGCTTCACGAAAATAGACTTAGGCATTAAGTTCATGCTTCACGATC
456 ATTCCAAGCTTCACGAAAATAGACTTAGGCATTAAGTTCATGCTTCACGATC
58780 AGCTAGCCTACTGCTCCTCGAATTAAAAGTCATTAGGCTCTTCGGCCTTTAAGTCTTCAAATAGC
1 AGCTAGCCTACTGCTCCTCGAATTAAAAGTCATTAGGCTCTTCGGCCTTTAAGTCTTCAAATAGC
58845 CTCTTATAAGTTTCTAATTGAATGAAATTGCCATGGTAAAATTGATATGCTTCTCCTTCTATAAA
66 CTCTTATAAGTTTCTAATTGAATGAAATTGCCATGGTAAAATTGATATGCTTCTCCTTCTATAAA
58910 TGAATCCACTTCTAAAATGCTCTAGCATTCTTCAGAATCATCTATGTATTTGAGAGAATGGAAGA
131 TGAATCCACTTCTAAAATGCTCTAGCATTCTTCAGAATCATCTATGTATTTGAGAGAATGGAAGA
58975 CATTCACTATGACACATTGGTCGGCCACCCTCATGGTCAGGTCACCCTTCTCGCAGTTGATAAGA
196 CATTCACTATGACACATTGGTCGGCCACCCTCATGGTCAGGTCACCCTTCTCGCAGTTGATAAGA
59040 ATGCGACCGGTAGCTAGGAATGGTCTCCCCAAAATTATGGGTATTGTGGTATCAACCTCACAGTC
261 ATGCGACCGGTAGCTAGGAATGGTCTCCCCAAAATTATGGGTATTGTGGTATCAACCTCACAGTC
59105 CAGAATAAGAAAATATACTGGAAATATGAACTTGTCAACCCATACAATGACATCCTCGATTCGCC
326 CAGAATAAGAAAATATACTGGAAATATGAACTTGTCAACCCATACAATGACATCCTCGATTCGCC
59170 CTTCAGGACGAATATGTGAACGATCAGCTAATTGCAAGATAACAGATGTGGGTCTCGTATTTCCT
391 CTTCAGGACGAATATGTGAACGATCAGCTAATTGCAAGATAACAGATGTGGGTCTCGTATTTCCT
59235 ATTCCAAGCTTCACGAAAATAGACTTAGGCATTAAGTTCATGCTT
456 ATTCCAAGCTTCACGAAAATAGACTTAGGCATTAAGTTCATGCTT
59280 GATCCAAGGT
Statistics
Matches: 500, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
507 500 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (507 bp):
AGCTAGCCTACTGCTCCTCGAATTAAAAGTCATTAGGCTCTTCGGCCTTTAAGTCTTCAAATAGC
CTCTTATAAGTTTCTAATTGAATGAAATTGCCATGGTAAAATTGATATGCTTCTCCTTCTATAAA
TGAATCCACTTCTAAAATGCTCTAGCATTCTTCAGAATCATCTATGTATTTGAGAGAATGGAAGA
CATTCACTATGACACATTGGTCGGCCACCCTCATGGTCAGGTCACCCTTCTCGCAGTTGATAAGA
ATGCGACCGGTAGCTAGGAATGGTCTCCCCAAAATTATGGGTATTGTGGTATCAACCTCACAGTC
CAGAATAAGAAAATATACTGGAAATATGAACTTGTCAACCCATACAATGACATCCTCGATTCGCC
CTTCAGGACGAATATGTGAACGATCAGCTAATTGCAAGATAACAGATGTGGGTCTCGTATTTCCT
ATTCCAAGCTTCACGAAAATAGACTTAGGCATTAAGTTCATGCTTCACGATC
Found at i:62846 original size:30 final size:29
Alignment explanation
Indices: 62812--62910 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 29
62802 AAGATCAGGC
* * *
62812 TGCAGCAAGTCATGGTCCAAAAGAATCAGT
1 TGCAGC-AGTCACGATCCAGAAGAATCAGT
*
62842 TGCAGCAGTTCACGATCCAGCAGAATCAGT
1 TGCAGCAG-TCACGATCCAGAAGAATCAGT
*
62872 TGCAGCAGGTCACGATCCAGTAGAATCAGT
1 TGCAGCA-GTCACGATCCAGAAGAATCAGT
62902 TGCAGCAGT
1 TGCAGCAGT
62911 GCATGGTTCC
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (29 bp):
TGCAGCAGTCACGATCCAGAAGAATCAGT
Found at i:63212 original size:20 final size:20
Alignment explanation
Indices: 63183--63221 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
63173 ATTCCACCAC
*
63183 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
63203 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
63222 CATGGGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:65077 original size:21 final size:21
Alignment explanation
Indices: 65053--65101 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
65043 AGATCTTGTA
65053 TAATGATAAATATATT-TATTT
1 TAAT-ATAAATATATTATATTT
**
65074 TAATATATTTATATTATATTT
1 TAATATAAATATATTATATTT
65095 TAATATA
1 TAATATA
65102 TTTTTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TAATATAAATATATTATATTT
Found at i:65101 original size:10 final size:10
Alignment explanation
Indices: 65069--65105 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
65059 TAAATATATT
65069 TATTTTAATA
1 TATTTTAATA
*
65079 TATTTATATTA
1 TATTT-TAATA
65090 TATTTTAATA
1 TATTTTAATA
65100 TATTTT
1 TATTTT
65106 TATAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTTTAATA
Found at i:65102 original size:21 final size:20
Alignment explanation
Indices: 65063--65104 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
65053 TAATGATAAA
65063 TATATTTATTTTAATATATT
1 TATATTTATTTTAATATATT
65083 TATATTATATTTTAATATATT
1 TATATT-TATTTTAATATATT
65104 T
1 T
65105 TTATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATTTATTTTAATATATT
Found at i:65107 original size:23 final size:23
Alignment explanation
Indices: 65063--65126 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
65053 TAATGATAAA
65063 TATATT-TATTTTAATATA--TT
1 TATATTATATTTTAATATATTTT
65083 TATATTATATTTTAATATATTTT
1 TATATTATATTTTAATATATTTT
* *
65106 TATAATA-ATATTTAAAATATT
1 TATATTATAT-TTTAATATATT
65127 ACAATTTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 6 0.16
21 12 0.32
22 2 0.05
23 18 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTATATTTTAATATATTTT
Found at i:66001 original size:129 final size:125
Alignment explanation
Indices: 65765--66002 Score: 377
Period size: 129 Copynumber: 1.9 Consensus size: 125
65755 CAAATATATC
65765 ATATTTTTAAGAGAAATGCACTATACTTCTCAAGTATGATCTCATTTAAATTGGTCCTCAAAGTT
1 ATATTTTTAAGAGAAATGCACTATACTTCTCAAGTATGATCTCATTTAAATTGGTCCTCAAAGTT
* * **
65830 TTGAATATTTTAATTTTATCCCTAAACTATGACTCTTTTTCTAATTAGTCCCTAAAGTTA
66 TTGAATATTTTAATCTTATCCCTAAACTATGAATCTCATTCTAATTAGTCCCTAAAGTTA
* *
65890 ATATTTTTAAGAGAACTGCACTATACATTCTTTAAGTATGATCCTCATTTTAAATTGGTCCTCAA
1 ATATTTTTAAGAGAAATGCACTATAC-TTC-TCAAGTATGAT-CTCA-TTTAAATTGGTCCTCAA
*
65955 AGTTTTGAATATTTTAATCTTATCCCTAAATTATGAATCTCATTCTAA
62 AGTTTTGAATATTTTAATCTTATCCCTAAACTATGAATCTCATTCTAA
66003 AAAAGTCGAC
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
125 25 0.25
126 3 0.03
127 10 0.10
128 4 0.04
129 60 0.59
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.42
Consensus pattern (125 bp):
ATATTTTTAAGAGAAATGCACTATACTTCTCAAGTATGATCTCATTTAAATTGGTCCTCAAAGTT
TTGAATATTTTAATCTTATCCCTAAACTATGAATCTCATTCTAATTAGTCCCTAAAGTTA
Done.