Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004572.1 Hibiscus syriacus cultivar Beakdansim tig00010175_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: 81599
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3584 original size:13 final size:13
Alignment explanation
Indices: 3557--3611 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
3547 TTACTTTTAA
3557 ATTTATTTA-AAT
1 ATTTATTTATAAT
3569 ATTTATTTATAAT
1 ATTTATTTATAAT
* * *
3582 ATTAATTTGTTAT
1 ATTTATTTATAAT
*
3595 -TTTATATTATATT
1 ATTTAT-TTATAAT
3608 ATTT
1 ATTT
3612 CATATTAATC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
12 13 0.39
13 17 0.52
14 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (13 bp):
ATTTATTTATAAT
Found at i:3639 original size:2 final size:2
Alignment explanation
Indices: 3632--3665 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3622 ACATAAATAA
3632 AT AT AT AT A- AT AT AT AT AT AT -T 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
3666 TTTTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3648 original size:11 final size:11
Alignment explanation
Indices: 3628--3662 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
3618 AATCACATAA
3628 ATAA-ATATAT
1 ATAATATATAT
3638 ATAATATATAT
1 ATAATATATAT
*
3649 ATATTATATAT
1 ATAATATATAT
3660 ATA
1 ATA
3663 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAATATATAT
Found at i:3648 original size:13 final size:13
Alignment explanation
Indices: 3627--3665 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3617 TAATCACATA
*
3627 AATAAATATATAT
1 AATATATATATAT
3640 AATATATATATAT
1 AATATATATATAT
*
3653 TATATATATATAT
1 AATATATATATAT
3666 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATATATATAT
Found at i:3663 original size:11 final size:11
Alignment explanation
Indices: 3632--3663 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3622 ACATAAATAA
*
3632 ATATATATAAT
1 ATATATATATT
3643 ATATATATATT
1 ATATATATATT
3654 ATATATATAT
1 ATATATATAT
3664 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATATATATT
Found at i:3666 original size:13 final size:13
Alignment explanation
Indices: 3632--3666 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
3622 ACATAAATAA
*
3632 ATATATATAATAT
1 ATATATATTATAT
3645 ATATATATTATAT
1 ATATATATTATAT
3658 ATATATATT
1 ATATATATT
3667 TTTAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:3858 original size:22 final size:24
Alignment explanation
Indices: 3833--3894 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
3823 CTTTCTGATA
*
3833 TATTTTTAA-ATAAA-TAATATTT
1 TATTTTAAATATAAATTAATATTT
3855 TATTTATAAATATAAATTAATATTT
1 TATTT-TAAATATAAATTAATATTT
3880 T-TTTTATAATTATAA
1 TATTTTA-AA-TATAA
3895 TTTCGAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
22 5 0.15
23 5 0.15
24 10 0.29
25 14 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTTAAATATAAATTAATATTT
Found at i:3885 original size:25 final size:24
Alignment explanation
Indices: 3842--3894 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
3832 ATATTTTTAA
3842 ATAAATAATATTTTATTTATAAAT
1 ATAAATAATATTTTATTTATAAAT
* *
3866 ATAAATTAATATTTTTTTTATAATT
1 ATAAA-TAATATTTTATTTATAAAT
3891 ATAA
1 ATAA
3895 TTTCGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATAAATAATATTTTATTTATAAAT
Found at i:14526 original size:113 final size:112
Alignment explanation
Indices: 14223--14859 Score: 979
Period size: 113 Copynumber: 5.7 Consensus size: 112
14213 TGTCAGTTAG
*
14223 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** * * * * * ** *
14288 ACTTTTTACTTGAATTCATCATTCGATGGATCAACAGTGT-CAGTTAG
66 ACTTTTTGCTCAAATCCATCATTTGATGGATCAGC-TTTTCCAGAAAA
*
14335 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
14400 ACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
66 ACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
* *
14447 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
14512 AACTTTTTCCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
65 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
* *
14560 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
14625 AACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
65 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
* * *
14673 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAGAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * *
14738 AACCTTTTGCTTGAATTCATCACTCGATGGATCAGCTTTTCCAGAAAA
65 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
14786 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
14851 ACTTTTTGC
66 ACTTTTTGC
14860 ATGACTCTAT
Statistics
Matches: 494, Mismatches: 29, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
111 2 0.00
112 168 0.34
113 324 0.66
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
Found at i:16324 original size:16 final size:16
Alignment explanation
Indices: 16303--16335 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16293 TTACTTTTAA
16303 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
16319 ATTTATTTATAATATT
1 ATTTATTTATAATATT
16335 A
1 A
16336 ATTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:16363 original size:17 final size:17
Alignment explanation
Indices: 16341--16374 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16331 TATTAATTTG
16341 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
16358 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
16375 ATCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:16389 original size:4 final size:4
Alignment explanation
Indices: 16380--16415 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
16370 TATTAATCAC
*
16380 ATAA ATAA ATAT ATAA ATAA ATAAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATA
16416 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:16397 original size:8 final size:8
Alignment explanation
Indices: 16384--16434 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
16374 AATCACATAA
16384 ATAAATAT
1 ATAAATAT
*
16392 ATAAATAA
1 ATAAATAT
*
16400 ATAAAATAA
1 AT-AAATAT
16409 ATAAATAT
1 ATAAATAT
*
16417 ATATATAT
1 ATAAATAT
*
16425 ATATATAT
1 ATAAATAT
16433 AT
1 AT
16435 TTTAAATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
8 31 0.79
9 8 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAAATAT
Found at i:16645 original size:27 final size:27
Alignment explanation
Indices: 16615--16669 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
16605 ATATTTTTAA
16615 ATAAATAAAT-ATTTTATTTATAAATAT
1 ATAAATAAATAATTTT-TTTATAAATAT
* *
16642 ATAAATTAATAATTTTTTTATAATTAT
1 ATAAATAAATAATTTTTTTATAAATAT
16669 A
1 A
16670 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAAATAAATAATTTTTTTATAAATAT
Found at i:24782 original size:33 final size:31
Alignment explanation
Indices: 24741--24881 Score: 130
Period size: 33 Copynumber: 4.5 Consensus size: 31
24731 TTAATCCATA
**
24741 ATTTATTATTAGTATTTTTTATTATATATTAGT
1 ATTTATTATTA-TATTTAATA-TATATATTAGT
* *
24774 ATTTATTA-TATATATAGTATATATATTATTAGA
1 ATTTATTATTATATTTA--ATATATA-TATTAGT
*
24807 ATTTATTA-TATATTAAATATAT-TATTAGT
1 ATTTATTATTATATTTAATATATATATTAGT
*
24836 ATTTA-TATCATATTT-ATATATATATTAGT
1 ATTTATTATTATATTTAATATATATATTAGT
24865 ATTGTATTATATATATT
1 ATT-TATTAT-TATATT
24882 AGTAGTTCAT
Statistics
Matches: 90, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
28 8 0.09
29 26 0.29
30 2 0.02
31 13 0.14
32 11 0.12
33 30 0.33
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.57
Consensus pattern (31 bp):
ATTTATTATTATATTTAATATATATATTAGT
Found at i:24793 original size:18 final size:17
Alignment explanation
Indices: 24758--24939 Score: 138
Period size: 18 Copynumber: 10.1 Consensus size: 17
24748 ATTAGTATTT
24758 TTTATTATATATTAGTA
1 TTTATTATATATTAGTA
24775 TTTATTATATATATAGTA
1 TTTATTATATAT-TAGTA
* *
24793 TATA-TAT-TATTAGAA
1 TTTATTATATATTAGTA
*
24808 TTTATTATATATTAAATA
1 TTTATTATATATT-AGTA
24826 TATTATTAGTATTTATATCA-TA
1 T-TTATTA-TA--TAT-T-AGTA
24848 TTTATATATATATTAGTA
1 TTTAT-TATATATTAGTA
24866 TTGTATTATATATATTAGTA
1 TT-TA-T-TATATATTAGTA
* *
24886 GTTCATTACATATTAGTA
1 -TTTATTATATATTAGTA
*
24904 TTTCATTACATATTA-TA
1 TTT-ATTATATATTAGTA
* *
24921 TTTATTATCTATTATTA
1 TTTATTATATATTAGTA
24938 TT
1 TT
24940 ACTTATTTAC
Statistics
Matches: 138, Mismatches: 11, Indels: 32
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.05
16 15 0.11
17 31 0.22
18 38 0.28
19 12 0.09
20 17 0.12
21 8 0.06
22 8 0.06
23 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTATTATATATTAGTA
Found at i:24826 original size:29 final size:29
Alignment explanation
Indices: 24763--24878 Score: 130
Period size: 29 Copynumber: 3.9 Consensus size: 29
24753 TATTTTTTAT
24763 TATA-TATTAGTATTTATTATATATATAGTATA
1 TATATTATTAGTATTTATTATATAT-TA--A-A
*
24795 TATATTATTAGAATTTATTATATATTAAA
1 TATATTATTAGTATTTATTATATATTAAA
*
24824 TATATTATTAGTATTTA-TATCATATT-TA
1 TATATTATTAGTATTTATTAT-ATATTAAA
24852 TATATATATTAGTATTGTATTATATAT
1 TATAT-TATTAGTATT-TATTATATAT
24879 ATTAGTAGTT
Statistics
Matches: 76, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
28 9 0.12
29 32 0.42
30 7 0.09
31 3 0.04
32 6 0.08
33 19 0.25
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (29 bp):
TATATTATTAGTATTTATTATATATTAAA
Found at i:24851 original size:11 final size:10
Alignment explanation
Indices: 24773--24881 Score: 57
Period size: 11 Copynumber: 10.4 Consensus size: 10
24763 TATATATTAG
24773 TATTTATTATA
1 TATTTA-TATA
*
24784 TATATAGTATA
1 TATTTA-TATA
24795 TATATTAT-TA
1 TAT-TTATATA
*
24805 GAATTTAT-TA
1 -TATTTATATA
*
24815 TATATTAAATA
1 TAT-TTATATA
24826 TA-TTAT-TA
1 TATTTATATA
24834 GTATTTATATCA
1 -TATTTATAT-A
24846 TATTTATATA
1 TATTTATATA
24856 TATATTAGTAT-
1 TAT-TTA-TATA
*
24867 TGTATTATATA
1 TAT-TTATATA
24878 TATT
1 TATT
24882 AGTAGTTCAT
Statistics
Matches: 78, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
8 2 0.03
9 7 0.09
10 23 0.29
11 40 0.51
12 6 0.08
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (10 bp):
TATTTATATA
Found at i:29992 original size:37 final size:37
Alignment explanation
Indices: 29939--30043 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
29929 CATTTTCGTC
29939 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
29976 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
30013 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
30044 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:30440 original size:18 final size:17
Alignment explanation
Indices: 30401--30443 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
30391 ATTATATGGA
30401 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
30417 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
30435 TATTATTAT
1 TATTATTAT
30444 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:35187 original size:183 final size:183
Alignment explanation
Indices: 34879--35232 Score: 620
Period size: 183 Copynumber: 1.9 Consensus size: 183
34869 ATTAAATCCG
34879 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATAA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATAA
** *
34944 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGTTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
35009 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTCAGTGATTTGTCCCTC
* *
35062 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGTCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATAA
*
35127 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTACATTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
35191 TTTGTCAGGTCAAAGACTTTGTGATAAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTCAGT
35233 TAAACCTGAT
Statistics
Matches: 162, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.01
183 161 0.99
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATAA
ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:36428 original size:36 final size:35
Alignment explanation
Indices: 36388--36501 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 35
36378 CACTCAAATT
36388 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACATA-TTTGTCTCACTTGAGAC
* * * * ** *
36424 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACATATTTGTCTCACTTGAGAC
*
36460 TGTTTTTCTTAAAACAATATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-ATATTTGTCTCACTTGAGAC
*
36496 CGTTTT
1 TGTTTT
36502 CACTCGAAAG
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 48 0.83
37 5 0.09
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (35 bp):
TGTTTTTCTTAAAACATATTTGTCTCACTTGAGAC
Found at i:36465 original size:72 final size:75
Alignment explanation
Indices: 36372--36546 Score: 227
Period size: 72 Copynumber: 2.4 Consensus size: 75
36362 ATGCAGATGA
* * *
36372 TTATCTCACTCAA-ATTTGTTTTTCTTAAAAC-ATACTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAATA-TTTGTCTCACTTGAGACCGTTTTCACTC
36434 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
36444 TTATTTCACTCAAGATTGTTTTTCTTAAAACAATATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAATATTTGTCTCACTTGAGACCGTTTTCACTCGA
36509 AAGAAGGCAT
66 AAGAAGGCAT
**
36519 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
36547 GAAGATTTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
72 49 0.54
73 14 0.15
74 1 0.01
75 8 0.09
76 19 0.21
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAATATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:36697 original size:39 final size:39
Alignment explanation
Indices: 36640--36718 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
36630 CCTTGAAATT
* *
36640 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACATAA
1 AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACATAA
* *
36679 AATTTTGTCTC-CCTTGAGACAGTTTCTCTTGAAACATAA
1 AATTTTGTCTCTCC-TGAGACAGTTTCCCTCGAAACATAA
36718 A
1 A
36719 CATTGAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACATAA
Found at i:36726 original size:104 final size:103
Alignment explanation
Indices: 36617--36934 Score: 496
Period size: 104 Copynumber: 3.1 Consensus size: 103
36607 ACAGTTTCTC
* *
36617 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACATAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACA-AAAAT
36682 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
36721 TTGAAAATATTTCCCTTGAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAAAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAAC-AAAAAT
36786 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * * *
36825 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGACAGTTTCCCTTGAAAC--GAATT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAAAAATT
** *
36888 TTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
36926 TTGAAAACA
1 TTGAAAACA
36935 ATTTAACGAA
Statistics
Matches: 199, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
101 48 0.24
104 150 0.75
105 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (103 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAAAAATT
TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:36881 original size:36 final size:36
Alignment explanation
Indices: 36834--36909 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
36824 ATTGAAAACA
* *
36834 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
36870 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
36906 TTTC
1 TTTC
36910 TCTCCAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:37306 original size:105 final size:105
Alignment explanation
Indices: 37078--37634 Score: 723
Period size: 105 Copynumber: 5.3 Consensus size: 105
37068 AACATCCGCT
* * * * * * *
37078 ATTTCAACTCCACGACGGAGGATATTGTGACACTCGAGACAACACAAGTTCAACTTCACAACAAA
1 ATTTCAACTTCACAACGAAGGATATTG-G--ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
37143 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
37187 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
37252 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
37292 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCATGACGAAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
37357 ACCACTGCTTGTCAACAACAACTTCCCAATCTCAGAGCTA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
37397 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
37462 ACTGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGAGTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * ** *
37497 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACATAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * ** *
37562 ACGGCTGATTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
37603 ATTTCAACTTCACGATA-G-AGGATATTGGACTC
1 ATTTCAACTTCAC-A-ACGAAGGATATTGGACTC
37635 GGAACAATGT
Statistics
Matches: 401, Mismatches: 39, Indels: 19
0.87 0.08 0.04
Matches are distributed among these distances:
100 80 0.20
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 199 0.50
106 82 0.20
107 2 0.00
108 1 0.00
109 24 0.06
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:38271 original size:37 final size:37
Alignment explanation
Indices: 38177--38273 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
38167 CATTTTCATC
38177 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
38214 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
38251 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
38274 GATATGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:38665 original size:17 final size:18
Alignment explanation
Indices: 38639--38678 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38629 ATTATATGGA
38639 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
38655 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
38673 TATTAT
1 TATTAT
38679 ATGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:41170 original size:17 final size:17
Alignment explanation
Indices: 41148--41183 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41138 TTATTAAAAG
*
41148 GACAAAAAAATTTGGGT
1 GACAAAAAAAATTGGGT
41165 GACAAAAAAAATTGGGT
1 GACAAAAAAAATTGGGT
41182 GA
1 GA
41184 TTCAATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (17 bp):
GACAAAAAAAATTGGGT
Found at i:43977 original size:17 final size:17
Alignment explanation
Indices: 43955--44005 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
43945 GTGTCGATCC
*
43955 TCCAAGTGTCATGTTCA
1 TCCAAGTGCCATGTTCA
43972 TCCAAGTGCCATGTTCA
1 TCCAAGTGCCATGTTCA
43989 TCCAAGTGCCATGTTCA
1 TCCAAGTGCCATGTTCA
44006 GGACGCCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (17 bp):
TCCAAGTGCCATGTTCA
Found at i:45337 original size:19 final size:19
Alignment explanation
Indices: 45313--45352 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
45303 GTTAACGGTA
*
45313 AGGTCAAAGTCAACGGTTC
1 AGGTCAAAGTCAACGGGTC
*
45332 AGGTCAAGGTCAACGGGTC
1 AGGTCAAAGTCAACGGGTC
45351 AG
1 AG
45353 ACCAGTTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.33, T:0.17
Consensus pattern (19 bp):
AGGTCAAAGTCAACGGGTC
Found at i:58416 original size:2 final size:2
Alignment explanation
Indices: 58409--58473 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
58399 CAAACCAAAT
58409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58451 TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
58474 CTCAAATATG
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59749 original size:20 final size:19
Alignment explanation
Indices: 59726--59773 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
59716 CTCAAAAACA
*
59726 TTTTTCAAATTTTTATTTTG
1 TTTTTCAAATTTGT-TTTTG
59746 TTTTTCAAAATTTGTTTTTG
1 TTTTTC-AAATTTGTTTTTG
59766 -TTTTCAAA
1 TTTTTCAAA
59774 AGAAAATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 11 0.42
21 7 0.27
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTTCAAATTTGTTTTTG
Found at i:59763 original size:19 final size:18
Alignment explanation
Indices: 59726--59774 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
59716 CTCAAAAACA
*
59726 TTTTTCAAATTTTTATTTT
1 TTTTTCAAA-ATTTATTTT
*
59745 GTTTTTCAAAATTTGTTTT
1 -TTTTTCAAAATTTATTTT
59764 TGTTTTCAAAA
1 T-TTTTCAAAA
59775 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTTCAAAATTTATTTT
Found at i:73205 original size:59 final size:59
Alignment explanation
Indices: 73132--73252 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 59
73122 AATAGATGGA
* * * *
73132 TAAGTGTCCCATCGAACCCTCTTAGTTGCAATGGAAAGCCAAACTCGATAATATGGCTC
1 TAAGTGTCCCATCGAACCCTCCTAGTCGCAATGAAAAGCAAAACTCGATAATATGGCTC
* * *
73191 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACTTGATAATATGGCTC
1 TAAGTGTCCCATCGAACCCTCCTAGTCGCAATGAAAAGCAAAACTCGATAATATGGCTC
73250 TAA
1 TAA
73253 CCAACCCTCC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (59 bp):
TAAGTGTCCCATCGAACCCTCCTAGTCGCAATGAAAAGCAAAACTCGATAATATGGCTC
Found at i:77687 original size:59 final size:59
Alignment explanation
Indices: 77593--77713 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
77583 AATAGATGGA
* *
77593 TAAGTGTCATATCGAACCCTCCTAGTCGCATTGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCATATCAAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
* *
77652 TAAGTGTCCTATCAAACCCTCCTAGTCGTAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCATATCAAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
77711 TAA
1 TAA
77714 CCGACCCTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (59 bp):
TAAGTGTCATATCAAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
Found at i:78654 original size:27 final size:27
Alignment explanation
Indices: 78616--78681 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
78606 TTTAAAAGTG
*
78616 TTGAGATCCTCTGTTATATATTTAGTA
1 TTGAGATCCTCTATTATATATTTAGTA
78643 TTGAGATCCTCTATTATATATTTAGTA
1 TTGAGATCCTCTATTATATATTTAGTA
78670 TTGAGATGCCTC
1 TTGAGAT-CCTC
78682 CATTCTAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (27 bp):
TTGAGATCCTCTATTATATATTTAGTA
Done.