Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003380.1 Hibiscus syriacus cultivar Beakdansim tig00007109_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: 40142
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:15149 original size:94 final size:94
Alignment explanation
Indices: 15043--15232 Score: 353
Period size: 94 Copynumber: 2.0 Consensus size: 94
15033 TAAATACATT
15043 CAAAACTATTGAAAATAAAATATAACAATGATCGTTTATAGATAGCATATAAACAAACCATTAAC
1 CAAAACTATTGAAAATAAAATATAACAATGATCGTTTATAGATAGCATATAAACAAACCATTAAC
15108 AAGTGAAGCAATGACATACAAAAACTGAA
66 AAGTGAAGCAATGACATACAAAAACTGAA
* *
15137 CAAAATTATTGAAAATAAAATATAACAATTATCGTTTATAGATAGCATATAAACAAACCATTAAC
1 CAAAACTATTGAAAATAAAATATAACAATGATCGTTTATAGATAGCATATAAACAAACCATTAAC
*
15202 AAGTGAAGTAATGACATACAAAAACTGAA
66 AAGTGAAGCAATGACATACAAAAACTGAA
15231 CA
1 CA
15233 CACCAACCAA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (94 bp):
CAAAACTATTGAAAATAAAATATAACAATGATCGTTTATAGATAGCATATAAACAAACCATTAAC
AAGTGAAGCAATGACATACAAAAACTGAA
Found at i:18700 original size:27 final size:30
Alignment explanation
Indices: 18658--18712 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
18648 TTTCTCCACC
18658 TATGGTTTCGTTTGTTT-TT-AATTTTGAA
1 TATGGTTTCGTTTGTTTCTTCAATTTTGAA
*
18686 TATGTTTTCG-TTGTTTCTTCAATTTTG
1 TATGGTTTCGTTTGTTTCTTCAATTTTG
18713 TTTATTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 11 0.46
29 7 0.29
ACGTcount: A:0.15, C:0.07, G:0.16, T:0.62
Consensus pattern (30 bp):
TATGGTTTCGTTTGTTTCTTCAATTTTGAA
Found at i:25504 original size:22 final size:20
Alignment explanation
Indices: 25479--25519 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
25469 AAATTAAAAA
25479 AAAGTAAAAAAAATCAATTGAC
1 AAAGT-AAAAAAAT-AATTGAC
*
25501 AAAGTAATAAAATAATTGA
1 AAAGTAAAAAAATAATTGA
25520 GAGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.63, C:0.05, G:0.10, T:0.22
Consensus pattern (20 bp):
AAAGTAAAAAAATAATTGAC
Found at i:25684 original size:21 final size:20
Alignment explanation
Indices: 25654--25709 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
25644 CATAACTCAG
*
25654 TTTTGAAATTCGCAACGCGA
1 TTTTCAAATTCGCAACGCGA
* * *
25674 TTTTCTAAATTCACAACGTGG
1 TTTTC-AAATTCGCAACGCGA
25695 TTTTCAAATTCGCAA
1 TTTTCAAATTCGCAA
25710 TACGAACTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTCAAATTCGCAACGCGA
Found at i:25818 original size:20 final size:20
Alignment explanation
Indices: 25762--25913 Score: 69
Period size: 20 Copynumber: 7.5 Consensus size: 20
25752 CGAATTTGGT
*
25762 ATTCGCAACACGAAATTTC-AA
1 ATTCGCAACACG--ATTTCTGA
** *
25783 ATTCGCAATTCAATTTCTGA
1 ATTCGCAACACGATTTCTGA
* *
25803 ATTCGCAACGCGATTTTCT-T
1 ATTCGCAACACGA-TTTCTGA
* * * * *
25823 TTTAGCAACGCGATTTTTAA
1 ATTCGCAACACGATTTCTGA
* *
25843 ACTCGCAACAAGATTTTCT-A
1 ATTCGCAACACGA-TTTCTGA
* *
25863 ATTCACAACACGAATTT-TGT
1 ATTCGCAACACG-ATTTCTGA
* * *
25883 TTTCGCAACTCGATTTCCGA
1 ATTCGCAACACGATTTCTGA
25903 ATTCGCAACAC
1 ATTCGCAACAC
25914 AAATTTTAAT
Statistics
Matches: 95, Mismatches: 29, Indels: 15
0.68 0.21 0.11
Matches are distributed among these distances:
19 14 0.15
20 62 0.65
21 19 0.20
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (20 bp):
ATTCGCAACACGATTTCTGA
Found at i:25889 original size:40 final size:40
Alignment explanation
Indices: 25845--25932 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
25835 ATTTTTAAAC
* * * **
25845 TCGCAACAAGATTTTCTAATTCACAACACGAATTTTGTTT
1 TCGCAACAAGATTTCCGAATTCACAACACAAATTTTAATT
** *
25885 TCGCAACTCGATTTCCGAATTCGCAACACAAATTTTAATT
1 TCGCAACAAGATTTCCGAATTCACAACACAAATTTTAATT
25925 TCGCAACA
1 TCGCAACA
25933 GTTTTTATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (40 bp):
TCGCAACAAGATTTCCGAATTCACAACACAAATTTTAATT
Found at i:25927 original size:20 final size:20
Alignment explanation
Indices: 25904--25955 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
25894 GATTTCCGAA
25904 TTCGCAACACAAATTTTAAT
1 TTCGCAACACAAATTTTAAT
** *
25924 TTCGC-A-ACAGTTTTTATT
1 TTCGCAACACAAATTTTAAT
25942 TTCGCAACACAAAT
1 TTCGCAACACAAAT
25956 GTTTTGGGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 14 0.56
19 2 0.08
20 9 0.36
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (20 bp):
TTCGCAACACAAATTTTAAT
Found at i:26917 original size:24 final size:24
Alignment explanation
Indices: 26866--26919 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
26856 GCATTCGAAA
*
26866 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
26890 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
26914 TTTGAT
1 TTTGAT
26920 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:27733 original size:38 final size:40
Alignment explanation
Indices: 27691--27828 Score: 117
Period size: 40 Copynumber: 3.4 Consensus size: 40
27681 TTAGTATATA
27691 TTTTATT-TTATTTTTAGATTATATATA-AATATATTA-TT
1 TTTTATTATTATTTTTA-ATTATATATATAATATATTACTT
*
27729 TTTTATTATCAGTTTTATTAATTTATATATATATATATATTTACTT
1 TTTTATTATTA--TTT-TTAA-TTATATATATA-ATATA-TTACTT
* * *
27775 TTTTA-T-TT-TTTTTATTTTATATATATATTATTTTTACTT
1 TTTTATTATTATTTTTA-ATTATATATATAATA-TATTACTT
27814 TTTTATTATTATTTT
1 TTTTATTATTATTTT
27829 ATTTATTTGT
Statistics
Matches: 81, Mismatches: 5, Indels: 24
0.74 0.05 0.22
Matches are distributed among these distances:
38 7 0.09
39 15 0.19
40 16 0.20
41 9 0.11
42 16 0.20
43 1 0.01
44 6 0.07
45 4 0.05
46 7 0.09
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (40 bp):
TTTTATTATTATTTTTAATTATATATATAATATATTACTT
Found at i:27779 original size:34 final size:36
Alignment explanation
Indices: 27741--27821 Score: 94
Period size: 39 Copynumber: 2.2 Consensus size: 36
27731 TTATTATCAG
27741 TTTTATTAATTTA-TATATATATA-TATATTTACTT
1 TTTTATTAATTTATTATATATATATTATATTTACTT
** *
27775 TTTTATTTTTTTTATTTTATATATATATTATTTTTACTT
1 TTTTA-TTAATTTA--TTATATATATATTATATTTACTT
27814 TTTTATTA
1 TTTTATTA
27822 TTATTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
34 5 0.13
35 6 0.16
38 12 0.32
39 15 0.39
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.69
Consensus pattern (36 bp):
TTTTATTAATTTATTATATATATATTATATTTACTT
Found at i:27787 original size:9 final size:9
Alignment explanation
Indices: 27773--27882 Score: 51
Period size: 9 Copynumber: 11.0 Consensus size: 9
27763 ATATATTTAC
27773 TTTTTTATT
1 TTTTTTATT
27782 TTTTTTATT
1 TTTTTTATT
27791 TTATATATATATT
1 TT-T-T-T-TATT
*
27804 ATTTTTACTT
1 TTTTTTA-TT
27814 TTTTATTATTAT
1 TTTT-TTA-T-T
27826 TTTATTTATT
1 TTT-TTTATT
*
27836 TGTTTTATT
1 TTTTTTATT
*
27845 TCTATATT-TT
1 T-T-TTTTATT
* *
27855 TTTCTTCTT
1 TTTTTTATT
27864 TTTCTTTATT
1 TTT-TTTATT
*
27874 TTTTATATT
1 TTTTTTATT
27883 ACTTACTATT
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
8 3 0.04
9 31 0.39
10 20 0.25
11 10 0.13
12 9 0.11
13 6 0.08
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTTTTATT
Found at i:27794 original size:40 final size:39
Alignment explanation
Indices: 27741--27832 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 39
27731 TTATTATCAG
* *
27741 TTTTATTAATTTATATATATATATATATTTACTTTTTTAT
1 TTTTTTTATTTTATATATATAT-TATATTTACTTTTTTAT
*
27781 TTTTTTTATTTTATATATATATTATTTTTACTTTTTTAT
1 TTTTTTTATTTTATATATATATTATATTTACTTTTTTAT
27820 TATTATTTTATTT
1 T-TT-TTTTATTT
27833 ATTTGTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 17 0.36
40 22 0.47
41 8 0.17
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (39 bp):
TTTTTTTATTTTATATATATATTATATTTACTTTTTTAT
Found at i:27809 original size:32 final size:35
Alignment explanation
Indices: 27758--27823 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
27748 AATTTATATA
27758 TATATATATATTTACTTTTTTA-TTTTTT-TTATTT
1 TATATATATATTTAC-TTTTTACTTTTTTATTATTT
27792 TATATATATA-TTA-TTTTTACTTTTTTATTATT
1 TATATATATATTTACTTTTTACTTTTTTATTATT
27824 ATTTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 6 0.20
32 6 0.20
33 8 0.27
34 10 0.33
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (35 bp):
TATATATATATTTACTTTTTACTTTTTTATTATTT
Found at i:27817 original size:25 final size:24
Alignment explanation
Indices: 27789--27865 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
27779 ATTTTTTTTA
27789 TTTTATATATATATTATTTTTACTT-
1 TTTTAT-TATATATT-TTTTTACTTC
* *
27814 TTTTATTAT-TATTTTATTTATTTG
1 TTTTATTATATATTTT-TTTACTTC
*
27838 TTTTATTTCTATATTTTTTT-CTTC
1 TTTTA-TTATATATTTTTTTACTTC
27862 TTTT
1 TTTT
27866 TCTTTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 2 0.05
23 10 0.23
24 14 0.32
25 12 0.27
26 6 0.14
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTTATTATATATTTTTTTACTTC
Found at i:27842 original size:32 final size:30
Alignment explanation
Indices: 27762--27845 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 30
27752 TATATATATA
*
27762 TATATATTTACTTTTTTATTTTTTTTATTT
1 TATATATTTATTTTTTTATTTTTTTTATTT
*
27792 TATATATATATTATTTTTACTTTTTTATTATTAT
1 TATATATTTATT-TTTTTA-TTTTTT-TTATT-T
27826 T-T-TATTTATTTGTTTTATTT
1 TATATATTTATTT-TTTTATTT
27846 CTATATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
30 10 0.22
31 10 0.22
32 18 0.39
33 6 0.13
34 2 0.04
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (30 bp):
TATATATTTATTTTTTTATTTTTTTTATTT
Found at i:27895 original size:85 final size:85
Alignment explanation
Indices: 27727--27900 Score: 187
Period size: 83 Copynumber: 2.0 Consensus size: 85
27717 AAATATATTA
27727 TTTTTTATTATCAGTTTTATTAATTTATATATATATATATATTTACTTTTTTATTTTTTTTATTT
1 TTTTTTATTATCAGTTTTATTAATTTATATATATATATATATTTA-TTTTTTATTTTTTTTATTT
27792 TATATATATATTATTTTTA-C
65 TATATATATATTATTTTTATC
* * * * * * *
27812 TTTTTTATTATTA-TTTTATTTATTTGT-TTTATTTCTATATTT-TTTTCTTCTTTTTCTTTATT
1 TTTTTTATTATCAGTTTTATTAATTTATATATATATATATATTTATTTT-TTATTTTT-TTTATT
*
27874 TTTTATAT-TACTTACTATTTTATC
64 TTATATATATA-TTA-T-TTTTATC
27898 TTT
1 TTT
27901 GTTTTCTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
81 4 0.05
82 9 0.12
83 28 0.37
84 13 0.17
85 17 0.23
86 4 0.05
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (85 bp):
TTTTTTATTATCAGTTTTATTAATTTATATATATATATATATTTATTTTTTATTTTTTTTATTTT
ATATATATATTATTTTTATC
Found at i:27988 original size:15 final size:16
Alignment explanation
Indices: 27970--28000 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27960 TATTTATTTC
27970 TTACC-TTTTTATCTA
1 TTACCTTTTTTATCTA
27985 TTACCTTTTTTATCTA
1 TTACCTTTTTTATCTA
28001 ATATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (16 bp):
TTACCTTTTTTATCTA
Found at i:30491 original size:8 final size:8
Alignment explanation
Indices: 30478--30516 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
30468 GAACATTTCA
*
30478 TGCATTCT
1 TGCATTTT
30486 TGCA-TTT
1 TGCATTTT
30493 TGCATTTT
1 TGCATTTT
*
30501 TGCCTTTT
1 TGCATTTT
30509 TGCATTTT
1 TGCATTTT
30517 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:31715 original size:9 final size:9
Alignment explanation
Indices: 31703--31752 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
31693 TAAAAAGGGC
31703 AAAAAGAAAA
1 AAAAAG-AAA
*
31713 AAAACAAAAA
1 AAAA-AGAAA
*
31723 AAAAAGCAA
1 AAAAAGAAA
*
31732 AAAAAGAAC
1 AAAAAGAAA
31741 AAAAAGAAA
1 AAAAAGAAA
31750 AAA
1 AAA
31753 GAAAAAGGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 21 0.64
10 11 0.33
11 1 0.03
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:31757 original size:23 final size:23
Alignment explanation
Indices: 31703--31769 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
31693 TAAAAAGGGC
31703 AAAAAGAAAAAA-AAC-AAAA-A
1 AAAAAGAAAAAAGAACAAAAAGA
31723 AAAAAGCAAAAAAAGAACAAAAAGA
1 AAAAAG--AAAAAAGAACAAAAAGA
* *
31748 AAAAAGAAAAAGGGACAAAAAG
1 AAAAAGAAAAAAGAACAAAAAG
31770 CACATGCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.15
22 6 0.15
23 17 0.43
24 4 0.10
25 7 0.17
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAGAACAAAAAGA
Found at i:32410 original size:22 final size:22
Alignment explanation
Indices: 32379--32433 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
32369 GCTATCCCAT
*
32379 CAAACATTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
32401 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
32423 CAAACCTTTGA
1 CAAACCTTTGA
32434 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:32853 original size:18 final size:18
Alignment explanation
Indices: 32830--32865 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32820 TCAACATCAA
* *
32830 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
32848 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
32866 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:33334 original size:36 final size:36
Alignment explanation
Indices: 33287--33549 Score: 265
Period size: 36 Copynumber: 7.4 Consensus size: 36
33277 ATTGAAAACA
* *
33287 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
33323 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
33360 TTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
33396 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* *
33425 TTT-TCTTAGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTT-GAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
33461 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
33498 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
33534 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
33550 ATCTTTGAAT
Statistics
Matches: 188, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
28 5 0.03
29 16 0.09
30 2 0.01
35 1 0.01
36 96 0.51
37 68 0.36
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:33408 original size:138 final size:137
Alignment explanation
Indices: 33231--33612 Score: 505
Period size: 138 Copynumber: 2.8 Consensus size: 137
33221 TGCTTTTTTA
* * * *
33231 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAACATTGAATATATTTCCCTTG
* * * *
33296 AAATAAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGT
65 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGT
33361 TTCTCTTG
130 TTCTCTTG
* * * *
33369 AAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTT-TCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACA-TTGAATATATTTCCCTT-
* * * *
33433 GAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
64 GAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
33498 TTTCTCTTG
129 TTTCTCTTG
* * * * * *
33507 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-CATTGAATATATTTCCCTTG
* *
33572 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
65 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACA
33613 CAAAATCTTC
Statistics
Matches: 209, Mismatches: 31, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
137 7 0.03
138 200 0.96
139 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (137 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACATTGAATATATTTCCCTTGA
AACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTT
TCTCTTG
Found at i:33611 original size:65 final size:65
Alignment explanation
Indices: 33507--33681 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 65
33497 GTTTCTCTTG
* ** * **
33507 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
33572 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
33637 TA
64 TA
* * *
33639 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
33682 CATATATCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
65 31 0.33
66 6 0.06
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:34447 original size:105 final size:105
Alignment explanation
Indices: 34285--34734 Score: 685
Period size: 105 Copynumber: 4.3 Consensus size: 105
34275 GCCATCCGCG
* * * * *
34285 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACGCAAGTTCAACTTCACGACAAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
34350 GGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* * *
34393 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
34458 ACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
34498 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
34563 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
34603 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
34668 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
34703 ATTTCAACTTCACGACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
34735 TGAACAATGC
Statistics
Matches: 322, Mismatches: 20, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
100 37 0.11
101 2 0.01
102 1 0.00
103 2 0.01
104 2 0.01
105 253 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:35840 original size:22 final size:20
Alignment explanation
Indices: 35794--35843 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
35784 TTTTCATGTA
35794 ATATTTTTTTTACATTTTAT
1 ATATTTTTTTTACATTTTAT
*
35814 GTATTTCTTTTTAC-TTTAGTAT
1 ATATTT-TTTTTACATTT--TAT
35836 ATATTTTT
1 ATATTTTT
35844 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 8 0.32
21 9 0.36
22 8 0.32
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.68
Consensus pattern (20 bp):
ATATTTTTTTTACATTTTAT
Found at i:35925 original size:43 final size:41
Alignment explanation
Indices: 35859--35982 Score: 123
Period size: 38 Copynumber: 3.0 Consensus size: 41
35849 TATTTTTAGA
*
35859 TATATATATAAATATATTA-TTTTTATTATCAGTTTTATTAATT
1 TATATATATATATAT-TTACTTTTTATTAT-A-TTTTATTAATT
* *
35902 TATATATATATATATTTAC-TTTT-TTAT-TTTTTTTATTT
1 TATATATATATATATTTACTTTTTATTATATTTTATTAATT
* *
35940 TATATATAT-TATTTTTACTTTTTTATTATTATTTTATTTATT
1 TATATATATATATATTTAC-TTTTTATTA-TATTTTATTAATT
35982 T
1 T
35983 GTTTTTTTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
37 8 0.12
38 18 0.26
39 4 0.06
40 3 0.04
41 5 0.07
42 16 0.24
43 14 0.21
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (41 bp):
TATATATATATATATTTACTTTTTATTATATTTTATTAATT
Found at i:35944 original size:28 final size:28
Alignment explanation
Indices: 35912--35990 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 28
35902 TATATATATA
35912 TATATTTACTTTTTTATTTTTTTTATT-T
1 TATATTTA-TTTTTTATTTTTTTTATTAT
* *
35940 TATATATATTATTTT-TACTTTTTTATTAT
1 TATATTTATT-TTTTAT-TTTTTTTATTAT
*
35969 TAT-TTTATTTATTTGTTTTTTT
1 TATATTTATTT-TTTATTTTTTT
35991 CTATATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 4 0.10
28 33 0.79
29 5 0.12
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (28 bp):
TATATTTATTTTTTATTTTTTTTATTAT
Found at i:35946 original size:30 final size:31
Alignment explanation
Indices: 35908--35969 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
35898 AATTTATATA
35908 TATATATATTTACTTTTTTA-TTTTTT-TTATTT
1 TATATATA-TTA--TTTTTACTTTTTTATTATTT
35940 TATATATATTATTTTTACTTTTTTATTATT
1 TATATATATTATTTTTACTTTTTTATTATT
35970 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 6 0.21
30 6 0.21
31 8 0.29
32 8 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (31 bp):
TATATATATTATTTTTACTTTTTTATTATTT
Found at i:35952 original size:23 final size:21
Alignment explanation
Indices: 35925--35982 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
35915 ATTTACTTTT
35925 TTATTTTTTTTATTTTATATATA
1 TTATTTTTTTTATTTT-TAT-TA
**
35948 TTATTTTTACT-TTTTTATTA
1 TTATTTTTTTTATTTTTATTA
*
35968 TTATTTTATTTATTT
1 TTATTTTTTTTATTT
35983 GTTTTTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.34
21 6 0.21
22 4 0.14
23 9 0.31
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTTTTTTTATTTTTATTA
Found at i:36131 original size:15 final size:16
Alignment explanation
Indices: 36113--36143 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36103 TATTTATTTC
36113 TTACC-TTTTTATCTA
1 TTACCTTTTTTATCTA
36128 TTACCTTTTTTATCTA
1 TTACCTTTTTTATCTA
36144 ATATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (16 bp):
TTACCTTTTTTATCTA
Found at i:38823 original size:16 final size:15
Alignment explanation
Indices: 38802--38836 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
38792 TACAAATTGA
*
38802 AATTAAACAACAAATC
1 AATTAAACAA-AAAAC
38818 AATTAAACAAAAAAC
1 AATTAAACAAAAAAC
38833 AATT
1 AATT
38837 TTTATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTAAACAAAAAAC
Done.