Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000953.1 Hibiscus syriacus cultivar Beakdansim tig00001907_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: 66675
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:11123 original size:28 final size:28
Alignment explanation
Indices: 11092--11147 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
11082 TTACAACTTG
11092 TATTTTTATATTTA-CTTTTATAATTTAA
1 TATTTTTA-ATTTATCTTTTATAATTTAA
* *
11120 TATTTTTAATTTATTTTTTATATTTTAA
1 TATTTTTAATTTATCTTTTATAATTTAA
11148 ATTATATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
TATTTTTAATTTATCTTTTATAATTTAA
Found at i:11124 original size:20 final size:20
Alignment explanation
Indices: 11051--11124 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
11041 TTATATACTT
11051 TAATTTAATATTTACTTTTA
1 TAATTTAATATTTACTTTTA
* ** *
11071 T-ATTTTATGATTTACAACTTG
1 TAATTTAAT-ATTTAC-TTTTA
* *
11092 TATTTTTATATTTACTTTTA
1 TAATTTAATATTTACTTTTA
11112 TAATTTAATATTT
1 TAATTTAATATTT
11125 TTAATTTATT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 6 0.15
20 20 0.49
21 9 0.22
22 6 0.15
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
TAATTTAATATTTACTTTTA
Found at i:11146 original size:14 final size:13
Alignment explanation
Indices: 11094--11144 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 13
11084 ACAACTTGTA
11094 TTTTTATATTTA-
1 TTTTTATATTTAT
*
11106 CTTTTATAATTTAAT
1 TTTTTAT-ATTT-AT
11121 ATTTTTA-ATTTAT
1 -TTTTTATATTTAT
11134 TTTTTATATTT
1 TTTTTATATTT
11145 TAAATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 12 0.38
13 10 0.31
14 5 0.16
16 5 0.16
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTATATTTAT
Found at i:18002 original size:20 final size:20
Alignment explanation
Indices: 17977--18045 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
17967 GCTGTTCGAA
17977 AAAGAAAATAAAAAAAAAAG
1 AAAGAAAATAAAAAAAAAAG
* ***
17997 AAAGAAACTGTTAAAAAAAG
1 AAAGAAAATAAAAAAAAAAG
* *
18017 AAA-AGACATGAGAAAAAAAAG
1 AAAGA-AAAT-AAAAAAAAAAG
18038 AAAGAAAA
1 AAAGAAAA
18046 AAACAACAAC
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
19 1 0.03
20 21 0.58
21 13 0.36
22 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAGAAAATAAAAAAAAAAG
Found at i:18014 original size:21 final size:22
Alignment explanation
Indices: 17988--18044 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
17978 AAGAAAATAA
*
17988 AAAAAAAAGAAAGAAAC-TG-T
1 AAAAAAAAGAAAGAAACATGAG
* *
18008 TAAAAAAAGAAA-AGACATGAG
1 AAAAAAAAGAAAGAAACATGAG
18029 AAAAAAAAGAAAGAAA
1 AAAAAAAAGAAAGAAA
18045 AAAACAACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 11 0.38
22 2 0.07
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.07
Consensus pattern (22 bp):
AAAAAAAAGAAAGAAACATGAG
Found at i:32690 original size:43 final size:43
Alignment explanation
Indices: 32580--32690 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 43
32570 ATGACTAACT
* * * * *
32580 TATTGCGGCA-TTTCTGCCACAAAAGCCGCTATATATCAAATC
1 TATTGCGGCATTTTTTACTACAAACGCCGCTATATATCAAATA
* * * * *
32622 TATTGTGTCATTTGTAACTAAAAACGCCGCTATATATCAAATA
1 TATTGCGGCATTTTTTACTACAAACGCCGCTATATATCAAATA
32665 TATTGCGGCATTTTTTACTACAAACG
1 TATTGCGGCATTTTTTACTACAAACG
32691 TCGTTAAATA
Statistics
Matches: 53, Mismatches: 15, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
42 8 0.15
43 45 0.85
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (43 bp):
TATTGCGGCATTTTTTACTACAAACGCCGCTATATATCAAATA
Found at i:34754 original size:158 final size:158
Alignment explanation
Indices: 34466--34772 Score: 596
Period size: 158 Copynumber: 1.9 Consensus size: 158
34456 CAAGTTCGTT
34466 GCTAATTTCCCATCTTTTTTTCGCTAACGACCTTATCCTCTATGCTAAACCCGATATGAATCAAG
1 GCTAATTTCCCATCTTTTTTTCGCTAACGACCTTATCCTCTATGCTAAACCCGATATGAATCAAG
34531 CTATTACAATTGAAAATATTCTTGATGTCTTGCTGTAATTCTCCATTAAAAAGTGCATACACGAC
66 CTATTACAATTGAAAATATTCTTGATGTCTTGCTGTAATTCTCCATTAAAAAGTGCATACACGAC
*
34596 TCTCGTCCAAGATCATTGGTAATGGCGC
131 TCTCGCCCAAGATCATTGGTAATGGCGC
*
34624 GCTAATTTCCCATCTTTTTTTCGCTAACGACCTTATCCTCTATGCTAAACCCGATTTGAATCAAG
1 GCTAATTTCCCATCTTTTTTTCGCTAACGACCTTATCCTCTATGCTAAACCCGATATGAATCAAG
34689 CTATTACAATTGAAAATATTCTTGATGTCTTGCTGTAATTCTCCATTAAAAAGTGCATACACGAC
66 CTATTACAATTGAAAATATTCTTGATGTCTTGCTGTAATTCTCCATTAAAAAGTGCATACACGAC
34754 TCTCGCCCAAGATCATTGG
131 TCTCGCCCAAGATCATTGG
34773 AATACCCCTC
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 147 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (158 bp):
GCTAATTTCCCATCTTTTTTTCGCTAACGACCTTATCCTCTATGCTAAACCCGATATGAATCAAG
CTATTACAATTGAAAATATTCTTGATGTCTTGCTGTAATTCTCCATTAAAAAGTGCATACACGAC
TCTCGCCCAAGATCATTGGTAATGGCGC
Found at i:36694 original size:23 final size:23
Alignment explanation
Indices: 36664--36708 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
36654 GCGAGTGAAA
36664 TGTTAAGTTAATTTGGGCTACGG
1 TGTTAAGTTAATTTGGGCTACGG
*
36687 TGTTAAGTTGATTTGGGCTACG
1 TGTTAAGTTAATTTGGGCTACG
36709 TGGGTGGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.40
Consensus pattern (23 bp):
TGTTAAGTTAATTTGGGCTACGG
Found at i:37913 original size:13 final size:13
Alignment explanation
Indices: 37895--37921 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37885 TAGACCTATT
37895 ATAAAATTATTTA
1 ATAAAATTATTTA
37908 ATAAAATTATTTA
1 ATAAAATTATTTA
37921 A
1 A
37922 ATTTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:38018 original size:23 final size:24
Alignment explanation
Indices: 37980--38030 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
37970 TGATTAAATA
*
37980 TAAATTATTATAGTTTAATTTATG
1 TAAATTATTATAGTTTAATTTAAG
38004 TAAATTA-TATAGTTTAATTTAAG
1 TAAATTATTATAGTTTAATTTAAG
38027 TAAA
1 TAAA
38031 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (24 bp):
TAAATTATTATAGTTTAATTTAAG
Found at i:38239 original size:12 final size:11
Alignment explanation
Indices: 38213--38252 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
38203 GATAATGATA
*
38213 ATTTAAATAAC
1 ATTTGAATAAC
*
38224 ATTTGATATAAA
1 ATTTGA-ATAAC
38236 ATTTGAATAAC
1 ATTTGAATAAC
38247 ATTTGA
1 ATTTGA
38253 GTTAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:38827 original size:25 final size:25
Alignment explanation
Indices: 38799--38876 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
38789 ATTATAGTGT
38799 ATTAA-ATAATAATTGCATGTTATTA
1 ATTAATATAAT-ATTGCATGTTATTA
* *
38824 ATTAATGTGATATTGCATGTTATTA
1 ATTAATATAATATTGCATGTTATTA
* * ***
38849 ATTCATGTTGCATTGCATGTTATTA
1 ATTAATATAATATTGCATGTTATTA
38874 ATT
1 ATT
38877 CATGTTACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 43 0.93
26 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.47
Consensus pattern (25 bp):
ATTAATATAATATTGCATGTTATTA
Found at i:38857 original size:13 final size:14
Alignment explanation
Indices: 38808--38883 Score: 67
Period size: 13 Copynumber: 5.9 Consensus size: 14
38798 TATTAAATAA
38808 TAATTGCATGTTAT
1 TAATTGCATGTTAT
* *
38822 TAATT-AATGTGA-
1 TAATTGCATGTTAT
38834 T-ATTGCATGTTAT
1 TAATTGCATGTTAT
38847 TAATT-CATG-T-T
1 TAATTGCATGTTAT
**
38858 GCATTGCATGTTAT
1 TAATTGCATGTTAT
38872 TAATT-CATGTTA
1 TAATTGCATGTTA
38884 CATTAGGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
11 7 0.15
12 11 0.23
13 18 0.38
14 12 0.25
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (14 bp):
TAATTGCATGTTAT
Found at i:38895 original size:25 final size:25
Alignment explanation
Indices: 38810--38887 Score: 120
Period size: 25 Copynumber: 3.1 Consensus size: 25
38800 TTAAATAATA
* * *
38810 ATTGCATGTTATTAATTAATGTGAT
1 ATTGCATGTTATTAATTCATGTTAC
*
38835 ATTGCATGTTATTAATTCATGTTGC
1 ATTGCATGTTATTAATTCATGTTAC
38860 ATTGCATGTTATTAATTCATGTTAC
1 ATTGCATGTTATTAATTCATGTTAC
38885 ATT
1 ATT
38888 AGGTGTTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (25 bp):
ATTGCATGTTATTAATTCATGTTAC
Found at i:39625 original size:29 final size:28
Alignment explanation
Indices: 39583--39654 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
39573 AATAAACTAT
39583 TTATA-ATTAAAATTAAAATTAATATAAA
1 TTATATATTAAAATTAAAATTAATAT-AA
* *
39611 TTATATATTATAATTAATATTAATATAA
1 TTATATATTAAAATTAAAATTAATATAA
*
39639 TTA-ATATTAATATTAA
1 TTATATATTAAAATTAA
39655 CTTATATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 11 0.28
28 10 0.26
29 18 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TTATATATTAAAATTAAAATTAATATAA
Found at i:39632 original size:6 final size:6
Alignment explanation
Indices: 39588--39671 Score: 60
Period size: 6 Copynumber: 15.2 Consensus size: 6
39578 ACTATTTATA
* *
39588 ATTAAA ATTAAA ATTAAT A-TAA- ATTATAT ATT-AT AATTAAT ATTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT -ATTAAT ATTAAT
*
39635 A-T-A- ATTAAT ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT A
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT A
39672 AAGTTTATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
3 1 0.02
4 4 0.06
5 18 0.28
6 37 0.57
7 5 0.08
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTAAT
Found at i:39722 original size:31 final size:31
Alignment explanation
Indices: 39687--39749 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
39677 TATAATTTGT
39687 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAAATATAGTCTATAA
* * *
39718 AATTAATATTAATATAAACTATATTTTATAA
1 AATTAATATTAATATAAAATATAGTCTATAA
39749 A
1 A
39750 TTATATAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (31 bp):
AATTAATATTAATATAAAATATAGTCTATAA
Found at i:39739 original size:24 final size:25
Alignment explanation
Indices: 39694--39740 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
39684 TGTAATTAAT
**
39694 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
39719 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
39741 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:39777 original size:66 final size:65
Alignment explanation
Indices: 39692--39872 Score: 172
Period size: 66 Copynumber: 2.7 Consensus size: 65
39682 TTTGTAATTA
*
39692 ATATTAATATAAAATATAGTCTATAAAATTAATATTAATATAAACTATATTTTATAAATTATATA
1 ATATT-ATATAAAATATAGT-TATAAAATTAATATTAATATAAACTATATTTTATAAACTATATA
39757 GT
64 GT
* ** * *
39759 ATAGTT-TATAAACTATAGTTAATTTAATTAATATTAATAT--AGTATAGTTTATAAACTATATA
1 ATA-TTATATAAAATATAGTT-ATAAAATTAATATTAATATAAACTATATTTTATAAACTATATA
*
39821 TT
64 GT
* ** *
39823 ATATTAGTATAAATTATAGTTA-AGATAATTAGCATTAATATAAATTATAT
1 ATATTA-TATAAAATATAGTTATA-A-AATTAATATTAATATAAACTATAT
39873 AGCACATTAA
Statistics
Matches: 92, Mismatches: 14, Indels: 16
0.75 0.11 0.13
Matches are distributed among these distances:
63 2 0.02
64 24 0.26
65 27 0.29
66 29 0.32
67 8 0.09
68 2 0.02
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (65 bp):
ATATTATATAAAATATAGTTATAAAATTAATATTAATATAAACTATATTTTATAAACTATATAGT
Found at i:39853 original size:65 final size:63
Alignment explanation
Indices: 39585--39865 Score: 198
Period size: 65 Copynumber: 4.3 Consensus size: 63
39575 TAAACTATTT
* * ** * *
39585 ATAATTAAAATTAAAATTAATATAAATTATATATTATA-ATTAATATTA-ATATAATTAATA-TT
1 ATAATTAATATTAATA-TAATATAGTTTATAAATTATATATT-ATATTATATA-AAAT-ATAGTT
39647 AA
62 AA
* * *
39649 TATTAACTT-ATATTAATATAATAAAGTTTATAATTTGTA-ATTAATATTAATATAAAATATAGT
1 -A-TAA-TTAATATTAATATAATATAGTTTATAAATTATATATT-ATATT-ATATAAAATATAGT
39712 CTATA
61 -TA-A
* * *
39717 A-AATTAATATTAATATAAACTATATTTTATAAATTATATAGTATAGTT-TATAAACTATAGTTA
1 ATAATTAATATTAATAT-AA-TATAGTTTATAAATTATATATTATA-TTATATAAAATATAGTTA
39780 A
63 A
* * * *
39781 TTTAATTAATATTAATATAGTATAGTTTATAAACTATATATTATATTAGTATAAATTATAGTTAA
1 -ATAATTAATATTAATATAATATAGTTTATAAATTATATATTATATTA-TATAAAATATAGTTAA
**
39846 GATAATTAGCATTAATATAA
1 -ATAATTAATATTAATATAA
39866 ATTATATAGC
Statistics
Matches: 174, Mismatches: 26, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
63 2 0.01
64 25 0.14
65 73 0.42
66 44 0.25
67 25 0.14
68 5 0.03
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (63 bp):
ATAATTAATATTAATATAATATAGTTTATAAATTATATATTATATTATATAAAATATAGTTAA
Found at i:40724 original size:22 final size:21
Alignment explanation
Indices: 40696--40758 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
40686 ACCCGTTCCA
*
40696 ACCCGACCTGACCCGTTGACCG
1 ACCCGACCCGA-CCGTTGACCG
*
40718 ACCCGACCCGACTGTTGACCCG
1 ACCCGACCCGACCGTTGA-CCG
*
40740 ACCCAACCCGACCGTTGAC
1 ACCCGACCCGACCGTTGAC
40759 TAGGTGCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.21, C:0.46, G:0.21, T:0.13
Consensus pattern (21 bp):
ACCCGACCCGACCGTTGACCG
Found at i:41553 original size:15 final size:15
Alignment explanation
Indices: 41521--41557 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
41511 TACATGATAC
41521 TTGA-TTCCTGAATA
1 TTGATTTCCTGAATA
41535 TTGATTTCCT-AATA
1 TTGATTTCCTGAATA
41549 TTTGATTTC
1 -TTGATTTC
41558 TGTATTTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (15 bp):
TTGATTTCCTGAATA
Found at i:47562 original size:29 final size:29
Alignment explanation
Indices: 47519--47588 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
47509 ATCGTTGACC
* *
47519 GGGTGCTAGTTTAGTAATTAATTCGAAATA
1 GGGTGCTATTTTAGTAATTAATT-GAAAAA
*
47549 -GGTGCTATTTTAGTAATTAATTTAAAAA
1 GGGTGCTATTTTAGTAATTAATTGAAAAA
47577 GGGTGCTATTTT
1 GGGTGCTATTTT
47589 TTGTAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.11
29 32 0.89
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.41
Consensus pattern (29 bp):
GGGTGCTATTTTAGTAATTAATTGAAAAA
Found at i:48372 original size:15 final size:15
Alignment explanation
Indices: 48339--48375 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
48329 TACATGATAC
48339 TTGA-TTCCTGAATA
1 TTGATTTCCTGAATA
48353 TTGATTTCCT-AATA
1 TTGATTTCCTGAATA
48367 TCTGATTTC
1 T-TGATTTC
48376 TGTATTTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (15 bp):
TTGATTTCCTGAATA
Found at i:49108 original size:20 final size:22
Alignment explanation
Indices: 49082--49139 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
49072 GTTATGTAGA
49082 TATAGTTCATATATAC-TATAC
1 TATAGTTCATATATACATATAC
* *
49103 -ATAGTT-ATACATACATGTAC
1 TATAGTTCATATATACATATAC
49123 TATAAGTTACATATATA
1 TAT-AGTT-CATATATA
49140 GTTTATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 7 0.24
20 10 0.34
21 2 0.07
22 4 0.14
24 6 0.21
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (22 bp):
TATAGTTCATATATACATATAC
Found at i:49306 original size:21 final size:21
Alignment explanation
Indices: 49282--49326 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
49272 GGGTTTAGTA
49282 TTTACGATTTA-AAGTTTAGGG
1 TTTACGATTTATAA-TTTAGGG
* *
49303 TTTAGGGTTTATAATTTAGGG
1 TTTACGATTTATAATTTAGGG
49324 TTT
1 TTT
49327 CTATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (21 bp):
TTTACGATTTATAATTTAGGG
Found at i:49362 original size:49 final size:48
Alignment explanation
Indices: 49309--49413 Score: 131
Period size: 49 Copynumber: 2.1 Consensus size: 48
49299 AGGGTTTAGG
** *
49309 GTTTATAATTTAGGGTTTCTATAAACTATATACTTTA-TTACTTTATATA
1 GTTTATAA--TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATA
* *
49358 GTTTATGCATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA
1 GTTTAT-AATAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATA
49407 GTTTATA
1 GTTTATA
49414 TATATATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
48 23 0.48
49 24 0.50
50 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.50
Consensus pattern (48 bp):
GTTTATAATAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATA
Found at i:49421 original size:15 final size:15
Alignment explanation
Indices: 49401--49437 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
49391 TAATTTACTT
*
49401 TATATAGTTTATATA
1 TATATAATTTATATA
49416 TATATAATTTATATA
1 TATATAATTTATATA
49431 TACTATA
1 TA-TATA
49438 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (15 bp):
TATATAATTTATATA
Found at i:49558 original size:2 final size:2
Alignment explanation
Indices: 49551--49717 Score: 134
Period size: 2 Copynumber: 85.0 Consensus size: 2
49541 TTCTATAAAC
* *
49551 TA TA TA TA TA TA TA -A TC TA TA GA T- TA CT- TA TA T- TA GT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* * * *
49590 TA TA CA TA TA TA CTA -A TA TA AA T- TA TA -A TT TA TA AA CTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
49631 TA TT TT TA TA GTT TA TA TA TA TA TA CA TA CA 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
49674 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
49716 TA
1 TA
49718 GAAAATTAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
1 8 0.06
2 118 0.89
3 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:49558 original size:84 final size:83
Alignment explanation
Indices: 49318--49560 Score: 242
Period size: 84 Copynumber: 2.9 Consensus size: 83
49308 GGTTTATAAT
49318 TTAGGGTTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAAC
1 TTAGGGTTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAAC
**
49383 TATATA-AGTAATTTACTT
66 TATATATA-TAATTTACGG
** * * * * * * * *
49401 TATATAGTTTATATATA-TATA-ATTTATATATACTATACATAGTTTATACATAAATG-TACTAT
1 T-TAGGGTTTCTATAAACTATATACTT-TAT-TACTTTATATAGTTTATGCAT-AGTGTTTCTAT
** * * *
49463 AAGTTACATATATAGTTTAGGGG
62 AAACTATATATATAATTTA-CGG
*
49486 TTAGGGTTTCTATAAACTATATACTTTATTACTTTATATAATTTATGCATAGTGTTTCTATAAAC
1 TTAGGGTTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAAC
49551 TATATATATA
66 TATATATATA
49561 TATAATCTAT
Statistics
Matches: 120, Mismatches: 31, Indels: 17
0.71 0.18 0.10
Matches are distributed among these distances:
82 3 0.03
83 11 0.09
84 91 0.76
85 12 0.10
86 3 0.03
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (83 bp):
TTAGGGTTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAAC
TATATATATAATTTACGG
Found at i:50190 original size:13 final size:13
Alignment explanation
Indices: 50138--50240 Score: 64
Period size: 13 Copynumber: 7.3 Consensus size: 13
50128 ATATACTTTT
*
50138 TATAGTTTATACACA
1 TATAGTTTAT--ATA
*
50153 TATAGTTTACATA
1 TATAGTTTATATA
50166 TATAGTTTATATA
1 TATAGTTTATATA
*
50179 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
50194 CATAATTTATATA
1 TATAGTTTATATA
*
50207 CATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
50225 TATAGTTTATA-A
1 TATAGTTTATATA
50237 TATA
1 TATA
50241 AATATAGTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
12 5 0.07
13 30 0.42
14 3 0.04
15 22 0.31
16 3 0.04
17 3 0.04
18 6 0.08
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.45
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:50234 original size:18 final size:19
Alignment explanation
Indices: 50208--50258 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
50198 ATTTATATAC
* *
50208 ATAGCTTATAATAAT-TAT
1 ATAGTTTATAATAATAAAT
50226 ATAGTTTATAAT-ATAAAT
1 ATAGTTTATAATAATAAAT
50244 ATAGTTTATATATAA
1 ATAGTTTATA-ATAA
50259 ACTTATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 23 0.82
19 2 0.07
20 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
ATAGTTTATAATAATAAAT
Found at i:50254 original size:15 final size:14
Alignment explanation
Indices: 50138--50255 Score: 62
Period size: 13 Copynumber: 7.9 Consensus size: 14
50128 ATATACTTTT
*
50138 TATAGTTTATACACA
1 TATAGTTTATATA-A
*
50153 TATAGTTTACAT-A
1 TATAGTTTATATAA
50166 TATAGTTTATAT-A
1 TATAGTTTATATAA
*
50179 TATAGTTCATATAAA
1 TATAGTTTATAT-AA
* *
50194 CATAATTTATAT-A
1 TATAGTTTATATAA
* *
50207 CATAGCTTATAATAATTA
1 TATAG-TT-T-AT-ATAA
50225 TATAGTTTATAATATAAA
1 TATAG-TT-T-ATAT-AA
50243 TATAGTTTATATA
1 TATAGTTTATATA
50256 TAAACTTATA
Statistics
Matches: 84, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
13 29 0.35
14 3 0.04
15 25 0.30
16 3 0.04
17 6 0.07
18 18 0.21
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (14 bp):
TATAGTTTATATAA
Found at i:50258 original size:17 final size:18
Alignment explanation
Indices: 50224--50259 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
50214 TATAATAATT
50224 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
50242 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
50259 A
1 A
50260 CTTATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:55273 original size:30 final size:31
Alignment explanation
Indices: 55216--55275 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
55206 CAACCATTCA
* * * *
55216 CAACTTTTCCAAAATTGCTGAATTGGTCCCC
1 CAACTTTTCAAAAATTGATAAAATGGTCCCC
55247 CAACTTTTCAAAAATT-ATAAAATGGTCCC
1 CAACTTTTCAAAAATTGATAAAATGGTCCC
55276 TAAATTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (31 bp):
CAACTTTTCAAAAATTGATAAAATGGTCCCC
Found at i:62071 original size:24 final size:24
Alignment explanation
Indices: 62039--62084 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
62029 TCTTCCTGAT
62039 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
62063 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
62085 CATGTCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:64252 original size:13 final size:13
Alignment explanation
Indices: 64234--64258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64224 AATTATTAGT
64234 ATAATAATAATAA
1 ATAATAATAATAA
64247 ATAATAATAATA
1 ATAATAATAATA
64259 TATTAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAATAA
Done.