Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001723.1 Hibiscus syriacus cultivar Beakdansim tig00003485_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: 54178
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:197 original size:15 final size:15
Alignment explanation
Indices: 168--211 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
158 CATTGACTTC
*
168 CTTCCTC-CTCACTT
1 CTTCCTCTCTCTCTT
182 CTTCCATCTCT-TCTT
1 CTTCC-TCTCTCTCTT
197 CTTCCTCTCTCTCTT
1 CTTCCTCTCTCTCTT
212 TTTCTTCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.38
15 14 0.54
16 2 0.08
ACGTcount: A:0.05, C:0.45, G:0.00, T:0.50
Consensus pattern (15 bp):
CTTCCTCTCTCTCTT
Found at i:200 original size:18 final size:18
Alignment explanation
Indices: 179--221 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
169 TTCCTCCTCA
179 CTTCTTC-CATCTCTTCTT
1 CTTCTTCTC-TCTCTTCTT
* *
197 CTTCCTCTCTCTCTTTTT
1 CTTCTTCTCTCTCTTCTT
215 CTTCTTC
1 CTTCTTC
222 ATATTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (18 bp):
CTTCTTCTCTCTCTTCTT
Found at i:447 original size:32 final size:32
Alignment explanation
Indices: 405--465 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
395 TTAATATCAC
*
405 CCCTTAACACCCCAACTTCTTTCACCACTTCA
1 CCCTCAACACCCCAACTTCTTTCACCACTTCA
* *
437 CCCTCAACACCTCTACTTCTTTCACCACT
1 CCCTCAACACCCCAACTTCTTTCACCACT
466 CCATCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.30
Consensus pattern (32 bp):
CCCTCAACACCCCAACTTCTTTCACCACTTCA
Found at i:524 original size:21 final size:21
Alignment explanation
Indices: 499--542 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
489 CCCCTTATGC
499 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
520 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
541 CT
1 CT
543 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:2745 original size:17 final size:18
Alignment explanation
Indices: 2723--2764 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
2713 AATATATCCG
*
2723 TATCATTT-TATCGGTTT
1 TATCATTTATACCGGTTT
2740 TATCATTTGATACCGGTTT
1 TATCATTT-ATACCGGTTT
2759 TATCAT
1 TATCAT
2765 ATTTTTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
19 14 0.64
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.52
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:2929 original size:19 final size:18
Alignment explanation
Indices: 2903--2960 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
2893 TCCGGTAACG
2903 TTTTACCGGTTTATCATT
1 TTTTACCGGTTTATCATT
*
2921 TTGTTACCGGTTTATCATA
1 TT-TTACCGGTTTATCATT
* *
2940 TTTTACCTGGTATATCGTT
1 TTTTACC-GGTTTATCATT
2959 TT
1 TT
2961 AATTTCTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.21
19 27 0.79
ACGTcount: A:0.17, C:0.16, G:0.14, T:0.53
Consensus pattern (18 bp):
TTTTACCGGTTTATCATT
Found at i:3597 original size:221 final size:222
Alignment explanation
Indices: 2993--3674 Score: 1072
Period size: 221 Copynumber: 3.1 Consensus size: 222
2983 ACTTTTATAC
* * *
2993 GTATAGACACTTTTATAAAAATGATATATATTTTTTTTAAAGTTATGTAATTTTGTTTCAATTTT
1 GTATGGACAC-TTTAT-AAAA--ATATATACTTTTTTTAAAGTTATGTAATTATGTTTCAATTTT
3058 TTTAATAGTGTTTCATG-TTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATT
62 TTTAATAGTG-TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATT
* *
3122 -TTTGA-TTTTTAATA-TTTATAAAATATTA-TTAGAATTTAAATTTAAC-A-ATTAACCAAATA
126 ATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGA
3181 TAATAATAAATATGTTTTCCACAGTGAAATAA
191 TAATAATAAATATGTTTTCCACAGTGAAATAA
3213 GTATGGACACTTTATAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
1 GTATGGACACTTTATAAAA--ATATATACTTTTTTTAAAGTTATGTAA-TTATGTTTCAA-TTTT
*
3278 TTTAATAGTGGTTCATGTTTTCCACCTACAATATT-ATTT-AGAATTTCATTTACACAAAAAATT
62 TTTAATAGT-GTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATT
3341 ATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGA
126 ATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGA
3406 TAATAATAAATATGTTTTCCACAGTGAAATAA
191 TAATAATAAATATGTTTTCCACAGTGAAATAA
*
3438 GTATGAACACTTTATAAAAATATATACTTTTTTTAAAGTTATGT-ATTATGTTTCAATTTTTTTA
1 GTATGGACACTTTATAAAAATATATACTTTTTTTAAAGTTATGTAATTATGTTTCAATTTTTTTA
*
3502 ATAGTGTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-ACAAATTATTTG
66 ATAGTGTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTG
3566 ATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAA-TTAACAATATTAACC-AAGATAAT
131 ATT-TTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAAT
3629 AATAAATA--TTTT-CACAGTGAAATAA
195 AATAAATATGTTTTCCACAGTGAAATAA
3654 GTATGGACACTTTTATAAAAA
1 GTATGGACAC-TTTATAAAAA
3675 GGATAGATAC
Statistics
Matches: 438, Mismatches: 10, Indels: 31
0.91 0.02 0.06
Matches are distributed among these distances:
216 22 0.05
217 14 0.03
218 32 0.07
219 79 0.18
220 83 0.19
221 88 0.20
222 15 0.03
223 43 0.10
224 1 0.00
225 61 0.14
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (222 bp):
GTATGGACACTTTATAAAAATATATACTTTTTTTAAAGTTATGTAATTATGTTTCAATTTTTTTA
ATAGTGTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTG
ATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATA
ATAAATATGTTTTCCACAGTGAAATAA
Found at i:15775 original size:3 final size:3
Alignment explanation
Indices: 15767--15792 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15757 TACTTGAAAA
15767 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
15793 GCTTAGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:19705 original size:2 final size:2
Alignment explanation
Indices: 19692--19725 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
19682 TCACAAATCT
19692 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19726 CGGGCCCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19866 original size:15 final size:15
Alignment explanation
Indices: 19826--19869 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
19816 ATGTATCTTT
*
19826 TATTCATTTTTTTTA
1 TATTCATTATTTTTA
* *
19841 TCTTTAGTTATTTTTA
1 TATTCA-TTATTTTTA
19857 TATTCATTATTTT
1 TATTCATTATTTT
19870 ATTTGTATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.70
Consensus pattern (15 bp):
TATTCATTATTTTTA
Found at i:21143 original size:10 final size:10
Alignment explanation
Indices: 21107--21135 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
21097 TCCTTTACCA
21107 TTTATTTATT
1 TTTATTTATT
21117 TTTATTTATT
1 TTTATTTATT
21127 TTTATTTAT
1 TTTATTTAT
21136 CTCTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:31581 original size:105 final size:105
Alignment explanation
Indices: 31399--32373 Score: 1700
Period size: 105 Copynumber: 9.3 Consensus size: 105
31389 TTTTACCCAA
* *
31399 AGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
31464 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
31504 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
31569 AAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
**
31609 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
31674 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
31714 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
31779 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
31819 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
31884 AAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
** *
31924 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
31989 AAGGGACCGTTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
32029 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
32094 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* ** * *
32134 AACCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
32199 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTTAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* *
32239 AGCCAATTTTAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
32304 AACGGACCGCTGGTTGTCAACAAACAACTTT-TCAATTTTAG
66 AAGGGACCGCTGGTTGTCAACAAAC-A-TTTCTCAATTTCAG
** * *
32345 AGCTCGTTTTCAACTTCACGACGAGGGAT
1 AGC-CAATTTCAACTTCACAACGAAGGAT
32374 TTCGTGCTCG
Statistics
Matches: 830, Mismatches: 37, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
105 793 0.96
106 14 0.02
107 23 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
Found at i:33741 original size:2 final size:2
Alignment explanation
Indices: 33734--33760 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33724 ATTATTTTAT
33734 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
33761 TTCTTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33962 original size:2 final size:2
Alignment explanation
Indices: 33949--33990 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
33939 TCACAAATCT
33949 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33991 CGGGCCCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34130 original size:15 final size:15
Alignment explanation
Indices: 34091--34133 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
34081 ATGTATCTTT
34091 TATTCATT-TTTTTA
1 TATTCATTATTTTTA
* *
34105 TCTTTAGTTATTTTTA
1 TATTCA-TTATTTTTA
34121 TATTCATTATTTT
1 TATTCATTATTTT
34134 ATTTGTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 10 0.43
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (15 bp):
TATTCATTATTTTTA
Found at i:34968 original size:2 final size:2
Alignment explanation
Indices: 34963--34992 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34953 AAAAAAAGGG
34963 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
34993 AAGAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35229 original size:15 final size:15
Alignment explanation
Indices: 35209--35252 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
35199 AAATACAAAT
35209 AAAATAATGAATATA
1 AAAATAATGAATATA
* *
35224 AAAATAACTAAAGATA
1 AAAATAA-TGAATATA
*
35240 AAAAAAATGAATA
1 AAAATAATGAATA
35253 AAAGATACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (15 bp):
AAAATAATGAATATA
Found at i:37109 original size:105 final size:105
Alignment explanation
Indices: 36979--38242 Score: 2169
Period size: 105 Copynumber: 12.0 Consensus size: 105
36969 TTGAAAACGA
* * *
36979 GCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCGTTCGTCGTGAAGTTGAACTTGCG
1 GCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
*
37044 TTGTCTGGAGTCCAACATCCTTCGTTGTGAAGTTAAAATTG
65 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTG
* * *
37085 GCTATAAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
37150 TGTCTGGAGTCCAATATCCTTCGTTGTGAAG-CAGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTA-AAATTG
* *
37190 GTTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
37255 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTG
*
37295 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
* *
37360 TGTCTGGAGTCCAATATCCTTCGTTGTGAAG-CAGAAATTA
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTA-AAATTG
* *
37400 GCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCAT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
37465 TGTCTGGAGTCCAATATCCTTCGTTGTGAAG-CAGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTA-AAATTG
*
37505 GTTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
37570 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTG
*
37610 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
37675 TGTCTGGAGTCCAATATCCTTCGTTGTGAAG-CAGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTA-AAATTG
*
37715 GCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
37780 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTG
37820 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
37885 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTG
*
37925 GCTCTAAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
37990 TGTCTGGAGTCCAATATCCTTCGTTGTGAAG-CAGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTA-AAATTG
*
38030 GCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
38095 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTG
38135 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1 GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
* *
38200 TATCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
66 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTG
38240 GCT
1 GCT
38243 TTGGGTAAAA
Statistics
Matches: 1104, Mismatches: 46, Indels: 17
0.95 0.04 0.01
Matches are distributed among these distances:
104 1 0.00
105 1088 0.99
106 15 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTG
Found at i:48510 original size:10 final size:10
Alignment explanation
Indices: 48497--48525 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
48487 TAAAATAGAG
48497 ATAAATAAAA
1 ATAAATAAAA
48507 ATAAATAAAA
1 ATAAATAAAA
48517 ATAAATAAA
1 ATAAATAAA
48526 TGGTAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:49789 original size:15 final size:15
Alignment explanation
Indices: 49769--49811 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
49759 AAATACAAAT
49769 AAAATAATGAATATA
1 AAAATAATGAATATA
* *
49784 AAAATAACTAAAGATA
1 AAAATAA-TGAATATA
49800 AAAA-AATGAATA
1 AAAATAATGAATA
49812 AAAGATACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 10 0.43
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAATAATGAATATA
Found at i:49923 original size:2 final size:2
Alignment explanation
Indices: 49912--49957 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
49902 AAGGGGCCCG
49912 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
49954 TA TA
1 TA TA
49958 AGATTTGTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:52536 original size:30 final size:30
Alignment explanation
Indices: 52452--52553 Score: 117
Period size: 29 Copynumber: 3.5 Consensus size: 30
52442 GATGGCCTTG
* * *
52452 GTCCCTGT-CTATTTAACA-TGAGTGGTCAA
1 GTCCCTGTACTATTTGACATTG-GTGGCCCA
52481 GT-CCT-TA-TATTTGACATTGGGTGGCCCA
1 GTCCCTGTACTATTTGACATT-GGTGGCCCA
52509 GTCCCTGTACTATTTGACATTGGTGGCCCA
1 GTCCCTGTACTATTTGACATTGGTGGCCCA
52539 GTCCC-GTACTATTTG
1 GTCCCTGTACTATTTG
52554 GTGCTTAACT
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.14
28 12 0.19
29 16 0.25
30 16 0.25
31 11 0.17
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (30 bp):
GTCCCTGTACTATTTGACATTGGTGGCCCA
Found at i:52922 original size:25 final size:24
Alignment explanation
Indices: 52880--52956 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 24
52870 AAAAATTGAT
52880 GAAGAAGTTTTAAAAATGGTTT-ATG
1 GAAGAA-TTTTAAAAAT-GTTTAATG
52905 GAAGAATTTTAAATAATGTTTAATG
1 GAAGAATTTTAAA-AATGTTTAATG
* *
52930 AAAGAATTTTGAAAAATGTTTGATG
1 GAAGAATTTT-AAAAATGTTTAATG
52955 GA
1 GA
52957 CATGAGCTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 11 0.24
25 32 0.70
26 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (24 bp):
GAAGAATTTTAAAAATGTTTAATG
Found at i:53102 original size:186 final size:187
Alignment explanation
Indices: 52768--53140 Score: 566
Period size: 186 Copynumber: 2.0 Consensus size: 187
52758 CCAGTCAGAG
*
52768 CATGAGGTTCTATGTTTATAGACATGTTTCAAATGCCAATATACTCAAAGGAGAATGTTTGTTTG
1 CATGAGCTTCTATGTTTATAGACATGTTTCAAATGCCAATATACTCAAAGGAGAATGTTTGTTTG
52833 AAATATTTTCTTCCTTTTCTATTTTTCAAAAGGTGAAAAAAATTGATGAAGAAGTTTTAAAAATG
66 AAATATTTTCTTCCTTTTCTATTTTTCAAAAGGTGAAAAAAATTGAT--AGAAGTTTTAAAAATG
52898 GTTTATGGAAGAATTTTAAATAATGTTTAATGAAAGAATTTTGAAAAATGTTTGATGGA
129 GTTTATGGAAGAATTTTAAATAATGTTTAATGAAAGAATTTTGAAAAATGTTTGATGGA
* *
52957 CATGAGCTTCTATG-TTATAAGACATGTTTCAAAATG-CAATTCTACTC-AA-GAGAGTTGTCTT
1 CATGAGCTTCTATGTTTAT-AGACATGTTTC-AAATGCCAA-TATACTCAAAGGAGA-ATGT-TT
53018 GTTTGAAAATATTTTTCTTCCTCTTTCTA-TTTTC-AAAGGTGAAAAAAA-TGAT-GAAGTTTT-
61 GTTTG-AAATA-TTTTCTTCCT-TTTCTATTTTTCAAAAGGTGAAAAAAATTGATAGAAGTTTTA
53078 AAAATGGTTTATGGAAGAATTTTAAATAATGTTTAATGAAAGAATTTTGAAAAATGTTTGATG
123 AAAATGGTTTATGGAAGAATTTTAAATAATGTTTAATGAAAGAATTTTGAAAAATGTTTGATG
53141 AAGTTTTTGA
Statistics
Matches: 173, Mismatches: 3, Indels: 19
0.89 0.02 0.10
Matches are distributed among these distances:
186 63 0.36
187 8 0.05
188 8 0.05
189 32 0.18
190 22 0.13
191 19 0.11
192 15 0.09
193 6 0.03
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (187 bp):
CATGAGCTTCTATGTTTATAGACATGTTTCAAATGCCAATATACTCAAAGGAGAATGTTTGTTTG
AAATATTTTCTTCCTTTTCTATTTTTCAAAAGGTGAAAAAAATTGATAGAAGTTTTAAAAATGGT
TTATGGAAGAATTTTAAATAATGTTTAATGAAAGAATTTTGAAAAATGTTTGATGGA
Found at i:53120 original size:25 final size:24
Alignment explanation
Indices: 53078--53142 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 24
53068 ATGAAGTTTT
*
53078 AAAATGGTTTATGGAAGAATTTT-A
1 AAAAT-GTTTATGAAAGAATTTTGA
53102 AATAATGTTTAATGAAAGAATTTTGA
1 AA-AATGTTT-ATGAAAGAATTTTGA
53128 AAAATGTTTGATGAA
1 AAAATGTTT-ATGAA
53143 GTTTTTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 6 0.17
25 27 0.75
26 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (24 bp):
AAAATGTTTATGAAAGAATTTTGA
Found at i:53752 original size:2 final size:2
Alignment explanation
Indices: 53745--53789 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
53735 CAAATTTATG
53745 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53784 TA TA TA
1 TA TA TA
53790 ATTACATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.