Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000243.1 Hibiscus syriacus cultivar Beakdansim tig00000428_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: 68640
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:22689 original size:2 final size:2
Alignment explanation
Indices: 22682--22706 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22672 CACAATATCC
22682 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
22707 CAGAAACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23580 original size:12 final size:12
Alignment explanation
Indices: 23563--23588 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23553 GTTATTATTA
23563 TTATTTTATTTT
1 TTATTTTATTTT
23575 TTATTTTATTTT
1 TTATTTTATTTT
23587 TT
1 TT
23589 TGAAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:23869 original size:3 final size:3
Alignment explanation
Indices: 23861--23887 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
23851 ATACTATGAG
23861 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
23888 GAAAAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:26021 original size:15 final size:14
Alignment explanation
Indices: 25989--26017 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25979 CCTAAAAAAC
25989 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
26003 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
26017 A
1 A
26018 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:26094 original size:32 final size:31
Alignment explanation
Indices: 26078--26189 Score: 104
Period size: 33 Copynumber: 3.5 Consensus size: 31
26068 AATATTTTTT
26078 AAACTATATATTATATTTAAAAAAGTTTTCA
1 AAACTATATATTATATTTAAAAAAGTTTTCA
* *
26109 AAACTATAT-TATATAGTTTTCAAAATGTTTT-A
1 AAACTATATAT-TATA--TTTAAAAAAGTTTTCA
* * *
26141 AAAATATTATATAAGT-TTTAAAAAACGTTTTTA
1 AAACTA-TATATTA-TATTTAAAAAA-GTTTTCA
26174 AAACTATATATTATAT
1 AAACTATATATTATAT
26190 AATTTATTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
30 1 0.02
31 21 0.33
32 18 0.28
33 22 0.34
34 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (31 bp):
AAACTATATATTATATTTAAAAAAGTTTTCA
Found at i:26100 original size:31 final size:32
Alignment explanation
Indices: 26057--26189 Score: 100
Period size: 31 Copynumber: 4.2 Consensus size: 32
26047 ATATAATACA
**
26057 TATATTTCAAAAATA-TTTTTTAAACTATATAT
1 TATATTTCAAAAA-AGTTTTCAAAACTATATAT
26089 TATATTT-AAAAAAGTTTTCAAAACTATAT-T
1 TATATTTCAAAAAAGTTTTCAAAACTATATAT
* *
26119 ATATAGTTTTC-AAAATGTTTT-AAAAATAT-TA-
1 -TATA--TTTCAAAAAAGTTTTCAAAACTATATAT
* *
26150 TATAAGTTTTAAAAAACGTTTTTAAAACTATATAT
1 TAT-A-TTTCAAAAAA-GTTTTCAAAACTATATAT
26185 TATAT
1 TATAT
26190 AATTTATTCA
Statistics
Matches: 81, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
30 8 0.10
31 28 0.35
32 19 0.23
33 20 0.25
34 3 0.04
35 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATTTCAAAAAAGTTTTCAAAACTATATAT
Found at i:26250 original size:107 final size:105
Alignment explanation
Indices: 26096--26354 Score: 264
Period size: 109 Copynumber: 2.4 Consensus size: 105
26086 TATTATATTT
* *
26096 AAAAAAGTTTTCAAAACTATA--TTATATAGTTTTCAAAATGTTTTAAAA-ATA--TTATATAAG
1 AAAAAAATTTTAAAAACTATATATTATATAGTTTTCAAAATGTTTTAAAACATATGTTATAT-A-
* *
26156 TTTTAAAAAACGTTTTTAAAACTATATATTATATAATTTATTCAAA
64 TTTTAAAAAACGTTTTAAAAACTATATATTATAT-AGTT-TTC--A
*
26202 AAAAAAATTTT-AAAACTATATATTATA-AGTTTTTAAAATGATTTTAAAACTATATGTTATATA
1 AAAAAAATTTTAAAAACTATATATTATATAGTTTTCAAAATG-TTTTAAAAC-ATATGTTATATA
** * *
26265 TTTTCTAAAATGTTTTAAAAACTATATGTTATATAGTTTTCA
64 TTTTAAAAAACGTTTTAAAAACTATATATTATATAGTTTTCA
* *
26307 AAAAATATTTTAAAAAACTATATATTACCCATA-TTTTCAAAATGTTTT
1 AAAAAAATTTT-AAAAACTATATATTA--TATAGTTTTCAAAATGTTTT
26355 CTTTTTAAAA
Statistics
Matches: 130, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
105 20 0.15
106 22 0.17
107 30 0.23
108 7 0.05
109 43 0.33
110 2 0.02
111 6 0.05
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (105 bp):
AAAAAAATTTTAAAAACTATATATTATATAGTTTTCAAAATGTTTTAAAACATATGTTATATATT
TTAAAAAACGTTTTAAAAACTATATATTATATAGTTTTCA
Found at i:27481 original size:249 final size:248
Alignment explanation
Indices: 26981--28007 Score: 1244
Period size: 249 Copynumber: 4.1 Consensus size: 248
26971 AACTCGACAA
* * * * * * * * * *
26981 TTTTATTGACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAACTGATATGACCTCGAAGTTGAG
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAG
** * *
27046 TGTAATCGAACCCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
66 TGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * * * * * * *
27111 TGCCTTAGAGCTGAGCGTAGTCGCACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGCCTTG
131 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTT-ACAGATAACCCTTCTAGACTTA
* * *
27176 AGTTATGCTGTAAATGATATGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTC
195 AGTTATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTC
* *
27230 TTTTGTTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAG
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAG
* *
27295 TGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCAAATGATG
66 TGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* *
27360 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTCTAGCCTTGA
131 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTCTAGACTTAA
* * * * * *
27425 GTTATGCTGTAAATGATATGCCCTTGAAGTTGAGTGTAATCGAACTTAAGGGTC
196 GTTATGCTGCAAATGATATGCCCTTG-AGCTGAGCGTAGTCGAACTCAAAGGTC
* * * * * * * *
27479 TTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTG-CCTTCGAAGCTGA
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTT-GAAGCTGA
** * * * *
27543 ACGTAGTCGAACTCGAA-GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGA
65 GTGTAATCGAACT-TAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * *
27607 TGTGCCTTGGAGCTGAACGTAGTCGAACTCGAGGGTCTTTGG---CAGATAGCCCTTCTCGACTT
129 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTCTAGACTT
* * *
27669 AAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
194 AAGTTATGCTGCAAATGATATGCCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTC
*
27724 -TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAG
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAG
*
27788 TGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
66 TGTAATCGAACTTAAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
* *
27853 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGA
127 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTA-CAGATAACCCTTCTAGA
* * * *
27918 CTTAAGTTATGCTGCAAATGATGTG-CCTTCAAAGCTGAACGTAGTCGAACTCGAAGGTC
191 CTTAAGTTATGCTGCAAATGATATGCCCTT--GAGCTGAGCGTAGTCGAACTCAAAGGTC
* * * *
27977 -TTGGTGGACAGATAGCCCTTCTGGCCTTGAG
1 TTTTGTTGACAGATAACCCTTCTAGCCTTGAG
28008 CTAAGCTGCA
Statistics
Matches: 667, Mismatches: 96, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
243 2 0.00
244 63 0.09
245 30 0.04
246 36 0.05
248 127 0.19
249 314 0.47
250 2 0.00
252 42 0.06
253 51 0.08
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (248 bp):
TTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAG
TGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATG
TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTCTAGACTTAA
GTTATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTC
Found at i:27653 original size:329 final size:329
Alignment explanation
Indices: 27071--27998 Score: 1272
Period size: 329 Copynumber: 2.8 Consensus size: 329
27061 GGGTCTTTGG
* * * * * * * * *
27071 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTT-AGAGCTGAGCGTAGTCG
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGA-AGCTGAGTGTAATCG
* * * * * * * *
27134 CACTCGAA-GGTCTTTTGTTGGCAGACAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGC
65 AACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
* * * *
27198 CGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTAACAGATAACCCTTCTAGCCTTGAGT
129 C-TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG-T-GCAGATAACCCTTCTAGACTTAAGT
* * * ** * ** *
27263 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAAC
191 TATGCTGCAAATGATGTG-CCTTGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGC
*
27328 CCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGG
255 CCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGG
*
27393 TCTTTGGTTA
320 TCTTTGGTGA
*
27403 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGTTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
* *
27468 ACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCT
66 ACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
* * * * *
27533 TCGAAGCTGAACGTAGTCGAACTCGAAGGTC-TTTG-GCAGATAGCCCTTCTCGACTTAAGCTAT
131 T-G-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTGCAGATAACCCTTCTAGACTTAAGTTAT
* *
27596 TCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTT
194 GCTGCAAATGATGTGCCTTGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTT
27661 CTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
259 CTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
27726 TGGTGA
324 TGGTGA
27732 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
*
27797 ACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
66 ACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
*
27862 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTA
131 T-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG-T-GCAGATAACCCTTCTAGACTTAAGTTA
* *
27927 TGCTGCAAATGATGTGCCTTCAAAGCTGAACGTAGTCGAACTCGAAGGTCTTGGTGGACAGATAG
193 TGCTGCAAATGATGTGCCTT-GAAGCTGAACGTAGTCGAACTCGAGGGTCTT--TGG-CAGATAG
27992 CCCTTCT
254 CCCTTCT
27999 GGCCTTGAGC
Statistics
Matches: 528, Mismatches: 55, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
328 25 0.05
329 245 0.46
330 33 0.06
332 82 0.16
333 101 0.19
334 25 0.05
335 3 0.01
336 14 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (329 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
ACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTGCAGATAACCCTTCTAGACTTAAGTTATGC
TGCAAATGATGTGCCTTGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCT
CGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG
GTGA
Found at i:28020 original size:84 final size:83
Alignment explanation
Indices: 27068--27998 Score: 975
Period size: 84 Copynumber: 11.2 Consensus size: 83
27058 CAGGGGTCTT
* * * *
27068 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * *
27133 GCACTCGAAGGTCTTTTGT
66 GAACTCAAAGGTC-TTTGG
* * * * *
27152 TGGCAGACAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCGTT-GAGCTGAGCGTAGT
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGT
* *
27216 CAAACTCAAAGGTCTTTTGT
65 CGAACTCAAAGGTC-TTTGG
** * * * * * * * *
27236 TAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAAT
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
* *
27301 CGAACTTAAGGGTC-TT--
65 CGAACTCAAAGGTCTTTGG
* * *
27317 TGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
27382 GAACTCAAAGGTCTTTGG
66 GAACTCAAAGGTCTTTGG
** * * * * * * * *
27400 TTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGTTGAGTGTAAT
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
* * *
27465 CGAACTTAAGGGTCTTTAGT
65 CGAACTCAAAGGTCTTT-GG
* * * *
27485 TGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGT
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGT
*
27550 CGAACTCGAAGGTC-TT--
65 CGAACTCAAAGGTCTTTGG
* * * * *
27566 TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTC
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *
27631 GAACTCGAGGGTC-TT--
66 GAACTCAAAGGTCTTTGG
* * * *
27646 TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
27711 GAACTCAAAGGTCTTTGG
66 GAACTCAAAGGTCTTTGG
* * * * * * * *
27729 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAAT
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
* * *
27794 CGAACTTAAGGGTCTTTAGT
65 CGAACTCAAAGGTCTTT-GG
*
27814 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
27879 GAACTCAAAGGTCTTTTGT
66 GAACTCAAAGGTC-TTTGG
* * ** *
27898 TAGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTCAAAGCTGAACGTAGT
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGT
*
27963 CGAACTCGAAGGTC-TTGG
65 CGAACTCAAAGGTCTTTGG
*
27981 TGGACAGATAGCCCTTCT
1 TGG-CAGATAACCCTTCT
27999 GGCCTTGAGC
Statistics
Matches: 719, Mismatches: 111, Indels: 34
0.83 0.13 0.04
Matches are distributed among these distances:
80 132 0.18
81 84 0.12
83 79 0.11
84 270 0.38
85 154 0.21
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (83 bp):
TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTGG
Found at i:34293 original size:15 final size:14
Alignment explanation
Indices: 34261--34289 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34251 CTAAAAAAAC
34261 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
34275 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
34289 A
1 A
34290 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:34371 original size:32 final size:32
Alignment explanation
Indices: 34327--34459 Score: 121
Period size: 32 Copynumber: 4.2 Consensus size: 32
34317 TTATAATACA
* * *
34327 TATATTTCAAAAATATTTTTTAAACTATATAT
1 TATATTTAAAAAATGTTTTTAAAACTATATAT
*
34359 TATATTTAAAAAA-GTTTTCAAAACTATAT-T
1 TATATTTAAAAAATGTTTTTAAAACTATATAT
** *
34389 ATATAGTTTTCAAAATG-TTTTAAAAATATTATAT
1 -TATA-TTTAAAAAATGTTTTTAAAACTA-TATAT
* *
34423 AAGT-TTTAAAAAACGTTTTTAAAACTATATAT
1 TA-TATTTAAAAAATGTTTTTAAAACTATATAT
34455 TATAT
1 TATAT
34460 AATTTATTCA
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
30 1 0.01
31 18 0.23
32 43 0.54
33 15 0.19
34 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATTTAAAAAATGTTTTTAAAACTATATAT
Found at i:34458 original size:37 final size:37
Alignment explanation
Indices: 34335--34608 Score: 197
Period size: 37 Copynumber: 7.7 Consensus size: 37
34325 CATATATTTC
* *
34335 AAAAATATTTTTTAAACTATATA-T-TAT-A--TTTA
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
*
34367 AAAAA-GTTTTCAAAAC--TATATTATAT-AGTTTT-
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
*
34399 CAAAATG-TTTT-AAA--A-ATATTATATAAGTTTTA
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
* *
34431 AAAAACGTTTTTAAAACTATATATTATATAATTTATTCAAA
1 AAAAATGTTTTTAAAACTATATATTATATAAGTT-TT---A
***
34472 AAAAAAAATTTTAAAACTATATATTATATAAGTTTT-
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
* * * *
34508 TAAAATGATTTTAAAACTATATGTTATATATA-TTTTC
1 AAAAATGTTTTTAAAACTATATATTATATA-AGTTTTA
* * *
34545 TAAAATGTTTTAAAAACTATATGTTATAT-AGTTTTCA
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTT-A
* *
34582 AAAAATATTTTAAAAAACTATATATTA
1 AAAAATGTTTT-TAAAACTATATATTA
34609 CCCATATTTT
Statistics
Matches: 198, Mismatches: 22, Indels: 38
0.77 0.09 0.15
Matches are distributed among these distances:
29 4 0.02
30 10 0.05
31 21 0.11
32 17 0.09
33 8 0.04
34 3 0.02
35 1 0.01
36 35 0.18
37 50 0.25
38 16 0.08
40 2 0.01
41 31 0.16
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
Found at i:35674 original size:16 final size:16
Alignment explanation
Indices: 35655--35699 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
35645 TTTTATCTTC
*
35655 TAATAATTTTATATAA
1 TAATAATTTTAAATAA
35671 TAAT-A-TTTAAATAA
1 TAATAATTTTAAATAA
35685 -AATAATTTTCAAATA
1 TAATAATTTT-AAATA
35700 TATTTTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.12
14 9 0.36
15 4 0.16
16 9 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:39802 original size:2 final size:2
Alignment explanation
Indices: 39795--39844 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
39785 GAGAAAAGGA
39795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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 AT AT AT
39837 AT AT AT AT
1 AT AT AT AT
39845 GATTAGAGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42151 original size:24 final size:24
Alignment explanation
Indices: 42115--42160 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
42105 GTAAACGGAG
*
42115 ATATCAGAAATCAAAATAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* *
42139 ATATCAGATATCAGAACAGAAT
1 ATATCAGAAATCAAAACAGAAT
42161 CTAGATCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:45577 original size:12 final size:12
Alignment explanation
Indices: 45521--45577 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
45511 AAATCAAAAT
*
45521 AGAATTCAGATC
1 AGAATTCAGAAC
*
45533 AG-ATATCATAAC
1 AGAAT-TCAGAAC
* *
45545 AGAATCCAGATC
1 AGAATTCAGAAC
*
45557 AGAAATCAGAAC
1 AGAATTCAGAAC
45569 AGAATTCAG
1 AGAATTCAG
45578 GTAATGTATC
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
11 2 0.06
12 30 0.88
13 2 0.06
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (12 bp):
AGAATTCAGAAC
Found at i:45577 original size:48 final size:47
Alignment explanation
Indices: 45506--45614 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
45496 AAACAAAGAT
* * * *
45506 ATCAGAAATCAAAATAGAATTCAGATCA-GATATCATAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAATG-TATCAGAACAGAATCCA
* *
45553 GATCAGAAATCAGAACAGAATTCAGGTAATGTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAATGTATCAGAACAGAATCCA
45601 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
45615 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAATGTATCAGAACAGAATCCA
Found at i:45613 original size:24 final size:25
Alignment explanation
Indices: 45506--45614 Score: 102
Period size: 24 Copynumber: 4.5 Consensus size: 25
45496 AAACAAAGAT
* *
45506 ATCAGAAATCAAAATAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
45530 ATCAGATATCATAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
45554 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
45578 GTAATG-TATCAGAACAGAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
45603 -TCAGAAATCAGA
1 ATCAGAAATCAGA
45615 TAAAATATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.04
24 62 0.89
25 5 0.07
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:50583 original size:9 final size:9
Alignment explanation
Indices: 50569--50593 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
50559 CCTATATGAA
50569 TATGTGATG
1 TATGTGATG
50578 TATGTGATG
1 TATGTGATG
50587 TATGTGA
1 TATGTGA
50594 AACATATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (9 bp):
TATGTGATG
Found at i:50976 original size:62 final size:63
Alignment explanation
Indices: 50794--50981 Score: 193
Period size: 62 Copynumber: 3.0 Consensus size: 63
50784 AGTCGAAGGT
** * *
50794 TTACCTATGTTCTACGGAACATATGGACAGAATTACCTATG-TCTTTTGGGACATATGGACAGAA
1 TTACCTATGTTCTAAAGAACATATGGACAG-TTTACCTATGTTC-TTTGGGACATATGGACAGTA
*** * * ** **
50858 TTACCTATG-TCTTTTGAGACATATGGACAATATACCTATGTTCTCAGAAACATATGGACAGTA
1 TTACCTATGTTCTAAAGA-ACATATGGACAGTTTACCTATGTTCTTTGGGACATATGGACAGTA
* *
50921 -TACCTATGTTCTAAAGAACATATGGACAGTTTACCTAGGTTCTTTGGGACCTATGGACAGT
1 TTACCTATGTTCTAAAGAACATATGGACAGTTTACCTATGTTCTTTGGGACATATGGACAGT
50982 TGTCGAGGTT
Statistics
Matches: 99, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
62 44 0.44
63 33 0.33
64 22 0.22
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (63 bp):
TTACCTATGTTCTAAAGAACATATGGACAGTTTACCTATGTTCTTTGGGACATATGGACAGTA
Found at i:50981 original size:31 final size:31
Alignment explanation
Indices: 50792--50982 Score: 170
Period size: 31 Copynumber: 6.1 Consensus size: 31
50782 AGAGTCGAAG
**
50792 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
* *
50823 GAATTACCTATG-TCTTTTGGGACATATGGACA
1 G-TTTACCTATGTTC-TTTGGAACATATGGACA
* *
50855 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 G-TTTACCTATGTTCTTTGGA-ACATATGGACA
* * ** *
50887 ATATACCTATGTTCTCAGAAACATATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
* ***
50918 GTATACCTATGTTCTAAAGAACATATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
* * *
50949 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTATGTTCTTTGGAACATATGGACA
50980 GTT
1 GTT
50983 GTCGAGGTTC
Statistics
Matches: 132, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
31 80 0.61
32 52 0.39
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTTTGGAACATATGGACA
Found at i:55314 original size:21 final size:20
Alignment explanation
Indices: 55284--55343 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
55274 TACTAAAGTT
* *
55284 AGTATCGATACCTAGTTTAG
1 AGTATTGATACCTAGTTAAG
*
55304 AAGTATTGATACTCTAGCTAAG
1 -AGTATTGATAC-CTAGTTAAG
55326 AGTATTGATACCCTAGTT
1 AGTATTGATA-CCTAGTT
55344 CCCTCAGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 25 0.76
22 8 0.24
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (20 bp):
AGTATTGATACCTAGTTAAG
Found at i:55405 original size:20 final size:20
Alignment explanation
Indices: 55369--55419 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
55359 ACCCCTTTTT
*
55369 AGTATCGGTAC-CAAGGGT-
1 AGTATCGATACTCAAGGGTC
55387 AGGTATCGATACTCAAGGGTC
1 A-GTATCGATACTCAAGGGTC
*
55408 AGTACCGATACT
1 AGTATCGATACT
55420 GAATGACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 9 0.32
20 17 0.61
21 1 0.04
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
AGTATCGATACTCAAGGGTC
Found at i:57687 original size:19 final size:19
Alignment explanation
Indices: 57659--57695 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
57649 ATCCATTCGG
57659 GTCAAACTTTAGATTTTTT
1 GTCAAACTTTAGATTTTTT
*
57678 GTCAATCTTTAGATTTTT
1 GTCAAACTTTAGATTTTT
57696 AGATTAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (19 bp):
GTCAAACTTTAGATTTTTT
Found at i:58420 original size:13 final size:14
Alignment explanation
Indices: 58399--58430 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
58389 TAGATTAAAA
58399 AATATAATATTTAT
1 AATATAATATTTAT
58413 AATA-AATATTTAT
1 AATATAATATTTAT
58426 AATAT
1 AATAT
58431 CAAATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATAATATTTAT
Found at i:67707 original size:20 final size:20
Alignment explanation
Indices: 67641--67761 Score: 133
Period size: 19 Copynumber: 6.2 Consensus size: 20
67631 TCAAGAAAAT
*
67641 TAAATCCTCCGGGTCA-TTG
1 TAAAACCTCCGGGTCATTTG
* *
67660 TAAAACATCCGGGTCATTTA
1 TAAAACCTCCGGGTCATTTG
*
67680 TAAAAACCTCCTGGTCATTTG
1 T-AAAACCTCCGGGTCATTTG
*
67701 TAAAACCTCCGGGTTATTT-
1 TAAAACCTCCGGGTCATTTG
*
67720 T-AAATCTCCGGGTCATTTG
1 TAAAACCTCCGGGTCATTTG
* *
67739 TAAAACCTCC-TGTAATTTG
1 TAAAACCTCCGGGTCATTTG
67758 TAAA
1 TAAA
67762 TCATTCAGAT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.18
19 27 0.32
20 26 0.31
21 17 0.20
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (20 bp):
TAAAACCTCCGGGTCATTTG
Found at i:67730 original size:18 final size:19
Alignment explanation
Indices: 67641--67742 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 19
67631 TCAAGAAAAT
67641 TAAATCCTCCGGGTCA-TTG
1 TAAAT-CTCCGGGTCATTTG
* *
67660 TAAAACATCCGGGTCATTTA
1 TAAATC-TCCGGGTCATTTG
* *
67680 TAAAAACCTCCTGGTCATTTG
1 T--AAATCTCCGGGTCATTTG
* *
67701 TAAAACCTCCGGGTTATTT-
1 T-AAATCTCCGGGTCATTTG
67720 TAAATCTCCGGGTCATTTG
1 TAAATCTCCGGGTCATTTG
67739 TAAA
1 TAAA
67743 ACCTCCTGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
18 16 0.23
19 18 0.26
20 19 0.28
21 12 0.17
22 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (19 bp):
TAAATCTCCGGGTCATTTG
Found at i:68024 original size:87 final size:87
Alignment explanation
Indices: 67863--68047 Score: 239
Period size: 87 Copynumber: 2.1 Consensus size: 87
67853 TCATTCGTAA
* * * *
67863 AACCTTCACGGAAGAGTAGTAAAGTAATTCAACCTCGAATCTGATCTTCATGGGAAGTAATGAAA
1 AACCTTCACGGAAGAGTAGTAAAGTAATCCAACCTCAAATCTAATATTCATGGGAAGTAATGAAA
67928 CAGATTCTTC-TCAAGCTAATTC
66 CAGATTCTTCTTC-AGCTAATTC
* * * * *
67950 AACCTTCATGGAAGAGTTGTGAAGTAATCCAACCTCAAATCTAATATTCATGGAGGAGTAGTGAA
1 AACCTTCACGGAAGAGTAGTAAAGTAATCCAACCTCAAATCTAATATTCATGG-GAAGTAATGAA
* *
68015 ACATA-TCTTCTTCAGTTAATTC
65 ACAGATTCTTCTTCAGCTAATTC
68037 AACCTTCACGG
1 AACCTTCACGG
68048 GTAGTGAAGT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 69 0.82
88 15 0.18
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (87 bp):
AACCTTCACGGAAGAGTAGTAAAGTAATCCAACCTCAAATCTAATATTCATGGGAAGTAATGAAA
CAGATTCTTCTTCAGCTAATTC
Found at i:68321 original size:13 final size:14
Alignment explanation
Indices: 68303--68331 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
68293 ATTTATATAC
68303 TATTATAT-ATTAT
1 TATTATATAATTAT
68316 TATTATATAATTAT
1 TATTATATAATTAT
68330 TA
1 TA
68332 CAAGGCCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATATAATTAT
Done.