Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007818.1 Hibiscus syriacus cultivar Beakdansim tig00110154_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: 290479
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:255295 original size:18 final size:18
Alignment explanation
Indices: 255274--255310 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
255264 GTAATTGGAG
255274 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
255292 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
255310 T
1 T
255311 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:255317 original size:24 final size:24
Alignment explanation
Indices: 255266--255318 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
255256 TTTCATATGT
* * *
255266 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
255290 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
255314 AATTT
1 AATTT
255319 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:255656 original size:39 final size:39
Alignment explanation
Indices: 255613--255699 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
255603 TCCGATGCTC
*
255613 ATCAAAATCCAAAGCTCATATGGTGGCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
255652 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
255691 ATCAAAATC
1 ATCAAAATC
255700 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:255837 original size:20 final size:20
Alignment explanation
Indices: 255810--255859 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
255800 AGTGTCCTTA
255810 GCGTTGCGAAATTGGAAATT-
1 GCGTTGCGAAATTGG-AATTC
*
255830 GGGTTGCGAAATTGGAATTC
1 GCGTTGCGAAATTGGAATTC
255850 GCGTTGCGAA
1 GCGTTGCGAA
255860 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.26, C:0.12, G:0.34, T:0.28
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAATTC
Found at i:256157 original size:23 final size:24
Alignment explanation
Indices: 256107--256157 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
256097 ATATGTCGTA
* *
256107 TATTATTTACGTTATAATCTTATT
1 TATTATTTACATTATAATCTTATG
256131 TATTATTATACATTA-AAT-TTATG
1 TATTATT-TACATTATAATCTTATG
256154 TATT
1 TATT
256158 GAGTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 10 0.42
25 6 0.25
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTATTTACATTATAATCTTATG
Found at i:257496 original size:16 final size:16
Alignment explanation
Indices: 257475--257506 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
257465 TAAGTTTTGA
257475 AGACTAAAACTATTAT
1 AGACTAAAACTATTAT
*
257491 AGACTAAAATTATTAT
1 AGACTAAAACTATTAT
257507 TATATCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (16 bp):
AGACTAAAACTATTAT
Found at i:257773 original size:20 final size:20
Alignment explanation
Indices: 257747--257816 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
257737 CACAGGTTCA
*
257747 AAAATCGTAACGCGAATAGG
1 AAAATCGCAACGCGAATAGG
*
257767 TAAATCGCAACGCGAATAGG
1 AAAATCGCAACGCGAATAGG
*
257787 AAAATCGCAACGCGAATAGT
1 AAAATCGCAACGCGAATAGG
*
257807 AATATCGCAA
1 AAAATCGCAA
257817 TGCTAATTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGAATAGG
Found at i:258156 original size:20 final size:20
Alignment explanation
Indices: 258129--258200 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
258119 AATTTGAAAA
258129 TCGCGTTGCGATTTTACTAT
1 TCGCGTTGCGATTTTACTAT
* *
258149 TCGTGTTGTGATTTTACTAT
1 TCGCGTTGCGATTTTACTAT
*
258169 TCACGTTGCGATTTT-CATAT
1 TCGCGTTGCGATTTTAC-TAT
258189 TCGCGTTGCGAT
1 TCGCGTTGCGAT
258201 AGTACTGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTACTAT
Found at i:258240 original size:57 final size:57
Alignment explanation
Indices: 258172--258314 Score: 252
Period size: 57 Copynumber: 2.5 Consensus size: 57
258162 TTACTATTCA
258172 CGTTGCGATTTTCATATTCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAG
1 CGTTGCGATTTTCATATTCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAG
258229 CGTTGCGATTTT-ACTATTCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAG
1 CGTTGCGATTTTCA-TATTCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAG
* *
258286 CGTTGCGATTTTCCTATTTGCGTTGCGAT
1 CGTTGCGATTTTCATATTCGCGTTGCGAT
258315 TTACCTATTC
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
56 1 0.01
57 81 0.99
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (57 bp):
CGTTGCGATTTTCATATTCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAG
Found at i:258310 original size:20 final size:20
Alignment explanation
Indices: 258285--258337 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
258275 TCGGTAATTA
*
258285 GCGTTGCGATTTTCCTATTT
1 GCGTTGCGATTTTCCTATTC
*
258305 GCGTTGCGATTTACCTATTC
1 GCGTTGCGATTTTCCTATTC
*
258325 GCGTTGTGATTTT
1 GCGTTGCGATTTT
258338 GGAGCTTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (20 bp):
GCGTTGCGATTTTCCTATTC
Found at i:260865 original size:15 final size:17
Alignment explanation
Indices: 260840--260876 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
260830 AAACGTCTTT
260840 TAAAATAA-TTTTAAGA
1 TAAAATAATTTTTAAGA
*
260856 -AAAATCATTTTTAAGA
1 TAAAATAATTTTTAAGA
260872 TAAAA
1 TAAAA
260877 ATTGGTCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (17 bp):
TAAAATAATTTTTAAGA
Found at i:261508 original size:3 final size:3
Alignment explanation
Indices: 261491--261531 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
261481 CTAATTGACT
*
261491 TAA TAA GAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
261532 ATATTGAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:261980 original size:16 final size:16
Alignment explanation
Indices: 261959--261989 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
261949 TTCCCCTTCT
261959 TTTTCATTTCATTTTC
1 TTTTCATTTCATTTTC
261975 TTTTCATTTCATTTT
1 TTTTCATTTCATTTT
261990 TAAAACAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCATTTCATTTTC
Found at i:262559 original size:3 final size:3
Alignment explanation
Indices: 262551--262600 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
262541 ACGATTGGGT
262551 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
262599 TT
1 TT
262601 TTGTGATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:267236 original size:15 final size:16
Alignment explanation
Indices: 267208--267239 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
267198 AAAATCTTTC
267208 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
267224 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
267239 T
1 T
267240 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:268014 original size:16 final size:16
Alignment explanation
Indices: 267990--268023 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
267980 TATCGCCGAC
*
267990 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
268006 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
268022 CG
1 CG
268024 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:270572 original size:81 final size:79
Alignment explanation
Indices: 270394--270681 Score: 238
Period size: 81 Copynumber: 3.6 Consensus size: 79
270384 ACAAACACTG
* * * *
270394 CAATAGAGTAGTACTTTAGTAGCATTTTTATATAAACGCCGCAATAGGTACATGTAGTGGCGTTT
1 CAATAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCGCAATAGGTACATATAGTGGCATTT
*
270459 TTCCATAAACGCCA
66 TTCCACAAACGCCA
* * * * *
270473 CAACAGAGTAGTACTTTAGCGGCATCTTTATACAAACTCCGCAATAGGTCCATCTATAGTGGCAT
1 CAATAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCGCAATAGGTACA--TATAGTGGCAT
**
270538 TTTTTGACAAACGCCA
64 TTTTCCACAAACGCCA
* * * * * * ** * *
270554 TAATAGATTAGTATTTTAGTGGCATTTTTATAAAAATGTCATAATAGGGTTCACCTATAGTGGCT
1 CAATAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCGCAATA-GG-T-ACATATAGTGGCA
* * *
270619 TTTTTCAATC-AATGTCA
63 TTTTTCCA-CAAACGCCA
* * * *
270636 CAACAGATTA-TAACTTTAGCGGCATTTTTACACAAACGCCGCAATA
1 CAATAGAGTAGT-ACTTTAGTGGCATTTTTATACAAACGCCGCAATA
270682 TTTGATAATT
Statistics
Matches: 161, Mismatches: 41, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
79 45 0.28
81 57 0.35
82 56 0.35
83 2 0.01
84 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (79 bp):
CAATAGAGTAGTACTTTAGTGGCATTTTTATACAAACGCCGCAATAGGTACATATAGTGGCATTT
TTCCACAAACGCCA
Found at i:274004 original size:42 final size:42
Alignment explanation
Indices: 273937--274234 Score: 258
Period size: 43 Copynumber: 7.0 Consensus size: 42
273927 TAATTAGCGG
*
273937 CGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGTGA
1 CGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGA
* * * * * *
273980 CATTTTTTCCAAAAACGTCGCTATATATCTTGACATTTTTC-A
1 CGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGA
* * * ** *
274022 GCGTTTGTTTCAAAAATGCCGCTATAGATATCGATTTTTTGCGG
1 -CGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGA
* * * *
274066 CGTTTGTTCCAAAAACGCCGCTATAGATATCGATCTTTTACGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGA
* * * * *
274109 TGTTTGTTCTAAAAAATGTCGTTATAGATCTGACCTTTTGCGA
1 CGTTTGTTC-CAAAAACGCCGCTATAGATCTGACCTTTTGCGA
* * *
274152 CGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGA
* * * *
274195 CGTTTGTT-CAAAAAAGTCGCTATATATCTAACCTTTTGCG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
274235 GCATTATATA
Statistics
Matches: 208, Mismatches: 41, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
41 11 0.05
42 57 0.27
43 124 0.60
44 16 0.08
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (42 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGA
Found at i:274081 original size:86 final size:84
Alignment explanation
Indices: 273934--274234 Score: 307
Period size: 86 Copynumber: 3.5 Consensus size: 84
273924 AGGTAATTAG
* * * * * *
273934 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGTGACATTTTTTCCAAAAACGTC
1 CGGCGTTTGT-TTCAAAAATGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTCCAAAAACGCC
* * *
273999 GCTATATATCTTGACATTTTT
65 GCTATAGATCTCGAC-TTTTA
* * ** *
274020 CAGCGTTTGTTTCAAAAATGCCGCTATAGATATCGATTTTTTGCGGCGTTTGTTCCAAAAACGCC
1 CGGCGTTTGTTTCAAAAATGCCGCTATAGATCT-GACCTTTTGCGACGTTTGTTCCAAAAACGCC
*
274085 GCTATAGATATCGATCTTTTA
65 GCTATAGATCTCGA-CTTTTA
* * * * *
274106 CGGTGTTTGTTCTAAAAAATGTCGTTATAGATCTGACCTTTTGCGACGTTTGTTCAAAAAACGCC
1 CGGCGTTTGTT-TCAAAAATGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTCCAAAAACGCC
* *
274171 GCTATAGATCTCAACCTTTTG
65 GCTATAGATCTCGA-CTTTTA
* * * *
274192 CGGCGTTTG-TTCAAAAAAGTCGCTATATATCTAACCTTTTGCG
1 CGGCGTTTGTTTCAAAAATGCCGCTATAGATCTGACCTTTTGCG
274235 GCATTATATA
Statistics
Matches: 177, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
84 28 0.16
85 21 0.12
86 109 0.62
87 19 0.11
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (84 bp):
CGGCGTTTGTTTCAAAAATGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTCCAAAAACGCCG
CTATAGATCTCGACTTTTA
Found at i:274166 original size:129 final size:128
Alignment explanation
Indices: 273933--274218 Score: 310
Period size: 129 Copynumber: 2.2 Consensus size: 128
273923 AAGGTAATTA
* ** * *
273933 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGTGACATTTTTTCCAAAAACGT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTTACGACATTTGTTCAAAAAACGT
* * * * **
273998 CGCTATATATCTTGACATTTTTCAGCGTTTGTTTCAAAAATGCCGCTATAGATATCGATTTTTT
65 CGCTATAGATCTTGACATTTTGCAGCGTTTGTTTCAAAAACGCCGCTATAGATATCAACCTTTT
* *** *
274062 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATCGATCTTTTACGGTGTTTGTTCTAAAAAATG
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTTACGACATTTGTTC-AAAAAACG
* * *
274127 TCGTTATAGATC-TGACCTTTTGC-GACGTTTG-TTCAAAAAACGCCGCTATAGATCTCAACCTT
64 TCGCTATAGATCTTGACATTTTGCAG-CGTTTGTTTC-AAAAACGCCGCTATAGATATCAACCTT
274189 TT
127 TT
* *
274191 GCGGCGTTTGTT-CAAAAAAGTCGCTATA
1 GCGGCGTTTGTTCCAAAAACGCCGCTATA
274219 TATCTAACCT
Statistics
Matches: 132, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
128 40 0.30
129 76 0.58
130 16 0.12
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (128 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTACGACATTTGTTCAAAAAACGTC
GCTATAGATCTTGACATTTTGCAGCGTTTGTTTCAAAAACGCCGCTATAGATATCAACCTTTT
Found at i:274331 original size:43 final size:43
Alignment explanation
Indices: 274263--274376 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
274253 TTTTGCGGCG
* * * **
274263 TTTGTTCCAAAAAAACGCTGCTATAGATATCGATTTTTTACGGGT
1 TTTGTTCCAAAAACAC-C-GCTATAGATATCGATCTTTTACAGCA
* *
274308 TTTGTTCCAAAAACCCCGCTATAGATATCGATCTTTTGCAGCA
1 TTTGTTCCAAAAACACCGCTATAGATATCGATCTTTTACAGCA
*
274351 TTTGTTCCAAAAACATCGCTATAGAT
1 TTTGTTCCAAAAACACCGCTATAGAT
274377 CTTAACATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
43 45 0.75
44 1 0.02
45 14 0.23
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (43 bp):
TTTGTTCCAAAAACACCGCTATAGATATCGATCTTTTACAGCA
Found at i:278128 original size:2 final size:2
Alignment explanation
Indices: 278121--278170 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
278111 TACTTTCATA
278121 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
278163 AT AT AT AT
1 AT AT AT AT
278171 CTACTTTTTT
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:285901 original size:111 final size:111
Alignment explanation
Indices: 285768--285987 Score: 413
Period size: 111 Copynumber: 2.0 Consensus size: 111
285758 AATAATTACA
285768 AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
1 AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
* *
285833 TTAAAACGTTAAACTGTTACCGTATCAGCAAAGTGTCGAGATATTT
66 TTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATATTT
285879 AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
1 AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
*
285944 TTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
66 TTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
285988 ATGATTTTCA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
AATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAA
TTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATATTT
Found at i:286073 original size:18 final size:19
Alignment explanation
Indices: 286050--286088 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
286040 TTATATTAGT
286050 AAAATA-TTAAATAAAGTA
1 AAAATACTTAAATAAAGTA
*
286068 AAAATACTTAAATAAATTA
1 AAAATACTTAAATAAAGTA
286087 AA
1 AA
286089 TACATAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATACTTAAATAAAGTA
Found at i:286346 original size:50 final size:49
Alignment explanation
Indices: 286292--286400 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 49
286282 AGATACCCAG
* * * * **
286292 GTATAGCGCGAATCAGGGGGCGCGCTATACTCACATGGCGCCAAATCATT
1 GTATAGCGCGAAGCA-GGGGAGCGCTATACCCACATGACGCCAAATCAGC
* * * *
286342 GTATATCACGAGGCAGGGGAGCGCTATACCCACGTGACGCCAAATCAGC
1 GTATAGCGCGAAGCAGGGGAGCGCTATACCCACATGACGCCAAATCAGC
286391 GTATAGCGCG
1 GTATAGCGCG
286401 GTTCAGGACG
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
49 36 0.77
50 11 0.23
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (49 bp):
GTATAGCGCGAAGCAGGGGAGCGCTATACCCACATGACGCCAAATCAGC
Found at i:286472 original size:29 final size:29
Alignment explanation
Indices: 286430--286506 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
286420 CTGCTACGGG
*
286430 TGTTAGATCGGAGAATATAATCTTACTGA
1 TGTTAGATCGGAGAATATAATCTGACTGA
286459 TGTTAGATCGGAGAATATAATCTGACTGA
1 TGTTAGATCGGAGAATATAATCTGACTGA
286488 TGTTAGATCGGTA-AATATA
1 TGTTAGATCGG-AGAATATA
286507 CCGATCACTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 45 0.98
30 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (29 bp):
TGTTAGATCGGAGAATATAATCTGACTGA
Found at i:287510 original size:15 final size:16
Alignment explanation
Indices: 287490--287531 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
287480 ACTATTTTAA
287490 ATATTTTAAAAAAT-T
1 ATATTTTAAAAAATAT
*
287505 ATATTTTATAAAATAT
1 ATATTTTAAAAAATAT
*
287521 ATACTTTAAAA
1 ATATTTTAAAA
287532 TCACTTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTTTAAAAAATAT
Found at i:287771 original size:15 final size:15
Alignment explanation
Indices: 287751--287779 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
287741 AAGTAGTTTA
287751 TCTAATTTTATAATG
1 TCTAATTTTATAATG
287766 TCTAATTTTATAAT
1 TCTAATTTTATAAT
287780 TTTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (15 bp):
TCTAATTTTATAATG
Found at i:287976 original size:22 final size:23
Alignment explanation
Indices: 287934--287978 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
287924 ATAATATTTT
*
287934 TTAATATTTCTAATCAGTTGATG
1 TTAATATTTCTAATCAATTGATG
*
287957 TTAATCTTTC-AATCAATTGATG
1 TTAATATTTCTAATCAATTGATG
287979 ATGTTCAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (23 bp):
TTAATATTTCTAATCAATTGATG
Found at i:289544 original size:17 final size:17
Alignment explanation
Indices: 289522--289574 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
289512 AATTAAAATT
289522 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
289539 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
289556 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
289573 TA
1 TA
289575 ACTTTGTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:289621 original size:17 final size:17
Alignment explanation
Indices: 289580--289626 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
289570 AACTAACTTT
289580 GTTAAATGAAATGCATA
1 GTTAAATGAAATGCATA
* *
289597 GCTGAATGAAATGCATA
1 GTTAAATGAAATGCATA
* *
289614 TTTAAATGCAATG
1 GTTAAATGAAATG
289627 AATGCTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (17 bp):
GTTAAATGAAATGCATA
Done.