Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006860.1 Hibiscus syriacus cultivar Beakdansim tig00017451_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: 70621
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:17002 original size:60 final size:59
Alignment explanation
Indices: 16899--17080 Score: 186
Period size: 60 Copynumber: 3.0 Consensus size: 59
16889 GTACCTAAAC
* *
16899 TTTTAAATATTTTAATTTT-ATCCTCAAATTATAACTCCCATTTTAAATCAGTCCTCAAAA
1 TTTT-AATATTTT-ATTTTCATCCTCAAATTATAACTCTCATTTTAAATTAGTCCTCAAAA
* * * *
16959 TTTTGAATATTTTATTTTCATCCTCAAATTATGACTCTTATTTTTTAACTTAGTCCTCAAAC
1 TTTT-AATATTTTATTTTCATCCTCAAATTATAACTCTCA--TTTTAAATTAGTCCTCAAAA
* * * * * * *
17021 TATTTAACATTTCATATTCATCCCCAAAATATAACCCTCATTCTAAATTAGTCCTCAAAA
1 T-TTTAATATTTTATTTTCATCCTCAAATTATAACTCTCATTTTAAATTAGTCCTCAAAA
17081 CGTTTTAGCA
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
59 5 0.05
60 47 0.47
62 45 0.45
63 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (59 bp):
TTTTAATATTTTATTTTCATCCTCAAATTATAACTCTCATTTTAAATTAGTCCTCAAAA
Found at i:17041 original size:62 final size:60
Alignment explanation
Indices: 16918--17080 Score: 159
Period size: 62 Copynumber: 2.7 Consensus size: 60
16908 TTTTAATTTT
* * *
16918 ATCCTCAAATTATAACTCCCATTTTAAATCAGTCCTCAAAATTTTGAATATTTTATTTTC
1 ATCCTCAAATTATAACTCCCATTTTAAATCAGTCCTCAAAATTTTGAACATTTCATATTC
* ** * * *
16978 ATCCTCAAATTATGACTCTTATTTTTTAACTTAGTCCTCAAACTATTT-AACATTTCATATTC
1 ATCCTCAAATTATAACTCCCA--TTTTAAATCAGTCCTCAAAAT-TTTGAACATTTCATATTC
* * * *
17040 ATCCCCAAAATATAAC-CCTCATTCTAAATTAGTCCTCAAAA
1 ATCCTCAAATTATAACTCC-CATTTTAAATCAGTCCTCAAAA
17081 CGTTTTAGCA
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
60 35 0.43
61 1 0.01
62 43 0.52
63 3 0.04
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (60 bp):
ATCCTCAAATTATAACTCCCATTTTAAATCAGTCCTCAAAATTTTGAACATTTCATATTC
Found at i:18815 original size:13 final size:13
Alignment explanation
Indices: 18797--18822 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18787 CGAGTAACTA
18797 CGTATACAAGATG
1 CGTATACAAGATG
18810 CGTATACAAGATG
1 CGTATACAAGATG
18823 TGTGTAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CGTATACAAGATG
Found at i:21926 original size:3 final size:3
Alignment explanation
Indices: 21920--22008 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
21910 TTCTTCTCGC
*
21920 TAT TAT TA- TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21966 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
22009 CTACTACTAC
Statistics
Matches: 82, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
2 6 0.07
3 76 0.93
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:21954 original size:26 final size:27
Alignment explanation
Indices: 21920--22011 Score: 145
Period size: 26 Copynumber: 3.5 Consensus size: 27
21910 TTCTTCTCGC
21920 TATTATTA-TACTATTATTATTATTAT
1 TATTATTATTACTATTATTATTATTAT
*
21946 TATTATTATTATTA-TATTATTATTAT
1 TATTATTATTACTATTATTATTATTAT
*
21972 TATTATTA-TATTATTATTATTATTAT
1 TATTATTATTACTATTATTATTATTAT
21998 TATTATTATTACTA
1 TATTATTATTACTA
22012 CTACTACTAC
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
25 5 0.08
26 48 0.79
27 8 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTATTATTACTATTATTATTATTAT
Found at i:43258 original size:8 final size:8
Alignment explanation
Indices: 43245--43334 Score: 69
Period size: 8 Copynumber: 11.0 Consensus size: 8
43235 AGGGCACTCG
43245 AAAAAAGA
1 AAAAAAGA
*
43253 AAAAAATA
1 AAAAAAGA
43261 AAATGAAA-A
1 AAA--AAAGA
43270 AGAAAAA-A
1 A-AAAAAGA
*
43278 GAAAAAG-
1 AAAAAAGA
43285 AAAAAAGA
1 AAAAAAGA
*
43293 AAAAAGGA
1 AAAAAAGA
43301 AGAAAAAGA
1 A-AAAAAGA
*
43310 AAGAAAGA
1 AAAAAAGA
*
43318 AAGAAAGA
1 AAAAAAGA
43326 AAGAAAAGA
1 AA-AAAAGA
43335 TAGATAAGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
7 11 0.16
8 38 0.56
9 14 0.21
10 5 0.07
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:43269 original size:13 final size:13
Alignment explanation
Indices: 43244--43332 Score: 89
Period size: 12 Copynumber: 6.9 Consensus size: 13
43234 TAGGGCACTC
43244 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
43257 -AATAAAATGAAAAA
1 GAA-AAAA-GAAAAA
43271 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
43284 GAAAAAAG-AAAA
1 GAAAAAAGAAAAA
**
43296 -AAGGAAGAAAAA
1 GAAAAAAGAAAAA
43308 GAAAGAAAG--AAA
1 GAAA-AAAGAAAAA
43320 GAAAGAAAGAAAA
1 GAAA-AAAGAAAA
43333 GATAGATAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
11 5 0.08
12 22 0.34
13 20 0.31
14 15 0.23
15 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:43271 original size:20 final size:20
Alignment explanation
Indices: 43244--43323 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 20
43234 TAGGGCACTC
43244 GAAAAAAGAAAAAA-ATAAAA
1 GAAAAAAGAAAAAAGA-AAAA
43264 TG-AAAAAGAAAAAAGAAAAA
1 -GAAAAAAGAAAAAAGAAAAA
43284 GAAAAAAGAAAAAAGGAAGAAA
1 GAAAAAAGAAAAAA-GAA-AAA
*
43306 -AAGAAAGAAAGAAAGAAA
1 GAAAAAAGAAA-AAAGAAA
43324 GAAAGAAAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
19 1 0.02
20 29 0.55
21 17 0.32
22 6 0.11
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (20 bp):
GAAAAAAGAAAAAAGAAAAA
Found at i:43308 original size:10 final size:10
Alignment explanation
Indices: 43246--43327 Score: 59
Period size: 9 Copynumber: 8.3 Consensus size: 10
43236 GGGCACTCGA
43246 AAAAAGAAA-
1 AAAAAGAAAG
43255 AAAATA-AAATG
1 AAAA-AGAAA-G
43266 AAAAAGAAA-
1 AAAAAGAAAG
43275 AAAGAA-AAAG
1 AAA-AAGAAAG
*
43285 AAAAA-AGA-
1 AAAAAGAAAG
*
43293 AAAAAGGAAG
1 AAAAAGAAAG
43303 AAAAAGAAAG
1 AAAAAGAAAG
43313 AAAGAAAGAAAG
1 -AA-AAAGAAAG
43325 AAA
1 AAA
43328 GAAAAGATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
8 5 0.08
9 18 0.31
10 17 0.29
11 11 0.19
12 8 0.14
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:43314 original size:4 final size:4
Alignment explanation
Indices: 43268--43347 Score: 75
Period size: 4 Copynumber: 21.2 Consensus size: 4
43258 ATAAAATGAA
*
43268 AAAG AAA- AAAG -AA- AAAG AAA- AAAG AAA- AAAG GAAG -AA- AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
43309 AAAG AAAG AAAG AAAG AAAG AAAAG ATAG ATAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG A-AAG AAAG A
43348 GAATAAGGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
3 17 0.27
4 40 0.62
5 7 0.11
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:45435 original size:42 final size:41
Alignment explanation
Indices: 45383--45473 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 41
45373 AGTTGGTAAG
* * * *
45383 TCCTTTGGGTCATCAGTAAGTCTTTCGAGCATGATGTTTAAA
1 TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATG-ATAAA
* *
45425 TCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAG
1 TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGATAAA
45466 TCCTTCGG
1 TCCTTCGG
45474 CCCATGGATA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 11 0.26
42 32 0.74
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGATAAA
Found at i:45460 original size:233 final size:231
Alignment explanation
Indices: 45053--46086 Score: 1276
Period size: 233 Copynumber: 4.4 Consensus size: 231
45043 TTATAAGTTA
* * * * *
45053 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATGGAAATTGTTAAAAAGTAAGGAAAATTTC
1 AAAAATGAGAAAGGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA-GAAAATTTC
* * * * *
45118 TTACATATTAAACTATTTTCAAAATTGGTAAATCCCTCGGGCCATCAGTAAGTCTTTCGAGCATG
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* ** * * *
45183 ATCCTTAAATCCTTCGGGTTGTCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTCCGGGAAGACA
130 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGGAAGACC
* * * *
45248 ATAAGACCTTTGGGTTGGATGTTTTCACATGTATGTCG
195 ATAAGACCTTCGGCTT-GATGTTTTCACATGTCTCTCG
*
45286 AAAAATGAGAAAGGTTTCTTATTTAAATCTGAAAATTAAAATTTTTGAAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAGGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAA-TTTC
* * *
45351 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTTGGGTCATCAGTAAGTCTTTCGAGCATG
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * *
45416 ATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGCCCATG-
130 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGG--GAAGA
* * *
45480 -GATAAGACCTTCGGGTATG-TTTTTTCACATGTCTCTCG
193 CCATAAGACCTTCGGCT-TGATGTTTTCACATGTCTCTCG
* * * *
45518 AAAAATGAGAATGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAATTGCC
1 AAAAATGAGAAAGGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAATT-TC
* * *
45583 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCCTTGGGGCCATCAGTAAGTCTTTCGAACAT
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGT-CCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * *
45648 GATGCATAAATCCTTCGGGTCATCTGCAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGACA-T
129 GATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGGA-AGA
* ** * *
45712 CCATAAGACCTTCAGGCATGATGTTTTCATGTGTCTGTTG
193 CCATAAGACCTTC-GGCTTGATGTTTTCACATGTCTCTCG
* *
45752 AAAAATGAGAAAGGTTT-TTCATTTAAATCTGAAAATTGAAATTTTAGAAAAGTAATAAAAATTT
1 AAAAATGAGAAAGGTTTCTT-ATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA-GAAAATTT
* *
45816 CTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAA
64 CTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * * *
45881 GATGCTTAAATCCTTCGTGTCATCTGTAAGTTTTTCGAGCAAGATAATAAGTCATTC---AAGCC
129 GATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGGAAG--
* * * *
45943 ATCCATAAGACCTCCGGCTAGGATGTTTTCACATGCCTCT-T
192 A-CCATAAGACCTTCGGCT-TGATGTTTTCACATGTCTCTCG
* *
45984 TAAAATAGAGAAAAGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
1 AAAAAT-GAGAAAGGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAA-TTT
* *
46049 TTTACCTAGTAAACCATTTCCAAAATTGGTAAGTCCTT
64 CTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
46087 TATACCATCC
Statistics
Matches: 697, Mismatches: 83, Indels: 42
0.85 0.10 0.05
Matches are distributed among these distances:
229 1 0.00
230 1 0.00
231 3 0.00
232 123 0.18
233 460 0.66
234 101 0.14
235 8 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (231 bp):
AAAAATGAGAAAGGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAATTTCT
TACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGGAAGACCA
TAAGACCTTCGGCTTGATGTTTTCACATGTCTCTCG
Found at i:45924 original size:466 final size:464
Alignment explanation
Indices: 45053--46084 Score: 1426
Period size: 466 Copynumber: 2.2 Consensus size: 464
45043 TTATAAGTTA
* *
45053 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATGGAAATTGTTAAAAAGTAAGGAAAATTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTAAAAAGTAA-GAAAATTTC
* * * * *
45118 TTACATATTAAACTATTTTCAAAATTGGTAAATCCCTCGGGCCATCAGTAAGTCTTTCGAGCATG
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAACATG
* ** * *
45183 ATCCTTAAATCCTTCGGGTTGTCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTCCGGGAAGACA
130 ATCCATAAATCCTTCGGGTCATCTGCAAGTCTTTCAAGCAAGATGATAAGTCCTCCGGGAAGACA
* **
45248 ATAAGACCTTTGGGTTGGATGTTTTCACATGTATGTCGAAAAATGAGAAAGGTTTCTTATTTAAA
195 ATAAGACCTTAGGCATGGATGTTTTCACATGTATGTCGAAAAATGAGAAAGGTTTCTTATTTAAA
* * *
45313 TCTGAAAATTAAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAGTTG
260 TCTGAAAATTAAAATTTTAGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAATTG
* * *
45378 GTAAGTCCTTTGGGTCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
325 GTAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGCTTAAATCCTTCGGGTCATCTGTA
* * * ** * * * *
45443 AGTCTTTCAAGCAAGATGATAAGTCCTTC-GGCCCATGGATAAGACCTTCGGGTATG-TTTTTTC
390 AGTCTTTCAAGCAAGATAATAAGTCATTCAAG-CCATCCATAAGACCTCCGGCTAGGATGTTTTC
*
45506 ACATGTCTCTCG
454 ACATGCCTCT-G
** * *
45518 AAAAATGAGAATGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAATTGCC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTAAAAAGTAAGAAAATT-TC
* *
45583 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCCTTGGGGCCATCAGTAAGTCTTTCGAACAT
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCC-TCGGGCCATCAGTAAGTCTTTCGAACAT
* ** *
45648 GATGCATAAATCCTTCGGGTCATCTGCAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGACA-T
129 GATCCATAAATCCTTCGGGTCATCTGCAAGTCTTTCAAGCAAGATGATAAGTCCTCCGGGA-AGA
* ** * *
45712 CCATAAGACCTTCAGGCAT-GATGTTTTCATGTGTCTGTTGAAAAATGAGAAAGGTTT-TTCATT
193 CAATAAGACCTT-AGGCATGGATGTTTTCACATGTATGTCGAAAAATGAGAAAGGTTTCTT-ATT
* *
45775 TAAATCTGAAAATTGAAATTTTAGAAAAGTAATAAAAATTTCTTACCTAGTAAACTATTTCCAAA
256 TAAATCTGAAAATTAAAATTTTAGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAA
*
45840 ATTGGTAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGCTTAAATCCTTCGTGTCATC
321 ATTGGTAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGCTTAAATCCTTCGGGTCATC
* *
45905 TGTAAGTTTTTCGAGCAAGATAATAAGTCATTCAAGCCATCCATAAGACCTCCGGCTAGGATGTT
386 TGTAAGTCTTTCAAGCAAGATAATAAGTCATTCAAGCCATCCATAAGACCTCCGGCTAGGATGTT
*
45970 TTCACATGCCTCTT
451 TTCACATGCCTCTG
* * *
45984 TAAAATAGAGAAAAGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
1 AAAAAT-GAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTAAAAAGTAAGAAAA-TTT
* *
46049 TTTACCTAGTAAACCATTTCCAAAATTGGTAAGTCC
64 CTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCC
46085 TTTATACCAT
Statistics
Matches: 497, Mismatches: 61, Indels: 16
0.87 0.11 0.03
Matches are distributed among these distances:
464 7 0.01
465 84 0.17
466 301 0.61
467 103 0.21
468 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (464 bp):
AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTAAAAAGTAAGAAAATTTCT
TACCTAGTAAACTATTTCCAAAATTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAACATGA
TCCATAAATCCTTCGGGTCATCTGCAAGTCTTTCAAGCAAGATGATAAGTCCTCCGGGAAGACAA
TAAGACCTTAGGCATGGATGTTTTCACATGTATGTCGAAAAATGAGAAAGGTTTCTTATTTAAAT
CTGAAAATTAAAATTTTAGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAATTGG
TAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGCTTAAATCCTTCGGGTCATCTGTAA
GTCTTTCAAGCAAGATAATAAGTCATTCAAGCCATCCATAAGACCTCCGGCTAGGATGTTTTCAC
ATGCCTCTG
Found at i:46670 original size:134 final size:134
Alignment explanation
Indices: 46441--46795 Score: 478
Period size: 134 Copynumber: 2.6 Consensus size: 134
46431 ATCAAACTTG
*
46441 ATTCAATCTTCCCTAAGTGACATCGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAGTGACATCGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAGAA
* * * * * * *
46506 GAAGCAGAACAGATCTCTCTCTTCCAAGATTTGATATTTCCTGAGTAACATTAGAATAAATCTGC
66 AAAGCGGAACAGATCACTCTCTTCCAAGATTTGATATTCCCTGAATAACAGTAGAACAAATCTGC
46571 CTCA
131 CTCA
* * * * *
46575 ATTCAATCTTCCCTGAGTAATATCGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTTAAGAA
1 ATTCAATCTTCCCTGAGTGACATCGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAGAA
* * * * * *
46640 AAAACGGAACAAATCACTCTCTTCCGAGATTTGATATTCCCTTAATAACAGTGGAACAAGTCTGC
66 AAAGCGGAACAGATCACTCTCTTCCAAGATTTGATATTCCCTGAATAACAGTAGAACAAATCTGC
**
46705 CTTG
131 CTCA
* *
46709 ATTCAATCTTCCCTGGGTGACAGT-GGAATTAATCAACATCCCCATATCTGATTTTCCCTCAAGA
1 ATTCAATCTTCCCTGAGTGACA-TCGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAGA
*
46773 AAAAGCGGAACAGATCCCTCTCT
65 AAAAGCGGAACAGATCACTCTCT
46796 CTTTCAAGAT
Statistics
Matches: 189, Mismatches: 31, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
134 188 0.99
135 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (134 bp):
ATTCAATCTTCCCTGAGTGACATCGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAGAA
AAAGCGGAACAGATCACTCTCTTCCAAGATTTGATATTCCCTGAATAACAGTAGAACAAATCTGC
CTCA
Found at i:46877 original size:94 final size:95
Alignment explanation
Indices: 46708--46886 Score: 254
Period size: 94 Copynumber: 1.9 Consensus size: 95
46698 AGTCTGCCTT
* * *
46708 GATTCAATCTTCCCTGGGTGACAGTGGAATTAATCAACATCCCCATATCTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATATGATTTTCCCTCAAGA
46773 AAAAGCGGAACAGATCCCTCTCTCTTTCAA
66 AAAAGCGGAACAGATCCCTCTCTCTTTCAA
* * ** *
46803 GATTCAATCTTCCCTGAGTGATAGTGGAATGAGTCAATGT-TCCATATATGATTTTCCCTCAA-A
1 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATATGATTTTCCCTCAAGA
*
46866 ACGAAGCGGAACAGATCCCTC
66 A-AAAGCGGAACAGATCCCTC
46887 ACTATATTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
93 2 0.03
94 38 0.51
95 34 0.46
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (95 bp):
GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATATGATTTTCCCTCAAGA
AAAAGCGGAACAGATCCCTCTCTCTTTCAA
Found at i:50750 original size:5 final size:5
Alignment explanation
Indices: 50720--50766 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
50710 TAGTCAGGGT
*
50720 TTTTA TTTT- TATTA TTGTTA -TTTA TTTTA TTTCTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTT-TA TTTTA TTTTA TT
50767 ATTTTTGCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 6 0.17
5 22 0.61
6 8 0.22
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:52624 original size:5 final size:5
Alignment explanation
Indices: 52607--52647 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
52597 GTGACGTTTC
52607 TATTA TA-TA TATTA TATTA TTATTA T-TATA TATTA TATTA T
1 TATTA TATTA TATTA TATTA -TATTA TAT-TA TATTA TATTA T
52648 TAAATTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 5 0.16
5 21 0.66
6 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:52656 original size:23 final size:21
Alignment explanation
Indices: 52607--52649 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
52597 GTGACGTTTC
52607 TATTA-TATATATTATATTAT
1 TATTATTATATATTATATTAT
52627 TATTATTATATATTATATTAT
1 TATTATTATATATTATATTAT
52648 TA
1 TA
52650 AATTATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATTATATATTATATTAT
Found at i:61325 original size:37 final size:37
Alignment explanation
Indices: 61274--61692 Score: 424
Period size: 37 Copynumber: 11.6 Consensus size: 37
61264 CATTCATAGG
* *
61274 ACCTTCACAAAAGAGTAGTAAAGTAATGCCAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
* * * * * *
61311 ACCTTCACGGAAGAGTACTAAAGTGAT-TCAA-TCCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
* *
61346 ACCTTCACAAAAGAGTAGTGAAGTTAAT--CATTTTTCA
1 ACCTTCACAGAAGAGTAGTGAAG-TAATGCCA-ATTTCA
* * * *
61383 ACTTTCACGGAAGAGTAGTGATGTTAAT-CAAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAG-TAATGCCAATTTCA
*
61420 ACCTTCACAAAAGAGTAGTGAAGTAATGCCAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
*
61457 ACCTTCACAAAAGAGTAGTGAAGTAATGCCAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
* *
61494 ACCTTCACAGAAGAGCAGTGAAGCAATGCCAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
* *
61531 ACCTTCATAGAAGAGTAGTGAAGTAATGCAAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
*
61568 ACCTTCACAGAAGAGTACTGAAGTCAAT---AATTCTCA
1 ACCTTCACAGAAGAGTAGTGAAGT-AATGCCAATT-TCA
*
61604 ACCTTCACGGAAGAGTAGTGAAG---T---AA-TTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
*
61634 ACCTTCACAGAAGAGTAGTGAAGTAAAT--C-ATTCTTA
1 ACCTTCACAGAAGAGTAGTGAAGT-AATGCCAATT-TCA
* *
61670 GCCTTCACGGAAGAGTAGTGAAG
1 ACCTTCACAGAAGAGTAGTGAAG
61693 CAAGATCCAA
Statistics
Matches: 329, Mismatches: 39, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
30 25 0.08
31 1 0.00
32 3 0.01
34 2 0.01
35 29 0.09
36 57 0.17
37 208 0.63
38 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (37 bp):
ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
Found at i:61636 original size:30 final size:30
Alignment explanation
Indices: 61564--61659 Score: 120
Period size: 30 Copynumber: 3.0 Consensus size: 30
61554 TAATGCAAAT
*
61564 TTCAACCTTCACAGAAGAGTACTGAAGTCAATAA
1 TTCAACCTTCACAGAAGAGTAGTGAAG----TAA
*
61598 TTCTCAACCTTCACGGAAGAGTAGTGAAGTAA
1 -T-TCAACCTTCACAGAAGAGTAGTGAAGTAA
61630 TTCAACCTTCACAGAAGAGTAGTGAAGTAA
1 TTCAACCTTCACAGAAGAGTAGTGAAGTAA
61660 ATCATTCTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
30 28 0.49
31 1 0.02
32 3 0.05
35 1 0.02
36 24 0.42
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (30 bp):
TTCAACCTTCACAGAAGAGTAGTGAAGTAA
Found at i:61675 original size:66 final size:66
Alignment explanation
Indices: 61564--61692 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 66
61554 TAATGCAAAT
*
61564 TTCAACCTTCACAGAAGAGTACTGAAGTCAATAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
1 TTCAACCTTCACAGAAGAGTACTGAAGTAAATAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
61629 A
66 A
* * * *
61630 TTCAACCTTCACAGAAGAGTAGTGAAGTAAATCATTCTTAGCCTTCACGGAAGAGTAGTGAAG
1 TTCAACCTTCACAGAAGAGTACTGAAGTAAATAATTCTCAACCTTCACGGAAGAGTAGTGAAG
61693 CAAGATCCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (66 bp):
TTCAACCTTCACAGAAGAGTACTGAAGTAAATAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
A
Found at i:61887 original size:5 final size:5
Alignment explanation
Indices: 61870--61916 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
61860 GTGACGTTTC
*
61870 TATTA TA-TA TATTA TATTA TTATTA TATAA TATTA TATTA TTATTA T
1 TATTA TATTA TATTA TATTA -TATTA TATTA TATTA TATTA -TATTA T
61917 TAAATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 4 0.11
5 23 0.62
6 10 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:61892 original size:3 final size:3
Alignment explanation
Indices: 61870--61918 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
61860 GTGACGTTTC
*
61870 TAT TA- TAT ATAT TA- TAT TAT TAT TAT ATAA TAT TA- TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
61914 TAT TA
1 TAT TA
61919 AATTATTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 6 0.15
3 28 0.72
4 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:61904 original size:21 final size:21
Alignment explanation
Indices: 61870--61924 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
61860 GTGACGTTTC
61870 TATTATAT-ATATTATATTAT
1 TATTATATAATATTATATTAT
61890 TATTATATAATATTATATTAT
1 TATTATATAATATTATATTAT
61911 TATTAT-TAA-ATTAT
1 TATTATATAATATTAT
61925 TTACAAGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.15
20 11 0.32
21 18 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTATATAATATTATATTAT
Found at i:67805 original size:14 final size:14
Alignment explanation
Indices: 67786--67812 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
67776 AAGAATTAAA
67786 AATATAATAATAAT
1 AATATAATAATAAT
67800 AATATAATAATAA
1 AATATAATAATAA
67813 CTATTTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATAATAATAAT
Found at i:68614 original size:97 final size:99
Alignment explanation
Indices: 68409--68614 Score: 380
Period size: 97 Copynumber: 2.1 Consensus size: 99
68399 CATCATCATC
* *
68409 ATTTTTAAAAAGAAATACTAGTTATAAACTTTTATAAAATTATTCATATTTTAAATTACTTACCC
1 ATTTTGAAAGAGAAATACTAGTTATAAACTTTTATAAAATTATTCATATTTTAAATTACTTACCC
68474 TCAAAGTTTTCCTATATTAGACTATATATATAGG
66 TCAAAGTTTTCCTATATTAGACTATATATATAGG
68508 ATTTTGAAAGAGAAATACTAGTTATAAACTTTTATAAAATTA-TCATATTTT-AATTACTTACCC
1 ATTTTGAAAGAGAAATACTAGTTATAAACTTTTATAAAATTATTCATATTTTAAATTACTTACCC
68571 TCAAAGTTTTCCTATATTAGACTATATATATAGG
66 TCAAAGTTTTCCTATATTAGACTATATATATAGG
68605 ATTTTGAAAG
1 ATTTTGAAAG
68615 GGTAAAAAAT
Statistics
Matches: 105, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
97 56 0.53
98 9 0.09
99 40 0.38
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (99 bp):
ATTTTGAAAGAGAAATACTAGTTATAAACTTTTATAAAATTATTCATATTTTAAATTACTTACCC
TCAAAGTTTTCCTATATTAGACTATATATATAGG
Done.