Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004796.1 Hibiscus syriacus cultivar Beakdansim tig00010807_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: 72991
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:3303 original size:2 final size:2
Alignment explanation
Indices: 3298--3333 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3288 ATATATATAT
3298 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3334 GAAGTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:8878 original size:21 final size:21
Alignment explanation
Indices: 8853--8897 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
8843 CTTTAACTTA
*
8853 AAACCCTAAATTATAAACC-CT
1 AAACCCTAAATCAT-AACCTCT
8874 AAACCCTAAATCATAACCTCT
1 AAACCCTAAATCATAACCTCT
8895 AAA
1 AAA
8898 TTATAAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAATCATAACCTCT
Found at i:16992 original size:23 final size:23
Alignment explanation
Indices: 16924--17025 Score: 93
Period size: 23 Copynumber: 4.5 Consensus size: 23
16914 AAGTATATTT
** *
16924 ATAATATTATGAAATTATTTTTAA
1 ATAATATTATTTAATTA-TTTAAA
16948 AT-AT-TTATTTAATT-TTTAAA
1 ATAATATTATTTAATTATTTAAA
* * *
16968 ATCATATTATTTATTTATTTGAA
1 ATAATATTATTTAATTATTTAAA
* *
16991 ATAATATTAATTAATTATTTCAA
1 ATAATATTATTTAATTATTTAAA
*
17014 ATAATATAATTT
1 ATAATATTATTT
17026 TTAAAATTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 7 0.11
21 2 0.03
22 17 0.27
23 36 0.56
24 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATAATATTATTTAATTATTTAAA
Found at i:17230 original size:24 final size:23
Alignment explanation
Indices: 17184--17269 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 23
17174 ATTTTAAAAT
*
17184 TAAATAAATATTTTTATAATATTA
1 TAAATATAT-TTTTTATAATATTA
17208 TAAATATATTTTTTATAATTATT-
1 TAAATATATTTTTTATAA-TATTA
* * * *
17231 T-CATATAATTTGTATAAAAATATA
1 TAAATATATTTTTTAT-AATAT-TA
17255 TAAAT-TATTTTTTAT
1 TAAATATATTTTTTAT
17270 TTTGAAATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
22 13 0.27
23 13 0.27
24 21 0.43
25 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
TAAATATATTTTTTATAATATTA
Found at i:17294 original size:35 final size:35
Alignment explanation
Indices: 17252--17342 Score: 150
Period size: 34 Copynumber: 2.6 Consensus size: 35
17242 GTATAAAAAT
17252 ATATAAATTATTTTTTATTTTGAAATAAAGTGAAA
1 ATATAAATTATTTTTTATTTTGAAATAAAGTGAAA
17287 ATATAAATTA-TTTTTATTTTGAAATAAAGTGAAA
1 ATATAAATTATTTTTTATTTTGAAATAAAGTGAAA
17321 AT-TAAAATTATTTTTTAATTTT
1 ATAT-AAATTATTTTTT-ATTTT
17343 ACTAACCTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 32 0.60
35 15 0.28
36 5 0.09
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (35 bp):
ATATAAATTATTTTTTATTTTGAAATAAAGTGAAA
Found at i:18989 original size:2 final size:2
Alignment explanation
Indices: 18976--19031 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
18966 ATCCTTCAGG
*
18976 CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19018 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
19032 TCTTCTTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:26468 original size:13 final size:12
Alignment explanation
Indices: 26427--26464 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
26417 CACTTTTATT
26427 AAATA-AAATAA
1 AAATATAAATAA
* *
26438 AAACATAATTAA
1 AAATATAAATAA
26450 AAATATAAATAA
1 AAATATAAATAA
26462 AAA
1 AAA
26465 ATATTATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATATAAATAA
Found at i:26700 original size:6 final size:6
Alignment explanation
Indices: 26689--26752 Score: 119
Period size: 6 Copynumber: 10.7 Consensus size: 6
26679 AGGAGGGAAA
26689 GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG
1 GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG
*
26737 GAAGTG CAAGTG GAAG
1 GAAGTG GAAGTG GAAG
26753 ACGGGTGGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.34, C:0.02, G:0.48, T:0.16
Consensus pattern (6 bp):
GAAGTG
Found at i:27109 original size:26 final size:24
Alignment explanation
Indices: 27058--27103 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
27048 AAAATATCAT
*
27058 TTTTTTAAATATTTTTCGGTTGAA
1 TTTTTTAAATATTTTTCAGTTGAA
27082 TTTTTTATAATA-TTTTCAGTTG
1 TTTTTTA-AATATTTTTCAGTTG
27104 CCAATTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.61
Consensus pattern (24 bp):
TTTTTTAAATATTTTTCAGTTGAA
Found at i:27735 original size:30 final size:31
Alignment explanation
Indices: 27699--27756 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
27689 GAAGGTTTGA
27699 GACT-AAAATATAAAGTTGTAAAAGTTATGT
1 GACTAAAAATATAAAGTTGTAAAAGTTATGT
* *
27729 GACTAAAAATATAAATTTTTAAAAGTTA
1 GACTAAAAATATAAAGTTGTAAAAGTTA
27757 CGTTTTGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.34
Consensus pattern (31 bp):
GACTAAAAATATAAAGTTGTAAAAGTTATGT
Found at i:29828 original size:24 final size:26
Alignment explanation
Indices: 29801--29859 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
29791 GAACTGTTCA
*
29801 TATATGATTTTAT-AA-GAATTGTTT
1 TATATGATTATATGAATGAATTGTTT
29825 TATATTGGATTATATGAATGAATTGTTT
1 TATA-T-GATTATATGAATGAATTGTTT
29853 TAATATG
1 T-ATATG
29860 CAAATTGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 7 0.24
27 3 0.10
28 11 0.38
29 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (26 bp):
TATATGATTATATGAATGAATTGTTT
Found at i:31591 original size:30 final size:30
Alignment explanation
Indices: 31549--31615 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
31539 CACACGATAT
* *
31549 TTTTAAA-ATTTTATTATT-TTTAAATTTT
1 TTTTAAATATTTTAATATTATTTAAATTTC
*
31577 TCTTTAAATATTTTAATATTATTTTAATTTC
1 T-TTTAAATATTTTAATATTATTTAAATTTC
31608 TTTTAAAT
1 TTTTAAAT
31616 TTCAAATATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 6 0.18
30 17 0.52
31 9 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTAAATATTTTAATATTATTTAAATTTC
Found at i:45537 original size:12 final size:11
Alignment explanation
Indices: 45510--45540 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
45500 GTGCGAAGCC
45510 TAAAAAATAGT
1 TAAAAAATAGT
*
45521 TAAAAAATGGT
1 TAAAAAATAGT
45532 TAAAAAATA
1 TAAAAAATA
45541 ATGTGATCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
TAAAAAATAGT
Found at i:46367 original size:182 final size:182
Alignment explanation
Indices: 46049--46504 Score: 723
Period size: 182 Copynumber: 2.5 Consensus size: 182
46039 ACTTTTTTAC
* * * * * *
46049 TATCGGTTTTATCATTTCGATACCGGTTTTGTCATATTTTTACCTTTTATATTATTATTGATCGA
1 TATCAGTTTTGTCATTTCGAAACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
46114 TACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* * *
46179 TGTCGATACTTATAATAAAGTATTAACACTTTCAATATATCCGGTAGTTCTT
131 TGTCGATACTTATAATAAAGTATCAACACTTTCAACATATCCGGTAGCTCTT
* * *
46231 TATTAGTTTTGTCATTTCGAAACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
1 TATCAGTTTTGTCATTTCGAAACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
46296 TACATTTTTATAAAGTATCGACATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* *
46361 TGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTT
131 TGTCGATACTTATAATAAAGTATCAACACTTTCAACATATCCGGTAGCTCTT
* * * *
46413 TATCGGTTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATAGA
1 TATCAGTTTTGTCATTTCGAAACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
46478 TACATTTTTATAAAGTATCGACATTTT
66 TACATTTTTATAAAGTATCGACATTTT
46505 TAATATATCT
Statistics
Matches: 250, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
182 250 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (182 bp):
TATCAGTTTTGTCATTTCGAAACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCAACACTTTCAACATATCCGGTAGCTCTT
Found at i:46573 original size:112 final size:112
Alignment explanation
Indices: 46375--46616 Score: 360
Period size: 112 Copynumber: 2.2 Consensus size: 112
46365 GATACTTATA
* *
46375 ATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTTTATCGGTTTTGTCATTTCGAGACCGGT
1 ATAAAGTATCGACACTTTCAACATATCTGGTAGCGCTTTATCGGTTTTGTCATTTAGAGACCGGT
* *
46440 TTTATCATATTTTTACCTGTTATATTGTTATGGATAGATACATTTTT
66 TTTACCATATTTTTACATGTTATATTGTTATGGATAGATACATTTTT
* * * * *
46487 ATAAAGTATCGACATTTTTAATATATCTGGTAGCGCTTTA-CATGTTTTGTCATTTATAGACCGG
1 ATAAAGTATCGACACTTTCAACATATCTGGTAGCGCTTTATC-GGTTTTGTCATTTAGAGACCGG
* * *
46551 TTTTGCCATTTTTTTGCATGTTATATTGTTATGGATAGATACATTTTT
65 TTTTACCATATTTTTACATGTTATATTGTTATGGATAGATACATTTTT
46599 ATAAAGTATCGACACTTT
1 ATAAAGTATCGACACTTT
46617 ATTGGCGCTA
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
111 1 0.01
112 115 0.99
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAACATATCTGGTAGCGCTTTATCGGTTTTGTCATTTAGAGACCGGT
TTTACCATATTTTTACATGTTATATTGTTATGGATAGATACATTTTT
Found at i:46722 original size:294 final size:294
Alignment explanation
Indices: 46193--46910 Score: 1096
Period size: 294 Copynumber: 2.4 Consensus size: 294
46183 GATACTTATA
** * ** * * ** * *
46193 ATAAAGTATTAACACTTTCAATATATCCGGTAGTTCTTTA-TTAGTTTTGTCATTTCGAAACCGA
1 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTGACAT-GTTTTGTCATTTATAGACCGG
*
46257 TTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTT
65 TTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
46322 TATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGA
130 TATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGA
* * * *
46387 CACTTTCAACATATCTGGTAGCTCTTTATCGGTTTTGTCATTTCGAGACCGGTTTTATCATATTT
195 CACTTTCAACATATCCGGTAGCTCTTTACCAGTTTTGTCATTTCGAGACCAGTTTTATCATATTT
46452 TTACCTGTTATATTGTTATGGATAGATACATTTTT
260 TTACCTGTTATATTGTTATGGATAGATACATTTTT
* * *
46487 ATAAAGTATCGACATTTTTAATATATCTGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTGACATGTTTTGTCATTTATAGACCGGT
* * * *
46552 TTTGCCATTTTTTTGCATGTTATATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* * * * *
46617 ATTGGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGTCGATACTTATAATAAATTATTGAC
131 ATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGAC
* * *
46682 ATTTTTAACATATCCGGTAGCTCTTTACCAGTTTTGTCATTTCGAGACCAGTTTTGTCATATTTT
196 ACTTTCAACATATCCGGTAGCTCTTTACCAGTTTTGTCATTTCGAGACCAGTTTTATCATATTTT
* *
46747 TACCTGTTATATTGTTATGGATCGATATATTTTT
261 TACCTGTTATATTGTTATGGATAGATACATTTTT
*
46781 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTGACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTGACATGTTTTGTCATTTATAGACCGGT
* *
46846 TTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
46911 CAATATATCC
Statistics
Matches: 382, Mismatches: 41, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
294 381 1.00
295 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (294 bp):
ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTGACATGTTTTGTCATTTATAGACCGGT
TTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
ATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGAC
ACTTTCAACATATCCGGTAGCTCTTTACCAGTTTTGTCATTTCGAGACCAGTTTTATCATATTTT
TACCTGTTATATTGTTATGGATAGATACATTTTT
Found at i:46866 original size:112 final size:112
Alignment explanation
Indices: 46669--47012 Score: 537
Period size: 112 Copynumber: 3.1 Consensus size: 112
46659 GATACTTATA
* * * * * * ** *
46669 ATAAATTATTGACATTTTTAACATATCCGGTAGCTCTTTACCAGTTTTGTCATTTCGAGACCAGT
1 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
46734 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
66 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
*
46781 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTGACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
46846 TTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
* * *
46893 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
46958 TTTGTCAT-TTTTTACATGTTATATTGTTATGGATCGATATATTTTT
66 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
47004 ATAAAGTAT
1 ATAAAGTAT
47013 TAACATTTTA
Statistics
Matches: 213, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
111 45 0.21
112 168 0.79
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
Found at i:47155 original size:293 final size:305
Alignment explanation
Indices: 46781--47623 Score: 1039
Period size: 293 Copynumber: 2.8 Consensus size: 305
46771 ATATATTTTT
* *
46781 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTGACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
46846 TTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
*
46911 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTACATG
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTACATG
* * *
46976 TTATATTGTTATGGATCGATATATTTTTATAAAGTATTAACA-TTT-TAT-T-AGCACTATAAC-
196 TTATATTGTTATAGATCAATATATTTTTATAAAGTATCAACACTTTATATATCAGCACTATAACG
47036 TTCT-TC-TCTTTTAAAT-TTCA-AAAG-T-G-TCCATAC-TTATA
261 TTCTGTCATCTTTTAAATGTT-ATAAAGTTGGATCCATACATTATA
* * * * * * ** *
47074 ATAAAGTATCAACACTTACAACATATCCGGTAGCTCTTTATCGGTTTTGTCATTTCGAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
47139 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* * * *
47204 CAATATATCCGATAGCGCTTTACCTATTTTGTCATTTATAGACCAATTTTGTCATTTTTTACTTG
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTACATG
* * * * *
47269 TTATATTGTTATAAATCAAAACATTTTTATAAAGTATCGACACTTTCAATATATCCGGCAGCGCT
196 TTATATTGTTATAGATCAATATATTTTTATAAAGTATCAACACTTT--ATATAT----CAGCACT
* * * * ** ** * * *
47334 TTACCTGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
255 ATAAC-GTTCTGTCA-TCTTTTAAATGTTATAAAG-T-TGGATCCATACATTATA
* *
47389 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTTATAGACTGG
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCA-TTTATAGACCGG
* * * *
47454 TTTTGTCAT-TTTTTACCTGTTATATTGTTATGGTTCAATATATTTTTATAAAGTATCAACACTT
65 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
* * * *
47518 TCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACC
130 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCA-TTTTTTACA
*
47583 TGTTATATTGTTATTGATCAATATATTTTTTATAAAGTATC
194 TGTTATATTGTTATAGATCAATATA-TTTTTATAAAGTATC
47624 GATACAAACC
Statistics
Matches: 462, Mismatches: 62, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
293 213 0.46
294 3 0.01
297 3 0.01
298 1 0.00
303 8 0.02
305 3 0.01
306 2 0.00
308 8 0.02
309 4 0.01
312 1 0.00
313 1 0.00
314 6 0.01
315 148 0.32
316 46 0.10
317 15 0.03
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (305 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTACATG
TTATATTGTTATAGATCAATATATTTTTATAAAGTATCAACACTTTATATATCAGCACTATAACG
TTCTGTCATCTTTTAAATGTTATAAAGTTGGATCCATACATTATA
Found at i:47165 original size:405 final size:406
Alignment explanation
Indices: 46375--47351 Score: 1494
Period size: 405 Copynumber: 2.4 Consensus size: 406
46365 GATACTTATA
* * * * * **
46375 ATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTTTATCGGTTTTGTCATTTCGAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
46440 TTTATCATATTTTTACCTGTTATATTGTTATGGATAGATACATTTTTATAAAGTATCGACATTTT
66 TTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* * * *
46505 TAATATATCTGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTTTGCCATTTTTTTGCAT
131 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGATTTTGCCATTTTTTTACAT
* * *
46570 GTTATATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCT
196 GTTATATTGTTATGGATAGATACATTTTTATAAAGTATCAACACTTTATTAGCACTATAACTTCT
* * * ** * **
46635 TTTCTTTTAAATTCTAAAAGTGTCGATACTTATAATAAATTATTGACATTTTTAACATATCCGGT
261 TCTCTTTTAAATTCTAAAAGTGTCCATACTTATAATAAAGTATCAACACTTACAACATATCCGGT
46700 AGCTCTTTACCAGTTTTGTCATTTCGAGACCAGTTTTGTCATATTTTTACCTGTTATATTGTTAT
326 AGCTCTTTACCAGTTTTGTCATTTCGAGACCAGTTTTGTCATATTTTTACCTGTTATATTGTTAT
*
46765 GGATCGATATATTTTT
391 GGATCGATACATTTTT
* *
46781 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTGACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
46846 TTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
*
46911 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGATTTTGTCA-TTTTTTACAT
131 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGATTTTGCCATTTTTTTACAT
* * * *
46975 GTTATATTGTTATGGATCGATATATTTTTATAAAGTATTAACATTTTATTAGCACTATAACTTCT
196 GTTATATTGTTATGGATAGATACATTTTTATAAAGTATCAACACTTTATTAGCACTATAACTTCT
47040 TCTCTTTTAAATT-TCAAAAGTGTCCATACTTATAATAAAGTATCAACACTTACAACATATCCGG
261 TCTCTTTTAAATTCT-AAAAGTGTCCATACTTATAATAAAGTATCAACACTTACAACATATCCGG
* *
47104 TAGCTCTTTATCGGTTTTGTCATTTCGAGACC-GATTTTGTCATATTTTTACCTGTTATATTGTT
325 TAGCTCTTTACCAGTTTTGTCATTTCGAGACCAG-TTTTGTCATATTTTTACCTGTTATATTGTT
47168 ATGGATCGATACATTTTT
389 ATGGATCGATACATTTTT
* * **
47186 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTATTTTGTCATTTATAGACCAAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * ** * *
47251 TTTGTCAT-TTTTTACTTGTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCGACACTTT
66 TTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
47315 CAATATATCCGGCAGCGCTTTACCTGTTTTGTCATTT
131 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTT
47352 TTTTACCTGT
Statistics
Matches: 521, Mismatches: 48, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
404 88 0.17
405 264 0.51
406 169 0.32
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (406 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGATTTTGCCATTTTTTTACAT
GTTATATTGTTATGGATAGATACATTTTTATAAAGTATCAACACTTTATTAGCACTATAACTTCT
TCTCTTTTAAATTCTAAAAGTGTCCATACTTATAATAAAGTATCAACACTTACAACATATCCGGT
AGCTCTTTACCAGTTTTGTCATTTCGAGACCAGTTTTGTCATATTTTTACCTGTTATATTGTTAT
GGATCGATACATTTTT
Found at i:47311 original size:111 final size:112
Alignment explanation
Indices: 47074--47351 Score: 396
Period size: 111 Copynumber: 2.5 Consensus size: 112
47064 CATACTTATA
* * * * * * * *
47074 ATAAAGTATCAACACTTACAACATATCCGGTAGCTCTTTATCGGTTTTGTCATTTCGAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTAGAGACCAAT
** * *
47139 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATATTTTTACCTGTTATATTGTTATAAATCAAAACATTTTT
* * *
47186 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTATTTTGTCATTTATAGACCAAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTAGAGACCAAT
*
47251 TTTGTCAT-TTTTTACTTGTTATATTGTTATAAATCAAAACATTTTT
66 TTTGTCATATTTTTACCTGTTATATTGTTATAAATCAAAACATTTTT
*
47297 ATAAAGTATCGACACTTTCAATATATCCGGCAGCGCTTTACCTGTTTTGTCATTT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTT
47352 TTTTACCTGT
Statistics
Matches: 147, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
111 85 0.58
112 62 0.42
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTAGAGACCAAT
TTTGTCATATTTTTACCTGTTATATTGTTATAAATCAAAACATTTTT
Found at i:47364 original size:92 final size:92
Alignment explanation
Indices: 47250--47444 Score: 320
Period size: 92 Copynumber: 2.1 Consensus size: 92
47240 TATAGACCAA
*
47250 TTTTGTCA-TTTTTTACTTGTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCGACACTT
1 TTTTGTCATTTTTTTACCTGTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCGACACTT
*
47314 TCAATATATCCGGCAGCGCTTTACCTG
66 TCAATATATCCGACAGCGCTTTACCTG
** * *
47341 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
1 TTTTGTCATTTTTTTACCTGTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCGACACTT
*
47406 TCAATATATCCGATAGCGCTTTACCTG
66 TCAATATATCCGACAGCGCTTTACCTG
47433 TTTTGTCATTTT
1 TTTTGTCATTTT
47445 ATAGACTGGT
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 8 0.08
92 88 0.92
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (92 bp):
TTTTGTCATTTTTTTACCTGTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCGACACTT
TCAATATATCCGACAGCGCTTTACCTG
Found at i:47476 original size:112 final size:112
Alignment explanation
Indices: 47340--47625 Score: 466
Period size: 112 Copynumber: 2.5 Consensus size: 112
47330 CGCTTTACCT
* *
47340 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACACT
*
47405 TTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTTATAGACTG
66 TTCAATATATCCGATAGCGCTTTACCTGTTTTGTCA-TTTATAGACCG
* *
47453 GTTTTGTCA-TTTTTTACCTGTTATATTGTTATGGTTCAATATATTTTTATAAAGTATCAACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACACT
* *
47517 TTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
66 TTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCG
* *
47564 GTTTTATCATTTTTTTACCTGTTATATTGTTATTGATCAATATATTTTTTATAAAGTATCGA
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATA-TTTTTATAAAGTATCGA
47626 TACAAACCGA
Statistics
Matches: 160, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
111 18 0.11
112 117 0.73
113 25 0.16
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (112 bp):
GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACACT
TTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCG
Found at i:47552 original size:204 final size:203
Alignment explanation
Indices: 47138--47555 Score: 701
Period size: 204 Copynumber: 2.1 Consensus size: 203
47128 TCGAGACCGA
*
47138 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
1 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
*
47203 TCAATATATCCGATAGCGCTTTACCTATTTTGTCATTTATAGACCAATTTTGTCATTTTTTACTT
66 TCAATATATCCGATAGCGCTTTACCTATTTTGTCATTTATAGACCAATTTTGTCATTTTTTACCT
*
47268 GTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCGACACTTTCAATATATCCGGCAGCGC
131 GTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCAACACTTTCAATATATCCGGCAGCGC
47333 TTTACCTG
196 TTTACCTG
47341 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
1 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
* ***
47406 TCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTTATAGACTGGTTTTGTCATTTTTTACC
66 TCAATATATCCGATAGCGCTTTACCTATTTTGTCA-TTTATAGACCAATTTTGTCATTTTTTACC
*** * * * *
47471 TGTTATATTGTTATGGTTCAATATATTTTTATAAAGTATCAACACTTTCAATATATCTGGTAGCG
130 TGTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCAACACTTTCAATATATCCGGCAGCG
47536 CTTTACCTG
195 CTTTACCTG
47545 TTTTGTCATTT
1 TTTTGTCATTT
47556 ATAGACCGGT
Statistics
Matches: 200, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
203 98 0.49
204 102 0.51
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (203 bp):
TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
TCAATATATCCGATAGCGCTTTACCTATTTTGTCATTTATAGACCAATTTTGTCATTTTTTACCT
GTTATATTGTTATAAATCAAAACATTTTTATAAAGTATCAACACTTTCAATATATCCGGCAGCGC
TTTACCTG
Found at i:48012 original size:2 final size:2
Alignment explanation
Indices: 48005--48032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47995 CACCCCAAAA
48005 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48033 AGCTGCTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:57751 original size:24 final size:25
Alignment explanation
Indices: 57707--57765 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
57697 TTTTGTCAAT
*
57707 TAAGTTAATAATAAAATATATTTAA
1 TAAGTTAATAATAAAACATATTTAA
* **
57732 TAAGTTAAT-GTAAAACATATTTTT
1 TAAGTTAATAATAAAACATATTTAA
57756 TAAGTTAATA
1 TAAGTTAATA
57766 TATACAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (25 bp):
TAAGTTAATAATAAAACATATTTAA
Done.