Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008367.1 Hibiscus syriacus cultivar Beakdansim tig00111119_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: 73592
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4770 original size:23 final size:23
Alignment explanation
Indices: 4732--4791 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
4722 TTAAATAAAT
4732 AAATAATAAAAAATTTA-TATAA
1 AAATAATAAAAAATTTATTATAA
* *
4754 AAATAATTAAAATATTTATTTTAA
1 AAATAA-TAAAAAATTTATTATAA
4778 AAAT-ATCAAAAAAT
1 AAATAAT-AAAAAAT
4792 GGACATCCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 7 0.22
23 17 0.53
24 8 0.25
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAATAAAAAATTTATTATAA
Found at i:4926 original size:42 final size:46
Alignment explanation
Indices: 4855--4945 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 46
4845 AAATAAAACT
*
4855 AAAATAATATATATAATATATATATATAAT-TTAAAATATTTATGTA
1 AAAATAATATATATAATATATATATATAATAAT-AAATATTTATGTA
*
4901 AAAATAATATATAT-ATA-AT-T-TATAATAATAAATATTTATTTA
1 AAAATAATATATATAATATATATATATAATAATAAATATTTATGTA
4943 AAA
1 AAA
4946 TATATCAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
42 21 0.50
43 2 0.05
44 2 0.05
45 3 0.07
46 14 0.33
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (46 bp):
AAAATAATATATATAATATATATATATAATAATAAATATTTATGTA
Found at i:6732 original size:3 final size:3
Alignment explanation
Indices: 6724--6833 Score: 186
Period size: 3 Copynumber: 36.7 Consensus size: 3
6714 ATTTTTATTA
6724 AAT AAT AAT AAT AAT ATAT AAT AAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
6769 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TTT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6817 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
6834 AACGAAATGA
Statistics
Matches: 101, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.02
3 96 0.95
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:7090 original size:76 final size:76
Alignment explanation
Indices: 6964--7322 Score: 567
Period size: 76 Copynumber: 4.7 Consensus size: 76
6954 GAAATGTTGA
* *
6964 AAACATCATGCACTGAAAGG-CTTACAGATAACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTG-CAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
*
7028 AAGGTTTTTTGG
65 AAGGCTTTTTGG
** *
7040 AAACATCATGCACTGCAGGACTTACAGATGACCCTTAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
7105 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
7116 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCGGG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCC-CG
7181 AAGGCTTTTTGG
65 AAGGCTTTTTGG
** *
7193 AAACATCATGCACTATAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
7258 AGGCTTTTTGG
66 AGGCTTTTTGG
7269 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCA
7323 TGCACTAAAG
Statistics
Matches: 265, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
75 3 0.01
76 176 0.66
77 86 0.32
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:7241 original size:153 final size:152
Alignment explanation
Indices: 6964--7556 Score: 586
Period size: 153 Copynumber: 3.7 Consensus size: 152
6954 GAAATGTTGA
*
6964 AAACATCATGCACTGAAAGG-CTTACAGATAACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTG-AAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
* * **
7028 AAGGTTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTTAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
7093 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
* * * *
7116 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCGGG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCC-CG
* *
7181 AAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
*
7246 AAAAGCTCCTGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
*
7269 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTAAAGG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCA---A--AAA-G
7334 ACTTACAGATGACCCGAAGG--TTTT-GATAACATCATGCACTGA-AGGACTTACAGATGACCCG
59 -----C---T--CCCGAAGGCTTTTTGGA-AACATCATGCACT-ACAGGACTTACAGATGACCCG
* * * * * *
7395 AAGGTTTTGATAACATCATGCACTGAAGGACTTACAGAAGACTCGAAGGTTTT-G
112 AAGGCTTTGA-AA-A-CAT-CA--AAAAG-C-TCCCGAAGGCT------TTTTGG
* * * *
7449 ATAACATCATGCACTGAAGGGCTTACAGATGATCTGAAGGTTTTTGAAAACATAAAAAAGCTCCC
1 A-AACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCC
**
7514 GAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
64 GAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATG
7557 TGGGAAATAG
Statistics
Matches: 374, Mismatches: 27, Indels: 65
0.80 0.06 0.14
Matches are distributed among these distances:
151 3 0.01
152 54 0.14
153 119 0.32
154 13 0.03
157 1 0.00
159 3 0.01
160 1 0.00
165 9 0.02
166 2 0.01
167 78 0.21
168 6 0.02
169 6 0.02
170 6 0.02
171 2 0.01
173 3 0.01
174 1 0.00
175 9 0.02
176 3 0.01
178 1 0.00
180 2 0.01
181 52 0.14
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (152 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:7373 original size:45 final size:45
Alignment explanation
Indices: 7270--7501 Score: 365
Period size: 45 Copynumber: 5.1 Consensus size: 45
7260 GCTTTTTGGA
* *
7270 AACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTTGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAT
*
7316 AACATCATGCACTAAAGGACTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAT
7361 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAT
* *
7406 AACATCATGCACTGAAGGACTTACAGAAGACTCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAT
* * * *
7451 AACATCATGCACTGAAGGGCTTACAGATGATCTGAAGGTTTTTGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAT
7497 AACAT
1 AACAT
7502 AAAAAAGCTC
Statistics
Matches: 173, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 126 0.73
46 47 0.27
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (45 bp):
AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAT
Found at i:8253 original size:22 final size:22
Alignment explanation
Indices: 8228--8304 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
8218 AATAAAGCTT
8228 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
8250 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
8272 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
8294 TCATCTTTGAA
1 TCATCTTTGAA
8305 GAGTGTAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:17180 original size:20 final size:21
Alignment explanation
Indices: 17135--17181 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
17125 TGACAAACAA
*
17135 ATAAATAAAATTTAATACTTG
1 ATAAATAAAATATAATACTTG
17156 A-AAATAAAATA-ATATACTT-
1 ATAAATAAAATATA-ATACTTG
17175 ATAAATA
1 ATAAATA
17182 TTATGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 20 0.87
21 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
ATAAATAAAATATAATACTTG
Found at i:17832 original size:22 final size:24
Alignment explanation
Indices: 17807--17857 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
17797 AATATTAAAT
17807 AAATAA-TAAAACATTTA-TCTAA
1 AAATAATTAAAACATTTATTCTAA
* *
17829 AAATAATTAAAATATTTATTTTAA
1 AAATAATTAAAACATTTATTCTAA
17853 AAATA
1 AAATA
17858 TCAAAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.24
23 10 0.40
24 9 0.36
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATAATTAAAACATTTATTCTAA
Found at i:18807 original size:22 final size:24
Alignment explanation
Indices: 18782--18832 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
18772 TTAAATAAAT
18782 AAATAA-TAAAACATTTATCT-AA
1 AAATAATTAAAACATTTATCTCAA
* *
18804 AAATAATTAAAATATTTATTTCAA
1 AAATAATTAAAACATTTATCTCAA
18828 AAATA
1 AAATA
18833 TCAAAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.24
23 12 0.48
24 7 0.28
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAATTAAAACATTTATCTCAA
Found at i:18838 original size:23 final size:23
Alignment explanation
Indices: 18782--18838 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
18772 TTAAATAAAT
18782 AAATAAT-AAAACATTTATCTAA
1 AAATAATCAAAACATTTATCTAA
* * *
18804 AAATAATTAAAATATTTATTTCAA
1 AAATAATCAAAACATTTATCT-AA
18828 AAAT-ATCAAAA
1 AAATAATCAAAA
18839 AATGGACATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.23
23 17 0.57
24 6 0.20
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAATCAAAACATTTATCTAA
Found at i:18958 original size:46 final size:45
Alignment explanation
Indices: 18905--18998 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
18895 AAATAAAACT
*
18905 AAAATAATATATATATAATATATATATAAT-TTAAAATATTTATGTA
1 AAAATAATATATATAT-ATA-ATATATAATAATAAAATATTTATGTA
* *
18951 AAAATAATATATATATATAATTTATAATAATAAAATATTTATTTA
1 AAAATAATATATATATATAATATATAATAATAAAATATTTATGTA
18996 AAA
1 AAA
18999 TATATTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 8 0.18
45 20 0.45
46 16 0.36
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (45 bp):
AAAATAATATATATATATAATATATAATAATAAAATATTTATGTA
Found at i:19020 original size:970 final size:976
Alignment explanation
Indices: 17320--19269 Score: 3340
Period size: 970 Copynumber: 2.0 Consensus size: 976
17310 CGCCAAGCTG
** *
17320 TCGTAACCGGTTTTCGTCCGGGCACGAATTTTTTACTTGGCGGGAAAAATAATGTAGATAAAAAT
1 TCGTAACCGGTTTTCGTCCGGGCACGAAAATTTTACTCGGCGGGAAAAATAATGTAGATAAAAAT
* *
17385 TGATTTTTGATTTAAAAATATTTTGGGGATCGCCATCGGCCTTTTGGGTCACGTAGGTCGAATAC
66 TGATTTTTGA--TAAAAATATTTTGGGGATCGCCATCGACCTTTTGAGTCACGTAGGTCGAATAC
* *
17450 CTAAAAATTATCTTTTAAAAGAGCTTTTAAGAAAACATCAGTCAAAAGATAAATCGGTCTGCGTT
129 CTAAAAATTATCTTTTAAAAAAGCTTTTAAGAAAACATCAGTCAAAAGATAAATCGATCTGCGTT
* *
17515 TTAACCAAAATTCGTTCTTTTTAATAATAAAAAGGGATTCGTGGTCGTTTACGTTTAGGGAAGGA
194 TTAACCAAAATTCATTCTTTTTAATAATAAAAAGGGATTCGTGGTCGGTTACGTTTAGGGAAGGA
17580 TTAGCACCCCTACAACGCCCAAAATTGGTACTTTATTAATTATAAATTGTCTCTATTATTGGAAA
259 TTAGCACCCCTACAACGCCCAAAATTGGTACTTTATTAATTATAAATTGTCTCTATTATTGGAAA
17645 TTTAAATATTCAAAAATATATTTAATTCATAATTCTTTTATTTCAAATTTATTAATATATTTTTA
324 TTTAAATATTCAAAAATATATTTAATTCATAATTCTTTTATTTCAAATTTATTAATATATTTTTA
*
17710 AGAAAATCTATTAATATATATAAGATATTTATTTATTTATAAATATCAGAAAAGGGCTTCTAGGT
389 AGAAAATCTATTAATATATATAAGATATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTAGGT
17775 GTATCAAGACAGCTCTTTTATTAATATTAAATAAATAATAAAACATTTATCTAAAAATAATTAAA
454 GTATCAAGACAGCTCTTTTATTAATATTAAATAAATAATAAAACATTTATCTAAAAATAATTAAA
*
17840 ATATTTATTTTAAAAATATCAAAAAATGGACATCCAGTTGTTTTAAGACTGCCCTTTCTTAACAT
519 ATATTTATTTCAAAAATATCAAAAAATGGACATCCAGTTGTTTTAAGACTGCCCTTTCTTAACAT
17905 TAAAAATAAATATTAAAATAAAACTAAATAATATATATATATATATAATATATAGATAATTTAAA
584 TAAAAATAAATATTAAAATAAAACT-AATAATATATATATATATATAATATATAGATAATTTAAA
17970 ATATTTATGTAAAAATAATATATATATATAATTTATAATAATAAAATATTTATTTAAAATATATC
648 ATATTTATGTAAAAATAATATATATATATAATTTATAATAATAAAATATTTATTTAAAATATATC
* * *
18035 AGAAAATGAACATCTAGTTGCTTTAAGACTGCATTTTCTTAATATTGAAAATAAATATTATATAT
713 AAAAAATGAACATCTAGTTGCTTTAAGACTGCACTTTATTAATATTGAAAATAAATATTATATAT
*
18100 GGTATTTCATATAAATATTAGTGAATAAAATATAAATAATGACAAACAAATATATAAATAAAGTA
778 GGTATTTCAAATAAATATTAGTGAATAAAATATAAATAATGACAAACAAATATATAAATAAAGTA
*
18165 CTAGTTTAAATATATTGAAAAATAAATTACAATATAGGAATAAAAT-AAATTTTATTAAATAATG
843 CTAGTTTAAATATATTGAAAAATAAATTACAATATAGGAATAAAATAAAATTATATTAAATAATG
*
18229 ACTAAAATGAAATAATTTAAAACTGTGGAATTAAATTATAAATTGAATGGTCAAAAATGAAAGTA
908 ACTAAAACGAAATAATTTAAAACTGTGGAATTAAATTATAAATTGAATGGTCAAAAATGAAAGTA
18294 ATTA
973 ATTA
* * *
18298 TCGTAACCGGTTTTCG-CCTGGGCACGAAAATTTTACTCGGCGGGAAAAGTGATGT-GA-ATAAA
1 TCGTAACCGGTTTTCGTCC-GGGCACGAAAATTTTACTCGGCGGGAAAAATAATGTAGATAAAAA
* *
18360 -TGA-TTTT--T-AAAATATTTTTGGGAGTCGCCATCGACCTTTTTGAGTCAGGTAGGTCGAATA
65 TTGATTTTTGATAAAAATATTTTGGGGA-TCGCCATCGACC-TTTTGAGTCACGTAGGTCGAATA
* * * * * * *
18420 CCTAAAAATTATTTTTTAAAAAAGTTTTTAAGAAAACATCTGTTAAAATATAAATTGATTTGCG-
128 CCTAAAAATTATCTTTTAAAAAAGCTTTTAAGAAAACATCAGTCAAAAGATAAATCGATCTGCGT
18484 TTTAACCAAAAATTCATTCTTTTTAGA-AATAAAAAGGGATTCGTGGTCGGTTACGTTTAGGGAA
193 TTTAACC-AAAATTCATTCTTTTTA-ATAATAAAAAGGGATTCGTGGTCGGTTACGTTTAGGGAA
*
18548 GGATTAGTA-CCCTACAACGCCCAAAATTGGTACTTTATTAATTATAAATTGTCTCTATTATTGG
256 GGATTAGCACCCCTACAACGCCCAAAATTGGTACTTTATTAATTATAAATTGTCTCTATTATTGG
18612 AAATTTAAATATTCAAAAATATATTTAATTCATAATTCTTTTATTTCAAATTTATTAATATATTT
321 AAATTTAAATATTCAAAAATATATTTAATTCATAATTCTTTTATTTCAAATTTATTAATATATTT
*
18677 TTAAGAAAATCTATTAATATATATAAGATATTTATTTATTTAGAAATATCAGAAAAATGGCTTCT
386 TTAAGAAAATCTATTAATATATATAAGATATTTATTTATTTAGAAATATCAG-AAAAGGGCTTCT
18742 AGGTGTATCAAGACAGCTCTTTTATTAATATTAAATAAATAAATAATAAAACATTTATCTAAAAA
450 AGGTGTATCAAGACAGCTCTTTTATTAATA-T---TAAATAAATAATAAAACATTTATCTAAAAA
*
18807 TAATTAAAATATTTATTTCAAAAATATCAAAAAATGGACATCTAGTTGTTTTAAGACTGCCCTTT
511 TAATTAAAATATTTATTTCAAAAATATCAAAAAATGGACATCCAGTTGTTTTAAGACTGCCCTTT
*
18872 CTTAACATTAAAAATAAATATTAAAATAAAACT-A-AA-ATA-ATATATATATAATATATATATA
576 CTTAACATTAAAAATAAATATTAAAATAAAACTAATAATATATATATATATATAATATATAGATA
18933 ATTTAAAATATTTATGTAAAAATAATATATATATATAATTTATAATAATAAAATATTTATTTAAA
641 ATTTAAAATATTTATGTAAAAATAATATATATATATAATTTATAATAATAAAATATTTATTTAAA
*
18998 ATATATTAAAAAAT-AGACATCTAGTTGCTTTAAGACTGCACTTTATTAATATTGAAAATAAATA
706 ATATATCAAAAAATGA-ACATCTAGTTGCTTTAAGACTGCACTTTATTAATATTGAAAATAAATA
*
19062 TTATATATGGTATTTCAAATAAATATTAGTGAATACAATATAAATAATGACAAACAAATATATAA
770 TTATATATGGTATTTCAAATAAATATTAGTGAATAAAATATAAATAATGACAAACAAATATATAA
19127 ATAAAGTACTAGTTTAAATATATTGAAAAATAAATTACAATATAGGAATAAAATAAAATTATATT
835 ATAAAGTACTAGTTTAAATATATTGAAAAATAAATTACAATATAGGAATAAAATAAAATTATATT
19192 AAATAATGACTAAAACGAAATAATTTAAAACTGTGGAATTAAATTATAAATTGAATGGTCAAAAA
900 AAATAATGACTAAAACGAAATAATTTAAAACTGTGGAATTAAATTATAAATTGAATGGTCAAAAA
19257 TGAAAGTAATTA
965 TGAAAGTAATTA
19269 T
1 T
19270 AATATTAGTG
Statistics
Matches: 925, Mismatches: 35, Indels: 31
0.93 0.04 0.03
Matches are distributed among these distances:
969 15 0.02
970 451 0.49
971 266 0.29
972 4 0.00
973 1 0.00
974 4 0.00
975 129 0.14
976 4 0.00
977 4 0.00
978 47 0.05
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (976 bp):
TCGTAACCGGTTTTCGTCCGGGCACGAAAATTTTACTCGGCGGGAAAAATAATGTAGATAAAAAT
TGATTTTTGATAAAAATATTTTGGGGATCGCCATCGACCTTTTGAGTCACGTAGGTCGAATACCT
AAAAATTATCTTTTAAAAAAGCTTTTAAGAAAACATCAGTCAAAAGATAAATCGATCTGCGTTTT
AACCAAAATTCATTCTTTTTAATAATAAAAAGGGATTCGTGGTCGGTTACGTTTAGGGAAGGATT
AGCACCCCTACAACGCCCAAAATTGGTACTTTATTAATTATAAATTGTCTCTATTATTGGAAATT
TAAATATTCAAAAATATATTTAATTCATAATTCTTTTATTTCAAATTTATTAATATATTTTTAAG
AAAATCTATTAATATATATAAGATATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGT
ATCAAGACAGCTCTTTTATTAATATTAAATAAATAATAAAACATTTATCTAAAAATAATTAAAAT
ATTTATTTCAAAAATATCAAAAAATGGACATCCAGTTGTTTTAAGACTGCCCTTTCTTAACATTA
AAAATAAATATTAAAATAAAACTAATAATATATATATATATATAATATATAGATAATTTAAAATA
TTTATGTAAAAATAATATATATATATAATTTATAATAATAAAATATTTATTTAAAATATATCAAA
AAATGAACATCTAGTTGCTTTAAGACTGCACTTTATTAATATTGAAAATAAATATTATATATGGT
ATTTCAAATAAATATTAGTGAATAAAATATAAATAATGACAAACAAATATATAAATAAAGTACTA
GTTTAAATATATTGAAAAATAAATTACAATATAGGAATAAAATAAAATTATATTAAATAATGACT
AAAACGAAATAATTTAAAACTGTGGAATTAAATTATAAATTGAATGGTCAAAAATGAAAGTAATT
A
Found at i:20795 original size:3 final size:3
Alignment explanation
Indices: 20787--20867 Score: 135
Period size: 3 Copynumber: 26.7 Consensus size: 3
20777 ATTTTTATTA
20787 AAT AAT AAT AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
**
20833 AAT AAT AAT AAT TTT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20868 AACGAAATGA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 70 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:24114 original size:32 final size:34
Alignment explanation
Indices: 24053--24115 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
24043 AGGCTTGATT
** *
24053 AAAACTTCTAATATATTTAGGGGTTTAATGAAAA
1 AAAACTTAAAATATATTTAGGGGTCTAATGAAAA
24087 AAAACTTAAAATAT-TTTA-GGGTCTAATGA
1 AAAACTTAAAATATATTTAGGGGTCTAATGA
24116 TTTTTCTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 10 0.38
33 4 0.15
34 12 0.46
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.35
Consensus pattern (34 bp):
AAAACTTAAAATATATTTAGGGGTCTAATGAAAA
Found at i:26236 original size:41 final size:42
Alignment explanation
Indices: 26151--26237 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 42
26141 TTTTCAAGGA
** *
26151 CTTTTGACTCAAAGGACTGATCCCCTAACAAGGGGATCGATC
1 CTTTTGACTCAAAGGACTGATCCCCTAACAAAAGAATCGATC
* * * *
26193 CTTTTGAC-CAAAGGATTGATCCCTTAAGAAAAGAATCGGTC
1 CTTTTGACTCAAAGGACTGATCCCCTAACAAAAGAATCGATC
26234 CTTT
1 CTTT
26238 GAATTTAAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 30 0.79
42 8 0.21
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (42 bp):
CTTTTGACTCAAAGGACTGATCCCCTAACAAAAGAATCGATC
Found at i:27115 original size:3 final size:3
Alignment explanation
Indices: 27107--27180 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
27097 ATTATTGTGA
27107 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27154 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
27181 GATGATGATG
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:27185 original size:3 final size:3
Alignment explanation
Indices: 27179--27216 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
27169 AATAATAATA
*
27179 ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
27217 ATAAACCTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:31613 original size:2 final size:2
Alignment explanation
Indices: 31606--31685 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
31596 ATACATTTAT
31606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31686 ACCGATTAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33221 original size:44 final size:44
Alignment explanation
Indices: 33139--33527 Score: 534
Period size: 44 Copynumber: 8.9 Consensus size: 44
33129 TGTTACCGAA
* * * *
33139 ATAAATGAAAATGCATAAC---GCATTAGTGGCATAAAGGTGTC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTGCC
* *
33180 ATAAATGACAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTGCC
* *
33224 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGTC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTGCC
* * *
33268 ATAAATGAAAATGCATAACGGTGCATTATTAGCAGAAAAGTGAC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTGCC
* * *
33312 ATATATGAAAATGTATAATGATGCATTATTGGCAGAAAAGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTGCC
* * *
33356 ACAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAAGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTGCC
* * *
33400 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTGCC
33444 ATAAATGAAAATGCATAACGATGCATTATTGGCAG-AAAGATGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAG-TGCC
* *
33488 ATAAATGAAAAATGTATAACGATGCATTATTGGGAGAAAA
1 ATAAATG-AAAATGCATAACGATGCATTATTGGCAGAAAA
33528 TGTACCACTC
Statistics
Matches: 313, Mismatches: 29, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
41 18 0.06
43 3 0.01
44 263 0.84
45 26 0.08
46 3 0.01
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTGCC
Found at i:34381 original size:71 final size:70
Alignment explanation
Indices: 34257--34394 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 70
34247 CTCCTTAGAT
** *
34257 CCGTAAGGAATTACCAGTTTGATCAGTCTAACCTATATAAGGAATTATTAGTTTGATTGAGCTGA
1 CCGTAAGGAATTACCAGTTTGATCAGTCTAACCTATATAAGGAATTACCAGTTTGATTAAGCTGA
34322 ACTTA
66 ACTTA
*
34327 CCGTAAGGAATTACCAAG-TTGATCGGTCTGAACCTATATAAGGAATTACCAGTTTGATTAAGCT
1 CCGTAAGGAATTACC-AGTTTGATCAGTCT-AACCTATATAAGGAATTACCAGTTTGATTAAGCT
34391 GAAC
64 GAAC
34395 CTACAGATAC
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 25 0.40
71 37 0.60
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (70 bp):
CCGTAAGGAATTACCAGTTTGATCAGTCTAACCTATATAAGGAATTACCAGTTTGATTAAGCTGA
ACTTA
Found at i:34393 original size:35 final size:35
Alignment explanation
Indices: 34260--34397 Score: 140
Period size: 35 Copynumber: 3.9 Consensus size: 35
34250 CTTAGATCCG
34260 TAAGGAATTACCAGTTTGATCAGTCT-AACCTATA
1 TAAGGAATTACCAGTTTGATCAGTCTGAACCTATA
** * * **
34294 TAAGGAATTATTAGTTTGATTGAG-CTGAACTTACCG
1 TAAGGAATTACCAGTTTGA-TCAGTCTGAACCTA-TA
*
34330 TAAGGAATTACCAAG-TTGATCGGTCTGAACCTATA
1 TAAGGAATTACC-AGTTTGATCAGTCTGAACCTATA
*
34365 TAAGGAATTACCAGTTTGATTAAG-CTGAACCTA
1 TAAGGAATTACCAGTTTGA-TCAGTCTGAACCTA
34398 CAGATACTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
34 21 0.26
35 35 0.43
36 24 0.29
37 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (35 bp):
TAAGGAATTACCAGTTTGATCAGTCTGAACCTATA
Found at i:36044 original size:14 final size:14
Alignment explanation
Indices: 36024--36093 Score: 59
Period size: 14 Copynumber: 5.0 Consensus size: 14
36014 GGTCAAAGTC
*
36024 AACGAGTTGACTCG
1 AACGAGTTGACTCA
* *
36038 GACGAGTTAACTCA
1 AACGAGTTGACTCA
* *
36052 AATGAGTTGACTCG
1 AACGAGTTGACTCA
* * *
36066 GACAAGTTAACTCA
1 AACGAGTTGACTCA
*
36080 AATGAGTTGACTCA
1 AACGAGTTGACTCA
36094 GTCCAGGTTG
Statistics
Matches: 40, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (14 bp):
AACGAGTTGACTCA
Found at i:36058 original size:28 final size:28
Alignment explanation
Indices: 36027--36092 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
36017 CAAAGTCAAC
*
36027 GAGTTGACTCGGACGAGTTAACTCAAAT
1 GAGTTGACTCGGACAAGTTAACTCAAAT
36055 GAGTTGACTCGGACAAGTTAACTCAAAT
1 GAGTTGACTCGGACAAGTTAACTCAAAT
36083 GAGTTGACTC
1 GAGTTGACTC
36093 AGTCCAGGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (28 bp):
GAGTTGACTCGGACAAGTTAACTCAAAT
Found at i:38240 original size:59 final size:59
Alignment explanation
Indices: 38172--38313 Score: 141
Period size: 60 Copynumber: 2.4 Consensus size: 59
38162 GAACACATTC
* *
38172 GGTCCATAAGGTCTTACCCTAGC-CGA-AG-AGTATATGCCTA-CCTGAGGGGAGTGTTCTTA-
1 GGTCCATAAGGTCTTACCCTAGCAC-ATAGCAAT-TATGCC-ACCCTGA-GGGAGT-TCCTTAG
** *
38231 GGTCCATAAGAACTTACCCAAAGCACATAGCAATTATGCCACCCTGAGGGAGTTCCTTAG
1 GGTCCATAAGGTCTTACCC-TAGCACATAGCAATTATGCCACCCTGAGGGAGTTCCTTAG
38291 GGTCCATAAGGTCTTACCACTAG
1 GGTCCATAAGGTCTTACC-CTAG
38314 GCCCATGGGC
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
59 22 0.32
60 29 0.43
61 15 0.22
62 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (59 bp):
GGTCCATAAGGTCTTACCCTAGCACATAGCAATTATGCCACCCTGAGGGAGTTCCTTAG
Found at i:38403 original size:35 final size:36
Alignment explanation
Indices: 38337--38458 Score: 142
Period size: 35 Copynumber: 3.4 Consensus size: 36
38327 CTTAGATCCG
* *
38337 TAAGGAATTATCAGTTCGATC-AGTCTTAACCTACA
1 TAAGGAATTACCAGTTCGATCGAGTCTGAACCTACA
* * *
38372 TAAGGAATTACTAGTTTGATCGAG-CTGAACCTTCCA
1 TAAGGAATTACCAGTTCGATCGAGTCTGAACC-TACA
* * *
38408 TAAGAAATTACCAGTCCGATCG-GTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGAGTCTGAACCTACA
38443 TAAGGAATTACCAGTT
1 TAAGGAATTACCAGTT
38459 TGATTTAGCT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
35 41 0.58
36 30 0.42
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (36 bp):
TAAGGAATTACCAGTTCGATCGAGTCTGAACCTACA
Found at i:38417 original size:36 final size:36
Alignment explanation
Indices: 38337--38472 Score: 129
Period size: 35 Copynumber: 3.8 Consensus size: 36
38327 CTTAGATCCG
* * *
38337 TAAGGAATTATCAGTTCGATC-AGTCTTAACCTA-CA
1 TAAGGAATTACCAGTTTGATCGAG-CTGAACCTATCA
*
38372 TAAGGAATTACTAGTTTGATCGAGCTGAACCT-TCCA
1 TAAGGAATTACCAGTTTGATCGAGCTGAACCTAT-CA
* **
38408 TAAGAAATTACCAGTCCGATCG-GTCTGAACCTAT-A
1 TAAGGAATTACCAGTTTGATCGAG-CTGAACCTATCA
**
38443 TAAGGAATTACCAGTTTGATTTAGCTGAAC
1 TAAGGAATTACCAGTTTGATCGAGCTGAAC
38473 TTGCAGAGAC
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
35 50 0.61
36 31 0.38
37 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (36 bp):
TAAGGAATTACCAGTTTGATCGAGCTGAACCTATCA
Found at i:38492 original size:71 final size:71
Alignment explanation
Indices: 38337--38472 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 71
38327 CTTAGATCCG
* * * * *
38337 TAAGGAATTATCAGTTCGATCAGTCTTAACCTACATAAGGAATTACTAGTTTGATCGAGCTGAAC
1 TAAGAAATTACCAGTCCGATCAGTCTGAACCTACATAAGGAATTACCAGTTTGATCGAGCTGAAC
38402 CTTCCA
66 CTTCCA
* * **
38408 TAAGAAATTACCAGTCCGATCGGTCTGAACCTATATAAGGAATTACCAGTTTGATTTAGCTGAAC
1 TAAGAAATTACCAGTCCGATCAGTCTGAACCTACATAAGGAATTACCAGTTTGATCGAGCTGAAC
38473 TTGCAGAGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (71 bp):
TAAGAAATTACCAGTCCGATCAGTCTGAACCTACATAAGGAATTACCAGTTTGATCGAGCTGAAC
CTTCCA
Found at i:40118 original size:14 final size:14
Alignment explanation
Indices: 40099--40129 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40089 TTAACTTTTC
40099 GGTCAAAGTCAACG
1 GGTCAAAGTCAACG
*
40113 GGTCAAAGTTAACG
1 GGTCAAAGTCAACG
40127 GGT
1 GGT
40130 TGACTCAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.19
Consensus pattern (14 bp):
GGTCAAAGTCAACG
Found at i:41670 original size:2 final size:2
Alignment explanation
Indices: 41663--41721 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
41653 TAATAAAAAT
41663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41705 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
41722 GGGGATGGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42663 original size:144 final size:143
Alignment explanation
Indices: 42401--42679 Score: 357
Period size: 144 Copynumber: 1.9 Consensus size: 143
42391 ATGAAATATC
* * *
42401 TTTCAAGAGAAATAATATTAAGTGCGATAAAATTTTTGTTTCAAGCAAAAAAATATCGATTTTTT
1 TTTCAAGAGAAATAATATCAAGTGAGATAAAATTTTTGTTTCAAGCAAAAAAATATCAATTTTTT
* *
42466 TGTATTTCAAGGGAAAATTCCTCAATCCTAACAAAAAAATTTATTTCAAGGAAAATTGTCTCGAG
66 TGTATTTCAAAGGAAAATTCCTCAATCCTAACAAAAAAATTTATTTCAAGG-AAACTGTCTCGAG
42531 TAAGACAAAAAAAT
130 TAAGACAAAAAAAT
* ** * *
42545 TTTCAAGAGAAACT-ATATCAAGTGAGATAAAATTTTTGTTTCGAGTGAAACAATCTCAATTTTT
1 TTTCAAGAGAAA-TAATATCAAGTGAGATAAAATTTTTGTTTCAAGCAAAAAAATATCAATTTTT
* * * **
42609 TTGTGTTTCAAAGGAAAATTCCTCAA-CC-GACACAAACTTTTAATTTCAAGGGAAACTGTCTCG
65 TTGTATTTCAAAGGAAAATTCCTCAATCCTAACAAAAAAATTT-ATTTCAA-GGAAACTGTCTCG
*
42672 AGTGAGAC
128 AGTAAGAC
42680 GAAATTCGAT
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
142 9 0.08
143 26 0.22
144 80 0.69
145 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (143 bp):
TTTCAAGAGAAATAATATCAAGTGAGATAAAATTTTTGTTTCAAGCAAAAAAATATCAATTTTTT
TGTATTTCAAAGGAAAATTCCTCAATCCTAACAAAAAAATTTATTTCAAGGAAACTGTCTCGAGT
AAGACAAAAAAAT
Found at i:42729 original size:144 final size:143
Alignment explanation
Indices: 42401--42730 Score: 326
Period size: 144 Copynumber: 2.3 Consensus size: 143
42391 ATGAAATATC
* ** * * ** * * *
42401 TTTCAAGAGAAA-TAATATTAAGTGCGATAAAATTTTTGTTTCAAGCAAAAAAATATCGATTTTT
1 TTTCAAGAGAAACT-ATATCAAGTGAAATAAAA-TTATGTTTCGAGTGAAACAATCTCAATTTTT
* *
42465 TTGTATTTCAAGGGAAAATTCCTCAATCCTAACAAAAAAATTTATTTCAAGGAAAATTGTCTCGA
64 TTGTATTTCAAAGGAAAATTCCTCAATCCTAACAAAAAAATTTATTTCAAGGAAAACTGTCTCGA
42530 GTAAGACAAAAAAAT
129 GTAAGACAAAAAAAT
* *
42545 TTTCAAGAGAAACTATATCAAGTGAGATAAAATTTTTGTTTCGAGTGAAACAATCTCAATTTTTT
1 TTTCAAGAGAAACTATATCAAGTGAAATAAAA-TTATGTTTCGAGTGAAACAATCTCAATTTTTT
* * * ** *
42610 TGTGTTTCAAAGGAAAATTCCTCAA-CC-GACACAAACTTTTAATTTCAAGGGAAACTGTCTCGA
65 TGTATTTCAAAGGAAAATTCCTCAATCCTAACAAAAAAATTT-ATTTCAAGGAAAACTGTCTCGA
* ***
42673 GTGAGACGAAATTCGAT
129 GTAAGAC-AAA-AAAAT
* * *
42690 GTTTCGAGGGAAACTATCTCAAGTGAAATAAAA-TATGTTTC
1 -TTTCAAGAGAAACTATATCAAGTGAAATAAAATTATGTTTC
42731 AATAGAAATT
Statistics
Matches: 156, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
142 9 0.06
143 28 0.18
144 88 0.56
145 3 0.02
146 28 0.18
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (143 bp):
TTTCAAGAGAAACTATATCAAGTGAAATAAAATTATGTTTCGAGTGAAACAATCTCAATTTTTTT
GTATTTCAAAGGAAAATTCCTCAATCCTAACAAAAAAATTTATTTCAAGGAAAACTGTCTCGAGT
AAGACAAAAAAAT
Found at i:42788 original size:112 final size:114
Alignment explanation
Indices: 42642--42845 Score: 306
Period size: 112 Copynumber: 1.8 Consensus size: 114
42632 CAACCGACAC
* * *
42642 AAACTTTTAATTTCAAGGGAAACTGTCTCGAGTGAGACGAAATTCGATGTTTCGAGGGAAACTAT
1 AAACTTTTAATTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTCGATGTTTCAAGGGAAACTAT
42707 CTC-AAGTGAAATAAAAT-ATGTTTCAATAGAAATTATATCAAGTGAGAT
66 CTCAAAG-GAAATAAAATAATGTTTCAATAGAAATTATATCAAGTGAGAT
** *
42755 AAACTTTT-ATTTTGAGGGAAAGTGTCTCAAGTGAGACAAAATTCGATGTTTCAAGGGAAACTAT
1 AAACTTTTAATTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTCGATGTTTCAAGGGAAACTAT
* *
42819 CTCAAAGGAGATAAACTAATGTTTCAA
66 CTCAAAGGAAATAAAATAATGTTTCAA
42846 GGGAAAACAA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
112 61 0.75
113 20 0.25
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.30
Consensus pattern (114 bp):
AAACTTTTAATTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTCGATGTTTCAAGGGAAACTAT
CTCAAAGGAAATAAAATAATGTTTCAATAGAAATTATATCAAGTGAGAT
Found at i:42822 original size:39 final size:39
Alignment explanation
Indices: 42652--42823 Score: 156
Period size: 39 Copynumber: 4.5 Consensus size: 39
42642 AAACTTTTAA
* * *
42652 TTTCAAGGGAAACTGTCTCGAGTGAGACGAAATTCGATG
1 TTTCAAGGGAAACTATCTCAAGTGAGACAAAATTCGATG
* * *
42691 TTTCGAGGGAAACTATCTCAAGTGAAATAAAA-T--ATG
1 TTTCAAGGGAAACTATCTCAAGTGAGACAAAATTCGATG
** * * * * **
42727 TTTCAATAGAAATTATATCAAGTGAGATAAACTTTTAT-
1 TTTCAAGGGAAACTATCTCAAGTGAGACAAAATTCGATG
* * *
42765 TTT-GAGGGAAAGTGTCTCAAGTGAGACAAAATTCGATG
1 TTTCAAGGGAAACTATCTCAAGTGAGACAAAATTCGATG
42803 TTTCAAGGGAAACTATCTCAA
1 TTTCAAGGGAAACTATCTCAA
42824 AGGAGATAAA
Statistics
Matches: 102, Mismatches: 26, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
36 28 0.27
37 25 0.25
38 7 0.07
39 42 0.41
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (39 bp):
TTTCAAGGGAAACTATCTCAAGTGAGACAAAATTCGATG
Found at i:54293 original size:3 final size:3
Alignment explanation
Indices: 54285--54342 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
54275 TACGTACTCT
54285 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54333 ATA ATA ATA A
1 ATA ATA ATA A
54343 CTTCTATTGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54415 original size:32 final size:34
Alignment explanation
Indices: 54379--54450 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 34
54369 TTAGCACGTT
***
54379 TAAAAT-T-AAAAACTTCATTTAAGTGTGTAATA
1 TAAAATATGAAAAACTTCATTTAAGTCCCTAATA
*
54411 TAAAATATGATAAACTTCATTTAAGTCCCTAATA
1 TAAAATATGAAAAACTTCATTTAAGTCCCTAATA
54445 TAAAAT
1 TAAAAT
54451 GTATAGGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 6 0.18
33 1 0.03
34 27 0.79
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (34 bp):
TAAAATATGAAAAACTTCATTTAAGTCCCTAATA
Found at i:57024 original size:63 final size:68
Alignment explanation
Indices: 56951--57099 Score: 161
Period size: 63 Copynumber: 2.3 Consensus size: 68
56941 CTATTTATTA
* *
56951 AATATTAAAAGATAATTATAGA-C-TTTGAATATTTCAAATT-AAA-ATAATATT-TA-TTTAAG
1 AATATTAAAAGATAATT-TAAATCTTTTGAATATTTCAAATTAAAAGATAATATTATAGTTTAAA
57010 TTTG
65 TTTG
* * * * *
57014 AATAGTAAAAG-GAGTTTAAATCTTTTGAATATTTTAAATTAAAAGATATTATTATATGTTTAAA
1 AATATTAAAAGATAATTTAAATCTTTTGAATATTTCAAATTAAAAGATAATATTATA-GTTTAAA
57078 TTTG
65 TTTG
57082 AATATTAAAAGAT-ATTTA
1 AATATTAAAAGATAATTTA
57100 GTTAGAGTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
61 3 0.04
62 4 0.06
63 26 0.38
64 3 0.04
65 7 0.10
66 2 0.03
68 23 0.34
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (68 bp):
AATATTAAAAGATAATTTAAATCTTTTGAATATTTCAAATTAAAAGATAATATTATAGTTTAAAT
TTG
Found at i:70051 original size:35 final size:35
Alignment explanation
Indices: 69929--70056 Score: 127
Period size: 35 Copynumber: 3.6 Consensus size: 35
69919 TCTTAGATCC
* * *
69929 ATAAGGAATTACCAGCTC-AGTCGGTCTGAACTTAT
1 ATAAGGAATTACCAGTTCGA-TTGGTCTGAACCTAT
* * *
69964 ATAAGGAATTACTAGTTTGATCTAGT-TGAACCT-T
1 ATAAGGAATTACCAGTTCGAT-TGGTCTGAACCTAT
*
69998 CCGTAAGGAATTACCAGTTCGATTGGTCTGAACCTAT
1 --ATAAGGAATTACCAGTTCGATTGGTCTGAACCTAT
*
70035 ATAAGGAATTACCAGTTTGATT
1 ATAAGGAATTACCAGTTCGATT
70057 AAGCTGGACC
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
34 1 0.01
35 45 0.60
36 28 0.37
37 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTCGATTGGTCTGAACCTAT
Found at i:70068 original size:35 final size:34
Alignment explanation
Indices: 69954--70068 Score: 115
Period size: 35 Copynumber: 3.3 Consensus size: 34
69944 CTCAGTCGGT
* *
69954 CTGAACTTATATAAGGAATTACTAGTTTGATCTAG
1 CTGAACCTATATAAGGAATTACCAGTTTGAT-TAG
* * * *
69989 TTGAACCT-TCCGTAAGGAATTACCAGTTCGATTGG
1 CTGAACCTAT--ATAAGGAATTACCAGTTTGATTAG
70024 TCTGAACCTATATAAGGAATTACCAGTTTGATTAAG
1 -CTGAACCTATATAAGGAATTACCAGTTTGATT-AG
*
70060 CTGGACCTA
1 CTGAACCTA
70069 CAGATACTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
34 1 0.02
35 36 0.56
36 26 0.41
37 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (34 bp):
CTGAACCTATATAAGGAATTACCAGTTTGATTAG
Done.