Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003141.1 Hibiscus syriacus cultivar Beakdansim tig00006606_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: 66115
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:8275 original size:19 final size:18
Alignment explanation
Indices: 8247--8283 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
8237 TGCGTATCAT
8247 AAAAATAAAAGAAAACAA
1 AAAAATAAAAGAAAACAA
*
8265 AAAAATGAAAAGGAAACAA
1 AAAAAT-AAAAGAAAACAA
8284 GTTAGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAATAAAAGAAAACAA
Found at i:10792 original size:4 final size:4
Alignment explanation
Indices: 10783--10844 Score: 58
Period size: 4 Copynumber: 15.0 Consensus size: 4
10773 AAAATAAAAT
10783 TAAA TAAA TAAA T-AA TAATA TAAA TAAA -ATAA TAAA T-AA TAATA TAAA
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TA-AA TAAA TAAA TAA-A TAAA
10831 TAATA TATAA TAAA
1 TAA-A TA-AA TAAA
10845 AACTATTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
3 7 0.14
4 27 0.54
5 15 0.30
6 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
TAAA
Found at i:10807 original size:12 final size:12
Alignment explanation
Indices: 10785--10840 Score: 82
Period size: 12 Copynumber: 4.8 Consensus size: 12
10775 AATAAAATTA
10785 AATAA-ATAAAT
1 AATAATATAAAT
10796 AATAATATAAAT
1 AATAATATAAAT
10808 AA-AATAATAAAT
1 AATAAT-ATAAAT
10820 AATAATATAAAT
1 AATAATATAAAT
10832 AAT-ATATAA
1 AATAATATAA
10841 TAAAAACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
11 14 0.33
12 25 0.60
13 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:10810 original size:24 final size:25
Alignment explanation
Indices: 10776--10844 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 25
10766 CTGTAGAAAA
10776 ATAA-AAT-TAAATAAATA-AAT-A
1 ATAATAATATAAATAAATATAATAA
10797 ATAAT-A--TAAATAAA-ATAATAA
1 ATAATAATATAAATAAATATAATAA
10818 ATAATAATATAAATAATATATAATAA
1 ATAATAATATAAATAA-ATATAATAA
10844 A
1 A
10845 AACTATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
19 1 0.03
20 11 0.28
21 11 0.28
22 1 0.03
24 7 0.17
25 1 0.03
26 8 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
ATAATAATATAAATAAATATAATAA
Found at i:10936 original size:38 final size:37
Alignment explanation
Indices: 10892--11161 Score: 207
Period size: 37 Copynumber: 7.3 Consensus size: 37
10882 ACAAAAAATA
* *
10892 TATATTATATATGTTTCCAAAAAAGCGTTTTAAAAAAC
1 TATATTATATATGTTTTCAAAAAA-CGTTTTTAAAAAC
10930 TATATTATATATGTTTTCAAAAATAC-TTTTT-AAAAC
1 TATATTATATATGTTTTCAAAAA-ACGTTTTTAAAAAC
* * * *
10966 TATGTATATTATACGTTTTC-AAAAATGTGTTTTTAAAAC
1 TATAT-TA-TATATGTTTTCAAAAAACGT-TTTTAAAAAC
* * *
11005 TATATAATATATGTTTTC-AACAACGTATTTTCAAAAC
1 TATATTATATATGTTTTCAAAAAACGT-TTTTAAAAAC
** *
11042 CGTATTATATA--TTTTCAAAAAATGATTTTTAAAAAC
1 TATATTATATATGTTTTCAAAAAACG-TTTTTAAAAAC
* * *
11078 TATA-TATTATATGCTTTC-AAAAACATTTTCTAAAGAC
1 TATATTA-TATATGTTTTCAAAAAACGTTTT-TAAAAAC
** * *
11115 TATA-TATGATATGTTTTCAAAAAATATTTTCAAAAAT
1 TATATTAT-ATATGTTTTCAAAAAACGTTTTTAAAAAC
*
11152 TACATTATAT
1 TATATTATAT
11162 TATTATATAT
Statistics
Matches: 187, Mismatches: 30, Indels: 31
0.75 0.12 0.12
Matches are distributed among these distances:
35 7 0.04
36 35 0.19
37 80 0.43
38 55 0.29
39 10 0.05
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.43
Consensus pattern (37 bp):
TATATTATATATGTTTTCAAAAAACGTTTTTAAAAAC
Found at i:11015 original size:75 final size:72
Alignment explanation
Indices: 10919--11150 Score: 215
Period size: 73 Copynumber: 3.1 Consensus size: 72
10909 CAAAAAAGCG
* *
10919 TTTTAAAAAACTATATTATATATGTTTTCAAAAATACTTTTTAAAACTATGTATATTATACGTTT
1 TTTTTAAAAACTATATAATATATGTTTTCAAAAATA-TTTTTAAAACTA-GTATATTATA-GTTT
10984 TCAAAAATG-
63 TCAAAAATGA
* * * *
10993 TGTTTTTAAAACTATATAATATATGTTTTCAACAACGTATTTTCAAAAC-CGTAT-TATATA-TT
1 T-TTTTAAAAACTATATAATATATGTTTTCAA-AA-ATATTTTTAAAACTAGTATAT-TATAGTT
11055 TTCAAAAAATGA
62 TTC-AAAAATGA
* * * *
11067 TTTTTAAAAACTATATATTATATGCTTTCAAAAACATTTTCTAAAGACTA-TATATGATATGTTT
1 TTTTTAAAAACTATATAATATATGTTTTCAAAAATATTTT-TAAA-ACTAGTATATTATA-GTTT
11131 TCAAAAAAT-A
63 TC-AAAAATGA
*
11141 TTTTCAAAAA
1 TTTTTAAAAA
11151 TTACATTATA
Statistics
Matches: 131, Mismatches: 15, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
71 5 0.04
72 10 0.08
73 43 0.33
74 21 0.16
75 39 0.30
76 11 0.08
77 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (72 bp):
TTTTTAAAAACTATATAATATATGTTTTCAAAAATATTTTTAAAACTAGTATATTATAGTTTTCA
AAAATGA
Found at i:11087 original size:110 final size:109
Alignment explanation
Indices: 10932--11149 Score: 266
Period size: 110 Copynumber: 2.0 Consensus size: 109
10922 TAAAAAACTA
* **
10932 TATTATATATGTTTTCAAAAATACTTTTTAAAACTATGTATATTATACGTTTTCAAAAATGTGTT
1 TATTATATA-GTTTTCAAAAATACTTTTTAAAACTA-GTATATTATACGCTTTCAAAAACAT-TT
* **
10997 TTTAAA-ACTATATAAT-ATATGTTTTCAACAACGTATTTTCAAAACCG
63 TCTAAAGACTATAT-ATGATATGTTTTCAA-AAAATATTTTCAAAACCG
*
11044 TATTATATA-TTTTCAAAAAATGA-TTTTTAAAAACTA-TATATTATATGCTTTCAAAAACATTT
1 TATTATATAGTTTTC-AAAAAT-ACTTTTT-AAAACTAGTATATTATACGCTTTCAAAAACATTT
11106 TCTAAAGACTATATATGATATGTTTTCAAAAAATATTTTCAAAA
63 TCTAAAGACTATATATGATATGTTTTCAAAAAATATTTTCAAAA
11150 ATTACATTAT
Statistics
Matches: 94, Mismatches: 7, Indels: 13
0.82 0.06 0.11
Matches are distributed among these distances:
109 22 0.23
110 44 0.47
111 11 0.12
112 17 0.18
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (109 bp):
TATTATATAGTTTTCAAAAATACTTTTTAAAACTAGTATATTATACGCTTTCAAAAACATTTTCT
AAAGACTATATATGATATGTTTTCAAAAAATATTTTCAAAACCG
Found at i:11096 original size:73 final size:73
Alignment explanation
Indices: 10899--11150 Score: 205
Period size: 75 Copynumber: 3.4 Consensus size: 73
10889 ATATATATTA
* * * * * *
10899 TATATGTTTCCAAAAAA-GCGTTTTAAAAAACTATATTATATATGTTTTCAAAAATACTTTT-TA
1 TATATGTTTTCAAAAAATG-ATTTTTAAAAACTATATAATATATGCTTTCAAAAACA-TTTTCTA
*
10962 AA-ACTATGTATAT
64 AAGAC----CATAT
* * * *
10975 TATACGTTTTC-AAAAATG-TGTTTTTAAAACTATATAATATATGTTTTCAACAACGTATTTTC-
1 TATATGTTTTCAAAAAATGAT-TTTTAAAAACTATATAATATATGCTTTCAAAAAC--ATTTTCT
*
11037 AAA-ACCGTAT
63 AAAGACCATAT
* *
11047 TATATATTTTCAAAAAATGATTTTTAAAAACTATATATTATATGCTTTCAAAAACATTTTCTAAA
1 TATATGTTTTCAAAAAATGATTTTTAAAAACTATATAATATATGCTTTCAAAAACATTTTCTAAA
*
11112 GACTATAT
66 GACCATAT
*
11120 ATGATATGTTTTCAAAAAAT-ATTTTCAAAAA
1 -T-ATATGTTTTCAAAAAATGATTTTTAAAAA
11151 TTACATTATA
Statistics
Matches: 146, Mismatches: 19, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
71 6 0.04
72 15 0.10
73 42 0.29
74 13 0.09
75 50 0.34
76 19 0.13
77 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (73 bp):
TATATGTTTTCAAAAAATGATTTTTAAAAACTATATAATATATGCTTTCAAAAACATTTTCTAAA
GACCATAT
Found at i:11159 original size:110 final size:108
Alignment explanation
Indices: 10892--11161 Score: 262
Period size: 110 Copynumber: 2.4 Consensus size: 108
10882 ACAAAAAATA
* ** *
10892 TATATTATATATGTTTCCAAAAAAGCGTTTTAAAAAACTATATTATATATGTTTTCAAAAATACT
1 TATA-TATATATGTTTTCAAAAAA-TATTTTCAAAAACTA-ATTATATA-GTTTTCAAAAATACT
* ** *
10957 TTTTAAAACTATGTATATTATACGTTTTCAAAAATGTGTTTTTAAAAC
62 TTTTAAAACTA-GTATATTATACGCTTTCAAAAACATGTTTCTAAAAC
** *
11005 TATATAATATATGTTTTCAACAACGTATTTTCAAAACCGT-ATTATATA-TTTTCAAAAAATGA-
1 TATAT-ATATATGTTTTCAA-AAAATATTTTCAAAAAC-TAATTATATAGTTTTC-AAAAAT-AC
*
11067 TTTTTAAAAACTA-TATATTATATGCTTTCAAAAACAT-TTTCTAAAGAC
61 TTTTT-AAAACTAGTATATTATACGCTTTCAAAAACATGTTTCTAAA-AC
*
11115 TATATATGATATGTTTTCAAAAAATATTTTCAAAAATTACATTATAT
1 TATATAT-ATATGTTTTCAAAAAATATTTTCAAAAACTA-ATTATAT
11162 TATTATATAT
Statistics
Matches: 131, Mismatches: 16, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
108 1 0.01
109 22 0.17
110 51 0.39
111 11 0.08
112 17 0.13
113 26 0.20
114 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.43
Consensus pattern (108 bp):
TATATATATATGTTTTCAAAAAATATTTTCAAAAACTAATTATATAGTTTTCAAAAATACTTTTT
AAAACTAGTATATTATACGCTTTCAAAAACATGTTTCTAAAAC
Found at i:14263 original size:2 final size:2
Alignment explanation
Indices: 14256--14290 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14246 TTTCGAAAAC
14256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14291 TCAAAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15040 original size:114 final size:114
Alignment explanation
Indices: 14829--15163 Score: 335
Period size: 114 Copynumber: 2.9 Consensus size: 114
14819 TTCTTATTAT
* * *
14829 GAACTTCTTCTATTTCATCGGATTAGTTCTTCTCATTATGAACCCTGCCATCATAAATGTTGACC
1 GAACTTCTTCTATCTCATCGGATGAGTTCTTCTCATTATGAACCCTGCAATCATAAATGTTGACC
* *
14894 CAACTCCTTTATGTGAAGGATGAACCTAGGTTGAACAAGTTCTCACTAG
66 CAACTCCTTTATGTGAAGGACGAACCTAGGTTGAACAAGTTCTCACTAC
* *
14943 GAACTTCTTCTATCTCATCGGATGAGTTCTTCTCATTATGAACCCTGTCAATGA-AAATGTTCGG
1 GAACTTCTTCTATCTCATCGGATGAGTTCTTCTCATTATGAACCCTG-CAATCATAAATGTT-GA
* * * * * *
15007 CCCACCAT-CTTCT-T-TGATA-GCCG-AGCTAGGGTTGAATAAGTTCTTATTAC
64 CCCAAC-TCCTT-TATGTGA-AGGACGAACCTA-GGTTGAACAAGTTCTCACTAC
* * * * * * * *
15057 GACCTTGTTCTCTCTCATCAGACGAGTTCTTCTCATTATGAACCCCT-CCATTATAAATGTTGAT
1 GAACTTCTTCTATCTCATCGGATGAGTTCTTCTCATTATGAA-CCCTGCAATCATAAATGTTGAC
* * *
15121 CCAACT-CTTTATATGAAGGATGAATCTAGGTTGAACAAGTTCT
65 CCAACTCCTTTATGTGAAGGACGAACCTAGGTTGAACAAGTTCT
15164 TCTCATTATG
Statistics
Matches: 182, Mismatches: 27, Indels: 25
0.78 0.12 0.11
Matches are distributed among these distances:
111 1 0.01
112 6 0.03
113 32 0.18
114 122 0.67
115 19 0.10
116 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (114 bp):
GAACTTCTTCTATCTCATCGGATGAGTTCTTCTCATTATGAACCCTGCAATCATAAATGTTGACC
CAACTCCTTTATGTGAAGGACGAACCTAGGTTGAACAAGTTCTCACTAC
Found at i:16432 original size:20 final size:20
Alignment explanation
Indices: 16366--16432 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
16356 TTGAACCCTC
* *
16366 TTTTTATTTTTCTT-TATCT
1 TTTTTCTTTTTCTTATTTCT
16385 TTTTATCTTTTT-TTCA-TTCAT
1 TTTT-TCTTTTTCTT-ATTTC-T
*
16406 TTCTTCTTTTTCTTATTTCT
1 TTTTTCTTTTTCTTATTTCT
16426 TTTTTCT
1 TTTTTCT
16433 GTAAGCGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
19 6 0.16
20 23 0.61
21 9 0.24
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTCTTTTTCTTATTTCT
Found at i:22779 original size:64 final size:64
Alignment explanation
Indices: 22697--22854 Score: 162
Period size: 63 Copynumber: 2.5 Consensus size: 64
22687 TTCAAGGTGT
* ** *
22697 ATCGATGCA-CATGAAGTGCATCGATGCACTCTGATAAAACAAAAACATCGAATGCCATT-AGTG
1 ATCGATGCATAATGAAGTGCATCGATGCAC-CCCATAAAACAAAAACATCGAATACCATTCA-TG
22760 C
64 C
* * * **
22761 ATCGATGCATAATG-AGTGCATCGATGCACCCCATTAAATACAAACATCGAATATGATTCATGC
1 ATCGATGCATAATGAAGTGCATCGATGCACCCCATAAAACAAAAACATCGAATACCATTCATGC
* * *
22824 ACCGATGCATAA-GTAGTGCATCGATGTACCC
1 ATCGATGCATAATGAAGTGCATCGATGCACCC
22855 GTTAAGGAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.01
63 51 0.64
64 25 0.31
65 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (64 bp):
ATCGATGCATAATGAAGTGCATCGATGCACCCCATAAAACAAAAACATCGAATACCATTCATGC
Found at i:23440 original size:22 final size:21
Alignment explanation
Indices: 23415--23480 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
23405 GAGGTCTTTT
23415 GGGATGTATTCAGTGGTCCTTC
1 GGGA-GTATTCAGTGGTCCTTC
* *
23437 GGGACGTGTCCAGTGGTCCTTC
1 GGGA-GTATTCAGTGGTCCTTC
23459 GGGA-TA-T-AGTGGTCCTTC
1 GGGAGTATTCAGTGGTCCTTC
23477 GGGA
1 GGGA
23481 CAAATACTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 15 0.38
20 1 0.03
22 23 0.59
ACGTcount: A:0.14, C:0.20, G:0.36, T:0.30
Consensus pattern (21 bp):
GGGAGTATTCAGTGGTCCTTC
Found at i:26670 original size:266 final size:255
Alignment explanation
Indices: 26159--26746 Score: 781
Period size: 266 Copynumber: 2.2 Consensus size: 255
26149 CTTATTCATA
* *
26159 TATTGAATAAAAATATTTTTTTATTATTTCAGGTCGGATCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCAGGTCGGGTCGGGTTTCTAATTCATATATTCAGGT
* *
26224 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTGGGTTGGTTTTTTTAAGTGTGATATTCA
66 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTTGCG-TGGTTTTTTTAAGTGTGATATTCA
** * * *
26289 GGTCGGGCCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATAT
130 GGTCGGGCCAAGTTTAGGGTGAAAAAAACCCGACCCAAAAAAATATATAATTTTACCTTATATAT
* *
26354 TTAGGAATAATTACAATAATACCCCTCTATATATATTGTTTTTCAATTAAGTCACTGTTTT
195 TTAGGAATAATTACAATAATACCCCTATATATATATTGTTTTTCAATTAAGTCAATGTTTT
* *
26415 TATTGAATAAAAATATTTTTTTATTATTTCAGGTCGGGTTGGATTTCTAATTCATATATTCAGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCAGGTCGGGTCGGGTTTCTAATTCATATATTCAGGT
* *
26480 TGGGTCGGGTGAAACTTTATTTTGTTCGGGTCAGG-T-CG-GG-TTTTTTAAGTGTGATATTTGG
66 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTTGCGTGGTTTTTTTAAGTGTGATA--T--
*
26541 GTCGAGTCTGGTCGGGTTCAAGTTTAGGGTGAAAAAAACGGGACCGACCCAAAAAAATATATAAT
127 -TC-A----GGTCGGG-CCAAGTTTAGGGTGAAAAAAAC----CCGACCCAAAAAAATATATAAT
26606 TTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATAATT-TTTTTCAATTAA
181 TTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATAT-ATTGTTTTTCAATTAA
26670 GTCAATGTTTT
245 GTCAATGTTTT
*
26681 TATTGAATAAAAATAATTTTTTTATTATTTTGTGTCATGTCGGGTCGGGTTTCTAATTCATATAT
1 TATTGAATAAAAAT-ATTTTTTTATTA---T-T-TCAGGTCGGGTCGGGTTTCTAATTCATATAT
26746 T
60 T
26747 GAATAAAAAT
Statistics
Matches: 291, Mismatches: 19, Indels: 28
0.86 0.06 0.08
Matches are distributed among these distances:
251 16 0.05
252 2 0.01
253 1 0.00
254 1 0.00
255 1 0.00
256 95 0.33
257 1 0.00
261 7 0.02
262 18 0.06
266 103 0.35
267 15 0.05
270 1 0.00
271 1 0.00
272 29 0.10
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (255 bp):
TATTGAATAAAAATATTTTTTTATTATTTCAGGTCGGGTCGGGTTTCTAATTCATATATTCAGGT
CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTTGCGTGGTTTTTTTAAGTGTGATATTCAG
GTCGGGCCAAGTTTAGGGTGAAAAAAACCCGACCCAAAAAAATATATAATTTTACCTTATATATT
TAGGAATAATTACAATAATACCCCTATATATATATTGTTTTTCAATTAAGTCAATGTTTT
Found at i:28384 original size:43 final size:43
Alignment explanation
Indices: 28334--28454 Score: 134
Period size: 43 Copynumber: 2.8 Consensus size: 43
28324 AAAGTCTTGC
** *
28334 TCTTTAGCGATGTTTTAGACACAAATGCTGCGAAAGTTCAAGT
1 TCTTTAGCGGCGTTTTAGACACAAACGCTGCGAAAGTTCAAGT
* * * * * * * *
28377 TCTTTAGCGGCATTTTAGACGCTAACACCGTGAAATTTCAGGT
1 TCTTTAGCGGCGTTTTAGACACAAACGCTGCGAAAGTTCAAGT
*
28420 TCTTTAGCGGCGTTTTAGAGACAAACGCTGCGAAA
1 TCTTTAGCGGCGTTTTAGACACAAACGCTGCGAAA
28455 TGTAAGAAAT
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTTAGACACAAACGCTGCGAAAGTTCAAGT
Found at i:28626 original size:48 final size:49
Alignment explanation
Indices: 28568--28726 Score: 169
Period size: 60 Copynumber: 3.0 Consensus size: 49
28558 ACTGAAATGT
*
28568 AACGTAGTTCACCAGTGTTCACTAGTAGAAACAAAACATTAACCTAAGA
1 AACGTAGTTCACCATTGTTCACTAGTAGAAACAAAACATTAACCTAAGA
* *
28617 AACG-AGTTCACCATTGTTCACTAGTAGAAACAAAGTTTACA-AACATCCAACTGAAATGT
1 AACGTAGTTCACCATTGTTCACTAGTAGAAACAAA----ACATTA-A--C--CT--AA-GA
28676 AACGTAGTTCACCATTGTTCACTAGTAGAAACAAAACATTAACCTAAGA
1 AACGTAGTTCACCATTGTTCACTAGTAGAAACAAAACATTAACCTAAGA
28725 AA
1 AA
28727 TCACCTAAGA
Statistics
Matches: 91, Mismatches: 5, Indels: 28
0.73 0.04 0.23
Matches are distributed among these distances:
48 29 0.32
49 7 0.08
50 2 0.02
51 1 0.01
52 6 0.07
54 2 0.02
56 6 0.07
57 1 0.01
58 2 0.02
59 5 0.05
60 30 0.33
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (49 bp):
AACGTAGTTCACCATTGTTCACTAGTAGAAACAAAACATTAACCTAAGA
Found at i:32495 original size:24 final size:22
Alignment explanation
Indices: 32466--32514 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
32456 AATTACTATT
* *
32466 ATATTTATTTATGAATATATAAAA
1 ATATTTATTCAT-AA-AAATAAAA
32490 ATATTTATTCATAAAAATAAAA
1 ATATTTATTCATAAAAATAAAA
32512 ATA
1 ATA
32515 CTATTAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 2 0.09
24 11 0.48
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATTTATTCATAAAAATAAAA
Found at i:33933 original size:3 final size:3
Alignment explanation
Indices: 33918--34003 Score: 102
Period size: 3 Copynumber: 29.0 Consensus size: 3
33908 TTAATATATT
* * * *
33918 TAA TAA -AA AAA TAA TAA TAA TAA TAA AAA TAA TAA TGA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
33965 TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34004 AATGGATAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:34011 original size:12 final size:11
Alignment explanation
Indices: 33920--34017 Score: 55
Period size: 12 Copynumber: 8.9 Consensus size: 11
33910 AATATATTTA
* *
33920 ATAAAAAAATA
1 ATAATAAAATG
*
33931 ATAATAATAATA
1 ATAATAA-AATG
*
33943 AAAATAATAATG
1 ATAATAA-AATG
*
33955 ATAATAATAT-
1 ATAATAAAATG
33965 -TAAT--AATG
1 ATAATAAAATG
33973 ATAATAATAAT-
1 ATAATAA-AATG
33984 ATTAATAATAATG
1 A-TAATAA-AATG
33997 ATAATAAAATGG
1 ATAATAAAAT-G
34009 ATAA-AAAAT
1 ATAATAAAAT
34018 AGTATCTTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
7 2 0.03
9 8 0.11
11 17 0.24
12 44 0.61
13 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:34497 original size:114 final size:114
Alignment explanation
Indices: 34251--34914 Score: 1057
Period size: 114 Copynumber: 5.8 Consensus size: 114
34241 GCTCTTGATG
* *
34251 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-CT
* * * * * *
34315 CTGGTAATG-TTGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACA
65 CTGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
*
34364 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
34429 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
*
34478 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* * * * * ***
34543 TGGAAAAG-GTGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
* * *
34591 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTGTGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
34656 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
34705 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
*
34770 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTCGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
*
34819 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* *
34884 TGG-AAACAATGATCCATCAATTTGATGAATT
66 TGGAAAAGAATGATCCATCAA-GTGATGAATT
34915 CAAATCTTTG
Statistics
Matches: 511, Mismatches: 36, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
112 1 0.00
113 185 0.36
114 325 0.64
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
Found at i:34657 original size:227 final size:227
Alignment explanation
Indices: 34251--34914 Score: 1098
Period size: 227 Copynumber: 2.9 Consensus size: 227
34241 GCTCTTGATG
*
34251 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CT
* * * *
34315 CTGGTAATGTTGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
65 CTGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
34380 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
130 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
34445 ATCAAGTGATGAATTTAAACAAAAGGTTGAACA
195 ATCAAGTGATGAATTTAAACAAAAGGTTGAACA
34478 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * *
34543 TGGAAAAGGTGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGA
66 TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
* *
34608 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTGTGAACTTTCTCTGGAAAAGAATGATCCA
131 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCA
34673 TCAAGTGATGAATTTAAACAAAAGGTTGAACA
196 TCAAGTGATGAATTTAAACAAAAGGTTGAACA
*
34705 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * *
34770 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTCGAACAAGTTCTTCTCATTATG
66 TGGAAAAG-ATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
* *
34835 AACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG-AAACAATGATCC
130 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
*
34899 ATCAATTTGATGAATT
195 ATCAA-GTGATGAATT
34915 CAAATCTTTG
Statistics
Matches: 407, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
226 1 0.00
227 302 0.74
228 104 0.26
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (227 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCA
TCAAGTGATGAATTTAAACAAAAGGTTGAACA
Found at i:34875 original size:341 final size:340
Alignment explanation
Indices: 34253--34889 Score: 1141
Period size: 341 Copynumber: 1.9 Consensus size: 340
34243 TCTTGATGAG
*
34253 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* * * *
34318 GTAATGTTGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GAAAAGATGATCCATCAACTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
34383 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCATC
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCATC
*
34448 AAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
196 AAGTGATGAATTTAAACAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
*
34513 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGGTGATCCACCAAATGATGGATTCAGGT
261 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGGTGATCCACCAAATGATGGATTCAGGT
34578 AAAAGGTTGAACAAA
326 AAAAGGTTGAACAAA
*
34593 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTGTGAACTTT-CTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
* * *
34657 GGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGA
65 GGAAAAG-ATGATCCATCAACTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGA
34722 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCA
129 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCA
*
34787 TCAAGTGATGAATTTAAACAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCT
194 TCAAGTGATGAATTTAAACAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
34852 TCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
259 TCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
34890 CAATGATCCA
Statistics
Matches: 283, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
339 1 0.00
340 65 0.23
341 217 0.77
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (340 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
GAAAAGATGATCCATCAACTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCATC
AAGTGATGAATTTAAACAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGGTGATCCACCAAATGATGGATTCAGGT
AAAAGGTTGAACAAA
Found at i:35609 original size:83 final size:83
Alignment explanation
Indices: 35470--35668 Score: 380
Period size: 83 Copynumber: 2.4 Consensus size: 83
35460 ATGCACTTCT
* *
35470 TCAGATCAAATAACTCAAAGAACGCTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
35535 ATGCTTGATTCTGTCTAA
66 ATGCTTGATTCTGTCTAA
35553 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
35618 ATGCTTGATTCTGTCTAA
66 ATGCTTGATTCTGTCTAA
35636 TCAGATCAGATAACTCAAAGAACACTTCCAGAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAA
35669 AATACTATGT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 114 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
ATGCTTGATTCTGTCTAA
Found at i:35704 original size:52 final size:52
Alignment explanation
Indices: 35618--35890 Score: 433
Period size: 52 Copynumber: 5.2 Consensus size: 52
35608 TCTAAACTCA
* * *
35618 ATGCT-TGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAA
1 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
35670 ATACTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
35722 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * *
35774 ATGCTATGTTATGAT-CAACCAGATCAGATAACTCAAAGAACATTTCCAGAAA
1 ATGCTATGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
35826 ATGCTATGTTCTGTCCAACCAGATCAGATAACTTAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
35878 ATGCTATGTTCTG
1 ATGCTATGTTCTG
35891 ATGATTTTCC
Statistics
Matches: 204, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
51 1 0.00
52 200 0.98
53 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (52 bp):
ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:36550 original size:16 final size:16
Alignment explanation
Indices: 36514--36551 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
36504 TGAATTTCCA
36514 AAAATAAATTGAATCT
1 AAAATAAATTGAATCT
*
36530 CAAATAAATTGAA-CTT
1 AAAATAAATTGAATC-T
36546 AAAATA
1 AAAATA
36552 GATAGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATAAATTGAATCT
Found at i:36875 original size:1 final size:1
Alignment explanation
Indices: 36869--36930 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
36859 ACCTTGACCC
* * * * ** * *
36869 TTTTTTTTTTTTTTTTCTTCTTTTCTTTTTTCTTTTTTTTTCCTTCTCTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
36931 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:36898 original size:26 final size:25
Alignment explanation
Indices: 36869--36930 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
36859 ACCTTGACCC
36869 TTTTTTTTTTTTTTTT-CTTCT-TT
1 TTTTTTTTTTTTTTTTCCTTCTCTT
36892 TCTTTTTTCTTTTTTTTTCCTTCTCTT
1 T-TTTTTT-TTTTTTTTTCCTTCTCTT
36919 TTTTTTTTTTTT
1 TTTTTTTTTTTT
36931 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 1 0.03
24 6 0.17
25 14 0.40
26 11 0.31
27 3 0.09
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (25 bp):
TTTTTTTTTTTTTTTTCCTTCTCTT
Found at i:36908 original size:31 final size:31
Alignment explanation
Indices: 36869--36933 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
36859 ACCTTGACCC
36869 TTTT-TTTTTTTTT--TT-TCTTCTTTTCTT
1 TTTTCTTTTTTTTTCCTTCTCTTCTTTTCTT
* *
36896 TTTTCTTTTTTTTTCCTTCTCTTTTTTTTTT
1 TTTTCTTTTTTTTTCCTTCTCTTCTTTTCTT
36927 TTTTCTT
1 TTTTCTT
36934 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 4 0.12
28 9 0.28
30 2 0.06
31 17 0.53
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (31 bp):
TTTTCTTTTTTTTTCCTTCTCTTCTTTTCTT
Found at i:46548 original size:18 final size:18
Alignment explanation
Indices: 46525--46559 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46515 ATACTTGCAA
46525 ATAAAACAT-ATAAATATT
1 ATAAAA-ATAATAAATATT
46543 ATAAAAATAATAAATAT
1 ATAAAAATAATAAATAT
46560 AAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATAATAAATATT
Found at i:48704 original size:3 final size:3
Alignment explanation
Indices: 48689--48771 Score: 96
Period size: 3 Copynumber: 28.0 Consensus size: 3
48679 TTAATATATT
* * * *
48689 TAA TAA -AA AAA TAA TAA TAA TAA AAA TAA TAA TGA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
48736 TAA TGA TAA TAA TAA TAT TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48772 AATGGATAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48779 original size:12 final size:11
Alignment explanation
Indices: 48689--48785 Score: 53
Period size: 12 Copynumber: 8.8 Consensus size: 11
48679 TTAATATATT
**
48689 TAATAAAAAAA
1 TAATAAAATGA
*
48700 TAATAATAATAA
1 TAATAA-AATGA
*
48712 AAATAATAATGA
1 TAATAA-AATGA
*
48724 TAATAATAT--
1 TAATAAAATGA
48733 TAAT--AATGA
1 TAATAAAATGA
48742 TAATAATAAT-A
1 TAATAA-AATGA
48753 TTAATAATAATGA
1 -TAATAA-AATGA
48766 TAATAAAATGGA
1 TAATAAAAT-GA
48778 TAA-AAAAT
1 TAATAAAAT
48786 AGTATCTTCA
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
7 2 0.03
9 8 0.11
11 17 0.24
12 43 0.61
13 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (11 bp):
TAATAAAATGA
Found at i:55706 original size:29 final size:29
Alignment explanation
Indices: 55673--55790 Score: 227
Period size: 29 Copynumber: 4.1 Consensus size: 29
55663 TCTACAGTGG
55673 CCTTGGAGGTCGCCATGGCATCCGGGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
55702 CCTTGGAGGTCGCCATGGCATCCGGGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
55731 CCTTGGAGGTCGCCATGGCATCCGGGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
*
55760 CCTTGGAGGTCGCCATGGCATCCGAGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
55789 CC
1 CC
55791 GACCTGTGTG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 88 1.00
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.17
Consensus pattern (29 bp):
CCTTGGAGGTCGCCATGGCATCCGGGCGA
Found at i:55875 original size:81 final size:81
Alignment explanation
Indices: 55783--55946 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
55773 CATGGCATCC
55783 GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGCCGCCATGCAATCAACATGGGACGTGGG
1 GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGCCGCCATGCAATCAACATGGGACGTGGG
55848 AATGCATGGGGGAGGG
66 AATGCATGGGGGAGGG
*
55864 GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGTCGCCATGCAATCAACATGGGACGTGGG
1 GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGCCGCCATGCAATCAACATGGGACGTGGG
55929 AATGCATGGGGGAGGG
66 AATGCATGGGGGAGGG
55945 GA
1 GA
55947 TGCATGCTGT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.26, C:0.18, G:0.37, T:0.19
Consensus pattern (81 bp):
GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGCCGCCATGCAATCAACATGGGACGTGGG
AATGCATGGGGGAGGG
Found at i:55978 original size:20 final size:20
Alignment explanation
Indices: 55953--56002 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
55943 GGGATGCATG
55953 CTGTGCATGGGACGTGGGAA
1 CTGTGCATGGGACGTGGGAA
55973 CTGTGCATGGGACGTGGGAA
1 CTGTGCATGGGACGTGGGAA
55993 CTGTGCATGG
1 CTGTGCATGG
56003 CCATGCACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.44, T:0.22
Consensus pattern (20 bp):
CTGTGCATGGGACGTGGGAA
Found at i:56525 original size:21 final size:21
Alignment explanation
Indices: 56500--56543 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
56490 AATCTAGTTA
56500 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
56521 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
56542 AT
1 AT
56544 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:56553 original size:28 final size:30
Alignment explanation
Indices: 56520--56582 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
56510 TAGTATAAAT
*
56520 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
56548 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
56578 TATTA
1 TATTA
56583 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:57131 original size:20 final size:21
Alignment explanation
Indices: 57087--57131 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
57077 AAATATTGTG
**
57087 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
57108 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
57128 TTTA
1 TTTA
57132 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:60354 original size:26 final size:26
Alignment explanation
Indices: 60325--60729 Score: 320
Period size: 26 Copynumber: 16.2 Consensus size: 26
60315 TTTGATGATT
60325 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
60351 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
60377 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
* *
60403 TA-AAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
60424 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
60448 TAGTAATGATTTGATAATAATCA-T-
1 TAGTAATGATTTGATAATAATCATTA
60472 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
60498 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
60524 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
60546 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
60570 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
60596 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
60622 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** * * *
60648 TAAAAATAATTTAATAATGAT--TTAAA
1 TAGTAATGATTTGATAATAATCATT--A
*
60674 TATTTAATGATTTGATAATAATCATTA
1 TA-GTAATGATTTGATAATAATCATTA
* * *
60701 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
60726 TAGT
1 TAGT
60730 TATTATTTAG
Statistics
Matches: 320, Mismatches: 31, Indels: 57
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.01
20 10 0.03
21 2 0.01
22 14 0.04
23 12 0.04
24 46 0.14
25 24 0.08
26 178 0.56
27 30 0.09
29 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:60583 original size:98 final size:104
Alignment explanation
Indices: 60470--60721 Score: 321
Period size: 98 Copynumber: 2.5 Consensus size: 104
60460 GATAATAATC
60470 ATTAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGA-T
1 ATTAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATT
* *
60534 T-TAATAATGATT-T-AAAT-A-TT-TAATGATTT-GAT
66 TATAATAATCATTATAAAATAATTTATAATGATTTAAAT
* *
60566 GATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTT-GATAATAATCATTATAATAATG
1 -A-TTAGTAATGATTTGATAATAATCATTATAATAATGATTTAG-TAATAATCATTATAAAAATG
60630 ATTTAGTAATAATCATTATAAAAATAATTTAATAATGATTTAAAT
63 ATTTA-TAATAATCATTAT-AAAATAATTT-ATAATGATTTAAAT
60675 ATT--TAATGATTTGATAATAATCATTATAATAATGATTTTA-TAATAAT
1 ATTAGTAATGATTTGATAATAATCATTATAATAATGA-TTTAGTAATAAT
60722 TATTTAGTTA
Statistics
Matches: 135, Mismatches: 5, Indels: 22
0.83 0.03 0.14
Matches are distributed among these distances:
97 2 0.01
98 58 0.43
99 2 0.01
101 10 0.07
102 1 0.01
104 4 0.03
105 39 0.29
106 5 0.04
107 2 0.01
108 10 0.07
109 2 0.01
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (104 bp):
ATTAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATT
TATAATAATCATTATAAAATAATTTATAATGATTTAAAT
Found at i:60666 original size:124 final size:124
Alignment explanation
Indices: 60270--60689 Score: 810
Period size: 124 Copynumber: 3.4 Consensus size: 124
60260 ATGTATTTAT
60270 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
60335 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
60394 TAATCATTAT-AAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
60458 TTGATAATAATCA-T-TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
60515 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
60580 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
60639 TAATCATTATAAAAATAATTTAATAATGATTTAAATATTTAATGATTTGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGAT
60690 AATAATCATT
Statistics
Matches: 292, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
121 53 0.18
122 68 0.23
123 68 0.23
124 103 0.35
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:60771 original size:105 final size:103
Alignment explanation
Indices: 60475--60781 Score: 325
Period size: 105 Copynumber: 3.0 Consensus size: 103
60465 TAATCATTAG
*
60475 TAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATAAAAATGA-TT--T
1 TAATGATTTGATAATAATCATTATAATAATGATTTGA-TAATAATCATTATAATAATGATTTAGT
*
60536 AATAATGATT-T--AAAT-A-TT--TAATGATTTGATGATTT
65 AATAAT-ATTATAAAAATAATTTAATAATGATTTAAT-A-TT
*
60571 AGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAG
1 --TAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTAG
60636 TAATAATCATTATAAAAATAATTTAATAATGATTTAAATATT
64 TAATAAT-ATTATAAAAATAATTTAATAATGATTT-AATATT
* * * * *
60678 TAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTA
1 TAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTAGTA
* * *
60742 ATTAT-TTATAATAATGATTTAATACTAATGATTTAATATT
66 ATAATATTATAAAAATAATTT-A-A-TAATGATTTAATATT
60782 ATTACTAATA
Statistics
Matches: 181, Mismatches: 13, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
98 54 0.30
99 3 0.02
101 10 0.06
102 14 0.08
103 1 0.01
104 28 0.15
105 55 0.30
106 2 0.01
107 2 0.01
108 10 0.06
109 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (103 bp):
TAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTAGTA
ATAATATTATAAAAATAATTTAATAATGATTTAATATT
Found at i:60772 original size:14 final size:14
Alignment explanation
Indices: 60328--60779 Score: 154
Period size: 14 Copynumber: 33.9 Consensus size: 14
60318 GATGATTTAG
*
60328 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
60342 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
60354 TAATGATTTGATAA
1 TAATGATTTAATAA
*
60368 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
60380 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
60394 TAATCA-TT-ATAA
1 TAATGATTTAATAA
60406 -AATGA-TT--TAA
1 TAATGATTTAATAA
*
60416 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
60432 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
60451 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
60465 TAATCA--T--TAG
1 TAATGATTTAATAA
*
60475 TAATGATTTGATAA
1 TAATGATTTAATAA
*
60489 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
60501 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
60515 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
60527 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
60538 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
60554 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
60573 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
60587 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
60599 TAATGATTTGATAA
1 TAATGATTTAATAA
*
60613 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
60625 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
60639 TAATCA-TT-ATAA
1 TAATGATTTAATAA
* *
60651 AAAT-AATT--TAA
1 TAATGATTTAATAA
*
60662 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
60678 TAATGATTTGATAA
1 TAATGATTTAATAA
*
60692 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
60704 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
60718 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
60730 T-ATTATTTAGTAA
1 TAATGATTTAATAA
60743 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
60753 TAATGATTTAATAC
1 TAATGATTTAATAA
60767 TAATGATTTAATA
1 TAATGATTTAATA
60780 TTATTACTAA
Statistics
Matches: 337, Mismatches: 54, Indels: 94
0.69 0.11 0.19
Matches are distributed among these distances:
10 14 0.04
11 40 0.12
12 84 0.25
13 35 0.10
14 100 0.30
15 9 0.03
16 31 0.09
18 2 0.01
19 18 0.05
20 4 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:63177 original size:15 final size:14
Alignment explanation
Indices: 63154--63184 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
63144 TACAACACTA
63154 AACTTTAATATAAT
1 AACTTTAATATAAT
63168 AACTTATAATATAAT
1 AACTT-TAATATAAT
63183 AA
1 AA
63185 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:63192 original size:16 final size:16
Alignment explanation
Indices: 63159--63205 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
63149 CACTAAACTT
*
63159 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
63174 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
63190 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
63206 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:63465 original size:42 final size:43
Alignment explanation
Indices: 63366--63494 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 43
63356 CAACAAACAA
*
63366 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTT
1 ATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTT
*
63412 ATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTT
1 ATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTT
* * *
63454 A-ACTATA-TAACTA-T--CAACATATACTAATTAAATAATTTTT
1 ATA-TA-ACTAACTATTAACAAAACAAACTAATTAAATAATTTTT
63494 A
1 A
63495 ATTTATGTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
39 12 0.16
40 10 0.14
41 2 0.03
42 18 0.24
43 14 0.19
44 5 0.07
45 6 0.08
46 7 0.09
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (43 bp):
ATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTT
Found at i:63685 original size:21 final size:21
Alignment explanation
Indices: 63655--63707 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
63645 TCCTTTCTTC
*
63655 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
63676 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
63697 TTCTTTCTTTC
1 TTCTTTCTTTC
63708 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:63698 original size:17 final size:16
Alignment explanation
Indices: 63678--63741 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
63668 TTCTCCCTTT
63678 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
*
63695 CTTTCTTTCTTTCTCGG
1 CTTTCTTTCTTTCTC-C
* **
63712 C-TGCAATCTCTTCTCC
1 CTTTCTTTCT-TTCTCC
63728 CTTTCTTTCTTTCT
1 CTTTCTTTCTTTCT
63742 TTTATAACCG
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
16 17 0.47
17 19 0.53
ACGTcount: A:0.03, C:0.36, G:0.05, T:0.56
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:63881 original size:27 final size:27
Alignment explanation
Indices: 63851--63906 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
63841 AATAATTCAC
63851 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
63878 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
63905 GG
1 GG
63907 GCTGTAGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (27 bp):
GGCTCAAATGGTTCACATGCATGCATT
Found at i:64007 original size:29 final size:29
Alignment explanation
Indices: 63973--64081 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
63963 GATGGAATGG
63973 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
64002 TGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
64031 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
64060 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
64082 CTCTATTCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 73 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.16
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:64178 original size:12 final size:13
Alignment explanation
Indices: 64146--64180 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
64136 TCGTATATGG
64146 CTCGTATGTCACC
1 CTCGTATGTCACC
64159 CTCGTATGTCACC
1 CTCGTATGTCACC
64172 C-CGTATGTC
1 CTCGTATGTC
64181 GCCTGGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.14, C:0.37, G:0.17, T:0.31
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:64544 original size:31 final size:31
Alignment explanation
Indices: 64506--64581 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
64496 TCAAAAAGCA
*
64506 TAAGATATGGTCACTTTTAATTTTATTTAAT
1 TAAGATATGGTCACTTTCAATTTTATTTAAT
**
64537 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCAATTTTATTTAAT
* *
64568 TAGGATGTGGTCAC
1 TAAGATATGGTCAC
64582 CTGAGTTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCAATTTTATTTAAT
Found at i:64742 original size:111 final size:112
Alignment explanation
Indices: 64544--64768 Score: 364
Period size: 111 Copynumber: 2.0 Consensus size: 112
64534 AATTAAGATA
*
64544 TGGTCACTTTCGTTTTTATTTAATTAGGATGTGGTCACCTGAGTTAACTACCGTTAACAAAAGTT
1 TGGTCACTTTCGTTTTTATTTAATTA-GA--TGGTCACCCGAGTTAACTACCGTTAACAAAAGTT
*
64609 AAATATTTTTTATATAATCACACATTTGGTCTCTGTTATTACATATTTTT
63 AAACATTTTTTATATAATCACACATTTGGTCTCTGTTATTACATATTTTT
**
64659 TGGTCACTTTCGTTTTTATTTAATTA-A-GGTCACCCCGAGTTAACTGTCGTTAACAAAAGTTAA
1 TGGTCACTTTCGTTTTTATTTAATTAGATGGTCA-CCCGAGTTAACTACCGTTAACAAAAGTTAA
64722 ACATTTTTTATATAATCACACATTTGGTCTCTGTTATTACATATTTT
65 ACATTTTTTATATAATCACACATTTGGTCTCTGTTATTACATATTTT
64769 CTTAATTTAG
Statistics
Matches: 105, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
110 5 0.05
111 73 0.70
113 1 0.01
115 26 0.25
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (112 bp):
TGGTCACTTTCGTTTTTATTTAATTAGATGGTCACCCGAGTTAACTACCGTTAACAAAAGTTAAA
CATTTTTTATATAATCACACATTTGGTCTCTGTTATTACATATTTTT
Found at i:64794 original size:111 final size:109
Alignment explanation
Indices: 64576--64796 Score: 302
Period size: 111 Copynumber: 2.0 Consensus size: 109
64566 ATTAGGATGT
* *
64576 GGTCACCTGAGTTAACTACCGTTAACAAAAGTTAAATATTTTTTATATAATCACACATTTGGTCT
1 GGTCACCCGAGTTAACTACCGTTAACAAAAGTTAAACATTTTTTATATAATCACACATTTGGTCT
* * * *
64641 CTGTTATTACATATTTTTTGGTCACTTTCGTTTTTATTTAATTAA
66 CTGTTATTACATATTTTCT-GTAACTTTCATTTTTATATAATTAA
**
64686 GGTCACCCCGAGTTAACTGTCGTTAACAAAAGTTAAACATTTTTTATATAATCACACATTTGGTC
1 GGTCA-CCCGAGTTAACTACCGTTAACAAAAGTTAAACATTTTTTATATAATCACACATTTGGTC
*
64751 TCTGTTATTACATATTTTCT-TAATTTAGTCATATTTTA-ATAATTAA
65 TCTGTTATTACATATTTTCTGTAACTT--TCAT-TTTTATATAATTAA
64797 AAAAATTAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
109 4 0.04
110 5 0.05
111 84 0.86
112 5 0.05
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (109 bp):
GGTCACCCGAGTTAACTACCGTTAACAAAAGTTAAACATTTTTTATATAATCACACATTTGGTCT
CTGTTATTACATATTTTCTGTAACTTTCATTTTTATATAATTAA
Found at i:65491 original size:22 final size:21
Alignment explanation
Indices: 65455--65498 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
65445 TAACTTATTG
* *
65455 AATATATTTTTATTTTCATTT
1 AATATATATTTATTTTAATTT
65476 AATATATAATTTATTTTAATTT
1 AATATAT-ATTTATTTTAATTT
65498 A
1 A
65499 TTAAAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
AATATATATTTATTTTAATTT
Done.