Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:228577 original size:132 final size:132
Alignment explanation
Indices: 228387--229234 Score: 940
Period size: 132 Copynumber: 6.5 Consensus size: 132
228377 GCTGCAGCCG
* ** **
228387 AGAGAAATAAATGTAAACCCTTTCTCTGTTGGACCCAATGCTCGC-ACGTTAGACCAGCAGTCGA
1 AGAGAAATAAATATAAACCCTTTCTCCATTGGTGCCAATGCTCGCAAC-TTAGACCAGCAGTCGA
* * *
228451 CTGTCGGGCCACTGCCTGTTTCGTTCCAATCGACGGGTAACAACTCGAATCCGAGACCGCCGAGG
65 CTGTCGGACCACTGCCTGTTTCGTTCCAATCGACGGGTAACAACTCGAATCCGACACCGCCAAGG
228516 CCA
130 CCA
* * *** * *
228519 AGAGAAATGAATATAAATCCTTTCTCCATTGGAATCAATGCTCGCAACTTAGATCAGCAGTC-AA
1 AGAGAAATAAATATAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAGCAGTCGAC
* * * * * **
228583 TGGTCAGACCGCTGCCTGTTTCGTTTCAATCCACGGGGAACAACTCGAATCCGACACCGAGAAGG
66 T-GTCGGACCACTGCCTGTTTCGTTCCAATCGACGGGTAACAACTCGAATCCGACACCGCCAAGG
228648 CCA
130 CCA
* * * * * *
228651 AGAGAAACAAATATAAACCCTTTTTCCACTGGAGCCAACGCTCGCAACGTAGACCAGCAGTCGAC
1 AGAGAAATAAATATAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAGCAGTCGAC
* * *
228716 TGTCGAACCACTGGCTGTTTCGTTCCAATTGACGGAG-AACAACTCGAATCCGACACCGCCAAGG
66 TGTCGGACCACTGCCTGTTTCGTTCCAATCGACGG-GTAACAACTCGAATCCGACACCGCCAAGG
*
228780 CCG
130 CCA
* * * * * * *
228783 AGAGAAACATATATAAACCCTTTCTCCTTTGGTGCCAAAGTTTGCAACGTAGACCAGCAGTCGAC
1 AGAGAAATAAATATAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAGCAGTCGAC
* * **
228848 TGTCAGACCACTGCCTGTTTCGTTCCAATCGACGGAG-AACAACTCAAATCCGACACCTTCAAGG
66 TGTCGGACCACTGCCTGTTTCGTTCCAATCGACGG-GTAACAACTCGAATCCGACACCGCCAAGG
228912 CCA
130 CCA
* * *
228915 ATAGAAATAACTAGAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAGCAGTCGAC
1 AGAGAAATAAATATAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAGCAGTCGAC
* * *
228980 TGTCGGACCACTGCCAGTTTCGTTCCAA-CG-C---T-----CT--AATCCAACTCCGCCAAGGC
66 TGTCGGACCACTGCCTGTTTCGTTCCAATCGACGGGTAACAACTCGAATCCGACACCGCCAAGGC
*
229033 TA
131 CA
* * *
229035 AGAGAAATAAATATAAATCCTTTCTCCATTGGTGCCACTGCTCGCAACTTAGACCAGCAGTCGCC
1 AGAGAAATAAATATAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAGCAGTCGAC
* *
229100 TGCCGGACCACTTCCTGTTTCGATT-CAATCGAC-GGTGAACAACTCGAATCCGACACCGCCAAG
66 TGTCGGACCACTGCCTGTTTCG-TTCCAATCGACGGGT-AACAACTCGAATCCGACACCGCCAAG
*
229163 GCCG
129 GCCA
* * * * * * * *
229167 AGAGAAACATATATAAACCCTTTTTCCATTGGTGCCAATGTTCGCAACGTAGATCAACAGTCAAC
1 AGAGAAATAAATATAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAGCAGTCGAC
229232 TGT
66 TGT
229235 GAGACCGCCA
Statistics
Matches: 600, Mismatches: 98, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
120 97 0.16
121 4 0.01
122 3 0.00
124 1 0.00
130 3 0.00
131 4 0.01
132 483 0.81
133 5 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (132 bp):
AGAGAAATAAATATAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAGCAGTCGAC
TGTCGGACCACTGCCTGTTTCGTTCCAATCGACGGGTAACAACTCGAATCCGACACCGCCAAGGC
CA
Found at i:229216 original size:384 final size:390
Alignment explanation
Indices: 228383--229267 Score: 1038
Period size: 384 Copynumber: 2.3 Consensus size: 390
228373 CTATGCTGCA
* * * ** ** *
228383 GCCGAGAGAAATAAATGTAAACCCTTTCTCTGTTGGACCCAATGCTCGC-ACGTTAGACCAGCAG
1 GCCGAGAGAAACATATATAAACCCTTTCTCCATTGGTGCCAATGTTCGCAACG-TAGACCAGCAG
* * * *
228447 TCGACTGTCGGGCCACTGCCTGTTTCGTTCCAATCGACGGGTAACAACTCGAATCCGAGACCGCC
65 TCGACTGTCAGACCACTGCCTGTTTCGTTCCAATCGACGGGTAACAACTCAAATCCGACACCGCC
* * * * *
228512 GAGGCCAAGAGAAATGAATATAAATCCTTTCTCCATTGGAATCAATGCTCGCAACTTAGATCAGC
130 AAGGCCAAGAGAAATGAATAGAAACCCTTTCTCCATTGGAACCAATGCTCGCAACTTAGACCAGC
* * *
228577 AGTCAATGGTCAGACCGCTGCCTGTTTCGTTTCAATCCACGGGGAACAACTCGAATCCGACACCG
195 AGTCAATGGTCAGACCACTGCCAGTTTCG-TT--ATCCAC---GAACAACTCGAATCCAACACCG
* *
228642 AGAAGGCCAAGAGAAACAAATATAAACCCTTTTTCCACTGGAGCCAACGCTCGCAACGTAGACCA
254 ACAAGGCCAAGAGAAACAAATATAAACCCTTTCTCCACTGGAGCCAACGCTCGCAACGTAGACCA
* * *
228707 GCAGTCGACTGTCGAACCACTGGCTGTTTCGTTCCAATTGACGGAGAACAACTCGAATCCGACAC
319 GCAGTCGACTGCCGAACCACTGCCTGTTTCGTTCCAATCGACGGAGAACAACTCGAATCCGACAC
228772 CGCCAAG
384 CGCCAAG
* * *
228779 GCCGAGAGAAACATATATAAACCCTTTCTCCTTTGGTGCCAAAGTTTGCAACGTAGACCAGCAGT
1 GCCGAGAGAAACATATATAAACCCTTTCTCCATTGGTGCCAATGTTCGCAACGTAGACCAGCAGT
**
228844 CGACTGTCAGACCACTGCCTGTTTCGTTCCAATCGACGGAG-AACAACTCAAATCCGACACCTTC
66 CGACTGTCAGACCACTGCCTGTTTCGTTCCAATCGACGG-GTAACAACTCAAATCCGACACCGCC
* **
228908 AAGGCCAATAGAAAT-AACTAGAAACCCTTTCTCCATTGGTGCCAATGCTCGCAACTTAGACCAG
130 AAGGCCAAGAGAAATGAA-TAGAAACCCTTTCTCCATTGGAACCAATGCTCGCAACTTAGACCAG
* * * * * *
228972 CAGTCGACT-GTCGGACCACTGCCAGTTTCG-T-T-C-C-AAC-GCTCTAATCCAACTCCGCCAA
194 CAGTC-AATGGTCAGACCACTGCCAGTTTCGTTATCCACGAACAACTCGAATCCAACACCGACAA
* * * * * *
229030 GGCTAAGAGAAATAAATATAAATCCTTTCTCCATTGGTGCC-ACTGCTCGCAACTTAGACCAGCA
258 GGCCAAGAGAAACAAATATAAACCCTTTCTCCACTGGAGCCAAC-GCTCGCAACGTAGACCAGCA
* * * *
229094 GTCGCCTGCCGGACCACTTCCTGTTTCGATT-CAATCGACGGTGAACAACTCGAATCCGACACCG
322 GTCGACTGCCGAACCACTGCCTGTTTCG-TTCCAATCGACGGAGAACAACTCGAATCCGACACCG
229158 CCAAG
386 CCAAG
* * *
229163 GCCGAGAGAAACATATATAAACCCTTTTTCCATTGGTGCCAATGTTCGCAACGTAGATCAACAGT
1 GCCGAGAGAAACATATATAAACCCTTTCTCCATTGGTGCCAATGTTCGCAACGTAGACCAGCAGT
* * * ** * * *
229228 CAACTGTGAGACCGCCACCTGTTTCGGTCCAGTCTACGGG
66 CGACTGTCAGACCACTGCCTGTTTCGTTCCAATCGACGGG
229268 GATTAGGAAC
Statistics
Matches: 421, Mismatches: 62, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
383 3 0.01
384 218 0.52
385 5 0.01
389 1 0.00
390 1 0.00
391 1 0.00
394 1 0.00
395 2 0.00
396 183 0.43
397 6 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (390 bp):
GCCGAGAGAAACATATATAAACCCTTTCTCCATTGGTGCCAATGTTCGCAACGTAGACCAGCAGT
CGACTGTCAGACCACTGCCTGTTTCGTTCCAATCGACGGGTAACAACTCAAATCCGACACCGCCA
AGGCCAAGAGAAATGAATAGAAACCCTTTCTCCATTGGAACCAATGCTCGCAACTTAGACCAGCA
GTCAATGGTCAGACCACTGCCAGTTTCGTTATCCACGAACAACTCGAATCCAACACCGACAAGGC
CAAGAGAAACAAATATAAACCCTTTCTCCACTGGAGCCAACGCTCGCAACGTAGACCAGCAGTCG
ACTGCCGAACCACTGCCTGTTTCGTTCCAATCGACGGAGAACAACTCGAATCCGACACCGCCAAG
Found at i:232967 original size:3 final size:3
Alignment explanation
Indices: 232961--232986 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
232951 ACAACTTCTC
232961 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
232987 GATTCATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:236319 original size:153 final size:153
Alignment explanation
Indices: 236162--236440 Score: 414
Period size: 153 Copynumber: 1.8 Consensus size: 153
236152 AGGTTTACTG
* * * * * * *
236162 GGAGAAGAACTAACTGTGAAGGCTCTGGAGAGGATAATCTCTAATGTAACTGATCAACAAAGCAA
1 GGAGAAGAACAAACTATCAAGGATCAGGAGAGGATAATCTCAAATGTAACCGATCAACAAAGCAA
* * * *
236227 AGGAGGCTTCTGTAACAATGTTCGGAGCCCAGCTAACTTGCAGAACTCTGATGTTAAAAGAAGAC
66 AGGAGGCTTCTGTAACAATGTTCAGAGCCCAGCTAACTTGCAAAACACTAATGTTAAAAGAAGAC
236292 GTACATTATTGAAACAAACATTT
131 GTACATTATTGAAACAAACATTT
**
236315 GGAGAAGAACAAACTATCAAGGATCAGGAGAGGATAATCTCAAATGTAACCGATCAACGTAGCAA
1 GGAGAAGAACAAACTATCAAGGATCAGGAGAGGATAATCTCAAATGTAACCGATCAACAAAGCAA
* * *
236380 TGGAGGGTTCTTTAACAATGTTCAGAGCCCAGCTAACTTGCAAAACACTAATGTTAAAAGA
66 AGGAGGCTTCTGTAACAATGTTCAGAGCCCAGCTAACTTGCAAAACACTAATGTTAAAAGA
236441 TCTACATTAT
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
153 110 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (153 bp):
GGAGAAGAACAAACTATCAAGGATCAGGAGAGGATAATCTCAAATGTAACCGATCAACAAAGCAA
AGGAGGCTTCTGTAACAATGTTCAGAGCCCAGCTAACTTGCAAAACACTAATGTTAAAAGAAGAC
GTACATTATTGAAACAAACATTT
Found at i:242234 original size:48 final size:48
Alignment explanation
Indices: 242158--242266 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 48
242148 CAAATTATAA
*
242158 TTGGTAATTAA-TTAAGTTTTATTTTAATTCTACTAGT-TGAAGATTAC
1 TTGGTAATTAAGTTAAGTTTTATTATAATTCTACT-GTCTGAAGATTAC
* * *
242205 TTGGTAATTAAGTTAAGTTTTATTATAATTTTAGTGTCTTAAGATTAC
1 TTGGTAATTAAGTTAAGTTTTATTATAATTCTACTGTCTGAAGATTAC
*
242253 TTGATAATTAAGTT
1 TTGGTAATTAAGTT
242267 TATTTAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
47 13 0.24
48 42 0.76
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.50
Consensus pattern (48 bp):
TTGGTAATTAAGTTAAGTTTTATTATAATTCTACTGTCTGAAGATTAC
Found at i:243815 original size:26 final size:26
Alignment explanation
Indices: 243779--243829 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
243769 AATCCGACAG
* *
243779 CCTTCTAGAAAATGCTGATTGGACCA
1 CCTTCTAGAAAATACTAATTGGACCA
* *
243805 CCTTTTAGAAATTACTAATTGGACC
1 CCTTCTAGAAAATACTAATTGGACC
243830 GCTTAAATCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (26 bp):
CCTTCTAGAAAATACTAATTGGACCA
Found at i:247881 original size:342 final size:342
Alignment explanation
Indices: 247251--247882 Score: 874
Period size: 342 Copynumber: 1.8 Consensus size: 342
247241 GAATCTCAAA
*
247251 TAAGGGATGTTTGTATTGAGAACTTGTAATATATAATCATTAAAATGAATGATGTCACTATCTTT
1 TAAGGGATGTTTGTATTAAGAACTTGTAATATATAATCATTAAAATGAATGATGTCACTATCTTT
* *
247316 ACATTAAAGAGAAAGCCCAAAGAACATGCAATATTTATCAAATGTCGAAACGTTTTTTATTAATT
66 ACATTAAAGAGAAAGCCCAAAGAACATGCAATATTTATCAAATGTCGAAACGTATTTTATTAATC
* *
247381 AAGTTGAGTTTTAAATGAAGATTATTAATAACCGAGTTGAAGTTTTAGCGAGCCATCTTAGCTTA
131 AAGTTGAGTTTTAAATGAAGATTATTAATAACCGAGTTGAAGTTTCAGCGAGCCATCTTAGCATA
* * * * *
247446 ACCTGTAGAGCGCGTGGCTTTTAACCACATGGTTATGGGTTCGATTATCATAAATGGTAACAACT
196 ACCTGTAGAGCACGTGGCTTTTAACCACATGGTTATGAGTTCGATTATCACAAATGGCAAAAACT
* *
247511 TTAAATAGTTGATGAAATTAATCTTTATTTAGTCGGTTAAAGGAATAAAAGAACTTGATGATGAT
261 TTAAATACTTGATGAAATTAAACTTTATTTAGTCGGTTAAAGGAATAAAAGAACTTGATGATGAT
247576 AAAAAGTGAAGATTTTT
326 AAAAAGTGAAGATTTTT
* * * * *
247593 TAAGGGATGTTTGTGTTAAGAATTTGTAATATATAATTATTAAAATGAATGATGTGACTATTTTT
1 TAAGGGATGTTTGTATTAAGAACTTGTAATATATAATCATTAAAATGAATGATGTCACTATCTTT
*** * *
247658 ACATTGGGGAGAAAGCTCAAAGAACATGCAATATTTATCGAATGTCGAAACGTATTTTATTAATC
66 ACATTAAAGAGAAAGCCCAAAGAACATGCAATATTTATCAAATGTCGAAACGTATTTTATTAATC
* * ***
247723 AAGTTGAGTTTTAAATTACGATTATTAATAACCGAGTTGAAGTTTCA-CTGAGTTGTCTTAG-AT
131 AAGTTGAGTTTTAAATGAAGATTATTAATAACCGAGTTGAAGTTTCAGC-GAGCCATCTTAGCAT
* * * **** * * *
247786 CAGCTGGTAGAGCATGTGGCTTTTAACTGTGTGGTTGTGAGTTTGATT-CCTACAAATGGCAAAA
195 AACCT-GTAGAGCACGTGGCTTTTAACCACATGGTTATGAGTTCGATTATC-ACAAATGGCAAAA
*
247850 ACTTTAAATACTTGATTAAATTAAACTTTATTT
258 ACTTTAAATACTTGATGAAATTAAACTTTATTT
247883 TGACCATTAA
Statistics
Matches: 249, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
341 6 0.02
342 243 0.98
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (342 bp):
TAAGGGATGTTTGTATTAAGAACTTGTAATATATAATCATTAAAATGAATGATGTCACTATCTTT
ACATTAAAGAGAAAGCCCAAAGAACATGCAATATTTATCAAATGTCGAAACGTATTTTATTAATC
AAGTTGAGTTTTAAATGAAGATTATTAATAACCGAGTTGAAGTTTCAGCGAGCCATCTTAGCATA
ACCTGTAGAGCACGTGGCTTTTAACCACATGGTTATGAGTTCGATTATCACAAATGGCAAAAACT
TTAAATACTTGATGAAATTAAACTTTATTTAGTCGGTTAAAGGAATAAAAGAACTTGATGATGAT
AAAAAGTGAAGATTTTT
Found at i:255937 original size:21 final size:21
Alignment explanation
Indices: 255913--255966 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
255903 TTAACTTTAC
* * *
255913 ATTCTTTTTTTATTGAATTTT
1 ATTCATTTTTAATTCAATTTT
*
255934 ATTCATTTTTAATTCATTTTT
1 ATTCATTTTTAATTCAATTTT
*
255955 ATTGATTTTTAA
1 ATTCATTTTTAA
255967 AAAAATGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.67
Consensus pattern (21 bp):
ATTCATTTTTAATTCAATTTT
Found at i:255948 original size:11 final size:10
Alignment explanation
Indices: 255919--255965 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
255909 TTACATTCTT
*
255919 TTTTTATTGA
1 TTTTTATTCA
*
255929 ATTTTATTCA
1 TTTTTATTCA
255939 TTTTTAATTCA
1 TTTTT-ATTCA
*
255950 TTTTTATTGA
1 TTTTTATTCA
255960 TTTTTA
1 TTTTTA
255966 AAAAAATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 22 0.69
11 10 0.31
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (10 bp):
TTTTTATTCA
Found at i:259127 original size:2 final size:2
Alignment explanation
Indices: 259120--259164 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
259110 TCAAATCATC
259120 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
259162 TA T
1 TA T
259165 GTCTATTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:259991 original size:18 final size:19
Alignment explanation
Indices: 259965--260005 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
259955 GGGATTGTGA
*
259965 TTTAGGGTTTTGGTATAAT
1 TTTAGGGTTTGGGTATAAT
259984 TTTA-GGTTTGGGTATAAT
1 TTTAGGGTTTGGGTATAAT
260002 TTTA
1 TTTA
260006 AATTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (19 bp):
TTTAGGGTTTGGGTATAAT
Found at i:272419 original size:25 final size:24
Alignment explanation
Indices: 272378--272432 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
272368 ATTATCAAGC
* *
272378 TCGACTTGAATTTAAAACTTAAAAT
1 TCGACTTGAA-ATAAAAATTAAAAT
* *
272403 TCGACTTGAAATAAAAATTGAAGT
1 TCGACTTGAAATAAAAATTAAAAT
272427 TCGACT
1 TCGACT
272433 CGAGCTCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (24 bp):
TCGACTTGAAATAAAAATTAAAAT
Found at i:276388 original size:29 final size:29
Alignment explanation
Indices: 276356--276431 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
276346 TATTATGTCC
276356 TTTAATTATTAAAAATTATAAAATAATTA
1 TTTAATTATTAAAAATTATAAAATAATTA
* * * *
276385 TTTAATTATTTATAATATTTTAAATTTATTA
1 TTTAATTA-TTA-AAAATTATAAAATAATTA
276416 TTT--TTATTAAAAATTA
1 TTTAATTATTAAAAATTA
276432 ACGATAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.13
28 3 0.08
29 11 0.28
30 3 0.08
31 17 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTAATTATTAAAAATTATAAAATAATTA
Found at i:277249 original size:58 final size:58
Alignment explanation
Indices: 277155--277265 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
277145 ATGGTCCCTT
* * *
277155 GACTATATGGTGTTACTTTGTTAAGTCTCTTGACTATTAAAAGTTACAAAATGATCCC
1 GACTATAGGGTGTTACTCTGTTAAGTCTCTTAACTATTAAAAGTTACAAAATGATCCC
* *
277213 GACTATAGGGTGTTGCTCTGTTGAGTC-CTTTAACTATTAAAAGTTACAAAATG
1 GACTATAGGGTGTTACTCTGTTAAGTCTC-TTAACTATTAAAAGTTACAAAATG
277266 GTCTCCCTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 1 0.02
58 46 0.98
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (58 bp):
GACTATAGGGTGTTACTCTGTTAAGTCTCTTAACTATTAAAAGTTACAAAATGATCCC
Found at i:281320 original size:14 final size:14
Alignment explanation
Indices: 281301--281327 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
281291 TGACTTTTTG
281301 GTCAAAGTCAACGA
1 GTCAAAGTCAACGA
281315 GTCAAAGTCAACG
1 GTCAAAGTCAACG
281328 GATTGACTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (14 bp):
GTCAAAGTCAACGA
Found at i:282339 original size:61 final size:61
Alignment explanation
Indices: 282221--282353 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
282211 ATTAAAGAGT
* * **
282221 AAAG-TACATAAATGGTCCCTCAACTATAGGGTGTTACTTTGTTGAATCTCTTGACTATTA
1 AAAGTTACAAAAATGGTCCCTCAACTATAGGGAGTTACTTTGTTGAATCTCTCAACTATTA
* * *
282281 GAAGTTATAAAAATGGTCCACT-AACTATAGGGAGTTACTTTTTTGAATC-CTCCAACTATTA
1 AAAGTTACAAAAATGGTCC-CTCAACTATAGGGAGTTACTTTGTTGAATCTCT-CAACTATTA
282342 AAAGTTACAAAA
1 AAAGTTACAAAA
282354 TGATCACCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 5 0.08
61 54 0.89
62 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (61 bp):
AAAGTTACAAAAATGGTCCCTCAACTATAGGGAGTTACTTTGTTGAATCTCTCAACTATTA
Found at i:288335 original size:181 final size:181
Alignment explanation
Indices: 288031--288388 Score: 707
Period size: 181 Copynumber: 2.0 Consensus size: 181
288021 TAAATGTCAT
288031 ATTGATCATTGAAGCGATCCAAAACGAAGTTCAAAAATTTGGTCAAAACAGATATAGAATTCACA
1 ATTGATCATTGAAGCGATCCAAAACGAAGTTCAAAAATTTGGTCAAAACAGATATAGAATTCACA
*
288096 AATAATTTATTCAAGTATAATTCTACTATCAGAAAATAATTTAATAAATGTCTAATTATTATTAC
66 AATAATTTATTCAAGTATAATTCTACTATCAGAAAATAATTTAATAAATGTCTAATTATTATTAA
288161 GACTTCATGCTAATCATTATCAAATAATTTAGCGTTCAAACTATCAATGTC
131 GACTTCATGCTAATCATTATCAAATAATTTAGCGTTCAAACTATCAATGTC
288212 ATTGATCATTGAAGCGATCCAAAACGAAGTTCAAAAATTTGGTCAAAACAGATATAGAATTCACA
1 ATTGATCATTGAAGCGATCCAAAACGAAGTTCAAAAATTTGGTCAAAACAGATATAGAATTCACA
288277 AATAATTTATTCAAGTATAATTCTACTATCAGAAAATAATTTAATAAATGTCTAATTATTATTAA
66 AATAATTTATTCAAGTATAATTCTACTATCAGAAAATAATTTAATAAATGTCTAATTATTATTAA
288342 GACTTCATGCTAATCATTATCAAATAATTTAGCGTTCAAACTATCAA
131 GACTTCATGCTAATCATTATCAAATAATTTAGCGTTCAAACTATCAA
288389 ATTGAATGTT
Statistics
Matches: 176, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 176 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.34
Consensus pattern (181 bp):
ATTGATCATTGAAGCGATCCAAAACGAAGTTCAAAAATTTGGTCAAAACAGATATAGAATTCACA
AATAATTTATTCAAGTATAATTCTACTATCAGAAAATAATTTAATAAATGTCTAATTATTATTAA
GACTTCATGCTAATCATTATCAAATAATTTAGCGTTCAAACTATCAATGTC
Found at i:288463 original size:24 final size:24
Alignment explanation
Indices: 288430--288482 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
288420 ATCCATTATT
*
288430 AACTCTTTTTGGTCAATTTCTTTTA
1 AACTCTTTTTGGTAAATTT-TTTTA
*
288455 AACTCTTTTTGGTAAATTTTTTTC
1 AACTCTTTTTGGTAAATTTTTTTA
288479 AACT
1 AACT
288483 TTGACTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.55
Consensus pattern (24 bp):
AACTCTTTTTGGTAAATTTTTTTA
Found at i:301164 original size:24 final size:26
Alignment explanation
Indices: 301118--301169 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 26
301108 CGCGTTGCGA
301118 TCGCGTTGCGATAGTTGAAAATCGCGT
1 TCGCGTTGCGA-AGTTGAAAATCGCGT
301145 TCGCGTTGCG-A-TTGAAAATCGCGT
1 TCGCGTTGCGAAGTTGAAAATCGCGT
301169 T
1 T
301170 GCGATTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 14 0.56
25 1 0.04
27 10 0.40
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (26 bp):
TCGCGTTGCGAAGTTGAAAATCGCGT
Found at i:301220 original size:48 final size:48
Alignment explanation
Indices: 301166--301272 Score: 128
Period size: 50 Copynumber: 2.2 Consensus size: 48
301156 TTGAAAATCG
* * *
301166 CGTTGCGATTTCCATTTCGCGTTGCGAT-TTTGCGATAG-CTACAGTTGT
1 CGTTGCGATTTCAAATT--CGTTGCGATAATTGCGATAGTCTACAGTTGT
*
301214 CGTTGCGATTTTAAATTCGTTGCGATAGCATTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTCAAATTCGTTGCGATA--ATTGCGATAGTCTACAGTTGT
301264 CGTTGCGAT
1 CGTTGCGAT
301273 AGTTGAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
46 9 0.18
48 14 0.27
49 9 0.18
50 19 0.37
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (48 bp):
CGTTGCGATTTCAAATTCGTTGCGATAATTGCGATAGTCTACAGTTGT
Found at i:301308 original size:18 final size:18
Alignment explanation
Indices: 301285--301388 Score: 77
Period size: 18 Copynumber: 5.5 Consensus size: 18
301275 TTGAAAATCG
301285 CGTTGCGATTTTCCATTT
1 CGTTGCGATTTTCCATTT
* **
301303 CGTTGCGATAGTTT-TATCG
1 CGTTGCGAT--TTTCCATTT
301322 CGTTGCGATTTTCCATTT
1 CGTTGCGATTTTCCATTT
* *
301340 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTTCCA-TT-T
*
301362 CGTTGCG-TTTTCCAAATT
1 CGTTGCGATTTTCC-ATTT
301380 CGTTGCGAT
1 CGTTGCGAT
301389 AGTTAAAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
17 3 0.05
18 28 0.42
19 16 0.24
20 8 0.12
21 3 0.05
22 8 0.12
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (18 bp):
CGTTGCGATTTTCCATTT
Found at i:301331 original size:37 final size:37
Alignment explanation
Indices: 301263--301395 Score: 160
Period size: 37 Copynumber: 3.5 Consensus size: 37
301253 TCTACAGTTG
301263 TCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGTTGCGATAGTT--AAATCGCGTTGCGATTTTCCATT
**
301302 TCGTTGCGATAGTTTTATCGCGTTGCGATTTTCCATT
1 TCGTTGCGATAGTTAAATCGCGTTGCGATTTTCCATT
* * *
301339 TCGTTGCGATAGTCTACAGTTGTCGTTGCG-TTTTCCAAAT
1 TCGTTGCGATAGT-TA-AATCG-CGTTGCGATTTTCC-ATT
301379 TCGTTGCGATAGTTAAA
1 TCGTTGCGATAGTTAAA
301396 AAAAAGATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
37 34 0.41
38 2 0.02
39 24 0.29
40 22 0.27
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (37 bp):
TCGTTGCGATAGTTAAATCGCGTTGCGATTTTCCATT
Found at i:301735 original size:19 final size:19
Alignment explanation
Indices: 301711--301758 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
301701 ACTGTAGACT
*
301711 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTAGAAA
301730 ATCGCAACGAATTTAGAAA
1 ATCGCAACGAATTTAGAAA
301749 ATCGCAACGA
1 ATCGCAACGA
301759 CAACTGTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTAGAAA
Found at i:301774 original size:22 final size:22
Alignment explanation
Indices: 301749--301821 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
301739 AATTTAGAAA
301749 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
**
301771 ATCGCAATGCGA-AA-TG--GAAA
1 ATCGCAA--CGACAACTGTAGACT
301791 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
301813 ATCGCAACG
1 ATCGCAACG
301822 CGAAATGGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 3 0.07
19 2 0.05
20 11 0.27
22 20 0.49
23 2 0.05
24 3 0.07
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:301796 original size:20 final size:20
Alignment explanation
Indices: 301771--301844 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
301761 ACTGTAGACT
*
301771 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
301791 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
301813 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
301833 ATCGCAACGCGA
1 ATCGCAACGCGA
301845 TTTTCAACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 26 0.60
21 2 0.05
22 15 0.35
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:301867 original size:41 final size:42
Alignment explanation
Indices: 301745--301869 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
301735 AACGAATTTA
*
301745 GAAAATCGCAACGACAACTGTAGACTATCGCAATGCGAAATG
1 GAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATG
301787 GAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATG
1 GAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATG
* * *
301829 GAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATG
1 GAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAATG
301870 CAATGCGAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
41 23 0.29
42 55 0.71
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (42 bp):
GAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATG
Found at i:303955 original size:2 final size:2
Alignment explanation
Indices: 303950--303978 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
303940 CACACACATA
303950 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
303979 TCAGATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:312644 original size:3 final size:3
Alignment explanation
Indices: 312630--312690 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
312620 TCTCTTTTAC
*
312630 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
312678 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
312691 TATGATAGTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:328931 original size:28 final size:27
Alignment explanation
Indices: 328871--328931 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
328861 TTTATCCTAA
* *
328871 TTTTTTTAAATTTATTTTAATTTCATT
1 TTTTTTTAAATTCATTTGAATTTCATT
* *
328898 TGTTTTTTAAATTCATTATGATTTTCCTT
1 T-TTTTTTAAATTCATT-TGAATTTCATT
328927 TTTTT
1 TTTTT
328932 AATATGATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.04
28 18 0.64
29 9 0.32
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTTTTTAAATTCATTTGAATTTCATT
Found at i:331811 original size:72 final size:72
Alignment explanation
Indices: 331694--331838 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
331684 GGCCCATAGC
331694 TCCATTGCTCTCAGTAAAAATCCTTGGTACATCTTAACCTGCTAATGTCATATATCAAAACTCAA
1 TCCATTGCTCTCAGTAAAAATCCTTGGTACATCTTAACCTGCTAATGTCATATATCAAAACTCAA
331759 GCAGAAG
66 GCAGAAG
331766 TCCATTGCTCTCAGTAAAAATCCTTGGTACATCTTAACCTGCTAATGTCATATATCAAAACTCAA
1 TCCATTGCTCTCAGTAAAAATCCTTGGTACATCTTAACCTGCTAATGTCATATATCAAAACTCAA
331831 GCAGAAG
66 GCAGAAG
331838 T
1 T
331839 GTCTATCACC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.30
Consensus pattern (72 bp):
TCCATTGCTCTCAGTAAAAATCCTTGGTACATCTTAACCTGCTAATGTCATATATCAAAACTCAA
GCAGAAG
Found at i:333780 original size:19 final size:19
Alignment explanation
Indices: 333756--333793 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
333746 ATTTTCTCGC
333756 TAGGGCTTTTGGGTTTGGG
1 TAGGGCTTTTGGGTTTGGG
333775 TAGGGCTTTTGGGTTTGGG
1 TAGGGCTTTTGGGTTTGGG
333794 GTTGGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.05, G:0.47, T:0.42
Consensus pattern (19 bp):
TAGGGCTTTTGGGTTTGGG
Found at i:337286 original size:83 final size:83
Alignment explanation
Indices: 337184--337349 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
337174 TTCAAGCTTG
337184 TGCAGCTGCTTCTCAGCTCCTGTTGTTGCGGCTGCTTCCGCAACCGCTGCAGGGACGGGAACTTC
1 TGCAGCTGCTTCTCAGCTCCTGTTGTTGCGGCTGCTTCCGCAACCGCTGCAGGGACGGGAACTTC
337249 CTCCGCCGCCTCAGTTGC
66 CTCCGCCGCCTCAGTTGC
337267 TGCAGCTGCTTCTCAGCTCCTGTTGTTGCGGCTGCTTCCGCAACCGCTGCAGGGACGGGAACTTC
1 TGCAGCTGCTTCTCAGCTCCTGTTGTTGCGGCTGCTTCCGCAACCGCTGCAGGGACGGGAACTTC
337332 CTCCGCCGCCTCAGTTGC
66 CTCCGCCGCCTCAGTTGC
337350 CATAAGTTGT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.11, C:0.36, G:0.28, T:0.25
Consensus pattern (83 bp):
TGCAGCTGCTTCTCAGCTCCTGTTGTTGCGGCTGCTTCCGCAACCGCTGCAGGGACGGGAACTTC
CTCCGCCGCCTCAGTTGC
Found at i:337671 original size:20 final size:21
Alignment explanation
Indices: 337646--337688 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
337636 GAGTCCGTGA
*
337646 TTAGAATCCTCGTATAAT-TT
1 TTAGAATCCTCATATAATATT
337666 TTAGAATCCTCATATAATATT
1 TTAGAATCCTCATATAATATT
337687 TT
1 TT
337689 TTAGCATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (21 bp):
TTAGAATCCTCATATAATATT
Found at i:345404 original size:18 final size:18
Alignment explanation
Indices: 345364--345399 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
345354 ATAAACTTAA
*
345364 AAAATTATACTCAAATCC
1 AAAATTATACACAAATCC
345382 AAAATTATATCACAAATC
1 AAAATTATA-CACAAATC
345400 TAAATCACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATTATACACAAATCC
Found at i:346901 original size:3 final size:3
Alignment explanation
Indices: 346875--346937 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
346865 GTCCGGATCT
*
346875 TTA TT- TTA TTT TTA TT- TT- TTA TTA TTA TTA TTA TTA TTA TTA CTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
346920 TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA
346938 CATGTACATT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
2 8 0.15
3 42 0.81
4 2 0.04
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:347188 original size:135 final size:134
Alignment explanation
Indices: 346941--347192 Score: 486
Period size: 134 Copynumber: 1.9 Consensus size: 134
346931 AATATTACAT
*
346941 GTACATTTTTTGAAGGCTTAATGGACAGCCCAGATTACAGACAAGCCCAATACACTCAAGGCCAC
1 GTACATTTTTTGAAGGCTTAATGGACAGCCCAGATTACAGACAAGCCCAATACACCCAAGGCCAC
347006 TTATGTGACCCATCAACCCAGAAGACCAACACATTAGGGTTTTTAAACCTTACTCGTCGGCCTTC
66 TTATGTGACCCATCAACCCAGAAGACCAACACATTAGGGTTTTTAAACCTTACTCGTCGGCCTTC
347071 TAGC
131 TAGC
347075 GTACATTTTTTGAAGGCTTAATGGACAGCCCAGATTACAGACAAGCCCAATACACCCAAGGCCCA
1 GTACATTTTTTGAAGGCTTAATGGACAGCCCAGATTACAGACAAGCCCAATACACCCAAGG-CCA
347140 CTTATGTGACCCATCAACCCAGAAGACCAACACATTAGGGTTTTTAAACCTTA
65 CTTATGTGACCCATCAACCCAGAAGACCAACACATTAGGGTTTTTAAACCTTA
347193 GCTCAACTGT
Statistics
Matches: 116, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
134 60 0.52
135 56 0.48
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (134 bp):
GTACATTTTTTGAAGGCTTAATGGACAGCCCAGATTACAGACAAGCCCAATACACCCAAGGCCAC
TTATGTGACCCATCAACCCAGAAGACCAACACATTAGGGTTTTTAAACCTTACTCGTCGGCCTTC
TAGC
Found at i:348448 original size:14 final size:15
Alignment explanation
Indices: 348424--348453 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
348414 TTAGTCCTAT
348424 TATTGTTTGTTATGA
1 TATTGTTTGTTATGA
348439 TATT-TTTGTTATGA
1 TATTGTTTGTTATGA
348453 T
1 T
348454 TGGACTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (15 bp):
TATTGTTTGTTATGA
Found at i:348729 original size:29 final size:26
Alignment explanation
Indices: 348655--348730 Score: 64
Period size: 29 Copynumber: 2.8 Consensus size: 26
348645 TATGTTTTAA
348655 CTATTTTGGTCCTTTTAAGTTTATGTTT
1 CTATTTTGGTCC-TTTAA-TTTATGTTT
* ** *
348683 -TATTTCGGTCCTCGAATTTCTGTTAAT
1 CTATTTTGGTCCTTTAATTTATGTT--T
348710 CCTATTTTGGTCCTTTAATTT
1 -CTATTTTGGTCCTTTAATTT
348731 TTTTTATTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
25 7 0.19
26 3 0.08
27 11 0.30
29 16 0.43
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.55
Consensus pattern (26 bp):
CTATTTTGGTCCTTTAATTTATGTTT
Found at i:351766 original size:22 final size:20
Alignment explanation
Indices: 351745--351783 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
351735 ATTCCCTCTT
*
351745 TTTGAGACCTTGAAACATTC
1 TTTGAGACATTGAAACATTC
*
351765 TTTGTGACATTGAAACATT
1 TTTGAGACATTGAAACATT
351784 GCATTTATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTGAGACATTGAAACATTC
Found at i:352380 original size:24 final size:24
Alignment explanation
Indices: 352336--352433 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 24
352326 TGAACCAGAT
*
352336 GCAAAGAGAAAGAAACAAAGACAAAA
1 GCAAAGA-AAAAAAACAAAGA-AAAA
352362 GCAAAGAAAAAAAAC-AAGAAAAA
1 GCAAAGAAAAAAAACAAAGAAAAA
* *
352385 ACAAAGAAAGAAAAAAAAAGAAAACA
1 GCAAAGAAA-AAAAACAAAGAAAA-A
** *
352411 ATAAAG-AAAAAGA-AAAGAAAAA
1 GCAAAGAAAAAAAACAAAGAAAAA
352433 G
1 G
352434 AAGACAAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
22 1 0.02
23 20 0.32
24 13 0.21
25 16 0.25
26 13 0.21
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (24 bp):
GCAAAGAAAAAAAACAAAGAAAAA
Found at i:352383 original size:11 final size:10
Alignment explanation
Indices: 352364--352435 Score: 56
Period size: 11 Copynumber: 6.6 Consensus size: 10
352354 AGACAAAAGC
352364 AAAGAAAAAAA
1 AAAG-AAAAAA
352375 ACAAGAAAAAA
1 A-AAGAAAAAA
352386 CAAAGAAAGAAA
1 -AAAGAAA-AAA
352398 AAA-AAAGAAA
1 AAAGAAA-AAA
* *
352408 ACAATAAAGAA
1 A-AAGAAAAAA
352419 AAAGAAAAGAA
1 AAAGAAAA-AA
352430 AAAGAA
1 AAAGAA
352436 GACAAAAGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
10 13 0.25
11 29 0.56
12 10 0.19
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.01
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:352389 original size:23 final size:23
Alignment explanation
Indices: 352337--352432 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 23
352327 GAACCAGATG
* *
352337 CAAAGAGAAAGAAACAAAGACAAAAG
1 CAAAGA-AAAAAAAC-AAGA-AAAAA
352363 CAAAGAAAAAAAACAAGAAAAAA
1 CAAAGAAAAAAAACAAGAAAAAA
*
352386 CAAAGAAAGAAAAAAAAAGAAAACAA
1 CAAAG-AA-AAAAAACAAGAAAA-AA
* *
352412 TAAAGAAAAAGAA-AAGAAAAA
1 CAAAGAAAAAAAACAAGAAAAA
352433 GAAGACAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.02
23 16 0.26
24 11 0.18
25 22 0.35
26 12 0.19
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.01
Consensus pattern (23 bp):
CAAAGAAAAAAAACAAGAAAAAA
Found at i:352397 original size:15 final size:14
Alignment explanation
Indices: 352344--352435 Score: 66
Period size: 14 Copynumber: 6.4 Consensus size: 14
352334 ATGCAAAGAG
* *
352344 AAAGAAACAAAGACA
1 AAAGAAAGAAA-AAA
352359 AAAGCAAAG-AAAAA
1 AAAG-AAAGAAAAAA
*
352373 AAA-CAAGAAAAAA
1 AAAGAAAGAAAAAA
352386 CAAAGAAAGAAAAAA
1 -AAAGAAAGAAAAAA
352401 AAAGAAA-ACAATAAA
1 AAAGAAAGA-AA-AAA
*
352416 GAA-AAAGAAAAGAA
1 AAAGAAAGAAAA-AA
352430 AAAGAA
1 AAAGAA
352436 GACAAAAGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
12 3 0.05
13 7 0.11
14 26 0.42
15 23 0.37
16 3 0.05
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (14 bp):
AAAGAAAGAAAAAA
Found at i:352418 original size:12 final size:10
Alignment explanation
Indices: 352391--352432 Score: 57
Period size: 11 Copynumber: 3.9 Consensus size: 10
352381 AAAAACAAAG
352391 AAAGAAAAAA
1 AAAGAAAAAA
352401 AAAGAAAACAA
1 AAAGAAAA-AA
352412 TAAAGAAAAAGA
1 -AAAGAAAAA-A
352424 AAAGAAAAA
1 AAAGAAAAA
352433 GAAGACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.28
11 12 0.41
12 9 0.31
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:352420 original size:18 final size:17
Alignment explanation
Indices: 352395--352435 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
352385 ACAAAGAAAG
352395 AAAA-AAAAAGAAAACA
1 AAAAGAAAAAGAAAACA
*
352411 ATAAAGAAAAAGAAAAGA
1 A-AAAGAAAAAGAAAACA
352429 AAAAGAA
1 AAAAGAA
352436 GACAAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 9 0.41
18 12 0.55
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAGAAAACA
Found at i:352428 original size:33 final size:33
Alignment explanation
Indices: 352371--352432 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
352361 AGCAAAGAAA
352371 AAAAACAAGAAAAAACAAAG-AAAGAAAAAAAA
1 AAAAACAAGAAAAAACAAAGAAAAGAAAAAAAA
* *
352403 AGAAAACAATAAAGAA-AAAGAAAAGAAAAA
1 A-AAAACAAGAAAAAACAAAGAAAAGAAAAA
352433 GAAGACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 5 0.19
33 21 0.81
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (33 bp):
AAAAACAAGAAAAAACAAAGAAAAGAAAAAAAA
Found at i:352442 original size:11 final size:11
Alignment explanation
Indices: 352368--352431 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 11
352358 AAAAGCAAAG
352368 AAAA-AAAACA
1 AAAAGAAAACA
*
352378 AGAA-AAAACAA
1 AAAAGAAAAC-A
352389 AGAAAGAAAA-A
1 A-AAAGAAAACA
352400 AAAAGAAAACA
1 AAAAGAAAACA
352411 ATAAAGAAAA-A
1 A-AAAGAAAACA
352422 GAAAAGAAAA
1 -AAAAGAAAA
352432 AGAAGACAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
10 16 0.35
11 15 0.33
12 11 0.24
13 4 0.09
ACGTcount: A:0.83, C:0.05, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAGAAAACA
Found at i:352455 original size:43 final size:41
Alignment explanation
Indices: 352338--352455 Score: 95
Period size: 43 Copynumber: 2.9 Consensus size: 41
352328 AACCAGATGC
*
352338 AAAGAGAAAGAAACA-AAGACAAAAG-CAAAGA-AA-AAAAA
1 AAAGA-AAAGAAAAAGAAGACAAAAGACAAAGACAATAAAAA
* * * *
352376 CAAGAAAA-AACAAAGAAAGA-AAAAAAAAGAAAACAATAAAGAA
1 AAAGAAAAGAA-AAAG-AAGACAAAAGACA-AAGACAATAAA-AA
352419 AAAGAAAAGAAAAAGAAGACAAAAGCACAAAGACAAT
1 AAAGAAAAGAAAAAGAAGACAAAAG-ACAAAGACAAT
352456 GAGTCCCTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
36 2 0.03
37 5 0.08
38 8 0.13
39 5 0.08
40 3 0.05
41 2 0.03
42 7 0.12
43 24 0.40
44 4 0.07
ACGTcount: A:0.75, C:0.08, G:0.14, T:0.02
Consensus pattern (41 bp):
AAAGAAAAGAAAAAGAAGACAAAAGACAAAGACAATAAAAA
Found at i:354102 original size:28 final size:28
Alignment explanation
Indices: 353995--354092 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
353985 TCTTGAGATA
*
353995 GTTTCTCTTGAAACAAAATCTTTGAGTCT
1 GTTTCTTTTGAAA-AAAATCTTTGAGTCT
*
354024 GTTCCTTTTGAATAAAAATCTTTGAGT-T
1 GTTTCTTTTGAA-AAAAATCTTTGAGTCT
354052 GTTTCTTTTGAAAAAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
354080 GTTTCTTTTGAAA
1 GTTTCTTTTGAAA
354093 CAAAGTTTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.22
28 26 0.41
29 23 0.36
30 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTCT
Found at i:354138 original size:59 final size:61
Alignment explanation
Indices: 354063--354217 Score: 244
Period size: 59 Copynumber: 2.6 Consensus size: 61
354053 TTTCTTTTGA
354063 AAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTG-TCTCTTGAGACAATTTCGTG
1 AAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGCTCTCTTGAGACAATTTCGTG
* *
354123 -AAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGATAATTTCGTG
1 AAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTG-CTCTCTTGAGACAATTTCGTG
*
354184 AAAAAAATATTTGAGT-TGTTTCTTTTGAAACAAA
1 -AAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAA
354218 AATCTTTGAG
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
59 38 0.44
61 19 0.22
62 17 0.20
63 13 0.15
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (61 bp):
AAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGCTCTCTTGAGACAATTTCGTG
Found at i:354219 original size:29 final size:30
Alignment explanation
Indices: 354186--354248 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
354176 ATTTCGTGAA
* *
354186 AAAAATATTTGAGT-TGTTTCTTTTGAAAC
1 AAAAATATTTGAGTCGGTTTCTTTGGAAAC
*
354215 AAAAATCTTTGAGTCGGTTTCTTTGGAAAC
1 AAAAATATTTGAGTCGGTTTCTTTGGAAAC
354245 AAAA
1 AAAA
354249 TTTTGTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (30 bp):
AAAAATATTTGAGTCGGTTTCTTTGGAAAC
Found at i:354219 original size:30 final size:31
Alignment explanation
Indices: 354185--354248 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
354175 AATTTCGTGA
* *
354185 AAAAAATATTTGAGT-TGTTTCTTTTGAAAC
1 AAAAAATATTTGAGTCGGTTTCTTTGGAAAC
*
354215 -AAAAATCTTTGAGTCGGTTTCTTTGGAAAC
1 AAAAAATATTTGAGTCGGTTTCTTTGGAAAC
354245 AAAA
1 AAAA
354249 TTTTGTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 13 0.45
30 13 0.45
31 3 0.10
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (31 bp):
AAAAAATATTTGAGTCGGTTTCTTTGGAAAC
Found at i:354236 original size:92 final size:93
Alignment explanation
Indices: 354123--354321 Score: 253
Period size: 92 Copynumber: 2.2 Consensus size: 93
354113 CAATTTCGTG
* * * *
354123 AAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGATA-ATT-TCGTGAA
1 AAAAATCTTTGAGTCGATTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACATATTCTCGTGAA
*
354186 AAAAATATTTGAGT-TGTTTC-TTTTGAAA
66 AAAAATATTTGAGTATG-CTCATTTTG-AA
* * *
354214 CAAAAATCTTTGAGTCGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACATTTTCTCTTGA
1 -AAAAATCTTTGAGTCGATTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACATATTCTCGTGA
* *
354279 AACAAATCTTTGAGTATGCTCATTTTGAA
65 AAAAAATATTTGAGTATGCTCATTTTGAA
354308 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
354322 TTGTTTCTAC
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
92 48 0.52
93 16 0.17
94 22 0.24
95 7 0.08
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (93 bp):
AAAAATCTTTGAGTCGATTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACATATTCTCGTGAA
AAAAATATTTGAGTATGCTCATTTTGAA
Found at i:354402 original size:122 final size:121
Alignment explanation
Indices: 354182--354402 Score: 293
Period size: 122 Copynumber: 1.8 Consensus size: 121
354172 GATAATTTCG
** * *
354182 TGAAAAAAATATTTGAGTTGTTTCTTTTGAAACAAAAATCTTTGAGTCGGTTTCTTTGGAAACAA
1 TGAAAAAAATATTTGAGTTGTTTCTACT-AAACAAAAATCTTTGAGTCGATTTCTTTGAAAACAA
* **
354247 AATTTTGTCTCTCTTGAGACATTTTCTCTTGAAACAAATCTTTGAGTATGCTCATTT
65 AATTTTGTCTCTCTTGAGACAGTTTCTAATGAAACAAATCTTTGAGTATGCTCATTT
* *
354304 TGAAAAAAATCTTTGAGTTTGTTTCTACT-AACAAAATCATCTTTGAGTCTATTTCTTT-AAAAC
1 TGAAAAAAATATTTGAG-TTGTTTCTACTAAACAAAA--ATCTTTGAGTCGATTTCTTTGAAAAC
* *
354367 CAAATTTTGTCTTTCTTGAGACAGTTTCTAATGAAA
63 AAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAA
354403 AAACAACTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
121 7 0.08
122 51 0.60
123 27 0.32
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.42
Consensus pattern (121 bp):
TGAAAAAAATATTTGAGTTGTTTCTACTAAACAAAAATCTTTGAGTCGATTTCTTTGAAAACAAA
ATTTTGTCTCTCTTGAGACAGTTTCTAATGAAACAAATCTTTGAGTATGCTCATTT
Found at i:354478 original size:273 final size:269
Alignment explanation
Indices: 353914--354491 Score: 644
Period size: 273 Copynumber: 2.1 Consensus size: 269
353904 ATCAAAATAC
* * *
353914 AAAATCTTTGAGTTTGTTTCTCTTGAAACAAACCATCTTTGAGTCGTTTCTCTTGAAACGAATTT
1 AAAATCTTTGAGTTTGTTTCTTTTGAAACAAA-AATCTTTGAGTCGTTTCTCTTGAAACAAATTT
* * * *
353979 TGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAGTCTGTTCCTTTTGAATAAAAATC
65 TGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTATGCTCATTTTGAATAAAAATC
** * *
354044 TTTGAGTTGTTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGTCTCTT
130 TTTGAGTTGTTTCTACTGAAAAAAATCTTTGAGTCTATTTCTTTTAAAACAAAGTTTTGTCTCTT
* * * * *
354109 GAGACAATTTCGTGAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGA
195 GAGACAATTTCATGAAAAAACTTTGAGTCTATTTCATTTGAAACAAAGTTTCGTCTCACTTGAGA
354174 TAATTTCGTGAAA
260 TAA--TCGT-AAA
*
354187 AAAATATTTGAG-TTGTTTCTTTTGAAACAAAAATCTTTGAGTCGGTTTCT-TTGGAAACAAAAT
1 AAAATCTTTGAGTTTGTTTCTTTTGAAACAAAAATCTTTGAGTC-GTTTCTCTT-GAAAC-AAAT
*
354250 TTTGTCTCTCTTGAGACATTTTCTCTTGAAAC-AAATCTTTGAGTATGCTCATTTTGAA-AAAAA
63 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTATGCTCATTTTGAATAAAAA
354313 TCTTTGAGTTTGTTTCTACT-AACAAAATCATCTTTGAGTCTATTTC-TTTAAAACCAAA-TTTT
128 TCTTTGAG-TTGTTTCTACTGAA-AAAA--ATCTTTGAGTCTATTTCTTTTAAAA-CAAAGTTTT
* *
354375 GTCTTTCTTGAGACAGTTTCTAATGAAAAAACAACTTTTGAGAT-TGTTTCATTTGAAACAAA-T
188 GTC--TCTTGAGACAATTTC--ATG--AAAA-AAC-TTTGAG-TCTATTTCATTTGAAACAAAGT
*
354438 TTCGTCTCACTT-A-A-GA-CGT-AA
244 TTCGTCTCACTTGAGATAATCGTAAA
*** *
354459 CCTATCTTTGAGTTTGTTTCTTTGGAAACAAAA
1 AAAATCTTTGAGTTTGTTTCTTTTGAAACAAAA
354492 TTTTGTCTAT
Statistics
Matches: 261, Mismatches: 26, Indels: 36
0.81 0.08 0.11
Matches are distributed among these distances:
271 28 0.11
272 75 0.29
273 76 0.29
274 23 0.09
275 14 0.05
277 3 0.01
278 1 0.00
279 5 0.02
280 13 0.05
281 22 0.08
282 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (269 bp):
AAAATCTTTGAGTTTGTTTCTTTTGAAACAAAAATCTTTGAGTCGTTTCTCTTGAAACAAATTTT
GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTATGCTCATTTTGAATAAAAATCT
TTGAGTTGTTTCTACTGAAAAAAATCTTTGAGTCTATTTCTTTTAAAACAAAGTTTTGTCTCTTG
AGACAATTTCATGAAAAAACTTTGAGTCTATTTCATTTGAAACAAAGTTTCGTCTCACTTGAGAT
AATCGTAAA
Found at i:354603 original size:36 final size:33
Alignment explanation
Indices: 354523--354656 Score: 114
Period size: 36 Copynumber: 4.0 Consensus size: 33
354513 TTCTTTTGAG
* *
354523 AAAA-ATCCTTGAGTCTGTTTCT-TTGGAAACAA
1 AAAACATCTTTGAGTATGTTTCTCTT-GAAACAA
* * *
354555 AATTTACCATCTTTGAGTCTGTTTCCCTTGAAACAA
1 AA---AACATCTTTGAGTATGTTTCTCTTGAAACAA
354591 AACAACAAATCTTTGAGTATGTTT-TCTTGAAAC-A
1 AA-AAC--ATCTTTGAGTATGTTTCTCTTGAAACAA
* *
354625 AAAACATCTTTGAGTTTGTTTCTCTCGAAACA
1 AAAACATCTTTGAGTATGTTTCTCTTGAAACA
354657 CCGATCTTGA
Statistics
Matches: 84, Mismatches: 9, Indels: 17
0.76 0.08 0.15
Matches are distributed among these distances:
31 15 0.18
32 10 0.12
33 3 0.04
34 5 0.06
35 9 0.11
36 40 0.48
37 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (33 bp):
AAAACATCTTTGAGTATGTTTCTCTTGAAACAA
Found at i:354637 original size:31 final size:33
Alignment explanation
Indices: 354562--354656 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 33
354552 CAAAATTTAC
* *
354562 CATCTTTGAGTCTGTTTCCCTTGAAACAAAACAA
1 CATCTTTGAGTATGTTTCTCTTGAAAC-AAACAA
354596 CAAATCTTTGAGTATGTTT-TCTTGAAACAAA-AA
1 C--ATCTTTGAGTATGTTTCTCTTGAAACAAACAA
* *
354629 CATCTTTGAGTTTGTTTCTCTCGAAACA
1 CATCTTTGAGTATGTTTCTCTTGAAACA
354657 CCGATCTTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
31 15 0.28
32 9 0.17
33 3 0.06
34 4 0.07
35 8 0.15
36 15 0.28
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (33 bp):
CATCTTTGAGTATGTTTCTCTTGAAACAAACAA
Found at i:355091 original size:133 final size:133
Alignment explanation
Indices: 354851--355184 Score: 449
Period size: 133 Copynumber: 2.5 Consensus size: 133
354841 ACCATAATCA
* * *
354851 CTAAAGATGGCCAGAACTCTTCATCA-AGTATGAGCCGTGTCATCCACCGAACAGACCTCCTCAT
1 CTAAAGATGACCAGAACTCTTCATCACA-TATGAGCCGTGTCATCCACCGACCAGATCT-CTCAT
* * * * *
354915 CATGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGC
64 CACGCAGGAGCCGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTATCAC
*
354980 CCTTC
129 CCTAC
354985 C-AAAGATGACCAGAACTCTTCATCACATATGAGCCGTGTCATCCACCGACCAGATCTCTTCATC
1 CTAAAGATGACCAGAACTCTTCATCACATATGAGCCGTGTCATCCACCGACCAGATCTC-TCATC
* * * *
355049 ACGCAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTAGGAACCGAGTTATCACC
65 ACGCAGGAGCCGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTATCACC
355114 CTAC
130 CTAC
* ** * *
355118 CTAAAGATGACCAGAACTCTTCATCACGTATGAGCATTGTCATCC-CTCAACCAGATTTCTCATC
1 CTAAAGATGACCAGAACTCTTCATCACATATGAGCCGTGTCATCCAC-CGACCAGATCTCTCATC
355182 ACG
65 ACG
355185 TATAGCATGT
Statistics
Matches: 178, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
132 1 0.01
133 125 0.70
134 52 0.29
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (133 bp):
CTAAAGATGACCAGAACTCTTCATCACATATGAGCCGTGTCATCCACCGACCAGATCTCTCATCA
CGCAGGAGCCGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTATCACCC
TAC
Found at i:355202 original size:37 final size:40
Alignment explanation
Indices: 355138--355224 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 40
355128 CCAGAACTCT
355138 TCATCACGTATGAGCATTGTCATCCCTCAACCAGATTT-C
1 TCATCACGTATGAGCATTGTCATCCCTCAACCAGATTTCC
355177 TCATCACGTAT-AGCA-TGTCATCCCTCAACCAGATTTCC
1 TCATCACGTATGAGCATTGTCATCCCTCAACCAGATTTCC
355215 TCATCACGTA
1 TCATCACGTA
355225 GTAGTTGTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
37 21 0.45
38 15 0.32
39 11 0.23
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.30
Consensus pattern (40 bp):
TCATCACGTATGAGCATTGTCATCCCTCAACCAGATTTCC
Found at i:355432 original size:3 final size:3
Alignment explanation
Indices: 355419--355476 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
355409 TCTTTTTTAT
*
355419 TTA TT- TTA TTA TTA TTA TTA -TA TTA TTA -TA TTA TTA TTA CTTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
355462 TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA
355477 CATTTACATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 6 0.13
3 39 0.83
4 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:355433 original size:11 final size:11
Alignment explanation
Indices: 355413--355469 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
355403 GTCCGGTCTT
355413 TTTTATTTATT-
1 TTTTA-TTATTA
355424 TTATTATTATTA
1 TT-TTATTATTA
*
355436 TTATATTATTA
1 TTTTATTATTA
*
355447 TATTATTATTA
1 TTTTATTATTA
*
355458 CTTT-TTATTA
1 TTTTATTATTA
355468 TT
1 TT
355470 AATATTACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 7 0.18
11 26 0.68
12 5 0.13
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:355469 original size:19 final size:20
Alignment explanation
Indices: 355420--355481 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 20
355410 CTTTTTTATT
355420 TATTTTATTATTATTATTA-
1 TATTTTATTATTATTATTAC
355439 TATTATTA-TATTATTATTAC
1 TATT-TTATTATTATTATTAC
*
355459 T-TTTTATTATTAATATTAC
1 TATTTTATTATTATTATTAC
355478 -ATTT
1 TATTT
355482 ACATTTTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
18 3 0.08
19 31 0.82
20 4 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTATTATTATTATTAC
Found at i:356280 original size:10 final size:10
Alignment explanation
Indices: 356265--356302 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
356255 TGGAGAGAAT
356265 TTTCTCTCTC
1 TTTCTCTCTC
356275 TTTCTC-C-C
1 TTTCTCTCTC
*
356283 CTTCTCTCTC
1 TTTCTCTCTC
356293 TTTCTCTCTC
1 TTTCTCTCTC
356303 GTAGGCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTCTCTCTC
Found at i:360483 original size:29 final size:29
Alignment explanation
Indices: 360440--360522 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
360430 CTCACCTAAC
360440 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
360470 TAAATGATGTAAGCAATGGCATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
360499 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
360523 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:361008 original size:18 final size:18
Alignment explanation
Indices: 360970--361022 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
360960 GATCGACCCG
*
360970 AAATAATATATTTATTTAA
1 AAATAATATTTTTA-TTAA
360989 AAATAATATTTTTATTAA
1 AAATAATATTTTTATTAA
* *
361007 AAAAAATATTGTTATT
1 AAATAATATTTTTATT
361023 CAATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 18 0.58
19 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
AAATAATATTTTTATTAA
Found at i:361030 original size:18 final size:18
Alignment explanation
Indices: 360985--361033 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
360975 ATATATTTAT
* *
360985 TTAAAAATAATATTTTTA
1 TTAAAAAAAATATTGTTA
361003 TTAAAAAAAATATTGTTA
1 TTAAAAAAAATATTGTTA
*
361021 TTCAATAAAAATA
1 TT-AAAAAAAATA
361034 AGAATTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAAAAAAAATATTGTTA
Found at i:361030 original size:21 final size:20
Alignment explanation
Indices: 360970--361034 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 20
360960 GATCGACCCG
360970 AAATAATATAT-TTATT-TAA
1 AAATAATAT-TGTTATTATAA
*
360989 AAATAATATTTTTATTA-AA
1 AAATAATATTGTTATTATAA
361008 AAA-AATATTGTTATTCAATAA
1 AAATAATATTGTTATT--ATAA
361029 AAATAA
1 AAATAA
361035 GAATTTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 12 0.31
19 19 0.49
20 1 0.03
21 5 0.13
22 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AAATAATATTGTTATTATAA
Found at i:368511 original size:18 final size:18
Alignment explanation
Indices: 368488--368558 Score: 115
Period size: 18 Copynumber: 3.9 Consensus size: 18
368478 AGGGATTATC
*
368488 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
368506 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
368524 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
368542 AGTGGTCATACGGGACA
1 AGTGGTCCTTCGGGACA
368559 AATTCTACGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:370065 original size:65 final size:64
Alignment explanation
Indices: 369910--370089 Score: 227
Period size: 65 Copynumber: 2.8 Consensus size: 64
369900 TGGAAAACTT
* * * * *
369910 AGTGCATCGGTGCACTA-AGTGTGCATCGATGCATAAAAGGCATTTGATGTTTTGAATAAACCTA
1 AGTGCATCGATGCA-TAGAGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAACCTA
* * * * *
369974 AGTGCATCGATGCATAGTGTGTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCATAGAGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAT-AAACCTA
* *
370039 AGTGCATCGATGCATGGAGAGTGCATCGATGCATAAACTGCATTCGATGTT
1 AGTGCATCGATGCATAGAGAGTGCATCGATGCATAAAATGCATTCGATGTT
370090 CAATTTATTT
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
63 2 0.02
64 47 0.47
65 52 0.51
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAGAGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAACCTA
Found at i:372913 original size:15 final size:15
Alignment explanation
Indices: 372893--372931 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
372883 TTCTTGTTCA
372893 TCTTCATCGGAACCT
1 TCTTCATCGGAACCT
372908 TCTTCATCGGAACCT
1 TCTTCATCGGAACCT
372923 TCTTCATCG
1 TCTTCATCG
372932 CTCCATGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.13, T:0.36
Consensus pattern (15 bp):
TCTTCATCGGAACCT
Found at i:374784 original size:64 final size:65
Alignment explanation
Indices: 374716--374842 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 65
374706 GGTGCACTAA
* * *
374716 GTGTGCATCGATACATAAAATGCATTCGATGTTTTGAAT-AAGCCTAAGTACATCGATGCATAGT
1 GTGTGCATCGATACATAAAATGCAATCGATGTTTTCAATAAAACCTAAGTACATCGATGCATAGT
* * * *
374780 GTGTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTGAGTGCATCGATGCATA
1 GTGTGCATCGATACATAAAATGCAATCGATGTTTTCAATAAAACCTAAGTACATCGATGCATA
374843 AACTGCATTC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
64 35 0.64
65 20 0.36
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (65 bp):
GTGTGCATCGATACATAAAATGCAATCGATGTTTTCAATAAAACCTAAGTACATCGATGCATAGT
Found at i:374855 original size:64 final size:63
Alignment explanation
Indices: 374719--374856 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
374709 GCACTAAGTG
* * * * ***
374719 TGCATCGATACATAAAATGCATTCGATGTTTTGAATAAGCCTAAGTACATCGATGCATAGTGTG
1 TGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAACCTAAGTACATCGATGCATAG-AAC
* * *
374783 TGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTGAGTGCATCGATGCATA-AAC
1 TGCATCGATGCATAAAATGCAATCGATGTTTTCAAT-AAACCTAAGTACATCGATGCATAGAAC
374846 TGCATTCGATG
1 TGCA-TCGATG
374857 TTCAATTTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 4 0.06
64 38 0.61
65 20 0.32
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAACCTAAGTACATCGATGCATAGAAC
Found at i:375874 original size:7 final size:7
Alignment explanation
Indices: 375862--375906 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
375852 ATTTATATTT
375862 TTTAAAA
1 TTTAAAA
375869 TTTAAAA
1 TTTAAAA
375876 TTTAAAA
1 TTTAAAA
**
375883 TTTAATT
1 TTTAAAA
*
375890 TTTAACA
1 TTTAAAA
375897 TTTGAAAA
1 TTT-AAAA
375905 TT
1 TT
375907 ATGATCATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (7 bp):
TTTAAAA
Found at i:379870 original size:19 final size:18
Alignment explanation
Indices: 379832--379871 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
379822 TGAAATAAAT
379832 TAAAAATAAAATAATGAA
1 TAAAAATAAAATAATGAA
379850 TAAACAATAATAATAAT-AA
1 TAAA-AATAA-AATAATGAA
379869 TAA
1 TAA
379872 TGGTGACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (18 bp):
TAAAAATAAAATAATGAA
Found at i:380035 original size:30 final size:31
Alignment explanation
Indices: 379967--380055 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
379957 GGTTAAATTA
* *
379967 GTCAAATTGATATATTATCTAAAGTTCAGTG
1 GTCAAAATGATATTTTATCTAAAGTTCAGTG
*
379998 ATCAAAATGATATTTTATCTAAAGTTCAG-G
1 GTCAAAATGATATTTTATCTAAAGTTCAGTG
*
380028 GTCAAAAT-ATTATTATATCTAAAGTTCA
1 GTCAAAATGA-TATTTTATCTAAAGTTCA
380056 AGAATCAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 1 0.02
30 25 0.48
31 26 0.50
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (31 bp):
GTCAAAATGATATTTTATCTAAAGTTCAGTG
Found at i:381020 original size:52 final size:52
Alignment explanation
Indices: 380929--381028 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 52
380919 ATGATCCTCA
* ** * *
380929 ATTATAGGACGTTGCTTTGTTGAGTCTTTCGATTATTAAAGGTTATAACCCG
1 ATTATAGGACGGTGCTTTGTTGAGTCCCTCAATTATTAAAAGTTATAACCCG
* * *
380981 ATTATAGGACGGTGTTTTTTTGAGTCCCTCAATTGTTAAAAGTTATAA
1 ATTATAGGACGGTGCTTTGTTGAGTCCCTCAATTATTAAAAGTTATAA
381029 AATGGTCACC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (52 bp):
ATTATAGGACGGTGCTTTGTTGAGTCCCTCAATTATTAAAAGTTATAACCCG
Found at i:382643 original size:19 final size:19
Alignment explanation
Indices: 382619--382656 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
382609 ATGAATGTTT
382619 TTAAAAAAATAATACTTAG
1 TTAAAAAAATAATACTTAG
*
382638 TTAAAAAAATAATAGTTAG
1 TTAAAAAAATAATACTTAG
382657 ATGACCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
TTAAAAAAATAATACTTAG
Found at i:383276 original size:37 final size:36
Alignment explanation
Indices: 383191--383326 Score: 170
Period size: 37 Copynumber: 3.8 Consensus size: 36
383181 TTTCGTCCTA
383191 CTAGGATTTAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTTAAACTCCTAAAAATAGGATAGAATTTT
*
383226 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTTAAACTCCTAAAAATAGGATAGA-ATTTT
* *
383261 GCTAGGATTTAAACTCCTAAAAATAGGATAGAGTTCTA
1 -CTAGGATTTAAACTCCTAAAAATAGGATAGAATT-TT
* * *
383299 CTAAGATTTAAATTCCTAAAGATAGGAT
1 CTAGGATTTAAACTCCTAAAAATAGGAT
383327 CCACAAGCAC
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
33 1 0.01
34 28 0.32
35 3 0.03
37 54 0.61
38 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (36 bp):
CTAGGATTTAAACTCCTAAAAATAGGATAGAATTTT
Found at i:383919 original size:2 final size:2
Alignment explanation
Indices: 383914--383942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
383904 TCTTATACTT
383914 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 T
383943 TATTTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:384133 original size:2 final size:2
Alignment explanation
Indices: 384128--384166 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
384118 TACTTTGATG
384128 TA TA 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 TA TA T
384167 TTCCTTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:384237 original size:9 final size:9
Alignment explanation
Indices: 384215--384249 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
384205 CTATTTTTTC
384215 TTTTATCTTA
1 TTTTAT-TTA
384225 -TTTATTTA
1 TTTTATTTA
384233 TTTTATTTA
1 TTTTATTTA
384242 TTTTATTT
1 TTTTATTT
384250 TTCCTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTATTTA
Found at i:384238 original size:13 final size:14
Alignment explanation
Indices: 384215--384250 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
384205 CTATTTTTTC
*
384215 TTTTATCTTATTTA
1 TTTTATTTTATTTA
384229 -TTTATTTTATTTA
1 TTTTATTTTATTTA
384242 TTTTATTTT
1 TTTTATTTT
384251 TCCTTTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:386901 original size:14 final size:14
Alignment explanation
Indices: 386882--386914 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
386872 AAAGAAGAAG
*
386882 AATTCATCTGAAAT
1 AATTCATCCGAAAT
386896 AATTCATCCGAAAT
1 AATTCATCCGAAAT
386910 AATTC
1 AATTC
386915 TATCATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (14 bp):
AATTCATCCGAAAT
Found at i:387238 original size:9 final size:9
Alignment explanation
Indices: 387224--387290 Score: 59
Period size: 9 Copynumber: 7.7 Consensus size: 9
387214 AGATCCAATC
387224 AAGAAAAAA
1 AAGAAAAAA
*
387233 AAG-AAAAG
1 AAGAAAAAA
*
387241 AAG-CAAAA
1 AAGAAAAAA
*
387249 GA-AAAAAA
1 AAGAAAAAA
387257 AAGAAAAAA
1 AAGAAAAAA
* *
387266 GAGAAACAA
1 AAGAAAAAA
387275 AAGAACAAAA
1 AAGAA-AAAA
387285 AAGAAA
1 AAGAAA
387291 GAACAAAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
8 16 0.36
9 21 0.47
10 8 0.18
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:387258 original size:19 final size:18
Alignment explanation
Indices: 387230--387284 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
387220 AATCAAGAAA
387230 AAAAAGAAAAGAAGCAAAAG
1 AAAAA-AAAAGAA-CAAAAG
387250 AAAAAAAAAGAA-AAAAG
1 AAAAAAAAAGAACAAAAG
*
387267 AGAAACAAAAGAACAAAA
1 A-AAAAAAAAGAACAAAA
387285 AAGAAAGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 6 0.19
18 10 0.31
19 11 0.34
20 5 0.16
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAACAAAAG
Found at i:387270 original size:28 final size:27
Alignment explanation
Indices: 387227--387290 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 27
387217 TCCAATCAAG
* *
387227 AAAAAA-AAGAAAAGAAGCAAAAGAAA
1 AAAAAAGAAAAAAAGAAACAAAAGAAA
*
387253 AAAAAAGAAAAAAGAGAAACAAAAGAAC
1 AAAAAAGAAAAAA-AGAAACAAAAGAAA
387281 AAAAAAGAAA
1 AAAAAAGAAA
387291 GAACAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 6 0.18
27 5 0.15
28 22 0.67
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAAAAAAGAAACAAAAGAAA
Found at i:387289 original size:19 final size:17
Alignment explanation
Indices: 387227--387317 Score: 64
Period size: 18 Copynumber: 5.3 Consensus size: 17
387217 TCCAATCAAG
*
387227 AAAAAAAAGAAAAGAAGC
1 AAAAAAAAAAAAAGAA-C
387245 AAAAGAAAAAAAAAGAA-
1 AAAA-AAAAAAAAAGAAC
*
387262 AAAAGAGAAACAAAAGAAC
1 AAAA-A-AAAAAAAAGAAC
*
387281 ---AAAAAAGAAAGAAC
1 AAAAAAAAAAAAAGAAC
**
387295 AAAAATAAAAAAGGGAAC
1 AAAAA-AAAAAAAAGAAC
387313 AAAAA
1 AAAAA
387318 GCACATGCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 1 0.02
17 8 0.14
18 28 0.47
19 11 0.19
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.01
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAC
Found at i:387293 original size:14 final size:14
Alignment explanation
Indices: 387246--387299 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
387236 AAAAGAAGCA
*
387246 AAAGAAAAAAAAAG
1 AAAGAACAAAAAAG
* * *
387260 AAAAAAGAGAAACA-
1 AAAGAACA-AAAAAG
387274 AAAGAACAAAAAAG
1 AAAGAACAAAAAAG
387288 AAAGAACAAAAA
1 AAAGAACAAAAA
387300 TAAAAAAGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 4 0.12
14 24 0.75
15 4 0.12
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAGAACAAAAAAG
Found at i:387304 original size:28 final size:28
Alignment explanation
Indices: 387244--387304 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
387234 AGAAAAGAAG
* *
387244 CAAAAGAAAAAAAAAGAAAAAAGAGAAA
1 CAAAAGAAAAAAAAAGAAAAAACAAAAA
* *
387272 CAAAAGAACAAAAAAGAAAGAACAAAAA
1 CAAAAGAAAAAAAAAGAAAAAACAAAAA
*
387300 TAAAA
1 CAAAA
387305 AAGGGAACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (28 bp):
CAAAAGAAAAAAAAAGAAAAAACAAAAA
Found at i:388826 original size:36 final size:36
Alignment explanation
Indices: 388786--388907 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 36
388776 ACTCATGATT
* * *
388786 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
* * * * *
388822 GTTT-TCACTAGAA-GAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAGATTTGTCTCCCTTGAGACA
* *
388857 GTTTCCCTTGAAACAA-ATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAGA-TTTGTCTCCCTTGAGACA
*
388893 GTTTCTCTTGAAACA
1 GTTTCTCTTAAAACA
388908 TAAACATTGA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
35 27 0.40
36 41 0.60
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
Found at i:388986 original size:37 final size:36
Alignment explanation
Indices: 388923--389047 Score: 171
Period size: 36 Copynumber: 3.4 Consensus size: 36
388913 ATTGAAAACA
* * *
388923 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
388959 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
* *
388996 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAG
389032 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
389048 ATCTTTGAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
35 4 0.05
36 43 0.54
37 33 0.41
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:388990 original size:138 final size:138
Alignment explanation
Indices: 388836--389110 Score: 383
Period size: 138 Copynumber: 2.0 Consensus size: 138
388826 TCACTAGAAG
* *
388836 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTC
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AATTTTCGTCTACCTTGAGACAGTTTCCC
* * * * * *
388900 TTGAAACATAAA-CATTGAAAACATTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCT
65 TTGAAACA-AAATCATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTTACT
388964 CTTGAAACAA
129 CTTGAAACAA
* *
388974 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAGTTTCCCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAATTTTCGTCTACCTTGAGACAGTTTCCCT
* *** *
389039 TGAAACAAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCT
66 TGAAACAAAATCATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTTACTCT
389104 TGAAACA
131 TGAAACA
389111 CAAAATCTTC
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 9 0.08
138 111 0.93
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (138 bp):
AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAATTTTCGTCTACCTTGAGACAGTTTCCCT
TGAAACAAAATCATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTTACTCT
TGAAACAA
Found at i:389109 original size:65 final size:65
Alignment explanation
Indices: 389005--389179 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 65
388995 GTTTCTCTTG
** * **
389005 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCT
389069 A
65 A
* *
389070 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
389135 TA
64 TA
* * *
389137 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
389180 CAGATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 25 0.26
66 12 0.13
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:389139 original size:67 final size:67
Alignment explanation
Indices: 388996--389178 Score: 219
Period size: 68 Copynumber: 2.7 Consensus size: 67
388986 CTTGAGACAG
* * ** * **
388996 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
389058 TTA
65 TTA
* *
389061 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
389126 TA
66 TA
* * *
389128 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
389179 ACAGATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 31 0.31
66 8 0.08
67 29 0.29
68 32 0.32
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:389946 original size:105 final size:103
Alignment explanation
Indices: 389783--390640 Score: 1234
Period size: 105 Copynumber: 8.3 Consensus size: 103
389773 GCCATCCGCG
* * * * * *
389783 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACGATGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
389848 GGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
63 GGGACCGCTGCTTGTCAACAACAACTT-CCAAT-TCAGAGCCA
*
389891 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
389956 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAAC-TTCCAAT-TCAGAGCCA
389996 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
390061 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATTCAGAGCCA
* *
390096 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
390161 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAAC-TTCCAAT-TCAGAGCCA
390201 ATTTCAACTTCACAACGAAGG--ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
390264 ACCGCTGCTTGCCAACAA-AA-TTTC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATTCAGAGCCA
* *
390299 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
390364 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTT-CCAAT-TCAGAGCCA
*
390404 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
390469 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCAATTCAGAGCCA
* * *
390504 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
390569 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTT-CCAATT-CAGAGCCA
* *
390610 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
390641 TGGAACAATG
Statistics
Matches: 688, Mismatches: 43, Indels: 40
0.89 0.06 0.05
Matches are distributed among these distances:
98 29 0.04
99 2 0.00
100 231 0.34
101 10 0.01
102 10 0.01
103 66 0.10
104 9 0.01
105 269 0.39
106 40 0.06
108 22 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (103 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCAATTCAGAGCCA
Found at i:390176 original size:205 final size:205
Alignment explanation
Indices: 389783--390640 Score: 1346
Period size: 205 Copynumber: 4.2 Consensus size: 205
389773 GCCATCCGCG
* * * * * *
389783 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACGATGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
389848 GGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGA
63 GGGACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGA
389913 TATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAAC
123 TATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAAC
389978 TTTCCAATCTCAGAGCCA
188 TTTCCAATCTCAGAGCCA
389996 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
390061 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
390126 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
390191 CTCAGAGCCA
196 CTCAGAGCCA
390201 ATTTCAACTTCACAACGAAGG--ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
390264 ACCGCTGCTTGCCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
390329 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
390394 CCCAGAGCCA
196 CTCAGAGCCA
*
390404 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
390469 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** * * * *
390534 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCG
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTT-CCA
*
390598 GT-TCCAGAGCCA
194 ATCT-CAGAGCCA
* *
390610 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
390641 TGGAACAATG
Statistics
Matches: 609, Mismatches: 31, Indels: 17
0.93 0.05 0.03
Matches are distributed among these distances:
203 198 0.33
205 284 0.47
206 46 0.08
207 1 0.00
208 2 0.00
209 2 0.00
210 51 0.08
211 3 0.00
213 22 0.04
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (205 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
CTCAGAGCCA
Found at i:391231 original size:34 final size:37
Alignment explanation
Indices: 391187--391288 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
391177 TTTCGTCCTA
391187 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
391222 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
391257 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
391289 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:391272 original size:37 final size:35
Alignment explanation
Indices: 391187--391322 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 35
391177 TTTCGTCCTA
391187 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
391222 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
391257 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
391294 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
391323 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:391916 original size:2 final size:2
Alignment explanation
Indices: 391911--391951 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
391901 CTTATAACTT
391911 TA TA TA 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 TA TA TA T
391952 TTTCGTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:392228 original size:22 final size:22
Alignment explanation
Indices: 392203--392270 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
392193 ATTACTTTAC
392203 TATTTTTTTCTTTTATCTTATT
1 TATTTTTTTCTTTTATCTTATT
*
392225 TA----TTTATTTTAT-TTATTT
1 TATTTTTTTCTTTTATCTTA-TT
* *
392243 TATTTTTTCCTTTTACCTTATT
1 TATTTTTTTCTTTTATCTTATT
*
392265 TGTTTT
1 TATTTT
392271 ATTTACCTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
17 3 0.09
18 13 0.37
22 16 0.46
23 3 0.09
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.75
Consensus pattern (22 bp):
TATTTTTTTCTTTTATCTTATT
Found at i:392235 original size:9 final size:9
Alignment explanation
Indices: 392203--392247 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
392193 ATTACTTTAC
392203 TATTTT-TT
1 TATTTTATT
*
392211 TCTTTTATCT
1 TATTTTAT-T
392221 TA-TTTATT
1 TATTTTATT
392229 TATTTTATT
1 TATTTTATT
392238 TATTTTATT
1 TATTTTATT
392247 T
1 T
392248 TTTCCTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 8 0.25
9 22 0.69
10 2 0.06
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (9 bp):
TATTTTATT
Found at i:392236 original size:13 final size:14
Alignment explanation
Indices: 392203--392248 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
392193 ATTACTTTAC
*
392203 TATTTT-TTTCTTT
1 TATTTTATTTATTT
*
392216 TATCTTATTTA-TT
1 TATTTTATTTATTT
392229 TATTTTATTTATTT
1 TATTTTATTTATTT
392243 TATTTT
1 TATTTT
392249 TTCCTTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:392275 original size:18 final size:17
Alignment explanation
Indices: 392224--392279 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
392214 TTTATCTTAT
**
392224 TTATTTATTTTATTTATT
1 TTATTT-TTTTATTTACC
392242 TTATTTTTTCCT-TTTACC
1 TTATTTTTT--TATTTACC
392260 TTATTTGTTTTATTTACC
1 TTATTT-TTTTATTTACC
392278 TT
1 TT
392280 GTTTATCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.12
18 24 0.75
19 4 0.12
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTTTTTATTTACC
Found at i:393994 original size:24 final size:22
Alignment explanation
Indices: 393959--394019 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
393949 TTTATCATTT
*
393959 TTAATTTTTTAATAAACTTTCTC
1 TTAATTTTTTAA-AAAATTTCTC
393982 TTAATTATTTTAAAAAATTTCATC
1 TTAATT-TTTTAAAAAATTTC-TC
*
394006 --ATTTTTTTAAAAAA
1 TTAATTTTTTAAAAAA
394020 AAAAACTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 10 0.29
22 3 0.09
23 13 0.38
24 8 0.24
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTTTTTAAAAAATTTCTC
Found at i:400425 original size:2 final size:2
Alignment explanation
Indices: 400418--400442 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
400408 CTAAAATGTT
400418 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 T
400443 TAATAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:401581 original size:3 final size:3
Alignment explanation
Indices: 401573--401661 Score: 88
Period size: 3 Copynumber: 28.0 Consensus size: 3
401563 TATATAAAGA
* * * *
401573 AAG AAG AAG AAG AAG AAT AGG AAG AAAG AAG AAG AAG AAG AAT AGG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG
*
401619 AAG AAAG AAG AAG AAG AAG AAG CATG AAG AAAG AATG AAG AAG
1 AAG -AAG AAG AAG AAG AAG AAG -AAG AAG -AAG AA-G AAG AAG
401662 GAGGAGGAGG
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
3 57 0.80
4 14 0.20
ACGTcount: A:0.63, C:0.01, G:0.31, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:401597 original size:25 final size:25
Alignment explanation
Indices: 401569--401661 Score: 150
Period size: 25 Copynumber: 3.6 Consensus size: 25
401559 AAGATATATA
401569 AAGAAAGAAGAAGAAGAAGAATAGG
1 AAGAAAGAAGAAGAAGAAGAATAGG
401594 AAGAAAGAAGAAGAAGAAGAATAGG
1 AAGAAAGAAGAAGAAGAAGAATAGG
* *
401619 AAGAAAGAAGAAGAAGAAGAAGCATG
1 AAGAAAGAAGAAGAAGAAGAA-TAGG
401645 AAGAAAGAATGAAGAAG
1 AAGAAAGAA-GAAGAAG
401662 GAGGAGGAGG
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 46 0.72
26 11 0.17
27 7 0.11
ACGTcount: A:0.63, C:0.01, G:0.31, T:0.04
Consensus pattern (25 bp):
AAGAAAGAAGAAGAAGAAGAATAGG
Found at i:401666 original size:3 final size:3
Alignment explanation
Indices: 401660--401684 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
401650 AGAATGAAGA
401660 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
401685 TGAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:402100 original size:18 final size:18
Alignment explanation
Indices: 402077--402112 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
402067 TCTCATTCTC
*
402077 TTGAAAATATTAAACACA
1 TTGAAAATACTAAACACA
402095 TTGAAAATACTAAACACA
1 TTGAAAATACTAAACACA
402113 GTTGTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (18 bp):
TTGAAAATACTAAACACA
Found at i:409022 original size:160 final size:157
Alignment explanation
Indices: 408758--409073 Score: 542
Period size: 160 Copynumber: 2.0 Consensus size: 157
408748 TTTTAACACT
*
408758 CTCTTAAGTTGGAGGTTTAAATATATTTCTAACCCCTAACTTGGACATTAAACACTCATGCTGCT
1 CTCTTAAGTTGGAGGTTTAAATATATCTCTAACCCCTAACTTGGACATTAAACACTCATGCTGCT
* *
408823 TCACACTCGGAGACTCTATGAAGATGTCTGCTAATTGTTCTGGGGTAGAAACGTGGCTTGTCTTA
66 TCACACTCAGAGACTCTATGAAGATGTCTGCTAATTGTTCTGGGGTAGAAACGCGGCTTGTCTTA
408888 ATTAGTCATTCTTGTATCTTTTCAAAAACA
131 ATTAGTC---CTTGTATCTTTTCAAAAACA
**
408918 CTCTTAAGTTGGAGGTTTAAATATATCTCTAACCCCTAACTTGGACATTAAACACTTGTGCTGCT
1 CTCTTAAGTTGGAGGTTTAAATATATCTCTAACCCCTAACTTGGACATTAAACACTCATGCTGCT
* *
408983 TCACACTCAGAGACTCTATGAAGATGTCTGCTAATTGTTCTGTGGTAGAAACGCGGCTTGTCTTT
66 TCACACTCAGAGACTCTATGAAGATGTCTGCTAATTGTTCTGGGGTAGAAACGCGGCTTGTCTTA
409048 ATTAGTCCTTGTATCTTTTCAAAAAC
131 ATTAGTCCTTGTATCTTTTCAAAAAC
409074 CTAGAGGCAA
Statistics
Matches: 149, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
157 19 0.13
160 130 0.87
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (157 bp):
CTCTTAAGTTGGAGGTTTAAATATATCTCTAACCCCTAACTTGGACATTAAACACTCATGCTGCT
TCACACTCAGAGACTCTATGAAGATGTCTGCTAATTGTTCTGGGGTAGAAACGCGGCTTGTCTTA
ATTAGTCCTTGTATCTTTTCAAAAACA
Found at i:423981 original size:74 final size:74
Alignment explanation
Indices: 423889--424040 Score: 304
Period size: 74 Copynumber: 2.1 Consensus size: 74
423879 TTAAGATATG
423889 ATATCAATGTAATTAATTTATGTTCATATAGAATTTTCATCTTGATAAATACTGTATACTAATTC
1 ATATCAATGTAATTAATTTATGTTCATATAGAATTTTCATCTTGATAAATACTGTATACTAATTC
423954 AGTTAAATC
66 AGTTAAATC
423963 ATATCAATGTAATTAATTTATGTTCATATAGAATTTTCATCTTGATAAATACTGTATACTAATTC
1 ATATCAATGTAATTAATTTATGTTCATATAGAATTTTCATCTTGATAAATACTGTATACTAATTC
424028 AGTTAAATC
66 AGTTAAATC
424037 ATAT
1 ATAT
424041 GTGCATATAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (74 bp):
ATATCAATGTAATTAATTTATGTTCATATAGAATTTTCATCTTGATAAATACTGTATACTAATTC
AGTTAAATC
Found at i:428733 original size:5 final size:5
Alignment explanation
Indices: 428725--428755 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
428715 AAATAATTAA
428725 AAATT AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT AAATT A
428756 CTAAAAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AAATT
Found at i:431589 original size:168 final size:168
Alignment explanation
Indices: 431311--431646 Score: 672
Period size: 168 Copynumber: 2.0 Consensus size: 168
431301 GAACTGCGAT
431311 GGTTTTTTATCAGGGATGATGTTTGCTATTTTGTATTCAAGCCTTGCTATGGTGTACTTTTTTTA
1 GGTTTTTTATCAGGGATGATGTTTGCTATTTTGTATTCAAGCCTTGCTATGGTGTACTTTTTTTA
431376 CCATTTAGGTTTAGGGAAGTTTTGAATGAAGCATCGGAATATAAATTTCAATAAATAAAATCTTT
66 CCATTTAGGTTTAGGGAAGTTTTGAATGAAGCATCGGAATATAAATTTCAATAAATAAAATCTTT
431441 AATTGCTGAGCAAAAAATATTAGGTGAATAATTCTGGA
131 AATTGCTGAGCAAAAAATATTAGGTGAATAATTCTGGA
431479 GGTTTTTTATCAGGGATGATGTTTGCTATTTTGTATTCAAGCCTTGCTATGGTGTACTTTTTTTA
1 GGTTTTTTATCAGGGATGATGTTTGCTATTTTGTATTCAAGCCTTGCTATGGTGTACTTTTTTTA
431544 CCATTTAGGTTTAGGGAAGTTTTGAATGAAGCATCGGAATATAAATTTCAATAAATAAAATCTTT
66 CCATTTAGGTTTAGGGAAGTTTTGAATGAAGCATCGGAATATAAATTTCAATAAATAAAATCTTT
431609 AATTGCTGAGCAAAAAATATTAGGTGAATAATTCTGGA
131 AATTGCTGAGCAAAAAATATTAGGTGAATAATTCTGGA
431647 ATAGCTGAAT
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (168 bp):
GGTTTTTTATCAGGGATGATGTTTGCTATTTTGTATTCAAGCCTTGCTATGGTGTACTTTTTTTA
CCATTTAGGTTTAGGGAAGTTTTGAATGAAGCATCGGAATATAAATTTCAATAAATAAAATCTTT
AATTGCTGAGCAAAAAATATTAGGTGAATAATTCTGGA
Found at i:432340 original size:27 final size:28
Alignment explanation
Indices: 432307--432360 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
432297 TTTTTAAAAT
432307 GAAGATTCTAAAAACAATTCC-ATTAAC
1 GAAGATTCTAAAAACAATTCCTATTAAC
**
432334 GAAGATTCTAAAAGTAATTCCTATTAA
1 GAAGATTCTAAAAACAATTCCTATTAA
432361 TTTTAATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (28 bp):
GAAGATTCTAAAAACAATTCCTATTAAC
Found at i:433391 original size:27 final size:28
Alignment explanation
Indices: 433358--433411 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
433348 TTTTTAAAAT
433358 GAAGATTCTAAAAACAATTCC-ATTAAC
1 GAAGATTCTAAAAACAATTCCTATTAAC
**
433385 GAAGATTCTAAAAGTAATTCCTATTAA
1 GAAGATTCTAAAAACAATTCCTATTAA
433412 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (28 bp):
GAAGATTCTAAAAACAATTCCTATTAAC
Found at i:435914 original size:29 final size:32
Alignment explanation
Indices: 435856--435915 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
435846 ATTTTAAATC
* *
435856 CCTAATTTTTTAACCTTAAACCTCTATTCATA
1 CCTAATTTTTTAACCTTAAACATCCATTCATA
435888 CCTAA-TTTTTAA-C-TAAACATCCATTCAT
1 CCTAATTTTTTAACCTTAAACATCCATTCAT
435916 GGAAAAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 1 0.04
31 7 0.27
32 5 0.19
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (32 bp):
CCTAATTTTTTAACCTTAAACATCCATTCATA
Found at i:436166 original size:30 final size:31
Alignment explanation
Indices: 436106--436170 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
436096 TATGTCATTA
**
436106 AAAAAATAAAGAAAAAACAAAATGCTATATG
1 AAAAAATAAAGAAAAAACAAAATGAAATATG
*
436137 AAAAAATAGAAG-AAAAA-AATATGAAATATG
1 AAAAAATA-AAGAAAAAACAAAATGAAATATG
436167 AAAA
1 AAAA
436171 TAACTTGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 14 0.47
31 13 0.43
32 3 0.10
ACGTcount: A:0.71, C:0.03, G:0.11, T:0.15
Consensus pattern (31 bp):
AAAAAATAAAGAAAAAACAAAATGAAATATG
Found at i:436832 original size:21 final size:20
Alignment explanation
Indices: 436815--436853 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
436805 TATATTTCTA
436815 TATTT-TTATGACACATTTT
1 TATTTCTTATGACACATTTT
* *
436834 TATTTCTTTTGACACGTTTT
1 TATTTCTTATGACACATTTT
436854 CGATCTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.59
Consensus pattern (20 bp):
TATTTCTTATGACACATTTT
Found at i:437631 original size:20 final size:21
Alignment explanation
Indices: 437606--437657 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
437596 TTTTCCCAAT
*
437606 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
437626 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
437647 TCGCAATGCGA
1 TCGCAATGCGA
437658 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:437701 original size:21 final size:21
Alignment explanation
Indices: 437667--437739 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
437657 ATACTGACTA
* *
437667 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
437688 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
437708 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
437729 TCGCAATGCGA
1 TCGCAATGCGA
437740 GTACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Done.