Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 15 of 343
Found at i:5247027 original size:17 final size:17
Alignment explanation
Indices: 5246990--5247027 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5246980 TTAGATTTTC
*
5246990 TTATTTGTATTTATTTG
1 TTATTTGTATTTATTTA
5247007 TTATTTGTGATTTA-TTA
1 TTATTTGT-ATTTATTTA
5247024 TTAT
1 TTAT
5247028 AACATTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (17 bp):
TTATTTGTATTTATTTA
Found at i:5250085 original size:3 final size:3
Alignment explanation
Indices: 5250077--5250105 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5250067 GATCCCAACA
5250077 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5250106 CTTCTACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5250580 original size:56 final size:58
Alignment explanation
Indices: 5250520--5250673 Score: 170
Period size: 56 Copynumber: 2.7 Consensus size: 58
5250510 AGTAGTTACG
* *
5250520 TAGGAATTAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAATAT-T-ATAT
1 TAGGAATTAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAACATCTCATAA
* * * * **
5250576 TAGGAATTAAATTGTTAAGAGATAATATCCTATTATAATATTTTATAACATCTCATAA
1 TAGGAATTAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAACATCTCATAA
* * * * *
5250634 T-GAAATCAAATTGCTAAAAAATAATATCACTTAATAATAT
1 TAGGAATTAAATTGCTAAAAGATAATATCCCATAATAATAT
5250674 ATTTTATCAT
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
56 44 0.56
57 31 0.39
58 4 0.05
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (58 bp):
TAGGAATTAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAACATCTCATAA
Found at i:5252285 original size:17 final size:18
Alignment explanation
Indices: 5252251--5252288 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5252241 CTGGTTAGAG
* *
5252251 TTTTAGCCATCTTTTCTT
1 TTTTAACCATCTTCTCTT
5252269 TTTTAACCATC-TCTCTT
1 TTTTAACCATCTTCTCTT
5252286 TTT
1 TTT
5252289 AATTCTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.13, C:0.24, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTAACCATCTTCTCTT
Found at i:5254509 original size:12 final size:12
Alignment explanation
Indices: 5254478--5254511 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
5254468 AAAAGAGAGA
5254478 AAATATTTGTCTG
1 AAAT-TTTGTCTG
5254491 AAGATTTTGTCTG
1 AA-ATTTTGTCTG
5254504 AAATTTTG
1 AAATTTTG
5254512 ATGTGGTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 12 0.60
14 2 0.10
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (12 bp):
AAATTTTGTCTG
Found at i:5266796 original size:46 final size:46
Alignment explanation
Indices: 5266721--5266902 Score: 258
Period size: 46 Copynumber: 4.0 Consensus size: 46
5266711 TTATCTTCGG
* * * * *
5266721 CATGATGCCATAGTGTCTTTCAACTATGGTCTTGCTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
*
5266767 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
5266813 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACCCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
5266859 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
5266903 TTCAGAAAGC
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.03
46 119 0.97
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:5268907 original size:50 final size:50
Alignment explanation
Indices: 5268848--5268948 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
5268838 GGGAAACAAG
5268848 TATGCTTATTAAAGAATAAGATTGTAAACATGAATGCTTGTGATGATATA
1 TATGCTTATTAAAGAATAAGATTGTAAACATGAATGCTTGTGATGATATA
*
5268898 TATGCTTATTAAAGAATAAGATTGTAAATATGAATGCTTGTGATGATATA
1 TATGCTTATTAAAGAATAAGATTGTAAACATGAATGCTTGTGATGATATA
5268948 T
1 T
5268949 CATGTTGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.38
Consensus pattern (50 bp):
TATGCTTATTAAAGAATAAGATTGTAAACATGAATGCTTGTGATGATATA
Found at i:5270058 original size:46 final size:46
Alignment explanation
Indices: 5270001--5270228 Score: 350
Period size: 46 Copynumber: 5.0 Consensus size: 46
5269991 TTTGACATGA
* * * * * *
5270001 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *
5270047 TGCCATGGTGTCTTTCAACCATGGTATTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5270093 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5270139 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5270185 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5270229 AGAGCACACT
Statistics
Matches: 171, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
45 4 0.02
46 167 0.98
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:5270285 original size:162 final size:162
Alignment explanation
Indices: 5270105--5270591 Score: 965
Period size: 162 Copynumber: 3.0 Consensus size: 162
5270095 CCATGGTATC
5270105 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
*
5270170 CATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
66 CATTTCATAACAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
5270235 CACTCCCGCGAACCTCATCCTTACAGTGGGAT
131 CACTCCCGCGAACCTCATCCTTACAGTGGGAT
5270267 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
5270332 CATTTCATAACAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
66 CATTTCATAACAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
5270397 CACTCCCGCGAACCTCATCCTTACAGTGGGAT
131 CACTCCCGCGAACCTCATCCTTACAGTGGGAT
5270429 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
5270494 CATTTCATAACAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
66 CATTTCATAACAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
5270559 CACTCCCGCGAACCTCATCCTTACAGTGGGAT
131 CACTCCCGCGAACCTCATCCTTACAGTGGGAT
5270591 T
1 T
5270592 ACCAGTCCAG
Statistics
Matches: 324, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 324 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.32
Consensus pattern (162 bp):
TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
CATTTCATAACAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
CACTCCCGCGAACCTCATCCTTACAGTGGGAT
Found at i:5270334 original size:46 final size:46
Alignment explanation
Indices: 5270267--5270390 Score: 221
Period size: 46 Copynumber: 2.7 Consensus size: 46
5270257 ACAGTGGGAT
*
5270267 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATC
*
5270313 TTTCAACCATGGTCTTACACATTTCATAACAGGCTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATC
*
5270359 TTTCAACCATGGTCTTACACATTTCATTTCAG
1 TTTCAACCATGGTCTTACACATTTCATATCAG
5270391 AGAGCACACT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATC
Found at i:5270481 original size:208 final size:205
Alignment explanation
Indices: 5270013--5270547 Score: 557
Period size: 208 Copynumber: 2.6 Consensus size: 205
5270003 CCATAGTGTC
* * * * *
5270013 TTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTGTCTTTCAACCATGGTATTACA
1 TTTCAACCATGGTCTTACACA-TTTCTATCA-GTTGCCATGGTATCTTTCAACCATGGTCTTACA
* *
5270078 CATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCC
64 CATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAACAGGCTGCC
* *** *
5270143 ATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATG
129 ATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCAGCCA--G-ATCCCGCAACCATC
* **
5270208 GTCTTACACATTTCA
191 ATCTTACACATGGCA
* *** *** ** * * *
5270223 TTTCAGAGAGCACACTCCCGCGA-ACCTC-ATC-CTT-ACAGTGGGAT-TTTCAACCATGGTCTT
1 TTTC--A-ACCATGGTCTTAC-ACATTTCTATCAGTTGCCA-TGGTATCTTTCAACCATGGTCTT
5270283 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAACAGGCT
61 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAACAGGCT
* *
5270348 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAG-AGCACA-CTCCCGCGAACC
126 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG-GCAGC-CAGATCCCGC-AACC
* *
5270411 -TCATCCTTACA-GTGGGA
188 ATCAT-CTTACACATGGCA
5270428 TTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 -TTTCAACCATGGTCTTACACATTTC-TATCA-GTTGCCATGGTATCTTTCAACCATGGTCTTAC
* *
5270493 ACATTTCATAACAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
63 ACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
5270548 TTCAGAGAGC
Statistics
Matches: 263, Mismatches: 45, Indels: 36
0.76 0.13 0.10
Matches are distributed among these distances:
202 1 0.00
203 9 0.03
204 1 0.00
205 10 0.04
206 14 0.05
207 7 0.03
208 197 0.75
209 9 0.03
210 4 0.02
211 2 0.01
212 3 0.01
213 6 0.02
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (205 bp):
TTTCAACCATGGTCTTACACATTTCTATCAGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
TTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAACAGGCTGCCAT
GGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCAGCCAGATCCCGCAACCATCATCTT
ACACATGGCA
Found at i:5270496 original size:46 final size:46
Alignment explanation
Indices: 5270429--5270552 Score: 221
Period size: 46 Copynumber: 2.7 Consensus size: 46
5270419 ACAGTGGGAT
*
5270429 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATC
*
5270475 TTTCAACCATGGTCTTACACATTTCATAACAGGCTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATC
*
5270521 TTTCAACCATGGTCTTACACATTTCATTTCAG
1 TTTCAACCATGGTCTTACACATTTCATATCAG
5270553 AGAGCACACT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATC
Found at i:5273410 original size:70 final size:70
Alignment explanation
Indices: 5273297--5273435 Score: 269
Period size: 70 Copynumber: 2.0 Consensus size: 70
5273287 GGGCATGTGA
5273297 GCCTTGCACATTGGAAAATTTTTAAAAAGTCACAAAAAATTCTTAGAGGTCTCAATTAAGTCCCA
1 GCCTTGCACATTGGAAAATTTTTAAAAAGTCACAAAAAATTCTTAGAGGTCTCAATTAAGTCCCA
5273362 ACTCT
66 ACTCT
*
5273367 GCCTTGCACCTTGGAAAATTTTTAAAAAGTCACAAAAAATTCTTAGAGGTCTCAATTAAGTCCCA
1 GCCTTGCACATTGGAAAATTTTTAAAAAGTCACAAAAAATTCTTAGAGGTCTCAATTAAGTCCCA
5273432 ACTC
66 ACTC
5273436 GATTATAATG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (70 bp):
GCCTTGCACATTGGAAAATTTTTAAAAAGTCACAAAAAATTCTTAGAGGTCTCAATTAAGTCCCA
ACTCT
Found at i:5279805 original size:17 final size:17
Alignment explanation
Indices: 5279783--5279818 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5279773 AAAAATAAGA
*
5279783 TTTTTACAATATTCATT
1 TTTTTAAAATATTCATT
*
5279800 TTTTTAAAATTTTCATT
1 TTTTTAAAATATTCATT
5279817 TT
1 TT
5279819 AAATTATGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTAAAATATTCATT
Found at i:5281392 original size:213 final size:214
Alignment explanation
Indices: 5280992--5281418 Score: 838
Period size: 213 Copynumber: 2.0 Consensus size: 214
5280982 TATCTTAATC
5280992 ATGATGGACATTCATTTAATAAGATATTCATAACAATATTCTATTTTTTGGCATCATTTTTATCG
1 ATGATGGACATTCATTTAATAAGATATTCATAACAATATTCTATTTTTTGGCATCATTTTTATCG
5281057 AATAATTATTAAGAACAAATATAAAATTTTTTTTTTCTAAATTTTGAATATATAAAACATTTAAA
66 AATAATTATTAAGAACAAATATAAAATTTTTTTTTTCTAAATTTTGAATATATAAAACATTTAAA
*
5281122 TCTTCAAAATTTAGACATGAAATAGGATAATTGTGCGTGTGGAATTTTTAGATTTTTAAATTTTA
131 TCTTCAAAATTTAGACATGAAATAGCATAATTGTGCGTGTGGAATTTTTAGATTTTTAAATTTTA
5281187 TATATAAATTATCATGTAT
196 TATATAAATTATCATGTAT
5281206 ATGATGGACATTCATTTAATAAGATATTCATAACAATATTCTATTTTTTGGCATCATTTTTATCG
1 ATGATGGACATTCATTTAATAAGATATTCATAACAATATTCTATTTTTTGGCATCATTTTTATCG
5281271 AATAATTATTAAGAACAAATAT-AAATTTTTTTTTTCTAAATTTTGAATATATAAAACATTTAAA
66 AATAATTATTAAGAACAAATATAAAATTTTTTTTTTCTAAATTTTGAATATATAAAACATTTAAA
5281335 TCTTCAAAATTTAGACATGAAATAGCATAATTGTGCGTGTGGAATTTTTAGATTTTTAAATTTTA
131 TCTTCAAAATTTAGACATGAAATAGCATAATTGTGCGTGTGGAATTTTTAGATTTTTAAATTTTA
5281400 TATATAAATTATCATGTAT
196 TATATAAATTATCATGTAT
5281419 TTTAGATTTG
Statistics
Matches: 212, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
213 125 0.59
214 87 0.41
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.44
Consensus pattern (214 bp):
ATGATGGACATTCATTTAATAAGATATTCATAACAATATTCTATTTTTTGGCATCATTTTTATCG
AATAATTATTAAGAACAAATATAAAATTTTTTTTTTCTAAATTTTGAATATATAAAACATTTAAA
TCTTCAAAATTTAGACATGAAATAGCATAATTGTGCGTGTGGAATTTTTAGATTTTTAAATTTTA
TATATAAATTATCATGTAT
Found at i:5282379 original size:27 final size:27
Alignment explanation
Indices: 5282345--5282400 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
5282335 AACCTAAACA
*
5282345 TCGGGTTAAAGTATTGGGATGTTACAT
1 TCGGGTTAAAGTACTGGGATGTTACAT
5282372 TCGGGTTAAAGTACTGGGATGTTACAT
1 TCGGGTTAAAGTACTGGGATGTTACAT
5282399 TC
1 TC
5282401 TATACTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.36
Consensus pattern (27 bp):
TCGGGTTAAAGTACTGGGATGTTACAT
Found at i:5284345 original size:15 final size:15
Alignment explanation
Indices: 5284321--5284366 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
5284311 ATATAAATAG
*
5284321 AAATAAAAATATAAT
1 AAATAGAAATATAAT
5284336 AAATAGAAATATAAT
1 AAATAGAAATATAAT
5284351 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
5284367 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:5284354 original size:23 final size:24
Alignment explanation
Indices: 5284287--5284357 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 24
5284277 TAAGAAAAAA
*
5284287 AGTAAT-AAT-GAAA-ATAATATT
1 AGTAATAAATAGAAATATAATAAT
5284308 AGTATATAAATAGAAATA-AA-AAT
1 AGTA-ATAAATAGAAATATAATAAT
5284331 A-TAATAAATAGAAATATAATAAT
1 AGTAATAAATAGAAATATAATAAT
5284354 AGTA
1 AGTA
5284358 GAAATATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
21 17 0.40
22 6 0.14
23 10 0.24
24 8 0.19
25 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (24 bp):
AGTAATAAATAGAAATATAATAAT
Found at i:5284363 original size:44 final size:44
Alignment explanation
Indices: 5284315--5284398 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 44
5284305 ATTAGTATAT
5284315 AAATAGAAATA-A-AAATATAATAAATAGA-AATATAATAATAGTAG
1 AAATAGAAATAGATAAATA-AA-AAATAGATAA-ATAATAATAGTAG
* *
5284359 AAATATAAATAGATAAATAAAAATTAGATAAATAATAATA
1 AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATA
5284399 ATATTAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
44 25 0.71
45 5 0.14
46 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (44 bp):
AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTAG
Found at i:5284386 original size:15 final size:14
Alignment explanation
Indices: 5284313--5284398 Score: 59
Period size: 15 Copynumber: 5.9 Consensus size: 14
5284303 ATATTAGTAT
*
5284313 ATAAATAGAAATA-
1 ATAAATAAAAATAG
*
5284326 AAAATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
5284342 A-AATATAATAATAG
1 ATAA-ATAAAAATAG
* *
5284356 TAGAAATATAAATAG
1 -ATAAATAAAAATAG
5284371 ATAAATAAAAATTAG
1 ATAAATAAAAA-TAG
*
5284386 ATAAATAATAATA
1 ATAAATAAAAATA
5284399 ATATTAGAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
13 3 0.05
14 19 0.32
15 34 0.58
16 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:5285033 original size:20 final size:20
Alignment explanation
Indices: 5285010--5285054 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5285000 CACATCAGTT
5285010 TTTTATCCTGAATTTCAGGA
1 TTTTATCCTGAATTTCAGGA
* *
5285030 TTTTATCCTGAATTTTAGTA
1 TTTTATCCTGAATTTCAGGA
5285050 TTTTA
1 TTTTA
5285055 ATTTGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (20 bp):
TTTTATCCTGAATTTCAGGA
Found at i:5291522 original size:5 final size:5
Alignment explanation
Indices: 5291512--5291575 Score: 80
Period size: 5 Copynumber: 13.4 Consensus size: 5
5291502 AATTAAAATA
*
5291512 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT A-TGT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
* *
5291560 -TTAT AATAT TTTAT AT
1 ATTAT ATTAT ATTAT AT
5291576 ATGTAATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
4 11 0.22
5 40 0.78
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:5291576 original size:25 final size:26
Alignment explanation
Indices: 5291509--5291585 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 26
5291499 TACAATTAAA
* *
5291509 ATAATTATATTATAT-TATATTATATT
1 ATAA-TATTTTATATATGTATTATATT
*
5291535 ATATTATATTATATATATGTATTAT-TT
1 ATA--ATATTTTATATATGTATTATATT
*
5291562 ATAATATTTTATATATGTAATATA
1 ATAATATTTTATATATGTATTATA
5291586 AAGCTAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 18 0.43
26 3 0.07
27 13 0.31
28 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
ATAATATTTTATATATGTATTATATT
Found at i:5292406 original size:21 final size:21
Alignment explanation
Indices: 5292380--5292423 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5292370 TTATCATGCC
*
5292380 TAAATGAACATATGTCACTCT
1 TAAATGAACATATATCACTCT
5292401 TAAATGAACATATATCACTCT
1 TAAATGAACATATATCACTCT
5292422 TA
1 TA
5292424 GAACGCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAATGAACATATATCACTCT
Found at i:5293215 original size:12 final size:12
Alignment explanation
Indices: 5293198--5293230 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5293188 GTTCGCCAAT
5293198 AAAAACATAAAG
1 AAAAACATAAAG
5293210 AAAAACAT-AAG
1 AAAAACATAAAG
5293221 -AAAACATAAA
1 AAAAACATAAA
5293231 AATAACTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 5 0.25
12 8 0.40
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAACATAAAG
Found at i:5295844 original size:48 final size:48
Alignment explanation
Indices: 5295782--5296256 Score: 833
Period size: 48 Copynumber: 9.9 Consensus size: 48
5295772 TATATATGTG
*
5295782 TGTGGTAAAGCCGAATGACTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
5295830 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATACGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
5295878 TGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 --TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
5295928 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
5295976 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
5296024 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
5296072 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* * * *
5296120 TATGGTAAAGCCGAATGGATAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
5296168 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
5296216 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
5296257 GTGTGTACAT
Statistics
Matches: 405, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
48 358 0.88
50 47 0.12
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
Found at i:5296452 original size:37 final size:37
Alignment explanation
Indices: 5296397--5296499 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
5296387 GGAAATATAT
**
5296397 TCCGGGTAAGACTTGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
5296434 TCTGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
5296471 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
5296500 GGACTATTCG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:5298768 original size:39 final size:40
Alignment explanation
Indices: 5298663--5298870 Score: 237
Period size: 40 Copynumber: 5.2 Consensus size: 40
5298653 TATTCGAATG
* * *
5298663 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
* *
5298704 ATATCCGGACTCAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
*
5298744 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
5298783 AAATCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5298823 ATAACCGGGC-AATGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATATCCGGGCTAA-GTCCCGAAGGCATTTGTGCGAGTTA-CT
5298863 ATATCCGG
1 ATATCCGG
5298871 TTAAATTCTG
Statistics
Matches: 143, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
39 39 0.27
40 76 0.53
41 27 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:5298804 original size:79 final size:80
Alignment explanation
Indices: 5298663--5298874 Score: 247
Period size: 79 Copynumber: 2.7 Consensus size: 80
5298653 TATTCGAATG
* * * ** *
5298663 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATATCCGGACTCAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAAGATCCGAAGGC
5298728 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACT
* *
5298744 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAG-TCTCGAAGG
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGATC-CGAAGG
5298806 CATTTGTGCGAGTTACT
64 CATTTGTGCGAGTTACT
* *
5298823 ATAACCGGGC-AATGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAA
1 ATATCCGGGCTAA-GTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAA
5298875 ATTCTGAAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
78 4 0.04
79 55 0.49
80 42 0.37
81 12 0.11
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGATCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:5300785 original size:24 final size:24
Alignment explanation
Indices: 5300758--5300807 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5300748 TGACCTATCT
5300758 TGCACACCCGATGAGTACCTAAAG
1 TGCACACCCGATGAGTACCTAAAG
*
5300782 TGCACACCCGATGAGTGCCTAAAG
1 TGCACACCCGATGAGTACCTAAAG
5300806 TG
1 TG
5300808 TACTATCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (24 bp):
TGCACACCCGATGAGTACCTAAAG
Found at i:5306982 original size:39 final size:40
Alignment explanation
Indices: 5306877--5307072 Score: 238
Period size: 40 Copynumber: 4.9 Consensus size: 40
5306867 TATTCGAATG
* * *
5306877 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
* *
5306918 ATATCCGGACTCAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
*
5306958 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5306997 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5307037 ATAACCGGGC-AATGTCCCGAAGGCATTTGAGCGAGT
1 ATATCCGGGCTAA-GTCCCGAAGGCATTTGTGCGAGT
5307073 AGTTATATCC
Statistics
Matches: 135, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
39 37 0.27
40 70 0.52
41 27 0.20
42 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:5307017 original size:79 final size:80
Alignment explanation
Indices: 5306877--5307072 Score: 238
Period size: 79 Copynumber: 2.5 Consensus size: 80
5306867 TATTCGAATG
* * * *
5306877 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATATCCGGACTCAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACTAAATCCGGACTAAGATCCGAAGGC
5306942 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACT
* * **
5306958 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGG
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAATCCGGACTAAGAT-CCGAAGG
5307020 CATTTGTGCGAGTTACT
64 CATTTGTGCGAGTTACT
* *
5307037 ATAACCGGGC-AATGTCCCGAAGGCATTTGAGCGAGT
1 ATATCCGGGCTAA-GTCCCGAAGGCATTTGTGCGAGT
5307073 AGTTATATCC
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.03
79 48 0.48
80 36 0.36
81 12 0.12
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAATCCGGACTAAGATCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:5309414 original size:106 final size:106
Alignment explanation
Indices: 5309208--5309415 Score: 251
Period size: 106 Copynumber: 2.0 Consensus size: 106
5309198 ACTATCACAG
* * *
5309208 CTTGCCAGGCCCACTGACGATCCCTGCTTCATCAAGTCCACTGGCAATTATAGTTTGCTAAATCT
1 CTTGCCAGGCCCACTGACGATCCCTACTTCATCAAGTCCACTAGCAATCATAGTTTGCTAAATCT
* * * **
5309273 ACTGGCAACCCTAGTTCGCTAGGCCTTTTGACGAACCCCAA
66 ACTGGCAACCCTAGCTCGCCAGACCTGCTGACGAACCCCAA
* * **
5309314 CTTGCCAGGCTCACTGGA-GATCCCTACTTCGTCAAG-CCTACTAGTGATCATAGTTCT-CTAAA
1 CTTGCCAGGCCCACT-GACGATCCCTACTTCATCAAGTCC-ACTAGCAATCATAGTT-TGCTAAA
*
5309376 TCTACTGGCAACCCTAGCTCGCCAGACCTGCTGGCGAACC
63 TCTACTGGCAACCCTAGCTCGCCAGACCTGCTGACGAACC
5309416 TCTTCTTGTA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
105 2 0.02
106 81 0.94
107 3 0.03
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (106 bp):
CTTGCCAGGCCCACTGACGATCCCTACTTCATCAAGTCCACTAGCAATCATAGTTTGCTAAATCT
ACTGGCAACCCTAGCTCGCCAGACCTGCTGACGAACCCCAA
Found at i:5310209 original size:21 final size:21
Alignment explanation
Indices: 5310183--5310222 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5310173 TATAGGTGGA
5310183 TCAACTCTCACGAGCTTCTAT
1 TCAACTCTCACGAGCTTCTAT
5310204 TCAACTCTCACGAGCTTCT
1 TCAACTCTCACGAGCTTCT
5310223 GTTTAGCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.10, T:0.33
Consensus pattern (21 bp):
TCAACTCTCACGAGCTTCTAT
Found at i:5316624 original size:17 final size:18
Alignment explanation
Indices: 5316591--5316626 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5316581 TGCTTCCAAG
5316591 AAGCACTTTTGGGACAAA
1 AAGCACTTTTGGGACAAA
*
5316609 AAGCTCTTTT-GGACAAA
1 AAGCACTTTTGGGACAAA
5316626 A
1 A
5316627 TCATTCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (18 bp):
AAGCACTTTTGGGACAAA
Found at i:5321460 original size:21 final size:20
Alignment explanation
Indices: 5321422--5321460 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5321412 TTCTACTGTT
* *
5321422 GTTGGTTCTTGCCTTCTTGG
1 GTTGGTACTTGCCATCTTGG
5321442 GTTGGTACTCTGCCATCTT
1 GTTGGTACT-TGCCATCTT
5321461 TGTTACCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.05, C:0.23, G:0.26, T:0.46
Consensus pattern (20 bp):
GTTGGTACTTGCCATCTTGG
Found at i:5377035 original size:15 final size:15
Alignment explanation
Indices: 5377015--5377043 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5377005 GAAATAAAAG
5377015 AAAGAAACAGAATGA
1 AAAGAAACAGAATGA
5377030 AAAGAAACAGAATG
1 AAAGAAACAGAATG
5377044 TGGAAACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAGAAACAGAATGA
Found at i:5377471 original size:23 final size:21
Alignment explanation
Indices: 5377424--5377464 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
5377414 TTTGGTTAAA
5377424 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
5377446 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
5377465 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:5380506 original size:13 final size:13
Alignment explanation
Indices: 5380454--5380523 Score: 68
Period size: 13 Copynumber: 5.3 Consensus size: 13
5380444 TTGTACATAT
5380454 ATTTCCATATAACC
1 ATTT-CATATAACC
* * *
5380468 AATTCATGTAAAC
1 ATTTCATATAACC
* *
5380481 ATTTCACACAACC
1 ATTTCATATAACC
*
5380494 ATTTTATATAACC
1 ATTTCATATAACC
*
5380507 AATTCATATAACC
1 ATTTCATATAACC
5380520 ATTT
1 ATTT
5380524 GTCATCTGGT
Statistics
Matches: 42, Mismatches: 14, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
13 39 0.93
14 3 0.07
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:5380668 original size:46 final size:47
Alignment explanation
Indices: 5380606--5380787 Score: 219
Period size: 46 Copynumber: 4.0 Consensus size: 47
5380596 TTATCTTCGA
* * ** **
5380606 CATGATGCCATAGTATCTTTCAATTATGGTCTTACTTGTTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCATGT
5380652 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA-TTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCATGT
* * *
5380698 CACGTTGCCATGGTATCTTTCAACCATGGTCTTAC-ACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCATGT
* * * *
5380744 CAGGTTGTCATGGTCTCTTTCAACCATGGTCTTAC-ACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCAT
5380788 TTCAGAGAGC
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 6 0.05
46 116 0.95
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (47 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCATGT
Found at i:5381197 original size:24 final size:23
Alignment explanation
Indices: 5381165--5381213 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5381155 ATCAGGTAGT
*
5381165 TCACAAAGAACCATATCGTGAAGC
1 TCACAAAGAACC-TATCGGGAAGC
* *
5381189 TCACGAAGAGCCTATCGGGAAGC
1 TCACAAAGAACCTATCGGGAAGC
5381212 TC
1 TC
5381214 CGGATAGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (23 bp):
TCACAAAGAACCTATCGGGAAGC
Found at i:5381210 original size:23 final size:23
Alignment explanation
Indices: 5381178--5381293 Score: 101
Period size: 23 Copynumber: 5.0 Consensus size: 23
5381168 CAAAGAACCA
*
5381178 TATCGTGAAGCTCACGAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* *
5381201 TATCGGGAAGCTC-CGGATAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* *
5381223 ATATATCGGGAAGTTCAAG-AGAGCAC
1 ---TATCGGGAAGCTCACGAAGAGC-C
* * *
5381249 TATCGAGAGGCTCACAAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
*
5381272 TATCAGGAAGCTCACGAAGAGC
1 TATCGGGAAGCTCACGAAGAGC
5381294 TGTATTTCGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
22 7 0.10
23 42 0.58
24 5 0.07
25 16 0.22
26 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (23 bp):
TATCGGGAAGCTCACGAAGAGCC
Found at i:5381223 original size:71 final size:71
Alignment explanation
Indices: 5381148--5381284 Score: 161
Period size: 71 Copynumber: 1.9 Consensus size: 71
5381138 AACTCAATAG
* * * *
5381148 AGCCA-AAATCAGGTAGTTCACAAAGAACCA-TATCGTGAAGCTCACGAAGAGCCTATCGGGAAG
1 AGCCATAAATCAGGAAGTTCA-AAAG-ACCACTATCGAGAAGCTCACAAAGAGCCTATCAGGAAG
5381211 CTCCGGAT
64 CTCCGGAT
* * * * *
5381219 AGCCATATATCGGGAAGTTCAAGAGAGCACTATCGAGAGGCTCACAAAGAGCCTATCAGGAAGCT
1 AGCCATAAATCAGGAAGTTCAAAAGACCACTATCGAGAAGCTCACAAAGAGCCTATCAGGAAGCT
5381284 C
66 C
5381285 ACGAAGAGCT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
70 3 0.05
71 40 0.73
72 12 0.22
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (71 bp):
AGCCATAAATCAGGAAGTTCAAAAGACCACTATCGAGAAGCTCACAAAGAGCCTATCAGGAAGCT
CCGGAT
Found at i:5383085 original size:15 final size:15
Alignment explanation
Indices: 5383065--5383094 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5383055 TTAAGTAAAA
5383065 AGGGCTAAATTGACT
1 AGGGCTAAATTGACT
5383080 AGGGCTAAATTGACT
1 AGGGCTAAATTGACT
5383095 TACCTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
AGGGCTAAATTGACT
Found at i:5392356 original size:23 final size:25
Alignment explanation
Indices: 5392300--5392358 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
5392290 ATATAATACA
5392300 TAAAAAATATT-AAAATAAATATTTT
1 TAAAAAA-ATTAAAAATAAATATTTT
* *
5392325 TCAACAAATTAAAAAT-AA-ATTTT
1 TAAAAAAATTAAAAATAAATATTTT
5392348 TAAAAAAATTA
1 TAAAAAAATTA
5392359 TGTATTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 14 0.48
24 5 0.17
25 10 0.34
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAAAAATTAAAAATAAATATTTT
Found at i:5404041 original size:26 final size:29
Alignment explanation
Indices: 5403994--5404047 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 29
5403984 TTTGATTTAA
*
5403994 TGTGTAATTTAATATGTAAATTTTAATTT
1 TGTGTAATTTAATATATAAATTTTAATTT
5404023 TGTGTAA-TT-ATATAT-AATTTTAATT
1 TGTGTAATTTAATATATAAATTTTAATT
5404048 GTGCTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 5 0.21
28 2 0.08
29 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (29 bp):
TGTGTAATTTAATATATAAATTTTAATTT
Found at i:5404242 original size:30 final size:30
Alignment explanation
Indices: 5404208--5404271 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5404198 AATTTGTGAG
** *
5404208 AATTGTATCAAATTAAAATTTAATGAATAA
1 AATTGTAAAAAATTAAAATTAAATGAATAA
* *
5404238 AATTGTAAAAAATTAAAGTTAAATGTATAA
1 AATTGTAAAAAATTAAAATTAAATGAATAA
5404268 AATT
1 AATT
5404272 ATTTTATCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.36
Consensus pattern (30 bp):
AATTGTAAAAAATTAAAATTAAATGAATAA
Found at i:5404615 original size:31 final size:31
Alignment explanation
Indices: 5404575--5404633 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
5404565 AAGACATTTA
5404575 TTTACATGTGTAG-AATTGAATCAAAATCACAG
1 TTTACATGTGT-GTAATTGAAT-AAAATCACAG
*
5404607 TTTA-ATGTGTGTAATTGCATAAAATCA
1 TTTACATGTGTGTAATTGAATAAAATCA
5404634 AAATTCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
31 13 0.52
32 4 0.16
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (31 bp):
TTTACATGTGTGTAATTGAATAAAATCACAG
Found at i:5405154 original size:28 final size:28
Alignment explanation
Indices: 5405113--5405170 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5405103 CAAGTTCACT
5405113 TTCAACCTACTAAAAACATAAAAACACA
1 TTCAACCTACTAAAAACATAAAAACACA
*
5405141 TTCAACCTAGTAAAAACATAAAAACACA
1 TTCAACCTACTAAAAACATAAAAACACA
5405169 TT
1 TT
5405171 TTCAATACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.21
Consensus pattern (28 bp):
TTCAACCTACTAAAAACATAAAAACACA
Found at i:5406387 original size:39 final size:39
Alignment explanation
Indices: 5406344--5406435 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 39
5406334 TCCACGAAAG
* *
5406344 GCTAGATCTCGTTACATTACTCGAGAATCTGCAACAAAT
1 GCTAGATCTCGTTACATTACCCAAGAATCTGCAACAAAT
* * * *
5406383 GCTAGATCTCGTTATATTACCCAATAGTTTGCAACAAAT
1 GCTAGATCTCGTTACATTACCCAAGAATCTGCAACAAAT
*
5406422 GCTAGATCTTGTTA
1 GCTAGATCTCGTTA
5406436 TAACTTGTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33
Consensus pattern (39 bp):
GCTAGATCTCGTTACATTACCCAAGAATCTGCAACAAAT
Found at i:5425596 original size:18 final size:17
Alignment explanation
Indices: 5425573--5425608 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
5425563 AGAGTGGATG
5425573 AGTTTGGACAAAAATATA
1 AGTTTGGACAAAAA-ATA
5425591 AGTTTGGACAAAAAATA
1 AGTTTGGACAAAAAATA
5425608 A
1 A
5425609 TGCACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25
Consensus pattern (17 bp):
AGTTTGGACAAAAAATA
Found at i:5426760 original size:21 final size:21
Alignment explanation
Indices: 5426736--5426789 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5426726 AATACGACAG
*
5426736 ATAATAAAAATGATAGTAATA
1 ATAATAAAAATAATAGTAATA
* *
5426757 ATAAAAAAAATAATGGTAATA
1 ATAATAAAAATAATAGTAATA
* *
5426778 CTATTAAAAATA
1 ATAATAAAAATA
5426790 GCAAGTATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (21 bp):
ATAATAAAAATAATAGTAATA
Found at i:5427073 original size:3 final size:3
Alignment explanation
Indices: 5426966--5427053 Score: 54
Period size: 3 Copynumber: 29.0 Consensus size: 3
5426956 AACAATATGC
* ** ** *
5426966 TAA TAA TAA TAA TAA TAAA CAA TAA TAA TAA TAA TGG TGG TTA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
5427012 TGAA -CA TAA TAA TAC TAA TAA TAAA TAA T-A TAA TAG TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
5427054 ACAGCCAACA
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
2 3 0.04
3 57 0.85
4 7 0.10
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5436224 original size:16 final size:16
Alignment explanation
Indices: 5436203--5436234 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5436193 AAGGTTATAT
5436203 CATACCGGGATAACAC
1 CATACCGGGATAACAC
5436219 CATACCGGGATAACAC
1 CATACCGGGATAACAC
5436235 GTGACCCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.19, T:0.12
Consensus pattern (16 bp):
CATACCGGGATAACAC
Found at i:5437586 original size:22 final size:21
Alignment explanation
Indices: 5437548--5437591 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
5437538 TAAAGAATGT
*
5437548 ATAAAATTATTAAATATTAAA
1 ATAAAATAATTAAATATTAAA
5437569 ATAAAATAATATAAATATTAAA
1 ATAAAATAAT-TAAATATTAAA
5437591 A
1 A
5437592 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAATAATTAAATATTAAA
Found at i:5437604 original size:22 final size:22
Alignment explanation
Indices: 5437558--5437600 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5437548 ATAAAATTAT
*
5437558 TAAATATTAAAATAAAATAATA
1 TAAATATTAAAATAAAATAAAA
*
5437580 TAAATATTAAAA-AAATTAAAA
1 TAAATATTAAAATAAAATAAAA
5437601 ATAATATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAATATTAAAATAAAATAAAA
Found at i:5448949 original size:22 final size:22
Alignment explanation
Indices: 5448925--5448967 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
5448915 TTAAATTTTT
5448925 AAAT-TTAAAAAGTAGAAATACTA
1 AAATCTTAAAAA-TA-AAATACTA
5448948 AAATCTTAAAAATAAAATAC
1 AAATCTTAAAAATAAAATAC
5448968 GGAGATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.26
Consensus pattern (22 bp):
AAATCTTAAAAATAAAATACTA
Found at i:5449947 original size:21 final size:21
Alignment explanation
Indices: 5449894--5449953 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
5449884 ATTGATGTAA
* *
5449894 AATTTTATAATATTATGTTTAT
1 AATTTTA-AATAATATTTTTAT
* * *
5449916 ACTATTGAATAATATTTTTAT
1 AATTTTAAATAATATTTTTAT
5449937 AATTTTAAATAAT-TTTT
1 AATTTTAAATAATATTTT
5449954 ACAATTTGGT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTTAAATAATATTTTTAT
Found at i:5450168 original size:9 final size:9
Alignment explanation
Indices: 5450146--5450198 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
5450136 AATGAAATTT
*
5450146 ATTTTTTAA
1 ATTTTTAAA
*
5450155 TTTTTTAAA
1 ATTTTTAAA
5450164 ATTTTTACAA
1 ATTTTTA-AA
*
5450174 ATTATTAAA
1 ATTTTTAAA
5450183 TATTTTTAATA
1 -ATTTTTAA-A
5450194 ATTTT
1 ATTTT
5450199 ATATTCTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 15 0.42
10 20 0.56
11 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:5457051 original size:15 final size:15
Alignment explanation
Indices: 5457031--5457064 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
5457021 TTATTTTTAA
5457031 TTTAATATTTAATGT
1 TTTAATATTTAATGT
5457046 TTTAATATTTAATGT
1 TTTAATATTTAATGT
5457061 TTTA
1 TTTA
5457065 GATGAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTAATATTTAATGT
Found at i:5464376 original size:18 final size:18
Alignment explanation
Indices: 5464355--5464421 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
5464345 AATCGGTTAA
*
5464355 TCAGTAACAATCATTTAT
1 TCAGTAACAGTCATTTAT
*
5464373 TCAGTATCAGT-AGTTTAT
1 TCAGTAACAGTCA-TTTAT
* * *
5464391 TCAATAACGGTCAATTAT
1 TCAGTAACAGTCATTTAT
*
5464409 TCAGTAGCAGTCA
1 TCAGTAACAGTCA
5464422 GTCTTTAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
17 1 0.03
18 36 0.95
19 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (18 bp):
TCAGTAACAGTCATTTAT
Found at i:5466691 original size:14 final size:14
Alignment explanation
Indices: 5466672--5466727 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
5466662 GAGTTACCTA
5466672 TTATATAATAACTC
1 TTATATAATAACTC
5466686 TTATATAATAACTC
1 TTATATAATAACTC
* * **
5466700 TT-GA-ACTTCCTC
1 TTATATAATAACTC
5466712 TTATATAATAACTC
1 TTATATAATAACTC
5466726 TT
1 TT
5466728 CGAAGTTACC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
12 7 0.22
13 2 0.06
14 23 0.72
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.45
Consensus pattern (14 bp):
TTATATAATAACTC
Found at i:5466727 original size:40 final size:42
Alignment explanation
Indices: 5466639--5466727 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
5466629 TTACCAGTCC
* *
5466639 AACTCTTATATAATAACTCTTCGGAGTTACCTATTATATAAT
1 AACTCTTATATAATAACTCTTCGAACTTACCTATTATATAAT
*
5466681 AACTCTTATATAATAACTCTT-GAACTT-CCTCTTATATAAT
1 AACTCTTATATAATAACTCTTCGAACTTACCTATTATATAAT
5466721 AACTCTT
1 AACTCTT
5466728 CGAAGTTACC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 19 0.43
41 4 0.09
42 21 0.48
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (42 bp):
AACTCTTATATAATAACTCTTCGAACTTACCTATTATATAAT
Found at i:5472430 original size:10 final size:9
Alignment explanation
Indices: 5472393--5472478 Score: 68
Period size: 10 Copynumber: 9.0 Consensus size: 9
5472383 GGTGTTTTAT
5472393 AATTA-AAA
1 AATTATAAA
5472401 TAATT-TAAA
1 -AATTATAAA
* *
5472410 ATTTATTAA
1 AATTATAAA
5472419 AATTATAGAA
1 AATTATA-AA
5472429 AACTTATAGAA
1 AA-TTATA-AA
5472440 AATTATAAA
1 AATTATAAA
5472449 ATATTATAAAA
1 A-ATTAT-AAA
*
5472460 AACTATTAAA
1 AATTA-TAAA
5472470 AATTATAAA
1 AATTATAAA
5472479 TATATATAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
8 3 0.05
9 22 0.34
10 24 0.38
11 15 0.23
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AATTATAAA
Found at i:5472503 original size:36 final size:34
Alignment explanation
Indices: 5472456--5472533 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 34
5472446 AAAATATTAT
5472456 AAAAAACTATTAAAAAT-TATAAATATATATAAGTG
1 AAAAAACTATTAAAAATAT-TAAA-ATATATAAGTG
*
5472491 CAAAAAATTATTAAAAATATTAAAATATATAAGTG
1 -AAAAAACTATTAAAAATATTAAAATATATAAGTG
5472526 AAAAAACT
1 AAAAAACT
5472534 CATGAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 7 0.18
35 11 0.28
36 20 0.51
37 1 0.03
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (34 bp):
AAAAAACTATTAAAAATATTAAAATATATAAGTG
Found at i:5473078 original size:30 final size:32
Alignment explanation
Indices: 5473042--5473138 Score: 80
Period size: 30 Copynumber: 3.2 Consensus size: 32
5473032 ATTTTAGTTC
* *
5473042 ATATAAAAATTTTTA-ATTTTTTAAT-AATTT
1 ATATAAAAATTTTTATAATTTATAATAAATTT
*
5473072 ATAT-AAATTTTTTATAATTTATAATAAATTT
1 ATATAAAAATTTTTATAATTTATAATAAATTT
* * *
5473103 -TAT--AAATTTTTAGTCATTTATTATAATTTT
1 ATATAAAAATTTTTA-TAATTTATAATAAATTT
*
5473133 TTATAA
1 ATATAA
5473139 TCTTTTTGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
29 17 0.31
30 29 0.54
31 8 0.15
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (32 bp):
ATATAAAAATTTTTATAATTTATAATAAATTT
Found at i:5473080 original size:21 final size:21
Alignment explanation
Indices: 5473056--5473111 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
5473046 AAAAATTTTT
5473056 AATTTTTTAATAATTTAT-ATA
1 AATTTTTT-ATAATTTATAATA
5473077 AATTTTTTATAATTTATAATA
1 AATTTTTTATAATTTATAATA
*
5473098 AATTTTATA-AATTT
1 AATTTTTTATAATTT
5473112 TTAGTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTTTATAATTTATAATA
Found at i:5473088 original size:20 final size:22
Alignment explanation
Indices: 5473056--5473103 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
5473046 AAAAATTTTT
5473056 AATTTTTTAATAATTTAT-ATA
1 AATTTTTTAATAATTTATAATA
5473077 AATTTTTT-ATAATTTATAATA
1 AATTTTTTAATAATTTATAATA
5473098 AATTTT
1 AATTTT
5473104 ATAAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTTTTTAATAATTTATAATA
Found at i:5473090 original size:10 final size:10
Alignment explanation
Indices: 5473051--5473145 Score: 70
Period size: 10 Copynumber: 9.4 Consensus size: 10
5473041 CATATAAAAA
5473051 TTTT-TAATT
1 TTTTATAATT
5473060 TTTTAATAA-T
1 TTTT-ATAATT
*
5473070 TTATATAAATT
1 TTTTAT-AATT
5473081 TTTTATAATT
1 TTTTATAATT
* * *
5473091 TATAATAA-A
1 TTTTATAATT
*
5473100 TTTTATAAAT
1 TTTTATAATT
*
5473110 TTTTAGTCATT
1 TTTTA-TAATT
*
5473121 TATTATAATT
1 TTTTATAATT
5473131 TTTTATAATCT
1 TTTTATAAT-T
5473142 TTTT
1 TTTT
5473146 GCACTTTTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
9 12 0.18
10 33 0.50
11 21 0.32
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:5473131 original size:50 final size:48
Alignment explanation
Indices: 5473043--5473139 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 48
5473033 TTTTAGTTCA
*
5473043 TATAAAAATTTTTAATTTTTTAATAATTTATATAAATTTTTTATAATT
1 TATAAAAATTTTTAAATTTTTAATAATTTATATAAATTTTTTATAATT
* *
5473091 TATAATAAATTTTATAAATTTTTAGTCATTTAT-TATAATTTTTTATAAT
1 TATAA-AAATTTT-TAAATTTTTAATAATTTATATA-AATTTTTTATAAT
5473140 CTTTTTGCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 5 0.12
49 9 0.21
50 29 0.67
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (48 bp):
TATAAAAATTTTTAAATTTTTAATAATTTATATAAATTTTTTATAATT
Found at i:5476027 original size:25 final size:27
Alignment explanation
Indices: 5475993--5476043 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
5475983 GAAATAATTT
* *
5475993 TTTTGGGAG-AAAGTAAAAA-GAAAAG
1 TTTTGAGAGAAAAATAAAAAGGAAAAG
5476018 TTTTGAGAGAAAAATAAAAAGGAAAA
1 TTTTGAGAGAAAAATAAAAAGGAAAA
5476044 AAATTTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 9 0.41
27 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.20
Consensus pattern (27 bp):
TTTTGAGAGAAAAATAAAAAGGAAAAG
Found at i:5488126 original size:28 final size:28
Alignment explanation
Indices: 5488082--5488137 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5488072 TTATTTTGGT
5488082 CCTTTTTTAAACAGTGCGCGTATGGGGA
1 CCTTTTTTAAACAGTGCGCGTATGGGGA
*
5488110 CCTTTTTTAAACGGTGCGCGTATGGGGA
1 CCTTTTTTAAACAGTGCGCGTATGGGGA
5488138 AGGATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (28 bp):
CCTTTTTTAAACAGTGCGCGTATGGGGA
Found at i:5490760 original size:19 final size:19
Alignment explanation
Indices: 5490736--5490780 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5490726 CGTCTCTTTT
*
5490736 TGCATT-CATTTCATGCATC
1 TGCATTGCATTTCAT-CATA
5490755 TGCATTGCATTTCATCATA
1 TGCATTGCATTTCATCATA
5490774 TGCATTG
1 TGCATTG
5490781 AATGTAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (19 bp):
TGCATTGCATTTCATCATA
Found at i:5493694 original size:5 final size:6
Alignment explanation
Indices: 5493679--5493713 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5493669 GAACGGTGCA
*
5493679 AAAAAT AAAAAT AAAAAT AAAAAC AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
5493714 AGGATCGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (6 bp):
AAAAAT
Found at i:5495220 original size:46 final size:46
Alignment explanation
Indices: 5495066--5495233 Score: 239
Period size: 46 Copynumber: 3.7 Consensus size: 46
5495056 CAAATCAGTT
*
5495066 GATTGAAGAAGATATAAATCCTATACCCCTGAGTTGCAGTGGGATG
1 GATTGAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
* *
5495112 GATTGAAGATA-ATACAAATCCTACACCCCTGAGTTGTAGTGGGATG
1 GATTGAAGA-AGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
* * *
5495158 GATTGAAGATGATACAAATCCTATACCCCTGAGCTACAGTGGGATG
1 GATTGAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
* * *
5495204 GATTGAAGAAGTTACAAATCTTGTACCCCT
1 GATTGAAGAAGATACAAATCCTATACCCCT
5495234 AAATTGCAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
46 107 0.99
47 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (46 bp):
GATTGAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
Found at i:5495262 original size:22 final size:22
Alignment explanation
Indices: 5495212--5495263 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
5495202 TGGATTGAAG
* * *
5495212 AAGTTACAAATCTTGTACCCCT
1 AAGTTGCAAATCCTATACCCCT
*
5495234 AAATTGCAAATCCTATACCCCT
1 AAGTTGCAAATCCTATACCCCT
*
5495256 GAGTTGCA
1 AAGTTGCA
5495264 GTAGGATAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (22 bp):
AAGTTGCAAATCCTATACCCCT
Found at i:5495309 original size:68 final size:68
Alignment explanation
Indices: 5495172--5495299 Score: 184
Period size: 68 Copynumber: 1.9 Consensus size: 68
5495162 GAAGATGATA
* * * * *
5495172 CAAATCCTATACCCCTGAGCTACAGTGGGATGGATTGAAGAAGTTACAAATCTTGTACCCCTAAA
1 CAAATCCTATACCCCTGAGCTACAGTAGGATAGATTGAAGAAGATACAAATCCTATACCCCTAAA
5495237 TTG
66 TTG
* * *
5495240 CAAATCCTATACCCCTGAGTTGCAGTAGGATAGATTGAAGATGATACAAATCCTATACCC
1 CAAATCCTATACCCCTGAGCTACAGTAGGATAGATTGAAGAAGATACAAATCCTATACCC
5495300 TTGAGTTGCA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 52 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (68 bp):
CAAATCCTATACCCCTGAGCTACAGTAGGATAGATTGAAGAAGATACAAATCCTATACCCCTAAA
TTG
Found at i:5495335 original size:46 final size:46
Alignment explanation
Indices: 5495240--5495336 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 46
5495230 CCCTAAATTG
* * *
5495240 CAAATCCTATACCCCTGAGTTGCAGTAGGATAGATTGAAGATGATA
1 CAAATCCTATACCCCTGAGTTGCAGTAGGATAGATGGAAGATAACA
* * * *
5495286 CAAATCCTATACCCTTGAGTTGCAGTGGGGTGGATGGAAGA-AACCA
1 CAAATCCTATACCCCTGAGTTGCAGTAGGATAGATGGAAGATAA-CA
5495332 CAAAT
1 CAAAT
5495337 TTTATCTCTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 1 0.02
46 42 0.98
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (46 bp):
CAAATCCTATACCCCTGAGTTGCAGTAGGATAGATGGAAGATAACA
Found at i:5495350 original size:114 final size:114
Alignment explanation
Indices: 5495126--5495336 Score: 314
Period size: 114 Copynumber: 1.9 Consensus size: 114
5495116 GAAGATAATA
* * *
5495126 CAAATCCTACACCCCTGAGTTGTAGTGGGATGGATTGAAGATGATACAAATCCTATACCCCTGAG
1 CAAATCCTACACCCCTGAGTTGCAGTAGGATAGATTGAAGATGATACAAATCCTATACCCCTGAG
* ***
5495191 CTACAGTGGGATGGATTGAAGAAGTTACAAATCTTGTACCCCTAAATTG
66 CTACAGTGGGATGGATGGAAGAAACCACAAATCTTGTACCCCTAAATTG
* *
5495240 CAAATCCTATACCCCTGAGTTGCAGTAGGATAGATTGAAGATGATACAAATCCTATACCCTTGAG
1 CAAATCCTACACCCCTGAGTTGCAGTAGGATAGATTGAAGATGATACAAATCCTATACCCCTGAG
* * *
5495305 TTGCAGTGGGGTGGATGGAAGAAACCACAAAT
66 CTACAGTGGGATGGATGGAAGAAACCACAAAT
5495337 TTTATCTCTC
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 85 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (114 bp):
CAAATCCTACACCCCTGAGTTGCAGTAGGATAGATTGAAGATGATACAAATCCTATACCCCTGAG
CTACAGTGGGATGGATGGAAGAAACCACAAATCTTGTACCCCTAAATTG
Found at i:5496148 original size:44 final size:44
Alignment explanation
Indices: 5495722--5496149 Score: 310
Period size: 44 Copynumber: 9.8 Consensus size: 44
5495712 TTATCATGGC
* * * *
5495722 CAATCTTATCTCCTTAAAGTTGCAGTGGAGCAGATTGAA-ACCA-
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-TAG
* * * * *
5495765 CAAGTCTTATCTTCCTAAAGTTGTAGTGGAGTAGACTAAAGATAG
1 CAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* *
5495810 CAAGTCTTATCTCCTTGAAGTTGCAGTGAAGCAGACT-AA-A-AG
1 CAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
** *
5495852 CAAGTCTTATCTTTCTGAAGTTGCAATGGAGCAGACTGAAGATAG
1 CAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* * *
5495897 CAGATCTTATCTCCCTGAAGTTGTAGTGGAGTAGA-TCG-A-A-AC
1 CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATAG
* * * * *
5495939 CATATTCTTTATCTCTCTAAAGTTGCAGTAGAGCAGGA-TAAAAATA-
1 CA-A-TC-TTATCTCCCTGAAGTTGCAGTGGAGCA-GACTGAAGATAG
* * * **
5495985 CAAACCTTATCTCCCTAAAGTTGCAGTAGAGCAGGTTGAAG-TAG
1 C-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
5496029 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
1 CAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* * * * **
5496074 CAGATC-T-TCTCCCTGAAATTACATTGGAGCAGACCGAAGCCA-
1 CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* *
5496116 CAATCCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 CAAT-CTTATCTCCCTGAAGTTGCAGTGGAGCAG
5496150 GATAAAAATA
Statistics
Matches: 310, Mismatches: 52, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
41 2 0.01
42 41 0.13
43 44 0.14
44 141 0.45
45 75 0.24
46 5 0.02
47 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
Found at i:5496582 original size:15 final size:16
Alignment explanation
Indices: 5496562--5496594 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5496552 CCAATTTTAG
*
5496562 AATTACAA-AACCCAA
1 AATTACAATAAACCAA
5496577 AATTACAATAAACCAA
1 AATTACAATAAACCAA
5496593 AA
1 AA
5496595 CCCAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.15
Consensus pattern (16 bp):
AATTACAATAAACCAA
Found at i:5515328 original size:14 final size:14
Alignment explanation
Indices: 5515309--5515355 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
5515299 TTACCTTACC
5515309 ATTTTAGTTTATAT
1 ATTTTAGTTTATAT
*
5515323 ATTTTAATTTA-AT
1 ATTTTAGTTTATAT
* *
5515336 ATTTTTTGTTTTTAT
1 A-TTTTAGTTTATAT
5515351 ATTTT
1 ATTTT
5515356 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (14 bp):
ATTTTAGTTTATAT
Found at i:5523879 original size:24 final size:22
Alignment explanation
Indices: 5523836--5523888 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
5523826 CGTGATACTT
* *
5523836 TTAAATTAAAATAAATAATTTA
1 TTAAATTAAAAAAAATAATTAA
5523858 TTAAATTATAAAAAAATAAATTAA
1 TTAAATTA-AAAAAAAT-AATTAA
*
5523882 TTTAATT
1 TTAAATT
5523889 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 8 0.31
23 7 0.27
24 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAATTAAAAAAAATAATTAA
Found at i:5526617 original size:21 final size:21
Alignment explanation
Indices: 5526566--5526610 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5526556 AAATGGCCTC
*
5526566 ACAGATCATTACGAGTTATAA
1 ACAGATCATTACGAGTGATAA
5526587 ACAGATCATTACGAGTGATAA
1 ACAGATCATTACGAGTGATAA
5526608 ACA
1 ACA
5526611 TTCCATTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (21 bp):
ACAGATCATTACGAGTGATAA
Found at i:5527274 original size:6 final size:6
Alignment explanation
Indices: 5527263--5527322 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
5527253 TAAAGATTGA
* * *
5527263 GTTTTT GTTTTT GTTTTT GTTGTGTT GTTGTT GTTGTT GTTTTT -TTGTT
1 GTTTTT GTTTTT GTTTTT GTT-T-TT GTTTTT GTTTTT GTTTTT GTTTTT
5527312 -TTTTT GTTTTT
1 GTTTTT GTTTTT
5527323 ACCCAGATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 8 0.17
6 33 0.70
7 1 0.02
8 5 0.11
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (6 bp):
GTTTTT
Found at i:5527293 original size:17 final size:17
Alignment explanation
Indices: 5527268--5527322 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
5527258 ATTGAGTTTT
5527268 TGTTTTTGTTTTTGTTG
1 TGTTTTTGTTTTTGTTG
* *
5527285 TGTTGTTGTTGTTGTTG
1 TGTTTTTGTTTTTGTTG
*
5527302 TTTTTTTGTTTTT-TTG
1 TGTTTTTGTTTTTGTTG
5527318 T-TTTT
1 TGTTTT
5527323 ACCCAGATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 4 0.12
16 4 0.12
17 25 0.76
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (17 bp):
TGTTTTTGTTTTTGTTG
Found at i:5527310 original size:8 final size:8
Alignment explanation
Indices: 5527270--5527322 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
5527260 TGAGTTTTTG
5527270 TTTTTGTT
1 TTTTTGTT
*
5527278 TTTGTTGTG
1 TTT-TTGTT
*
5527287 TTGTTGTT
1 TTTTTGTT
*
5527295 GTTGTTGTT
1 -TTTTTGTT
5527304 TTTTTGTT
1 TTTTTGTT
5527312 TTTTTGTT
1 TTTTTGTT
5527320 TTT
1 TTT
5527323 ACCCAGATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 25 0.64
9 14 0.36
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (8 bp):
TTTTTGTT
Found at i:5529150 original size:16 final size:16
Alignment explanation
Indices: 5529129--5529161 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5529119 TGACATGTGG
5529129 TAAAAAGTT-ATAAAAA
1 TAAAAA-TTAATAAAAA
5529145 TAAAAATTAATAAAAA
1 TAAAAATTAATAAAAA
5529161 T
1 T
5529162 TATAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
TAAAAATTAATAAAAA
Found at i:5529223 original size:28 final size:27
Alignment explanation
Indices: 5529129--5529226 Score: 87
Period size: 28 Copynumber: 3.6 Consensus size: 27
5529119 TGACATGTGG
* *
5529129 TAAAAAGTTAT-AAAAATA-AAAATTAA
1 TAAAAA-TTATAAAAAATATTAAATTTA
5529155 TAAAAATTAT-AAAAATGATTAAATTTTA
1 TAAAAATTATAAAAAAT-ATTAAA-TTTA
*
5529183 TTAACAA-TATAAAAAATATTAAATTTA
1 -TAAAAATTATAAAAAATATTAAATTTA
*
5529210 TAAAAAATTGTAAAAAA
1 T-AAAAATTATAAAAAA
5529227 CTATAATATA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
25 10 0.17
26 8 0.13
27 11 0.18
28 20 0.33
29 11 0.18
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (27 bp):
TAAAAATTATAAAAAATATTAAATTTA
Found at i:5530547 original size:22 final size:21
Alignment explanation
Indices: 5530497--5530547 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
5530487 TTTTGTTTAC
**
5530497 AATTTT-TTATAATTTCTTCT
1 AATTTTATTATAATTTCAACT
**
5530517 AATAATATTATTAATTTCAACT
1 AATTTTATTA-TAATTTCAACT
5530539 AATTTTATT
1 AATTTTATT
5530548 TCAATTATCC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 4 0.17
21 3 0.13
22 16 0.70
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTATTATAATTTCAACT
Found at i:5530613 original size:21 final size:21
Alignment explanation
Indices: 5530589--5530629 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5530579 TTTATAATTT
*
5530589 TTTCTAGATTATGTATATATA
1 TTTCTAAATTATGTATATATA
* *
5530610 TTTCTAAATTTTTTATATAT
1 TTTCTAAATTATGTATATAT
5530630 TTATTTCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTCTAAATTATGTATATATA
Found at i:5530640 original size:21 final size:22
Alignment explanation
Indices: 5530602--5530653 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
5530592 CTAGATTATG
*
5530602 TATATATATTTCTAAATTTTTTA
1 TATATTTATTTC-AAATTTTTTA
5530625 TATATTTATTTC-AATTTTTTA
1 TATATTTATTTCAAATTTTTTA
*
5530646 TATTTTTA
1 TATATTTA
5530654 ATGTGTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 16 0.59
23 11 0.41
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
TATATTTATTTCAAATTTTTTA
Found at i:5538638 original size:46 final size:45
Alignment explanation
Indices: 5538490--5538717 Score: 191
Period size: 46 Copynumber: 5.0 Consensus size: 45
5538480 TTATTTGTGT
*
5538490 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAT-A-TTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-TGAGATAT-A-A
* * *
5538536 GCCAGTGTAAGACCATGTCTGGGACGTGGCATCGGCATTGAGACGATAA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTGAGA-TATAA
* * *
5538585 -CTAGTGTAAGATATGTCTGGGACATGCATCAGCCTCGAGATATAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-GAGATATAA
* *
5538630 GCCAGTGTAAGACATGTCTGGAACATGCATCGG-CTACAAGATAT--
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT--GAGATATAA
* * *
5538674 GTCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATGA-ATAT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTGAGATAT
5538718 GTGAGAGCCA
Statistics
Matches: 150, Mismatches: 20, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
44 15 0.10
45 20 0.13
46 65 0.43
47 26 0.17
48 19 0.13
49 2 0.01
50 1 0.01
51 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTGAGATATAA
Found at i:5538727 original size:94 final size:94
Alignment explanation
Indices: 5538492--5538761 Score: 263
Period size: 94 Copynumber: 2.9 Consensus size: 94
5538482 ATTTGTGTGC
*
5538492 CAGTGTAAGACATGTCTGGGACATGCATCGGCCAT-ATTA-TGAGAGCCAGTGTAAGACCATGTC
1 CAGTGTAAGACATGTCTGGGACATGCATCGG-CATGAATATTGAGAGCCAGTGTAAGACCATGTC
* * *
5538555 TGGGACGTGGCATCGGCATTGAGACGATAACT
65 T-GGACATGGCATCGGCA-TGACAAGATAACT
* * *
5538587 -AGTGTAAGATATGTCTGGGACATGCATCAGCCTCGAGATA-T-A-AGCCAGTGTAAGA-CATGT
1 CAGTGTAAGACATGTCTGGGACATGCATCGGCAT-GA-ATATTGAGAGCCAGTGTAAGACCATGT
**
5538647 CTGGAACAT-GCATCGGC-T-ACAAGATATGT
64 CTGG-ACATGGCATCGGCATGACAAGATAACT
* * *
5538676 CAGTGTAAGACCATGTCTAGGACATGGCATCGGCATGAATATGTGAGAGCCATTGTAAAACCATG
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATGAATAT-TGAGAGCCAGTGTAAGACCATG
*
5538741 TCTCGGACATGGCATCAGCAT
63 TCT-GGACATGGCATCGGCAT
5538762 TATACCCTAT
Statistics
Matches: 144, Mismatches: 16, Indels: 28
0.77 0.09 0.15
Matches are distributed among these distances:
89 7 0.05
90 13 0.09
91 14 0.10
92 19 0.13
93 13 0.09
94 52 0.36
95 13 0.09
96 12 0.08
97 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (94 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGGCATGAATATTGAGAGCCAGTGTAAGACCATGTCT
GGACATGGCATCGGCATGACAAGATAACT
Found at i:5538733 original size:140 final size:142
Alignment explanation
Indices: 5538490--5538759 Score: 320
Period size: 138 Copynumber: 1.9 Consensus size: 142
5538480 TTATTTGTGT
* * *
5538490 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCCAGTGTAAGACCATGTC
1 GCCAGTGTAAGACATGTCTGGAACATGCATCGGCCATATCAAGAGAGCCAGTGTAAGACCATGTC
* * * * * *
5538555 TGGGACGTGGCATCGGCATTGAGACGATAACTAGTGTAAGA-TATGTCTGGGACAT-GCATCAGC
66 TAGGACATGGCATCGGCATTGAGACGATAACCAGTGTAAAACCATGTCTCGGACATGGCATCAGC
5538618 CTCGAGATATAA
131 CTCGAGATATAA
* *
5538630 GCCAGTGTAAGACATGTCTGGAACATGCATCGG-C-TA-CAAGATATGTCAGTGTAAGACCATGT
1 GCCAGTGTAAGACATGTCTGGAACATGCATCGGCCATATCAAGAGA-GCCAGTGTAAGACCATGT
* * *
5538692 CTAGGACATGGCATCGGCA-TGAATATG-TGAGAGCCATTGTAAAACCATGTCTCGGACATGGCA
65 CTAGGACATGGCATCGGCATTG-AGACGAT-A-A-CCAGTGTAAAACCATGTCTCGGACATGGCA
5538755 TCAGC
126 TCAGC
5538760 ATTATACCCT
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
137 7 0.06
138 40 0.37
139 2 0.02
140 40 0.37
141 12 0.11
142 8 0.07
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (142 bp):
GCCAGTGTAAGACATGTCTGGAACATGCATCGGCCATATCAAGAGAGCCAGTGTAAGACCATGTC
TAGGACATGGCATCGGCATTGAGACGATAACCAGTGTAAAACCATGTCTCGGACATGGCATCAGC
CTCGAGATATAA
Found at i:5539088 original size:28 final size:28
Alignment explanation
Indices: 5539048--5539105 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5539038 TGCTTATGAG
*
5539048 AATGATTTTGTGATGACCTTGTGATTAT
1 AATGATTTTGTGATGACCTGGTGATTAT
5539076 AATGATTTTGTGATGACCTGGTGATTAT
1 AATGATTTTGTGATGACCTGGTGATTAT
5539104 AA
1 AA
5539106 GTCTATACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (28 bp):
AATGATTTTGTGATGACCTGGTGATTAT
Found at i:5553485 original size:23 final size:23
Alignment explanation
Indices: 5553439--5553485 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5553429 TTTAGCTCAG
* *
5553439 TTAGTTTACTTAACAATTTAATT
1 TTAGTTTACTAAACAAATTAATT
5553462 TTAGTTTA-TAAACAAATTATATT
1 TTAGTTTACTAAACAAATTA-ATT
5553485 T
1 T
5553486 GAATTTGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAGTTTACTAAACAAATTAATT
Found at i:5554901 original size:11 final size:11
Alignment explanation
Indices: 5554863--5554923 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
5554853 ACATTAACAA
5554863 CAAAATAGTAC
1 CAAAATAGTAC
* * *
5554874 CAACATAATAG
1 CAAAATAGTAC
*
5554885 TAAAATAGTAC
1 CAAAATAGTAC
* *
5554896 TAAAATAGTGC
1 CAAAATAGTAC
5554907 CAAAA-AGTAC
1 CAAAATAGTAC
*
5554917 GAAAATA
1 CAAAATA
5554924 ATAGGATTTT
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
10 8 0.21
11 30 0.79
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAC
Found at i:5564161 original size:43 final size:43
Alignment explanation
Indices: 5564114--5564253 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 43
5564104 TGAGATTATA
* * *
5564114 TGTAAGACCATGTCTGAGACATTGGCATTG-TATTGTGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTA-TATGATTACG
* *
5564157 TGTAAGACCATGTCTGGGACATTGACATCGTTATATGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTATATGATTACG
* * * * *
5564200 TGTAGGACCATGTCTGGGACATTGGAATCGATATGA-GATAACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTAT-ATGATTACG
5564243 TGTAAGACCAT
1 TGTAAGACCAT
5564254 ATCTAGGATA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 79 0.96
44 3 0.04
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTTATATGATTACG
Found at i:5573156 original size:18 final size:18
Alignment explanation
Indices: 5573133--5573201 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 18
5573123 TCCTCAAATG
5573133 CAGCAGCCACAGCAACAT
1 CAGCAGCCACAGCAACAT
5573151 CAGCAG-CAGCAGC-A-A-
1 CAGCAGCCA-CAGCAACAT
* * * *
5573166 CAGCAACTACTGCAACAA
1 CAGCAGCCACAGCAACAT
*
5573184 CAGCAGCTACAGCAACAT
1 CAGCAGCCACAGCAACAT
5573202 GCTCAACAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
15 8 0.20
16 3 0.08
17 4 0.10
18 25 0.62
ACGTcount: A:0.41, C:0.35, G:0.17, T:0.07
Consensus pattern (18 bp):
CAGCAGCCACAGCAACAT
Found at i:5581892 original size:11 final size:11
Alignment explanation
Indices: 5581876--5581900 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5581866 CTCCAATTTG
5581876 TTTTTTTGTTT
1 TTTTTTTGTTT
5581887 TTTTTTTGTTT
1 TTTTTTTGTTT
5581898 TTT
1 TTT
5581901 GCAGATACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:5588136 original size:29 final size:27
Alignment explanation
Indices: 5588057--5588137 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 27
5588047 CGTTAATAAA
*
5588057 TAAATTTTAAATTAAAAAATAAAGGAAT
1 TAAATTTTAAATT-AAAAATATAGGAAT
*
5588085 TAAATTTTTAAAAATAAAAATATA-GAGAT
1 TAAA-TTTT-AAATTAAAAATATAGGA-AT
5588114 TAAATTTTAAATGTAGAAAATATA
1 TAAATTTTAAAT-TA-AAAATATA
5588138 ATAAATCTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 3 0.07
28 12 0.27
29 26 0.58
30 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (27 bp):
TAAATTTTAAATTAAAAATATAGGAAT
Found at i:5593598 original size:21 final size:22
Alignment explanation
Indices: 5593562--5593609 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
5593552 TATTTGTCTA
*
5593562 TTATTTTTTCATTGTTTTACTG
1 TTATTTTTTCACTGTTTTACTG
*
5593584 TTATTTTTT-ACTGTTTTGCTG
1 TTATTTTTTCACTGTTTTACTG
5593605 TTATT
1 TTATT
5593610 AACACTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.69
Consensus pattern (22 bp):
TTATTTTTTCACTGTTTTACTG
Found at i:5597294 original size:17 final size:17
Alignment explanation
Indices: 5597260--5597298 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5597250 ACAATTTCAT
5597260 ATTTTGAAATTTTATAA
1 ATTTTGAAATTTTATAA
*
5597277 ATTTT-AAATATTTTTAA
1 ATTTTGAAAT-TTTATAA
5597294 ATTTT
1 ATTTT
5597299 TTTATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTGAAATTTTATAA
Found at i:5607988 original size:44 final size:42
Alignment explanation
Indices: 5607910--5608065 Score: 133
Period size: 44 Copynumber: 3.6 Consensus size: 42
5607900 TTATTGCTAT
* *
5607910 TATTATTATGTTTCTATT-TGTATTTATTTTTTTATTCTAATAC
1 TATTATTATATTTCTATTAT-TATTTATTTATTTATT-TAATAC
* **
5607953 TATTATTAT-TTATCTAATTATTATTTATCTATTTATATTTCTAC
1 TATTATTATATT-TCT-ATTATTATTTATTTATTTAT-TTAATAC
5607997 TATTATTATATTTCTATTTATTATATT-TTTATTTCTATTTATATAC
1 TATTATTATATTTCTA-TTATTAT-TTATTTA-TT-TATTTA-ATAC
*
5608043 TAATATTAT-TTTC-ATTATTATTT
1 TATTATTATATTTCTATTATTATTT
5608066 TTCTCATATA
Statistics
Matches: 95, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
42 4 0.04
43 20 0.21
44 43 0.45
45 14 0.15
46 14 0.15
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (42 bp):
TATTATTATATTTCTATTATTATTTATTTATTTATTTAATAC
Found at i:5608021 original size:15 final size:15
Alignment explanation
Indices: 5607912--5608030 Score: 67
Period size: 15 Copynumber: 8.1 Consensus size: 15
5607902 ATTGCTATTA
*
5607912 TTATTATGTTTCTATT
1 TTATTATATTTCTA-T
5607928 TGTATT-TATTT-T-T
1 T-TATTATATTTCTAT
* * *
5607941 TTATTCTAATACTA-
1 TTATTATATTTCTAT
*
5607955 TTATTAT-TTATCTAA
1 TTATTATATT-TCTAT
5607970 TTATTAT-TTATCTA-
1 TTATTATATT-TCTAT
5607984 -T-TTATATTTCTACT
1 TTATTATATTTCTA-T
5607998 ATTATTATATTTCTAT
1 -TTATTATATTTCTAT
*
5608014 TTATTATATTTTTAT
1 TTATTATATTTCTAT
5608029 TT
1 TT
5608031 CTATTTATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
12 12 0.14
13 9 0.11
14 10 0.12
15 31 0.37
16 7 0.08
17 15 0.18
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (15 bp):
TTATTATATTTCTAT
Found at i:5608029 original size:29 final size:30
Alignment explanation
Indices: 5607898--5608020 Score: 92
Period size: 29 Copynumber: 4.2 Consensus size: 30
5607888 TATTTTAATA
** *
5607898 TATTATTGCTATTATTATTATGTTTCTATT
1 TATTATTTATATTATTATTATATTTCTATT
* * * * * *
5607928 T-GTATTTATTTTTTTATTCTAATACTA-T
1 TATTATTTATATTATTATTATATTTCTATT
* *
5607956 TATTATTTATCTAATTATTAT-TTATCTATT
1 TATTATTTATATTATTATTATATT-TCTATT
* *
5607986 TA-TATTTCTACTATTATTATATTTCTATT
1 TATTATTTATATTATTATTATATTTCTATT
5608015 TATTAT
1 TATTAT
5608021 ATTTTTATTT
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
28 3 0.04
29 56 0.82
30 9 0.13
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (30 bp):
TATTATTTATATTATTATTATATTTCTATT
Found at i:5608072 original size:15 final size:14
Alignment explanation
Indices: 5607952--5608069 Score: 75
Period size: 15 Copynumber: 8.1 Consensus size: 14
5607942 TATTCTAATA
*
5607952 CTATTATTATTTAT
1 CTATTATTATTTTT
*
5607966 CTAATTATTATTTAT
1 CT-ATTATTATTTTT
*
5607981 CTATT-TATATTTCTA
1 CTATTAT-TATTT-TT
*
5607996 CTATTATTATATTT
1 CTATTATTATTTTT
5608010 CTATTTATTATATTTT
1 CTA-TTATTAT-TTTT
5608026 -TATT-TCTATTTATAT
1 CTATTAT-TATTT-T-T
*
5608041 ACTAATATTA-TTTT
1 -CTATTATTATTTTT
5608055 C-ATTATTATTTTT
1 CTATTATTATTTTT
5608068 CT
1 CT
5608070 CATATATGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 28
0.70 0.06 0.24
Matches are distributed among these distances:
12 6 0.07
13 10 0.12
14 21 0.25
15 34 0.41
16 6 0.07
17 5 0.06
18 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (14 bp):
CTATTATTATTTTT
Found at i:5608203 original size:25 final size:25
Alignment explanation
Indices: 5608175--5608269 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 25
5608165 CTCATTTCAA
5608175 ATTTTTATACATTATTTATTTTAAT
1 ATTTTTATACATTATTTATTTTAAT
* * * *
5608200 ATTTTCATATATTATGTATTTCAAACT
1 ATTTTTATACATTATTTATTT-TAA-T
* * *
5608227 TTTTTTCACACATTATATATTTTGAAT
1 ATTTTT-ATACATTATTTATTTT-AAT
* *
5608254 -TGTTTATATATTATTT
1 ATTTTTATACATTATTT
5608270 TTAAAGAGTT
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
25 26 0.50
26 6 0.12
27 6 0.12
28 14 0.27
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTTTTATACATTATTTATTTTAAT
Found at i:5609720 original size:20 final size:18
Alignment explanation
Indices: 5609680--5609722 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5609670 TATTAATTAC
*
5609680 ATTAATATTTTTTTAATA
1 ATTAATATTTTTTTAAAA
5609698 ATTAATATTCTTTTTAAAAA
1 ATTAATATT-TTTTT-AAAA
5609718 ATTAA
1 ATTAA
5609723 AACTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 5 0.23
20 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAATATTTTTTTAAAA
Found at i:5610252 original size:12 final size:12
Alignment explanation
Indices: 5610232--5610261 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5610222 TTAGTCGTTG
5610232 ATTTAAAAATTTT
1 ATTTAAAAA-TTT
5610245 ATTTAAAAATTT
1 ATTTAAAAATTT
5610257 ATTTA
1 ATTTA
5610262 TATTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTTAAAAATTT
Found at i:5620270 original size:22 final size:22
Alignment explanation
Indices: 5620242--5620286 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5620232 GGTTGTTGTG
5620242 TAGGAATAT-TCTGTAAATATTT
1 TAGGAATATCT-TGTAAATATTT
*
5620264 TAGGAATATCTTGTAGATATTT
1 TAGGAATATCTTGTAAATATTT
5620286 T
1 T
5620287 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATCTTGTAAATATTT
Found at i:5624868 original size:22 final size:22
Alignment explanation
Indices: 5624840--5624884 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5624830 AGGGGGAGTG
5624840 TAGGAATAT-TCTGTAAATATTT
1 TAGGAATATCT-TGTAAATATTT
*
5624862 TAGGAATATCTTGTAGATATTT
1 TAGGAATATCTTGTAAATATTT
5624884 T
1 T
5624885 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATCTTGTAAATATTT
Found at i:5628442 original size:46 final size:46
Alignment explanation
Indices: 5628390--5628662 Score: 397
Period size: 46 Copynumber: 6.0 Consensus size: 46
5628380 AGTGTGCTCT
5628390 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5628436 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5628482 CTGATATG-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
5628527 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** **
5628573 GTGACATGAAAAGAATAAGACCACAGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
5628619 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
5628663 TCACGTCAAA
Statistics
Matches: 210, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
45 46 0.22
46 164 0.78
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:5628554 original size:91 final size:92
Alignment explanation
Indices: 5628390--5628662 Score: 397
Period size: 91 Copynumber: 3.0 Consensus size: 92
5628380 AGTGTGCTCT
5628390 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
5628455 ACCATGGTTGAAAGATACCATGGCAAC
66 ACCATGGTTGAAAGATACCATGGCAAC
*
5628482 CTGATATG-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
5628546 ACCATGGTTGAAAGATACCATGGCAAC
66 ACCATGGTTGAAAGATACCATGGCAAC
* * * ** ** * * *
5628573 GTGACATGAAAAGAATAAGACCACAGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAATGTGTAA
* * *
5628637 GACCATAGTTGAAAGACACTATGGCA
65 GACCATGGTTGAAAGATACCATGGCA
5628663 TCACGTCAAA
Statistics
Matches: 164, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
91 89 0.54
92 75 0.46
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (92 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
ACCATGGTTGAAAGATACCATGGCAAC
Found at i:5628685 original size:137 final size:137
Alignment explanation
Indices: 5628405--5628662 Score: 338
Period size: 137 Copynumber: 1.9 Consensus size: 137
5628395 ATGAAATGTG
* * ** **
5628405 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCACAGTTGAAAGA
* * * * * *
5628470 TACCATGGCAACCTGATATGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
66 TACCATGGCAACATGACATGAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACCTGATATA
***
5628535 AGATGTG
131 AGATAAA
*
5628542 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCACAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCACAGTTGAAAGA
*
5628607 TACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
66 TACCATGGCAACATGACATG--AATGAGTAAGACCATAGTTGAAAGACACCATGGCA
5628663 TCACGTCAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
136 1 0.01
137 74 0.70
138 31 0.29
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.21
Consensus pattern (137 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCACAGTTGAAAGA
TACCATGGCAACATGACATGAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACCTGATATA
AGATAAA
Found at i:5628968 original size:23 final size:25
Alignment explanation
Indices: 5628923--5628969 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5628913 AATAAATATA
*
5628923 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
5628948 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
5628970 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:5631819 original size:24 final size:24
Alignment explanation
Indices: 5631792--5631842 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5631782 TTAGGACTAG
* * *
5631792 TTTAGCATTGTTTTTGAGGAGTGT
1 TTTAACATTATTTTTGAGAAGTGT
*
5631816 TTTAACATTATTTTTGTGAAGTGT
1 TTTAACATTATTTTTGAGAAGTGT
5631840 TTT
1 TTT
5631843 TAAAAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.55
Consensus pattern (24 bp):
TTTAACATTATTTTTGAGAAGTGT
Found at i:5632132 original size:100 final size:101
Alignment explanation
Indices: 5631997--5632208 Score: 338
Period size: 100 Copynumber: 2.1 Consensus size: 101
5631987 TTCAAATTAG
* * *
5631997 TTAATATTATGATATTTTAATAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATACTTTA
1 TTAATATTA-AATATCTTAATAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATAATTTA
*
5632062 ACATATGAAATATAAATTTTAAA-ATTTTTTTAAAAAA
65 ACATATAAAATATAAATTTTAAATA-TTTTTTAAAAAA
*
5632099 -TAATATTAAATATCTTAGTAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATAATTTAA
1 TTAATATTAAATATCTTAATAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATAATTTAA
*
5632163 TATATAAAATATAAATTTTAAATATTTTTTAAAAAA
66 CATATAAAATATAAATTTTAAATATTTTTTAAAAAA
5632199 TTAATATTAA
1 TTAATATTAA
5632209 TTATTTATAA
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
100 84 0.82
101 18 0.18
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (101 bp):
TTAATATTAAATATCTTAATAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATAATTTAA
CATATAAAATATAAATTTTAAATATTTTTTAAAAAA
Found at i:5632176 original size:19 final size:19
Alignment explanation
Indices: 5632154--5632263 Score: 51
Period size: 22 Copynumber: 5.2 Consensus size: 19
5632144 TTTGTTGTTA
5632154 ATAATTTAATATATAAAAT
1 ATAATTTAATATATAAAAT
* *
5632173 ATAAATTTTAAATATTTTTTAAAAA
1 AT-AA-TTT-AATA---TATAAAAT
*
5632198 ATTAATATTAATTATTTATAAAT
1 A-TAAT-TTAA-TATATA-AAAT
* *
5632221 TTAATTTGAATATATAAATT
1 ATAATTT-AATATATAAAAT
*
5632241 ATATTTTAA-ATAATAAAAT
1 ATAATTTAATAT-ATAAAAT
5632260 ATAA
1 ATAA
5632264 CCAATAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
18 2 0.03
19 13 0.19
20 10 0.14
21 10 0.14
22 14 0.20
23 3 0.04
24 3 0.04
25 13 0.19
26 1 0.01
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (19 bp):
ATAATTTAATATATAAAAT
Done.