Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold246
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: 866086
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.32
Warning! 37936 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:208386 original size:22 final size:21
Alignment explanation
Indices: 208361--208404 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
208351 AAATGAAATC
208361 CAAAGCACGGGAAATTGGCTTA
1 CAAAGCA-GGGAAATTGGCTTA
** *
208383 CAAATTAGGGAAATTGTCTTA
1 CAAAGCAGGGAAATTGGCTTA
208404 C
1 C
208405 GCTTCTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (21 bp):
CAAAGCAGGGAAATTGGCTTA
Found at i:210897 original size:16 final size:15
Alignment explanation
Indices: 210872--210903 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
210862 GTGCTTGATT
210872 TATGATTTGGTATAA
1 TATGATTTGGTATAA
210887 TATGCATTTGGTATAA
1 TATG-ATTTGGTATAA
210903 T
1 T
210904 TTGTTTACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (15 bp):
TATGATTTGGTATAA
Found at i:211412 original size:46 final size:46
Alignment explanation
Indices: 211289--211437 Score: 211
Period size: 46 Copynumber: 3.3 Consensus size: 46
211279 CTTGAATCAA
***
211289 GTTTTTGCAATAAACAACAATACTTAAATAATCAAATTTATAATAAT
1 GTTTTTGCAATAAACAACAATACTTAAATAATCAAACACA-AATAAT
211336 GTTTTTGCAATAAACAAC-A-A--T--ATAATCAAACACAAATAAT
1 GTTTTTGCAATAAACAACAATACTTAAATAATCAAACACAAATAAT
*
211376 GTTTTTGCAATAAACAACAATACTTAAATAATCAAACAGAAATAAT
1 GTTTTTGCAATAAACAACAATACTTAAATAATCAAACACAAATAAT
211422 GTTTTTGCAATAAACA
1 GTTTTTGCAATAAACA
211438 TTAAAGTATT
Statistics
Matches: 92, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
40 24 0.26
41 11 0.12
42 1 0.01
43 1 0.01
44 1 0.01
45 1 0.01
46 35 0.38
47 18 0.20
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.32
Consensus pattern (46 bp):
GTTTTTGCAATAAACAACAATACTTAAATAATCAAACACAAATAAT
Found at i:227757 original size:16 final size:16
Alignment explanation
Indices: 227725--227759 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
227715 AAAATATAGG
* *
227725 AAAATATTAGTTTAAA
1 AAAATATTAGCTGAAA
227741 AAAATATTAGCTGAAA
1 AAAATATTAGCTGAAA
227757 AAA
1 AAA
227760 TAAGTATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (16 bp):
AAAATATTAGCTGAAA
Found at i:228411 original size:19 final size:19
Alignment explanation
Indices: 228355--228451 Score: 59
Period size: 19 Copynumber: 4.8 Consensus size: 19
228345 AAATTAAATC
*
228355 TCTAAGATTACAAAATCATATA
1 TCTAAGATTAC-ATATC--ATA
* *
228377 TTCTAATATTGCATATCATA
1 -TCTAAGATTACATATCATA
*
228397 TCTAAGATTATATATATCATA
1 TCTAAGA-T-TACATATCATA
** *
228418 TCTTGGATTGCATATCATA
1 TCTAAGATTACATATCATA
* *
228437 TTTAAGATTGCATAT
1 TCTAAGATTACATAT
228452 TCTCAAAAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
19 27 0.46
20 5 0.08
21 14 0.24
22 4 0.07
23 9 0.15
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.41
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:228432 original size:21 final size:21
Alignment explanation
Indices: 228389--228451 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
228379 CTAATATTGC
*
228389 ATATCATATCTAAGATTATAT
1 ATATCATATCTAAGATTACAT
** *
228410 ATATCATATCTTGGATTGC--
1 ATATCATATCTAAGATTACAT
* *
228429 ATATCATATTTAAGATTGCAT
1 ATATCATATCTAAGATTACAT
228450 AT
1 AT
228452 TCTCAAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (21 bp):
ATATCATATCTAAGATTACAT
Found at i:228824 original size:15 final size:15
Alignment explanation
Indices: 228800--228829 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
228790 CCAGCAAAAT
*
228800 ATTTTTAACTTGTAA
1 ATTTTCAACTTGTAA
228815 ATTTTCAACTTGTAA
1 ATTTTCAACTTGTAA
228830 GTTGTGTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
ATTTTCAACTTGTAA
Found at i:229115 original size:19 final size:19
Alignment explanation
Indices: 229091--229129 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
229081 AAATTGATAA
*
229091 ACATATAATATAACACAAT
1 ACATATAATATAAAACAAT
*
229110 ACATATCATATAAAACAAT
1 ACATATAATATAAAACAAT
229129 A
1 A
229130 ATAATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (19 bp):
ACATATAATATAAAACAAT
Found at i:231228 original size:45 final size:44
Alignment explanation
Indices: 231159--231253 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 44
231149 CTTCCTACGG
231159 AAACAGACAAGCAGGTTACCCAAAA-TAGGAAATTAAGAAAAAGAA
1 AAACAGACAAGCAGGTTACCCAAAACTA-GAAATTAAG-AAAAGAA
*
231204 AAACAGACAAGCAGGTTACTCAAAACTAGAAATTAAGAAAAGAA
1 AAACAGACAAGCAGGTTACCCAAAACTAGAAATTAAGAAAAGAA
231248 AAACAG
1 AAACAG
231254 GAGCTAGTCC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 13 0.27
45 33 0.69
46 2 0.04
ACGTcount: A:0.58, C:0.14, G:0.17, T:0.12
Consensus pattern (44 bp):
AAACAGACAAGCAGGTTACCCAAAACTAGAAATTAAGAAAAGAA
Found at i:231306 original size:25 final size:26
Alignment explanation
Indices: 231277--231325 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
231267 AAGAAATGCG
231277 TGTCAAAAGACAGAG-AAAAAAAACT
1 TGTCAAAAGACAGAGTAAAAAAAACT
*
231302 TGTCAACAGACAGAGTAAAAAAAA
1 TGTCAAAAGACAGAGTAAAAAAAA
231326 TTAGATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.12
Consensus pattern (26 bp):
TGTCAAAAGACAGAGTAAAAAAAACT
Found at i:233279 original size:15 final size:15
Alignment explanation
Indices: 233255--233284 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
233245 CCAGCAAAAT
*
233255 ATTTTTAACTTGTAA
1 ATTTTCAACTTGTAA
233270 ATTTTCAACTTGTAA
1 ATTTTCAACTTGTAA
233285 GTTGTGTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
ATTTTCAACTTGTAA
Found at i:235233 original size:16 final size:16
Alignment explanation
Indices: 235208--235239 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
235198 TAGTGAGCCA
235208 CGTGTCTGTGGTTAAT
1 CGTGTCTGTGGTTAAT
*
235224 CGTGTGTGTGGTTAAT
1 CGTGTCTGTGGTTAAT
235240 AAATCTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.34, T:0.44
Consensus pattern (16 bp):
CGTGTCTGTGGTTAAT
Found at i:235632 original size:15 final size:15
Alignment explanation
Indices: 235586--235634 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
235576 AAAATCTAAA
235586 AAAAACTAAATTCTT
1 AAAAACTAAATTCTT
* *
235601 AAAAA-TACAAAT-AT
1 AAAAACTA-AATTCTT
235615 AAAAACTAAATTCTT
1 AAAAACTAAATTCTT
235630 AAAAA
1 AAAAA
235635 TTGAAAAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAACTAAATTCTT
Found at i:237623 original size:111 final size:112
Alignment explanation
Indices: 237418--237637 Score: 343
Period size: 111 Copynumber: 2.0 Consensus size: 112
237408 AACTGCTTGT
* * * **
237418 TCACTCCGATGTTCAAACAAATATTTAGATAGATATTTGAATAGTAATTTGTACAATAAATCTTT
1 TCACTCCGATCTTCAAACAAATATTTAGATAGATATTGGAATAGTAATCTACACAATAAATCTTT
*
237483 GGATAGCTTTAAGTCAACTTAGATGTGGGCCTTTTTTTTATTTTGAC
66 GGATAGATTTAAGTCAACTTAGATGTGGGCCTTTTTTTTATTTTGAC
*
237530 TCACTCC-ATCTTCAAACAAATATTTAGATAGATCTTGGAATAGTAATCTACACAATAAATCTTT
1 TCACTCCGATCTTCAAACAAATATTTAGATAGATATTGGAATAGTAATCTACACAATAAATCTTT
* * *
237594 GGATAGATTTAAGTCAAGTTAGATGTGGGCTTTTTTTTTTTTTT
66 GGATAGATTTAAGTCAACTTAGATGTGGGCCTTTTTTTTATTTT
237638 TTTGACATCC
Statistics
Matches: 98, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
111 91 0.93
112 7 0.07
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (112 bp):
TCACTCCGATCTTCAAACAAATATTTAGATAGATATTGGAATAGTAATCTACACAATAAATCTTT
GGATAGATTTAAGTCAACTTAGATGTGGGCCTTTTTTTTATTTTGAC
Found at i:239847 original size:18 final size:19
Alignment explanation
Indices: 239824--239859 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
239814 CATGTATCTA
*
239824 TACATA-TTATTATTTTAT
1 TACATATTTATGATTTTAT
239842 TACATATTTATGATTTTA
1 TACATATTTATGATTTTA
239860 GTTCATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (19 bp):
TACATATTTATGATTTTAT
Found at i:242939 original size:533 final size:533
Alignment explanation
Indices: 241933--242998 Score: 1889
Period size: 533 Copynumber: 2.0 Consensus size: 533
241923 CCAAACTTTT
241933 TCTTTTCCTCGATCTAGCTTCGTATTTGAACTTTCTGGATCTAAATAAATAAATTTAATCATTAA
1 TCTTTTCCTCGATCTAGCTTCGTATTTGAACTTTCTGGATCTAAATAAATAAATTTAATCATTAA
241998 CCTAATACATTTCATGTGCATGTGTAACATTCTCTATAACTCCATTATTATTTATAGTGCATTCA
66 CCTAATACATTTCATGTGCATGTGTAACATTCTCTATAACTCCATTATTATTTATAGTGCATTCA
* * *
242063 AAGCTATCTCACTGAGTCACTGTCACTAAATTATTTATATCTTGAGCTACGGAATTCCAAATTAA
131 AAGATATCTCACTGAGTCACTGTCACTAAATTATTTATATCTTGAGCTACAGAACTCCAAATTAA
*
242128 GATCCGTTAATTTTCCTTGAAACTAGACTCACATATCTTATTACCATAAAATTTTAAGAATTTTT
196 GATCCGTTAATTTTCCTTGAAACTAGACTCACATATATTATTACCATAAAATTTTAAGAATTTTT
* *
242193 GGTTCAGCCAATAAGTACATTTTATTCTTTAAAATTTCCCCTATTTCACTGTCTGACAGTTCCGA
261 GGTCCAGCCAATAAGTACAGTTTATTCTTTAAAATTTCCCCTATTTCACTGTCTGACAGTTCCGA
* *
242258 CCCCTCTTCACTAAAATTTAATTATATCATTGTACATAATTCAGATGATGTTTTTGTTTGTTTCT
326 CCCCTCTTCACTAAAATTTAATTATATCATTGTACAGAATTCAGATGATGTTTTCGTTTGTTTCT
* * *
242323 TCTGAAAATATACTCATTAAGGATTTTTACCATATAAATTATAACTCATAATAATTTTTTTACAA
391 TCTGAAAATAGACTCATTAAGGATTCTGACCATATAAATTATAACTCATAATAATTTTTTTACAA
*
242388 TTTTTAATGATTTTCCAAAGTTAGAACAGGGGAACCCGAATTCATTCTAACCTTGTCTCACAAAA
456 TTTTTAATGATTTTCCAAAGTCAGAACAGGGGAACCCGAATTCATTCTAACCTTGTCTCACAAAA
242453 TCTATTATATCTC
521 TCTATTATATCTC
*
242466 TCTTTTCCTCGATCTAGCTTCGTATTTGAACTTTTTGGATCTAAATAAATAAATTTAATCATTAA
1 TCTTTTCCTCGATCTAGCTTCGTATTTGAACTTTCTGGATCTAAATAAATAAATTTAATCATTAA
* * *
242531 TCTAATACATTTCATGTTCATGTGTAACATTCTCTATAACTCCATTTTTATTTATAGTGCATTCA
66 CCTAATACATTTCATGTGCATGTGTAACATTCTCTATAACTCCATTATTATTTATAGTGCATTCA
*
242596 AAGATGTCTCACTGAGTCACTGTCACTAAATTATTTATATCTTGAGCTACAGAACTCCAAATTAA
131 AAGATATCTCACTGAGTCACTGTCACTAAATTATTTATATCTTGAGCTACAGAACTCCAAATTAA
* * *
242661 TATCCGTTAATTTTCCTTGAAACTAGACTCACATATATTATTACCATAAAATTTTCATAATTTTT
196 GATCCGTTAATTTTCCTTGAAACTAGACTCACATATATTATTACCATAAAATTTTAAGAATTTTT
* *
242726 GGTCCAGCCAATAAGTACAGTTTATTCTTTAAAATTTCCCTTGTTTCACTGTCTGACAGTTCCGA
261 GGTCCAGCCAATAAGTACAGTTTATTCTTTAAAATTTCCCCTATTTCACTGTCTGACAGTTCCGA
242791 CCCCTCTTCACTAAAATTTAATTATATCATTGTACAGAATTCAGATGATGTTTTCGTTTGTTTCT
326 CCCCTCTTCACTAAAATTTAATTATATCATTGTACAGAATTCAGATGATGTTTTCGTTTGTTTCT
* * *
242856 TTTGAAAATAGACTCATTAAGTATTCTGACCATATAAATTATAACTCATAATCATTTTTTTACAA
391 TCTGAAAATAGACTCATTAAGGATTCTGACCATATAAATTATAACTCATAATAATTTTTTTACAA
* *
242921 TTTTTAATGATTTTCCAAAGTCAGAATAGGGGAACCCGAATTCATTCTGACCTTGTCTCACAAAA
456 TTTTTAATGATTTTCCAAAGTCAGAACAGGGGAACCCGAATTCATTCTAACCTTGTCTCACAAAA
242986 TCTATTATATCTC
521 TCTATTATATCTC
242999 GTGATTTACA
Statistics
Matches: 506, Mismatches: 27, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
533 506 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (533 bp):
TCTTTTCCTCGATCTAGCTTCGTATTTGAACTTTCTGGATCTAAATAAATAAATTTAATCATTAA
CCTAATACATTTCATGTGCATGTGTAACATTCTCTATAACTCCATTATTATTTATAGTGCATTCA
AAGATATCTCACTGAGTCACTGTCACTAAATTATTTATATCTTGAGCTACAGAACTCCAAATTAA
GATCCGTTAATTTTCCTTGAAACTAGACTCACATATATTATTACCATAAAATTTTAAGAATTTTT
GGTCCAGCCAATAAGTACAGTTTATTCTTTAAAATTTCCCCTATTTCACTGTCTGACAGTTCCGA
CCCCTCTTCACTAAAATTTAATTATATCATTGTACAGAATTCAGATGATGTTTTCGTTTGTTTCT
TCTGAAAATAGACTCATTAAGGATTCTGACCATATAAATTATAACTCATAATAATTTTTTTACAA
TTTTTAATGATTTTCCAAAGTCAGAACAGGGGAACCCGAATTCATTCTAACCTTGTCTCACAAAA
TCTATTATATCTC
Found at i:248509 original size:54 final size:54
Alignment explanation
Indices: 248442--248647 Score: 412
Period size: 54 Copynumber: 3.8 Consensus size: 54
248432 ATCCTTACAG
248442 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
248496 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
248550 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
248604 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCAT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCAT
248648 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 152 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (54 bp):
CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
Found at i:251573 original size:14 final size:13
Alignment explanation
Indices: 251550--251581 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
251540 AAATTTTCAC
251550 GAAATCATTTCGT
1 GAAATCATTTCGT
251563 GAAATCGATTTCGT
1 GAAATC-ATTTCGT
251577 GAAAT
1 GAAAT
251582 TGTAGGCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (13 bp):
GAAATCATTTCGT
Found at i:256962 original size:151 final size:152
Alignment explanation
Indices: 256687--256994 Score: 476
Period size: 151 Copynumber: 2.0 Consensus size: 152
256677 AAGGTTCTAC
256687 GTGAAAGTGTGACTAAAGTGAATCCGGGTGCTGGTCTTAAGTTCTACCAATGGCTGGGCATACCG
1 GTGAAAGTGTGACTAAAGTGAATCCGGGTGCTGGTCTTAAGTTCTACCAATGGCTGGGCATACCG
* * * *
256752 ACATGTGTTGCGGATACCTGACAGCTTGTGTGAGCAACACTGAGTAGTAATAAAAGACTGACAGC
66 ACATGTGTTGCAGATACCTGACAGCTTGTGTGAGCAACACTGAATAGAAACAAAAGACTGACAGC
*
256817 TTGTGTGAGCAGACCCGT-AAT
131 TTGTGTGAGCAGACCCGTGAAA
* * * *
256838 GTGAAAGTGTGGCTAAAGTGAATCTGGGTGCTGGTCTTAAGTTCTACCAGTGGCTGGGTATACC-
1 GTGAAAGTGTGACTAAAGTGAATCCGGGTGCTGGTCTTAAGTTCTACCAATGGCTGGGCATACCG
* * * *
256902 AGTATGTGTTGCAGATACCTGACAGCTTGTGTGAGCAGCACTGAATAGAAACGAATGACTGACAG
66 A-CATGTGTTGCAGATACCTGACAGCTTGTGTGAGCAACACTGAATAGAAACAAAAGACTGACAG
256967 CTTGTGTGAGCAGACCCGTGAAA
130 CTTGTGTGAGCAGACCCGTGAAA
256990 GTGAA
1 GTGAA
256995 TAGCTCGAGA
Statistics
Matches: 142, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
150 1 0.01
151 134 0.94
152 7 0.05
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (152 bp):
GTGAAAGTGTGACTAAAGTGAATCCGGGTGCTGGTCTTAAGTTCTACCAATGGCTGGGCATACCG
ACATGTGTTGCAGATACCTGACAGCTTGTGTGAGCAACACTGAATAGAAACAAAAGACTGACAGC
TTGTGTGAGCAGACCCGTGAAA
Found at i:263312 original size:54 final size:54
Alignment explanation
Indices: 263230--263338 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
263220 TAAGCCTTAA
*
263230 GTTTCTAAGCACTTAGTGCACTTGGGTTGACTTTAATATATGGTCAACTCTGCC
1 GTTTCTAAGCACTTAGTGCACTTGGGTTGACTTTAATATATGGTCAACCCTGCC
*
263284 GTTTCTAAGCACTTAGTGCACTTGGGTTGGCTTTAATATATGGTCAACCCTGCC
1 GTTTCTAAGCACTTAGTGCACTTGGGTTGACTTTAATATATGGTCAACCCTGCC
263338 G
1 G
263339 CCTGAGTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (54 bp):
GTTTCTAAGCACTTAGTGCACTTGGGTTGACTTTAATATATGGTCAACCCTGCC
Found at i:278478 original size:12 final size:12
Alignment explanation
Indices: 278461--278488 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
278451 CTAAATCCTT
278461 TCTCTAATATTC
1 TCTCTAATATTC
278473 TCTCTAATATTC
1 TCTCTAATATTC
278485 TCTC
1 TCTC
278489 AAATTCCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCTAATATTC
Found at i:278494 original size:22 final size:21
Alignment explanation
Indices: 278459--278551 Score: 75
Period size: 22 Copynumber: 4.2 Consensus size: 21
278449 AACTAAATCC
278459 TTTCTCT-AATATTCTCTCTAA
1 TTTCTCTCAA-ATTCTCTCTAA
278480 TATTCTCTCAAATTC-CTCTCAA
1 T-TTCTCTCAAATTCTCTCT-AA
*
278502 TTTCCTCTCAATTTGCTCTC-AA
1 TTT-CTCTCAAATT-CTCTCTAA
* *
278524 CTTCCTCTCAAATTTCTCTCAAA
1 -TTTCTCTCAAA-TTCTCTCTAA
278547 TTTCT
1 TTTCT
278552 ATTTAAAAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
21 7 0.12
22 40 0.68
23 9 0.15
24 3 0.05
ACGTcount: A:0.23, C:0.30, G:0.01, T:0.46
Consensus pattern (21 bp):
TTTCTCTCAAATTCTCTCTAA
Found at i:278549 original size:11 final size:11
Alignment explanation
Indices: 278470--278551 Score: 87
Period size: 11 Copynumber: 7.4 Consensus size: 11
278460 TTCTCTAATA
*
278470 TTCTCTCTAAT
1 TTCTCTCAAAT
278481 ATTCTCTCAAAT
1 -TTCTCTCAAAT
*
278493 TCCTCTC-AAT
1 TTCTCTCAAAT
278503 TTCCTCTC-AAT
1 TT-CTCTCAAAT
*
278514 TTGCTCTCAACT
1 TT-CTCTCAAAT
*
278526 TCCTCTCAAAT
1 TTCTCTCAAAT
278537 TTCTCTCAAAT
1 TTCTCTCAAAT
278548 TTCT
1 TTCT
278552 ATTTAAAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
10 4 0.07
11 43 0.72
12 13 0.22
ACGTcount: A:0.22, C:0.32, G:0.01, T:0.45
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:280108 original size:21 final size:21
Alignment explanation
Indices: 280069--280108 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
280059 ATCATATAAA
*
280069 TTACAAATTACAATTATTTTT
1 TTACAAATTACAATGATTTTT
* *
280090 TTACAATTTATAATGATTT
1 TTACAAATTACAATGATTT
280109 ATCAAAGTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
TTACAAATTACAATGATTTTT
Found at i:282804 original size:126 final size:125
Alignment explanation
Indices: 282514--282925 Score: 637
Period size: 126 Copynumber: 3.3 Consensus size: 125
282504 CAGACCATGC
* * *
282514 GCTACTGTAGCAAAAGCGCGTCCACGTGGAAGCTTCTTTCAATACTTCTGCTGACAAAGCATCTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * * *
282579 GCTTAAAGCATTTTTGACACTGTTTGTTCAAAAAGTCTACTCGAAATTATTTTTTCAGGG
66 ACTTAAAGCGTTTTTGACACTGTTTGCTCAAAAAGTCTACTCGAAATTATTTTTTCAGGA
* *
282639 GCTACTGTAGCAAAAGC-CTGTACACGTGAGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCC
1 GCTACTGTAGCAAAAGCGC-GTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCC
* *
282703 TAATTAAAGCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATTATTCTTTCAGGA
65 TACTTAAAGCGTTTTTGACACTGTTTGCTCAAAAA-GTCTACTCGAAATTATTTTTTCAGGA
*
282765 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTCCTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * *
282830 TCTTAAAGCGTCTTTGACACTGTTTGCTCAGAAATGTCTACTCGAAATTATTTTTTCAGGA
66 ACTTAAAGCGTTTTTGACACTGTTTGCTCA-AAAAGTCTACTCGAAATTATTTTTTCAGGA
* *
282891 CCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTT
282926 TTTTAAATTA
Statistics
Matches: 262, Mismatches: 21, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
124 1 0.00
125 88 0.34
126 169 0.65
127 4 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (125 bp):
GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
ACTTAAAGCGTTTTTGACACTGTTTGCTCAAAAAGTCTACTCGAAATTATTTTTTCAGGA
Found at i:283143 original size:95 final size:89
Alignment explanation
Indices: 282962--283187 Score: 274
Period size: 95 Copynumber: 2.4 Consensus size: 89
282952 AGTAACCTTA
*
282962 AACCCGGAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACCTTAAACTAATTTATTAA
1 AACCCTGAACCCTAATTTATTTGA-TTTTTACTTAAAAACCCTAAACCTTAAACTAATTTATTAA
*
283027 AAAATTTTAATTAATTTACTCAAGT
65 AAAATTTTAATTAAATTACTCAAGT
* *
283052 AACCCTGAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAA-CTCTAAACCCTAATTTGAT
1 AACCCTGAACCCTAATTTATTTGATTTTTACTTAAAAACCCTAAACCT-TAAA--CTAATTT-A-
**
283116 TTTTAAAATTTTTTAATTAAATTACTCAAGT
61 --TTAAAAAATTTTAATTAAATTACTCAAGT
* * *
283147 AACCCTAAACCCTAATTTAGTTGAATTTTTTCTTACAAAAC
1 AACCCTGAACCCTAATTTATTTG-ATTTTTACTTA-AAAAC
283188 AATAAACACG
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
88 2 0.02
89 23 0.19
90 23 0.19
91 7 0.06
92 1 0.01
95 47 0.40
96 10 0.08
97 5 0.04
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (89 bp):
AACCCTGAACCCTAATTTATTTGATTTTTACTTAAAAACCCTAAACCTTAAACTAATTTATTAAA
AAATTTTAATTAAATTACTCAAGT
Found at i:283943 original size:71 final size:72
Alignment explanation
Indices: 283825--283968 Score: 254
Period size: 71 Copynumber: 2.0 Consensus size: 72
283815 TTTATTAAAT
* *
283825 AATATTATAATTATTTTTAAATGTGAATTTAGTAATATGATGAAAAATAAAGGGCATTCTCTCAC
1 AATATTATAA-TATATTTAAAAGTGAATTTAGTAATATGATGAAAAATAAAGGGCATTCTCTCAC
283890 ATCAAAAG
65 ATCAAAAG
283898 AATATTATAA-ATATTTAAAAGTGAATTTAGTAATATGATGAAAAATAAAGGGCATTCTCTCACA
1 AATATTATAATATATTTAAAAGTGAATTTAGTAATATGATGAAAAATAAAGGGCATTCTCTCACA
283962 TCAAAAG
66 TCAAAAG
283969 TTTTTCTAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
71 59 0.86
73 10 0.14
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (72 bp):
AATATTATAATATATTTAAAAGTGAATTTAGTAATATGATGAAAAATAAAGGGCATTCTCTCACA
TCAAAAG
Found at i:284094 original size:24 final size:24
Alignment explanation
Indices: 284036--284096 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
284026 TAGATGTTCA
* *
284036 ACCTTTCATATTCCTCAACTTTTC
1 ACCTTTCATCTTCCTCAACTCTTC
*
284060 ACCTTTCATCTTCCTTAACTCTTC
1 ACCTTTCATCTTCCTCAACTCTTC
*
284084 ACCTTTAATCTTC
1 ACCTTTCATCTTC
284097 TTGTAACCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (24 bp):
ACCTTTCATCTTCCTCAACTCTTC
Found at i:284966 original size:18 final size:20
Alignment explanation
Indices: 284929--284968 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
284919 CTAGTGTCAA
*
284929 ATAATATTTCTAATATTTTT
1 ATAATATTTATAATATTTTT
284949 ATAA-ATTTATAA-ATTTTT
1 ATAATATTTATAATATTTTT
284967 AT
1 AT
284969 TTTTATTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATAATATTTATAATATTTTT
Found at i:292048 original size:19 final size:19
Alignment explanation
Indices: 292026--292075 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
292016 AATAATTTAT
292026 AAATTAATTTATAA-GAATA
1 AAATTAATTT-TAAGGAATA
* *
292045 AAATTTATTTTAAGGAATC
1 AAATTAATTTTAAGGAATA
*
292064 AATTTAATTTTA
1 AAATTAATTTTA
292076 TTTAGTGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (19 bp):
AAATTAATTTTAAGGAATA
Found at i:293088 original size:10 final size:10
Alignment explanation
Indices: 293019--293137 Score: 55
Period size: 10 Copynumber: 12.8 Consensus size: 10
293009 TTCATGTGGC
293019 TTAAAAACT-T
1 TTAAAAA-TAT
* *
293029 TTAAACATAC
1 TTAAAAATAT
*
293039 TTATAAAT-T
1 TTAAAAATAT
293048 ATTAAAAA-AT
1 -TTAAAAATAT
293058 TGTAAAAAT-T
1 T-TAAAAATAT
293068 TT-AAAA-A-
1 TTAAAAATAT
293075 -TAAAAATAT
1 TTAAAAATAT
*
293084 TTAAATAT-T
1 TTAAAAATAT
293093 TTAAAAA-AT
1 TTAAAAATAT
* *
293102 CTAAGAATA-
1 TTAAAAATAT
*
293111 TTAAAAATGT
1 TTAAAAATAT
*
293121 TTAAATAT-T
1 TTAAAAATAT
293130 TTAAAAAT
1 TTAAAAAT
293138 TAAATTAAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 5 0.06
9 30 0.37
10 41 0.51
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:293123 original size:28 final size:26
Alignment explanation
Indices: 293050--293125 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 26
293040 TATAAATTAT
293050 TAAAAA-ATTGTAAAAATTTT-AAAAA
1 TAAAAATATT-TAAAAATTTTAAAAAA
*
293075 TAAAAATATTTAAATATTTTAAAAAA
1 TAAAAATATTTAAAAATTTTAAAAAA
*
293101 TCTAAGAATA-TTAAAAATGTTTAAA
1 --TAAAAATATTTAAAAAT-TTTAAA
293126 TATTTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 15 0.35
26 8 0.19
27 7 0.16
28 13 0.30
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (26 bp):
TAAAAATATTTAAAAATTTTAAAAAA
Found at i:293154 original size:62 final size:62
Alignment explanation
Indices: 293047--293163 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 62
293037 ACTTATAAAT
**
293047 TATTAAAAAATTGTAAAAATTTTAAAAATAAAAATATTTAAATATTTTAAAAAATCTAAGAA
1 TATTAAAAAATTGTAAAAATTTTAAAAATAAAAATAAATAAATATTTTAAAAAATCTAAGAA
* * * * * *
293109 TATT-AAAAATGTTTAAATATTTTAAAAATTAAATTAAATATATATTTTAGAAAAT
1 TATTAAAAAAT-TGTAAAAATTTTAAAAATAAAAATAAATAAATATTTTAAAAAAT
293164 ATAAAAGTCC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 6 0.13
62 40 0.87
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (62 bp):
TATTAAAAAATTGTAAAAATTTTAAAAATAAAAATAAATAAATATTTTAAAAAATCTAAGAA
Found at i:296662 original size:51 final size:51
Alignment explanation
Indices: 296519--296698 Score: 159
Period size: 51 Copynumber: 3.5 Consensus size: 51
296509 AAAGTGATGG
* * ** * *
296519 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTAATACGCATACCGGATAGTAAT-GA
* * * *
296569 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTAATACGCATACCGGATAGTAAT-GA
* * * ** * * *
296620 TCACTTGTGGAGTACTATGTGTAGGCTAATACGTGTATCGGATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTAATACGCATACCGGATAGTAATGA
296671 TCACATGTGTAGTACTATGTGCAGGCTA
1 TCACATGTGTAGTACTATGTGCAGGCTA
296699 CTATGTAACA
Statistics
Matches: 104, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
50 37 0.36
51 65 0.62
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTAATACGCATACCGGATAGTAATGA
Found at i:300049 original size:11 final size:10
Alignment explanation
Indices: 300023--300047 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
300013 TCTGACTTTG
300023 AAAAATTGTA
1 AAAAATTGTA
300033 AAAAATTGTA
1 AAAAATTGTA
300043 AAAAA
1 AAAAA
300048 ATAATTATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAAATTGTA
Found at i:312251 original size:19 final size:19
Alignment explanation
Indices: 312229--312270 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
312219 CAAAATTTTT
*
312229 AAAAATATA-TAAATACATC
1 AAAAA-ATACTAAAAACATC
*
312248 AAAAAATACTAAAAACATT
1 AAAAAATACTAAAAACATC
312267 AAAA
1 AAAA
312271 TAAATGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAATACTAAAAACATC
Found at i:314132 original size:60 final size:60
Alignment explanation
Indices: 313981--314167 Score: 290
Period size: 60 Copynumber: 3.2 Consensus size: 60
313971 GAGTACCAGC
*
313981 TCTGATGAATTTCAAGAAGCAAGAGAAGAACAGAGTCCAATGAAGTCTCCACTAAAA-C-
1 TCTGATGAATTTCAAGAAGCAAGAGAAGAACAGAGTCCGATGAAGTCTCCACTAAAACCT
* * *
314039 -CTGATGAATTTCATGAAGCAAGGGAAGAACAGAGTCCGATGAAGTCTCCATTAAAACCT
1 TCTGATGAATTTCAAGAAGCAAGAGAAGAACAGAGTCCGATGAAGTCTCCACTAAAACCT
* * *
314098 TCTGATGAATTTCAAGAAGCAAGAGAAGAACAGAGTCCGATGAAGGCTCCACCAAAACTT
1 TCTGATGAATTTCAAGAAGCAAGAGAAGAACAGAGTCCGATGAAGTCTCCACTAAAACCT
314158 TCTGATGAAT
1 TCTGATGAAT
314168 CTGTATTCAT
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
57 52 0.45
58 1 0.01
60 63 0.54
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (60 bp):
TCTGATGAATTTCAAGAAGCAAGAGAAGAACAGAGTCCGATGAAGTCTCCACTAAAACCT
Found at i:330089 original size:11 final size:10
Alignment explanation
Indices: 330062--330091 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
330052 ATGTTTATTC
330062 AAAATTTTTA
1 AAAATTTTTA
330072 AAAATTTTTA
1 AAAATTTTTA
330082 AAATATTTTT
1 AAA-ATTTTT
330092 TTTTGATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:330214 original size:37 final size:37
Alignment explanation
Indices: 330171--330243 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
330161 TTTTAATAAT
*
330171 TTTTTTTACAATCTTTTATG-ATTTCTAATAAATTTTA
1 TTTTTTTACAATATTTTA-GAATTTCTAATAAATTTTA
*
330208 TTTTTTTACAATATTTTAGAATTTCTAATAATTTTT
1 TTTTTTTACAATATTTTAGAATTTCTAATAAATTTT
330244 GTAACTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 32 0.97
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (37 bp):
TTTTTTTACAATATTTTAGAATTTCTAATAAATTTTA
Found at i:330527 original size:31 final size:31
Alignment explanation
Indices: 330461--330533 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
330451 TTAAATTTTT
* * *
330461 TAATAATTCTTTTACAATCTTTGATGATTTT
1 TAATAATTTTTTTACAATATTTGATGATTTC
*
330492 TAATAATTTTTTTACAATATTTTA-GAATTTC
1 TAATAATTTTTTTACAATATTTGATG-ATTTC
330523 TAATAATTTTT
1 TAATAATTTTT
330534 ATATCGTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (31 bp):
TAATAATTTTTTTACAATATTTGATGATTTC
Found at i:330581 original size:10 final size:10
Alignment explanation
Indices: 330448--330581 Score: 53
Period size: 10 Copynumber: 13.2 Consensus size: 10
330438 CTTTTACTAG
330448 TTTTTA-AAT
1 TTTTTATAAT
330457 TTTTTAATAAT
1 TTTTT-ATAAT
*
330468 TCTTTTACAAT
1 T-TTTTATAAT
* * *
330479 CTTTGATGAT
1 TTTTTATAAT
*
330489 TTTTAATAATT
1 TTTTTATAA-T
*
330500 TTTTTACAAT
1 TTTTTATAAT
* *
330510 ATTTTAGAAT
1 TTTTTATAAT
* *
330520 TTCTAATAA-
1 TTTTTATAAT
330529 TTTTTAT-AT
1 TTTTTATAAT
* * *
330538 CGTTTGATATT
1 -TTTTTATAAT
330549 TTTTTAATAAAT
1 TTTTT-AT-AAT
330561 TTTATT-T-AT
1 TTT-TTATAAT
330570 TTTTTATAAT
1 TTTTTATAAT
330580 TT
1 TT
330582 AAAAAAATCA
Statistics
Matches: 89, Mismatches: 24, Indels: 23
0.65 0.18 0.17
Matches are distributed among these distances:
8 3 0.03
9 16 0.18
10 39 0.44
11 20 0.22
12 9 0.10
13 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:338305 original size:12 final size:12
Alignment explanation
Indices: 338290--338342 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
338280 TTTTATGTAA
338290 TATCTGTATATG
1 TATCTGTATATG
*
338302 TATCTGTATCTG
1 TATCTGTATATG
*
338314 TATATGTATATG
1 TATCTGTATATG
* * *
338326 TATATGCACATG
1 TATCTGTATATG
338338 TATCT
1 TATCT
338343 TTCTTTGCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.47
Consensus pattern (12 bp):
TATCTGTATATG
Found at i:338309 original size:6 final size:6
Alignment explanation
Indices: 338294--338331 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
338284 ATGTAATATC
* *
338294 TGTATA TGTATC TGTATC TGTATA TGTATA TGTATA TG
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TG
338332 CACATGTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:338313 original size:18 final size:18
Alignment explanation
Indices: 338290--338342 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
338280 TTTTATGTAA
338290 TATCTGTATATGTATCTG
1 TATCTGTATATGTATCTG
*
338308 TATCTGTATATGTATATG
1 TATCTGTATATGTATCTG
* * *
338326 TATATGCACATGTATCT
1 TATCTGTATATGTATCT
338343 TTCTTTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.47
Consensus pattern (18 bp):
TATCTGTATATGTATCTG
Found at i:341318 original size:19 final size:19
Alignment explanation
Indices: 341294--341336 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
341284 ATGTGTTGTT
*
341294 TAATTTGGTCTTTTTTTTG
1 TAATTTGCTCTTTTTTTTG
*
341313 TAATTTTGCTTTTTTTTTTG
1 TAA-TTTGCTCTTTTTTTTG
341333 TAAT
1 TAAT
341337 ATTAAGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.70
Consensus pattern (19 bp):
TAATTTGCTCTTTTTTTTG
Found at i:344899 original size:22 final size:22
Alignment explanation
Indices: 344874--344962 Score: 92
Period size: 22 Copynumber: 4.0 Consensus size: 22
344864 CACGACCATA
**
344874 TGCCTCCTCGTACACGGCCGTG
1 TGCCTCCTCCCACACGGCCGTG
* ** *
344896 TGCCTCCTCCCACATGATCGCG
1 TGCCTCCTCCCACACGGCCGTG
344918 TGCCTCCTCCCACACGGTCC-TG
1 TGCCTCCTCCCACACGG-CCGTG
344940 TGCCTCCTCCCACACAGG-CGTG
1 TGCCTCCTCCCACAC-GGCCGTG
344962 T
1 T
344963 TGACCCCCAC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.02
22 50 0.93
23 3 0.06
ACGTcount: A:0.11, C:0.45, G:0.21, T:0.22
Consensus pattern (22 bp):
TGCCTCCTCCCACACGGCCGTG
Found at i:352290 original size:22 final size:20
Alignment explanation
Indices: 352265--352304 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
352255 CCGGCCCAAT
352265 TTTTAATAAACACAAAAAATTA
1 TTTTAA-AAACA-AAAAAATTA
*
352287 TTTTAAAAATAAAAAAAT
1 TTTTAAAAACAAAAAAAT
352305 AAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTTAAAAACAAAAAAATTA
Found at i:352844 original size:79 final size:80
Alignment explanation
Indices: 352699--352858 Score: 277
Period size: 79 Copynumber: 2.0 Consensus size: 80
352689 TAACTTCTCA
352699 AAAAAGTTATGATTCAGTTTCAACCCTATATATATATATTTTTGGTTTGCCCCTAATCAACGCAA
1 AAAAAGTTATGATTCAGTTTCAACCCTATATATATATATTTTTGGTTTGCCCCTAATCAACGCAA
352764 CATTTCTCGACCACT
66 CATTTCTCGACCACT
* * * *
352779 AAAAAGTTATGATTCAGTTTCAACCCTAT-TTTTTTTTTTTTTGGTTTGCCCCTAATCAACGCAA
1 AAAAAGTTATGATTCAGTTTCAACCCTATATATATATATTTTTGGTTTGCCCCTAATCAACGCAA
352843 CATTTCTCGACCACT
66 CATTTCTCGACCACT
352858 A
1 A
352859 TTGAAATTGA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 47 0.62
80 29 0.38
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (80 bp):
AAAAAGTTATGATTCAGTTTCAACCCTATATATATATATTTTTGGTTTGCCCCTAATCAACGCAA
CATTTCTCGACCACT
Found at i:354200 original size:68 final size:67
Alignment explanation
Indices: 354126--354493 Score: 224
Period size: 68 Copynumber: 5.4 Consensus size: 67
354116 ATTTTCATAG
354126 ATTTAATATTAAATTTAATTTAATAATTATCTTAATAATATTTTATTAATTTAATATTATAGTGA
1 ATTTAATATTAAATTTAATTTAATAATTATCTTAATAATATTTTATTAATTTAATATTATAGTGA
354191 TT
66 TT
* * * *
354193 ATCTTAATATTAAATTAAATTAAATATTTATCCTGTAGATAAGTATTCTATTAA-TT--TA--AT
1 AT-TTAATATTAAATTTAATTTAATAATTAT-CT-TA-ATAA-TATTTTATTAATTTAATATTAT
354253 A--G---
61 AGTGATT
* * * * * * *
354255 ATTTAATATTAAATATAATCTAATATTTATCCTGATAAGTATTATATTAATTTAATATTAAAGTG
1 ATTTAATATTAAATTTAATTTAATAATTATCTTAATAA-TATTTTATTAATTTAATATTATAGTG
354320 ATT
65 ATT
* * * * * **
354323 AAGTTTAATCA-T-AATTGATTCTACTAGAGAATTTGATTTTAAATTAAATATTTCA--AAAATA
1 -A-TTTAAT-ATTAAATTTAAT-T--TA-ATAA-TT-ATCTT-AA-T-AATATTTTATTAATTTA
** * *
354384 ATATTATTTTCATAG
54 ATATTATAGTGAT-T
* *
354399 ATTTAATATTAAATTTAATTTAATAATTATCTTAATAATATTTTATTAATTTAATATTAAAGTGG
1 ATTTAATATTAAATTTAATTTAATAATTATCTTAATAATATTTTATTAATTTAATATTATAGTGA
354464 TT
66 TT
* *
354466 ATCTTAAAATTAAATTAAATTTAATAAT
1 AT-TTAATATTAAATTTAATTTAATAAT
354494 ATTTTATTAA
Statistics
Matches: 223, Mismatches: 45, Indels: 65
0.67 0.14 0.20
Matches are distributed among these distances:
58 15 0.07
59 3 0.01
60 1 0.00
61 26 0.12
62 2 0.01
63 2 0.01
65 2 0.01
66 8 0.04
67 8 0.04
68 62 0.28
69 14 0.06
70 11 0.05
71 10 0.04
72 14 0.06
73 3 0.01
74 10 0.04
75 23 0.10
76 1 0.00
77 6 0.03
78 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (67 bp):
ATTTAATATTAAATTTAATTTAATAATTATCTTAATAATATTTTATTAATTTAATATTATAGTGA
TT
Found at i:354266 original size:61 final size:58
Alignment explanation
Indices: 354196--354311 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 58
354186 AGTGATTATC
*
354196 TTAATATTAAAT-TAAAT-TAAATATTTATCCTGTAGATAAGTATTCTATTAATTTAATAGAT
1 TTAATATTAAATAT-AATCT-AATATTTATCC--T-GATAAGTATTATATTAATTTAATAGAT
354257 TTAATATTAAATATAATCTAATATTTATCCTGATAAGTATTATATTAATTTAATA
1 TTAATATTAAATATAATCTAATATTTATCCTGATAAGTATTATATTAATTTAATA
354312 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
58 23 0.44
59 1 0.02
61 26 0.50
62 2 0.04
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (58 bp):
TTAATATTAAATATAATCTAATATTTATCCTGATAAGTATTATATTAATTTAATAGAT
Found at i:354492 original size:56 final size:56
Alignment explanation
Indices: 354430--354546 Score: 234
Period size: 56 Copynumber: 2.1 Consensus size: 56
354420 AATAATTATC
354430 TTAATAATATTTTATTAATTTAATATTAAAGTGGTTATCTTAAAATTAAATTAAAT
1 TTAATAATATTTTATTAATTTAATATTAAAGTGGTTATCTTAAAATTAAATTAAAT
354486 TTAATAATATTTTATTAATTTAATATTAAAGTGGTTATCTTAAAATTAAATTAAAT
1 TTAATAATATTTTATTAATTTAATATTAAAGTGGTTATCTTAAAATTAAATTAAAT
354542 TTAAT
1 TTAAT
354547 GTTTACATTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (56 bp):
TTAATAATATTTTATTAATTTAATATTAAAGTGGTTATCTTAAAATTAAATTAAAT
Found at i:358649 original size:18 final size:18
Alignment explanation
Indices: 358626--358670 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
358616 CAAGGTCACT
*
358626 ATCAATAGT-GTCGCTAGC
1 ATCAATA-TCGTCACTAGC
*
358644 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTAGC
358662 ATCAATATC
1 ATCAATATC
358671 AATATCATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (18 bp):
ATCAATATCGTCACTAGC
Found at i:359197 original size:30 final size:31
Alignment explanation
Indices: 359163--359230 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
359153 AATAAACACC
*
359163 AAAAATTTATTTTAAAAATA-AAAAAATTAA
1 AAAAATGTATTTTAAAAATATAAAAAATTAA
* **
359193 AAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATGTATTTTAAAAATA-TAAAAAATTAA
359225 AAAAAT
1 AAAAAT
359231 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 18 0.58
32 13 0.42
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (31 bp):
AAAAATGTATTTTAAAAATATAAAAAATTAA
Found at i:360398 original size:12 final size:12
Alignment explanation
Indices: 360381--360410 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
360371 TTAAAAAAAA
360381 TTAAAAAGTATT
1 TTAAAAAGTATT
360393 TTAAAAAGTATT
1 TTAAAAAGTATT
360405 TTAAAA
1 TTAAAA
360411 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (12 bp):
TTAAAAAGTATT
Found at i:380933 original size:89 final size:90
Alignment explanation
Indices: 380781--380960 Score: 353
Period size: 89 Copynumber: 2.0 Consensus size: 90
380771 AAATAATCAT
380781 AAATATAAAAAAAATTATTTTTGAAATTTTCTTGATAATTATATATATTTTTATTAAATTGATAT
1 AAATATAAAAAAAATTATTTTTGAAATTTTCTTGATAATTATATATATTTTTATTAAATTGATAT
380846 CACAAATCAACTTAACACCAATTGG
66 CACAAATCAACTTAACACCAATTGG
380871 AAATAT-AAAAAAATTATTTTTGAAATTTTCTTGATAATTATATATATTTTTATTAAATTGATAT
1 AAATATAAAAAAAATTATTTTTGAAATTTTCTTGATAATTATATATATTTTTATTAAATTGATAT
380935 CACAAATCAACTTAACACCAATTGG
66 CACAAATCAACTTAACACCAATTGG
380960 A
1 A
380961 TACAACCTAA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 84 0.93
90 6 0.07
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (90 bp):
AAATATAAAAAAAATTATTTTTGAAATTTTCTTGATAATTATATATATTTTTATTAAATTGATAT
CACAAATCAACTTAACACCAATTGG
Found at i:381329 original size:14 final size:14
Alignment explanation
Indices: 381310--381352 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
381300 GTTTTTTACT
381310 AAAATATTATAACA
1 AAAATATTATAACA
**
381324 AAAATAAAAATTAACA
1 AAAAT-ATTA-TAACA
381340 AAAATATTATAAC
1 AAAATATTATAAC
381353 TTTTTGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 9 0.39
15 4 0.17
16 10 0.43
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATATTATAACA
Found at i:381594 original size:19 final size:19
Alignment explanation
Indices: 381567--381636 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
381557 TTCAACACAT
*
381567 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
**
381586 TTTTAATTTAATAA-AATA
1 TTTTAATTTAATAACTCTA
* *
381604 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
381623 TTTTAATTTAATAA
1 TTTTAATTTAATAA
381637 ACTATTAAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:381616 original size:37 final size:37
Alignment explanation
Indices: 381572--381642 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
381562 CACATTTTTT
381572 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
*
381609 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATT
381643 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
Found at i:381891 original size:18 final size:19
Alignment explanation
Indices: 381854--381892 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
381844 TCAACTCATT
* *
381854 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
381873 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
381891 TT
1 TT
381893 CTCATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:381899 original size:18 final size:19
Alignment explanation
Indices: 381859--381901 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
381849 TCATTTTTTT
* *
381859 ATTTAATAACTCTATTTTA
1 ATTTAATAACACTATTCTA
*
381878 ATTTAATAA-ACTATTCTC
1 ATTTAATAACACTATTCTA
381896 ATTTAA
1 ATTTAA
381902 ATTAAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATAACACTATTCTA
Found at i:381961 original size:18 final size:19
Alignment explanation
Indices: 381898--381956 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
381888 CTATTCTCAT
381898 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
381917 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
381935 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
381954 TTA
1 TTA
381957 CTTAATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:382156 original size:20 final size:19
Alignment explanation
Indices: 382117--382157 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
382107 ACTTAATAGT
* *
382117 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
382136 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
382156 TT
1 TT
382158 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:386401 original size:9 final size:9
Alignment explanation
Indices: 386382--386425 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
386372 TTTACATCCC
386382 AAAAAATTAT
1 AAAAAA-TAT
386392 AAAAAATAT
1 AAAAAATAT
386401 ATAAAAATAT
1 A-AAAAATAT
*
386411 TAAAAATAT
1 AAAAAATAT
386420 AAAAAA
1 AAAAAA
386426 ACTTTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 17 0.55
10 14 0.45
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAAAATAT
Found at i:386403 original size:11 final size:11
Alignment explanation
Indices: 386382--386436 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 11
386372 TTTACATCCC
386382 AAAAAAT-TAT
1 AAAAAATATAT
386392 AAAAAATATAT
1 AAAAAATATAT
386403 -AAAAATAT-T
1 AAAAAATATAT
386412 -AAAAATATA-
1 AAAAAATATAT
*
386421 AAAAAACTTTAT
1 AAAAAA-TATAT
386433 AAAA
1 AAAA
386437 CCCTAAACCC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 9 0.23
10 20 0.51
11 6 0.15
12 4 0.10
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAAATATAT
Found at i:386426 original size:19 final size:19
Alignment explanation
Indices: 386382--386426 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
386372 TTTACATCCC
*
386382 AAAAAATTATAAAAAATAT
1 AAAAAAATATAAAAAATAT
* *
386401 ATAAAAATATTAAAAATAT
1 AAAAAAATATAAAAAATAT
386420 AAAAAAA
1 AAAAAAA
386427 CTTTATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAAATATAAAAAATAT
Found at i:395070 original size:45 final size:45
Alignment explanation
Indices: 395000--395398 Score: 555
Period size: 45 Copynumber: 8.9 Consensus size: 45
394990 GCTTCGCTTT
* * * *
395000 GATCTACTTCGCTGCCAATACAGGAAAATAAGATCTGTTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * *
395045 GATCTACTTCGCTGCTAATATAGGAAGACAAGATCTGTTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * *
395090 GATATACTTCACTGCCAATATAGGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * * *
395135 GATCTACTTCGCTACCAATATAGGAAGACAATATATGCTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
*
395180 GATCTACTTCGCTGCCGATACAGGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * *
395225 GATCTACTTCTCTACCAATATAGGAAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* *
395270 GATCTACTTCGCTGCCGATACAGGAAGACAAGATCTGTTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * *
395315 GATCTACTTCACTGCCAATACAAGAAGATAAGATTTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
*
395360 GATTTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
395399 CTTTTCAGAC
Statistics
Matches: 311, Mismatches: 43, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 311 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (45 bp):
GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
Found at i:399892 original size:16 final size:16
Alignment explanation
Indices: 399871--399905 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
399861 TTCTATGATG
399871 AAATGTCATGCAGACA
1 AAATGTCATGCAGACA
*
399887 AAATGTCATGCAGCCA
1 AAATGTCATGCAGACA
399903 AAA
1 AAA
399906 CAGAACACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGTCATGCAGACA
Found at i:404911 original size:21 final size:21
Alignment explanation
Indices: 404885--404929 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
404875 ATATTTGGTA
404885 TGTAGGCAATGCTGTTCAATT
1 TGTAGGCAATGCTGTTCAATT
404906 TGTAGGCAATGCTGTTCAATT
1 TGTAGGCAATGCTGTTCAATT
404927 TGT
1 TGT
404930 TGTCAGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.40
Consensus pattern (21 bp):
TGTAGGCAATGCTGTTCAATT
Found at i:406107 original size:13 final size:13
Alignment explanation
Indices: 406085--406173 Score: 133
Period size: 13 Copynumber: 6.8 Consensus size: 13
406075 CACTCAAATG
406085 TCTCAAAAGCACT
1 TCTCAAAAGCACT
* *
406098 TTTGAAAAGCACT
1 TCTCAAAAGCACT
406111 TCTCAAAAGCACT
1 TCTCAAAAGCACT
*
406124 TCTGAAAAGCACT
1 TCTCAAAAGCACT
* *
406137 TTTGAAAAGCACT
1 TCTCAAAAGCACT
406150 TCTCAAAAGCACT
1 TCTCAAAAGCACT
406163 TCTCAAAAGCA
1 TCTCAAAAGCA
406174 ATGAAGAACT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 68 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (13 bp):
TCTCAAAAGCACT
Found at i:406141 original size:39 final size:39
Alignment explanation
Indices: 406085--406173 Score: 169
Period size: 39 Copynumber: 2.3 Consensus size: 39
406075 CACTCAAATG
406085 TCTCAAAAGCACTTTTGAAAAGCACTTCTCAAAAGCACT
1 TCTCAAAAGCACTTTTGAAAAGCACTTCTCAAAAGCACT
*
406124 TCTGAAAAGCACTTTTGAAAAGCACTTCTCAAAAGCACT
1 TCTCAAAAGCACTTTTGAAAAGCACTTCTCAAAAGCACT
406163 TCTCAAAAGCA
1 TCTCAAAAGCA
406174 ATGAAGAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (39 bp):
TCTCAAAAGCACTTTTGAAAAGCACTTCTCAAAAGCACT
Found at i:407744 original size:8 final size:8
Alignment explanation
Indices: 407731--407755 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
407721 AAATAGTGGA
407731 AGAAATTG
1 AGAAATTG
407739 AGAAATTG
1 AGAAATTG
407747 AGAAATTG
1 AGAAATTG
407755 A
1 A
407756 ACACACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Found at i:413106 original size:42 final size:42
Alignment explanation
Indices: 413058--413305 Score: 374
Period size: 42 Copynumber: 5.9 Consensus size: 42
413048 GCGTTTACAA
413058 AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCGCTTAG
* *
413100 AAAAAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 -AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCGCTTAG
* * * * *
413143 GAAAAAATGCTGCTAAAGACAATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCGCTTAG
413185 AAAAAAACGCCGCTAAAGACCATG-TACTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTA-TTTAGCGGCGCTTAG
413227 AAAAAAACGCCGCTAAAGACCATG-TACTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTA-TTTAGCGGCGCTTAG
* *
413269 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1 AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCG
413306 TTTATTCTTA
Statistics
Matches: 189, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
41 1 0.01
42 147 0.78
43 41 0.22
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCGCTTAG
Found at i:413329 original size:126 final size:127
Alignment explanation
Indices: 413058--413305 Score: 412
Period size: 126 Copynumber: 2.0 Consensus size: 127
413048 GCGTTTACAA
*
413058 AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGACCA
1 AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGACCA
* * * *
413123 TGTTCTTTAGCGGCGCTTAGGAAAAAATGCTGCTAAAGACAATGTTCTTTAGCGGCGCTTAG
66 TGTACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACAATGTTCTTTAGCGGCGCTTAG
413185 AAAAAAACGCCGCTAAAGACCATG-TACTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGACC
1 AAAAAAACGCCGCTAAAGACCATGTTA-TTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGACC
413248 ATGTACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATC-ATGTTCTTTAGCGGCG
65 ATGTACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGA-CAATGTTCTTTAGCGGCG
413306 TTTATTCTTA
Statistics
Matches: 114, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
126 74 0.65
127 40 0.35
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (127 bp):
AAAAAAACGCCGCTAAAGACCATGTTATTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGACCA
TGTACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACAATGTTCTTTAGCGGCGCTTAG
Found at i:413733 original size:21 final size:21
Alignment explanation
Indices: 413706--413755 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
413696 TTTTGGCCTG
* *
413706 CTCTGCTTCTCTCGTTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
413727 TTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
413748 CTCTGCTT
1 CTCTGCTT
413756 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.42, G:0.18, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:416963 original size:3 final size:3
Alignment explanation
Indices: 416955--417010 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
416945 TGTACTTGGA
* * *
416955 AAT AAT AAT TAT AAT ATT AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
417003 AAT AAT AA
1 AAT AAT AA
417011 AATTTAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:416978 original size:18 final size:18
Alignment explanation
Indices: 416955--417010 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
416945 TGTACTTGGA
*
416955 AATAATAATTATAATATT
1 AATAATAATTATAATAAT
416973 AATAATAATTATAATAAT
1 AATAATAATTATAATAAT
*
416991 AATAATAATAATAATAAT
1 AATAATAATTATAATAAT
417009 AA
1 AA
417011 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAATAATTATAATAAT
Found at i:418304 original size:18 final size:20
Alignment explanation
Indices: 418281--418323 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
418271 TATATTTTTT
418281 TATTTT-TA-ATCAAATATA
1 TATTTTGTATATCAAATATA
*
418299 TATTTTGTATATTAAATATA
1 TATTTTGTATATCAAATATA
418319 TATTT
1 TATTT
418324 AATATGAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 2 0.09
20 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTTTGTATATCAAATATA
Found at i:418311 original size:27 final size:26
Alignment explanation
Indices: 418245--418304 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
418235 TGAGTAAAAA
418245 ATAT-TTTTTTTATTTTTAATCAAAT
1 ATATATTTTTTTATTTTTAATCAAAT
418270 ATATATTTTTTTATTTTTAATCAAAT
1 ATATATTTTTTTATTTTTAATCAAAT
418296 ATATATTTT
1 ATATATTTT
418305 GTATATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.12
26 30 0.88
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATATTTTTTTATTTTTAATCAAAT
Found at i:418313 original size:24 final size:26
Alignment explanation
Indices: 418245--418313 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 26
418235 TGAGTAAAAA
* *
418245 ATAT-TTTTTTTATTTTTAATCAAAT
1 ATATATTTTTGTATTATTAATCAAAT
* *
418270 ATATATTTTTTTATTTTTAATCAAAT
1 ATATATTTTTGTATTATTAATCAAAT
418296 ATATA-TTTTGTA-TATTAA
1 ATATATTTTTGTATTATTAA
418314 ATATATATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.12
25 10 0.24
26 26 0.63
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (26 bp):
ATATATTTTTGTATTATTAATCAAAT
Found at i:418321 original size:24 final size:24
Alignment explanation
Indices: 418268--418321 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
418258 TTTTAATCAA
* * *
418268 ATATATATTTTTTTATTTTTAATC
1 ATATATATTTTTGTATATTAAATC
*
418292 AAATATATATTTTGTATATTAAAT-
1 ATATATAT-TTTTGTATATTAAATC
418316 ATATAT
1 ATATAT
418322 TTAATATGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATATATATTTTTGTATATTAAATC
Found at i:435290 original size:27 final size:26
Alignment explanation
Indices: 435259--435316 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
435249 TCTAATAAAA
435259 TATTAAAACATATAAATTTAACT-ATTT
1 TATTAAAACA-AT-AATTTAACTAATTT
*
435286 TATTAAAACAATATTTTAACTAAATTT
1 TATTAAAACAATAATTTAACT-AATTT
435313 TATT
1 TATT
435317 TTTTATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 8 0.29
26 2 0.07
27 18 0.64
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTAAAACAATAATTTAACTAATTT
Found at i:439553 original size:28 final size:28
Alignment explanation
Indices: 439521--439575 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
439511 ACCGACCCGA
* **
439521 AATAACATTAACCGAATTGAAATTTTTC
1 AATAAAATTAACCGAACCGAAATTTTTC
439549 AATAAAATTAACCGAACCGAAATTTTT
1 AATAAAATTAACCGAACCGAAATTTTT
439576 TCGGTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (28 bp):
AATAAAATTAACCGAACCGAAATTTTTC
Found at i:439654 original size:9 final size:9
Alignment explanation
Indices: 439642--439701 Score: 84
Period size: 9 Copynumber: 6.7 Consensus size: 9
439632 TTTTGTTAAA
439642 AATTAACCG
1 AATTAACCG
*
439651 AATTACCCG
1 AATTAACCG
439660 AATTAACCG
1 AATTAACCG
*
439669 AATTAATCG
1 AATTAACCG
*
439678 AATTACCCG
1 AATTAACCG
*
439687 AATTACCCG
1 AATTAACCG
439696 AATTAA
1 AATTAA
439702 ATTACTACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:439665 original size:18 final size:18
Alignment explanation
Indices: 439642--439701 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
439632 TTTTGTTAAA
439642 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
**
439660 AATTAACCGAATTAATCG
1 AATTAACCGAATTACCCG
*
439678 AATTACCCGAATTACCCG
1 AATTAACCGAATTACCCG
439696 AATTAA
1 AATTAA
439702 ATTACTACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:439673 original size:27 final size:27
Alignment explanation
Indices: 439642--439701 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
439632 TTTTGTTAAA
439642 AATTAACCGAATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
* *
439669 AATTAATCGAATTACCCGAATTACCCG
1 AATTAACCGAATTACCCGAATTAACCG
439696 AATTAA
1 AATTAA
439702 ATTACTACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTAACCG
Found at i:439828 original size:18 final size:18
Alignment explanation
Indices: 439788--439831 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
439778 AATTTTTATG
*
439788 ATTGGGTTGGGTTAGGTA
1 ATTGGGTTGGGTTAGATA
439806 ATTGGGTTGGGTT-GAATA
1 ATTGGGTTGGGTTAG-ATA
*
439824 CTTGGGTT
1 ATTGGGTT
439832 TGAATTGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTAGATA
Found at i:442329 original size:25 final size:23
Alignment explanation
Indices: 442294--442353 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
442284 ACATGTGACG
*
442294 AATA-ATT-TTTTGTGGGAAGAAA
1 AATATATTGTTTTGT-GAAAGAAA
*
442316 AATATATTGATTTTGTGAAAGGAA
1 AATATATTG-TTTTGTGAAAGAAA
*
442340 AATATTTTGTTTTG
1 AATATATTGTTTTG
442354 ACCCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 14 0.44
25 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (23 bp):
AATATATTGTTTTGTGAAAGAAA
Found at i:446691 original size:34 final size:35
Alignment explanation
Indices: 446647--446713 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
446637 CAGTAAAATA
*
446647 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
446681 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
446714 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:448631 original size:40 final size:41
Alignment explanation
Indices: 448577--448661 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 41
448567 GAAATAGTAG
448577 CAAAACAACAACAGTAAAATAGAAGAAAGAGCAGCAAAACA
1 CAAAACAACAACAGTAAAATAGAAGAAAGAGCAGCAAAACA
* *
448618 CAAAAC-ACAACAGTAAAATAGTAGAAAGAGCGGCAAAACA
1 CAAAACAACAACAGTAAAATAGAAGAAAGAGCAGCAAAACA
448658 CAAA
1 CAAA
448662 TCTTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 36 0.86
41 6 0.14
ACGTcount: A:0.61, C:0.18, G:0.15, T:0.06
Consensus pattern (41 bp):
CAAAACAACAACAGTAAAATAGAAGAAAGAGCAGCAAAACA
Found at i:459750 original size:31 final size:33
Alignment explanation
Indices: 459712--459777 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
459702 ACCTAGTGGC
459712 TTAAATAAAGA-CTTTTAAATAGTTC-ATG-CAT
1 TTAAATAAA-ATCTTTTAAATAGTTCAATGACAT
* *
459743 TTAAATAAAATTTTTTGAATAGTTCAATGACAT
1 TTAAATAAAATCTTTTAAATAGTTCAATGACAT
459776 TT
1 TT
459778 TGTAACTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 1 0.03
31 21 0.70
32 3 0.10
33 5 0.17
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (33 bp):
TTAAATAAAATCTTTTAAATAGTTCAATGACAT
Found at i:461822 original size:62 final size:59
Alignment explanation
Indices: 461707--461832 Score: 157
Period size: 63 Copynumber: 2.1 Consensus size: 59
461697 CCAAATTAGG
* *
461707 AAAAATTGTCAAGTTCAAACGTCAAATTAAAAAAAAAAACCTTAGGTATCAAAATAGGAGAA
1 AAAAATTGTCAAGTTCAAACG-CAAATCAAAAAAAAAAACCTTAAGTATCAAAATA--AGAA
*
461769 AAAAAGTTGTCAAGTTCAAGTAC-CAAATCAAATAAAAAAA-CTTAAGTATCAAAATAAGAA
1 AAAAA-TTGTCAAGTTCAA--ACGCAAATCAAAAAAAAAAACCTTAAGTATCAAAATAAGAA
461829 AAAA
1 AAAA
461833 TGTAACCAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
60 8 0.14
62 20 0.34
63 28 0.48
65 2 0.03
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.21
Consensus pattern (59 bp):
AAAAATTGTCAAGTTCAAACGCAAATCAAAAAAAAAAACCTTAAGTATCAAAATAAGAA
Found at i:463741 original size:18 final size:18
Alignment explanation
Indices: 463718--463760 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
463708 GTACAAGGTG
463718 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
463736 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
463754 TAATTAA
1 TAATTAA
463761 AAACTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:464077 original size:20 final size:20
Alignment explanation
Indices: 464054--464095 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
464044 CAACATGTTT
464054 TTAAAAAAAAAATCTTTTTC
1 TTAAAAAAAAAATCTTTTTC
* * *
464074 TTAATAATAAAATGTTTTTC
1 TTAAAAAAAAAATCTTTTTC
464094 TT
1 TT
464096 TTTCATTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAAAAAAAAATCTTTTTC
Found at i:471352 original size:24 final size:23
Alignment explanation
Indices: 471295--471356 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
471285 TCCATTTCCA
*
471295 CCAAAACCACCACCCTTTCCACCT
1 CCAAAACCACCA-CCTCTCCACCT
***
471319 CCAGCTCCACCACCTACTCCACCT
1 CCAAAACCACCACCT-CTCCACCT
471343 CCAAAACCACCACC
1 CCAAAACCACCACC
471357 CTTGCCAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.29, C:0.56, G:0.02, T:0.13
Consensus pattern (23 bp):
CCAAAACCACCACCTCTCCACCT
Found at i:471502 original size:30 final size:30
Alignment explanation
Indices: 471468--471527 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
471458 CACCACCAAT
* *
471468 TCCATGGCCTCCTCCCTTACCAATTCCACC
1 TCCATAGCCTCCTCCCTTACCAATCCCACC
* * *
471498 TCCATATCCTCCTCCTTTGCCAATCCCACC
1 TCCATAGCCTCCTCCCTTACCAATCCCACC
471528 ACCCTTTCCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.17, C:0.50, G:0.05, T:0.28
Consensus pattern (30 bp):
TCCATAGCCTCCTCCCTTACCAATCCCACC
Found at i:471572 original size:78 final size:78
Alignment explanation
Indices: 471475--471764 Score: 458
Period size: 78 Copynumber: 3.7 Consensus size: 78
471465 AATTCCATGG
* * * * *
471475 CCTCCTCCCTTACCAATTCCACCTCCATA-TCCTCCTCCTTTGCCAATCCCACCACCCTTTCCGA
1 CCTCCACCCTTTCCAATTCCACCACCA-ACACCTCCTCCTTTGCCAATCCCACCACCCTTTCCTA
471539 TGCCACCTCCGTAT
65 TGCCACCTCCGTAT
* * *
471553 CCTCCACCCTTTCCGATTCCACCTCCAACACCTCCTCCTTTGCCAATCCCACCACCTTTTCCTAT
1 CCTCCACCCTTTCCAATTCCACCACCAACACCTCCTCCTTTGCCAATCCCACCACCCTTTCCTAT
471618 GCCACCTCCGTAT
66 GCCACCTCCGTAT
*
471631 CCTCCACCCTTTCCGATTCCACCACCAACACCTCCTCCTTTGCCAATCCCACCACCCTTTCCTAT
1 CCTCCACCCTTTCCAATTCCACCACCAACACCTCCTCCTTTGCCAATCCCACCACCCTTTCCTAT
471696 GCCACCTCCGTAT
66 GCCACCTCCGTAT
*
471709 CCACCA-CCTTTCCCAATTCCACCACCAACACCTCCTCCTTTGCCAATCCCACCACC
1 CCTCCACCCTTT-CCAATTCCACCACCAACACCTCCTCCTTTGCCAATCCCACCACC
471765 ATATCCACCA
Statistics
Matches: 200, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
77 6 0.03
78 194 0.97
ACGTcount: A:0.18, C:0.51, G:0.04, T:0.26
Consensus pattern (78 bp):
CCTCCACCCTTTCCAATTCCACCACCAACACCTCCTCCTTTGCCAATCCCACCACCCTTTCCTAT
GCCACCTCCGTAT
Found at i:471587 original size:30 final size:30
Alignment explanation
Indices: 471526--471587 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
471516 GCCAATCCCA
* *
471526 CCACCCTTTCCGATGCCACCTCCGTATCCT
1 CCACCCTTTCCGATGCCACCTCCGAAACCT
*
471556 CCACCCTTTCCGATTCCACCTCC-AACACCT
1 CCACCCTTTCCGATGCCACCTCCGAA-ACCT
471586 CC
1 CC
471588 TCCTTTGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.16, C:0.53, G:0.06, T:0.24
Consensus pattern (30 bp):
CCACCCTTTCCGATGCCACCTCCGAAACCT
Found at i:471731 original size:30 final size:28
Alignment explanation
Indices: 471679--471784 Score: 77
Period size: 30 Copynumber: 3.5 Consensus size: 28
471669 TTTGCCAATC
* * *
471679 CCACCACCCTTTCCTATGCCACCTCCGTAT
1 CCACCA-CCTTTCCAATCCCACCACC-TAT
* * *
471709 CCACCACCTTTCCCAATTCCACCACCAACA
1 CCACCACCTTT-CCAATCCCACCACCTA-T
* *
471739 CCTCCTCCTTTGCCAATCCCACCACCATAT
1 CCACCACCTTT-CCAATCCCACCACC-TAT
471769 CCACCACCTTTACCAA
1 CCACCACCTTT-CCAA
471785 AGTCTCCACC
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
29 6 0.10
30 52 0.88
31 1 0.02
ACGTcount: A:0.24, C:0.51, G:0.03, T:0.23
Consensus pattern (28 bp):
CCACCACCTTTCCAATCCCACCACCTAT
Found at i:478508 original size:12 final size:12
Alignment explanation
Indices: 478491--478533 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
478481 CTTGAAGCTC
478491 GATTTGGTATTG
1 GATTTGGTATTG
*
478503 GATTTGGT-TTT
1 GATTTGGTATTG
*
478514 GATTTGGCATTG
1 GATTTGGTATTG
*
478526 AATTTGGT
1 GATTTGGT
478534 TTCATTAGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.16, C:0.02, G:0.30, T:0.51
Consensus pattern (12 bp):
GATTTGGTATTG
Found at i:478517 original size:23 final size:23
Alignment explanation
Indices: 478491--478535 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
478481 CTTGAAGCTC
* *
478491 GATTTGGTATTGGATTTGGTTTT
1 GATTTGGCATTGAATTTGGTTTT
478514 GATTTGGCATTGAATTTGGTTT
1 GATTTGGCATTGAATTTGGTTT
478536 CATTAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.02, G:0.29, T:0.53
Consensus pattern (23 bp):
GATTTGGCATTGAATTTGGTTTT
Found at i:479966 original size:20 final size:20
Alignment explanation
Indices: 479908--479968 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
479898 CATTTGATTC
* *
479908 TTTTATAATTTTATATTTA-T
1 TTTTATTATATTA-ATTTATT
* *
479928 TTTTGTTCTATGTAA-TTATT
1 TTTTATTATAT-TAATTTATT
479948 TTTTATTATATTAATTTATT
1 TTTTATTATATTAATTTATT
479968 T
1 T
479969 AATGTTCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 6 0.19
20 24 0.75
21 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTATTATATTAATTTATT
Found at i:483188 original size:18 final size:18
Alignment explanation
Indices: 483150--483190 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
483140 TGTTAAAACT
*
483150 TAAAATAATATTATTTAA
1 TAAAATAATATTATATAA
483168 TAAAATAATA-TATATACA
1 TAAAATAATATTATATA-A
483186 TAAAA
1 TAAAA
483191 ACATATAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATAATATTATATAA
Found at i:488125 original size:6 final size:6
Alignment explanation
Indices: 488120--488154 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
488110 CCACCACCAA
* *
488120 TTCCAA TTCCAG TTCCAG TTCCAG TTCCAG CTCCA
1 TTCCAG TTCCAG TTCCAG TTCCAG TTCCAG TTCCA
488155 CTACCACCAG
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:0.20, C:0.37, G:0.11, T:0.31
Consensus pattern (6 bp):
TTCCAG
Found at i:488166 original size:21 final size:21
Alignment explanation
Indices: 488140--488215 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
488130 AGTTCCAGTT
488140 CCAGTTCCAGCTCCACTACCA
1 CCAGTTCCAGCTCCACTACCA
** *
488161 CCAGTTCCAATTCCACCACCA
1 CCAGTTCCAGCTCCACTACCA
* * * *
488182 CCAATTCCAGTTCCAATTCCA
1 CCAGTTCCAGCTCCACTACCA
488203 CCAGTTCCAGCTC
1 CCAGTTCCAGCTC
488216 TAGTTCCAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.25, C:0.45, G:0.08, T:0.22
Consensus pattern (21 bp):
CCAGTTCCAGCTCCACTACCA
Found at i:488169 original size:27 final size:27
Alignment explanation
Indices: 488134--488479 Score: 157
Period size: 27 Copynumber: 12.1 Consensus size: 27
488124 AATTCCAGTT
*
488134 CCAGTTCCAGTTCCAGCTCCACTACCA
1 CCAGTTCCAGTTCCAGCTCCACCACCA
*
488161 CCAGTTCCAATTCCA---CCACCACCA
1 CCAGTTCCAGTTCCAGCTCCACCACCA
**
488185 --A-TTCCAGTTCCAATTCCACCAGTTCCA
1 CCAGTTCCAGTTCCAGCTCCACCA---CCA
* *
488212 GCTCTAGTTCCAGTTCCACCACCACCACCA
1 -C-C-AGTTCCAGTTCCAGCTCCACCACCA
*
488242 CCAGTTCCAGTTCCAGATCCACCACCACCACCA
1 CCAGTTCCAGTTCCAG------CTCCACCACCA
*
488275 CCAGTTCCAGTTCCAGATCCACCACCA
1 CCAGTTCCAGTTCCAGCTCCACCACCA
*** * *
488302 CCACCACCAGTTCCAGTTCCAGTTCCACCT
1 CCAGTTCCAGTTCCAGCTCCA---CCACCA
* * * * *
488332 CCAGCTCCA-TAACCAACTCCAACTCCATCT
1 CCAGTTCCAGT-TCCAGCTCC-A--CCACCA
* ** *
488362 CCATTTTTAGTTCCAGTTCCACCACCA
1 CCAGTTCCAGTTCCAGCTCCACCACCA
* *
488389 CCAATTCCAATTCCAGCTCCAGCTCCACCAGA
1 CCAGTTCCAGTTCCAGCTCCA---CCACC--A
* * *
488421 TCCAGTTCTAGCTCCAGCTCCACTACCA
1 -CCAGTTCCAGTTCCAGCTCCACCACCA
* *
488449 CCAATTCCAGTTCCAGTTCCACCACCA
1 CCAGTTCCAGTTCCAGCTCCACCACCA
488476 CCAG
1 CCAG
488480 CTCCTCTAGC
Statistics
Matches: 243, Mismatches: 46, Indels: 60
0.70 0.13 0.17
Matches are distributed among these distances:
21 10 0.04
22 1 0.00
24 14 0.06
27 101 0.42
28 2 0.01
29 3 0.01
30 47 0.19
31 2 0.01
32 2 0.01
33 61 0.25
ACGTcount: A:0.25, C:0.45, G:0.09, T:0.22
Consensus pattern (27 bp):
CCAGTTCCAGTTCCAGCTCCACCACCA
Found at i:488176 original size:15 final size:15
Alignment explanation
Indices: 488158--488211 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
488148 AGCTCCACTA
488158 CCACCAGTTCCAATT
1 CCACCAGTTCCAATT
***
488173 CCACCACCACCAATT
1 CCACCAGTTCCAATT
488188 ---CCAGTTCCAATT
1 CCACCAGTTCCAATT
488200 CCACCAGTTCCA
1 CCACCAGTTCCA
488212 GCTCTAGTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
12 9 0.30
15 21 0.70
ACGTcount: A:0.28, C:0.44, G:0.06, T:0.22
Consensus pattern (15 bp):
CCACCAGTTCCAATT
Found at i:488202 original size:33 final size:33
Alignment explanation
Indices: 488173--488330 Score: 170
Period size: 33 Copynumber: 5.0 Consensus size: 33
488163 AGTTCCAATT
*
488173 CCACCACCACCAATTCCAGTTCCAATTCCACCA
1 CCACCACCACCAGTTCCAGTTCCAATTCCACCA
*** * * *
488206 GTTCCAGCTCTAGTTCCAG-T-----TCCACCA
1 CCACCACCACCAGTTCCAGTTCCAATTCCACCA
488233 CCACCACCACCAGTTCCAGTTCCAGA-TCCACCA
1 CCACCACCACCAGTTCCAGTTCCA-ATTCCACCA
488266 CCACCACCACCAGTTCCAGTTCCAGA-TCCACCA
1 CCACCACCACCAGTTCCAGTTCCA-ATTCCACCA
*
488299 CCACCACCACCAGTTCCAGTTCCAGTTCCACC
1 CCACCACCACCAGTTCCAGTTCCAATTCCACC
488331 TCCAGCTCCA
Statistics
Matches: 104, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
27 20 0.19
28 1 0.01
32 1 0.01
33 82 0.79
ACGTcount: A:0.25, C:0.47, G:0.09, T:0.19
Consensus pattern (33 bp):
CCACCACCACCAGTTCCAGTTCCAATTCCACCA
Found at i:488416 original size:33 final size:33
Alignment explanation
Indices: 488373--488478 Score: 98
Period size: 33 Copynumber: 3.4 Consensus size: 33
488363 CATTTTTAGT
* *
488373 TCCAGTTCCACCACCACCAATTCCAATTCCAGC
1 TCCAGCTCCACCACCACCAATTCCAGTTCCAGC
* *
488406 TCCAGCT---CCACCA--GA-TCCAGTTCTAGC
1 TCCAGCTCCACCACCACCAATTCCAGTTCCAGC
* *
488433 TCCAGCTCCACTACCACCAATTCCAGTTCCAGT
1 TCCAGCTCCACCACCACCAATTCCAGTTCCAGC
* *
488466 TCCACCACCACCA
1 TCCAGCTCCACCA
488479 GCTCCTCTAG
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
27 17 0.30
28 1 0.02
30 11 0.20
32 1 0.02
33 26 0.46
ACGTcount: A:0.25, C:0.45, G:0.08, T:0.21
Consensus pattern (33 bp):
TCCAGCTCCACCACCACCAATTCCAGTTCCAGC
Found at i:488457 original size:21 final size:21
Alignment explanation
Indices: 488433--488472 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
488423 CAGTTCTAGC
488433 TCCAGCTCCACTACCACCAAT
1 TCCAGCTCCACTACCACCAAT
* * *
488454 TCCAGTTCCAGTTCCACCA
1 TCCAGCTCCACTACCACCA
488473 CCACCAGCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.45, G:0.07, T:0.23
Consensus pattern (21 bp):
TCCAGCTCCACTACCACCAAT
Found at i:490238 original size:29 final size:29
Alignment explanation
Indices: 490205--490260 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
490195 TTTTATTCCT
490205 TTTAATAATAAAGAGACTAAATTGATCAA
1 TTTAATAATAAAGAGACTAAATTGATCAA
* * *
490234 TTTAATAATAGAGGGACTAATTTGATC
1 TTTAATAATAAAGAGACTAAATTGATC
490261 TTGTCCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (29 bp):
TTTAATAATAAAGAGACTAAATTGATCAA
Found at i:495839 original size:38 final size:38
Alignment explanation
Indices: 495786--495861 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
495776 AGAACATGTA
* * * * *
495786 CTTTAGCGGCGCTTTTGTCACAAATGCCTCTAAAGAAC
1 CTTTAACGGCACTTTTATCACAAACGCCGCTAAAGAAC
495824 CTTTAACGGCACTTTTATCACAAACGCCGCTAAAGAAC
1 CTTTAACGGCACTTTTATCACAAACGCCGCTAAAGAAC
495862 ATGACCTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (38 bp):
CTTTAACGGCACTTTTATCACAAACGCCGCTAAAGAAC
Found at i:495888 original size:43 final size:43
Alignment explanation
Indices: 495770--495900 Score: 141
Period size: 43 Copynumber: 3.2 Consensus size: 43
495760 TAGACAATGT
* *
495770 CGCTAAAGAACATGTA-CTTTAGCGGCGCTTTTGTCACAAATGC
1 CGCTAAAGAACATG-ACCTTTAGCGGCGCTTTTATCACAAACGC
* * *
495813 CTCTAAAG---A--ACCTTTAACGGCACTTTTATCACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGC
*
495851 CGCTAAAGAACATGACCTTTAGCGGCGCCTTTT-TCACAAACAC
1 CGCTAAAGAACATGACCTTTAGCGGCG-CTTTTATCACAAACGC
495894 CGCTAAA
1 CGCTAAA
495901 AGTACCGTTC
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
37 1 0.01
38 30 0.42
40 1 0.01
41 1 0.01
43 34 0.47
44 5 0.07
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (43 bp):
CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGC
Found at i:496699 original size:13 final size:14
Alignment explanation
Indices: 496673--496701 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
496663 ACAAACAAAG
496673 AATTAAATCATTAT
1 AATTAAATCATTAT
496687 AATTAAA-CATTAT
1 AATTAAATCATTAT
496700 AA
1 AA
496702 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAATCATTAT
Found at i:497822 original size:27 final size:28
Alignment explanation
Indices: 497775--497831 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
497765 AAAATATATT
497775 AAATATATATATTAAGTTTTTTATGTTTA
1 AAATATATATATTAAG-TTTTTATGTTTA
*
497804 AAATATATATATTTA-TTTTTATGTTTA
1 AAATATATATATTAAGTTTTTATGTTTA
497831 A
1 A
497832 GTTTTTAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 13 0.48
29 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (28 bp):
AAATATATATATTAAGTTTTTATGTTTA
Found at i:499172 original size:9 final size:9
Alignment explanation
Indices: 499154--499197 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
499144 TTTTGTTACA
499154 ACAATTAAT
1 ACAATTAAT
*
499163 ACAATCAAT
1 ACAATTAAT
499172 ACAATT-A-
1 ACAATTAAT
499179 ACAATTAAT
1 ACAATTAAT
499188 ACAATTAAT
1 ACAATTAAT
499197 A
1 A
499198 ATTTGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 23 0.74
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (9 bp):
ACAATTAAT
Found at i:499188 original size:16 final size:16
Alignment explanation
Indices: 499163--499200 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
499153 AACAATTAAT
*
499163 ACAATCAATACAATTA
1 ACAATTAATACAATTA
499179 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
499195 ATAATT
1 ACAATT
499201 TGATAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:499291 original size:16 final size:16
Alignment explanation
Indices: 499270--499311 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
499260 AATAATTTGA
*
499270 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
499286 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
499302 TAGTTTTAAT
1 TAATTTTAAT
499312 TTGAGTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:501932 original size:12 final size:12
Alignment explanation
Indices: 501917--501942 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
501907 ATCATCCTCT
501917 TCATCAGATTCA
1 TCATCAGATTCA
501929 TCATCAGATTCA
1 TCATCAGATTCA
501941 TC
1 TC
501943 CCTCGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:503699 original size:9 final size:9
Alignment explanation
Indices: 503688--503840 Score: 99
Period size: 9 Copynumber: 17.6 Consensus size: 9
503678 TATTTATGTA
*
503688 TTATGTAAA
1 TTATGTAAG
*
503697 TTACGTAAG
1 TTATGTAAG
503706 TTATG-AGAG
1 TTATGTA-AG
*
503715 TTATATAAG
1 TTATGTAAG
503724 TTATG-ATA-
1 TTATGTA-AG
* *
503732 TTATATATAT
1 TTATGTA-AG
503742 TTATGT-A-
1 TTATGTAAG
503749 TTATGTAAG
1 TTATGTAAG
503758 CTT-TGTAAG
1 -TTATGTAAG
*
503767 TTATGTGAG
1 TTATGTAAG
503776 TTATGTAAG
1 TTATGTAAG
*
503785 TTATGTATG
1 TTATGTAAG
* * *
503794 ATATAT-AT
1 TTATGTAAG
503802 TTATGT-A-
1 TTATGTAAG
*
503809 TCATGTAAG
1 TTATGTAAG
*
503818 TTATGTGAG
1 TTATGTAAG
503827 TTATGTAAG
1 TTATGTAAG
503836 TTATG
1 TTATG
503841 ATATGATATA
Statistics
Matches: 113, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
7 11 0.10
8 16 0.14
9 78 0.69
10 8 0.07
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:503747 original size:61 final size:59
Alignment explanation
Indices: 503652--503868 Score: 288
Period size: 61 Copynumber: 3.7 Consensus size: 59
503642 AGTATAATTA
* *
503652 AGTTATGCAAGTTATGATATGATATATATTTATGTATTATGTAAATTACGTAAGTTATGAG
1 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAATT--GTAAGTTATGTG
* * *
503713 AGTTATATAAGTTATGATATTATATATATTTATGTATTATGTAAGCTTTGTAAGTTATGTG
1 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAA--ATTGTAAGTTATGTG
*
503774 AGTTATGTAAGTTATG-TATGATATATATTTATG---TA--T-CA-TGTAAGTTATGTG
1 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAATTGTAAGTTATGTG
503825 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAA
1 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAA
503869 GNNNNNNNNN
Statistics
Matches: 137, Mismatches: 10, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
51 29 0.21
52 17 0.12
55 3 0.02
57 3 0.02
60 16 0.12
61 67 0.49
63 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.47
Consensus pattern (59 bp):
AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAATTGTAAGTTATGTG
Done.