Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 36 of 82
Found at i:13190192 original size:61 final size:61
Alignment explanation
Indices: 13190039--13190391 Score: 259
Period size: 61 Copynumber: 5.7 Consensus size: 61
13190029 AGTTAGGGAG
* * *
13190039 TTTTCAAAATTCAAACCTGTTTTGAGATAGGTGGAGCCTAGATAAAGTT-TACG-ATCTAAAAAA
1 TTTTC-AAA-TCAAACCTGTTTTGAGATAGGTCGAGCCTAGATTAAGTTATAGGAAT-T--AAAA
13190102 A
61 A
* **
13190103 TTTTCAAATCAAATCTGTTTTGAGATAGGTCGAGCCTAGATTAAG-TATAGGAAATTTTAAA
1 TTTTCAAATCAAACCTGTTTTGAGATAGGTCGAGCCTAGATTAAGTTATAGG-AATTAAAAA
* * * * * * * * **
13190164 TTTTAAAATCGAACCTGTTTTAAGATAGGTTGAGACTAGGTTAAGTTTAAAAGCTAAAAAAAAAA
1 TTTTCAAATCAAACCTGTTTTGAGATAGGTCGAGCCTAGATTAAG-TT-ATAG--GAATTAAAAA
* * * * * * *
13190229 ATTTCAAATCAAACCTATTTTGAGATAAGTTGAACCTAGATTAAG-TCTAGGAATTTCAAAA
1 TTTTCAAATCAAACCTGTTTTGAGATAGGTCGAGCCTAGATTAAGTTATAGGAA-TTAAAAA
** * * * * * *
13190290 TAAT-AAATCGAACCTGTTTTGAGATAGGTCAAGCTTGGATTAAGCT-TAGGAGTTAAAAAA
1 TTTTCAAATCAAACCTGTTTTGAGATAGGTCGAGCCTAGATTAAGTTATAGGAATT-AAAAA
* *
13190350 TTTTCAAATCAAATCTGTTTTGAGATAAGTCGAGCCTAGATT
1 TTTTCAAATCAAACCTGTTTTGAGATAGGTCGAGCCTAGATT
13190392 TGTTGGCTCC
Statistics
Matches: 222, Mismatches: 55, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
59 2 0.01
60 45 0.20
61 79 0.36
62 39 0.18
63 6 0.03
64 10 0.05
65 41 0.18
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (61 bp):
TTTTCAAATCAAACCTGTTTTGAGATAGGTCGAGCCTAGATTAAGTTATAGGAATTAAAAA
Found at i:13190349 original size:126 final size:123
Alignment explanation
Indices: 13190094--13190391 Score: 361
Period size: 126 Copynumber: 2.4 Consensus size: 123
13190084 AGTTTACGAT
*
13190094 CTAAAAAAATTTTCAAATCAAATCTGTTTTGAGATAGGTCGAGCCTAGATTAAGTATAGGAAATT
1 CTAAAAAAATTTTCAAATCAAATCTGTTTTGAGATAAGTCGAGCCTAGATTAAGTATAGGAAATT
* ** ** *
13190159 TTAAATTTTAAAATCGAACCTGTTTTAAGATAGGTTGAGACTAGGTTAAGTTTAAAAG
66 TAAAATAATAAAATCGAACCTGTTTTAAGATAGGTCAAGACTAGGTTAAGCTTAAAAG
* * * * * *
13190217 CTAAAAAAAAAAATTTCAAATCAAACCTATTTTGAGATAAGTTGAACCTAGATTAAGTCTAGG-A
1 CT---AAAAAAATTTTCAAATCAAATCTGTTTTGAGATAAGTCGAGCCTAGATTAAGTATAGGAA
* * **
13190281 ATTTCAAAATAAT-AAATCGAACCTGTTTTGAGATAGGTCAAG-CTTGGATTAAGCTTAGGAG
63 ATTT-AAAATAATAAAATCGAACCTGTTTTAAGATAGGTCAAGACTAGG-TTAAGCTTAAAAG
*
13190342 -TTAAAAAATTTTCAAATCAAATCTGTTTTGAGATAAGTCGAGCCTAGATT
1 CTAAAAAAATTTTCAAATCAAATCTGTTTTGAGATAAGTCGAGCCTAGATT
13190392 TGTTGGCTCC
Statistics
Matches: 147, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
121 43 0.29
123 2 0.01
124 5 0.03
125 41 0.28
126 56 0.38
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (123 bp):
CTAAAAAAATTTTCAAATCAAATCTGTTTTGAGATAAGTCGAGCCTAGATTAAGTATAGGAAATT
TAAAATAATAAAATCGAACCTGTTTTAAGATAGGTCAAGACTAGGTTAAGCTTAAAAG
Found at i:13190730 original size:74 final size:74
Alignment explanation
Indices: 13190641--13190831 Score: 262
Period size: 74 Copynumber: 2.6 Consensus size: 74
13190631 TATTGTGAGA
*
13190641 CAGAAAAGACTTAGTCAACCAAGAAGCATGGTTAGTTGACTAAGTGCTCACTGCTAGAAACTT-C
1 CAGAAAAGACTTAGTCAACCAAGAAGCATGGTTAGTCGACTAAGTGCTCACTGCTAGAAA-TTGC
13190705 AATTAGGAAA-
65 AATTA-GAAAG
* * * **
13190715 TAGAGAAGACTTAGTCGACCAAGAAGCATGGTTAGTCGACTAAGTGCTCACTGCTAGAAATTGGG
1 CAGAAAAGACTTAGTCAACCAAGAAGCATGGTTAGTCGACTAAGTGCTCACTGCTAGAAATTGCA
13190780 ATTAGAAAG
66 ATTAGAAAG
* * *
13190789 CAGAAAAGACTTAGTCAACTAAGAAGTAT-GTTAGTCAACTAAG
1 CAGAAAAGACTTAGTCAACCAAGAAGCATGGTTAGTCGACTAAG
13190832 AGCACACTAT
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
73 19 0.18
74 84 0.82
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (74 bp):
CAGAAAAGACTTAGTCAACCAAGAAGCATGGTTAGTCGACTAAGTGCTCACTGCTAGAAATTGCA
ATTAGAAAG
Found at i:13194218 original size:61 final size:60
Alignment explanation
Indices: 13194153--13194299 Score: 161
Period size: 60 Copynumber: 2.5 Consensus size: 60
13194143 ACCTGTTTTA
*
13194153 AGATAGGTTGAGCCTAGATTAAGTTTAAGAGCTAAAAAAAAATTAAATCAAACTTATTGTG
1 AGATAGGTCGAGCCTAGATTAAGTTTAAGA-CTAAAAAAAAATTAAATCAAACTTATTGTG
* * * *** * ** * *
13194214 AGATAGGTCGAACCTAGATCAAGTCTAAGACTTTCAAAATATTAAATTGAACTTGTTTTG
1 AGATAGGTCGAGCCTAGATTAAGTTTAAGACTAAAAAAAAATTAAATCAAACTTATTGTG
*
13194274 AGATAAGTCGAG-CTAGATTAAGTTTA
1 AGATAGGTCGAGCCTAGATTAAGTTTA
13194300 GGAATTTCAA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 12 0.17
60 32 0.46
61 26 0.37
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (60 bp):
AGATAGGTCGAGCCTAGATTAAGTTTAAGACTAAAAAAAAATTAAATCAAACTTATTGTG
Found at i:13194284 original size:60 final size:59
Alignment explanation
Indices: 13194189--13194317 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 59
13194179 AAGAGCTAAA
* * *
13194189 AAAAAATTAAATCAAACTTATTGTGAGATAGGTCGAACCTAGATCAAGTCTAAGACTTTC
1 AAAATATTAAATCAAACTTATTGTGAGATAAGTCG-ACCTAGATCAAGTCTAAGAATTTC
** * * * * * *
13194249 AAAATATTAAATTGAACTTGTTTTGAGATAAGTCGAGCTAGATTAAGTTTAGGAATTTC
1 AAAATATTAAATCAAACTTATTGTGAGATAAGTCGACCTAGATCAAGTCTAAGAATTTC
*
13194308 AAAATTTTAA
1 AAAATATTAA
13194318 CCTATTTTGA
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
59 28 0.49
60 29 0.51
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (59 bp):
AAAATATTAAATCAAACTTATTGTGAGATAAGTCGACCTAGATCAAGTCTAAGAATTTC
Found at i:13196163 original size:217 final size:218
Alignment explanation
Indices: 13195784--13196195 Score: 753
Period size: 217 Copynumber: 1.9 Consensus size: 218
13195774 GAATAGTTGT
13195784 TAAAAATATATATAATAATAAAATAAAATGATAAGTAGGTTAGTTTGTTATAAATATGTATTTCC
1 TAAAAATATATATAATAATAAAATAAAATGATAAGTAGGTTAGTTTGTTATAAATATGTATTTCC
13195849 CTAATTATGCATCATGAAAAAAATATATGTATAAGAAAATATAAAGATATAGTTTAGTAAACCTG
66 CTAATTATGCATCATGAAAAAAATATATGTATAAGAAAATATAAAGATATAGTTTAGTAAACCTG
13195914 AATATATATATATATATATATATAAGAAGAGAGAGAGAGAG-AGA-AGAAATATAGTAT-AGAAA
131 AATATATATATATATATATATATAAGAAGAGAGAGAGAGAGAAGAGA-AAATATAGTATGAGAAA
13195976 AGTAAAAAANAAGGAAGTTGAGTCA
195 AGTAAAAAA-AAGGAAGTTGAGTCA
13196001 TAAAAATATATATAAATAAT-AAATAAAATGATAAGTAGGTTAGTTTGTTATAAATATGTATTTC
1 TAAAAATATATAT-AATAATAAAATAAAATGATAAGTAGGTTAGTTTGTTATAAATATGTATTTC
13196065 CCTAATTATGCATCATGAAAAAAATATATGTATAAGAAAATATAAAGATATAGTTTAGTAAACCT
65 CCTAATTATGCATCATGAAAAAAATATATGTATAAGAAAATATAAAGATATAGTTTAGTAAACCT
13196130 GAATATATATATATATATATATAT-AGAAAGAGAGAGAGAGAGAAGAGAAAATATAGTATGAGAA
130 GAATATATATATATATATATATATAAG-AAGAGAGAGAGAGAGAAGAGAAAATATAGTATGAGAA
13196194 AA
194 AA
13196196 AAAATTAAGT
Statistics
Matches: 190, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
216 2 0.01
217 161 0.85
218 20 0.11
219 7 0.04
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (218 bp):
TAAAAATATATATAATAATAAAATAAAATGATAAGTAGGTTAGTTTGTTATAAATATGTATTTCC
CTAATTATGCATCATGAAAAAAATATATGTATAAGAAAATATAAAGATATAGTTTAGTAAACCTG
AATATATATATATATATATATATAAGAAGAGAGAGAGAGAGAAGAGAAAATATAGTATGAGAAAA
GTAAAAAAAAGGAAGTTGAGTCA
Found at i:13197493 original size:364 final size:366
Alignment explanation
Indices: 13196786--13197514 Score: 1074
Period size: 364 Copynumber: 2.0 Consensus size: 366
13196776 TATTTTAAAC
* *
13196786 TTGTTCATTTGGCACCATTCATTATTTTATCTTGACATGGCATACAACATGTTTATTTTGCTAAT
1 TTGTTCATTTGGCACCATTCATGATTTTATCTTGACATGGCATACAACATGTTTATTTTACTAAT
13196851 GGGTCAAAAACCTCGATGATGGGATTTTCTCAAAAGACTTGTAGAGATGAGTTCTTTCGAGGATA
66 GGGTCAAAAACCTCGATGATGGGATTTTCTCAAAAGACTTGTAGAGATGAGTTCTTTCGAGGATA
* * * * *
13196916 TTCTTAAGTGAGAAAAATTTCTAAACTTCACCTAAGCACTGGGATGGTTTATGTATGATTTTTTT
131 TCCTTAAGTGAGAAAAATTTCTAAACTTCACCAAAGCACTGGGATGGTCTATGAACGATTTTTTT
* * * * **
13196981 CATACATGGTTTTTGTTTTCGATTTTTTAAAATTGGTAAATCATGACATCATTTTGTAATTACAT
196 CATACATGGTTTTTGTTTCCCATTATTTAAAATTGGGAAATCATGACATCATTTCATAATTACAT
*
13197046 CATGTGCATCCATAAAGTAGAATAATCAAACTTTGGTTTTAAAAAAGCAAAACAAATACAATAAT
261 CATGTGCATCCATAAAGTAGAATAATCAAACTTTGGTTTTAAAAAAGCAAAACAAATAAAATAAT
* * *
13197111 GATAACAATGAGTTAGAAAGAAAGATTTTAAACAAAGAAAT
326 GAAAACAATGAATTAGAAAGAAAGATTTTAAAAAAAGAAAT
* *
13197152 TTGTTCATTTGGCACCATTCATGATTTTATCTTGACATGGCATACGACATGTTTATTTTATTAAT
1 TTGTTCATTTGGCACCATTCATGATTTTATCTTGACATGGCATACAACATGTTTATTTTACTAAT
* * * * *
13197217 GGGTCGAGAACC-CAGTTGATGGGATTTTCTCGAAAA-ACTTGTAGGGATGAGTTCTTTTGAGGA
66 GGGTCAAAAACCTC-GATGATGGGATTTTCTC-AAAAGACTTGTAGAGATGAGTTCTTTCGAGGA
* * * * ** *
13197280 TATCCTTAGGTGAGGAAACTTT-TAGACTTGGCCAAAGCATTGGGATGGTCTATGAACGA-TTTT
129 TATCCTTAAGTGAGAAAAATTTCTAAACTTCACCAAAGCACTGGGATGGTCTATGAACGATTTTT
*
13197343 TTCGATACATGG-TTTTGTTTCCCATTATTTAAAATTGGGAAATCATGACATCATTTCATAATTC
194 TTC-ATACATGGTTTTTGTTTCCCATTATTTAAAATTGGGAAATCATGACATCATTTCATAATTA
*
13197407 CATCATGTGCATCCATAAAGTCA-AATAATTAAACTTTGGTTTTAAAAAAGCAAAACAAATAAAA
258 CATCATGTGCATCCATAAAGT-AGAATAATCAAACTTTGGTTTTAAAAAAGCAAAACAAATAAAA
*
13197471 TAATGAAAATAATGAATTAGAAAGAAAGATTTTAAAAAAAGAAA
322 TAATGAAAACAATGAATTAGAAAGAAAGATTTTAAAAAAAGAAA
13197515 CAAGACATGT
Statistics
Matches: 325, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
364 152 0.47
365 39 0.12
366 130 0.40
367 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (366 bp):
TTGTTCATTTGGCACCATTCATGATTTTATCTTGACATGGCATACAACATGTTTATTTTACTAAT
GGGTCAAAAACCTCGATGATGGGATTTTCTCAAAAGACTTGTAGAGATGAGTTCTTTCGAGGATA
TCCTTAAGTGAGAAAAATTTCTAAACTTCACCAAAGCACTGGGATGGTCTATGAACGATTTTTTT
CATACATGGTTTTTGTTTCCCATTATTTAAAATTGGGAAATCATGACATCATTTCATAATTACAT
CATGTGCATCCATAAAGTAGAATAATCAAACTTTGGTTTTAAAAAAGCAAAACAAATAAAATAAT
GAAAACAATGAATTAGAAAGAAAGATTTTAAAAAAAGAAAT
Found at i:13207461 original size:95 final size:96
Alignment explanation
Indices: 13207307--13207503 Score: 233
Period size: 96 Copynumber: 2.1 Consensus size: 96
13207297 ATAAGTGATG
* * *
13207307 AAAATTTACCATTTGCATTAACAAGATATTTTATGAAATATTCCAATTATGTTATTTTTTGT-CC
1 AAAATTTACCATTTACATTAACAAAATATTTTATGAAATATTCCAATTATATTATTTTTTGTACC
13207371 AAAAAATCAACAAAATTGT-AAGTACAATTG-C
66 AAAAAATCAACAAAATT-TAAAGTACAA-TGAC
* * * *
13207402 AAAATTTATCATTTACATTAACAAAATATATTTCAT-AAATATTTCAGTTCTATTATTTTTT-TA
1 AAAATTTACCATTTACATTAACAAAATAT-TTT-ATGAAATATTCCAATTATATTATTTTTTGTA
* * *
13207465 TCTAAAAATCAACGAAATTTAAAGTACAATGAC
64 CCAAAAAATCAACAAAATTTAAAGTACAATGAC
13207498 AAAATT
1 AAAATT
13207504 AAATATTGAG
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
95 30 0.34
96 55 0.63
97 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (96 bp):
AAAATTTACCATTTACATTAACAAAATATTTTATGAAATATTCCAATTATATTATTTTTTGTACC
AAAAAATCAACAAAATTTAAAGTACAATGAC
Found at i:13224314 original size:37 final size:37
Alignment explanation
Indices: 13224255--13224373 Score: 186
Period size: 37 Copynumber: 3.2 Consensus size: 37
13224245 TAATGTTGTG
*
13224255 TGATAATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
* *
13224292 TGATGATGTT-AGAGTGTACGAGTAGAGAGTGCACACA
1 TGATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACACA
*
13224329 TGATGATGTTGAAGTATGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
13224366 TGATGATG
1 TGATGATG
13224374 ATATTGCATT
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.01
37 72 0.97
38 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.34, T:0.25
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:13242444 original size:28 final size:27
Alignment explanation
Indices: 13242413--13242467 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
13242403 ATTTGGAGTA
* *
13242413 TAGGGGCGAAATGGTAATTTTGCCACCC
1 TAGGGGCAAAACGGTAATTTTG-CACCC
13242441 TAGGGGCAAAACGGTAATTTTGCACCC
1 TAGGGGCAAAACGGTAATTTTGCACCC
13242468 CCAAAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (27 bp):
TAGGGGCAAAACGGTAATTTTGCACCC
Found at i:13247880 original size:30 final size:30
Alignment explanation
Indices: 13247846--13247907 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
13247836 GCAAGGAAAA
13247846 GGATTCGA-AAAATAATCCTAAGGAGGTTAG
1 GGATTC-ACAAAATAATCCTAAGGAGGTTAG
*
13247876 GGATTCACAAAATAATCCTGAGGAGGTTAG
1 GGATTCACAAAATAATCCTAAGGAGGTTAG
13247906 GG
1 GG
13247908 TCCTAGTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (30 bp):
GGATTCACAAAATAATCCTAAGGAGGTTAG
Found at i:13256781 original size:29 final size:29
Alignment explanation
Indices: 13256720--13256783 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
13256710 GTAAATTTTT
** *
13256720 AAAAATTACACTTTTGCCCCCGTAAAGTG
1 AAAAATTACACTTTTGCCCCCAAAAACTG
*
13256749 AAAAATTACATTTTTG-CCCCAAAAACTG
1 AAAAATTACACTTTTGCCCCCAAAAACTG
13256777 AAAAATT
1 AAAAATT
13256784 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTGCCCCCAAAAACTG
Found at i:13259123 original size:42 final size:42
Alignment explanation
Indices: 13259063--13259192 Score: 172
Period size: 42 Copynumber: 3.1 Consensus size: 42
13259053 TGTTGATGTG
13259063 GACCCGGCTATGTGCGAGTAGGAGTGTGCAT-ACTCCGATGAT
1 GACCCGGCTATGTGCGAGTAGGAGTGTGCATAACT-CGATGAT
* * *
13259105 GACCCGGCTATGTACGAGTAGGACTGTGCATAAGTCGATGAT
1 GACCCGGCTATGTGCGAGTAGGAGTGTGCATAACTCGATGAT
* ** * *
13259147 GACCCGGCTATGTGTGAGTAGGAGTACGCATAAGTCGATGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGTGCATAACTCGATGAT
13259189 GACC
1 GACC
13259193 TAGCCATGTG
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 76 0.97
43 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGTGCATAACTCGATGAT
Found at i:13261734 original size:2 final size:2
Alignment explanation
Indices: 13261727--13261777 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
13261717 CAAATCGTAN
13261727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13261769 TA TA TA TA T
1 TA TA TA TA T
13261778 GTAGCCTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13264402 original size:11 final size:11
Alignment explanation
Indices: 13264362--13264394 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
13264352 TTATAAAAAT
*
13264362 ATTATTATTTA
1 ATTATTATTTC
13264373 ATTATTATTTC
1 ATTATTATTTC
13264384 ATTATTATTTC
1 ATTATTATTTC
13264395 TTCATTATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTATTTC
Found at i:13269280 original size:68 final size:68
Alignment explanation
Indices: 13269081--13269268 Score: 268
Period size: 68 Copynumber: 2.8 Consensus size: 68
13269071 TAATTTGCAT
*
13269081 GAAAGCATGATGAATGCCATTAGATTATGTATATGATATATATTCCATGTACTACATGAGATGAT
1 GAAAGCATGATGAATGCCATTAGATTATGTATATGATATATATTCCATATACTACATGAGATGAT
13269146 TGA
66 TGA
* * * *
13269149 GAAAGCATGATGAATGCCATTAGATTGTGTATTTGATTTATATTCCTTATACTACATGAGATGAT
1 GAAAGCATGATGAATGCCATTAGATTATGTATATGATATATATTCCATATACTACATGAGATGAT
13269214 TGA
66 TGA
* * * * * * *
13269217 GAAAGTATGAAGAATGCCATGAGATTATGTACATGATGTAAATTTCATATAC
1 GAAAGCATGATGAATGCCATTAGATTATGTATATGATATATATTCCATATAC
13269269 CTTATGAGAT
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 105 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (68 bp):
GAAAGCATGATGAATGCCATTAGATTATGTATATGATATATATTCCATATACTACATGAGATGAT
TGA
Found at i:13271554 original size:21 final size:19
Alignment explanation
Indices: 13271521--13271561 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
13271511 ACATGTTGAG
13271521 TAGTTAATTTATGTTATTT
1 TAGTTAATTTATGTTATTT
13271540 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTATGTTATTT
13271561 T
1 T
13271562 CTTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (19 bp):
TAGTTAATTTATGTTATTT
Found at i:13275439 original size:29 final size:28
Alignment explanation
Indices: 13275387--13275452 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
13275377 ATGTCTATGG
* **
13275387 GTAATTTTTCAGTTTTTTGGGCAAAAAT
1 GTAATTTTTCACTTTTACGGGCAAAAAT
*
13275415 GTAATTTTTCACTTTTACGTGGCAAAAGT
1 GTAATTTTTCACTTTTACG-GGCAAAAAT
*
13275444 GTAAATTTT
1 GTAATTTTT
13275453 AAAAATTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (28 bp):
GTAATTTTTCACTTTTACGGGCAAAAAT
Found at i:13280707 original size:29 final size:29
Alignment explanation
Indices: 13280665--13280739 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
13280655 ATATGCTCAT
13280665 AATGTATCGATACATTTTCTCCAGAACCA
1 AATGTATCGATACATTTTCTCCAGAACCA
*
13280694 AATGCATCGATACATTTTCTCCAGAACCA
1 AATGTATCGATACATTTTCTCCAGAACCA
13280723 AATGTATCGATACATTT
1 AATGTATCGATACATTT
13280740 CATCGATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (29 bp):
AATGTATCGATACATTTTCTCCAGAACCA
Found at i:13281805 original size:68 final size:67
Alignment explanation
Indices: 13281635--13281808 Score: 233
Period size: 67 Copynumber: 2.6 Consensus size: 67
13281625 TAATGTGAAT
* * * * * *
13281635 GAAAGTATGAAAAATGCCATTAGATTATGTGTATGATGTATATTCCATATACTACTTAAGATTTT
1 GAAAGTATGAAGAATGCCATGAGATTATGTATATGATGTATATTCCATATACTACATAAAATATT
13281700 GA
66 GA
* * *
13281702 GAAAGCATGATGAATGCCATTG-GATTGTGTATATGATGTATATTCCATATACTACATAAAATGA
1 GAAAGTATGAAGAATGCCA-TGAGATTATGTATATGATGTATATTCCATATACTACATAAAAT-A
13281766 TTGA
64 TTGA
*
13281770 GAAAGTATGAAGAATGCGATGAGATTATGTATATGATGT
1 GAAAGTATGAAGAATGCCATGAGATTATGTATATGATGT
13281809 TAATATGCCA
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
67 54 0.59
68 37 0.41
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (67 bp):
GAAAGTATGAAGAATGCCATGAGATTATGTATATGATGTATATTCCATATACTACATAAAATATT
GA
Found at i:13293975 original size:19 final size:20
Alignment explanation
Indices: 13293948--13293993 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
13293938 AGGAGACAAG
*
13293948 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
13293967 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
13293986 ATAATATT
1 ATAATATT
13293994 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:13294518 original size:27 final size:27
Alignment explanation
Indices: 13294488--13294545 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
13294478 TTGGAGAAAA
*
13294488 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGGTAATTTT-CCACCACC
*
13294515 AGGGGCAAAATTGTAATTTTCCACCACC
1 A-GGGCAAAATGGTAATTTTCCACCACC
13294543 AGG
1 AGG
13294546 ACATTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACC
Found at i:13297101 original size:15 final size:15
Alignment explanation
Indices: 13297081--13297118 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
13297071 CAGATATTTT
13297081 GATTTTAAAGCTTTG
1 GATTTTAAAGCTTTG
* *
13297096 GATTTTAAAGTTTTT
1 GATTTTAAAGCTTTG
13297111 GATTTTAA
1 GATTTTAA
13297119 GGTTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (15 bp):
GATTTTAAAGCTTTG
Found at i:13306611 original size:3 final size:3
Alignment explanation
Indices: 13306603--13306627 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13306593 ATCTACAAAT
13306603 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
13306628 GACATTTACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13306971 original size:26 final size:25
Alignment explanation
Indices: 13306872--13307054 Score: 70
Period size: 26 Copynumber: 6.9 Consensus size: 25
13306862 GTACACATGA
*
13306872 TGTTATACACTATGTTGAAAAAATAT
1 TGTTACACACTATGTT-AAAAAATAT
* * * *
13306898 TATTATTATACGTCATG-TACAAAAACA-
1 TGTTA-CACAC-T-ATGTTA-AAAAATAT
*
13306925 TGTTACACACCATGGTTAAAAAATAT
1 TGTTACACACTAT-GTTAAAAAATAT
13306951 TGTTACACACTATGTTGAAAACAAAATATTAT
1 TGTTACACACTATGTT----A-AAAA-A-TAT
*
13306983 TGTTACATACTATG-TACAAAAATA-
1 TGTTACACACTATGTTA-AAAAATAT
* * *
13307007 TGTTACAC-GTCGTGATTAAAAAAGAT
1 TGTTACACACT-ATG-TTAAAAAATAT
* * *
13307033 TGTTACACGCCACGTTAAAAAA
1 TGTTACACACTATGTTAAAAAA
13307055 AAATATTGTT
Statistics
Matches: 120, Mismatches: 18, Indels: 39
0.68 0.10 0.22
Matches are distributed among these distances:
23 1 0.01
24 11 0.09
25 26 0.22
26 33 0.28
27 15 0.12
28 8 0.07
29 4 0.03
30 4 0.03
31 2 0.02
32 16 0.13
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (25 bp):
TGTTACACACTATGTTAAAAAATAT
Found at i:13307010 original size:82 final size:82
Alignment explanation
Indices: 13306872--13307068 Score: 224
Period size: 82 Copynumber: 2.4 Consensus size: 82
13306862 GTACACATGA
* *
13306872 TGTTATACACTATGTTG--AAAAAATATTATTATT-ATACGTCATGTACAAAAACATGTTACACA
1 TGTTACACACTATGTTGAAAAAAAATATTATTGTTAATACGTCATGTACAAAAACATGTTACACA
* *
13306934 CCATGGTTAAAAAATAT
66 CCATGATTAAAAAAGAT
*
13306951 TGTTACACACTATGTTGAAAACAAAATATTATTGTTACATAC-T-ATGTACAAAAATATGTTACA
1 TGTTACACACTATGTTGAAAA-AAAATATTATTGTTA-ATACGTCATGTACAAAAACATGTTACA
** *
13307014 CGTCGTGATTAAAAAAGAT
64 CACCATGATTAAAAAAGAT
* * * * *
13307033 TGTTACACGCCACGTTAAAAAAAAATATTGTTGTTA
1 TGTTACACACTATGTTGAAAAAAAATATTATTGTTA
13307069 TTCGCTATGG
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
79 16 0.16
81 16 0.16
82 63 0.63
83 1 0.01
84 4 0.04
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (82 bp):
TGTTACACACTATGTTGAAAAAAAATATTATTGTTAATACGTCATGTACAAAAACATGTTACACA
CCATGATTAAAAAAGAT
Found at i:13307085 original size:81 final size:82
Alignment explanation
Indices: 13306889--13307092 Score: 200
Period size: 82 Copynumber: 2.5 Consensus size: 82
13306879 CACTATGTTG
* * ** * * *
13306889 AAAAAATATTATTATT--ATACGTCATGTACAAAAACATGTTACACACCATGGTTAAAAAATATT
1 AAAAAATATTATTGTTACATAC-T-ATGGACAAAAACATGTTACACGTCGTGATTAAAAAAGATT
* *
13306952 GTTACACACTATGTTGAAA
64 GTTACACACCACGTTGAAA
* * *
13306971 ACAAAATATTATTGTTACATACTATGTACAAAAATATGTTACACGTCGTGATTAAAAAAGATTGT
1 AAAAAATATTATTGTTACATACTATGGACAAAAACATGTTACACGTCGTGATTAAAAAAGATTGT
*
13307036 TACACGCCACGTT-AAA
66 TACACACCACGTTGAAA
* * * *
13307052 AAAAAATATTGTTGTTA-TTCGCTATGGATAAAAACATGTTA
1 AAAAAATATTATTGTTACAT-ACTATGGACAAAAACATGTTA
13307093 GACGCTATGT
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
80 1 0.01
81 35 0.35
82 60 0.59
83 1 0.01
84 4 0.04
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (82 bp):
AAAAAATATTATTGTTACATACTATGGACAAAAACATGTTACACGTCGTGATTAAAAAAGATTGT
TACACACCACGTTGAAA
Found at i:13316466 original size:24 final size:24
Alignment explanation
Indices: 13316434--13316481 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
13316424 CTGTTCATCA
13316434 AGCTATACCCTCAAAAAATAGTGG
1 AGCTATACCCTCAAAAAATAGTGG
13316458 AGCTATACCCTCAAAAAATAGTGG
1 AGCTATACCCTCAAAAAATAGTGG
13316482 CTTAATTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
AGCTATACCCTCAAAAAATAGTGG
Found at i:13317379 original size:86 final size:81
Alignment explanation
Indices: 13317199--13317425 Score: 330
Period size: 86 Copynumber: 2.7 Consensus size: 81
13317189 TTAAATTACT
* * * * *
13317199 TATAAATTTTTTATATTAGCTGAATTTATAAACTAACAAATGTAAAA-TTAGTTTACATTACTTG
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTTA-TTTATATTACTTG
*
13317263 TGATGCAAATTTAAATA
65 TGATGCAAACTTAAATA
13317280 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTTATTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTTATTTATATTACTTG-
13317345 ACTATGATGCAAACTTAAATA
65 ----TGATGCAAACTTAAATA
*
13317366 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTA
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTTATTTATATTA
13317426 ACAACAATTG
Statistics
Matches: 133, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
81 55 0.41
82 3 0.02
86 75 0.56
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (81 bp):
TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTTATTTATATTACTTGT
GATGCAAACTTAAATA
Found at i:13317441 original size:28 final size:28
Alignment explanation
Indices: 13317400--13317453 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
13317390 CTTGTAAACT
13317400 AACAAATGTAAAATTAATTTATATTAAC
1 AACAAATGTAAAATTAATTTATATTAAC
* *
13317428 AACAATTGTCAAATTAATTTATATTA
1 AACAAATGTAAAATTAATTTATATTA
13317454 CTTGAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (28 bp):
AACAAATGTAAAATTAATTTATATTAAC
Found at i:13317514 original size:114 final size:113
Alignment explanation
Indices: 13317314--13317538 Score: 387
Period size: 114 Copynumber: 2.0 Consensus size: 113
13317304 CTTGTAAACT
*
13317314 AACAAATGTAAAATTTATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTA
1 AACAAATGTAAAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTA
* **
13317379 TATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTAAC
66 TATTAATTGAACTTGTAAACTAA-AAATACAAAATTAATTTATATTAAC
* *
13317428 AACAATTGTCAAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTA
1 AACAAATGTAAAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTA
13317493 TATTAATTGAACTTGTAAACTAAAAATACAAAATTAATTTATATTA
66 TATTAATTGAACTTGTAAACTAAAAATACAAAATTAATTTATATTA
13317539 CTTGAACTAT
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 21 0.20
114 84 0.80
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (113 bp):
AACAAATGTAAAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTA
TATTAATTGAACTTGTAAACTAAAAATACAAAATTAATTTATATTAAC
Found at i:13317520 original size:41 final size:40
Alignment explanation
Indices: 13317445--13317600 Score: 152
Period size: 44 Copynumber: 3.7 Consensus size: 40
13317435 GTCAAATTAA
* *
13317445 TTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATT
1 TTTATATTAATTGAACT-TG-T--AAACTAAAATATATAAAATT
*
13317489 TTTATATTAATTGAACTTGTAAACTAAAA-ATACAAAATT
1 TTTATATTAATTGAACTTGTAAACTAAAATATATAAAATT
* * *
13317528 AATTTATATTACTTGAACTATGATGCAAACTTAAATATTTAAAATT
1 --TTTATATTAATTGAACT-TG-T--AAACTAAAATATATAAAATT
*
13317574 TTTATATTAGTTGAACTTGTAAACTAA
1 TTTATATTAATTGAACTTGTAAACTAA
13317601 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
39 9 0.09
40 14 0.15
41 16 0.17
42 4 0.04
43 5 0.05
44 32 0.33
45 8 0.08
46 8 0.08
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (40 bp):
TTTATATTAATTGAACTTGTAAACTAAAATATATAAAATT
Found at i:13317541 original size:85 final size:85
Alignment explanation
Indices: 13317438--13317600 Score: 308
Period size: 85 Copynumber: 1.9 Consensus size: 85
13317428 AACAATTGTC
13317438 AAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAATTGA
1 AAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAATTGA
13317503 ACTTGTAAACTAAAAATACA
66 ACTTGTAAACTAAAAATACA
* *
13317523 AAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATTTAAAATTTTTATATTAGTTGA
1 AAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAATTGA
13317588 ACTTGTAAACTAA
66 ACTTGTAAACTAA
13317601 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (85 bp):
AAATTAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAATTGA
ACTTGTAAACTAAAAATACA
Found at i:13334086 original size:17 final size:17
Alignment explanation
Indices: 13334064--13334096 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13334054 AAATATGCAC
13334064 ATACTTAGGGGGAGCAT
1 ATACTTAGGGGGAGCAT
13334081 ATACTTAGGGGGAGCA
1 ATACTTAGGGGGAGCA
13334097 ATCTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.36, T:0.21
Consensus pattern (17 bp):
ATACTTAGGGGGAGCAT
Found at i:13338302 original size:25 final size:25
Alignment explanation
Indices: 13338273--13338329 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
13338263 TGGTCGTAAT
* *
13338273 CACGTGTATCAACTTGTGGCCTAGC
1 CACGTATATCAACCTGTGGCCTAGC
* *
13338298 CACGTATATCAACCTGTTGCCTTGC
1 CACGTATATCAACCTGTGGCCTAGC
13338323 CACGTAT
1 CACGTAT
13338330 TGATATCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (25 bp):
CACGTATATCAACCTGTGGCCTAGC
Found at i:13339860 original size:21 final size:20
Alignment explanation
Indices: 13339832--13339871 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
13339822 AGCTTTTCTT
13339832 CTTTCTTCTCTCTCCTTTCG
1 CTTTCTTCTCTCTCCTTTCG
*
13339852 CTTTCCTTCTTTCTCCTTTC
1 CTTT-CTTCTCTCTCCTTTC
13339872 TTCCTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.40, G:0.03, T:0.57
Consensus pattern (20 bp):
CTTTCTTCTCTCTCCTTTCG
Found at i:13339889 original size:18 final size:18
Alignment explanation
Indices: 13339830--13339882 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
13339820 CTAGCTTTTC
* *
13339830 TTCTTTCTTCTCTCTCCT
1 TTCTTCCTTCTTTCTCCT
13339848 TTCGCTTTCCTTCTTTCTCCT
1 TT--C-TTCCTTCTTTCTCCT
13339869 TTCTTCCTT-TTTCT
1 TTCTTCCTTCTTTCT
13339883 TGCTTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.17
18 8 0.27
19 1 0.03
20 1 0.03
21 15 0.50
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (18 bp):
TTCTTCCTTCTTTCTCCT
Found at i:13344862 original size:21 final size:21
Alignment explanation
Indices: 13344841--13344880 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13344831 AACATTTTGT
13344841 TTCA-AATGTATCAATACATG
1 TTCATAATGTATCAATACATG
* *
13344861 TTCATGATGTATCGATACAT
1 TTCATAATGTATCAATACAT
13344881 TTAGCCTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
TTCATAATGTATCAATACATG
Found at i:13354125 original size:21 final size:21
Alignment explanation
Indices: 13354099--13354148 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
13354089 GCAGAGTTGA
*
13354099 AGGAGTTGAAAGTATAATTGC
1 AGGAGTTGAAAGTACAATTGC
13354120 AGGAGTTGAAAGTACAATTGC
1 AGGAGTTGAAAGTACAATTGC
*
13354141 AAGAGTTG
1 AGGAGTTG
13354149 GTGGACAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.30, T:0.26
Consensus pattern (21 bp):
AGGAGTTGAAAGTACAATTGC
Found at i:13360361 original size:80 final size:80
Alignment explanation
Indices: 13360221--13360444 Score: 319
Period size: 80 Copynumber: 2.8 Consensus size: 80
13360211 CGTGAGTTCC
* * *
13360221 ATTTATGAGATT--GTAACATGTATGCCATGAGATGTATGTGTTAAGTATA-TCATGTTCACTAT
1 ATTTATGAGATTACG-AA-ATGTATGCCATGAGATGTATGTGTTGAG-ATAGTCATATACACTAT
13360283 GGGCTAAGCATGTAAGTG
63 GGGCTAAGCATGTAAGTG
* *
13360301 ATTTATGAGGTTACGAAATGTATTCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
1 ATTTATGAGATTACGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
* *
13360366 CTAGGCATGTACGTG
66 CTAAGCATGTAAGTG
* *
13360381 ATTTATGAGATTATGAAATGTATGCCATGAGATGTATGTTTTGAGATAGTCATATACACTATGG
1 ATTTATGAGATTACGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGG
13360445 CCAAAGTATG
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
79 3 0.02
80 124 0.95
81 2 0.02
82 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (80 bp):
ATTTATGAGATTACGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
CTAAGCATGTAAGTG
Found at i:13361478 original size:54 final size:53
Alignment explanation
Indices: 13361407--13361566 Score: 248
Period size: 54 Copynumber: 2.9 Consensus size: 53
13361397 ATAAGCACAT
* *
13361407 ACACCACCATCTCACCCAGTTCATGTGCATCCCCCGACATCGTGCACATAGCCGG
1 ACACC-CCATCTCACCCAGCTCATGTGCATCCCCC-ACATCGTGCACATAGCCAG
* *
13361462 ACACCCCGTCTCACCCAACTCATGTGCATCCCCTCACATCGTGCACATAGCCAG
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCC-CACATCGTGCACATAGCCAG
13361516 ACACCCCATCTCACCCAGCTCATGTGCATCTCCCCACATCGTGCACATAGC
1 ACACCCCATCTCACCCAGCTCATGTGCATC-CCCCACATCGTGCACATAGC
13361567 TAGAGTCATC
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
54 88 0.91
55 9 0.09
ACGTcount: A:0.24, C:0.44, G:0.14, T:0.19
Consensus pattern (53 bp):
ACACCCCATCTCACCCAGCTCATGTGCATCCCCCACATCGTGCACATAGCCAG
Found at i:13362883 original size:19 final size:19
Alignment explanation
Indices: 13362837--13362885 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
13362827 GCTATGCCCA
* *
13362837 CTCTCTTTTTTTTTTCTTT
1 CTCTCTTTCTTGTTTCTTT
13362856 CT-TCTTTTCTTGTTTCTTT
1 CTCTC-TTTCTTGTTTCTTT
13362875 CTCTCTTTCTT
1 CTCTCTTTCTT
13362886 CTTCTCCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 22 0.85
20 2 0.08
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (19 bp):
CTCTCTTTCTTGTTTCTTT
Found at i:13363038 original size:32 final size:35
Alignment explanation
Indices: 13363001--13363095 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 35
13362991 TAACAGCATC
*
13363001 AACTCTT-GT-TTTCTCTCT-CAAATTTGCAGCAA
1 AACTCTTCGTATTTCTCTCTAAAAATTTGCAGCAA
* * *
13363033 AACTCTTCTTATTTCTTTCTAAAAATTTGTAGCAA
1 AACTCTTCGTATTTCTCTCTAAAAATTTGCAGCAA
**
13363068 AACTCTTTATATTTC-CTTCTAAAAATTT
1 AACTCTTCGTATTTCTC-TCTAAAAATTT
13363096 ACAACACGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 7 0.13
33 1 0.02
34 8 0.15
35 36 0.69
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.45
Consensus pattern (35 bp):
AACTCTTCGTATTTCTCTCTAAAAATTTGCAGCAA
Found at i:13363061 original size:35 final size:35
Alignment explanation
Indices: 13363020--13363095 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
13363010 TTTCTCTCTC
*
13363020 AAATTTGCAGCAAAACTCTTCT-TATTTCTTTCTAA
1 AAATTTGCAGCAAAACTCTT-TATATTTCCTTCTAA
*
13363055 AAATTTGTAGCAAAACTCTTTATATTTCCTTCTAA
1 AAATTTGCAGCAAAACTCTTTATATTTCCTTCTAA
13363090 AAATTT
1 AAATTT
13363096 ACAACACGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 1 0.03
35 37 0.97
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.43
Consensus pattern (35 bp):
AAATTTGCAGCAAAACTCTTTATATTTCCTTCTAA
Found at i:13368429 original size:39 final size:39
Alignment explanation
Indices: 13368363--13368450 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 39
13368353 ATTCAGTCTT
* *
13368363 GCTGCAGCAAAATTGTGACCCAGAAACAGAAAGTTTCTC
1 GCTGCAGCAAAATTATGACCCAAAAACAGAAAGTTTCTC
* *
13368402 GCTGTAGCGAAATTATGACCCAAAAACAGAAAGTTTCTC
1 GCTGCAGCAAAATTATGACCCAAAAACAGAAAGTTTCTC
*
13368441 ACTGCAGCAA
1 GCTGCAGCAA
13368451 GAATGAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (39 bp):
GCTGCAGCAAAATTATGACCCAAAAACAGAAAGTTTCTC
Found at i:13368867 original size:43 final size:43
Alignment explanation
Indices: 13368816--13368925 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 43
13368806 TCACCAGCTC
*** *
13368816 ATGCGCACTCCCTACTCGCACAT-GGTTGGGTCATCATCGGGTG
1 ATGCGCACTCCCTACTCGCACATAACCT-GGTCATCATCGGCTG
* * * * *
13368859 ATGTGCACTCTCTACTCACACATAACCTGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCTGGTCATCATCGGCTG
13368902 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
13368926 GCCGAGTCAA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 53 0.98
44 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCTGGTCATCATCGGCTG
Found at i:13381553 original size:21 final size:21
Alignment explanation
Indices: 13381511--13381553 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
13381501 CTTGTACCGG
*
13381511 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
13381532 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
13381553 T
1 T
13381554 TGACCAGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:13398357 original size:35 final size:35
Alignment explanation
Indices: 13398318--13398401 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
13398308 TGATGTGGGC
**
13398318 GGGAGTGCATGTGATGATATTGAAATGTGCGTGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
* *** *
13398353 GGGAGTGCACATGATGATGTTGCCTTGTGTGTGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
13398388 GGGAGTGCACATGA
1 GGGAGTGCACATGA
13398402 GTTGAGTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.30
Consensus pattern (35 bp):
GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
Found at i:13398437 original size:2 final size:2
Alignment explanation
Indices: 13398430--13398460 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13398420 GGTGTACATG
13398430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13398461 GTATGCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13402709 original size:16 final size:16
Alignment explanation
Indices: 13402679--13402708 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13402669 GTAAAATTTA
13402679 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
13402695 GATTTTGATT-TTTT
1 GATTTTGATTCTTTT
13402709 TTATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:13402913 original size:21 final size:21
Alignment explanation
Indices: 13402882--13402941 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
13402872 TCCATTCTAT
*
13402882 TTCA-AATGTATCCATACATG
1 TTCATAATGTATCGATACATG
* *
13402902 TTCATGATGTATCGGTACATG
1 TTCATAATGTATCGATACATG
13402923 TTCATAATGTATCGATACA
1 TTCATAATGTATCGATACA
13402942 ATTTTTTTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
TTCATAATGTATCGATACATG
Found at i:13418699 original size:34 final size:35
Alignment explanation
Indices: 13418634--13418738 Score: 104
Period size: 35 Copynumber: 3.0 Consensus size: 35
13418624 CTTACCCAGC
* * ***
13418634 TTATGTGAACTCCTTACACGCACAAGGCAATATCA
1 TTATGTGCACTCCCTACACGCACATTTCAATATCA
13418669 TTATGTGCACTCCCT-CACGCACATTTCAATATCA
1 TTATGTGCACTCCCTACACGCACATTTCAATATCA
** * * * *
13418703 CCATGCGCACTCCCTACATGTACATTTTAATATCA
1 TTATGTGCACTCCCTACACGCACATTTCAATATCA
13418738 T
1 T
13418739 CACACGCACT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
34 28 0.49
35 29 0.51
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (35 bp):
TTATGTGCACTCCCTACACGCACATTTCAATATCA
Found at i:13418747 original size:35 final size:34
Alignment explanation
Indices: 13418675--13418749 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 34
13418665 ATCATTATGT
**
13418675 GCACTCCCTCACGCACATTTCAATATCACCATGC
1 GCACTCCCTCACGCACATTTCAATATCACCACAC
* * * *
13418709 GCACTCCCTACATGTACATTTTAATATCATCACAC
1 GCACTCCCT-CACGCACATTTCAATATCACCACAC
13418744 GCACTC
1 GCACTC
13418750 TTGCCTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 9 0.26
35 25 0.74
ACGTcount: A:0.28, C:0.37, G:0.08, T:0.27
Consensus pattern (34 bp):
GCACTCCCTCACGCACATTTCAATATCACCACAC
Found at i:13419831 original size:19 final size:19
Alignment explanation
Indices: 13419807--13419854 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
13419797 TGGCAAGGTG
13419807 AAATGGCATGGGAGCATGA
1 AAATGGCATGGGAGCATGA
* **
13419826 AAATGGCATTGGGTGGGTGA
1 AAATGGCA-TGGGAGCATGA
13419846 AAATGGCAT
1 AAATGGCAT
13419855 TCTGAGCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.33, C:0.08, G:0.38, T:0.21
Consensus pattern (19 bp):
AAATGGCATGGGAGCATGA
Found at i:13419866 original size:20 final size:20
Alignment explanation
Indices: 13419807--13419866 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
13419797 TGGCAAGGTG
*
13419807 AAATGGCA-TGGGAGCATGA
1 AAATGGCATTCGGAGCATGA
* * **
13419826 AAATGGCATTGGGTGGGTGA
1 AAATGGCATTCGGAGCATGA
*
13419846 AAATGGCATTCTGAGCATGA
1 AAATGGCATTCGGAGCATGA
13419866 A
1 A
13419867 GGTGGAGGAG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 8 0.25
20 24 0.75
ACGTcount: A:0.33, C:0.10, G:0.35, T:0.22
Consensus pattern (20 bp):
AAATGGCATTCGGAGCATGA
Found at i:13420282 original size:14 final size:14
Alignment explanation
Indices: 13420263--13420304 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
13420253 CCTTGAATGA
13420263 AATATTAATATT-TT
1 AATATT-ATATTATT
13420277 AATATTATATTATT
1 AATATTATATTATT
**
13420291 AATAAAATATTATT
1 AATATTATATTATT
13420305 TTATTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTATATTATT
Found at i:13420835 original size:19 final size:19
Alignment explanation
Indices: 13420811--13420850 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
13420801 GGTGGTAAGG
13420811 TGAAAATAGCATGGGAGCA
1 TGAAAATAGCATGGGAGCA
* *
13420830 TGAAAATGGCGTGGGAGCA
1 TGAAAATAGCATGGGAGCA
13420849 TG
1 TG
13420851 GACAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.38, T:0.17
Consensus pattern (19 bp):
TGAAAATAGCATGGGAGCA
Found at i:13424504 original size:38 final size:41
Alignment explanation
Indices: 13424462--13424649 Score: 183
Period size: 41 Copynumber: 4.7 Consensus size: 41
13424452 ATATTGCCCA
*
13424462 TGTGCACGATATGGGGGGATGCACATGATG-GCAT-TAGC-
1 TGTGCACGATGTGGGGGGATGCACATGATGAGCATATAGCT
* *
13424500 TGTGCACGATGTGGTGGGATGCACATGATGATG-ATATCGCT
1 TGTGCACGATGTGGGGGGATGCACATGATGA-GCATATAGCT
* * * * * * *
13424541 TATGCATGATGTGGGGGGATGCATA-AAGCGATCATATTGCT
1 TGTGCACGATGTGGGGGGATGCACATGA-TGAGCATATAGCT
* *
13424582 TGTGCACGATGTGGGGGGATGCACACGATGA-C-TCTAGCTT
1 TGTGCACGATGTGGGGGGATGCACATGATGAGCATATAGC-T
*
13424622 TGTGCACGATATGGGGGGATGCACATGA
1 TGTGCACGATGTGGGGGGATGCACATGA
13424650 GCTGGGTGAG
Statistics
Matches: 122, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
38 28 0.23
39 6 0.05
40 33 0.27
41 54 0.44
42 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.26
Consensus pattern (41 bp):
TGTGCACGATGTGGGGGGATGCACATGATGAGCATATAGCT
Found at i:13425627 original size:175 final size:175
Alignment explanation
Indices: 13425331--13425666 Score: 627
Period size: 175 Copynumber: 1.9 Consensus size: 175
13425321 AAAGGCATTC
* * * *
13425331 TCGCTGCAGTGACGTTGGGATTTAGTTATTAATCGAACGAGGGTTTCTCAACTGGCCGAGGATTT
1 TCGCTGCAGCGACATTGGGATTTAGTTATTAACCGAACGAGGGTTTCTCAACTAGCCGAGGATTT
13425396 CTCACTAAACCTCCTCATTTTAAACTTAACTCATTTAATCCTTAATGTTAGAAGTCCATGCTCTG
66 CTCACTAAACCTCCTCATTTTAAACTTAACTCATTTAATCCTTAATGTTAGAAGTCCATGCTCTG
13425461 ATATGGTAGCAAAGAAGTGAAAGATAGGACAACGAGAATGCCTTT
131 ATATGGTAGCAAAGAAGTGAAAGATAGGACAACGAGAATGCCTTT
13425506 TCGCTGCAGCGACATTGGGATTTAGTTATTAACCGAACGAGGGTTTCTCAACTAGCCGAGGATTT
1 TCGCTGCAGCGACATTGGGATTTAGTTATTAACCGAACGAGGGTTTCTCAACTAGCCGAGGATTT
*
13425571 CTCACTAAACCTCCTCATTTTAAACTTAACTCATTTAATCCTTAATGTTGGAAGTCCATGCTCTG
66 CTCACTAAACCTCCTCATTTTAAACTTAACTCATTTAATCCTTAATGTTAGAAGTCCATGCTCTG
13425636 ATATGGTAGCAAAGAAGTGAAAGATAGGACA
131 ATATGGTAGCAAAGAAGTGAAAGATAGGACA
13425667 GCAAGTGAAC
Statistics
Matches: 156, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 156 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (175 bp):
TCGCTGCAGCGACATTGGGATTTAGTTATTAACCGAACGAGGGTTTCTCAACTAGCCGAGGATTT
CTCACTAAACCTCCTCATTTTAAACTTAACTCATTTAATCCTTAATGTTAGAAGTCCATGCTCTG
ATATGGTAGCAAAGAAGTGAAAGATAGGACAACGAGAATGCCTTT
Found at i:13425744 original size:39 final size:40
Alignment explanation
Indices: 13425697--13425795 Score: 137
Period size: 39 Copynumber: 2.5 Consensus size: 40
13425687 ACCAAAATAA
* *
13425697 AAAGTTTTTCGCTGCAGCGAAATTTCTACCCA-AAAACAG
1 AAAGTTTTTCGCTGCAGCGAAATTGCAACCCAGAAAACAG
* *
13425736 AATGTTTTTCGTTGCAGCGAAATTGCAACCCAGAAAACAG
1 AAAGTTTTTCGCTGCAGCGAAATTGCAACCCAGAAAACAG
**
13425776 AAAGTTTCCCGCTGCAGCGA
1 AAAGTTTTTCGCTGCAGCGA
13425796 GAATGCATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 28 0.55
40 23 0.45
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (40 bp):
AAAGTTTTTCGCTGCAGCGAAATTGCAACCCAGAAAACAG
Found at i:13427056 original size:19 final size:20
Alignment explanation
Indices: 13427022--13427059 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
13427012 GAAGAAGACT
13427022 AGCTGCTAGAAAATTCAAGA
1 AGCTGCTAGAAAATTCAAGA
13427042 AGCTGCTAG-AAATTCAAG
1 AGCTGCTAGAAAATTCAAG
13427060 GTATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (20 bp):
AGCTGCTAGAAAATTCAAGA
Found at i:13427585 original size:54 final size:54
Alignment explanation
Indices: 13427463--13427596 Score: 162
Period size: 54 Copynumber: 2.5 Consensus size: 54
13427453 TCACAAATGT
* * * * *
13427463 ACATGAGTTGGGTGAGACGAGGTGTCTGGCTATGTGCACAATGTGGGGGGATGC
1 ACATGAGTCGGGTGAGATGGGGTGTCCGACTATGTGCACAATGTGGGGGGATGC
* * *
13427517 ACATGA-ACTTGGTGAGATGGGGTGTCCGACTATGTGCATAATGTGGGGGGATGC
1 ACATGAGTC-GGGTGAGATGGGGTGTCCGACTATGTGCACAATGTGGGGGGATGC
*
13427571 ACATCAGTCGGGTGAGATGGTGGTGT
1 ACATGAGTCGGGTGAGATGG-GGTGT
13427597 ATGTGCTTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
54 60 0.91
55 6 0.09
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.25
Consensus pattern (54 bp):
ACATGAGTCGGGTGAGATGGGGTGTCCGACTATGTGCACAATGTGGGGGGATGC
Found at i:13431657 original size:19 final size:20
Alignment explanation
Indices: 13431625--13431662 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
13431615 AAAGAGAAAA
13431625 GAAATGAAAAGAAA-ACAAG
1 GAAATGAAAAGAAAGACAAG
13431644 GAAAT-AAAATGAAAGACAA
1 GAAATGAAAA-GAAAGACAA
13431663 TTAGCTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.08
Consensus pattern (20 bp):
GAAATGAAAAGAAAGACAAG
Found at i:13437939 original size:61 final size:61
Alignment explanation
Indices: 13437718--13437931 Score: 293
Period size: 61 Copynumber: 3.5 Consensus size: 61
13437708 GTACAACATC
* ** * * *
13437718 ACCGGCATGTGCACTGCCCACTCCACACATGCATGGCTGTAATTATCACGACATCAACATT
1 ACCGGCATGTGCACTGCCCACTCCGCACATGCACAGTTGTAATTATCACGACAACATCATT
** * * * *
13437779 ACCGGCATGTGCACTGCCCACTTTGAACATGCACAGTTCTAATTATCATGACAGCATCATT
1 ACCGGCATGTGCACTGCCCACTCCGCACATGCACAGTTGTAATTATCACGACAACATCATT
* * *
13437840 ATCGGCATGTGCACTACCCACTCCGCACATGCACAGTTGTAATGATCACGACAACATCATT
1 ACCGGCATGTGCACTGCCCACTCCGCACATGCACAGTTGTAATTATCACGACAACATCATT
13437901 ACCGGCATGTGCACTGCCCACTCCGCACATG
1 ACCGGCATGTGCACTGCCCACTCCGCACATG
13437932 TATAGTTGCA
Statistics
Matches: 131, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 131 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.23
Consensus pattern (61 bp):
ACCGGCATGTGCACTGCCCACTCCGCACATGCACAGTTGTAATTATCACGACAACATCATT
Found at i:13443632 original size:38 final size:39
Alignment explanation
Indices: 13443590--13443692 Score: 104
Period size: 38 Copynumber: 2.6 Consensus size: 39
13443580 ATAGTGCCCG
*
13443590 TGTGCACGATGTCGGGGGATGTACACGAT-G-GCACTGAT-
1 TGTGCACGATGT-GGGGGATGTACACGATGGTGC-CGGATA
* * * *
13443628 TGTGCATGATGTGGGAGGATGCACATGATGGTGCCGGCTA
1 TGTGCACGATGTGGG-GGATGTACACGATGGTGCCGGATA
13443668 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGT-GGGGGATGTACA
13443693 TGAGCCGGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
37 3 0.06
38 22 0.42
39 4 0.08
40 21 0.40
41 3 0.06
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGATGTACACGATGGTGCCGGATA
Found at i:13445278 original size:38 final size:40
Alignment explanation
Indices: 13445192--13445294 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 40
13445182 ACTTGGCTCA
* *
13445192 TGTACATCCCCCCACATCATGCACATAGCTGGTACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCTAGTACCATCG
* * *
13445232 TGTGCATCCCCCCACATCGTGCACA-ATC-AGTGCCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCTAGTACCATCG
13445270 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
13445295 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 32 0.56
39 2 0.04
40 23 0.40
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACATAGCTAGTACCATCG
Found at i:13445287 original size:19 final size:19
Alignment explanation
Indices: 13445227--13445290 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
13445217 TAGCTGGTAC
*
13445227 CATCGTGTGCATCCCCCCA
1 CATCGTGTACATCCCCCCA
* ****
13445246 CATCGTGCACAATCAGTGC-
1 CATCGTGTAC-ATCCCCCCA
13445265 CATCGTGTACATCCCCCCA
1 CATCGTGTACATCCCCCCA
13445284 CATCGTG
1 CATCGTG
13445291 CACACGGGCA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 4 0.12
19 24 0.75
20 4 0.12
ACGTcount: A:0.20, C:0.41, G:0.17, T:0.22
Consensus pattern (19 bp):
CATCGTGTACATCCCCCCA
Found at i:13446209 original size:19 final size:21
Alignment explanation
Indices: 13446167--13446210 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
13446157 AGGGAAGAAG
*
13446167 AAGACAGCTGTTGGAAATTTC
1 AAGACAGCTGCTGGAAATTTC
13446188 AAGA-AGCTGCTGGAAA-TTC
1 AAGACAGCTGCTGGAAATTTC
13446207 AAGA
1 AAGA
13446211 TATTTATAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 11 0.50
21 4 0.18
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (21 bp):
AAGACAGCTGCTGGAAATTTC
Found at i:13449714 original size:2 final size:2
Alignment explanation
Indices: 13449707--13449737 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13449697 TATAATGTTG
13449707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13449738 CTATGTCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13449901 original size:41 final size:41
Alignment explanation
Indices: 13449849--13449953 Score: 142
Period size: 41 Copynumber: 2.6 Consensus size: 41
13449839 ATATTGCCTG
* * *
13449849 TGTGCACGATGTGGGGGGATGCAT-ATGATGATGATATCACT
1 TGTGCAAGATGTGGGGGGATGCATAAAG-CGATGATATCACT
*
13449890 TGTGCAAGATGTGGGGGGATGCATAAAGCGATGATATTACT
1 TGTGCAAGATGTGGGGGGATGCATAAAGCGATGATATCACT
13449931 TGTGCACA-ATGTGGGGGGATGCA
1 TGTGCA-AGATGTGGGGGGATGCA
13449954 CACGATGACT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
41 55 0.95
42 3 0.05
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.27
Consensus pattern (41 bp):
TGTGCAAGATGTGGGGGGATGCATAAAGCGATGATATCACT
Found at i:13450169 original size:54 final size:54
Alignment explanation
Indices: 13449967--13450171 Score: 230
Period size: 54 Copynumber: 3.8 Consensus size: 54
13449957 GATGACTTCT
* * * * *
13449967 GCTATGTGCACAATGTAGGGGGATTCACATGAGCTGGGTAAGATGAGGTGTTCG
1 GCTATGTGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGACGAGGTGTCCG
* * * * *
13450021 GGTATGTCCACAATGTGGGGGGATGCACATGGGTTGGGTGAGACGAGGTGTCTG
1 GCTATGTGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGACGAGGTGTCCG
*** * * *
13450075 GCTATGTGCTTGATGTGGGGGAACGCACATGAGCTGGGTGAGACGAGATGTCCG
1 GCTATGTGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGACGAGGTGTCCG
* * * *
13450129 ACTATGTGCACGATGTGGGGGGATACACATGAGCTAGGTGAGA
1 GCTATGTGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGA
13450172 AGGTGGTGTA
Statistics
Matches: 123, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 123 1.00
ACGTcount: A:0.22, C:0.14, G:0.40, T:0.23
Consensus pattern (54 bp):
GCTATGTGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGACGAGGTGTCCG
Found at i:13458645 original size:21 final size:21
Alignment explanation
Indices: 13458621--13458688 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
13458611 GTTCATGCAA
*
13458621 TTCATGTCAAAGACTGATGCC
1 TTCATGACAAAGACTGATGCC
* * *
13458642 TTCATAACAGAGACAGATGCC
1 TTCATGACAAAGACTGATGCC
*
13458663 TTCATGACAAGGACTGATGCC
1 TTCATGACAAAGACTGATGCC
*
13458684 ATCAT
1 TTCAT
13458689 TCAAAGTCCA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (21 bp):
TTCATGACAAAGACTGATGCC
Found at i:13468719 original size:63 final size:63
Alignment explanation
Indices: 13468547--13468719 Score: 238
Period size: 63 Copynumber: 2.7 Consensus size: 63
13468537 GTACCATTGT
* * * *
13468547 GTGATAATTGTAACCGTGCATGTGCTGAGTGGGCAGTGCACATGCCAGTTGAATGACAATGTT
1 GTGATAATTGCAACCGTGCATGTGCTGAGTGGGCAGTGCACATGCCGGTTGAATAACAATGTC
* * * *
13468610 GTGATAATTGCAACCGTGCTTGTGCTAAGTGGGCAATGCACATGCCGGTTGAGTAACAATGTC
1 GTGATAATTGCAACCGTGCATGTGCTGAGTGGGCAGTGCACATGCCGGTTGAATAACAATGTC
* * * *
13468673 GTGATAATTACAACTGTGCATGTGCGGAGTGGGCAGTGCACGTGCCG
1 GTGATAATTGCAACCGTGCATGTGCTGAGTGGGCAGTGCACATGCCG
13468720 ATAATGATGC
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 95 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (63 bp):
GTGATAATTGCAACCGTGCATGTGCTGAGTGGGCAGTGCACATGCCGGTTGAATAACAATGTC
Found at i:13470515 original size:12 final size:11
Alignment explanation
Indices: 13470497--13470527 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
13470487 CTTGGATTGA
13470497 AAAAAAAAAAG
1 AAAAAAAAAAG
13470508 AAAGAAAAAAAG
1 AAA-AAAAAAAG
13470520 AAAAAAAA
1 AAAAAAAA
13470528 GGAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:13470518 original size:17 final size:18
Alignment explanation
Indices: 13470495--13470534 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
13470485 AGCTTGGATT
*
13470495 GAAAAAAA-AAAAGAAA-
1 GAAAAAAAGAAAAAAAAG
13470511 GAAAAAAAGAAAAAAAAG
1 GAAAAAAAGAAAAAAAAG
13470529 GAAAAA
1 GAAAAA
13470535 TATGAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 7 0.33
18 6 0.29
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
GAAAAAAAGAAAAAAAAG
Found at i:13476471 original size:21 final size:21
Alignment explanation
Indices: 13476445--13476486 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13476435 AAACAGAAGG
13476445 TTTCTCACTGCAGCGAAATTC
1 TTTCTCACTGCAGCGAAATTC
* *
13476466 TTTCTCATTGCTGCGAAATTC
1 TTTCTCACTGCAGCGAAATTC
13476487 AGTTGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (21 bp):
TTTCTCACTGCAGCGAAATTC
Found at i:13476972 original size:38 final size:40
Alignment explanation
Indices: 13476886--13476988 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 40
13476876 ACCCGGCTCA
**
13476886 TGTACATCCCCCCACATTGTGCAC-ATAGCTGGCACCATCG
1 TGTACATCCCCCCACATCATGCACAATAGCTGG-ACCATCG
*
13476926 TGTGCATCCCCCCACATCATGCACAATTAG-T-G-CCATCG
1 TGTACATCCCCCCACATCATGCACAA-TAGCTGGACCATCG
*
13476964 TGTACATCCCCCCACATCCTGCACA
1 TGTACATCCCCCCACATCATGCACA
13476989 CAGGCACTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 29 0.52
40 22 0.39
41 2 0.04
42 3 0.05
ACGTcount: A:0.23, C:0.40, G:0.15, T:0.22
Consensus pattern (40 bp):
TGTACATCCCCCCACATCATGCACAATAGCTGGACCATCG
Found at i:13477905 original size:19 final size:21
Alignment explanation
Indices: 13477866--13477905 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13477856 GAAGAAGACC
13477866 AGCTGCTGGAAAATCTCAAGA
1 AGCTGCTGGAAAATCTCAAGA
13477887 AGCTGCTGG-AAAT-TCAAGA
1 AGCTGCTGGAAAATCTCAAGA
13477906 TATTTATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (21 bp):
AGCTGCTGGAAAATCTCAAGA
Found at i:13478987 original size:63 final size:63
Alignment explanation
Indices: 13478868--13479040 Score: 258
Period size: 63 Copynumber: 2.8 Consensus size: 63
13478858 TACCATTGTG
*
13478868 TGATAATTGTAACCGTGCATGTGC-GAGTGGGTAGTGCACATGCCGGTTGAATGACAATATTA
1 TGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGACAATATTA
* * * *
13478930 TGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTACAAATGCCGGTTGAATGACAATGTTG
1 TGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGACAATATTA
** * *
13478993 TGATAATTACAGCCGTGCATGTGCGGAATGGGCAGTGCACATGCCGGT
1 TGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGT
13479041 AATGATGCAC
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
62 24 0.24
63 75 0.76
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (63 bp):
TGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGACAATATTA
Found at i:13481401 original size:28 final size:28
Alignment explanation
Indices: 13481347--13481494 Score: 172
Period size: 28 Copynumber: 5.2 Consensus size: 28
13481337 AGACAAAAAT
* * * *
13481347 ATGTTATCATGTCTAAATTGAGACAAAT
1 ATGTTTTCTTGTCTAAATTAAGACAAAC
* *
13481375 ATGTTTTCTTGTCTAAATTAAGCCAAAAAA
1 ATGTTTTCTTGTCTAAATTAAG--ACAAAC
13481405 AT-TTTTCTTGTCTTAAATTAAGACAAAC
1 ATGTTTTCTTGTC-TAAATTAAGACAAAC
* *
13481433 ATATTTTCTTGTATAAATTAAGACCAAAC
1 ATGTTTTCTTGTCTAAATTAAGA-CAAAC
*
13481462 ATGTTTTCTTATCTAAATTAAGACAAAC
1 ATGTTTTCTTGTCTAAATTAAGACAAAC
13481490 ATGTT
1 ATGTT
13481495 AAAACTGTCA
Statistics
Matches: 104, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
28 45 0.43
29 44 0.42
30 15 0.14
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (28 bp):
ATGTTTTCTTGTCTAAATTAAGACAAAC
Found at i:13481422 original size:58 final size:57
Alignment explanation
Indices: 13481332--13481494 Score: 186
Period size: 58 Copynumber: 2.8 Consensus size: 57
13481322 TTTTGTCTTT
* * * * * * *
13481332 AATTCAGACAAAAATATGTTATCATGTCTAAATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACCAAAA-ATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTATA
*
13481390 AATTAAG-CCAAAAAAAT-TTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTATA
1 AATTAAGACC--AAAAATGTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTGTATA
* *
13481448 AATTAAGACCAAACATGTTTTCTTATCTAAATTAAGACAAACATGTT
1 AATTAAGACCAAAAATGTTTTCTTGTCTAAATTAAGACAAACATGTT
13481495 AAAACTGTCA
Statistics
Matches: 89, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
57 33 0.37
58 50 0.56
59 6 0.07
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (57 bp):
AATTAAGACCAAAAATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTATA
Found at i:13481439 original size:29 final size:28
Alignment explanation
Indices: 13481332--13481491 Score: 167
Period size: 29 Copynumber: 5.5 Consensus size: 28
13481322 TTTTGTCTTT
* * *
13481332 AATTCAGACAAAAATATGTTATCATGTCTA
1 AATTAAGACAAACATAT-TT-TCTTGTCTA
* * *
13481362 AATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
* * *
13481390 AATTAAGCCAAAAAAATTTTTCTTGTCTTA
1 AATTAAGACAAACATA-TTTTCTTGTC-TA
*
13481420 AATTAAGACAAACATATTTTCTTGTATA
1 AATTAAGACAAACATATTTTCTTGTCTA
* *
13481448 AATTAAGACCAAACATGTTTTCTTATCTA
1 AATTAAGA-CAAACATATTTTCTTGTCTA
13481477 AATTAAGACAAACAT
1 AATTAAGACAAACAT
13481492 GTTAAAACTG
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 36 0.32
29 46 0.41
30 29 0.26
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTGTCTA
Found at i:13486770 original size:3 final size:3
Alignment explanation
Indices: 13486762--13486795 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
13486752 TTTCCAACAG
13486762 CTT CTT CTT CTT CTT CTT CTT CGTT CTT CCTT CT
1 CTT CTT CTT CTT CTT CTT CTT C-TT CTT -CTT CT
13486796 CACGTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:13506223 original size:32 final size:32
Alignment explanation
Indices: 13506187--13506335 Score: 122
Period size: 35 Copynumber: 4.5 Consensus size: 32
13506177 TTTACCGGGA
*
13506187 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * *
13506219 TCAACCACAACCTTTCACAA-TAGTTTTT-AACTGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAA-AGGC
*
13506254 TCAACCAAAACCCAAAGTGATTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * * **
13506286 TCAACCACAACCTACAATAATGGTTTTTCACAGAA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCAAAGGC
13506321 TCAACCAAAACCCAA
1 TCAACCAAAACCCAA
13506336 CAACTAGCTT
Statistics
Matches: 92, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
31 2 0.02
32 32 0.35
33 5 0.05
34 5 0.05
35 46 0.50
36 2 0.02
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:13506245 original size:35 final size:32
Alignment explanation
Indices: 13506195--13506298 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
13506185 GATCAACTAA
13506195 AACC-CAAAGTGGTTTTTCAAAGGCTCAACCAC
1 AACCTCAAAGT-GTTTTTCAAAGGCTCAACCAC
* *
13506227 AACCTTTCACAA-TAGTTTTT-AACTGGCTCAACCAA
1 AACC--TCA-AAGT-GTTTTTCAA-AGGCTCAACCAC
13506262 AACC-CAAAGTGATTTTTCAAAGGCTCAACCAC
1 AACCTCAAAGTG-TTTTTCAAAGGCTCAACCAC
13506294 AACCT
1 AACCT
13506299 ACAATAATGG
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
31 3 0.05
32 26 0.45
33 2 0.03
34 2 0.03
35 23 0.40
36 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.25
Consensus pattern (32 bp):
AACCTCAAAGTGTTTTTCAAAGGCTCAACCAC
Found at i:13506258 original size:67 final size:67
Alignment explanation
Indices: 13506160--13506335 Score: 237
Period size: 67 Copynumber: 2.6 Consensus size: 67
13506150 GCTTAGCCAA
* * *
13506160 AACCTTTCACAATAGTTTTTACCGGGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATAGTTTTTAACGGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
13506225 AC
66 AC
* *
13506227 AACCTTTCACAATAGTTTTTAACTGGCTCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
1 AACCTTTCACAATAGTTTTTAACGGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
13506292 AC
66 AC
* * * * * *
13506294 AACC-TACAATAATGGTTTTTCACAGAATCAACCAAAACCCAA
1 AACCTTTC-ACAATAGTTTTTAACGGGATCAACCAAAACCCAA
13506336 CAACTAGCTT
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
66 2 0.02
67 94 0.98
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATAGTTTTTAACGGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
AC
Found at i:13513949 original size:67 final size:67
Alignment explanation
Indices: 13513832--13514006 Score: 219
Period size: 67 Copynumber: 2.6 Consensus size: 67
13513822 GCTTAGCCAA
* * * *
13513832 AACCTTTCACAATAGTTTTT-ACCGGATCAACTAAAACCCAAAGTTATTTTTCAAAGCCTCAATC
1 AACCTTTCACAATAGTTTTTCACGGGATCAACAAAAACCCAAAGTGATTTTTCAAAGCCTCAACC
13513896 AC
66 AC
* * * * *
13513898 GACCTTTCACAATAGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATAGTTTTTCACGGGATCAACAAAAACCCAAAGTGATTTTTCAAAGCCTCAACC
13513963 AC
66 AC
* * *
13513965 AACC-TACAACAATGGTTTTTCATGGGATCAACAAAAACCCAA
1 AACCTTTC-ACAATAGTTTTTCACGGGATCAACAAAAACCCAA
13514007 CAACTAACTT
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
66 21 0.23
67 72 0.77
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATAGTTTTTCACGGGATCAACAAAAACCCAAAGTGATTTTTCAAAGCCTCAACC
AC
Found at i:13513986 original size:35 final size:34
Alignment explanation
Indices: 13513878--13513986 Score: 98
Period size: 35 Copynumber: 3.2 Consensus size: 34
13513868 CCCAAAGTTA
* * * *
13513878 TTTTTCAAAGCCTCAATCACGACCTTTC-ACAATAG
1 TTTTTCAAAGGCTCAACCACAACC--TCAACAATGG
** * *
13513913 TTTTTCACGGGCTCAACCAAAACC-CAA-AGTGG
1 TTTTTCAAAGGCTCAACCACAACCTCAACAATGG
13513945 TTTTTCAAAGGCTCAACCACAACCTACAACAATGG
1 TTTTTCAAAGGCTCAACCACAACCT-CAACAATGG
13513980 TTTTTCA
1 TTTTTCA
13513987 TGGGATCAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
32 25 0.43
33 1 0.02
34 3 0.05
35 29 0.50
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (34 bp):
TTTTTCAAAGGCTCAACCACAACCTCAACAATGG
Found at i:13513996 original size:35 final size:33
Alignment explanation
Indices: 13513906--13514009 Score: 111
Period size: 32 Copynumber: 3.1 Consensus size: 33
13513896 ACGACCTTTC
* *
13513906 ACAATAGTTTTTCACGGGCTCAACCAAAACCCA
1 ACAATGGTTTTTCAAGGGCTCAACCAAAACCCA
* * *
13513939 A-AGTGGTTTTTCAAAGGCTCAACCACAACCTACA
1 ACAATGGTTTTTCAAGGGCTCAACCAAAACC--CA
* * *
13513973 ACAATGGTTTTTCATGGGATCAACAAAAACCCA
1 ACAATGGTTTTTCAAGGGCTCAACCAAAACCCA
13514006 ACAA
1 ACAA
13514010 CTAACTTTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
32 24 0.42
33 7 0.12
34 3 0.05
35 23 0.40
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.22
Consensus pattern (33 bp):
ACAATGGTTTTTCAAGGGCTCAACCAAAACCCA
Found at i:13524129 original size:17 final size:17
Alignment explanation
Indices: 13524107--13524162 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
13524097 TTTTAAAAAA
13524107 AATAAAAAAAATATTTT
1 AATAAAAAAAATATTTT
*
13524124 AATAAAAAAATATATATT
1 AATAAAAAAA-ATATTTT
*
13524142 AATAATAACAAA-ATTTT
1 AATAA-AAAAAATATTTT
13524159 AATA
1 AATA
13524163 TAAGAAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 18 0.53
18 12 0.35
19 4 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAAAAAAATATTTT
Found at i:13524133 original size:18 final size:18
Alignment explanation
Indices: 13524110--13524162 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
13524100 TAAAAAAAAT
13524110 AAAAAAAATATTTTAATA
1 AAAAAAAATATTTTAATA
* *
13524128 AAAAAATATATATTAATA
1 AAAAAAAATATTTTAATA
* *
13524146 ATAACAAA-ATTTTAATA
1 AAAAAAAATATTTTAATA
13524163 TAAGAAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAAAAATATTTTAATA
Found at i:13534186 original size:17 final size:17
Alignment explanation
Indices: 13534157--13534189 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13534147 TTCTTGATAA
13534157 AATAAAACTTCTTATTG
1 AATAAAACTTCTTATTG
13534174 AATAATAAC-TCTTATT
1 AATAA-AACTTCTTATT
13534190 TTGTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAAAACTTCTTATTG
Found at i:13534382 original size:30 final size:28
Alignment explanation
Indices: 13534331--13534495 Score: 174
Period size: 27 Copynumber: 5.8 Consensus size: 28
13534321 TTAAGACATC
*
13534331 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGAC-AAAATATTTT
* *
13534361 ATCTTGTCTAAATTGAGAC-AAATATGTT
1 -TCTTGTCTAAATTAAGACAAAATATTTT
* *
13534389 TCTTGTCTAGATTAAGATAAAAAATATTTT
1 TCTTGTCTAAATTAAG--ACAAAATATTTT
13534419 TCTTGTCTTAAATTAAGAC-AAATATTTT
1 TCTTGTC-TAAATTAAGACAAAATATTTT
* * *
13534447 T-TTATCTAAATTAAAACCAAATATGTTT
1 TCTTGTCTAAATTAAGACAAAATAT-TTT
13534475 TCTTGTCTAAATTAAGACAAA
1 TCTTGTCTAAATTAAGACAAA
13534496 CATGTTAAAG
Statistics
Matches: 113, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
26 10 0.09
27 24 0.21
28 22 0.19
29 18 0.16
30 24 0.21
31 15 0.13
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAAATATTTT
Found at i:13534425 original size:57 final size:56
Alignment explanation
Indices: 13534341--13534501 Score: 200
Period size: 57 Copynumber: 2.8 Consensus size: 56
13534331 TCTTGTCTTT
* * *
13534341 AATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTCTTGTCTA
1 AATTAAGAAAAAAATATTTT-TCTTGTCTAAATTAAGACAAATATGTTTCTTATCTA
* *
13534398 GATTAAGATAAAAAATATTTTTCTTGTCTTAAATTAAGACAAATAT-TTTTTTATCTA
1 AATTAAGA-AAAAAATATTTTTCTTGTC-TAAATTAAGACAAATATGTTTCTTATCTA
** *
13534455 AATTAA-AACCAAATATGTTTTCTTGTCTAAATTAAGACAAACATGTT
1 AATTAAGAAAAAAATAT-TTTTCTTGTCTAAATTAAGACAAATATGTT
13534502 AAAGCTGTCA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
55 23 0.25
56 13 0.14
57 28 0.31
58 27 0.30
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (56 bp):
AATTAAGAAAAAAATATTTTTCTTGTCTAAATTAAGACAAATATGTTTCTTATCTA
Found at i:13534475 original size:29 final size:27
Alignment explanation
Indices: 13534352--13534495 Score: 146
Period size: 28 Copynumber: 5.1 Consensus size: 27
13534342 ATTAAGACAA
* *
13534352 AAATATTTTATCTTGTCTAAATTGAGAC
1 AAATATTTT-TCTTGTCTAAATTAAAAC
* * *
13534380 AAATATGTTTCTTGTCTAGATTAAGATAAA
1 AAATATTTTTCTTGTCTAAATT-A-A-AAC
*
13534410 AAATATTTTTCTTGTCTTAAATTAAGAC
1 AAATATTTTTCTTGTC-TAAATTAAAAC
*
13534438 AAATATTTTT-TTATCTAAATTAAAACC
1 AAATATTTTTCTTGTCTAAATTAAAA-C
*
13534465 AAATATGTTTTCTTGTCTAAATTAAGAC
1 AAATAT-TTTTCTTGTCTAAATTAAAAC
13534493 AAA
1 AAA
13534496 CATGTTAAAG
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
26 9 0.09
27 23 0.24
28 27 0.28
29 15 0.16
30 17 0.18
31 5 0.05
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (27 bp):
AAATATTTTTCTTGTCTAAATTAAAAC
Found at i:13551081 original size:21 final size:21
Alignment explanation
Indices: 13551057--13551117 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
13551047 TAATTCATGT
13551057 CAAAGACTGATGCCTTCATAA
1 CAAAGACTGATGCCTTCATAA
* *
13551078 CAAAGACAGATGCCTTCATGA
1 CAAAGACTGATGCCTTCATAA
* *
13551099 CAAGGACTGATGCCATCAT
1 CAAAGACTGATGCCTTCAT
13551118 TCAAAGTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
CAAAGACTGATGCCTTCATAA
Found at i:13553203 original size:3 final size:3
Alignment explanation
Indices: 13553195--13553241 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
13553185 CACTTTTCTC
* * * *
13553195 TAG TAG TAG TAG TAA TAA TAG GAG TAG TAG TAG TAG TGG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
13553242 ACTATATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
TAG
Found at i:13557931 original size:63 final size:63
Alignment explanation
Indices: 13557832--13558004 Score: 238
Period size: 63 Copynumber: 2.7 Consensus size: 63
13557822 GGTACCATTG
* *
13557832 TGTGATAATTGTAACCGTGCATGTGCTGAGTGGGCAGTGCACATGCCAGTTGAATGATAATGT
1 TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCAGTTGAATGACAATGT
* * **
13557895 TGTGATAATTGTAACCGTGCATGTACGGAGTGGGCAGTGCACATGCGGGTTGAATGACAATGT
1 TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCAGTTGAATGACAATGT
* ** * * *
13557958 CGTGATAATTACAACCATGGATGTGCAGAGTGGGCAATGCACATGCC
1 TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCC
13558005 GGTAATGATG
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 96 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (63 bp):
TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCAGTTGAATGACAATGT
Found at i:13559808 original size:9 final size:10
Alignment explanation
Indices: 13559783--13559821 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
13559773 TTGGATTGAA
*
13559783 AAAAAAAAGA
1 AAAAAAAAGG
13559793 AAGAAAAAAGG
1 AA-AAAAAAGG
*
13559804 AAAAAAAAGT
1 AAAAAAAAGG
13559814 AAAAAAAA
1 AAAAAAAA
13559822 TGAGAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:13559809 original size:10 final size:10
Alignment explanation
Indices: 13559782--13559821 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
13559772 CTTGGATTGA
13559782 AAAAAAAAAG
1 AAAAAAAAAG
13559792 AAAGAAAAAAG
1 AAA-AAAAAAG
*
13559803 GAAAAAAAAG
1 AAAAAAAAAG
13559813 TAAAAAAAA
1 -AAAAAAAA
13559822 TGAGAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:13562857 original size:22 final size:22
Alignment explanation
Indices: 13562827--13562882 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
13562817 AAGCCATACA
13562827 AGAATATTGAAGTTTGAAGTTGC
1 AGAA-ATTGAAGTTTGAAGTTGC
13562850 AGAAATTGAAGTTTGAAGTTGC
1 AGAAATTGAAGTTTGAAGTTGC
13562872 AGAAATTGAAG
1 AGAAATTGAAG
13562883 GTAAACATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.30
Consensus pattern (22 bp):
AGAAATTGAAGTTTGAAGTTGC
Found at i:13566186 original size:28 final size:30
Alignment explanation
Indices: 13566128--13566187 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
13566118 TTTTTGAAAT
*
13566128 TTACACTTTTGCCCCCGTAAAAGTGAAAAA
1 TTACACTTTTGCCCCCGAAAAAGTGAAAAA
* *
13566158 TTACATTTTTG-CCCC-AAAAATTGAAAAA
1 TTACACTTTTGCCCCCGAAAAAGTGAAAAA
13566186 TT
1 TT
13566188 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 4 0.15
30 10 0.37
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (30 bp):
TTACACTTTTGCCCCCGAAAAAGTGAAAAA
Found at i:13566806 original size:63 final size:62
Alignment explanation
Indices: 13566728--13566899 Score: 218
Period size: 63 Copynumber: 2.7 Consensus size: 62
13566718 GGTACCATTG
* *
13566728 TGTGATAATTATAACCATGCATGTGCGGATTGGGCAGTGCACATGTCGGTTGAATGACAATGT
1 TGTGATAATTATAACCGTGCATGTGCGGAGTGGGCAGTGCACATG-CGGTTGAATGACAATGT
* * * * *
13566791 TGTGATAATTGTAACCGTGCATGTGCGAAGTGGGTAATGCACATGCTGGTTGAATGATAATGT
1 TGTGATAATTATAACCGTGCATGTGCGGAGTGGGCAGTGCACATGC-GGTTGAATGACAATGT
* * ** *
13566854 CGTGATAATTACAACCGTGCATGTGTAGAGTGGGCAGTGGACATGC
1 TGTGATAATTATAACCGTGCATGTGCGGAGTGGGCAGTGCACATGC
13566900 CGGTAATGAT
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
62 1 0.01
63 91 0.99
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (62 bp):
TGTGATAATTATAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCGGTTGAATGACAATGT
Found at i:13569032 original size:17 final size:17
Alignment explanation
Indices: 13569012--13569044 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13569002 TTCTTGATAA
13569012 AATAA-AACTCCTTATTG
1 AATAATAACT-CTTATTG
13569029 AATAATAACTCTTATT
1 AATAATAACTCTTATT
13569045 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAATAACTCTTATTG
Found at i:13569227 original size:30 final size:29
Alignment explanation
Indices: 13569193--13569352 Score: 143
Period size: 29 Copynumber: 5.5 Consensus size: 29
13569183 ACTCTTATCT
* *
13569193 TTAATTTAGACAAAAATATTTTATCATGTC
1 TTAATTAAGACAAAAATATTTT-TCTTGTC
*
13569223 TTAATTGAGAC--AAATATGTTTTCTTGTC
1 TTAATTAAGACAAAAATAT-TTTTCTTGTC
13569251 -TAGATTAAGACAAAAAATATTTTTCTTGTC
1 TTA-ATTAAGAC-AAAAATATTTTTCTTGTC
*
13569281 TTAAATTAAGA-AAAACATA-TTTTCTTGTA
1 TT-AATTAAGACAAAA-ATATTTTTCTTGTC
* * *
13569310 TAAATTAAGACCAAACAT-GTTTTCTTGTC
1 TTAATTAAGA-CAAAAATATTTTTCTTGTC
*
13569339 TAAATTAAGACAAA
1 TTAATTAAGACAAA
13569353 CATGTTAAAG
Statistics
Matches: 112, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
27 2 0.02
28 31 0.28
29 38 0.34
30 26 0.23
31 14 0.12
32 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (29 bp):
TTAATTAAGACAAAAATATTTTTCTTGTC
Found at i:13569305 original size:59 final size:58
Alignment explanation
Indices: 13569195--13569355 Score: 184
Period size: 59 Copynumber: 2.8 Consensus size: 58
13569185 TCTTATCTTT
* * * * * *
13569195 AATTTAGACAAAAATATTTTATCATGTCTT-AATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTT-TCTTGTCTTAAATTAAGACAAACATATTTTCTTGTATA
* *
13569253 GATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGAAAAACATATTTTCTTGTATA
1 AATTAAGAC-AAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTATA
* *
13569312 AATTAAGACCAAACAT-GTTTTCTTGTC-TAAATTAAGACAAACAT
1 AATTAAGA-CAAAAATATTTTTCTTGTCTTAAATTAAGACAAACAT
13569356 GTTAAAGTTG
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 16 0.18
58 25 0.28
59 46 0.52
60 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.39
Consensus pattern (58 bp):
AATTAAGACAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTATA
Found at i:13569349 original size:29 final size:28
Alignment explanation
Indices: 13569219--13569358 Score: 163
Period size: 29 Copynumber: 4.9 Consensus size: 28
13569209 TATTTTATCA
* * *
13569219 TGTCTTAATTGAGACAAATATGTTTTCT
1 TGTCTAAATTAAGACAAACATGTTTTCT
* * *
13569247 TGTCTAGATTAAGACAAAAAATATTTTTCT
1 TGTCTAAATTAAGAC-AAACAT-GTTTTCT
* *
13569277 TGTCTTAAATTAAGAAAAACATATTTTCT
1 TGTC-TAAATTAAGACAAACATGTTTTCT
*
13569306 TGTATAAATTAAGACCAAACATGTTTTCT
1 TGTCTAAATTAAGA-CAAACATGTTTTCT
13569335 TGTCTAAATTAAGACAAACATGTT
1 TGTCTAAATTAAGACAAACATGTT
13569359 AAAGTTGTCA
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
28 32 0.34
29 39 0.41
30 15 0.16
31 9 0.09
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (28 bp):
TGTCTAAATTAAGACAAACATGTTTTCT
Found at i:13571877 original size:36 final size:36
Alignment explanation
Indices: 13571810--13571880 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
13571800 ATACGCAAGC
* *
13571810 AAGTCAAATACGACAACGAATCTTCCCTGCAGCGAA
1 AAGTCAAATACGAAAACGAATCTTCACTGCAGCGAA
* * * *
13571846 AAGTCAAATACGAAAATGAATTTTTATTGCAGCGA
1 AAGTCAAATACGAAAACGAATCTTCACTGCAGCGA
13571881 CGTTGGAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (36 bp):
AAGTCAAATACGAAAACGAATCTTCACTGCAGCGAA
Found at i:13573460 original size:19 final size:21
Alignment explanation
Indices: 13573418--13573463 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
13573408 AGAGAAGAAG
13573418 AAGATAGTTGCTAGAAATTTC
1 AAGATAGTTGCTAGAAATTTC
*
13573439 AAGA-AGTTGCTGGAAA-TTC
1 AAGATAGTTGCTAGAAATTTC
13573458 AAGATA
1 AAGATA
13573464 TTTATAGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (21 bp):
AAGATAGTTGCTAGAAATTTC
Found at i:13578188 original size:37 final size:38
Alignment explanation
Indices: 13578131--13578242 Score: 174
Period size: 37 Copynumber: 3.0 Consensus size: 38
13578121 TGATAATGTT
* *
13578131 GAAGTGTGAGAGTAGAGAGTGCACACATGATGATGATA
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
*
13578169 G-AGTGTGCGAGTAGGGAGTGCACACATGATGATG-TT
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
*
13578205 GAAGTGTTCGAGTAGGGAGTGCACACATGATGATGATA
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
13578243 TTGCATTGAG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 2 0.03
37 63 0.94
38 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.23
Consensus pattern (38 bp):
GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
Found at i:13578704 original size:44 final size:44
Alignment explanation
Indices: 13578641--13578728 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
13578631 TCTTAGCTTT
13578641 CTAATGGTCTAAAATCAAGGTCAATTGGACTTCTCTAGTGGGAG
1 CTAATGGTCTAAAATCAAGGTCAATTGGACTTCTCTAGTGGGAG
*
13578685 CTAATGGTCTAAAATCAAGGTTAATTGGACTTCTCTAGTGGGAG
1 CTAATGGTCTAAAATCAAGGTCAATTGGACTTCTCTAGTGGGAG
13578729 ATATACTAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (44 bp):
CTAATGGTCTAAAATCAAGGTCAATTGGACTTCTCTAGTGGGAG
Found at i:13586189 original size:19 final size:19
Alignment explanation
Indices: 13586133--13586194 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
13586123 CGGCTCATGT
13586133 ACATCCCCCCACATCGTGC
1 ACATCCCCCCACATCGTGC
* *
13586152 ACATAGCCGGCCC-CATCGTGT
1 ACAT--CC-CCCCACATCGTGC
*
13586173 GCATCCCCCCACATCGTGC
1 ACATCCCCCCACATCGTGC
13586192 ACA
1 ACA
13586195 ATCAGTGCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 3 0.09
19 15 0.45
21 12 0.36
22 3 0.09
ACGTcount: A:0.21, C:0.47, G:0.16, T:0.16
Consensus pattern (19 bp):
ACATCCCCCCACATCGTGC
Found at i:13587584 original size:26 final size:26
Alignment explanation
Indices: 13587524--13587585 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
13587514 ACCATATACC
*
13587524 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
13587550 CATCATCATCATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
13587576 CATCATCATC
1 CATCATCATC
13587586 TCATATGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.32, C:0.42, G:0.03, T:0.23
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:13587786 original size:42 final size:42
Alignment explanation
Indices: 13587605--13587788 Score: 269
Period size: 42 Copynumber: 4.4 Consensus size: 42
13587595 ACGGCTTATG
* * * *
13587605 CGCATATAGCAGGGTCAGCAACGGCTTATGTGCACTCCCACT
1 CGCACATAGCCGGGTCAGCAACGACTTATGTGCACTCCTACT
* *
13587647 CACACATAGTCGGGTCAGCAACGACTTATGTGCACTCCTACT
1 CGCACATAGCCGGGTCAGCAACGACTTATGTGCACTCCTACT
* * * *
13587689 GGCACATAGTCGGGTCAGCAACGGCTTATGTGCACTCTTACT
1 CGCACATAGCCGGGTCAGCAACGACTTATGTGCACTCCTACT
13587731 CGCACATAGCCGGGTCAGCAACGACTTATGTGCACTCCTACT
1 CGCACATAGCCGGGTCAGCAACGACTTATGTGCACTCCTACT
*
13587773 CGCACATAACCGGGTC
1 CGCACATAGCCGGGTC
13587789 CAAATCAACA
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 127 1.00
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (42 bp):
CGCACATAGCCGGGTCAGCAACGACTTATGTGCACTCCTACT
Found at i:13597394 original size:37 final size:38
Alignment explanation
Indices: 13597342--13597453 Score: 174
Period size: 37 Copynumber: 3.0 Consensus size: 38
13597332 TGATAATGTT
* *
13597342 GAAGTGTGCGAGTAGGGAGTGCATATATGATGATGATA
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
* *
13597380 G-AGTGTGCGAGTAGGGAGTGCACACATAATGATG-TT
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
13597416 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
13597454 TTGCATTGAG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
36 2 0.03
37 62 0.94
38 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.37, T:0.24
Consensus pattern (38 bp):
GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
Found at i:13597620 original size:24 final size:23
Alignment explanation
Indices: 13597588--13597632 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
13597578 AATTGCTCCC
*
13597588 AAATTGCTTTTCATTTCAACAAAA
1 AAATGGCTTTTCATTT-AACAAAA
*
13597612 AAATGGCTTTTGATTTAACAA
1 AAATGGCTTTTCATTTAACAA
13597633 GACCCATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATGGCTTTTCATTTAACAAAA
Found at i:13603367 original size:35 final size:35
Alignment explanation
Indices: 13603327--13603395 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
13603317 CAAAATTTTA
*
13603327 ATACAAGAAAAACTC-TTTCTTTTTAAAAAAAATTG
1 ATACAAGAAAAACTCATTT-TTCTTAAAAAAAATTG
13603362 ATACAAGAAAAACTCATTTTTCTTAAAAAAAATT
1 ATACAAGAAAAACTCATTTTTCTTAAAAAAAATT
13603396 AAAGAGAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 29 0.91
36 3 0.09
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (35 bp):
ATACAAGAAAAACTCATTTTTCTTAAAAAAAATTG
Found at i:13604262 original size:21 final size:21
Alignment explanation
Indices: 13604236--13604277 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13604226 GGCAGCAAGT
*
13604236 TTCTCACTGCAGGGAAATTCA
1 TTCTCACTGCAGCGAAATTCA
*
13604257 TTCTCACTGCAGCGAGATTCA
1 TTCTCACTGCAGCGAAATTCA
13604278 GACGACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (21 bp):
TTCTCACTGCAGCGAAATTCA
Found at i:13604891 original size:49 final size:49
Alignment explanation
Indices: 13604819--13604938 Score: 170
Period size: 49 Copynumber: 2.4 Consensus size: 49
13604809 CATTCATTGT
* * * *
13604819 CATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCGTACTTTCA
1 CATAGCCGGGTCATAATCATCATCGGCTTATACGCACTCCCTACTTGCA
* *
13604868 CATAGCTGGGTCATAATCATCATCGGTTTATACGCACTCCCTACTTGCA
1 CATAGCCGGGTCATAATCATCATCGGCTTATACGCACTCCCTACTTGCA
13604917 CATAGCCGGGTCA-ATATCATCA
1 CATAGCCGGGTCATA-ATCATCA
13604939 CATAACATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
48 1 0.02
49 62 0.98
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (49 bp):
CATAGCCGGGTCATAATCATCATCGGCTTATACGCACTCCCTACTTGCA
Found at i:13604978 original size:2 final size:2
Alignment explanation
Indices: 13604973--13604999 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13604963 ACATATATTC
13604973 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13605000 CATACCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.