Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:378824 original size:29 final size:29
Alignment explanation
Indices: 378734--378821 Score: 133
Period size: 29 Copynumber: 3.1 Consensus size: 29
378724 AATCTTTCTA
* *
378734 TTATAGAGACTGGTTTAAATTAATCTCTT
1 TTATAGACATTGGTTTAAATTAATCTCTT
*
378763 TTATAGACATTGGTTTAAATTAATCTCAT
1 TTATAGACATTGGTTTAAATTAATCTCTT
*
378792 TTATAGATATTGGTTTAAATTAATC-CTT
1 TTATAGACATTGGTTTAAATTAATCTCTT
378820 TT
1 TT
378822 TATTATTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 4 0.07
29 50 0.93
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (29 bp):
TTATAGACATTGGTTTAAATTAATCTCTT
Found at i:396264 original size:71 final size:71
Alignment explanation
Indices: 396178--396550 Score: 268
Period size: 71 Copynumber: 5.2 Consensus size: 71
396168 AGATCAAATT
* * * *
396178 TTGTTTCGAGCGAGACGAGAATTTTCAAGAGAAAATATCTCAAGTAAGATTAGATTTTGTTTAGA
1 TTGTCTCGAGTGAGACGAGAATTTTCAAGAGAAAATATCTCAAGTGAGATTAAATTTTGTTTAGA
396243 GAGAAA
66 GAGAAA
* * *
396249 TTGTCTCGAGTGAGACCAGAA-TTT---G-GAAAGTATCTCAAGTGAGATTAAATTTTGTTTTGA
1 TTGTCTCGAGTGAGACGAGAATTTTCAAGAGAAAATATCTCAAGTGAGATTAAATTTTGTTTAGA
396309 GAGAAAA
66 GAG-AAA
* * * ** *
396316 TTGTCTTGAGTGAGACGAAAAATTGATTTTGAAGA-AACCTATCTCAAGTGAGATAAAATTTTTG
1 TTGTCTCGAGTGAGACG--AGA---ATTTTCAAGAGAAAATATCTCAAGTGAGATTAAA-TTTTG
*
396380 TTTAAAGAGAAA
60 TTTAGAGAGAAA
* * * * * *
396392 CTATCTTGAGTGAGACAAGAATTTTCAA-AGGAAAAATATCTCAAGTGAGATTAAATTTCGTTTC
1 TTGTCTCGAGTGAGACGAGAATTTTCAAGA-G-AAAATATCTCAAGTGAGATTAAATTTTGTTTA
*
396456 GAGAG-GA
64 GAGAGAAA
* * * * * *
396463 TTGTCTCAAGTGAGAGGA-AATTGTTCTTTAAG-GAAAGCTATCTCGAGTGTGA-TAAAATTTGT
1 TTGTCTCGAGTGAGACGAGAATT-TTC---AAGAGAAA-ATATCTCAAGTGAGATTAAATTTTGT
396525 TTAGAG-GAAA
61 TTAGAGAGAAA
*
396535 TGGTCTC-ATGTGAGAC
1 TTGTCTCGA-GTGAGAC
396551 AAAATTTATG
Statistics
Matches: 237, Mismatches: 42, Indels: 45
0.73 0.13 0.14
Matches are distributed among these distances:
66 34 0.14
67 19 0.08
69 2 0.01
70 8 0.03
71 43 0.18
72 41 0.17
73 36 0.15
74 4 0.02
76 38 0.16
77 12 0.05
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (71 bp):
TTGTCTCGAGTGAGACGAGAATTTTCAAGAGAAAATATCTCAAGTGAGATTAAATTTTGTTTAGA
GAGAAA
Found at i:396307 original size:127 final size:125
Alignment explanation
Indices: 396069--396305 Score: 347
Period size: 127 Copynumber: 1.9 Consensus size: 125
396059 CGAGTGAGAT
* * *
396069 GAATTTCCAAGGGAAAATATCTCAAGTGAGATTAGATTGTGTTTCGAGAGAAATTGTCTCATGTG
1 GAATTTCCAAGAGAAAATATCTCAAGTAAGATTAGATTGTGTTTAGAGAGAAATTGTCTCATGTG
396134 AGACAAAAATTTTCATGGGAAAGTATCTCAAGTGAGATCAAATTTTGTTTCGAGCGAGACGA
66 AGACAAAAA-TTT-ATGGGAAAGTATCTCAAGTGAGATCAAATTTTGTTTCGAGCGAGACGA
* *
396196 GAATTTTCAAGAGAAAATATCTCAAGTAAGATTAGATTTTGTTTAGAGAGAAATTGTCTCGA-GT
1 GAATTTCCAAGAGAAAATATCTCAAGTAAGATTAGATTGTGTTTAGAGAGAAATTGTCTC-ATGT
* * *
396260 GAGACCAGAA-TT-T-GGAAAGTATCTCAAGTGAGATTAAATTTTGTTT
65 GAGACAAAAATTTATGGGAAAGTATCTCAAGTGAGATCAAATTTTGTTT
396306 TGAGAGAAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
122 32 0.32
123 1 0.01
125 2 0.02
127 65 0.64
128 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.32
Consensus pattern (125 bp):
GAATTTCCAAGAGAAAATATCTCAAGTAAGATTAGATTGTGTTTAGAGAGAAATTGTCTCATGTG
AGACAAAAATTTATGGGAAAGTATCTCAAGTGAGATCAAATTTTGTTTCGAGCGAGACGA
Found at i:396809 original size:51 final size:52
Alignment explanation
Indices: 396738--396861 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 52
396728 TTTTCTTATG
* *
396738 TAACCT-ATAGAAAGGAAAAATAGTGATC-TTAAG-AA-AGAAAAATTTGA-AA
1 TAACCTCAT-GAAAGGAAAAA-AATAATCTTTAAGAAATAGAAAAATTTGAGAA
* *
396787 GTAAGCTCATGAGA-GAAAAAAATAATCTTTAAGAAATAGAAAAATTTGAGAA
1 -TAACCTCATGAAAGGAAAAAAATAATCTTTAAGAAATAGAAAAATTTGAGAA
*
396839 TATCCTCATGAAAGGAAAAAAAT
1 TAACCTCATGAAAGGAAAAAAAT
396862 GAATGATGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
48 5 0.08
49 11 0.18
50 10 0.16
51 24 0.39
52 11 0.18
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (52 bp):
TAACCTCATGAAAGGAAAAAAATAATCTTTAAGAAATAGAAAAATTTGAGAA
Found at i:401215 original size:21 final size:22
Alignment explanation
Indices: 401182--401225 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
401172 AAAAATATAT
* *
401182 AAATAACTCAAAT-GAAATAAA
1 AAATAACTAAAATAGAAACAAA
*
401203 AAATAATTAAAATAGAAACAAA
1 AAATAACTAAAATAGAAACAAA
401225 A
1 A
401226 TTGCTGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (22 bp):
AAATAACTAAAATAGAAACAAA
Found at i:403714 original size:13 final size:13
Alignment explanation
Indices: 403698--403722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
403688 GAAAATTATG
403698 AAAGAAAATAAAC
1 AAAGAAAATAAAC
403711 AAAGAAAATAAA
1 AAAGAAAATAAA
403723 GAGAATGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAGAAAATAAAC
Found at i:409838 original size:22 final size:21
Alignment explanation
Indices: 409796--409879 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 21
409786 TAAATTATAA
409796 ATAAAATAAATATTTTAATATT
1 ATAAAATAAATATTTT-ATATT
*
409818 ATAAGAATAAACATTTTATATT
1 ATAA-AATAAATATTTTATATT
*
409840 ATAAAAATAAATATTTTAGATT
1 AT-AAAATAAATATTTTATATT
*
409862 ATATACATAAAATATTTT
1 ATA-AAAT-AAATATTTT
409880 TATACTAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.02
22 31 0.57
23 22 0.41
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAAAATAAATATTTTATATT
Found at i:410172 original size:18 final size:19
Alignment explanation
Indices: 410131--410172 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
410121 TTTAGATCAT
410131 TAATTAATAAAATTTAGAA
1 TAATTAATAAAATTTAGAA
410150 T-ATTAAT-AAATATTA-AA
1 TAATTAATAAAAT-TTAGAA
410167 TAATTA
1 TAATTA
410173 TTAAGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.33
18 13 0.62
19 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAATTAATAAAATTTAGAA
Found at i:411349 original size:26 final size:26
Alignment explanation
Indices: 411313--411367 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
411303 ATTTAAGATT
*
411313 AATTTATGTTCAATTGAATGGATATG
1 AATTTATGTTCAATTGAATAGATATG
411339 AATTTATGTTCAATTGAATAGATATG
1 AATTTATGTTCAATTGAATAGATATG
411365 AAT
1 AAT
411368 GTAAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (26 bp):
AATTTATGTTCAATTGAATAGATATG
Found at i:411588 original size:31 final size:31
Alignment explanation
Indices: 411542--411609 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
411532 TTATAATACA
* *
411542 GTCCCTCAACATTTAGTCTGTTTACAATATG
1 GTCCCCCAACATTTAGTCCGTTTACAATATG
* *
411573 GTCCCCCAACTTTTAGTCCGTTTGCAATATG
1 GTCCCCCAACATTTAGTCCGTTTACAATATG
411604 GTCCCC
1 GTCCCC
411610 GACGTAACCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCGTTTACAATATG
Found at i:422115 original size:25 final size:25
Alignment explanation
Indices: 422085--422155 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
422075 GACAGAACTT
*
422085 TTAAAAAGTGATTTTTAAAAGTTTTG
1 TTAAAAAGTGA-TTTTAAAAGTGTTG
* *
422111 -TAAAAAATAACTTTTAAAAGTGTTG
1 TTAAAAAGTGA-TTTTAAAAGTGTTG
*
422136 TTTAAAAGTGCATTTTAAAA
1 TTAAAAAGTG-ATTTTAAAA
422156 TTTAACTCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
25 21 0.58
26 14 0.39
27 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (25 bp):
TTAAAAAGTGATTTTAAAAGTGTTG
Found at i:422371 original size:16 final size:16
Alignment explanation
Indices: 422346--422385 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
422336 ACTCATTAAT
*
422346 AATATTTTTTATAAATA
1 AATATATTTTATAAA-A
422363 AA-ATATTTTATAAAA
1 AATATATTTTATAAAA
422378 AATATATT
1 AATATATT
422386 ATCTACATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.76
17 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATTTTATAAAA
Found at i:423414 original size:17 final size:17
Alignment explanation
Indices: 423392--423429 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
423382 ATTCATTAAT
423392 AATATTTTTATATA-AGA
1 AATATTTTTAT-TAGAGA
423409 AATA-TTTTATTAGAGA
1 AATATTTTTATTAGAGA
423425 AATAT
1 AATAT
423430 ACTATCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.11
16 13 0.68
17 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
AATATTTTTATTAGAGA
Found at i:424415 original size:29 final size:29
Alignment explanation
Indices: 424374--424437 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
424364 CCAACAAATT
* * *
424374 TAAAA-AAGAAATAAAAACAGTAAT-TAAA
1 TAAAATAAAAAATAAAAA-AATAATGAAAA
424402 TAAAATAAAAAATAAAAAAATAATGAAAA
1 TAAAATAAAAAATAAAAAAATAATGAAAA
424431 TAAAATA
1 TAAAATA
424438 TAAGTACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (29 bp):
TAAAATAAAAAATAAAAAAATAATGAAAA
Found at i:424485 original size:2 final size:2
Alignment explanation
Indices: 424478--424520 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
424468 AATAAGATAA
424478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
424520 A
1 A
424521 AAAGATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:426739 original size:106 final size:106
Alignment explanation
Indices: 426554--427122 Score: 951
Period size: 106 Copynumber: 5.4 Consensus size: 106
426544 TTTATGTTCC
* * * * *
426554 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATCGGCTCTGGAA-CTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAGTTGGGAAATTATTTGTTGACA
426618 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
65 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
* * *
426660 GAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTATGAAGTTGGGAAATTATTCGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
* * *
426725 TCAGCTGCCCCTTCGCCATGAAGTTGAACTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
* *
426766 GAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAGTTGAGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
426831 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
* *
426872 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTCGCTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
426937 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
* *
426978 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGAGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
427043 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
* *
427084 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
427123 AGATAAAACC
Statistics
Matches: 432, Mismatches: 30, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
105 3 0.01
106 429 0.99
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:438685 original size:20 final size:18
Alignment explanation
Indices: 438662--438705 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
438652 AAATATGCAT
438662 ATAAATTAATGTAAGATAAA
1 ATAAATTAAT-T-AGATAAA
438682 ATAAATTAATTAGATAAA
1 ATAAATTAATTAGATAAA
438700 ACTAAA
1 A-TAAA
438706 AAAAGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 10 0.43
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (18 bp):
ATAAATTAATTAGATAAA
Found at i:441012 original size:22 final size:22
Alignment explanation
Indices: 440982--441025 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
440972 CAGTTACAGA
440982 GTAAATGCAAGAGTTACAAATG
1 GTAAATGCAAGAGTTACAAATG
* *
441004 GTAATTGCATGAGTTACAAATG
1 GTAAATGCAAGAGTTACAAATG
441026 ACTAGACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (22 bp):
GTAAATGCAAGAGTTACAAATG
Found at i:452654 original size:14 final size:14
Alignment explanation
Indices: 452635--452664 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
452625 AACGAACGTT
452635 AACGAACACAAACG
1 AACGAACACAAACG
*
452649 AACGAACATAAACG
1 AACGAACACAAACG
452663 AA
1 AA
452665 TACAATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.23, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:452979 original size:24 final size:24
Alignment explanation
Indices: 452949--453014 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
452939 GTCCGCTGTT
*
452949 CGAACATAAATGAACGAACATATA
1 CGAACATAAATGAACGAACATAAA
* * *
452973 TGAACATAAATGATCAAACATAAA
1 CGAACATAAATGAACGAACATAAA
452997 CGAACATATAATCGAACG
1 CGAACATA-AAT-GAACG
453015 TTCACGAAGG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
24 27 0.82
25 3 0.09
26 3 0.09
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.18
Consensus pattern (24 bp):
CGAACATAAATGAACGAACATAAA
Found at i:453512 original size:2 final size:2
Alignment explanation
Indices: 453505--453537 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
453495 TAATAGTGTT
453505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
453538 TCTAAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:456281 original size:14 final size:13
Alignment explanation
Indices: 456257--456290 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
456247 CATAGTTGAA
456257 CAGTCTTCATATG
1 CAGTCTTCATATG
456270 CAGTCATTCATATG
1 CAGTC-TTCATATG
456284 CACGTCT
1 CA-GTCT
456291 GTAATGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 11 0.58
15 3 0.16
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:460199 original size:141 final size:141
Alignment explanation
Indices: 459945--460226 Score: 492
Period size: 141 Copynumber: 2.0 Consensus size: 141
459935 ATCTGAAAGA
*
459945 GAAAAAGTTTTGGGAGTAAGCTAGGAAGCTCAGTGTGTTCCAATAAGTGTCATATAAAACATGTT
1 GAAAAAGTTTTGAGAGTAAGCTAGGAAGCTCAGTGTGTTCCAATAAGTGTCATATAAAACATGTT
*
460010 GATACATTTCAAATCAGATTTCAGAAATCATAGAGTAAAGATGGAAGTAAAGTTTTTATTTATAA
66 GATACATTTCAAATCAGATTTCAGAAATCATAGAGTAAAGATGGAAGTAAAGTTTTTAATTATAA
*
460075 CATATAACTAC
131 CAGATAACTAC
* * * *
460086 GAAAAAGTTTTTAGAGTGAGTTAGGAAGCTCAGTGTGTTCCAATAAGTGTTATATAAAACATGTT
1 GAAAAAGTTTTGAGAGTAAGCTAGGAAGCTCAGTGTGTTCCAATAAGTGTCATATAAAACATGTT
*
460151 GATACATTTCAAATCAGGTTTCAGAAATCATAGAGTAAAGATGGAAGTAAAGTTTTTAATTATAA
66 GATACATTTCAAATCAGATTTCAGAAATCATAGAGTAAAGATGGAAGTAAAGTTTTTAATTATAA
460216 CAGATAACTAC
131 CAGATAACTAC
460227 CCTCCACACT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 133 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (141 bp):
GAAAAAGTTTTGAGAGTAAGCTAGGAAGCTCAGTGTGTTCCAATAAGTGTCATATAAAACATGTT
GATACATTTCAAATCAGATTTCAGAAATCATAGAGTAAAGATGGAAGTAAAGTTTTTAATTATAA
CAGATAACTAC
Found at i:460950 original size:16 final size:16
Alignment explanation
Indices: 460929--460959 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
460919 TTAACTTTTC
*
460929 GGTCAAAGTCAAAGTG
1 GGTCAAAGCCAAAGTG
460945 GGTCAAAGCCAAAGT
1 GGTCAAAGCCAAAGT
460960 CAAATCTGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16
Consensus pattern (16 bp):
GGTCAAAGCCAAAGTG
Found at i:461028 original size:20 final size:20
Alignment explanation
Indices: 461000--461037 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
460990 AATTGGTCAA
*
461000 ACTGGTTCGAGTTGACTCAG
1 ACTGATTCGAGTTGACTCAG
*
461020 ACTGATTCGGGTTGACTC
1 ACTGATTCGAGTTGACTC
461038 GAGCGACTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (20 bp):
ACTGATTCGAGTTGACTCAG
Found at i:468569 original size:20 final size:20
Alignment explanation
Indices: 468546--468614 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
468536 ACTGGTTTGG
*
468546 GTTGACTCAGACCAATTCGA
1 GTTGACTCAGACCGATTCGA
468566 GTTGACTCAGACCGATTCGA
1 GTTGACTCAGACCGATTCGA
468586 GTTGACTCAGACCGATTCGA
1 GTTGACTCAGACCGATTCGA
468606 GTTGACTCA
1 GTTGACTCA
468615 ACTGACTTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (20 bp):
GTTGACTCAGACCGATTCGA
Found at i:468577 original size:40 final size:40
Alignment explanation
Indices: 468532--468619 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
468522 AGTCAACGGG
* * *
468532 TCAGACTGGTTTGGGTTGACTCAGACCAATTCGAGTTGAC
1 TCAGACTGATTCGAGTTGACTCAGACCAATTCGAGTTGAC
* *
468572 TCAGACCGATTCGAGTTGACTCAGACCGATTCGAGTTGAC
1 TCAGACTGATTCGAGTTGACTCAGACCAATTCGAGTTGAC
468612 TCA-ACTGA
1 TCAGACTGA
468620 CTTGGTCAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 4 0.10
40 38 0.90
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (40 bp):
TCAGACTGATTCGAGTTGACTCAGACCAATTCGAGTTGAC
Found at i:476300 original size:19 final size:19
Alignment explanation
Indices: 476276--476323 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
476266 GAAATTATAA
476276 AAATTAGAATTATAA-AAAT
1 AAATTAGAATTA-AAGAAAT
*
476295 AAATTAAAATTAAAGAAAT
1 AAATTAGAATTAAAGAAAT
*
476314 AATTTAGAAT
1 AAATTAGAAT
476324 ATTGTACGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
AAATTAGAATTAAAGAAAT
Found at i:477867 original size:15 final size:17
Alignment explanation
Indices: 477840--477885 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
477830 ATGTTAATAA
477840 AATAATAATAAATTTAAT
1 AATAA-AATAAATTTAAT
*
477858 -ATAAAA-AAATTTATT
1 AATAAAATAAATTTAAT
477873 AATAAAATAAATT
1 AATAAAATAAATT
477886 AGAGTGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 8 0.32
16 8 0.32
17 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAAAATAAATTTAAT
Found at i:484775 original size:28 final size:29
Alignment explanation
Indices: 484736--484800 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
484726 TTATAATATT
484736 TATTTATAATAAA-ATTTAAATTATT-TCA
1 TATTTATAATAAAGATTTAAATT-TTATCA
* *
484764 TATTTATTATAAAGATTTATATTTTATCA
1 TATTTATAATAAAGATTTAAATTTTATCA
*
484793 TATATATA
1 TATTTATA
484801 GTTTAAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (29 bp):
TATTTATAATAAAGATTTAAATTTTATCA
Found at i:485762 original size:35 final size:35
Alignment explanation
Indices: 485716--485785 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
485706 TTTTCCAAAA
* *
485716 GCCTAAGACCAAGGGAACACATTTCTAGCTATCAT
1 GCCTAAGACCAAGAGAACACATTTCTAACTATCAT
485751 GCCTAAGACCAAGAGAACACATTTCTAACTATCAT
1 GCCTAAGACCAAGAGAACACATTTCTAACTATCAT
485786 ATGCCATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (35 bp):
GCCTAAGACCAAGAGAACACATTTCTAACTATCAT
Found at i:497046 original size:197 final size:193
Alignment explanation
Indices: 496580--497083 Score: 550
Period size: 197 Copynumber: 2.6 Consensus size: 193
496570 TTTTGTGACA
* * * * * *
496580 AAATAAATTTTACATAATTTCTTGTTTTGAGTAAATTTAATATGTTATTGTGACTAAAT-ATTTT
1 AAATAAATTTAAAATAATTTCTTATTTTGACTAAATTTAATATGTTATTGTGATTAAATAAATTT
* * *
496644 TTTACAATTTATTATTATGAAAGATTATCATTTGTCATAA--TTTTATATTGAGAATTAATATTT
66 TTCACAATTTATTATTATGAAA-ATTAT-TTTTTTCATAATTTTTTATATTGAGAATTAATATTT
* ** ** * * *
496707 GTTATAAATAATTATTATGACTAAGTAATTTATCAAGATTTGTAATCTTGAGAAAATATTGTGAT
129 GTTATAAATAATTATTATGACTAAATAAACTATCAAGATGAGT-ATCTTGAGAAAATATTATAAC
496772 T
193 T
* * * * *
496773 AAATAAATTTGACATAATTTCTTATTTTGACTAAATTTCATATGTTTTTGTGGTTAAATAAATTT
1 AAATAAATTTAAAATAATTTCTTATTTTGACTAAATTTAATATGTTATTGTGATTAAATAAATTT
* * * *
496838 TTCATAATTTATTATTGTGAAAAATATTTTTTTTATAAATTTTTTATATTGAGAAATTAATATTT
66 TTCACAATTTATTATTATGAAAATTATTTTTTTCAT-AATTTTTTATATTGAG-AATTAATATTT
* * *
496903 GTTATAAATTATTATTATGACTAAATAAAACTGTCATA-ATGAGT-TGTTGAGAAAATATTATAA
129 GTTATAAATAATTATTATGACTAAAT-AAACTATCA-AGATGAGTATCTTGAGAAAATATTATAA
496966 CT
192 CT
* * *
496968 AAATAAATTTAAAATAGTTTTTTTTATTTTGACTAAATTTAATATGTTACTGTGATTAAATAAAT
1 AAATAAATTTAAAATA--ATTTCTTATTTTGACTAAATTTAATATGTTATTGTGATTAAATAAAT
** *
497033 TTACCACAATTTATTAATTTTGCAAAATTATTTTTTTCATAATTTATTTAT
64 TTTTCACAATTTATT-ATTATG-AAAATTATTTTTTTCATAATTT-TTTAT
497084 GTGGTTAAAT
Statistics
Matches: 259, Mismatches: 40, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
192 6 0.02
193 58 0.22
194 23 0.09
195 43 0.17
196 35 0.14
197 63 0.24
198 11 0.04
199 20 0.08
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (193 bp):
AAATAAATTTAAAATAATTTCTTATTTTGACTAAATTTAATATGTTATTGTGATTAAATAAATTT
TTCACAATTTATTATTATGAAAATTATTTTTTTCATAATTTTTTATATTGAGAATTAATATTTGT
TATAAATAATTATTATGACTAAATAAACTATCAAGATGAGTATCTTGAGAAAATATTATAACT
Found at i:500227 original size:179 final size:175
Alignment explanation
Indices: 499915--500234 Score: 430
Period size: 179 Copynumber: 1.8 Consensus size: 175
499905 TAAGTAAAAT
* * * *
499915 TTATAGTTACAAAATTTGCCACTATATAATTTTTTGTGCCAAAAAATGGAGTAAAATATTTATGA
1 TTATAGTTACAAAATATGCCACTATATAATTTTTTGTGCCAAAAAATAGAGGAAAACATTTATGA
* *
499980 CAATATATTTCTCACTATAATTAAAATATATAACTACAAACAAAATTTGTCACCAAAAATTTGAA
66 CAATACATTTCTCACTATAATTAAAATATATAACTACAAACAAAATTTGTCACCAAAAATTAGAA
500045 TCTCATTATTTGTTGTGATAGTTTTTCTGTAACAAAAATTATAAG
131 TCTCATTATTTGTTGTGATAGTTTTTCTGTAACAAAAATTATAAG
* * *
500090 TTATAGTTACAAAATATGTCACTATATAACTTTCGTTTTTGCGCTAAAAACTAGAGGAAAACATT
1 TTATAGTTACAAAATATGCCACTATATAA-TTT--TTTGTGC-C-AAAAAATAGAGGAAAACATT
* * * **
500155 TATGACTATACATTTTTTCACTATAATT-AAA-ATATGACTACAAACAAAAATTT-TCATGAAAA
61 TATGACAATACA-TTTCTCACTATAATTAAAATATATAACTACAAAC-AAAATTTGTCACCAAAA
500217 ATTAGAATCTCATTATTT
124 ATTAGAATCTCATTATTT
500235 CCTGTGACAA
Statistics
Matches: 124, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
175 27 0.22
176 3 0.02
178 6 0.05
179 38 0.31
180 36 0.29
181 14 0.11
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (175 bp):
TTATAGTTACAAAATATGCCACTATATAATTTTTTGTGCCAAAAAATAGAGGAAAACATTTATGA
CAATACATTTCTCACTATAATTAAAATATATAACTACAAACAAAATTTGTCACCAAAAATTAGAA
TCTCATTATTTGTTGTGATAGTTTTTCTGTAACAAAAATTATAAG
Found at i:502043 original size:17 final size:18
Alignment explanation
Indices: 502021--502066 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
502011 AAATATAGTT
502021 TTATTTAATAAATTGA-A
1 TTATTTAATAAATTGATA
*
502038 TTATTTAA-AATTTGATA
1 TTATTTAATAAATTGATA
502055 TTAATTTAATAA
1 TT-ATTTAATAA
502067 TAATTTTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 11 0.44
18 6 0.24
19 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TTATTTAATAAATTGATA
Found at i:503097 original size:3 final size:3
Alignment explanation
Indices: 503083--503112 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
503073 ATCTCTACTT
*
503083 CTC CTT CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
503113 ACTCGCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
CTC
Found at i:505947 original size:22 final size:22
Alignment explanation
Indices: 505922--505966 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
505912 TATTTCTACC
505922 ATCCATGAAACCTTAGTTTCCA
1 ATCCATGAAACCTTAGTTTCCA
505944 ATCCATGAAACCTTAGTTTCCA
1 ATCCATGAAACCTTAGTTTCCA
505966 A
1 A
505967 AGCATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (22 bp):
ATCCATGAAACCTTAGTTTCCA
Found at i:506180 original size:15 final size:15
Alignment explanation
Indices: 506160--506190 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
506150 TTAAACGGTC
506160 GAATGATTTGAACCG
1 GAATGATTTGAACCG
506175 GAATGATTTGAACCG
1 GAATGATTTGAACCG
506190 G
1 G
506191 CCAGACCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (15 bp):
GAATGATTTGAACCG
Found at i:507083 original size:20 final size:20
Alignment explanation
Indices: 507055--507092 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
507045 TCAATTTTTA
* *
507055 AAATTTATTTTTGAAATTAT
1 AAATATATTTTTAAAATTAT
507075 AAATATATTTTTAAAATT
1 AAATATATTTTTAAAATT
507093 TTATTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATATATTTTTAAAATTAT
Found at i:507326 original size:2 final size:2
Alignment explanation
Indices: 507319--507348 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
507309 CTCGTGAATT
507319 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
507349 AATTGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:513972 original size:21 final size:21
Alignment explanation
Indices: 513946--513985 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
513936 GAGAAATTGT
513946 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
513967 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
513986 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:517828 original size:20 final size:21
Alignment explanation
Indices: 517791--517853 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 21
517781 TTTTGGTGGA
* * *
517791 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTTCCCCTAT
*
517811 GAGGGAACCGATTTCCCCTTT
1 GAGGGAACCGATTTCCCCTAT
*
517832 GAAGGGGAACCGATTCCCCCTA
1 G-A-GGGAACCGATTTCCCCTA
517854 GGGGAATCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 10 0.29
21 7 0.21
22 1 0.03
23 16 0.47
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTTCCCCTAT
Found at i:517875 original size:18 final size:19
Alignment explanation
Indices: 517834--517875 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
517824 TCCCCTTTGA
*
517834 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCT
*
517853 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATACCCCCT
517872 -GGGG
1 AGGGG
517876 TTCTGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:530648 original size:16 final size:16
Alignment explanation
Indices: 530627--530658 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
530617 TGTGAACAAG
530627 AATTTATTTGAGTTAT
1 AATTTATTTGAGTTAT
530643 AATTTATTTGAGTTAT
1 AATTTATTTGAGTTAT
530659 GGCTATACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
AATTTATTTGAGTTAT
Found at i:532204 original size:26 final size:26
Alignment explanation
Indices: 532175--532234 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
532165 CATTCAAATT
532175 TATGATTATCACT-ATTTGATTCGGAC
1 TATGATTATCACTGA-TTGATTCGGAC
* * *
532201 TATGATTATTATTGATTGATTCGTAC
1 TATGATTATCACTGATTGATTCGGAC
532227 TATG-TTAT
1 TATGATTAT
532235 GACTTGTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 4 0.13
26 25 0.83
27 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (26 bp):
TATGATTATCACTGATTGATTCGGAC
Found at i:535332 original size:16 final size:18
Alignment explanation
Indices: 535311--535347 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
535301 ATTTCATTGT
535311 TACGTC-CAACA-ATAAG
1 TACGTCACAACATATAAG
535327 TACGTCATCAACATATAAG
1 TACGTCA-CAACATATAAG
535346 TA
1 TA
535348 TAGAATCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (18 bp):
TACGTCACAACATATAAG
Found at i:543004 original size:23 final size:23
Alignment explanation
Indices: 542978--543068 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
542968 GGACATTATA
542978 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
* * *
543001 TGGCACTTCGGTGCAATTCTATG
1 TGGCACTACGGTGCATTTCTACG
*
543024 TGGCACTACAGTGCATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
* *
543047 T-GCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCATTTCTACG
543069 AGCTGTGGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
22 18 0.31
23 40 0.69
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTACG
Found at i:548295 original size:103 final size:102
Alignment explanation
Indices: 548128--548405 Score: 297
Period size: 103 Copynumber: 2.7 Consensus size: 102
548118 TCCTAGTAGG
* * * * * * * *
548128 GTATCGATACCGAGGTATTTTTTAAACCATCAAATATAATTTTAGTATAAGTACTCATAGGAGTA
1 GTATCGATACTGAGGTATTTTTCAAAACATCAAATGTAATTTTGGTATGA-TACTCGTAAGAGTA
* * *
548193 TCGATACTTAGGGTAAGGTATTAATACTCTAAGAAGGA
65 TCGATACTAAGGATAAGGTATCAATACTCTAAGAAGGA
* * * *
548231 GTATTGATATTGAGGTATTTTTCAAAACATCGAATGCAATTTTGGTATTGATACTCGTAAGAGTA
1 GTATCGATACTGAGGTATTTTTCAAAACATCAAATGTAATTTTGGTA-TGATACTCGTAAGAGTA
* * *
548296 TCAATACTAAGGATAGGGTATCAATACTCTCAGAAGGA
65 TCGATACTAAGGATAAGGTATCAATACTCTAAGAAGGA
* * * * * *
548334 GTATCGATACTAACGTATTTTCCAAAGCATCAAATGTAATTTTGGTACTGATACTTG-GAGAAGT
1 GTATCGATACTGAGGTATTTTTCAAAACATCAAATGTAATTTTGGTA-TGATACTCGTAAG-AGT
548398 ATCGATAC
64 ATCGATAC
548406 CATATGATGG
Statistics
Matches: 143, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
102 2 0.01
103 139 0.97
104 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (102 bp):
GTATCGATACTGAGGTATTTTTCAAAACATCAAATGTAATTTTGGTATGATACTCGTAAGAGTAT
CGATACTAAGGATAAGGTATCAATACTCTAAGAAGGA
Found at i:555078 original size:29 final size:29
Alignment explanation
Indices: 555036--555150 Score: 131
Period size: 29 Copynumber: 3.9 Consensus size: 29
555026 TACCGGGGGT
*
555036 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
555065 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
555094 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
** *
555123 AGCAACGCCCATGCACGCCCAACGACCT
1 AG-GTCG-CCATGCACGCCCAGCGACCT
555151 CCATGCACGC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
29 51 0.73
30 2 0.03
31 17 0.24
ACGTcount: A:0.20, C:0.43, G:0.25, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:555123 original size:58 final size:60
Alignment explanation
Indices: 555033--555150 Score: 177
Period size: 58 Copynumber: 2.0 Consensus size: 60
555023 CAGTACCGGG
** *
555033 GGTAGGTCGCCATGCACGCCCGGCGACCTACCAG-GTCG-CCATGCACGCCCAGCGACCT
1 GGTAGGTCGCCATGCACGCCCGGCGACCTACCAGCAACGCCCATGCACGCCCAACGACCT
* *
555091 GGTAGGTCGCCATGCATGCCCTGCGACCTACCAGCAACGCCCATGCACGCCCAACGACCT
1 GGTAGGTCGCCATGCACGCCCGGCGACCTACCAGCAACGCCCATGCACGCCCAACGACCT
555151 CCATGCACGC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
58 32 0.60
59 2 0.04
60 19 0.36
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (60 bp):
GGTAGGTCGCCATGCACGCCCGGCGACCTACCAGCAACGCCCATGCACGCCCAACGACCT
Found at i:555163 original size:30 final size:30
Alignment explanation
Indices: 555100--555253 Score: 211
Period size: 30 Copynumber: 5.1 Consensus size: 30
555090 TGGTAGGTCG
* **
555100 CCATGCATGCCCTGCGACCTACCA-GCAACGC
1 CCATGCACGCCCAACGACCT-CCATGC-ACGC
555131 CCATGCACGCCCAACGACCTCCATGCACGC
1 CCATGCACGCCCAACGACCTCCATGCACGC
* *
555161 CCATGAACGCCCAACGACCTCCATGCATGC
1 CCATGCACGCCCAACGACCTCCATGCACGC
* * *
555191 CCAGGCACGTCCAACGACCTCCATGCACGG
1 CCATGCACGCCCAACGACCTCCATGCACGC
555221 CCATGCACGCCCAACGACCTCCATGCACGC
1 CCATGCACGCCCAACGACCTCCATGCACGC
555251 CCA
1 CCA
555254 GCTCGCCAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
30 90 0.83
31 19 0.17
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.11
Consensus pattern (30 bp):
CCATGCACGCCCAACGACCTCCATGCACGC
Found at i:555926 original size:21 final size:21
Alignment explanation
Indices: 555901--555944 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
555891 AATTTAGTTA
555901 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
555922 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
555943 AT
1 AT
555945 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:555958 original size:28 final size:28
Alignment explanation
Indices: 555921--555974 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
555911 TAGTATAAAT
*
555921 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
555949 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
555975 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:559151 original size:35 final size:34
Alignment explanation
Indices: 559111--559271 Score: 88
Period size: 35 Copynumber: 5.2 Consensus size: 34
559101 TTTGATAGTA
559111 ATGATTAGTAATAATGAAATTATTATTAATTATGT
1 ATGATTAGTAATAATGAAATTATTATTAATTAT-T
* * * *
559146 ATGATT--TGAT-A-GTAATGA-T-TT-AGTA--
1 ATGATTAGTAATAATGAAATTATTATTAATTATT
*
559171 ATGATTAGTAATAATGAAATTATTATTAATTTTT
1 ATGATTAGTAATAATGAAATTATTATTAATTATT
* * * *
559205 AATGATT--TGAT-A-GTAATGA-T-TT-AGTA--
1 -ATGATTAGTAATAATGAAATTATTATTAATTATT
559231 ATGATTAGTAATAATGAAATTATTATTAATTATGT
1 ATGATTAGTAATAATGAAATTATTATTAATTAT-T
559266 ATGATT
1 ATGATT
559272 TGATAGTAAT
Statistics
Matches: 88, Mismatches: 18, Indels: 40
0.60 0.12 0.27
Matches are distributed among these distances:
25 12 0.14
27 6 0.07
28 7 0.08
29 14 0.16
30 4 0.05
31 14 0.16
32 7 0.08
33 6 0.07
35 18 0.20
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (34 bp):
ATGATTAGTAATAATGAAATTATTATTAATTATT
Found at i:559171 original size:11 final size:11
Alignment explanation
Indices: 559155--559242 Score: 54
Period size: 11 Copynumber: 7.6 Consensus size: 11
559145 TATGATTTGA
559155 TAGTAATGATT
1 TAGTAATGATT
559166 TAGTAATGATT
1 TAGTAATGATT
* *
559177 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
559191 TATTATTAATT
1 TAGTAATGATT
*
559202 T-TTAATGATTT
1 TAGTAATGA-TT
559213 GATAGTAATGATT
1 --TAGTAATGATT
559226 TAGTAATGA-T
1 TAGTAATGATT
559236 TAGTAAT
1 TAGTAAT
559243 AATGAAATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
10 13 0.21
11 25 0.41
12 5 0.08
13 10 0.16
14 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:559179 original size:21 final size:20
Alignment explanation
Indices: 559155--559243 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
559145 TATGATTTGA
559155 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
559176 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * * *
559194 TATTAATTTTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
559215 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
559236 TAGTAATA
1 TAGTAATA
559244 ATGAAATTAT
Statistics
Matches: 48, Mismatches: 14, Indels: 13
0.64 0.19 0.17
Matches are distributed among these distances:
18 12 0.25
19 2 0.04
20 5 0.10
21 22 0.46
22 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:559352 original size:25 final size:25
Alignment explanation
Indices: 559324--559428 Score: 84
Period size: 25 Copynumber: 4.0 Consensus size: 25
559314 TATTAATTTT
*
559324 TAATGATTTGATCGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
* * * * *
559349 TAATGATTAGTAATAATTTATTATTAATATT
1 TAATGATT--TGAT-AGTAATGATT--TA-G
* *
559380 TAATGATTTGATATTAATGATTTTG
1 TAATGATTTGATAGTAATGATTTAG
559405 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
559429 CGACTTGAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
25 30 0.49
26 1 0.02
27 3 0.05
28 14 0.23
29 3 0.05
30 2 0.03
31 8 0.13
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.49
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:559396 original size:14 final size:14
Alignment explanation
Indices: 559380--559427 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
559370 TATTAATATT
*
559380 TAATGATTTGATAT
1 TAATGATTTGATAG
559394 TAATGATTT--T-G
1 TAATGATTTGATAG
559405 TAATGATTTGATAG
1 TAATGATTTGATAG
559419 TAATGATTT
1 TAATGATTT
559428 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:559422 original size:60 final size:60
Alignment explanation
Indices: 559042--559412 Score: 560
Period size: 60 Copynumber: 6.2 Consensus size: 60
559032 GTATTTATAA
* *
559042 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTAATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
559102 --TTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATT--TAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATAGTAAT
*
559162 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
559222 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATAGTAAT
* * *
559282 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATCGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
559342 GATTTAGTAATGATTAGTAATAAT----TTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
559398 GATTTTGTAATGATT
1 GATTTAGTAATGATT
559413 TGATAGTAAT
Statistics
Matches: 287, Mismatches: 16, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
56 43 0.15
58 2 0.01
59 6 0.02
60 227 0.79
61 7 0.02
62 2 0.01
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:561769 original size:30 final size:31
Alignment explanation
Indices: 561732--561806 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
561722 TTTCCCTTAA
561732 ACAACTAATAAACTATTCTTTAA-TATAAATT
1 ACAACTAATAAACTATT-TTTAATTATAAATT
*
561763 A-AACTAATAAA-TGATTTTTAATTATAATTT
1 ACAACTAATAAACT-ATTTTTAATTATAAATT
*
561793 ACTACTAA-AAACTA
1 ACAACTAATAAACTA
561807 ATTAACTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 6 0.16
30 25 0.66
31 7 0.18
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (31 bp):
ACAACTAATAAACTATTTTTAATTATAAATT
Found at i:562008 original size:21 final size:21
Alignment explanation
Indices: 561984--562023 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
561974 TTTCTATATG
561984 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
562005 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
562024 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:562104 original size:18 final size:18
Alignment explanation
Indices: 562051--562105 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
562041 TTGTTTTACC
*
562051 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
562069 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
562081 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
562098 CTAATTTA
1 CTAATTTA
562106 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:562164 original size:35 final size:37
Alignment explanation
Indices: 562125--562196 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
562115 TCTTTTATAT
562125 AACTT-AA-ACTAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTA-TATAATAA
562160 AACTTAAACTACTAATAAACTAATTTTTTATATAATA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAATA
562197 TAAATTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
35 5 0.15
36 2 0.06
38 18 0.55
39 8 0.24
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.42
Consensus pattern (37 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAATAA
Found at i:562256 original size:27 final size:29
Alignment explanation
Indices: 562221--562285 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
562211 AAAATATAAC
*
562221 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
562248 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
562276 TTAATTATTT
1 TTAAATATTT
562286 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:562606 original size:12 final size:11
Alignment explanation
Indices: 562575--562610 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
562565 ACGTTCACGG
562575 GCTGCAATAAT
1 GCTGCAATAAT
*
562586 GCAGCAATAAGT
1 GCTGCAATAA-T
562598 GCTGCAATAAT
1 GCTGCAATAAT
562609 GC
1 GC
562611 AGTTGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (11 bp):
GCTGCAATAAT
Found at i:562864 original size:33 final size:33
Alignment explanation
Indices: 562801--562866 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
562791 AAGCATGGAC
*
562801 TGCATGGTGACCTTTGGCGAGCTGGACGTGCAT
1 TGCATGGTGACCTTTGGCGAGATGGACGTGCAT
* *
562834 TGCATGGTGACCTTTGGCGATATGGGCGTGCAT
1 TGCATGGTGACCTTTGGCGAGATGGACGTGCAT
562867 GGGCGTGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.15, C:0.20, G:0.36, T:0.29
Consensus pattern (33 bp):
TGCATGGTGACCTTTGGCGAGATGGACGTGCAT
Found at i:562870 original size:10 final size:10
Alignment explanation
Indices: 562855--562880 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
562845 CTTTGGCGAT
562855 ATGGGCGTGC
1 ATGGGCGTGC
562865 ATGGGCGTGC
1 ATGGGCGTGC
562875 ATGGGC
1 ATGGGC
562881 ATGGAGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.50, T:0.19
Consensus pattern (10 bp):
ATGGGCGTGC
Found at i:562935 original size:29 final size:29
Alignment explanation
Indices: 562900--562986 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
562890 GTTGGCTGGT
*
562900 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
562929 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
562958 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
562987 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:563358 original size:19 final size:19
Alignment explanation
Indices: 563334--563370 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
563324 AAATTTGATA
*
563334 ATGTGACATATGTCATATG
1 ATGTGACATATATCATATG
563353 ATGTGACATATATCATAT
1 ATGTGACATATATCATAT
563371 CATTAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (19 bp):
ATGTGACATATATCATATG
Found at i:571344 original size:31 final size:31
Alignment explanation
Indices: 571309--571382 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
571299 ATTTGAACAC
***
571309 TTTTGGTCACTTATGTTATTGTTTTACTAAG
1 TTTTGGTCACTTATGTTATCAATTTACTAAG
*
571340 TTTTGGTCACTTATGTTATCAATTTATTAAG
1 TTTTGGTCACTTATGTTATCAATTTACTAAG
*
571371 TTTTGATCACTT
1 TTTTGGTCACTT
571383 GAACTTGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.54
Consensus pattern (31 bp):
TTTTGGTCACTTATGTTATCAATTTACTAAG
Found at i:572014 original size:19 final size:20
Alignment explanation
Indices: 571985--572022 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
571975 AACACTCATA
571985 TCTTCTTCTTCTTCATTTTC
1 TCTTCTTCTTCTTCATTTTC
572005 TCTT-TTCTTCTTCATTTT
1 TCTTCTTCTTCTTCATTTT
572023 TTTAGTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (20 bp):
TCTTCTTCTTCTTCATTTTC
Found at i:573077 original size:22 final size:22
Alignment explanation
Indices: 573060--573126 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
573050 CTCGTATAAA
573060 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
573082 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
573104 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
573126 T
1 T
573127 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:573396 original size:30 final size:31
Alignment explanation
Indices: 573346--573404 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
573336 TAGACATAGT
*
573346 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
* *
573376 ATTTACATACTTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
573405 GAACTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:573461 original size:29 final size:28
Alignment explanation
Indices: 573419--573490 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
573409 TTTTCTGCAT
*
573419 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGA-CA
* *
573448 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAAGACA
573476 ACTTCATGTCATGTA
1 A-TTCATGTCATGTA
573491 TCATAATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAAGACA
Found at i:573910 original size:67 final size:67
Alignment explanation
Indices: 573794--573966 Score: 224
Period size: 67 Copynumber: 2.6 Consensus size: 67
573784 TTTTTCTCAT
* * *
573794 GGGGGAATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAATTCATATACGAT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
573858 GA
66 GA
* * * *
573860 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
573925 GA
66 GA
* * *
573927 AGGGGTATCGGTT-CCCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCCTG--GGGGTACCGATTCCCCT
573967 AACCCAGAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
66 27 0.29
67 51 0.54
68 16 0.17
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
GA
Found at i:573954 original size:22 final size:22
Alignment explanation
Indices: 573923--573965 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
573913 ATCATATTCG
* *
573923 TTGAAGGGGTATCGGTTCCCCC
1 TTGAAGGGGTACCGATTCCCCC
*
573945 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
573966 TAACCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (22 bp):
TTGAAGGGGTACCGATTCCCCC
Found at i:579812 original size:22 final size:22
Alignment explanation
Indices: 579795--579861 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
579785 CTCGTATAAA
579795 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
579817 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
579839 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
579861 T
1 T
579862 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:580131 original size:30 final size:31
Alignment explanation
Indices: 580081--580139 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
580071 TAGACATAGT
*
580081 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
* *
580111 ATTTACATACTTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
580140 GAACTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:580200 original size:29 final size:28
Alignment explanation
Indices: 580154--580225 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
580144 TTTTCTGCAT
*
580154 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGA-CA
* * *
580183 ATTCATGTCATGTGATACATTTAATACA
1 ATTCATGTCATGTAATACATATAAGACA
580211 ACTTCATGTCATGTA
1 A-TTCATGTCATGTA
580226 TCATAATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 2 0.05
29 35 0.95
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAAGACA
Found at i:580660 original size:67 final size:66
Alignment explanation
Indices: 580523--580694 Score: 204
Period size: 66 Copynumber: 2.6 Consensus size: 66
580513 TTTTTCTCAT
* * *
580523 GGGGGAATCGGTTCCCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAATTCATATACGA
1 GGGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGA
580587 TGA
64 TGA
* * * *
580590 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
580655 A
66 A
* * *
580656 AGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
580695 AACCCAGAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 13 0.14
66 51 0.55
67 28 0.30
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
A
Found at i:580682 original size:21 final size:21
Alignment explanation
Indices: 580652--580694 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
580642 ATCATATTCG
* *
580652 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
580673 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
580694 T
1 T
580695 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:587486 original size:7 final size:7
Alignment explanation
Indices: 587474--587507 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
587464 GTGAAAAGGT
587474 ATATGTG
1 ATATGTG
587481 ATATGTG
1 ATATGTG
587488 ATATGTG
1 ATATGTG
587495 ATATGTG
1 ATATGTG
587502 ATATGT
1 ATATGT
587508 ATAAGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
ATATGTG
Found at i:587488 original size:21 final size:21
Alignment explanation
Indices: 587468--587507 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
587458 TTTCTCGTGA
587468 AAAGGT-ATATGTGATATGTG
1 AAAGGTGATATGTGATATGTG
* *
587488 ATATGTGATATGTGATATGT
1 AAAGGTGATATGTGATATGT
587508 ATAAGTAATA
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:0.33, C:0.00, G:0.28, T:0.40
Consensus pattern (21 bp):
AAAGGTGATATGTGATATGTG
Found at i:589045 original size:31 final size:31
Alignment explanation
Indices: 589010--589083 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
589000 TTCAATGTTC
**
589010 AAGTGACCAAAACTTAATAAAATGATAA-AGT
1 AAGTGACCAAAACTTAATAAAACAATAACA-T
589041 AAGTGACCAAAACTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
589072 AAGTGACCAAAA
1 AAGTGACCAAAA
589084 GTGTACAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:589294 original size:31 final size:31
Alignment explanation
Indices: 589220--589284 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
589210 TAACCTTCAA
*
589220 TGACCACATCTTAATTAAAATGAAAAGAAAG
1 TGACCAAATCTTAATTAAAATGAAAAGAAAG
589251 TGACCAAATCTTAATTAAAATGAAACA-AAAG
1 TGACCAAATCTTAATTAAAATGAAA-AGAAAG
589282 TGA
1 TGA
589285 TTGAATCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (31 bp):
TGACCAAATCTTAATTAAAATGAAAAGAAAG
Found at i:593815 original size:18 final size:18
Alignment explanation
Indices: 593792--593840 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
593782 GGTAGGGTTG
*
593792 AATTTAATTGATTAGTCA
1 AATTTAATTGATCAGTCA
593810 AATTTAATTGATCAGTCA
1 AATTTAATTGATCAGTCA
593828 AATTTAATTGATC
1 AATTTAATTGATC
593841 TCCTCCTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (18 bp):
AATTTAATTGATCAGTCA
Found at i:594162 original size:144 final size:144
Alignment explanation
Indices: 593828--594163 Score: 367
Period size: 144 Copynumber: 2.3 Consensus size: 144
593818 TGATCAGTCA
* * *
593828 AATTTAATTGATCTCCTCCTGTAA-CTTGGACTTTCGGTGCTGCATTTATTGCCGTGGGGACCAA
1 AATTTAATTGTTCTCCTCCTG-AAGCTTGGACTTTCGGTGCTCCATTTGTTGCCGTGGGGACCAA
* * ** *
593892 TTCATTTTCAATTTGTTTATTCGTTGCATGCACATAGCTATTCAATTGATTATCTTGCTCCATTG
65 TGCATTTTCAATTTGTTTATTCGTTGAATGCACATAGCTATTCAATTGATTATCTCACTCCAATG
* *
593957 TGGAAGGTGGGGGCG
130 TGAAAGGTAGGGGCG
*** ** * *
593972 AA-TTAATTTGTTCAAGTCCTGAAGCTTGGACAATCGGTGCTTCATTTGTTGTCGTGGGGACCAA
1 AATTTAA-TTGTTCTCCTCCTGAAGCTTGGACTTTCGGTGCTCCATTTGTTGCCGTGGGGACCAA
* * * * *
594036 TGC-TTTTCCCATTTGTTTATTCGTTGAATTCACAT-GGTAATTCAAATT-ATTGTGTCACTCCA
65 TGCATTTT-CAATTTGTTTATTCGTTGAATGCACATAGCT-ATTC-AATTGATTATCTCACTCCA
*
594098 ATGTGAAAGGTAGGGTCG
127 ATGTGAAAGGTAGGGGCG
* *
594116 AATTTAATTGTTCTCCTCCTGCAGCTTGGACTTTCGGTGCACCATTTG
1 AATTTAATTGTTCTCCTCCTGAAGCTTGGACTTTCGGTGCTCCATTTG
594164 GATCTTGTAG
Statistics
Matches: 156, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
143 12 0.08
144 136 0.87
145 8 0.05
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (144 bp):
AATTTAATTGTTCTCCTCCTGAAGCTTGGACTTTCGGTGCTCCATTTGTTGCCGTGGGGACCAAT
GCATTTTCAATTTGTTTATTCGTTGAATGCACATAGCTATTCAATTGATTATCTCACTCCAATGT
GAAAGGTAGGGGCG
Found at i:595089 original size:169 final size:169
Alignment explanation
Indices: 594810--595152 Score: 686
Period size: 169 Copynumber: 2.0 Consensus size: 169
594800 TAGAAATAAA
594810 ATTAAGGGCAGCTCCAAGAAATTGCCCAACCAAGGAGAGTTTCCATTCAGCAATACCGGCATCAA
1 ATTAAGGGCAGCTCCAAGAAATTGCCCAACCAAGGAGAGTTTCCATTCAGCAATACCGGCATCAA
594875 ATACCTCTGGAGGAGGTTGAACTGATGGGAACCCTTCACGCGATTTCGGTGGAAAATACTCTAAC
66 ATACCTCTGGAGGAGGTTGAACTGATGGGAACCCTTCACGCGATTTCGGTGGAAAATACTCTAAC
594940 ACCTACCCTGATGAGCACCCGAACAATTTCCTCCACTCC
131 ACCTACCCTGATGAGCACCCGAACAATTTCCTCCACTCC
594979 ATTAAGGGCAGCTCCAAGAAATTGCCCAACCAAGGAGAGTTTCCATTCAGCAATACCGGCATCAA
1 ATTAAGGGCAGCTCCAAGAAATTGCCCAACCAAGGAGAGTTTCCATTCAGCAATACCGGCATCAA
595044 ATACCTCTGGAGGAGGTTGAACTGATGGGAACCCTTCACGCGATTTCGGTGGAAAATACTCTAAC
66 ATACCTCTGGAGGAGGTTGAACTGATGGGAACCCTTCACGCGATTTCGGTGGAAAATACTCTAAC
595109 ACCTACCCTGATGAGCACCCGAACAATTTCCTCCACTCC
131 ACCTACCCTGATGAGCACCCGAACAATTTCCTCCACTCC
595148 ATTAA
1 ATTAA
595153 AAGGAAGAAG
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 174 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (169 bp):
ATTAAGGGCAGCTCCAAGAAATTGCCCAACCAAGGAGAGTTTCCATTCAGCAATACCGGCATCAA
ATACCTCTGGAGGAGGTTGAACTGATGGGAACCCTTCACGCGATTTCGGTGGAAAATACTCTAAC
ACCTACCCTGATGAGCACCCGAACAATTTCCTCCACTCC
Found at i:595835 original size:13 final size:14
Alignment explanation
Indices: 595813--595847 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
595803 GATGACTAAT
*
595813 TTTATTTTAATTTA
1 TTTATTTTAATATA
595827 TTT-TTTTAATATA
1 TTTATTTTAATATA
595840 TTTATTTT
1 TTTATTTT
595848 TCACCAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTAATATA
Found at i:596081 original size:24 final size:25
Alignment explanation
Indices: 596054--596119 Score: 91
Period size: 24 Copynumber: 2.7 Consensus size: 25
596044 TTAAATTCAT
596054 AATATTTTATATATTAACTTA-AAA
1 AATATTTTATATATTAACTTATAAA
*
596078 AATATTTTTTATATTAACTTATTAAA
1 AATATTTTATATATTAACTTA-TAAA
*
596104 TATATTTTAT-TATTAA
1 AATATTTTATATATTAA
596120 TTCAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.54
25 6 0.16
26 11 0.30
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATTTTATATATTAACTTATAAA
Found at i:598119 original size:20 final size:20
Alignment explanation
Indices: 598094--598142 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
598084 TTTAGATAAG
598094 ATTAAATTATATATTTTTAA
1 ATTAAATTATATATTTTTAA
** *
598114 ATTAAAAAATTTATTTTTAA
1 ATTAAATTATATATTTTTAA
598134 ATTAAATTA
1 ATTAAATTA
598143 ATAATAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAAATTATATATTTTTAA
Found at i:608996 original size:27 final size:27
Alignment explanation
Indices: 608964--609017 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
608954 AAAACAAATT
608964 ATTAATTATAATCATT-AGATTAATAAA
1 ATTAATTATAATCATTGA-ATTAATAAA
*
608991 ATTAATTATGATCATTGAATTAATAAA
1 ATTAATTATAATCATTGAATTAATAAA
609018 TTTTTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.41
Consensus pattern (27 bp):
ATTAATTATAATCATTGAATTAATAAA
Found at i:609627 original size:19 final size:20
Alignment explanation
Indices: 609591--609629 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
609581 TAATAATAAC
609591 TTTAAATTATTAATTTTTTA
1 TTTAAATTATTAATTTTTTA
609611 TTTAAATTATT-ATTTTTTA
1 TTTAAATTATTAATTTTTTA
609630 AATAATTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTAAATTATTAATTTTTTA
Found at i:609667 original size:17 final size:18
Alignment explanation
Indices: 609656--609694 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
609646 ATTATTAATT
609656 TTATTAGATTATATAAGA
1 TTATTAGATTATATAAGA
* *
609674 TTATTA-ATTTTATTAGA
1 TTATTAGATTATATAAGA
609691 TTAT
1 TTAT
609695 ATAAAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TTATTAGATTATATAAGA
Found at i:609675 original size:27 final size:27
Alignment explanation
Indices: 609645--609698 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
609635 TTCATTCGTT
609645 GATTATTAATTTTATTAGATTATATAA
1 GATTATTAATTTTATTAGATTATATAA
609672 GATTATTAATTTTATTAGATTATATAA
1 GATTATTAATTTTATTAGATTATATAA
609699 AATGATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (27 bp):
GATTATTAATTTTATTAGATTATATAA
Found at i:610493 original size:23 final size:23
Alignment explanation
Indices: 610456--610555 Score: 89
Period size: 23 Copynumber: 4.3 Consensus size: 23
610446 TATGTAATAA
*
610456 ATGCATACATTATACATACATGC
1 ATGCATACATCATACATACATGC
*
610479 ATGCATGCATCATACATACATGC
1 ATGCATACATCATACATACATGC
610502 ATGTTC-TACAT-AGTACATACAT-C
1 ATG--CATACATCA-TACATACATGC
* * *
610525 ATACATACATAACTACATAACATAC
1 ATGCATACATCA-TACAT-ACATGC
610550 ATGCAT
1 ATGCAT
610556 TCATGCATCA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.02
22 5 0.08
23 34 0.53
24 17 0.27
25 7 0.11
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (23 bp):
ATGCATACATCATACATACATGC
Found at i:610529 original size:11 final size:11
Alignment explanation
Indices: 610459--610551 Score: 59
Period size: 11 Copynumber: 8.3 Consensus size: 11
610449 GTAATAAATG
*
610459 CATACATTATA
1 CATACATCATA
*
610470 CATACATGCATG
1 CATACAT-CATA
*
610482 CATGCATCATA
1 CATACATCATA
*
610493 CATACATGCATGTT
1 CATACAT-CA--TA
610507 C-TACAT-AGTA
1 CATACATCA-TA
610517 CATACATCATA
1 CATACATCATA
*
610528 CATACATAACTA
1 CATACATCA-TA
610540 CATA-A-CATA
1 CATACATCATA
610549 CAT
1 CAT
610552 GCATTCATGC
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
9 5 0.08
10 4 0.06
11 33 0.50
12 17 0.26
13 5 0.08
14 2 0.03
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (11 bp):
CATACATCATA
Found at i:611083 original size:43 final size:43
Alignment explanation
Indices: 611034--611122 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
611024 AATCGTTTTG
* * * *
611034 ACCTGAACTGATATCGATTGGAGCTGAAATTAACCCGTCTCGA
1 ACCTGAACTAATATCGATCGGAGCTGAAATCAACCCGTCTCAA
* *
611077 ACCTGAATTAATATTGATCGGAGCTGAAATCAACCCGTCTCAA
1 ACCTGAACTAATATCGATCGGAGCTGAAATCAACCCGTCTCAA
611120 ACC
1 ACC
611123 CGAATTGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ACCTGAACTAATATCGATCGGAGCTGAAATCAACCCGTCTCAA
Found at i:611128 original size:43 final size:43
Alignment explanation
Indices: 611044--611128 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
611034 ACCTGAACTG
* * * *
611044 ATATCGATTGGAGCTGAAATTAACCCGTCTCGAACCTGAATTA
1 ATATCGATCGGAGCTGAAATCAACCCGTCTCAAACCCGAATTA
*
611087 ATATTGATCGGAGCTGAAATCAACCCGTCTCAAACCCGAATT
1 ATATCGATCGGAGCTGAAATCAACCCGTCTCAAACCCGAATT
611129 GAATCTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (43 bp):
ATATCGATCGGAGCTGAAATCAACCCGTCTCAAACCCGAATTA
Found at i:611516 original size:43 final size:43
Alignment explanation
Indices: 611450--611576 Score: 202
Period size: 43 Copynumber: 3.0 Consensus size: 43
611440 CTGTTAAAAG
* *
611450 TTACAAAATGATCACT-TGACTATTCATTATGTTCCAAACTAAC
1 TTACAAAATGATCACTCT-TCTATTCATTATGTTCTAAACTAAC
*
611493 TTACAAAATTATCACTCTTCTATTCATTATGTTCTAAACTAAC
1 TTACAAAATGATCACTCTTCTATTCATTATGTTCTAAACTAAC
*
611536 TTACAAAATGATCACTCTTTTATTCATTATGTTCTAAACTA
1 TTACAAAATGATCACTCTTCTATTCATTATGTTCTAAACTA
611577 GTCATTTTCC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
43 77 0.99
44 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (43 bp):
TTACAAAATGATCACTCTTCTATTCATTATGTTCTAAACTAAC
Found at i:616138 original size:212 final size:213
Alignment explanation
Indices: 615770--616196 Score: 838
Period size: 212 Copynumber: 2.0 Consensus size: 213
615760 GATACGGGAG
615770 GAAGAAGAAAGCAAGAAGAAGAAGATAACTCTCTTCCCCCCCCCCACGTGAATCATTCATATAAA
1 GAAGAAGAAAGCAAGAAGAAGAAGATAACTCTCTTCCCCCCCCCCACGTGAATCATTCATATAAA
615835 GGGGGGAAATATCTTTCTTGTCAAATGACCATTTTGCTCTTTAATTCCTTGGATAATTACTAACA
66 GGGGGGAAATATCTTTCTTGTCAAATGACCATTTTGCTCTTTAATTCCTTGGATAATTACTAACA
615900 ACTTTCAGGAAATATTCCTAAATAAATCATTGAACTATTCAACTATTCTACTTTAATCACCAAAT
131 ACTTTCAGGAAATATTCCTAAATAAATCATTGAACTATTCAACTATTCTACTTTAATCACCAAAT
615965 TCTAAAATTTTACAATTT
196 TCTAAAATTTTACAATTT
615983 GAAGAAGAAAGCAAGAAGAAGAAGATAACTCTCTT-CCCCCCCCCACGTGAATCATTCATATAAA
1 GAAGAAGAAAGCAAGAAGAAGAAGATAACTCTCTTCCCCCCCCCCACGTGAATCATTCATATAAA
616047 GGGGGGAAATATCTTTCTTGTCAAATGACCATTTTGCTCTTTAATTCCTTGGATAATTACTAACA
66 GGGGGGAAATATCTTTCTTGTCAAATGACCATTTTGCTCTTTAATTCCTTGGATAATTACTAACA
616112 ACTTTCAGGAAATATTCCTAAATAAATCATTGAACTATTCAACTATTCTACTTTAATCACCAAAT
131 ACTTTCAGGAAATATTCCTAAATAAATCATTGAACTATTCAACTATTCTACTTTAATCACCAAAT
*
616177 TCTGAAATTTTACAATTT
196 TCTAAAATTTTACAATTT
616195 GA
1 GA
616197 TCACTAACCC
Statistics
Matches: 213, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
212 178 0.84
213 35 0.16
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (213 bp):
GAAGAAGAAAGCAAGAAGAAGAAGATAACTCTCTTCCCCCCCCCCACGTGAATCATTCATATAAA
GGGGGGAAATATCTTTCTTGTCAAATGACCATTTTGCTCTTTAATTCCTTGGATAATTACTAACA
ACTTTCAGGAAATATTCCTAAATAAATCATTGAACTATTCAACTATTCTACTTTAATCACCAAAT
TCTAAAATTTTACAATTT
Found at i:619975 original size:17 final size:17
Alignment explanation
Indices: 619953--619993 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
619943 ATAAAGGGTC
619953 GATCCAAGAGTTTCTAG
1 GATCCAAGAGTTTCTAG
619970 GATCCAAGAGTTTCTAG
1 GATCCAAGAGTTTCTAG
*
619987 AATCCAA
1 GATCCAA
619994 TGGATCGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (17 bp):
GATCCAAGAGTTTCTAG
Found at i:621317 original size:31 final size:31
Alignment explanation
Indices: 621282--621352 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
621272 TAAAAGGGGT
621282 TTTGGGTTTCTTAGTTGGGTATGATTTTTTA
1 TTTGGGTTTCTTAGTTGGGTATGATTTTTTA
621313 TTTGGGTTTCTTAGTTGGGTATGATTTTTTA
1 TTTGGGTTTCTTAGTTGGGTATGATTTTTTA
621344 TTTGGGTTT
1 TTTGGGTTT
621353 AGGGTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.11, C:0.03, G:0.27, T:0.59
Consensus pattern (31 bp):
TTTGGGTTTCTTAGTTGGGTATGATTTTTTA
Found at i:621319 original size:18 final size:18
Alignment explanation
Indices: 621296--621350 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
621286 GGTTTCTTAG
621296 TTGGGTATGATTTTTTAT
1 TTGGGTATGATTTTTTAT
* *
621314 TT-GG---G-TTTCTTAG
1 TTGGGTATGATTTTTTAT
621327 TTGGGTATGATTTTTTAT
1 TTGGGTATGATTTTTTAT
621345 TTGGGT
1 TTGGGT
621351 TTAGGGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
17 3 0.11
18 14 0.50
ACGTcount: A:0.13, C:0.02, G:0.27, T:0.58
Consensus pattern (18 bp):
TTGGGTATGATTTTTTAT
Found at i:622976 original size:32 final size:31
Alignment explanation
Indices: 622935--622999 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
622925 TTTGATATTG
* *
622935 AACTTTAGATAAAATATCACTTTGACTCTCTA
1 AACTTTAGATAAAATATCAATTTAACTCT-TA
*
622967 AACTTTAGATAAGATATCAATTTAACTCTTA
1 AACTTTAGATAAAATATCAATTTAACTCTTA
622998 AA
1 AA
623000 TTCAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (31 bp):
AACTTTAGATAAAATATCAATTTAACTCTTA
Found at i:623069 original size:16 final size:16
Alignment explanation
Indices: 623048--623078 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
623038 TTACCGTCAT
*
623048 TCACTATTGATTGTTG
1 TCACTATTGAATGTTG
623064 TCACTATTGAATGTT
1 TCACTATTGAATGTT
623079 ATATCCCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (16 bp):
TCACTATTGAATGTTG
Found at i:624019 original size:9 final size:9
Alignment explanation
Indices: 624005--624222 Score: 75
Period size: 9 Copynumber: 24.4 Consensus size: 9
623995 AGAGAAGAAA
624005 AAAATAAAT
1 AAAATAAAT
*
624014 AAAATAGAT
1 AAAATAAAT
624023 AAAATAAAT
1 AAAATAAAT
*
624032 AAAATAAAGG
1 AAAATAAA-T
*
624042 AAAGT-AAT
1 AAAATAAAT
624050 AATAATGATAAT
1 AA-AAT-A-AAT
* **
624062 -ATATACGT
1 AAAATAAAT
*
624070 AATAA-AAAC
1 AA-AATAAAT
* *
624079 AAGATAAAA
1 AAAATAAAT
624088 ATAAATAAAT
1 A-AAATAAAT
624098 -AAATAAAT
1 AAAATAAAT
*
624106 AAAATACAT
1 AAAATAAAT
*
624115 ATAATAAGAT
1 AAAATAA-AT
*
624125 -ATATAAA-
1 AAAATAAAT
624132 AAAAT-AA-
1 AAAATAAAT
624139 AAAAT-AAT
1 AAAATAAAT
624147 AAAATAAA-
1 AAAATAAAT
*
624155 ATAA-AAAT
1 AAAATAAAT
** *
624163 AAAAGGATT
1 AAAATAAAT
624172 AAAATAAAAT
1 AAAAT-AAAT
624182 AGAAATAAA-
1 A-AAATAAAT
*
624191 AAGTATAAAT
1 AA-AATAAAT
**
624201 AATAATGTAT
1 AA-AATAAAT
624211 AAAA-AAAT
1 AAAATAAAT
624219 AAAA
1 AAAA
624223 AATTAATAGT
Statistics
Matches: 152, Mismatches: 37, Indels: 41
0.66 0.16 0.18
Matches are distributed among these distances:
7 12 0.08
8 34 0.22
9 69 0.45
10 29 0.19
11 5 0.03
12 3 0.02
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (9 bp):
AAAATAAAT
Found at i:624095 original size:4 final size:4
Alignment explanation
Indices: 624086--624159 Score: 62
Period size: 4 Copynumber: 17.8 Consensus size: 4
624076 AACAAGATAA
* * *
624086 AAAT AAAT AAAT AAAT AAAT AAAAT ACAT ATAAT AAGAT ATAT AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A-AAT AA-AT AAAT AAAT AAAT
624137 AAA- AAAT -AAT AAAAT AAAAT AAA
1 AAAT AAAT AAAT -AAAT -AAAT AAA
624160 AATAAAAGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
3 6 0.10
4 34 0.59
5 18 0.31
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:624152 original size:5 final size:5
Alignment explanation
Indices: 624085--624191 Score: 59
Period size: 5 Copynumber: 21.8 Consensus size: 5
624075 AAACAAGATA
* *
624085 AAAAT -AAAT -AAAT -AAAT -AAAT AAAAT -ACAT ATAAT AAGATAT ATAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-A-AT A-AAAT
** *
624132 AAAAT AAAA- AATAAT AAAAT AAAAT AAAAAT AAAA- GGATT AAAAT AAAAT
1 AAAAT AAAAT AA-AAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
624182 AGAAAT AAAA
1 A-AAAT AAAA
624192 AGTATAAATA
Statistics
Matches: 81, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
4 25 0.31
5 37 0.46
6 14 0.17
7 4 0.05
8 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:624166 original size:25 final size:25
Alignment explanation
Indices: 624069--624192 Score: 89
Period size: 25 Copynumber: 5.0 Consensus size: 25
624059 AATATATACG
*
624069 TAATAAAA-ACAAGATAAAAATAAATA
1 TAATAAAATA-AA-ATAAAAATAAAAA
* *
624095 -AAT-AAAT-AAAT-AAAATACATA
1 TAATAAAATAAAATAAAAATAAAAA
*
624116 TAATAAGATATATAA-AAAAATAAAAAA
1 TAATAA-A-ATAAAATAAAAAT-AAAAA
*
624143 TAATAAAATAAAATAAAAATAAAAG
1 TAATAAAATAAAATAAAAATAAAAA
* * *
624168 GATTAAAATAAAATAGAAATAAAAA
1 TAATAAAATAAAATAAAAATAAAAA
624193 GTATAAATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
21 9 0.11
22 5 0.06
23 3 0.04
24 4 0.05
25 35 0.44
26 14 0.18
27 9 0.11
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (25 bp):
TAATAAAATAAAATAAAAATAAAAA
Found at i:624199 original size:25 final size:25
Alignment explanation
Indices: 624131--624199 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
624121 AGATATATAA
*
624131 AAAAATAAAAAATAATAAAATAAAAT
1 AAAAATAAAAAGT-ATAAAATAAAAT
*
624157 AAAAAT-AAAAGGATTAAAATAAAAT
1 AAAAATAAAAAGTA-TAAAATAAAAT
*
624182 AGAAATAAAAAGTATAAA
1 AAAAATAAAAAGTATAAA
624200 TAATAATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.03
25 24 0.65
26 12 0.32
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (25 bp):
AAAAATAAAAAGTATAAAATAAAAT
Found at i:624281 original size:24 final size:23
Alignment explanation
Indices: 624215--624283 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
624205 ATGTATAAAA
** *
624215 AAATAAAAAATTAATAGTAATAGG
1 AAATAAAAAA-TAATAAAAATAGC
*
624239 AAATAAGAAAAAAAT-AAAATGAGC
1 AAATAA-AAAATAATAAAAAT-AGC
624263 AAATAAAAAATAATAAAAATA
1 AAATAAAAAATAATAAAAATA
624284 ATAAAATGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 11 0.30
24 22 0.59
25 4 0.11
ACGTcount: A:0.71, C:0.01, G:0.09, T:0.19
Consensus pattern (23 bp):
AAATAAAAAATAATAAAAATAGC
Found at i:624292 original size:32 final size:31
Alignment explanation
Indices: 624239--624298 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
624229 TAGTAATAGG
624239 AAATAAGAAAAAAATAAAATGAGCAAATAAA
1 AAATAAGAAAAAAATAAAATGAGCAAATAAA
* *
624270 AAATAATAAAAATAATAAAATGATCAAAT
1 AAATAAGAAAAA-AATAAAATGAGCAAAT
624299 TATAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.18
Consensus pattern (31 bp):
AAATAAGAAAAAAATAAAATGAGCAAATAAA
Found at i:624298 original size:16 final size:16
Alignment explanation
Indices: 624251--624303 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
624241 ATAAGAAAAA
*
624251 AATAAAATGAGCAAAT
1 AATAAAATGATCAAAT
* *
624267 AA-AAAATAATAAAAAT
1 AATAAAATGAT-CAAAT
624283 AATAAAATGATCAAAT
1 AATAAAATGATCAAAT
*
624299 TATAA
1 AATAA
624304 TAAAAATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 6 0.21
16 16 0.55
17 7 0.24
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.23
Consensus pattern (16 bp):
AATAAAATGATCAAAT
Found at i:624449 original size:22 final size:22
Alignment explanation
Indices: 624421--624467 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
624411 CCTTATAAAG
624421 AACAAGGGACCAAATCTTCAAA
1 AACAAGGGACCAAATCTTCAAA
624443 AACAAGGGACCAAATCTTCAAA
1 AACAAGGGACCAAATCTTCAAA
624465 AAC
1 AAC
624468 GCTCAGATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.23, G:0.13, T:0.13
Consensus pattern (22 bp):
AACAAGGGACCAAATCTTCAAA
Found at i:629764 original size:36 final size:36
Alignment explanation
Indices: 629529--629644 Score: 180
Period size: 36 Copynumber: 3.2 Consensus size: 36
629519 TAATGTACTC
629529 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
*
629566 AAAA-AAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
629601 AAAACAAATTTTGTCTCTCTTGAAACGGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
629637 AAAACAAA
1 AAAACAAA
629645 AACTTTGAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 31 0.42
36 38 0.52
37 4 0.05
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:629781 original size:36 final size:36
Alignment explanation
Indices: 629657--630023 Score: 248
Period size: 36 Copynumber: 10.5 Consensus size: 36
629647 CTTTGAATTT
* *
629657 GTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* * *
629694 GTTT-CTTTTAGAACTAAATTTTGTCACTCTTGAGACA
1 GTTTCCCTTGA-AAC-AAATTTTGTCTCTCTTGAGACA
* * * * *
629731 TTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGAAA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
629767 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CA
* * *
629796 GTTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
629832 ATTT-CTTTTAGAACTAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGA-AAC-AAATTTTGTCTCTCTTGAGACA
* * * *
629869 TTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
629905 GTTTCTCTTGAAACAAA------ATCTC-TGA-ATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
629933 TGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 -GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * *
629970 GTTTCTTTTGGAACTAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
630007 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
630024 ATCTTTGAAT
Statistics
Matches: 255, Mismatches: 50, Indels: 51
0.72 0.14 0.14
Matches are distributed among these distances:
28 3 0.01
29 37 0.15
30 7 0.03
35 11 0.04
36 100 0.39
37 90 0.35
38 7 0.03
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:630022 original size:102 final size:101
Alignment explanation
Indices: 629847--630082 Score: 296
Period size: 102 Copynumber: 2.3 Consensus size: 101
629837 TTTTAGAACT
* * * ** * *
629847 AAATTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC
1 AAATTTCGTCTCACTTGAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
*
629912 TTGAAACAAAATCTCTGAATATG-TTTTCCTTGAAAC
66 TTGAAACAAAATCTCTGAATATGTTTTTCATT-AAAC
* * *
629948 AAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTCTTGAGATAGTTTCC
1 AAATTTCGTCTCACTTGAGACAGTTTCTTTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCC
* *
630013 CTTGAAACAAAATCTTTGAATCTGTTTTTCATTAAAC
65 CTTGAAACAAAATCTCTGAATATGTTTTTCATTAAAC
**
630050 AAATTTAC-TCTCACTCAAGACAGTTTCTTTTGA
1 AAATTT-CGTCTCACTTGAGACAGTTTCTTTTGA
630083 GACAGTTTCT
Statistics
Matches: 116, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
101 29 0.25
102 79 0.68
103 8 0.07
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (101 bp):
AAATTTCGTCTCACTTGAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
TTGAAACAAAATCTCTGAATATGTTTTTCATTAAAC
Found at i:630023 original size:138 final size:139
Alignment explanation
Indices: 629530--630004 Score: 742
Period size: 138 Copynumber: 3.4 Consensus size: 139
629520 AATGTACTCA
* * *
629530 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTA-AA-AAAATTTTGTCTCTCTTGAGACAT
1 AAACAAAGTTTCGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT
* * * * * *
629593 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAAACGGTTTCCCTTAAAACAAAAACTTTGAATTTG
66 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
629658 TTTTCCTTG
131 TTTTCCTTG
* * *
629667 AAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTTTTAGAACTAAATTTTGTCACTCTTGAGACAT
1 AAACAAAGTTTCGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT
* *
629732 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATCTTTGAATCTG
66 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
*
629797 TTTTCCTTT
131 TTTTCCTTG
*
629806 AAACAAA-TTTCGTCTCTCTTGAGACAATTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT
1 AAACAAAGTTTCGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT
* *
629870 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTCTGAATATG
66 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
629935 TTTTCCTTG
131 TTTTCCTTG
* *
629944 AAACAAA-TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTCTTGAGA
1 AAACAAAGTTTCGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGA
630005 TAGTTTCCCT
Statistics
Matches: 312, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
137 35 0.11
138 182 0.58
139 95 0.30
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (139 bp):
AAACAAAGTTTCGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT
TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
TTTTCCTTG
Found at i:630087 original size:15 final size:15
Alignment explanation
Indices: 630067--630097 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
630057 CTCTCACTCA
*
630067 AGACAGTTTCTTTTG
1 AGACAGTTTCTATTG
630082 AGACAGTTTCTATTG
1 AGACAGTTTCTATTG
630097 A
1 A
630098 AACACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (15 bp):
AGACAGTTTCTATTG
Found at i:631303 original size:21 final size:21
Alignment explanation
Indices: 631265--631305 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
631255 GAGGTTTATA
*
631265 TTTTAAAAAAATATGTTTTGC
1 TTTTAAAAAAATAGGTTTTGC
631286 TTTTAAAAAAAGT-GGTTTTG
1 TTTTAAAAAAA-TAGGTTTTG
631306 AAAAGCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (21 bp):
TTTTAAAAAAATAGGTTTTGC
Done.