Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 87 of 203
Found at i:27652239 original size:27 final size:22
Alignment explanation
Indices: 27652185--27652234 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
27652175 AAACAAATAA
27652185 GAATG-TTAGTTTTCCTGAAGT
1 GAATGATTAGTTTTCCTGAAGT
27652206 GAATGATTAGTTTTCCTGAAGT
1 GAATGATTAGTTTTCCTGAAGT
27652228 GAATGAT
1 GAATGAT
27652235 ATGATGGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (22 bp):
GAATGATTAGTTTTCCTGAAGT
Found at i:27652837 original size:15 final size:15
Alignment explanation
Indices: 27652817--27652845 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27652807 ATATCGTATC
27652817 TTGGATTTCTCTATT
1 TTGGATTTCTCTATT
27652832 TTGGATTTCTCTAT
1 TTGGATTTCTCTAT
27652846 CTTAGTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TTGGATTTCTCTATT
Found at i:27657002 original size:68 final size:64
Alignment explanation
Indices: 27656788--27657009 Score: 182
Period size: 64 Copynumber: 3.4 Consensus size: 64
27656778 CATAATTTTG
* ** * * *
27656788 GCTCTCTTGTGCACATGGTGCACACATAGTATCACCCATGTGACCTAGCCA-CTTTA-TCTCGTA
1 GCTCTCTTGT-CACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTCTATTCTCATA
* * * * * * * *
27656851 GCTCTCTTGTTTACATGGTGTCCTTCACCTGGAACCACACATGCAACCTAGCTACATCTA-TCT-
1 GCTCTCTTG-TCACATGGTG---TACACATAGTATCACCCATGCAACCTAGCTACCTCTATTCTC
27656914 AGTA
62 A-TA
27656918 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTCATAATGTCTC
1 GCTCTCTTGTC-ACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTC-T-AT-TCTC
27656983 ATA
62 ATA
*
27656986 GCTCTCTTGTACACATGGTATACA
1 GCTCTCTTGT-CACATGGTGTACA
27657010 TCTCGTATTA
Statistics
Matches: 123, Mismatches: 23, Indels: 21
0.74 0.14 0.13
Matches are distributed among these distances:
63 17 0.14
64 29 0.24
65 1 0.01
66 23 0.19
67 25 0.20
68 26 0.21
69 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (64 bp):
GCTCTCTTGTCACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTCTATTCTCATA
Found at i:27657537 original size:30 final size:30
Alignment explanation
Indices: 27657503--27657560 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27657493 TTCTTAACTC
27657503 AAACTTTGGCAAAATTACAATTTTGCCCTT
1 AAACTTTGGCAAAATTACAATTTTGCCCTT
* * * *
27657533 AAACTTTTGCATATTTACACTTTTGCCC
1 AAACTTTGGCAAAATTACAATTTTGCCC
27657561 CTAGGCTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCTT
Found at i:27665201 original size:44 final size:44
Alignment explanation
Indices: 27665130--27665258 Score: 147
Period size: 42 Copynumber: 3.0 Consensus size: 44
27665120 GTTAACATTG
* ** *
27665130 ATCTGAGATATCGTGTAAGACTGTGTCTGGGACACAGGCCTCG-
1 ATCTGAGATTTCGTGTAAGACCATGTCTGGGACACAGGCATCGT
* *
27665173 ATTTGAGATTTACGTGTAAGACCATGTCTGGGACATAGGCATCGT
1 ATCTGAGATTT-CGTGTAAGACCATGTCTGGGACACAGGCATCGT
* * *
27665218 ATCT--GATTTCGTGTAAGACCCTGTCTGGGACAGAGTCATCG
1 ATCTGAGATTTCGTGTAAGACCATGTCTGGGACACAGGCATCG
27665259 AAACTGAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 29 0.39
43 14 0.19
44 28 0.38
45 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (44 bp):
ATCTGAGATTTCGTGTAAGACCATGTCTGGGACACAGGCATCGT
Found at i:27678161 original size:39 final size:39
Alignment explanation
Indices: 27678118--27678201 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
27678108 GCAATTAGCT
*
27678118 TGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCC
1 TGCTAGGTATAAACCTGAACTTATCACCAGCACGAGGCC
* *
27678157 TGCTAGGTATAAACCTGAATTTATCACCAGCAGGAGGCC
1 TGCTAGGTATAAACCTGAACTTATCACCAGCACGAGGCC
27678196 TGCTAG
1 TGCTAG
27678202 ACATTAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (39 bp):
TGCTAGGTATAAACCTGAACTTATCACCAGCACGAGGCC
Found at i:27682789 original size:39 final size:39
Alignment explanation
Indices: 27682615--27682773 Score: 228
Period size: 39 Copynumber: 4.1 Consensus size: 39
27682605 TGTGAATATA
*
27682615 TATATGCGAGAATTATATCCGGACTTCAGGTCCGTAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* * *
27682654 TATAAGCGAGAATTATATCTGGACTTCATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* * *
27682693 TATATGCGAGAATTATATCCAGACTTTATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* * *
27682732 TATATGCGAGAATTATATCCGGGCTTTAGGTCCGTAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
27682771 TAT
1 TAT
27682774 GTGCTGGACA
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 108 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (39 bp):
TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
Found at i:27697391 original size:49 final size:49
Alignment explanation
Indices: 27697252--27697598 Score: 607
Period size: 49 Copynumber: 7.2 Consensus size: 49
27697242 TTAGGATTTT
** *
27697252 ATGTGATGAATGTG-AA-TGTGCATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
27697299 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
27697346 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
27697395 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
27697444 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
27697493 ATGTGATGAATGTGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAA--TGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
27697542 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
27697591 ATGTGATG
1 ATGTGATG
27697599 GCCTAATGGC
Statistics
Matches: 290, Mismatches: 2, Indels: 14
0.95 0.01 0.05
Matches are distributed among these distances:
47 69 0.24
48 2 0.01
49 209 0.72
51 10 0.03
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.31
Consensus pattern (49 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
Found at i:27697603 original size:20 final size:20
Alignment explanation
Indices: 27697578--27697618 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
27697568 TATGTGATAA
27697578 GGCCTAATGGCCGATGTGAT
1 GGCCTAATGGCCGATGTGAT
27697598 GGCCTAATGGCCGATGTGAT
1 GGCCTAATGGCCGATGTGAT
27697618 G
1 G
27697619 AATGTGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.24
Consensus pattern (20 bp):
GGCCTAATGGCCGATGTGAT
Found at i:27697611 original size:69 final size:67
Alignment explanation
Indices: 27697520--27697665 Score: 256
Period size: 67 Copynumber: 2.1 Consensus size: 67
27697510 AAGTGTATAT
27697520 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
1 ATGTGAT--GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAA
27697585 TGGCCG
62 TGGCCG
27697591 ATGTGATGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
1 ATGTGATGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
27697656 CG
66 CG
27697658 ATGTGATG
1 ATGTGATG
27697666 AATGTGAAAG
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
67 35 0.47
69 33 0.44
71 7 0.09
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (67 bp):
ATGTGATGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
CG
Found at i:27697635 original size:116 final size:115
Alignment explanation
Indices: 27697471--27697712 Score: 423
Period size: 116 Copynumber: 2.1 Consensus size: 115
27697461 GTGTATATAT
27697471 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGTGAAAGTGTATATATGTGATAAGGCCTAA
1 ATGTGAT--GGCCTAATGGCCGATGTGATGAA-GTGTGAAAGTGTATATATGTGATAAGGCCTAA
*
27697536 TGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
63 TGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCAAATGGCCG
27697591 ATGTGATGGCCTAATGGCCGATGTGATGAA-TGTGAAAGTGTATATATGTGATAAGGCCTAATGG
1 ATGTGATGGCCTAATGGCCGATGTGATGAAGTGTGAAAGTGTATATATGTGATAAGGCCTAATGG
27697655 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCAAATGGCCG
66 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCAAATGGCCG
27697705 ATGTGATG
1 ATGTGATG
27697713 AATGTGAAAG
Statistics
Matches: 121, Mismatches: 1, Indels: 6
0.95 0.01 0.05
Matches are distributed among these distances:
114 34 0.28
116 57 0.47
118 23 0.19
120 7 0.06
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (115 bp):
ATGTGATGGCCTAATGGCCGATGTGATGAAGTGTGAAAGTGTATATATGTGATAAGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCAAATGGCCG
Found at i:27697651 original size:47 final size:47
Alignment explanation
Indices: 27697591--27697786 Score: 297
Period size: 47 Copynumber: 4.2 Consensus size: 47
27697581 CTAATGGCCG
27697591 ATGTGAT--GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
27697636 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
27697683 ATGTGATAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * * * * *
27697730 ATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAA
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
27697777 ATGTGATAAG
1 ATGTGATAAG
27697787 TCCCGAAGGG
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
45 7 0.05
47 131 0.95
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (47 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
Found at i:27714047 original size:2 final size:2
Alignment explanation
Indices: 27714040--27714068 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27714030 TTAAGCTTAA
27714040 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
27714069 TCAAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27716864 original size:16 final size:15
Alignment explanation
Indices: 27716843--27716881 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
27716833 ATTAATAAAA
27716843 AAATATTTATTTTTAG
1 AAATATTTATTTTT-G
* *
27716859 AAATATTCATTTTTT
1 AAATATTTATTTTTG
27716874 AAATATTT
1 AAATATTT
27716882 GATGACATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (15 bp):
AAATATTTATTTTTG
Found at i:27717852 original size:31 final size:32
Alignment explanation
Indices: 27717805--27717865 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
27717795 ACAATTCAGC
27717805 TCTTTTTAAAAGATTGATGG-TCAAATTTAATTT
1 TCTTTTT-AAAGATTGA-GGATCAAATTTAATTT
27717838 TCTTTTT-AAGATTGAGGATCAAATTTAA
1 TCTTTTTAAAGATTGAGGATCAAATTTAA
27717866 CTCCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 2 0.07
31 18 0.67
33 7 0.26
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (32 bp):
TCTTTTTAAAGATTGAGGATCAAATTTAATTT
Found at i:27719252 original size:68 final size:68
Alignment explanation
Indices: 27719140--27719401 Score: 328
Period size: 68 Copynumber: 3.9 Consensus size: 68
27719130 TCGAAATTAA
* * *
27719140 GAGTCCGCCAAGACATTAAACATGGATTCATAATGTGTAAGACCATAGCTAGGATATGACAATAT
1 GAGTCCGCCAAGACATTAAACATGGGTTCATAATGTGTAAGACCATAGCTAGGCTATGACAACAT
27719205 ATG
66 ATG
* * * * * *
27719208 AAGTCCTCCAAGACATTAAACTTGAGTTTATAATGTGTATGACCATAGCTAGGCTATGACAACAT
1 GAGTCCGCCAAGACATTAAACATGGGTTCATAATGTGTAAGACCATAGCTAGGCTATGACAACAT
27719273 ATG
66 ATG
* * * * * *
27719276 GAGTTCGCTAGGACATTAAACATGGGTTCATACTGTGTAAGACCATATCTAGGCTATGGCAACAT
1 GAGTCCGCCAAGACATTAAACATGGGTTCATAATGTGTAAGACCATAGCTAGGCTATGACAACAT
27719341 ATG
66 ATG
** * * *
27719344 GAGTCTACCAAAACATTAAACATGGGTTCATACAT-TGTAAGACCATAGTTGGGCTATG
1 GAGTCCGCCAAGACATTAAACATGGGTTCATA-ATGTGTAAGACCATAGCTAGGCTATG
27719402 GTGCCAGATA
Statistics
Matches: 162, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
68 161 0.99
69 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (68 bp):
GAGTCCGCCAAGACATTAAACATGGGTTCATAATGTGTAAGACCATAGCTAGGCTATGACAACAT
ATG
Found at i:27721057 original size:29 final size:29
Alignment explanation
Indices: 27721015--27721119 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
27721005 CACCATCGGT
*
27721015 ACATAGTACCTGATAAATATAAAACTGAA
1 ACATAGTACCTGATAAATATAACACTGAA
* * * * *
27721044 ACATAGTGCTTGATAACTATAACACCGAT
1 ACATAGTACCTGATAAATATAACACTGAA
*
27721073 ACAAAGTACCTGATAAATATAATCACT-AA
1 ACATAGTACCTGATAAATATAA-CACTGAA
*
27721102 CACATAGTGCCTGATAAA
1 -ACATAGTACCTGATAAA
27721120 CCCTAATGAC
Statistics
Matches: 60, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 42 0.70
30 18 0.30
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (29 bp):
ACATAGTACCTGATAAATATAACACTGAA
Found at i:27724798 original size:40 final size:40
Alignment explanation
Indices: 27724741--27724821 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
27724731 CTCGAGAGTG
*
27724741 TTAGTTAACCTAAGGTTAAGGACAACGACTACCTCAAGTC
1 TTAGTTAACCTAAGGTTAAGGACAACGACTACATCAAGTC
*
27724781 TTAGTTAACCTAGGGTTAAGGACAACGACTACATCAAGTC
1 TTAGTTAACCTAAGGTTAAGGACAACGACTACATCAAGTC
27724821 T
1 T
27724822 ATAAATAGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (40 bp):
TTAGTTAACCTAAGGTTAAGGACAACGACTACATCAAGTC
Found at i:27733524 original size:22 final size:22
Alignment explanation
Indices: 27733466--27733517 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
27733456 TGTAACACCC
*
27733466 TGAATTTTGGGGTTAGAAGTTT
1 TGAATTTTGGGGTTAAAAGTTT
*
27733488 TGACTTTTGGGGTTAAAAGTTT
1 TGAATTTTGGGGTTAAAAGTTT
27733510 TGAATTTT
1 TGAATTTT
27733518 TCGGTTAGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (22 bp):
TGAATTTTGGGGTTAAAAGTTT
Found at i:27740507 original size:33 final size:33
Alignment explanation
Indices: 27740460--27740523 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
27740450 TGGATTGCCA
27740460 TCTGGGGTCTTCTTCTGGAATCTGTTGTTAGTT
1 TCTGGGGTCTTCTTCTGGAATCTGTTGTTAGTT
27740493 TCTGGGGT-TCTCTTCTGGAATCTGTTGTTAG
1 TCTGGGGTCT-TCTTCTGGAATCTGTTGTTAG
27740524 CCGTTCTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (33 bp):
TCTGGGGTCTTCTTCTGGAATCTGTTGTTAGTT
Found at i:27747280 original size:59 final size:59
Alignment explanation
Indices: 27747181--27747295 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
27747171 GCATACATTA
* * *
27747181 AACCTACAGGGGAGACACGGTCATGTCGCCTAGCCATGTGTGACACACGGCTGAGTCAG
1 AACCTACAAGGGACACACGGTCATGTCGCCTAGCCATGTGTCACACACGGCTGAGTCAG
* * * **
27747240 AACCTACAAGGGACACATGGTCGTGTCGCCTGGCTGTGTGTCACACACGGCTGAGT
1 AACCTACAAGGGACACACGGTCATGTCGCCTAGCCATGTGTCACACACGGCTGAGT
27747296 TAGACGCTCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.23, C:0.27, G:0.30, T:0.19
Consensus pattern (59 bp):
AACCTACAAGGGACACACGGTCATGTCGCCTAGCCATGTGTCACACACGGCTGAGTCAG
Found at i:27748114 original size:41 final size:41
Alignment explanation
Indices: 27748066--27748210 Score: 229
Period size: 41 Copynumber: 3.5 Consensus size: 41
27748056 AAGTATAGAT
27748066 AGGGGCACGTATGTGCAATTCAAGGGTATCGAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAAGGGTATCGAAGTACAAAC
* * * *
27748107 AGAGGCACTTATGTGCAATTCAAGGGTA-CTGAAATACAAAT
1 AGGGGCACGTATGTGCAATTCAAGGGTATC-GAAGTACAAAC
*
27748148 AGGGGCACGTATGTGCAATTCAGGGGTATCGAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAAGGGTATCGAAGTACAAAC
27748189 AGGGGCACGTATGTGCAATTCA
1 AGGGGCACGTATGTGCAATTCA
27748211 TTATTATTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 1 0.01
41 91 0.98
42 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAAGGGTATCGAAGTACAAAC
Found at i:27750097 original size:11 final size:13
Alignment explanation
Indices: 27750077--27750108 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
27750067 AATAAAATAA
27750077 TAAAATATC-ATT
1 TAAAATATCAATT
27750089 TAAAA-ATCAATT
1 TAAAATATCAATT
27750101 TAAAATAT
1 TAAAATAT
27750109 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 13 0.72
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCAATT
Found at i:27763138 original size:56 final size:50
Alignment explanation
Indices: 27762911--27763159 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
27762901 GATCATAACA
* * * * * *
27762911 TGCCAAAGCCATGTCCCAAACATGATCTTAAATGGGTTA-TTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGG--ACCTCTCATCTCGG
* * **
27762962 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
27763012 TGCCAACGCCATGTCCTAGACATAGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
27763062 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * *
27763117 ATGCCAATGCCATGTCCCAGACATGGTCTTAAATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27763160 TTACCCAAAT
Statistics
Matches: 171, Mismatches: 20, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 95 0.56
51 29 0.17
53 5 0.03
55 2 0.01
56 39 0.23
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:27769420 original size:30 final size:29
Alignment explanation
Indices: 27769385--27769441 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
27769375 CCTCGACTCT
*
27769385 AACTTTGT-CAAAATTATGATTTTTCCCCTA
1 AACTTT-TACAAAATTA-CATTTTTCCCCTA
*
27769415 AACTTTTACATAATTACATTTTTCCCC
1 AACTTTTACAAAATTACATTTTTCCCC
27769442 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.44
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTTCCCCTA
Found at i:27776549 original size:125 final size:125
Alignment explanation
Indices: 27776333--27776861 Score: 679
Period size: 125 Copynumber: 4.2 Consensus size: 125
27776323 ATTTTTGCAG
* * *
27776333 TCGCGCCCCCGTGTACGCGTTTTTGCTACAGTAGGTCCTGGAA-AAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * *
27776397 TCTGAGCAAATAGTATAAAAAAT-GCTTCAAGCAAGATGCTATATGCGAAGAATTTGTGAAA
66 TCTGAGCAAATA--ATATAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * *
27776458 TCGCGCCCTCATGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACATT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* *
27776523 TCTGAGCAAATAATATAAAATCGCTTCTACCAGGATG-TTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAATATAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * *
27776582 TCGCGCCCACGTGGACGTGCTTTTGCTACAGTAGGTCCT-GAAAAAATTATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* ** * * *
27776646 TCTGAGCAAATAGTATAAAAAAAGCTTCAAGCAGGATGCTATTTGAGAAGAATTTCTGAAA
66 TCTGAGCAAATAATAT-AAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * * * * *
27776707 TCGTGCCCTCATGGACGCGCTTTTTCTACAGTTGGTCCTGGAAGAAATAATTTTGAGTTGATGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * * *
27776772 TTTGAGCAAATAGTACAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAATATAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* *
27776832 TCACGCCCACGTGGACGCACTTTTGCTACA
1 TCGCGCCCACGTGGACGCGCTTTTGCTACA
27776862 ATAGCATGTT
Statistics
Matches: 347, Mismatches: 52, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
123 37 0.11
124 80 0.23
125 163 0.47
126 67 0.19
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (125 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
TCTGAGCAAATAATATAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
Found at i:27776780 original size:249 final size:250
Alignment explanation
Indices: 27776303--27776861 Score: 868
Period size: 249 Copynumber: 2.2 Consensus size: 250
27776293 AAAATCAAAG
* * * * * * * *
27776303 CAGGATGATTTATCAGAAGGATTTTTGCAGTCGCGCCCCCGTGTACGCGTTTTTGCTACAGTAGG
1 CAGGATGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
* *
27776368 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAAGA
66 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAGCTTCAAGCAAGA
* *
27776433 TGCTATATGCGAAGAATTTGTGAAATCGCGCCCTCATGGACGCGCTTTTGCTACAGTTGGTCCTG
131 TGCTATATGAGAAGAATTTCTGAAATCGCGCCCTCATGGACGCGCTTTTGCTACAGTTGGTCCTG
*
27776498 GAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAATATAAAATCGCTTCTAC
196 GAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAATACAAAATCGCTTCTAC
*
27776553 CAGGATG-TTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGTGCTTTTGCTACAGTAGG
1 CAGGATGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
* *
27776617 TCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAGCTTCAAGCAGGA
66 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAGCTTCAAGCAAGA
* * *
27776682 TGCTATTTGAGAAGAATTTCTGAAATCGTGCCCTCATGGACGCGCTTTTTCTACAGTTGGTCCTG
131 TGCTATATGAGAAGAATTTCTGAAATCGCGCCCTCATGGACGCGCTTTTGCTACAGTTGGTCCTG
* ** * *
27776747 GAAGAAATAATTTTGAGTTGATGTTTTTGAGCAAATAGTACAAAATCGCTTCTAC
196 GAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAATACAAAATCGCTTCTAC
* * *
27776802 CAGGATGCTTTATGAGAAGAATTTGTGAAATCACGCCCACGTGGACGCACTTTTGCTACA
1 CAGGATGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACA
27776862 ATAGCATGTT
Statistics
Matches: 281, Mismatches: 27, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
249 225 0.80
250 56 0.20
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (250 bp):
CAGGATGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAGCTTCAAGCAAGA
TGCTATATGAGAAGAATTTCTGAAATCGCGCCCTCATGGACGCGCTTTTGCTACAGTTGGTCCTG
GAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAATACAAAATCGCTTCTAC
Found at i:27778169 original size:22 final size:22
Alignment explanation
Indices: 27778144--27778342 Score: 163
Period size: 22 Copynumber: 8.8 Consensus size: 22
27778134 ACGGTTTAGA
27778144 GTTTTTAAGTTTAGGGTTTGTG
1 GTTTTTAAGTTTAGGGTTTGTG
*
27778166 GTTTTTAAGTTAAGGGTTTAGT-
1 GTTTTTAAGTTTAGGGTTT-GTG
*
27778188 GTTTTTAGGTTTAGGGTTTGTG
1 GTTTTTAAGTTTAGGGTTTGTG
27778210 GTTTTTAAGTTAATAATTAGGGTTTG-G
1 GTTTTTAAG----T--TTAGGGTTTGTG
* **
27778237 GTTTTTTAAGTTTAGTGTTTAAG
1 G-TTTTTAAGTTTAGGGTTTGTG
* * *
27778260 GTTTTTAGGTTTAGGTTTTGGG
1 GTTTTTAAGTTTAGGGTTTGTG
* * **
27778282 GGTTTTAGGTTTAGGGTTTAAG
1 GTTTTTAAGTTTAGGGTTTGTG
*
27778304 GTTTTTAAGTTTAGAGTTTAG-G
1 GTTTTTAAGTTTAGGGTTT-GTG
*
27778326 G-TTTTAAGTTAAGGGTT
1 GTTTTTAAGTTTAGGGTT
27778343 ATGATTAGGG
Statistics
Matches: 145, Mismatches: 21, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
21 16 0.11
22 103 0.71
23 4 0.03
24 1 0.01
26 1 0.01
27 2 0.01
28 18 0.12
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (22 bp):
GTTTTTAAGTTTAGGGTTTGTG
Found at i:27778200 original size:44 final size:44
Alignment explanation
Indices: 27778131--27778342 Score: 185
Period size: 44 Copynumber: 4.7 Consensus size: 44
27778121 AGGTACAGTA
* * **
27778131 TTAACGGTTTAGAGTTTTTAAGTTTAGGGTTTGTGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTTTTAAG
* * **
27778175 TTAAGGGTTTAGTGTTTTTAGGTTTAGGGTTTGTGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTTTTAAG
* *
27778219 TTAATAATTAGGGTTT-GGGTTTTTTAAGTTTAGTGTTTAAGGTTTTTAGG
1 -T--T-A--AGGGTTTAGGG-TTTTTAAGTTTAGGGTTTAAGGTTTTTAAG
* * * * *
27778269 TTTAGGTTTTGGGGGTTTTAGGTTTAGGGTTTAAGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTTTTAAG
* * *
27778313 TTTAGAGTTTAGGG-TTTTAAGTTAAGGGTT
1 TTAAGGGTTTAGGGTTTTTAAGTTTAGGGTT
27778343 ATGATTAGGG
Statistics
Matches: 140, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
43 14 0.10
44 84 0.60
45 4 0.03
47 2 0.01
48 1 0.01
49 3 0.02
50 32 0.23
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.50
Consensus pattern (44 bp):
TTAAGGGTTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTTTTAAG
Found at i:27778247 original size:72 final size:72
Alignment explanation
Indices: 27778154--27778288 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
27778144 GTTTTTAAGT
* *
27778154 TTAGGGTTTGTGGTTTTTAAGTTAAGGGTTT-AGTGTTTTTAGGTTTAGGGTTTGTGGTTTTTAA
1 TTAGGGTTTGTGGTTTTTAAGTTAAGGGTTTAAG-GTTTTTAGGTTTAGGGTTTGGGGGTTTTAA
27778218 GTTAATAA
65 GTTAATAA
* * *
27778226 TTAGGGTTTG-GGTTTTTTAAGTTTAGTGTTTAAGGTTTTTAGGTTTAGGTTTTGGGGGTTTTA
1 TTAGGGTTTGTGG-TTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGGGGGTTTTA
27778289 GGTTTAGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
71 2 0.04
72 52 0.93
73 2 0.04
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (72 bp):
TTAGGGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGGGGGTTTTAAG
TTAATAA
Found at i:27778645 original size:21 final size:21
Alignment explanation
Indices: 27778621--27778665 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
27778611 TTTTGTCCAG
*
27778621 CTTCCGGCGGCGATTGTGGTT
1 CTTCCGGCGGCGATTCTGGTT
*
27778642 CTTCCGGCGGGGATTCTGGTT
1 CTTCCGGCGGCGATTCTGGTT
27778663 CTT
1 CTT
27778666 GCAATAGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.24, G:0.36, T:0.36
Consensus pattern (21 bp):
CTTCCGGCGGCGATTCTGGTT
Found at i:27780183 original size:19 final size:21
Alignment explanation
Indices: 27780158--27780205 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
27780148 AACCTTTTTA
27780158 ATTTAATGTT-ATTTATAA-TG
1 ATTTAATGTTAATTT-TAATTG
*
27780178 -TTTAATCTTAATTTTAATTG
1 ATTTAATGTTAATTTTAATTG
27780198 ATTTAATG
1 ATTTAATG
27780206 CTATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 11 0.48
20 6 0.26
21 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (21 bp):
ATTTAATGTTAATTTTAATTG
Found at i:27780569 original size:12 final size:12
Alignment explanation
Indices: 27780525--27780578 Score: 72
Period size: 12 Copynumber: 4.3 Consensus size: 12
27780515 TATGCATAGG
27780525 CATTCTTTCTTA
1 CATTCTTTCTTA
*
27780537 CATTTATTTCTGTA
1 CA-TTCTTTCT-TA
*
27780551 AATTCTTTCTTA
1 CATTCTTTCTTA
27780563 CATTCTTTCTTA
1 CATTCTTTCTTA
27780575 CATT
1 CATT
27780579 TGCATTTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
12 19 0.53
13 14 0.39
14 3 0.08
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.57
Consensus pattern (12 bp):
CATTCTTTCTTA
Found at i:27780686 original size:19 final size:19
Alignment explanation
Indices: 27780648--27780687 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
27780638 TATAATTACT
*
27780648 TACATGAATATAATTTTAA
1 TACATGAATATAATTATAA
27780667 TACATGAATAT-ATATATAA
1 TACATGAATATAAT-TATAA
27780686 TA
1 TA
27780688 TATTCAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
TACATGAATATAATTATAA
Found at i:27785013 original size:12 final size:12
Alignment explanation
Indices: 27784962--27785006 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
27784952 ATTAAATACG
27784962 AATTTGAGAG-A
1 AATTTGAGAGAA
*
27784973 AATTTG-GAAGGA
1 AATTTGAG-AGAA
27784985 AA-TTGAGAGAA
1 AATTTGAGAGAA
27784996 AATTTGAGAGA
1 AATTTGAGAGA
27785007 GGATTTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 1 0.03
11 16 0.55
12 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (12 bp):
AATTTGAGAGAA
Found at i:27795345 original size:18 final size:18
Alignment explanation
Indices: 27795322--27795359 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
27795312 TCATAATCAC
27795322 TTGAAAATTTCTTTTCAT
1 TTGAAAATTTCTTTTCAT
27795340 TTGAAAATTTCTTTTCAT
1 TTGAAAATTTCTTTTCAT
27795358 TT
1 TT
27795360 CTCATCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (18 bp):
TTGAAAATTTCTTTTCAT
Found at i:27801433 original size:45 final size:45
Alignment explanation
Indices: 27801369--27801556 Score: 220
Period size: 45 Copynumber: 4.2 Consensus size: 45
27801359 TACTACGTGT
* *
27801369 ACTGGGTACCATTAATTATAAAGGTGGTTGCTGTGTGCTGATTCC
1 ACTGGGTATCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * * *
27801414 ACTGGGTATGATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
1 ACTGGGTATCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCC
* *
27801459 ACCGGGTA-CTATTAATTATAAAGGTGGTTGCTATGTGTTGATTCC
1 ACTGGGTATC-ATTAATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * * * *
27801504 ACCGAGTATCATTGACTATAAGGGTGG-TGCTATGTGCTGA-TCC
1 ACTGGGTATCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCC
*
27801547 ACTGTGTATC
1 ACTGGGTATC
27801557 TGTTATTATT
Statistics
Matches: 124, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
43 11 0.09
44 12 0.10
45 100 0.81
46 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.36
Consensus pattern (45 bp):
ACTGGGTATCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCC
Found at i:27801530 original size:90 final size:88
Alignment explanation
Indices: 27801372--27801548 Score: 246
Period size: 90 Copynumber: 2.0 Consensus size: 88
27801362 TACGTGTACT
* * * * *
27801372 GGGTACCATTAATTATAAAGGTGGTTGCTGTGTGCTGATTCCACTGGGTATGATTGATTATAAAG
1 GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAGTATCATTGACTATAAAG
* *
27801437 GTGGTTGTTGTGTGCTGATTCCACC
66 GTGG-TGCTATGTGCTGA-TCCACC
* * *
27801462 GGGTACTATTAATTATAAAGGTGGTTGCTATGTGTTGATTCCACCGAGTATCATTGACTATAAGG
1 GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAGTATCATTGACTATAAAG
27801527 GTGGTGCTATGTGCTGATCCAC
66 GTGGTGCTATGTGCTGATCCAC
27801549 TGTGTATCTG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 5 0.06
89 11 0.14
90 61 0.79
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.36
Consensus pattern (88 bp):
GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAGTATCATTGACTATAAAG
GTGGTGCTATGTGCTGATCCACC
Found at i:27808197 original size:12 final size:11
Alignment explanation
Indices: 27808171--27808204 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
27808161 TAGACCCAAC
27808171 TTGAATTAATT
1 TTGAATTAATT
*
27808182 TTGAATCTATTT
1 TTGAAT-TAATT
27808194 TTGAATTAATT
1 TTGAATTAATT
27808205 CACTTGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (11 bp):
TTGAATTAATT
Found at i:27810151 original size:44 final size:44
Alignment explanation
Indices: 27810085--27810203 Score: 159
Period size: 44 Copynumber: 2.7 Consensus size: 44
27810075 TACCATGGTG
**
27810085 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-C
1 AATCTTATCTCTTTGAAGTTGCAGTGGAGCAGATTAAAGCCATC
* * *
27810128 AATCCTTATCTCTTTGAAGTTGCAATGGAGAAGATTAAAGCCATT
1 AAT-CTTATCTCTTTGAAGTTGCAGTGGAGCAGATTAAAGCCATC
* *
27810173 AATCTTATCTCTTTGAAGTTTCGGTGGAGCA
1 AATCTTATCTCTTTGAAGTTGCAGTGGAGCA
27810204 TATTGAAACA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 3 0.05
44 59 0.91
45 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (44 bp):
AATCTTATCTCTTTGAAGTTGCAGTGGAGCAGATTAAAGCCATC
Found at i:27810461 original size:45 final size:42
Alignment explanation
Indices: 27810411--27810598 Score: 144
Period size: 45 Copynumber: 4.3 Consensus size: 42
27810401 GCTACAAACC
27810411 ACAAATCTTATACCCTCAAAGTTGCAGTAGAGCAGATTGAAGAT
1 ACAAATCTTAT-CCCT-AAAGTTGCAGTAGAGCAGATTGAAGAT
* * *
27810455 AGCAAATCTTATCGCTCTGAAGTTGCAGTAGAGCAGATTAAAGTT
1 A-CAAATCTTATC-C-CTAAAGTTGCAGTAGAGCAGATTGAAGAT
* * * * * *
27810500 ATAAACCTTACCCCTGAAGTTGCAGT-GAGACAGATTGATGGT
1 ACAAATCTTATCCCTAAAGTTGCAGTAGAG-CAGATTGAAGAT
* * ** * * *
27810542 ATAGATCTTACTTCCCTAAAGTTATAGTGGAGTAGATCGAAGAT
1 ACAAATCTTA--TCCCTAAAGTTGCAGTAGAGCAGATTGAAGAT
27810586 AGCAAATCTTATC
1 A-CAAATCTTATC
27810599 TTTCTGAACT
Statistics
Matches: 115, Mismatches: 21, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
41 3 0.03
42 30 0.26
43 3 0.03
44 31 0.27
45 46 0.40
46 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (42 bp):
ACAAATCTTATCCCTAAAGTTGCAGTAGAGCAGATTGAAGAT
Found at i:27810552 original size:42 final size:42
Alignment explanation
Indices: 27810429--27810544 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 42
27810419 TATACCCTCA
* * * * *
27810429 AAGTTGCAGTAGAGCAGATTGAAGATAGCAAATCTTATCGCTCTG
1 AAGTTGCAGTAGAGCAGATTAAAGGTA-TAAACCTTA-C-CCCTG
*
27810474 AAGTTGCAGTAGAGCAGATTAAAGTTATAAACCTTACCCCTG
1 AAGTTGCAGTAGAGCAGATTAAAGGTATAAACCTTACCCCTG
* *
27810516 AAGTTGCAGT-GAGACAGATTGATGGTATA
1 AAGTTGCAGTAGAG-CAGATTAAAGGTATA
27810545 GATCTTACTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
41 3 0.05
42 26 0.42
43 1 0.02
44 7 0.11
45 25 0.40
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (42 bp):
AAGTTGCAGTAGAGCAGATTAAAGGTATAAACCTTACCCCTG
Found at i:27812355 original size:52 final size:54
Alignment explanation
Indices: 27812299--27812408 Score: 156
Period size: 53 Copynumber: 2.1 Consensus size: 54
27812289 AACATTATTC
*
27812299 ATATTTGA-TTTATCAATTT-ATCATTCTTTTTAC-TTTAAAATATTTAAATTTA
1 ATATTT-ATTTTATCAATTTGATCATTATTTTTACTTTTAAAATATTTAAATTTA
* *
27812351 ATA-TTATTTTATCTATTTGTTCATTATTTTTACTTTTAAAATATTTAAATTTA
1 ATATTTATTTTATCAATTTGATCATTATTTTTACTTTTAAAATATTTAAATTTA
27812404 ATATT
1 ATATT
27812409 ATATGTATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
50 1 0.02
51 12 0.24
52 15 0.29
53 22 0.43
54 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (54 bp):
ATATTTATTTTATCAATTTGATCATTATTTTTACTTTTAAAATATTTAAATTTA
Found at i:27812404 original size:53 final size:55
Alignment explanation
Indices: 27812319--27812424 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 55
27812309 TATCAATTTA
*
27812319 TCATTCTTTTTACTTTAAAATATTTAAATTTAATATTAT-T-T-TATCTATTTGT
1 TCATTATTTTTACTTTAAAATATTTAAATTTAATATTATATGTATATCTATTTGT
27812371 TCATTATTTTTACTTTTAAAATATTTAAATTTAATATTATATGTATATCTATTT
1 TCATTATTTTTAC-TTTAAAATATTTAAATTTAATATTATATGTATATCTATTT
27812425 ATCTCCAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
52 12 0.24
53 26 0.53
54 1 0.02
55 1 0.02
56 9 0.18
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (55 bp):
TCATTATTTTTACTTTAAAATATTTAAATTTAATATTATATGTATATCTATTTGT
Found at i:27820806 original size:4 final size:4
Alignment explanation
Indices: 27820793--27820838 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
27820783 AAGGTTGAAG
*
27820793 AAAT -AAT AAAT AAAT GAAT AAAT AAAT AAAT AAA- ATAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAA
27820839 ATAGTTTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 4 0.11
4 32 0.86
5 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:27822172 original size:44 final size:44
Alignment explanation
Indices: 27822064--27822286 Score: 227
Period size: 44 Copynumber: 5.0 Consensus size: 44
27822054 GATTTGTAAC
* * * *
27822064 TTGTAGCTTCAATCTATTCCACCGCAA-TGTC-AGAGAAATAAGATT
1 TTGTAGCTTCAATCTACTCCACTGTAACT-TCAAG-GAGATAAGA-T
* * *
27822109 TTCTATCTTCAATCTGCTCCACTGTAACTTCAAGGAGATAAGAT
1 TTGTAGCTTCAATCTACTCCACTGTAACTTCAAGGAGATAAGAT
* * *
27822153 TTGTAGCTTCAATCTGCTCCACTGCAACTTCATGGAGATAAGAT
1 TTGTAGCTTCAATCTACTCCACTGTAACTTCAAGGAGATAAGAT
* *
27822197 TCGTAGCTTCAATCTACTCCACTGTAACTT-TAGAGAGATAAGAT
1 TTGTAGCTTCAATCTACTCCACTGTAACTTCAAG-GAGATAAGAT
** * * * *
27822241 TCATAGCTTCAATCTATTCCACTGTAACTTTAGGGAGATACGAT
1 TTGTAGCTTCAATCTACTCCACTGTAACTTCAAGGAGATAAGAT
27822285 TT
1 TT
27822287 ACTACGGTTA
Statistics
Matches: 152, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.01
44 116 0.76
45 32 0.21
46 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
TTGTAGCTTCAATCTACTCCACTGTAACTTCAAGGAGATAAGAT
Found at i:27822235 original size:88 final size:86
Alignment explanation
Indices: 27822064--27822285 Score: 250
Period size: 88 Copynumber: 2.5 Consensus size: 86
27822054 GATTTGTAAC
* * * *
27822064 TTGTAGCTTCAATCTATTCCACCGCAA-TGTCAGAGAAATAAGATTTTCTATCTTCAATCTGCTC
1 TTGTAGCTTCAATCTATTCCACTGCAACT-TCAG-GAGATAAGA--TTCTAGCTTCAATCTACTC
27822128 CACTGTAACTTCAAGGAGATAAGAT
62 CACTGTAACTTCAAGGAGATAAGAT
**
27822153 TTGTAGCTTCAATCTGCTCCACTGCAACTTCATGGAGATAAGATTCGTAGCTTCAATCTACTCCA
1 TTGTAGCTTCAATCTATTCCACTGCAACTTCA-GGAGATAAGATTC-TAGCTTCAATCTACTCCA
*
27822218 CTGTAACTT-TAGAGAGATAAGAT
64 CTGTAACTTCAAG-GAGATAAGAT
** * * *
27822241 TCATAGCTTCAATCTATTCCACTGTAACTTTAGGGAGATACGATT
1 TTGTAGCTTCAATCTATTCCACTGCAACTTCA-GGAGATAAGATT
27822286 TACTACGGTT
Statistics
Matches: 114, Mismatches: 15, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
87 5 0.04
88 72 0.63
89 35 0.31
90 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (86 bp):
TTGTAGCTTCAATCTATTCCACTGCAACTTCAGGAGATAAGATTCTAGCTTCAATCTACTCCACT
GTAACTTCAAGGAGATAAGAT
Found at i:27829026 original size:4 final size:4
Alignment explanation
Indices: 27829012--27829060 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
27829002 AAAAAGGTTG
* *
27829012 AATA AAT- AATA AATA AATA AATA ACTA AATA ACTA AA-A TAATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA -AATA AATA
27829059 AA
1 AA
27829061 ACACTTTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 4 0.11
4 33 0.87
5 1 0.03
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:27829040 original size:12 final size:11
Alignment explanation
Indices: 27829012--27829060 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
27829002 AAAAAGGTTG
27829012 AATAAATAATA
1 AATAAATAATA
27829023 AATAAATAAATA
1 AATAAAT-AATA
*
27829035 ACTAAATAACT-
1 AATAAATAA-TA
27829046 -A-AAATAATA
1 AATAAATAATA
27829055 AATAAA
1 AATAAA
27829061 ACACTTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
8 1 0.03
9 6 0.19
10 1 0.03
11 12 0.39
12 11 0.35
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (11 bp):
AATAAATAATA
Found at i:27834265 original size:17 final size:17
Alignment explanation
Indices: 27834243--27834276 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27834233 ATGTTAATTC
27834243 AATAATATTTTTTTGAT
1 AATAATATTTTTTTGAT
27834260 AATAATATTTTTTTGAT
1 AATAATATTTTTTTGAT
27834277 TCATGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
AATAATATTTTTTTGAT
Found at i:27847703 original size:26 final size:26
Alignment explanation
Indices: 27847674--27847725 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
27847664 AGGGACCTCT
27847674 CACATAGACAATCCTGGAAGACTTCC
1 CACATAGACAATCCTGGAAGACTTCC
* * *
27847700 CACATAGACAGTTCTGGCAGACTTCC
1 CACATAGACAATCCTGGAAGACTTCC
27847726 ACGTAGATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (26 bp):
CACATAGACAATCCTGGAAGACTTCC
Found at i:27847846 original size:26 final size:26
Alignment explanation
Indices: 27847817--27847936 Score: 105
Period size: 26 Copynumber: 4.6 Consensus size: 26
27847807 TTATTAAATG
27847817 GTCCTTGCAGACTTTCCCATTAGATA
1 GTCCTTGCAGACTTTCCCATTAGATA
* * * *
27847843 GTCCGTGCGGACCTTCCTATTAGATA
1 GTCCTTGCAGACTTTCCCATTAGATA
* * * * *
27847869 GTCCCTACAAACTTTCCCATCAGATG
1 GTCCTTGCAGACTTTCCCATTAGATA
** **
27847895 GTCCTTGTGGACTTTTTCATTAGATA
1 GTCCTTGCAGACTTTCCCATTAGATA
**
27847921 GTCCACGCAGACTTTC
1 GTCCTTGCAGACTTTC
27847937 AACATTTACA
Statistics
Matches: 68, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
26 68 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (26 bp):
GTCCTTGCAGACTTTCCCATTAGATA
Found at i:27847935 original size:52 final size:52
Alignment explanation
Indices: 27847808--27847936 Score: 127
Period size: 52 Copynumber: 2.5 Consensus size: 52
27847798 GGACTTCCCT
* * * *
27847808 TATTAAATGGTCCTTGCAGACTTTCCCATTAGATAGTCCGTGCGGACCTTCC
1 TATTAGATAGTCCCTGCAGACTTTCCCATCAGATAGTCCGTGCGGACCTTCC
* * * * * **
27847860 TATTAGATAGTCCCTACAAACTTTCCCATCAGATGGTCCTTGTGGA-CTTTT
1 TATTAGATAGTCCCTGCAGACTTTCCCATCAGATAGTCCGTGCGGACCTTCC
27847911 TCATTAGATAGTCCAC-GCAGACTTTC
1 T-ATTAGATAGTCC-CTGCAGACTTTC
27847937 AACATTTACA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
51 4 0.06
52 57 0.92
53 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (52 bp):
TATTAGATAGTCCCTGCAGACTTTCCCATCAGATAGTCCGTGCGGACCTTCC
Found at i:27854002 original size:22 final size:23
Alignment explanation
Indices: 27853956--27854002 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
27853946 AACATTGAAG
*
27853956 AATTTCGATTATAATATATAGGA
1 AATTTCGATTATAATATATACGA
27853979 AATTT-GATTATAAGTAT-TACGA
1 AATTTCGATTATAA-TATATACGA
27854001 AA
1 AA
27854003 ATGATGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (23 bp):
AATTTCGATTATAATATATACGA
Found at i:27854004 original size:23 final size:23
Alignment explanation
Indices: 27853956--27854004 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
27853946 AACATTGAAG
*
27853956 AATTTCGATTATAATATATAGGA
1 AATTTCGATTATAATATATAGAA
27853979 AATTT-GATTATAAGTAT-TACGAA
1 AATTTCGATTATAA-TATATA-GAA
27854002 AAT
1 AAT
27854005 GATGTCATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (23 bp):
AATTTCGATTATAATATATAGAA
Found at i:27864572 original size:22 final size:22
Alignment explanation
Indices: 27864540--27864581 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27864530 TATATAATTA
*
27864540 ATATTACTTGAATAGTTATGAG
1 ATATTACTTGAATAATTATGAG
*
27864562 ATATTAGTTGAATAATTATG
1 ATATTACTTGAATAATTATG
27864582 TCTCTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (22 bp):
ATATTACTTGAATAATTATGAG
Found at i:27864836 original size:127 final size:127
Alignment explanation
Indices: 27864673--27864926 Score: 499
Period size: 127 Copynumber: 2.0 Consensus size: 127
27864663 ATAGGAGCGA
*
27864673 GATCTCATTCAGAAGACATACATAAAATTCTCAGAAGGTCTTTCTGTCTTTCCTCCATCTTCTGC
1 GATCTCATTCAGAAGACATACATAAAATTCTCAGAAGGTCTTTCTGTCTTTCCTCCATATTCTGC
27864738 TATTATTAGATTGTTTTATAAAGAATTTTTATAGTAATTCTTTATAGAAATTGATTTGCTTG
66 TATTATTAGATTGTTTTATAAAGAATTTTTATAGTAATTCTTTATAGAAATTGATTTGCTTG
27864800 GATCTCATTCAGAAGACATACATAAAATTCTCAGAAGGTCTTTCTGTCTTTCCTCCATATTCTGC
1 GATCTCATTCAGAAGACATACATAAAATTCTCAGAAGGTCTTTCTGTCTTTCCTCCATATTCTGC
27864865 TATTATTAGATTGTTTTATAAAGAATTTTTATAGTAATTCTTTATAGAAATTGATTTGCTTG
66 TATTATTAGATTGTTTTATAAAGAATTTTTATAGTAATTCTTTATAGAAATTGATTTGCTTG
27864927 TTATGCTATG
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (127 bp):
GATCTCATTCAGAAGACATACATAAAATTCTCAGAAGGTCTTTCTGTCTTTCCTCCATATTCTGC
TATTATTAGATTGTTTTATAAAGAATTTTTATAGTAATTCTTTATAGAAATTGATTTGCTTG
Found at i:27878141 original size:25 final size:25
Alignment explanation
Indices: 27878105--27878168 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
27878095 AATCGATATA
* * **
27878105 CTCACTCAAGCTGTAGATTGGTATG
1 CTCACACAAGCTGTAAATCAGTATG
* *
27878130 CTCTCACAAGCTATAAATCAGTATG
1 CTCACACAAGCTGTAAATCAGTATG
27878155 CTCACACAAGCTGT
1 CTCACACAAGCTGT
27878169 GGGTCGAAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (25 bp):
CTCACACAAGCTGTAAATCAGTATG
Found at i:27881073 original size:27 final size:27
Alignment explanation
Indices: 27881036--27881243 Score: 213
Period size: 27 Copynumber: 7.7 Consensus size: 27
27881026 CTTAGGCTAA
*
27881036 AAAATTACCGAAATACCCTCGAAGGGT
1 AAAATTACCAAAATACCCTCGAAGGGT
*
27881063 AAAATTACCGAAATACCCTCGAAGGGT
1 AAAATTACCAAAATACCCTCGAAGGGT
* * * * *
27881090 AAAATTATCGAAATACCATCGAATGAT
1 AAAATTACCAAAATACCCTCGAAGGGT
*
27881117 AAAATTACCAAAATACCC-CCATAGGG-
1 AAAATTACCAAAATACCCTCGA-AGGGT
*
27881143 AAAATTTACTAAAATACCCTCGAAGGGT
1 AAAA-TTACCAAAATACCCTCGAAGGGT
* * * *
27881171 AAAATGACTAATATACCCTTCGCAGGGT
1 AAAATTACCAAAATACCC-TCGAAGGGT
* * *
27881199 AAAATGATCAAAATACCCCCGAAGGGT
1 AAAATTACCAAAATACCCTCGAAGGGT
* *
27881226 AAAATGACTAAAATACCC
1 AAAATTACCAAAATACCC
27881244 CCATATGGTA
Statistics
Matches: 154, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
26 6 0.04
27 119 0.77
28 29 0.19
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGAAGGGT
Found at i:27881240 original size:82 final size:82
Alignment explanation
Indices: 27881036--27881269 Score: 235
Period size: 82 Copynumber: 2.9 Consensus size: 82
27881026 CTTAGGCTAA
* * * ** * *
27881036 AAAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGA
1 AAAATGACCAAAATACCCCCGAAGGGTAAAATTACTAAAATACCCTCGAAGGGTAAAATGA-CTA
*
27881101 A-ATA-CCATCGAATGAT
65 ATATACCCATCGAAGGAT
*
27881117 AAAATTACCAAAATACCCCC-ATAGGG-AAAATTTACTAAAATACCCTCGAAGGGTAAAATGACT
1 AAAATGACCAAAATACCCCCGA-AGGGTAAAA-TTACTAAAATACCCTCGAAGGGTAAAATGACT
* * *
27881180 AATATACCCTTCGCAGGGT
64 AATATACCCATCGAAGGAT
* * * * * *
27881199 AAAATGATCAAAATACCCCCGAAGGGTAAAATGACTAAAATACCC-CCATATGGTAAAATGATTG
1 AAAATGACCAAAATACCCCCGAAGGGTAAAATTACTAAAATACCCTCGA-AGGGTAAAATGACTA
27881263 ATATACC
65 ATATACC
27881270 TTAGGAGTTG
Statistics
Matches: 129, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
80 8 0.06
81 54 0.42
82 62 0.48
83 5 0.04
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (82 bp):
AAAATGACCAAAATACCCCCGAAGGGTAAAATTACTAAAATACCCTCGAAGGGTAAAATGACTAA
TATACCCATCGAAGGAT
Found at i:27881253 original size:27 final size:26
Alignment explanation
Indices: 27881116--27881259 Score: 132
Period size: 27 Copynumber: 5.3 Consensus size: 26
27881106 CATCGAATGA
* *
27881116 TAAAATTACCAAAATACCCCCATAGGG
1 TAAAATGACTAAAATACCCCCA-AGGG
* *
27881143 -AAAATTTACTAAAATACCCTCGAAGGG
1 TAAAA-TGACTAAAATACCC-CCAAGGG
*
27881170 TAAAATGACTAATATACCCTTCGC-AGGG
1 TAAAATGACTAAAATACCC--C-CAAGGG
27881198 TAAAATGA-TCAAAATACCCCCGAAGGG
1 TAAAATGACT-AAAATACCCCC-AAGGG
*
27881225 TAAAATGACTAAAATACCCCCATATGG
1 TAAAATGACTAAAATACCCCCA-AGGG
27881252 TAAAATGA
1 TAAAATGA
27881260 TTGATATACC
Statistics
Matches: 100, Mismatches: 7, Indels: 20
0.79 0.06 0.16
Matches are distributed among these distances:
25 1 0.01
26 6 0.06
27 64 0.64
28 29 0.29
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (26 bp):
TAAAATGACTAAAATACCCCCAAGGG
Found at i:27881517 original size:26 final size:26
Alignment explanation
Indices: 27881441--27881518 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
27881431 ACAAATACTG
* * * * *
27881441 TTACTGGTAACTTTGCTACGTTACTG
1 TTACTGGCAACTTTGCTGCGATATTA
* * *
27881467 TTATTGGCAGCTCTGCTGC-ATTATTA
1 TTACTGGCAACTTTGCTGCGA-TATTA
27881493 TTACTGGCAACTTTGCTGCGATATTA
1 TTACTGGCAACTTTGCTGCGATATTA
27881519 GTGTGTTGGC
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
26 38 0.97
27 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (26 bp):
TTACTGGCAACTTTGCTGCGATATTA
Found at i:27881680 original size:22 final size:24
Alignment explanation
Indices: 27881627--27881675 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
27881617 TATTGTTTAC
*
27881627 TGTACTGGGCTAAAGCCCACATTG
1 TGTACTGAGCTAAAGCCCACATTG
*
27881651 TGTACTGAGCTAAGGCCCACATTG
1 TGTACTGAGCTAAAGCCCACATTG
27881675 T
1 T
27881676 ACTGATACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
TGTACTGAGCTAAAGCCCACATTG
Found at i:27888610 original size:27 final size:27
Alignment explanation
Indices: 27888572--27888819 Score: 268
Period size: 27 Copynumber: 9.2 Consensus size: 27
27888562 CCTGGGCTAA
**
27888572 AAAATTACCAAAATACCCTCGAAGTTT
1 AAAATTACCAAAATACCCTCGAAGGGT
* * *
27888599 AAAATTATCAAAATACACTAGAAGGGT
1 AAAATTACCAAAATACCCTCGAAGGGT
* * *
27888626 AAACTTACCGAAATACCTTCGAAGGGT
1 AAAATTACCAAAATACCCTCGAAGGGT
* *
27888653 AAAATTACCGAAATATCCTCGAAGGGT
1 AAAATTACCAAAATACCCTCGAAGGGT
* * *
27888680 AAAATTATCGAAATACCC-CCATAGGGT
1 AAAATTACCAAAATACCCTCGA-AGGGT
*
27888707 AAAATTACCAAAATACCCTCGAAGGAT
1 AAAATTACCAAAATACCCTCGAAGGGT
*
27888734 AAAATGACCAAAATACTCCT-GAAGGGT
1 AAAATTACCAAAATAC-CCTCGAAGGGT
* *
27888761 AAAATGACCAAAATACCCTCGAAGGAT
1 AAAATTACCAAAATACCCTCGAAGGGT
* * *
27888788 AAAATGACTAAAATACCC-CCATAGGGT
1 AAAATTACCAAAATACCCTCGA-AGGGT
27888815 AAAAT
1 AAAAT
27888820 GACTGATATA
Statistics
Matches: 189, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.04
27 177 0.94
28 5 0.03
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.21
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGAAGGGT
Found at i:27890385 original size:17 final size:18
Alignment explanation
Indices: 27890352--27890392 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
27890342 AAGGTAACCA
27890352 TTTATATTTCTATTAGT-T
1 TTTA-ATTTCTATTAGTCT
27890370 TTTAATTT-TATCTAGTCT
1 TTTAATTTCTAT-TAGTCT
27890388 TTTAA
1 TTTAA
27890393 ATGAAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.14
17 8 0.38
18 10 0.48
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTAATTTCTATTAGTCT
Found at i:27891442 original size:17 final size:17
Alignment explanation
Indices: 27891422--27891483 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
27891412 TTGAATGTTA
27891422 TGTGATTATATGAGTAT
1 TGTGATTATATGAGTAT
*
27891439 TGTGATATATGCTTGAATGT-T
1 TGTGAT-TAT--ATG-A-GTAT
27891460 ATGTGATTATATGAGTAT
1 -TGTGATTATATGAGTAT
27891478 TGTGAT
1 TGTGAT
27891484 ATAACCTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
17 14 0.39
18 5 0.14
19 2 0.06
20 2 0.06
21 5 0.14
22 8 0.22
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.47
Consensus pattern (17 bp):
TGTGATTATATGAGTAT
Found at i:27891450 original size:39 final size:39
Alignment explanation
Indices: 27891395--27891530 Score: 218
Period size: 39 Copynumber: 3.5 Consensus size: 39
27891385 CATATTTTTA
*
27891395 AGTATTGTGATGTATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
27891434 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
** *
27891473 AGTATTGTGATATAACCTTAAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
27891512 TGTAATGTGATATATGCTT
1 AGTATTGTGATATATGCTT
27891531 AAAACTGTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.46
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
Found at i:27897774 original size:39 final size:39
Alignment explanation
Indices: 27897719--27897859 Score: 210
Period size: 39 Copynumber: 3.6 Consensus size: 39
27897709 AACATGTTTT
*
27897719 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
27897758 TGAGTATTGTGGTATATGCTTAAATTTTATATGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
27897797 TGAGTATTGTGACATATCCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
27897836 TGTGTAATGTGATATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
27897860 AATGAATATG
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:27900419 original size:13 final size:13
Alignment explanation
Indices: 27900394--27900426 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27900384 TTTGTTTATC
*
27900394 TTTA-TTTATTTA
1 TTTATTTTAGTTA
27900406 TTTATTTTAGTTA
1 TTTATTTTAGTTA
27900419 TTTATTTT
1 TTTATTTT
27900427 TAGTCCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTATTTTAGTTA
Found at i:27900419 original size:17 final size:18
Alignment explanation
Indices: 27900383--27900425 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
27900373 TGTCTAATTC
* *
27900383 ATTTGTTTATCTTTATTT
1 ATTTATTTATCTTTAGTT
27900401 ATTTATTTAT-TTTAGTT
1 ATTTATTTATCTTTAGTT
27900418 ATTTATTT
1 ATTTATTT
27900426 TTAGTCCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (18 bp):
ATTTATTTATCTTTAGTT
Found at i:27901595 original size:57 final size:58
Alignment explanation
Indices: 27901508--27901621 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
27901498 AGAAATGGTG
* * *
27901508 AAAATGGAGAAATAGGAAACATTTGGAAATGATTATGGTTTTCTCAAAAATGAAAATT
1 AAAATAGAGAAATACGAAACATTTGGAAATGAATATGGTTTTCTCAAAAATGAAAATT
* * *
27901566 AAAATAGAGAAAT-CGAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAAT
1 AAAATAGAGAAATACGAAACATTTGGAAATGAATATGGTTTTCTCAAAAATGAAAAT
27901622 GACCTGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 38 0.76
58 12 0.24
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (58 bp):
AAAATAGAGAAATACGAAACATTTGGAAATGAATATGGTTTTCTCAAAAATGAAAATT
Found at i:27903042 original size:28 final size:28
Alignment explanation
Indices: 27903010--27903065 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
27903000 TTCATGCTTG
27903010 GTCTGTTAATTTATTTTTAAGATCCAAA
1 GTCTGTTAATTTATTTTTAAGATCCAAA
27903038 GTCTGTTAATTTATTTTTAAGATCCAAA
1 GTCTGTTAATTTATTTTTAAGATCCAAA
27903066 CTATCAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (28 bp):
GTCTGTTAATTTATTTTTAAGATCCAAA
Found at i:27905513 original size:16 final size:16
Alignment explanation
Indices: 27905492--27905537 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
27905482 GGGGTCGAAC
27905492 TTCTCTAATTCAAATT
1 TTCTCTAATTCAAATT
*
27905508 TTCTCTAATTTAAATT
1 TTCTCTAATTCAAATT
27905524 TTCT-TGAATTCAAA
1 TTCTCT-AATTCAAA
27905538 GCTATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 1 0.04
16 26 0.96
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.50
Consensus pattern (16 bp):
TTCTCTAATTCAAATT
Found at i:27906438 original size:7 final size:7
Alignment explanation
Indices: 27906426--27906474 Score: 80
Period size: 7 Copynumber: 7.0 Consensus size: 7
27906416 GTAAATAAAT
27906426 ATTATTA
1 ATTATTA
27906433 ATTATTA
1 ATTATTA
27906440 ATTATTA
1 ATTATTA
27906447 ATTATTA
1 ATTATTA
*
27906454 ATTATTT
1 ATTATTA
*
27906461 ATAATTA
1 ATTATTA
27906468 ATTATTA
1 ATTATTA
27906475 TTCAATTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTATTA
Found at i:27906483 original size:21 final size:21
Alignment explanation
Indices: 27906426--27906483 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
27906416 GTAAATAAAT
*
27906426 ATTATTAATT-ATTAATTATTA
1 ATTATTAATTAATT-ATAATTA
*
27906447 ATTATTAATTATTTATAATTA
1 ATTATTAATTAATTATAATTA
27906468 ATTATT-ATTCAATTAT
1 ATTATTAATT-AATTAT
27906484 GTTTAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 3 0.09
21 27 0.84
22 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTAATTAATTATAATTA
Found at i:27906530 original size:20 final size:21
Alignment explanation
Indices: 27906492--27906530 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27906482 ATGTTTAAAT
*
27906492 AAAATTATTAGTATATATTTA
1 AAAATTATTACTATATATTTA
*
27906513 AAAATTTTTACTAT-TATT
1 AAAATTATTACTATATATT
27906531 GTTGGTACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
AAAATTATTACTATATATTTA
Found at i:27909822 original size:35 final size:34
Alignment explanation
Indices: 27909770--27909835 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
27909760 CTATGAAAAT
27909770 TTTAACTTTAAAATTAAATATAA-AAATTAATGAA
1 TTTAACTTTAAAATTAAA-ATAATAAATTAATGAA
* *
27909804 TTTAATTTTAGAATTTAAAATAATAAATTAAT
1 TTTAACTTTA-AAATTAAAATAATAAATTAAT
27909836 AACACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (34 bp):
TTTAACTTTAAAATTAAAATAATAAATTAATGAA
Found at i:27909981 original size:19 final size:19
Alignment explanation
Indices: 27909959--27910024 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
27909949 ACAGTAACGA
*
27909959 AAAATTAAACACCACACAT
1 AAAATTAAACACCAAACAT
* * *
27909978 AAAATTACACAGACAGTAACAA
1 AAAATTAAACA-CCA--AACAT
*
27910000 AAAATTAAACACCATACAT
1 AAAATTAAACACCAAACAT
27910019 AAAATT
1 AAAATT
27910025 TATCAAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.59, C:0.20, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATTAAACACCAAACAT
Found at i:27910004 original size:22 final size:22
Alignment explanation
Indices: 27909943--27910006 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
27909933 AAAAATTAAA
*
27909943 ACACAGACAGTAACGAAAAATT
1 ACACAGACAGTAACAAAAAATT
* * * *
27909965 AAACA-CCA--CACATAAAATT
1 ACACAGACAGTAACAAAAAATT
27909984 ACACAGACAGTAACAAAAAATT
1 ACACAGACAGTAACAAAAAATT
27910006 A
1 A
27910007 AACACCATAC
Statistics
Matches: 30, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
19 12 0.40
20 2 0.07
21 2 0.07
22 14 0.47
ACGTcount: A:0.58, C:0.20, G:0.08, T:0.14
Consensus pattern (22 bp):
ACACAGACAGTAACAAAAAATT
Found at i:27910045 original size:41 final size:41
Alignment explanation
Indices: 27909943--27910024 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
27909933 AAAAATTAAA
*
27909943 ACACAGACAGTAACGAAAAATTAAACACCACACATAAAATT
1 ACACAGACAGTAACAAAAAATTAAACACCACACATAAAATT
*
27909984 ACACAGACAGTAACAAAAAATTAAACACCATACATAAAATT
1 ACACAGACAGTAACAAAAAATTAAACACCACACATAAAATT
27910025 TATCAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.57, C:0.21, G:0.06, T:0.16
Consensus pattern (41 bp):
ACACAGACAGTAACAAAAAATTAAACACCACACATAAAATT
Found at i:27910358 original size:30 final size:30
Alignment explanation
Indices: 27910296--27910360 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
27910286 ACTTTTCCCT
* * *
27910296 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCCTCCCACTATCCACC
*
27910326 CAAAACTTTTACTCCCCTCCC-CTATCTACC
1 CAAAACTTTTACT-CCCTCCCACTATCCACC
27910356 CAAAA
1 CAAAA
27910361 TCCATTTCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (30 bp):
CAAAACTTTTACTCCCTCCCACTATCCACC
Found at i:27910602 original size:18 final size:17
Alignment explanation
Indices: 27910576--27910633 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
27910566 ACTCCCCCTA
*
27910576 TTTACTTTCCCTCAAACT
1 TTTATTTTCCC-CAAACT
*
27910594 TTTATTTT-CCAAAACTT
1 TTTATTTTCCCCAAAC-T
27910611 TTTATTTTTCCCCTAAACT
1 TTTA-TTTTCCCC-AAACT
27910630 TTTA
1 TTTA
27910634 CTTCTCACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 11 0.33
19 7 0.21
20 4 0.12
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTATTTTCCCCAAACT
Found at i:27910926 original size:18 final size:18
Alignment explanation
Indices: 27910905--27910939 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27910895 AAAAATCATA
27910905 TTTTTACATT-TAATATAT
1 TTTTTA-ATTCTAATATAT
27910923 TTTTTAATTCTAATATA
1 TTTTTAATTCTAATATA
27910940 CATAGTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTAATTCTAATATAT
Found at i:27911639 original size:23 final size:23
Alignment explanation
Indices: 27911589--27911640 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
27911579 GTTAGGTGTC
* *
27911589 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
27911612 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
27911635 AGTATG
1 AGTATG
27911641 TTCAATTGCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:27916074 original size:146 final size:148
Alignment explanation
Indices: 27915900--27916196 Score: 395
Period size: 146 Copynumber: 2.0 Consensus size: 148
27915890 TTTGTGGCGT
* * * * * *
27915900 CGCTGTTGTTTATCTATTGCGGCGTTTTTAAT-AAAAACGTCACAAAAAATTATTTTATTTGGAA
1 CGCTATTGCTTATCTATTGCGGCATTTTT-ATGAAAAACGCCACAAAAAATTACTTTATTTGAAA
* *
27915964 TAAAACGACATTGTTTTGTTAT-ATAAAATGG-CGCTA-TTTTTTAAAATAAAATTATTTTTTGT
65 TAAAACGACAATGTTTTGCTATGATAAAA-GGACGCTATTTTTTTAAAATAAAATTATTTTTTGT
27916026 GGCGTTTTTAAAAAAAACGC
129 GGCGTTTTTAAAAAAAACGC
* * * *
27916046 CGCTATTGCTTATCTTTTGTGGCATTTTTATGAAAAACGCCGCAACAAATTACTTTATTTGAAAT
1 CGCTATTGCTTATCTATTGCGGCATTTTTATGAAAAACGCCACAAAAAATTACTTTATTTGAAAT
* *
27916111 AAAACGACAATGTTTTGCTATGCTAAAAGGACGCTATTTTTTTAAAGTAAAATTATTTTTTGTGG
66 AAAACGACAATGTTTTGCTATGATAAAAGGACGCTATTTTTTTAAAATAAAATTATTTTTTGTGG
* * *
27916176 CTTTTTTTATAAAAACGC
131 CGTTTTTAAAAAAAACGC
27916194 CGC
1 CGC
27916197 AAAAAATTAT
Statistics
Matches: 130, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
145 2 0.02
146 73 0.56
147 10 0.08
148 45 0.35
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (148 bp):
CGCTATTGCTTATCTATTGCGGCATTTTTATGAAAAACGCCACAAAAAATTACTTTATTTGAAAT
AAAACGACAATGTTTTGCTATGATAAAAGGACGCTATTTTTTTAAAATAAAATTATTTTTTGTGG
CGTTTTTAAAAAAAACGC
Found at i:27917718 original size:41 final size:40
Alignment explanation
Indices: 27917661--27917983 Score: 353
Period size: 41 Copynumber: 8.0 Consensus size: 40
27917651 ATAAAAAAGG
* * * *
27917661 GCATTAGTGGCCCTTCTTCAAAAATGCCGCTAAAGGGCCGA
1 GCATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCCGA
*
27917702 GCATTAGCGGCGCTTCTTCAAAAA-GCCGCTAAAAGGCCCCA
1 GCATTAGCGGCGCTT-TTCAAAAACGCCGCT-AAAGGCCCGA
** *
27917743 GCATTAGCGGCGC-TACCAAAAACGTCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCCGA
* * * *
27917782 GCATTAGCGGCACTTTATAAAAAACGTCGCTAAAGACCCGA
1 GCATTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGGCCCGA
* *
27917823 GCATTAGCGGTGCTTTATCAAAAACGCCGCTAAAGGCCCAA
1 GCATTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGGCCCGA
* * *
27917864 ACATTAGCGGCGTTTTTTTAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCG-CTTTTCAAAAACGCCGCTAAAGGCCCGA
* ** *
27917905 GCATTAGCGACGCTTTTTTAAAATGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCCGA
* * *
27917945 GCATTAGCAGCACTTTTTCAAAAATGCCGCTAAAGGCCC
1 GCATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCC
27917984 CAAAAACTCA
Statistics
Matches: 242, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
39 27 0.11
40 48 0.20
41 164 0.68
42 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.20
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:27918168 original size:12 final size:12
Alignment explanation
Indices: 27918151--27918176 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27918141 GTTTTTTCCC
27918151 AAACGCCGCTAA
1 AAACGCCGCTAA
27918163 AAACGCCGCTAA
1 AAACGCCGCTAA
27918175 AA
1 AA
27918177 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:27922382 original size:21 final size:21
Alignment explanation
Indices: 27922356--27922416 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
27922346 TTAAAAACAG
*
27922356 CTGTGGCGGTGAGATTAGTTA
1 CTGTGGCGGTGAGATTAGATA
*
27922377 CTGTGGCGGTGAGATTGGATA
1 CTGTGGCGGTGAGATTAGATA
* **
27922398 CTGTAGCAATGAGATTAGA
1 CTGTGGCGGTGAGATTAGA
27922417 AACAATTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.10, G:0.36, T:0.30
Consensus pattern (21 bp):
CTGTGGCGGTGAGATTAGATA
Found at i:27926099 original size:13 final size:13
Alignment explanation
Indices: 27926081--27926108 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
27926071 ATATTTCATC
27926081 TTTAAGAGGAGAG
1 TTTAAGAGGAGAG
27926094 TTTAAGAGGAGAG
1 TTTAAGAGGAGAG
27926107 TT
1 TT
27926109 GGATAACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
TTTAAGAGGAGAG
Found at i:27930730 original size:30 final size:30
Alignment explanation
Indices: 27930689--27930749 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
27930679 CTACTTCGGT
*
27930689 TGGTAGGGACTATCGCACCTCAAGCCAAAC
1 TGGTAGGGACTACCGCACCTCAAGCCAAAC
*
27930719 TGGTAGTGACTACCGCACCTCAAGCCAAAC
1 TGGTAGGGACTACCGCACCTCAAGCCAAAC
27930749 T
1 T
27930750 CGCTTACTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (30 bp):
TGGTAGGGACTACCGCACCTCAAGCCAAAC
Found at i:27932912 original size:39 final size:39
Alignment explanation
Indices: 27932862--27932957 Score: 165
Period size: 39 Copynumber: 2.5 Consensus size: 39
27932852 GGAGTTGTAA
* *
27932862 GTGACTATTCATCTACATCACTTCAGTGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
*
27932901 GTGACTATTCATCTTCATCACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
27932940 GTGACTATTCATCTACAT
1 GTGACTATTCATCTACAT
27932958 GCATGTGTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (39 bp):
GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
Found at i:27932991 original size:16 final size:16
Alignment explanation
Indices: 27932970--27933024 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
27932960 ATGTGTGTAA
27932970 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
27932986 CTCTTCA-CATTTCTAA--
1 CTCTTCATC--TTC-AAGT
27933002 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
27933018 CTCTTCA
1 CTCTTCA
27933025 CATACTTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 21 0.64
17 4 0.12
18 2 0.06
ACGTcount: A:0.20, C:0.33, G:0.04, T:0.44
Consensus pattern (16 bp):
CTCTTCATCTTCAAGT
Found at i:27933008 original size:32 final size:32
Alignment explanation
Indices: 27932967--27933027 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
27932957 TGCATGTGTG
27932967 TAACTCTTCATCTTCAAGTCTCTTCACATTTC
1 TAACTCTTCATCTTCAAGTCTCTTCACATTTC
27932999 TAACTCTTCATCTTCAAGTCTCTTCACAT
1 TAACTCTTCATCTTCAAGTCTCTTCACAT
27933028 ACTTAGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.03, T:0.43
Consensus pattern (32 bp):
TAACTCTTCATCTTCAAGTCTCTTCACATTTC
Found at i:27937344 original size:43 final size:41
Alignment explanation
Indices: 27937296--27937405 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 41
27937286 CTTCATCACA
* *
27937296 TATAGGAGTTGTAAGTGACTATTCATCTACATCACTTCAGTGC
1 TATAGGAGTTGT--GTGACTATTCATCTACATCACTTAAATGC
* *
27937339 TATAGGAG-T-TGTGACTATTTATCTTCATCACTTAAATGC
1 TATAGGAGTTGTGTGACTATTCATCTACATCACTTAAATGC
*
27937378 TATAGGAG-T-TGTGAGTATTCATCTACAT
1 TATAGGAGTTGTGTGACTATTCATCTACAT
27937406 GCATGTGTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
39 50 0.83
41 1 0.02
42 1 0.02
43 8 0.13
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (41 bp):
TATAGGAGTTGTGTGACTATTCATCTACATCACTTAAATGC
Found at i:27937368 original size:39 final size:39
Alignment explanation
Indices: 27937310--27937405 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 39
27937300 GGAGTTGTAA
* *
27937310 GTGACTATTCATCTACATCACTTCAGTGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
* *
27937349 GTGACTATTTATCTTCATCACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
*
27937388 GTGAGTATTCATCTACAT
1 GTGACTATTCATCTACAT
27937406 GCATGTGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (39 bp):
GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
Found at i:27937439 original size:16 final size:16
Alignment explanation
Indices: 27937418--27937472 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
27937408 ATGTGTGTAA
27937418 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
27937434 CTCTTCA-CATTTCTAA--
1 CTCTTCATC--TTC-AAGT
*
27937450 CTCTTCATTTTCAAGT
1 CTCTTCATCTTCAAGT
27937466 CTCTTCA
1 CTCTTCA
27937473 CATACCTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 21 0.66
17 3 0.09
18 2 0.06
ACGTcount: A:0.20, C:0.31, G:0.04, T:0.45
Consensus pattern (16 bp):
CTCTTCATCTTCAAGT
Found at i:27937456 original size:32 final size:32
Alignment explanation
Indices: 27937415--27937475 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
27937405 TGCATGTGTG
27937415 TAACTCTTCATCTTCAAGTCTCTTCACATTTC
1 TAACTCTTCATCTTCAAGTCTCTTCACATTTC
*
27937447 TAACTCTTCATTTTCAAGTCTCTTCACAT
1 TAACTCTTCATCTTCAAGTCTCTTCACAT
27937476 ACCTAGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.44
Consensus pattern (32 bp):
TAACTCTTCATCTTCAAGTCTCTTCACATTTC
Found at i:27939189 original size:20 final size:20
Alignment explanation
Indices: 27939127--27939206 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
27939117 ACTTTCAGGC
* * * *
27939127 TATGACTCAACATATGTTGC
1 TATGGCTCAACATAGGCTGT
*
27939147 TATGGCTCAACACAAGAGCTGT
1 TATGGCTCAACA-TAG-GCTGT
27939169 TATGGCTCAACATAGGCTGT
1 TATGGCTCAACATAGGCTGT
*
27939189 TATGGCTCAACACAGGCT
1 TATGGCTCAACATAGGCT
27939207 ACGTGTTGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
20 33 0.65
21 3 0.06
22 15 0.29
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (20 bp):
TATGGCTCAACATAGGCTGT
Found at i:27944302 original size:26 final size:25
Alignment explanation
Indices: 27944254--27944305 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
27944244 CATGTTTTCT
* *
27944254 TCTAAATCTAACATAAAATTAAAAA
1 TCTAAATCTAAAATAAAACTAAAAA
*
27944279 TCTAAATCCTAAAATATAACTAAAAA
1 TCTAAAT-CTAAAATAAAACTAAAAA
27944305 T
1 T
27944306 AAAAACAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (25 bp):
TCTAAATCTAAAATAAAACTAAAAA
Found at i:27945934 original size:33 final size:33
Alignment explanation
Indices: 27945895--27945958 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
27945885 TCCGCACAGA
27945895 AGAGATAGTCCACTAGGACAGTAAACACAGAAT
1 AGAGATAGTCCACTAGGACAGTAAACACAGAAT
* *
27945928 AGAGATAGTCCATTGGGACAGTAAACACAGA
1 AGAGATAGTCCACTAGGACAGTAAACACAGA
27945959 GCTAGTCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (33 bp):
AGAGATAGTCCACTAGGACAGTAAACACAGAAT
Found at i:27952628 original size:29 final size:29
Alignment explanation
Indices: 27952586--27952643 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
27952576 CTCGTACAGG
27952586 ATTCGGATGATGTTACCGTTTGTTTCTCT
1 ATTCGGATGATGTTACCGTTTGTTTCTCT
27952615 ATTCGGATGATGTTACCGTTTGTTTCTCT
1 ATTCGGATGATGTTACCGTTTGTTTCTCT
27952644 TGAAAATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (29 bp):
ATTCGGATGATGTTACCGTTTGTTTCTCT
Found at i:27953516 original size:2 final size:2
Alignment explanation
Indices: 27953509--27953533 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27953499 CTTCTAGAAT
27953509 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
27953534 ATTTGACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:27953935 original size:23 final size:23
Alignment explanation
Indices: 27953909--27953959 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
27953899 ACCTACTTTC
* *
27953909 TTACTGTAATAATTTTCGGGGTA
1 TTACAGTAATAATTTTCGGGATA
*
27953932 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAATAATTTTCGGGATA
27953955 TTACA
1 TTACA
27953960 TCGTTGGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAATAATTTTCGGGATA
Found at i:27962642 original size:20 final size:19
Alignment explanation
Indices: 27962617--27962655 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
27962607 TGATTCTCCG
27962617 AATGCCCAGTCCGGTCCTA
1 AATGCCCAGTCCGGTCCTA
*
27962636 NAATGCCGAGTCCGGTCCTA
1 -AATGCCCAGTCCGGTCCTA
27962656 TTTTTGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.21
Consensus pattern (19 bp):
AATGCCCAGTCCGGTCCTA
Found at i:27964618 original size:20 final size:20
Alignment explanation
Indices: 27964593--27964630 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27964583 CGGGTGTGAC
*
27964593 ACTATGGCTTAACATAGGCT
1 ACTATGGCTCAACATAGGCT
27964613 ACTATGGCTCAACATAGG
1 ACTATGGCTCAACATAGG
27964631 AATGTCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ACTATGGCTCAACATAGGCT
Found at i:27967068 original size:4 final size:4
Alignment explanation
Indices: 27967059--27967085 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
27967049 TCTATTGTAT
27967059 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
27967086 TTATCTACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:27968002 original size:28 final size:29
Alignment explanation
Indices: 27967957--27968028 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
27967947 TTCACTTTTT
* ** *
27967957 TATATATGTTATTTATTTTGAA-TATATG
1 TATATATATTATCCATTTTAAATTATATG
27967985 TATATATATTATCCATTTTAAATTTATATG
1 TATATATATTATCCATTTTAAA-TTATATG
27968015 TACATATATATTAT
1 T--ATATATATTAT
27968029 TTATTTCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.50
30 7 0.19
32 11 0.31
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (29 bp):
TATATATATTATCCATTTTAAATTATATG
Found at i:27970279 original size:24 final size:25
Alignment explanation
Indices: 27970237--27970294 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
27970227 ATGTCTCTTT
*
27970237 TTACA-TTCATTCCATTCATCTGCA
1 TTACATTTCATTACATTCATCTGCA
*
27970261 TTACATTTCATTACA-TCATTTGCA
1 TTACATTTCATTACATTCATCTGCA
*
27970285 -TAAATTTCAT
1 TTACATTTCAT
27970295 GAAAGAGCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.30
24 13 0.43
25 8 0.27
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.45
Consensus pattern (25 bp):
TTACATTTCATTACATTCATCTGCA
Found at i:27973206 original size:18 final size:18
Alignment explanation
Indices: 27973167--27973232 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 18
27973157 AATATTTGAA
27973167 AAAAAAG-AGAAAAGAAAGG
1 AAAAAAGAAGAAAAG-AA-G
27973186 AAAAGAAGAA-AAAAGAAG
1 AAAA-AAGAAGAAAAGAAG
*
27973204 AAAGAAAGAAAGAAGAAAAAG
1 AAA-AAAG-AAGAA-AAGAAG
27973225 AAAAAAGA
1 AAAAAAGA
27973233 GAGGCCAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
18 7 0.17
19 10 0.25
20 14 0.35
21 9 0.22
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAGAAAAGAAG
Found at i:27973215 original size:31 final size:30
Alignment explanation
Indices: 27973164--27973232 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
27973154 AAAAATATTT
* *
27973164 GAAAAAA-AAGAGAAAAGAAAGGAA-AAGAA
1 GAAAAAAGAAGAAAAAAGAAA-GAAGAAAAA
27973193 GAAAAAAGAAGAAAGAAAGAAAGAAGAAAAA
1 GAAAAAAGAAGAAA-AAAGAAAGAAGAAAAA
27973224 GAAAAAAGA
1 GAAAAAAGA
27973233 GAGGCCAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 7 0.20
30 8 0.23
31 20 0.57
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (30 bp):
GAAAAAAGAAGAAAAAAGAAAGAAGAAAAA
Found at i:27974944 original size:3 final size:3
Alignment explanation
Indices: 27974936--27974996 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
27974926 ATAATCAAAT
* *
27974936 ATA ATA ATA ACA ATA ATAA ATA GTA ATA ATA ATA ATA ATA ATA GCA-A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA --ATA
27974983 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
27974997 TAAGTGATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 1 0.02
3 44 0.88
4 4 0.08
5 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:27974951 original size:22 final size:22
Alignment explanation
Indices: 27974926--27974996 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
27974916 TAACACATAT
27974926 ATAATCAAATA-TAATAATAACA
1 ATAAT-AAATAGTAATAATAACA
*
27974948 ATAATAAATAGTAATAATAATA
1 ATAATAAATAGTAATAATAACA
* *
27974970 ATAAT-AATAGCAAATAATAATA
1 ATAATAAATAG-TAATAATAACA
27974992 ATAAT
1 ATAAT
27974997 TAAGTGATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.22
22 35 0.78
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (22 bp):
ATAATAAATAGTAATAATAACA
Found at i:27977187 original size:45 final size:45
Alignment explanation
Indices: 27977090--27977180 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
27977080 AGAACAGATC
* * *
27977090 ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGGAGCAG
1 ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAA
*
27977135 ACTGAAGATAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGCAA
1 ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAA
27977180 A
1 A
27977181 TCGAAGACAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (45 bp):
ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAA
Found at i:27977276 original size:44 final size:44
Alignment explanation
Indices: 27977228--27977424 Score: 163
Period size: 44 Copynumber: 4.5 Consensus size: 44
27977218 AAACCAATCC
*
27977228 TATCTCCCTAAAGTTGTAGTGGAGTGGATTAAAACCACAGATCT
1 TATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACCACAGATCT
* * * * * *
27977272 TATCTCTCTGAAGTTGCAGTGGAGTAGA-CAGAAGA-AATCA-ATCC
1 TATCTCCCTAAAGTTGCAGTGGAGTGGATTA-AA-ACCA-CAGATCT
* *
27977316 TATCTTCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGATCT
1 TATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACCACAGATCT
* * * * * * *
27977360 TATCTCTCTGAAGTTGCAGTAGAGTAGA-TCACATC-CAG-TCT
1 TATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACCACAGATCT
* *
27977401 TATCTCCTTGAAGTTGCAGTGGAG
1 TATCTCCCTAAAGTTGCAGTGGAG
27977425 CAGACAAAAG
Statistics
Matches: 120, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
41 24 0.20
42 3 0.03
43 8 0.07
44 81 0.68
45 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
TATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACCACAGATCT
Found at i:27977347 original size:88 final size:88
Alignment explanation
Indices: 27977222--27977516 Score: 298
Period size: 88 Copynumber: 3.4 Consensus size: 88
27977212 TTAAATAAAC
* *
27977222 CAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
1 CAATCCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGAAGTT
*
27977287 GCAGTGGAGTAGACAGAAGAAAT
66 GCAGTAGAGTAGACAGAAGAAAT
*
27977310 CAATCCTATCTTCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGAAGTT
1 CAATCCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGAAGTT
*
27977375 GCAGTAGAGTAGATC-----ACAT
66 GCAGTAGAGTAGA-CAGAAGAAAT
* * * * * * * *
27977394 CCAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACA-AAAGAAGCCACAAACCTTATCTCTCTG
1 -CAATCCTATCTCCCTAAAGTTGCAGTGGAG-TGA-ATTAA-AA-CCACAGATCTTATCTCTCTG
* *** *
27977458 AAGTTGCAGTAGAGCAGGTTGAAGTAA-
61 AAGTTGCAGTAGAGTAGACAGAAGAAAT
* *
27977485 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGT
1 CAA-TCCTATCTCCCTAAAGTTGCAGTGGAGT
27977517 AGACAGAAGT
Statistics
Matches: 173, Mismatches: 22, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
84 3 0.02
85 25 0.14
86 4 0.02
87 3 0.02
88 108 0.62
89 1 0.01
90 2 0.01
91 26 0.15
92 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (88 bp):
CAATCCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGAAGTT
GCAGTAGAGTAGACAGAAGAAAT
Found at i:27977508 original size:44 final size:45
Alignment explanation
Indices: 27977396--27977555 Score: 137
Period size: 44 Copynumber: 3.6 Consensus size: 45
27977386 GATCACATCC
* * * *
27977396 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACAAAAG-AAGCCACA
1 AGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACAGAAGTAA--C-TA
** * ***
27977443 AACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGTAAC-A
1 AGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACAGAAGTAACTA
* * **
27977487 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGTTGCTA
1 AGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACAGAAGTAACTA
*
27977532 ATTC-TATCTCCCTGAAGTTGCAGT
1 AGTCTTATCTCCCTGAAGTTGCAGT
27977556 GCAGCGAATT
Statistics
Matches: 91, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
44 54 0.59
45 4 0.04
46 1 0.01
47 30 0.33
48 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACAGAAGTAACTA
Found at i:27998912 original size:26 final size:26
Alignment explanation
Indices: 27998883--27998940 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
27998873 CCCTATATAT
27998883 GGCTCTTCATGAGCTTCCCGATTAAA
1 GGCTCTTCATGAGCTTCCCGATTAAA
** * *
27998909 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTCATGAGCTTCCCGATTAAA
27998935 GGCTCT
1 GGCTCT
27998941 CTGGAGCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCCGATTAAA
Found at i:27998952 original size:26 final size:26
Alignment explanation
Indices: 27998892--27999013 Score: 85
Period size: 26 Copynumber: 4.9 Consensus size: 26
27998882 TGGCTCTTCA
*
27998892 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTCTG
* *
27998918 TGAGCTTCCTGATTAATGGCTCTCTG
1 TGAGCTTCCCGATTAAAGGCTCTCTG
* * * *
27998944 -GAGCTTTCC-AATATA-GCTCGCT-
1 TGAGCTTCCCGATTAAAGGCTCTCTG
* * *
27998966 TGAACTTCCCGA-TAAATGGCTATCCG
1 TGAGCTTCCCGATTAAA-GGCTCTCTG
* *
27998992 -GAGCTTCTCGATTAATGGCTCT
1 TGAGCTTCCCGATTAAAGGCTCT
27999014 TCGGAGCTAC
Statistics
Matches: 71, Mismatches: 19, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
23 16 0.23
24 4 0.06
25 25 0.35
26 26 0.37
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTCTG
Found at i:27999008 original size:25 final size:25
Alignment explanation
Indices: 27998970--27999021 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
27998960 CTCGCTTGAA
27998970 CTTCCCGATAAATGGCTATCCGGAG
1 CTTCCCGATAAATGGCTATCCGGAG
* * * *
27998995 CTTCTCGATTAATGGCTCTTCGGAG
1 CTTCCCGATAAATGGCTATCCGGAG
27999020 CT
1 CT
27999022 ACCTGTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (25 bp):
CTTCCCGATAAATGGCTATCCGGAG
Found at i:27999146 original size:25 final size:24
Alignment explanation
Indices: 27999067--27999129 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 24
27999057 GCTCTTGTGG
27999067 GCTTCTCGTTATACAGCCCAGATAA
1 GCTTCTCGTTATACAGCCCA-ATAA
* *
27999092 GTTTCCCGTTATACAGCCCGAATAA
1 GCTTCTCGTTATACAGCCC-AATAA
27999117 GCTTCTCGTTATA
1 GCTTCTCGTTATA
27999130 TAGCTCACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (24 bp):
GCTTCTCGTTATACAGCCCAATAA
Done.