Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 117 of 126
Found at i:35104328 original size:15 final size:16
Alignment explanation
Indices: 35104296--35104333 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
35104286 AACCTGAAAC
*
35104296 TGAAAAAGCTTGAGCT
1 TGAAAAAGCTTGAACT
*
35104312 TGAAAAATC-TGAACT
1 TGAAAAAGCTTGAACT
35104327 TGAAAAA
1 TGAAAAA
35104334 AACTCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (16 bp):
TGAAAAAGCTTGAACT
Found at i:35118225 original size:32 final size:32
Alignment explanation
Indices: 35118154--35118226 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
35118144 ACTCAAACTC
* *
35118154 ATTTTATTTTTATTTTTAAAAATATTTATATT
1 ATTTTATTTTAATATTTAAAAATATTTATATT
*
35118186 ATGTTATTTTAATATTTAATAAAT-TTATATATT
1 ATTTTATTTTAATATTTAA-AAATATT-TATATT
35118219 -TTTTATTT
1 ATTTTATTT
35118227 ATTAATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (32 bp):
ATTTTATTTTAATATTTAAAAATATTTATATT
Found at i:35118757 original size:37 final size:37
Alignment explanation
Indices: 35118714--35118788 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
35118704 CTTTCCCTTT
* * *
35118714 TTAAAATAAGCATGAATTGTTTGAACTGAGAAAGAGA
1 TTAAAATAAGAATGAATAGTTTGAACTAAGAAAGAGA
*
35118751 TTAAAATAATAATGAATAGTTTGAACTAAGAAAGAGA
1 TTAAAATAAGAATGAATAGTTTGAACTAAGAAAGAGA
35118788 T
1 T
35118789 ATTTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (37 bp):
TTAAAATAAGAATGAATAGTTTGAACTAAGAAAGAGA
Found at i:35118973 original size:26 final size:25
Alignment explanation
Indices: 35118905--35118966 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
35118895 TTTTTTAATG
35118905 ATTTATTTTA-ATTA-T-AATTTTTA
1 ATTT-TTTTATATTATTGAATTTTTA
*
35118928 ATTTTTTTGTATTATTGAATTTTTA
1 ATTTTTTTATATTATTGAATTTTTA
35118953 TATTTTTTTATATT
1 -ATTTTTTTATATT
35118967 TTAGAATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 4 0.12
23 8 0.24
24 1 0.03
25 8 0.24
26 12 0.36
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (25 bp):
ATTTTTTTATATTATTGAATTTTTA
Found at i:35127706 original size:57 final size:58
Alignment explanation
Indices: 35127609--35127722 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 58
35127599 AAAATGAGTT
* *
35127609 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTAGGTTTAAAAATATTTGAGTTTA
1 GTTTATAAGTGTTATTTAAGAATAAAATTATATTTAGGTTTAAAAATATTTGAGTTTA
* * *
35127667 GTTTATAAGTGTT-TTTAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTT
1 GTTTATAAGTGTTATTTAAGAATAAAATTATATTTAGGTTTAAAAATATTTGAGTTT
35127723 TAAATTTTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 39 0.76
58 12 0.24
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (58 bp):
GTTTATAAGTGTTATTTAAGAATAAAATTATATTTAGGTTTAAAAATATTTGAGTTTA
Found at i:35128398 original size:17 final size:17
Alignment explanation
Indices: 35128369--35128451 Score: 94
Period size: 17 Copynumber: 4.8 Consensus size: 17
35128359 TTAAAAATTA
*
35128369 AAATTTTAATTTATTTT
1 AAATTTAAATTTATTTT
*
35128386 AAGTTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
35128403 AAACTTAAACTTATTTTTT
1 AAATTTAAA-TT-TATTTT
* *
35128422 GAGTTTAAATTTATTTT
1 AAATTTAAATTTATTTT
35128439 AAATTTAAATTTA
1 AAATTTAAATTTA
35128452 GAATTTAATT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
17 38 0.72
18 4 0.08
19 11 0.21
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:35129149 original size:24 final size:23
Alignment explanation
Indices: 35129100--35129145 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
35129090 TCATGGTATT
* *
35129100 TAATAAATATAGTAATAAATACA
1 TAATAAATATAATAATAAATAAA
35129123 TAATAAATAATAATAAT-AATAAA
1 TAATAAAT-ATAATAATAAATAAA
35129146 ATAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
TAATAAATATAATAATAAATAAA
Found at i:35130256 original size:29 final size:29
Alignment explanation
Indices: 35130218--35130340 Score: 111
Period size: 30 Copynumber: 4.1 Consensus size: 29
35130208 AGAAATCATA
* * *
35130218 TTTAACCCCTGAACCTTCTAAAAATTATAT
1 TTTAA-CCCTAAAACTTCTAAAAATTACAT
* * *
35130248 TTTGACCCTCAAACTTTCCAAAAATTACAT
1 TTTAACCCTAAAAC-TTCTAAAAATTACAT
* * *
35130278 TTTAACCCTCAAACTTCTTAAAAATCATAT
1 TTTAACCCTAAAACTTC-TAAAAATTACAT
* *
35130308 TTTAACCCTTAAACTTTTCAAAAATTACAT
1 TTTAACCCTAAAACTTCT-AAAAATTACAT
35130338 TTT
1 TTT
35130341 GCCTCCAAAC
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
29 11 0.14
30 66 0.86
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
TTTAACCCTAAAACTTCTAAAAATTACAT
Found at i:35130273 original size:30 final size:29
Alignment explanation
Indices: 35130232--35130489 Score: 186
Period size: 29 Copynumber: 8.8 Consensus size: 29
35130222 ACCCCTGAAC
*
35130232 CTTCTAAAAATTATATTTTGACCCTCAAA
1 CTTCCAAAAATTATATTTTGACCCTCAAA
* *
35130261 CTTTCCAAAAATTACATTTTAACCCTCAAA
1 C-TTCCAAAAATTATATTTTGACCCTCAAA
* * * *
35130291 CTTCTTAAAAATCATATTTTAACCCTTAAA
1 CTTC-CAAAAATTATATTTTGACCCTCAAA
* *
35130321 CTTTTCAAAAATTACATTTTG--CCTCCAAA
1 C-TTCCAAAAATTATATTTTGACCCT-CAAA
* * * *
35130350 CTTCCAAAAATCACATTTTTG-CTCTCGAA
1 CTTCCAAAAATTATA-TTTTGACCCTCAAA
* * *
35130379 CTTCCAAAAATTCTATTTTTGCCCCT-GAA
1 CTTCCAAAAATTATA-TTTTGACCCTCAAA
*
35130408 CTTCCAAAAATTCCAT-TTTTGTCCCT-AAA
1 CTTCCAAAAATT--ATATTTTGACCCTCAAA
** * * *
35130437 CTTCCAAAAATTCCATTTTTACTCTCGAA
1 CTTCCAAAAATTATATTTTGACCCTCAAA
* *
35130466 CTTCCAAAAATCATATTTTTACCC
1 CTTCCAAAAATTATATTTTGACCC
35130490 CGAATTTTTC
Statistics
Matches: 184, Mismatches: 34, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
28 22 0.12
29 94 0.51
30 65 0.35
31 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
CTTCCAAAAATTATATTTTGACCCTCAAA
Found at i:35130351 original size:29 final size:30
Alignment explanation
Indices: 35130237--35130576 Score: 154
Period size: 29 Copynumber: 11.6 Consensus size: 30
35130227 TGAACCTTCT
* *
35130237 AAAAATTATATTTTGACCCTCAAACTTTCC
1 AAAAATTACATTTTAACCCTCAAACTTTCC
*
35130267 AAAAATTACATTTTAACCCTCAAAC-TTCTT
1 AAAAATTACATTTTAACCCTCAAACTTTC-C
* * * *
35130297 AAAAATCATATTTTAACCCTTAAACTTTTC
1 AAAAATTACATTTTAACCCTCAAACTTTCC
*
35130327 AAAAATTACATTTT--GCCTCCAAAC-TTCC
1 AAAAATTACATTTTAACCCT-CAAACTTTCC
* ** * *
35130355 AAAAATCACATTTTTGCTCTCGAAC-TTCC
1 AAAAATTACATTTTAACCCTCAAACTTTCC
** *
35130384 AAAAATT-CTATTTTTGCCC-CTGAAC-TTCC
1 AAAAATTAC-ATTTTAACCCTC-AAACTTTCC
* **
35130413 AAAAATTCCATTTTTGTCCCT-AAAC-TTCC
1 AAAAATTACA-TTTTAACCCTCAAACTTTCC
* * * *
35130442 AAAAATTCCATTTTTACTCTCGAAC-TTCC
1 AAAAATTACATTTTAACCCTCAAACTTTCC
* * * **
35130471 AAAAATCATATTTTTACCC-CGAATTTTTCC
1 AAAAATTACATTTTAACCCTC-AAACTTTCC
* * * *
35130501 -AAAATGACATTTTTACCCCTAAAACTTT-T
1 AAAAATTACA-TTTTAACCCTCAAACTTTCC
* ** *
35130530 TAAAATTTTATTTTAACCCT-AAACTCTCC
1 AAAAATTACATTTTAACCCTCAAACTTTCC
* * *
35130559 GAAACTT-CATTTTGACCC
1 AAAAATTACATTTTAACCC
35130577 CGATTTTTCC
Statistics
Matches: 242, Mismatches: 51, Indels: 36
0.74 0.16 0.11
Matches are distributed among these distances:
28 44 0.18
29 107 0.44
30 89 0.37
31 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTCAAACTTTCC
Found at i:35130505 original size:58 final size:58
Alignment explanation
Indices: 35130262--35130516 Score: 173
Period size: 58 Copynumber: 4.4 Consensus size: 58
35130252 ACCCTCAAAC
* * * * * **
35130262 TTTCCAAAAATTACATTTTAACCCTCAAACTTCTTAAAAATCATATTTTAACCCTTAAACT
1 TTTCCAAAAATTACATTTTTACTCTCAAACTTC-CAAAAATCACATTTTTACCC-CGAA-T
** * *
35130323 TTT-CAAAAATTACATTTTGCCTC-CAAACTTCCAAAAATCACATTTTTGCTCTCGAA-
1 TTTCCAAAAATTACATTTTTACTCTCAAACTTCCAAAAATCACATTTTTAC-CCCGAAT
* * * * ** * *
35130379 CTTCCAAAAATT-CTATTTTTGC-CCCTGAACTTCCAAAAATTC-CATTTTTGTCCCTAAA
1 TTTCCAAAAATTAC-ATTTTTACTCTC-AAACTTCCAAAAA-TCACATTTTTACCCCGAAT
* * * *
35130437 CTTCCAAAAATTCCATTTTTACTCTCGAACTTCCAAAAATCATATTTTTACCCCGAATT
1 TTTCCAAAAATTACATTTTTACTCTCAAACTTCCAAAAATCACATTTTTACCCCGAA-T
*
35130496 TTTCC-AAAATGACATTTTTAC
1 TTTCCAAAAATTACATTTTTAC
35130517 CCCTAAAACT
Statistics
Matches: 156, Mismatches: 27, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
56 4 0.03
57 21 0.13
58 93 0.60
59 18 0.12
60 17 0.11
61 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (58 bp):
TTTCCAAAAATTACATTTTTACTCTCAAACTTCCAAAAATCACATTTTTACCCCGAAT
Found at i:35130505 original size:87 final size:85
Alignment explanation
Indices: 35130238--35130523 Score: 258
Period size: 87 Copynumber: 3.3 Consensus size: 85
35130228 GAACCTTCTA
* * * * * *
35130238 AAAATTATA-TTTTGACCCTCAAACTTTCCAAAAATTACATTTTAACCCTCAAACTTCTTAAAAA
1 AAAATTACATTTTTG-CCCT-AAAC-TTCCAAAAATTCCATTTTTACTCTCGAACTTC-CAAAAA
* ** *
35130302 TCATATTTTAACCCTTAAACTTTTCA
62 TCATATTTTTACCC-CGAA-TTTTCC
* *
35130328 AAAATTACA-TTTTGCCTCCAAACTTCCAAAAA-TCACATTTTTGCTCTCGAACTTCCAAAAATT
1 AAAATTACATTTTTGCC-CTAAACTTCCAAAAATTC-CATTTTTACTCTCGAACTTCCAAAAA-T
* *
35130391 C-TATTTTTGCCCCTGAA-CTTCC
63 CATATTTTTACCCC-GAATTTTCC
*
35130413 AAAAATTCCATTTTTGTCCCTAAACTTCCAAAAATTCCATTTTTACTCTCGAACTTCCAAAAATC
1 -AAAATTACATTTTTG-CCCTAAACTTCCAAAAATTCCATTTTTACTCTCGAACTTCCAAAAATC
35130478 ATATTTTTACCCCGAATTTTTCC
64 ATATTTTTACCCCGAA-TTTTCC
* *
35130501 AAAATGACATTTTTACCCCTAAA
1 AAAATTACATTTTT-GCCCTAAA
35130524 ACTTTTTAAA
Statistics
Matches: 162, Mismatches: 22, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
85 3 0.02
86 13 0.08
87 91 0.56
88 35 0.22
89 6 0.04
90 14 0.09
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (85 bp):
AAAATTACATTTTTGCCCTAAACTTCCAAAAATTCCATTTTTACTCTCGAACTTCCAAAAATCAT
ATTTTTACCCCGAATTTTCC
Found at i:35130989 original size:97 final size:98
Alignment explanation
Indices: 35130803--35130995 Score: 298
Period size: 97 Copynumber: 2.0 Consensus size: 98
35130793 TCCAAAATAT
* *
35130803 TTAAAATCAAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGC
1 TTAAAATCAAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCATTAACTTACTAGGCGC
*
35130868 GATTTTTCTTCAAACCGGGATAATCGAATACCC
66 GACTTTTCTTCAAACCGGGATAATCGAATACCC
* * * *
35130901 TTAAAA-CAAGTCAATGTTTCTTTATCTCTGGTTTTGAAAATTTGTGCATTAACTTACTAGGCGC
1 TTAAAATCAAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCATTAACTTACTAGGCGC
* *
35130965 GACTTTTCTTCAAATCGGGGTAATCGAATAC
66 GACTTTTCTTCAAACCGGGATAATCGAATAC
35130996 TCTTTTCGAA
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 80 0.93
98 6 0.07
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (98 bp):
TTAAAATCAAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCATTAACTTACTAGGCGC
GACTTTTCTTCAAACCGGGATAATCGAATACCC
Found at i:35133841 original size:20 final size:21
Alignment explanation
Indices: 35133780--35133871 Score: 114
Period size: 22 Copynumber: 4.3 Consensus size: 21
35133770 ATTATATTAT
35133780 TGTTTTGGTGCTGGTTTTTTAC
1 TGTTTTGGTGCT-GTTTTTTAC
*
35133802 TGTTTTGATTGCTGTTTTTTAC
1 TGTTTTG-GTGCTGTTTTTTAC
*
35133824 TGTTTTGGTACT-TTTTTTAC
1 TGTTTTGGTGCTGTTTTTTAC
* * *
35133844 TGTTTTGGTGTTTTTTTTTAT
1 TGTTTTGGTGCTGTTTTTTAC
35133865 TGTTTTG
1 TGTTTTG
35133872 ATTGTTGTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
20 18 0.29
21 17 0.27
22 23 0.37
23 4 0.06
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.66
Consensus pattern (21 bp):
TGTTTTGGTGCTGTTTTTTAC
Found at i:35133844 original size:9 final size:10
Alignment explanation
Indices: 35133793--35133849 Score: 62
Period size: 10 Copynumber: 5.5 Consensus size: 10
35133783 TTTGGTGCTG
35133793 GTTTTTTACT
1 GTTTTTTACT
*
35133803 GTTTTGATTGCT
1 GTTTT--TTACT
35133815 GTTTTTTACT
1 GTTTTTTACT
*
35133825 GTTTTGGTACT
1 GTTTT-TTACT
35133836 -TTTTTTACT
1 GTTTTTTACT
35133845 GTTTT
1 GTTTT
35133850 GGTGTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.10
10 22 0.56
11 4 0.10
12 9 0.23
ACGTcount: A:0.09, C:0.09, G:0.16, T:0.67
Consensus pattern (10 bp):
GTTTTTTACT
Found at i:35133877 original size:22 final size:21
Alignment explanation
Indices: 35133793--35133882 Score: 92
Period size: 22 Copynumber: 4.2 Consensus size: 21
35133783 TTTGGTGCTG
*
35133793 GTTTTTTACTGTTTTGATTGCT
1 GTTTTTTACTGTTTTG-TTGTT
* **
35133815 GTTTTTTACTGTTTTGGTACT
1 GTTTTTTACTGTTTTGTTGTT
*
35133836 -TTTTTTACTGTTTTGGTGTT
1 GTTTTTTACTGTTTTGTTGTT
* *
35133856 TTTTTTTATTGTTTTGATTGTT
1 GTTTTTTACTGTTTTG-TTGTT
35133878 GTTTT
1 GTTTT
35133883 GAGCTATTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.31
21 17 0.29
22 24 0.41
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (21 bp):
GTTTTTTACTGTTTTGTTGTT
Found at i:35133893 original size:23 final size:22
Alignment explanation
Indices: 35133867--35133925 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
35133857 TTTTTTATTG
*
35133867 TTTTGATTGTTGTTTTGAGCTA
1 TTTTTATTGTTGTTTTGAGCTA
* *
35133889 TTTTTTATTG-T-TTTGGTGCTA
1 -TTTTTATTGTTGTTTTGAGCTA
*
35133910 TTTTTACTGTTGTTTT
1 TTTTTATTGTTGTTTT
35133926 TGTTGCTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.28
21 9 0.31
22 4 0.14
23 8 0.28
ACGTcount: A:0.10, C:0.05, G:0.19, T:0.66
Consensus pattern (22 bp):
TTTTTATTGTTGTTTTGAGCTA
Found at i:35133899 original size:20 final size:21
Alignment explanation
Indices: 35133876--35133914 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35133866 GTTTTGATTG
35133876 TTGTTTT-GAGCTATTTTTTA
1 TTGTTTTGGAGCTATTTTTTA
*
35133896 TTGTTTTGGTGCTATTTTT
1 TTGTTTTGGAGCTATTTTT
35133915 ACTGTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67
Consensus pattern (21 bp):
TTGTTTTGGAGCTATTTTTTA
Found at i:35133932 original size:24 final size:23
Alignment explanation
Indices: 35133885--35133989 Score: 71
Period size: 21 Copynumber: 4.8 Consensus size: 23
35133875 GTTGTTTTGA
* *
35133885 GCTATTTTT-TATTG-TTTTGGT
1 GCTATTTTTCTGTTGTTTTTGTT
35133906 GCTATTTTTACTGTTGTTTTTGTT
1 GCTATTTTT-CTGTTGTTTTTGTT
* *
35133930 GCT-GTTTT-TGTTG-TTTTCTT
1 GCTATTTTTCTGTTGTTTTTGTT
* * *
35133950 GTTATTTTTGCTGCTGTTTTGGTT
1 GCTATTTTT-CTGTTGTTTTTGTT
*
35133974 GTTA-TTTT-TGTTGTTT
1 GCTATTTTTCTGTTGTTT
35133990 GAATGTTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
20 8 0.12
21 25 0.37
23 16 0.24
24 18 0.27
ACGTcount: A:0.06, C:0.07, G:0.20, T:0.68
Consensus pattern (23 bp):
GCTATTTTTCTGTTGTTTTTGTT
Found at i:35133938 original size:44 final size:44
Alignment explanation
Indices: 35133885--35133989 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
35133875 GTTGTTTTGA
* * * *
35133885 GCTATTTTTTATTGTTTTGGTGCTATTTTTACTGTTGTTTTTGTT
1 GCTA-TTTTTGTTGTTTTCGTGCTATTTTTACTGCTGTTTTGGTT
* * * *
35133930 GCTGTTTTTGTTGTTTTCTTGTTATTTTTGCTGCTGTTTTGGTT
1 GCTATTTTTGTTGTTTTCGTGCTATTTTTACTGCTGTTTTGGTT
*
35133974 GTTATTTTTGTTGTTT
1 GCTATTTTTGTTGTTT
35133990 GAATGTTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 47 0.94
45 3 0.06
ACGTcount: A:0.06, C:0.07, G:0.20, T:0.68
Consensus pattern (44 bp):
GCTATTTTTGTTGTTTTCGTGCTATTTTTACTGCTGTTTTGGTT
Found at i:35133941 original size:73 final size:74
Alignment explanation
Indices: 35133802--35133941 Score: 167
Period size: 73 Copynumber: 1.9 Consensus size: 74
35133792 GGTTTTTTAC
* * ** *
35133802 TGTTTTGATTGCTGTTTTTTACTGTTTTGGTACTTTTTTTACTGTTTTGGTGTTTTTTTTTATTG
1 TGTTTTGA-TGCTATTTTTTACTGTTTTGGTACTATTTTTACTGTTTTGGTGTTGCTGTTTATTG
35133867 TTTTGATTGT
65 TTTTGATTGT
* * **
35133877 TGTTTTGA-GCTATTTTTTATTGTTTTGGTGCTATTTTTACTGTTGTTTTTGTTGCTGTTT-TTG
1 TGTTTTGATGCTATTTTTTACTGTTTTGGTACTATTTTTACTGTT-TTGGTGTTGCTGTTTATTG
35133940 TT
65 TT
35133942 GTTTTCTTGT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 37 0.67
74 10 0.18
75 8 0.15
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (74 bp):
TGTTTTGATGCTATTTTTTACTGTTTTGGTACTATTTTTACTGTTTTGGTGTTGCTGTTTATTGT
TTTGATTGT
Found at i:35133959 original size:32 final size:33
Alignment explanation
Indices: 35133917--35133985 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
35133907 CTATTTTTAC
* * *
35133917 TGTTGTTTTTGTTGCTGTTTTTGTTGTT-TTCT
1 TGTTATTTTTGCTGCTGTTTTGGTTGTTATTCT
*
35133949 TGTTATTTTTGCTGCTGTTTTGGTTGTTATTTT
1 TGTTATTTTTGCTGCTGTTTTGGTTGTTATTCT
35133982 TGTT
1 TGTT
35133986 GTTTGAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.03, C:0.06, G:0.22, T:0.70
Consensus pattern (33 bp):
TGTTATTTTTGCTGCTGTTTTGGTTGTTATTCT
Found at i:35141302 original size:29 final size:28
Alignment explanation
Indices: 35141245--35141301 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
35141235 ATCGATACTT
*
35141245 ATGTTTATTTTTTTTATCCGTATTTAAA
1 ATGTTTATTTTTTTCATCCGTATTTAAA
35141273 ATGTTTATTTTTTTCATCCGTATTTAAA
1 ATGTTTATTTTTTTCATCCGTATTTAAA
35141301 A
1 A
35141302 AAAAAACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.58
Consensus pattern (28 bp):
ATGTTTATTTTTTTCATCCGTATTTAAA
Found at i:35143666 original size:57 final size:57
Alignment explanation
Indices: 35143595--35143724 Score: 140
Period size: 57 Copynumber: 2.3 Consensus size: 57
35143585 AATACTGTAA
** * * *
35143595 CAAATTAGGAAAAAATG-CCAGTTCAAG-CATCAAATTGGCTCAAAAAAGTTTAGGTAT
1 CAAATTATAAAAAAATGTCAAGTT-AAGACATCAAATTGG-ACAAAAAAATTTAGGTAT
* * * *
35143652 CAAATTATTAAAAAATGTCAAGTTTAGATATCGAATTGGACAAAAAAATTTAGGTAT
1 CAAATTATAAAAAAATGTCAAGTTAAGACATCAAATTGGACAAAAAAATTTAGGTAT
35143709 CAAATT-TAAAAAAATG
1 CAAATTATAAAAAAATG
35143725 ATAAATTCAG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
56 9 0.15
57 39 0.63
58 14 0.23
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.28
Consensus pattern (57 bp):
CAAATTATAAAAAAATGTCAAGTTAAGACATCAAATTGGACAAAAAAATTTAGGTAT
Found at i:35145962 original size:9 final size:10
Alignment explanation
Indices: 35145938--35146028 Score: 57
Period size: 9 Copynumber: 9.4 Consensus size: 10
35145928 AAAATTATTA
* *
35145938 TTTTAGAAAA
1 TTTTATAAAT
35145948 TTTTA-AAA-
1 TTTTATAAAT
*
35145956 TTTT-TAATT
1 TTTTATAAAT
*
35145965 TTTTATATAT
1 TTTTATAAAT
*
35145975 TCTTTAGAAAT
1 T-TTTATAAAT
*
35145986 CTTTTATAATT
1 -TTTTATAAAT
35145997 TTTTATAAAT
1 TTTTATAAAT
*
35146007 ATTT-TAAAT
1 TTTTATAAAT
*
35146016 TTTT-GAAAT
1 TTTTATAAAT
35146025 TTTT
1 TTTT
35146029 TTGTAATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
8 6 0.09
9 23 0.35
10 21 0.32
11 14 0.22
12 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:35146000 original size:10 final size:10
Alignment explanation
Indices: 35145956--35146039 Score: 57
Period size: 11 Copynumber: 8.3 Consensus size: 10
35145946 AATTTTAAAA
35145956 TTTT-TAATT
1 TTTTATAATT
35145965 TTTTATATATT
1 TTTTATA-ATT
* * *
35145976 CTTTAGAAATC
1 TTTTA-TAATT
35145987 TTTTATAATT
1 TTTTATAATT
*
35145997 TTTTATAAATA
1 TTTTAT-AATT
35146008 TTTTA-AATT
1 TTTTATAATT
*
35146017 TTTGA-AATTT
1 TTTTATAA-TT
*
35146027 TTTTGTAATT
1 TTTTATAATT
35146037 TTT
1 TTT
35146040 ATTGTGAGAG
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
9 13 0.22
10 21 0.36
11 23 0.40
12 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:35146214 original size:21 final size:24
Alignment explanation
Indices: 35146170--35146217 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
35146160 CGAATTACTT
*
35146170 ATTCGAATTGACTCGAATAATTCA
1 ATTCGAATTAACTCGAATAATTCA
35146194 ATTCG-ATTAACTC-AA-AATTCA
1 ATTCGAATTAACTCGAATAATTCA
35146215 ATT
1 ATT
35146218 TTTTTCGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 2 0.09
23 7 0.30
24 5 0.22
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (24 bp):
ATTCGAATTAACTCGAATAATTCA
Found at i:35148204 original size:18 final size:20
Alignment explanation
Indices: 35148167--35148215 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
35148157 ATTACAAAAT
*
35148167 AATTCAAAATCATTT-TTAA
1 AATTCAAAATCATTTATAAA
35148186 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATCATTTATAAA
35148205 AATTTCAAAAT
1 AA-TTCAAAAT
35148216 TTATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 15 0.56
20 8 0.30
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTCAAAATCATTTATAAA
Found at i:35148261 original size:21 final size:19
Alignment explanation
Indices: 35148225--35148272 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
35148215 TTTATATTTT
35148225 TAAAAATTATAAAAAAATC
1 TAAAAATTATAAAAAAATC
*
35148244 TAAAGAATATATAGAAAAAGT-
1 TAAA-AAT-TATA-AAAAAATC
35148265 TAAAAATT
1 TAAAAATT
35148273 TTCTAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 5 0.20
20 6 0.24
21 8 0.32
22 6 0.24
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (19 bp):
TAAAAATTATAAAAAAATC
Found at i:35148514 original size:21 final size:20
Alignment explanation
Indices: 35148489--35148536 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
35148479 CAATTCACTC
35148489 GATTTGA-TTCGACTCGACCT
1 GATTTGATTTC-ACTCGACCT
* *
35148509 GAATTTCATTTCACTCGACTT
1 G-ATTTGATTTCACTCGACCT
35148530 GATTTGA
1 GATTTGA
35148537 AAAAATTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 6 0.26
21 14 0.61
22 3 0.13
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
GATTTGATTTCACTCGACCT
Found at i:35154118 original size:23 final size:23
Alignment explanation
Indices: 35154090--35154152 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
35154080 TGTGTAATCG
*
35154090 TCAATAGCTCAAATTCGGTTCAA
1 TCAATAGCTCGAATTCGGTTCAA
**
35154113 TCAATAGCTCGAGCTCGGTTCAA
1 TCAATAGCTCGAATTCGGTTCAA
35154136 TCAATAGCTCGAATTCG
1 TCAATAGCTCGAATTCG
35154153 ATTCGATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (23 bp):
TCAATAGCTCGAATTCGGTTCAA
Found at i:35158604 original size:2 final size:2
Alignment explanation
Indices: 35158599--35158624 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35158589 ACATATATAT
35158599 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
35158625 CATTTAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35162993 original size:18 final size:18
Alignment explanation
Indices: 35162970--35163014 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
35162960 AACATTTCCC
35162970 TTTAATTAATTTAAAATT-
1 TTTAATTAA-TTAAAATTA
*
35162988 TTTAATTAATTAAATTTA
1 TTTAATTAATTAAAATTA
35163006 TTTAATTAA
1 TTTAATTAA
35163015 AAAATCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATTAATTAAAATTA
Found at i:35164896 original size:11 final size:11
Alignment explanation
Indices: 35164835--35164947 Score: 66
Period size: 11 Copynumber: 9.9 Consensus size: 11
35164825 ATGTTATTTC
*
35164835 TATTATTTTCT
1 TATTATTTTAT
* *
35164846 TACTGTTTTAT
1 TATTATTTTAT
* *
35164857 TGTCATTTTAT
1 TATTATTTTAT
* *
35164868 TATTATGTAAT
1 TATTATTTTAT
35164879 TATTATTTTAT
1 TATTATTTTAT
35164890 TATTATTATT-T
1 TATTATT-TTAT
* *
35164901 AAATATTGTATGAT
1 TATTATT-T-T-AT
* *
35164915 TTTTGTTTTAT
1 TATTATTTTAT
*
35164926 TATTAATTTTAC
1 TATT-ATTTTAT
35164938 TATTATTTTA
1 TATTATTTTA
35164948 AAATATTTAC
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
11 56 0.76
12 13 0.18
13 1 0.01
14 4 0.05
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.65
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:35170571 original size:11 final size:11
Alignment explanation
Indices: 35170551--35170625 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
35170541 AAGCCTCTCA
*
35170551 TCTTTCCTTTC
1 TCTTTTCTTTC
*
35170562 TCTTTTCTTTT
1 TCTTTTCTTTC
*
35170573 TCTCATTCATTTC
1 TCT-TTTC-TTTC
35170586 T-TATTTCTTTC
1 TCT-TTTCTTTC
35170597 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
35170609 TATTTTCTTCC
1 TCTTTTCTTTC
35170620 TCTTTT
1 TCTTTT
35170626 AATCACACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 29 0.57
12 18 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:35170612 original size:22 final size:22
Alignment explanation
Indices: 35170558--35170622 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
35170548 TCATCTTTCC
*
35170558 TTTCTCTTTTCTTTTTCTCATTCA
1 TTTCT-TTTTCTTTCTCTC-TTCA
* *
35170582 TTTCTTATTTCTTTCTCTTTTCT
1 TTTCTT-TTTCTTTCTCTCTTCA
*
35170605 TTTCTATTTTCTTCCTCT
1 TTTCT-TTTTCTTTCTCT
35170623 TTTAATCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTCTTCA
Found at i:35171029 original size:21 final size:21
Alignment explanation
Indices: 35170995--35171062 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
35170985 ACCCATTAAG
*
35170995 CCCAAATCCTATTTAAACCAAA
1 CCCAAATTC-ATTTAAACCAAA
*
35171017 CCCACATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
*
35171038 CTCAAATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
35171059 CCCA
1 CCCA
35171063 TTTGAACCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 34 0.83
22 7 0.17
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
CCCAAATTCATTTAAACCAAA
Found at i:35171064 original size:15 final size:15
Alignment explanation
Indices: 35171046--35171075 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35171036 AACTCAAATT
35171046 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
35171061 CATTTGAACCAAACC
1 CATTTAAACCAAACC
35171076 AAACGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:35172267 original size:3 final size:3
Alignment explanation
Indices: 35172255--35172293 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
35172245 TAGAATATTC
35172255 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35172294 TTGGGATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:35177657 original size:11 final size:11
Alignment explanation
Indices: 35177637--35177711 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
35177627 AAGCCTCTCA
*
35177637 TCTTTCCTTTC
1 TCTTTTCTTTC
*
35177648 TCTTTTCTTTT
1 TCTTTTCTTTC
*
35177659 TCTCATTCATTTC
1 TCT-TTTC-TTTC
35177672 T-TATTTCTTTC
1 TCT-TTTCTTTC
35177683 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
35177695 TATTTTCTTCC
1 TCTTTTCTTTC
35177706 TCTTTT
1 TCTTTT
35177712 AATCACACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 29 0.57
12 18 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:35177698 original size:22 final size:22
Alignment explanation
Indices: 35177644--35177708 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
35177634 TCATCTTTCC
*
35177644 TTTCTCTTTTCTTTTTCTCATTCA
1 TTTCT-TTTTCTTTCTCTC-TTCA
* *
35177668 TTTCTTATTTCTTTCTCTTTTCT
1 TTTCTT-TTTCTTTCTCTCTTCA
*
35177691 TTTCTATTTTCTTCCTCT
1 TTTCT-TTTTCTTTCTCT
35177709 TTTAATCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTCTTCA
Found at i:35178114 original size:21 final size:21
Alignment explanation
Indices: 35178080--35178147 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
35178070 ACTCATTAAG
*
35178080 CCCAAATCCTATTTAAACCAAA
1 CCCAAATTC-ATTTAAACCAAA
*
35178102 CCCACATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
35178123 CCCAAATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
35178144 CCCA
1 CCCA
35178148 TTTGAACCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
21 36 0.84
22 7 0.16
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCAAATTCATTTAAACCAAA
Found at i:35178149 original size:15 final size:15
Alignment explanation
Indices: 35178131--35178160 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35178121 AACCCAAATT
35178131 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
35178146 CATTTGAACCAAACC
1 CATTTAAACCAAACC
35178161 AAACGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:35178232 original size:21 final size:20
Alignment explanation
Indices: 35178197--35178255 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
35178187 AGTTAAACCA
* *
35178197 TTGACCGATGTTGACTGGCG
1 TTGACCGACGTTGACCGGCG
*
35178217 TTGACCGACCGTTGACCGGTG
1 TTGACCGA-CGTTGACCGGCG
**
35178238 TTGATTGATCGTTGACCG
1 TTGACCGA-CGTTGACCG
35178256 CTGATCGTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.15, C:0.22, G:0.32, T:0.31
Consensus pattern (20 bp):
TTGACCGACGTTGACCGGCG
Found at i:35178277 original size:20 final size:20
Alignment explanation
Indices: 35178249--35178300 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
35178239 TGATTGATCG
*
35178249 TTGACCGCTGATCGTTGACT
1 TTGACCGCTGACCGTTGACT
*
35178269 TTGATCGCTGACCGTTGACT
1 TTGACCGCTGACCGTTGACT
*
35178289 TTGACCGTTGAC
1 TTGACCGCTGAC
35178301 TTTTTCGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGACCGCTGACCGTTGACT
Found at i:35178293 original size:13 final size:13
Alignment explanation
Indices: 35178277--35178303 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35178267 CTTTGATCGC
35178277 TGACCGTTGACTT
1 TGACCGTTGACTT
35178290 TGACCGTTGACTT
1 TGACCGTTGACTT
35178303 T
1 T
35178304 TTCGAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (13 bp):
TGACCGTTGACTT
Found at i:35179360 original size:3 final size:3
Alignment explanation
Indices: 35179348--35179377 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
35179338 TATTTTATTC
35179348 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35179378 TTGGGATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:35179947 original size:22 final size:21
Alignment explanation
Indices: 35179904--35179955 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
35179894 TTTATCATTA
35179904 AATAAA-TT-TAAAAAATAAT
1 AATAAATTTATAAAAAATAAT
*
35179923 AATAAATTTATAAATAAATATT
1 AATAAATTTATAAA-AAATAAT
*
35179945 AATAATTTTAT
1 AATAAATTTAT
35179956 TTAAGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 2 0.07
21 4 0.14
22 16 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAAATTTATAAAAAATAAT
Found at i:35181028 original size:21 final size:20
Alignment explanation
Indices: 35180986--35181028 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
35180976 AAATTTAAAG
*
35180986 TTTAAGAATTTTATTTGAGA
1 TTTAAGAATTTTATTTAAGA
35181006 TTTAA-AATTTATAGTTTAAGA
1 TTTAAGAATTT-TA-TTTAAGA
35181027 TT
1 TT
35181029 AATGACTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTAAGAATTTTATTTAAGA
Found at i:35181976 original size:2 final size:2
Alignment explanation
Indices: 35181969--35182000 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35181959 ATTTCCACCG
35181969 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
35182001 TCCACCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35185883 original size:199 final size:198
Alignment explanation
Indices: 35185510--35186238 Score: 911
Period size: 199 Copynumber: 3.7 Consensus size: 198
35185500 TGTATTGACA
* * * * * * * **
35185510 GGTTAAAGGTCAGTGACCAAACAAGCATTGCCAACATAGGTTGCTTAGCATTGTGGTACGTCCCA
1 GGTTAGAGGTTAGTGACCTAACAGGCACTGCCAACATAGGTTGGTTGGTGTTGTGGTACGTCCCA
* * *
35185575 TGTGATCATGTTTGTGTCGTAGGTTATCTTGTTCTAATGTCATAATCTTGTGCAATACCAACTAA
66 TGTGATCATGTTTGTGTCGTAGGTTATCTTGTTCTAATGTCATAGTCTCGTGCAGTACCAACTAA
* *
35185640 TGAGTGTGCTTTCTCATCGTACAAGCTGTCCGTTAGACAAGAGGCTATTACAAAGAGTTAGGGGT
131 TGAGTGTGCTTTCTCATCGTACAAGCCGTCCATTAGACAAGAGGCTATTACAAA-AGTTAGGGGT
35185705 TAGG
195 TAGG
* * * *
35185709 GGTTAGAGGTTAGTGACCTAACAGGCATTGCTAACATAGGTTGGTTGGTGTTGTGGTATGTCTCA
1 GGTTAGAGGTTAGTGACCTAACAGGCACTGCCAACATAGGTTGGTTGGTGTTGTGGTACGTCCCA
* * *
35185774 TGTGATCATGTTTGTGTCGTAGGCTATCTTGTTCTAATGTCATTGTCCCGTGCAGTACCAACTAA
66 TGTGATCATGTTTGTGTCGTAGGTTATCTTGTTCTAATGTCATAGTCTCGTGCAGTACCAACTAA
* * * *
35185839 TGAGTGTGCTTTCTCATCGAACAAGCCATCTATTAGAGAAGAGGCTATTACAAAAAGTTAGGGGT
131 TGAGTGTGCTTTCTCATCGTACAAGCCGTCCATTAGACAAGAGGCTATTAC-AAAAGTTAGGGGT
35185904 TAGG
195 TAGG
*
35185908 GGTTAGAGGTTAAAGGTTAGTGACCTAACAGGCACTACCAACATAGGTTGGTTGGTGTTGTGGTA
1 GGTT--A-G----AGGTTAGTGACCTAACAGGCACTGCCAACATAGGTTGGTTGGTGTTGTGGTA
* * * * *
35185973 CGTCCCATGTGATCATGTTTGTGTTGTAGGTTATCTTGTTCTAATGTCATAGTCTTGCGTAGTAG
59 CGTCCCATGTGATCATGTTTGTGTCGTAGGTTATCTTGTTCTAATGTCATAGTCTCGTGCAGTAC
* *
35186038 CAACTAATGAGTGTGCTTTCTTATCGTACAAGCCGTCCATTAGACAAGAGGTTATTAC-AAAG--
124 CAACTAATGAGTGTGCTTTCTCATCGTACAAGCCGTCCATTAGACAAGAGGCTATTACAAAAGTT
35186100 A---GTTAGG
189 AGGGGTTAGG
* * * *
35186107 GG-T--AGGTTAGTGACCTAACTA-GCACGGCCAACATAGGTTAGTTGGTGTTGTGGTACATCAC
1 GGTTAGAGGTTAGTGACCTAAC-AGGCACTGCCAACATAGGTTGGTTGGTGTTGTGGTACGTCCC
* * * ** *
35186168 ATGTGATCATGTTTGTGTCCTAGGTTATCTTGTTCTTATGTCATAGTTTCGTATAGTATCAACTA
65 ATGTGATCATGTTTGTGTCGTAGGTTATCTTGTTCTAATGTCATAGTCTCGTGCAGTACCAACTA
35186233 ATGAGT
130 ATGAGT
35186239 CATCGTACAA
Statistics
Matches: 466, Mismatches: 55, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
189 114 0.24
190 1 0.00
198 1 0.00
199 184 0.39
200 3 0.01
201 1 0.00
202 2 0.00
204 4 0.01
206 156 0.33
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (198 bp):
GGTTAGAGGTTAGTGACCTAACAGGCACTGCCAACATAGGTTGGTTGGTGTTGTGGTACGTCCCA
TGTGATCATGTTTGTGTCGTAGGTTATCTTGTTCTAATGTCATAGTCTCGTGCAGTACCAACTAA
TGAGTGTGCTTTCTCATCGTACAAGCCGTCCATTAGACAAGAGGCTATTACAAAAGTTAGGGGTT
AGG
Found at i:35187515 original size:21 final size:21
Alignment explanation
Indices: 35187490--35187543 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
35187480 AACATGAACT
* * *
35187490 CTAAACCATAAACTTTAAACC
1 CTAAACCTTAAACCTCAAACC
* *
35187511 CTAAAGCTTAGACCTCAAACC
1 CTAAACCTTAAACCTCAAACC
35187532 CTAAACCTTAAA
1 CTAAACCTTAAA
35187544 ACCCTGGACT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.30, G:0.04, T:0.22
Consensus pattern (21 bp):
CTAAACCTTAAACCTCAAACC
Found at i:35192296 original size:17 final size:17
Alignment explanation
Indices: 35192274--35192312 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35192264 AGGTGGAGAA
* * *
35192274 CTTGTTCGTTGAGAGTT
1 CTTGTTAGTAGAGAATT
35192291 CTTGTTAGTAGAGAATT
1 CTTGTTAGTAGAGAATT
35192308 CTTGT
1 CTTGT
35192313 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTAGTAGAGAATT
Found at i:35192963 original size:32 final size:30
Alignment explanation
Indices: 35192898--35192972 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
35192888 CAAATGATTT
35192898 TAAAATTATTAAAATTATTTTTTAAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAAATA
* * **
35192928 TAAATTTGTTAAAATTATTTTTTTTGAAATAA
1 TAAAATTATTAAAATTA-TTTTTTAAAAAT-A
35192960 TAAAATTATTAAA
1 TAAAATTATTAAA
35192973 TAATTTTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 15 0.41
31 10 0.27
32 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAAATA
Found at i:35193811 original size:21 final size:21
Alignment explanation
Indices: 35193768--35193832 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
35193758 AAAATTATTT
35193768 AATAATTTT-ATTATTTCAAAAA
1 AATAATTTTAATT-TTT-AAAAA
35193790 AATAATTTTAATTTTTAAAAA
1 AATAATTTTAATTTTTAAAAA
*
35193811 AATATTTTTAATAATTTTAAAA
1 AATAATTTTAAT--TTTTAAAA
35193833 TCATTTGCTG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
21 16 0.41
22 12 0.31
23 11 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAATTTTAATTTTTAAAAA
Found at i:35194803 original size:30 final size:31
Alignment explanation
Indices: 35194742--35194806 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
35194732 TTATAGAATT
* *
35194742 GTCATTAAACTATTTAAAAGTTTTCATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
*
35194773 GTCACTAAACTATTCGAAAGTTTT-ATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
35194803 GTCA
1 GTCA
35194807 TTGGACTGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTTTCATTTAA
Found at i:35198555 original size:33 final size:34
Alignment explanation
Indices: 35198502--35198567 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
35198492 AGTAAAACAG
35198502 TGAAAAAACAATAAAAAAAATAGAAGCAAAATAA
1 TGAAAAAACAATAAAAAAAATAGAAGCAAAATAA
*
35198536 TGAAAAAACAAT-AAGAAAATAGAAGCAAAATA
1 TGAAAAAACAATAAAAAAAATAGAAGCAAAATA
35198568 GCAAGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 19 0.61
34 12 0.39
ACGTcount: A:0.71, C:0.06, G:0.11, T:0.12
Consensus pattern (34 bp):
TGAAAAAACAATAAAAAAAATAGAAGCAAAATAA
Found at i:35203758 original size:60 final size:60
Alignment explanation
Indices: 35203666--35203810 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 60
35203656 GTCTTTGTTA
* * * * ** * *
35203666 TTACCCTATGTGCTAGGTTTATTATGTGATTGCTTTTGATTTGTTGCAATCTG-CTTTTTG
1 TTACTCTATGTGCTAGATTTATCATGTAATTGCTTTTGACGTGTTGCAATATGTC-TTTTC
* *
35203726 TTACTCTATGTGCCAGACTTATCATGTAATTGCTTTTGACGTGTTGCAATATGTCTTTTC
1 TTACTCTATGTGCTAGATTTATCATGTAATTGCTTTTGACGTGTTGCAATATGTCTTTTC
35203786 TTACTCTATGTGCTAGATTTATCAT
1 TTACTCTATGTGCTAGATTTATCAT
35203811 TATGTTTAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 71 0.99
61 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (60 bp):
TTACTCTATGTGCTAGATTTATCATGTAATTGCTTTTGACGTGTTGCAATATGTCTTTTC
Found at i:35207612 original size:36 final size:36
Alignment explanation
Indices: 35207566--35207695 Score: 235
Period size: 36 Copynumber: 3.6 Consensus size: 36
35207556 GCTAGGTCAG
* *
35207566 TAGA-TGTTTATTGCTTCAGATCAGTCACAGAATGT
1 TAGATTGTTTATTGCATCAGATCAGTCACATAATGT
35207601 TAGATTGTTTATTGCATCAGATCAGTCACATAATGT
1 TAGATTGTTTATTGCATCAGATCAGTCACATAATGT
35207637 TAGATTGTTTATTGCATCAGATCAGTCACATAATGT
1 TAGATTGTTTATTGCATCAGATCAGTCACATAATGT
35207673 TAGATTGTTTATTGCATCAGATC
1 TAGATTGTTTATTGCATCAGATC
35207696 CATCTTATTC
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
35 4 0.04
36 88 0.96
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (36 bp):
TAGATTGTTTATTGCATCAGATCAGTCACATAATGT
Found at i:35225842 original size:18 final size:20
Alignment explanation
Indices: 35225816--35225872 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
35225806 TAATTCATCT
*
35225816 ATTCTTATA-ATA-ATATAC
1 ATTCATATATATATATATAC
*
35225834 ATTCATATATATATATATAT
1 ATTCATATATATATATATAC
35225854 ATAT-ATATATATATATATA
1 AT-TCATATATATATATATA
35225873 TATGGACGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 3 0.09
20 22 0.65
21 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTCATATATATATATATAC
Found at i:35225845 original size:2 final size:2
Alignment explanation
Indices: 35225838--35225875 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
35225828 ATATACATTC
35225838 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
35225876 GGACGCATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35235164 original size:20 final size:21
Alignment explanation
Indices: 35235139--35235178 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35235129 TGATTAATTT
*
35235139 ATTTTTTATCTTAC-GTTATA
1 ATTTTTAATCTTACTGTTATA
*
35235159 ATTTTTAATTTTACTGTTAT
1 ATTTTTAATCTTACTGTTAT
35235179 CGTTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTTTTAATCTTACTGTTATA
Found at i:35236765 original size:126 final size:128
Alignment explanation
Indices: 35236468--35236817 Score: 363
Period size: 126 Copynumber: 2.7 Consensus size: 128
35236458 TTCAAAATTT
* * * * * * ** *
35236468 AAAAATCATAAGTTCGTATAATGGTAAATTTGCATTTTAATCCCTCCAAAAATTTATGATTCATT
1 AAAAAT-ACAAGTTAGTATAATGATAAATTTGTAATTTGA-CCCAGCAAAAATTTATGATTCATC
* *
35236533 TTTGATCC-CTTAAAGCAATTTTTTGGCTTCACCTCTGATTTACTTTGTAGCCCCTTTAAAATTT
64 TTTGACCCTCTTAAAGCAATTTCTT---TTCACCTCTGATTTACTTTGTAGCCCCTTT-AAA-TT
35236597 AAAAA
124 AAAAA
*
35236602 AAAAATACAAGTTAGTATAATGATAAATTTGTAATTTGTCCCCAGCAAAAATTTATGATTCATCT
1 AAAAATACAAGTTAGTATAATGATAAATTTGTAATTTG-ACCCAGCAAAAATTTATGATTCATCT
* * *
35236667 TTGACCCTCTTAAAGCAATTTGCTTTTC-CC-CTGATTTGCTTTGTTGCCTCTTT-AA-TAAAAA
65 TTGACCCTCTTAAAGCAATTT-CTTTTCACCTCTGATTTACTTTGTAGCCCCTTTAAATTAAAAA
* * *
35236728 AAAATTACAAGTTAGTATAATGGTTAAATTT-TAATTTGACCCATCAAAAAATTTATGATTCATC
1 AAAAATACAAGTTAGTATAAT-GATAAATTTGTAATTTGACCCAGC-AAAAATTTATGATTCATC
* *
35236792 TCTGGCCCT-TTAAAGCAATTTTCTTT
64 TTTGACCCTCTTAAAGCAA-TTTCTTT
35236818 GTAGCCTTTT
Statistics
Matches: 189, Mismatches: 21, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
125 18 0.10
126 61 0.32
127 8 0.04
128 2 0.01
130 20 0.11
131 2 0.01
132 3 0.02
133 54 0.29
134 19 0.10
135 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (128 bp):
AAAAATACAAGTTAGTATAATGATAAATTTGTAATTTGACCCAGCAAAAATTTATGATTCATCTT
TGACCCTCTTAAAGCAATTTCTTTTCACCTCTGATTTACTTTGTAGCCCCTTTAAATTAAAAA
Found at i:35236917 original size:111 final size:113
Alignment explanation
Indices: 35236722--35236924 Score: 281
Period size: 111 Copynumber: 1.8 Consensus size: 113
35236712 GCCTCTTTAA
* *
35236722 TAAAAAAAAATTACAAGTTAGTATAATGGTTAAATTTTAATTTGACCCATCAAAAAATTTATGAT
1 TAAAAAAAAAATACAAGCTAGTATAATGGTTAAATTTTAATTTGACCCATCAAAAAATTTATGAT
* *
35236787 TCATCTCTGGCCCTTTAAAGCAATTTTCTTTGTAGCCTTTTTAAAATT
66 TCATCTCTGACCCTCTAAAGCAATTTTCTTTGTAGCCTTTTTAAAATT
*
35236835 TAAAAAAAAAATA-AA-CTAGTATAATGG-TAAATTTTTAATTTGACCCCTTC-AAAAATTTATG
1 TAAAAAAAAAATACAAGCTAGTATAATGGTTAAA-TTTTAATTTGA-CCCATCAAAAAATTTATG
* *
35236896 ATTCATCTTTTA-CCTCCTAAAGCAATTTT
64 ATTCATCTCTGACCCT-CTAAAGCAATTTT
35236925 TTGCTTCCTC
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
110 7 0.09
111 54 0.68
112 7 0.09
113 12 0.15
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (113 bp):
TAAAAAAAAAATACAAGCTAGTATAATGGTTAAATTTTAATTTGACCCATCAAAAAATTTATGAT
TCATCTCTGACCCTCTAAAGCAATTTTCTTTGTAGCCTTTTTAAAATT
Found at i:35237750 original size:21 final size:21
Alignment explanation
Indices: 35237726--35237765 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35237716 ACATTATATA
35237726 TATTAATTAATTATAATAAAT
1 TATTAATTAATTATAATAAAT
* *
35237747 TATTAATTTATTATTATAA
1 TATTAATTAATTATAATAA
35237766 TTAAGTCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTAATTAATTATAATAAAT
Found at i:35238215 original size:17 final size:18
Alignment explanation
Indices: 35238195--35238232 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
35238185 TTACGACTTG
35238195 AAATATATT-TGAT-ATAA
1 AAAT-TATTATGATAATAA
35238212 AAATTATTATGATAATAA
1 AAATTATTATGATAATAA
35238230 AAA
1 AAA
35238233 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 8 0.42
18 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATTATTATGATAATAA
Found at i:35238239 original size:27 final size:29
Alignment explanation
Indices: 35238209--35238268 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
35238199 ATATTTGATA
35238209 TAAAAATT-ATTATGAT-AATAAAAAATT
1 TAAAAATTAATTATGATAAATAAAAAATT
* * *
35238236 T-AAAATTAATTTTGTTAAATATAAAATT
1 TAAAAATTAATTATGATAAATAAAAAATT
35238264 TAAAA
1 TAAAA
35238269 TGAAAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 6 0.22
27 7 0.26
28 11 0.41
29 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAAAATTAATTATGATAAATAAAAAATT
Found at i:35238905 original size:4 final size:4
Alignment explanation
Indices: 35238896--35238924 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
35238886 ATTAATTTTG
35238896 TTAT TTAT TTAT TTAT TTAT TTA- TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
35238925 TTATGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:35238924 original size:71 final size:69
Alignment explanation
Indices: 35238832--35239039 Score: 350
Period size: 71 Copynumber: 3.0 Consensus size: 69
35238822 TCTTATTATT
35238832 TTTATTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGT
1 TTTATTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG-
35238897 TATTTA
65 T-TTTA
35238903 TTTATTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG-
1 TTTATTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGT
35238967 -TTA
66 TTTA
* * *
35238970 TTTATTTATTTATTTATTA-TTGTATGAATATAAATAAATAAATGTAAAATAATATTACTTTTGT
1 TTTATTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGT
35239034 TTTA
66 TTTA
35239038 TT
1 TT
35239040 GTTTATTATT
Statistics
Matches: 132, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
66 41 0.31
67 22 0.17
68 5 0.04
71 64 0.48
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (69 bp):
TTTATTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGT
TTTA
Found at i:35246452 original size:50 final size:50
Alignment explanation
Indices: 35246349--35246455 Score: 117
Period size: 50 Copynumber: 2.1 Consensus size: 50
35246339 GCCACGACGG
* * * * * * *
35246349 CGAATCTCATATACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGTAATGA
1 CGAATCTCATATACCTAAAACTATAGAGAGGCAAATTGAAGCCGCAATAA
**
35246399 CGAATCTCAT-TCACCTAAAACTATAGAGAGGCAAATTGAAGTTGCAATAA
1 CGAATCTCATAT-ACCTAAAACTATAGAGAGGCAAATTGAAGCCGCAATAA
35246449 CGAATCT
1 CGAATCT
35246456 TATACTCCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
49 1 0.02
50 46 0.98
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (50 bp):
CGAATCTCATATACCTAAAACTATAGAGAGGCAAATTGAAGCCGCAATAA
Found at i:35246562 original size:40 final size:40
Alignment explanation
Indices: 35246507--35246779 Score: 261
Period size: 40 Copynumber: 6.9 Consensus size: 40
35246497 ATCTCTTACT
35246507 CAGAGGGCAGATTGAAGACCATCCGATCTTTTACCCCGAC
1 CAGAGGGCAGATTGAAGACCATCCGATCTTTTACCCCGAC
* * * *
35246547 CAGAGGGTAGATTGAAGATCATCCGATCTCTTACTCCGAC
1 CAGAGGGCAGATTGAAGACCATCCGATCTTTTACCCCGAC
* * **
35246587 CATG-GGGCAGATTGAA-ACAATCCAATCTTTTACCCTAAC
1 CA-GAGGGCAGATTGAAGACCATCCGATCTTTTACCCCGAC
* * *
35246626 CAAAGGGCAGATTGAAGACCATCCGATCTCTTACCCTGAC
1 CAGAGGGCAGATTGAAGACCATCCGATCTTTTACCCCGAC
* * * * * **
35246666 CATAGGGCAAATTGAAG-CAATCCAATTTTTTACCCTAAC
1 CAGAGGGCAGATTGAAGACCATCCGATCTTTTACCCCGAC
* * * *
35246705 TAGAGGGCAGATTGAAAACCATTCGATCTCTTACCCCGAC
1 CAGAGGGCAGATTGAAGACCATCCGATCTTTTACCCCGAC
* *
35246745 CACG-GGGCAAATTGAA-ACAATCC-ATTCTTTTACCC
1 CA-GAGGGCAGATTGAAGACCATCCGA-TCTTTTACCC
35246780 TTAAAACTAT
Statistics
Matches: 187, Mismatches: 40, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.01
39 74 0.40
40 110 0.59
41 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (40 bp):
CAGAGGGCAGATTGAAGACCATCCGATCTTTTACCCCGAC
Found at i:35246639 original size:79 final size:79
Alignment explanation
Indices: 35246480--35246780 Score: 362
Period size: 79 Copynumber: 3.9 Consensus size: 79
35246470 TGAAATGAGT
* * * * *
35246480 AGATTGAAGGCCATCCGATCTCTTACT-C-A-GA--GGGCAGATTGAAGACCATCCGATCTTTTA
1 AGATTGAAGACCATCCGATCTCTTACTCCGACCATGGGGCAAATTGAA-ACAATCCAATCTTTTA
** *
35246540 CCCCGACCAGAGGGT
65 CCCTAACCAGAGGGC
* *
35246555 AGATTGAAGATCATCCGATCTCTTACTCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTAC
1 AGATTGAAGACCATCCGATCTCTTACTCCGACCATGGGGCAAATTGAAACAATCCAATCTTTTAC
*
35246620 CCTAACCAAAGGGC
66 CCTAACCAGAGGGC
* * *
35246634 AGATTGAAGACCATCCGATCTCTTAC-CCTGACCATAGGGCAAATTGAAGCAATCCAATTTTTTA
1 AGATTGAAGACCATCCGATCTCTTACTCC-GACCATGGGGCAAATTGAAACAATCCAATCTTTTA
*
35246698 CCCTAACTAGAGGGC
65 CCCTAACCAGAGGGC
* * * * *
35246713 AGATTGAAAACCATTCGATCTCTTACCCCGACCACGGGGCAAATTGAAACAATCCATTCTTTTAC
1 AGATTGAAGACCATCCGATCTCTTACTCCGACCATGGGGCAAATTGAAACAATCCAATCTTTTAC
35246778 CCT
66 CCT
35246781 TAAAACTATA
Statistics
Matches: 196, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
75 25 0.13
76 1 0.01
77 1 0.01
78 3 0.02
79 152 0.78
80 14 0.07
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (79 bp):
AGATTGAAGACCATCCGATCTCTTACTCCGACCATGGGGCAAATTGAAACAATCCAATCTTTTAC
CCTAACCAGAGGGC
Found at i:35246739 original size:119 final size:118
Alignment explanation
Indices: 35246510--35246740 Score: 270
Period size: 119 Copynumber: 1.9 Consensus size: 118
35246500 TCTTACTCAG
* * * *
35246510 AGGGCAGATTGAAGACCATCCGATCTTTTACCCCGACCAGAGGGTAGATTGAAGATCATCCGATC
1 AGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAGAGGGCAAATTGAAGA-CATCCAATC
* *
35246575 TCTTACTCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAA
65 TCTTACTCCAACCATGGGGCAGATTGAAACAATCCAATCTCTTACCCTAACCAA
* * *
35246629 AGGGCAGATTGAAGACCATCCGATCTCTTACCCTGACCATAGGGCAAATTGAAG-CAATCCAATT
1 AGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAGAGGGCAAATTGAAGAC-ATCCAATC
* * * * *
35246693 TTTTAC-CCTAACTA-GAGGGCAGATTGAAAACCATTCGATCTCTTACCC
65 TCTTACTCC-AACCATG-GGGCAGATTG-AAACAATCCAATCTCTTACCC
35246741 CGACCACGGG
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
117 4 0.04
118 24 0.26
119 66 0.70
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (118 bp):
AGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAGAGGGCAAATTGAAGACATCCAATCT
CTTACTCCAACCATGGGGCAGATTGAAACAATCCAATCTCTTACCCTAACCAA
Found at i:35247365 original size:58 final size:60
Alignment explanation
Indices: 35247303--35247438 Score: 183
Period size: 59 Copynumber: 2.3 Consensus size: 60
35247293 ATTTTTCTTA
* *
35247303 TTATTTTTATTTATTTATTATTTTTATGAATATAAAT-AA-ATA-TAAAATAATATTTATT
1 TTATTTTTATTTATTTATTA-TTGTATGAATATAAATAAATATAGTAAAATAATATTAATT
35247361 TTATTATTTATTTATTTATTATTGTATGAATATAAATAAATATATGTAAAATAATATTAATT
1 TTATT-TTTATTTATTTATTATTGTATGAATATAAATAAATATA-GTAAAATAATATTAATT
*
35247423 TT-GTTTTA-TTATTTAT
1 TTATTTTTATTTATTTAT
35247439 AATAAACAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
58 20 0.29
59 25 0.36
60 7 0.10
61 1 0.01
62 17 0.24
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (60 bp):
TTATTTTTATTTATTTATTATTGTATGAATATAAATAAATATAGTAAAATAATATTAATT
Found at i:35249023 original size:20 final size:21
Alignment explanation
Indices: 35248981--35249035 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
35248971 TTTAATAACA
* *
35248981 TTTATTTAAAT-TAATTTTCT
1 TTTATTCAAATATCATTTTCT
35249001 TTTATTCAAATATCATTTT-T
1 TTTATTCAAATATCATTTTCT
35249021 TTT-TTCAAATCATCA
1 TTTATTCAAAT-ATCA
35249036 ATTAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.23
20 18 0.58
21 6 0.19
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTATTCAAATATCATTTTCT
Found at i:35249027 original size:19 final size:22
Alignment explanation
Indices: 35248994--35249035 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
35248984 ATTTAAATTA
35248994 ATTTTCTTTTATTCAAAT-ATC
1 ATTTTCTTTTATTCAAATCATC
35249015 ATTTT-TTTT-TTCAAATCATC
1 ATTTTCTTTTATTCAAATCATC
35249035 A
1 A
35249036 ATTAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 8 0.40
21 5 0.25
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTCTTTTATTCAAATCATC
Found at i:35260967 original size:1 final size:1
Alignment explanation
Indices: 35260961--35260988 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
35260951 CTCTCTCTCT
35260961 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
35260989 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:35264283 original size:62 final size:62
Alignment explanation
Indices: 35264176--35264331 Score: 199
Period size: 62 Copynumber: 2.5 Consensus size: 62
35264166 GAAATTTAAG
* * *
35264176 TCCCGAAAATCCCCAAA-ATTTTAAACTTAAACCAAAATCCTCAAACCCAACAACCTTAAAAA
1 TCCC-AAAATCCCCAAATTTTTTAAACCTAAACCAAAATCCTCAAACCCAACAACCCTAAAAA
* *
35264238 TCCCAAAATCCCCAAATTTTTTAAACCTAATCCAAATTTCC-CAAACCCAACAACCCTAAAAA
1 TCCCAAAATCCCCAAATTTTTTAAACCTAAACCAAA-ATCCTCAAACCCAACAACCCTAAAAA
* * *
35264300 TCTCGAAAATCCCTAAATTTTTAAAACCTAAA
1 TC-CCAAAATCCCCAAATTTTTTAAACCTAAA
35264332 TCCCCAAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
61 12 0.15
62 42 0.51
63 28 0.34
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (62 bp):
TCCCAAAATCCCCAAATTTTTTAAACCTAAACCAAAATCCTCAAACCCAACAACCCTAAAAA
Found at i:35264634 original size:18 final size:20
Alignment explanation
Indices: 35264611--35264655 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
35264601 AGGTAAATAT
35264611 TTTATTTTTTTAA-TTT-AA
1 TTTATTTTTTTAACTTTAAA
35264629 TTTA-TTTTTTAACTTTAAA
1 TTTATTTTTTTAACTTTAAA
35264648 TTT-TTTTT
1 TTTATTTTT
35264656 ATTGACATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 7 0.29
19 9 0.38
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTTTTTAACTTTAAA
Found at i:35264638 original size:17 final size:18
Alignment explanation
Indices: 35264611--35264656 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
35264601 AGGTAAATAT
35264611 TTTATTTTTTTAA-TTTAA
1 TTTA-TTTTTTAACTTTAA
35264629 TTTATTTTTTAACTTTAA
1 TTTATTTTTTAACTTTAA
*
35264647 ATT-TTTTTTA
1 TTTATTTTTTA
35264657 TTGACATGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTTTTAACTTTAA
Found at i:35267323 original size:68 final size:68
Alignment explanation
Indices: 35267214--35267353 Score: 271
Period size: 68 Copynumber: 2.1 Consensus size: 68
35267204 ATCCACTAAC
*
35267214 AATATTGGGGAACGATTCTATTATTGTAAGTAGATTTGAACTTCGTTTCAAGCAAATAGAGACTC
1 AATATTGGGGAACAATTCTATTATTGTAAGTAGATTTGAACTTCGTTTCAAGCAAATAGAGACTC
35267279 GTA
66 GTA
35267282 AATATTGGGGAACAATTCTATTATTGTAAGTAGATTTGAACTTCGTTTCAAGCAAATAGAGACTC
1 AATATTGGGGAACAATTCTATTATTGTAAGTAGATTTGAACTTCGTTTCAAGCAAATAGAGACTC
35267347 GTA
66 GTA
35267350 AATA
1 AATA
35267354 CCATAGAACT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (68 bp):
AATATTGGGGAACAATTCTATTATTGTAAGTAGATTTGAACTTCGTTTCAAGCAAATAGAGACTC
GTA
Found at i:35269139 original size:23 final size:25
Alignment explanation
Indices: 35269095--35269142 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
35269085 AATATTTATA
35269095 TTATATTATTTTAATATTTAATAAAT
1 TTATATTATTTT-ATATTTAATAAAT
35269121 TTATA-TATTTT-TATTTAATAAA
1 TTATATTATTTTATATTTAATAAA
35269143 AAATTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.50
25 6 0.27
26 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTATATTATTTTATATTTAATAAAT
Found at i:35271661 original size:28 final size:27
Alignment explanation
Indices: 35271609--35271660 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
35271599 CAAAAATAGT
*
35271609 TTTTATTTAATTATAATATAATTTTCA
1 TTTTATTAAATTATAATATAATTTTCA
35271636 TTTTATTAAAATTAT-ATATAATTTT
1 TTTTATT-AAATTATAATATAATTTT
35271661 TTACAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTTATTAAATTATAATATAATTTTCA
Found at i:35271677 original size:22 final size:22
Alignment explanation
Indices: 35271613--35271677 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
35271603 AATAGTTTTT
* * * *
35271613 ATTTAATTATAATATAATTTTC
1 ATTTTATTAAAATATAATTATA
35271635 ATTTTATTAAAAT-T-ATATATA
1 ATTTTATTAAAATATAAT-TATA
35271656 ATTTT-TTACAAATATAATTATA
1 ATTTTATTA-AAATATAATTATA
35271678 TCCATATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 5 0.14
21 12 0.34
22 16 0.46
23 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTATTAAAATATAATTATA
Found at i:35279638 original size:10 final size:10
Alignment explanation
Indices: 35279609--35279659 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
35279599 AATCTGAATC
35279609 ATTTAAAAATA
1 ATTT-AAAATA
*
35279620 TAATTAAAATA
1 -ATTTAAAATA
35279631 ATTTAAAAT-
1 ATTTAAAATA
*
35279640 -TTAAAAATA
1 ATTTAAAATA
35279649 ATTTAAAATA
1 ATTTAAAATA
35279659 A
1 A
35279660 GGTCATAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 7 0.21
10 17 0.52
11 6 0.18
12 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTTAAAATA
Found at i:35290311 original size:86 final size:86
Alignment explanation
Indices: 35290209--35290382 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 86
35290199 TTACTTCTTT
*
35290209 TTTCTTTCATATATTTTTATTTTTGGTAATTGAATACAATGCGAAAACATGGGTGCAAGTAAAAG
1 TTTCTTTCATATATTTTTATTTTTGGTAATTGAATACAATGCAAAAACATGGGTGCAAGTAAAAG
35290274 CATGTTGGTTCATGTAGTTTG
66 CATGTTGGTTCATGTAGTTTG
35290295 TTTCTTTCATATATTTTTATTTTTGGTAATTGAATACAATGCAAAAACATGGGTGCAAGTAAAAG
1 TTTCTTTCATATATTTTTATTTTTGGTAATTGAATACAATGCAAAAACATGGGTGCAAGTAAAAG
35290360 CATGTTGGTTCATGTAGTTTG
66 CATGTTGGTTCATGTAGTTTG
35290381 TT
1 TT
35290383 GGATTTCCGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (86 bp):
TTTCTTTCATATATTTTTATTTTTGGTAATTGAATACAATGCAAAAACATGGGTGCAAGTAAAAG
CATGTTGGTTCATGTAGTTTG
Found at i:35295406 original size:35 final size:35
Alignment explanation
Indices: 35295365--35295436 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
35295355 GAAAATAGTC
35295365 AAATATAGTAGCAACTGGCAAGAAAATGCAGATAA
1 AAATATAGTAGCAACTGGCAAGAAAATGCAGATAA
35295400 AAATATAGTAGCAACTGGCAAGAAAATGCAGATAA
1 AAATATAGTAGCAACTGGCAAGAAAATGCAGATAA
35295435 AA
1 AA
35295437 GGTAGAGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.53, C:0.11, G:0.19, T:0.17
Consensus pattern (35 bp):
AAATATAGTAGCAACTGGCAAGAAAATGCAGATAA
Found at i:35301924 original size:30 final size:31
Alignment explanation
Indices: 35301866--35301933 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
35301856 TTACAAAATG
* *
35301866 ATCATTAAACTATTTGAAAATTTTTATTTAA
1 ATCATTGAACTATTTGAAAATCTTTATTTAA
*
35301897 ATCATTGACCTATTTGAAAA-CTTTATTTAA
1 ATCATTGAACTATTTGAAAATCTTTATTTAA
*
35301927 TTCATTG
1 ATCATTG
35301934 GGCGGTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (31 bp):
ATCATTGAACTATTTGAAAATCTTTATTTAA
Found at i:35302699 original size:3 final size:3
Alignment explanation
Indices: 35302638--35302682 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
35302628 TGGAAGAGTG
*
35302638 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35302683 TAAGCTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:35303271 original size:16 final size:16
Alignment explanation
Indices: 35303250--35303280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35303240 GTGTTTTCAT
*
35303250 AAAAATTTAAAATTTA
1 AAAAATATAAAATTTA
35303266 AAAAATATAAAATTT
1 AAAAATATAAAATTT
35303281 TACCATATTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATATAAAATTTA
Found at i:35307339 original size:23 final size:23
Alignment explanation
Indices: 35307325--35307428 Score: 99
Period size: 23 Copynumber: 4.5 Consensus size: 23
35307315 TAATGTTCAT
35307325 GAACATGTTCATTTAACTTAATC
1 GAACATGTTCATTTAACTTAATC
*
35307348 GAACATGTTCA-TGAACATTAATC
1 GAACATGTTCATTTAAC-TTAATC
*
35307371 GAACATGTTCA--CAAGCATTAATC
1 GAACATGTTCATTTAA-C-TTAATC
*
35307394 GAACATGTTCA-TTAACATATAATT
1 GAACATGTTCATTTAAC-T-TAATC
*
35307418 GAACACGTTCA
1 GAACATGTTCA
35307429 CGAATAATGT
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
22 6 0.08
23 50 0.69
24 16 0.22
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (23 bp):
GAACATGTTCATTTAACTTAATC
Found at i:35308697 original size:24 final size:22
Alignment explanation
Indices: 35308665--35308749 Score: 64
Period size: 24 Copynumber: 3.7 Consensus size: 22
35308655 CCAAACAACC
*
35308665 AAAACAGCAGCAAAAATAATAGAA
1 AAAATAGCA-CAAAAATAATA-AA
*
35308689 AAAATAGCAACAAAAATAACAATA
1 AAAATAGC-ACAAAAATAATAA-A
* * *
35308713 AAAA-AACACCAAAATAGTAAAA
1 AAAATAGCACAAAAATAAT-AAA
*
35308735 AAAATAGCACCAAAA
1 AAAATAGCACAAAAA
35308750 CAGTAATCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
22 13 0.26
23 14 0.28
24 22 0.44
25 1 0.02
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.09
Consensus pattern (22 bp):
AAAATAGCACAAAAATAATAAA
Found at i:35308754 original size:23 final size:22
Alignment explanation
Indices: 35308687--35308764 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 22
35308677 AAAATAATAG
*
35308687 AAAAAATAGCAACAAAAA-TAA
1 AAAAAATAGCACCAAAAAGTAA
* *
35308708 CAATAAAAAAACACCAAAATAGTAA
1 -AA-AAAATAGCACCAAAA-AGTAA
35308733 AAAAAATAGCACCAAAACAGTAA
1 AAAAAATAGCACCAAAA-AGTAA
**
35308756 TCAAAATAG
1 AAAAAATAG
35308765 TAAAAAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
22 2 0.04
23 37 0.82
24 3 0.07
25 3 0.07
ACGTcount: A:0.68, C:0.14, G:0.06, T:0.12
Consensus pattern (22 bp):
AAAAAATAGCACCAAAAAGTAA
Found at i:35308798 original size:20 final size:20
Alignment explanation
Indices: 35308757--35308806 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
35308747 AAACAGTAAT
*
35308757 CAAAATAGTAAAAAAAATAC
1 CAAAATAGTAAAAAAAACAC
* *
35308777 CAAAATAGTAAAAACACCAC
1 CAAAATAGTAAAAAAAACAC
*
35308797 CAAAACAGTA
1 CAAAATAGTA
35308807 CCAAAACAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.64, C:0.18, G:0.06, T:0.12
Consensus pattern (20 bp):
CAAAATAGTAAAAAAAACAC
Found at i:35312924 original size:3 final size:3
Alignment explanation
Indices: 35312918--35312953 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
35312908 AGCTTTTTTT
*
35312918 TGA TGA TGA TGA TGA TGA TGA TGA CGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
35312954 GTAATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:35319277 original size:22 final size:23
Alignment explanation
Indices: 35319243--35319287 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
35319233 TCGCCTATAT
35319243 TATTATTATTATTTAAATATTTA
1 TATTATTATTATTTAAATATTTA
*
35319266 TATTA-TATTATTTTAATATTTA
1 TATTATTATTATTTAAATATTTA
35319288 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATTATTATTTAAATATTTA
Found at i:35327081 original size:21 final size:22
Alignment explanation
Indices: 35327057--35327097 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35327047 AATATGACTT
*
35327057 TTTTTTTTGT-ATATATTTTAA
1 TTTTATTTGTCATATATTTTAA
35327078 TTTTATTTGTCATATATTTT
1 TTTTATTTGTCATATATTTT
35327098 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTATTTGTCATATATTTTAA
Found at i:35328554 original size:21 final size:21
Alignment explanation
Indices: 35328530--35328576 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
35328520 CTCGAGACCA
*
35328530 TAAACTTTAAATCCAA-AACT
1 TAAACTTTAAATCAAATAACT
35328550 CTAAACTTTAAATCAAATAACT
1 -TAAACTTTAAATCAAATAACT
35328572 TAAAC
1 TAAAC
35328577 CCTAAACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACTTTAAATCAAATAACT
Found at i:35329427 original size:14 final size:15
Alignment explanation
Indices: 35329398--35329435 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
35329388 CGTTATTTCG
*
35329398 AAGAAAAAAAAGAAA
1 AAGAAAAAGAAGAAA
35329413 AAGAAAAAGAA-AAA
1 AAGAAAAAGAAGAAA
35329427 AAGAAAAAG
1 AAGAAAAAG
35329436 CAGTTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAGAAA
Found at i:35330977 original size:21 final size:21
Alignment explanation
Indices: 35330938--35330977 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35330928 AATACTTTAT
*
35330938 AATATTATTATTGATATTTCA
1 AATATTATTATTGAAATTTCA
*
35330959 AATATTATTATTTAAATTT
1 AATATTATTATTGAAATTT
35330978 TTTATTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
AATATTATTATTGAAATTTCA
Found at i:35333514 original size:12 final size:12
Alignment explanation
Indices: 35333486--35333518 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
35333476 TTTTTATATT
35333486 TAAAAGTTAATA
1 TAAAAGTTAATA
*
35333498 T-AAAGTTTATA
1 TAAAAGTTAATA
35333509 TAAAAGTTAA
1 TAAAAGTTAA
35333519 CACAAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (12 bp):
TAAAAGTTAATA
Found at i:35339666 original size:20 final size:20
Alignment explanation
Indices: 35339637--35339674 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35339627 GAAGATGTAG
* *
35339637 AGAAATTGGAAATAGGAAGT
1 AGAAAGTGGAAAAAGGAAGT
35339657 AGAAAGTGGAAAAAGGAA
1 AGAAAGTGGAAAAAGGAA
35339675 ATGAAATAGA
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:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (20 bp):
AGAAAGTGGAAAAAGGAAGT
Found at i:35356871 original size:19 final size:17
Alignment explanation
Indices: 35356841--35356884 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
35356831 TCACTTGCTA
35356841 TAAAAATCTAAAAATATG
1 TAAAAATCTAAAAAT-TG
*
35356859 TATAAAATTTAAAAATTG
1 TA-AAAATCTAAAAATTG
35356877 TAAAAATC
1 TAAAAATC
35356885 CAAATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (17 bp):
TAAAAATCTAAAAATTG
Found at i:35356940 original size:27 final size:27
Alignment explanation
Indices: 35356910--35356974 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
35356900 ACTATAAAAA
* *
35356910 TAAAAATTATTTAAATA-TTTAATAATT
1 TAAAAAATATTAAAATATTTTAA-AATT
35356937 TAAAAAATATTAAAATATTTTAAAATT
1 TAAAAAATATTAAAATATTTTAAAATT
35356964 TAATAAAATAT
1 TAA-AAAATAT
35356975 ATATTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAAAAATATTAAAATATTTTAAAATT
Found at i:35359696 original size:15 final size:15
Alignment explanation
Indices: 35359672--35359705 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35359662 TTTTTATATG
35359672 TTTTTATAATTTATAA
1 TTTTTATAATTT-TAA
35359688 TTTTT-TAATTTTAA
1 TTTTTATAATTTTAA
35359702 TTTT
1 TTTT
35359706 AATTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 6 0.33
16 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATAATTTTAA
Found at i:35359718 original size:22 final size:21
Alignment explanation
Indices: 35359678--35359721 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 21
35359668 TATGTTTTTA
35359678 TAATTTATAATTTTTTAATTT
1 TAATTTATAATTTTTTAATTT
35359699 TAATTT-TAATTTTTCATAATTT
1 TAATTTATAATTTTT--TAATTT
35359721 T
1 T
35359722 TGGAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 7 0.33
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TAATTTATAATTTTTTAATTT
Found at i:35367560 original size:29 final size:29
Alignment explanation
Indices: 35367528--35367583 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
35367518 TAAATTAGAA
* ** *
35367528 AAATAAAAAGATTTGATTTTAAATTTTTT
1 AAATAAAAAAATTAAATTTAAAATTTTTT
35367557 AAATAAAAAAATTAAATTTAAAATTTT
1 AAATAAAAAAATTAAATTTAAAATTTT
35367584 GTCAAAGTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
AAATAAAAAAATTAAATTTAAAATTTTTT
Found at i:35369675 original size:12 final size:12
Alignment explanation
Indices: 35369658--35369682 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35369648 ATGGAACAAC
35369658 ACAACTGTTGTA
1 ACAACTGTTGTA
35369670 ACAACTGTTGTA
1 ACAACTGTTGTA
35369682 A
1 A
35369683 TATTTGTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ACAACTGTTGTA
Found at i:35369915 original size:5 final size:5
Alignment explanation
Indices: 35369907--35369945 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
35369897 TTTTTTTCCA
*
35369907 AAAAC AAAAG AAAAG AAAAG AAAAG AAAAG AAAA- AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
35369946 GAACTGCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:35370751 original size:183 final size:181
Alignment explanation
Indices: 35370431--35370985 Score: 826
Period size: 183 Copynumber: 3.0 Consensus size: 181
35370421 CTGTCATACC
* * *
35370431 CTCAGTTGTAGCTGGTTTCAGAGTCAATTCTAAACTCAGACTCGGTCTAGGCCCTTTT-GTCTTG
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACT-TGACTCAGTCTAGG-CCTTTTCGTCTTG
35370495 TATCTTGCTATATCTTGGGAAGTGCTGTGGTTGGTTGGTATGTGCTCCTTGTTGATGCTGGGGGT
64 TATCTTGCTATATCTTGGGAAGTGCTGTGGTTGGTTGGTATGTGCTCCTTG-TGATGCTGGGGGT
* *
35370560 TGTAGTTGCAGTGATTTGATCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
128 TGTAGTTGCAGTGGTTTGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
* *
35370614 CTCAGCTGTAGTTGGTTTCAGAGTCAATTCTAAACTTGTACTCAGTCTAGGCCTTTTCTTCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTTG-ACTCAGTCTAGGCCTTTTCGTCTTGT
*
35370679 ATCTTGCTATATCTCGGGAAGTGCTGTGGTTGGTTGGTATGTGCTCCTTTGTGATGCTGGGGGTT
65 ATCTTGCTATATCTTGGGAAGTGCTGTGGTTGGTTGGTATGTGCTCC-TTGTGATGCTGGGGGTT
* *
35370744 GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACGTCTGCCAAATGATA
129 GTAGTTGCAGTGGTTTGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
*
35370797 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTTGAACTCAGTCTAGGCCTCTTCGTCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTTG-ACTCAGTCTAGGCCTTTTCGTCTTGT
* * * * *
35370862 ATCTTGCTATACCTTGGGAAGTTCTGTTGG-TGGTTGGTATGGGCTCCATGTCGATGCCGGGGGT
65 ATCTTGCTATATCTTGGGAAGTGCTG-TGGTTGGTTGGTATGTGCTCCTTGT-GATGCTGGGGGT
* * * * * *
35370926 TGTAGTTGCAGTGGTTTGGCCTAGTTCATGGTTTAAGACCTCTGCCGAATGATC
128 TGTAGTTGCAGTGGTTTGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
35370980 CTCAGT
1 CTCAGT
35370986 CTCAGAAGGC
Statistics
Matches: 340, Mismatches: 27, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
182 10 0.03
183 324 0.95
184 6 0.02
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.37
Consensus pattern (181 bp):
CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTTGACTCAGTCTAGGCCTTTTCGTCTTGTA
TCTTGCTATATCTTGGGAAGTGCTGTGGTTGGTTGGTATGTGCTCCTTGTGATGCTGGGGGTTGT
AGTTGCAGTGGTTTGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
Found at i:35371538 original size:21 final size:21
Alignment explanation
Indices: 35371514--35371553 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35371504 GAGAGAATTT
35371514 GAGAAATTAAG-GAAAGTAAGA
1 GAGAAATTAAGAG-AAGTAAGA
*
35371535 GAGAATTTAAGAGAAGTAA
1 GAGAAATTAAGAGAAGTAA
35371554 CAGCTACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (21 bp):
GAGAAATTAAGAGAAGTAAGA
Found at i:35372726 original size:6 final size:6
Alignment explanation
Indices: 35372715--35372803 Score: 62
Period size: 6 Copynumber: 15.2 Consensus size: 6
35372705 GGGCCCAACA
* * **
35372715 AAATTT AAATTT -ATTTT AAAATTT AAGTTT ATTTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT
* *
35372763 --ATTGG AAATTT AAATTT --ATTAT AAATTT AAATTC AAATTT A
1 AAATT-T AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT A
35372804 TGTAAATGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
4 6 0.09
5 5 0.08
6 43 0.67
7 10 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:35372737 original size:18 final size:18
Alignment explanation
Indices: 35372714--35372795 Score: 105
Period size: 18 Copynumber: 4.7 Consensus size: 18
35372704 CGGGCCCAAC
35372714 AAAATTTAAATTTATTTT
1 AAAATTTAAATTTATTTT
*
35372732 AAAATTTAAGTTTATTTT
1 AAAATTTAAATTTATTTT
* *
35372750 TAAATTTAAATTTA-TTG
1 AAAATTTAAATTTATTTT
* *
35372767 GAAATTTAAATTTATTAT
1 AAAATTTAAATTTATTTT
35372785 -AAATTTAAATT
1 AAAATTTAAATT
35372796 CAAATTTATG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
17 26 0.46
18 30 0.54
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
AAAATTTAAATTTATTTT
Found at i:35372773 original size:17 final size:18
Alignment explanation
Indices: 35372715--35372795 Score: 103
Period size: 17 Copynumber: 4.6 Consensus size: 18
35372705 GGGCCCAACA
*
35372715 AAATTTAAATTTATTTTA
1 AAATTTAAATTTATTTTT
*
35372733 AAATTTAAGTTTATTTTT
1 AAATTTAAATTTATTTTT
**
35372751 AAATTTAAATTTA-TTGG
1 AAATTTAAATTTATTTTT
*
35372768 AAATTTAAATTTA-TTAT
1 AAATTTAAATTTATTTTT
35372785 AAATTTAAATT
1 AAATTTAAATT
35372796 CAAATTTATG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
17 28 0.50
18 28 0.50
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
AAATTTAAATTTATTTTT
Found at i:35373428 original size:17 final size:19
Alignment explanation
Indices: 35373394--35373429 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
35373384 TATTGTACCC
35373394 ATTTATTAATATATAATAA
1 ATTTATTAATATATAATAA
35373413 ATTT-TTAATA-ATAATAA
1 ATTTATTAATATATAATAA
35373430 TAATAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATTAATATATAATAA
Found at i:35374717 original size:28 final size:28
Alignment explanation
Indices: 35374634--35374778 Score: 116
Period size: 28 Copynumber: 5.0 Consensus size: 28
35374624 CTCAAGAGAT
* *
35374634 CCCTAAACTATC-CGAAAATCATATTTTGA
1 CCCTAAACT-TCACAAAAATCACATTTT-A
* *
35374663 CCCTTAAACTTTAAAAAAAAATCACATTTTA
1 CCC-TAAAC-TT-CACAAAAATCACATTTTA
* *
35374694 CCTCTAAACTTCAC-AAAATTACATTTTTC
1 CC-CTAAACTTCACAAAAATCACA-TTTTA
*
35374723 CCCTGAACTTC-CAAAAATCACATTTTTA
1 CCCTAAACTTCACAAAAATCACA-TTTTA
*
35374751 CCCGTAAACTTCACAAAAATTACATTTT
1 CCC-TAAACTTCACAAAAATCACATTTT
35374779 TGCCCCCAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 18
0.75 0.10 0.14
Matches are distributed among these distances:
27 1 0.01
28 32 0.34
29 21 0.22
30 18 0.19
31 9 0.10
32 13 0.14
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (28 bp):
CCCTAAACTTCACAAAAATCACATTTTA
Found at i:35374770 original size:30 final size:29
Alignment explanation
Indices: 35374634--35374843 Score: 144
Period size: 30 Copynumber: 7.1 Consensus size: 29
35374624 CTCAAGAGAT
* * *
35374634 CCCTAAACTATCCGAAAATCATATTTTGAC
1 CCCTAAACT-TCCAAAAATCACATTTTTAC
* **
35374664 CCTTAAACTTTAAAAAAAAATCACA-TTTTAC
1 CCCTAAAC-TT--CCAAAAATCACATTTTTAC
* *
35374695 CTCTAAACTT-CACAAAATTACATTTTT-C
1 CCCTAAACTTCCA-AAAATCACATTTTTAC
*
35374723 CCCTGAACTTCCAAAAATCACATTTTTAC
1 CCCTAAACTTCCAAAAATCACATTTTTAC
* * *
35374752 CCGTAAACTTCACAAAAATTACATTTTTGC
1 CCCTAAACTTC-CAAAAATCACATTTTTAC
* *
35374782 CCCCAAACTTTCCAAAATTC-CATTTTTAAC
1 CCCTAAAC-TTCCAAAAATCACATTTTT-AC
* *
35374812 CCC-AAACCTTTCAAAAATTACCA-TTTTAC
1 CCCTAAA-CTTCCAAAAATCA-CATTTTTAC
35374841 CCC
1 CCC
35374844 CCGAATATTT
Statistics
Matches: 142, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.01
28 30 0.21
29 39 0.27
30 47 0.33
31 17 0.12
32 8 0.06
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.32
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATCACATTTTTAC
Found at i:35374874 original size:29 final size:28
Alignment explanation
Indices: 35374795--35375078 Score: 125
Period size: 29 Copynumber: 9.7 Consensus size: 28
35374785 CAAACTTTCC
* * **
35374795 AAAATTCCATTTTTAACCCCAAACCTTTCA
1 AAAATTCCA-TTTTGACCCCGAATATTT-A
*
35374825 AAAATTACCATTTT-ACCCCCCGAATATTTT
1 AAAATT-CCATTTTGA--CCCCGAATATTTA
*
35374855 AAAATTCCATTTTTGACCCC-AAAACTTTCA
1 AAAATTCCA-TTTTGACCCCGAATA-TTT-A
* *
35374885 AAAATTACCATTTT-ACCCTTGAATATCTA
1 AAAATT-CCATTTTGACCC-CGAATATTTA
** * *
35374914 AAAATTCCACTTTTGACCCTAAACATTCA
1 AAAATTCCA-TTTTGACCCCGAATATTTA
*
35374943 AAAATTTACCATTTT-ACCCCTAA-ATGTCTA
1 AAAA-TT-CCATTTTGACCCCGAATAT-T-TA
* * *
35374973 AAAATTCTATTTTGACCCCAAACT-TTTC
1 AAAATTCCATTTTGACCCCGAA-TATTTA
* *
35375001 AAAATTACCATTTT-ACCCCCGAATGTCTA
1 AAAATT-CCATTTTGA-CCCCGAATATTTA
* ** *
35375030 AAAATTCCATTTTTGATCCCGAACCTTCCA
1 AAAATTCCA-TTTTGACCCCGAATATT-TA
35375060 AAAATTTCCATTTT-ACCCC
1 AAAA-TTCCATTTTGACCCC
35375079 CCTGAGTGTC
Statistics
Matches: 199, Mismatches: 29, Indels: 53
0.71 0.10 0.19
Matches are distributed among these distances:
28 26 0.13
29 88 0.44
30 58 0.29
31 27 0.14
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTGACCCCGAATATTTA
Found at i:35374952 original size:59 final size:58
Alignment explanation
Indices: 35374795--35375079 Score: 349
Period size: 59 Copynumber: 4.8 Consensus size: 58
35374785 CAAACTTTCC
* * *
35374795 AAAATTCCATTTTTAACCCCAAACCTTTCAAAAATTACCATTTTACCCCCCGAATATTTT
1 AAAATTCCATTTTTGACCCCAAA-CTTTCAAAAATTACCATTTTA-CCCCCGAATATCTA
**
35374855 AAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCTTGAATATCTA
1 AAAATTCCATTTTTGACCCC-AAACTTTCAAAAATTACCATTTTACCCCCGAATATCTA
* * * ** *
35374914 AAAATTCCACTTTTGACCCTAAACATTCAAAAATTTACCATTTTACCCCTAAATGTCTA
1 AAAATTCCATTTTTGACCCCAAACTTTCAAAAA-TTACCATTTTACCCCCGAATATCTA
* *
35374973 AAAATTCTA-TTTTGACCCCAAACTTTTC-AAAATTACCATTTTACCCCCGAATGTCTA
1 AAAATTCCATTTTTGACCCCAAAC-TTTCAAAAATTACCATTTTACCCCCGAATATCTA
* * * *
35375030 AAAATTCCATTTTTGATCCCGAACCTTCCAAAAATTTCCATTTTACCCCC
1 AAAATTCCATTTTTGA-CCCCAAACTTTCAAAAATTACCATTTTACCCCC
35375080 CTGAGTGTCC
Statistics
Matches: 198, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
57 31 0.16
58 38 0.19
59 86 0.43
60 40 0.20
61 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCCAAACTTTCAAAAATTACCATTTTACCCCCGAATATCTA
Found at i:35374966 original size:30 final size:29
Alignment explanation
Indices: 35374679--35375019 Score: 169
Period size: 30 Copynumber: 11.7 Consensus size: 29
35374669 AACTTTAAAA
* *
35374679 AAAAATCA-CATTTTACCTCTAAAC-TTC
1 AAAAATTACCATTTTACCCCTAAACATTC
* *
35374706 ACAAAATTA-CATTTTTCCCCTGAAC-TTCC
1 A-AAAATTACCATTTTACCCCTAAACATT-C
* *
35374735 AAAAATCA-CATTTTTACCCGTAAAC-TTCAC
1 AAAAATTACCA-TTTTACCCCTAAACATT--C
* * *
35374765 AAAAATTA-CATTTTTGCCCCCAAACTTTC
1 AAAAATTACCA-TTTTACCCCTAAACATTC
* *
35374794 CAAAATT-CCATTTTTAACCCC-AAACCTTTC
1 AAAAATTACCA-TTTT-ACCCCTAAA-CATTC
** * *
35374824 AAAAATTACCATTTTACCCCCCGAATATTT
1 AAAAATTACCATTTTA-CCCCTAAACATTC
* * *
35374854 TAAAATT-CCATTTTTGACCCCAAAACTTTC
1 AAAAATTACCA-TTTT-ACCCCTAAACATTC
* * *
35374884 AAAAATTACCATTTTACCCTTGAATA-TC
1 AAAAATTACCATTTTACCCCTAAACATTC
35374912 TAAAAATT-CCACTTTTGA-CCCTAAACATTC
1 -AAAAATTACCA-TTTT-ACCCCTAAACATTC
35374942 AAAAATTTACCATTTTACCCCT-AA-ATGTC
1 AAAAA-TTACCATTTTACCCCTAAACAT-TC
* *
35374971 TAAAAATT-CTATTTTGACCCC-AAACTTTTC
1 -AAAAATTACCATTTT-ACCCCTAAAC-ATTC
35375001 -AAAATTACCATTTTACCCC
1 AAAAATTACCATTTTACCCC
35375020 CGAATGTCTA
Statistics
Matches: 248, Mismatches: 38, Indels: 55
0.73 0.11 0.16
Matches are distributed among these distances:
27 1 0.00
28 53 0.21
29 84 0.34
30 95 0.38
31 15 0.06
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCTAAACATTC
Done.