Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 50 of 171
Found at i:20898275 original size:31 final size:31
Alignment explanation
Indices: 20898240--20898486 Score: 156
Period size: 31 Copynumber: 7.4 Consensus size: 31
20898230 CTTCATCTCT
20898240 GAAATTGAAGTAAGAGCAACGTCATCCCCTC
1 GAAATTGAAGTAAGAGCAACGTCATCCCCTC
* * * *
20898271 GAAATTGAAGTAGAGTGGATAAC-ACATCTTTACCTC
1 GAAATTGAAGTA-AG-AG-CAACGTCATC---CCCTC
* *
20898307 TGAAATTGAAGTAAGAGCAACGTCATCCCGTT
1 -GAAATTGAAGTAAGAGCAACGTCATCCCCTC
* * * *
20898339 GAAATTGAAGTAGAGTGGATAAC-ACATCTTCATCTC
1 GAAATTGAAGTA-AG-AG-CAACGTCATC--C-CCTC
20898375 TGAAATTGAAGTAAGAGCAACGTCATCCCCTC
1 -GAAATTGAAGTAAGAGCAACGTCATCCCCTC
** * **
20898407 GAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
1 GAAATTGAAGTA-A---GAGCA-ACGTCATCCCCTC
*
20898443 TGAAATTAAAGTAAGAGCAACGTCATCCCCTC
1 -GAAATTGAAGTAAGAGCAACGTCATCCCCTC
20898475 GAAATTGAAGTA
1 GAAATTGAAGTA
20898487 GAGTGGATAA
Statistics
Matches: 162, Mismatches: 32, Indels: 44
0.68 0.13 0.18
Matches are distributed among these distances:
31 47 0.29
32 20 0.12
33 14 0.09
34 12 0.07
35 14 0.09
36 20 0.12
37 35 0.22
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (31 bp):
GAAATTGAAGTAAGAGCAACGTCATCCCCTC
Found at i:20898946 original size:76 final size:76
Alignment explanation
Indices: 20898818--20898966 Score: 217
Period size: 76 Copynumber: 2.0 Consensus size: 76
20898808 CTAAGATCAA
** *
20898818 TTCCTATCCTCTTGAAAATGAAGTAAAGTTGGATATCAAGCCGTTATTTCTGAAATTGAAGTAAG
1 TTCCTATCCTCTTGAAAATGAAGTAAAGCGGGATATCAAGCCGTTATCTCTGAAATTGAAGTAAG
20898883 AGCAAGATCGT
66 AGCAAGATCGT
* * * * *
20898894 TTCCTATCGTCTTGAAATTGAAGTAAAGCGGGATATTAAGTCTTTATCTCTGAAATTGAAGTAAG
1 TTCCTATCCTCTTGAAAATGAAGTAAAGCGGGATATCAAGCCGTTATCTCTGAAATTGAAGTAAG
*
20898959 AGTAAGAT
66 AGCAAGAT
20898967 AAAGCACCAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (76 bp):
TTCCTATCCTCTTGAAAATGAAGTAAAGCGGGATATCAAGCCGTTATCTCTGAAATTGAAGTAAG
AGCAAGATCGT
Found at i:20899536 original size:24 final size:23
Alignment explanation
Indices: 20899509--20899562 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
20899499 ATTCATTTAC
**
20899509 AAATTTGAATTTATCTTAAAATTT
1 AAATTTGAATCAAT-TTAAAATTT
* *
20899533 AAATTTAAATCAATTTTAAATTT
1 AAATTTGAATCAATTTAAAATTT
20899556 AAATTTG
1 AAATTTG
20899563 TGTTAAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
AAATTTGAATCAATTTAAAATTT
Found at i:20899568 original size:17 final size:17
Alignment explanation
Indices: 20899548--20899580 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
20899538 TAAATCAATT
20899548 TTAAATTTAAATTTGTG
1 TTAAATTTAAATTTGTG
20899565 TTAAATTTAAATTTGT
1 TTAAATTTAAATTTGT
20899581 TAAATTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TTAAATTTAAATTTGTG
Found at i:20899644 original size:12 final size:12
Alignment explanation
Indices: 20899627--20899688 Score: 70
Period size: 14 Copynumber: 4.8 Consensus size: 12
20899617 ATTAAAGTCC
20899627 AAGGCCCAATTA
1 AAGGCCCAATTA
*
20899639 AAGGCCTAATTA
1 AAGGCCCAATTA
20899651 CAATGGCCCAAATTA
1 -AA-GGCCC-AATTA
20899666 AAGGCCCAATTATA
1 AAGGCCCAA-T-TA
20899680 AAGGCCCAA
1 AAGGCCCAA
20899689 ATAGGCCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 13 0.30
13 8 0.19
14 17 0.40
15 5 0.12
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (12 bp):
AAGGCCCAATTA
Found at i:20899667 original size:27 final size:27
Alignment explanation
Indices: 20899627--20899690 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
20899617 ATTAAAGTCC
*
20899627 AAGGCCC-AATTAAAGGCCTAATTACA
1 AAGGCCCAAATTAAAGGCCCAATTACA
* *
20899653 ATGGCCCAAATTAAAGGCCCAATTATA
1 AAGGCCCAAATTAAAGGCCCAATTACA
20899680 AAGGCCCAAAT
1 AAGGCCCAAAT
20899691 AGGCCCAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 6 0.18
27 27 0.82
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (27 bp):
AAGGCCCAAATTAAAGGCCCAATTACA
Found at i:20899766 original size:15 final size:15
Alignment explanation
Indices: 20899746--20899776 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20899736 CGTGCCTCTG
20899746 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
20899761 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
20899776 C
1 C
20899777 CATCCGCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:20900240 original size:7 final size:7
Alignment explanation
Indices: 20900228--20900288 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
20900218 TAAAAATATT
20900228 ATTAATA
1 ATTAATA
20900235 ATTAATA
1 ATTAATA
20900242 ATT-ATA
1 ATTAATA
20900248 ATTAAT-
1 ATTAATA
* *
20900254 ATTTATG
1 ATTAATA
*
20900261 ACT-ATA
1 ATTAATA
*
20900267 GTTAAT-
1 ATTAATA
20900273 ATTAATA
1 ATTAATA
20900280 ATTAATA
1 ATTAATA
20900287 AT
1 AT
20900289 ATTGAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 19 0.43
7 25 0.57
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (7 bp):
ATTAATA
Found at i:20900286 original size:13 final size:13
Alignment explanation
Indices: 20900227--20900286 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 13
20900217 ATAAAAATAT
20900227 TATTAATAATTAA
1 TATTAATAATTAA
20900240 TAATT-ATAATTAA
1 T-ATTAATAATTAA
20900253 TATTTATGACTATAGTTAA
1 TA-TTA--A-TA-A-TTAA
20900272 TATTAATAATTAA
1 TATTAATAATTAA
20900285 TA
1 TA
20900287 ATATTGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
12 1 0.03
13 18 0.46
14 4 0.10
15 2 0.05
16 2 0.05
17 2 0.05
18 4 0.10
19 6 0.15
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (13 bp):
TATTAATAATTAA
Found at i:20901459 original size:30 final size:31
Alignment explanation
Indices: 20901425--20901486 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
20901415 CCAAACAATT
* * *
20901425 CAAAAATTATATTTTGA-CCCTAAAACTTTC
1 CAAAAATTACATTTTAACCCCTAAAAATTTC
20901455 CAAAAATTACATTTTAACCCCTAAAAATTTC
1 CAAAAATTACATTTTAACCCCTAAAAATTTC
20901486 C
1 C
20901487 TAAATCCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (31 bp):
CAAAAATTACATTTTAACCCCTAAAAATTTC
Found at i:20901629 original size:58 final size:59
Alignment explanation
Indices: 20901488--20901653 Score: 246
Period size: 60 Copynumber: 2.8 Consensus size: 59
20901478 AAAATTTCCT
* *
20901488 AAATCCCATTTTTAACCCCGATTTCACTGAAAATTTACCATTTTACCCCCAAAGCTTCTA
1 AAATTCCATTTTTAACCCCGATTTCACTGAAAA-TTACCATTTTACCCCCAAACCTTCTA
* * *
20901548 AAATTCCATTTTTAACCCTGATTTCACTGAAAATTACCATTTTACCTCGAAACCTT-TA
1 AAATTCCATTTTTAACCCCGATTTCACTGAAAATTACCATTTTACCCCCAAACCTTCTA
* *
20901606 AAATTCCATTTTTAACCCCGATTTCAC-CAAAATTACCATTTTGCCCCC
1 AAATTCCATTTTTAACCCCGATTTCACTGAAAATTACCATTTTACCCCC
20901654 GGGTATCCAT
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
57 17 0.18
58 28 0.29
59 20 0.21
60 31 0.32
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (59 bp):
AAATTCCATTTTTAACCCCGATTTCACTGAAAATTACCATTTTACCCCCAAACCTTCTA
Found at i:20907492 original size:21 final size:21
Alignment explanation
Indices: 20907433--20907492 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
20907423 TATTATTTTT
* *
20907433 ATTAAAATTTTATATATAGGC
1 ATTATAATTTTATATATTGGC
*
20907454 ATCT-TAATTTT-TAATATTTGC
1 AT-TATAATTTTAT-ATATTGGC
20907475 ATTATAATTTTATATATT
1 ATTATAATTTTATATATT
20907493 ATTATAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTATAATTTTATATATTGGC
Found at i:20908795 original size:262 final size:257
Alignment explanation
Indices: 20908337--20908852 Score: 626
Period size: 262 Copynumber: 2.0 Consensus size: 257
20908327 CTAAGAACAT
* * * * *
20908337 TTTTTTTCAAATGTTAGGGTTGTAAATTCGGTTGTATTAAAGGCATCCTTCTGCCAAAAAAAAAA
1 TTTTTGTCAAATGTTAGGATTATAAATTCGGTTGTATAAAAGGCATCCTTATGCCAAAAAAAAAA
** * **
20908402 AAGCCTCTTATCATCTTTTTAGGTCTTATCCATTATTCCTTTCATTATATTTAGGTTTTTTGGTT
66 AAGCCTCTTATCATCTTTTTAGGTCTTATCCATTATTCCTTTCACCATATTTAGGCTTTTAAGTT
* * * ** * *
20908467 TTCATTTCTTAGCTTAGTTAGTGATTGTTAGTTTCTTCATTTTTGTTGTAGCTTTAGTTTTCTTG
131 TCCATTTCTTAACTTAGTTAGTGATTGCTAGTTTCTTCATTTTTACTATAACTTTAGTTTTCTTG
* *** * *
20908532 CAATCAAACATAAAACTTT-TCTTGTTATTTTGAATTCTCTTTAGAGCATTCAATATATTTCA
196 CAATCAAA-ACAAAACTTTCTCTTGTTATTCAAAATTCTCTTTAAAACATTCAATATATTTCA
* *
20908594 TTTTTGTCAAATGTTAGGATTATAAATTTGGTTGTATAAAAGAG-ATCTTTATGCCAAACAAAAA
1 TTTTTGTCAAATGTTAGGATTATAAATTCGGTTGTATAAAAG-GCATCCTTATGCCAAA-AAAAA
* * * * * *
20908658 AAAAGCCACTTTTAT-TTTTTTTTTGGTCTTCTCCATTATTCCTTTC-CCATGTTTAGGCTTTTA
64 AAAAG-C-CTCTTATCATCTTTTTAGGTCTTATCCATTATTCCTTTCACCATATTTAGGCTTTTA
* *
20908721 AGTTTCCATTTCTTAACTTAGTTAATCCTTGGTTGCTAGTTTCTTCATTTTTACTATAACTTTAG
127 AGTTTCCATTTCTTAACTTAGTT-A---GTGATTGCTAGTTTCTTCATTTTTACTATAACTTTAG
20908786 TTTTCTTGCAATCAAAACAAAACTTTCTCTTGTTATTCAAAATTCTCTTTAAAACATTCAATATA
188 TTTTCTTGCAATCAAAACAAAACTTTCTCTTGTTATTCAAAATTCTCTTTAAAACATTCAATATA
20908851 TT
253 TT
20908853 CTCTTTATAA
Statistics
Matches: 217, Mismatches: 33, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
257 49 0.23
258 43 0.20
259 29 0.13
260 6 0.03
261 9 0.04
262 81 0.37
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (257 bp):
TTTTTGTCAAATGTTAGGATTATAAATTCGGTTGTATAAAAGGCATCCTTATGCCAAAAAAAAAA
AAGCCTCTTATCATCTTTTTAGGTCTTATCCATTATTCCTTTCACCATATTTAGGCTTTTAAGTT
TCCATTTCTTAACTTAGTTAGTGATTGCTAGTTTCTTCATTTTTACTATAACTTTAGTTTTCTTG
CAATCAAAACAAAACTTTCTCTTGTTATTCAAAATTCTCTTTAAAACATTCAATATATTTCA
Found at i:20908855 original size:23 final size:22
Alignment explanation
Indices: 20908820--20908872 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
20908810 TTCTCTTGTT
20908820 ATTCAAAATTCTCTTTA-AAAC
1 ATTCAAAATTCTCTTTATAAAC
20908841 ATTCAATATATTCTCTTTATAAAC
1 ATTCAA-A-ATTCTCTTTATAAAC
*
20908865 TTTCAAAA
1 ATTCAAAA
20908873 GTGTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.21
22 2 0.07
23 11 0.39
24 9 0.32
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTCAAAATTCTCTTTATAAAC
Found at i:20910109 original size:29 final size:29
Alignment explanation
Indices: 20910077--20910134 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
20910067 GTTAAACTTG
* *
20910077 GGAAAAAATATTATAAAATTTATAAAAAT
1 GGAAAAAATACTAGAAAATTTATAAAAAT
** *
20910106 GGAAAATTTACTGGAAAATTTATAAAAAT
1 GGAAAAAATACTAGAAAATTTATAAAAAT
20910135 TCAAAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (29 bp):
GGAAAAAATACTAGAAAATTTATAAAAAT
Found at i:20912724 original size:59 final size:60
Alignment explanation
Indices: 20912646--20912832 Score: 218
Period size: 59 Copynumber: 3.1 Consensus size: 60
20912636 TTAATATAAT
* * * *
20912646 ATTTAGTACTTGAACTTGACACTTTTTTCTAATATAATAACTAAACTTTTTTT-GACTCA
1 ATTTGGTACTTGAACTTGACACTTTTTTCTAATTTGATACCTAAACTTTTTTTAGACTCA
* * * *
20912705 ATTTGGTACTTGAATTTGACAC-TTTTTCTTAATTTGTTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTTC-TAATTTGATACCTAAACTTTTTTTAGACTCA
* * * ** *
20912765 ATTTGGTACCTGAACTTGGCA-TTTTTTCTAATTTGGTACCTAAGGTTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGACACTTTTTTCTAATTTGATACCTAAACTTTTTTTAGACTCA
20912824 ATTTGGTAC
1 ATTTGGTAC
20912833 CTATATTTAT
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
58 6 0.06
59 74 0.68
60 29 0.27
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (60 bp):
ATTTGGTACTTGAACTTGACACTTTTTTCTAATTTGATACCTAAACTTTTTTTAGACTCA
Found at i:20913170 original size:31 final size:31
Alignment explanation
Indices: 20913040--20913161 Score: 121
Period size: 31 Copynumber: 4.0 Consensus size: 31
20913030 CCCCAAACAG
* * *
20913040 TTAAGTACCAACTTTA-AAAAAAGTGTCAAAT
1 TTAAGTACCAA-ATTAGGAAAAAGTGTCAAGT
20913071 TTAAGTACCAAATTAGGAAAAAGTGTCAAGT
1 TTAAGTACCAAATTAGGAAAAAGTGTCAAGT
* *
20913102 TTAAGTATCAAATT-GGACCAAAA----AAAGT
1 TTAAGTACCAAATTAGGA--AAAAGTGTCAAGT
*
20913130 TTAGGTACCAAATTAGGAAAAAGTGTCAAGT
1 TTAAGTACCAAATTAGGAAAAAGTGTCAAGT
20913161 T
1 T
20913162 CGGGTACCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
27 4 0.05
28 16 0.21
29 3 0.04
30 6 0.08
31 42 0.56
32 4 0.05
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (31 bp):
TTAAGTACCAAATTAGGAAAAAGTGTCAAGT
Found at i:20914414 original size:18 final size:18
Alignment explanation
Indices: 20914391--20914425 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20914381 GCTTTTCCTC
*
20914391 TGCCTTATGGCATGTTTA
1 TGCCTTATGGCACGTTTA
20914409 TGCCTTATGGCACGTTT
1 TGCCTTATGGCACGTTT
20914426 TCGTCTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (18 bp):
TGCCTTATGGCACGTTTA
Found at i:20915633 original size:3 final size:3
Alignment explanation
Indices: 20915625--20915651 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20915615 TGTATCATAA
20915625 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
20915652 CATGAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20916477 original size:16 final size:17
Alignment explanation
Indices: 20916449--20916480 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20916439 ATATAATATA
20916449 ATATAATATTTTACCTT
1 ATATAATATTTTACCTT
20916466 ATATAA-ATTTTACCT
1 ATATAATATTTTACCT
20916481 CCTCCCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATAATATTTTACCTT
Found at i:20926230 original size:3 final size:3
Alignment explanation
Indices: 20926224--20926268 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
20926214 GGTTATGATG
20926224 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
20926269 TCAATGGTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20930183 original size:73 final size:72
Alignment explanation
Indices: 20930106--20930256 Score: 160
Period size: 72 Copynumber: 2.1 Consensus size: 72
20930096 ACGCCCACGT
*
20930106 GCGTGTACCAAACCGTGTGAACATACTGTT-TTGAGAATACAAAAACAGTGAGTTACACGGTCTG
1 GCGTGTACCAAACCGTGTGAACATACTGTTGCTGA-AAT-CAAAAACAGTGAGTTACACGGTCTG
20930170 GACCCACAG
64 GACCCACAG
* * * * * ** * * *
20930179 GCGTGTGCCAGACTGTGTGGACGTGTTGTTGCTGAAATGAGAAATAGTGAGTTACACGGTCTGGA
1 GCGTGTACCAAACCGTGTGAACATACTGTTGCTGAAATCAAAAACAGTGAGTTACACGGTCTGGA
**
20930244 CCCATGG
66 CCCACAG
20930251 GCGTGT
1 GCGTGT
20930257 GCCAGACCAT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
72 35 0.55
73 26 0.41
74 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (72 bp):
GCGTGTACCAAACCGTGTGAACATACTGTTGCTGAAATCAAAAACAGTGAGTTACACGGTCTGGA
CCCACAG
Found at i:20930326 original size:73 final size:72
Alignment explanation
Indices: 20930156--20930342 Score: 205
Period size: 73 Copynumber: 2.6 Consensus size: 72
20930146 AAAAACAGTG
* * * * **
20930156 AGTTACACGGTCTGGACCCACAGGCGTGTGCCAGACTGTGTGGACGTGTTGTTGCTGAAATGAGA
1 AGTTACACGGTCTGGACCCACGGGCGTGTGCCAGACCGTGTGGACATGTTATACCTGAAATGAGA
* * *
20930221 AATAGTG
66 AACAATA
* * * *
20930228 AGTTACACGGTCTGGACCCATGGGCGTGTGCCAGACCATGTGGTCATGTTATACCATGGAATCG-
1 AGTTACACGGTCTGGACCCACGGGCGTGTGCCAGACCGTGTGGACATGTTATACC-TGAAAT-GA
20930292 GAAACAATA
64 GAAACAATA
* * *
20930301 AGTTACACGGTCTGGACACACGGGCGTGGGCTAGACCGTGTG
1 AGTTACACGGTCTGGACCCACGGGCGTGTGCCAGACCGTGTG
20930343 ACACCCACGG
Statistics
Matches: 95, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
72 46 0.48
73 48 0.51
74 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (72 bp):
AGTTACACGGTCTGGACCCACGGGCGTGTGCCAGACCGTGTGGACATGTTATACCTGAAATGAGA
AACAATA
Found at i:20931125 original size:29 final size:27
Alignment explanation
Indices: 20931075--20931141 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 27
20931065 GGATGGGAGG
* *
20931075 GGAGTAAAAGTTTAGGAGAAAAAATGGAA
1 GGAGTAAAAGTTAAAGAGAAAAAA-GG-A
*
20931104 GGAGTAAAAGTTGAAAGA-AAAATAGGA
1 GGAGTAAAAGTT-AAAGAGAAAAAAGGA
20931131 GAGAGTAAAAG
1 G-GAGTAAAAG
20931142 ATTTGGGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 11 0.33
29 17 0.52
30 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (27 bp):
GGAGTAAAAGTTAAAGAGAAAAAAGGA
Found at i:20932462 original size:13 final size:12
Alignment explanation
Indices: 20932446--20932478 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20932436 AATTAAATTA
20932446 TAAAATATTCATT
1 TAAAATATT-ATT
20932459 TAAAATA-TATT
1 TAAAATATTATT
20932470 TAAAATATT
1 TAAAATATT
20932479 TGTTTTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 2 0.11
13 7 0.37
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:20932707 original size:23 final size:23
Alignment explanation
Indices: 20932662--20932707 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
20932652 AAAACATAGT
**
20932662 AAAATATAAAATTATATACAAAA
1 AAAATATAAAACAATATACAAAA
20932685 AAAATATAAACACAATATA-AAAA
1 AAAATATAAA-ACAATATACAAAA
20932708 TACAAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAATATAAAACAATATACAAAA
Found at i:20933205 original size:20 final size:20
Alignment explanation
Indices: 20933180--20933218 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20933170 CATATATACT
20933180 TAATAAAAATTCAAAAAAAA
1 TAATAAAAATTCAAAAAAAA
* *
20933200 TAATAAATATTTAAAAAAA
1 TAATAAAAATTCAAAAAAA
20933219 TAAAAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
TAATAAAAATTCAAAAAAAA
Found at i:20939150 original size:38 final size:38
Alignment explanation
Indices: 20939108--20939188 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
20939098 AATGTTTTTA
*
20939108 AGACCCATACAATCCTAACCAAAACATTCGAATAATTT
1 AGACCCATACAATACTAACCAAAACATTCGAATAATTT
20939146 AGACCCATACAATACTAACCAAAACATTCGAATAATTT
1 AGACCCATACAATACTAACCAAAACATTCGAATAATTT
20939184 AGACC
1 AGACC
20939189 AAGTCCGGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.22
Consensus pattern (38 bp):
AGACCCATACAATACTAACCAAAACATTCGAATAATTT
Found at i:20943459 original size:26 final size:26
Alignment explanation
Indices: 20943424--20943476 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
20943414 TCGATTAATT
20943424 ACTTTAATTAAGTCGGAGGTCGGTTA
1 ACTTTAATTAAGTCGGAGGTCGGTTA
20943450 ACTTTAATTAAGTCGGAGGTCGGTTA
1 ACTTTAATTAAGTCGGAGGTCGGTTA
20943476 A
1 A
20943477 AGGTTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.34
Consensus pattern (26 bp):
ACTTTAATTAAGTCGGAGGTCGGTTA
Found at i:20949866 original size:2 final size:2
Alignment explanation
Indices: 20949859--20949897 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20949849 GTTTTCTGTA
20949859 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
20949898 CCAGACAGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20953618 original size:57 final size:55
Alignment explanation
Indices: 20953581--20953992 Score: 310
Period size: 57 Copynumber: 7.2 Consensus size: 55
20953571 GGGTGAAAGC
* *
20953581 GTAATTTTGG-GAAAATTCGGGGTTAAAAATGGGATTTTAGAAAGTTCAGGGTAAAATG
1 GTAATTTTGGTG-AAATT-AGGGTTAAAAATGGGATTTT-G-AACTTCAGGGTAAAATG
* *
20953639 GTAATTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAGTTCGGGGGTAAAATG
1 GTAATTTTGGTGAAATTAGGGTTAAAAATGGGATTTT-GAACTTC-AGGGTAAAATG
* ** * **
20953696 ATAATTTTCGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAGTTGGGGGTAAAATG
1 GTAATTTT-GGTGAAATTAGGGTTAAAAATGGGATTTT-GAACTTCAGGGTAAAATG
* * * * *
20953753 GTAATTTTGGTAAAATTGGGGTT-AAAA-GGAATTTTGGAAAGTTTAGGGGTAAAATG
1 GTAATTTTGGTGAAATTAGGGTTAAAAATGGGATTTT-G-AACTTCA-GGGTAAAATG
** * ** * *
20953809 ACAATTTTTTGTGAAATCGGGGTTAAAAATAGGATTTTGGAAGTTCAGGGTAAAATG
1 GTAA-TTTTGGTGAAATTAGGGTTAAAAATGGGATTTT-GAACTTCAGGGTAAAATG
* ** * * *
20953866 GTAATTTTTGGTAAAATCGGGGTT-AAAATGGAATTTTAGAAAGTTTAGGGGTAAAATG
1 GTAA-TTTTGGTGAAATTAGGGTTAAAAATGGGATTTT-G-AACTTCA-GGGTAAAATG
* * * * *
20953924 ATAATTTTCGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATG
1 GTAATTTT-GGTGAAATTAGGGTTAAAAATGGGATTTT-G-AACTTCAGGGTAAAATG
20953982 GTAATATTTGG
1 GTAAT-TTTGG
20953993 AAGTTTTGGG
Statistics
Matches: 305, Mismatches: 36, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
54 9 0.03
55 9 0.03
56 43 0.14
57 111 0.36
58 101 0.33
59 32 0.10
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (55 bp):
GTAATTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGAACTTCAGGGTAAAATG
Found at i:20953623 original size:29 final size:29
Alignment explanation
Indices: 20953583--20953992 Score: 194
Period size: 29 Copynumber: 14.3 Consensus size: 29
20953573 GTGAAAGCGT
20953583 AATTTTGGGAAAATTCGGGGTTAAAAATGG
1 AATTTTGGG-AAATTCGGGGTTAAAAATGG
* * *
20953613 GATTTT-AGAAAGTTCAGGG-T-AAAATGG
1 AATTTTGGGAAA-TTCGGGGTTAAAAATGG
*
20953640 TAATTTTGGTGAAATT-AGGGTTAAAAATGG
1 -AATTTTGG-GAAATTCGGGGTTAAAAATGG
* * * *
20953670 GATTTT-GGAAGTTCGGGGGT-AAAATGAT
1 AATTTTGGGAAATTCGGGGTTAAAAATG-G
20953698 AATTTTCGGTGAAA-TCGGGGTTAAAAATGG
1 AATTTT-GG-GAAATTCGGGGTTAAAAATGG
* * *
20953728 GATTTT-GGAAGTT-GGGGGT-AAAATGG
1 AATTTTGGGAAATTCGGGGTTAAAAATGG
*
20953754 TAATTTTGGTAAAATT-GGGGTT-AAAA-GG
1 -AATTTTGG-GAAATTCGGGGTTAAAAATGG
* *
20953782 AATTTT-GGAAAGTTTAGGGG-T-AAAATGAC
1 AATTTTGGGAAA--TTCGGGGTTAAAAATG-G
*
20953811 AATTTTTTGTGAAA-TCGGGGTTAAAAATAGG
1 AA--TTTTGGGAAATTCGGGGTTAAAAAT-GG
* *
20953842 -ATTTT-GGAAGTTCAGGG-T-AAAATGG
1 AATTTTGGGAAATTCGGGGTTAAAAATGG
* *
20953867 TAATTTTTGGTAAAATCGGGGTT-AAAATGG
1 -AA-TTTTGGGAAATTCGGGGTTAAAAATGG
* * *
20953897 AATTTT-AGAAAGTTTAGGGG-T-AAAATGAT
1 AATTTTGGGAAA--TTCGGGGTTAAAAATG-G
20953926 AATTTTCGGTGAAATT-GGGGTTAAAAATGG
1 AATTTT-GG-GAAATTCGGGGTTAAAAATGG
20953956 AATTTT-GGAAAGTTCGGGG-T-AAAATGG
1 AATTTTGGGAAA-TTCGGGGTTAAAAATGG
20953983 TAATATTTGG
1 -AAT-TTTGG
20953993 AAGTTTTGGG
Statistics
Matches: 294, Mismatches: 40, Indels: 92
0.69 0.09 0.22
Matches are distributed among these distances:
25 5 0.02
26 13 0.04
27 63 0.21
28 64 0.22
29 67 0.23
30 49 0.17
31 24 0.08
32 9 0.03
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (29 bp):
AATTTTGGGAAATTCGGGGTTAAAAATGG
Found at i:20953951 original size:115 final size:113
Alignment explanation
Indices: 20953597--20954033 Score: 572
Period size: 115 Copynumber: 3.8 Consensus size: 113
20953587 TTGGGAAAAT
* * *
20953597 TCGGGGTTAAAAATGGGATTTTAGAAAGTTCAGGGTAAAATGGTAATTTTGGTGAAATTAGGGTT
1 TCGGGGTTAAAAATGGGATTTT-GGAAGTTCAGGGTAAAATGGTAATTTTGGTAAAATTGGGGTT
* * **
20953662 AAAAATGGGATTTTGGAAGTTCGGGGGTAAAATGATAATTTTCGGTGAAA
65 -AAAATGGAATTTTGAAAGTTTAGGGGTAAAATGATAATTTTCGGTGAAA
**
20953712 TCGGGGTTAAAAATGGGATTTTGGAAGTTGGGGGTAAAATGGTAATTTTGGTAAAATTGGGGTTA
1 TCGGGGTTAAAAATGGGATTTTGGAAGTTCAGGGTAAAATGGTAATTTTGGTAAAATTGGGGTTA
* **
20953777 AAA-GGAATTTTGGAAAGTTTAGGGGTAAAATGACAATTTTTTGTGAAA
66 AAATGGAATTTT-GAAAGTTTAGGGGTAAAATGATAATTTTCGGTGAAA
* *
20953825 TCGGGGTTAAAAATAGGATTTTGGAAGTTCAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTT
1 TCGGGGTTAAAAATGGGATTTTGGAAGTTCAGGGTAAAATGGTAA-TTTTGGTAAAATTGGGGTT
20953890 AAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGATAATTTTCGGTGAAA
65 AAAATGGAATTTT-GAAAGTTTAGGGGTAAAATGATAATTTTCGGTGAAA
* * * **
20953940 TTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAATATTTGG-AAGTTTTGGGG
1 TCGGGGTTAAAAATGGGATTTTGG-AAGTTCAGGGTAAAATGGTAAT-TTTGGTAA-AATTGGGG
* *
20954004 TCAAAATGTAATTTTTTGAACAGTTTAGGG
63 TTAAAATGGAA--TTTTGAA-AGTTTAGGG
20954034 ACCTATAAGC
Statistics
Matches: 284, Mismatches: 29, Indels: 15
0.87 0.09 0.05
Matches are distributed among these distances:
112 7 0.02
113 76 0.27
114 59 0.21
115 87 0.31
116 39 0.14
117 3 0.01
118 13 0.05
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (113 bp):
TCGGGGTTAAAAATGGGATTTTGGAAGTTCAGGGTAAAATGGTAATTTTGGTAAAATTGGGGTTA
AAATGGAATTTTGAAAGTTTAGGGGTAAAATGATAATTTTCGGTGAAA
Found at i:20954004 original size:58 final size:56
Alignment explanation
Indices: 20953581--20953991 Score: 431
Period size: 58 Copynumber: 7.2 Consensus size: 56
20953571 GGGTGAAAGC
* * * *
20953581 GTAATTTTGGGAAAATTCGGGGTTAAAAATGGGATTTTAGAAAGTTCAGGGTAAAATG
1 GTAATTTTGTG-AAATT-GGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATG
* *
20953639 GTAATTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGG-AAGTTCGGGGGTAAAATG
1 GTAATTTT-GTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTC-GGGGTAAAATG
* * * *
20953696 ATAATTTTCGGTGAAATCGGGGTTAAAAATGGGATTTTGG-AAGTTGGGGGTAAAATG
1 GTAATTTT--GTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATG
* *
20953753 GTAATTTTGGTAAAATTGGGGTT-AAAA-GGAATTTTGGAAAGTTTAGGGGTAAAATG
1 GTAATTTT-GTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG-TTCGGGGTAAAATG
** * *
20953809 ACAATTTTTTGTGAAATCGGGGTTAAAAATAGG-ATTTTGG-AAGTTCAGGGTAAAATG
1 GTAA--TTTTGTGAAATTGGGGTTAAAAAT-GGAATTTTGGAAAGTTCGGGGTAAAATG
* * * *
20953866 GTAATTTTTGGTAAAATCGGGGTT-AAAATGGAATTTTAGAAAGTTTAGGGGTAAAATG
1 GTAA-TTTT-GTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG-TTCGGGGTAAAATG
*
20953924 ATAATTTTCGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATG
1 GTAATTTT--GTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATG
20953982 GTAATATTTG
1 GTAAT-TTTG
20953992 GAAGTTTTGG
Statistics
Matches: 305, Mismatches: 31, Indels: 35
0.82 0.08 0.09
Matches are distributed among these distances:
54 9 0.03
55 9 0.03
56 50 0.16
57 102 0.33
58 103 0.34
59 30 0.10
60 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (56 bp):
GTAATTTTGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATG
Found at i:20955952 original size:6 final size:6
Alignment explanation
Indices: 20955943--20956008 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
20955933 TATAATAATG
* * * *
20955943 TTAAAT TTAAA- TTAAAT TCAAAT TTAAA- TTGAAT TCAAA- ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
20955988 TTAAAA TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
20956009 TATCAAAATG
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
5 16 0.36
6 29 0.64
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:20955959 original size:11 final size:11
Alignment explanation
Indices: 20955943--20955998 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
20955933 TATAATAATG
20955943 TTAAATTTAAA-
1 TTAAA-TTAAAT
20955954 TTAAATTCAAAT
1 TTAAATT-AAAT
*
20955966 TTAAATTGAAT
1 TTAAATTAAAT
* *
20955977 TCAAAATAAAT
1 TTAAATTAAAT
20955988 TTAAAATTAAA
1 TT-AAATTAAA
20955999 ATAAATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 2 0.06
11 20 0.56
12 14 0.39
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:20955965 original size:17 final size:17
Alignment explanation
Indices: 20955945--20955981 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20955935 TAATAATGTT
20955945 AAATTTAAATTAAATTC
1 AAATTTAAATTAAATTC
*
20955962 AAATTTAAATTGAATTC
1 AAATTTAAATTAAATTC
20955979 AAA
1 AAA
20955982 ATAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTAAATTC
Found at i:20955999 original size:17 final size:18
Alignment explanation
Indices: 20955974--20956017 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
20955964 ATTTAAATTG
20955974 AATTCAAAATAAATTTAA
1 AATTCAAAATAAATTTAA
20955992 AATT-AAAATAAATTTAA
1 AATTCAAAATAAATTTAA
*
20956009 TA-TCAAAAT
1 AATTCAAAAT
20956018 GGTTTGGGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 19 0.79
18 4 0.17
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTCAAAATAAATTTAA
Found at i:20956428 original size:91 final size:91
Alignment explanation
Indices: 20956276--20956447 Score: 335
Period size: 91 Copynumber: 1.9 Consensus size: 91
20956266 GGGTTTTATT
*
20956276 TTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGG
1 TTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATACCCAGCTTTACTTCAATTTCAAGAGG
20956341 ATAGGAAATGATCTTGATGCTCTGTC
66 ATAGGAAATGATCTTGATGCTCTGTC
20956367 TTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATACCCAGCTTTACTTCAATTTCAAGAGG
1 TTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATACCCAGCTTTACTTCAATTTCAAGAGG
20956432 ATAGGAAATGATCTTG
66 ATAGGAAATGATCTTG
20956448 CTCTTACTTC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (91 bp):
TTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATACCCAGCTTTACTTCAATTTCAAGAGG
ATAGGAAATGATCTTGATGCTCTGTC
Found at i:20956464 original size:38 final size:38
Alignment explanation
Indices: 20956365--20956675 Score: 230
Period size: 38 Copynumber: 8.1 Consensus size: 38
20956355 TGATGCTCTG
* **
20956365 TCTTGCTCTTACTTCAATTTC-AGAGAGATAAAGACTTGA
1 TCTTGCTCTTACTTCAATTTCAAGAG-GAT-AGGAAATGA
**
20956404 TACCCAGCT-TTACTTCAATTTCAAGAGGATAGGAAATGA
1 T--CTTGCTCTTACTTCAATTTCAAGAGGATAGGAAATGA
* **
20956443 TCTTGCTCTTACTTCAATTTC-AGA-GATAAAGACTTGTTA
1 TCTTGCTCTTACTTCAATTTCAAGAGGAT-AGGAAATG--A
*** *
20956482 TCCAACTC-TACTTCAATTTCAAGAGGATAGGAAAAGA
1 TCTTGCTCTTACTTCAATTTCAAGAGGATAGGAAATGA
* **
20956519 TCTTGCTCTTACTTCAATTTC-AGA-GATAAAGACTTGATA
1 TCTTGCTCTTACTTCAATTTCAAGAGGAT-AGGAAATG--A
**
20956558 TCCAGCT-TTACTTCAATTTCAAGAGGATAGGAAATGA
1 TCTTGCTCTTACTTCAATTTCAAGAGGATAGGAAATGA
**
20956595 TCTTGCTCTTACTTCAATTTCAA-A-GATAGAGACTTGTTA
1 TCTTGCTCTTACTTCAATTTCAAGAGGATAG-GAAATG--A
***
20956634 TCCAACTC-TACTTCAATTTCAAGAGGATAGGAAATGA
1 TCTTGCTCTTACTTCAATTTCAAGAGGATAGGAAATGA
20956671 TCTTG
1 TCTTG
20956676 ATGCTCTGTC
Statistics
Matches: 210, Mismatches: 41, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
36 11 0.05
37 39 0.19
38 79 0.38
39 46 0.22
40 27 0.13
41 8 0.04
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (38 bp):
TCTTGCTCTTACTTCAATTTCAAGAGGATAGGAAATGA
Found at i:20956500 original size:76 final size:76
Alignment explanation
Indices: 20956365--20956675 Score: 514
Period size: 76 Copynumber: 4.1 Consensus size: 76
20956355 TGATGCTCTG
* * *
20956365 TCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATACCCAGCTTTACTTCAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGA
20956430 GGATAGGAAATGA
64 GGATAGGAAATGA
*
20956443 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
*
20956508 ATAGGAAAAGA
66 ATAGGAAATGA
* *
20956519 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
20956584 ATAGGAAATGA
66 ATAGGAAATGA
* * *
20956595 TCTTGCTCTTACTTCAATTTCAAAGATAGAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
20956660 ATAGGAAATGA
66 ATAGGAAATGA
20956671 TCTTG
1 TCTTG
20956676 ATGCTCTGTC
Statistics
Matches: 219, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
76 198 0.90
78 21 0.10
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (76 bp):
TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
ATAGGAAATGA
Found at i:20956643 original size:152 final size:156
Alignment explanation
Indices: 20956276--20956840 Score: 690
Period size: 152 Copynumber: 3.4 Consensus size: 156
20956266 GGGTTTTATT
* * *
20956276 TTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGG
1 TTGCTCTTACTTCAATTTCA-A-AGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
20956341 ATAGGAAATGATCTTGATGCTCTGTCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATA
64 ATAGGAAA-GA---TGA-----T-TCTTGCTCTTACTTCAATTTCA-AGAGATAAAGACTTGATA
*
20956406 CCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGATC
118 TCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGATC
*
20956445 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAAAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
20956510 AGGAAA-A-GA-TCTTGCTCTTACTTCAATTTC-AGAGATAAAGACTTGATATCCAGCTTTACTT
66 AGGAAAGATGATTCTTGCTCTTACTTCAATTTCAAGAGATAAAGACTTGATATCCAGCTTTACTT
20956571 CAATTTCAAGAGGATAGGAAATGATC
131 CAATTTCAAGAGGATAGGAAATGATC
*
20956597 TTGCTCTTACTTCAATTTCAAAGATAGAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAAAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
*
20956662 AGGAAATGATCTTGATGCTCTGTCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATC
66 AGGAAA-GA---TGA-----T-TCTTGCTCTTACTTCAATTTCA-AGAGATAAAGACTTGATATC
20956727 CTA-CTTTACTTCAATTTCAAGAGGATAGGAAATGATGC
120 C-AGCTTTACTTCAATTTCAAGAGGATAGGAAATGAT-C
** *
20956765 TTTATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTACTATCCAACTTTACTTCAATTTC
1 ----T-T-GCTCTTACTTCAATTTCA-A-AGATAAAGACTTGTTATCCAACTCTACTTCAATTTC
*
20956830 AATAGGATAGG
58 AAGAGGATAGG
20956841 GAATGATGTT
Statistics
Matches: 358, Mismatches: 13, Indels: 43
0.86 0.03 0.10
Matches are distributed among these distances:
152 125 0.35
154 22 0.06
158 2 0.01
161 2 0.01
165 22 0.06
167 100 0.28
168 2 0.01
169 20 0.06
172 1 0.00
173 1 0.00
174 18 0.05
175 1 0.00
176 42 0.12
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (156 bp):
TTGCTCTTACTTCAATTTCAAAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
AGGAAAGATGATTCTTGCTCTTACTTCAATTTCAAGAGATAAAGACTTGATATCCAGCTTTACTT
CAATTTCAAGAGGATAGGAAATGATC
Found at i:20956748 original size:91 final size:88
Alignment explanation
Indices: 20956594--20956847 Score: 356
Period size: 85 Copynumber: 2.9 Consensus size: 88
20956584 ATAGGAAATG
* *
20956594 ATCTTGCTCTTACTTCAATTTCA-A-AGATAGAGACTTGTTATCCAACTCTACTTCAATTTCAAG
1 ATCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAG
20956657 AGGATAGGAAATGATCTTGATGCTCT
66 AGGATAGG-AATGA--TTGATGCTCT
* *
20956683 GTCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCTACTTTACTTCAATTTCAAG
1 ATCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAG
*
20956748 AGGATAGGAA--A-TGATGCTTT
66 AGGATAGGAATGATTGATGCTCT
* ** *
20956768 ATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTACTATCCAACTTTACTTCAATTTCAAT
1 ATCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAG
20956833 AGGATAGGGAATGAT
66 AGGATA-GGAATGAT
20956848 GTTTGATTTA
Statistics
Matches: 148, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
85 73 0.49
86 4 0.03
88 2 0.01
89 22 0.15
90 3 0.02
91 44 0.30
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (88 bp):
ATCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAG
AGGATAGGAATGATTGATGCTCT
Found at i:20956821 original size:40 final size:38
Alignment explanation
Indices: 20956692--20956830 Score: 136
Period size: 40 Copynumber: 3.4 Consensus size: 38
20956682 TGTCTTGCTC
*
20956692 TTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCTACT
1 TTACTTCAATTTCAGAGAGATAAAGAC-T-TTATCCAACT
* *
20956732 TTACTTCAATTTCA-AGAGGATAGGAAATGATGCTTTATCTAGCT
1 TTACTTCAATTTCAGAGA-GAT---AAA-GA--CTTTATCCAACT
20956776 CTTACTTCAATTTCAGAGAGATAAAGACTTACTATCCAACT
1 -TTACTTCAATTTCAGAGAGATAAAGACTT--TATCCAACT
20956817 TTACTTCAATTTCA
1 TTACTTCAATTTCA
20956831 ATAGGATAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
39 6 0.07
40 31 0.37
41 9 0.11
42 3 0.04
43 3 0.04
44 9 0.11
45 18 0.22
46 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (38 bp):
TTACTTCAATTTCAGAGAGATAAAGACTTTATCCAACT
Found at i:20957082 original size:50 final size:51
Alignment explanation
Indices: 20957028--20957129 Score: 120
Period size: 50 Copynumber: 2.0 Consensus size: 51
20957018 GGTACACGGT
**
20957028 CCGCCATTGAGA-CTTAGACCTTTCCC-TTTTGTATCTTTGTGGTACTG-GAC
1 CCGCCATTGAGATCTTAGACCTTTCCCGTCGTGT-T-TTTGTGGTACTGAGAC
* * *
20957078 CCGCCGTTGCGATCTTAGATCTTTCCCGTCGTGTTTTTGTGGTACTGAGAC
1 CCGCCATTGAGATCTTAGACCTTTCCCGTCGTGTTTTTGTGGTACTGAGAC
20957129 C
1 C
20957130 TGTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 22 0.50
51 18 0.41
52 4 0.09
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (51 bp):
CCGCCATTGAGATCTTAGACCTTTCCCGTCGTGTTTTTGTGGTACTGAGAC
Found at i:20958433 original size:18 final size:18
Alignment explanation
Indices: 20958402--20958500 Score: 107
Period size: 18 Copynumber: 5.5 Consensus size: 18
20958392 CGACCTCTCC
*
20958402 TTTTC-TTTTCTCTTTTT
1 TTTTCTTTTTTTCTTTTT
20958419 TTTTCTTTTTTTCTTTTT
1 TTTTCTTTTTTTCTTTTT
*
20958437 TTTTC--TTCTTCTTTTT
1 TTTTCTTTTTTTCTTTTT
20958453 CTTTTCTTTTATCTT-TTTCTT
1 -TTTTCTTTT-T-TTCTTT-TT
*
20958474 TTTTCTTTTTTTCTTCTT
1 TTTTCTTTTTTTCTTTTT
20958492 TTTTCTTTT
1 TTTTCTTTT
20958501 ATTCACTGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
16 10 0.14
17 10 0.14
18 29 0.41
19 5 0.07
20 12 0.17
21 4 0.06
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTCTTTTTTTCTTTTT
Found at i:20958468 original size:42 final size:40
Alignment explanation
Indices: 20958404--20958500 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 40
20958394 ACCTCTCCTT
20958404 TTCTTTTCTCTTTTTTTTTCTTTTT-TTCTTTT-TTTTTCTTC
1 TTCTTTT-TCTTTTTTTTTCTTTTTCTT-TTTTCTTTTT-TTC
20958445 TTCTTTTTCTTTTCTTTTATCTTTTTCTTTTTTCTTTTTTTC
1 TTCTTTTTCTTTT-TTTT-TCTTTTTCTTTTTTCTTTTTTTC
20958487 TTCTTTTTTCTTTT
1 TTC-TTTTTCTTTT
20958501 ATTCACTGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
40 6 0.12
41 11 0.22
42 17 0.33
43 17 0.33
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (40 bp):
TTCTTTTTCTTTTTTTTTCTTTTTCTTTTTTCTTTTTTTC
Found at i:20963915 original size:59 final size:59
Alignment explanation
Indices: 20963852--20964310 Score: 528
Period size: 58 Copynumber: 7.9 Consensus size: 59
20963842 GGGAAAATTT
*
20963852 GGGGTTAAAAATAGG-ATTTTGGAAAGTTCGAGAGTAAAATGGTAATTTTTGGTGAAATC
1 GGGGTTAAAAAT-GGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATC
* * * * *
20963911 GGGGTTACAAAATGGGATTTT-GAAAGTTCGGGGGTAAAACGGTAATTTTTGGTAAAATT
1 GGGGTTA-AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATC
* * *
20963970 AGGGTT-AAAATGGAATTTTGGAAAGTT-TAGGGCTAAAATGATAATTTTTGGTGAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGG-TAAAATGGTAATTTTTGGTGAAATC
* * * * *
20964028 GGGGTTAAAAATGGGATTTTGG-AAGTTCGGGGGTAAAATAGTAATTTTCGGTAAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATC
* * * *
20964086 AGGGTT-AAAATGGAATTTTGGAAAGTT-TAGGGGTAAAATGATAATTTTTTGTGAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGGTGAAATC
* * * * * * *
20964144 TGGGATAAAAATGGGATTTTGG-AAGTTCGAGGGTAGAACGGTAATTTTTTGTAAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATC
* *
20964202 GGGGTT-AAAATGGAATTTTGGAAAGTT-TAGGGGT-AAATGATAATTTTTGGTGAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGGTGAAATC
*
20964259 GAGGTTAAAAATGGAATTTTGGAAAGTTC-AGGGGTAAAATGGTAATTTTTGG
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGG
20964311 AAGTTTTGGG
Statistics
Matches: 336, Mismatches: 49, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
57 67 0.20
58 165 0.49
59 94 0.28
60 10 0.03
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATC
Found at i:20964090 original size:116 final size:116
Alignment explanation
Indices: 20963820--20964310 Score: 677
Period size: 116 Copynumber: 4.2 Consensus size: 116
20963810 ATTTTGACTC
* ** *
20963820 TCGGGGGTGAAAAC-GTAA-TTTTGGGAAAATTTGGGGTTAAAAATAGG-ATTTTGGAAAG-TTC
1 TCGGGGGT-AAAACGGTAATTTTTGGTAAAA-TCAGGGTT-AAAAT-GGAATTTTGGAAAGTTTA
* * *
20963881 GAGAGTAAAATGGTAATTTTTGGTGAAATCGGGGTTACAAAATGGGATTTTGAAAGT
62 G-GGGTAAAATGATAATTTTTGGTGAAATCGGGGTTA-AAAATGGGATTTTGGAAGT
* *
20963938 TCGGGGGTAAAACGGTAATTTTTGGTAAAATTAGGGTTAAAATGGAATTTTGGAAAGTTTAGGGC
1 TCGGGGGTAAAACGGTAATTTTTGGTAAAATCAGGGTTAAAATGGAATTTTGGAAAGTTTAGGGG
20964003 TAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAGT
66 TAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAGT
** *
20964054 TCGGGGGTAAAATAGTAATTTTCGGTAAAATCAGGGTTAAAATGGAATTTTGGAAAGTTTAGGGG
1 TCGGGGGTAAAACGGTAATTTTTGGTAAAATCAGGGTTAAAATGGAATTTTGGAAAGTTTAGGGG
* * *
20964119 TAAAATGATAATTTTTTGTGAAATCTGGGATAAAAATGGGATTTTGGAAGT
66 TAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAGT
* * * *
20964170 TCGAGGGTAGAACGGTAATTTTTTGTAAAATCGGGGTTAAAATGGAATTTTGGAAAGTTTAGGGG
1 TCGGGGGTAAAACGGTAATTTTTGGTAAAATCAGGGTTAAAATGGAATTTTGGAAAGTTTAGGGG
* *
20964235 T-AAATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGT
66 TAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGG-AAGT
* *
20964286 TCAGGGGTAAAATGGTAATTTTTGG
1 TCGGGGGTAAAACGGTAATTTTTGG
20964311 AAGTTTTGGG
Statistics
Matches: 336, Mismatches: 32, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
115 40 0.12
116 211 0.63
117 53 0.16
118 22 0.07
119 10 0.03
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (116 bp):
TCGGGGGTAAAACGGTAATTTTTGGTAAAATCAGGGTTAAAATGGAATTTTGGAAAGTTTAGGGG
TAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAGT
Found at i:20966314 original size:17 final size:18
Alignment explanation
Indices: 20966287--20966330 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
20966277 ATTTAAATTG
20966287 AATTCAAAATAAATTTAA
1 AATTCAAAATAAATTTAA
20966305 AATT-AAAATAAATTTAA
1 AATTCAAAATAAATTTAA
*
20966322 TA-TCAAAAT
1 AATTCAAAAT
20966331 GGTTTGGGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 19 0.79
18 4 0.17
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTCAAAATAAATTTAA
Found at i:20974583 original size:39 final size:41
Alignment explanation
Indices: 20974529--20974605 Score: 122
Period size: 39 Copynumber: 1.9 Consensus size: 41
20974519 TGCAAATTCG
20974529 AATTTAGTCCTTATTCAAATATT-T-ACATTTTTTTTTATC
1 AATTTAGTCCTTATTCAAATATTATGACATTTTTTTTTATC
* *
20974568 AATTTAGTCTTTATTCAAATATTATGACTTTTTTTTTT
1 AATTTAGTCCTTATTCAAATATTATGACATTTTTTTTT
20974606 TTTACTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 22 0.65
40 1 0.03
41 11 0.32
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.58
Consensus pattern (41 bp):
AATTTAGTCCTTATTCAAATATTATGACATTTTTTTTTATC
Found at i:20974726 original size:18 final size:18
Alignment explanation
Indices: 20974697--20974739 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20974687 TTTTAAAGTA
*
20974697 ATAAAAATATTAAAATATT
1 ATAAAAACATT-AAATATT
20974716 A-AAAAACATTAAATATT
1 ATAAAAACATTAAATATT
20974733 ATAAAAA
1 ATAAAAA
20974740 GTTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAAAACATTAAATATT
Found at i:20975574 original size:21 final size:21
Alignment explanation
Indices: 20975554--20975602 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 21
20975544 TGAAATATCA
20975554 ATAAATAAT-TAAAAAAAATC
1 ATAAATAATATAAAAAAAATC
*
20975574 ATATATAATATAAGAAAAAGATTC
1 ATAAATAATATAA-AAAAA-A-TC
20975598 ATAAA
1 ATAAA
20975603 AAAACTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
22 5 0.22
23 1 0.04
24 6 0.26
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAATAATATAAAAAAAATC
Found at i:20976089 original size:3 final size:3
Alignment explanation
Indices: 20976081--20976118 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
20976071 TGAAATTGTT
20976081 ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20976119 TGTTACAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:20983729 original size:23 final size:25
Alignment explanation
Indices: 20983703--20983750 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
20983693 CTTCAAAGTA
20983703 TTAAC-TAATTAAA-ATAATTAATT
1 TTAACATAATTAAAGATAATTAATT
20983726 TTAACATTAATTAAATGATAATTAA
1 TTAACA-TAATTAAA-GATAATTAA
20983751 GATGTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
25 8 0.38
27 8 0.38
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (25 bp):
TTAACATAATTAAAGATAATTAATT
Found at i:20991651 original size:57 final size:58
Alignment explanation
Indices: 20991590--20991926 Score: 368
Period size: 58 Copynumber: 5.8 Consensus size: 58
20991580 GAAAATTTGG
* * ** * *
20991590 GGTTAAAATGGGATTTTAGAAGGTTCGGGGGT-AAATGGTAATTTTTAGTAAAATCGA
1 GGTTAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * *
20991647 GGTTAAAATGAGG-TTTT-AAAGAGTTT-GAGAGTAAAATGGTAA-TTTTGATGAAATCGA
1 GGTTAAAATG-GGATTTTGGAA-AGTTTAG-GGGTAAAATGGTAATTTTTGGTGAAATCGA
* *
20991704 GGTTAAAAATGGGATTTTGGAAAGTTTA-GGGTAAAATGGTAA-TTTTGGTGAAATTGG
1 GGTT-AAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * * *
20991761 GGTTAAAAAAGGGATTTTGGAAAATTTAGGGGTAAAATGGTAATTTTTGGTAAAAACAGA
1 GGTT-AAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATC-GA
* * * *
20991821 GGTTAAAA-GAGATTTTGGAAAGTTTAGCGATAAAATGGTAATTTTTGGTGAAATCGG
1 GGTTAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
*
20991878 GGTTAAGAATGAGATTTTGGAAAGTTTAGGGGT-AAATGGTAATTTTTGG
1 GGTTAA-AATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGG
20991927 ACAGTCGAGG
Statistics
Matches: 240, Mismatches: 27, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
56 3 0.01
57 96 0.40
58 99 0.41
59 37 0.15
60 5 0.02
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (58 bp):
GGTTAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
Found at i:20991710 original size:29 final size:28
Alignment explanation
Indices: 20991678--20991807 Score: 88
Period size: 29 Copynumber: 4.5 Consensus size: 28
20991668 AGTTTGAGAG
*
20991678 TAAAATGGTAATTTTGATGAAATCGAGGT
1 TAAAATGGTAATTTTG-TGAAATTGAGGT
* * *
20991707 TAAAAATGG-GATTTTG-GAAAGTTTAGGG
1 T-AAAATGGTAATTTTGTGAAA-TTGAGGT
*
20991735 TAAAATGGTAATTTTGGTGAAATTGGGGT
1 TAAAATGGTAATTTT-GTGAAATTGAGGT
* * * *
20991764 TAAAAAAGG-GATTTTG-GAAAATTTAGGGG
1 T-AAAATGGTAATTTTGTG-AAATTGA-GGT
20991793 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
20991808 TGGTAAAAAC
Statistics
Matches: 77, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
27 12 0.16
28 22 0.29
29 26 0.34
30 17 0.22
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.35
Consensus pattern (28 bp):
TAAAATGGTAATTTTGTGAAATTGAGGT
Found at i:20991741 original size:115 final size:115
Alignment explanation
Indices: 20991590--20991925 Score: 348
Period size: 115 Copynumber: 2.9 Consensus size: 115
20991580 GAAAATTTGG
* * ** * * *
20991590 GGTTAAAATGGGATTTTAGAAGGTTCGGGGGT-AAATGGTAATTTTTAGTAAAATCGAGGTTAAA
1 GGTTAAAATGGGATTTTGGAAAGTT-TAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAA
* *
20991654 ATGAGGTTTT-AAAGAGTTT-GAGAGTAAAATGGTAA-TTTTGATGAAATC-GA
65 ATGAGGTTTTGAAA-A-TTTAG-GAGTAAAATGGTAATTTTTGATAAAAACAGA
*
20991704 GGTTAAAAATGGGATTTTGGAAAGTTTAGGGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAA
1 GGTT-AAAATGGGATTTTGGAAAGTTTAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAA
* * *
20991768 A-AAGGGATTTTGGAAAATTTAGGGGTAAAATGGTAATTTTTGGTAAAAACAGA
65 ATGA-GG-TTTT-GAAAATTTAGGAGTAAAATGGTAATTTTTGATAAAAACAGA
* *
20991821 GGTTAAAA-GAGATTTTGGAAAGTTTAGCGATAAAATGGTAATTTTTGGTGAAATCGGGGTTAAG
1 GGTTAAAATGGGATTTTGGAAAGTTTAG-GGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAA-
* * *
20991885 AATGAGATTTTGGAAAGTTTAGGGGT-AAATGGTAATTTTTG
64 AATGAGGTTTT-GAAAATTTAGGAGTAAAATGGTAATTTTTG
20991926 GACAGTCGAG
Statistics
Matches: 190, Mismatches: 19, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
113 1 0.01
114 29 0.15
115 66 0.35
116 43 0.23
117 47 0.25
118 3 0.02
119 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (115 bp):
GGTTAAAATGGGATTTTGGAAAGTTTAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAA
TGAGGTTTTGAAAATTTAGGAGTAAAATGGTAATTTTTGATAAAAACAGA
Found at i:20993079 original size:12 final size:12
Alignment explanation
Indices: 20993061--20993093 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20993051 ATATTATTTA
20993061 TTATTTAATA-T
1 TTATTTAATACT
20993072 TGTATTTAATACT
1 T-TATTTAATACT
20993085 TTATTTAAT
1 TTATTTAAT
20993094 GCATTTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 17 0.85
13 2 0.10
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (12 bp):
TTATTTAATACT
Found at i:20993758 original size:16 final size:17
Alignment explanation
Indices: 20993724--20993758 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20993714 GTAATTTGGC
20993724 TTTTGTAAATGGACTAT
1 TTTTGTAAATGGACTAT
20993741 TTTTGTAAATGGAC-AT
1 TTTTGTAAATGGACTAT
20993757 TT
1 TT
20993759 AATTTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.49
Consensus pattern (17 bp):
TTTTGTAAATGGACTAT
Found at i:20993809 original size:17 final size:16
Alignment explanation
Indices: 20993770--20993813 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
20993760 ATTTATTCTT
20993770 AAATTTAAA-TTTATA
1 AAATTTAAATTTTATA
20993785 ATATATTTAAATTTTATA
1 A-A-ATTTAAATTTTATA
20993803 CAAATTTAAAT
1 -AAATTTAAAT
20993814 CCAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 15 0.60
18 7 0.28
19 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTAAATTTTATA
Found at i:20994507 original size:201 final size:200
Alignment explanation
Indices: 20994158--20994595 Score: 648
Period size: 201 Copynumber: 2.2 Consensus size: 200
20994148 TTCATTGATC
* * * *
20994158 TGGTCTTCTTCTCTGTGTCTCATCAGGAAGATGACCGCAATTCTGTTTTAATTCGCTTCTCTGGA
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCTCAATGCTGTTTTAATTCGCTTCTCTGGA
* * *
20994223 TCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTG
66 TCTCCTCAAGAAGACAAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATTG
* * *
20994288 CTTCGTCCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGAG-TCTGAGTG
131 CTTCGTCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGAGCT-TGAGCG
* *
20994352 TTGAGT
195 CTAAGT
* *
20994358 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCTC-CTCGCTTGTTTTGATTCGCTTCTCTG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCTCAAT-GC-TGTTTTAATTCGCTTCTCTG
* *
20994422 GATCTCTTCAAGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTAT
64 GATCTCCTCAAGAAGACAAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTAT
*
20994487 TGCTTCGTCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGTGCTTGAGC
129 TGCTTCGTCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGAGCTTGAGC
20994552 GCTAAGT
194 GCTAAGT
* *
20994559 TGGTGTTC-TCACTGTATCTCATCAGGAAAGATGACCT
1 TGGTATTCTTCTCTGTATCTCATCAGG-AAGATGACCT
20994596 TTTTATTGCT
Statistics
Matches: 215, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
199 1 0.00
200 53 0.25
201 160 0.74
202 1 0.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (200 bp):
TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCTCAATGCTGTTTTAATTCGCTTCTCTGGA
TCTCCTCAAGAAGACAAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATTG
CTTCGTCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGAGCTTGAGCGC
TAAGT
Found at i:20994666 original size:116 final size:116
Alignment explanation
Indices: 20994451--20994709 Score: 328
Period size: 116 Copynumber: 2.2 Consensus size: 116
20994441 ATCTGGTCCA
* * *
20994451 CTTCTCTGTATCTCATCAGG-AAGCTAACCTTTTTATTGCTTCGTCCTGCTTCTCAGTATCTCAT
1 CTTCACTGTATCTCATCAGGAAAGATAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* *
20994515 CAGGAAGCTGGGTTCGAAGATTTACTCGTGCTTGAGCGCTAAGTTGGTGTT
66 CAGGAAGCTGGGTTCGAAGATTTACTCGAGCTTGAGCGCTAAGTTGGTATT
* * * *
20994566 C-TCACTGTATCTCATCAGGAAAGATGACCTTTTTATTGCTTTCGACTTGCTTCTCTGTGTCTCA
1 CTTCACTGTATCTCATCAGGAAAGATAACCTTTTTATTGC-TTCGACCTGCTTCTCAGTATCTCA
* * * * * *
20994630 TCAGGAA-ATCGTGTTCGAAGATTTGCTCGAGTTTGAGCGTTGAGTTGGTATT
65 TCAGGAAGCT-GGGTTCGAAGATTTACTCGAGCTTGAGCGCTAAGTTGGTATT
*
20994682 CTTCTCTGTATCTCATCAGG-AAGATAAC
1 CTTCACTGTATCTCATCAGGAAAGATAAC
20994710 TGCCTCGCTT
Statistics
Matches: 123, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
114 17 0.14
115 19 0.15
116 70 0.57
117 17 0.14
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (116 bp):
CTTCACTGTATCTCATCAGGAAAGATAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGGTTCGAAGATTTACTCGAGCTTGAGCGCTAAGTTGGTATT
Found at i:21007133 original size:28 final size:28
Alignment explanation
Indices: 21007044--21007133 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
21007034 AAATCGAGGT
* * *
21007044 TAAAAATGGATTTTGGAAAGTTTAGGGG
1 TAAAAAGGGATTTTGGAAAATTTAAGGG
* * ** *
21007072 TAAAATGGTAATTTTTGGTAAAA-TCGAGGT
1 TAAAAAGG-GA-TTTTGG-AAAATTTAAGGG
21007102 TAAAAAGGGATTTTGGAAAATTTAAGGG
1 TAAAAAGGGATTTTGGAAAATTTAAGGG
21007130 TAAA
1 TAAA
21007134 TGGTAATTTT
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
27 4 0.09
28 20 0.44
29 2 0.04
30 16 0.36
31 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.27, T:0.32
Consensus pattern (28 bp):
TAAAAAGGGATTTTGGAAAATTTAAGGG
Found at i:21007169 original size:57 final size:58
Alignment explanation
Indices: 21006782--21007205 Score: 345
Period size: 58 Copynumber: 7.4 Consensus size: 58
21006772 GACTCTTGAG
** * * * ** ***
21006782 GGGTAAAAT-GTAATTTTTAGGAAAAATTGGGGTTAAAAATGGGATTTTAGAAGGTTCGG
1 GGGTAAAATGGTAATTTTT-GGTGAAATCGAGGTT-AAAATGGGATTTTGGAAAATTTAA
* * *
21006841 GGGTAAAATGGTAATTTTTAGTAAAATCGAGGTTAAAATGTGG-TTTT-GAAAAGTTCGAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATG-GGATTTTGGAAAA-TT-TAA
* * * * * *
21006900 -GGTAAAACGATAA-TTTTGGTGAAATCGGGGTCAAAAATGGGATTTT-GAAAAGTTCAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGT-TAAAATGGGATTTTGGAAAA-TTTAA
* * * * **
21006957 GGGTAAAATGGTAA-TTTTGATGAAATCTG-GGTT-AAATGAGATTTTAGAAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAATGGGATTTTGGAAAATTTAA
* * *
21007013 GGG--AAATGCTAATTTTTGGTGAAATCGAGGTTAAAAAT-GGATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGGATTTTGGAAAATTTAA
* *
21007069 GGGTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAAGGGATTTTGGAAAATTTAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGGATTTTGGAAAATTTAA
* * *
21007127 GGGT-AAATGGTAATTTTTGGTGAAATAG-GGTTAAGAATGGGATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAA-AATGGGATTTTGGAAAATTTAA
*
21007184 GGGTAAAAATGATAATTTTTGG
1 GGGT-AAAATGGTAATTTTTGG
21007206 ACAGTCCAGG
Statistics
Matches: 303, Mismatches: 43, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
54 9 0.03
55 16 0.05
56 39 0.13
57 78 0.26
58 114 0.38
59 38 0.13
60 9 0.03
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGGATTTTGGAAAATTTAA
Found at i:21009098 original size:17 final size:15
Alignment explanation
Indices: 21009059--21009102 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
21009049 ATTTAATCTT
21009059 AAATTTAAATTTATA
1 AAATTTAAATTTATA
21009074 ATAGATTTAAATTGTATA
1 A-A-ATTTAAATT-TATA
21009092 CAAATTTAAAT
1 -AAATTTAAAT
21009103 CCAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 17 0.68
18 5 0.20
19 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATTTAAATTTATA
Found at i:21009889 original size:15 final size:16
Alignment explanation
Indices: 21009863--21009892 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21009853 GCATGTGGAA
21009863 TTGGGTTTAAGATTTT
1 TTGGGTTTAAGATTTT
21009879 TTGGG-TTAAGATTT
1 TTGGGTTTAAGATTT
21009893 AGGGTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (16 bp):
TTGGGTTTAAGATTTT
Found at i:21012725 original size:20 final size:20
Alignment explanation
Indices: 21012689--21012733 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
21012679 TCATTAAGTT
*
21012689 TTAATTAATCTCTTTTAATC
1 TTAATTAAGCTCTTTTAATC
*
21012709 TTAATTAAGCT-TATTTACTC
1 TTAATTAAGCTCT-TTTAATC
21012729 TTAAT
1 TTAAT
21012734 ACAAATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.31, C:0.13, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAATTAAGCTCTTTTAATC
Found at i:21023771 original size:39 final size:38
Alignment explanation
Indices: 21023692--21023775 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 38
21023682 AAAAGTTAAC
21023692 GGTCAAAGTCAACATCAACGATCAAAGTCAACAAGTTT
1 GGTCAAAGTCAACATCAACGATCAAAGTCAACAAGTTT
*
21023730 GGTCAAAGTCAACAGGTCAACGGGTC-AA-TCAACAAGTTT
1 GGTCAAAGTCAACA--TCAAC-GATCAAAGTCAACAAGTTT
21023769 GGTCAAA
1 GGTCAAA
21023776 TTGAATTGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
38 14 0.33
39 18 0.43
40 7 0.17
41 3 0.07
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (38 bp):
GGTCAAAGTCAACATCAACGATCAAAGTCAACAAGTTT
Found at i:21025337 original size:23 final size:22
Alignment explanation
Indices: 21025311--21025447 Score: 86
Period size: 22 Copynumber: 6.2 Consensus size: 22
21025301 AAAAACGCAT
21025311 AAAAATAACATCCAAACAACAAC
1 AAAAATAACA-CCAAACAACAAC
* * *
21025334 AAAAA-AAC-CAAAATAACAGC
1 AAAAATAACACCAAACAACAAC
21025354 AAAAATAACACCAAAACAACAAC
1 AAAAATAACACC-AAACAACAAC
* * * *
21025377 AAAAAATAATA-AAAATAGCAAC
1 -AAAAATAACACCAAACAACAAC
* *
21025399 -AAAATAGCACCAAAACAATAA-
1 AAAAATAACACC-AAACAACAAC
* *
21025420 ATAAATAGCACCAAAACAACAATC
1 AAAAATAACACC-AAACAACAA-C
21025444 AAAA
1 AAAA
21025448 CAGTAAAAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
20 21 0.24
21 3 0.03
22 37 0.43
23 13 0.15
24 12 0.14
ACGTcount: A:0.68, C:0.20, G:0.03, T:0.09
Consensus pattern (22 bp):
AAAAATAACACCAAACAACAAC
Found at i:21025369 original size:11 final size:11
Alignment explanation
Indices: 21025312--21025380 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
21025302 AAAACGCATA
21025312 AAAATAACATCC
1 AAAATAACA-CC
* *
21025324 -AAACAACAAC
1 AAAATAACACC
21025334 AAAA-AA-ACC
1 AAAATAACACC
*
21025343 AAAATAACAGCA
1 AAAATAACA-CC
21025355 AAAATAACACC
1 AAAATAACACC
* *
21025366 AAAACAACAAC
1 AAAATAACACC
21025377 AAAA
1 AAAA
21025381 AATAATAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
9 6 0.13
10 5 0.11
11 25 0.54
12 10 0.22
ACGTcount: A:0.70, C:0.23, G:0.01, T:0.06
Consensus pattern (11 bp):
AAAATAACACC
Found at i:21025393 original size:33 final size:33
Alignment explanation
Indices: 21025354--21025458 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
21025344 AAATAACAGC
*
21025354 AAAAATAACACCAAAACAACAACAAAA-AATAA
1 AAAAATAGCACCAAAACAACAACAAAACAATAA
* * * *
21025386 TAAAAATAGCAACAAAATAGCACCAAAACAATAA
1 -AAAAATAGCACCAAAACAACAACAAAACAATAA
* *
21025420 ATAAATAGCACCAAAACAACAATCAAAACAGTAA
1 AAAAATAGCACCAAAACAACAA-CAAAACAATAA
21025454 AAAAA
1 AAAAA
21025459 ATACTAAAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
33 39 0.67
34 19 0.33
ACGTcount: A:0.69, C:0.18, G:0.04, T:0.10
Consensus pattern (33 bp):
AAAAATAGCACCAAAACAACAACAAAACAATAA
Found at i:21025410 original size:44 final size:43
Alignment explanation
Indices: 21025311--21025416 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 43
21025301 AAAAACGCAT
* *
21025311 AAAAATAACATCC-AAACAACAACAAAAAAACCAAAATAACAGC
1 AAAAATAACA-CCAAAACAACAACAAAAAAACAAAAATAACAAC
* *
21025354 AAAAATAACACCAAAACAACAACAAAAAATAATAAAAATAGCAAC
1 AAAAATAACACCAAAACAACAAC-AAAAA-AACAAAAATAACAAC
*
21025399 -AAAATAGCACCAAAACAA
1 AAAAATAACACCAAAACAA
21025417 TAAATAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
42 2 0.04
43 20 0.36
44 22 0.40
45 11 0.20
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.08
Consensus pattern (43 bp):
AAAAATAACACCAAAACAACAACAAAAAAACAAAAATAACAAC
Found at i:21025520 original size:19 final size:19
Alignment explanation
Indices: 21025493--21025535 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
21025483 ACACTAAAAC
*
21025493 AACAAAAAACAA-TAACCAA
1 AACAAAAAAAAAGT-ACCAA
*
21025512 AACAGAAAAAAAGTACCAA
1 AACAAAAAAAAAGTACCAA
21025531 AACAA
1 AACAA
21025536 CAATATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.72, C:0.19, G:0.05, T:0.05
Consensus pattern (19 bp):
AACAAAAAAAAAGTACCAA
Found at i:21026227 original size:29 final size:32
Alignment explanation
Indices: 21026165--21026235 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 32
21026155 ATTAATAAAA
*
21026165 AAAAATTATACTTTGATTCTTCTAAAAATAAT
1 AAAAATTATACTTTAATTCTTCTAAAAATAAT
*
21026197 AAAAATTA-A-TTTAATTCTT-TAAAAATTAT
1 AAAAATTATACTTTAATTCTTCTAAAAATAAT
*
21026226 AAAAAATATA
1 AAAAATTATA
21026236 AATTATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.46
30 10 0.29
31 1 0.03
32 8 0.23
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (32 bp):
AAAAATTATACTTTAATTCTTCTAAAAATAAT
Found at i:21026231 original size:30 final size:33
Alignment explanation
Indices: 21026158--21026232 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 33
21026148 ATTTTAAATT
* *
21026158 AATAAAAAAAAATTATACTTTGATTCTTCTAAA
1 AATAATAAAAAATTATACTTTAATTCTTCTAAA
21026191 AATAAT-AAAAATTA-A-TTTAATTCTT-TAAA
1 AATAATAAAAAATTATACTTTAATTCTTCTAAA
*
21026220 AATTATAAAAAAT
1 AATAATAAAAAAT
21026233 ATAAATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 9 0.24
30 15 0.39
31 1 0.03
32 8 0.21
33 5 0.13
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.37
Consensus pattern (33 bp):
AATAATAAAAAATTATACTTTAATTCTTCTAAA
Found at i:21026238 original size:16 final size:16
Alignment explanation
Indices: 21026218--21026260 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
21026208 TAATTCTTTA
21026218 AAAATTATAAA-AAAT
1 AAAATTATAAACAAAT
*
21026233 ATAAATTATTAAACTAAT
1 A-AAATTA-TAAACAAAT
21026251 AAAATTATAA
1 AAAATTATAA
21026261 TTTAATGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 9 0.38
17 10 0.42
18 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTATAAACAAAT
Found at i:21027483 original size:6 final size:6
Alignment explanation
Indices: 21027474--21027539 Score: 68
Period size: 6 Copynumber: 11.3 Consensus size: 6
21027464 AATTTTATTT
21027474 ATTTAA ATTT-A ATTT-- ATTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
21027520 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
21027540 AAAAATTAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.08
5 9 0.17
6 33 0.63
8 6 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
ATTTAA
Found at i:21027512 original size:20 final size:20
Alignment explanation
Indices: 21027474--21027539 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
21027464 AATTTTATTT
21027474 ATTTAAATTTAATTTATTTAA
1 ATTTAAATTTAA-TTATTTAA
21027495 ATTTAAATTTAATTATTTAA
1 ATTTAAATTTAATTATTTAA
* *
21027515 ATTT-ACTTTGA--ATTTAA
1 ATTTAAATTTAATTATTTAA
21027532 ATTTAAAT
1 ATTTAAAT
21027540 AAAAATTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.24
18 2 0.05
19 5 0.12
20 12 0.29
21 12 0.29
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTTAAATTTAATTATTTAA
Found at i:21029648 original size:30 final size:30
Alignment explanation
Indices: 21029609--21029900 Score: 376
Period size: 30 Copynumber: 9.7 Consensus size: 30
21029599 CCCCAAACAA
* * *
21029609 TCCAGAAATTGCATTTTAACCTCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
21029640 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
21029670 TCCAAAATTATATTTTGACCCAAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
21029700 TCCAAAATTACATTTTGACCTCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
21029729 TCCAAAAATTACATTTT-ACCCTAAAACTTT
1 TCC-AAAATTACATTTTGACCCCAAAACTTT
* *
21029759 TCCAAAATCATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
21029789 TCCAAAATTACATTTTAACCCCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
21029818 TCCAAAATTATATTTTCACCTCAAAAACTTT
1 TCCAAAATTACATTTTGACC-CCAAAACTTT
* *
21029849 TCCAAAAATATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
21029879 ACCAAAATTACCATTTT-ACCCC
1 TCCAAAATTA-CATTTTGACCCC
21029901 CGAATCTTTT
Statistics
Matches: 230, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
29 44 0.19
30 157 0.68
31 29 0.13
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:21029782 original size:90 final size:88
Alignment explanation
Indices: 21029609--21029896 Score: 416
Period size: 89 Copynumber: 3.2 Consensus size: 88
21029599 CCCCAAACAA
* * *
21029609 TCCAGAAATTGCATTTTAACCTCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
1 TCCA-AAATTACATTTTAACCTCAAAAC-TTTCCAAAATTACATTTTCACCCAAAAACTTTTCCA
*
21029674 AAATTATATTTTGACCCAAAAACTTT
64 AAA-TATATTTTGACCCCAAAACTTT
* *
21029700 TCCAAAATTACATTTTGACCTCAAAACTTTCCAAAAATTACATTTT-ACCCTAAAACTTTTCCAA
1 TCCAAAATTACATTTTAACCTCAAAACTTTCC-AAAATTACATTTTCACCCAAAAACTTTTCCAA
21029764 AATCATATTTTGACCCCAAAACTTT
65 AAT-ATATTTTGACCCCAAAACTTT
* *
21029789 TCCAAAATTACATTTTAACCCCAAAACTTTCCAAAATTATATTTTCACCTCAAAAACTTTTCCAA
1 TCCAAAATTACATTTTAACCTCAAAACTTTCCAAAATTACATTTTCACC-CAAAAACTTTTCC-A
21029854 AAATATATTTTGACCCCAAAACTTT
64 AAATATATTTTGACCCCAAAACTTT
*
21029879 ACCAAAATTACCATTTTA
1 TCCAAAATTA-CATTTTA
21029897 CCCCCGAATC
Statistics
Matches: 182, Mismatches: 9, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
88 13 0.07
89 77 0.42
90 76 0.42
91 16 0.09
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (88 bp):
TCCAAAATTACATTTTAACCTCAAAACTTTCCAAAATTACATTTTCACCCAAAAACTTTTCCAAA
ATATATTTTGACCCCAAAACTTT
Found at i:21029984 original size:59 final size:59
Alignment explanation
Indices: 21029882--21030260 Score: 562
Period size: 59 Copynumber: 6.4 Consensus size: 59
21029872 AAACTTTACC
*
21029882 AAAATTACCATTTTACCCCCGAATCTTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAATC-TTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * * * * *
21029942 AAAATTACCATTTTGCCCTCGAAGCTTCTAAAATTCCGTTTTTTACCCCGATTTCATCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
*
21030001 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * * *
21030060 AAAATTACTACTTTACCCCCGAAGCTTCTAAAATTCCATTTTTCACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
21030119 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCTATTTTTCACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
21030178 AAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTAAACCCCGATTGCACC-
1 -AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
*
21030237 AAAATTACCATTTTGCCCCCGAAT
1 AAAATTACCATTTTACCCCCGAAT
21030261 ATCCATAAGT
Statistics
Matches: 288, Mismatches: 30, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
58 23 0.08
59 189 0.66
60 76 0.26
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:21030256 original size:29 final size:27
Alignment explanation
Indices: 21029879--21030258 Score: 114
Period size: 29 Copynumber: 12.9 Consensus size: 27
21029869 CCAAAACTTT
*
21029879 ACCAAAATTACCATTTTACCCCCGAATCTT
1 ACCAAAATT-CCATTTTACCCCCG-AT-TC
*** *
21029909 TTTAAAATTCCATTTTTAACCCCGATTTC
1 ACCAAAATTCCA-TTTTACCCCCGA-TTC
* * **
21029938 ACCAAAAATTACCATTTTGCCCTCGAAGC
1 ACC-AAAATT-CCATTTTACCCCCGATTC
* * *
21029967 TTCTAAAATTCCGTTTTTTA-CCCCGATTTC
1 -ACCAAAATTCC--ATTTTACCCCCGA-TTC
* *
21029997 ATCGAAAATTACCATTTTACCCCCGAATC
1 A-CCAAAATT-CCATTTTACCCCCGATTC
*** *
21030026 TTTTAAAATTCCATTTTTAACCCCGATTTC
1 -ACCAAAATTCCA-TTTTACCCCCGA-TTC
* * * **
21030056 ATCGAAAATTACTACTTTACCCCCGAAGC
1 A-CCAAAATT-CCATTTTACCCCCGATTC
* * *
21030085 TTCTAAAATTCCATTTTTCACCCCGATTTC
1 -ACCAAAATTCCATTTTAC-CCCCGA-TTC
*
21030115 ACCGAAAATTACCATTTTACCCCCGAATC
1 ACC-AAAATT-CCATTTTACCCCCGATTC
*** * *
21030144 TTTTAAAATTCTATTTTTCACCCCGATTTC
1 -ACCAAAATTCCATTTTAC-CCCCGA-TTC
*
21030174 ACCGAAAAATTACCATTTTACCCCCGAATC
1 ACC--AAAATT-CCATTTTACCCCCGATTC
*** *
21030204 TTTTAAAATTCCATTTTAAACCCCGATTGC
1 -ACCAAAATTCCATTTT-ACCCCCGATT-C
*
21030234 ACCAAAATTACCATTTTGCCCCCGA
1 ACCAAAATT-CCATTTTACCCCCGA
21030259 ATATCCATAA
Statistics
Matches: 249, Mismatches: 70, Indels: 63
0.65 0.18 0.16
Matches are distributed among these distances:
28 25 0.10
29 96 0.39
30 94 0.38
31 27 0.11
32 7 0.03
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.35
Consensus pattern (27 bp):
ACCAAAATTCCATTTTACCCCCGATTC
Found at i:21042672 original size:31 final size:31
Alignment explanation
Indices: 21042567--21042744 Score: 115
Period size: 31 Copynumber: 5.4 Consensus size: 31
21042557 CTTAATCTCT
21042567 GAAATTGAAGTAAGAGCAACGTCATCCCCT-
1 GAAATTGAAGTAAGAGCAACGTCATCCCCTC
* * * * ***
21042597 GAAATTGAAATAGAGTGGATAACAAGTCTTGATCTC
1 GAAATTGAAGTA-AG-AG-CAAC--GTCATCCCCTC
21042633 TGAAATTGAAGTAAGAGCAACGTCATCCCCTC
1 -GAAATTGAAGTAAGAGCAACGTCATCCCCTC
** * **
21042665 GAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
1 GAAATTGAAGTA-A---GAGCA-ACGTCATCCCCTC
* *
21042701 TGAAATTGAAGTAAGAGCAACGTCATCCCTTT
1 -GAAATTGAAGTAAGAGCAACGTCATCCCCTC
21042733 GAAATTGAAGTA
1 GAAATTGAAGTA
21042745 GAGTGGATAA
Statistics
Matches: 109, Mismatches: 26, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
30 11 0.10
31 26 0.24
32 17 0.16
33 6 0.06
34 3 0.03
35 10 0.09
36 13 0.12
37 23 0.21
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (31 bp):
GAAATTGAAGTAAGAGCAACGTCATCCCCTC
Found at i:21042677 original size:141 final size:138
Alignment explanation
Indices: 21042377--21042856 Score: 713
Period size: 141 Copynumber: 3.5 Consensus size: 138
21042367 ACCTTTTCCT
*
21042377 ATCCCCTTGAAATGAAGTAGAGTAGAGTGGATAACACGTCTTCGTCTCTGAAATTGAAGTAAGAG
1 ATCCCCTTGAAATG-AGTAGAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAG
* *
21042442 CAACGTCATCCCTTGAAATTGAAGAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
65 CAACGTCATCCCTTGAAATTGAA-A-TAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTA
21042507 AGAGCAACGTC
128 AGAGCAACGTC
*
21042518 ATCCCCTTGAAATGAGTAGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAAGAG
1 ATCCCCTTGAAATGAGTAG-AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAG
*
21042583 CAACGTCATCCCCTGAAATTGAAATAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAG
65 CAACGTCATCCCTTGAAATTGAAATAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAG
21042648 AGCAACGTC
130 AGCAACGTC
* *
21042657 ATCCCCTCGAAAT-TG-A-AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 ATCCCCTTGAAATGAGTAGAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
* *
21042719 AACGTCATCCCTTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTTTGAAATTGAAGTAAG
66 AACGTCATCCC-TTGAAATTGAAATAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAG
21042784 AGCAACGTC
130 AGCAACGTC
* * * * * *
21042793 GTCCTCTTGAAACTGA--A-A-TAGAGTTGGATAACATGCCTTTATTTCTGAAATTGAAGTAAGA
1 ATCCCCTTGAAA-TGAGTAGAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGA
21042854 GCA
64 GCA
21042857 CGATCATTTC
Statistics
Matches: 315, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
135 56 0.18
136 73 0.23
137 40 0.13
138 1 0.00
139 60 0.19
140 6 0.02
141 79 0.25
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (138 bp):
ATCCCCTTGAAATGAGTAGAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
AACGTCATCCCTTGAAATTGAAATAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAGA
GCAACGTC
Found at i:21042703 original size:68 final size:68
Alignment explanation
Indices: 21042397--21042856 Score: 681
Period size: 68 Copynumber: 6.7 Consensus size: 68
21042387 AATGAAGTAG
*
21042397 AGTAGAGTGGATAACACGTCTTCGTCTCTGAAATTGAAGTAAGAGCAACGTCAT-CCCTTGAAAT
1 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAAT
21042461 TGAA
66 TG-A
21042465 GAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAA
1 -AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAA
21042530 TGAGTAGA
65 T---T-GA
*
21042538 AGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCC-TGAAAT
1 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAAT
21042602 TGA
66 TGA
* * * *
21042605 AATAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAAT
1 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAAT
21042670 TGA
66 TGA
*
21042673 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCTTTGAAAT
1 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAAT
21042738 TGA
66 TGA
* * * * * *
21042741 AGTAGAGTGGATAACAAGTCTTGATCTTTGAAATTGAAGTAAGAGCAACGTCGTCCTCTTGAAAC
1 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAAT
21042806 TGA
66 TGA
* * * * *
21042809 AATAGAGTTGGATAACATGCCTTTATTTCTGAAATTGAAGTAAGAGCA
1 AGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
21042857 CGATCATTTC
Statistics
Matches: 360, Mismatches: 24, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
67 57 0.16
68 139 0.39
69 88 0.24
70 10 0.03
71 6 0.02
72 57 0.16
73 2 0.01
74 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (68 bp):
AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAAT
TGA
Found at i:21043223 original size:6 final size:6
Alignment explanation
Indices: 21043214--21043281 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
21043204 TTTTAATTTT
*
21043214 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
21043262 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
21043282 AAAAATTAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
8 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:21043235 original size:17 final size:16
Alignment explanation
Indices: 21043205--21043278 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
21043195 AAATTGATTT
*
21043205 TTTAATTTTATTTAAA
1 TTTAAATTTATTTAAA
21043221 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
21043238 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
21043252 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTTAAA
21043269 TTTAAATTTA
1 TTTAAATTTA
21043279 AATAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 27 0.53
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:21043258 original size:31 final size:31
Alignment explanation
Indices: 21043220--21043279 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
21043210 TTTTATTTAA
*
21043220 ATTTAAATTTATTTTAAATTTAAATTTAATT
1 ATTTAAATTTACTTTAAATTTAAATTTAATT
*
21043251 ATTTAAATTTACTTTGAATTTAAATTTAA
1 ATTTAAATTTACTTTAAATTTAAATTTAA
21043280 ATAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTTAAATTTACTTTAAATTTAAATTTAATT
Found at i:21045447 original size:30 final size:29
Alignment explanation
Indices: 21045378--21045529 Score: 189
Period size: 30 Copynumber: 5.0 Consensus size: 29
21045368 CCCCAAACAA
* *
21045378 TCCAGAAATTGCATTTTAACCCCAAAACTT
1 TCCA-AAATTACATTTTGACCCCAAAACTT
21045408 TCCAAAATTACATTTTGACCCCAAAACTT
1 TCCAAAATTACATTTTGACCCCAAAACTT
*
21045437 TCCAAAAATTACATTTTGACCCTAAAAACTTT
1 TCC-AAAATTACATTTTGACCC-CAAAAC-TT
*
21045469 TCCAAAATTATATTTTGACCCCAAAACTT
1 TCCAAAATTACATTTTGACCCCAAAACTT
*
21045498 TACCAAAATTACCATTTT-ACCCACAAATCTT
1 T-CCAAAATTA-CATTTTGACCC-CAAAACTT
21045529 T
1 T
21045530 TAAATTCCAT
Statistics
Matches: 109, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
29 29 0.27
30 40 0.37
31 35 0.32
32 5 0.05
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
TCCAAAATTACATTTTGACCCCAAAACTT
Found at i:21045530 original size:61 final size:61
Alignment explanation
Indices: 21045378--21045530 Score: 199
Period size: 61 Copynumber: 2.5 Consensus size: 61
21045368 CCCCAAACAA
* *
21045378 TCCAGAAATTGCATTTTAACCC-CAAAAC-TTTCCAAAATTACATTTTGACCCCAAAACTT
1 TCCAAAAATTACATTTTAACCCACAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTT
* *
21045437 TCCAAAAATTACATTTTGACCCTA-AAAACTTTTCCAAAATTATATTTTGACCCCAAAACTT
1 TCCAAAAATTACATTTTAACCC-ACAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTT
*
21045498 TACC-AAAATTACCATTTT-ACCCACAAATCTTTT
1 T-CCAAAAATTA-CATTTTAACCCACAAAACTTTT
21045531 AAATTCCATT
Statistics
Matches: 83, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
59 19 0.23
60 6 0.07
61 50 0.60
62 8 0.10
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.33
Consensus pattern (61 bp):
TCCAAAAATTACATTTTAACCCACAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTT
Found at i:21045593 original size:29 final size:27
Alignment explanation
Indices: 21045502--21045720 Score: 89
Period size: 29 Copynumber: 7.5 Consensus size: 27
21045492 AAACTTTACC
*
21045502 AAAATTACCATTTTACCCACAAATCTT-T
1 AAAATT-CCATTTTACCC-CGAATCTTCT
* * ** *
21045530 TAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCA-TTTT-ACCCCGA-ATCTTCT
*
21045560 AAAATTACCATTTTACCCTCGAATCTTTT
1 AAAATT-CCATTTTACCC-CGAATCTTCT
* * * * *
21045589 AAAATTCCGTTTTTAACCTCGATTTCATCG
1 AAAATTCC-ATTTT-ACCCCGA-ATCTTCT
* * *
21045619 AAAATTACTACTTTACCCCCGAAGCTTCT
1 AAAATT-CCATTTTA-CCCCGAATCTTCT
* * ** *
21045648 AAAATTTCATTTTTTACCCCGATTTCACCG
1 AAAATTCCA--TTTTACCCCGA-ATCTTCT
*
21045678 AAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATT-CCATTTTA-CCCCGAATCTTCT
21045707 AAAATTCCATTTTA
1 AAAATTCCATTTTA
21045721 AACCCCGATT
Statistics
Matches: 135, Mismatches: 40, Indels: 32
0.65 0.19 0.15
Matches are distributed among these distances:
27 3 0.02
28 22 0.16
29 54 0.40
30 50 0.37
31 6 0.04
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (27 bp):
AAAATTCCATTTTACCCCGAATCTTCT
Found at i:21045604 original size:59 final size:59
Alignment explanation
Indices: 21045502--21045753 Score: 357
Period size: 59 Copynumber: 4.3 Consensus size: 59
21045492 AAACTTTACC
* *
21045502 AAAATTACCATTTTACCCACAAATCTTTT-AAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * *
21045560 AAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCGTTTTTAACCTCGATTTCATCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * * * *
21045619 AAAATTACTACTTTACCCCCGAAGCTTCTAAAATTTCATTTTTTACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
21045678 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTAAACCCCGATTGCACC-
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
21045736 AAAATTACCATTTT-CCCC
1 AAAATTACCATTTTACCCC
21045754 AGGATATCCA
Statistics
Matches: 170, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
57 4 0.02
58 41 0.24
59 125 0.74
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:21048850 original size:20 final size:18
Alignment explanation
Indices: 21048825--21048878 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
21048815 ATATTCAAAA
*
21048825 AATTATTATTTTATATTCAT
1 AATTA-TATTTTATA-TAAT
21048845 AATTATATTTT-TATAAT
1 AATTATATTTTATATAAT
*
21048862 AATTATATTTTAAATAA
1 AATTATATTTTATATAA
21048879 AAACATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 14 0.45
18 6 0.19
19 6 0.19
20 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTATATTTTATATAAT
Found at i:21060164 original size:40 final size:40
Alignment explanation
Indices: 21060119--21060199 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
21060109 AAATACATAA
* *
21060119 ATATTTTTTTATATTT-ATTAGAATTTCTTAGAATTAGGAT
1 ATATTTTTATATATTTCATTA-AATTTCTTAAAATTAGGAT
*
21060159 ATATTTTTATATATTTCTTTAAATTTCTTAAAATTAGGAT
1 ATATTTTTATATATTTCATTAAATTTCTTAAAATTAGGAT
21060199 A
1 A
21060200 AAATTAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 34 0.92
41 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (40 bp):
ATATTTTTATATATTTCATTAAATTTCTTAAAATTAGGAT
Found at i:21070082 original size:23 final size:22
Alignment explanation
Indices: 21070056--21070153 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 22
21070046 ACACTAGCGC
*
21070056 GCTCTCCGTTTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACTTT-CGT
* *
21070079 GCTCTCTGTTTAGCACGTTTCAT
1 GCTCTCCGTTTAGCAC-TTTCGT
*
21070102 GCTCTCCGTTATTAGCACTTCTTGT
1 GCTCTCCG-T-TTAGCACTT-TCGT
* * *
21070127 TCTCTCTGATTAGCACTTTGCGT
1 GCTCTCCGTTTAGCACTTT-CGT
21070150 GCTC
1 GCTC
21070154 AATACTTTGT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
22 1 0.02
23 37 0.63
24 6 0.10
25 15 0.25
ACGTcount: A:0.11, C:0.28, G:0.18, T:0.43
Consensus pattern (22 bp):
GCTCTCCGTTTAGCACTTTCGT
Found at i:21070197 original size:23 final size:22
Alignment explanation
Indices: 21070167--21070231 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 22
21070157 ACTTTGTGTA
*
21070167 CTCTCTGTTTAGCACTGTGTATG
1 CTCTCTGTTTAGCACT-TATATG
* *
21070190 CTCTCTGTTGCCCAGCACTTATGTG
1 CTCTCTGTT---TAGCACTTATATG
21070215 CTCTCTGTTTAGCACTT
1 CTCTCTGTTTAGCACTT
21070232 CAGTACTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
22 7 0.20
23 9 0.26
25 13 0.37
26 6 0.17
ACGTcount: A:0.12, C:0.28, G:0.18, T:0.42
Consensus pattern (22 bp):
CTCTCTGTTTAGCACTTATATG
Found at i:21070219 original size:87 final size:87
Alignment explanation
Indices: 21070070--21070231 Score: 211
Period size: 87 Copynumber: 1.9 Consensus size: 87
21070060 TCCGTTTAGC
* * ** * *
21070070 ACTTTGTGTGCTCTCTGTTTAGCACGTTTCATGCTCTCCGTTATTAGCACTTCTTGTTCTCTCTG
1 ACTTTGTGTACTCTCTGTTTAGCACGTGTCATGCTCTCCGTTACCAGCACTTCATGTGCTCTCTG
21070135 ATTAGCACTTTGCGTGCTCAAT
66 ATTAGCACTTTGCGTGCTCAAT
* *
21070157 ACTTTGTGTACTCTCTGTTTAGCACTGTGT-ATGCTCTCTGTTGCCCAGCACTT-ATGTGCTCTC
1 ACTTTGTGTACTCTCTGTTTAGCAC-GTGTCATGCTCTCCGTT-ACCAGCACTTCATGTGCTCTC
*
21070220 TGTTTAGCACTT
64 TGATTAGCACTT
21070232 CAGTACTCTC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 54 0.84
88 10 0.16
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (87 bp):
ACTTTGTGTACTCTCTGTTTAGCACGTGTCATGCTCTCCGTTACCAGCACTTCATGTGCTCTCTG
ATTAGCACTTTGCGTGCTCAAT
Found at i:21070240 original size:22 final size:21
Alignment explanation
Indices: 21070164--21070246 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 21
21070154 AATACTTTGT
21070164 GTACTCTCTGTTTAGCACTGT-
1 GTACTCTCTGTTTAGCACT-TA
*
21070185 GTATGCTCTCTGTTGCCCAGCACTTA
1 GTA--CTCTCTGTT---TAGCACTTA
*
21070211 TGTGCTCTCTGTTTAGCACTTCA
1 -GTACTCTCTGTTTAGCACTT-A
*
21070234 GTACTCTCCGTTT
1 GTACTCTCTGTTT
21070247 GTTCTATATC
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
21 3 0.06
22 18 0.37
23 10 0.20
25 10 0.20
26 6 0.12
27 2 0.04
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41
Consensus pattern (21 bp):
GTACTCTCTGTTTAGCACTTA
Found at i:21073499 original size:19 final size:17
Alignment explanation
Indices: 21073475--21073522 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
21073465 AAATTTTAAA
21073475 TTTAAATTTACTTTAAATT
1 TTTAAATTTAC--TAAATT
*
21073494 TTTAAATGTCTACTACATT
1 TTTAAAT-T-TACTAAATT
21073513 TTTAAATTTA
1 TTTAAATTTA
21073523 AATTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
18 1 0.04
19 19 0.73
20 1 0.04
21 3 0.12
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTACTAAATT
Found at i:21074634 original size:16 final size:16
Alignment explanation
Indices: 21074602--21074648 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
21074592 TCAAACAATA
*
21074602 AGAGAAGA-AGAAAAGG
1 AGAGAAGAGAG-AGAGG
21074618 AGAGAAGAGAGAGAGG
1 AGAGAAGAGAGAGAGG
21074634 AGA-AAGAGGAGAGAG
1 AGAGAAGA-GAGAGAG
21074649 TTCTTTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 4 0.14
16 22 0.79
17 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (16 bp):
AGAGAAGAGAGAGAGG
Found at i:21074643 original size:25 final size:23
Alignment explanation
Indices: 21074602--21074647 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
21074592 TCAAACAATA
21074602 AGAGAAGAAGAAAAGGAGAGAAG
1 AGAGAAGAAGAAAAGGAGAGAAG
*
21074625 AGAGAGAGGAGAAAGAGGAGAGA
1 AGAGA-AGAAGAAA-AGGAGAGA
21074648 GTTCTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (23 bp):
AGAGAAGAAGAAAAGGAGAGAAG
Found at i:21075214 original size:30 final size:30
Alignment explanation
Indices: 21075065--21075459 Score: 268
Period size: 30 Copynumber: 13.2 Consensus size: 30
21075055 TTTTGATCTA
* * *
21075065 TAAAC-TTTCTCAAAATCATATTTTAACCTCC
1 TAAACTTTTC-CAAAATTACATTTTGACC-CC
* *
21075096 -AAACTTTAT-CAAAATCACATTTTGACCCT
1 TAAACTTT-TCCAAAATTACATTTTGACCCC
** *
21075125 TAAAC-TTTCTTGAAATAACATTTTGA-CCC
1 TAAACTTTTC-CAAAATTACATTTTGACCCC
* * *
21075154 TCAAACTTTTCCAAAATCAAAATTTGACCCC
1 T-AAACTTTTCCAAAATTACATTTTGACCCC
* * *
21075185 CAAACTTTTCCAAAATAAAATTTTGACCCC
1 TAAACTTTTCCAAAATTACATTTTGACCCC
* *
21075215 TAAA-TGTTTCTAAAATTACATTTT-AGCCC
1 TAAACT-TTTCCAAAATTACATTTTGACCCC
* * * *
21075244 TAAAACTTTTCTAAAATTTCATTTTAAACCC
1 T-AAACTTTTCCAAAATTACATTTTGACCCC
* ** * *
21075275 TTAACTTTT-CAAAATTGTATTTTAACCAC
1 TAAACTTTTCCAAAATTACATTTTGACCCC
* **
21075304 TAAACTTCTCCAAAATTACATTTTGACCTT
1 TAAACTTTTCCAAAATTACATTTTGACCCC
* * *
21075334 TATACTTCTCCAAAATTACA-TTTGACTCC
1 TAAACTTTTCCAAAATTACATTTTGACCCC
* * * *
21075363 TAAACTTCTCTAAAATCACATTTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTGACCCC
* * * **
21075393 CAAACCTTTCCAAAATTAAATTTTGACCAT
1 TAAACTTTTCCAAAATTACATTTTGACCCC
* * *
21075423 TAAACTTCTCTAAAATCACATTTTGACCCC
1 TAAACTTTTCCAAAATTACATTTTGACCCC
*
21075453 CAAACTT
1 TAAACTT
21075460 CTATAAAATC
Statistics
Matches: 288, Mismatches: 62, Indels: 29
0.76 0.16 0.08
Matches are distributed among these distances:
28 1 0.00
29 57 0.20
30 214 0.74
31 15 0.05
32 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
TAAACTTTTCCAAAATTACATTTTGACCCC
Found at i:21075349 original size:89 final size:89
Alignment explanation
Indices: 21075293--21075476 Score: 226
Period size: 89 Copynumber: 2.1 Consensus size: 89
21075283 TCAAAATTGT
* * * *
21075293 ATTTTAACCACTAAA-CTTCTCCAAAATTACATTTTGACCTTTATACTTCTCCAAAATTACATTT
1 ATTTTAACCACCAAACCTT-TCCAAAATTAAATTTTGACCATTAAACTTCTCCAAAATTACATTT
*
21075357 GACTCCTAAACTTCTCTAAAATCAC
65 AACTCCTAAACTTCTCTAAAATCAC
* * *
21075382 ATTTTAACCCCCAAACCTTTCCAAAATTAAATTTTGACCATTAAACTTCTCTAAAATCACATTTT
1 ATTTTAACCACCAAACCTTTCCAAAATTAAATTTTGACCATTAAACTTCTCCAAAATTACA-TTT
* * * * *
21075447 GACCCCCAAACTTCTATAAAATCAT
65 AACTCCTAAACTTCTCTAAAATCAC
21075472 ATTTT
1 ATTTT
21075477 TGACCCTTCT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
89 50 0.61
90 32 0.39
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (89 bp):
ATTTTAACCACCAAACCTTTCCAAAATTAAATTTTGACCATTAAACTTCTCCAAAATTACATTTA
ACTCCTAAACTTCTCTAAAATCAC
Found at i:21075489 original size:53 final size:53
Alignment explanation
Indices: 21075431--21075535 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 53
21075421 ATTAAACTTC
* * *
21075431 TCTAAAATCACATTTTGACCCCCAAACTTCTAT-AAAATCATATTTTTGACCCT
1 TCTAAAATCACAGTTTAACCCCAAAACTTCT-TCAAAATCATATTTTTGACCCT
* * * *
21075484 TCTAAAATCATAGTTTAACCCTAAAACTTCTTCAAAATTATATTTTTTACCC
1 TCTAAAATCACAGTTTAACCCCAAAACTTCTTCAAAATCATATTTTTGACCC
21075536 CCTAAACTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.02
53 43 0.98
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (53 bp):
TCTAAAATCACAGTTTAACCCCAAAACTTCTTCAAAATCATATTTTTGACCCT
Found at i:21075576 original size:28 final size:29
Alignment explanation
Indices: 21075544--21075598 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
21075534 CCCCTAAACT
21075544 TTTCTAAAATTACA-TTTTGACCCCGTAG
1 TTTCTAAAATTACATTTTTGACCCCGTAG
*
21075572 TTTCTAAAATTTCATTTTTGACCCCGT
1 TTTCTAAAATTACATTTTTGACCCCGT
21075599 TTTTTCGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (29 bp):
TTTCTAAAATTACATTTTTGACCCCGTAG
Found at i:21075604 original size:29 final size:28
Alignment explanation
Indices: 21075543--21075604 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
21075533 CCCCCTAAAC
21075543 TTTTCTAAAATTACATTTTGACCCCGTA
1 TTTTCTAAAATTACATTTTGACCCCGTA
* * *
21075571 GTTTCTAAAATTTCATTTTTGACCCCGTT
1 TTTTCTAAAATTACA-TTTTGACCCCGTA
21075600 TTTTC
1 TTTTC
21075605 GTTTTCTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTTCTAAAATTACATTTTGACCCCGTA
Found at i:21076473 original size:323 final size:323
Alignment explanation
Indices: 21075877--21076473 Score: 840
Period size: 323 Copynumber: 1.8 Consensus size: 323
21075867 AGACAACGTT
* * ** * *
21075877 CTTTCGTGTGAAAATTTCGAAAAATTATTTCCTAACGTGCTGGGTGTGATTTTTCGTATAATTCG
1 CTTTCGTATGAAAATTTCAAAAAATTATGCCCTAACGTGCTGGGTATGATTTTTCGTACAATTCG
* * *
21075942 CGCGATCGAATATCCTCTTTAAAACCTTTCAAAGTGTCCTTCAATTTCGAAATTTCGAGAACATC
66 CACGATCGAATATCCTCTTTAAAACCTTTCAAAATGTCCTTCAATTTCGAAATTCCGAGAACATC
* *
21076007 GTGTCCTAACGTGTTGGACACGACTTCAATTCTCCGAGAAATTCGAAACACAGGGACATTTTTCT
131 GTGTCCTAACGTGTTGGACACAACTTCAATTCTCCGAGAAATTCGAAACACACGGACATTTTTCT
* * * * * *
21076072 TCAAATCTAATTTTTGAAAATCACGTGAAATAAGTTATGTGTCCGAGGATTGTATTTTAAACTTC
196 TCAAATCTAATTTTTGAAAATCACGTGAAATAAGTTATGAGTACAAAGATCGTATTTTAAAATTC
*
21076137 ATTCGAAATTTCAAGTTCTCAAAAAAATATACAAATAATTTTAAACAAAAACGAGGCAATATC
261 ACTCGAAATTTCAAGTTCTCAAAAAAATATACAAATAATTTTAAACAAAAACGAGGCAATATC
* *
21076200 CTTTCGTATGAAAGTTTCAAAAAATTATGCCCTAACGTGCTGGGTATGATTTTTCGTACAATTCT
1 CTTTCGTATGAAAATTTCAAAAAATTATGCCCTAACGTGCTGGGTATGATTTTTCGTACAATTCG
* * * *
21076265 TACGATCGAATATCCTCTTTAAAATCTTTCAAAATGTCTTTCAATTTCGAAATTCCGAGAACGTC
66 CACGATCGAATATCCTCTTTAAAACCTTTCAAAATGTCCTTCAATTTCGAAATTCCGAGAACATC
* *
21076330 GTGTCCTAACGTGTTGGACACAACTTCAATTCTTCG-GAAAATTCGAAACACACGGACGTTTTTA
131 GTGTCCTAACGTGTTGGACACAACTTCAATTCTCCGAG-AAATTCGAAACACACGGACATTTTT-
* * * * * *
21076394 C-TCAAATTTGATTTTTGAAAATCATC-TGAAGTTATTTATGAGTACAAATATCGTATTTTAAAA
194 CTTCAAATCTAATTTTTGAAAATCA-CGTGAAATAAGTTATGAGTACAAAGATCGTATTTTAAAA
* *
21076457 TTCGCTCGAGATTTCAA
258 TTCACTCGAAATTTCAA
21076474 AGTTTTAATA
Statistics
Matches: 237, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
322 1 0.00
323 234 0.99
324 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (323 bp):
CTTTCGTATGAAAATTTCAAAAAATTATGCCCTAACGTGCTGGGTATGATTTTTCGTACAATTCG
CACGATCGAATATCCTCTTTAAAACCTTTCAAAATGTCCTTCAATTTCGAAATTCCGAGAACATC
GTGTCCTAACGTGTTGGACACAACTTCAATTCTCCGAGAAATTCGAAACACACGGACATTTTTCT
TCAAATCTAATTTTTGAAAATCACGTGAAATAAGTTATGAGTACAAAGATCGTATTTTAAAATTC
ACTCGAAATTTCAAGTTCTCAAAAAAATATACAAATAATTTTAAACAAAAACGAGGCAATATC
Found at i:21079203 original size:16 final size:15
Alignment explanation
Indices: 21079178--21079219 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
21079168 AAAAATTTTA
21079178 AAAATA-TTTTATTT
1 AAAATATTTTTATTT
21079192 AATAATATTTTTATCTT
1 AA-AATATTTTTAT-TT
21079209 AAAATATTTTT
1 AAAATATTTTT
21079220 GAAAAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 4 0.16
16 15 0.60
17 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
AAAATATTTTTATTT
Found at i:21085045 original size:27 final size:29
Alignment explanation
Indices: 21084997--21085059 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
21084987 TAAGTTTATG
*
21084997 TATTTTTTATATCTAAATTTTA-TCT-TA
1 TATTTTTTATATCTAAAATTTAGTCTATA
* *
21085024 TATTTTTTAT-TTTAAAAATTTAGTCTATT
1 TATTTTTTATATCT-AAAATTTAGTCTATA
21085053 TATTTTT
1 TATTTTT
21085060 CGAAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 17 0.57
28 3 0.10
29 8 0.27
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (29 bp):
TATTTTTTATATCTAAAATTTAGTCTATA
Found at i:21089710 original size:5 final size:5
Alignment explanation
Indices: 21089695--21089732 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
21089685 TAGAATGAAG
21089695 GAAAA GAAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA
1 GAAAA G-AAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA
21089733 GAGAATATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:21094308 original size:16 final size:16
Alignment explanation
Indices: 21094289--21094319 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21094279 TAAAAGTTTC
21094289 ATTATTTAATATAATA
1 ATTATTTAATATAATA
21094305 ATTATTTAATATAAT
1 ATTATTTAATATAAT
21094320 TAAGTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATTTAATATAATA
Found at i:21096170 original size:29 final size:29
Alignment explanation
Indices: 21096129--21096205 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
21096119 TGTAAATTTG
*
21096129 GAAAGTTTAGGGGTCAAAATGCAATTTTTA
1 GAAAGTAT-GGGGTCAAAATGCAATTTTTA
* * **
21096159 -AAGGATTTGGGGTC-AAATGTGATTTTTA
1 GAAAG-TATGGGGTCAAAATGCAATTTTTA
21096187 GAAAGTATGGGGTCAAAAT
1 GAAAGTATGGGGTCAAAAT
21096206 CAAGGTTTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 20 0.51
29 16 0.41
30 3 0.08
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (29 bp):
GAAAGTATGGGGTCAAAATGCAATTTTTA
Found at i:21096235 original size:30 final size:29
Alignment explanation
Indices: 21096188--21096353 Score: 119
Period size: 29 Copynumber: 5.7 Consensus size: 29
21096178 TGATTTTTAG
* * *
21096188 AAAGTATG-GGGTCAAAATCAAGGTTTGGA
1 AAAGTTTGAGGGTTAAAAT-AAGTTTTGGA
*
21096217 AAAGTTTGAGGGTTAAAATATAATTTTTGGA
1 AAAGTTTGAGGGTT-AAA-ATAAGTTTTGGA
* *
21096248 AAA-TTTGAGGGTTAAATATAATTTTTAG-
1 AAAGTTTGAGGGTTAAA-ATAAGTTTTGGA
* * **
21096276 AGAGTTTG-GGGTTAAAATATGATTTTTAA
1 AAAGTTTGAGGGTTAAAATAAG-TTTTGGA
*
21096305 AAAGTTTGGGGGTTAAAATCAAAGTTTTGG-
1 AAAGTTTGAGGGTTAAAAT--AAGTTTTGGA
*
21096335 AAAGTTTGA-GGTCAAAATA
1 AAAGTTTGAGGGTTAAAATA
21096354 TAATTTTTAA
Statistics
Matches: 112, Mismatches: 16, Indels: 20
0.76 0.11 0.14
Matches are distributed among these distances:
27 4 0.04
28 14 0.12
29 40 0.36
30 32 0.29
31 18 0.16
32 4 0.04
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAGTTTGAGGGTTAAAATAAGTTTTGGA
Found at i:21096273 original size:29 final size:29
Alignment explanation
Indices: 21096211--21096361 Score: 130
Period size: 29 Copynumber: 5.1 Consensus size: 29
21096201 AAAATCAAGG
21096211 TTTGGAAAAGTTTGAGGGTTAAAATATAATT
1 TTTGGAAAA-TTTGAGGGTT-AAATATAATT
21096242 TTTGGAAAATTTGAGGGTTAAATATAATT
1 TTTGGAAAATTTGAGGGTTAAATATAATT
* * * *
21096271 TTTAGAGAGTTTG-GGGTTAAAATATGATT
1 TTTGGAAAATTTGAGGGTT-AAATATAATT
* * *
21096300 TTT-AAAAAGTTTGGGGGTTAAA-ATCAAAGT
1 TTTGGAAAA-TTTGAGGGTTAAATAT--AATT
* *
21096330 TTTGGAAAGTTTGA-GGTCAAAATATAATT
1 TTTGGAAAATTTGAGGGT-TAAATATAATT
21096359 TTT
1 TTT
21096362 AAATAAAATA
Statistics
Matches: 98, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
28 9 0.09
29 48 0.49
30 27 0.28
31 14 0.14
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.40
Consensus pattern (29 bp):
TTTGGAAAATTTGAGGGTTAAATATAATT
Found at i:21096360 original size:59 final size:59
Alignment explanation
Indices: 21096180--21096364 Score: 191
Period size: 59 Copynumber: 3.2 Consensus size: 59
21096170 GTCAAATGTG
* * * *
21096180 ATTTTTAGAAAGTAT-GGGGTCAAAATC-AAGGTTTGGAAAAGTTTGAGGGTTAAAATATA
1 ATTTTTAAAAAGTTTGGGGGTTAAAATCAAAGTTTTGG-AAAGTTTGA-GGTTAAAATATA
* * * * * * *
21096239 ATTTTTGGAAAA-TTTGAGGGTT-AAAT-ATAATTTTTAGAGAGTTTGGGGTTAAAATATG
1 ATTTTT-AAAAAGTTTGGGGGTTAAAATCA-AAGTTTTGGAAAGTTTGAGGTTAAAATATA
*
21096297 ATTTTTAAAAAGTTTGGGGGTTAAAATCAAAGTTTTGGAAAGTTTGAGGTCAAAATATA
1 ATTTTTAAAAAGTTTGGGGGTTAAAATCAAAGTTTTGGAAAGTTTGAGGTTAAAATATA
21096356 ATTTTTAAA
1 ATTTTTAAA
21096365 TAAAATAGGG
Statistics
Matches: 100, Mismatches: 19, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
57 4 0.04
58 26 0.26
59 56 0.56
60 14 0.14
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (59 bp):
ATTTTTAAAAAGTTTGGGGGTTAAAATCAAAGTTTTGGAAAGTTTGAGGTTAAAATATA
Found at i:21098218 original size:3 final size:3
Alignment explanation
Indices: 21098210--21098248 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
21098200 TACTTCCCAA
21098210 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
21098249 GAATAGAATA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21099308 original size:7 final size:7
Alignment explanation
Indices: 21099298--21099349 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
21099288 AATGATCAAA
21099298 GTCAACG
1 GTCAACG
*
21099305 GTCAA-A
1 GTCAACG
21099311 GTCAACG
1 GTCAACG
21099318 GTCAACG
1 GTCAACG
21099325 GTCATA--
1 GTCA-ACG
21099331 GTCAACG
1 GTCAACG
21099338 GTCAACG
1 GTCAACG
21099345 GTCAA
1 GTCAA
21099350 AGTCAAAGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 1 0.03
6 9 0.23
7 28 0.72
8 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:21099321 original size:20 final size:20
Alignment explanation
Indices: 21099298--21099355 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
21099288 AATGATCAAA
21099298 GTCAACGGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
*
21099318 GTCAACGGTCATAGTCAACG
1 GTCAACGGTCAAAGTCAACG
21099338 GTCAACGGTCAAAGTCAA
1 GTCAACGGTCAAAGTCAA
21099356 AGTCAATGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (20 bp):
GTCAACGGTCAAAGTCAACG
Found at i:21099354 original size:13 final size:13
Alignment explanation
Indices: 21099282--21099355 Score: 71
Period size: 13 Copynumber: 5.6 Consensus size: 13
21099272 TTTTTCGAAA
* *
21099282 AAAGTCAATGATC
1 AAAGTCAACGGTC
21099295 AAAGTCAACGGTC
1 AAAGTCAACGGTC
21099308 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
21099321 AACGGTCATA--GTC
1 AA-AGTCA-ACGGTC
*
21099334 AACGGTCAACGGTC
1 AA-AGTCAACGGTC
21099348 AAAGTCAA
1 AAAGTCAA
21099356 AGTCAATGGT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
12 1 0.02
13 42 0.79
14 9 0.17
15 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (13 bp):
AAAGTCAACGGTC
Done.