Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008241.1 Hibiscus syriacus cultivar Beakdansim tig00110889_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1355325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:912386 original size:33 final size:33
Alignment explanation
Indices: 912340--912418 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
912330 AATCGCAATG
**
912340 CGATTTTGGTTTCGCGTTGCGATTATCTCGTTA
1 CGATTTTAATTTCGCGTTGCGATTATCTCGTTA
* * * *
912373 CGATTTTAATTTCGCGTTGTGATTCTCTTGTTG
1 CGATTTTAATTTCGCGTTGCGATTATCTCGTTA
*
912406 CGATTTTCATTTC
1 CGATTTTAATTTC
912419 TCTCGTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (33 bp):
CGATTTTAATTTCGCGTTGCGATTATCTCGTTA
Found at i:912421 original size:21 final size:20
Alignment explanation
Indices: 912398--912473 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
912388 GTTGTGATTC
912398 TCTTGTTGCGATTTTCATTT
1 TCTTGTTGCGATTTTCATTT
* * **
912418 CTCTCGTTGTGATAGTCATTT
1 -TCTTGTTGCGATTTTCATTT
912439 TCGTT-TTGCGATTTTCATTT
1 TC-TTGTTGCGATTTTCATTT
*
912459 TCATGTTGCGATTTT
1 TCTTGTTGCGATTTT
912474 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 26 0.59
21 17 0.39
ACGTcount: A:0.12, C:0.16, G:0.17, T:0.55
Consensus pattern (20 bp):
TCTTGTTGCGATTTTCATTT
Found at i:913058 original size:20 final size:20
Alignment explanation
Indices: 913033--913243 Score: 194
Period size: 20 Copynumber: 10.4 Consensus size: 20
913023 TAAAAATCGA
913033 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
913053 GTTGCGATTTTACGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
913074 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * * *
913094 ATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
*
913114 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
* * *
913134 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
* *
913154 GTTGTGATTTACGGATATGC
1 GTTGCGATTTACGGATACGC
* *
913174 GTTACGATTTTAC--ATATTGTC
1 GTTGCGA-TTTACGGATA-CG-C
*
913195 GTTGTGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
913215 GTTACGATTTTACGGATACTC
1 GTTGCGA-TTTACGGATACGC
913236 GTTGCGAT
1 GTTGCGAT
913244 AGTCAGAATC
Statistics
Matches: 151, Mismatches: 31, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.02
20 98 0.65
21 47 0.31
22 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:913116 original size:40 final size:41
Alignment explanation
Indices: 913033--913243 Score: 300
Period size: 41 Copynumber: 5.2 Consensus size: 41
913023 TAAAAATCGA
*
913033 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
913074 GTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
913114 GTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* * * * *
913154 GTTGTGATTTACGGATATGCGTTACGATTTTACATATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* * * *
913195 GTTGTGATTTACGGATACGCGTTACGATTTTACGGATACTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
913236 GTTGCGAT
1 GTTGCGAT
913244 AGTCAGAATC
Statistics
Matches: 153, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
40 73 0.48
41 80 0.52
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (41 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
Found at i:913182 original size:60 final size:60
Alignment explanation
Indices: 913033--913243 Score: 205
Period size: 61 Copynumber: 3.5 Consensus size: 60
913023 TAAAAATCGA
* *
913033 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATATGCGTTGCGA-TTTACGTATCGTCGTTGCGATTTACGGATACGC
* * * * * *
913094 ATTGCGATTTACGTAT-TCTCGTTGCGATTTACAG-ATACG-CGTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATAT-GCGTTGCGATTTAC-GTAT-CGTCGTTGCGATTTACGGATACGC
* * * * *
913154 GTTGTGATTTACGGATATGCGTTACGATTTTACATATTGTCGTTGTGATTTACGGATACGC
1 GTTGCGATTTACGGATATGCGTTGCGA-TTTACGTATCGTCGTTGCGATTTACGGATACGC
*
913215 GTTACGATTTTACGGATACT-CGTTGCGAT
1 GTTGCGA-TTTACGGATA-TGCGTTGCGAT
913244 AGTCAGAATC
Statistics
Matches: 119, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
60 46 0.39
61 55 0.46
62 17 0.14
63 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (60 bp):
GTTGCGATTTACGGATATGCGTTGCGATTTACGTATCGTCGTTGCGATTTACGGATACGC
Found at i:913300 original size:21 final size:21
Alignment explanation
Indices: 913252--913305 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
913242 ATAGTCAGAA
*
913252 TCGCGTTGCGA-TTTATATGT
1 TCGCGTTGCGATTTTATATAT
* *
913272 TCGTGTTGCGATTTTTTATAT
1 TCGCGTTGCGATTTTATATAT
913293 TCGCGTTGCGATT
1 TCGCGTTGCGATT
913306 CTGGAAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.13, C:0.15, G:0.24, T:0.48
Consensus pattern (21 bp):
TCGCGTTGCGATTTTATATAT
Found at i:913317 original size:21 final size:21
Alignment explanation
Indices: 913293--913387 Score: 63
Period size: 20 Copynumber: 4.6 Consensus size: 21
913283 TTTTTTATAT
*
913293 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGGAAAA
* * **
913314 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGAAAA
* *
913335 TCGCATTGCGATTCTGGGAAC
1 TCGCATTGCGATTCTGGAAAA
*
913356 T-G-ATTTGCGATTCTGG-AGA
1 TCGCA-TTGCGATTCTGGAAAA
*
913375 TCGCGTTGCGATT
1 TCGCATTGCGATT
913388 TTTATTTCGC
Statistics
Matches: 55, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
19 3 0.05
20 25 0.45
21 24 0.44
22 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTCTGGAAAA
Found at i:913509 original size:14 final size:14
Alignment explanation
Indices: 913490--913517 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
913480 TTATTTTCTC
913490 TAATAATAATCAAA
1 TAATAATAATCAAA
913504 TAATAATAATCAAA
1 TAATAATAATCAAA
913518 ACGGCCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATAATCAAA
Found at i:917964 original size:14 final size:14
Alignment explanation
Indices: 917945--917971 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
917935 ACTTAATATC
917945 ACACAAGAATCATA
1 ACACAAGAATCATA
917959 ACACAAGAATCAT
1 ACACAAGAATCAT
917972 GTTAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (14 bp):
ACACAAGAATCATA
Found at i:920115 original size:16 final size:13
Alignment explanation
Indices: 920080--920136 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
920070 ACTATCTTCT
920080 ATTTAATAACTCA
1 ATTTAATAACTCA
920093 ATTTAATAACTCA
1 ATTTAATAACTCA
920106 ACTGTTTAATAACTCA
1 A---TTTAATAACTCA
***
920122 AGAAAATAACTCA
1 ATTTAATAACTCA
920135 AT
1 AT
920137 CTGGCCCTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 24 0.65
16 13 0.35
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (13 bp):
ATTTAATAACTCA
Found at i:921103 original size:41 final size:41
Alignment explanation
Indices: 921058--921187 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 41
921048 ACAAACGCTT
921058 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
1 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
* ** * * * * *
921099 CAATATAGTGGTAAA-CTAGCAGCGTTTTA-CCATAAACGCCA
1 CAATAGA-TTATAAATTTTGCGGCGATTTAGCCA-AAACGCCG
* * * *
921140 CAATAGAGTATAAATTTTGCGGTGATTGAGTCAAAACGCCG
1 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
921181 CAATAGA
1 CAATAGA
921188 GTGGTAAATT
Statistics
Matches: 65, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
40 7 0.11
41 51 0.78
42 7 0.11
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (41 bp):
CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
Found at i:921191 original size:82 final size:83
Alignment explanation
Indices: 921058--921227 Score: 243
Period size: 82 Copynumber: 2.1 Consensus size: 83
921048 ACAAACGCTT
* * *
921058 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCGCAATATAGTGGTAAACTAGCAGCG
1 CAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGTGGTAAACTAGCAGCG
*
921123 TTTT-ACCATAAACGCCA
66 TTTTGACCAAAAACGCCA
* * * * *
921140 CAATAGAGTATAAATTTTGCGGTGATTGAGTCAAAACGCCGCAATAGAGTGGTAAATTGGCTGCG
1 CAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGTGGTAAACTAGCAGCG
*
921205 TTTTGACCAAAAACGCCG
66 TTTTGACCAAAAACGCCA
921223 CAATA
1 CAATA
921228 TATTACACAT
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
82 61 0.79
83 16 0.21
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (83 bp):
CAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGTGGTAAACTAGCAGCG
TTTTGACCAAAAACGCCA
Found at i:921216 original size:41 final size:40
Alignment explanation
Indices: 921088--921227 Score: 124
Period size: 41 Copynumber: 3.4 Consensus size: 40
921078 GGCGATTTAG
* * *
921088 CCAAAACGCCGCAATATAGTGGTAAACTAGCAGCGTTTT-A
1 CCAAAACGCCGCAATAGAGTGGTAAA-TTGCTGCGTTTTGA
* * * *
921128 CCATAAACGCCACAATAGAGT-ATAAATT-TTGCGGTGATTGA
1 CCA-AAACGCCGCAATAGAGTGGTAAATTGCTGC-GT-TTTGA
*
921169 GTCAAAACGCCGCAATAGAGTGGTAAATTGGCTGCGTTTTGA
1 -CCAAAACGCCGCAATAGAGTGGTAAATT-GCTGCGTTTTGA
921211 CCAAAAACGCCGCAATA
1 CC-AAAACGCCGCAATA
921228 TATTACACAT
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
38 2 0.03
39 3 0.04
40 9 0.12
41 33 0.42
42 26 0.33
43 2 0.03
44 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (40 bp):
CCAAAACGCCGCAATAGAGTGGTAAATTGCTGCGTTTTGA
Found at i:921993 original size:23 final size:21
Alignment explanation
Indices: 921946--921985 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
921936 CGAGCAATTA
921946 GTTTTTTACTGAACACGAAAT
1 GTTTTTTACTGAACACGAAAT
921967 GTTTTTTACTGAACACGAA
1 GTTTTTTACTGAACACGAA
921986 TGATGTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
GTTTTTTACTGAACACGAAAT
Found at i:923223 original size:12 final size:12
Alignment explanation
Indices: 923206--923231 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
923196 TTTAGTTCAT
923206 CATTTCATCACC
1 CATTTCATCACC
923218 CATTTCATCACC
1 CATTTCATCACC
923230 CA
1 CA
923232 CTAAAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (12 bp):
CATTTCATCACC
Found at i:927389 original size:43 final size:43
Alignment explanation
Indices: 927317--927452 Score: 122
Period size: 42 Copynumber: 3.3 Consensus size: 43
927307 GTTTTTGAAG
* * * *
927317 AAACGCCGCTAA-A-CATCAACTATTGCGGCGTTTGT-CTGCC
1 AAACGCCGCTAATATCAACACCTATTGCGGCGTTTGTAATGAC
* * *
927357 AAATGCCGTTAAATATCAACACCTATTGCGGCGTTT-TAATGAT
1 AAACGCCGCT-AATATCAACACCTATTGCGGCGTTTGTAATGAC
* *
927400 AAACGCCGCTAATATCAATACCTTTTGCGGCGTTTGT--TGAAC
1 AAACGCCGCTAATATCAACACCTATTGCGGCGTTTGTAATG-AC
*
927442 AATCGCCGCTA
1 AAACGCCGCTA
927453 TGTTGTAACC
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
40 8 0.10
41 4 0.05
42 36 0.47
43 29 0.38
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAATATCAACACCTATTGCGGCGTTTGTAATGAC
Found at i:927449 original size:42 final size:42
Alignment explanation
Indices: 927301--927452 Score: 106
Period size: 42 Copynumber: 3.7 Consensus size: 42
927291 TAAAATCTAC
* * *
927301 TGCGGCGTTTT-TGAAGAAACGCCGCTAA-A-C-ATCAACTAT
1 TGCGGCGTTTTATGAACAATCGCCGCTAATATCAAT-ACCTAT
* * * *
927340 TGCGGCGTTTGTCTG-CCAAAT-GCCGTTAAATATCAACACCTAT
1 TGCGGCGTTT-TATGAAC-AATCGCCGCT-AATATCAATACCTAT
*
927383 TGCGGCGTTTTAATGATA-AA-CGCCGCTAATATCAATACCTTT
1 TGCGGCGTTTT-ATGA-ACAATCGCCGCTAATATCAATACCTAT
927425 TGCGGCGTTTGT-TGAACAATCGCCGCTA
1 TGCGGCGTTT-TATGAACAATCGCCGCTA
927453 TGTTGTAACC
Statistics
Matches: 88, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
39 10 0.11
40 7 0.08
41 11 0.12
42 33 0.38
43 26 0.30
44 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (42 bp):
TGCGGCGTTTTATGAACAATCGCCGCTAATATCAATACCTAT
Found at i:928817 original size:38 final size:36
Alignment explanation
Indices: 928766--928837 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 36
928756 TTTTATCTAT
*
928766 CCCTAAACCATTAAAATAAACCGAATACAATTTAAAAG
1 CCCTAAACCATTAAAA-AAACCGAA-ACAACTTAAAAG
* *
928804 CCCTAATCCATTAAAAAAACCTAAACAACTTAAA
1 CCCTAAACCATTAAAAAAACCGAAACAACTTAAA
928838 TAAAACCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.29
37 7 0.23
38 15 0.48
ACGTcount: A:0.53, C:0.24, G:0.03, T:0.21
Consensus pattern (36 bp):
CCCTAAACCATTAAAAAAACCGAAACAACTTAAAAG
Found at i:928826 original size:18 final size:18
Alignment explanation
Indices: 928767--928827 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
928757 TTTATCTATC
*
928767 CCTAAACCATTAAAATAAA
1 CCTAATCCATTAAAA-AAA
* * * **
928786 CCGAATACAATTTAAAAGC
1 CCTAAT-CCATTAAAAAAA
928805 CCTAATCCATTAAAAAAA
1 CCTAATCCATTAAAAAAA
928823 CCTAA
1 CCTAA
928828 ACAACTTAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 3
0.68 0.25 0.07
Matches are distributed among these distances:
18 13 0.43
19 10 0.33
20 7 0.23
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.21
Consensus pattern (18 bp):
CCTAATCCATTAAAAAAA
Found at i:928847 original size:21 final size:20
Alignment explanation
Indices: 928776--928853 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 20
928766 CCCTAAACCA
*
928776 TTAAAATAAACCGAATACAA-
1 TTAAAA-AAACCTAATACAAC
* ** *
928796 TTTAAAAGCCCTAAT-CCA-
1 TTAAAAAAACCTAATACAAC
928814 TTAAAAAAACCTAA-ACAAC
1 TTAAAAAAACCTAATACAAC
928833 TTAAATAAAACCCTAATACAA
1 TTAAA-AAAA-CCTAATACAA
928854 AGAAAATCCT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
18 15 0.34
19 11 0.25
20 9 0.20
21 5 0.11
22 4 0.09
ACGTcount: A:0.55, C:0.21, G:0.03, T:0.22
Consensus pattern (20 bp):
TTAAAAAAACCTAATACAAC
Found at i:928900 original size:73 final size:73
Alignment explanation
Indices: 928817--929036 Score: 195
Period size: 73 Copynumber: 3.0 Consensus size: 73
928807 TAATCCATTA
*
928817 AAAAAACCTAAACAACTTAAATAAAACCCTAATACAAAGAAAATCCTAAATCACATAAAAAACTC
1 AAAAACCCTAAACAACTTAAATAAAACCCTAATACAAAGAAAATCCTAAATCACATAAAAAACTC
928882 TAAACCAC
66 TAAACCAC
* * * ** * * * *
928890 AAAAACCCTAAACTACTTCAACATTAAAAAAACCCTAA-CCCAA-ACCA-CTTTAACCCCA-AAA
1 AAAAACCCTAAACAACTT-AA-A-T---AAAACCCTAATACAAAGAAAATCCTAAATCACATAAA
928951 AAAC-CTAAA-C-C
60 AAACTCTAAACCAC
**
928962 AAAAACTTATAAACAACTT-AATAAAACCCTAATACAATTAGAAAATCCTAAATCACATAAAAAA
1 AAAAAC-CCTAAACAACTTAAATAAAACCCTAATACAA--AGAAAATCCTAAATCACATAAAAAA
929026 CTCTAAACCAC
63 CTCTAAACCAC
929037 TTTAAAAAAA
Statistics
Matches: 110, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
66 10 0.09
67 2 0.02
69 2 0.02
70 3 0.03
71 8 0.07
72 14 0.13
73 31 0.28
74 8 0.07
75 9 0.08
76 8 0.07
77 2 0.02
78 3 0.03
79 10 0.09
ACGTcount: A:0.55, C:0.26, G:0.01, T:0.18
Consensus pattern (73 bp):
AAAAACCCTAAACAACTTAAATAAAACCCTAATACAAAGAAAATCCTAAATCACATAAAAAACTC
TAAACCAC
Found at i:929044 original size:20 final size:19
Alignment explanation
Indices: 929019--929080 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 19
929009 CTAAATCACA
929019 TAAAAAACTCTAAACCACTT
1 TAAAAAAC-CTAAACCACTT
929039 TAAAAAAAAACCTAAACCACTT
1 T---AAAAAACCTAAACCACTT
*
929061 TAAAAACACCTAAACTACTT
1 TAAAAA-ACCTAAACCACTT
929081 CAACATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 5 0.14
20 13 0.35
22 12 0.32
23 7 0.19
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAAAAACCTAAACCACTT
Found at i:929053 original size:22 final size:23
Alignment explanation
Indices: 929020--929066 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
929010 TAAATCACAT
929020 AAAAAACTCTAAACCACTTTAAA
1 AAAAAACTCTAAACCACTTTAAA
929043 AAAAAAC-CTAAACCACTTTAAA
1 AAAAAACTCTAAACCACTTTAAA
929065 AA
1 AA
929067 CACCTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (23 bp):
AAAAAACTCTAAACCACTTTAAA
Found at i:929160 original size:173 final size:167
Alignment explanation
Indices: 928872--929309 Score: 676
Period size: 173 Copynumber: 2.6 Consensus size: 167
928862 CTAAATCACA
928872 TAAAAAACTCTAAACCAC---AAAAACCCTAAACTACTTCAACATTAAAAAAACCCTAACCC-AA
1 TAAAAAAC-CTAAACCACTTTAAAAACCCTAAACTACTTCAACATTAAAAAAA---T-ACCCTAA
*
928933 ACCACTTTAACCCCAAAAAAACCTAAACCAAAAAC-TTATAAACAACTTAATAAAACCCTAATAC
61 ACCACTTTAACCCCAAAAAAACCTAAACCAGAAACTTTATAAACAACTTAATAAAACCCTAATAC
928997 AATTAGAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
126 AATTAGAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
929039 TAAAAAAAAACCTAAACCACTTTAAAAACACCTAAACTACTTCAACATTAAAAAAATACCCTAAA
1 T---AAAAAACCTAAACCACTTTAAAAAC-CCTAAACTACTTCAACATTAAAAAAATACCCTAAA
929104 CCACTTTAACCCCCAAAAAAACCTAAACCAGAAACTTTATAAACAACTTAAATAAAACCCTAATA
62 CCACTTTAA-CCCCAAAAAAACCTAAACCAGAAACTTTATAAACAACTT-AATAAAACCCTAATA
*
929169 CAATTAGAAAATCCTAAATCACATAAAACACTCTAAACCACTT
125 CAATTAGAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
*
929212 TAAAAAGCCTAAAACCACTTT-AAAACTCCTAAACTACTTCAACATT-AAAAAA-ACCCTAAACC
1 TAAAAAACCT-AAACCACTTTAAAAAC-CCTAAACTACTTCAACATTAAAAAAATACCCTAAACC
929274 ACTTTAACCCCAAAAAAACCTAAACCAGAAACTTTA
64 ACTTTAACCCCAAAAAAACCTAAACCAGAAACTTTA
929310 AACCGTAAGT
Statistics
Matches: 255, Mismatches: 4, Indels: 24
0.90 0.01 0.08
Matches are distributed among these distances:
167 30 0.12
168 17 0.07
169 19 0.07
170 52 0.20
171 34 0.13
172 19 0.07
173 84 0.33
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.20
Consensus pattern (167 bp):
TAAAAAACCTAAACCACTTTAAAAACCCTAAACTACTTCAACATTAAAAAAATACCCTAAACCAC
TTTAACCCCAAAAAAACCTAAACCAGAAACTTTATAAACAACTTAATAAAACCCTAATACAATTA
GAAAATCCTAAATCACATAAAAAACTCTAAACCACTT
Found at i:929223 original size:19 final size:19
Alignment explanation
Indices: 929201--929250 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
929191 ATAAAACACT
929201 CTAAACCACTTTAAAAAGC
1 CTAAACCACTTTAAAAAGC
**
929220 CTAAAACCACTTTAAAACTC
1 CT-AAACCACTTTAAAAAGC
*
929240 CTAAACTACTT
1 CTAAACCACTT
929251 CAACATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.44, C:0.28, G:0.02, T:0.26
Consensus pattern (19 bp):
CTAAACCACTTTAAAAAGC
Found at i:934410 original size:203 final size:201
Alignment explanation
Indices: 934064--934468 Score: 767
Period size: 203 Copynumber: 2.0 Consensus size: 201
934054 TATCTTACAA
934064 CAATTTCACCTGGGAAGCCTCAAGTCCGATAGAGTGTCCTCGAGGAGTGTGAGTTGTCTTTGAAT
1 CAATTTCACCTGGGAAGCCTCAAGTCCGATAGAGTGTCCTCGAGGAGTGTGAGTTGTCTTTGAAT
*
934129 TGAACTTACTTCGATCCTATATATATATATATAAACTGATATACTAACATAGTCGATTTGCATAT
66 TGAACTTACTTCGATCCTATATATATATATATAAACTGATATACTAACATAGTCAATTTGCATAT
934194 CTCAATCTTTCCAGGAACTTGGTTGAGAGCTACTCTACAACAGCAAATAAATTGTAAGCATATT-
131 CTCAATCTTTCCAGGAACTTGGTTGAGAGCTACTCTACAACAGCAAATAAATTGTAAGCATATTC
934258 TTGTGC
196 TTGTGC
934264 CAATTTCACCTGGGAAGCCTCAAGTCCGATAGAGTGTCCTCGAGGGAGCGTGTGAGTTGTCTTTG
1 CAATTTCACCTGGGAAGCCTCAAGTCCGATAGAGTGTCCTCGA-GGA--GTGTGAGTTGTCTTTG
934329 AATTGAACTTACTTCGATCCTATATATATATATATAAACTGATATACTAACATAGTCAATTTGCA
63 AATTGAACTTACTTCGATCCTATATATATATATATAAACTGATATACTAACATAGTCAATTTGCA
934394 TATCTCAATCTTTCCAGGAACTTGGTTGAGAGCTACTCTACAACAGCAAATAAATTGTAAGCATA
128 TATCTCAATCTTTCCAGGAACTTGGTTGAGAGCTACTCTACAACAGCAAATAAATTGTAAGCATA
934459 TTCTTGTGC
193 TTCTTGTGC
934468 C
1 C
934469 TTGATTTATG
Statistics
Matches: 200, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
200 43 0.22
201 3 0.01
203 147 0.74
204 7 0.04
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (201 bp):
CAATTTCACCTGGGAAGCCTCAAGTCCGATAGAGTGTCCTCGAGGAGTGTGAGTTGTCTTTGAAT
TGAACTTACTTCGATCCTATATATATATATATAAACTGATATACTAACATAGTCAATTTGCATAT
CTCAATCTTTCCAGGAACTTGGTTGAGAGCTACTCTACAACAGCAAATAAATTGTAAGCATATTC
TTGTGC
Found at i:938344 original size:2 final size:2
Alignment explanation
Indices: 938339--938402 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
938329 TTTTTTTAAA
938339 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
938380 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
938403 ATTTTAATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:938551 original size:20 final size:20
Alignment explanation
Indices: 938526--938597 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
938516 GACCAACAAA
938526 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
938546 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
* * *
938566 TTCGAAACGCGAAAGT-CAAA
1 TTCGCAACGCG-AATTCCAAT
938586 TTCGCAACGCGA
1 TTCGCAACGCGA
938598 TAGTCAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
19 3 0.07
20 35 0.85
21 2 0.05
22 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:938602 original size:20 final size:20
Alignment explanation
Indices: 938566--938611 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
938556 AGTTTCCAAT
*
938566 TTCGAAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
938586 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
938606 TTCGCA
1 TTCGCA
938612 GCTCGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:938894 original size:20 final size:20
Alignment explanation
Indices: 938871--938925 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
938861 GATTTTGCAA
*
938871 TTCGCAACGCGAATTTGACT
1 TTCGCGACGCGAATTTGACT
**
938891 TTCGCGTTGCGAATTTGACT
1 TTCGCGACGCGAATTTGACT
*
938911 TTCGCGACGCTAATT
1 TTCGCGACGCGAATT
938926 ACCTATATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (20 bp):
TTCGCGACGCGAATTTGACT
Found at i:941776 original size:2 final size:2
Alignment explanation
Indices: 941771--941799 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
941761 ATTAAAAAAT
941771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
941800 TAAAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:948165 original size:38 final size:38
Alignment explanation
Indices: 948114--948189 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
948104 GTAGTATTTG
948114 TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
1 TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
948152 TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
1 TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
948190 AGATCGGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (38 bp):
TGTACTCACAAAGCGGGTAATGTTACGTGTAATTACAT
Found at i:948269 original size:17 final size:17
Alignment explanation
Indices: 948244--948282 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
948234 ACCCTTAAAA
948244 ATTTAAAATTATCATAT
1 ATTTAAAATTATCATAT
* * *
948261 ATTTTAAATTTTTATAT
1 ATTTAAAATTATCATAT
948278 ATTTA
1 ATTTA
948283 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAAAATTATCATAT
Found at i:948449 original size:37 final size:37
Alignment explanation
Indices: 948366--948455 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
948356 GTCCTACTAG
* * * *
948366 GATTCAAACTCCTAAAAATATGACAGAATTTTGCTAT
1 GATTCAAACTCCTAAAAATAGGACAGAATTCTACAAT
* *
948403 GATTCAAACTCCTAAAAATAGGATAGAGTTCTACAAT
1 GATTCAAACTCCTAAAAATAGGACAGAATTCTACAAT
* *
948440 TATTTAAACTCCTAAA
1 GATTCAAACTCCTAAA
948456 GATATGATCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (37 bp):
GATTCAAACTCCTAAAAATAGGACAGAATTCTACAAT
Found at i:949020 original size:14 final size:14
Alignment explanation
Indices: 948982--949024 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 14
948972 TATATTATTA
948982 TTTTTTATCTATGTT
1 TTTTTTA-CTATGTT
948997 TACTTATTTACTATGTT
1 T--TT-TTTACTATGTT
949014 TTTTTTACTAT
1 TTTTTTACTAT
949025 TTATATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
17 10 0.40
18 4 0.16
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (14 bp):
TTTTTTACTATGTT
Found at i:949177 original size:9 final size:9
Alignment explanation
Indices: 949165--949204 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
949155 TATTTTTATA
949165 TATTTATTT
1 TATTTATTT
949174 TATTTATTT
1 TATTTATTT
**
949183 TATTTATAC
1 TATTTATTT
949192 TATTTA-TT
1 TATTTATTT
949200 TATTT
1 TATTT
949205 TCATTATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (9 bp):
TATTTATTT
Found at i:949184 original size:22 final size:23
Alignment explanation
Indices: 949126--949205 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 23
949116 TACTATTTAG
* *
949126 TATTTTATTT-TATTATACATAC
1 TATTTTATTTATTTTATATATAC
* *
949148 -ATTTT-TATATTTT-TATATATT
1 TATTTTATTTATTTTATATATA-C
*
949169 TATTTTATTTATTTTATTTATAC
1 TATTTTATTTATTTTATATATAC
949192 TA-TTTATTTATTTT
1 TATTTTATTTATTTT
949206 CATTATGTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 7 0.15
21 8 0.17
22 17 0.37
23 9 0.20
24 5 0.11
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTATTTATTTTATATATAC
Found at i:949186 original size:18 final size:17
Alignment explanation
Indices: 949159--949204 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
949149 TTTTTATATT
* **
949159 TTTATATATTTATTTTA
1 TTTATTTATTTATACTA
949176 TTTATTTTATTTATACTA
1 TTTA-TTTATTTATACTA
949194 TTTATTTATTT
1 TTTATTTATTT
949205 TCATTATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTATTTATACTA
Found at i:949201 original size:13 final size:12
Alignment explanation
Indices: 949083--949202 Score: 58
Period size: 13 Copynumber: 10.1 Consensus size: 12
949073 TTAATAATAT
949083 TATATTTATTT-
1 TATATTTATTTA
949094 T-TCATTTATTTA
1 TAT-ATTTATTTA
*
949106 T-TA-TTATTGA
1 TATATTTATTTA
*
949116 TACTATTTAGTATTT
1 TA-TATTTA-T-TTA
949131 TAT-TTTA-TTA
1 TATATTTATTTA
* ** *
949141 TACATACATTTT
1 TATATTTATTTA
949153 TATA-TT-TTTA
1 TATATTTATTTA
949163 TATATTTATTTTA
1 TATATTTA-TTTA
*
949176 TTTATTTTATTTA
1 TATA-TTTATTTA
949189 TACTATTTATTTA
1 TA-TATTTATTTA
949202 T
1 T
949203 TTTCATTATG
Statistics
Matches: 81, Mismatches: 14, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
10 19 0.23
11 14 0.17
12 9 0.11
13 28 0.35
14 8 0.10
15 3 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (12 bp):
TATATTTATTTA
Found at i:952888 original size:7 final size:7
Alignment explanation
Indices: 952876--952951 Score: 55
Period size: 8 Copynumber: 9.7 Consensus size: 7
952866 AATCAAGAAC
952876 AAAAAAG
1 AAAAAAG
952883 AAAAAAAG
1 -AAAAAAG
952891 CAAAAAAG
1 -AAAAAAG
*
952899 CAAAAAAA
1 -AAAAAAG
952907 AAACAAAG
1 AAA-AAAG
952915 AAAAAAG
1 AAAAAAG
952922 AGAAACAAG
1 A-AAA-AAG
952931 AACAAAA-
1 AA-AAAAG
952938 ATCAAAAAG
1 A--AAAAAG
952947 AAAAA
1 AAAAA
952952 GGGACAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
7 13 0.22
8 37 0.64
9 8 0.14
ACGTcount: A:0.80, C:0.08, G:0.11, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:952896 original size:16 final size:16
Alignment explanation
Indices: 952875--952951 Score: 72
Period size: 16 Copynumber: 4.8 Consensus size: 16
952865 CAATCAAGAA
952875 CAAAAAAGAAAAAAAG
1 CAAAAAAGAAAAAAAG
952891 CAAAAAAGCAAAAAAA-
1 CAAAAAAG-AAAAAAAG
952907 -AAACAAAGAAAAAAGAG
1 CAAA-AAAGAAAAAA-AG
* *
952924 -AAACAAGAACAAAAAT
1 CAAAAAAGAA-AAAAAG
952940 C-AAAAAGAAAAA
1 CAAAAAAGAAAAA
952952 GGGACAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
15 12 0.23
16 26 0.50
17 14 0.27
ACGTcount: A:0.79, C:0.09, G:0.10, T:0.01
Consensus pattern (16 bp):
CAAAAAAGAAAAAAAG
Found at i:952925 original size:9 final size:8
Alignment explanation
Indices: 952876--952926 Score: 59
Period size: 8 Copynumber: 6.2 Consensus size: 8
952866 AATCAAGAAC
952876 AAAAAAGA
1 AAAAAAGA
*
952884 AAAAAAGC
1 AAAAAAGA
952892 AAAAAAGCA
1 AAAAAAG-A
952901 AAAAAA-A
1 AAAAAAGA
*
952908 AACAAAGA
1 AAAAAAGA
952916 AAAAAGAGA
1 AAAAA-AGA
952925 AA
1 AA
952927 CAAGAACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 6 0.17
8 19 0.53
9 11 0.31
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:952938 original size:32 final size:32
Alignment explanation
Indices: 952876--952951 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
952866 AATCAAGAAC
952876 AAAAAAGAAAAAAAGCAAAAAAGCAAAAAAA-
1 AAAAAAGAAAAAAAGCAAAAAAGCAAAAAAAT
*
952907 AAACAAAGAAAAAAGAG-AAACAAG-AACAAAAAT
1 AAA-AAAGAAAAAA-AGCAAAAAAGCAA-AAAAAT
*
952940 CAAAAAGAAAAA
1 AAAAAAGAAAAA
952952 GGGACAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 5 0.13
32 30 0.77
33 4 0.10
ACGTcount: A:0.80, C:0.08, G:0.11, T:0.01
Consensus pattern (32 bp):
AAAAAAGAAAAAAAGCAAAAAAGCAAAAAAAT
Found at i:953794 original size:22 final size:22
Alignment explanation
Indices: 953720--953796 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
953710 GCTACCCTAT
* *
953720 CAAACCGTTGAGCATCAAGTGC
1 CAAACCTTTGAGCATCAAATGC
*
953742 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
953764 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
953786 CAAACCTTTGA
1 CAAACCTTTGA
953797 CCAAACATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:954885 original size:106 final size:106
Alignment explanation
Indices: 954597--956396 Score: 2758
Period size: 106 Copynumber: 17.0 Consensus size: 106
954587 ATATCGTGTC
* * * *
954597 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
954662 -ATTTCAGAGCCAATTTC-ACTTAACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
954701 ACTCCAGACAATGCAAGTTCAACTTCACGACG-A-GGATCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
954764 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
954805 ACTCCATACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
954870 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
954911 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
954976 AATTTTAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
955017 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAATAAACAACTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
955082 AATTTCAGATCTAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
955123 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
955188 AATTTCAGAGCCAATTTCAACTTAACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
955229 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
955294 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
955335 ACTCCATACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
955400 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
955441 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTC-ATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
955505 AATTTTAGAGCC-ATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
955545 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT-CC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
955609 AATTTCAGATCTAATTTCAACTTCACAGCTAAGGATA-TGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
955649 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
955714 AATTTCATAGCCAATTTCAACTTCACAAC-AACGATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAA-G--GATATTGG
*
955757 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
955822 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
955863 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
955928 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
955969 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAATAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
956034 AATTTC-GAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
956075 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
956140 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
956181 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
956246 AATTTCAGAGCCAATTTCAACTTCACAACAAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
956287 ACTCAAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
956352 GATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
956393 ACTC
1 ACTC
956397 GGAACAATGC
Statistics
Matches: 1546, Mismatches: 135, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
102 26 0.02
103 18 0.01
104 226 0.15
105 82 0.05
106 1093 0.71
107 5 0.00
108 94 0.06
109 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:957532 original size:29 final size:28
Alignment explanation
Indices: 957482--957558 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 28
957472 TTCTTTGCGT
* *
957482 TATATTATATTATTTTCCTATTATTATA
1 TATATTATATTATATTACTATTATTATA
* *
957510 TATATATATATTATATTATTATTTTTATA
1 TATAT-TATATTATATTACTATTATTATA
*
957539 TATGTT-TACTTAT-TTACTAT
1 TATATTATA-TTATATTACTAT
957559 GTTTTTTACT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 8 0.20
28 10 0.24
29 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (28 bp):
TATATTATATTATATTACTATTATTATA
Found at i:973279 original size:2 final size:2
Alignment explanation
Indices: 973272--973304 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
973262 GCTAAAATCC
973272 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
973305 TTGTTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:976138 original size:33 final size:33
Alignment explanation
Indices: 976099--976188 Score: 171
Period size: 33 Copynumber: 2.7 Consensus size: 33
976089 ATGTGGTTTG
976099 TTTATTTTCTATTTGTCTATTCCTGATTCTTGA
1 TTTATTTTCTATTTGTCTATTCCTGATTCTTGA
*
976132 TTTATTTTCTATTTCTCTATTCCTGATTCTTGA
1 TTTATTTTCTATTTGTCTATTCCTGATTCTTGA
976165 TTTATTTTCTATTTGTCTATTCCT
1 TTTATTTTCTATTTGTCTATTCCT
976189 TCTCTGAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.14, C:0.17, G:0.07, T:0.62
Consensus pattern (33 bp):
TTTATTTTCTATTTGTCTATTCCTGATTCTTGA
Found at i:976153 original size:26 final size:26
Alignment explanation
Indices: 976108--976159 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
976098 GTTTATTTTC
*
976108 TATTTGTCTATTCCTGATTCTTGATT
1 TATTTGTCTATTCCTGATTCCTGATT
976134 TATTT-TCTATTTCTCT-ATTCCTGATT
1 TATTTGTCTA-TTC-CTGATTCCTGATT
976160 CTTGATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 17 0.74
27 2 0.09
ACGTcount: A:0.15, C:0.17, G:0.08, T:0.60
Consensus pattern (26 bp):
TATTTGTCTATTCCTGATTCCTGATT
Found at i:980454 original size:20 final size:21
Alignment explanation
Indices: 980431--980475 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
980421 TGGGTACCGA
* *
980431 ATACTATAA-GGTCGGTATCG
1 ATACTAAAATGGTCAGTATCG
*
980451 ATACTAAAATGGTTAGTATCG
1 ATACTAAAATGGTCAGTATCG
980472 ATAC
1 ATAC
980476 CATCGTACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (21 bp):
ATACTAAAATGGTCAGTATCG
Found at i:982167 original size:16 final size:16
Alignment explanation
Indices: 982146--982190 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
982136 ACAGTTTTTC
*
982146 TTCTTCTTCCTTCTTT
1 TTCTTCTTCCTTCTTG
982162 TTCTTCTT-CTTCATTG
1 TTCTTCTTCCTTC-TTG
982178 TTC--CTTCCTTCTT
1 TTCTTCTTCCTTCTT
982191 CTCACAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 13 0.50
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.64
Consensus pattern (16 bp):
TTCTTCTTCCTTCTTG
Found at i:983961 original size:11 final size:11
Alignment explanation
Indices: 983945--983983 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
983935 TCGGTTGTGA
983945 GAAGAAGGAAG
1 GAAGAAGGAAG
983956 GAAGAAGGAAG
1 GAAGAAGGAAG
* *
983967 AAAGGAGGAA-
1 GAAGAAGGAAG
983977 GAAGAAG
1 GAAGAAG
983984 AAACTGTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (11 bp):
GAAGAAGGAAG
Found at i:984316 original size:16 final size:17
Alignment explanation
Indices: 984295--984328 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
984285 TTTTATTATT
*
984295 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
984311 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
984328 A
1 A
984329 AAACAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:992345 original size:20 final size:19
Alignment explanation
Indices: 992320--992361 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
992310 TAAGTGTAGA
992320 TAATTTA-AATACTATATTTT
1 TAATTTACAATA-TA-ATTTT
992340 TAATTTACAATATAATTTT
1 TAATTTACAATATAATTTT
992359 TAA
1 TAA
992362 AATGAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATTTACAATATAATTTT
Found at i:992422 original size:19 final size:19
Alignment explanation
Indices: 992398--992435 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
992388 AACGCAATCT
992398 CAACTAGCTAAATTTTAAA
1 CAACTAGCTAAATTTTAAA
992417 CAACTAGCTAAATTTTAAA
1 CAACTAGCTAAATTTTAAA
992436 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
CAACTAGCTAAATTTTAAA
Found at i:995372 original size:109 final size:110
Alignment explanation
Indices: 995182--995400 Score: 406
Period size: 109 Copynumber: 2.0 Consensus size: 110
995172 CTAGTAGTAT
995182 CAGACTAACAACAACAACCAATAACACCTACCAAGTGGAAGATAGGTAGGTACTAATTTGTTCTC
1 CAGACTAACAACAACAACCAATAACACCTACCAAGTGGAAGATAGGTAGGTACTAATTTGTTCTC
995247 AGTGTTTGATATCCGAGTTTCTCATGC-T-TTTGGTATCATATTC
66 AGTGTTTGATATCCGAGTTTCTCATGCTTGTTTGGTATCATATTC
*
995290 CAGACTAACAACAACAACCAATAACACCTCTCCAAGTGGAAGATAGGTAGGTACTAATTTGTTCT
1 CAGACTAACAACAACAACCAATAACACCT-ACCAAGTGGAAGATAGGTAGGTACTAATTTGTTCT
995355 CAGTGTTTGATATCCGAGTTTCTCATGCTTGTTTGGTATCATATTC
65 CAGTGTTTGATATCCGAGTTTCTCATGCTTGTTTGGTATCATATTC
995401 ATGGACGGTT
Statistics
Matches: 107, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
108 29 0.27
109 62 0.58
110 1 0.01
111 15 0.14
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (110 bp):
CAGACTAACAACAACAACCAATAACACCTACCAAGTGGAAGATAGGTAGGTACTAATTTGTTCTC
AGTGTTTGATATCCGAGTTTCTCATGCTTGTTTGGTATCATATTC
Found at i:995905 original size:73 final size:73
Alignment explanation
Indices: 995786--995936 Score: 286
Period size: 73 Copynumber: 2.1 Consensus size: 73
995776 TTTCATAATT
995786 TTAATCAAAAATTAAAACATTGAATTAAAATATTTTAAAAAAATACACAATAAAGCGTA-ATTTT
1 TTAATCAAAAATTAAAACATTGAATTAAAATATTTTAAAAAAATACACAAT-AAGCGTATATTTT
995850 GATAAAAGA
65 GATAAAAGA
995859 TTAATCAAAAATTAAAACATTGAATTAAAATATTTTAAAAAAATACACAATAAGCGTATATTTTG
1 TTAATCAAAAATTAAAACATTGAATTAAAATATTTTAAAAAAATACACAATAAGCGTATATTTTG
995924 ATAAAAGA
66 ATAAAAGA
995932 TTAAT
1 TTAAT
995937 TTTAATATTA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
72 7 0.09
73 70 0.91
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (73 bp):
TTAATCAAAAATTAAAACATTGAATTAAAATATTTTAAAAAAATACACAATAAGCGTATATTTTG
ATAAAAGA
Found at i:997216 original size:13 final size:13
Alignment explanation
Indices: 997198--997222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
997188 TCAATTCGTC
997198 ACACGTATGTATA
1 ACACGTATGTATA
997211 ACACGTATGTAT
1 ACACGTATGTAT
997223 TTTAAGAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ACACGTATGTATA
Found at i:998803 original size:39 final size:39
Alignment explanation
Indices: 998760--998881 Score: 217
Period size: 39 Copynumber: 3.1 Consensus size: 39
998750 CTCATGATTT
**
998760 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
998799 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
*
998838 TATCAAAGTCATGATAAACATTATCATACATAATAGTCA
1 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
998877 TATCA
1 TATCA
998882 TATACTTTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (39 bp):
TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
Found at i:999073 original size:18 final size:17
Alignment explanation
Indices: 999032--999086 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
999022 AACTCATAAT
*
999032 TTATTTCAGATTCATAAC
1 TTATTTCA-ATTCATAGC
*
999050 TAATTTCATATTCATAGC
1 TTATTTCA-ATTCATAGC
999068 TTATTTTCAAGTTCATAGC
1 TTA-TTTCAA-TTCATAGC
999087 CCAATGCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 18 0.58
19 13 0.42
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.45
Consensus pattern (17 bp):
TTATTTCAATTCATAGC
Found at i:1001805 original size:30 final size:29
Alignment explanation
Indices: 1001762--1001828 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
1001752 TCAAAACACA
*
1001762 TAAATTTTAAAAATTACACTTTTGGTCTC
1 TAAATTTTAAAAATTACACTTTTAGTCTC
* * *
1001791 TAAATATTTGAAAATTACATTTTTAGTCTT
1 TAAAT-TTTAAAAATTACACTTTTAGTCTC
*
1001821 TTAATTTT
1 TAAATTTT
1001829 TCCAAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (29 bp):
TAAATTTTAAAAATTACACTTTTAGTCTC
Found at i:1004050 original size:26 final size:26
Alignment explanation
Indices: 1004014--1004065 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1004004 ACTTGTCTCT
1004014 CCAAAGATCATAAAATCATCCGCAAA
1 CCAAAGATCATAAAATCATCCGCAAA
*
1004040 CCAAAGATCATACAATCATCCGCAAA
1 CCAAAGATCATAAAATCATCCGCAAA
1004066 AAACAGGTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.29, G:0.08, T:0.15
Consensus pattern (26 bp):
CCAAAGATCATAAAATCATCCGCAAA
Found at i:1008838 original size:19 final size:18
Alignment explanation
Indices: 1008804--1008849 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
1008794 TTCTGTAATA
* *
1008804 ATTTATTTATATTTATTT
1 ATTTATTTAAATTTATTG
1008822 ATTTATTTCAAATTTATTG
1 ATTTATTT-AAATTTATTG
1008841 ATTTATTTA
1 ATTTATTTA
1008850 TTTCGAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTATTTAAATTTATTG
Found at i:1008867 original size:23 final size:23
Alignment explanation
Indices: 1008813--1008878 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
1008803 AATTTATTTA
*
1008813 TATTTATTTATTTATTTCAAATT
1 TATTTATTTATTTATTTCGAATT
*
1008836 TATTGATTTATTTATTTCGAATCT
1 TATTTATTTATTTATTTCGAAT-T
*
1008860 T-TTTATTTAATTA-TTCGAA
1 TATTTATTTATTTATTTCGAA
1008879 GGGATTTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 6 0.16
23 30 0.79
24 2 0.05
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.61
Consensus pattern (23 bp):
TATTTATTTATTTATTTCGAATT
Found at i:1008868 original size:4 final size:4
Alignment explanation
Indices: 1008741--1008852 Score: 59
Period size: 4 Copynumber: 26.8 Consensus size: 4
1008731 GGAGGTAATT
* * *
1008741 TTTA TTTA TTTA TTTA CTTTGAA TTTT TTTAA TTT- TTTGA GTAA TTTA
1 TTTA TTTA TTTA TTTA -TTT--A TTTA TTT-A TTTA TTT-A TTTA TTTA
* * * *
1008789 TTTA TTTC TGTA ATAA TTTA TTTA --TA TTTA TTTA TTTA TTTCAAA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT---A TTTA
*
1008838 TTGA TTTA TTTA TTT
1 TTTA TTTA TTTA TTT
1008853 CGAATCTTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 22
0.68 0.13 0.18
Matches are distributed among these distances:
2 2 0.02
3 3 0.04
4 61 0.75
5 7 0.09
6 3 0.04
7 5 0.06
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:1011055 original size:28 final size:27
Alignment explanation
Indices: 1010997--1011056 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
1010987 AAATTTGTAA
*
1010997 TTTTTTAGTTAATCAAACTCTATTTTC
1 TTTTTTAGTTAATCAAACTCCATTTTC
**
1011024 TTTTTTAGTTAATTGAACTCCATTTTC
1 TTTTTTAGTTAATCAAACTCCATTTTC
1011051 TTTTTT
1 TTTTTT
1011057 TAAATAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (27 bp):
TTTTTTAGTTAATCAAACTCCATTTTC
Found at i:1011141 original size:17 final size:17
Alignment explanation
Indices: 1011095--1011180 Score: 118
Period size: 18 Copynumber: 4.9 Consensus size: 17
1011085 TTTTTTTTAA
1011095 AATTTGTTTAAATTATT
1 AATTTGTTTAAATTATT
**
1011112 AATTAACTTTAAATTATT
1 AATT-TGTTTAAATTATT
1011130 AATTTGTTTAAATTATT
1 AATTTGTTTAAATTATT
*
1011147 AATTAAGTTTAAATTATT
1 AATT-TGTTTAAATTATT
*
1011165 AATTTGTTTAAGTTAT
1 AATTTGTTTAAATTAT
1011181 CCTTGAACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
17 29 0.48
18 31 0.52
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (17 bp):
AATTTGTTTAAATTATT
Found at i:1011141 original size:35 final size:35
Alignment explanation
Indices: 1011095--1011180 Score: 154
Period size: 35 Copynumber: 2.5 Consensus size: 35
1011085 TTTTTTTTAA
1011095 AATTTGTTTAAATTATTAATTAACTTTAAATTATT
1 AATTTGTTTAAATTATTAATTAACTTTAAATTATT
*
1011130 AATTTGTTTAAATTATTAATTAAGTTTAAATTATT
1 AATTTGTTTAAATTATTAATTAACTTTAAATTATT
*
1011165 AATTTGTTTAAGTTAT
1 AATTTGTTTAAATTAT
1011181 CCTTGAACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (35 bp):
AATTTGTTTAAATTATTAATTAACTTTAAATTATT
Found at i:1022835 original size:21 final size:21
Alignment explanation
Indices: 1022811--1022863 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1022801 GGAGAGGCAT
*
1022811 TATCGATACTCTTCCCCTCAA
1 TATCGATACTCTCCCCCTCAA
1022832 TATCGATACTCTCCCCCTCAA
1 TATCGATACTCTCCCCCTCAA
*
1022853 TATTGATACTC
1 TATCGATACTC
1022864 CCTACTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.36, G:0.06, T:0.34
Consensus pattern (21 bp):
TATCGATACTCTCCCCCTCAA
Found at i:1023014 original size:2 final size:2
Alignment explanation
Indices: 1023007--1023041 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1022997 TAAAAATTTA
1023007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1023042 ACAAGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1023520 original size:21 final size:21
Alignment explanation
Indices: 1023494--1023555 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1023484 AATATGATAG
1023494 ATAAACTATCATATCAATATC
1 ATAAACTATCATATCAATATC
* *
1023515 ATAAACTGTTATATCAATATC
1 ATAAACTATCATATCAATATC
* *
1023536 ATACACTGA-CATATTAATAT
1 ATAAACT-ATCATATCAATAT
1023556 TGTAACAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.35
Consensus pattern (21 bp):
ATAAACTATCATATCAATATC
Found at i:1023970 original size:20 final size:20
Alignment explanation
Indices: 1023945--1023999 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1023935 TTAGTTCATG
1023945 GAATATAAGATTATCGGTGA
1 GAATATAAGATTATCGGTGA
*
1023965 GAATATAAGATTATCGGTGG
1 GAATATAAGATTATCGGTGA
* *
1023985 GAATGTAAAATTATC
1 GAATATAAGATTATC
1024000 AGGAAATATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (20 bp):
GAATATAAGATTATCGGTGA
Found at i:1024463 original size:21 final size:21
Alignment explanation
Indices: 1024434--1024486 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1024424 ATTCTATATA
1024434 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
1024455 TCGCGTTGCGATTTTCTTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1024476 TCGCAATGCGA
1 TCGCATTGCGA
1024487 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1024501 original size:20 final size:20
Alignment explanation
Indices: 1024476--1024607 Score: 151
Period size: 20 Copynumber: 6.7 Consensus size: 20
1024466 TTTTCTTAAT
1024476 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1024496 TCGCAACGCGAATTTGAAAAA
1 TCGCAATGCGAATACG-TAAA
* *
1024517 TCGCAATGTGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1024537 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1024557 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1024577 TCGCATTGCG-ATA-ATAAA
1 TCGCAATGCGAATACGTAAA
1024595 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1024608 CTGGCTATCG
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.14
19 5 0.05
20 61 0.66
21 14 0.15
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1024522 original size:41 final size:40
Alignment explanation
Indices: 1024476--1024581 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 40
1024466 TTTTCTTAAT
* **
1024476 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGAAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATACG-AAAA
* * * *
1024517 TCGCAATGTGATTACGTAAATCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATACGAAAA
*
1024557 TCGCAATGCAAATACGTAAATCGCA
1 TCGCAATGCGAATACGTAAATCGCA
1024582 TTGCGATAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 25 0.45
41 30 0.55
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCAAATACGAAAA
Found at i:1024780 original size:22 final size:22
Alignment explanation
Indices: 1024755--1024816 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
1024745 ACATCCGTCC
*
1024755 CCATCTCCGACGAAATTAGTCT
1 CCATCTCCGACGAAATCAGTCT
* *
1024777 CCATCTCCAACGATATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
1024799 CCATCTCCGACGAAATCA
1 CCATCTCCGACGAAATCA
1024817 TTCACGGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.29, C:0.35, G:0.11, T:0.24
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:1025050 original size:20 final size:20
Alignment explanation
Indices: 1024995--1025058 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1024985 GAAATTCAGT
* *
1024995 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGATTCAC
*
1025015 GTTGCGATAGTCAGATTCAC
1 ATTGCGATAGTCAGATTCAC
*
1025035 ATTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGATTCAC
1025055 ATTG
1 ATTG
1025059 ATATTTACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (20 bp):
ATTGCGATAGTCAGATTCAC
Found at i:1025072 original size:20 final size:20
Alignment explanation
Indices: 1025049--1025162 Score: 147
Period size: 20 Copynumber: 5.7 Consensus size: 20
1025039 CGATAGTCAG
** *
1025049 ATTCGCATTGATATTTACAT
1 ATTCGCATTGCGATTTACGT
1025069 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1025089 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1025109 AATCGCATTGCGATTTTTCAA
1 ATTCGCATTGCGA-TTTACGT
*
1025130 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1025150 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1025163 ATTAGGAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 65 0.81
21 15 0.19
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1025078 original size:40 final size:38
Alignment explanation
Indices: 1025029--1025162 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 38
1025019 CGATAGTCAG
* ** *
1025029 ATTCACATTGCGATAGTCAGATTCGCATTGATATTTACAT
1 ATTCGCATTGCGAT--TCAGATTCGCATTGCGATTTACGT
*
1025069 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTCA-G-ATTCGCATTGCGATTTACGT
* * *
1025109 AATCGCATTGCGATTTTTCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGA---TTCAGATTCGCATTGCGATTTACGT
1025150 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1025163 ATTAGGAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 42 0.53
41 31 0.39
43 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (38 bp):
ATTCGCATTGCGATTCAGATTCGCATTGCGATTTACGT
Found at i:1025146 original size:41 final size:40
Alignment explanation
Indices: 1025049--1025162 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 40
1025039 CGATAGTCAG
** * **
1025049 ATTCGCATTGATATTTACATATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACAA
* *
1025089 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTTCAA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA-TTTACAA
*
1025130 ATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
1025163 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
40 29 0.45
41 35 0.55
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACAA
Found at i:1025183 original size:21 final size:21
Alignment explanation
Indices: 1025159--1025204 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1025149 TATTCGCATT
1025159 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1025180 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1025201 GCGA
1 GCGA
1025205 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1031288 original size:60 final size:60
Alignment explanation
Indices: 1031198--1031323 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
1031188 AAAAAGGATC
* * ** *
1031198 AATTTAGAATGAAGGTCATAGTTTGGGGATGAAATTGAAATATTCAAAAATTTAAGGACT
1 AATTTAGAATGAAGGTCAAAATTTAAGGATGAAATTAAAATATTCAAAAATTTAAGGACT
* * * *
1031258 AATTTAGAATGATA-GTCAAAATTTAAGGATGAAATTAAAATATTTAAAAGTTTAGGGATT
1 AATTTAGAATGA-AGGTCAAAATTTAAGGATGAAATTAAAATATTCAAAAATTTAAGGACT
1031318 AATTTA
1 AATTTA
1031324 AAGTGAATGT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 55 0.98
61 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.34
Consensus pattern (60 bp):
AATTTAGAATGAAGGTCAAAATTTAAGGATGAAATTAAAATATTCAAAAATTTAAGGACT
Found at i:1031650 original size:14 final size:14
Alignment explanation
Indices: 1031626--1031694 Score: 92
Period size: 14 Copynumber: 5.2 Consensus size: 14
1031616 GTTCGTGAAT
1031626 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
* *
1031640 GTACAGTTATGTTC
1 GTTCGGTTATGTTC
1031654 G-T---TTATGTTC
1 GTTCGGTTATGTTC
1031664 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
1031678 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
1031692 GTT
1 GTT
1031695 TATGTTCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.19
11 1 0.02
14 38 0.79
ACGTcount: A:0.10, C:0.13, G:0.26, T:0.51
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:1031676 original size:38 final size:38
Alignment explanation
Indices: 1031626--1031701 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
1031616 GTTCGTGAAT
1031626 GTTCGGTTATGTTCGTACAGTTATGTTCGTTTATGTTC
1 GTTCGGTTATGTTCGTACAGTTATGTTCGTTTATGTTC
* *
1031664 GTTCGGTTATGTTCGTTCGGTTATGTTCGTTTATGTTC
1 GTTCGGTTATGTTCGTACAGTTATGTTCGTTTATGTTC
1031702 ATTCATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.11, C:0.13, G:0.25, T:0.51
Consensus pattern (38 bp):
GTTCGGTTATGTTCGTACAGTTATGTTCGTTTATGTTC
Found at i:1031679 original size:24 final size:24
Alignment explanation
Indices: 1031624--1031680 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1031614 ACGTTCGTGA
*
1031624 ATGTTCGGTTATGTTCGTACAGTT
1 ATGTTCGTTTATGTTCGTACAGTT
* *
1031648 ATGTTCGTTTATGTTCGTTCGGTT
1 ATGTTCGTTTATGTTCGTACAGTT
1031672 ATGTTCGTT
1 ATGTTCGTT
1031681 CGGTTATGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.51
Consensus pattern (24 bp):
ATGTTCGTTTATGTTCGTACAGTT
Found at i:1031711 original size:24 final size:24
Alignment explanation
Indices: 1031664--1031714 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1031654 GTTTATGTTC
* *
1031664 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
1031688 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
1031712 GTT
1 GTT
1031715 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:1031712 original size:38 final size:38
Alignment explanation
Indices: 1031631--1031714 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 38
1031621 TGAATGTTCG
* *
1031631 GTTATGTTCGTACAGTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTACAGTTATGTTCGTTTATGTTCATTCA
* *
1031669 GTTATGTTCGTTCGGTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTACAGTTATGTTCGTTTATGTTCATTCA
*
1031707 TTTATGTT
1 GTTATGTT
1031715 TAACCCAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.13, C:0.12, G:0.21, T:0.54
Consensus pattern (38 bp):
GTTATGTTCGTACAGTTATGTTCGTTTATGTTCATTCA
Found at i:1032657 original size:16 final size:16
Alignment explanation
Indices: 1032636--1032699 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
1032626 GGTCTCCAAC
1032636 GTTTATGTTCGTTTAT
1 GTTTATGTTCGTTTAT
*
1032652 GTTTATGTTCATGTTCA-
1 GTTTATGTTC--GTTTAT
* *
1032669 -TTTATGTCCGTGTT-C
1 GTTTATGTTCGT-TTAT
1032684 GTTTATGTTCGTTTAT
1 GTTTATGTTCGTTTAT
1032700 TTATTAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
14 2 0.05
15 3 0.08
16 28 0.76
18 4 0.11
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.58
Consensus pattern (16 bp):
GTTTATGTTCGTTTAT
Found at i:1032785 original size:16 final size:16
Alignment explanation
Indices: 1032764--1032796 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1032754 AAAAAAAATT
1032764 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
*
1032780 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
1032796 T
1 T
1032797 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:1045722 original size:30 final size:30
Alignment explanation
Indices: 1045686--1045749 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
1045676 AATAAAAAGT
*
1045686 ACATTTGTAAGCTAACAAGATCTGCAAATA
1 ACATTTGTAAGCTAACAAGACCTGCAAATA
1045716 ACATTTGTAAGCTAACAAGACCTGCAAATA
1 ACATTTGTAAGCTAACAAGACCTGCAAATA
1045746 ACAT
1 ACAT
1045750 ATATAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (30 bp):
ACATTTGTAAGCTAACAAGACCTGCAAATA
Found at i:1050070 original size:2 final size:2
Alignment explanation
Indices: 1050063--1050098 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1050053 AACTTGGGTA
1050063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1050099 GAGTTAGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1051245 original size:21 final size:17
Alignment explanation
Indices: 1051203--1051239 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1051193 CATCGTATTA
1051203 ATTGAAAGATGTTAAAC
1 ATTGAAAGATGTTAAAC
1051220 ATTGAAAGATGTTAAAC
1 ATTGAAAGATGTTAAAC
1051237 ATT
1 ATT
1051240 CATTGAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (17 bp):
ATTGAAAGATGTTAAAC
Found at i:1060437 original size:24 final size:26
Alignment explanation
Indices: 1060390--1060440 Score: 88
Period size: 24 Copynumber: 2.0 Consensus size: 26
1060380 TATGTGATTT
1060390 TCTTGGTTTTCAAAGAAACAAAATTG
1 TCTTGGTTTTCAAAGAAACAAAATTG
1060416 TCTTGGTTTTC-AA-AAACAAAATTG
1 TCTTGGTTTTCAAAGAAACAAAATTG
1060440 T
1 T
1060441 GTAGCTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 12 0.48
25 2 0.08
26 11 0.44
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (26 bp):
TCTTGGTTTTCAAAGAAACAAAATTG
Found at i:1062099 original size:61 final size:62
Alignment explanation
Indices: 1062015--1062137 Score: 223
Period size: 61 Copynumber: 2.0 Consensus size: 62
1062005 TGAAAAACAA
1062015 ATTTTAGGTTCTCGTATAAAAGAAGGGATAGTGCGAGTGTCTTAGACA-TCATGAACGTTTT
1 ATTTTAGGTTCTCGTATAAAAGAAGGGATAGTGCGAGTGTCTTAGACATTCATGAACGTTTT
1062076 ATTTTAGGTTCTCGT-TATAAAGAAGGGATAGTGCGAGTGTCTTAGACATTCATGAACGTTTT
1 ATTTTAGGTTCTCGTATA-AAAGAAGGGATAGTGCGAGTGTCTTAGACATTCATGAACGTTTT
1062138 CTTCATCTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
60 2 0.03
61 45 0.75
62 13 0.22
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.36
Consensus pattern (62 bp):
ATTTTAGGTTCTCGTATAAAAGAAGGGATAGTGCGAGTGTCTTAGACATTCATGAACGTTTT
Found at i:1063367 original size:21 final size:23
Alignment explanation
Indices: 1063341--1063382 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1063331 AAATTAAGAT
1063341 AAATGAATTT-TAAG-ATTTTTC
1 AAATGAATTTCTAAGTATTTTTC
*
1063362 AAATGATTTTCTAAGTATTTT
1 AAATGAATTTCTAAGTATTTT
1063383 CATATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (23 bp):
AAATGAATTTCTAAGTATTTTTC
Found at i:1063735 original size:19 final size:20
Alignment explanation
Indices: 1063687--1063763 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
1063677 TTTACACTTA
1063687 GGGAACCGATTCCCCTCAAG
1 GGGAACCGATTCCCCTCAAG
*
1063707 GGGAACCGATTCTCCTCAA-
1 GGGAACCGATTCCCCTCAAG
*
1063726 GGGTACCGATTCCCCTCAAG
1 GGGAACCGATTCCCCTCAAG
*
1063746 GGGTACCGATTCCCCTCA
1 GGGAACCGATTCCCCTCA
1063764 CGCTTCAACT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
19 17 0.32
20 36 0.68
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.19
Consensus pattern (20 bp):
GGGAACCGATTCCCCTCAAG
Found at i:1063745 original size:39 final size:39
Alignment explanation
Indices: 1063686--1063763 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
1063676 TTTTACACTT
*
1063686 AGGGAACCGATTCCCCTCAAGGGGAACCGATTCTCCTCA
1 AGGGAACCGATTCCCCTCAAGGGGAACCGATTCCCCTCA
* *
1063725 AGGGTACCGATTCCCCTCAAGGGGTACCGATTCCCCTCA
1 AGGGAACCGATTCCCCTCAAGGGGAACCGATTCCCCTCA
1063764 CGCTTCAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (39 bp):
AGGGAACCGATTCCCCTCAAGGGGAACCGATTCCCCTCA
Found at i:1066835 original size:32 final size:34
Alignment explanation
Indices: 1066786--1066874 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 34
1066776 TCATATATTT
* *
1066786 TATAACATATACA-ATAATCAT-T-AACACATACA
1 TATATCATAT-CATATAATCATATAAAAACATACA
*
1066818 TATATCATATCATATAATTCATATCAAAAACATATA
1 TATATCATATCATATAA-TCATAT-AAAAACATACA
1066854 TATAT-ATAT-ATATAAT-ATATA
1 TATATCATATCATATAATCATATA
1066875 TATATATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
31 3 0.06
32 17 0.35
33 5 0.10
34 7 0.14
35 4 0.08
36 13 0.27
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (34 bp):
TATATCATATCATATAATCATATAAAAACATACA
Found at i:1066856 original size:2 final size:2
Alignment explanation
Indices: 1066849--1066931 Score: 159
Period size: 2 Copynumber: 42.0 Consensus size: 2
1066839 TATCAAAAAC
1066849 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1066890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1066932 CATACATTGT
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1067916 original size:24 final size:20
Alignment explanation
Indices: 1067862--1067899 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1067852 TTCCCCTTGA
1067862 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
1067882 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
1067900 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:1068026 original size:43 final size:45
Alignment explanation
Indices: 1067926--1068027 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 45
1067916 TCACTACCCA
* * *
1067926 TGCATCGATACACCAATCACCTTCGATGTTTTTCATTTTAAGGGCG
1 TGCATCGATACACCAATCACATTCGATGTTTTTCA-TTTAAGAGAG
* *
1067972 TGCATCAATACACTAAT-ACATTCGATGTTTCTTC-TTTAA-AGAG
1 TGCATCGATACACCAATCACATTCGATGTTT-TTCATTTAAGAGAG
1068015 TGCATCGATACAC
1 TGCATCGATACAC
1068028 ATTGAATGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 14 0.29
44 5 0.10
45 12 0.24
46 18 0.37
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (45 bp):
TGCATCGATACACCAATCACATTCGATGTTTTTCATTTAAGAGAG
Found at i:1068739 original size:24 final size:24
Alignment explanation
Indices: 1068706--1068752 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1068696 CAAGGGGAGA
1068706 AAAATTACACGAAAAAATAGCGAGG
1 AAAATTACACGAAAAAATA-CGAGG
*
1068731 AAAA-TACACGAGAAAATACGAG
1 AAAATTACACGAAAAAATACGAG
1068753 AGATTACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.57, C:0.13, G:0.19, T:0.11
Consensus pattern (24 bp):
AAAATTACACGAAAAAATACGAGG
Found at i:1072176 original size:20 final size:20
Alignment explanation
Indices: 1072148--1072186 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1072138 CAAGAAATTA
1072148 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
1072168 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1072187 CCCTTGAAAA
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:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:1081596 original size:17 final size:17
Alignment explanation
Indices: 1081549--1081587 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1081539 TCGATCGGTT
*
1081549 TAAATA-ATTTAATT-A
1 TAAATATATTTATTTAA
1081564 TAAATATATTTATTTAA
1 TAAATATATTTATTTAA
1081581 TAAATAT
1 TAAATAT
1081588 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 7 0.33
17 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATATATTTATTTAA
Found at i:1082348 original size:30 final size:30
Alignment explanation
Indices: 1082312--1082413 Score: 129
Period size: 30 Copynumber: 3.5 Consensus size: 30
1082302 ATTTTTTATT
* *
1082312 TAAGTACCTAAAGTTTTTTTTTTGTCAAAA
1 TAAGTACCTAAAGTTATTTTTTGGTCAAAA
* *
1082342 TAAGTA-CTAAAATTACCTTTTTGGTCAAAA
1 TAAGTACCTAAAGTTA-TTTTTTGGTCAAAA
1082372 TAAGTACCTAAAG-TATTTTTTGGTCAAAA
1 TAAGTACCTAAAGTTATTTTTTGGTCAAAA
*
1082401 -AAGTACTTAAAGT
1 TAAGTACCTAAAGT
1082414 ATTCAATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.18
29 20 0.32
30 26 0.42
31 5 0.08
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (30 bp):
TAAGTACCTAAAGTTATTTTTTGGTCAAAA
Found at i:1084570 original size:25 final size:27
Alignment explanation
Indices: 1084542--1084591 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
1084532 TCAAAATATT
*
1084542 ATACTTAAATTAAT-TA-ATATATACC
1 ATACATAAATTAATATATATATATACC
*
1084567 ATACATAAATTTATATATATATATA
1 ATACATAAATTAATATATATATATA
1084592 TTAAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 2 0.10
27 7 0.33
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (27 bp):
ATACATAAATTAATATATATATATACC
Found at i:1085846 original size:21 final size:21
Alignment explanation
Indices: 1085820--1085869 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 21
1085810 AGATATTTGT
1085820 AATATTTGATATTAAATCTAG
1 AATATTTGATATTAAATCTAG
1085841 AATATTTGATATTAAATCTAG
1 AATATTTGATATTAAATCTAG
1085862 AATTATTT
1 AA-TATTT
1085870 ATAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (21 bp):
AATATTTGATATTAAATCTAG
Found at i:1092062 original size:19 final size:19
Alignment explanation
Indices: 1092038--1092079 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1092028 ATGACCAACA
1092038 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
1092057 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
1092076 AAAT
1 AAAT
1092080 TACAACGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:1092089 original size:19 final size:19
Alignment explanation
Indices: 1092038--1092092 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
1092028 ATGACCAACA
* *
1092038 AAATCGCAATGCGATCTCT
1 AAATCACAACGCGATCTCT
* *
1092057 AAATCGCAATGCGATCTCT
1 AAATCACAACGCGATCTCT
*
1092076 AAATTACAACGCGATCT
1 AAATCACAACGCGATCT
1092093 TCAGTATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (19 bp):
AAATCACAACGCGATCTCT
Found at i:1092142 original size:20 final size:20
Alignment explanation
Indices: 1092119--1092207 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
1092109 GTTTCCAGAT
*
1092119 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * *
1092139 TCGCAATGCGAATATAT-A-AA
1 TCGCAACGCG-AT-TCTGACTA
1092159 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
1092179 TCGCAACTCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
1092199 TCGCAACGC
1 TCGCAACGC
1092208 TGAATTTCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
18 2 0.04
19 3 0.05
20 46 0.82
21 3 0.05
22 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1093300 original size:14 final size:14
Alignment explanation
Indices: 1093271--1093307 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1093261 AAAGGAAGAA
1093271 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1093286 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1093300 GAAGAAAA
1 GAAGAAAA
1093308 TACCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1095808 original size:20 final size:21
Alignment explanation
Indices: 1095785--1095841 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
1095775 TGAAACTTAA
1095785 AATCGCAACACGAAAATGA-T
1 AATCGCAACACGAAAATGACT
1095805 AATCGCAACACGAAAATGACT
1 AATCGCAACACGAAAATGACT
1095826 -ATCGCAACGA-GAAAAT
1 AATCGCAAC-ACGAAAAT
1095842 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.49, C:0.21, G:0.16, T:0.14
Consensus pattern (21 bp):
AATCGCAACACGAAAATGACT
Found at i:1096284 original size:22 final size:22
Alignment explanation
Indices: 1096256--1096310 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1096246 GGATATAGAC
1096256 GGATTTCGCCGGAGATGGGGAT
1 GGATTTCGCCGGAGATGGGGAT
*
1096278 GGATTTCGTCGGAGATGGGGAT
1 GGATTTCGCCGGAGATGGGGAT
*
1096300 GGATGTCGCCG
1 GGATTTCGCCG
1096311 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.16, C:0.15, G:0.45, T:0.24
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAT
Found at i:1098481 original size:15 final size:15
Alignment explanation
Indices: 1098461--1098502 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
1098451 GCGACCAAGC
1098461 AGGTCGCCATGCAGA
1 AGGTCGCCATGCAGA
1098476 AGGTCGCCATGCAGA
1 AGGTCGCCATGCAGA
1098491 AGGTCGCCATGC
1 AGGTCGCCATGC
1098503 GTTCTTCACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.24, C:0.29, G:0.33, T:0.14
Consensus pattern (15 bp):
AGGTCGCCATGCAGA
Found at i:1104786 original size:33 final size:33
Alignment explanation
Indices: 1104749--1104816 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1104739 TTACATGCAA
1104749 CATAATGTCCCAGGAAACATTGAAATCCTTGAC
1 CATAATGTCCCAGGAAACATTGAAATCCTTGAC
1104782 CATAATGTCCCAGGAAACATTGAAATCCTTGAC
1 CATAATGTCCCAGGAAACATTGAAATCCTTGAC
1104815 CA
1 CA
1104817 CCTTTTCGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.24
Consensus pattern (33 bp):
CATAATGTCCCAGGAAACATTGAAATCCTTGAC
Found at i:1107192 original size:22 final size:20
Alignment explanation
Indices: 1107167--1107237 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 20
1107157 TTTTATTTAG
*
1107167 TATATTATGTTTTATTATCATA
1 TATATTAT-TATTATTAT-ATA
*
1107189 TATATTATTATTCTTATATA
1 TATATTATTATTATTATATA
1107209 TATATATATATATATATATATATA
1 TATAT-TAT-TAT-TAT-TATATA
1107233 TATAT
1 TATAT
1107238 ATGTAATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.19
21 10 0.24
22 11 0.26
23 2 0.05
24 11 0.26
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (20 bp):
TATATTATTATTATTATATA
Found at i:1107196 original size:12 final size:11
Alignment explanation
Indices: 1107179--1107239 Score: 69
Period size: 10 Copynumber: 5.9 Consensus size: 11
1107169 TATTATGTTT
1107179 TATTATCATATA
1 TATTAT-ATATA
1107191 TATTAT-TAT-
1 TATTATATATA
*
1107200 TCTTATATATA
1 TATTATATATA
1107211 TA-TATATATA
1 TATTATATATA
1107221 TA-TATATATA
1 TATTATATATA
1107231 TA-TATATAT
1 TATTATATAT
1107240 GTAATTATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 5 0.11
10 33 0.73
11 1 0.02
12 6 0.13
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
TATTATATATA
Found at i:1107208 original size:2 final size:2
Alignment explanation
Indices: 1107203--1107239 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1107193 TTATTATTCT
1107203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1107240 GTAATTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1107436 original size:12 final size:13
Alignment explanation
Indices: 1107392--1107437 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
1107382 TCCTTCGACA
*
1107392 TATTTTTTATTTT
1 TATTATTTATTTT
1107405 TATT-TTTATTTT
1 TATTATTTATTTT
*
1107417 TGTGTATTTA-TTT
1 TAT-TATTTATTTT
1107430 TATTATTT
1 TATTATTT
1107438 TGCTCACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 15 0.52
13 10 0.34
14 4 0.14
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.78
Consensus pattern (13 bp):
TATTATTTATTTT
Found at i:1108696 original size:16 final size:15
Alignment explanation
Indices: 1108676--1108708 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1108666 TTATCGATGA
1108676 ATTTTTATATAAATG
1 ATTTTTATATAAATG
*
1108691 ATTTTTATTTAAAT-
1 ATTTTTATATAAATG
1108705 ATTT
1 ATTT
1108709 AGAATTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTTTATATAAATG
Done.