Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 59 of 193
Found at i:18640790 original size:46 final size:46
Alignment explanation
Indices: 18640719--18640831 Score: 129
Period size: 46 Copynumber: 2.5 Consensus size: 46
18640709 AAGTGCTGGG
* ** * * *
18640719 GAAACAATAAGCACACACACAGCAAATCAGTAGGTACATGCAGTG-
1 GAAACAGTAAGCACACACAGTGCAAATCAGTAAGCACATACAGTGC
* *
18640764 GAAAACAGTAATCACACACAGTGCAAATCAGTAAGCACATATAGTGC
1 G-AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACATACAGTGC
*
18640811 GAATCAGTAAGCACACACAGT
1 GAAACAGTAAGCACACACAGT
18640832 ACTGAACAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
45 1 0.02
46 54 0.96
47 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (46 bp):
GAAACAGTAAGCACACACAGTGCAAATCAGTAAGCACATACAGTGC
Found at i:18648043 original size:23 final size:23
Alignment explanation
Indices: 18648012--18648096 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
18648002 GGGGAAACAA
18648012 TAAGCACACACAGTGCAAATCAG
1 TAAGCACACACAGTGCAAATCAG
* ** *
18648035 TAGGCACACGTAGTACAAAAT-AG
1 TAAGCACACACAGTGC-AAATCAG
*
18648058 TAAGCACACACAATGCAAATCAG
1 TAAGCACACACAGTGCAAATCAG
18648081 TAAGCACACACAGTGC
1 TAAGCACACACAGTGC
18648097 TGAACAGTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
22 4 0.08
23 42 0.84
24 4 0.08
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.14
Consensus pattern (23 bp):
TAAGCACACACAGTGCAAATCAG
Found at i:18648104 original size:23 final size:22
Alignment explanation
Indices: 18648006--18648108 Score: 98
Period size: 23 Copynumber: 4.5 Consensus size: 22
18647996 AGTGCTGGGG
*
18648006 AAACAATAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
* ** *
18648028 AAATCAGTAGGCACACGTAGTAC
1 AAA-CAGTAAGCACACACAGTGC
* *
18648051 AAAATAGTAAGCACACACAATGC
1 -AAACAGTAAGCACACACAGTGC
18648074 AAATCAGTAAGCACACACAGTGC
1 AAA-CAGTAAGCACACACAGTGC
*
18648097 TGAACAGTAAGC
1 -AAACAGTAAGC
18648109 GCGCTAATGT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
22 6 0.10
23 52 0.83
24 5 0.08
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:18648106 original size:46 final size:46
Alignment explanation
Indices: 18648006--18648108 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
18647996 AGTGCTGGGG
* * * **
18648006 AAACAATAAGCACACACAGTGCAAATCAGTAGGCACACGTAGTACA
1 AAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTACA
* * *
18648052 AAATAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTGCT
1 AAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTACA
*
18648098 GAACAGTAAGC
1 AAACAGTAAGC
18648109 GCGCTAATGT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (46 bp):
AAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTACA
Found at i:18654495 original size:2 final size:2
Alignment explanation
Indices: 18654488--18654527 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
18654478 CCCTCCCTCC
*
18654488 CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18654528 GCGGTAAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:18656621 original size:118 final size:117
Alignment explanation
Indices: 18656466--18656701 Score: 348
Period size: 118 Copynumber: 2.0 Consensus size: 117
18656456 TGATGGATTT
* * *
18656466 TGTTTGATATGTTAATTTTTAGGGTTTTACTTGTGATGTTAAGTTTCAAG-TTTTTTTAATAGAT
1 TGTTTGATATGTTAATTTTTAGGGTTTGACTTATGATGTTAAGTGTCAAGTTTTTTTTAATAGAT
*
18656530 TGATGGGTGTTCAAAGTCTGGATTTTTTTTTCTAATGGGTGTTCTAAGTTTGGA
66 TGATGGGTGTTCAAAGTCTAGA--TTTTTTTCTAATGGGTGTTCTAAGTTTGGA
* ** *
18656584 TGTTTGATATGTTAATTTTTAGGGTTTGATTTATGATGTTAAGTGTCTGGTTTTTTTTAATGGAT
1 TGTTTGATATGTTAATTTTTAGGGTTTGACTTATGATGTTAAGTGTCAAGTTTTTTTTAATAGAT
** *
18656649 TGATGGGTGTTTTAAGTCTAGATTTTTTTCTAATGTGTGTTCTAAGTTTGGA
66 TGATGGGTGTTCAAAGTCTAGATTTTTTTCTAATGGGTGTTCTAAGTTTGGA
18656701 T
1 T
18656702 TTCAATTTGT
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 30 0.28
118 44 0.42
119 32 0.30
ACGTcount: A:0.20, C:0.04, G:0.23, T:0.52
Consensus pattern (117 bp):
TGTTTGATATGTTAATTTTTAGGGTTTGACTTATGATGTTAAGTGTCAAGTTTTTTTTAATAGAT
TGATGGGTGTTCAAAGTCTAGATTTTTTTCTAATGGGTGTTCTAAGTTTGGA
Found at i:18659586 original size:14 final size:13
Alignment explanation
Indices: 18659548--18659586 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
18659538 TATTATTTGC
18659548 ATTTTTAA-TTTA
1 ATTTTTAATTTTA
18659560 ATTTTTATATTTTA
1 ATTTTTA-ATTTTA
18659574 ATTTTTTAATTTT
1 A-TTTTTAATTTT
18659587 TTTCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.29
13 1 0.04
14 10 0.42
15 6 0.25
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTAATTTTA
Found at i:18669054 original size:77 final size:77
Alignment explanation
Indices: 18668962--18669521 Score: 288
Period size: 82 Copynumber: 7.2 Consensus size: 77
18668952 TAAAATTCTA
* * * * * * *
18668962 AAACAAATTCAAAATCAATTCTGTTGAATGACATAAATAAATTTTGAAACAGAATTATTTAATTA
1 AAACAAAATCAAAATCAATTCTATTGAACGACAGAAATAAATCTCGAAACAGAATTATTCAATTA
*
18669027 ATTCTTGTTTGG
66 ATCCTTGTTTGG
* * * *
18669039 AAACAAAATGAAAATCAATTCTATTGAACGGCAGGAATAAATCTCGAAACATAATTATTCAATTA
1 AAACAAAATCAAAATCAATTCTATTGAACGACAGAAATAAATCTCGAAACAGAATTATTCAATTA
18669104 ATCCTTGTTTGG
66 ATCCTTGTTTGG
* * * * * *
18669116 AAACAAAATCAGACTAGAATAAAATCTATTGAAC-AGCGGGAATAACTCCCGAAACAGAATTATT
1 AAACAAAATC--A--A-AATCAATTCTATTGAACGA-CAGAAATAAATCTCGAAACAGAATTATT
* * *
18669180 CTATTAATTCTTATTTGG
60 CAATTAATCCTTGTTTGG
* * ** * *
18669198 AAACAAAATTAAAATAGAATAAAATCTATTTTATGACAGGAATAAATCTC-AAACAGAATTATTC
1 AAACAAAATCAAAAT-CAAT----TCTATTGAACGACAGAAATAAATCTCGAAACAGAATTATTC
* *
18669262 AATTAATCATTGTTTCG
61 AATTAATCCTTGTTTGG
* * * * ** ** * * *
18669279 AAAAAAAATTAAAATAAAATAAAATCTGTTGAACGGTAGGCATAAATCCCAAAATA-ATATTATT
1 AAACAAAATCAAAAT-CAAT----TCTATTGAACGACAGAAATAAATCTCGAAACAGA-ATTATT
*
18669343 CAATTAATCCTTGTTTTG
60 CAATTAATCCTTGTTTGG
* * * * * *
18669361 -----AAAT---AA--AA-TCTGTTGAAAG-TAGGAATAAATCCCGAAACAGAATCATTCAATTA
1 AAACAAAATCAAAATCAATTCTATTGAACGACAGAAATAAATCTCGAAACAGAATTATTCAATTA
*
18669414 ATCCTTTTTTGG
66 ATCCTTGTTTGG
* * ** * * * * *
18669426 AAACAAAATCAAAATAGAATAAAATCTGTTGAACGGTAGGAATAAATCCCTAAACAGATTTATTA
1 AAACAAAATCAAAAT-CAAT----TCTATTGAACGACAGAAATAAATCTCGAAACAGAATTATTC
*
18669491 AATTAATTCTT-TTTGG
61 AATTAATCCTTGTTTGG
18669507 AAACAAAATCAAAAT
1 AAACAAAATCAAAAT
18669522 AGAATAAAAT
Statistics
Matches: 388, Mismatches: 63, Indels: 60
0.76 0.12 0.12
Matches are distributed among these distances:
65 38 0.10
66 11 0.03
70 4 0.01
71 2 0.01
73 2 0.01
74 2 0.01
76 2 0.01
77 81 0.21
78 3 0.01
79 1 0.00
80 1 0.00
81 98 0.25
82 142 0.37
83 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (77 bp):
AAACAAAATCAAAATCAATTCTATTGAACGACAGAAATAAATCTCGAAACAGAATTATTCAATTA
ATCCTTGTTTGG
Found at i:18669177 original size:82 final size:82
Alignment explanation
Indices: 18669007--18669370 Score: 382
Period size: 82 Copynumber: 4.5 Consensus size: 82
18668997 AATAAATTTT
* * * *
18669007 GAAACAGAATTATTTAATTAATTCTTGTTTGGAAACAAAATGAAAAT-CAAT----TCTATTGAA
1 GAAACAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTATTGAA
*
18669067 CGGCAGGAATAAATCTC
66 CGGCAGGAATAAATCCC
* * *
18669084 GAAACATAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAGACTAGAATAAAATCTATTGAA
1 GAAACAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTATTGAA
* * *
18669149 CAGCGGGAATAACTCCC
66 CGGCAGGAATAAATCCC
* * * * **
18669166 GAAACAGAATTATTCTATTAATTCTTATTTGGAAACAAAATTAAAATAGAATAAAATCTATTTTA
1 GAAACAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTATTGAA
* * *
18669231 TGACAGGAATAAATCTC
66 CGGCAGGAATAAATCCC
* * * * * *
18669248 -AAACAGAATTATTCAATTAATCATTGTTTCGAAAAAAAATTAAAATAAAATAAAATCTGTTGAA
1 GAAACAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTATTGAA
* *
18669312 CGGTAGGCATAAATCCC
66 CGGCAGGAATAAATCCC
* * * *
18669329 AAAATA-ATATTATTCAATTAATCCTTGTTTTGAAATAAAATC
1 GAAACAGA-ATTATTCAATTAATCCTTGTTTGGAAACAAAATC
18669371 TGTTGAAAGT
Statistics
Matches: 234, Mismatches: 46, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
77 41 0.18
78 3 0.01
81 67 0.29
82 123 0.53
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (82 bp):
GAAACAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTATTGAA
CGGCAGGAATAAATCCC
Found at i:18669343 original size:163 final size:164
Alignment explanation
Indices: 18669008--18669369 Score: 396
Period size: 163 Copynumber: 2.2 Consensus size: 164
18668998 ATAAATTTTG
* * * * * ** *
18669008 AAACAGAATTATTTAATTAATTCTTGTTTGGAAACAAAATGAAAAT-CAAT----TCTATTGAAC
1 AAACAGAATTATTCAATTAATCCTTATTTGGAAACAAAATTAAAATAGAATAAAATCTATTTTAT
* * * * * * * *
18669068 GGCAGGAATAAATCTCGAAACATAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAGACTAG
66 GACAGGAATAAATCTCGAAACAGAATTATTCAATTAATCATTGTTTCGAAAAAAAATCAAAATAA
* * *
18669133 AATAAAATCTATTGAACAGCGGGAATAACTCCCG
131 AATAAAATCTATTGAACAGCAGGAATAAATCCCA
* *
18669167 AAACAGAATTATTCTATTAATTCTTATTTGGAAACAAAATTAAAATAGAATAAAATCTATTTTAT
1 AAACAGAATTATTCAATTAATCCTTATTTGGAAACAAAATTAAAATAGAATAAAATCTATTTTAT
*
18669232 GACAGGAATAAATCTC-AAACAGAATTATTCAATTAATCATTGTTTCGAAAAAAAATTAAAATAA
66 GACAGGAATAAATCTCGAAACAGAATTATTCAATTAATCATTGTTTCGAAAAAAAATCAAAATAA
* * * *
18669296 AATAAAATCTGTTGAACGGTAGGCATAAATCCCA
131 AATAAAATCTATTGAACAGCAGGAATAAATCCCA
* * * *
18669330 AAATA-ATATTATTCAATTAATCCTTGTTTTGAAATAAAAT
1 AAACAGA-ATTATTCAATTAATCCTTATTTGGAAACAAAAT
18669370 CTGTTGAAAG
Statistics
Matches: 167, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
159 42 0.25
160 3 0.02
162 1 0.01
163 99 0.59
164 22 0.13
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (164 bp):
AAACAGAATTATTCAATTAATCCTTATTTGGAAACAAAATTAAAATAGAATAAAATCTATTTTAT
GACAGGAATAAATCTCGAAACAGAATTATTCAATTAATCATTGTTTCGAAAAAAAATCAAAATAA
AATAAAATCTATTGAACAGCAGGAATAAATCCCA
Found at i:18669409 original size:65 final size:66
Alignment explanation
Indices: 18669295--18669435 Score: 189
Period size: 65 Copynumber: 2.2 Consensus size: 66
18669285 AATTAAAATA
* * * *
18669295 AAATAAAATCTGTTGAACGGTAGGCATAAATCCCAAAATAATATTATTCAATTAATCCTTGTTTT
1 AAATAAAATCTGTTGAACAGTAGGAATAAATCCCAAAACAATATCATTCAATTAATCCTT-TTTT
18669360 -G
65 GG
*
18669361 AAATAAAATCTGTTGAA-AGTAGGAATAAATCCCGAAACAGA-ATCATTCAATTAATCCTTTTTT
1 AAATAAAATCTGTTGAACAGTAGGAATAAATCCCAAAACA-ATATCATTCAATTAATCCTTTTTT
18669424 GG
65 GG
*
18669426 AAACAAAATC
1 AAATAAAATC
18669436 AAAATAGAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 4 0.06
65 45 0.67
66 18 0.27
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (66 bp):
AAATAAAATCTGTTGAACAGTAGGAATAAATCCCAAAACAATATCATTCAATTAATCCTTTTTTG
G
Found at i:18669411 original size:147 final size:145
Alignment explanation
Indices: 18669235--18669516 Score: 395
Period size: 147 Copynumber: 1.9 Consensus size: 145
18669225 ATTTTATGAC
* * *
18669235 AGGAATAAATCTCAAACAGAATTATTCAATTAATCATTGTTTCGAAAAAAAATTAAAATAAAATA
1 AGGAATAAATCCCAAACAGAATCATTCAATTAATCATTGTTTCGAAAAAAAATCAAAATAAAATA
* * * *
18669300 AAATCTGTTGAACGGTAGGCATAAATCCCAAAATA-ATATTATTCAATTAATCCTTGTTTTGAAA
66 AAATCTGTTGAACGGTAGGAATAAATCCCAAAACAGAT-TTATTAAATTAATCCTT-TTTGGAAA
*
18669364 TAAAATCTGTTGAAAGT
129 CAAAATCTGTTGAAAGT
* * * * *
18669381 AGGAATAAATCCCGAAACAGAATCATTCAATTAATCCTTTTTTGGAAACAAAATCAAAATAGAAT
1 AGGAATAAATCCC-AAACAGAATCATTCAATTAATCATTGTTTCGAAAAAAAATCAAAATAAAAT
* *
18669446 AAAATCTGTTGAACGGTAGGAATAAATCCCTAAACAGATTTATTAAATTAATTCTTTTTGGAAAC
65 AAAATCTGTTGAACGGTAGGAATAAATCCCAAAACAGATTTATTAAATTAATCCTTTTTGGAAAC
18669511 AAAATC
130 AAAATC
18669517 AAAATAGAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
146 25 0.21
147 92 0.77
148 2 0.02
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (145 bp):
AGGAATAAATCCCAAACAGAATCATTCAATTAATCATTGTTTCGAAAAAAAATCAAAATAAAATA
AAATCTGTTGAACGGTAGGAATAAATCCCAAAACAGATTTATTAAATTAATCCTTTTTGGAAACA
AAATCTGTTGAAAGT
Found at i:18669512 original size:81 final size:82
Alignment explanation
Indices: 18669362--18669570 Score: 314
Period size: 81 Copynumber: 2.6 Consensus size: 82
18669352 CTTGTTTTGA
* * * *
18669362 AATAAAATCTGTTGAA-AGTAGGAATAAATCCCGAAACAGAATCATTCAATTAATCCTTTTTTGG
1 AATAAAATCTGTTGAACGGTAGGAATAAATCCCGAAACAGATTTATTAAATTAATCCTTTTTTGG
18669426 AAACAAAATCAAAATAG
66 AAACAAAATCAAAATAG
* *
18669443 AATAAAATCTGTTGAACGGTAGGAATAAATCCCTAAACAGATTTATTAAATTAATTC-TTTTTGG
1 AATAAAATCTGTTGAACGGTAGGAATAAATCCCGAAACAGATTTATTAAATTAATCCTTTTTTGG
18669507 AAACAAAATCAAAATAG
66 AAACAAAATCAAAATAG
*** *
18669524 AATAAAATCTGTTGAACGACGGGAATAAATCCCGAAACAAATTTATT
1 AATAAAATCTGTTGAACGGTAGGAATAAATCCCGAAACAGATTTATT
18669571 CATTTTTAAT
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
81 82 0.71
82 34 0.29
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (82 bp):
AATAAAATCTGTTGAACGGTAGGAATAAATCCCGAAACAGATTTATTAAATTAATCCTTTTTTGG
AAACAAAATCAAAATAG
Found at i:18669554 original size:228 final size:229
Alignment explanation
Indices: 18669133--18669572 Score: 575
Period size: 228 Copynumber: 1.9 Consensus size: 229
18669123 ATCAGACTAG
* * * * *
18669133 AATAAAATCTATTGAACAGCGGGAATAACTCCCGAAACAGAATTATTCTATTAATTCTTATTTGG
1 AATAAAATCTATTGAACAGCAGGAATAAATCCCGAAACAGAATCATTCAATTAATCCTTATTTGG
* ** * * *
18669198 AAACAAAATTAAAATAGAATAAAATCTATTTTATGACAGGAATAAATCTCAAACAGAATTATTCA
66 AAACAAAATCAAAATAGAATAAAATCTATTGAACGACAGGAATAAATCCCAAACAGAATTATTAA
* ** *
18669263 ATTAATCATTGTTTCGAAAAAAAATTAAAATAAAATAAAATCTGTTGAACGGTAGGCATAAATCC
131 ATTAATCATTGTTTCGAAAAAAAATCAAAATAAAATAAAATCTGTTGAACGACAGGAATAAATCC
18669328 C-AAA-ATAATATTATTCAATTAATCCTTGTTTTGA
196 CGAAACA-AAT-TTATTCAATTAATCCTTGTTTTGA
* * *
18669362 AATAAAATCTGTTGAA-AGTAGGAATAAATCCCGAAACAGAATCATTCAATTAATCCTTTTTTGG
1 AATAAAATCTATTGAACAGCAGGAATAAATCCCGAAACAGAATCATTCAATTAATCCTTATTTGG
* ** *
18669426 AAACAAAATCAAAATAGAATAAAATCTGTTGAACGGTAGGAATAAATCCCTAAACAGATTTATTA
66 AAACAAAATCAAAATAGAATAAAATCTATTGAACGACAGGAATAAATCCC-AAACAGAATTATTA
* * * *
18669491 AATTAATTC-TT-TTTGGAAACAAAATCAAAATAGAATAAAATCTGTTGAACGACGGGAATAAAT
130 AATTAA-TCATTGTTTCGAAAAAAAATCAAAATAAAATAAAATCTGTTGAACGACAGGAATAAAT
18669554 CCCGAAACAAATTTATTCA
194 CCCGAAACAAATTTATTCA
18669573 TTTTTAATTT
Statistics
Matches: 181, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
228 137 0.76
229 41 0.23
230 3 0.02
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.30
Consensus pattern (229 bp):
AATAAAATCTATTGAACAGCAGGAATAAATCCCGAAACAGAATCATTCAATTAATCCTTATTTGG
AAACAAAATCAAAATAGAATAAAATCTATTGAACGACAGGAATAAATCCCAAACAGAATTATTAA
ATTAATCATTGTTTCGAAAAAAAATCAAAATAAAATAAAATCTGTTGAACGACAGGAATAAATCC
CGAAACAAATTTATTCAATTAATCCTTGTTTTGA
Found at i:18672237 original size:21 final size:21
Alignment explanation
Indices: 18672190--18672238 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
18672180 TTTAGTTAAT
18672190 TTTTTAAAATTTTAATATTCA
1 TTTTTAAAATTTTAATATTCA
*
18672211 TATTTAAAATTTCTAACTA-T-A
1 TTTTTAAAATTT-TAA-TATTCA
18672232 TTTTTAA
1 TTTTTAA
18672239 TGTCTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 18 0.75
22 4 0.17
23 2 0.08
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTAAAATTTTAATATTCA
Found at i:18672425 original size:2 final size:2
Alignment explanation
Indices: 18672418--18672446 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18672408 TCATCTAATT
18672418 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
18672447 ACCTCACTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:18674648 original size:25 final size:23
Alignment explanation
Indices: 18674620--18674665 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
18674610 GTTGGATCCA
18674620 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
18674645 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
18674666 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:18676690 original size:6 final size:5
Alignment explanation
Indices: 18676635--18676700 Score: 51
Period size: 5 Copynumber: 11.8 Consensus size: 5
18676625 AGTGCATAAT
* *
18676635 TAAAA TAAAA TTAAAAA TGAAA TAGAAC TAAAA CTAAAAA TAAAA TAAAA
1 TAAAA TAAAA -T-AAAA TAAAA TA-AAA TAAAA -T-AAAA TAAAA TAAAA
18676685 TGAAAA TGAAAA TAAA
1 T-AAAA T-AAAA TAAA
18676701 TGTACTAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
5 24 0.47
6 19 0.37
7 8 0.16
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:18676702 original size:16 final size:16
Alignment explanation
Indices: 18676636--18676700 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
18676626 GTGCATAATT
18676636 AAAATAAAATTAAAAATG
1 AAAATAAAA-T-AAAATG
* *
18676654 -AAATAGAACTAAAACTA
1 AAAATA-AAATAAAA-TG
18676671 AAAATAAAATAAAATG
1 AAAATAAAATAAAATG
18676687 AAAATGAAAATAAA
1 AAAAT-AAAATAAA
18676701 TGTACTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 10 0.26
17 22 0.56
18 7 0.18
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAATG
Found at i:18679888 original size:25 final size:23
Alignment explanation
Indices: 18679860--18679905 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
18679850 GTTGGATCCA
18679860 AATTAAATTCTAAAAACATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
18679885 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
18679906 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:18682519 original size:49 final size:50
Alignment explanation
Indices: 18682405--18682532 Score: 195
Period size: 49 Copynumber: 2.6 Consensus size: 50
18682395 TATGTTTTTA
* *
18682405 ATAGTCTTCATCTAATCTGTCACCCTCTCACTCTCCATATATATATTAATC
1 ATAGTCTTCATCTAATCTCTCACTCTCTCACTCTCCA-ATATATATTAATC
* *
18682456 ATAGTCTTCATCTAATCTCACATTCTCTCACTCTCC-ATATATATTAATC
1 ATAGTCTTCATCTAATCTCTCACTCTCTCACTCTCCAATATATATTAATC
*
18682505 ATAGTCTTCTTCTAATCTCTCACTCTCT
1 ATAGTCTTCATCTAATCTCTCACTCTCT
18682533 ATATATATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
49 38 0.54
51 32 0.46
ACGTcount: A:0.26, C:0.30, G:0.03, T:0.41
Consensus pattern (50 bp):
ATAGTCTTCATCTAATCTCTCACTCTCTCACTCTCCAATATATATTAATC
Found at i:18683694 original size:41 final size:41
Alignment explanation
Indices: 18683649--18683737 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 41
18683639 CTAATCTTTC
* * *
18683649 ACTCTCTGACTATCCACATATATTAGTCATAGTCTTCATCT
1 ACTCTCTCACTATCCACAAATATTAATCATAGTCTTCATCT
* * *
18683690 ACTCTCTCACTCTCCATAAATATTAATCATAGTCTTCATTT
1 ACTCTCTCACTATCCACAAATATTAATCATAGTCTTCATCT
*
18683731 AATCTCT
1 ACTCTCT
18683738 TACCCTCTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.28, C:0.27, G:0.04, T:0.40
Consensus pattern (41 bp):
ACTCTCTCACTATCCACAAATATTAATCATAGTCTTCATCT
Found at i:18694343 original size:37 final size:38
Alignment explanation
Indices: 18694246--18694343 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
18694236 ATTTCCGAAA
* * *
18694246 TGCACCCAAGACTATCGCTACATAAATATTCTTCAAAT
1 TGCACCCAAGAATATTGCTGCATAAATATTCTTCAAAT
* * * *
18694284 TGCA-TCTAGAACTATTGTTGCATAAGTATTCTTC-AAT
1 TGCACCCAAGAA-TATTGCTGCATAAATATTCTTCAAAT
*
18694321 TGCACCCAAGAATGTTGCTGCAT
1 TGCACCCAAGAATATTGCTGCAT
18694344 GAACATGTCC
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
37 20 0.43
38 27 0.57
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (38 bp):
TGCACCCAAGAATATTGCTGCATAAATATTCTTCAAAT
Found at i:18694367 original size:26 final size:26
Alignment explanation
Indices: 18694329--18694385 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
18694319 ATTGCACCCA
*
18694329 AGAA-TGTTGCTGCATGAACATGTCC
1 AGAATTGTCGCTGCATGAACATGTCC
*
18694354 AGAATTGTCGCTGCATGAACGTGTCC
1 AGAATTGTCGCTGCATGAACATGTCC
*
18694380 AAAATT
1 AGAATT
18694386 ACGCCAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (26 bp):
AGAATTGTCGCTGCATGAACATGTCC
Found at i:18694751 original size:45 final size:45
Alignment explanation
Indices: 18694700--18694786 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
18694690 GCGACGCAAG
18694700 AGGGAGAGTAAGGGAGCATTTCAAGTAAACTAGGAATAGAGTACT
1 AGGGAGAGTAAGGGAGCATTTCAAGTAAACTAGGAATAGAGTACT
18694745 AGGGAGAGTAAGGGAGCATTTCAAGTAAACTAGGAATAGAGT
1 AGGGAGAGTAAGGGAGCATTTCAAGTAAACTAGGAATAGAGT
18694787 GCTCCATCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.40, C:0.08, G:0.32, T:0.20
Consensus pattern (45 bp):
AGGGAGAGTAAGGGAGCATTTCAAGTAAACTAGGAATAGAGTACT
Found at i:18695798 original size:25 final size:26
Alignment explanation
Indices: 18695770--18695823 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
18695760 TTTCTTTTAA
*
18695770 AAGTGCTGAAATTATATTT-ATATAT
1 AAGTGCAGAAATTATATTTAATATAT
18695795 AAGTGCAGAAATTATATTTCAATATAT
1 AAGTGCAGAAATTATATTT-AATATAT
18695822 AA
1 AA
18695824 ATTCTATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 18 0.69
27 8 0.31
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (26 bp):
AAGTGCAGAAATTATATTTAATATAT
Found at i:18702850 original size:4 final size:4
Alignment explanation
Indices: 18702841--18702879 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
18702831 TTCATCTAAT
*
18702841 CTCC CTCC CTCC CTCC CTCC CTCTC TTCCC CTCC CTCC C
1 CTCC CTCC CTCC CTCC CTCC CTC-C CT-CC CTCC CTCC C
18702880 CCTTTCTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 26 0.84
5 4 0.13
6 1 0.03
ACGTcount: A:0.00, C:0.72, G:0.00, T:0.28
Consensus pattern (4 bp):
CTCC
Found at i:18704748 original size:67 final size:67
Alignment explanation
Indices: 18704640--18704774 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
18704630 AATTGACATA
* * *
18704640 TAAACCAAATATCATATTTACACATAACCAATTCACATACCATTTCATGTAATCATTCCCTAACC
1 TAAACCAAACATCATATTTACACATAACCAATTAACATACCATTTCATGTAATCATTCCCGAACC
18704705 AT
66 AT
18704707 TAAACCAAACATCATATTTACACATAACCAATTAACATACCATTTCATGTAATCATTCCCGAACC
1 TAAACCAAACATCATATTTACACATAACCAATTAACATACCATTTCATGTAATCATTCCCGAACC
18704772 AT
66 AT
18704774 T
1 T
18704775 TCTTATAGCC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.30
Consensus pattern (67 bp):
TAAACCAAACATCATATTTACACATAACCAATTAACATACCATTTCATGTAATCATTCCCGAACC
AT
Found at i:18705362 original size:40 final size:40
Alignment explanation
Indices: 18705318--18705405 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
18705308 TCGACCTTTG
**
18705318 TCCTTTCGGATAAC-GTCCTTTTTAACCTTTTCATTTATTA
1 TCCTTTCGGAT-ACTGTCCTTTCCAACCTTTTCATTTATTA
*
18705358 TCCTTTCGGATTCTGTCCTTTCCAACCTTTTCATTTATTA
1 TCCTTTCGGATACTGTCCTTTCCAACCTTTTCATTTATTA
*
18705398 TCTTTTCG
1 TCCTTTCG
18705406 AATATAATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.16, C:0.25, G:0.08, T:0.51
Consensus pattern (40 bp):
TCCTTTCGGATACTGTCCTTTCCAACCTTTTCATTTATTA
Found at i:18705415 original size:15 final size:15
Alignment explanation
Indices: 18705397--18705446 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
18705387 TTCATTTATT
18705397 ATCTTTTCGAATATA
1 ATCTTTTCGAATATA
18705412 ATCTTTTC-AA-AT-
1 ATCTTTTCGAATATA
* *
18705424 ATCCTTTCGGATATA
1 ATCTTTTCGAATATA
*
18705439 ACCTTTTC
1 ATCTTTTC
18705447 AATGATATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 4 0.14
15 14 0.50
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (15 bp):
ATCTTTTCGAATATA
Found at i:18705431 original size:27 final size:28
Alignment explanation
Indices: 18705381--18705615 Score: 155
Period size: 28 Copynumber: 8.4 Consensus size: 28
18705371 TGTCCTTTCC
* * *
18705381 AACCTTTTCATTTATTATCTTTTCGAATAT
1 AACCTTTTCA--TAATATCCTTTCGGATAT
*
18705411 AATCTTTTCA-AATATCCTTTCGGATAT
1 AACCTTTTCATAATATCCTTTCGGATAT
*
18705438 AACCTTTTCAATGATATCCTTTCGGATAT
1 AACCTTTTC-ATAATATCCTTTCGGATAT
* * *
18705467 -CCCTTTTCATAGTATCCTTACGGATAT
1 AACCTTTTCATAATATCCTTTCGGATAT
*
18705494 AACCTTTTCAATAATATCCTTATAGG-TAT
1 AACCTTTTC-ATAATATCCTT-TCGGATAT
* * *
18705523 -TCCTTTTCATTGATATCCTTGCGGAT-T
1 AACCTTTTCA-TAATATCCTTTCGGATAT
* *
18705550 -TCTCTCTTCTATAATATCCTTAT-GGATAT
1 AAC-CTTTTC-ATAATATCCTT-TCGGATAT
* * *
18705579 -TCCTTTTCATTGATATCCTTGCGGATAT
1 AACCTTTTCA-TAATATCCTTTCGGATAT
*
18705607 -CCCTTTTCA
1 AACCTTTTCA
18705616 CATGATTTTA
Statistics
Matches: 167, Mismatches: 25, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
27 45 0.27
28 78 0.47
29 33 0.20
30 11 0.07
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (28 bp):
AACCTTTTCATAATATCCTTTCGGATAT
Found at i:18705483 original size:56 final size:56
Alignment explanation
Indices: 18705414--18705615 Score: 227
Period size: 56 Copynumber: 3.6 Consensus size: 56
18705404 CGAATATAAT
* * *
18705414 CTTTTCA-A-ATATCCTTTCGGATATAACCTTTTCAATGATATCCTT-TCGGATATCC
1 CTTTTCATAGATATCCTTGCGGATAT-ACCTTTTCAATAATATCCTTAT-GGATATTC
*
18705469 CTTTTCATAG-TATCCTTACGGATATAACCTTTTCAATAATATCCTTATAGG-TATTC
1 CTTTTCATAGATATCCTTGCGGATAT-ACCTTTTCAATAATATCCTTAT-GGATATTC
* * * *
18705525 CTTTTCATTGATATCCTTGCGGAT-TTCTCTCTTCTATAATATCCTTATGGATATTC
1 CTTTTCATAGATATCCTTGCGGATATAC-CTTTTCAATAATATCCTTATGGATATTC
* *
18705581 CTTTTCATTGATATCCTTGCGGATATCCCTTTTCA
1 CTTTTCATAGATATCCTTGCGGATATACCTTTTCA
18705616 CATGATTTTA
Statistics
Matches: 128, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
55 10 0.08
56 101 0.79
57 17 0.13
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (56 bp):
CTTTTCATAGATATCCTTGCGGATATACCTTTTCAATAATATCCTTATGGATATTC
Found at i:18705542 original size:84 final size:86
Alignment explanation
Indices: 18705407--18705621 Score: 219
Period size: 84 Copynumber: 2.6 Consensus size: 86
18705397 ATCTTTTCGA
* * *
18705407 ATATAATCTTTTC-A-AATATCCTTTCGGATATAACCTTTTCAATGATATCCTTTCGGATATCCC
1 ATATAACCTTTTCAATAATATCCTTTAGGATATAACCTTTTCAATGATATCCTTGCGGATATCCC
* *
18705470 TTTTC-ATAGTATCCTTACGG
66 TCTTCTATAATATCCTTACGG
* * * *
18705490 ATATAACCTTTTCAATAATATCCTTATAGG-TAT-TCCTTTTCATTGATATCCTTGCGGATTTCT
1 ATATAACCTTTTCAATAATATCCTT-TAGGATATAACCTTTTCAATGATATCCTTGCGGATATCC
*
18705553 CTCTTCTATAATATCCTTATGG
65 CTCTTCTATAATATCCTTACGG
* * * ** *
18705575 ATAT-TCCTTTTCATTGATATCCTTGCGGATAT-CCCTTTTCACATGAT
1 ATATAACCTTTTCAATAATATCCTTTAGGATATAACCTTTTCA-ATGAT
18705622 TTTAGAGGAA
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
83 14 0.13
84 59 0.54
85 33 0.30
86 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (86 bp):
ATATAACCTTTTCAATAATATCCTTTAGGATATAACCTTTTCAATGATATCCTTGCGGATATCCC
TCTTCTATAATATCCTTACGG
Found at i:18709310 original size:25 final size:23
Alignment explanation
Indices: 18709282--18709327 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
18709272 GTTGGATCAA
18709282 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
18709307 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
18709328 CCCTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:18710390 original size:18 final size:17
Alignment explanation
Indices: 18710369--18710424 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 17
18710359 TCTTTTTCTC
18710369 TTCTTTTTTCCAATTTTT
1 TTCTTTTTT-CAATTTTT
*
18710387 TTCTTTTTTTAATTTTT
1 TTCTTTTTTCAATTTTT
18710404 TTCTTTTTTTTCAATTTTT
1 TTC--TTTTTTCAATTTTT
18710423 TT
1 TT
18710425 GACTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 10 0.29
18 9 0.26
19 15 0.44
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTTTTTTCAATTTTT
Found at i:18710400 original size:17 final size:17
Alignment explanation
Indices: 18710369--18710434 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 17
18710359 TCTTTTTCTC
*
18710369 TTCTTTTTTCCAATTTTT
1 TTCTTTTTT-TAATTTTT
18710387 TTCTTTTTTTAATTTTT
1 TTCTTTTTTTAATTTTT
18710404 TTCTTTTTTTTCAATTTTT
1 TTC-TTTTTTT-AATTTTT
18710423 TTGACTTTTTTT
1 TT--CTTTTTTT
18710435 TTCTAAATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
17 10 0.23
18 16 0.37
19 9 0.21
20 7 0.16
21 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (17 bp):
TTCTTTTTTTAATTTTT
Found at i:18710403 original size:38 final size:37
Alignment explanation
Indices: 18710361--18710434 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 37
18710351 CATTTTTATC
18710361 TTTTTCTCTTCTTTTTTCCAATTTTTTT-CTTTTTTTAA
1 TTTTTCTCTT-TTTTTT-CAATTTTTTTACTTTTTTTAA
*
18710399 TTTTTTTCTTTTTTTTCAATTTTTTTGACTTTTTTT
1 TTTTTCTCTTTTTTTTCAATTTTTTT-ACTTTTTTT
18710435 TTCTAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 10 0.30
37 6 0.18
38 17 0.52
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.77
Consensus pattern (37 bp):
TTTTTCTCTTTTTTTTCAATTTTTTTACTTTTTTTAA
Found at i:18711375 original size:12 final size:12
Alignment explanation
Indices: 18711358--18711453 Score: 76
Period size: 12 Copynumber: 8.0 Consensus size: 12
18711348 AAAAGTGCAT
18711358 AATTAAAATAAA
1 AATTAAAATAAA
18711370 AATTAAAAT-AA
1 AATTAAAATAAA
18711381 AA-TAAAACT-AA
1 AATTAAAA-TAAA
* *
18711392 AACTAAAACTACA
1 AATTAAAA-TAAA
*
18711405 AATAAAAAT-AA
1 AATTAAAATAAA
18711416 AATTAAAAATTAAA
1 AATT-AAAA-TAAA
18711430 AATT-AAATGAAA
1 AATTAAAAT-AAA
*
18711442 AATGAAAATAAA
1 AATTAAAATAAA
18711454 TGTGCTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
10 5 0.07
11 14 0.20
12 33 0.47
13 12 0.17
14 6 0.09
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (12 bp):
AATTAAAATAAA
Found at i:18711377 original size:6 final size:6
Alignment explanation
Indices: 18711358--18711436 Score: 65
Period size: 6 Copynumber: 13.2 Consensus size: 6
18711348 AAAAGTGCAT
* * * *
18711358 AATTAA AATAAA AATTAA AA-TAA AA-TAA AACTAA AACTAA AACTACA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTA-A
*
18711405 AA-TAA AAATAA AATTAAA AATTAAA AATTAA A
1 AATTAA AATTAA AATT-AA AATT-AA AATTAA A
18711437 TGAAAAATGA
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
5 13 0.20
6 37 0.56
7 16 0.24
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (6 bp):
AATTAA
Found at i:18714253 original size:22 final size:22
Alignment explanation
Indices: 18714225--18714270 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
18714215 TAGAATTCAT
18714225 TAGAGGGTTCATCTGCCCTAGG
1 TAGAGGGTTCATCTGCCCTAGG
18714247 TAGAGGGTTCATCTGCCCTAGG
1 TAGAGGGTTCATCTGCCCTAGG
18714269 TA
1 TA
18714271 TTTAGGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (22 bp):
TAGAGGGTTCATCTGCCCTAGG
Found at i:18715668 original size:20 final size:20
Alignment explanation
Indices: 18715634--18715680 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
18715624 AATTTTGTCT
*
18715634 TTTTCTTCTTCTTTTCTCCAA
1 TTTT-TTCTTCTTTTCTCAAA
* *
18715655 TTTTTTCTTTTTTTTTCAAA
1 TTTTTTCTTCTTTTCTCAAA
18715675 TTTTTT
1 TTTTTT
18715681 TCAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTCTTCTTTTCTCAAA
Found at i:18717652 original size:18 final size:19
Alignment explanation
Indices: 18717617--18717666 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
18717607 AATAGATATG
*
18717617 GAGAGTGAGAGTGAAGGAGA
1 GAGAGAGAGAG-GAAGGAGA
* *
18717637 TAGAGAG-GAGGAAGGATA
1 GAGAGAGAGAGGAAGGAGA
18717655 GAGAGAGAGAGG
1 GAGAGAGAGAGG
18717667 GAGGGATGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 13 0.52
19 7 0.28
20 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.08
Consensus pattern (19 bp):
GAGAGAGAGAGGAAGGAGA
Found at i:18717670 original size:26 final size:26
Alignment explanation
Indices: 18717651--18717706 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
18717641 GAGGAGGAAG
*
18717651 GATAGAGAGAGAGAGGGAGGGATGGA
1 GATAGAGAGAGAAAGGGAGGGATGGA
*
18717677 GATAGAGAGAGAAAGGGGAGGGAGGGA
1 GATAGAGAGAGAAA-GGGAGGGATGGA
18717704 GAT
1 GAT
18717707 TAGATGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.54, T:0.07
Consensus pattern (26 bp):
GATAGAGAGAGAAAGGGAGGGATGGA
Found at i:18717673 original size:20 final size:20
Alignment explanation
Indices: 18717617--18717685 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
18717607 AATAGATATG
* * *
18717617 GAGAGTGAGAGTGAAGGAGA
1 GAGAGAGAGAGGGAAGGATA
*
18717637 TAGAGAG-GA-GGAAGGATA
1 GAGAGAGAGAGGGAAGGATA
* *
18717655 GAGAGAGAGAGGGAGGGATG
1 GAGAGAGAGAGGGAAGGATA
*
18717675 GAGATAGAGAG
1 GAGAGAGAGAG
18717686 AGAAAGGGGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 13 0.33
19 4 0.10
20 22 0.56
ACGTcount: A:0.41, C:0.00, G:0.51, T:0.09
Consensus pattern (20 bp):
GAGAGAGAGAGGGAAGGATA
Found at i:18717686 original size:22 final size:23
Alignment explanation
Indices: 18717632--18717688 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 23
18717622 TGAGAGTGAA
18717632 GGAGATAGAGAG-GAGGAAGGAT
1 GGAGATAGAGAGAGAGGAAGGAT
* *
18717654 --AGAGAGAGAGAG-GGAGGGAT
1 GGAGATAGAGAGAGAGGAAGGAT
18717674 GGAGATAGAGAGAGA
1 GGAGATAGAGAGAGA
18717689 AAGGGGAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 16 0.57
21 1 0.04
22 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.51, T:0.07
Consensus pattern (23 bp):
GGAGATAGAGAGAGAGGAAGGAT
Found at i:18717693 original size:22 final size:22
Alignment explanation
Indices: 18717632--18717693 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
18717622 TGAGAGTGAA
18717632 GGAGATAGAGAGGAGGAA-GGAT
1 GGAGATAGAGA-GAGGAAGGGAT
* *
18717654 --AGAGAGAGAGAGGGAGGGAT
1 GGAGATAGAGAGAGGAAGGGAT
*
18717674 GGAGATAGAGAGAGAAAGGG
1 GGAGATAGAGAGAGGAAGGG
18717694 GAGGGAGGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 5 0.16
20 12 0.38
22 15 0.47
ACGTcount: A:0.42, C:0.00, G:0.52, T:0.06
Consensus pattern (22 bp):
GGAGATAGAGAGAGGAAGGGAT
Found at i:18720448 original size:20 final size:21
Alignment explanation
Indices: 18720410--18720448 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18720400 AAATTAGAGT
*
18720410 GAAATTGTTTGAGTTTTGATA
1 GAAATTGTTAGAGTTTTGATA
18720431 GAAATTGTTAGA-TTTTGA
1 GAAATTGTTAGAGTTTTGA
18720449 AGCTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
GAAATTGTTAGAGTTTTGATA
Found at i:18721016 original size:16 final size:16
Alignment explanation
Indices: 18720995--18721044 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
18720985 ATATCCTTAA
18720995 GGATATTATTGAAAAG
1 GGATATTATTGAAAAG
18721011 GGATATTCA-T---AA-
1 GGATATT-ATTGAAAAG
18721023 GGATATTATTGAAAAG
1 GGATATTATTGAAAAG
18721039 GGATAT
1 GGATAT
18721045 CCGCAAGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
11 1 0.04
12 8 0.29
13 2 0.07
15 2 0.07
16 14 0.50
17 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.32
Consensus pattern (16 bp):
GGATATTATTGAAAAG
Found at i:18721036 original size:56 final size:56
Alignment explanation
Indices: 18720942--18721085 Score: 171
Period size: 56 Copynumber: 2.6 Consensus size: 56
18720932 TTACTCTAAA
** * * **
18720942 ATTATGTGAAAAGGGATATCCGCATGGATATCAATGAAAAGGAATATCCTTAAGGAT
1 ATTAT-TGAAAAGGGATATCCATAAGGATATTAATGAAAAGGAATATCCGCAAGGAT
* * *
18720999 ATTATTGAAAAGGGATATTCATAAGGATATTATTGAAAAGGGATATCCGCAAGGAT
1 ATTATTGAAAAGGGATATCCATAAGGATATTAATGAAAAGGAATATCCGCAAGGAT
* * *
18721055 ATCAATGAAAAGGAATATCCATAAGGATATT
1 ATTATTGAAAAGGGATATCCATAAGGATATT
18721086 GTCGAAACCA
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
56 69 0.93
57 5 0.07
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (56 bp):
ATTATTGAAAAGGGATATCCATAAGGATATTAATGAAAAGGAATATCCGCAAGGAT
Found at i:18721039 original size:15 final size:15
Alignment explanation
Indices: 18720993--18721044 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
18720983 GAATATCCTT
18720993 AAGGATATTATTGAA
1 AAGGATATTATTGAA
* * *
18721008 AAGG-GA-TATTCAT
1 AAGGATATTATTGAA
18721021 AAGGATATTATTGAA
1 AAGGATATTATTGAA
18721036 AAGGGATAT
1 AA-GGATAT
18721045 CCGCAAGGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
13 9 0.32
14 2 0.07
15 11 0.39
16 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.31
Consensus pattern (15 bp):
AAGGATATTATTGAA
Found at i:18721092 original size:28 final size:28
Alignment explanation
Indices: 18720942--18721085 Score: 153
Period size: 28 Copynumber: 5.1 Consensus size: 28
18720932 TTACTCTAAA
* ** *
18720942 ATTATGTGAAAAGGGATATCCGCATGGAT
1 ATTAT-TGAAAAGGAATATCCATAAGGAT
* * *
18720971 ATCAATGAAAAGGAATATCCTTAAGGAT
1 ATTATTGAAAAGGAATATCCATAAGGAT
* *
18720999 ATTATTGAAAAGGGATATTCATAAGGAT
1 ATTATTGAAAAGGAATATCCATAAGGAT
* **
18721027 ATTATTGAAAAGGGATATCCGCAAGGAT
1 ATTATTGAAAAGGAATATCCATAAGGAT
* *
18721055 ATCAATGAAAAGGAATATCCATAAGGAT
1 ATTATTGAAAAGGAATATCCATAAGGAT
18721083 ATT
1 ATT
18721086 GTCGAAACCA
Statistics
Matches: 95, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
28 92 0.97
29 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (28 bp):
ATTATTGAAAAGGAATATCCATAAGGAT
Found at i:18722530 original size:59 final size:59
Alignment explanation
Indices: 18722467--18722630 Score: 211
Period size: 59 Copynumber: 2.8 Consensus size: 59
18722457 GGAACTTCGA
*
18722467 GGGCAAGAATGTAATTTTTGGAGGTTTTGGGGTTAAAAATGGAATTCTTAAAAGTTTGG
1 GGGCAAAAATGTAATTTTTGGAGGTTTTGGGGTTAAAAATGGAATTCTTAAAAGTTTGG
** * ** * * *
18722526 GGGCAAAAATGTAATTTTTTAAGGTTTCGGGGTTAAACTTGGATTTTTTGAAAGTTTGG
1 GGGCAAAAATGTAATTTTTGGAGGTTTTGGGGTTAAAAATGGAATTCTTAAAAGTTTGG
* ** *
18722585 GGTCAAAAATGTAATTTTTGGAAATTTTGGGGTCAAAAATGGAATT
1 GGGCAAAAATGTAATTTTTGGAGGTTTTGGGGTTAAAAATGGAATT
18722631 TTGGAGAAGT
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 86 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (59 bp):
GGGCAAAAATGTAATTTTTGGAGGTTTTGGGGTTAAAAATGGAATTCTTAAAAGTTTGG
Found at i:18722534 original size:29 final size:29
Alignment explanation
Indices: 18722408--18722652 Score: 172
Period size: 30 Copynumber: 8.4 Consensus size: 29
18722398 TTCAAAAAAA
* * *
18722408 TGGGATCAAAAAT--AAATTTTGAAATTT
1 TGGGGTCAAAAATGGAATTTTTGAAAGTT
* * * * *
18722435 TAGGGTCAAATATAGAATTTTTGGAACTT
1 TGGGGTCAAAAATGGAATTTTTGAAAGTT
* * * * *
18722464 CGAGGG-CAAGAATGTAATTTTTGGAGGTTT
1 TG-GGGTCAAAAATGGAATTTTTGAAAG-TT
* * *
18722494 TGGGGTTAAAAATGGAATTCTTAAAAGTT
1 TGGGGTCAAAAATGGAATTTTTGAAAGTT
* * * *
18722523 TGGGGGCAAAAATGTAATTTTTTAAGGTT
1 TGGGGTCAAAAATGGAATTTTTGAAAGTT
* ** *
18722552 TCGGGGTTAAACTTGGATTTTTTGAAAGTT
1 T-GGGGTCAAAAATGGAATTTTTGAAAGTT
* *
18722582 TGGGGTCAAAAATGTAATTTTTGGAAATTT
1 TGGGGTCAAAAATGGAATTTTT-GAAAGTT
*
18722612 TGGGGTCAAAAATGGAATTTTGGAGAAGTT
1 TGGGGTCAAAAATGGAATTTTTGA-AAGTT
*
18722642 TAGGGTCAAAA
1 TGGGGTCAAAA
18722653 CATAATTTTT
Statistics
Matches: 164, Mismatches: 46, Indels: 13
0.74 0.21 0.06
Matches are distributed among these distances:
27 10 0.06
29 73 0.45
30 81 0.49
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
TGGGGTCAAAAATGGAATTTTTGAAAGTT
Found at i:18722659 original size:59 final size:58
Alignment explanation
Indices: 18722413--18722665 Score: 176
Period size: 59 Copynumber: 4.3 Consensus size: 58
18722403 AAAAATGGGA
* * * * * *
18722413 TCAAAAATAAATTTT-GAAATTTTAGGGTCAAATATAGAATTTTTG-GAACTTCGAGGG
1 TCAAAAATAATTTTTGGAAATTTTGGGGTCAAAAATGGAATTTTTGAGAAGTT-TAGGG
* ** * * * *
18722470 -CAAGAATGTAATTTTTGGAGGTTTTGGGGTTAAAAATGGAATTCTT-AAAAGTTTGGGG
1 TCAA-AA-ATAATTTTTGGAAATTTTGGGGTCAAAAATGGAATTTTTGAGAAGTTTAGGG
* * * * * ** * *
18722528 GCAAAAATGTAATTTTT-TAAGGTTTCGGGGTTAAACTTGGATTTTTTGA-AAGTTTGGGG
1 TCAAAAA--TAATTTTTGGAA-ATTTTGGGGTCAAAAATGGAATTTTTGAGAAGTTTAGGG
*
18722587 TCAAAAATGTAATTTTTGGAAATTTTGGGGTCAAAAATGGAATTTTGGAGAAGTTTAGGG
1 TCAAAAA--TAATTTTTGGAAATTTTGGGGTCAAAAATGGAATTTTTGAGAAGTTTAGGG
18722647 TCAAAACATAATTTTTGGA
1 TCAAAA-ATAATTTTTGGA
18722666 CAGTTTAGGG
Statistics
Matches: 153, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
56 3 0.02
57 2 0.01
58 13 0.08
59 116 0.76
60 18 0.12
61 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (58 bp):
TCAAAAATAATTTTTGGAAATTTTGGGGTCAAAAATGGAATTTTTGAGAAGTTTAGGG
Found at i:18722663 original size:30 final size:28
Alignment explanation
Indices: 18722568--18722675 Score: 110
Period size: 30 Copynumber: 3.7 Consensus size: 28
18722558 TTAAACTTGG
* *
18722568 ATTTTTTGAAAGTTTGGGGTCAAAAATGTA
1 ATTTTTGGAAAGTTTAGGGTCAAAAA--TA
* *
18722598 ATTTTTGGAAATTTTGGGGTCAAAAATGGA
1 ATTTTTGGAAAGTTTAGGGTCAAAAAT--A
18722628 A-TTTTGGAGAAGTTTAGGGTCAAAACATA
1 ATTTTTGGA-AAGTTTAGGGTCAAAA-ATA
*
18722657 ATTTTTGGACAGTTTAGGG
1 ATTTTTGGAAAGTTTAGGG
18722676 ACCTCCAAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.01
29 18 0.26
30 47 0.69
31 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (28 bp):
ATTTTTGGAAAGTTTAGGGTCAAAAATA
Found at i:18723657 original size:12 final size:12
Alignment explanation
Indices: 18723640--18723678 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
18723630 GGTTTTTTAT
18723640 TTAATAATATTA
1 TTAATAATATTA
*
18723652 TTAATATTATTA
1 TTAATAATATTA
18723664 TT-ATAATAGTTA
1 TTAATAATA-TTA
18723676 TTA
1 TTA
18723679 TTATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TTAATAATATTA
Found at i:18724284 original size:28 final size:28
Alignment explanation
Indices: 18724252--18724321 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
18724242 GTTTGGGCCC
18724252 ATTTGGGCTTGTAAGCTTTGGATATTCA
1 ATTTGGGCTTGTAAGCTTTGGATATTCA
18724280 ATTTGGGCTTGTAAGCTTTGGATATTCA
1 ATTTGGGCTTGTAAGCTTTGGATATTCA
* *
18724308 ACTTGGGCATGTAA
1 ATTTGGGCTTGTAA
18724322 TTGGACATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (28 bp):
ATTTGGGCTTGTAAGCTTTGGATATTCA
Found at i:18724560 original size:29 final size:29
Alignment explanation
Indices: 18724478--18724566 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
18724468 GGCTTCAACA
* *
18724478 GATATTATTGAAAAGGTTATATCCGTAAG
1 GATATCATTGAAAAGGTTATATCCGAAAG
* * *
18724507 GATA-C-TAAGAAAAGG-GATATTCGAAAG
1 GATATCAT-TGAAAAGGTTATATCCGAAAG
* *
18724534 GATATCATTGAAATGGTTATATCCGAAAA
1 GATATCATTGAAAAGGTTATATCCGAAAG
18724563 GATA
1 GATA
18724567 AAAAATGAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
27 14 0.30
28 14 0.30
29 18 0.39
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (29 bp):
GATATCATTGAAAAGGTTATATCCGAAAG
Found at i:18724642 original size:40 final size:40
Alignment explanation
Indices: 18724552--18724668 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
18724542 TGAAATGGTT
* *
18724552 ATATCCGAAAAGATAAAAAATGAAAAGGTTGAAAAGGACA
1 ATATCCGAAAGGATAATAAATGAAAAGGTTGAAAAGGACA
* * *
18724592 AAATCTGAAAGGATAATAACTGAAAAGGTTGAAAAGGA-A
1 ATATCCGAAAGGATAATAAATGAAAAGGTTGAAAAGGACA
* * * *
18724631 GTTATCCGAAAGGACAATAAATTAAAAGGTCGAAAAGG
1 -ATATCCGAAAGGATAATAAATGAAAAGGTTGAAAAGG
18724669 TAAATTTATT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.02
40 63 0.98
ACGTcount: A:0.53, C:0.08, G:0.22, T:0.17
Consensus pattern (40 bp):
ATATCCGAAAGGATAATAAATGAAAAGGTTGAAAAGGACA
Found at i:18730241 original size:6 final size:6
Alignment explanation
Indices: 18730232--18730306 Score: 95
Period size: 6 Copynumber: 13.2 Consensus size: 6
18730222 AAAAAAAATA
* * *
18730232 TTATTT TTATTT TTATTT TCATTT TTATTT TTATTT TCATTT TTAGTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
18730280 TTA-TT TTA-TT TTA-TT TT-TTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT TTATTT T
18730307 AATTATGCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
5 18 0.29
6 44 0.71
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:18730250 original size:5 final size:5
Alignment explanation
Indices: 18730236--18730307 Score: 72
Period size: 5 Copynumber: 13.0 Consensus size: 5
18730226 AAAATATTAT
18730236 TTTTA TTTTTA TTTTCA TTTTTA TTTTTA TTTTCA TTTTTA GTTTTA TTTTA
1 TTTTA -TTTTA TTTT-A -TTTTA -TTTTA TTTT-A -TTTTA -TTTTA TTTTA
*
18730288 TTTTA TTTTT TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA
18730308 ATTATGCACT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
5 31 0.53
6 20 0.34
7 8 0.14
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:18730257 original size:18 final size:17
Alignment explanation
Indices: 18730232--18730306 Score: 109
Period size: 18 Copynumber: 4.4 Consensus size: 17
18730222 AAAAAAAATA
18730232 TTATTTTTATTTTTATT
1 TTATTTTTATTTTTATT
18730249 TTCATTTTTATTTTTATT
1 TT-ATTTTTATTTTTATT
*
18730267 TTCATTTTTAGTTTTATT
1 TT-ATTTTTATTTTTATT
18730285 TTA-TTTTATTTTT-TT
1 TTATTTTTATTTTTATT
18730300 TTATTTT
1 TTATTTT
18730307 AATTATGCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
15 5 0.09
16 12 0.22
17 3 0.06
18 34 0.63
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.80
Consensus pattern (17 bp):
TTATTTTTATTTTTATT
Found at i:18731258 original size:14 final size:14
Alignment explanation
Indices: 18731240--18731278 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
18731230 AAAAAAAGTC
18731240 GAAAAGAAAAATTGA
1 GAAAA-AAAAATTGA
18731255 -AAAAAAATAATTGA
1 GAAAAAAA-AATTGA
18731269 GAAAAAAAAA
1 GAAAAAAAAA
18731279 GAAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 12 0.55
15 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
GAAAAAAAAATTGA
Found at i:18733223 original size:10 final size:10
Alignment explanation
Indices: 18733208--18733236 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
18733198 TTAGTTTAAT
18733208 AATTTAGTTA
1 AATTTAGTTA
18733218 AATTTAGTTA
1 AATTTAGTTA
18733228 AATTTAGTT
1 AATTTAGTT
18733237 TAAAACAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (10 bp):
AATTTAGTTA
Found at i:18734835 original size:20 final size:20
Alignment explanation
Indices: 18734798--18734835 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18734788 AGTTATTTAA
*
18734798 ATTATTTAATTAATGAAATT
1 ATTATTTAATCAATGAAATT
18734818 ATTATTTAGATCAA-GAAA
1 ATTATTTA-ATCAATGAAA
18734836 CGAGAGAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (20 bp):
ATTATTTAATCAATGAAATT
Found at i:18735118 original size:56 final size:56
Alignment explanation
Indices: 18735021--18735171 Score: 171
Period size: 56 Copynumber: 2.7 Consensus size: 56
18735011 TTCCACTAAA
* * * ***
18735021 ATTATGTGAAAAGG-GATATCCGCAAGGATATCAATGAAAAGGAATACCCTTGAGGAT
1 ATTAT-TGAAAAGGTTATATCCGAAAGGATA-CTATGAAAAGGAATACCCGAAAGGAT
* * *
18735078 ATTATTGAAAAGGTTATATCCGTAAGGATACTATGAAAAGGGATATCCGAAAGGAT
1 ATTATTGAAAAGGTTATATCCGAAAGGATACTATGAAAAGGAATACCCGAAAGGAT
* *
18735134 ATCATTGAAAAGGTTATATCCGAAAGGATA-TTTGAAAA
1 ATTATTGAAAAGGTTATATCCGAAAGGATACTATGAAAA
18735172 AATTATATCC
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
55 7 0.09
56 56 0.68
57 19 0.23
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.26
Consensus pattern (56 bp):
ATTATTGAAAAGGTTATATCCGAAAGGATACTATGAAAAGGAATACCCGAAAGGAT
Found at i:18735156 original size:29 final size:28
Alignment explanation
Indices: 18735027--18735185 Score: 137
Period size: 28 Copynumber: 5.7 Consensus size: 28
18735017 TAAAATTATG
* * *
18735027 TGAAAAGGGATATCCGCAAGGATATCAA
1 TGAAAAGGTATATCCGAAAGGATATCAT
* * *** *
18735055 TGAAAAGGAATACCCTTGAGGATATTAT
1 TGAAAAGGTATATCCGAAAGGATATCAT
*
18735083 TGAAAAGGTTATATCCGTAAGGATA-C-T
1 TGAAAAGG-TATATCCGAAAGGATATCAT
*
18735110 ATGAAAAGGGATATCCGAAAGGATATCAT
1 -TGAAAAGGTATATCCGAAAGGATATCAT
18735139 TGAAAAGGTTATATCCGAAAGGATAT--T
1 TGAAAAGG-TATATCCGAAAGGATATCAT
**
18735166 TGAAAAAATTATATCCGAAA
1 TG-AAAAGGTATATCCGAAA
18735186 AAATAATAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
27 29 0.27
28 50 0.46
29 29 0.27
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (28 bp):
TGAAAAGGTATATCCGAAAGGATATCAT
Found at i:18735177 original size:27 final size:28
Alignment explanation
Indices: 18735073--18735185 Score: 106
Period size: 27 Copynumber: 4.0 Consensus size: 28
18735063 AATACCCTTG
** *
18735073 AGGATATTATTGAAAAGGTTATATCCGTA
1 AGGATA-TATTGAAAAAATTATATCCGAA
***
18735102 AGGATACTA-TG-AAAAGGGATATCCGAA
1 AGGATA-TATTGAAAAAATTATATCCGAA
**
18735129 AGGATATCATTGAAAAGGTTATATCCGAA
1 AGGATAT-ATTGAAAAAATTATATCCGAA
18735158 AGGATAT-TTGAAAAAATTATATCCGAA
1 AGGATATATTGAAAAAATTATATCCGAA
18735185 A
1 A
18735186 AAATAATAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.01
27 38 0.54
28 4 0.06
29 28 0.39
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.27
Consensus pattern (28 bp):
AGGATATATTGAAAAAATTATATCCGAA
Found at i:18738220 original size:28 final size:24
Alignment explanation
Indices: 18738163--18738209 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
18738153 AGAAATAATC
18738163 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
18738187 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
18738210 ATTTGAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:18738222 original size:24 final size:24
Alignment explanation
Indices: 18738163--18738225 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
18738153 AGAAATAATC
* *
18738163 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTA
*
18738187 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAATCAAACTCTGTTTATTTA
* *
18738211 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
18738226 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTATTTA
Found at i:18740205 original size:24 final size:24
Alignment explanation
Indices: 18740151--18740223 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
18740141 GAAATGATCA
* *
18740151 TTCAGTTAAACTCTGTTTAATT-T
1 TTCAATTAAACTCTGTTTATTTGT
*
18740174 TTCAATTAAACTCTATTTATTTGT
1 TTCAATTAAACTCTGTTTATTTGT
*
18740198 TTCAATTAAACTTTGTTTATTTGT
1 TTCAATTAAACTCTGTTTATTTGT
18740222 TT
1 TT
18740224 GAGTCAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 19 0.43
24 25 0.57
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (24 bp):
TTCAATTAAACTCTGTTTATTTGT
Found at i:18742281 original size:20 final size:21
Alignment explanation
Indices: 18742246--18742312 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 21
18742236 GTTAATATAG
*
18742246 GAGAGTGAGAGTGAAGGAGAGA
1 GAGAGTGGGAG-GAAGGAGAGA
18742268 GAGAG-GGGAGGAAGG-GAGA
1 GAGAGTGGGAGGAAGGAGAGA
*
18742287 GAGAGTGGGATGAATGGAGAGA
1 GAGAGTGGGAGGAA-GGAGAGA
18742309 GAGA
1 GAGA
18742313 TAGATACAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.22
20 12 0.30
21 6 0.15
22 13 0.32
ACGTcount: A:0.39, C:0.00, G:0.54, T:0.07
Consensus pattern (21 bp):
GAGAGTGGGAGGAAGGAGAGA
Found at i:18746081 original size:28 final size:28
Alignment explanation
Indices: 18746041--18746222 Score: 136
Period size: 28 Copynumber: 6.5 Consensus size: 28
18746031 ACTTATGTGT
*
18746041 AAAAGG-ATATCCGCAAGTATATCAATG
1 AAAAGGAATATCCGCAAGGATATCAATG
* * *
18746068 AAAAGGAATATCCGTAAGGATATTATTG
1 AAAAGGAATATCCGCAAGGATATCAATG
* *
18746096 AAAA-CAGATATCCGCAGGGATATCAATG
1 AAAAGGA-ATATCCGCAAGGATATCAATG
* * * *
18746124 AAAAGGAATATCCGTAAGAATATTATTG
1 AAAAGGAATATCCGCAAGGATATCAATG
* ** * *
18746152 AAAAGGTTATATTTGTAAGGATA-CTATG
1 AAAAGG-AATATCCGCAAGGATATCAATG
* * * *
18746180 AAAAGGGATATTCGAAAGGATATCATTG
1 AAAAGGAATATCCGCAAGGATATCAATG
*
18746208 AAAAGGTTATATCCG
1 AAAAGG-AATATCCG
18746223 AAAAGATAAA
Statistics
Matches: 120, Mismatches: 29, Indels: 10
0.75 0.18 0.06
Matches are distributed among these distances:
27 20 0.17
28 81 0.68
29 19 0.16
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (28 bp):
AAAAGGAATATCCGCAAGGATATCAATG
Found at i:18746181 original size:56 final size:57
Alignment explanation
Indices: 18746047--18746222 Score: 214
Period size: 56 Copynumber: 3.1 Consensus size: 57
18746037 GTGTAAAAGG
* *
18746047 ATATCCGCAAGTATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAACAG--
1 ATATCCGCAAGGATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAA-GGTT
* *
18746103 ATATCCGCAGGGATATCAATGAAAAGGAATATCCGTAAGAATATTATTGAAAAGGTT
1 ATATCCGCAAGGATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAAGGTT
** * * * * * *
18746160 ATATTTGTAAGGATA-CTATGAAAAGGGATATTCGAAAGGATATCATTGAAAAGGTT
1 ATATCCGCAAGGATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAAGGTT
18746216 ATATCCG
1 ATATCCG
18746223 AAAAGATAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
55 1 0.01
56 90 0.88
57 11 0.11
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.27
Consensus pattern (57 bp):
ATATCCGCAAGGATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAAGGTT
Found at i:18746182 original size:84 final size:83
Alignment explanation
Indices: 18746041--18746222 Score: 195
Period size: 84 Copynumber: 2.2 Consensus size: 83
18746031 ACTTATGTGT
* *
18746041 AAAAGGATATCCGCAAGTATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAACAGATA
1 AAAAGGATATCCGCAAGAATATCAATGAAAAGGAATATCCGTAAGGATACTATTGAAAACAGATA
* *
18746106 TCCGCAGGGATATCAATG
66 TCCGAAAGGATATCAATG
* * * * ** **
18746124 AAAAGGAATATCCGTAAGAATATTATTGAAAAGGTTATATTTGTAAGGATACTA-TGAAAAGGGA
1 AAAAGG-ATATCCGCAAGAATATCAATGAAAAGG-AATATCCGTAAGGATACTATTGAAAACAGA
* *
18746188 TATTCGAAAGGATATCATTG
64 TATCCGAAAGGATATCAATG
18746208 AAAAGGTTATATCCG
1 AAAAGG--ATATCCG
18746223 AAAAGATAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
83 6 0.07
84 53 0.65
85 22 0.27
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (83 bp):
AAAAGGATATCCGCAAGAATATCAATGAAAAGGAATATCCGTAAGGATACTATTGAAAACAGATA
TCCGAAAGGATATCAATG
Found at i:18746281 original size:40 final size:40
Alignment explanation
Indices: 18746218--18746332 Score: 128
Period size: 40 Copynumber: 2.9 Consensus size: 40
18746208 AAAAGGTTAT
*
18746218 ATCCGAAAA-GATAAAAACTGAAAAGGTTGAAAAGGACAG-A
1 ATCC-AAAAGGATAATAACTGAAAAGGTTGAAAAGGA-AGTA
*
18746258 ATCCAAAAGGATAATAACTGAAAAGGTTGAAAAGGAAGTT
1 ATCCAAAAGGATAATAACTGAAAAGGTTGAAAAGGAAGTA
* * * *
18746298 ATCCGAAAGGACAATTAA-TTAAAAGGTCGAAAAGG
1 ATCCAAAAGGATAA-TAACTGAAAAGGTTGAAAAGG
18746333 TAAATTTATT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
39 6 0.09
40 57 0.86
41 3 0.05
ACGTcount: A:0.51, C:0.10, G:0.23, T:0.17
Consensus pattern (40 bp):
ATCCAAAAGGATAATAACTGAAAAGGTTGAAAAGGAAGTA
Found at i:18749728 original size:28 final size:28
Alignment explanation
Indices: 18749621--18749810 Score: 134
Period size: 28 Copynumber: 6.8 Consensus size: 28
18749611 TAAAATTATG
* * * * *
18749621 TGAAAAGGGATATCCGCATGAATATAAA
1 TGAAAAGGAATATCCGTAAGGATATCAA
* *
18749649 TGAAAAGGAATATCCATAAGGATAT-TA
1 TGAAAAGGAATATCCGTAAGGATATCAA
* ** *
18749676 TAGAAAAGGGATATCCACAATGATATCAA
1 T-GAAAAGGAATATCCGTAAGGATATCAA
* * *
18749705 TGAAAAGGAATACCCGTAAGGATATTAT
1 TGAAAAGGAATATCCGTAAGGATATCAA
** *
18749733 TGAAAATGTTATATCCGTAAGGATA-CTA
1 TGAAAA-GGAATATCCGTAAGGATATCAA
* *
18749761 TGAAAATGG-ATATCCGAAAGGATATCAT
1 TGAAAA-GGAATATCCGTAAGGATATCAA
* *
18749789 TGAAAAGGTTATATCCGAAAGG
1 TGAAAAGG-AATATCCGTAAGG
18749811 TTATTTGAAA
Statistics
Matches: 129, Mismatches: 27, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
27 18 0.14
28 82 0.64
29 29 0.22
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.25
Consensus pattern (28 bp):
TGAAAAGGAATATCCGTAAGGATATCAA
Found at i:18749757 original size:29 final size:29
Alignment explanation
Indices: 18749722--18749815 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 29
18749712 GAATACCCGT
*
18749722 AAGGATATTATTGAAAATGTTATATCCGT
1 AAGGATATTATTGAAAATGTTATATCCGA
* *
18749751 AAGGATACTA-TGAAAATG-GATATCCGA
1 AAGGATATTATTGAAAATGTTATATCCGA
* *
18749778 AAGGATATCATTGAAAAGGTTATATCCGA
1 AAGGATATTATTGAAAATGTTATATCCGA
*
18749807 AAGGTTATT
1 AAGGATATT
18749816 TGAAAAGATT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 15 0.28
28 15 0.28
29 24 0.44
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (29 bp):
AAGGATATTATTGAAAATGTTATATCCGA
Found at i:18749764 original size:56 final size:56
Alignment explanation
Indices: 18749615--18749810 Score: 182
Period size: 56 Copynumber: 3.5 Consensus size: 56
18749605 TTCCTCTAAA
** * * * * *
18749615 ATTATGTGAAAAGGGATATCCGCATGAATATAAATGAAAAGGAATATCCATAAGGAT
1 ATTAT-TGAAAAGTTATATCCGAAAGGATATCAATGAAAAGGAATATCCGTAAGGAT
* ** * *
18749672 ATTATAGAAAAGGGATATCC-ACAATGATATCAATGAAAAGGAATACCCGTAAGGAT
1 ATTATTGAAAAGTTATATCCGA-AAGGATATCAATGAAAAGGAATATCCGTAAGGAT
* * *
18749728 ATTATTGAAAATGTTATATCCGTAAGGATA-CTATGAAAATGG-ATATCCGAAAGGAT
1 ATTATTGAAAA-GTTATATCCGAAAGGATATCAATGAAAA-GGAATATCCGTAAGGAT
*
18749784 ATCATTGAAAAGGTTATATCCGAAAGG
1 ATTATTGAAAA-GTTATATCCGAAAGG
18749811 TTATTTGAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
56 96 0.83
57 20 0.17
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (56 bp):
ATTATTGAAAAGTTATATCCGAAAGGATATCAATGAAAAGGAATATCCGTAAGGAT
Found at i:18749830 original size:27 final size:28
Alignment explanation
Indices: 18749722--18749831 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 28
18749712 GAATACCCGT
*
18749722 AAGGATATTATTGAAAATG-TTATATCCGT
1 AAGGATA-TATTGAAAA-GATTATATCCGA
*
18749751 AAGGATACTA-TG-AAA-ATGGATATCCGA
1 AAGGATA-TATTGAAAAGAT-TATATCCGA
*
18749778 AAGGATATCATTGAAAAGGTTATATCCGA
1 AAGGATAT-ATTGAAAAGATTATATCCGA
* *
18749807 AAGGTTAT-TTGAAAAGATTGTATCC
1 AAGGATATATTGAAAAGATTATATCC
18749832 AAAAATATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.03
27 33 0.49
28 4 0.06
29 27 0.40
30 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (28 bp):
AAGGATATATTGAAAAGATTATATCCGA
Found at i:18749902 original size:40 final size:40
Alignment explanation
Indices: 18749838--18749942 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
18749828 ATCCAAAAAT
* * * *
18749838 ATAATAAATGAAAAGTTTGGAAAGGATAG-AATCTGAAAGG
1 ATAATAAATGAAAAGGTCGAAAAGGA-AGTAATCCGAAAGG
* *
18749878 ATAATAAATGAAAAGGTCGAAAAGGACGTTATCCGAAAGG
1 ATAATAAATGAAAAGGTCGAAAAGGAAGTAATCCGAAAGG
*
18749918 ATAATAAATAAAAAGGTCGAAAAGG
1 ATAATAAATGAAAAGGTCGAAAAGG
18749943 TAAATTTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 56 0.98
ACGTcount: A:0.51, C:0.06, G:0.24, T:0.19
Consensus pattern (40 bp):
ATAATAAATGAAAAGGTCGAAAAGGAAGTAATCCGAAAGG
Found at i:18750601 original size:67 final size:67
Alignment explanation
Indices: 18750472--18750601 Score: 224
Period size: 67 Copynumber: 1.9 Consensus size: 67
18750462 TAAGAACTGA
* * *
18750472 TTAGGGAATGATTACATGAAATGGTATGTGAATTGGCTATGTGTAAATATGATGTTTGGTTTAAT
1 TTAGGGAATGATTACAGGAAATGGTATGTGAATTGGCTATGTGTAAATATGATGTCTAGTTTAAT
18750537 GG
66 GG
*
18750539 TTAGGGAATGATTACAGGAAATGGTATGTGAATTGGTTATGTGTAAATATGATGTCTAGTTTA
1 TTAGGGAATGATTACAGGAAATGGTATGTGAATTGGCTATGTGTAAATATGATGTCTAGTTTA
18750602 TATGTCAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (67 bp):
TTAGGGAATGATTACAGGAAATGGTATGTGAATTGGCTATGTGTAAATATGATGTCTAGTTTAAT
GG
Found at i:18755212 original size:20 final size:20
Alignment explanation
Indices: 18755186--18755234 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
18755176 TGAGAGTGAT
18755186 AGAGAGAGAGAGGGGGAGGG
1 AGAGAGAGAGAGGGGGAGGG
* * * *
18755206 AGGGAGAGATAGTGGGATGG
1 AGAGAGAGAGAGGGGGAGGG
18755226 AGAGAGAGA
1 AGAGAGAGA
18755235 CAGATACAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.57, T:0.06
Consensus pattern (20 bp):
AGAGAGAGAGAGGGGGAGGG
Found at i:18762027 original size:45 final size:45
Alignment explanation
Indices: 18761976--18762065 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
18761966 GAACAGATGG
* *
18761976 AGTACTCTATTCCTAGTTTACTCGAAATGCTCCCTTATTCTCCCT
1 AGTACTCTATTCCTAGTTTACTCGAAATGCTCCCCTACTCTCCCT
18762021 AGTACTCTATTCCTAGTTTACTCGAAATGCTCCCCTACTCTCCCT
1 AGTACTCTATTCCTAGTTTACTCGAAATGCTCCCCTACTCTCCCT
18762066 CTTGCATTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.38
Consensus pattern (45 bp):
AGTACTCTATTCCTAGTTTACTCGAAATGCTCCCCTACTCTCCCT
Found at i:18765320 original size:13 final size:14
Alignment explanation
Indices: 18765286--18765325 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
18765276 TGGAAATAGA
*
18765286 TATATGAAATGATT
1 TATATGAAGTGATT
18765300 T-TATGAAGTG-TT
1 TATATGAAGTGATT
18765312 TATATGAAGT-ATT
1 TATATGAAGTGATT
18765325 T
1 T
18765326 GTAGAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 3 0.13
13 19 0.83
14 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.47
Consensus pattern (14 bp):
TATATGAAGTGATT
Found at i:18773505 original size:47 final size:41
Alignment explanation
Indices: 18773399--18773528 Score: 215
Period size: 41 Copynumber: 3.2 Consensus size: 41
18773389 TGAGAGGGTA
*
18773399 AGAGATTAGATGAAGACTATGATTAATATTTATGGAGAGTG
1 AGAGAGTAGATGAAGACTATGATTAATATTTATGGAGAGTG
18773440 AGAGAGTAGATGAAGACTATGATTAATATTTATGGAGAGTG
1 AGAGAGTAGATGAAGACTATGATTAATATTTATGGAGAGTG
* * * *
18773481 AGAGAGTAGATGAAGACTATGACTAATATATGTGGAGAGTC
1 AGAGAGTAGATGAAGACTATGATTAATATTTATGGAGAGTG
18773522 AGAGAGT
1 AGAGAGT
18773529 GAAAGATTAG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.39, C:0.04, G:0.29, T:0.28
Consensus pattern (41 bp):
AGAGAGTAGATGAAGACTATGATTAATATTTATGGAGAGTG
Found at i:18776164 original size:15 final size:15
Alignment explanation
Indices: 18776144--18776187 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
18776134 AGTTGTTCAC
18776144 TTCTTCTTGTTCTTG
1 TTCTTCTTGTTCTTG
18776159 TTCTTCTTGTTCTTG
1 TTCTTCTTGTTCTTG
*
18776174 TTCTTCTTCTTCTT
1 TTCTTCTTGTTCTT
18776188 ATATGGGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.68
Consensus pattern (15 bp):
TTCTTCTTGTTCTTG
Found at i:18776165 original size:9 final size:9
Alignment explanation
Indices: 18776143--18776187 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
18776133 TAGTTGTTCA
18776143 CTTCTTCTT
1 CTTCTTCTT
* *
18776152 GTTCTTGTT
1 CTTCTTCTT
*
18776161 CTTCTTGTT
1 CTTCTTCTT
*
18776170 CTTGTTCTT
1 CTTCTTCTT
18776179 CTTCTTCTT
1 CTTCTTCTT
18776188 ATATGGGACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.00, C:0.24, G:0.09, T:0.67
Consensus pattern (9 bp):
CTTCTTCTT
Found at i:18776185 original size:6 final size:6
Alignment explanation
Indices: 18776143--18776187 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
18776133 TAGTTGTTCA
* * * *
18776143 CTTCTT CTTGTT CTTGTT CTTCTT GTTCTT GTTCTT CTTCTT CTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTT
18776188 ATATGGGACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.24, G:0.09, T:0.67
Consensus pattern (6 bp):
CTTCTT
Found at i:18778861 original size:6 final size:6
Alignment explanation
Indices: 18778850--18778903 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
18778840 GTGTTTAATT
* * * *
18778850 AAAATA AAAATA AAAAT- AAAAT- AAAATA AAACTG AAAATG AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
18778896 AAAATA AA
1 AAAATA AA
18778904 TATACTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:18778867 original size:12 final size:12
Alignment explanation
Indices: 18778850--18778903 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
18778840 GTGTTTAATT
*
18778850 AAAATAAAAATA
1 AAAATAAAAATG
18778862 AAAAT-AAAAT-
1 AAAATAAAAATG
*
18778872 AAAATAAAACTG
1 AAAATAAAAATG
*
18778884 AAAATGAAAATG
1 AAAATAAAAATG
18778896 AAAATAAA
1 AAAATAAA
18778904 TATACTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.14
11 9 0.25
12 22 0.61
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:18778938 original size:21 final size:21
Alignment explanation
Indices: 18778912--18778957 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
18778902 AATATACTAA
*
18778912 TTTTTTAG-AATTTT-TCAATT
1 TTTTTTTGAAATTTTCTC-ATT
18778932 TTTTTTTGAAATTTTCTCATT
1 TTTTTTTGAAATTTTCTCATT
18778953 TTTTT
1 TTTTT
18778958 AAAAACGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTTTGAAATTTTCTCATT
Found at i:18784748 original size:17 final size:17
Alignment explanation
Indices: 18784728--18784767 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
18784718 ATATAAGTGC
18784728 ATAAATTATATTTCTAT
1 ATAAATTATATTTCTAT
18784745 ATAAATTATATTTCTAT
1 ATAAATTATATTTCTAT
18784762 ATAAAT
1 ATAAAT
18784768 ATGGCTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAAATTATATTTCTAT
Found at i:18805222 original size:26 final size:24
Alignment explanation
Indices: 18805186--18805241 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
18805176 TGATTTAATT
*
18805186 TATTATTAATTAATATTAGAATATAA
1 TATTATAAATTAATATT-GAAT-TAA
* *
18805212 TATTATAAATTATTATTTAATTAA
1 TATTATAAATTAATATTGAATTAA
18805236 TATTAT
1 TATTAT
18805242 CTTATTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 9 0.33
25 3 0.11
26 15 0.56
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTATAAATTAATATTGAATTAA
Found at i:18805513 original size:14 final size:14
Alignment explanation
Indices: 18805494--18805520 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18805484 GCTCAAACGA
18805494 AAAAGGGAAGGAAG
1 AAAAGGGAAGGAAG
18805508 AAAAGGGAAGGAA
1 AAAAGGGAAGGAA
18805521 AAAGAAAAAG
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:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AAAAGGGAAGGAAG
Found at i:18812947 original size:40 final size:40
Alignment explanation
Indices: 18812903--18813009 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
18812893 AATTGATAAA
18812903 GGATTAAATTGTAAAAGAAGTTATAAGTTTTGTGATAGAG
1 GGATTAAATTGTAAAAGAAGTTATAAGTTTTGTGATAGAG
18812943 GGATTAAATTGTAAAAGAAGTTATAAGTTTTGTGATAGAG
1 GGATTAAATTGTAAAAGAAGTTATAAGTTTTGTGATAGAG
* *
18812983 GGATTAAATTG--AAAGAAATTTTAAGTT
1 GGATTAAATTGTAAAAGAAGTTATAAGTT
18813010 AGGGTTTTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
38 14 0.22
40 51 0.78
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (40 bp):
GGATTAAATTGTAAAAGAAGTTATAAGTTTTGTGATAGAG
Found at i:18814971 original size:18 final size:19
Alignment explanation
Indices: 18814919--18814972 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
18814909 AGGTGGAACT
18814919 TGAGGAGAAGAAGGAA-AA
1 TGAGGAGAAGAAGGAAGAA
*
18814937 TAAGGA-AGAGAAGGAAGAA
1 TGAGGAGA-AGAAGGAAGAA
18814956 -GAGGAGAAGAAGGAAGA
1 TGAGGAGAAGAAGGAAGA
18814973 TGCCCTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 1 0.03
18 27 0.87
19 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.04
Consensus pattern (19 bp):
TGAGGAGAAGAAGGAAGAA
Found at i:18815411 original size:17 final size:18
Alignment explanation
Indices: 18815372--18815415 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
18815362 ATGCATAGCA
* *
18815372 TTTAGTTGTCATTGCACT
1 TTTATTTGTCACTGCACT
18815390 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTGCACT
18815407 TTTATTTGT
1 TTTATTTGT
18815416 TAGTACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (18 bp):
TTTATTTGTCACTGCACT
Found at i:18816030 original size:21 final size:22
Alignment explanation
Indices: 18815997--18816039 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
18815987 AGTCACGAAC
*
18815997 AAAATAAAAAAGAAGA-AAAAG
1 AAAACAAAAAAGAAGAGAAAAG
*
18816018 AAAACAAAGAAGAAGAGAAAAG
1 AAAACAAAAAAGAAGAGAAAAG
18816040 TAGAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (22 bp):
AAAACAAAAAAGAAGAGAAAAG
Found at i:18819713 original size:26 final size:26
Alignment explanation
Indices: 18819631--18819720 Score: 72
Period size: 26 Copynumber: 3.5 Consensus size: 26
18819621 ATTTTGGGCG
* * * *
18819631 CAATTCTCGACATGCTCATACAACGA
1 CAATTCTGGACAAGTTCATGCAACGA
* * * *
18819657 CAAGTCTGGACATGTTCATGCAGCAA
1 CAATTCTGGACAAGTTCATGCAACGA
* **
18819683 TAATTCTGGACAAGTTTTTGCAACGA
1 CAATTCTGGACAAGTTCATGCAACGA
*
18819709 CAATTCTAGACA
1 CAATTCTGGACA
18819721 TGCTCATGTA
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (26 bp):
CAATTCTGGACAAGTTCATGCAACGA
Found at i:18825352 original size:15 final size:15
Alignment explanation
Indices: 18825325--18825364 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
18825315 CTTCAGCTAA
18825325 TCTCCCTCC-CTCTC
1 TCTCCCTCCTCTCTC
18825339 TC-CTCCTCCTCTCTC
1 TCTC-CCTCCTCTCTC
18825354 TCTCCCTCCTC
1 TCTCCCTCCTC
18825365 CTTTTCTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 7 0.30
15 14 0.61
16 1 0.04
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (15 bp):
TCTCCCTCCTCTCTC
Found at i:18825372 original size:19 final size:18
Alignment explanation
Indices: 18825329--18825380 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
18825319 AGCTAATCTC
*
18825329 CCTCCCTCTCT-CCTCCT
1 CCTCTCTCTCTCCCTCCT
18825346 CCTCTCTCTCTCCCTCCT
1 CCTCTCTCTCTCCCTCCT
* *
18825364 CCTTTTCTCACTCCCTC
1 CC-TCTCTCTCTCCCTC
18825381 ACACTCACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 10 0.33
18 8 0.27
19 12 0.40
ACGTcount: A:0.02, C:0.60, G:0.00, T:0.38
Consensus pattern (18 bp):
CCTCTCTCTCTCCCTCCT
Found at i:18825710 original size:3 final size:3
Alignment explanation
Indices: 18825702--18825729 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18825692 CAGTCTCAAG
18825702 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
18825730 TGAACAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:18828301 original size:246 final size:245
Alignment explanation
Indices: 18827861--18828501 Score: 771
Period size: 246 Copynumber: 2.6 Consensus size: 245
18827851 AATCAAAATC
* * * *
18827861 AATTCTGTTGAACGACAGGAATAAATCTAGAAACAGAATTATTTAATTAATTTTTGTTTGGAAAC
1 AATT-TGTTGTACGACAGGAATAAATCTCGAAACAGAATTATTAAATTAATATTT-TTTGGAAAC
* *
18827926 AAAATCAAAAT-CAAT----TCTATTGAACGGTAGGAATAAATCTCGAAACAGAATTATTCAATT
64 AAAATCAAAATAGAATAAAATCTATTGAACGGTAGGAATAAATCTCGAAATAGAATTATTCAATT
** * *
18827986 AATTCTTGTTTGGAAACAAAATTAAAATAGAATAAAATCTGTTGAACAGCGTGAATAAATCCCGA
129 AATTCTTGTTCAGAAACAAAATCAAAATAGAATAAAATCTGTTGAACAGCGGGAATAAATCCCGA
* * *
18828051 AACAGAATTATTCTATTAATTCTTGTTTGGAAACAAAATCAGAATAGAATAA
194 AACAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAA
*
18828103 AATTTGTTGTACGACAGGAATAAATCTCGAAACAGAATTATTCAATTAATGATTTTTTGGAAACA
1 AATTTGTTGTACGACAGGAATAAATCTCGAAACAGAATTATTAAATTAAT-ATTTTTTGGAAACA
* * * *
18828168 AAATTAAAATAGAATAAAATCTCTTCAACGGTGGGAATAAATCTCGAAATAGAATTATTCAATTA
65 AAATCAAAATAGAATAAAATCTATTGAACGGTAGGAATAAATCTCGAAATAGAATTATTCAATTA
* * * * *
18828233 ATCCTTGTTCAGAAACAAAATCAAAGTAGAATAAAATTTGTTTAAC-GACGGGAATAAATCTCGA
130 ATTCTTGTTCAGAAACAAAATCAAAATAGAATAAAATCTGTTGAACAG-CGGGAATAAATCCCGA
*
18828297 AACAGAATTATTCAATTAATCCTTTTTTGGAAACAAAATCAAAATAGAATAA
194 AACAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAA
* * * ***
18828349 AATTTGTT-TAACGGCAAGAATAAAT-TCAGAAACA-AATTTATTAAATTAATCCTTTTTAAAAA
1 AATTTGTTGT-ACGACAGGAATAAATCTC-GAAACAGAA-TTATTAAATTAAT-ATTTTTTGGAA
* ** * * *
18828411 ACAAAATCACAATAGAATAAAATC-AGTTGAACGACAGGAATAAATCTCGAAATATATTTATTGA
62 ACAAAATCAAAATAGAATAAAATCTA-TTGAACGGTAGGAATAAATCTCGAAATAGAATTATTCA
* *
18828475 ATTTTAATTTTTATTCAGAAACAAAAT
126 A--TTAATTCTTGTTCAGAAACAAAAT
18828502 ATGTTTTTCA
Statistics
Matches: 342, Mismatches: 44, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
241 62 0.18
242 10 0.03
245 6 0.02
246 243 0.71
248 21 0.06
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (245 bp):
AATTTGTTGTACGACAGGAATAAATCTCGAAACAGAATTATTAAATTAATATTTTTTGGAAACAA
AATCAAAATAGAATAAAATCTATTGAACGGTAGGAATAAATCTCGAAATAGAATTATTCAATTAA
TTCTTGTTCAGAAACAAAATCAAAATAGAATAAAATCTGTTGAACAGCGGGAATAAATCCCGAAA
CAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAA
Found at i:18828472 original size:82 final size:81
Alignment explanation
Indices: 18827864--18828462 Score: 676
Period size: 82 Copynumber: 7.4 Consensus size: 81
18827854 CAAAATCAAT
* * **
18827864 TCTGTTGAACGACAGGAATAAATCTAGAAACAGAATTATTTAATTAATTTTTGTTTGGAAACAAA
1 TCTGTTGAACGACAGGAATAAATCTCGAAACAGAATTATTCAATTAATCCTT-TTTGGAAACAAA
*
18827929 ATCAAAAT-CAAT----
65 ATCAAAATAGAATAAAA
* ** *
18827941 TCTATTGAACGGTAGGAATAAATCTCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAA
1 TCTGTTGAACGACAGGAATAAATCTCGAAACAGAATTATTCAATTAATCCTT-TTTGGAAACAAA
*
18828006 ATTAAAATAGAATAAAA
65 ATCAAAATAGAATAAAA
* * *
18828023 TCTGTTGAAC-AGC-GTGAATAAATCCCGAAACAGAATTATTCTATTAATTCTTGTTTGGAAACA
1 TCTGTTGAACGA-CAG-GAATAAATCTCGAAACAGAATTATTCAATTAATCCTT-TTTGGAAACA
*
18828086 AAATCAGAATAGAATAAAA
63 AAATCAAAATAGAATAAAA
* * **
18828105 TTTGTTGTACGACAGGAATAAATCTCGAAACAGAATTATTCAATTAATGATTTTTTGGAAACAAA
1 TCTGTTGAACGACAGGAATAAATCTCGAAACAGAATTATTCAATTAAT-CCTTTTTGGAAACAAA
*
18828170 ATTAAAATAGAATAAAA
65 ATCAAAATAGAATAAAA
* * *** * **
18828187 TCTCTTCAACGGTGGGAATAAATCTCGAAATAGAATTATTCAATTAATCCTTGTTCAGAAACAAA
1 TCTGTTGAACGACAGGAATAAATCTCGAAACAGAATTATTCAATTAATCCTT-TTTGGAAACAAA
*
18828252 ATCAAAGTAGAATAAAA
65 ATCAAAATAGAATAAAA
* * *
18828269 TTTGTTTAACGACGGGAATAAATCTCGAAACAGAATTATTCAATTAATCCTTTTTTGGAAACAAA
1 TCTGTTGAACGACAGGAATAAATCTCGAAACAGAATTATTCAATTAATCC-TTTTTGGAAACAAA
18828334 ATCAAAATAGAATAAAA
65 ATCAAAATAGAATAAAA
* * * * * **
18828351 TTTGTTTAACGGCAAGAATAAAT-TCAGAAACA-AATTTATTAAATTAATCCTTTTTAAAAAACA
1 TCTGTTGAACGACAGGAATAAATCTC-GAAACAGAA-TTATTCAATTAATCCTTTTT-GGAAACA
*
18828414 AAATCACAATAGAATAAAA
63 AAATCAAAATAGAATAAAA
*
18828433 TCAGTTGAACGACAGGAATAAATCTCGAAA
1 TCTGTTGAACGACAGGAATAAATCTCGAAA
18828463 TATATTTATT
Statistics
Matches: 448, Mismatches: 58, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
77 66 0.15
78 3 0.01
81 12 0.03
82 359 0.80
83 8 0.02
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.30
Consensus pattern (81 bp):
TCTGTTGAACGACAGGAATAAATCTCGAAACAGAATTATTCAATTAATCCTTTTTGGAAACAAAA
TCAAAATAGAATAAAA
Found at i:18829010 original size:50 final size:50
Alignment explanation
Indices: 18828947--18829070 Score: 187
Period size: 50 Copynumber: 2.5 Consensus size: 50
18828937 AAAATACAAT
* *
18828947 ATCTGAA-AAAACAATATAAATAAATATTTATATTTATGTAAAACAACAG
1 ATCTGAACAAAACAATTTAAATAAATATTTATATTTATATAAAACAACAG
* * *
18828996 ATCTGAACAAAACAATTTAAATAAATATTTATTTTTATATAAAACACCAT
1 ATCTGAACAAAACAATTTAAATAAATATTTATATTTATATAAAACAACAG
*
18829046 ATCTGAACAAAACAATTTAGATAAA
1 ATCTGAACAAAACAATTTAAATAAA
18829071 CAAGTTTTGA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 7 0.10
50 61 0.90
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.31
Consensus pattern (50 bp):
ATCTGAACAAAACAATTTAAATAAATATTTATATTTATATAAAACAACAG
Found at i:18831517 original size:20 final size:20
Alignment explanation
Indices: 18831462--18831517 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
18831452 ATCTAATCTC
*
18831462 CCTCCC-CCCTCTCTCGC-T
1 CCTCCCTCCCTCTCTCTCTT
*
18831480 CC-CCCTCCCTCCCTCTCTT
1 CCTCCCTCCCTCTCTCTCTT
*
18831499 CCTCCCTCCCTCTCACTCT
1 CCTCCCTCCCTCTCTCTCT
18831518 CACTCTCCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.10
18 11 0.35
19 3 0.10
20 14 0.45
ACGTcount: A:0.02, C:0.66, G:0.02, T:0.30
Consensus pattern (20 bp):
CCTCCCTCCCTCTCTCTCTT
Found at i:18831525 original size:22 final size:19
Alignment explanation
Indices: 18831458--18831518 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 19
18831448 CATCATCTAA
*
18831458 TCTCCCTCCCCCCTCTCTCGC
1 TCTCCCTCCCTCC-CTCTC-C
*
18831479 TCCCCCTCCCTCCCTCT-C
1 TCTCCCTCCCTCCCTCTCC
18831497 T-T-CCTCCCTCCCTCTCAC
1 TCTCCCTCCCTCCCTCTC-C
18831515 TCTC
1 TCTC
18831519 ACTCTCCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
16 13 0.39
18 4 0.12
19 1 0.03
20 4 0.12
21 11 0.33
ACGTcount: A:0.02, C:0.66, G:0.02, T:0.31
Consensus pattern (19 bp):
TCTCCCTCCCTCCCTCTCC
Found at i:18835294 original size:18 final size:17
Alignment explanation
Indices: 18835273--18835317 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
18835263 TGTCTTTTTC
18835273 TTCTCTTTTTTTCTCAAT
1 TTCTCTTTTTTT-TCAAT
18835291 TTCTCTTTTTTTTCAAT
1 TTCTCTTTTTTTTCAAT
*
18835308 TTTTCTTTTT
1 TTCTCTTTTT
18835318 GACTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (17 bp):
TTCTCTTTTTTTTCAAT
Found at i:18835341 original size:11 final size:11
Alignment explanation
Indices: 18835290--18835341 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
18835280 TTTTTCTCAA
18835290 TTTCTCTTTTT
1 TTTCTCTTTTT
*
18835301 TTTCAATTTTTCTT
1 TTTC--TCTTT-TT
**
18835315 TTTGACTTTTT
1 TTTCTCTTTTT
18835326 TTTCTCTTTTT
1 TTTCTCTTTTT
18835337 TTTCT
1 TTTCT
18835342 TTTCTGAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
11 20 0.62
12 3 0.09
13 4 0.12
14 5 0.16
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTCTCTTTTT
Found at i:18835344 original size:17 final size:17
Alignment explanation
Indices: 18835259--18835344 Score: 59
Period size: 19 Copynumber: 4.7 Consensus size: 17
18835249 CTCGGACATA
*
18835259 TTTTTGTCTTTTTCTTCT
1 TTTTTTTCTTTTTC-TCT
*
18835277 CTTTTTTTCTCAATTTCTCT
1 -TTTTTTTCT--TTTTCTCT
18835297 TTTTTTTCAATTTTTCT-T
1 TTTTTTTC--TTTTTCTCT
*
18835315 TTTGACTTT-TTTTTCTCT
1 TTT--TTTTCTTTTTCTCT
18835333 TTTTTTTCTTTT
1 TTTTTTTCTTTT
18835345 CTGAACATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
16 3 0.06
17 11 0.20
18 8 0.15
19 21 0.39
20 6 0.11
21 5 0.09
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTTTCTTTTTCTCT
Found at i:18836399 original size:6 final size:6
Alignment explanation
Indices: 18836390--18836479 Score: 83
Period size: 6 Copynumber: 14.8 Consensus size: 6
18836380 AGTGCATAAT
* * * *
18836390 AAAATA AAAATAA AAAATA AAAAAA AAAACTA AAACTA AAACTA AAAATG
1 AAAATA AAAAT-A AAAATA AAAATA AAAA-TA AAAATA AAAATA AAAATA
* * * *
18836440 AAAATG AAAATG AAAATG AAAATG AAAATA AAAA-A AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
18836480 GTAATAATTT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.07
6 60 0.80
7 10 0.13
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:18836411 original size:125 final size:125
Alignment explanation
Indices: 18836179--18836412 Score: 434
Period size: 125 Copynumber: 1.9 Consensus size: 125
18836169 CAATTTTCCG
18836179 AGCAAACTAATAAGAAAATAGACAAACGCAAGTAACAGAGGGAGATAACAACTAAAAAGATCATA
1 AGCAAACTAATAAGAAAATAGACAAACGCAAGTAACAGAGGGAGATAACAACTAAAAAGATCATA
* *
18836244 GGAATAAAAATAGTGCATAATAAAACTAAAACTAAAACTAAAAATGAAAATGAAAATGAA
66 GGAATAAAAATAGTGCATAATAAAACTAAAAATAAAAATAAAAATGAAAATGAAAATGAA
18836304 AGCAAACTAATAAGAAAATAGACAAACGCAAGTAACAGAGGGAGATAACAACTAAAAAGATCATA
1 AGCAAACTAATAAGAAAATAGACAAACGCAAGTAACAGAGGGAGATAACAACTAAAAAGATCATA
18836369 GGAATAAAAATAGTGCATAATAAAA-TAAAAATAAAAAATAAAAA
66 GGAATAAAAATAGTGCATAATAAAACTAAAAAT-AAAAATAAAAA
18836413 AAAAAACTAA
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
124 6 0.06
125 100 0.94
ACGTcount: A:0.61, C:0.10, G:0.14, T:0.15
Consensus pattern (125 bp):
AGCAAACTAATAAGAAAATAGACAAACGCAAGTAACAGAGGGAGATAACAACTAAAAAGATCATA
GGAATAAAAATAGTGCATAATAAAACTAAAAATAAAAATAAAAATGAAAATGAAAATGAA
Found at i:18836511 original size:19 final size:20
Alignment explanation
Indices: 18836487--18836529 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
18836477 AATGTAATAA
18836487 TTTTTTGAA-TTTTTTATTT
1 TTTTTTGAATTTTTTTATTT
18836506 TTTTTTGAATTTTTTTATTT
1 TTTTTTGAATTTTTTTATTT
18836526 TTTT
1 TTTT
18836530 AAAAAATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (20 bp):
TTTTTTGAATTTTTTTATTT
Found at i:18840471 original size:25 final size:23
Alignment explanation
Indices: 18840443--18840488 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
18840433 GTTGGTTCCA
18840443 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
18840468 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
18840489 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:18849150 original size:14 final size:13
Alignment explanation
Indices: 18849127--18849172 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
18849117 GTTAGTTTAT
*
18849127 TTTA-ATTATAGA
1 TTTATATTATATA
18849139 CTTTATATTATATA
1 -TTTATATTATATA
18849153 TTTATATT-TATA
1 TTTATATTATATA
18849165 TTTATATT
1 TTTATATT
18849173 TGTGAATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 12 0.39
13 12 0.39
14 7 0.23
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTATATTATATA
Found at i:18849160 original size:6 final size:6
Alignment explanation
Indices: 18849140--18849173 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
18849130 AATTATAGAC
18849140 TTTATA TTATATA TTTATA TTTATA TTTATA TTT
1 TTTATA TT-TATA TTTATA TTTATA TTTATA TTT
18849174 GTGAATGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:18860351 original size:6 final size:6
Alignment explanation
Indices: 18860340--18860369 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
18860330 AATAAATAGT
18860340 AAAATA AAAATA AAAAT- AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA A
18860370 TTGGGTTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:18860353 original size:11 final size:11
Alignment explanation
Indices: 18860340--18860369 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
18860330 AATAAATAGT
18860340 AAAATAAAAATA
1 AAAAT-AAAATA
18860352 AAAATAAAATA
1 AAAATAAAATA
18860363 AAAATAA
1 AAAATAA
18860370 TTGGGTTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:18860361 original size:17 final size:18
Alignment explanation
Indices: 18860329--18860369 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
18860319 TATAATAAAT
*
18860329 AAATAAATAGTAAAATAA
1 AAATAAATAATAAAATAA
18860347 AAATAAA-AATAAAATAA
1 AAATAAATAATAAAATAA
18860364 AAATAA
1 AAATAA
18860370 TTGGGTTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATAAATAATAAAATAA
Done.