Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 126 of 135
Found at i:41341536 original size:11 final size:11
Alignment explanation
Indices: 41341518--41341551 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41341508 AACATTTTAT
*
41341518 TAAATTTAAAT
1 TAAATTTAAAA
*
41341529 TGAATTTAAAA
1 TAAATTTAAAA
41341540 TAAATTTAAAA
1 TAAATTTAAAA
41341551 T
1 T
41341552 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:41341560 original size:22 final size:21
Alignment explanation
Indices: 41341518--41341578 Score: 50
Period size: 22 Copynumber: 2.8 Consensus size: 21
41341508 AACATTTTAT
**
41341518 TAAATTTAAATTGAATTTAAAA
1 TAAATTTAAATT-AAAATAAAA
*
41341540 TAAATTTAAAATTAAAATAAAT
1 TAAATTT-AAATTAAAATAAAA
* *
41341562 TTAATTTCAAAGTAAAA
1 TAAATTT-AAATTAAAA
41341579 ATGGTTTGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAATTTAAATTAAAATAAAA
Found at i:41341577 original size:17 final size:16
Alignment explanation
Indices: 41341524--41341568 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
41341514 TTATTAAATT
*
41341524 TAAATTGAATTTAAAA
1 TAAATTTAATTTAAAA
*
41341540 TAAATTTAAAATTAAAA
1 TAAATTT-AATTTAAAA
41341557 TAAATTTAATTT
1 TAAATTTAATTT
41341569 CAAAGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:41347927 original size:2 final size:2
Alignment explanation
Indices: 41347922--41347955 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41347912 TATATATATA
41347922 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41347956 AATTCATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:41364496 original size:28 final size:29
Alignment explanation
Indices: 41364433--41364496 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
41364423 ATTTTGAAAT
* *
41364433 TTAAAATATAGAAAAACTAAATTTCTAAA
1 TTAAAAAATACAAAAACTAAATTTCTAAA
*
41364462 --AATAAAATACAAAAATTAAATTTC-AAA
1 TTAA-AAAATACAAAAACTAAATTTCTAAA
41364489 TTAAAAAA
1 TTAAAAAA
41364497 AAAAGTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
27 5 0.17
28 22 0.76
29 2 0.07
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (29 bp):
TTAAAAAATACAAAAACTAAATTTCTAAA
Found at i:41367929 original size:29 final size:29
Alignment explanation
Indices: 41367890--41367969 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 29
41367880 CCTAAAAAGC
* * *
41367890 GCGTTTACGTGGAAGTGTTTTTCAACAAA
1 GCGTCTACGTGGAAGCGTTTTTCAAAAAA
41367919 GCGTCTACGTGGAAGCGTTTTTCAAAAAA
1 GCGTCTACGTGGAAGCGTTTTTCAAAAAA
*
41367948 GCGTCTACGTGGAAACGTTTTT
1 GCGTCTACGTGGAAGCGTTTTT
41367970 GCGCACAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (29 bp):
GCGTCTACGTGGAAGCGTTTTTCAAAAAA
Found at i:41368166 original size:235 final size:233
Alignment explanation
Indices: 41367692--41368175 Score: 736
Period size: 235 Copynumber: 2.1 Consensus size: 233
41367682 AAGCGCGGTG
* *
41367692 ACGTGGAAGCGTTTTTCAAAAAAGCATCCACGTGGAAGCGTTTTTACGCACGAGAAGGTGACCAT
1 ACGTGGAAGCGTTTTTCAAAAAAGCATCCACGTGGAAACGTTTTTACGCACAAGAAGGTGACCAT
**
41367757 TGGGGAAAACACGTGCAAAAAAGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAGT
66 TGGGGAAAACACGTGCAAAAAAGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAAC
*
41367822 GCGCTTTTGCCCGACACAACAAAAAAAGCTTACGTGAAAGCATTTTTCTGATTTATTCCCTAAAA
131 GCGCTTTTACCCGACACAACAAAAAAAGCTTACGTGAAAGCATTTTTCTGATTTATTCCCTAAAA
* * * *
41367887 AGCGCGTTTACGTGGAAGTGTTTTTCAACAAAGCGTCT
196 AGCGCGTTGACGTGGAAGTGGTTTTCAAAAAAGCGTCC
* * * *
41367925 ACGTGGAAGCGTTTTTCAAAAAAGCGTCTACGTGGAAACGTTTTTGCGCACAAGAAGGTGACTAT
1 ACGTGGAAGCGTTTTTCAAAAAAGCATCCACGTGGAAACGTTTTTACGCACAAGAAGGTGACCAT
* **
41367990 TGGGGGAAAACACAG-GTAAAAGCGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCA
66 T-GGGGAAAACAC-GTGCAAAAAAGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCA
* * * * *
41368054 ACGCGCTTTTACCTGACACAACGAAAAAAGGCTTACGTGGAAGCATTTTTCTGATTTATTCCTTG
129 ACGCGCTTTTACCCGACACAAC-AAAAAAAGCTTACGTGAAAGCATTTTTCTGATTTATTCCCTA
41368119 AAAAGCGCGTTGACGTGGAAGTGGTTTTCAAAAAAGCGTCC
193 AAAAGCGCGTTGACGTGGAAGTGGTTTTCAAAAAAGCGTCC
*
41368160 ACGTGGAAGTGTTTTT
1 ACGTGGAAGCGTTTTT
41368176 GCGCAAGAGA
Statistics
Matches: 226, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
233 60 0.27
234 75 0.33
235 91 0.40
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (233 bp):
ACGTGGAAGCGTTTTTCAAAAAAGCATCCACGTGGAAACGTTTTTACGCACAAGAAGGTGACCAT
TGGGGAAAACACGTGCAAAAAAGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAAC
GCGCTTTTACCCGACACAACAAAAAAAGCTTACGTGAAAGCATTTTTCTGATTTATTCCCTAAAA
AGCGCGTTGACGTGGAAGTGGTTTTCAAAAAAGCGTCC
Found at i:41368279 original size:206 final size:206
Alignment explanation
Indices: 41367925--41368328 Score: 623
Period size: 206 Copynumber: 2.0 Consensus size: 206
41367915 CAAAGCGTCT
* *
41367925 ACGTGGAAGCGTTTTTCAAAAAAGCGTCTACGTGGAAACGTTTTTGCGCACAAGAAGGTGACTAT
1 ACGTGGAAGCGGTTTTCAAAAAAGCGTCCACGTGGAAACGTTTTTGCGCACAAGAAGGTGACTAT
* *
41367990 TGGGGGAAAACACAGGTAAAAGCGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAA
66 TGGGGGAAAACACAGGCAAAAGCGCGCCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAA
* * *
41368055 CGCGCTTTTACCTGACACAACGAAAAAAGGCTTACGTGGAAGCATTTTTCTGATTTATTCCTTGA
131 CGCGCTTTTACCTGACACAACGAAAAAAAGCTTACGTGGAAGCATTTTTATGATTTATTCCCTGA
41368120 AAAGCGCGTTG
196 AAAGCGCGTTG
* **
41368131 ACGTGGAAGTGGTTTTCAAAAAAGCGTCCACGTGGAAGTGTTTTTGCGCA-AGAGAAGGTGA-TC
1 ACGTGGAAGCGGTTTTCAAAAAAGCGTCCACGTGGAAACGTTTTTGCGCACA-AGAAGGTGACT-
* * *
41368194 ATTGGGGGAAAACACGGGCAAAAGCGCGCCCACATGGGAGCTTTTTTGAAAAACGCTTCCATATC
64 ATTGGGGGAAAACACAGGCAAAAGCGCGCCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATC
* * * *
41368259 AGCGCGTTTTTGCCTGACACAACGAAAAAAAGCTTACGTGGAAGTATTTTTATGATTTATTCCCT
129 AACGCGCTTTTACCTGACACAACGAAAAAAAGCTTACGTGGAAGCATTTTTATGATTTATTCCCT
41368324 GAAAA
194 GAAAA
41368329 CGACGTCACA
Statistics
Matches: 179, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
205 2 0.01
206 177 0.99
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (206 bp):
ACGTGGAAGCGGTTTTCAAAAAAGCGTCCACGTGGAAACGTTTTTGCGCACAAGAAGGTGACTAT
TGGGGGAAAACACAGGCAAAAGCGCGCCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAA
CGCGCTTTTACCTGACACAACGAAAAAAAGCTTACGTGGAAGCATTTTTATGATTTATTCCCTGA
AAAGCGCGTTG
Found at i:41374128 original size:11 final size:11
Alignment explanation
Indices: 41374058--41374130 Score: 56
Period size: 11 Copynumber: 6.1 Consensus size: 11
41374048 TAGCTTTGGG
*
41374058 TTTAAATTAAT
1 TTTAAATTTAT
41374069 TTTAAATTTAT
1 TTTAAATTTAT
*
41374080 TTTAAAATTTAAAA
1 TTT-AAATTT--AT
*
41374094 TTTAAAATTACTT
1 TTTAAATTTA--T
*
41374107 ATTTAAGTTTAT
1 -TTTAAATTTAT
41374119 TTTAAATTTAT
1 TTTAAATTTAT
41374130 T
1 T
41374131 CAAATTTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
11 25 0.51
12 7 0.14
13 5 0.10
14 12 0.24
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:41374909 original size:3 final size:3
Alignment explanation
Indices: 41374901--41374934 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
41374891 ATAAAAATGC
*
41374901 TAA TAA TAA TAA TAA TAA TAA TTAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
41374935 ATAAAAAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:41375500 original size:27 final size:27
Alignment explanation
Indices: 41375461--41375529 Score: 129
Period size: 27 Copynumber: 2.5 Consensus size: 27
41375451 ACCGAGACTG
41375461 ACGGTCGGAGGAGCGTGGAACGTTCCCA
1 ACGG-CGGAGGAGCGTGGAACGTTCCCA
41375489 ACGGCGGAGGAGCGTGGAACGTTCCCA
1 ACGGCGGAGGAGCGTGGAACGTTCCCA
41375516 ACGGCGGAGGAGCG
1 ACGGCGGAGGAGCG
41375530 ACCGGCGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 37 0.90
28 4 0.10
ACGTcount: A:0.22, C:0.25, G:0.43, T:0.10
Consensus pattern (27 bp):
ACGGCGGAGGAGCGTGGAACGTTCCCA
Found at i:41376174 original size:30 final size:30
Alignment explanation
Indices: 41376138--41376284 Score: 204
Period size: 30 Copynumber: 4.9 Consensus size: 30
41376128 AAATTGTCCA
* * *
41376138 AAAATTACATTTCGACCCTAAAACTTTTTG
1 AAAATTACATTTTGACCCCAAAACTTTTTC
* * *
41376168 AAAATTATATTTTGACCCCAAAACTTTCTG
1 AAAATTACATTTTGACCCCAAAACTTTTTC
* *
41376198 AAAATTACATTTTGACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTTC
* *
41376228 AAAATTATAGTTTGACCCCAAAACTTTTTC
1 AAAATTACATTTTGACCCCAAAACTTTTTC
41376258 AAAATTACATTTTGACCCCAAAACTTT
1 AAAATTACATTTTGACCCCAAAACTTT
41376285 CAAAAATTGC
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 102 1.00
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTTC
Found at i:41376299 original size:90 final size:89
Alignment explanation
Indices: 41376124--41376312 Score: 242
Period size: 90 Copynumber: 2.1 Consensus size: 89
41376114 CTCTGTAAGT
* * *
41376124 CCCTAAA-TTGTCCAAAAATTACATTTCGACCCTAAAACTTTTTGAAAATTATATTTTGACCCCA
1 CCCTAAACTTGTCCAAAAATTACATTTCGACCCCAAAACTTTTTCAAAATTACATTTTGACCCCA
*
41376188 AAACTTTCTGAAAATTACATTTTGA
66 AAACTTTCTAAAAATTACATTTT-A
* *
41376213 CCCCTAAACTTTTCC-AAAATTATAGTTT-GACCCCAAAACTTTTTCAAAATTACATTTTGACCC
1 -CCCTAAACTTGTCCAAAAATTACA-TTTCGACCCCAAAACTTTTTCAAAATTACATTTTGACCC
*
41376276 CAAAACTTTC-AAAAATTGCCATTTTA
64 CAAAACTTTCTAAAAATT-ACATTTTA
41376302 CCCTCAAACTT
1 CCCT-AAACTT
41376313 CCCTAAATCC
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
88 4 0.05
89 13 0.15
90 63 0.72
91 8 0.09
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (89 bp):
CCCTAAACTTGTCCAAAAATTACATTTCGACCCCAAAACTTTTTCAAAATTACATTTTGACCCCA
AAACTTTCTAAAAATTACATTTTA
Found at i:41376348 original size:59 final size:58
Alignment explanation
Indices: 41376285--41376480 Score: 164
Period size: 59 Copynumber: 3.3 Consensus size: 58
41376275 CCAAAACTTT
* * *
41376285 CAAAAATTGCCATTTTACCCTCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCTCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * * * * * ** * **
41376344 CAAAACTTACCGTTTT-GCCTCCGAACTTTCCAAAATTTCATTTTTGACCATGTTTTTGC
1 CAAAAATTACCATTTTACCCT-CAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * *
41376403 CAAAATTTACCATTTTATTCCC-CAAGCTTTCCAAATTCCA-TTTTAGCCCCGATTTCAC
1 CAAAAATTACCATTTTA--CCCTCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
*
41376461 AAAAAATTACCATTTTACCC
1 CAAAAATTACCATTTTACCC
41376481 CTAAAAACCC
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
56 3 0.03
58 29 0.28
59 61 0.59
60 8 0.08
62 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.06, T:0.36
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCTCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
Found at i:41377933 original size:24 final size:24
Alignment explanation
Indices: 41377912--41377963 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
41377902 AATCAATGTC
*
41377912 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
41377936 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
41377960 AAAT
1 AAAT
41377964 CTTTTAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:41380502 original size:19 final size:19
Alignment explanation
Indices: 41380465--41380503 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41380455 CTTTATATAT
**
41380465 TTTTAGAATTTTTTTAAAA
1 TTTTAGAATTTTTGAAAAA
*
41380484 TTTTATAATTTTTGAAAAA
1 TTTTAGAATTTTTGAAAAA
41380503 T
1 T
41380504 ATAAAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTAGAATTTTTGAAAAA
Found at i:41380678 original size:9 final size:9
Alignment explanation
Indices: 41380658--41380691 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
41380648 TTATTCAAGT
*
41380658 TAACTAGAA
1 TAACTTGAA
*
41380667 TAATTTGAA
1 TAACTTGAA
41380676 TAACTTGAA
1 TAACTTGAA
41380685 TAACTTG
1 TAACTTG
41380692 GAATCGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (9 bp):
TAACTTGAA
Found at i:41382352 original size:30 final size:28
Alignment explanation
Indices: 41382316--41382376 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
41382306 TTATGTTATC
41382316 TTAATTTTAT-AACAATTTACAACACATATT
1 TTAATTTTATGAA-AATTTAC-A-ACATATT
*
41382346 TTAATTTTATGAATATTTACAACATATT
1 TTAATTTTATGAAAATTTACAACATATT
41382374 TTA
1 TTA
41382377 TTACAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.34
29 1 0.03
30 16 0.55
31 2 0.07
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.48
Consensus pattern (28 bp):
TTAATTTTATGAAAATTTACAACATATT
Found at i:41386144 original size:29 final size:29
Alignment explanation
Indices: 41386080--41386394 Score: 253
Period size: 30 Copynumber: 10.7 Consensus size: 29
41386070 GACATTCAGA
* * ***
41386080 GGTAAAAATGTAACTTTT-AAAGTTTTAG
1 GGTAAAAATGTAATTTTTGGAAGTTCGGG
41386108 GGTCAAAAATAG-AATTTTTGGAAGTTCGGG
1 GGT-AAAAAT-GTAATTTTTGGAAGTTCGGG
*
41386138 GGTAAAAAATGTAATTTTTGGAAGTTACGAG
1 GGT-AAAAATGTAATTTTTGGAAGTT-CGGG
* * *
41386169 GTTAAAAATGGAATTTTTGGAAGTT-TGG
1 GGTAAAAATGTAATTTTTGGAAGTTCGGG
* *
41386197 GGTAAAAATGTAATTTTTGAAAGTTTC-GA
1 GGTAAAAATGTAATTTTTGGAAG-TTCGGG
* *
41386226 TGTCAAAAATGGAATTTTTGGAAGTTCGGG
1 GGT-AAAAATGTAATTTTTGGAAGTTCGGG
* **
41386256 GGTAAAAATGTAATTTTTGGAGGTT-ATG
1 GGTAAAAATGTAATTTTTGGAAGTTCGGG
* * **
41386284 GATCAAAAATGGAATTTTTGGAAGTTTAGG
1 GGT-AAAAATGTAATTTTTGGAAGTTCGGG
**
41386314 GGTAAAAATGTAATTTTTGGAAGTTTTAGG
1 GGTAAAAATGTAATTTTTGGAAG-TTCGGG
* * *
41386344 GTTAAAAATGTAATTTTAGAGAAGTTTGGG
1 GGTAAAAATGTAATTTTTG-GAAGTTCGGG
** * *
41386374 GGTCGAAATATAATTTCTGGA
1 GGTAAAAATGTAATTTTTGGA
41386395 TAATTTAAGG
Statistics
Matches: 235, Mismatches: 39, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
28 27 0.11
29 82 0.35
30 117 0.50
31 9 0.04
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
GGTAAAAATGTAATTTTTGGAAGTTCGGG
Found at i:41386234 original size:58 final size:57
Alignment explanation
Indices: 41386080--41386374 Score: 342
Period size: 58 Copynumber: 5.0 Consensus size: 57
41386070 GACATTCAGA
* * * * *
41386080 GGTAAAAATGTAACTTTT-AAAGTTTTAGGGTCAAAAATAGAATTTTTGGAAGTTCGGG
1 GGTAAAAATGTAATTTTTGGAAGTTTGA-GGTCAAAAATGGAATTTTTGGAAGTT-TGG
* *
41386138 GGTAAAAAATGTAATTTTTGGAAGTTACGAGGTTAAAAATGGAATTTTTGGAAGTTTGG
1 GGT-AAAAATGTAATTTTTGGAAGTT-TGAGGTCAAAAATGGAATTTTTGGAAGTTTGG
* * *
41386197 GGTAAAAATGTAATTTTTGAAAGTTTCGATGTCAAAAATGGAATTTTTGGAAGTTCGGG
1 GGTAAAAATGTAATTTTTGGAAGTTT-GAGGTCAAAAATGGAATTTTTGGAAGTT-TGG
* *
41386256 GGTAAAAATGTAATTTTTGGAGGTTATG-GATCAAAAATGGAATTTTTGGAAGTTTAGG
1 GGTAAAAATGTAATTTTTGGAAGTT-TGAGGTCAAAAATGGAATTTTTGGAAGTTT-GG
* * * *
41386314 GGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAATGTAATTTTAGAGAAGTTTGG
1 GGTAAAAATGTAATTTTTGGAAGTTTGA-GGTCAAAAATGGAATTTTTG-GAAGTTTGG
41386373 GG
1 GG
41386375 GTCGAAATAT
Statistics
Matches: 204, Mismatches: 23, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
57 1 0.00
58 100 0.49
59 65 0.32
60 37 0.18
61 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
GGTAAAAATGTAATTTTTGGAAGTTTGAGGTCAAAAATGGAATTTTTGGAAGTTTGG
Found at i:41387421 original size:12 final size:12
Alignment explanation
Indices: 41387404--41387448 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
41387394 TCTTTTTTTT
41387404 ATATTATTATTA
1 ATATTATTATTA
41387416 ATATTATTATTA
1 ATATTATTATTA
*
41387428 ACGCATTTATTATTA
1 A--TA-TTATTATTA
41387443 ATATTA
1 ATATTA
41387449 ACCAACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 16 0.57
13 1 0.04
14 1 0.04
15 10 0.36
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (12 bp):
ATATTATTATTA
Found at i:41388147 original size:17 final size:17
Alignment explanation
Indices: 41388124--41388189 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 17
41388114 GATAATTTTT
41388124 AATTCAAAATAAATTTA
1 AATTCAAAATAAATTTA
* * *
41388141 AACTCAACATGAATTTA
1 AATTCAAAATAAATTTA
* *
41388158 AATTTAAAATAAATTCA
1 AATTCAAAATAAATTTA
*
41388175 AATTTAAAATAAATT
1 AATTCAAAATAAATT
41388190 AACATTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTCAAAATAAATTTA
Found at i:41388196 original size:17 final size:16
Alignment explanation
Indices: 41388155--41388201 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 16
41388145 CAACATGAAT
41388155 TTAAATTTAAAATAAA
1 TTAAATTTAAAATAAA
41388171 TTCAAATTTAAAATAAA
1 TT-AAATTTAAAATAAA
41388188 TTAACATTTAAAAT
1 TTAA-ATTTAAAAT
41388202 TAAAAGTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:41389024 original size:206 final size:204
Alignment explanation
Indices: 41388531--41389026 Score: 724
Period size: 205 Copynumber: 2.4 Consensus size: 204
41388521 TCTGGTTTCA
* * * ** * *
41388531 TTGATTTGATCTTCTTTTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA-CGCATCATTTGTTTCAATTCGCTT
* * * * * *
41388596 CTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTTTTCGTGTCTCATCAGGAAGCTAACCAT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTTCTCGTATCTCATCAGGAAGCTAACCAT
* *
41388661 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGTTCGAAGATTTGCACACATC
130 TTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGTTGGGTTCGAAGATTTGCACAAATC
41388726 GAGCATGGGC
195 GAGCATGGGC
41388736 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCATTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGAC-GCATCATTTGTTTCAATTCGCTT
*
41388801 CTCTGTATCTTATCAGGAAGACGAATTTGGTCCAC-TTCTCAGTATCTCATCAGGAAGCTAACCA
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTTCTC-GTATCTCATCAGGAAGCTAACCA
* *
41388865 TTTTATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCAAA
129 TTTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGTT-GGGTTCGAAGATTTGCACAAA
* * *
41388930 TCGATCGTGGGT
193 TCGAGCATGGGC
* *
41388942 TTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGATCGCATCGTTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA-CGCATCATTTGTTTCAATTCGCTT
*
41389007 CTCTATATCTCATCAGGAAG
65 CTCTGTATCTCATCAGGAAG
41389027 CTAACCATTT
Statistics
Matches: 262, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
204 5 0.02
205 149 0.57
206 107 0.41
207 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (204 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACGCATCATTTGTTTCAATTCGCTTC
TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTTCTCGTATCTCATCAGGAAGCTAACCATT
TTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGTTGGGTTCGAAGATTTGCACAAATCG
AGCATGGGC
Found at i:41389122 original size:169 final size:169
Alignment explanation
Indices: 41388835--41389195 Score: 598
Period size: 169 Copynumber: 2.1 Consensus size: 169
41388825 ATTTGGTCCA
41388835 CTTCTC-AGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCAT
1 CTTCTCTA-TATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCAT
* * *
41388899 CAGGAAGTTGGGGTTCGAAGATTTGCTCAAATCGATCGTGGGTTTGATTTGGTCTTCTTCTCAGT
65 CAGGAAGCTGGGGTTCGAAAATTTGCTCAAATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGT
*
41388964 ATCTCATCGGGAAGATGATCGCATCGTTTGTTTCAATTCG
130 ATCTCATCAGGAAGATGATCGCATCGTTTGTTTCAATTCG
*
41389004 CTTCTCTATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCTATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* * *
41389069 AGGAAGCTGGGGTTCGAAAATTTGCTCATATCGAGCGTTGGTTTGATTTGGTCTTCTTCTTAGTA
66 AGGAAGCTGGGGTTCGAAAATTTGCTCAAATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
* *
41389134 TCTCATTAGGAAGATGATTGCATCGTTTGTTTCAATTCG
131 TCTCATCAGGAAGATGATCGCATCGTTTGTTTCAATTCG
* *
41389173 TTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTATATCTCATCAGGAAG
41389196 ACGAATTTGG
Statistics
Matches: 179, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
169 178 0.99
170 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (169 bp):
CTTCTCTATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
AGGAAGCTGGGGTTCGAAAATTTGCTCAAATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
TCTCATCAGGAAGATGATCGCATCGTTTGTTTCAATTCG
Found at i:41389329 original size:375 final size:374
Alignment explanation
Indices: 41388640--41389375 Score: 1213
Period size: 375 Copynumber: 2.0 Consensus size: 374
41388630 CTTTTTCGTG
*
41388640 TCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGG
1 TCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTGGG
*
41388705 GTTCGAAGATTTGCACACATCGAGCATGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGA
66 GTTCGAAAATTTGCACACATCGAGCATGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGA
*
41388770 AGATGACTGCATCATTTGTTTCAATTCGCTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCCA
131 AGATGACTGCATCATTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCA
41388835 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
196 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* * *
41388900 AGGAAGTTGGGGTTCGAAGATTTGCTCAAATCGATCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
261 AGGAAGCTGGGGTTCGAAGATTTACTCAAATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
**
41388965 TCTCATCGGGAAGATGA-TCGCATCGTTTGTTTCAATTCGCTTCTCTATA
326 TCTCATCAAGAAGATGACT-GCATCGTTTGTTTCAATTCGCTTCTCTATA
*
41389014 TCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGG
1 TCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAG-TGG
* * * * * * *
41389079 GGTTCGAAAATTTGCTCATATCGAGCGTTGGTTTGATTTGGTCTTCTTCTTAGTATCTCATTAGG
65 GGTTCGAAAATTTGCACACATCGAGCATGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGG
* * *
41389144 AAGATGATTGCATCGTTTGTTTCAATTCGTTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCC
130 AAGATGACTGCATCATTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCC
* * * * * *
41389209 ACTTCTCCGTATCTCCTGAGGAAGTTAACCATTTTATTGCTTCGACCTGCTTCTTAGTATCTCAT
195 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCAT
*
41389274 CAGGAAGCTGGGGTTCGAAGATTTACTCATATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGT
260 CAGGAAGCTGGGGTTCGAAGATTTACTCAAATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGT
41389339 ATCTCATCAAGAAGATGACTGCATCGTTTGTTTCAAT
325 ATCTCATCAAGAAGATGACTGCATCGTTTGTTTCAAT
41389376 AATCGCAATC
Statistics
Matches: 334, Mismatches: 26, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
374 60 0.18
375 273 0.82
376 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (374 bp):
TCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTGGG
GTTCGAAAATTTGCACACATCGAGCATGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGA
AGATGACTGCATCATTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCA
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
AGGAAGCTGGGGTTCGAAGATTTACTCAAATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTA
TCTCATCAAGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCTATA
Found at i:41389504 original size:39 final size:38
Alignment explanation
Indices: 41389461--41389604 Score: 134
Period size: 39 Copynumber: 3.7 Consensus size: 38
41389451 GATGGTTGCA
* *
41389461 ATCTGCCCTAGACTCGGGGTAAGAGATTGGTTGACGATG
1 ATCTGCCCCAGACTCGGGGTAAAAGATTGGTT-ACGATG
*
41389500 ATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGTTAC-A--
1 ATCTGCCCCAGACTCGGGGTAAAAGAT----TGGTTACGATG
* * * *
41389539 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTAATGATG
1 ATCTGCCCCAGACTCGGGGTAAAAGATTGGTT-ACGATG
41389578 ATCTGCCCCA-AGCTCGGGGTAAAAGAT
1 ATCTGCCCCAGA-CTCGGGGTAAAAGAT
41389605 CAAATGGCTG
Statistics
Matches: 85, Mismatches: 11, Indels: 18
0.75 0.10 0.16
Matches are distributed among these distances:
35 5 0.06
36 1 0.01
37 1 0.01
39 70 0.82
41 1 0.01
42 2 0.02
43 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (38 bp):
ATCTGCCCCAGACTCGGGGTAAAAGATTGGTTACGATG
Found at i:41389516 original size:78 final size:78
Alignment explanation
Indices: 41389406--41389643 Score: 336
Period size: 78 Copynumber: 3.1 Consensus size: 78
41389396 TCTGGGTAGA
* * * **
41389406 AGATTGGTTGATGATGATCTGCTCCAAGCTCGGAGTAAAAGGTCGGATGGTTGCAATCTGCCCTA
1 AGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGTTGCAATCTGCCCTA
*
41389471 GACTCGGGGTAAG
66 GGCTCGGGGTAAG
* * *
41389484 AGATTGGTTGACGATGATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGTTACAATCTG-CCTC
1 AGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGTTGCAATCTGCCCT-
41389548 AGGCTCGGGGTAAG
65 AGGCTCGGGGTAAG
* *
41389562 AGATTGGTTAATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCAATCTGTCCC-
1 AGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGTTGCAATCTG-CCCT
*
41389626 AGGCTCGGGGTAAA
65 AGGCTCGGGGTAAG
41389640 AGAT
1 AGAT
41389644 CAAATGGCTT
Statistics
Matches: 142, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
77 3 0.02
78 137 0.96
80 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (78 bp):
AGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGTTGCAATCTGCCCTA
GGCTCGGGGTAAG
Found at i:41389596 original size:117 final size:114
Alignment explanation
Indices: 41389500--41389762 Score: 332
Period size: 117 Copynumber: 2.3 Consensus size: 114
41389490 GTTGACGATG
41389500 ATCTGCCCCAAACTCGGGGTAAAAGATCAAATGG-TTACAATCTG-CCTCAGGCTCGGGGTAAGA
1 ATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGCTT-CAATCTGCCCT-AGGCTCGGGGTAAGA
*
41389563 GATTGGTTAATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCA
64 GATTAGTTAATGATGATCTGCCCCAAGCTCGGGGTAAAAGAT---ATGGCTGCA
* **
41389617 ATCTGTCCCAGGCTCGGGGTAAAAGATCAAATGGCTTCAATCTGCCCTAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGCTTCAATCTGCCCTAGGCTCGGGGTAAGAGA
* * * * *
41389682 TTAGTTGATGATGATTTGCCCCAAGCTCAGGGTAAAAGATCAAACGGCTTCA
66 TTAGTTAATGATGATCTGCCCCAAGCTCGGGGTAAAAGAT---ATGGCTGCA
* * *
41389734 ATCTTCCCCAAGCTCGGGGTAAGAGATCA
1 ATCTGCCCCAAACTCGGGGTAAAAGATCA
41389763 GAATCTTAAT
Statistics
Matches: 131, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
117 126 0.96
118 5 0.04
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (114 bp):
ATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGCTTCAATCTGCCCTAGGCTCGGGGTAAGAGA
TTAGTTAATGATGATCTGCCCCAAGCTCGGGGTAAAAGATATGGCTGCA
Found at i:41389621 original size:39 final size:39
Alignment explanation
Indices: 41389500--41389762 Score: 221
Period size: 39 Copynumber: 6.7 Consensus size: 39
41389490 GTTGACGATG
* * *
41389500 ATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGTTACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCA
* * * ** *
41389539 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTAAT-GATG--
1 ATCTGCCCCAAGCTCGGGGTAAAAGA-T--CAAATGGCTGCA
41389578 ATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCA
* * *
41389617 ATCTGTCCCAGGCTCGGGGTAAAAGATCAAATGGCTTCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCA
* * * * * * *
41389656 ATCTGCCCTAGGCTCGGGGTAAGAGAT-TAGTTGATG-A
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCA
* * * *
41389693 TGATTTGCCCCAAGCTCAGGGTAAAAGATCAAACGGCTTCA
1 --ATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCA
* *
41389734 ATCTTCCCCAAGCTCGGGGTAAGAGATCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCA
41389763 GAATCTTAAT
Statistics
Matches: 174, Mismatches: 40, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
36 3 0.02
37 4 0.02
38 5 0.03
39 152 0.87
40 4 0.02
41 3 0.02
42 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCA
Found at i:41391901 original size:11 final size:11
Alignment explanation
Indices: 41391882--41391951 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
41391872 GGATCAAATT
41391882 TTAATTTTAAA
1 TTAATTTTAAA
* *
41391893 TTAAGTTTAGA
1 TTAATTTTAAA
*
41391904 TTGATTTTAAA
1 TTAATTTTAAA
*
41391915 TTTATTTTTAAA
1 -TTAATTTTAAA
* *
41391927 TTTAAATTTAGA
1 -TTAATTTTAAA
**
41391939 TTTGTTTTAAA
1 TTAATTTTAAA
41391950 TT
1 TT
41391952 TAAATTTAAC
Statistics
Matches: 44, Mismatches: 14, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
11 26 0.59
12 18 0.41
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
TTAATTTTAAA
Found at i:41391925 original size:12 final size:12
Alignment explanation
Indices: 41391881--41391960 Score: 67
Period size: 12 Copynumber: 6.9 Consensus size: 12
41391871 TGGATCAAAT
41391881 TTTAATTTTAAA
1 TTTAATTTTAAA
* *
41391893 -TTAAGTTTAGA
1 TTTAATTTTAAA
*
41391904 -TTGATTTTAAA
1 TTTAATTTTAAA
*
41391915 TTTATTTTTAAA
1 TTTAATTTTAAA
* *
41391927 TTTAAATTTAGA
1 TTTAATTTTAAA
*
41391939 TTT-GTTTTAAA
1 TTTAATTTTAAA
*
41391950 TTTAAATTTAA
1 TTTAATTTTAA
41391961 CTAAATTTGA
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
11 25 0.49
12 26 0.51
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:41391930 original size:6 final size:6
Alignment explanation
Indices: 41391909--41391960 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
41391899 TTAGATTGAT
** * **
41391909 TTTAAA TTTATT TTTAAA TTTAAA TTTAGA TTT-GT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41391956 TTTAA
1 TTTAA
41391961 CTAAATTTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:41391937 original size:35 final size:34
Alignment explanation
Indices: 41391881--41391973 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 34
41391871 TGGATCAAAT
*
41391881 TTTAATTTTAAATTAAGTTTAGA-TTGATTTTAAA
1 TTTAATTTTAAATTAAATTTAGATTTG-TTTTAAA
*
41391915 TTTATTTTTAAATTTAAATTTAGATTTGTTTTAAA
1 TTTAATTTTAAA-TTAAATTTAGATTTGTTTTAAA
* *
41391950 TTTAAATTT-AACTAAATTTGAGAT
1 TTTAATTTTAAATTAAATTT-AGAT
41391974 AATTATAAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 7 0.14
34 17 0.33
35 24 0.47
36 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.54
Consensus pattern (34 bp):
TTTAATTTTAAATTAAATTTAGATTTGTTTTAAA
Found at i:41392059 original size:26 final size:26
Alignment explanation
Indices: 41392030--41392086 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
41392020 ATTTTACAAA
41392030 CCCAAATTGAACCCGAAAC-CAAAAGG
1 CCCAAATTGAACCC-AAACACAAAAGG
* *
41392056 CCC-AATTGGACCCAATCACAAAAGG
1 CCCAAATTGAACCCAAACACAAAAGG
*
41392081 TCCAAA
1 CCCAAA
41392087 ACAAACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 18 0.69
26 5 0.19
ACGTcount: A:0.44, C:0.32, G:0.14, T:0.11
Consensus pattern (26 bp):
CCCAAATTGAACCCAAACACAAAAGG
Found at i:41394043 original size:30 final size:30
Alignment explanation
Indices: 41394009--41394247 Score: 178
Period size: 29 Copynumber: 8.1 Consensus size: 30
41393999 TATATTTCGA
* *
41394009 ACCTC-AAATTTCTCCAAAATTACATTTTT
1 ACCTCAAAACTTCTCAAAAATTACATTTTT
** *
41394038 GACCTCAAAACTT-TTGAAAACTACA-TTTT
1 -ACCTCAAAACTTCTCAAAAATTACATTTTT
* * *
41394067 ACCCCTAAACTT-TCAAAAATTACATTTTG
1 ACCTCAAAACTTCTCAAAAATTACATTTTT
* *
41394096 ACCCCAAAACTTC-CTAAAATTACATTTTT
1 ACCTCAAAACTTCTCAAAAATTACATTTTT
*
41394125 ACCCTC-GAACTTC-CAAAAATTACATTTTTT
1 A-CCTCAAAACTTCTCAAAAATTACA-TTTTT
*
41394155 ACCTCAAAACTTCT-AAAAATCACATTTTT
1 ACCTCAAAACTTCTCAAAAATTACATTTTT
* *
41394184 ACCTCCAAAA-TAC-C-AAAATTCCATTTTT
1 ACCT-CAAAACTTCTCAAAAATTACATTTTT
** *
41394212 AACCTCAAAAAAAT-TCAAAAATTACCATTTTG
1 -ACCTC-AAAACTTCTCAAAAATTA-CATTTTT
41394244 ACCT
1 ACCT
41394248 TGGATGTCCA
Statistics
Matches: 169, Mismatches: 25, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
28 32 0.19
29 72 0.43
30 44 0.26
31 15 0.09
32 6 0.04
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (30 bp):
ACCTCAAAACTTCTCAAAAATTACATTTTT
Found at i:41394089 original size:58 final size:59
Alignment explanation
Indices: 41394010--41394221 Score: 213
Period size: 58 Copynumber: 3.6 Consensus size: 59
41394000 ATATTTCGAA
* * *
41394010 CCTCAAATTTCTCCAAAATTACATTTTTGACCTCAAAACTT-TTGAAAACTACA-TTTTAC
1 CCTCAAACTTC-CAAAAATTACATTTTTGACCTCAAAACTTCCT-AAAACTACATTTTTAC
* * *
41394069 CC-CTAAACTTTCAAAAATTACA-TTTTGACCCCAAAACTTCCTAAAATTACATTTTTAC
1 CCTC-AAACTTCCAAAAATTACATTTTTGACCTCAAAACTTCCTAAAACTACATTTTTAC
* * *
41394127 CCTCGAACTTCCAAAAATTACATTTTTTACCTCAAAACTT-CTAAAAATCACATTTTTA-
1 CCTCAAACTTCCAAAAATTACATTTTTGACCTCAAAACTTCCTAAAACT-ACATTTTTAC
* * * *
41394185 CCTCCAAAATACC-AAAATTCCATTTTTAACCTCAAAA
1 CCT-CAAACTTCCAAAAATTACATTTTTGACCTCAAAA
41394222 AAATTCAAAA
Statistics
Matches: 130, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
57 24 0.18
58 68 0.52
59 38 0.29
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.34
Consensus pattern (59 bp):
CCTCAAACTTCCAAAAATTACATTTTTGACCTCAAAACTTCCTAAAACTACATTTTTAC
Found at i:41394404 original size:29 final size:29
Alignment explanation
Indices: 41394345--41394405 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
41394335 AAATTTTTCC
* *
41394345 AAAATTACCATTTTACCCTCGAGAGTTCA
1 AAAATTACCATTTTACCCCCGAGAGTCCA
*
41394374 AAAATTATCATTTTACCCCCGAGTA-TCCA
1 AAAATTACCATTTTACCCCCGAG-AGTCCA
41394403 AAA
1 AAA
41394406 GTTTCAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAGAGTCCA
Found at i:41400027 original size:7 final size:7
Alignment explanation
Indices: 41400015--41400086 Score: 53
Period size: 7 Copynumber: 10.3 Consensus size: 7
41400005 TGAATAAAAG
41400015 AAAAGAA
1 AAAAGAA
41400022 AAAAG-A
1 AAAAGAA
*
41400028 AGAAGAA
1 AAAAGAA
41400035 AACAA-AA
1 AA-AAGAA
41400042 ACAAA-AA
1 A-AAAGAA
*
41400049 CAAAACAAA
1 -AAAA-GAA
*
41400058 AAAACAA
1 AAAAGAA
41400065 AAAAGAA
1 AAAAGAA
41400072 AAAAG-A
1 AAAAGAA
41400078 AAAAGAA
1 AAAAGAA
41400085 AA
1 AA
41400087 GGAGAGGTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
6 11 0.20
7 33 0.61
8 8 0.15
9 2 0.04
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:41400035 original size:13 final size:12
Alignment explanation
Indices: 41400010--41400086 Score: 59
Period size: 13 Copynumber: 6.2 Consensus size: 12
41400000 TTCAATGAAT
41400010 AAAAGAAAAGAA
1 AAAAGAAAAGAA
41400022 AAAAGAAGAAGAA
1 AAAAGAA-AAGAA
* *
41400035 AACA-AAAACAA
1 AAAAGAAAAGAA
*
41400046 AAACA-AAACAAAA
1 AAA-AGAAA-AGAA
*
41400059 AAACAAAAAAGAA
1 AAA-AGAAAAGAA
41400072 AAAAGAAAAAGAA
1 AAAAG-AAAAGAA
41400085 AA
1 AA
41400087 GGAGAGGTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
11 6 0.11
12 14 0.26
13 31 0.57
14 3 0.06
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:41400042 original size:6 final size:6
Alignment explanation
Indices: 41400033--41400067 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
41400023 AAAGAAGAAG
*
41400033 AAAACA AAAACA AAAACA AAACAAA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAA-ACA AAAACA AAAA
41400068 AGAAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:41400087 original size:5 final size:6
Alignment explanation
Indices: 41400010--41400086 Score: 50
Period size: 6 Copynumber: 12.5 Consensus size: 6
41400000 TTCAATGAAT
* * * * *
41400010 AAAAG- AAAAGAA AAAAGA AGAAG- AAAACA AAAACA AAAACA AAACAAA
1 AAAAGA AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA-AGA
*
41400058 AAAACAA AAAAGAA AAAAGA AAAAGA AAA
1 AAAA-GA AAAAG-A AAAAGA AAAAGA AAA
41400087 GGAGAGGTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
5 8 0.13
6 31 0.51
7 22 0.36
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:41401211 original size:50 final size:50
Alignment explanation
Indices: 41401084--41401391 Score: 223
Period size: 51 Copynumber: 6.1 Consensus size: 50
41401074 CAGGTTTAAC
* * ***
41401084 AGGGAAAGATTTAAG-CCGCGACGGCGGATCCAGTA-CCGTGAAGAC-AA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCCCAAAAGACAAA
*
41401131 AGGGAAAGATCTAAGACCGCAACGACGGATCCAGTACCACCAAAAGACAAA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACC-CCAAAAGACAAA
* ** * ** * *
41401182 AGGGAAAGGTCTAAG-TTGCAACGGTGGATCGTGTACCTCAAAAGACATGA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCCCAAAAGACA-AA
* * * *
41401232 CGAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGCAAAAAGACAAA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTAC-CCCAAAAGACAAA
* * * * * ** * * *
41401283 AGGGAAAGGTCTGAG-TCGTAAAGGCGGATCGTGTACCTCAGAAGACACGAC
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCCCAAAAGACA--AA
* * * *
41401334 A-GGAAAGATCTAAGACCGCAATGGTGGATCCAGTACCGCAAAAAAACAAAA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACC-CCAAAAGAC-AAA
41401385 AGGGAAA
1 AGGGAAA
41401392 AGTCATTATC
Statistics
Matches: 194, Mismatches: 54, Indels: 21
0.72 0.20 0.08
Matches are distributed among these distances:
47 14 0.07
48 18 0.09
49 17 0.09
50 62 0.32
51 64 0.33
52 18 0.09
53 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (50 bp):
AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCCCAAAAGACAAA
Found at i:41401261 original size:101 final size:101
Alignment explanation
Indices: 41401133--41401391 Score: 367
Period size: 101 Copynumber: 2.6 Consensus size: 101
41401123 GAAGACAAAG
* * *
41401133 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCACCAAAAGACAAAAGGGAAAGGTCTAAGT
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGT
* * * *
41401198 TGCAACGGTGGATCGTGTACCTCAAAAGACATGAC-
66 CGCAAAGGCGGATCGTGTACCTCAAAAGACACGACA
* *
41401233 GAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGCAAAAAGACAAAAGGGAAAGGTCTGAG
1 G-GAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAG
* *
41401298 TCGTAAAGGCGGATCGTGTACCTCAGAAGACACGACA
65 TCGCAAAGGCGGATCGTGTACCTCAAAAGACACGACA
* * *
41401335 GGAAAGATCTAAGACCGCAATGGTGGATCCAGTACCGCAAAAAAACAAAAAGGGAAA
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAAAGAC-AAAAGGGAAA
41401392 AGTCATTATC
Statistics
Matches: 141, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
100 1 0.01
101 129 0.91
102 11 0.08
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.13
Consensus pattern (101 bp):
GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGT
CGCAAAGGCGGATCGTGTACCTCAAAAGACACGACA
Found at i:41401653 original size:38 final size:38
Alignment explanation
Indices: 41401611--41401692 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
41401601 AATTCAAGAA
*
41401611 GGGCAAAATGAAG-ATTCTGATCTCTTGCCCCGAGCCAG
1 GGGCAAAATGAAGCATT-TGATCTCTTACCCCGAGCCAG
* * *
41401649 GGGCAGATTGAAGTCATTTGATCTCTTACCCCGAGCCTG
1 GGGCAAAATGAAG-CATTTGATCTCTTACCCCGAGCCAG
41401688 GGGCA
1 GGGCA
41401693 GATCATCATC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 11 0.29
39 24 0.63
40 3 0.08
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (38 bp):
GGGCAAAATGAAGCATTTGATCTCTTACCCCGAGCCAG
Found at i:41401681 original size:39 final size:39
Alignment explanation
Indices: 41401628--41401773 Score: 145
Period size: 39 Copynumber: 3.7 Consensus size: 39
41401618 ATGAAGATTC
* *
41401628 TGATCTCTTGCCCCGAGCCAGGGGCAGATTGAAGTCATT
1 TGATCTCTTACCCCGAGCCTGGGGCAGATTGAAGTCATT
* *
41401667 TGATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-TCAAT
1 TGATCTCTTACCCCGAGCCTGGGGCAGAT--TGAAGTCATT
** * *
41401706 CAATCTCTTACCCCGAG-CTCGGGGCAGATTGTAGCCATT
1 TGATCTCTTACCCCGAGCCT-GGGGCAGATTGAAGTCATT
* * *
41401745 TGATTTTTTACCCCGAGCCTGGGACAGAT
1 TGATCTCTTACCCCGAGCCTGGGGCAGAT
41401774 CACTATCAAC
Statistics
Matches: 87, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
37 1 0.01
38 3 0.03
39 79 0.91
40 3 0.03
41 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (39 bp):
TGATCTCTTACCCCGAGCCTGGGGCAGATTGAAGTCATT
Found at i:41401782 original size:78 final size:78
Alignment explanation
Indices: 41401630--41401775 Score: 222
Period size: 78 Copynumber: 1.9 Consensus size: 78
41401620 GAAGATTCTG
* * *
41401630 ATCTCTTGCCCCGAGCCAGGGGCAGATTGAAGTCATTTGATCTCTTACCCCGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGAAGCCATTTGATCTCTTACCCCGAGCCTGGGACAGA
41401695 TCATCATCAATCA
66 TCATCATCAATCA
* * *
41401708 ATCTCTTACCCCGAGCTC-GGGGCAGATTGTAGCCATTTGATTTTTTACCCCGAGCCTGGGACAG
1 ATCTCTTACCCCGAGC-CAGGGGCAGATTGAAGCCATTTGATCTCTTACCCCGAGCCTGGGACAG
41401772 ATCA
65 ATCA
41401776 CTATCAACCA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 60 0.98
79 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCAGGGGCAGATTGAAGCCATTTGATCTCTTACCCCGAGCCTGGGACAGA
TCATCATCAATCA
Found at i:41402172 original size:200 final size:200
Alignment explanation
Indices: 41401824--41402661 Score: 1185
Period size: 200 Copynumber: 4.2 Consensus size: 200
41401814 GATCATGCAC
* * * * **
41401824 AAAC-AGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCAGTGCTCGATGC
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACCCA-CGCTCGATAT
* * * * *
41401888 GAGCAAATCTTCGAACCCTAGCTTCTTGATGAGATGCTGAGAAGCAGGTCAAAACAATAAAATGG
65 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGG
41401953 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
130 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
41402018 GAATTG
195 GAATTG
* * *
41402024 AAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATGCCAACCTATGCTCGATATG
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACCCACGCTCGATATG
* *
41402089 AGCAAATCTTCGAACCCTAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
66 AGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* *
41402154 TAGCTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCG
131 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
41402219 AATTG
196 AATTG
* *
41402224 AAACAAGTGAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATGCCAACCCACGCTCAATATG
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACCCACGCTCGATATG
* * *
41402289 AGCAAATCTTCGAGCCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAATGGT
66 AGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
*
41402354 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
131 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
*
41402419 GATTG
196 AATTG
** * * * *
41402424 AAACAAACGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAAT-CAAACCCACGCT
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATAC--AG-AGAAG----TATGCCAACCCACGCT
* *
41402488 CGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATA
59 CGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATA
* * * * * * * *
41402553 AAATGGTTAGCCTCCTGATGAGACACGGAGAAGTGAACCAAATCCATCTTCCTGATAAAATACAG
124 AAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAG
*
41402618 AGAAACGAATTG
189 AGAAGCGAATTG
** *
41402630 AAACAAACGACGCGGTCATCTTCCTGATGAGA
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGA
41402662 CACTAAGAAG
Statistics
Matches: 578, Mismatches: 52, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
200 359 0.62
201 44 0.08
202 2 0.00
203 5 0.01
206 166 0.29
207 2 0.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (200 bp):
AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACCCACGCTCGATATG
AGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
AATTG
Found at i:41403019 original size:11 final size:11
Alignment explanation
Indices: 41403000--41403057 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
41402990 GGATCAAATT
41403000 TTAATTTTAAA
1 TTAATTTTAAA
* *
41403011 TTAAGTTTAGA
1 TTAATTTTAAA
*
41403022 TTGATTTTAAA
1 TTAATTTTAAA
* *
41403033 TTTATTGTAAA
1 TTAATTTTAAA
*
41403044 TTTAAATTTAAA
1 -TTAATTTTAAA
41403056 TT
1 TT
41403058 TAGATTTGTT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
11 28 0.78
12 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (11 bp):
TTAATTTTAAA
Found at i:41403059 original size:29 final size:29
Alignment explanation
Indices: 41403027--41403083 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
41403017 TTAGATTGAT
41403027 TTTAAATTTATTGTAAATTTAAATTTAAA
1 TTTAAATTTATTGTAAATTTAAATTTAAA
* * * *
41403056 TTTAGATTTGTTTTAGATTTAAATTTAA
1 TTTAAATTTATTGTAAATTTAAATTTAA
41403084 CTAAATTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (29 bp):
TTTAAATTTATTGTAAATTTAAATTTAAA
Found at i:41405194 original size:29 final size:29
Alignment explanation
Indices: 41405097--41405272 Score: 162
Period size: 30 Copynumber: 6.0 Consensus size: 29
41405087 CCATGAAGGT
* * *
41405097 CCCT-AAACTGTCCAAAAATTATATTTTGA
1 CCCTAAAACT-TCCCAAAATTACATTTTTA
*
41405126 -CCTCCAAACTTCTCCAAAATTACATTTTTGA
1 CCCT-AAAACTTC-CCAAAATTACATTTTT-A
41405157 CCCTAAAACTTCCCAAAATTACATTTTTA
1 CCCTAAAACTTCCCAAAATTACATTTTTA
* * *
41405186 CCCTTAAACTTCCAAAAATTACATGTTTGA
1 CCCTAAAACTTCCCAAAATTACAT-TTTTA
*
41405216 -CCTCAAAATTTCCCAAAATTACATTTTTA
1 CCCT-AAAACTTCCCAAAATTACATTTTTA
* * * *
41405245 CCCTCAAACTT-TCGAAATTCCATTTTTA
1 CCCTAAAACTTCCCAAAATTACATTTTTA
41405273 ACCTCGAAAA
Statistics
Matches: 123, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
28 17 0.14
29 37 0.30
30 58 0.47
31 8 0.07
32 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCTAAAACTTCCCAAAATTACATTTTTA
Found at i:41405229 original size:59 final size:60
Alignment explanation
Indices: 41405097--41405255 Score: 200
Period size: 59 Copynumber: 2.7 Consensus size: 60
41405087 CCATGAAGGT
* * * * *
41405097 CCCT-AAACTGTCCAAAAATTATATTTTGA-CCTCCAAACTTCTCCAAAATTACATTTTTGA
1 CCCTAAAACT-TCCCAAAATTACATTTTTACCCT-CAAACTTCTCAAAAATTACATGTTTGA
*
41405157 CCCTAAAACTTCCCAAAATTACATTTTTACCCTTAAACTTC-CAAAAATTACATGTTTGA
1 CCCTAAAACTTCCCAAAATTACATTTTTACCCTCAAACTTCTCAAAAATTACATGTTTGA
*
41405216 -CCTCAAAATTTCCCAAAATTACATTTTTACCCTCAAACTT
1 CCCT-AAAACTTCCCAAAATTACATTTTTACCCTCAAACTT
41405256 TCGAAATTCC
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
58 3 0.03
59 50 0.57
60 27 0.31
61 8 0.09
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (60 bp):
CCCTAAAACTTCCCAAAATTACATTTTTACCCTCAAACTTCTCAAAAATTACATGTTTGA
Found at i:41405300 original size:59 final size:58
Alignment explanation
Indices: 41405111--41405306 Score: 168
Period size: 59 Copynumber: 3.3 Consensus size: 58
41405101 AAACTGTCCA
* * * * * *
41405111 AAAATTATATTTTGA-CCTCCAAACTTCTCCAAAATTACATTTTTGACC-CTAAAACTTCCC
1 AAAATTACATTTTTACCCT-CAAACTTC-CAAAAATTACATGTTTAACCTC-AAAA-TTTCC
* *
41405171 AAAATTACATTTTTACCCTTAAACTTCCAAAAATTACATGTTTGACCTCAAAATTTCCC
1 AAAATTACATTTTTACCCTCAAACTTCCAAAAATTACATGTTTAACCTCAAAATTT-CC
* * * * *
41405230 AAAATTACATTTTTACCCTCAAACTTTC-GAAATTCCATTTTTAACCTCGAAAAATTT-T
1 AAAATTACATTTTTACCCTCAAACTTCCAAAAATTACATGTTTAACCTC--AAAATTTCC
41405288 AAAATTACCA-TTTTACCCT
1 AAAATTA-CATTTTTACCCT
41405307 TAGATGTCCA
Statistics
Matches: 117, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
58 34 0.29
59 52 0.44
60 28 0.24
61 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAATTACATTTTTACCCTCAAACTTCCAAAAATTACATGTTTAACCTCAAAATTTCC
Found at i:41405465 original size:29 final size:29
Alignment explanation
Indices: 41405406--41405466 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
41405396 AAATTTTCCC
* *
41405406 AAAATTACCATTTTACCCTCGAGAGTTCA
1 AAAAATACCATTTTACCCTCGAGAGTCCA
*
41405435 AAAAATACCATTTTGCCCTCGAGTA-TCCA
1 AAAAATACCATTTTACCCTCGAG-AGTCCA
41405464 AAA
1 AAA
41405467 GTCTCATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (29 bp):
AAAAATACCATTTTACCCTCGAGAGTCCA
Found at i:41407850 original size:59 final size:58
Alignment explanation
Indices: 41407802--41407999 Score: 220
Period size: 59 Copynumber: 3.4 Consensus size: 58
41407792 TTTGGACATC
* *
41407802 CGAGGGTAAAAATGTAATTTTTGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGTT
1 CGAGGGTAAAAATGTAATTTTTGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTA
** *
41407860 TAAGGGTAAAAATGTAATTTTTGAAAGTTACGGGGTCAAAAATGGAATTTTTGGAAGTTA
1 CGAGGGTAAAAATGTAATTTTTG-AAGTTTCGGGGTCAAAAATGGAATTTTTGGAAG-TA
* * * * *
41407920 CG-GGATCAAAAATGGAATTTTTGGAAGTTTGGGGGT-AAAAATGTAATTTTTGGAAGTT
1 CGAGGGT-AAAAATGTAATTTTT-GAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTA
* * *
41407978 TGGGGGTCAAAAATGGAATTTT
1 CGAGGGT-AAAAATGTAATTTT
41408000 AGAGAAGTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
58 23 0.19
59 71 0.59
60 25 0.21
61 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (58 bp):
CGAGGGTAAAAATGTAATTTTTGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTA
Found at i:41407860 original size:30 final size:30
Alignment explanation
Indices: 41407805--41408014 Score: 257
Period size: 30 Copynumber: 7.1 Consensus size: 30
41407795 GGACATCCGA
*
41407805 GGGT-AAAAATGTAATTTTT-GAAGTTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCG
* **
41407833 GGGTCAAAAATGGAATTTTTAGAAGTTTAA
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCG
* * *
41407863 GGGT-AAAAATGTAATTTTTGAAAGTTACG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCG
*
41407892 GGGTCAAAAATGGAATTTTTGGAAGTTACG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCG
* *
41407922 GGATCAAAAATGGAATTTTTGGAAGTTTGG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCG
* *
41407952 GGGT-AAAAATGTAATTTTTGGAAGTTTGG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCG
* *
41407981 GGGTCAAAAATGGAATTTTAGAGAAGTTTTG
1 GGGTCAAAAATGGAATTTTTG-GAAGTTTCG
41408012 GGG
1 GGG
41408015 GTCGAAATAT
Statistics
Matches: 158, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
28 4 0.03
29 65 0.41
30 78 0.49
31 11 0.07
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (30 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTTCG
Found at i:41407940 original size:89 final size:89
Alignment explanation
Indices: 41407805--41408008 Score: 295
Period size: 89 Copynumber: 2.3 Consensus size: 89
41407795 GGACATCCGA
* * *
41407805 GGGT-AAAAATGTAATTTTT-GAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGTTTAAGGGTA
1 GGGTCAAAAATGGAATTTTTGGAAGTTACGGGATCAAAAATGGAATTTTTAGAAGTTTAAGGGTA
41407868 AAAATGTAATTTTTGAAAGTTACG
66 AAAATGTAATTTTTGAAAGTTACG
* **
41407892 GGGTCAAAAATGGAATTTTTGGAAGTTACGGGATCAAAAATGGAATTTTTGGAAGTTTGGGGGTA
1 GGGTCAAAAATGGAATTTTTGGAAGTTACGGGATCAAAAATGGAATTTTTAGAAGTTTAAGGGTA
* **
41407957 AAAATGTAATTTTTGGAAGTTTGG
66 AAAATGTAATTTTTGAAAGTTACG
*
41407981 GGGTCAAAAATGGAATTTTAGAGAAGTT
1 GGGTCAAAAATGGAATTTTTG-GAAGTT
41408009 TTGGGGGTCG
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
87 4 0.04
88 14 0.13
89 80 0.77
90 6 0.06
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (89 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTACGGGATCAAAAATGGAATTTTTAGAAGTTTAAGGGTA
AAAATGTAATTTTTGAAAGTTACG
Found at i:41409792 original size:17 final size:17
Alignment explanation
Indices: 41409772--41409854 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
41409762 GATAATTTTT
41409772 AATTCAAAATAAATTCA
1 AATTCAAAATAAATTCA
* *
41409789 AATTTAAAATAAATTTA
1 AATTCAAAATAAATTCA
* * * *
41409806 AACTCAACATGAATTTA
1 AATTCAAAATAAATTCA
*
41409823 AATTTAAAATAAATTCA
1 AATTCAAAATAAATTCA
*
41409840 AATTAAAAATAAATT
1 AATTCAAAATAAATT
41409855 AAAACTTAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.34
Consensus pattern (17 bp):
AATTCAAAATAAATTCA
Found at i:41409864 original size:34 final size:34
Alignment explanation
Indices: 41409772--41409866 Score: 118
Period size: 34 Copynumber: 2.8 Consensus size: 34
41409762 GATAATTTTT
* *
41409772 AATTCAAAATAAATTCAAATTTAAAATAAATTTA
1 AATTCAAAATAAATTAAAATTTAAAATAAATTCA
* * * *
41409806 AACTCAACATGAATTTAAATTTAAAATAAATTCA
1 AATTCAAAATAAATTAAAATTTAAAATAAATTCA
* *
41409840 AATTAAAAATAAATTAAAACTTAAAAT
1 AATTCAAAATAAATTAAAATTTAAAAT
41409867 TAAAAGTTGG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (34 bp):
AATTCAAAATAAATTAAAATTTAAAATAAATTCA
Found at i:41409865 original size:17 final size:17
Alignment explanation
Indices: 41409777--41409866 Score: 92
Period size: 17 Copynumber: 5.3 Consensus size: 17
41409767 TTTTTAATTC
*
41409777 AAAATAAATTCAAATTT
1 AAAATAAATTCAAACTT
* *
41409794 AAAATAAATTTAAACTC
1 AAAATAAATTCAAACTT
* * * *
41409811 AACATGAATTTAAATTT
1 AAAATAAATTCAAACTT
41409828 AAAATAAATTCAAA-TT
1 AAAATAAATTCAAACTT
*
41409844 AAAAATAAATTAAAACTT
1 -AAAATAAATTCAAACTT
41409862 AAAAT
1 AAAAT
41409867 TAAAAGTTGG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
16 2 0.03
17 56 0.93
18 2 0.03
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (17 bp):
AAAATAAATTCAAACTT
Found at i:41410469 original size:29 final size:29
Alignment explanation
Indices: 41410434--41410501 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
41410424 TCAAGTACAG
* *
41410434 ATATAATACGGATACAGTTACAGATGCAA
1 ATATAATACAGATACAGTTACAAATGCAA
* * *
41410463 ATGTAATACAGATACAGTTGCAAATGCAT
1 ATATAATACAGATACAGTTACAAATGCAA
41410492 ATATAATACA
1 ATATAATACA
41410502 AATATAATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (29 bp):
ATATAATACAGATACAGTTACAAATGCAA
Found at i:41410471 original size:23 final size:23
Alignment explanation
Indices: 41410445--41410488 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
41410435 TATAATACGG
*
41410445 ATACAGTTACAGATGCAAATGTA
1 ATACAGATACAGATGCAAATGTA
*
41410468 ATACAGATACAGTTGCAAATG
1 ATACAGATACAGATGCAAATG
41410489 CATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (23 bp):
ATACAGATACAGATGCAAATGTA
Found at i:41410504 original size:40 final size:40
Alignment explanation
Indices: 41410460--41410540 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
41410450 GTTACAGATG
* *
41410460 CAAATGTAATACAGATACAGTTGCAAATGCATATATAATA
1 CAAATATAATACAGATACAGTTACAAATGCATATATAATA
* *
41410500 CAAATATAATACAGATACAGTTACATATGCATATATGATA
1 CAAATATAATACAGATACAGTTACAAATGCATATATAATA
41410540 C
1 C
41410541 CCCCCATCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (40 bp):
CAAATATAATACAGATACAGTTACAAATGCATATATAATA
Found at i:41411569 original size:3 final size:3
Alignment explanation
Indices: 41411561--41411610 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
41411551 ACAAAGGCAT
41411561 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41411609 AT
1 AT
41411611 TTATAAAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41411959 original size:18 final size:17
Alignment explanation
Indices: 41411936--41411984 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
41411926 GGGATTTTTT
41411936 AAAATGAAATAAAAAAA
1 AAAATGAAATAAAAAAA
* *
41411953 CAAAATGAAAGAACAAAA
1 -AAAATGAAATAAAAAAA
41411971 AAAATGAAACTAAA
1 AAAATGAAA-TAAA
41411985 GGGATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (17 bp):
AAAATGAAATAAAAAAA
Found at i:41415112 original size:18 final size:18
Alignment explanation
Indices: 41415078--41415113 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41415068 GGGATTTTTT
*
41415078 AAAATGAAATAAAAAAAC
1 AAAATGAAAGAAAAAAAC
41415096 AAAATGAAAGAACAAAAA
1 AAAATGAAAGAA-AAAAA
41415114 ATCGAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.78, C:0.06, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAATGAAAGAAAAAAAC
Found at i:41416577 original size:18 final size:18
Alignment explanation
Indices: 41416539--41416597 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
41416529 CGAGGAGGCT
*
41416539 TCGGGCAG-AAGAGCGTCC
1 TCGGGCAGAAAGAACGT-C
41416557 TCGGGCAGAAAGAACGTC
1 TCGGGCAGAAAGAACGTC
* *
41416575 TCGAGCAGAGA-AACGATC
1 TCGGGCAGAAAGAACG-TC
41416593 TCGGG
1 TCGGG
41416598 AGCCGAGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.11
18 24 0.69
19 7 0.20
ACGTcount: A:0.29, C:0.24, G:0.36, T:0.12
Consensus pattern (18 bp):
TCGGGCAGAAAGAACGTC
Found at i:41417739 original size:49 final size:49
Alignment explanation
Indices: 41417686--41418181 Score: 332
Period size: 49 Copynumber: 10.1 Consensus size: 49
41417676 ACCGTGGTAG
* * * *
41417686 CTTAAATCTTTCCTTTCATGTTTTTGAGGTATAAGGTTCGTCGTTGTGA
1 CTTAAACCTTTCCCTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGCGA
* * * * * * * *
41417735 CTTAAACCATTCCCTCCATATCTTCGTGGTACT--GGATTCGCTGTTGCGG
1 CTTAAACCTTTCCCTTCATGTTTTTGAGGTA-TAAGG-TTCGCCGTTGCGA
* * **
41417784 CTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTAAGA
1 CTTAAACCTTTCCCTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGCGA
* * * * *
41417833 CTTAAACCTTTCCCTTCAT-ATCTTCATGGTACT--GGATTCGCTGTTGCGG
1 CTTAAACCTTTCCCTTCATGTTTTTGA-GGTA-TAAGG-TTCGCCGTTGCGA
* * * *
41417882 CTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA
1 CTTAAACCTTTCCCTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGCGA
* * * * * *
41417931 -TTGAAACCTTTCTCTCCATATCTTTGTGGTACTGAA--TTCGCCGTTGCAA
1 CTT-AAACCTTTCCCTTCATGTTTTTGAGGTA-T-AAGGTTCGCCGTTGCGA
* * *
41417980 CTTAAATCTTTCCCTTCATGTTTCTGAAGTATAAGGTTCGCCGTTGCGA
1 CTTAAACCTTTCCCTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGCGA
* * * * * * *
41418029 CTTAAACCTTTCCCTCCATATTTTTGTGGTACT--GGATTTGCTGTTGTGG
1 CTTAAACCTTTCCCTTCATGTTTTTGAGGTA-TAAGG-TTCGCCGTTGCGA
* * * * *
41418078 CTTAAATCTTTCCTTTCATGTTTTTAAGGTATAAGGTTCGCCGCTGTGA
1 CTTAAACCTTTCCCTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGCGA
* * * * * *
41418127 CTTAAACCTTTTCCTCCATATTTTCGTGGTATTAA-ATTCGCCGTTGC-A
1 CTTAAACCTTTCCCTTCATGTTTTTGAGGTA-TAAGGTTCGCCGTTGCGA
41418175 GCTTAAA
1 -CTTAAA
41418182 ATTTTCCCAT
Statistics
Matches: 333, Mismatches: 92, Indels: 44
0.71 0.20 0.09
Matches are distributed among these distances:
47 2 0.01
48 15 0.05
49 297 0.89
50 17 0.05
51 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (49 bp):
CTTAAACCTTTCCCTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGCGA
Found at i:41417802 original size:98 final size:98
Alignment explanation
Indices: 41417685--41418189 Score: 672
Period size: 98 Copynumber: 5.2 Consensus size: 98
41417675 CACCGTGGTA
* * * * *
41417685 GCTTAAATCTTTCCTTTCATGTTTTTGAGGTATAAGGTTCGTCGTTGTGACTTAAACCATTCCCT
1 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
41417750 CCATATCTTCGTGGTACTGGATTCGCTGTTGCG
66 CCATATCTTCGTGGTACTGGATTCGCTGTTGCG
**
41417783 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTAAGACTTAAACCTTTCCCT
1 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
* *
41417848 TCATATCTTCATGGTACTGGATTCGCTGTTGCG
66 CCATATCTTCGTGGTACTGGATTCGCTGTTGCG
* * *
41417881 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA-TTGAAACCTTTCTC
1 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTT-AAACCTTTCCC
* * * *
41417945 TCCATATCTTTGTGGTACTGAATTCGCCGTTGCA
65 TCCATATCTTCGTGGTACTGGATTCGCTGTTGCG
* *
41417979 ACTTAAATCTTTCCCTTCATGTTTCTGAAGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
1 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
* * * *
41418044 CCATATTTTTGTGGTACTGGATTTGCTGTTGTG
66 CCATATCTTCGTGGTACTGGATTCGCTGTTGCG
* * * * * *
41418077 GCTTAAATCTTTCCTTTCATGTTTTTAAGGTATAAGGTTCGCCGCTGTGACTTAAACCTTTTCCT
1 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
* * ** * *
41418142 CCATATTTTCGTGGTATTAAATTCGCCGTTGCA
66 CCATATCTTCGTGGTACTGGATTCGCTGTTGCG
41418175 GCTTAAAAT-TTTCCC
1 GCTT-AAATCTTTCCC
41418190 ATCTCATCTT
Statistics
Matches: 357, Mismatches: 47, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
97 2 0.01
98 349 0.98
99 6 0.02
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (98 bp):
GCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
CCATATCTTCGTGGTACTGGATTCGCTGTTGCG
Found at i:41417953 original size:196 final size:196
Alignment explanation
Indices: 41417685--41418386 Score: 726
Period size: 196 Copynumber: 3.6 Consensus size: 196
41417675 CACCGTGGTA
* * *
41417685 GCTTAAATCTTTCCTTTCATGTTTTTGAGGTATAAGGTTCGTCGTTGTGACTTAAACCATTCCCT
1 GCTTAAATCTTTCCTTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGTGACTTAAACCTTTCTCT
* * * *
41417750 CCATATCTTCGTGGTACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTA
66 CCATATCTTCGTGGTACTGAATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTTTCTGAAGTA
*
41417815 TAAGGTTCGCCGTTAAGACTTAAACCTTTCCCTTCATATCTTCATGGTACTGGATTCGCTGTTGC
131 TAAGGTTCGCCGTTAAGACTTAAACCTTTCCCTCCATATCTTCATGGTACTGGATTCGCTGTTGC
41417880 G
196 G
* * * * *
41417881 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA-TTGAAACCTTTCTC
1 GCTTAAATCTTTCCTTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGTGACTT-AAACCTTTCTC
* *
41417945 TCCATATCTTTGTGGTACTGAATTCGCCGTTGCAACTTAAATCTTTCCCTTCATGTTTCTGAAGT
65 TCCATATCTTCGTGGTACTGAATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTTTCTGAAGT
** * ** *
41418010 ATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATTTTTGTGGTACTGGATTTGCTGTTG
130 ATAAGGTTCGCCGTTAAGACTTAAACCTTTCCCTCCATATCTTCATGGTACTGGATTCGCTGTTG
*
41418075 TG
195 CG
* *
41418077 GCTTAAATCTTTCCTTTCATGTTTTTAAGGTATAAGGTTCGCCGCTGTGACTTAAACCTTT-TCC
1 GCTTAAATCTTTCCTTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGTGACTTAAACCTTTCT-C
* * * *
41418141 TCCATATTTTCGTGGTATTAAATTCGCCGTTGCAGCTTAAAAT-TTTCCCATCTCAT-CTTCATG
65 TCCATATCTTCGTGGTACTGAATTCGCCGTTGCAGCTT-AAATCTTTCCC-T-TCATGTTTC-TG
* * * * * * ** * * *
41418204 --G-A-ACCGGATTCACCGTTGCAA-CCTCAATCC-CT-CCTATAATATCTGCTAAGGTACCAGG
126 AAGTATA-AGG-TTCGCCGTT--AAGACTTAAACCTTTCCCT-CCATATCTTC-ATGGTA-CTGG
* *
41418262 -TCCGCTGTTACG
184 ATTCGCTGTTGCG
* * * * * *
41418274 GCTTAAATCTTTCCTTTTATGTTTTTTAGGTATAAGGTTCACCGCTGTGACTTAAACTTTTCCCT
1 GCTTAAATCTTTCCTTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGTGACTTAAACCTTTCTCT
* * * * * *
41418339 CCATATTTTCGTGGTATTAAATTCACCGTTGCGGCTTAAATTTTTCCC
66 CCATATCTTCGTGGTACTGAATTCGCCGTTGCAGCTTAAATCTTTCCC
41418387 ATCTCATCTT
Statistics
Matches: 428, Mismatches: 62, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
194 1 0.00
195 9 0.02
196 281 0.66
197 128 0.30
198 9 0.02
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (196 bp):
GCTTAAATCTTTCCTTTCATGTTTTTGAGGTATAAGGTTCGCCGTTGTGACTTAAACCTTTCTCT
CCATATCTTCGTGGTACTGAATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTTTCTGAAGTA
TAAGGTTCGCCGTTAAGACTTAAACCTTTCCCTCCATATCTTCATGGTACTGGATTCGCTGTTGC
G
Found at i:41418311 original size:197 final size:197
Alignment explanation
Indices: 41418076--41418463 Score: 670
Period size: 197 Copynumber: 2.0 Consensus size: 197
41418066 TTGCTGTTGT
*
41418076 GGCTTAAATCTTTCCTTTCATGTTTTTAAGGTATAAGGTTCGCCGCTGTGACTTAAACCTTTT-C
1 GGCTTAAATCTTTCCTTTCATGTTTTTAAGGTATAAGGTTCACCGCTGTGACTTAAA-CTTTTCC
*
41418140 CTCCATATTTTCGTGGTATTAAATTCGCCGTTGCAGCTTAAAATTTTCCCATCTCATCTTCATGG
65 CTCCATATTTTCGTGGTATTAAATTCACCGTTGCAGCTTAAAATTTTCCCATCTCATCTTCATGG
41418205 AACCGGATTCACCGTTGCAACCTCAATCCCTCCTATAATATCTGCTAAGGTACCAGGTCCGCTGT
130 AACCGGATTCACCGTTGCAACCTCAATCCCTCCTATAATATCTGCTAAGGTACCAGGTCCGCTGT
41418270 TAC
195 TAC
* *
41418273 GGCTTAAATCTTTCCTTTTATGTTTTTTAGGTATAAGGTTCACCGCTGTGACTTAAACTTTTCCC
1 GGCTTAAATCTTTCCTTTCATGTTTTTAAGGTATAAGGTTCACCGCTGTGACTTAAACTTTTCCC
* *
41418338 TCCATATTTTCGTGGTATTAAATTCACCGTTGCGGCTTAAATTTTTCCCATCTCATCTTCATGGA
66 TCCATATTTTCGTGGTATTAAATTCACCGTTGCAGCTTAAAATTTTCCCATCTCATCTTCATGGA
* * * *
41418403 ACCTGATTCACCGTTGCGACCTCAATCCTTCCTATAATATCTGCTAAGGTACCGGGTCCGC
131 ACCGGATTCACCGTTGCAACCTCAATCCCTCCTATAATATCTGCTAAGGTACCAGGTCCGC
41418464 CATTGCGGCC
Statistics
Matches: 180, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
196 5 0.03
197 175 0.97
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.37
Consensus pattern (197 bp):
GGCTTAAATCTTTCCTTTCATGTTTTTAAGGTATAAGGTTCACCGCTGTGACTTAAACTTTTCCC
TCCATATTTTCGTGGTATTAAATTCACCGTTGCAGCTTAAAATTTTCCCATCTCATCTTCATGGA
ACCGGATTCACCGTTGCAACCTCAATCCCTCCTATAATATCTGCTAAGGTACCAGGTCCGCTGTT
AC
Found at i:41423909 original size:17 final size:17
Alignment explanation
Indices: 41423889--41423940 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
41423879 TAAACCTTAG
41423889 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
* *
41423906 TTTATGTTAAATTTGAA
1 TTTATTTTAAATTTAAA
*
41423923 TTTATTTTGAATTTAAA
1 TTTATTTTAAATTTAAA
41423940 T
1 T
41423941 GTTTAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:41425815 original size:161 final size:162
Alignment explanation
Indices: 41425518--41425851 Score: 555
Period size: 161 Copynumber: 2.1 Consensus size: 162
41425508 AGTTTTCAAT
41425518 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGATTTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGATTTATTTATGTA
* * * *
41425583 CCTAGTCCCTGTCATTTTTAATTTGTTTTCATTTAATCTTTAAATCAACTTTTATTTAATTACAG
66 CCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTAGTTAATTACAA
41425648 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
* *
41425680 TTAGTCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTC-ATTTTATTTAT-T
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGA-TTTATTTATGT
* *
41425743 ATCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAATTTTTAGTTAATTACA
65 ACCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTAGTTAATTACA
* *
41425808 AAATTGGCCCAAGAATTTTTTAGGATTTATAAA
130 AAATTGGCCCAAGAATTTTTCAAGATTTATAAA
41425841 TTAGTCCTTTG
1 TTAGTCCTTTG
41425852 GCTTCTGGGT
Statistics
Matches: 161, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
161 103 0.64
162 58 0.36
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCACTTTTCGATTTATTTATGTA
CCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTAGTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTATAAA
Found at i:41425960 original size:30 final size:30
Alignment explanation
Indices: 41425924--41426125 Score: 96
Period size: 30 Copynumber: 6.8 Consensus size: 30
41425914 CCCTGGATTG
41425924 TCCAAAAATTACCATTTTACCCCTAAAGTC
1 TCCAAAAATTACCATTTTACCCCTAAAGTC
* ***
41425954 TCC-AAAATT-CCATTTTTA-ACCTCGGTGTC
1 TCCAAAAATTACCA-TTTTACCCCT-AAAGTC
* * *
41425983 ACCAAAAATTACCATTTTACCCTTAAACTC
1 TCCAAAAATTACCATTTTACCCCTAAAGTC
* * * **
41426013 TTC-AAAATT-CCATTTTTAACCCTGATTTC
1 TCCAAAAATTACCA-TTTTACCCCTAAAGTC
* *
41426042 ACCAAAAATTACCATTTTGCCCCCTAAAACGT-
1 TCCAAAAATTACCATTTT-ACCCCT-AAA-GTC
* * ****
41426074 TCC-AAAA-TCCCATTTTTAACCCTGGTTTC
1 TCCAAAAATTACCA-TTTTACCCCTAAAGTC
*
41426103 ACCAAAAATTACCATTTTACCCC
1 TCCAAAAATTACCATTTTACCCC
41426126 CCGAACTTTC
Statistics
Matches: 121, Mismatches: 36, Indels: 30
0.65 0.19 0.16
Matches are distributed among these distances:
28 10 0.08
29 36 0.30
30 47 0.39
31 24 0.20
32 3 0.02
33 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTACCCCTAAAGTC
Found at i:41425970 original size:29 final size:30
Alignment explanation
Indices: 41425928--41426096 Score: 91
Period size: 29 Copynumber: 5.7 Consensus size: 30
41425918 GGATTGTCCA
41425928 AAAATTACCA-TTTTACCCCTAAAGTCTCC
1 AAAATTACCATTTTTACCCCTAAAGTCTCC
* *** *
41425957 AAAATT-CCATTTTTA-ACCTCGGTGTCACC
1 AAAATTACCATTTTTACCCCT-AAAGTCTCC
* * *
41425986 AAAAATTACCA-TTTTACCCTTAAACTCTTC
1 -AAAATTACCATTTTTACCCCTAAAGTCTCC
* * ** *
41426016 AAAATT-CCATTTTTAACCCTGATTTCACC
1 AAAATTACCATTTTTACCCCTAAAGTCTCC
**
41426045 AAAAATTACCATTTTGCCCCCTAAAACGT-TCC
1 -AAAATTACCATTTTTACCCCT-AAA-GTCTCC
* *
41426077 AAAA-TCCCATTTTTAACCCT
1 AAAATTACCATTTTTACCCCT
41426097 GGTTTCACCA
Statistics
Matches: 99, Mismatches: 31, Indels: 19
0.66 0.21 0.13
Matches are distributed among these distances:
28 9 0.09
29 34 0.34
30 32 0.32
31 20 0.20
32 3 0.03
33 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTTACCCCTAAAGTCTCC
Found at i:41425999 original size:59 final size:59
Alignment explanation
Indices: 41425925--41426151 Score: 305
Period size: 59 Copynumber: 3.8 Consensus size: 59
41425915 CCTGGATTGT
* *
41425925 CCAAAAATTACCATTTTACCCCTAAAGTCTCCAAAATTCCATTTTTAA-CCTCGGTGTCA
1 CCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCCT-GGTTTCA
* * *
41425984 CCAAAAATTACCATTTTACCCTTAAACTCTTCAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCCTGGTTTCA
* *
41426043 CCAAAAATTACCATTTTGCCCCCTAAAACGT-TCCAAAATCCCATTTTTAACCCTGGTTTCA
1 CCAAAAATTACCATTTT-ACCCCT-AAAC-TCTCCAAAATTCCATTTTTAACCCTGGTTTCA
** *
41426104 CCAAAAATTACCATTTTACCCCCCGAACTTTCCAAAATTCCATTTTTA
1 CCAAAAATTACCATTTTA-CCCCTAAACTCTCCAAAATTCCATTTTTA
41426152 GCCCCGATTT
Statistics
Matches: 148, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
59 68 0.46
60 27 0.18
61 52 0.35
62 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCCTGGTTTCA
Found at i:41426168 original size:29 final size:28
Alignment explanation
Indices: 41426015--41426168 Score: 64
Period size: 30 Copynumber: 5.1 Consensus size: 28
41426005 TTAAACTCTT
*
41426015 CAAAATTCCATTTTTAACCCTGATTTCA
1 CAAAATTCCATTTTTAACCCCGATTTCA
** * *
41426043 CCAAAAATTACCA-TTTTGCCCCCTAAAACGTTC-
1 -C-AAAATT-CCATTTTTAACCCC---GA-TTTCA
* * *
41426076 CAAAATCCCATTTTTAACCCTGGTTTCA
1 CAAAATTCCATTTTTAACCCCGATTTCA
*
41426104 CCAAAAATTACCA-TTTTACCCCCCGAACTTTC-
1 -C-AAAATT-CCATTTTTA-ACCCCG-A-TTTCA
*
41426136 CAAAATTCCATTTTTAGCCCCGATTTCA
1 CAAAATTCCATTTTTAACCCCGATTTCA
41426164 TCAAA
1 -CAAA
41426169 GTTTCCAAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 34
0.64 0.12 0.24
Matches are distributed among these distances:
27 7 0.08
28 1 0.01
29 14 0.15
30 37 0.41
31 23 0.25
32 1 0.01
33 5 0.05
34 3 0.03
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (28 bp):
CAAAATTCCATTTTTAACCCCGATTTCA
Found at i:41426183 original size:38 final size:38
Alignment explanation
Indices: 41426132--41426206 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
41426122 CCCCCCGAAC
* *
41426132 TTTCCAAAATTCCATTTTTAGCCCCGATTTCATCAAAG
1 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAG
41426170 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAA
1 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAA
41426207 AATTACCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (38 bp):
TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAG
Found at i:41435025 original size:6 final size:6
Alignment explanation
Indices: 41435007--41435089 Score: 73
Period size: 6 Copynumber: 13.8 Consensus size: 6
41434997 TTAAATTGAT
* *
41435007 TTTAAA TTT--A TTTAAA TTTAAA TTTAATTA TTTAAA TTT-AC TTTGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA
** *
41435054 TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA
41435090 CATTAAAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
4 4 0.06
5 4 0.06
6 45 0.70
7 5 0.08
8 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:41435035 original size:11 final size:11
Alignment explanation
Indices: 41434997--41435066 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
41434987 TAATTTAGAG
* *
41434997 TTAAATTGATT
1 TTAAATTTAAT
41435008 TTAAATTT-AT
1 TTAAATTTAAT
41435018 TTAAATTTAAAT
1 TTAAATTT-AAT
41435030 TT-AA-TT-AT
1 TTAAATTTAAT
*
41435038 TTAAATTTACT
1 TTAAATTTAAT
*
41435049 TTGAATTTAAAT
1 TTAAATTT-AAT
41435061 TTAAAT
1 TTAAAT
41435067 AAAAATTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
8 4 0.09
9 2 0.04
10 13 0.28
11 17 0.36
12 11 0.23
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:41436860 original size:30 final size:30
Alignment explanation
Indices: 41436824--41437059 Score: 298
Period size: 30 Copynumber: 7.9 Consensus size: 30
41436814 AAATTGTCCA
41436824 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
41436854 AAAATTATATTTTAACCCTAAAACTTTCCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* *
41436884 AAAATTACATTTTAACCCTAAAACTTTCCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
41436914 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
41436944 ATAATTACATTTTGACCCTGAAACTCTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
** *
41436974 AAAACCACATTTAGACCCTAAAA-TTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* *
41437003 TAAAATTATATTTTGAACCCTAAAACTTTT-A
1 -AAAATTACATTTTG-ACCCTAAAACTTTTCC
*
41437034 AAAATTACCATTTT-ACCCTCAAACTT
1 AAAATTA-CATTTTGACCCTAAAACTT
41437060 CCCTAAATCC
Statistics
Matches: 180, Mismatches: 22, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
29 16 0.09
30 146 0.81
31 14 0.08
32 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTAAAACTTTTCC
Found at i:41449022 original size:68 final size:68
Alignment explanation
Indices: 41448903--41449773 Score: 1418
Period size: 68 Copynumber: 12.8 Consensus size: 68
41448893 ACCTTTTCCT
* * * *
41448903 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTAATATCTGAAATTGAAGTAAGAGTAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
41448968 CGTC
65 CGTC
* *
41448972 ATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449037 GTC
66 GTC
*
41449040 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449105 GTC
66 GTC
* *
41449108 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTAAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449173 GTC
66 GTC
*
41449176 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449241 GTC
66 GTC
41449244 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449309 GTC
66 GTC
* * * ** *
41449312 GTCCTCTTGAAATTAAAGTAGAAAGGATAACGCGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449377 GTC
66 GTC
* *
41449380 ATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449445 GTC
66 GTC
*
41449448 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449513 GTC
66 GTC
* * * ** * * *
41449516 GTCCTCTTGAAATTAAAGTAGAAAGGATAACGCGTCTTCATCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449581 GTC
66 GTC
*
41449584 ATCCCCTTGAAATTGAAGTAAAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449649 GTC
66 GTC
* * ** * *
41449652 GTCCTCTTGAAATTGAAGTAGAAAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41449717 GTC
66 GTC
*
41449720 ATCTCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAA
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAA
41449774 AAATTGAAGT
Statistics
Matches: 745, Mismatches: 57, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
68 722 0.97
69 23 0.03
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (68 bp):
ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:41450118 original size:27 final size:27
Alignment explanation
Indices: 41450088--41450142 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
41450078 TTTTTTTTTA
*
41450088 ATTTAGAGTTAAATTGATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
* *
41450115 ATTTAAATTTAAATTTATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
41450142 A
1 A
41450143 AATTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (27 bp):
ATTTAAAGTTAAATTGATTTTAAATTT
Found at i:41450124 original size:6 final size:6
Alignment explanation
Indices: 41450106--41450205 Score: 91
Period size: 6 Copynumber: 16.8 Consensus size: 6
41450096 TTAAATTGAT
*
41450106 TTTAAA TTT--A TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A
* * ** *
41450153 TTTAAA TTT-AC TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
41450201 TTTAA
1 TTTAA
41450206 CATTAAAAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 55 0.71
7 5 0.06
8 6 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:41450124 original size:17 final size:17
Alignment explanation
Indices: 41450106--41450179 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
41450096 TTAAATTGAT
41450106 TTTAAATTTA-TTTAAA
1 TTTAAATTTACTTTAAA
*
41450122 TTTAAATTTATTTTAAA
1 TTTAAATTTACTTTAAA
*
41450139 TTTAAATTTA-ATT--A
1 TTTAAATTTACTTTAAA
*
41450153 TTTAAATTTACTTTGAA
1 TTTAAATTTACTTTAAA
41450170 TTTAAATTTA
1 TTTAAATTTA
41450180 AATAAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 12 0.23
17 27 0.52
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:41450136 original size:11 final size:10
Alignment explanation
Indices: 41450096--41450173 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 10
41450086 TAATTTAGAG
*
41450096 TTAAATTGATT
1 TTAAATTTA-T
41450107 TTAAATTTAT
1 TTAAATTTAT
41450117 TT-AA---AT
1 TTAAATTTAT
41450123 TTAAATTTATT
1 TTAAATTTA-T
41450134 TTAAATTTAAAT
1 TTAAATTT--AT
41450146 TT-AA-TTAT
1 TTAAATTTAT
41450154 TTAAATTTACT
1 TTAAATTTA-T
*
41450165 TTGAATTTA
1 TTAAATTTA
41450174 AATTTAAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
8 4 0.07
9 4 0.07
10 9 0.16
11 28 0.51
12 3 0.05
13 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:41451983 original size:30 final size:30
Alignment explanation
Indices: 41451947--41452298 Score: 412
Period size: 30 Copynumber: 11.7 Consensus size: 30
41451937 AAAGTGTCCA
41451947 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
41451977 AAAATTATATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
*
41452007 AAAATTACATTTT-AACCTCAAAACTTTTCC
1 AAAATTACATTTTGACCCT-AAAACTTTTCC
*
41452037 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* *
41452067 AAAATTACATTTTGGCCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
*
41452097 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
41452127 AAAATTATATTTTAACCCTAAAACTTTCCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
41452157 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
41452187 ACAATTACATTTTGA-CCTCGAAACTCTTCC
1 AAAATTACATTTTGACCCT-AAAACTTTTCC
** * *
41452217 AAAACCACATTTAGACCCCAAAA-TTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* *
41452246 TAAAATTATATTTTGGA-CCTCGAAAC-TTT-C
1 -AAAATTACATTTT-GACCCT-AAAACTTTTCC
41452276 AAAATTACCATTTT-ACCCCTAAA
1 AAAATTA-CATTTTGA-CCCTAAA
41452299 CTTCCCTAAA
Statistics
Matches: 276, Mismatches: 35, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.00
29 20 0.07
30 242 0.88
31 13 0.05
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTAAAACTTTTCC
Found at i:41452037 original size:60 final size:60
Alignment explanation
Indices: 41451947--41452301 Score: 461
Period size: 60 Copynumber: 5.9 Consensus size: 60
41451937 AAAGTGTCCA
* *
41451947 AAAATTACATTTTGACC-CTAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCTC-AAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
*
41452007 AAAATTACATTTTAACCTCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCTCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* *
41452067 AAAATTACATTTTGGCCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCTCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * * *
41452127 AAAATTATATTTTAACC-CTAAAACTTTCCCAAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCTC-AAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * * ** *
41452187 ACAATTACATTTTGACCTCGAAACTCTTCCAAAACCACATTTAGACCCCAAAA-TTTTCC
1 AAAATTACATTTTGACCTCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * *
41452246 TAAAATTATATTTTGGACCTCGAAAC-TTT-CAAAATTACCATTTT-ACCCCTAAACTT
1 -AAAATTACATTTT-GACCTCAAAACTTTTCCAAAATTA-CATTTTGACCCCAAAACTT
41452302 CCCTAAATCC
Statistics
Matches: 260, Mismatches: 28, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.08
60 226 0.87
61 13 0.05
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (60 bp):
AAAATTACATTTTGACCTCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:41452343 original size:59 final size:57
Alignment explanation
Indices: 41452275--41452492 Score: 188
Period size: 59 Copynumber: 3.7 Consensus size: 57
41452265 TCGAAACTTT
* * *
41452275 CAAAATTACCATTTTACCCCTAAACTTCCCTAAATCCCATTTTTAACCCCGATTCCAC
1 CAAAATTACCATTTTACCCCTAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * * * ** * **
41452333 CAAAACTTACCGTTTTGCCTCC-AAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAA-TTACCATTTTACC-CCTAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* ** *
41452392 CAAAATTTATCATTTTATTCCTCAAACTTTCCAAATTCCATTCTTAACCCCGATTTCAC
1 CAAAA-TTACCATTTTACCCCT-AAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
* **
41452451 AAAAATTACCATTTTACCCCTAAA-AATCCAAATTACCATTTT
1 CAAAATTACCATTTTACCCCTAAACTTTCCAAATT-CCATTTT
41452493 GCCCCCGGGT
Statistics
Matches: 121, Mismatches: 34, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
56 8 0.07
57 9 0.07
58 20 0.17
59 73 0.60
60 11 0.09
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (57 bp):
CAAAATTACCATTTTACCCCTAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
Found at i:41455921 original size:32 final size:32
Alignment explanation
Indices: 41455885--41455996 Score: 83
Period size: 32 Copynumber: 3.5 Consensus size: 32
41455875 ATTAATTTAG
41455885 ATATTAAATTATTTAATATAATGATACATCAA
1 ATATTAAATTATTTAATATAATGATACATCAA
* * **
41455917 ATATTTAAAAT-TTTAA-ATTAATGA-AAAT-TT
1 ATA-TTAAATTATTTAATA-TAATGATACATCAA
* *
41455947 ATATTCAAATAATTTAATATAATCATACA-CGAA
1 ATATT-AAATTATTTAATATAATGATACATC-AA
41455980 ATA-TAAATTTATTTAAT
1 ATATTAAA-TTATTTAAT
41455997 TTTTTAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
29 2 0.03
30 6 0.10
31 17 0.28
32 26 0.43
33 9 0.15
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
ATATTAAATTATTTAATATAATGATACATCAA
Found at i:41457006 original size:13 final size:13
Alignment explanation
Indices: 41456988--41457013 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41456978 TGAGAAGTAG
41456988 ATGCCGAACCCAA
1 ATGCCGAACCCAA
41457001 ATGCCGAACCCAA
1 ATGCCGAACCCAA
41457014 CTCAGGTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.08
Consensus pattern (13 bp):
ATGCCGAACCCAA
Found at i:41458734 original size:17 final size:17
Alignment explanation
Indices: 41458699--41458760 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
41458689 TTTTATTTTA
* *
41458699 AAAATATTTAAAATTATT
1 AAAATA-TTAATATAATT
41458717 AAAATATTAATATAATT
1 AAAATATTAATATAATT
* * * *
41458734 ATATTTTTCATATAATAT
1 AAAATATTAATATAAT-T
41458752 AAAATATTA
1 AAAATATTA
41458761 TATGAAGACA
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
17 21 0.64
18 12 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTAATATAATT
Found at i:41459328 original size:625 final size:625
Alignment explanation
Indices: 41458139--41459356 Score: 2436
Period size: 625 Copynumber: 1.9 Consensus size: 625
41458129 GGGGGGGGGG
41458139 GAAGACAAACTTGCGACTACATATTGGGAAAAATATTTTTCATTTATTCTTTTACTTCTTATATA
1 GAAGACAAACTTGCGACTACATATTGGGAAAAATATTTTTCATTTATTCTTTTACTTCTTATATA
41458204 CAAAAATATAGCTTAAACAATAAGATTTATATATATTTAGAAACTCATATAAACAATATAATTCT
66 CAAAAATATAGCTTAAACAATAAGATTTATATATATTTAGAAACTCATATAAACAATATAATTCT
41458269 GTAATAAATAAAATATAAGTAAATAATTATTGCTAATTTGATGTAAATCTTTTGATTTAATCGGG
131 GTAATAAATAAAATATAAGTAAATAATTATTGCTAATTTGATGTAAATCTTTTGATTTAATCGGG
41458334 ATAATATAGTTCAATCGGTTTTTTGATATACTCGATGAAGGTGTACATACATTCTATGATTTGAT
196 ATAATATAGTTCAATCGGTTTTTTGATATACTCGATGAAGGTGTACATACATTCTATGATTTGAT
41458399 TTCAGGATAAGGGATAATTGCAAGGAGGAAAACACTCCAAAGGTTTGTTTAGGTTTTACGGAAAA
261 TTCAGGATAAGGGATAATTGCAAGGAGGAAAACACTCCAAAGGTTTGTTTAGGTTTTACGGAAAA
41458464 TATTTTTTGTATTTTTTTGTGTTTGTTTCATATAAAATAATTTAATCAACGAAAAATAACTTAAA
326 TATTTTTTGTATTTTTTTGTGTTTGTTTCATATAAAATAATTTAATCAACGAAAAATAACTTAAA
41458529 GGTCAACGTAAAATAATCTCTTTTTCCTATAAAATGACTTACCCTTTTGAAAAGGGTAAGTTATT
391 GGTCAACGTAAAATAATCTCTTTTTCCTATAAAATGACTTACCCTTTTGAAAAGGGTAAGTTATT
41458594 TTTTCGAAAAAGAGCTCTTCTATAGTTAATTTTATTTTTATATAAAAATTAACTTAAATCAAATT
456 TTTTCGAAAAAGAGCTCTTCTATAGTTAATTTTATTTTTATATAAAAATTAACTTAAATCAAATT
41458659 TAATATAATTATATTGATAATAAATTTTATTTTTATTTTAAAAATATTTAAAATTATTAAAATAT
521 TAATATAATTATATTGATAATAAATTTTATTTTTATTTTAAAAATATTTAAAATTATTAAAATAT
41458724 TAATATAATTATATTTTTCATATAATATAAAATATTATAT
586 TAATATAATTATATTTTTCATATAATATAAAATATTATAT
41458764 GAAGACAAACTTGCGACTACATATTGGGAAAAATATTTTTCATTTATTCTTTTACTTCTTATATA
1 GAAGACAAACTTGCGACTACATATTGGGAAAAATATTTTTCATTTATTCTTTTACTTCTTATATA
41458829 CAAAAATATAGCTTAAACAATAAGATTTATATATATTTAGAAACTCATATAAACAATATAATTCT
66 CAAAAATATAGCTTAAACAATAAGATTTATATATATTTAGAAACTCATATAAACAATATAATTCT
41458894 GTAATAAATAAAATATAAGTAAATAATTATTGCTAATTTGATGTAAATCTTTTGATTTAATCGGG
131 GTAATAAATAAAATATAAGTAAATAATTATTGCTAATTTGATGTAAATCTTTTGATTTAATCGGG
41458959 ATAATATAGTTCAATCGGTTTTTTGATATACTCGATGAAGGTGTACATACATTCTATGATTTGAT
196 ATAATATAGTTCAATCGGTTTTTTGATATACTCGATGAAGGTGTACATACATTCTATGATTTGAT
41459024 TTCAGGATAAGGGATAATTGCAAGGAGGAAAACACTCCAAAGGTTTGTTTAGGTTTTACGGAAAA
261 TTCAGGATAAGGGATAATTGCAAGGAGGAAAACACTCCAAAGGTTTGTTTAGGTTTTACGGAAAA
41459089 TATTTTTTGTATTTTTTTGTGTTTGTTTCATATAAAATAATTTAATCAACGAAAAATAACTTAAA
326 TATTTTTTGTATTTTTTTGTGTTTGTTTCATATAAAATAATTTAATCAACGAAAAATAACTTAAA
41459154 GGTCAACGTAAAATAATCTCTTTTTCCTATAAAATGACTTACCCTTTTGAAAAGGGTAAGTTATT
391 GGTCAACGTAAAATAATCTCTTTTTCCTATAAAATGACTTACCCTTTTGAAAAGGGTAAGTTATT
41459219 TTTTCGAAAAAGAGCTCTTCTATAGTTAATTTTATTTTTATATAAAAATTAACTTAAATCAAATT
456 TTTTCGAAAAAGAGCTCTTCTATAGTTAATTTTATTTTTATATAAAAATTAACTTAAATCAAATT
41459284 TAATATAATTATATTGATAATAAATTTTATTTTTATTTTAAAAATATTTAAAATTATTAAAATAT
521 TAATATAATTATATTGATAATAAATTTTATTTTTATTTTAAAAATATTTAAAATTATTAAAATAT
41459349 TAATATAA
586 TAATATAA
41459357 AATATTATAT
Statistics
Matches: 593, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
625 593 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (625 bp):
GAAGACAAACTTGCGACTACATATTGGGAAAAATATTTTTCATTTATTCTTTTACTTCTTATATA
CAAAAATATAGCTTAAACAATAAGATTTATATATATTTAGAAACTCATATAAACAATATAATTCT
GTAATAAATAAAATATAAGTAAATAATTATTGCTAATTTGATGTAAATCTTTTGATTTAATCGGG
ATAATATAGTTCAATCGGTTTTTTGATATACTCGATGAAGGTGTACATACATTCTATGATTTGAT
TTCAGGATAAGGGATAATTGCAAGGAGGAAAACACTCCAAAGGTTTGTTTAGGTTTTACGGAAAA
TATTTTTTGTATTTTTTTGTGTTTGTTTCATATAAAATAATTTAATCAACGAAAAATAACTTAAA
GGTCAACGTAAAATAATCTCTTTTTCCTATAAAATGACTTACCCTTTTGAAAAGGGTAAGTTATT
TTTTCGAAAAAGAGCTCTTCTATAGTTAATTTTATTTTTATATAAAAATTAACTTAAATCAAATT
TAATATAATTATATTGATAATAAATTTTATTTTTATTTTAAAAATATTTAAAATTATTAAAATAT
TAATATAATTATATTTTTCATATAATATAAAATATTATAT
Found at i:41459497 original size:13 final size:14
Alignment explanation
Indices: 41459481--41459522 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
41459471 TTTCAATTTT
41459481 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
41459494 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
41459509 ATTTTAAATAATAT
1 ATTTT-AATAATAT
41459523 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:41459507 original size:16 final size:16
Alignment explanation
Indices: 41459485--41459521 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
41459475 AATTTTATTT
41459485 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
41459502 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
41459517 TAATA
1 TAATA
41459522 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:41459574 original size:15 final size:15
Alignment explanation
Indices: 41459554--41459610 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
41459544 ATTCAATATT
41459554 AATATTTTAATAATA
1 AATATTTTAATAATA
*
41459569 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
41459588 AATATATTAATAATA
1 AATATTTTAATAATA
41459603 AATATTTT
1 AATATTTT
41459611 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:41461327 original size:23 final size:24
Alignment explanation
Indices: 41461301--41461345 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
41461291 ATCTTATTTG
41461301 TTTTTGTAATTTT-ATTTTTATCA
1 TTTTTGTAATTTTAATTTTTATCA
* *
41461324 TTTTTTTAGTTTTAATTTTTAT
1 TTTTTGTAATTTTAATTTTTAT
41461346 TTATAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTTGTAATTTTAATTTTTATCA
Found at i:41468398 original size:13 final size:12
Alignment explanation
Indices: 41468380--41468419 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
41468370 AAATCAAATC
41468380 AAATTTTAATTGA
1 AAATTTTAATT-A
41468393 AAATTTTAAGTTA
1 AAATTTTAA-TTA
*
41468406 AAAGTTTAATTA
1 AAATTTTAATTA
41468418 AA
1 AA
41468420 TTAATATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 5 0.20
13 18 0.72
14 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (12 bp):
AAATTTTAATTA
Found at i:41469073 original size:13 final size:12
Alignment explanation
Indices: 41469040--41469080 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
41469030 ATAAAATTAT
41469040 TAAATATTAAAA
1 TAAATATTAAAA
41469052 TAAA-A-TAAAA
1 TAAATATTAAAA
41469062 TAAATATTTAAAA
1 TAAATA-TTAAAA
*
41469075 AAAATA
1 TAAATA
41469081 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 9 0.36
11 2 0.08
12 4 0.16
13 10 0.40
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAATATTAAAA
Found at i:41469084 original size:23 final size:22
Alignment explanation
Indices: 41469040--41469088 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
41469030 ATAAAATTAT
41469040 TAAATATTAAAATAAAATAAAA
1 TAAATATTAAAATAAAATAAAA
41469062 TAAATATTTAAAA-AAAATAAAA
1 TAAATA-TTAAAATAAAATAAAA
41469084 -AAATA
1 TAAATA
41469089 ATATGAACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.19
22 15 0.58
23 6 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAATATTAAAATAAAATAAAA
Found at i:41475544 original size:22 final size:22
Alignment explanation
Indices: 41475531--41475585 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
41475521 TATTTTAATC
41475531 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* *
41475553 TTAAATTTAAATTTAAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
41475576 TTAAAATTTA
1 TT-AAATTTA
41475586 ATATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.28
23 15 0.52
24 6 0.21
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:41475561 original size:6 final size:6
Alignment explanation
Indices: 41475514--41475586 Score: 66
Period size: 6 Copynumber: 12.7 Consensus size: 6
41475504 CATTTGAAAA
* * *
41475514 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
41475559 TTAAAT TTAAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
41475587 TATTATTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 28 0.51
7 10 0.18
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:41475587 original size:12 final size:11
Alignment explanation
Indices: 41475511--41475587 Score: 84
Period size: 12 Copynumber: 6.8 Consensus size: 11
41475501 AACCATTTGA
*
41475511 AAATTAAATTT
1 AAATTTAATTT
*
41475522 -ATTTTAATCTT
1 AAATTTAAT-TT
*
41475533 AAATTTACTTT
1 AAATTTAATTT
*
41475544 AAATTCAATTT
1 AAATTTAATTT
41475555 AAATTTAAATTT
1 AAATTT-AATTT
41475567 AAATTTAATTT
1 AAATTTAATTT
41475578 AAAATTTAAT
1 -AAATTTAAT
41475588 ATTATTATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.42
12 26 0.47
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:41475782 original size:15 final size:14
Alignment explanation
Indices: 41475762--41475817 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
41475752 CGTGCCTCTG
41475762 CTGCCACCACCAGC
1 CTGCCACCACCAGC
41475776 TCTGCCACCACCAG-
1 -CTGCCACCACCAGC
41475790 CT-CCATCCACCATGCC
1 CTGCCA-CCACCA-G-C
41475806 CTGCCACCACCA
1 CTGCCACCACCA
41475818 TTAAACCTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 8 0.22
14 1 0.03
15 13 0.36
16 8 0.22
17 3 0.08
ACGTcount: A:0.21, C:0.55, G:0.11, T:0.12
Consensus pattern (14 bp):
CTGCCACCACCAGC
Found at i:41477599 original size:29 final size:30
Alignment explanation
Indices: 41477496--41477712 Score: 155
Period size: 29 Copynumber: 7.5 Consensus size: 30
41477486 AAACTTTTCC
* *
41477496 AAAATTA-CATTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTAACCCCGATTTCATCT
* * * *
41477525 AAAATTACTATTTTACCCCCGA-ATC-TTT
1 AAAATTACCATTTTAACCCCGATTTCATCT
* * *
41477553 TAAA-TCCCATTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTAACCCCGATTTCATCT
* ** *
41477582 AAAATTACCATTTTACCCCCGA-AGCTTCT
1 AAAATTACCATTTTAACCCCGATTTCATCT
* * *
41477611 AAAATT-TCATTTTTAACCCCGATTTCACCG
1 AAAATTACCA-TTTTAACCCCGATTTCATCT
* ** * *
41477641 AAAATTACCATTTT-ACCCCTAAATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCATCT
*
41477670 AAAATT-CCATTTTTAACCTCGATTTCATC-
1 AAAATTACCA-TTTTAACCCCGATTTCATCT
41477699 AAAATTACCATTTT
1 AAAATTACCATTTT
41477713 GCCCCCGGGT
Statistics
Matches: 137, Mismatches: 41, Indels: 20
0.69 0.21 0.10
Matches are distributed among these distances:
27 14 0.10
28 10 0.07
29 61 0.45
30 50 0.36
31 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCATCT
Found at i:41477638 original size:116 final size:116
Alignment explanation
Indices: 41477496--41477719 Score: 344
Period size: 116 Copynumber: 1.9 Consensus size: 116
41477486 AAACTTTTCC
* *
41477496 AAAATTACATTTTAACCCCGATTTCACCAAAAATTACTATTTTACCCCCGAATCTTTT-AAATCC
1 AAAATTACATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATCC
41477560 CA-TTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAAGCTTCT
66 CATTTTTAACCCCGATTTCATC-AAAATTACCATTTTACCCCCGAAGCTTCT
* * * *
41477611 AAAATTTCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAAATT
1 AAAATTACA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATC
* *
41477676 CCATTTTTAACCTCGATTTCATCAAAATTACCATTTTGCCCCCG
65 CCATTTTTAACCCCGATTTCATCAAAATTACCATTTTACCCCCG
41477720 GGTATCCATA
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
115 8 0.08
116 45 0.46
117 27 0.28
118 18 0.18
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.36
Consensus pattern (116 bp):
AAAATTACATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATCC
CATTTTTAACCCCGATTTCATCAAAATTACCATTTTACCCCCGAAGCTTCT
Found at i:41477643 original size:59 final size:57
Alignment explanation
Indices: 41477496--41477719 Score: 288
Period size: 59 Copynumber: 3.9 Consensus size: 57
41477486 AAACTTTTCC
* * *
41477496 AAAATTACATTTTAACCCCGATTTCACCAAAAATTACTATTTTACCCCCGAATCTTT
1 AAAATTCCATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTT
* * * *
41477553 TAAATCCCATTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATTCCATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTT-T
* **
41477611 AAAATTTCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTT
1 AAAATTCCA-TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATC-TTT
* * *
41477670 AAAATTCCATTTTTAACCTCGATTTCATC-AAAATTACCATTTTGCCCCCG
1 AAAATTCCA-TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCG
41477720 GGTATCCATA
Statistics
Matches: 144, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
57 49 0.34
58 25 0.17
59 68 0.47
60 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.36
Consensus pattern (57 bp):
AAAATTCCATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTT
Found at i:41489818 original size:38 final size:37
Alignment explanation
Indices: 41489675--41490423 Score: 447
Period size: 38 Copynumber: 21.4 Consensus size: 37
41489665 GTCATCCCCT
* *
41489675 TGAAATTGAAGTAGAGTGGATAACACGTCCTAATCTC
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
** * **
41489712 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCCCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
* * *
41489743 TGAAATTGGAGTAGAGTGGATAATACATC--C-TCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
* *
41489776 TGAAATTGAAGTAGAGTGGATAACATTGCCTTCATCTC
1 TGAAATTGAAGTAGAGTGGATAACA-CGTCTTCATCTC
** * * *
41489814 TGAAATTGAAGT-GA---GAGCA-ATGTCATCCTCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
*
41489845 TGAAAATGAAGTAGAGTTGGATAACACGTCTTCATCTC
1 TGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTC
* * *
41489883 TGAAATTGAAGTA-A---G--AGCAGCGCCTTCATCCC
1 TGAAATTGAAGTAGAGTGGATAACA-CGTCTTCATCTC
*
41489915 TTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCC
1 -TGAAATTGAAGTAGAGTGGATAACACGTCTTCAT-CTC
* *
41489954 TTGAAATTGAAGTAGAGTGGATAACACGCCTTCATCCC
1 -TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
* *
41489992 TTGAAATTGAAGTAGAGTGGATAACACGTCTTTATTTC
1 -TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
* ** * **
41490030 TGAAACTGAAGTA-A---GAGCA-ACGTCATCCCCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
* *
41490061 TGAAATTGAAGTAGAGTGGATAACACGCCTTCATCCC
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
*
41490098 TTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
** * **
41490136 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCCCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
41490167 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
** * *
41490204 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCTCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
* * *
41490235 TGAAATTGAAGTAGAGTTGAATATCAAGTCCTT-ATCTC
1 TGAAATTGAAGTAGAG-TGGATAACACGT-CTTCATCTC
* ** * *
41490273 TGAAAATGAAGT--A--GGAGCA-ACGTCATCCTCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
* * *
41490304 TGAAATTGAAGTAGAGTTGAATATCAAGTCCTT-ATCTC
1 TGAAATTGAAGTAGAG-TGGATAACACGT-CTTCATCTC
* *
41490342 TGAAATTGAAGTA-A---G--AACAACGTCATCCTCT-
1 TGAAATTGAAGTAGAGTGGATAAC-ACGTCTTCATCTC
* * *
41490373 TGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTC
1 TGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTC
41490411 TGAAATTGAAGTA
1 TGAAATTGAAGTA
41490424 AGAGCAAGAT
Statistics
Matches: 541, Mismatches: 105, Indels: 131
0.70 0.14 0.17
Matches are distributed among these distances:
31 94 0.17
32 70 0.13
33 55 0.10
34 6 0.01
35 9 0.02
36 33 0.06
37 88 0.16
38 146 0.27
39 40 0.07
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (37 bp):
TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
Found at i:41489849 original size:69 final size:68
Alignment explanation
Indices: 41489768--41490111 Score: 395
Period size: 69 Copynumber: 4.8 Consensus size: 68
41489758 GTGGATAATA
* * *
41489768 CATCCTCTTGAAATTGAAGTAGAGTGGATAACATTGCCTTCATCTCTGAAATTGAAGTGAGAGCA
1 CATCC-CTTGAAATTGAAGTAGAGTGGATAACA-CGTCTTCATCTCTGAAATTGAAGTAAGAGCA
*
41489833 ATG-T
64 ACGCT
*
41489837 CATCCTCTTGAAAATGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 CATCC-CTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
*
41489902 GCGCCTT
64 ACG-C-T
*
41489909 CATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCCTTGAAATTGAAGTAGAGTGG
1 CATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCAT-CTC-TGAAATTGAAGTA-A---G
**
41489974 ATAACACGCCTT
60 AGCA-ACG-C-T
* * *
41489986 CATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATTTCTGAAACTGAAGTAAGAGCAAC
1 CATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
41490051 G-T
66 GCT
* *
41490053 CATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTCATCCCTTGAAATTGAAGTA
1 CAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC-TGAAATTGAAGTA
41490112 GAGTGGATAA
Statistics
Matches: 240, Mismatches: 22, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
67 4 0.02
68 37 0.15
69 64 0.27
70 30 0.12
71 22 0.09
72 19 0.08
73 1 0.00
74 1 0.00
75 12 0.05
76 4 0.02
77 46 0.19
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (68 bp):
CATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
GCT
Found at i:41490075 original size:106 final size:106
Alignment explanation
Indices: 41489666--41490216 Score: 671
Period size: 106 Copynumber: 5.2 Consensus size: 106
41489656 GATCCCAACG
* *
41489666 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCCTAATCTCTGAAATTGAAGTAAGAGCA
1 TCAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
*
41489731 ACGTCATCCCCTTGAAATTGGAGTAGAGTGGAT-A-A----T
65 ACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCT
* * * *
41489767 ACATCCTCTTGAAATTGAAGTAGAGTGGATAACATTGCCTTCATCTCTGAAATTGAAGTGAGAGC
1 TCATCC-CTTGAAATTGAAGTAGAGTGGATAACA-CGTCTTCATCTCTGAAATTGAAGTAAGAGC
* * * *
41489832 AATGTCATCCTCTTGAAAATGAAGTAGAGTTGGATAACACGTCT
64 AACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGCCT
* * * *
41489876 TCATCTC-TGAAATTGAAGTA-A---G--AGCAGCGCCTTCATCCCTTGAAATTGAAGTAGAGTG
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACA-CGTCTTCATCTC-TGAAATTGAAGTA-A---
**
41489934 GATAACACGTCTTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCT
60 GAGCA-ACG---TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCT
* * *
41489985 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATTTCTGAAACTGAAGTAAGAGCAA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
41490050 CGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCT
66 CGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCT
*
41490091 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
*
41490156 CGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
66 CGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCT
*
41490197 TCATCTC-TGAAATTGAAGTA
1 TCATCCCTTGAAATTGAAGTA
41490217 AGAGCAACGT
Statistics
Matches: 389, Mismatches: 36, Indels: 46
0.83 0.08 0.10
Matches are distributed among these distances:
100 2 0.01
101 43 0.11
102 62 0.16
103 7 0.02
104 1 0.00
105 14 0.04
106 152 0.39
107 15 0.04
108 1 0.00
109 27 0.07
110 39 0.10
111 1 0.00
113 1 0.00
114 13 0.03
115 8 0.02
116 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (106 bp):
TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
CGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCT
Found at i:41490171 original size:31 final size:31
Alignment explanation
Indices: 41490136--41490385 Score: 162
Period size: 31 Copynumber: 7.4 Consensus size: 31
41490126 TCTTTATCTC
*
41490136 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCTCT
** * *
41490167 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCTCT
41490203 CTGAAATTGAAGTAAGAGCAACGTCATCCTCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCTCT
* **
41490235 TGAAATTGAAGT-AGAGTTGAATATCAAGTCCTTATCT
1 TGAAATTGAAGTAAGAG--CAACGTC-A-TCC---TCT
* *
41490272 CTGAAAATGAAGTAGGAGCAACGTCATCCTCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCTCT
* **
41490304 TGAAATTGAAGT-AGAGTTGAATATCAAGTCCTTATCT
1 TGAAATTGAAGTAAGAG--CAACGTC-A-TCC---TCT
*
41490341 CTGAAATTGAAGTAAGAACAACGTCATCCTCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCTCT
41490373 TGAAATTGAAGTA
1 TGAAATTGAAGTA
41490386 GAGTTGGATA
Statistics
Matches: 169, Mismatches: 26, Indels: 48
0.70 0.11 0.20
Matches are distributed among these distances:
30 7 0.04
31 49 0.29
32 25 0.15
33 5 0.03
34 6 0.04
35 9 0.05
36 12 0.07
37 27 0.16
38 23 0.14
39 6 0.04
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCTCT
Found at i:41490285 original size:174 final size:179
Alignment explanation
Indices: 41489904--41490286 Score: 530
Period size: 174 Copynumber: 2.1 Consensus size: 179
41489894 TAAGAGCAGC
41489904 GCCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCCTTGAAATTGAAGTAG
1 GCCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCCTTGAAATTGAAGTAG
* * *
41489969 AGTGGATAACACGCCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATTTCTGAA
66 A--GGAGAACACG-C-TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAA
* *
41490034 ACTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAC
127 ACTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGAATAACAA
* *
41490087 GCCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTAT-CTC-TGAAATTGAAGTA-
1 GCCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCCTTGAAATTGAAGTAG
* *
41490149 A-GAGCA-ACG-TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATT
66 AGGAGAACACGCTCAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAACT
* *
41490211 GAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGAATATCAA
130 GAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAG-TGAATAACAA
* *
41490262 GTCCTT-ATCTC-TGAAAATGAAGTAG
1 G-CCTTCATCCCTTGAAATTGAAGTAG
41490287 GAGCAACGTC
Statistics
Matches: 184, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
173 4 0.02
174 97 0.53
175 12 0.07
176 7 0.04
177 3 0.02
180 1 0.01
181 13 0.07
182 2 0.01
183 45 0.24
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (179 bp):
GCCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCCTTGAAATTGAAGTAG
AGGAGAACACGCTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAACTG
AAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGAATAACAA
Found at i:41490299 original size:69 final size:69
Alignment explanation
Indices: 41490091--41490430 Score: 535
Period size: 69 Copynumber: 5.0 Consensus size: 69
41490081 TAACACGCCT
* * *
41490091 TCATCC-CTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGC
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCCTTATCTCTGAAATTGAAGTAAGAGC
41490154 AACG
66 AACG
* * *
41490158 TCATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGT-CTTCATCTCTGAAATTGAAGTAAGAG
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCCTT-ATCTCTGAAATTGAAGTAAGAG
41490221 CAACG
65 CAACG
* * *
41490226 TCATCCTCTTGAAATTGAAGTAGAGTTGAATATCAAGTCCTTATCTCTGAAAATGAAGTAGGAGC
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCCTTATCTCTGAAATTGAAGTAAGAGC
41490291 AACG
66 AACG
* *
41490295 TCATCCTCTTGAAATTGAAGTAGAGTTGAATATCAAGTCCTTATCTCTGAAATTGAAGTAAGAAC
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCCTTATCTCTGAAATTGAAGTAAGAGC
41490360 AACG
66 AACG
*
41490364 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGC
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCCTTATCTCTGAAATTGAAGTAAGAGC
41490429 AA
66 AA
41490431 GATCATTTCC
Statistics
Matches: 256, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
67 8 0.03
68 81 0.32
69 164 0.64
70 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (69 bp):
TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCCTTATCTCTGAAATTGAAGTAAGAGC
AACG
Found at i:41490794 original size:22 final size:22
Alignment explanation
Indices: 41490781--41490835 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
41490771 TATTTTAATC
41490781 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* * *
41490803 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
41490826 TTAAAATTTA
1 TT-AAATTTA
41490836 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:41490811 original size:6 final size:6
Alignment explanation
Indices: 41490764--41490836 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
41490754 CATTTGAAAA
* * *
41490764 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
41490809 TTAAAT TTGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
41490837 TATTATTATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 27 0.50
7 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:41490811 original size:17 final size:17
Alignment explanation
Indices: 41490784--41490830 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
41490774 TTTAATCTTA
*
41490784 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
41490800 AATTTAAATTTAAATTTG
1 AATTT-AATTTAAATTTC
41490818 AATTTAATTTAAA
1 AATTTAATTTAAA
41490831 ATTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 5 0.19
17 15 0.56
18 7 0.26
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:41490821 original size:12 final size:12
Alignment explanation
Indices: 41490764--41490836 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
41490754 CATTTGAAAA
41490764 TTAAATTT--AT
1 TTAAATTTAAAT
*
41490774 TTTAATCTTAAAT
1 TTAAAT-TTAAAT
*
41490787 TT-ACTTTAAA-
1 TTAAATTTAAAT
*
41490797 TTCAATTTAAAT
1 TTAAATTTAAAT
*
41490809 TTAAATTTGAAT
1 TTAAATTTAAAT
41490821 TT-AATTTAAAAT
1 TTAAATTT-AAAT
41490833 TTAA
1 TTAA
41490837 TATTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
11 19 0.38
12 19 0.38
13 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:41490837 original size:12 final size:11
Alignment explanation
Indices: 41490761--41490837 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
41490751 AACCATTTGA
*
41490761 AAATTAAATTT
1 AAATTTAATTT
*
41490772 -ATTTTAATCTT
1 AAATTTAAT-TT
*
41490783 AAATTTACTTT
1 AAATTTAATTT
*
41490794 AAATTCAATTT
1 AAATTTAATTT
41490805 AAATTTAAATTT
1 AAATTT-AATTT
*
41490817 GAATTTAATTT
1 AAATTTAATTT
41490828 AAAATTTAAT
1 -AAATTTAAT
41490838 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.43
12 24 0.45
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:41491034 original size:15 final size:14
Alignment explanation
Indices: 41491014--41491069 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
41491004 CGTAACTCTG
41491014 CTGCCACCACCAGC
1 CTGCCACCACCAGC
41491028 TCTGCCACCACCAG-
1 -CTGCCACCACCAGC
41491042 CT-CCATCCACCATGCC
1 CTGCCA-CCACCA-G-C
41491058 CTGCCACCACCA
1 CTGCCACCACCA
41491070 TTAAACCTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 8 0.22
14 1 0.03
15 13 0.36
16 8 0.22
17 3 0.08
ACGTcount: A:0.21, C:0.55, G:0.11, T:0.12
Consensus pattern (14 bp):
CTGCCACCACCAGC
Found at i:41492645 original size:162 final size:162
Alignment explanation
Indices: 41492471--41492780 Score: 507
Period size: 162 Copynumber: 1.9 Consensus size: 162
41492461 CTTTTCAATT
* *
41492471 TAGTCCTTTGACTTTTTTGATTGCACCAGAGGTTGCCACGTGTCATTTTTTGGATTATTTCTGCA
1 TAGTCCTTTGACTTTTTTGACTACACCAGAGGTTGCCACGTGTCATTTTTTGGATTATTTCTGCA
*
41492536 TTTAATCCTTTTTATTTTTAATTTGTTTTAATTTAATC-CCAAATCGACTTT-ATTTTAATTACA
66 TTTAATCCTTTTTATTTTTAATTTGTTTTAATTTAATCTCCAAATCGACTTTCA-CTTAATTACA
41492599 AAATCGGCCCAATAATTTTTCAAAGTTTATAAAC
130 AAATCGGCCCAA-AATTTTTCAAAGTTTATAAAC
41492633 TAGTCCTTTGACTTTTTTGACTACACCAGAGGTTGCCACGTGTCATTTTTTGGATTATTTCTGCA
1 TAGTCCTTTGACTTTTTTGACTACACCAGAGGTTGCCACGTGTCATTTTTTGGATTATTTCTGCA
* ** *
41492698 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCTTTAAATCGACTTTCACTTAATTCCAA
66 TTTAATCCTTTTTATTTTTAATTTGTTTTAATTTAATCTCCAAATCGACTTTCACTTAATTACAA
* *
41492763 AATTGGTCCAAAATTTTT
131 AATCGGCCCAAAATTTTT
41492781 TCAAGATTTT
Statistics
Matches: 137, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
162 107 0.78
163 29 0.21
164 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.47
Consensus pattern (162 bp):
TAGTCCTTTGACTTTTTTGACTACACCAGAGGTTGCCACGTGTCATTTTTTGGATTATTTCTGCA
TTTAATCCTTTTTATTTTTAATTTGTTTTAATTTAATCTCCAAATCGACTTTCACTTAATTACAA
AATCGGCCCAAAATTTTTCAAAGTTTATAAAC
Done.