Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015277.1 Kokia drynarioides strain JFW-HI SEQ_130322, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 544247
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 933 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3225 original size:41 final size:41
Alignment explanation
Indices: 3174--3257 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
3164 ACACTGACAA
* * *
3174 TTTATAGCTATGAATAACTTAAAACTGTAACATCAACAATG
1 TTTATAGCTATGAACAACTCAAAACTGCAACATCAACAATG
* *
3215 TTTATAGCTATGAACAACTCAAAACTGCAACTTCATCAATG
1 TTTATAGCTATGAACAACTCAAAACTGCAACATCAACAATG
3256 TT
1 TT
3258 AGTATCATGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (41 bp):
TTTATAGCTATGAACAACTCAAAACTGCAACATCAACAATG
Found at i:14238 original size:38 final size:38
Alignment explanation
Indices: 14195--14271 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
14185 AACTAATTGA
* *
14195 AGTTGTTATAGACGCTACAATAAAGGAAGATAATTCAG
1 AGTTGTTACAGACGCTACAATAAAGGAAGATAATGCAG
* *
14233 AGTTGTTACAGACGCTATAGTAAAGGAAGATAATGCAG
1 AGTTGTTACAGACGCTACAATAAAGGAAGATAATGCAG
14271 A
1 A
14272 TCTCGATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (38 bp):
AGTTGTTACAGACGCTACAATAAAGGAAGATAATGCAG
Found at i:16867 original size:37 final size:38
Alignment explanation
Indices: 16774--16871 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 38
16764 ATTTTCGGAA
16774 TGCACTCAAG-ATAGTCGCTGCATAAATATTCTTCAAAT
1 TGCACTCAAGAAT-GTCGCTGCATAAATATTCTTCAAAT
* * *
16812 TGCA-TCTAGAACTATCGCTGCATAAGTATTCTTC-AAT
1 TGCACTCAAGAA-TGTCGCTGCATAAATATTCTTCAAAT
*
16849 TGCACCCAAGAATGTCGCTGCAT
1 TGCACTCAAGAATGTCGCTGCAT
16872 GAACATGTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
37 21 0.41
38 29 0.57
39 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (38 bp):
TGCACTCAAGAATGTCGCTGCATAAATATTCTTCAAAT
Found at i:27355 original size:21 final size:22
Alignment explanation
Indices: 27331--27383 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
27321 CACAAGAGAT
*
27331 CCAAGGTGCA-TTACAGGGGCA
1 CCAAAGTGCATTTACAGGGGCA
*
27352 CCAAAGTGCATTTACGGGGGCA
1 CCAAAGTGCATTTACAGGGGCA
* *
27374 TCGAAGTGCA
1 CCAAAGTGCA
27384 AACACAAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.28, C:0.23, G:0.32, T:0.17
Consensus pattern (22 bp):
CCAAAGTGCATTTACAGGGGCA
Found at i:27413 original size:21 final size:22
Alignment explanation
Indices: 27369--27416 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
27359 GCATTTACGG
*
27369 GGGCATCGAAGTGCAAACACAA
1 GGGCACCGAAGTGCAAACACAA
* *
27391 GGGCACCGGAGTGC-AATACAA
1 GGGCACCGAAGTGCAAACACAA
27412 GGGCA
1 GGGCA
27417 TAGGAGCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.35, C:0.23, G:0.33, T:0.08
Consensus pattern (22 bp):
GGGCACCGAAGTGCAAACACAA
Found at i:27422 original size:21 final size:22
Alignment explanation
Indices: 27369--27422 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
27359 GCATTTACGG
*
27369 GGGCATCGAAGTGCAAACACAA
1 GGGCATCGGAGTGCAAACACAA
* *
27391 GGGCACCGGAGTGC-AATACAA
1 GGGCATCGGAGTGCAAACACAA
*
27412 GGGCATAGGAG
1 GGGCATCGGAG
27423 CATCGAGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.35, C:0.20, G:0.35, T:0.09
Consensus pattern (22 bp):
GGGCATCGGAGTGCAAACACAA
Found at i:28559 original size:23 final size:23
Alignment explanation
Indices: 28529--28699 Score: 218
Period size: 23 Copynumber: 7.4 Consensus size: 23
28519 GTTACAAATA
*
28529 TGATTTGTGCTTAAATATTAATT
1 TGATTTGTGCTTAAATATTAATG
*
28552 TGATTTGTGCTTACATATTAATG
1 TGATTTGTGCTTAAATATTAATG
28575 TGATTTGTGCTTAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
* * *
28598 TGATTTCTGCTTAAATTTTAATA
1 TGATTTGTGCTTAAATATTAATG
*
28621 TGATTTAG-GCTTAAATATTAGTG
1 TGATTT-GTGCTTAAATATTAATG
*
28644 TGATTTATGCTTAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
* * *
28667 TGATTTATGTTTGAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
*
28690 TAAATTTGTG
1 T-GATTTGTG
28700 GGTATGTTAT
Statistics
Matches: 129, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
23 123 0.95
24 6 0.05
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (23 bp):
TGATTTGTGCTTAAATATTAATG
Found at i:28768 original size:36 final size:36
Alignment explanation
Indices: 28691--28768 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 36
28681 ATATTAATGT
* * * *
28691 AAATTTGTGGGTATGTTATTCATGCCGTAAGACAGT
1 AAATATGTGGGTATGCTATTCATGCCATAAGACAGC
* **
28727 AAATATGTGGGTATGCTATTCATGTCATGTGACAGC
1 AAATATGTGGGTATGCTATTCATGCCATAAGACAGC
*
28763 GAATAT
1 AAATAT
28769 ATTGTGTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (36 bp):
AAATATGTGGGTATGCTATTCATGCCATAAGACAGC
Found at i:29224 original size:46 final size:45
Alignment explanation
Indices: 29156--29248 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 45
29146 TTATCATTAA
*
29156 TTGTGTTAAAAGTTAATGTGATTTATGCTTAAATATTAATGTGAT
1 TTGTGTTAAAAGTTAATATGATTTATGCTTAAATATTAATGTGAT
* *
29201 TTGTGCTTAAATGTTAATATGATTTATGTTTAAATATTAATGTGAT
1 TTGTG-TTAAAAGTTAATATGATTTATGCTTAAATATTAATGTGAT
29247 TT
1 TT
29249 ATGAGTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 5 0.11
46 39 0.89
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.49
Consensus pattern (45 bp):
TTGTGTTAAAAGTTAATATGATTTATGCTTAAATATTAATGTGAT
Found at i:29258 original size:46 final size:46
Alignment explanation
Indices: 29162--29258 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
29152 TTAATTGTGT
* * * **
29162 TAAAAGTTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCT
1 TAAATGTTAATATGATTTATGCTTAAATATTAATGTGATTTATGAG
*
29208 TAAATGTTAATATGATTTATGTTTAAATATTAATGTGATTTATGAG
1 TAAATGTTAATATGATTTATGCTTAAATATTAATGTGATTTATGAG
29254 TAAAT
1 TAAAT
29259 AAACCTATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.46
Consensus pattern (46 bp):
TAAATGTTAATATGATTTATGCTTAAATATTAATGTGATTTATGAG
Found at i:29259 original size:23 final size:23
Alignment explanation
Indices: 29168--29251 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
29158 GTGTTAAAAG
29168 TTAATGTGATTTATGCTTAAATA
1 TTAATGTGATTTATGCTTAAATA
* *
29191 TTAATGTGATTTGTGCTTAAATG
1 TTAATGTGATTTATGCTTAAATA
* *
29214 TTAATATGATTTATGTTTAAATA
1 TTAATGTGATTTATGCTTAAATA
29237 TTAATGTGATTTATG
1 TTAATGTGATTTATG
29252 AGTAAATAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.50
Consensus pattern (23 bp):
TTAATGTGATTTATGCTTAAATA
Found at i:30092 original size:41 final size:40
Alignment explanation
Indices: 30047--30133 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
30037 GAGGCACTTT
* *
30047 TAGCGGTGTTTGGACAAAAAACGCCACAAAAGGTAAATCAA
1 TAGCGGTGTTTCGAC-AAAAACGCCACAAAAGGTAAAGCAA
** * * *
30088 TAGCGGTGTTTCTTCATAAACGCCGCAAAAGGTAAAGCAT
1 TAGCGGTGTTTCGACAAAAACGCCACAAAAGGTAAAGCAA
30128 TAGCGG
1 TAGCGG
30134 CGCTTGTGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 27 0.69
41 12 0.31
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (40 bp):
TAGCGGTGTTTCGACAAAAACGCCACAAAAGGTAAAGCAA
Found at i:30173 original size:41 final size:41
Alignment explanation
Indices: 30115--30302 Score: 265
Period size: 41 Copynumber: 4.6 Consensus size: 41
30105 AAACGCCGCA
* *
30115 AAAGGT-AAAGCATTAGCGGCGCTTGTGGAAAAGCGCCACT
1 AAAGGTCAGAGCATTAGCGGCGCTTGTGGGAAAGCGCCACT
30155 AAAGGTCAGAGCATTAGCGGCGCTTGTGGGAAAGCG-CAGCT
1 AAAGGTCAGAGCATTAGCGGCGCTTGTGGGAAAGCGCCA-CT
* * *
30196 AAAGGTCAGAGCATTAGCGACACTTGTGGGAAAGCGCTACT
1 AAAGGTCAGAGCATTAGCGGCGCTTGTGGGAAAGCGCCACT
* * *
30237 AAAAGTCAGAGCATTAGCGGCGGTTG-GGGCAAAGCGCCGCT
1 AAAGGTCAGAGCATTAGCGGCGCTTGTGGG-AAAGCGCCACT
30278 AAAGGTCAGAGCATTAGCGGCGCTT
1 AAAGGTCAGAGCATTAGCGGCGCTT
30303 TCTCATAAAC
Statistics
Matches: 131, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
40 11 0.08
41 119 0.91
42 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.33, T:0.18
Consensus pattern (41 bp):
AAAGGTCAGAGCATTAGCGGCGCTTGTGGGAAAGCGCCACT
Found at i:36127 original size:43 final size:43
Alignment explanation
Indices: 36070--36296 Score: 328
Period size: 43 Copynumber: 5.3 Consensus size: 43
36060 TTTGTTAATG
*
36070 TTAGTGGCGTTTGTGGGAAAAGCGCCGCTGAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTGAAGACCATGTTCT
*
36113 TTAGCGGCATTTGTGGGAAAAGCGCCGCTGAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTGAAGACCATGTTCT
* *
36156 TTAGCGGCGTTTTTGGGAAAAGCGCCACTGAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTGAAGACCATGTTCT
* * * * *
36199 TTAGCGGCATTTGTGGGAAAAGCGTCGCTAAAGACCATGGTAT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTGAAGACCATGTTCT
* ** *
36242 TTAGTGGCGTTTGTGCAAAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTGAAGACCATGTTCT
*
36285 ATAGCGGCGTTT
1 TTAGCGGCGTTT
36297 TTCCTTATAA
Statistics
Matches: 163, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 163 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTGAAGACCATGTTCT
Found at i:37049 original size:17 final size:16
Alignment explanation
Indices: 37027--37074 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
37017 AAAACAATGT
* *
37027 TAAAAGAAATGGAAAAG
1 TAAAAGAAA-AGAAAAA
37044 TAAAAGAGAAAGAAAAA
1 TAAAAGA-AAAGAAAAA
37061 TAAAAGAAAA-AAAA
1 TAAAAGAAAAGAAAA
37075 GTTAAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.14
16 3 0.11
17 19 0.68
18 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (16 bp):
TAAAAGAAAAGAAAAA
Found at i:49264 original size:21 final size:21
Alignment explanation
Indices: 49238--49287 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
49228 ACTTCTATCA
*
49238 ATACAAGTGACAGTTTTACCG
1 ATACAAGTGACACTTTTACCG
* *
49259 ATACAAGTGTCTCTTTTACCG
1 ATACAAGTGACACTTTTACCG
*
49280 AAACAAGT
1 ATACAAGT
49288 CTTACTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (21 bp):
ATACAAGTGACACTTTTACCG
Found at i:51279 original size:131 final size:131
Alignment explanation
Indices: 51045--51427 Score: 730
Period size: 131 Copynumber: 2.9 Consensus size: 131
51035 TTAAGCTTAC
51045 TTAATCATTTTTAGCCTTAATTAATGATTCTTTTAACACCTAAATGCCATGATATTCCACTATCT
1 TTAATCATTTTTAGCCTTAATTAATGATTCTTTTAACACCTAAATGCCATGATATTCCACTATCT
*
51110 TAACCTTTATTGGCTAATTTCCCTATTCAGTCCTTCTAATAAAACAATTCTATTTTTACCAAGAA
66 TAACCTCTATTGGCTAATTTCCCTATTCAGTCCTTCTAATAAAACAATTCTATTTTTACCAAGAA
51175 A
131 A
*
51176 TTAATCATTTTTAGCCTTAATTAATGATTCTTTTAACACCTAAATGCCATGATATTCCACTATAT
1 TTAATCATTTTTAGCCTTAATTAATGATTCTTTTAACACCTAAATGCCATGATATTCCACTATCT
*
51241 TAACCTCTATTGGCTAATTTCCCTATTCAGTCCTTCTAATAAAACAATTCTATTTTTACCATGAA
66 TAACCTCTATTGGCTAATTTCCCTATTCAGTCCTTCTAATAAAACAATTCTATTTTTACCAAGAA
51306 A
131 A
*
51307 TTAATCATTTTTAGCCTTAATTAATGATTCTTTTAACACCTAAATGTCATGATATTCCACTATCT
1 TTAATCATTTTTAGCCTTAATTAATGATTCTTTTAACACCTAAATGCCATGATATTCCACTATCT
51372 TAACCTCTATTGGCTAATTTCCCTATTCAGTCCTTCTAATAAAACAATTCTATTTT
66 TAACCTCTATTGGCTAATTTCCCTATTCAGTCCTTCTAATAAAACAATTCTATTTT
51428 CACCTTTTGC
Statistics
Matches: 247, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 247 1.00
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (131 bp):
TTAATCATTTTTAGCCTTAATTAATGATTCTTTTAACACCTAAATGCCATGATATTCCACTATCT
TAACCTCTATTGGCTAATTTCCCTATTCAGTCCTTCTAATAAAACAATTCTATTTTTACCAAGAA
A
Found at i:54876 original size:101 final size:100
Alignment explanation
Indices: 54748--55109 Score: 347
Period size: 101 Copynumber: 3.6 Consensus size: 100
54738 AGTAAATGGT
* * * *
54748 AAATCCTATACCCTTGAGGTTATAGTGGGTCGGATTAAAGTTACAAAAACAAATCTCAATCTCCC
1 AAATCCTATACCCTTGAAGTTACAGTGGATCGGATTAAAGTTACAAAAACAGATCTCAATCTCCC
54813 TAAGGTTACAATGGAATGGAGTGAAACTTCAACATC
66 TAAGGTTACAATGGAATGGAGTGAAACTTCAACA-C
* * * * * * **
54849 AAATCCTATATCCTTAAAGTTACAGTGGATCAGATTAAAATGAC--TAATGGATCTCAATCTCCC
1 AAATCCTATACCCTTGAAGTTACAGTGGATCGGATTAAAGTTACAAAAACAGATCTCAATCTCCC
* * * * * * *
54912 TGATGTTATAGTGGAATAGAGTG-AAGTTATAACACC
66 TAAGGTTACAATGGAATGGAGTGAAACTT-CAACA-C
* * *
54948 AAATCCTATACCCCTGAAGTTACAGTGGATCGGATTAAAGTTACAAAATCAGATCTTAATCTCCC
1 AAATCCTATACCCTTGAAGTTACAGTGGATCGGATTAAAGTTACAAAAACAGATCTCAATCTCCC
* * *
55013 CAAGGCTACAATGGAATGGAGTGAAGCTTCAACAC
66 TAAGGTTACAATGGAATGGAGTGAAACTTCAACAC
* * * ** **
55048 GAAATCTTAT-CTTCTTGAAGTTACAGTGAAGT-GGATTAAAACTACAGTAACAGATCTCAATC
1 -AAATCCTATAC-CCTTGAAGTTACAGTGGA-TCGGATTAAAGTTACAAAAACAGATCTCAATC
55110 CTTCTAAAGT
Statistics
Matches: 203, Mismatches: 51, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
98 4 0.02
99 76 0.37
100 2 0.01
101 117 0.58
102 4 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (100 bp):
AAATCCTATACCCTTGAAGTTACAGTGGATCGGATTAAAGTTACAAAAACAGATCTCAATCTCCC
TAAGGTTACAATGGAATGGAGTGAAACTTCAACAC
Found at i:54934 original size:99 final size:99
Alignment explanation
Indices: 54800--55053 Score: 269
Period size: 99 Copynumber: 2.5 Consensus size: 99
54790 ACAAAAACAA
* * * *
54800 ATCTCAATCTCCCTAAGGTTACAATGGAATGGAGTGAAACTT-CAACATCAAATCCTATATCCTT
1 ATCTCAATCTCCCTAAGGTTACAATGGAATAGAGTG-AACTTACAACACCAAATCCTATACCCCT
54864 AAAGTTACAGTGGATCAGATTAAAATGACTAATGG
65 AAAGTTACAGTGGATCAGATTAAAATGACTAATGG
* * * * * * *
54899 ATCTCAATCTCCCTGATGTTATAGTGGAATAGAGTGAAGTTATAACACCAAATCCTATACCCCTG
1 ATCTCAATCTCCCTAAGGTTACAATGGAATAGAGTGAACTTACAACACCAAATCCTATACCCCTA
* * * * *
54964 AAGTTACAGTGGATCGGATTAAAGTTACAAAATCAG
66 AAGTTACAGTGGATCAGATTAAAATGAC-TAAT-GG
* * * * *
55000 ATCTTAATCTCCCCAAGGCTACAATGGAATGGAGTGAAGCTT-CAACACGAAATC
1 ATCTCAATCTCCCTAAGGTTACAATGGAATAGAGTGAA-CTTACAACACCAAATC
55054 TTATCTTCTT
Statistics
Matches: 124, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
98 4 0.03
99 74 0.60
100 3 0.02
101 41 0.33
102 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (99 bp):
ATCTCAATCTCCCTAAGGTTACAATGGAATAGAGTGAACTTACAACACCAAATCCTATACCCCTA
AAGTTACAGTGGATCAGATTAAAATGACTAATGG
Found at i:55219 original size:46 final size:46
Alignment explanation
Indices: 55151--55413 Score: 235
Period size: 46 Copynumber: 5.7 Consensus size: 46
55141 TACATCACCA
* * *
55151 CATCCAATTTTATACCCCTAAATTCAGATGGGCAGATTGAAGCCAC
1 CATCCAATATTATACCCCTAAATCCAGAGGGGCAGATTGAAGCCAC
* * * * * * *
55197 CA-CCATAGATTATACCCATAAATCCAAATGAGC-GAGTTAAAACCAC
1 CATCCA-ATATTATACCCCTAAATCCAGAGGGGCAGA-TTGAAGCCAC
* * *
55243 CATCCAATCTTATACCCCTAAATCCAGGGGGGCAAATTGAAGCCAC
1 CATCCAATATTATACCCCTAAATCCAGAGGGGCAGATTGAAGCCAC
* * * * *
55289 CATCTAATCTTATACCCCTAAATCCAAAAGGGTAGATTGAAGCCAC
1 CATCCAATATTATACCCCTAAATCCAGAGGGGCAGATTGAAGCCAC
* * * * *
55335 CATCCAATCTTATACCCTTAAATTCAGAGGGGTAGATTGAAGCTAC
1 CATCCAATATTATACCCCTAAATCCAGAGGGGCAGATTGAAGCCAC
* *
55381 CAGATCAAATCA-TATACCTCTAAATCCAGAGGG
1 C--ATCCAAT-ATTATACCCCTAAATCCAGAGGG
55414 TCCAATCGAA
Statistics
Matches: 175, Mismatches: 35, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
45 5 0.03
46 142 0.81
47 4 0.02
48 24 0.14
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (46 bp):
CATCCAATATTATACCCCTAAATCCAGAGGGGCAGATTGAAGCCAC
Found at i:55311 original size:92 final size:92
Alignment explanation
Indices: 55147--55408 Score: 291
Period size: 92 Copynumber: 2.8 Consensus size: 92
55137 AAGTTACATC
* * *
55147 ACCA-CATCCAATTTTATACCCCTAAATTCAGATGGGCAGATTGAAGCCACCACCATAGA--TTA
1 ACCACCATCCAATCTTATACCCCTAAATTCAGAGGGGCAGATTGAAGCCACCATC-TA-ATCTTA
*
55209 TACCCATAAATCCAAATGAGCG-AG-TTAAA
64 TACCCCTAAATCCAAA--AGCGTAGATTAAA
* * *
55238 ACCACCATCCAATCTTATACCCCTAAATCCAGGGGGGCAAATTGAAGCCACCATCTAATCTTATA
1 ACCACCATCCAATCTTATACCCCTAAATTCAGAGGGGCAGATTGAAGCCACCATCTAATCTTATA
* *
55303 CCCCTAAATCCAAAAGGGTAGATTGAA
66 CCCCTAAATCCAAAAGCGTAGATTAAA
* * * * * *
55330 GCCACCATCCAATCTTATACCCTTAAATTCAGAGGGGTAGATTGAAGCTACCAGATCAAATCATA
1 ACCACCATCCAATCTTATACCCCTAAATTCAGAGGGGCAGATTGAAGCCACC--ATCTAATCTTA
*
55395 TACCTCTAAATCCA
64 TACCCCTAAATCCA
55409 GAGGGTCCAA
Statistics
Matches: 145, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
90 4 0.03
91 8 0.06
92 111 0.77
94 22 0.15
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (92 bp):
ACCACCATCCAATCTTATACCCCTAAATTCAGAGGGGCAGATTGAAGCCACCATCTAATCTTATA
CCCCTAAATCCAAAAGCGTAGATTAAA
Found at i:56599 original size:21 final size:21
Alignment explanation
Indices: 56573--56615 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
56563 CAAGAGAAAA
56573 AACGGTACTGTTTTGGGCACC
1 AACGGTACTGTTTTGGGCACC
56594 AACGGTACTGTTTTGGGCACC
1 AACGGTACTGTTTTGGGCACC
56615 A
1 A
56616 TTTTAATGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
AACGGTACTGTTTTGGGCACC
Found at i:61370 original size:36 final size:36
Alignment explanation
Indices: 61290--61370 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
61280 CTGTTGTGAA
*
61290 AGTGAATATGTGCGTATGTTATTCATGCCATAAGAT
1 AGTGAATATGTGCGTATGTTATTCATGCCATAAGAC
** * * ***
61326 AGAAAATATGTGGGTATGTTATTCATGTCATGTTAC
1 AGTGAATATGTGCGTATGTTATTCATGCCATAAGAC
61362 AGTGAATAT
1 AGTGAATAT
61371 ATTGTGTTGA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (36 bp):
AGTGAATATGTGCGTATGTTATTCATGCCATAAGAC
Found at i:61794 original size:23 final size:23
Alignment explanation
Indices: 61768--61900 Score: 203
Period size: 23 Copynumber: 5.8 Consensus size: 23
61758 ATTAAATGTG
* *
61768 TTAAATATTAATGTGATTTGTAC
1 TTAAATATTAATGTGATTTATGC
*
61791 TTAAATATTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
61814 TTAAATATTTATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
61837 TTAAATATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
*
61860 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
*
61883 TTAAATATTCATGTGATT
1 TTAAATATTAATGTGATT
61901 AAATGTGACT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 102 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTATGC
Found at i:61981 original size:58 final size:58
Alignment explanation
Indices: 61880--62032 Score: 193
Period size: 58 Copynumber: 2.6 Consensus size: 58
61870 ATGTGATTTG
* * *
61880 TGCTTAAATATTCATGTGATTAAATGTGACTAAATGCGATTAATATGTGATGTGATAAA
1 TGCTTAAATATTCATGTGATT-AATGCGATTAAATGTGATTAATATGTGATGTGATAAA
* * *
61939 TG-TTGAAATATTCATGTGACTAATGCGATTAAATGTGATTAATATGTGTTGTGTTAAA
1 TGCTT-AAATATTCATGTGATTAATGCGATTAAATGTGATTAATATGTGATGTGATAAA
* * *
61997 TGCTTAAGTACTCATGTGATTAATGCAATT-AATGTG
1 TGCTTAAATATTCATGTGATTAATGCGATTAAATGTG
62033 TAAAAGAATG
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
57 6 0.07
58 57 0.70
59 19 0.23
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (58 bp):
TGCTTAAATATTCATGTGATTAATGCGATTAAATGTGATTAATATGTGATGTGATAAA
Found at i:62905 original size:29 final size:30
Alignment explanation
Indices: 62872--62931 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 30
62862 AGATTCTTGA
* *
62872 TAAAATTTTTAGGGTTT-GAT-TATTTAAAT
1 TAAAA-TTTTAAGGTTTCGATGTATTAAAAT
62901 TAAAATTTTAAGGTTTCGATGTATTAAAAT
1 TAAAATTTTAAGGTTTCGATGTATTAAAAT
62931 T
1 T
62932 TTAAGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 10 0.37
29 8 0.30
30 9 0.33
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (30 bp):
TAAAATTTTAAGGTTTCGATGTATTAAAAT
Found at i:62949 original size:24 final size:24
Alignment explanation
Indices: 62899--62949 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
62889 GATTATTTAA
* **
62899 ATTAAAATTTTAAGGTTTCGATGT
1 ATTAAAATTTTAAGGTTTCAAAAT
62923 ATTAAAATTTTAAGGATTT-AAAAT
1 ATTAAAATTTTAAGG-TTTCAAAAT
62947 ATT
1 ATT
62950 GATTTGGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (24 bp):
ATTAAAATTTTAAGGTTTCAAAAT
Found at i:66751 original size:27 final size:27
Alignment explanation
Indices: 66719--66798 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
66709 TGTATAAGCA
66719 ATATTCTGTTCTGGGCTCGAATGAGCT
1 ATATTCTGTTCTGGGCTCGAATGAGCT
* * * * *
66746 ATATTCTATTTTGGGCTCAAAAGAGCA
1 ATATTCTGTTCTGGGCTCGAATGAGCT
66773 ATAATT-TG-TCTAGGG-TCGAATGAGCT
1 AT-ATTCTGTTCT-GGGCTCGAATGAGCT
66799 TCTGTAACGG
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
26 10 0.24
27 28 0.68
28 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (27 bp):
ATATTCTGTTCTGGGCTCGAATGAGCT
Found at i:70953 original size:28 final size:28
Alignment explanation
Indices: 70910--71000 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 28
70900 TTAACAATTG
*
70910 CTCTGTATTCTAGCTCGTAAGAGCGTAA
1 CTCTGTATTCTGGCTCGTAAGAGCGTAA
* * *
70938 CTCTGTGTTCTGGCTCGAAAGAGCATAA
1 CTCTGTATTCTGGCTCGTAAGAGCGTAA
* * *
70966 CTCTGTAATCTGGCTCGTATGAGCGTTA
1 CTCTGTATTCTGGCTCGTAAGAGCGTAA
*
70994 TTCTGTA
1 CTCTGTA
71001 ATCTTACTCA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (28 bp):
CTCTGTATTCTGGCTCGTAAGAGCGTAA
Found at i:71132 original size:27 final size:27
Alignment explanation
Indices: 71102--71191 Score: 130
Period size: 27 Copynumber: 3.3 Consensus size: 27
71092 ATGTGTAACA
71102 ATATTCTGTTCTGGGCTCGAATGAGCT
1 ATATTCTGTTCTGGGCTCGAATGAGCT
* *
71129 ATATTTTGTTCTGGGCTCGAATGAGCA
1 ATATTCTGTTCTGGGCTCGAATGAGCT
71156 ATAATT-TGTT-TGGGCTCGAATGAGCT
1 AT-ATTCTGTTCTGGGCTCGAATGAGCT
71182 ATATTTCTGT
1 ATA-TTCTGT
71192 AACGGTTCGA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.02
26 19 0.33
27 34 0.60
28 3 0.05
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (27 bp):
ATATTCTGTTCTGGGCTCGAATGAGCT
Found at i:74884 original size:17 final size:18
Alignment explanation
Indices: 74862--74895 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
74852 CATTAATTAA
74862 AAAGAAATGAAA-GAAAG
1 AAAGAAATGAAATGAAAG
74879 AAAGAAATGAAATGAAA
1 AAAGAAATGAAATGAAA
74896 TAATAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (18 bp):
AAAGAAATGAAATGAAAG
Found at i:75745 original size:27 final size:27
Alignment explanation
Indices: 75707--75786 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
75697 TAAAATTATG
*
75707 TGAAAAAGTTATATCCGAAAGGATATT
1 TGAAAAGGTTATATCCGAAAGGATATT
* *
75734 TGAAAAGGTTATATCCGAATGGATATC
1 TGAAAAGGTTATATCCGAAAGGATATT
* *
75761 TGAAAAGG-AATATCCGTAAGGATATT
1 TGAAAAGGTTATATCCGAAAGGATATT
75787 ATTGAAAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 14 0.30
27 32 0.70
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (27 bp):
TGAAAAGGTTATATCCGAAAGGATATT
Found at i:75828 original size:28 final size:28
Alignment explanation
Indices: 75796--76033 Score: 235
Period size: 28 Copynumber: 8.5 Consensus size: 28
75786 TATTGAAAAT
* *
75796 GATATCAATTAAAAGGAATATCCATAAG
1 GATATCAATGAAAAGGAATATCCGTAAG
* * * ** *
75824 GATATTATTTAAAAGGTGTATCCGCAAG
1 GATATCAATGAAAAGGAATATCCGTAAG
* *
75852 GATATAAATGAAAAGGAATATCCATAAG
1 GATATCAATGAAAAGGAATATCCGTAAG
** *
75880 GATATCAATGAAAAAAAATATTCGTAAG
1 GATATCAATGAAAAGGAATATCCGTAAG
* * * * *
75908 GATATTATTGGAAAGGGATATCCGCAAG
1 GATATCAATGAAAAGGAATATCCGTAAG
*
75936 GATATCAATGAAAAGGAATATCTGTAAG
1 GATATCAATGAAAAGGAATATCCGTAAG
* * * * *
75964 GCTATTATTGAAAAGGGATATCCGCAAG
1 GATATCAATGAAAAGGAATATCCGTAAG
*
75992 GATATCAATGAAAAGGAATATTCGTAAG
1 GATATCAATGAAAAGGAATATCCGTAAG
*
76020 GATA-CTATGAAAAG
1 GATATCAATGAAAAG
76034 ATTATATCTG
Statistics
Matches: 165, Mismatches: 45, Indels: 1
0.78 0.21 0.00
Matches are distributed among these distances:
27 9 0.05
28 156 0.95
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (28 bp):
GATATCAATGAAAAGGAATATCCGTAAG
Found at i:75993 original size:84 final size:84
Alignment explanation
Indices: 75796--76033 Score: 264
Period size: 84 Copynumber: 2.8 Consensus size: 84
75786 TATTGAAAAT
* * * *
75796 GATATCAATTAAAAGGAATATCCATAAGGATATTATTTAAAAGGTG-TATCCGCAAGGATATAAA
1 GATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAAGG-GATATCCGCAAGGATATCAA
75860 TGAAAAGGAATATCCATAAG
65 TGAAAAGGAATATCCATAAG
** * *
75880 GATATCAATGAAAAAAAATATTCGTAAGGATATTATTGGAAAGGGATATCCGCAAGGATATCAAT
1 GATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAAGGGATATCCGCAAGGATATCAAT
**
75945 GAAAAGGAATATCTGTAAG
66 GAAAAGGAATATCCATAAG
* * * * * * * * * * *
75964 GCTATTATTGAAAAGGGATATCCGCAAGGATATCAATGAAAAGGAATATTCGTAAGGATA-CTAT
1 GATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAAGGGATATCCGCAAGGATATCAAT
76028 GAAAAG
66 GAAAAG
76034 ATTATATCTG
Statistics
Matches: 128, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
83 10 0.08
84 118 0.92
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (84 bp):
GATATCAATGAAAAGGAATATCCGTAAGGATATTATTGAAAAGGGATATCCGCAAGGATATCAAT
GAAAAGGAATATCCATAAG
Found at i:78334 original size:17 final size:18
Alignment explanation
Indices: 78312--78345 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
78302 CATTAATTAA
78312 AAAGAAATGAAA-GAAAG
1 AAAGAAATGAAATGAAAG
78329 AAAGAAATGAAATGAAA
1 AAAGAAATGAAATGAAA
78346 TAATAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (18 bp):
AAAGAAATGAAATGAAAG
Found at i:81606 original size:28 final size:28
Alignment explanation
Indices: 81565--81812 Score: 221
Period size: 28 Copynumber: 8.9 Consensus size: 28
81555 CTGAAATTAT
** *
81565 TGAAAAGGGGTATCCGCAAGGATATCAA
1 TGAAAAGGAATATCCGTAAGGATATCAA
* * * * *
81593 TGAAAAGAAATATCCATAAGGATGTTAT
1 TGAAAAGGAATATCCGTAAGGATATCAA
*
81621 TGAAAAGGAATATTCGTAAGGATATCAA
1 TGAAAAGGAATATCCGTAAGGATATCAA
* * * *
81649 TGAAAAGTAATATCTGTAAGGATATTAC
1 TGAAAAGGAATATCCGTAAGGATATCAA
* * * * *
81677 TGGAAAGGGATATCTGCAATGATATCAA
1 TGAAAAGGAATATCCGTAAGGATATCAA
* * * *
81705 TGAAAAAGAATATCCTTAAGGATATTAT
1 TGAAAAGGAATATCCGTAAGGATATCAA
* *
81733 TG-AAAGGGATAACCGTAAGGATATCAA
1 TGAAAAGGAATATCCGTAAGGATATCAA
* *
81760 TGAAAAGGAATATTCGTAAGGATA-CTA
1 TGAAAAGGAATATCCGTAAGGATATCAA
* *
81787 TGAAAAGGTTATATCCGAAAGGATAT
1 TGAAAAGG-AATATCCGTAAGGATAT
81813 TTGAAAAGGT
Statistics
Matches: 169, Mismatches: 48, Indels: 5
0.76 0.22 0.02
Matches are distributed among these distances:
27 31 0.18
28 138 0.82
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.26
Consensus pattern (28 bp):
TGAAAAGGAATATCCGTAAGGATATCAA
Found at i:81647 original size:56 final size:56
Alignment explanation
Indices: 81560--81812 Score: 287
Period size: 56 Copynumber: 4.5 Consensus size: 56
81550 TTGCTCTGAA
* *
81560 ATTATTGAAAAGGGGTATCCGCAAGGATATCAATGAAAAGAAATATCCATAAGGAT
1 ATTATTGAAAAGGGATATCCGCAAGGATATCAATGAAAAGAAATATCCGTAAGGAT
* * * * * *
81616 GTTATTGAAAAGGAATATTCGTAAGGATATCAATGAAAAGTAATATCTGTAAGGAT
1 ATTATTGAAAAGGGATATCCGCAAGGATATCAATGAAAAGAAATATCCGTAAGGAT
* * * * *
81672 ATTACTGGAAAGGGATATCTGCAATGATATCAATGAAAA-AGAATATCCTTAAGGAT
1 ATTATTGAAAAGGGATATCCGCAAGGATATCAATGAAAAGA-AATATCCGTAAGGAT
* * * *
81728 ATTATTG-AAAGGGATAACCGTAAGGATATCAATGAAAAGGAATATTCGTAAGGAT
1 ATTATTGAAAAGGGATATCCGCAAGGATATCAATGAAAAGAAATATCCGTAAGGAT
* * *
81783 ACTA-TGAAAAGGTTATATCCGAAAGGATAT
1 ATTATTGAAAAGG-GATATCCGCAAGGATAT
81813 TTGAAAAGGT
Statistics
Matches: 162, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
54 2 0.01
55 48 0.30
56 112 0.69
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.26
Consensus pattern (56 bp):
ATTATTGAAAAGGGATATCCGCAAGGATATCAATGAAAAGAAATATCCGTAAGGAT
Found at i:81801 original size:111 final size:112
Alignment explanation
Indices: 81565--81812 Score: 324
Period size: 111 Copynumber: 2.2 Consensus size: 112
81555 CTGAAATTAT
* *
81565 TGAAAAGGGGTATCCGCAAGGATATCAATGAAAAGAAATATCCATAAGGATGTTATTGAAAAGGA
1 TGAAAAGGGATATCCGCAAGGATATCAATGAAAAGAAATATCCATAAGGATATTATTGAAAAGGA
** * *
81630 ATATTCGTAAGGATATCAATGAAAAGTAATATCTGTAAGGATATTAC
66 ATAACCGTAAGGATATCAATGAAAAGGAATATCTGTAAGGATACTAC
* * * *
81677 TGGAAAGGGATATCTGCAATGATATCAATGAAAA-AGAATATCCTTAAGGATATTATTG-AAAGG
1 TGAAAAGGGATATCCGCAAGGATATCAATGAAAAGA-AATATCCATAAGGATATTATTGAAAAGG
*
81740 GATAACCGTAAGGATATCAATGAAAAGGAATAT-TCGTAAGGATACTA-
65 AATAACCGTAAGGATATCAATGAAAAGGAATATCT-GTAAGGATACTAC
* *
81787 TGAAAAGGTTATATCCGAAAGGATAT
1 TGAAAAGG-GATATCCGCAAGGATAT
81813 TTGAAAAGGT
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
110 8 0.07
111 59 0.50
112 50 0.43
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.26
Consensus pattern (112 bp):
TGAAAAGGGATATCCGCAAGGATATCAATGAAAAGAAATATCCATAAGGATATTATTGAAAAGGA
ATAACCGTAAGGATATCAATGAAAAGGAATATCTGTAAGGATACTAC
Found at i:81829 original size:15 final size:15
Alignment explanation
Indices: 81787--81833 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
81777 AAGGATACTA
*
81787 TGAAAAGGTTATATC
1 TGAAAAGGTTATATT
*
81802 CG-AAAGG--ATATT
1 TGAAAAGGTTATATT
81814 TGAAAAGGTTATATT
1 TGAAAAGGTTATATT
81829 TGAAA
1 TGAAA
81834 CGATAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 5 0.19
15 11 0.42
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (15 bp):
TGAAAAGGTTATATT
Found at i:81833 original size:27 final size:28
Alignment explanation
Indices: 81749--81853 Score: 97
Period size: 27 Copynumber: 3.7 Consensus size: 28
81739 GGATAACCGT
* * *
81749 AAGGATATCAATGAAAAGG-AATATTCGT
1 AAGGATA-CTATGAAAAGGTTATATTCGA
*
81777 AAGGATACTATGAAAAGGTTATATCCGA
1 AAGGATACTATGAAAAGGTTATATTCGA
* *
81805 AAGGATA-TTTGAAAAGGTTATATTTGA
1 AAGGATACTATGAAAAGGTTATATTCGA
* *
81832 AACGATAATAAATGAAAAGGTT
1 AAGGATACT--ATGAAAAGGTT
81854 GAAAAGGACG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
27 33 0.52
28 21 0.33
30 10 0.16
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.28
Consensus pattern (28 bp):
AAGGATACTATGAAAAGGTTATATTCGA
Found at i:84417 original size:23 final size:22
Alignment explanation
Indices: 84386--84459 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
84376 CCGACCCAAC
*
84386 CTGAGCCATTGACTTTGATCGAA
1 CTGACCCATTGACTTTGA-CGAA
*
84409 CTGACCCATTAACTTTGACAGAA
1 CTGACCCATTGACTTTGAC-GAA
* * *
84432 -TCGACCCGTTGAATTTGCCGAA
1 CT-GACCCATTGACTTTGACGAA
84454 CTGACC
1 CTGACC
84460 TGTTAACTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
22 9 0.21
23 33 0.79
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (22 bp):
CTGACCCATTGACTTTGACGAA
Found at i:85678 original size:6 final size:6
Alignment explanation
Indices: 85667--85693 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
85657 TATTCAGTTT
85667 TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT
85694 AAATACGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:85798 original size:49 final size:49
Alignment explanation
Indices: 85721--85818 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
85711 AATGAATGTG
* * * * *
85721 GATGTTAAGGTTGCGAGAGGGTAGAATTACAGTAGTGACCTTCAGGATC
1 GATGTTAAGGTTACGAGAGGGTAAAATTACAGCAATGACCTTCAAGATC
*
85770 GATGTTAAGGTTACGAGAGGGTAAAATTATAGCAATGACCTTCAAGATC
1 GATGTTAAGGTTACGAGAGGGTAAAATTACAGCAATGACCTTCAAGATC
85819 AAGTCATATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (49 bp):
GATGTTAAGGTTACGAGAGGGTAAAATTACAGCAATGACCTTCAAGATC
Found at i:89748 original size:23 final size:23
Alignment explanation
Indices: 89722--89806 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
89712 ACTCGAGCAA
*
89722 TTGACTTTAATCGAACTGGCTAG
1 TTGACTTTAATCGAACTGACTAG
* * *
89745 TTGACTTTGACCGAACCGACTAG
1 TTGACTTTAATCGAACTGACTAG
***
89768 TTGACTTTGGGCGAACTGACCT-G
1 TTGACTTTAATCGAACTGA-CTAG
*
89791 TTGACTTTAATTGAAC
1 TTGACTTTAATCGAAC
89807 CAAATCGTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
23 48 0.96
24 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (23 bp):
TTGACTTTAATCGAACTGACTAG
Found at i:91692 original size:26 final size:26
Alignment explanation
Indices: 91656--91713 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
91646 TGTGTTAGTG
*
91656 TGCTTGAGTATGGGTGTATTGCATTA
1 TGCTTGAGTATGGGTGCATTGCATTA
91682 TGCTTGAGTATGGGTGCATTGCATTA
1 TGCTTGAGTATGGGTGCATTGCATTA
91708 TGCTTG
1 TGCTTG
91714 TGATTGTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.17, C:0.10, G:0.31, T:0.41
Consensus pattern (26 bp):
TGCTTGAGTATGGGTGCATTGCATTA
Found at i:92031 original size:6 final size:6
Alignment explanation
Indices: 92020--92058 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
92010 TATTCAGTTT
92020 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TAT
92059 AAATACGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:93890 original size:293 final size:293
Alignment explanation
Indices: 93363--93950 Score: 1158
Period size: 293 Copynumber: 2.0 Consensus size: 293
93353 TAAGGACTAA
93363 AATGTTAAAATGATGAAAATATATGTATTTGTTGTGAAATAATTGGTTAAAGGAATTTGTATGAA
1 AATGTTAAAATGATGAAAATATATGTATTTGTTGTGAAATAATTGGTTAAAGGAATTTGTATGAA
93428 GGTTGTAGATATTCGACTGGTATGGATTGAACTTGGAAATGGTTATTTTGTATGTTTTAGGTTTA
66 GGTTGTAGATATTCGACTGGTATGGATTGAACTTGGAAATGGTTATTTTGTATGTTTTAGGTTTA
93493 AGGACTAAATTGAACAAAAGTGAAAGTATAGGGGTAATTTAGTAAATTTCCAAAAAAGGAAATAA
131 AGGACTAAATTGAACAAAAGTGAAAGTATAGGGGTAATTTAGTAAATTTCCAAAAAAGGAAATAA
93558 ATGCAAGAAGTGATTTAATGTGGGAATTAATGATTTATTGATTTAGATCACGAGTGGGCTGCAGA
196 ATGCAAGAAGTGATTTAATGTGGGAATTAATGATTTATTGATTTAGATCACGAGTGGGCTGCAGA
*
93623 TCGAGGAAAAGGGAAAATTACAGAATAGTCCCT
261 TCAAGGAAAAGGGAAAATTACAGAATAGTCCCT
93656 AATGTTAAAATGATGAAAATATATGTATTTGTTGTGAAATAATTGGTTAAAGGAATTTGTATGAA
1 AATGTTAAAATGATGAAAATATATGTATTTGTTGTGAAATAATTGGTTAAAGGAATTTGTATGAA
*
93721 GGTTGTAGATATTCGATTGGTATGGATTGAACTTGGAAATGGTTATTTTGTATGTTTTAGGTTTA
66 GGTTGTAGATATTCGACTGGTATGGATTGAACTTGGAAATGGTTATTTTGTATGTTTTAGGTTTA
93786 AGGACTAAATTGAACAAAAGTGAAAGTATAGGGGTAATTTAGTAAATTTCCAAAAAAGGAAATAA
131 AGGACTAAATTGAACAAAAGTGAAAGTATAGGGGTAATTTAGTAAATTTCCAAAAAAGGAAATAA
93851 ATGCAAGAAGTGATTTAATGTGGGAATTAATGATTTATTGATTTAGATCACGAGTGGGCTGCAGA
196 ATGCAAGAAGTGATTTAATGTGGGAATTAATGATTTATTGATTTAGATCACGAGTGGGCTGCAGA
93916 TCAAGGAAAAGGGAAAATTACAGAATAGTCCCT
261 TCAAGGAAAAGGGAAAATTACAGAATAGTCCCT
93949 AA
1 AA
93951 AGTTTAGCCT
Statistics
Matches: 293, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
293 293 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (293 bp):
AATGTTAAAATGATGAAAATATATGTATTTGTTGTGAAATAATTGGTTAAAGGAATTTGTATGAA
GGTTGTAGATATTCGACTGGTATGGATTGAACTTGGAAATGGTTATTTTGTATGTTTTAGGTTTA
AGGACTAAATTGAACAAAAGTGAAAGTATAGGGGTAATTTAGTAAATTTCCAAAAAAGGAAATAA
ATGCAAGAAGTGATTTAATGTGGGAATTAATGATTTATTGATTTAGATCACGAGTGGGCTGCAGA
TCAAGGAAAAGGGAAAATTACAGAATAGTCCCT
Found at i:94157 original size:28 final size:25
Alignment explanation
Indices: 94092--94178 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
94082 ATCCTATCCT
* *
94092 GTAAAAGCGATATTCTGTTTGGGTC
1 GTAAGAGCGATATTCTGTTTGGCTC
* *
94117 GAAAGAGCAATATTCTGAATTCTGGCTC
1 GTAAGAGCGATATTCTG--TT-TGGCTC
* *
94145 GTAAGAGCGATATTCAGTCTGGCTC
1 GTAAGAGCGATATTCTGTTTGGCTC
*
94170 GAAAGAGCG
1 GTAAGAGCG
94179 TTGTTTTGTC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
25 28 0.56
26 1 0.02
27 2 0.04
28 19 0.38
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (25 bp):
GTAAGAGCGATATTCTGTTTGGCTC
Found at i:97208 original size:27 final size:28
Alignment explanation
Indices: 97149--97209 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
97139 GTACCGATAT
*
97149 GAAAAAAAAGATTAGGTACCTAAAATGG
1 GAAAAAAAAGATTAGATACCTAAAATGG
* * * *
97177 AAAAAAAAAGTTTAGATA-CTTAAGTGG
1 GAAAAAAAAGATTAGATACCTAAAATGG
97204 GAAAAA
1 GAAAAA
97210 TGTTATAGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
GAAAAAAAAGATTAGATACCTAAAATGG
Found at i:102398 original size:28 final size:30
Alignment explanation
Indices: 102354--102409 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
102344 TATCTGTATT
*
102354 TTTTTATATTTAAATATATGTTTATATTAA
1 TTTTTATATTTAAATATATGTATATATTAA
*
102384 TTTTTA-ATTT-AATATTTGTATATATT
1 TTTTTATATTTAAATATATGTATATATT
102410 TTTGTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
29 4 0.17
30 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTTTATATTTAAATATATGTATATATTAA
Found at i:102417 original size:28 final size:27
Alignment explanation
Indices: 102352--102433 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 27
102342 CTTATCTGTA
* *
102352 TTTTTTTATATTTAAATATATGTTTATAT
1 TTTTTTTA-ATTT-AATATTTGTATATAT
*
102381 TAATTTTTAATTTAATATTTGTATATAT
1 T-TTTTTTAATTTAATATTTGTATATAT
*
102409 TTTTGTTT-A-TTAAAATTT-TATATAT
1 TTTT-TTTAATTTAATATTTGTATATAT
102434 AATTATTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
25 7 0.15
26 8 0.17
27 3 0.07
28 17 0.37
29 5 0.11
30 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (27 bp):
TTTTTTTAATTTAATATTTGTATATAT
Found at i:103167 original size:25 final size:25
Alignment explanation
Indices: 103105--103167 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
103095 AAATAATCTT
*
103105 TAAAATTAAATAGAACAATTAATAA
1 TAAAATTAAATATAACAATTAATAA
* *
103130 TAAAATCAAATATAATAATTAATAA
1 TAAAATTAAATATAACAATTAATAA
*
103155 TAAATTTAAATAT
1 TAAAATTAAATAT
103168 GTTTAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (25 bp):
TAAAATTAAATATAACAATTAATAA
Found at i:104497 original size:2 final size:2
Alignment explanation
Indices: 104490--104526 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
104480 TATGTACATG
104490 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104527 GAGAATCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:106479 original size:51 final size:51
Alignment explanation
Indices: 106383--106479 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
106373 CGATATATAG
* * * *
106383 CATAAGACCATAGATGAAAGATGCTATGCCAGTCTAGTATGAGGTACATAA
1 CATAAGACCATAGATGAAAGATGCCATGACAGACTAGTATAAGGTACATAA
* *
106434 CATAAGACCATGGATGAAAGATGCCATGACA-ACATTGTATAAGGTA
1 CATAAGACCATAGATGAAAGATGCCATGACAGAC-TAGTATAAGGTA
106480 TAACGTATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 1 0.03
51 38 0.97
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (51 bp):
CATAAGACCATAGATGAAAGATGCCATGACAGACTAGTATAAGGTACATAA
Found at i:106724 original size:33 final size:33
Alignment explanation
Indices: 106633--106793 Score: 137
Period size: 33 Copynumber: 4.9 Consensus size: 33
106623 CATGGAATCC
* * *
106633 ACAAAGATAGTCCATTGGGACAGTAAACATAGA
1 ACAAAGATAGTCTATTGGGACAATAAACACAGA
* * *** * *
106666 ATAGAGATAGTCCCCTAGGATAATAAACACAGA
1 ACAAAGATAGTCTATTGGGACAATAAACACAGA
*
106699 ACAAAGATAGTCTATTGGGACAATAAACACATA
1 ACAAAGATAGTCTATTGGGACAATAAACACAGA
* * * *
106732 AAAAAAATAGT-TCGTCGGGACAATAAACACAGA
1 ACAAAGATAGTCT-ATTGGGACAATAAACACAGA
* *
106765 ACATAA-ATAGTCTGTTGGGACAGTAAACA
1 ACA-AAGATAGTCTATTGGGACAATAAACA
106794 TAGATATAGT
Statistics
Matches: 101, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
32 1 0.01
33 97 0.96
34 3 0.03
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (33 bp):
ACAAAGATAGTCTATTGGGACAATAAACACAGA
Found at i:106742 original size:66 final size:66
Alignment explanation
Indices: 106633--106793 Score: 182
Period size: 66 Copynumber: 2.4 Consensus size: 66
106623 CATGGAATCC
* * * * * *
106633 ACAAAGATAGTCCATTGGGACAGTAAACATAGAATAGAGATAGTCCC-CTAGGATAATAAACACA
1 ACAAAGATAGTCTATTGGGACAGTAAACACAGAAAAAAAATAGTCCCTC-AGGACAATAAACACA
106697 GA
65 GA
* * * * *
106699 ACAAAGATAGTCTATTGGGACAATAAACACATAAAAAAAATAGTTCGTCGGGACAATAAACACAG
1 ACAAAGATAGTCTATTGGGACAGTAAACACAGAAAAAAAATAGTCCCTCAGGACAATAAACACAG
106764 A
66 A
*
106765 ACATAA-ATAGTCTGTTGGGACAGTAAACA
1 ACA-AAGATAGTCTATTGGGACAGTAAACA
106794 TAGATATAGT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
66 77 0.96
67 3 0.04
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (66 bp):
ACAAAGATAGTCTATTGGGACAGTAAACACAGAAAAAAAATAGTCCCTCAGGACAATAAACACAG
A
Found at i:109691 original size:67 final size:67
Alignment explanation
Indices: 109583--109721 Score: 190
Period size: 67 Copynumber: 2.1 Consensus size: 67
109573 CCTCAAATAG
* * * *
109583 GTTACATGTGTAAAATCTTAGCTCGACTATGGAAACATGTGGAGTCCTCTAGGACATTGAACATG
1 GTTACATGTATAAAACCTTAGCTCGACTATGGAAACATGTGGAGTCCACTAGGACATTAAACATG
109648 GA
66 GA
* * *
109650 GTTACATGTATAAGACCTTAGCTTGGCTAT-GACAACATGTGGAGTCCACTAGGACATTAAACAT
1 GTTACATGTATAAAACCTTAGCTCGACTATGGA-AACATGTGGAGTCCACTAGGACATTAAACAT
*
109714 GGG
65 GGA
109717 GTTAC
1 GTTAC
109722 TGACCGCCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 2 0.03
67 61 0.97
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (67 bp):
GTTACATGTATAAAACCTTAGCTCGACTATGGAAACATGTGGAGTCCACTAGGACATTAAACATG
GA
Found at i:117678 original size:68 final size:68
Alignment explanation
Indices: 117549--117686 Score: 204
Period size: 68 Copynumber: 2.0 Consensus size: 68
117539 GCAGTTAGAG
* * *
117549 TTAGAATAAGAGAAATTGTAAGGAATAAGGTCAGTGCAATTGAATCAAAGACTATATAAATAAAC
1 TTAGAATAAGAAAAATTGTAAGGAATAAGGTCAGTGCAATTGAATCAAAGACTACAGAAATAAAC
117614 GAA
66 GAA
* * * * *
117617 TTAGAATAATAAAAATTGTAAGGAATAATGTTAGTGCAATTGAATCAAAGACTGCAGAAATAAAT
1 TTAGAATAAGAAAAATTGTAAGGAATAAGGTCAGTGCAATTGAATCAAAGACTACAGAAATAAAC
117682 GAA
66 GAA
117685 TT
1 TT
117687 TAAACAGTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (68 bp):
TTAGAATAAGAAAAATTGTAAGGAATAAGGTCAGTGCAATTGAATCAAAGACTACAGAAATAAAC
GAA
Found at i:122199 original size:13 final size:13
Alignment explanation
Indices: 122181--122214 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
122171 GTATGTATAA
122181 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
122194 TTTTC-TTTCTTT
1 TTTTCTTTTCTTT
*
122206 TTGTCTTTT
1 TTTTCTTTT
122215 TTTATGTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:126425 original size:33 final size:33
Alignment explanation
Indices: 126383--126449 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
126373 GGGGATACAC
* *
126383 CGACAGCAAATAGCTTTACATTAGGAAATGCGT
1 CGACAGCAAATAGCTTTACATCAGAAAATGCGT
*
126416 CGACAGCAAATAGCTTTTCATCAGAAAATGCGT
1 CGACAGCAAATAGCTTTACATCAGAAAATGCGT
126449 C
1 C
126450 AACAATTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (33 bp):
CGACAGCAAATAGCTTTACATCAGAAAATGCGT
Found at i:128956 original size:18 final size:18
Alignment explanation
Indices: 128935--128980 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
128925 CAAAACCGTT
128935 TGCGTCGACATCGGTAGA
1 TGCGTCGACATCGGTAGA
128953 TGCGTCGACATCGGTAGA
1 TGCGTCGACATCGGTAGA
128971 TGCGTCGACA
1 TGCGTCGACA
128981 ATTTCGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.22
Consensus pattern (18 bp):
TGCGTCGACATCGGTAGA
Found at i:133394 original size:25 final size:25
Alignment explanation
Indices: 133365--133417 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
133355 AAAATCACAA
133365 AATTTAAACTGTAGTCTCCTCAAAT
1 AATTTAAACTGTAGTCTCCTCAAAT
133390 AATTTAAACTGTAGTCTCCTCAAAT
1 AATTTAAACTGTAGTCTCCTCAAAT
133415 AAT
1 AAT
133418 ATAGATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (25 bp):
AATTTAAACTGTAGTCTCCTCAAAT
Found at i:136146 original size:40 final size:40
Alignment explanation
Indices: 136041--136197 Score: 149
Period size: 40 Copynumber: 4.0 Consensus size: 40
136031 TATTCACCGG
* * *
136041 CTCATAGCCTGCTAAGTC-GAAGCTTGAATGTT-ACATCGA
1 CTCATAGCCTGCTAAG-CAGAAGCTTGAATATTAACACCAA
* * * * * *
136080 CTCATGGGCTGCTAAGCCA-AAACTTGAATATGAACATCGA
1 CTCATAGCCTGCTAAG-CAGAAGCTTGAATATTAACACCAA
** * *
136120 CTCATAGGTTGTTAAGCAGCAGCTTGAATATTAACACCAA
1 CTCATAGCCTGCTAAGCAGAAGCTTGAATATTAACACCAA
*
136160 CTCATAGCCTGCTAAGCTGAAGCTTGAATATTAACACC
1 CTCATAGCCTGCTAAGCAGAAGCTTGAATATTAACACC
136198 GAATTTAACA
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
39 27 0.28
40 69 0.72
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (40 bp):
CTCATAGCCTGCTAAGCAGAAGCTTGAATATTAACACCAA
Found at i:144635 original size:13 final size:13
Alignment explanation
Indices: 144614--144655 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
144604 TTGAATGAGA
*
144614 AAAAG-AAAAGAA
1 AAAAGAAAAAGAG
144626 AAAGAGAAAAAGAG
1 AAA-AGAAAAAGAG
*
144640 AAAAGAAAAAAAG
1 AAAAGAAAAAGAG
144653 AAA
1 AAA
144656 TATTGCTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 3 0.12
13 14 0.54
14 9 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:144641 original size:21 final size:20
Alignment explanation
Indices: 144613--144655 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
144603 GTTGAATGAG
*
144613 AAAAAGAAAAGAAAAAGAGA
1 AAAAAGAAAAGAAAAAAAGA
144633 AAAAGAGAAAAGAAAAAAAGA
1 AAAA-AGAAAAGAAAAAAAGA
144654 AA
1 AA
144656 TATTGCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAAAAGA
Found at i:161135 original size:3 final size:3
Alignment explanation
Indices: 161127--161179 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
161117 GAGAAGGATC
*
161127 AAG AAG AAG AAG AAG AAG AAG AAGG AA- AGG AAG AAG -AG AAAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG -AAG AAG
*
161172 AAA AAG AA
1 AAG AAG AA
161180 CCTGCCGAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 3 0.07
3 34 0.81
4 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:167065 original size:48 final size:48
Alignment explanation
Indices: 167010--167108 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
167000 AAATGGATAC
167010 ACATAGCTTCATCTGTCGGAACAATCTCCCGAGCATACTTGCTGAGGT
1 ACATAGCTTCATCTGTCGGAACAATCTCCCGAGCATACTTGCTGAGGT
*
167058 ACATAGCTTCGTCTGTCGGAACAATCTCCCGAGCATACTTGCTGAGGT
1 ACATAGCTTCATCTGTCGGAACAATCTCCCGAGCATACTTGCTGAGGT
167106 ACA
1 ACA
167109 CAAATTTTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (48 bp):
ACATAGCTTCATCTGTCGGAACAATCTCCCGAGCATACTTGCTGAGGT
Found at i:185719 original size:24 final size:25
Alignment explanation
Indices: 185686--185733 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
185676 GTTAAGAGTA
*
185686 AAAATTGTCATTGCAAAAGTAATAC
1 AAAATTGTCAGTGCAAAAGTAATAC
*
185711 AAAA-TGTCAGTGCAAATGTAATA
1 AAAATTGTCAGTGCAAAAGTAATA
185734 TAAATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATTGTCAGTGCAAAAGTAATAC
Found at i:198534 original size:23 final size:22
Alignment explanation
Indices: 198497--198544 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
198487 TTAACCTTAG
* *
198497 TTAATTATAATTATTTCTTTAA
1 TTAATTATAATTATTTATTAAA
*
198519 TTAATTCATTATTATTTATTAAA
1 TTAATT-ATAATTATTTATTAAA
198542 TTA
1 TTA
198545 GTGTTAGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTATAATTATTTATTAAA
Found at i:202065 original size:46 final size:46
Alignment explanation
Indices: 202013--202100 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
202003 ACTACTAATT
* ** ** *
202013 TGTAATATTAGTTATGTACTTGGACGATGTTGTAGTTATCATGTGG
1 TGTAATACTAGTTATACACTTGGAAAATATTGTAGTTATCATGTGG
202059 TGTAATACTAGTTATACACTTGGAAAATATTGTAGTTATCAT
1 TGTAATACTAGTTATACACTTGGAAAATATTGTAGTTATCAT
202101 CAATTTGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (46 bp):
TGTAATACTAGTTATACACTTGGAAAATATTGTAGTTATCATGTGG
Found at i:202406 original size:22 final size:21
Alignment explanation
Indices: 202373--202412 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
202363 AAATATTAAT
202373 TTTTCCAGAAAAAGTAATTCA
1 TTTTCCAGAAAAAGTAATTCA
202394 TTTTCCAGAAAAAGTAATT
1 TTTTCCAGAAAAAGTAATT
202413 TCTGAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (21 bp):
TTTTCCAGAAAAAGTAATTCA
Found at i:208444 original size:40 final size:40
Alignment explanation
Indices: 208400--208475 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
208390 GTCTCGATAC
*
208400 CTCGTTTTCTAAAACCACTTGACTTCTAAACTAAACTACT
1 CTCGTTTTCTAAAACCACTTGACTTCTAAACCAAACTACT
*
208440 CTCGTTTTCTAAAACCACTTGACTTTTAAACCAAAC
1 CTCGTTTTCTAAAACCACTTGACTTCTAAACCAAAC
208476 CACTTATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (40 bp):
CTCGTTTTCTAAAACCACTTGACTTCTAAACCAAACTACT
Found at i:210862 original size:53 final size:54
Alignment explanation
Indices: 210787--211084 Score: 396
Period size: 53 Copynumber: 5.6 Consensus size: 54
210777 GTAAATGTAA
* *
210787 AAAGGTCCGATAACTCTGTGTCATCATGAGTTATATGAATCCTATTATGAG-TT
1 AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGAGATT
* * *
210840 AAAGGGT-GGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTAC-AGATT
1 AAA-GGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGAGATT
* * *
210893 AAAGGTCCGATGACTTTGTGCCATCGTGAGTTATATGAATCCTATTACGA-ATT
1 AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGAGATT
210946 AAAGGTCCGATGA--CTGTGTCATCATGAGTTATATGAATCCTATTACG-GATT
1 AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGAGATT
* * *
210997 AAACGTCTGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTATG-GATT
1 AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGAGATT
* * *
211050 AAAAGGTCCAATGACTCTGTCTCATCGTGAGTTAT
1 -AAAGGTCCGATGACTCTGTGTCATCATGAGTTAT
211085 CAAATGTGAA
Statistics
Matches: 217, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
51 45 0.21
52 5 0.02
53 134 0.62
54 33 0.15
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (54 bp):
AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGAGATT
Found at i:211009 original size:104 final size:105
Alignment explanation
Indices: 210791--211084 Score: 403
Period size: 104 Copynumber: 2.8 Consensus size: 105
210781 ATGTAAAAAG
* * *
210791 GTCCGATAACTCTGTGTCATCATGAGTTATATGAATCCTATTATGAGTTAAAGGGT-GGATGACT
1 GTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTATGAATTAAA-GGTCCGATGAC-
* *
210855 CTATGTCATCGTGAGTTATATGAATCCTATTACAGATTAAAG
64 CTGTGTCATCGTGAGTTATATGAATCCTATTACAGATTAAAC
* * * *
210897 GTCCGATGACTTTGTGCCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCGATGA-CT
1 GTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTATGAATTAAAGGTCCGATGACCT
* *
210961 GTGTCATCATGAGTTATATGAATCCTATTACGGATTAAAC
66 GTGTCATCGTGAGTTATATGAATCCTATTACAGATTAAAC
* * *
211001 GTCTGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTATGGATTAAAAGGTCCAATGACT
1 GTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTATGAATT-AAAGGTCCGATGAC-
*
211066 CTGTCTCATCGTGAGTTAT
64 CTGTGTCATCGTGAGTTAT
211085 CAAATGTGAA
Statistics
Matches: 164, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
104 81 0.49
105 15 0.09
106 51 0.31
107 17 0.10
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (105 bp):
GTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTATGAATTAAAGGTCCGATGACCT
GTGTCATCGTGAGTTATATGAATCCTATTACAGATTAAAC
Found at i:211020 original size:157 final size:159
Alignment explanation
Indices: 210787--211084 Score: 435
Period size: 157 Copynumber: 1.9 Consensus size: 159
210777 GTAAATGTAA
* *
210787 AAAGGTCCGATAACTCTGTGTCATCATGAGTTATATGAATCCTATTATGAGTTAAAGGGTGGATG
1 AAAGGTCCGATAAC-CTGTGTCATCATGAGTTATATGAATCCTATTAGGAGTTAAAGCGTGGATG
* * *
210852 ACTCTATGTCATCGTGAGTTATATGAATCCTATTACAGATT-AAAGGTCCGATGACTTTGTGC-C
65 ACTCTATGTCATCATGAGTTATATGAATCCTATTACAGATTAAAAGGTCCAATGACTCTGT-CTC
210915 ATCGTGAGTTATATGAATCCTATTACGAATT
129 ATCGTGAGTTATATGAATCCTATTACGAATT
* *
210946 AAAGGTCCGATGA-CTGTGTCATCATGAGTTATATGAATCCTATTACGGA-TTAAA-CGTCTGAT
1 AAAGGTCCGATAACCTGTGTCATCATGAGTTATATGAATCCTATTA-GGAGTTAAAGCGT-GGAT
* **
211008 GACTCTGTGTCATCATGAGTTATATGAATCCTATTATGGATTAAAAGGTCCAATGACTCTGTCTC
64 GACTCTATGTCATCATGAGTTATATGAATCCTATTACAGATTAAAAGGTCCAATGACTCTGTCTC
211073 ATCGTGAGTTAT
129 ATCGTGAGTTAT
211085 CAAATGTGAA
Statistics
Matches: 125, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
156 2 0.02
157 79 0.63
158 32 0.26
159 12 0.10
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (159 bp):
AAAGGTCCGATAACCTGTGTCATCATGAGTTATATGAATCCTATTAGGAGTTAAAGCGTGGATGA
CTCTATGTCATCATGAGTTATATGAATCCTATTACAGATTAAAAGGTCCAATGACTCTGTCTCAT
CGTGAGTTATATGAATCCTATTACGAATT
Found at i:218126 original size:54 final size:53
Alignment explanation
Indices: 217944--218130 Score: 275
Period size: 53 Copynumber: 3.5 Consensus size: 53
217934 GCAAAAAGTT
* *
217944 CGATGACTTTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAAAGGTC
1 CGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTC
* * * * *
217997 AGATGATTTTGTGTTATCGTGAGTTATATGAATCCTATTATGGATTAAAGGTC
1 CGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTC
* *
218050 TGATGACTCTGTGTCATAGTGAGTTATATGAATCCTATTACGGATTAAAAGGTC
1 CGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT-AAAGGTC
*
218104 CGATGACTCTGTGTCACCGTGAGTTAT
1 CGATGACTCTGTGTCATCGTGAGTTAT
218131 CAAATGTGAA
Statistics
Matches: 119, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
53 88 0.74
54 31 0.26
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (53 bp):
CGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTC
Found at i:223515 original size:14 final size:14
Alignment explanation
Indices: 223496--223527 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
223486 ATATAAATTT
*
223496 TTTTCTTTTTTTTC
1 TTTTCTTCTTTTTC
223510 TTTTCTTCTTTTTC
1 TTTTCTTCTTTTTC
223524 TTTT
1 TTTT
223528 ATAAATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:226178 original size:51 final size:50
Alignment explanation
Indices: 226102--226202 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 50
226092 TTGCCACTAC
226102 AAAGATAAGACACTAAGTCTGCATCCAATAAATACAATGACTTGGATTGT
1 AAAGATAAGACACTAAGTCTGCATCCAATAAATACAATGACTTGGATTGT
*
226152 NAAAGATAAGACACTAAGTCTGCATCCAATAAATGCAATGACTTGGATTGT
1 -AAAGATAAGACACTAAGTCTGCATCCAATAAATACAATGACTTGGATTGT
226203 CCTTTTTCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (50 bp):
AAAGATAAGACACTAAGTCTGCATCCAATAAATACAATGACTTGGATTGT
Found at i:234971 original size:52 final size:52
Alignment explanation
Indices: 234890--235077 Score: 236
Period size: 52 Copynumber: 3.6 Consensus size: 52
234880 GTAAATGAAA
*
234890 AAGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
* * * *
234942 AAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGGTTTT
1 AAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
* * * *
234994 GAGGTCCGATGACTATGT-TGCATCGTGATTATATAAATCCTTTACGGATTA-
1 AAGGTCCGATGACTATGTGT-CATCATGAGTATATGAATCCTTTACGGATTAT
* * *
235045 AGAGGTTCGGTGATTATGTGTCATCATGAGTAT
1 A-AGGTCCGATGACTATGTGTCATCATGAGTAT
235078 TAAATGAAAT
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
51 1 0.01
52 114 0.98
53 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
Found at i:245630 original size:12 final size:14
Alignment explanation
Indices: 245595--245639 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 14
245585 AATAAGAGAA
245595 AAGAGAAGAAGAAGG
1 AAGAGAAGAA-AAGG
245610 AAGAGAAGAAAAGG
1 AAGAGAAGAAAAGG
*
245624 AA-A-AAGAAAATG
1 AAGAGAAGAAAAGG
245636 AAGA
1 AAGA
245640 AGCTTTTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 10 0.36
13 2 0.07
14 6 0.21
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
AAGAGAAGAAAAGG
Found at i:254502 original size:52 final size:52
Alignment explanation
Indices: 254423--254616 Score: 307
Period size: 52 Copynumber: 3.7 Consensus size: 52
254413 TAAATGAAAA
* * * *
254423 AGGTCCGATAACTATTTGTCATTGTGAGTATATGAATTCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
254475 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGGTTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
254527 AGGTCCGATGACTATGTGTAATTGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
254579 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATC
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATC
254617 TTGTACAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 130 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:256266 original size:21 final size:21
Alignment explanation
Indices: 256240--256289 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
256230 ATTATTCTTC
256240 GTACT-ATAAACCCTAAAGTAA
1 GTACTAAT-AACCCTAAAGTAA
*
256261 GTACTAATTACCCTAAAGTAA
1 GTACTAATAACCCTAAAGTAA
256282 GTACTAAT
1 GTACTAAT
256290 TACTTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (21 bp):
GTACTAATAACCCTAAAGTAA
Found at i:256290 original size:21 final size:21
Alignment explanation
Indices: 256249--256292 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
256239 CGTACTATAA
256249 ACCCTAAAGTAAGTACTAATT
1 ACCCTAAAGTAAGTACTAATT
256270 ACCCTAAAGTAAGTACTAATT
1 ACCCTAAAGTAAGTACTAATT
256291 AC
1 AC
256293 TTTTACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (21 bp):
ACCCTAAAGTAAGTACTAATT
Found at i:262649 original size:31 final size:32
Alignment explanation
Indices: 262579--262653 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
262569 CTCATATATA
*
262579 TAAAGCTTGCAACTTCAAATGCTTCGCAAGTG
1 TAAAGCTCGCAACTTCAAATGCTTCGCAAGTG
* * *
262611 TAGAGCTCGTAACTTCAAGTGC-TCGC-AGATG
1 TAAAGCTCGCAACTTCAAATGCTTCGCAAG-TG
262642 TAAAGCTCGCAA
1 TAAAGCTCGCAA
262654 GTACAGAGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.06
31 16 0.44
32 18 0.50
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (32 bp):
TAAAGCTCGCAACTTCAAATGCTTCGCAAGTG
Found at i:262651 original size:15 final size:14
Alignment explanation
Indices: 262631--262695 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 14
262621 AACTTCAAGT
262631 GCTCGCAGATGTAAA
1 GCTCGCA-ATGTAAA
262646 GCTCGCAA-GTACAGA
1 GCTCGCAATGTA-A-A
*
262661 GCTCACAACTGTAAA
1 GCTCGCAA-TGTAAA
*
262676 TGCTCGCATGTGTAAA
1 -GCTCGCA-ATGTAAA
262692 GCTC
1 GCTC
262696 TCCACTACGA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 20 0.49
16 13 0.32
17 3 0.07
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (14 bp):
GCTCGCAATGTAAA
Found at i:271270 original size:4 final size:4
Alignment explanation
Indices: 271261--271287 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
271251 AAGAACCAAA
271261 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
271288 ACACTAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:304645 original size:40 final size:40
Alignment explanation
Indices: 304590--304671 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
304580 TTAGGGAGAT
*
304590 GATGATGATGGGGTTGAAGTTGAACAACCTATTTCTCATG
1 GATGATGATAGGGTTGAAGTTGAACAACCTATTTCTCATG
*
304630 GATGATGATAGGGTTGAAGTTGAACAACCTCTTTCTCATG
1 GATGATGATAGGGTTGAAGTTGAACAACCTATTTCTCATG
304670 GA
1 GA
304672 AAAAAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (40 bp):
GATGATGATAGGGTTGAAGTTGAACAACCTATTTCTCATG
Found at i:324041 original size:40 final size:40
Alignment explanation
Indices: 323986--324069 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
323976 CTCCTTATCT
323986 GCTTTGTAATCTAGGATTATGAAATCGACAGGGAACAAGA
1 GCTTTGTAATCTAGGATTATGAAATCGACAGGGAACAAGA
324026 GCTTTGTAATCTAGGATTATGAAATCGACAGGGAACAAGA
1 GCTTTGTAATCTAGGATTATGAAATCGACAGGGAACAAGA
324066 GCTT
1 GCTT
324070 ATCAACTTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (40 bp):
GCTTTGTAATCTAGGATTATGAAATCGACAGGGAACAAGA
Found at i:330069 original size:123 final size:123
Alignment explanation
Indices: 329737--330105 Score: 580
Period size: 126 Copynumber: 3.0 Consensus size: 123
329727 GATTACGTTA
* * * *
329737 AATATT-AAAACATGAAAATTAATATCCTTTTGAAAAGGGTATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
*
329801 ATATTTCTTTAAAGGAATATTTCCATTTTAATAT-AAGATATTATATAAAAGGAAATTG
66 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAA-ATATTATATAAAAGGAAATTC
* *
329859 AATATTAAAAAAAATATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATGAACCTTC
1 AATATT---AAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
329924 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAAATATTATATAAAAGGAAATTC
63 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAAATATTATATAAAAGGAAATTC
*
329985 AATATTAAAAACATGGAAGTTAATATACTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* * *
330050 ATATTTCTCTAAAGGAATATTTCCATTTTAATATGAGATATTAAATAAAAAGGAAA
66 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAAATATTATAT-AAAAGGAAA
330106 GATAGCAAAA
Statistics
Matches: 228, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
122 6 0.03
123 99 0.43
124 9 0.04
126 112 0.49
127 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (123 bp):
AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAAATATTATATAAAAGGAAATTC
Found at i:340749 original size:21 final size:21
Alignment explanation
Indices: 340723--340766 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
340713 CTCTCCTTCC
* *
340723 TCCTTGTGCTTCTTCTTTTTG
1 TCCTTGTGCTTCCTCTTCTTG
340744 TCCTTGTGCTTCCTCTTCTTG
1 TCCTTGTGCTTCCTCTTCTTG
340765 TC
1 TC
340767 ATTCAAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.14, T:0.57
Consensus pattern (21 bp):
TCCTTGTGCTTCCTCTTCTTG
Found at i:341784 original size:43 final size:43
Alignment explanation
Indices: 341723--341810 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
341713 CCCCATCTCT
341723 GGGTACAATCCCCCTTTGTTTACATAGCAGCATGATTAAAGAA
1 GGGTACAATCCCCCTTTGTTTACATAGCAGCATGATTAAAGAA
341766 GGGTACAATCCCCCTTTGTTTACATAGCAGCATGATTAAAGAA
1 GGGTACAATCCCCCTTTGTTTACATAGCAGCATGATTAAAGAA
341809 GG
1 GG
341811 AAACAATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (43 bp):
GGGTACAATCCCCCTTTGTTTACATAGCAGCATGATTAAAGAA
Found at i:344134 original size:84 final size:84
Alignment explanation
Indices: 343993--344159 Score: 298
Period size: 84 Copynumber: 2.0 Consensus size: 84
343983 ACAATGTAGG
343993 CCAATAGGATCCTGATTGTAAAACCTTTGCAACAATCCTTACACCGCCAAAATGGCCTCCATAGG
1 CCAATAGGATCCTGATTGTAAAACCTTTGCAACAATCCTTACACCGCCAAAATGGCCTCCATAGG
344058 GAGCATCATGGCAATGTCC
66 GAGCATCATGGCAATGTCC
* * * *
344077 CCAATAGGATCCTGATTGTAAAACCTTTGGAATAGTCCTTACACTGCCAAAATGGCCTCCATAGG
1 CCAATAGGATCCTGATTGTAAAACCTTTGCAACAATCCTTACACCGCCAAAATGGCCTCCATAGG
344142 GAGCATCATGGCAATGTC
66 GAGCATCATGGCAATGTC
344160 TCAAGATAGA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (84 bp):
CCAATAGGATCCTGATTGTAAAACCTTTGCAACAATCCTTACACCGCCAAAATGGCCTCCATAGG
GAGCATCATGGCAATGTCC
Found at i:346160 original size:2 final size:2
Alignment explanation
Indices: 346143--346178 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
346133 CGTAAAACAA
*
346143 AT AT A- AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
346179 AAAGAGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:351121 original size:59 final size:59
Alignment explanation
Indices: 350948--351106 Score: 205
Period size: 60 Copynumber: 2.7 Consensus size: 59
350938 TAAGAATTTG
* * **
350948 TATTATAGACAACGAGAAACACTTGATTAGATAAAATTTTCAAAAGAAAAAAAATGTATG
1 TATTATAGACAA-GAGAAACACTTGATTAGATAAATTTTTCAAAAGAAAAAAAAAGTACA
* *
351008 TATTATAGACCAAAAAAAACACTTGATTAGATAAATTTTTCAAAAGAATAAAAAAAGTACA
1 TATTATAGA-CAAGAGAAACACTTGATTAGATAAATTTTTCAAAAGAA-AAAAAAAGTACA
*
351069 TATTATAGAC-AGAGAAACACTT-ATTTAGATAATTTTTT
1 TATTATAGACAAGAGAAACACTTGA-TTAGATAAATTTTT
351107 TTAAAAAAGA
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
58 1 0.01
59 23 0.26
60 42 0.48
61 21 0.24
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (59 bp):
TATTATAGACAAGAGAAACACTTGATTAGATAAATTTTTCAAAAGAAAAAAAAAGTACA
Found at i:356830 original size:62 final size:63
Alignment explanation
Indices: 356764--356906 Score: 180
Period size: 62 Copynumber: 2.3 Consensus size: 63
356754 ATCTTGGACC
* ** *
356764 AAAAAAAAATTCAAGCCATAATGAGAGAACAATTGTCAAGTTCAGGACCTAACTTAGAC-AAA
1 AAAAAAAAATTCAAGCCATAATGAGAGAACAATTATCAAGTTCAAAACCTAACTTAAACAAAA
* * * * * *
356826 AAAAAAACATTTAAACCCTAATGTGAGAACAATTATCAAGTTTAAAACCTAACTTAAACAAAAA
1 AAAAAAAAATTCAAGCCATAATGAGAGAACAATTATCAAGTTCAAAACCTAACTTAAAC-AAAA
356890 AAAAAAAAATTCAAGCC
1 AAAAAAAAATTCAAGCC
356907 CCAATATGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
62 49 0.74
64 17 0.26
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.20
Consensus pattern (63 bp):
AAAAAAAAATTCAAGCCATAATGAGAGAACAATTATCAAGTTCAAAACCTAACTTAAACAAAA
Found at i:367367 original size:18 final size:18
Alignment explanation
Indices: 367344--367380 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
367334 AATAGACAAG
367344 GTTTGTAAGTAGAGGCTA
1 GTTTGTAAGTAGAGGCTA
367362 GTTTGTAAGTAGAGGCTA
1 GTTTGTAAGTAGAGGCTA
367380 G
1 G
367381 AGGATTGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.32
Consensus pattern (18 bp):
GTTTGTAAGTAGAGGCTA
Found at i:369145 original size:18 final size:18
Alignment explanation
Indices: 369122--369160 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
369112 CTGAATTTTT
369122 TAATTCGAAT-AACTCGAA
1 TAATTCGAATAAAC-CGAA
369140 TAATTCGAATAAACCGAA
1 TAATTCGAATAAACCGAA
369158 TAA
1 TAA
369161 AACTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (18 bp):
TAATTCGAATAAACCGAA
Found at i:369341 original size:34 final size:34
Alignment explanation
Indices: 369298--369373 Score: 127
Period size: 34 Copynumber: 2.2 Consensus size: 34
369288 CATAAACTAC
*
369298 ACCCAAATATTTTTAATTTTTTA-CATTTTATCTT
1 ACCCAAATATTTTTAATTTTTTATC-TTTTAACTT
369332 ACCCAAATATTTTTAATTTTTTATCTTTTAACTT
1 ACCCAAATATTTTTAATTTTTTATCTTTTAACTT
369366 ACCCAAAT
1 ACCCAAAT
369374 GTTGTTGACT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 39 0.98
35 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (34 bp):
ACCCAAATATTTTTAATTTTTTATCTTTTAACTT
Found at i:370265 original size:23 final size:23
Alignment explanation
Indices: 370238--370313 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
370228 CGAGGAAGTA
370238 ACTTCAACTTGGGCCGCTCAGGT
1 ACTTCAACTTGGGCCGCTCAGGT
** ** *
370261 ACTTC-TGTTGGGGTGC-GAGGAAGT
1 ACTTCAACTTGGGCCGCTCA-G--GT
370285 AACTTCAACTTGGGCCGCTCAGGT
1 -ACTTCAACTTGGGCCGCTCAGGT
370309 ACTTC
1 ACTTC
370314 TGTTGGTGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
21 1 0.03
22 8 0.22
23 10 0.27
24 4 0.11
25 5 0.14
26 8 0.22
27 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.28
Consensus pattern (23 bp):
ACTTCAACTTGGGCCGCTCAGGT
Found at i:370280 original size:48 final size:48
Alignment explanation
Indices: 370224--370319 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
370214 CCAATGGCTT
370224 GGTGCGAGGAAGTAACTTCAACTTGGGCCGCTCAGGTACTTCTGTTGG
1 GGTGCGAGGAAGTAACTTCAACTTGGGCCGCTCAGGTACTTCTGTTGG
370272 GGTGCGAGGAAGTAACTTCAACTTGGGCCGCTCAGGTACTTCTGTTGG
1 GGTGCGAGGAAGTAACTTCAACTTGGGCCGCTCAGGTACTTCTGTTGG
370320 TGATGGCAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (48 bp):
GGTGCGAGGAAGTAACTTCAACTTGGGCCGCTCAGGTACTTCTGTTGG
Found at i:371709 original size:3 final size:3
Alignment explanation
Indices: 371701--371754 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
371691 AGAAGCTATG
* *
371701 GAA GAA GAA GAA GGA GGA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
371749 GAA GAA
1 GAA GAA
371755 AGGGGGGGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:378786 original size:18 final size:18
Alignment explanation
Indices: 378760--378794 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
378750 TTAATTTTAT
*
378760 AATTTGAATAACTCAAAA
1 AATTCGAATAACTCAAAA
378778 AATTCGAATAACTCAAA
1 AATTCGAATAACTCAAA
378795 TAATATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (18 bp):
AATTCGAATAACTCAAAA
Found at i:382993 original size:3 final size:3
Alignment explanation
Indices: 382985--383015 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
382975 CAGTAGACCT
382985 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
383016 ACATAAGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:391242 original size:15 final size:14
Alignment explanation
Indices: 391224--391264 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
391214 TAAATCTATA
391224 ATAATATATAATATT
1 ATAATATA-AATATT
391239 ATAATATAAATATT
1 ATAATATAAATATT
391253 -TAA-A-AAATATT
1 ATAATATAAATATT
391264 A
1 A
391265 AAATGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.28
12 1 0.04
13 3 0.12
14 6 0.24
15 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATATAAATATT
Found at i:391883 original size:7 final size:8
Alignment explanation
Indices: 391865--391901 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
391855 TTATTAAAAG
391865 AAAATTTA
1 AAAATTTA
391873 AAAATTTA
1 AAAATTTA
*
391881 AAAAATTA
1 AAAATTTA
*
391889 AAAAATTA
1 AAAATTTA
391897 AAAAT
1 AAAAT
391902 GGTTGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAATTTA
Found at i:406972 original size:21 final size:20
Alignment explanation
Indices: 406948--406996 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
406938 TTTAATCAAA
*
406948 ATTAAAAAAAAAAACTTAAGT
1 ATTAAAAAAAAAAA-TTAAAT
*
406969 ATTAAATTAAAAAAATTAAAT
1 ATTAAA-AAAAAAAATTAAAT
406990 A-TAAAAA
1 ATTAAAAA
406997 TGAATATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 12 0.50
22 7 0.29
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
ATTAAAAAAAAAAATTAAAT
Found at i:406997 original size:22 final size:22
Alignment explanation
Indices: 406955--406995 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
406945 AAAATTAAAA
* *
406955 AAAAAAACTTAAGTATTAAATT
1 AAAAAAACTTAAATATAAAATT
406977 AAAAAAA-TTAAATATAAAA
1 AAAAAAACTTAAATATAAAA
406996 ATGAATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAAAACTTAAATATAAAATT
Found at i:407635 original size:18 final size:17
Alignment explanation
Indices: 407595--407650 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
407585 TCATCTCTTG
407595 AAAAATTAAAAATATTAA
1 AAAAATTAAAAATA-TAA
* *
407613 TAAAATCTAAACATATAA
1 AAAAAT-TAAAAATATAA
407631 AAAAATTAAAAAATATAA
1 AAAAATT-AAAAATATAA
407649 AA
1 AA
407651 TATCTTTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 24 0.75
19 7 0.22
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAATTAAAAATATAA
Found at i:407639 original size:27 final size:25
Alignment explanation
Indices: 407596--407653 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
407586 CATCTCTTGA
* *
407596 AAAAT-TAAAAATATTAATAAAATCT
1 AAAATATAAAAAAATTAA-AAAATAT
407621 AAACATATAAAAAAATTAAAAAATAT
1 AAA-ATATAAAAAAATTAAAAAATAT
407647 AAAATAT
1 AAAATAT
407654 CTTTTACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.24
26 11 0.38
27 11 0.38
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAATATAAAAAAATTAAAAAATAT
Found at i:423320 original size:19 final size:19
Alignment explanation
Indices: 423296--423335 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
423286 CTACTATCAA
423296 AGACAAATGCTGGTTGTTT
1 AGACAAATGCTGGTTGTTT
423315 AGACAAATGCTGGTTGTTT
1 AGACAAATGCTGGTTGTTT
423334 AG
1 AG
423336 GCATTGGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (19 bp):
AGACAAATGCTGGTTGTTT
Found at i:428172 original size:15 final size:17
Alignment explanation
Indices: 428152--428184 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
428142 CTTATCAACA
428152 AATTAAAC-TA-AAAAT
1 AATTAAACATATAAAAT
428167 AATTAAACATATAAAAT
1 AATTAAACATATAAAAT
428184 A
1 A
428185 TAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAACATATAAAAT
Found at i:430482 original size:13 final size:13
Alignment explanation
Indices: 430464--430492 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
430454 TAGTTTCTCC
430464 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
430477 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
430490 TTT
1 TTT
430493 CCTTTCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:430486 original size:12 final size:12
Alignment explanation
Indices: 430464--430497 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
430454 TAGTTTCTCC
430464 TTTTTCTTTTTTT
1 TTTTTC-TTTTTT
430477 TTTTTCTTTTTT
1 TTTTTCTTTTTT
*
430489 TTTTCCTTT
1 TTTTTCTTT
430498 CCTTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:430587 original size:2 final size:2
Alignment explanation
Indices: 430574--430603 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
430564 TTTATTCTTT
430574 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
430604 TAGTTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:432037 original size:13 final size:13
Alignment explanation
Indices: 432019--432047 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
432009 TAGTTTCTCC
432019 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
432032 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
432045 TTT
1 TTT
432048 CCTTTCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:432041 original size:12 final size:12
Alignment explanation
Indices: 432019--432052 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
432009 TAGTTTCTCC
432019 TTTTTCTTTTTTT
1 TTTTTC-TTTTTT
432032 TTTTTCTTTTTT
1 TTTTTCTTTTTT
*
432044 TTTTCCTTT
1 TTTTTCTTT
432053 CCTTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:432142 original size:2 final size:2
Alignment explanation
Indices: 432129--432158 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
432119 TTTATTCTTT
432129 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
432159 TAGTTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:432374 original size:13 final size:12
Alignment explanation
Indices: 432330--432385 Score: 60
Period size: 13 Copynumber: 4.5 Consensus size: 12
432320 ATATAATAAG
432330 ATAATATTAATT
1 ATAATATTAATT
*
432342 A-AATAATAATTT
1 ATAATATTAA-TT
*
432354 ATACTATTATATT
1 ATAATATTA-ATT
432367 ATAATATTAATT
1 ATAATATTAATT
432379 AATAATA
1 -ATAATA
432386 ATTTAAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 7 0.19
12 7 0.19
13 21 0.58
14 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATATTAATT
Found at i:435627 original size:19 final size:20
Alignment explanation
Indices: 435603--435651 Score: 55
Period size: 24 Copynumber: 2.3 Consensus size: 20
435593 TTTTAGTTAT
435603 TCGAATT-ATTCGAGTAAAC
1 TCGAATTGATTCGAGTAAAC
435622 TCGAATAATTTGATTCGAGTAAAC
1 TCG---AA-TTGATTCGAGTAAAC
435646 TCGAAT
1 TCGAAT
435652 AATTTGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
19 3 0.12
20 1 0.04
21 2 0.08
22 2 0.08
23 2 0.08
24 15 0.60
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
TCGAATTGATTCGAGTAAAC
Found at i:435637 original size:24 final size:24
Alignment explanation
Indices: 435610--435665 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
435600 TATTCGAATT
435610 ATTCGAGTAAACTCGAATAATTTG
1 ATTCGAGTAAACTCGAATAATTTG
435634 ATTCGAGTAAACTCGAATAATTTG
1 ATTCGAGTAAACTCGAATAATTTG
435658 ATTCGAGT
1 ATTCGAGT
435666 TTCGAGATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (24 bp):
ATTCGAGTAAACTCGAATAATTTG
Done.