Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 20
Found at i:454322 original size:99 final size:99
Alignment explanation
Indices: 454202--454399 Score: 315
Period size: 99 Copynumber: 2.0 Consensus size: 99
454192 TTATAATATC
454202 ATATATATACAAAAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCACGGCTTTATGG
1 ATATATATACAAAAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCACGGCTTTATGG
** *
454267 ATAAGATTCGGCTAGCCTGATAAACGTGATTATA
66 ATAAGATTCAACTAACCTGATAAACGTGATTATA
* * * *
454301 ATATCTATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATATATACAAAAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCACGGCTTTATGG
* *
454366 ATAAGATTCAACTAACCTGATAAAGGTGTTTATA
66 ATAAGATTCAACTAACCTGATAAACGTGATTATA
454400 TATTGAGCTG
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 90 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (99 bp):
ATATATATACAAAAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCACGGCTTTATGG
ATAAGATTCAACTAACCTGATAAACGTGATTATA
Found at i:455418 original size:151 final size:152
Alignment explanation
Indices: 455214--455619 Score: 557
Period size: 151 Copynumber: 2.6 Consensus size: 152
455204 TTTTGTAGCT
* * *
455214 TTCAGAGTCAATTT-AACTTCACAGTGAAGGATATTGGACTCAAAACAACACAAGATTGGATTTC
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAATACAAGATTGGATTTC
*
455278 AACTTCACAACGAAGGATATCCAATTCAAATCTCAACTTCACAACGAATGGG-CGACTGTTTGAC
66 AACTTCACAACGAAGGATATCCAATTCAAATCTCAACTTCACAACGAA-GGGACGACTGTCTGAC
455342 GACAAACAACTTTCC-AGTTTCA
130 GACAAACAACTTTCCAAGTTTCA
*
455364 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAGTACAAGATTGGATTTC
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAATACAAGATTGGATTTC
* * * * *
455429 AACTTCACAACGAATGATATCTAATTGAAATCTCAACTTCACAGCGAAGGGACGATTGTCTGACG
66 AACTTCACAACGAAGGATATCCAATTCAAATCTCAACTTCACAACGAAGGGACGACTGTCTGACG
*
455494 ACAAACAACTTTCCAAGTTTCG
131 ACAAACAACTTTCCAAGTTTCA
* * * *
455516 TTCAGAGTCAATTTCAACTCCAAAGCGAAGGATATTGAACTCGAAGCGACACAATTTACTCGAGA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCG-A---A-ACAA--TA--CAAGA
*
455581 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
57 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
455620 ACCAATTTGG
Statistics
Matches: 224, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
150 17 0.08
151 115 0.51
152 46 0.21
153 1 0.00
156 1 0.00
157 3 0.01
159 2 0.01
161 39 0.17
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (152 bp):
TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAATACAAGATTGGATTTC
AACTTCACAACGAAGGATATCCAATTCAAATCTCAACTTCACAACGAAGGGACGACTGTCTGACG
ACAAACAACTTTCCAAGTTTCA
Found at i:455676 original size:65 final size:65
Alignment explanation
Indices: 455571--455877 Score: 289
Period size: 65 Copynumber: 4.9 Consensus size: 65
455561 GCGACACAAT
* * *
455571 TTACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
1 TTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTAAAAC
* *
455636 TTACTCAAGATTGGATTTCAACTTCACGACGAAGGTTATCCAGCTCAAAACCAATTTGGTAAAAC
1 TTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTAAAAC
* * * * ** * * * *
455701 -AATTC----TTGGATTTCAACTTCACAACGAAGAATAT-C-A-TGC-CCA-CAA-GTAGCAATA
1 TTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACT-CAAAACCAATTTGGTAAAA
455755 C
65 C
* * * * *
455756 -AACTCGAGATTGGATTTCAACTTCA-GAACGAAGGATATCCAACTTAAAGCCAATTTGGAAAAA
1 TTACTCAAGATTGGATTTCAACTTCACG-ACGAAGGATATCCAACTCAAAACCAATTTGGTAAAA
455819 C
65 C
* * *
455820 TTACTCAAGAATGGATTTCAACTTCACGACGAAGGATATCCAGCTCAAAGGCCAATTT
1 TTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAA-ACCAATTT
455878 AGAAAAACAA
Statistics
Matches: 194, Mismatches: 33, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
55 10 0.05
56 3 0.02
57 2 0.01
58 1 0.01
59 27 0.14
60 27 0.14
61 1 0.01
62 1 0.01
63 3 0.02
64 9 0.05
65 101 0.52
66 9 0.05
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (65 bp):
TTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTAAAAC
Found at i:455837 original size:184 final size:185
Alignment explanation
Indices: 455573--455920 Score: 572
Period size: 184 Copynumber: 1.9 Consensus size: 185
455563 GACACAATTT
**
455573 ACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAACTT
1 ACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGAAAAACTT
* * * *
455638 ACTCAAGATTGGATTTCAACTTCACGACGAAGGTTATCCAGCTCAAA-ACCAATTTGGTAAAACA
66 ACTCAAGAATGGATTTCAACTTCACGACGAAGGATATCCAGCTCAAAGACCAATTTAGAAAAACA
455702 ATTCTTGGATTTCAACTTCACAACGAAGAATATCATGCCCACAAGTAGCAATACA
131 ATTCTTGGATTTCAACTTCACAACGAAGAATATCATGCCCACAAGTAGCAATACA
* * *
455757 ACTCGAGATTGGATTTCAACTTCAGAACGAAGGATATCCAACTTAAAGCCAATTTGGAAAAACTT
1 ACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGAAAAACTT
*
455822 ACTCAAGAATGGATTTCAACTTCACGACGAAGGATATCCAGCTCAAAGGCCAATTTAGAAAAACA
66 ACTCAAGAATGGATTTCAACTTCACGACGAAGGATATCCAGCTCAAAGACCAATTTAGAAAAACA
* * *
455887 ATTCTTGGGTTTCAACTTCTCAACGAAGGATATC
131 ATTCTTGGATTTCAACTTCACAACGAAGAATATC
455921 CAATTCAAGG
Statistics
Matches: 150, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
184 105 0.70
185 45 0.30
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (185 bp):
ACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGAAAAACTT
ACTCAAGAATGGATTTCAACTTCACGACGAAGGATATCCAGCTCAAAGACCAATTTAGAAAAACA
ATTCTTGGATTTCAACTTCACAACGAAGAATATCATGCCCACAAGTAGCAATACA
Found at i:456205 original size:84 final size:84
Alignment explanation
Indices: 456058--456381 Score: 488
Period size: 84 Copynumber: 3.9 Consensus size: 84
456048 TCCCCAGCCT
* * * * *
456058 ATTTACAGCATAGATCAAGGAAAGAA-AGGTCATCTGCCAACAAAAGACCTTCGAGTTTGATTAC
1 ATTTGCAGCATAGCTCAAGGCAAGAAGAGCT-ATCTGCCAACAAAAGACCTTCGAGTTCGATTAC
456122 ACTCAGCTCAAAGGCACATC
65 ACTCAGCTCAAAGGCACATC
* * * *
456142 ATTTGCAGCATAGCTCAGGGCAAGAAGACCTATCTGCCAACAAAAGACCTTTGAGTTCAATTACA
1 ATTTGCAGCATAGCTCAAGGCAAGAAGAGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
456207 CTCAGCTCAAAGGCACATC
66 CTCAGCTCAAAGGCACATC
* * *
456226 ATTTGCAGCATAGCTCAAGGCGAGAAGAGCTATCTTCCAACAAAAGAGCTTCGAGTTCGATTACA
1 ATTTGCAGCATAGCTCAAGGCAAGAAGAGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
456291 CTCAGCTCAAAGGCACATC
66 CTCAGCTCAAAGGCACATC
* * *
456310 ATTTGCAACATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAGCTCAAGGCAAGAAGAGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
*
456375 TTCAGCT
66 CTCAGCT
456382 TAAGGCCATG
Statistics
Matches: 217, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
84 215 0.99
85 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (84 bp):
ATTTGCAGCATAGCTCAAGGCAAGAAGAGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
CTCAGCTCAAAGGCACATC
Found at i:457127 original size:3 final size:3
Alignment explanation
Indices: 457119--457149 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
457109 TAAAGTAAAT
457119 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
457150 AAAAATAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:457893 original size:112 final size:111
Alignment explanation
Indices: 457308--458089 Score: 932
Period size: 112 Copynumber: 7.1 Consensus size: 111
457298 TCACTCAAGA
* * * * * *
457308 AATATCAGATAT-GGGGATGTTGATCCATTAAATTGGGGCAGACTTATTCCGCTTTCACTCTGGG
1 AATATCAGATATGGGGGA-GTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCAGGG
* * * **
457372 AATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTC--AAAAGGG
65 AATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGG
* ** * * * *
457417 GATATCAGATATGGGGGAGTTGATTTATTGAATAGGGGCAGACTTGTTTCGCTGTCACTCAGTGA
1 AATATCAGATATGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCAGGGA
* *
457482 ATATCAAATCTTGGAAGAGAGTGACATGTTCCGCTTCTTCTAAGGG
66 ATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGG
* * * * *
457528 AATATCAGATTTGGGAGAGATGATCCATTGAATCGGGGCAGACTTGTTCCACTGCCACTCATGGA
1 AATATCAGATATGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCAGGGA
* * *
457593 ATATCAAATATTGGAAGAGAGTG-TATGTTCCACTTCTTCTAAGGG
66 ATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGG
* * *
457638 AATATCAGATATGGGGGAGATGATCCATTGAATCAGGGCAGACTTGTTCCATTGTCACTCAGGGA
1 AATATCAGATATGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCAGGGA
*
457703 ATATCAAATCTT-G--GA-AGTGATATGTTCCGCTTCTTCTAAGGG
66 ATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGG
* * * * * * *
457745 GATATCAGATTTGGGGGAGTTAATCCATTGAATCGGGACATACTTGTTCCGCTGTCACTCAGTGA
1 AATATCAGATATGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCAGGGA
* * * * * *
457810 ATACCAAATCTTGGAAGAGAGGGTTTTTTTCCTCTTATTCTAAAGGG
66 ATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCT-AAGGG
* * * *
457857 AATATCAGATCTAGGGGAGTTGATCCATTGAATCGGGACAGACTTGTTTCACTGTCACTCAGGGA
1 AATATCAGATATGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCAGGGA
* * * *
457922 ATATTAAATATTGGAAGAGAGGGATCTGTTTCGCTTCTTCTAAAGGG
66 ATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCT-AAGGG
* * * * *
457969 AATATCAGATTTAGGGGAGTTGATCCATTGAATTGGGGTAGACTTGTTCCACTGTCACTAAGGGA
1 AATATCAGATATGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCAGGGA
* * *
458034 ATATCAGATCTTGGAATAGAGTGATATGTTCCGCTTCTTCTAAGGG
66 ATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGG
458080 AATATCAGAT
1 AATATCAGAT
458090 CTGTAAATTA
Statistics
Matches: 577, Mismatches: 87, Indels: 16
0.85 0.13 0.02
Matches are distributed among these distances:
106 4 0.01
107 89 0.15
108 1 0.00
109 82 0.14
110 97 0.17
111 111 0.19
112 193 0.33
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (111 bp):
AATATCAGATATGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCAGGGA
ATATCAAATCTTGGAAGAGAGGGATATGTTCCGCTTCTTCTAAGGG
Found at i:464449 original size:3 final size:3
Alignment explanation
Indices: 464441--464473 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
464431 TAAGGTAAAT
464441 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA
464474 TATATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:465292 original size:7 final size:7
Alignment explanation
Indices: 465282--465314 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
465272 AAGGGGAAAA
465282 TGGAGAT
1 TGGAGAT
465289 TGGAGAT
1 TGGAGAT
465296 TGGAGAT
1 TGGAGAT
465303 TGGAGAT
1 TGGAGAT
465310 TGGAG
1 TGGAG
465315 GACCTTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.45, T:0.27
Consensus pattern (7 bp):
TGGAGAT
Found at i:467355 original size:17 final size:17
Alignment explanation
Indices: 467333--467366 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
467323 TTCCTCTTGA
* *
467333 CTTATTTTTCTTTGTAT
1 CTTATTTGTATTTGTAT
467350 CTTATTTGTATTTGTAT
1 CTTATTTGTATTTGTAT
467367 TTTTGTTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.09, T:0.68
Consensus pattern (17 bp):
CTTATTTGTATTTGTAT
Found at i:471007 original size:23 final size:23
Alignment explanation
Indices: 470977--471025 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
470967 TGGTGGTTGG
*
470977 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGAATATTTA-ACTTTAT
*
471000 TTTAATGGAATATTTAAGTTTAT
1 TTTAATGGAATATTTAACTTTAT
471023 TTT
1 TTT
471026 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (23 bp):
TTTAATGGAATATTTAACTTTAT
Found at i:471533 original size:11 final size:11
Alignment explanation
Indices: 471517--471541 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
471507 TTCTTTTCAT
471517 TTTATTTACTG
1 TTTATTTACTG
471528 TTTATTTACTG
1 TTTATTTACTG
471539 TTT
1 TTT
471542 TTACCATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTATTTACTG
Found at i:477571 original size:17 final size:16
Alignment explanation
Indices: 477538--477573 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
477528 TAGGCTTTTC
*
477538 TTTATTTTTATTTTAT
1 TTTATTTTTAATTTAT
477554 TTTATTTTGTAATTTAT
1 TTTATTTT-TAATTTAT
477571 TTT
1 TTT
477574 TGATCTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTATTTTTAATTTAT
Found at i:481171 original size:23 final size:23
Alignment explanation
Indices: 481141--481189 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
481131 TGGTAGTTGG
*
481141 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
481164 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
481187 TTT
1 TTT
481190 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:484159 original size:56 final size:56
Alignment explanation
Indices: 484058--484163 Score: 167
Period size: 56 Copynumber: 1.9 Consensus size: 56
484048 GAGGAACATA
* *
484058 TCAAGTCTGATCTCCCCTGAAAGAAGAGTATAGCAAACCCCTCTTCCAAAGATTTC
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTAGAACAAACCCCTCTTCCAAAGATTTC
* * *
484114 TCAAGTCTGATCTCCCCTGAAAGAAGAGTGGAACAGACCCGTCTTCCAAA
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTAGAACAAACCCCTCTTCCAAA
484164 ATTGATCTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (56 bp):
TCAAGTCTGATCTCCCCTGAAAGAAGAGTAGAACAAACCCCTCTTCCAAAGATTTC
Found at i:484423 original size:56 final size:56
Alignment explanation
Indices: 484337--484481 Score: 202
Period size: 56 Copynumber: 2.6 Consensus size: 56
484327 GAAGAACATA
** * * *
484337 TCAAGTCTGATCTTGCTTGAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTC
1 TCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGCAGACCCATCGTCCAAAGAATTC
484393 TCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGCAGACCCATCGTCCAAAGAATTC
1 TCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGCAGACCCATCGTCCAAAGAATTC
* * * *
484449 TCGAGTCTTATCTCCC-TGAAAGAATAATGGAGC
1 TCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGC
484482 TCAAAATTGA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 15 0.19
56 65 0.81
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (56 bp):
TCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGCAGACCCATCGTCCAAAGAATTC
Found at i:484428 original size:138 final size:138
Alignment explanation
Indices: 483968--484442 Score: 614
Period size: 138 Copynumber: 3.4 Consensus size: 138
483958 AAATGGATCA
* * ****
483968 AAAGATTTCTCGAGTCTTATCT-CCCTGAAAGAAGAGTGGAGCAGGTTTATCTTCCAAAATTGAT
1 AAAGATTTCTCAAGTCTGATCTCCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAATTGAT
* * * * **
484032 CTGACTACCCAAAAAAGAGGAACATATCAAGTCTGATCTCCCCTGAAAGAAGAGTATAGCAAACC
66 CTGACTACCCGAATAAGAAGAACATATCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGCAAACC
*
484097 CCTCTTCC
131 CGTCTTCC
* *
484105 AAAGATTTCTCAAGTCTGATCTCCCCTGAAAGAAGAGTGGAACAGACCCGTCTTCCAAAATTGAT
1 AAAGATTTCTCAAGTCTGATCTCCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAATTGAT
* * * *
484170 CTAACTACCCG-ATAA-AAGGGAACATATCAAGTCTGATCTCCCCTGGAAAAAAAAAAGTGGAGC
66 CTGACTACCCGAATAAGAA--GAACATATCAAGTCTGATCT-CCCTTG--AAAGAAGAGTGGAGC
**
484233 AAACTTGTCTTCC
126 AAACCCGTCTTCC
* * *
484246 TAAGATTTCTCAAGTCTGATCTCCCCTGAAAGAAGAGTGAAGCAGACCCGTCTTCCAAAATTGAT
1 AAAGATTTCTCAAGTCTGATCTCCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAATTGAT
* ** *
484311 CTGACTATCCGAATAAGAAGAACATATCAAGTCTGATCTTGCTTGAAAGAAGAGTGGAGCAGACC
66 CTGACTACCCGAATAAGAAGAACATATCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGCAAACC
484376 CGTCTTCC
131 CGTCTTCC
* *
484384 AAAGATTTCTCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGCAGACCCATCGTCCAAA
1 AAAGATTTCTCAAGTCTGATCTCCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAA
484443 GAATTCTCGA
Statistics
Matches: 291, Mismatches: 39, Indels: 15
0.84 0.11 0.04
Matches are distributed among these distances:
136 1 0.00
137 23 0.08
138 142 0.49
139 4 0.01
140 3 0.01
141 112 0.38
142 4 0.01
143 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (138 bp):
AAAGATTTCTCAAGTCTGATCTCCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAATTGAT
CTGACTACCCGAATAAGAAGAACATATCAAGTCTGATCTCCCTTGAAAGAAGAGTGGAGCAAACC
CGTCTTCC
Found at i:484710 original size:3 final size:3
Alignment explanation
Indices: 484687--484734 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
484677 GTCCATATAT
* *
484687 TTA TTT TTA TGA TTA -TA TTA TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
484732 TTA
1 TTA
484735 AATAATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:487004 original size:6 final size:6
Alignment explanation
Indices: 486993--487018 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
486983 ATTGACGTTA
486993 TTAATT TTAATT TTAATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TT
487019 TATATTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTAATT
Found at i:488624 original size:24 final size:24
Alignment explanation
Indices: 488596--488643 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
488586 TAAGATATAA
*
488596 ATTTTTTATATTTAT-AGTTATGT
1 ATTTTTTTTATTTATAAGTTATGT
* *
488619 ATTTTTTTTCTTTCTAAGTTATGT
1 ATTTTTTTTATTTATAAGTTATGT
488643 A
1 A
488644 AAATGAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (24 bp):
ATTTTTTTTATTTATAAGTTATGT
Found at i:489545 original size:116 final size:116
Alignment explanation
Indices: 489341--489688 Score: 651
Period size: 116 Copynumber: 3.0 Consensus size: 116
489331 GGAGGGAGCC
489341 AGCGTCGCCGTCTCCGGCAATAAATTGGCAGCTTCGTAGGAACTGCTCAGGGTTTCAAAAAACGG
1 AGCGTCGCCGTCTCCGGCAATAAATTGGCAGCTTCGTAGGAACTGCTCAGGGTTTCAAAAAACGG
*
489406 ACCGCGACCGCGATTTCGTCCGCGATATAGCGGTTTTGCCGTTGTCCGAGT
66 ACCGCGACCGCGATTTCGTCCGCGATATAGCGGTTTCGCCGTTGTCCGAGT
* *
489457 AGCGTCGCCGTTTCCGGCAATAAATTGGCAGTTTCGTAGGAACTGCTCAGGGTTTCAAAAAACGG
1 AGCGTCGCCGTCTCCGGCAATAAATTGGCAGCTTCGTAGGAACTGCTCAGGGTTTCAAAAAACGG
489522 ACCGCGACCGCGATTTCGTCCGCGATATAGCGGTTTCGCCGTTGTCCGAGT
66 ACCGCGACCGCGATTTCGTCCGCGATATAGCGGTTTCGCCGTTGTCCGAGT
*
489573 AGCGTCGCCGTCTCCGGCAATAAATTGGCAGCTTCGTAGGAACTGCTCAGGGTTTCAAAAAACAG
1 AGCGTCGCCGTCTCCGGCAATAAATTGGCAGCTTCGTAGGAACTGCTCAGGGTTTCAAAAAACGG
*
489638 ACCGCGACCGCGATTTCGTCCGCGATATAACGGTTTCGCCGTTGTCCGAGT
66 ACCGCGACCGCGATTTCGTCCGCGATATAGCGGTTTCGCCGTTGTCCGAGT
489689 TACCCGCGAC
Statistics
Matches: 225, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 225 1.00
ACGTcount: A:0.21, C:0.27, G:0.28, T:0.24
Consensus pattern (116 bp):
AGCGTCGCCGTCTCCGGCAATAAATTGGCAGCTTCGTAGGAACTGCTCAGGGTTTCAAAAAACGG
ACCGCGACCGCGATTTCGTCCGCGATATAGCGGTTTCGCCGTTGTCCGAGT
Found at i:489718 original size:21 final size:21
Alignment explanation
Indices: 489692--489766 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
489682 TCCGAGTTAC
489692 CCGCGACGGCCGTAATAGCGT
1 CCGCGACGGCCGTAATAGCGT
489713 CCGCGACGGCCGTAATAGCGT
1 CCGCGACGGCCGTAATAGCGT
** * *
489734 CCGCGACGATCGCAATAGCGC
1 CCGCGACGGCCGTAATAGCGT
*
489755 CCGTGACGGCCG
1 CCGCGACGGCCG
489767 CAATCACGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.19, C:0.36, G:0.33, T:0.12
Consensus pattern (21 bp):
CCGCGACGGCCGTAATAGCGT
Found at i:491493 original size:18 final size:18
Alignment explanation
Indices: 491449--491496 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
491439 TTTTAAAAGA
* *
491449 AAATATATAAATATTTTTC
1 AAATATAT-AATATTATAC
*
491468 AACT-TATAATATTATAC
1 AAATATATAATATTATAC
491485 AAATATATAATA
1 AAATATATAATA
491497 AGGACAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 11 0.46
18 10 0.42
19 3 0.12
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:492132 original size:20 final size:21
Alignment explanation
Indices: 492107--492158 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
492097 TTTTCCCAAT
*
492107 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
492127 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
492148 TCGCAATGCGA
1 TCGCAATGCGA
492159 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:492237 original size:20 final size:20
Alignment explanation
Indices: 492189--492237 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
492179 TAATACAAAA
*
492189 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
492209 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
492229 TCGCAACGC
1 TCGCAACGC
492238 AATAATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:492457 original size:22 final size:22
Alignment explanation
Indices: 492429--492472 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
492419 CACTCTCTCA
492429 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
492451 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
492473 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:492760 original size:20 final size:20
Alignment explanation
Indices: 492735--492783 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
492725 GCGATTCTCT
492735 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
492755 CGTTGCGGTAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
492775 TGTTGCGAT
1 CGTTGCGAT
492784 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:492984 original size:25 final size:24
Alignment explanation
Indices: 492930--492984 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
492920 TGTTTATTAT
* *
492930 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
492954 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
492980 TGTTT
1 TGTTT
492985 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:494134 original size:18 final size:18
Alignment explanation
Indices: 494113--494157 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
494103 TCCACTTCGG
*
494113 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
494131 GAGCTATCACCTCACTCA
1 GAGCCATCACCTCACCCA
494149 GAGCCATCA
1 GAGCCATCA
494158 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:494673 original size:20 final size:19
Alignment explanation
Indices: 494650--494727 Score: 76
Period size: 20 Copynumber: 4.3 Consensus size: 19
494640 CGCAACACGA
494650 AAATGACTATCGCAATGCAG
1 AAATGACTATCGCAATGC-G
*
494670 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
**
494689 AAATGAAAATCGCAA--CG
1 AAATGACTATCGCAATGCG
*
494706 AAA--A-AATCGCAATGCG
1 AAATGACTATCGCAATGCG
494722 AAATGA
1 AAATGA
494728 AATCGCAACG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 8 0.16
15 1 0.02
16 5 0.10
17 5 0.10
18 1 0.02
19 13 0.26
20 17 0.34
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.17
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:494700 original size:19 final size:19
Alignment explanation
Indices: 494658--494773 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
494648 GAAAATGACT
***
494658 ATCGCAATGCAGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
494678 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
494697 ATCGCAA--CG-AA--AAA
1 ATCGCAATGCGAAATGAAA
494711 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
494729 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
494743 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
494762 ATCGCAATGCGA
1 ATCGCAATGCGA
494774 TTTTCATTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.25
16 8 0.10
17 4 0.05
18 10 0.13
19 27 0.34
20 10 0.13
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:494713 original size:14 final size:14
Alignment explanation
Indices: 494694--494751 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
494684 ATGCGAAATG
494694 AAAATCGCAACGAA
1 AAAATCGCAACGAA
494708 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
*
494724 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
494740 AAAATCGCAACG
1 AAAATCGCAACG
494752 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:494736 original size:32 final size:33
Alignment explanation
Indices: 494678--494768 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
494668 AGAAATGGCT
494678 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
494711 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
494743 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
494769 TGCGATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:494804 original size:14 final size:14
Alignment explanation
Indices: 494785--494875 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
494775 TTTCATTTCG
*
494785 CGTTGCGATTTTGT
1 CGTTGCGATTTTTT
494799 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
494815 CGCATTGCGATTTTTT
1 CG--TTGCGATTTTTT
494831 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
*
494848 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
494864 CGTTGCGATTTT
1 CGTTGCGATTTT
494876 CATTTCGCAT
Statistics
Matches: 66, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
14 27 0.41
15 3 0.05
16 13 0.20
17 5 0.08
18 12 0.18
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:494845 original size:65 final size:66
Alignment explanation
Indices: 494769--494891 Score: 230
Period size: 65 Copynumber: 1.9 Consensus size: 66
494759 AAAATCGCAA
*
494769 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCATTTCGCATTGCGATTTTTTCG
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTTTCG
494833 T
66 T
494834 TGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
494892 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 37 0.66
66 19 0.34
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (66 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTTTCG
T
Found at i:494849 original size:33 final size:33
Alignment explanation
Indices: 494769--494891 Score: 221
Period size: 33 Copynumber: 3.8 Consensus size: 33
494759 AAAATCGCAA
*
494769 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
*
494802 TGCGA-TTTCATTTCGCATTGCGATTTTTTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
494834 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
494867 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
494892 AGCCATTTCC
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 30 0.35
33 56 0.65
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
Found at i:494910 original size:20 final size:19
Alignment explanation
Indices: 494876--494931 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
494866 TTGCGATTTT
*
494876 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
494895 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
494915 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
494932 TTTAAGTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:495396 original size:42 final size:42
Alignment explanation
Indices: 495299--495387 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
495289 GACTCACCTG
* * *
495299 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
* * *
495341 TCCTCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
495383 TCATC
1 TCATC
495388 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.44, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:496825 original size:14 final size:14
Alignment explanation
Indices: 496806--496841 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
496796 ATTGTTTAAT
496806 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
496820 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
496834 TGATTTGT
1 TGATTTGT
496842 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:496987 original size:14 final size:14
Alignment explanation
Indices: 496968--497002 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
496958 GAAACTGACT
496968 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
496982 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
496996 ATCGCAA
1 ATCGCAA
497003 TGCGATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:497051 original size:20 final size:20
Alignment explanation
Indices: 497026--497101 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
497016 TCGCATTACG
*
497026 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
497046 ATTTTCGTGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
497067 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
497086 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
497102 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.43
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:497340 original size:20 final size:20
Alignment explanation
Indices: 497315--497406 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
497305 TTGAAGATGA
497315 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
497335 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* * **
497355 TTACGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** ** *
497376 TTGCGATAGTCAGTGTCGCG
1 TTGCGATTTTCAGAATCTCG
497396 TTGCGATTTTC
1 TTGCGATTTTC
497407 CTAATTCGCA
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:498234 original size:24 final size:24
Alignment explanation
Indices: 498207--498260 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
498197 GTATTCAAAA
*
498207 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
498231 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
498255 TTTGAT
1 TTTGAT
498261 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:498452 original size:12 final size:12
Alignment explanation
Indices: 498435--498459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
498425 ATATAATCCT
498435 GAAGAAGAAAAA
1 GAAGAAGAAAAA
498447 GAAGAAGAAAAA
1 GAAGAAGAAAAA
498459 G
1 G
498460 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:500775 original size:19 final size:19
Alignment explanation
Indices: 500753--500844 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
500743 GGAAATTACT
500753 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
500772 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
500786 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
500805 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
500819 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
500838 ATCGCAA
1 ATCGCAA
500845 CGAGGGAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 18 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 25 0.45
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:500795 original size:33 final size:33
Alignment explanation
Indices: 500753--500866 Score: 176
Period size: 33 Copynumber: 3.5 Consensus size: 33
500743 GGAAATTACT
500753 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
500786 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
500818 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
500852 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
500867 TATTTCGCAT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.01
33 70 0.97
34 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:500895 original size:14 final size:14
Alignment explanation
Indices: 500876--500911 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
500866 TTATTTCGCA
500876 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
500890 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
500904 TTACGATT
1 TTGCGATT
500912 TTCATTTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:501055 original size:14 final size:14
Alignment explanation
Indices: 501036--501072 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
501026 CATCAATTAA
501036 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
501050 ACAAATCACCTTTT
1 ACAAATCAACTTTT
501064 ACAAATCAA
1 ACAAATCAA
501073 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:502495 original size:21 final size:20
Alignment explanation
Indices: 502429--502495 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
502419 GTGAATCGGG
*
502429 CTCTTGAATGGTGGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
* * ** *
502449 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAG-GGA
502471 CTCTTGAACGGTGGGAGAGGA
1 CTCTTGAACGGTGGGAG-GGA
502492 CTCT
1 CTCT
502496 CGAGAAATGA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGA
Found at i:502514 original size:42 final size:42
Alignment explanation
Indices: 502468--502631 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 42
502458 CGATGACAGT
* * * * *
502468 GGCCTCTTGAACGGTGGGAGAGGACTCTCGAGAAATGATAGG
1 GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGATAGG
* * * *
502510 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGT
1 GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGATAGG
* * * *
502552 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGATAGG
* *
502594 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGA
502632 CAGGAGAGTC
Statistics
Matches: 99, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 99 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGATAGG
Found at i:502570 original size:84 final size:84
Alignment explanation
Indices: 502459--502634 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
502449 CCTCTTCAAC
502459 GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGAAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGAAATGATAGGGGCCTCTTCAACGA
502524 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
* *
502543 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGAAATGATAGGGGCCTCTTCAACGA
502608 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
502627 GATGACAG
1 GATGACAG
502635 GAGAGTCAGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGAAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:503029 original size:91 final size:90
Alignment explanation
Indices: 502853--503037 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
502843 ATTTCAAACT
*
502853 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
502918 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAACAACCGAATAAATTTAC
502946 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
503010 GTATTGGCAACAACCGAATAAATTTAC
64 GAATTGGCAACAACCGAATAAATTTAC
503037 T
1 T
503038 ATGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAACAACCGAATAAATTTAC
Found at i:504806 original size:33 final size:33
Alignment explanation
Indices: 504749--504836 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
504739 ACGAGATAAT
504749 GAGAATCGCAACGCAGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
504783 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
504816 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
504837 AAATCCCAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:504841 original size:19 final size:19
Alignment explanation
Indices: 504724--504907 Score: 181
Period size: 19 Copynumber: 10.1 Consensus size: 19
504714 TCTTTTGGTT
*
504724 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
504743 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
504763 AGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
504781 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
504797 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
504814 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
504830 GAAATGAAAATCCCAACGC
1 GAAATGAAAATCGCAACGC
504849 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
504868 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
504887 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
504906 GA
1 GA
504908 TTTTGGTTTT
Statistics
Matches: 137, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
14 17 0.12
15 2 0.01
16 4 0.03
17 3 0.02
18 3 0.02
19 79 0.58
20 27 0.20
21 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:504939 original size:18 final size:19
Alignment explanation
Indices: 504903--504946 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
504893 AAAATCGCAA
* *
504903 TGCGATTTTGGTTTTGCG-
1 TGCGATTTTGATTTCGCGT
*
504921 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
504940 TGCGATT
1 TGCGATT
504947 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.09, C:0.14, G:0.27, T:0.50
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:505567 original size:40 final size:40
Alignment explanation
Indices: 505523--505598 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
505513 GAAAGTCAAA
* * *
505523 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTAT
*
505563 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
505599 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTAT
Found at i:505585 original size:20 final size:20
Alignment explanation
Indices: 505503--505595 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
505493 CGCTATGTAA
* **
505503 ATCGCGTTGCGAAAGTCAAA
1 ATCGCGTTGCGATAGTCAGT
*
505523 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
505543 ATCTCGTTGCGATTTTGT-A-T
1 ATCGCGTTGCGA--TAGTCAGT
*
505563 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
505583 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
505596 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.05
19 1 0.02
20 54 0.89
21 1 0.02
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:505775 original size:28 final size:28
Alignment explanation
Indices: 505707--505775 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
505697 GAAATGCAAC
* *
505707 GCGAATTTGCGAAAATGGAGATCGCGTT
1 GCGAATTAGCGATAATGGAGATCGCGTT
505735 GCGAATTAGCGATAATGGAGATCGCGTT
1 GCGAATTAGCGATAATGGAGATCGCGTT
505763 GCGAATTAGCGAT
1 GCGAATTAGCGAT
505776 CGCATTGCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (28 bp):
GCGAATTAGCGATAATGGAGATCGCGTT
Found at i:512810 original size:23 final size:23
Alignment explanation
Indices: 512783--512858 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
512773 GAGTCGAGGG
*
512783 TTCTATGCGGTCATTCGGGACAA
1 TTCTACGCGGTCATTCGGGACAA
* * *
512806 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCATTCGGGACAA
* *
512829 TTCTACGCGGTCCGTT-GGGACAT
1 TTCTACGCGGT-CATTCGGGACAA
512852 TTCTACG
1 TTCTACG
512859 TGGCACTTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 43 0.93
24 3 0.07
ACGTcount: A:0.16, C:0.25, G:0.26, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCATTCGGGACAA
Found at i:512884 original size:24 final size:23
Alignment explanation
Indices: 512852--512908 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 23
512842 GTTGGGACAT
512852 TTCTACGTGGCACTTCGGTGCATA
1 TTCTACGTGGCACTTCGGTGCA-A
*
512876 TTCTACGTGGTACTTCGGTGCAA
1 TTCTACGTGGCACTTCGGTGCAA
*
512899 TTCTATGTGG
1 TTCTACGTGG
512909 AAGTTTCGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 10 0.32
24 21 0.68
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (23 bp):
TTCTACGTGGCACTTCGGTGCAA
Found at i:518169 original size:15 final size:15
Alignment explanation
Indices: 518149--518191 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
518139 AAGGAGTAGC
518149 ATCGATACCAATGGT
1 ATCGATACCAATGGT
518164 ATCGATACCAATGGT
1 ATCGATACCAATGGT
*
518179 ATCGATACTAATG
1 ATCGATACCAATG
518192 AACAAGTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (15 bp):
ATCGATACCAATGGT
Found at i:518650 original size:21 final size:21
Alignment explanation
Indices: 518607--518650 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
518597 TTAAAGTTTA
* *
518607 TTACATGATATGATTACATGT
1 TTACATGATATAAGTACATGT
518628 TTACATGAATATAAGTACA-GT
1 TTACATG-ATATAAGTACATGT
518649 TT
1 TT
518651 TGATTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (21 bp):
TTACATGATATAAGTACATGT
Found at i:518876 original size:23 final size:23
Alignment explanation
Indices: 518820--518944 Score: 133
Period size: 23 Copynumber: 5.4 Consensus size: 23
518810 GAGTCGAGGG
** * *
518820 TTCTACGCAGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGACAT
* *
518843 TTCTACGTGGTCGTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* *
518866 TTTTACGTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* *
518889 TTCTACGCGATCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
** *
518912 TTCTATATGGTCCTTCGGAACAT
1 TTCTACGTGGTCCTTCGGGACAT
518935 TTCTACGTGG
1 TTCTACGTGG
518945 AACTTTGGTG
Statistics
Matches: 81, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:518935 original size:69 final size:70
Alignment explanation
Indices: 518820--518987 Score: 184
Period size: 69 Copynumber: 2.4 Consensus size: 70
518810 GAGTCGAGGG
* * * * **
518820 TTCTACGC-AGTCCTTCGGGATAATTCTACGTGGTCGTTCAGGACATTTTTACGTGGTCCTTTGG
1 TTCTACGCGA-TCCTTCGGGACAATTCTACATGGTCCTTCAGGACATTTCTACGTGGAACTTTGG
518884 -GACAT-
65 TG-CATA
* *
518889 TTCTACGCGATCCTTCGGGACATTTCTATATGGTCCTTC-GGAACATTTCTACGTGGAACTTTGG
1 TTCTACGCGATCCTTCGGGACAATTCTACATGGTCCTTCAGG-ACATTTCTACGTGGAACTTTGG
518953 TGCATA
65 TGCATA
*
518959 TTCTACGCG-TCACTTCGGTACAATTCTAC
1 TTCTACGCGATC-CTTCGGGACAATTCTAC
518988 CCAGTACACA
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
68 2 0.02
69 56 0.67
70 25 0.30
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (70 bp):
TTCTACGCGATCCTTCGGGACAATTCTACATGGTCCTTCAGGACATTTCTACGTGGAACTTTGGT
GCATA
Found at i:523296 original size:9 final size:9
Alignment explanation
Indices: 523282--523353 Score: 60
Period size: 9 Copynumber: 7.7 Consensus size: 9
523272 AACAATGTAT
523282 GAAACAGAG
1 GAAACAGAG
523291 GAAACAG-G
1 GAAACAGAG
523299 CTGAAACAGAG
1 --GAAACAGAG
523310 GAAACAG-G
1 GAAACAGAG
523318 CTGAAACAGAG
1 --GAAACAGAG
523329 GAAACAG-G
1 GAAACAGAG
*
523337 CTAAAGCAGAG
1 -GAAA-CAGAG
523348 GAAACA
1 GAAACA
523354 AGCTAAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
8 3 0.06
9 26 0.50
10 20 0.38
11 3 0.06
ACGTcount: A:0.50, C:0.15, G:0.31, T:0.04
Consensus pattern (9 bp):
GAAACAGAG
Found at i:523360 original size:19 final size:19
Alignment explanation
Indices: 523281--523353 Score: 130
Period size: 19 Copynumber: 3.8 Consensus size: 19
523271 GAACAATGTA
523281 TGAAACAGAGGAAACAGGC
1 TGAAACAGAGGAAACAGGC
523300 TGAAACAGAGGAAACAGGC
1 TGAAACAGAGGAAACAGGC
523319 TGAAACAGAGGAAACAGGC
1 TGAAACAGAGGAAACAGGC
523338 T-AAAGCAGAGGAAACA
1 TGAAA-CAGAGGAAACA
523354 AGCTAAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
18 3 0.06
19 50 0.94
ACGTcount: A:0.49, C:0.15, G:0.30, T:0.05
Consensus pattern (19 bp):
TGAAACAGAGGAAACAGGC
Found at i:525515 original size:19 final size:19
Alignment explanation
Indices: 525479--525517 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
525469 TCACTATAAT
*
525479 TAAAATTTATAACTAAAAA
1 TAAAATTTATAACAAAAAA
525498 TAAAATTTATTAA-AAAAAA
1 TAAAATTTA-TAACAAAAAA
525517 T
1 T
525518 TGAATCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTTATAACAAAAAA
Found at i:528766 original size:20 final size:20
Alignment explanation
Indices: 528720--528767 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
528710 AGTTAGTGGC
* ** *
528720 ATTGATACCTAGAGGTTAGT
1 ATTGATACCTAAAGGCCAAT
*
528740 ATCGATACCTAAAGGCCAAT
1 ATTGATACCTAAAGGCCAAT
528760 ATTGATAC
1 ATTGATAC
528768 TGAGGGGCTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (20 bp):
ATTGATACCTAAAGGCCAAT
Found at i:536506 original size:24 final size:24
Alignment explanation
Indices: 536462--536507 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
536452 TTTTAATAAT
**
536462 AAAAATATTTTTTTTTCAAAAAAG
1 AAAAATATTTTTTTTAAAAAAAAG
536486 AAAAATATTTTTTTTAAAAAAA
1 AAAAATATTTTTTTTAAAAAAA
536508 TCAGACCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAAATATTTTTTTTAAAAAAAAG
Found at i:540198 original size:12 final size:12
Alignment explanation
Indices: 540181--540224 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
540171 GTTATCATGA
*
540181 ACATCACCGTGC
1 ACATCATCGTGC
* *
540193 ACATCATCTTGA
1 ACATCATCGTGC
540205 ACATCATCGTGC
1 ACATCATCGTGC
540217 ACATCATC
1 ACATCATC
540225 TTGAATAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (12 bp):
ACATCATCGTGC
Found at i:540206 original size:24 final size:24
Alignment explanation
Indices: 540178--540229 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
540168 TTGGTTATCA
540178 TGAACATCACCGTGCACATCATCT
1 TGAACATCACCGTGCACATCATCT
*
540202 TGAACATCATCGTGCACATCATCT
1 TGAACATCACCGTGCACATCATCT
540226 TGAA
1 TGAA
540230 TAAGATCTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (24 bp):
TGAACATCACCGTGCACATCATCT
Found at i:541970 original size:20 final size:20
Alignment explanation
Indices: 541942--541987 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
541932 CTGTTCGAGG
*
541942 CAACTCGAACAAGCCTAAGT
1 CAACCCGAACAAGCCTAAGT
*
541962 CAACCCGAACCAGCCTAAGT
1 CAACCCGAACAAGCCTAAGT
541982 CAACCC
1 CAACCC
541988 AAAATGATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.39, G:0.13, T:0.11
Consensus pattern (20 bp):
CAACCCGAACAAGCCTAAGT
Found at i:546706 original size:115 final size:115
Alignment explanation
Indices: 546500--546730 Score: 444
Period size: 115 Copynumber: 2.0 Consensus size: 115
546490 AGCATTGTCC
546500 TCAATGCTTACTAAAACTAAGGAAAATGAAATTATATGCTATGAATGCAATGCAAGGTACCTTGT
1 TCAATGCTTACTAAAACTAAGGAAAATGAAATTATATGCTATGAATGCAATGCAAGGTACCTTGT
546565 CTTCATGCAGGTGGTGGTGCAACGGTCACATGACGGGTGCGCTTTCTCAG
66 CTTCATGCAGGTGGTGGTGCAACGGTCACATGACGGGTGCGCTTTCTCAG
546615 TCAATGCTTACTAAAACTAAGGAAAATGAAATTATATGCTATGAATGCAATGCAAGGTACCTTGT
1 TCAATGCTTACTAAAACTAAGGAAAATGAAATTATATGCTATGAATGCAATGCAAGGTACCTTGT
* *
546680 CTTCATGCAGGTGGTGGTGCAGCGGTCACATGACGGGTGTGCTTTCTCAG
66 CTTCATGCAGGTGGTGGTGCAACGGTCACATGACGGGTGCGCTTTCTCAG
546730 T
1 T
546731 TTTACGGGGC
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (115 bp):
TCAATGCTTACTAAAACTAAGGAAAATGAAATTATATGCTATGAATGCAATGCAAGGTACCTTGT
CTTCATGCAGGTGGTGGTGCAACGGTCACATGACGGGTGCGCTTTCTCAG
Found at i:555021 original size:21 final size:21
Alignment explanation
Indices: 554997--555038 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
554987 TCTCCTAAAG
554997 AAAGGCTACTCTCGCAGCTCC
1 AAAGGCTACTCTCGCAGCTCC
*
555018 AAAGGCTACTCTCGTAGCTCC
1 AAAGGCTACTCTCGCAGCTCC
555039 TACAACCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AAAGGCTACTCTCGCAGCTCC
Found at i:556265 original size:31 final size:31
Alignment explanation
Indices: 556173--556280 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
556163 AAGTATTCCC
* * *
556173 TTGGGTAGGCTCTCAGACCCCAAGGTACTTTCT
1 TTGGGTAGGCTCTAAGGCCCCAAGGTA--TTCA
* * *
556206 TTGGGTATGCTCTGAGGCTCCAAGGTATTCA
1 TTGGGTAGGCTCTAAGGCCCCAAGGTATTCA
* * *
556237 TTGGGTAGGTTCTAAGGCCCCAATGTATTTCC
1 TTGGGTAGGCTCTAAGGCCCCAAGGTA-TTCA
*
556269 TTAGGTAGGCTC
1 TTGGGTAGGCTC
556281 ACACTTTTGG
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
31 25 0.41
32 13 0.21
33 23 0.38
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (31 bp):
TTGGGTAGGCTCTAAGGCCCCAAGGTATTCA
Found at i:560906 original size:31 final size:32
Alignment explanation
Indices: 560832--560944 Score: 174
Period size: 31 Copynumber: 3.5 Consensus size: 32
560822 CCCCGAGATG
* *
560832 TTCCCTTGGGTGGGCTCTAAGGCCCCAAGGTGC
1 TTCCCTTGGGTAGGCTCTAAGGCCCCAAGGT-A
*
560865 TTCCCTTGGGTAGGCTCTAGGGCCCCAAGGTA
1 TTCCCTTGGGTAGGCTCTAAGGCCCCAAGGTA
560897 TT-CCTTGGGTAGGCTCTAAGGCCCCAAGGTA
1 TTCCCTTGGGTAGGCTCTAAGGCCCCAAGGTA
*
560928 TTCCCTTAGGTAGGCTC
1 TTCCCTTGGGTAGGCTC
560945 ACACTTTTAG
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 30 0.41
32 15 0.20
33 29 0.39
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (32 bp):
TTCCCTTGGGTAGGCTCTAAGGCCCCAAGGTA
Found at i:562565 original size:21 final size:21
Alignment explanation
Indices: 562541--562588 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
562531 TTGGCTTTTA
562541 TCTCTACCCTTGTCATCTTTG
1 TCTCTACCCTTGTCATCTTTG
562562 TCTCTACCCTTGTCATCTTTG
1 TCTCTACCCTTGTCATCTTTG
562583 TCTCTA
1 TCTCTA
562589 TTTCTCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.10, C:0.33, G:0.08, T:0.48
Consensus pattern (21 bp):
TCTCTACCCTTGTCATCTTTG
Found at i:563512 original size:21 final size:22
Alignment explanation
Indices: 563488--563532 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
563478 TTTTATTCGT
563488 TTTAAATAGC-TATT-TGTTAAA
1 TTTAAATA-CTTATTATGTTAAA
*
563509 TTTATATACTTATTATGTTAAA
1 TTTAAATACTTATTATGTTAAA
563531 TT
1 TT
563533 ATGTCCATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 11 0.52
22 9 0.43
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (22 bp):
TTTAAATACTTATTATGTTAAA
Found at i:567959 original size:20 final size:20
Alignment explanation
Indices: 567934--567971 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
567924 AAAAGCTTCA
567934 TTTAGTCGACTCTGAATTCC
1 TTTAGTCGACTCTGAATTCC
*
567954 TTTAGTTGACTCTGAATT
1 TTTAGTCGACTCTGAATT
567972 AATCAGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (20 bp):
TTTAGTCGACTCTGAATTCC
Found at i:575371 original size:22 final size:21
Alignment explanation
Indices: 575317--575371 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 21
575307 ATAGTCGCAA
* *
575317 TGGTATCGATACTCATCTTTG
1 TGGTATTGATACTCATCTCTG
*
575338 -GGTATT-AGTACTCCTCTCCTG
1 TGGTATTGA-TACTCATCT-CTG
575359 TGGTATTGATACT
1 TGGTATTGATACT
575372 TCCCCAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.04
20 13 0.48
21 2 0.07
22 10 0.37
23 1 0.04
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (21 bp):
TGGTATTGATACTCATCTCTG
Found at i:575649 original size:20 final size:22
Alignment explanation
Indices: 575612--575666 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
575602 TCAAGGTCAC
575612 GAGTATCGATAC-CACTTGA-G
1 GAGTATCGATACTCACTTGATG
*
575632 TAGTATCGATACTC-CTTGATG
1 GAGTATCGATACTCACTTGATG
*
575653 GGGTATCGATACTC
1 GAGTATCGATACTC
575667 TCCTTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (22 bp):
GAGTATCGATACTCACTTGATG
Found at i:576790 original size:2 final size:2
Alignment explanation
Indices: 576783--576818 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
576773 GGCATCGACA
576783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
576819 CAAGGATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:580861 original size:2 final size:2
Alignment explanation
Indices: 580856--580894 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
580846 AACATTGTAA
580856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
580895 AATGGCCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:586669 original size:2 final size:2
Alignment explanation
Indices: 586662--586696 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
586652 ATAACCATTA
586662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
586697 ATAATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:587186 original size:14 final size:14
Alignment explanation
Indices: 587162--587240 Score: 85
Period size: 14 Copynumber: 5.9 Consensus size: 14
587152 TTGGTAATAT
*
587162 GTTCTTTTATGTTC
1 GTTCGTTTATGTTC
* *
587176 ATTCATTTATGTTC
1 GTTCGTTTATGTTC
587190 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
587204 GTTCGTTTA--TT-
1 GTTCGTTTATGTTC
*
587215 -TTCGTTTATGTAC
1 GTTCGTTTATGTTC
*
587228 GTTCATTTATGTT
1 GTTCGTTTATGTT
587241 TAGCCTAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
10 8 0.15
12 3 0.06
14 43 0.80
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:587202 original size:28 final size:27
Alignment explanation
Indices: 587161--587240 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 27
587151 TTTGGTAATA
* *
587161 TGTTCTTTTATGTTCATTCATTTATGT
1 TGTTCGTTTATGTTCGTTCATTTATGT
*
587188 TCGTTCGTTTATGTTCGTTCGTTTA--T
1 T-GTTCGTTTATGTTCGTTCATTTATGT
*
587214 T-TTCGTTTATGTACGTTCATTTATGT
1 TGTTCGTTTATGTTCGTTCATTTATGT
587240 T
1 T
587241 TAGCCTAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 20 0.44
26 4 0.09
27 1 0.02
28 20 0.44
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.60
Consensus pattern (27 bp):
TGTTCGTTTATGTTCGTTCATTTATGT
Found at i:587434 original size:10 final size:10
Alignment explanation
Indices: 587412--587453 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
587402 GAAACAAAAA
*
587412 TTATTTTCAT
1 TTATGTTCAT
*
587422 TTATGTTCGT
1 TTATGTTCAT
*
587432 TTACGTTCAT
1 TTATGTTCAT
587442 TTATGTTCAT
1 TTATGTTCAT
587452 TT
1 TT
587454 CTTGTGCTCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.62
Consensus pattern (10 bp):
TTATGTTCAT
Found at i:587524 original size:23 final size:23
Alignment explanation
Indices: 587436--587524 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 23
587426 GTTCGTTTAC
*
587436 GTTCATTTATGTTCATTTCTTGT
1 GTTCATTTATGTTCATTTATTGT
* * ** * *
587459 GCTCGTTTACATTCGTTCATTTGT
1 GTTCATTTATGTTCATTTA-TTGT
**
587483 GTTCATTTATGTTTGTTTATTGT
1 GTTCATTTATGTTCATTTATTGT
*
587506 GTTCGTTTATGTTCATTTA
1 GTTCATTTATGTTCATTTA
587525 CATCCGTTCG
Statistics
Matches: 49, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
23 32 0.65
24 17 0.35
ACGTcount: A:0.13, C:0.12, G:0.16, T:0.58
Consensus pattern (23 bp):
GTTCATTTATGTTCATTTATTGT
Found at i:587851 original size:18 final size:18
Alignment explanation
Indices: 587825--587864 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
587815 AATATATATC
*
587825 TTAACTTAAATTCAAATA
1 TTAAATTAAATTCAAATA
*
587843 TTAAATTAAATTCACATA
1 TTAAATTAAATTCAAATA
587861 TTAA
1 TTAA
587865 TTTTCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAATTAAATTCAAATA
Found at i:587910 original size:30 final size:29
Alignment explanation
Indices: 587870--588114 Score: 217
Period size: 30 Copynumber: 8.1 Consensus size: 29
587860 ATTAATTTTC
587870 AAAAAGTATATTTTATTTTTATCTTTAACTT
1 AAAAA-TATATTTTATTTTTATC-TTAACTT
* *
587901 AAAAATATATATTATTTTTATTTTAACTT
1 AAAAATATATTTTATTTTTATCTTAACTT
* *
587930 AAAAAGTATATTTTATTTCTAACTTAACTT
1 AAAAA-TATATTTTATTTTTATCTTAACTT
* * *
587960 AAAAAATATTTTTTATTTTAATAGAGCTCAACTTT
1 -AAAAATATATTTTATTTT--T--ATCTTAAC-TT
*
587995 AAAAATAT-TTTTATTTTTATCTTACATTT
1 AAAAATATATTTTATTTTTATCTTA-ACTT
** * *
588024 CTAAATATATTTTATTCTTATCTTAATTT
1 AAAAATATATTTTATTTTTATCTTAACTT
* *
588053 AAAAAATATATGTTATTCTTATCTTAATCTT
1 -AAAAATATATTTTATTTTTATCTTAA-CTT
* *
588084 -TAAAT-TATTTTATTTTTATCTTAATTT
1 AAAAATATATTTTATTTTTATCTTAACTT
588111 AAAA
1 AAAA
588115 GTATCCAAAA
Statistics
Matches: 177, Mismatches: 25, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
27 2 0.01
28 19 0.11
29 32 0.18
30 85 0.48
31 13 0.07
32 1 0.01
33 9 0.05
34 14 0.08
35 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (29 bp):
AAAAATATATTTTATTTTTATCTTAACTT
Found at i:587920 original size:24 final size:25
Alignment explanation
Indices: 587888--587956 Score: 59
Period size: 29 Copynumber: 2.6 Consensus size: 25
587878 TATTTTATTT
*
587888 TTATCTTTAACTTAAAAA-TATATA
1 TTATTTTTAACTTAAAAAGTATATA
*
587912 TTATTTTTATTTTAACTTAAAAAGTATATT
1 TTA----T-TTTTAACTTAAAAAGTATATA
*
587942 TTATTTCTAACTTAA
1 TTATTTTTAACTTAA
587957 CTTAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
24 3 0.08
25 10 0.28
26 1 0.03
28 1 0.03
29 13 0.36
30 8 0.22
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (25 bp):
TTATTTTTAACTTAAAAAGTATATA
Found at i:588069 original size:93 final size:94
Alignment explanation
Indices: 587899--588069 Score: 222
Period size: 93 Copynumber: 1.8 Consensus size: 94
587889 TATCTTTAAC
*
587899 TTAAAAATATATATTATTTTTATTTTAACTTAAAAAGTATATTTTATTTCTAACTTAACTTAAAA
1 TTAAAAATATATATTATTTTTATCTTAACTTAAAAAGTATATTTTATTTCTAACTTAACTTAAAA
* *
587964 AATATTTTTTATTTTAATAGAGCTCAACT
66 AATATATGTTATTTTAATAGAGCTCAACT
* * ** * *
587993 TTAAAAATAT-TTTTATTTTTATCTTACATTTCTAAA-TATATTTTA-TTCTTATCTTAATTTAA
1 TTAAAAATATATATTATTTTTATCTTA-ACTTAAAAAGTATATTTTATTTC-TAACTTAACTTAA
588055 AAAATATATGTTATT
64 AAAATATATGTTATT
588070 CTTATCTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
92 3 0.05
93 47 0.71
94 16 0.24
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (94 bp):
TTAAAAATATATATTATTTTTATCTTAACTTAAAAAGTATATTTTATTTCTAACTTAACTTAAAA
AATATATGTTATTTTAATAGAGCTCAACT
Found at i:588093 original size:58 final size:59
Alignment explanation
Indices: 587995--588114 Score: 174
Period size: 58 Copynumber: 2.1 Consensus size: 59
587985 GCTCAACTTT
* *
587995 AAAAATATTTTTATTTTTATCTTACATTTCTAAATATATTTTATTCTTATCTTAATTTA
1 AAAAATATTGTTATTCTTATCTTACATTTCTAAATATATTTTATTCTTATCTTAATTTA
*
588054 AAAAATATATGTTATTCTTATCTTA-ATCTT-TAAAT-TATTTTATTTTTATCTTAATTTA
1 AAAAATAT-TGTTATTCTTATCTTACAT-TTCTAAATATATTTTATTCTTATCTTAATTTA
588112 AAA
1 AAA
588115 GTATCCAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
58 25 0.45
59 15 0.27
60 16 0.29
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (59 bp):
AAAAATATTGTTATTCTTATCTTACATTTCTAAATATATTTTATTCTTATCTTAATTTA
Found at i:593098 original size:12 final size:11
Alignment explanation
Indices: 593057--593291 Score: 87
Period size: 11 Copynumber: 22.0 Consensus size: 11
593047 ACATTTAATA
593057 TATTATTATA-
1 TATTATTATAT
*
593067 TAGT-TTATA-
1 TATTATTATAT
*
593076 TA-TAGTATAT
1 TATTATTATAT
593086 TACTTATTATAT
1 TA-TTATTATAT
* *
593098 TATTATTTTAG
1 TATTATTATAT
593109 TA-TATT-TA-
1 TATTATTATAT
*
593117 CATATATATATAT
1 TAT-TAT-TATAT
593130 ATATTA-TATAT
1 -TATTATTATAT
593141 TA-TATTATA-
1 TATTATTATAT
593150 TA-TATTATAT
1 TATTATTATAT
* *
593160 TAGTAATATA-
1 TATTATTATAT
*
593170 T-TTAGTATA-
1 TATTATTATAT
593179 TATTATTATTAT
1 TATTATTA-TAT
*
593191 TA-TATTATAG
1 TATTATTATAT
593201 TA-TATT-TA-
1 TATTATTATAT
593209 TATGTATTATAT
1 TAT-TATTATAT
593221 GTATATATTATAT
1 -TAT-TATTATAT
*
593234 T-TATATTTTAT
1 TAT-TATTATAT
**
593245 ATATTGGTATAT
1 -TATTATTATAT
* *
593257 GTAATA-TATAG
1 -TATTATTATAT
593268 TATTATTATTAT
1 TATTATTA-TAT
593280 TATTATTTATAT
1 TATTA-TTATAT
593292 ATATATTTTT
Statistics
Matches: 176, Mismatches: 23, Indels: 50
0.71 0.09 0.20
Matches are distributed among these distances:
8 4 0.02
9 33 0.19
10 42 0.24
11 45 0.26
12 33 0.19
13 17 0.10
14 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (11 bp):
TATTATTATAT
Found at i:593125 original size:2 final size:2
Alignment explanation
Indices: 593118--593297 Score: 87
Period size: 2 Copynumber: 98.0 Consensus size: 2
593108 GTATATTTAC
593118 AT AT AT AT AT AT AT AT -T AT AT AT -T AT AT -T AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
593156 AT AT -T AGT A- AT AT AT TT AGT AT AT AT -T AT -T AT -T AT -T AT
1 AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * *
593194 AT -T AT AGT AT AT TT AT AT GT AT -T AT AT GT AT AT AT -T AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
593234 TT AT AT -T TT AT AT AT -T GGT AT AT GT A- AT AT AT AGT AT -T AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A-T AT AT AT
*
593274 -T AT -T AT -T AT -T AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
593298 TTTTATTTAA
Statistics
Matches: 136, Mismatches: 16, Indels: 52
0.67 0.08 0.25
Matches are distributed among these distances:
1 21 0.15
2 106 0.78
3 9 0.07
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (2 bp):
AT
Found at i:593135 original size:41 final size:43
Alignment explanation
Indices: 593055--593295 Score: 171
Period size: 43 Copynumber: 5.3 Consensus size: 43
593045 ACACATTTAA
593055 TATATTATTA-TATAGTTTATATATAGTATAT-TACTTATTATATTAT
1 TATATTA-TAGTATA-TTTATATATA-TATATATA--TATTATATTAT
*
593101 TAT-TT-TAGTATATTTACATATATATATATATATTATA-TAT
1 TATATTATAGTATATTTATATATATATATATATATTATATTAT
593141 TATATTATA-TATATTATATTAGTAATATATTTAGTATATATTATTATTAT
1 TATATTATAGTATATT-TA-TA-T-ATATA--TA-TATATATTA-TATTAT
*
593191 TATATTATAGTATATTTATATGTATTATATGTATATATTATA-T-T
1 TATATTATAGTATATTTATA--TA-TATATATATATATTATATTAT
* *
593235 TATATTTTA-TATATTGGTATATGTA-ATATATAGTATTATTATTAT
1 TATATTATAGTATATT--TATATATATATATATA-TATTA-TATTAT
593280 TATTATTTATA-TATAT
1 TA-TA-TTATAGTATAT
593296 ATTTTTATTT
Statistics
Matches: 164, Mismatches: 7, Indels: 47
0.75 0.03 0.22
Matches are distributed among these distances:
40 6 0.04
41 21 0.13
42 16 0.10
43 23 0.14
44 15 0.09
45 15 0.09
46 7 0.04
47 20 0.12
48 10 0.06
49 5 0.03
50 20 0.12
51 6 0.04
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (43 bp):
TATATTATAGTATATTTATATATATATATATATATTATATTAT
Found at i:593211 original size:57 final size:57
Alignment explanation
Indices: 593063--593297 Score: 152
Period size: 58 Copynumber: 4.1 Consensus size: 57
593053 AATATATTAT
* * * *
593063 TATATAGTTTATATA-TAGTATATTA-CTTA-TTATATTATTATTTTAGTATATTTACA
1 TATATA-TATATATATTA-TATATTATATTATTTATATTATTATTGTAATATATTTACA
* *
593119 TATATATATATATATTATATATTATATTATATATATTA-TATTAGTAATATATTTA-G
1 TATATATATATATATTATATATTATATTATTTATATTATTATT-GTAATATATTTACA
*
593175 TATATAT-TAT-TATTATTATATTATAGTATATTTATATGTATTATATGT-ATATA-TTATA
1 TATATATATATATATTA-TATATTATA-T-TATTTATAT-TATTAT-TGTAATATATTTACA
* * * * * * *
593233 TTTATATTTTATATATTGGTATATGTA-A-TATATAGTATTATTATTATTAT-TATTTATA
1 TATATA-TATATATATT-ATATAT-TATATTATTTA-TATTATTATTGTAATATATTTACA
593291 TATATAT
1 TATATAT
593298 TTTTATTTAA
Statistics
Matches: 147, Mismatches: 13, Indels: 37
0.75 0.07 0.19
Matches are distributed among these distances:
54 5 0.03
55 26 0.18
56 23 0.16
57 33 0.22
58 35 0.24
59 9 0.06
60 4 0.03
61 10 0.07
62 2 0.01
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (57 bp):
TATATATATATATATTATATATTATATTATTTATATTATTATTGTAATATATTTACA
Found at i:593246 original size:92 final size:91
Alignment explanation
Indices: 593054--593295 Score: 268
Period size: 92 Copynumber: 2.6 Consensus size: 91
593044 GACACATTTA
* *
593054 ATATATTATTATA-TAGT-TTATATATAGTATATTACTTATTA-TATTATTATTTTAGTATATTT
1 ATATA-TATTATATTAGTAATATAT-TAGTATA-TA-TTATTATTATTA-TATTATAGTATATTT
593116 ACATATATATATATATATTATATATTATATT
61 ACATATATATATATATATTATATATTATATT
*
593147 ATATATATTATATTAGTAATATATTTAGTATATATTATTATTATTATATTATAGTATATTTATAT
1 ATATATATTATATTAGTAATATA-TTAGTATATATTATTATTATTATATTATAGTATATTTACA-
*
593212 GTATTATATGTATATATTATAT-TTATATT
64 -TA-TATATATATATATTATATATTATATT
* *
593241 TTATATATTGGTA-TATGTAATATA-TAGTAT-TATTATTATTATTAT-TTATA-TATAT
1 ATATATATT-ATATTA-GTAATATATTAGTATATATTATTATTATTATATTATAGTATAT
593296 ATTTTTATTT
Statistics
Matches: 134, Mismatches: 6, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
90 5 0.04
91 5 0.04
92 44 0.33
93 22 0.16
94 30 0.22
95 28 0.21
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (91 bp):
ATATATATTATATTAGTAATATATTAGTATATATTATTATTATTATATTATAGTATATTTACATA
TATATATATATATTATATATTATATT
Found at i:593255 original size:28 final size:27
Alignment explanation
Indices: 593055--593300 Score: 136
Period size: 28 Copynumber: 8.7 Consensus size: 27
593045 ACACATTTAA
*
593055 TATATTAT-TATATAGTTTA-TATATAG
1 TATATTATATATATATTTTATTAT-TAG
593081 TATATTACT-TATTATATTATTATT-TTAG
1 TATATTA-TATA-TATATT-TTATTATTAG
* *
593109 TATATT-TACATATATATATATATATTA-
1 TATATTATATATATAT-TTTAT-TATTAG
*
593136 TATATTATATTATATATATTA-TATTAG
1 TATATTATA-TATATATTTTATTATTAG
*
593163 TAATATATTTAGTATATATTATTATTATTA-
1 T-ATAT-TATA-TATATATT-TTATTATTAG
*
593193 TATTATAGTATATTTATATGTATTA-TATGTA-
1 TA-TAT--TATATATATAT-T-TTATTAT-TAG
* *
593224 TATATTATATTTATATTTTATATATTGG
1 TATATTATATATATATTTTAT-TATTAG
*
593252 TATATGTAATATATAGTATTATTATTATTAT
1 TATAT-T-ATATATA-TATT-TTATTATTAG
593283 TAT-TTATATATATATTTT
1 TATATTATATATATATTTT
593301 TATTTAATTA
Statistics
Matches: 178, Mismatches: 16, Indels: 52
0.72 0.07 0.21
Matches are distributed among these distances:
26 26 0.15
27 19 0.11
28 51 0.29
29 23 0.13
30 27 0.15
31 28 0.16
32 4 0.02
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (27 bp):
TATATTATATATATATTTTATTATTAG
Found at i:595788 original size:30 final size:30
Alignment explanation
Indices: 595753--595983 Score: 241
Period size: 30 Copynumber: 7.8 Consensus size: 30
595743 TGGGAAAAAC
* * * * *
595753 AACTTAAAAGACCAAAATAGCACAAACAAG
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
595783 AACTTAAAGGACTAAAATAG-AAAAATAAA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
*
595812 AACTTAAAGGACTAAAATAGAAAAAATAAA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
*
595842 AACTTAAAGGACTAAAATAGCAAAAATAGA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
* * * *
595872 AACTTAAGGGACT-AAATAGTAAATACAAA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
* * * *
595901 CATTTAAAGGACTAAAATAGCAACAACAAA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
* * * * * *
595931 AACTTAAGGGACCAACATGGCCAAAATAGA
1 AACTTAAAGGACTAAAATAGCAAAAATAAA
* *
595961 CATTTAAAGGACTAAAATAGCAA
1 AACTTAAAGGACTAAAATAGCAA
595984 CATAAATTTA
Statistics
Matches: 164, Mismatches: 35, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
29 48 0.29
30 116 0.71
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (30 bp):
AACTTAAAGGACTAAAATAGCAAAAATAAA
Found at i:595829 original size:59 final size:61
Alignment explanation
Indices: 595753--595983 Score: 235
Period size: 59 Copynumber: 3.9 Consensus size: 61
595743 TGGGAAAAAC
*
595753 AACTTAAAAGACCAAAATAGCACAAACAAGA-ACTTAAAGGACTAAAATAG-AAAAATAAA
1 AACTTAAAGGACCAAAATAGCACAAACAAGACACTTAAAGGACTAAAATAGCAAAAATAAA
* * * * * *
595812 AACTTAAAGGACTAAAATAGAAAAAATAA-AAACTTAAAGGACTAAAATAGCAAAAATAGA
1 AACTTAAAGGACCAAAATAGCACAAACAAGACACTTAAAGGACTAAAATAGCAAAAATAAA
* * * * * *
595872 AACTTAAGGGA-CTAAATAGTA-AATACAA-ACATTTAAAGGACTAAAATAGCAACAACAAA
1 AACTTAAAGGACCAAAATAGCACAA-ACAAGACACTTAAAGGACTAAAATAGCAAAAATAAA
* * * *
595931 AACTTAAGGGACCAACATGGC-CAAA-ATAGACATTTAAAGGACTAAAATAGCAA
1 AACTTAAAGGACCAAAATAGCACAAACA-AGACACTTAAAGGACTAAAATAGCAA
595984 CATAAATTTA
Statistics
Matches: 145, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
58 4 0.03
59 92 0.63
60 49 0.34
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (61 bp):
AACTTAAAGGACCAAAATAGCACAAACAAGACACTTAAAGGACTAAAATAGCAAAAATAAA
Found at i:595884 original size:89 final size:89
Alignment explanation
Indices: 595753--595989 Score: 266
Period size: 89 Copynumber: 2.7 Consensus size: 89
595743 TGGGAAAAAC
*
595753 AACTTAAAAGACCAAAATAGCACAAACA-AG-AACTTAAAGGACTAAAATAGAAAAATAAAA-AC
1 AACTTAAAGGACCAAAATAGCA-AAA-ATAGAAACTTAAAGGACTAAAATAG-AAAATAAAACAC
*
595815 TTAAAGGACTAAAATAGAAAAAATAAA
63 TTAAAGGACTAAAATAGAAAAAACAAA
* * * *
595842 AACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAAGGGACT-AAATAGTAAATACAAACATTT
1 AACTTAAAGGACCAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGAAAATA-AAACACTT
* *
595906 AAAGGACTAAAATAGCAACAACAAA
65 AAAGGACTAAAATAGAAAAAACAAA
* * * * * * *
595931 AACTTAAGGGACCAACATGGCCAAAATAGACATTTAAAGGACTAAAATAGCAACATAAA
1 AACTTAAAGGACCAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAG-AAAATAAA
595990 TTTAAGGGAC
Statistics
Matches: 124, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
87 6 0.05
88 14 0.11
89 92 0.74
90 8 0.06
91 4 0.03
ACGTcount: A:0.58, C:0.13, G:0.12, T:0.16
Consensus pattern (89 bp):
AACTTAAAGGACCAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGAAAATAAAACACTTA
AAGGACTAAAATAGAAAAAACAAA
Found at i:595996 original size:26 final size:26
Alignment explanation
Indices: 595962--596014 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
595952 CAAAATAGAC
595962 ATTTAAA-GGACTAAAATAGCAACATAA
1 ATTTAAAGGGACT-AAATAGCAA-ATAA
595989 ATTT-AAGGGACTAAATAGCAAATAA
1 ATTTAAAGGGACTAAATAGCAAATAA
596014 A
1 A
596015 AATAATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.20
26 11 0.44
27 9 0.36
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (26 bp):
ATTTAAAGGGACTAAATAGCAAATAA
Found at i:598063 original size:130 final size:129
Alignment explanation
Indices: 597677--598073 Score: 492
Period size: 131 Copynumber: 3.0 Consensus size: 129
597667 ATCTTTAGGA
* * *
597677 AGGG-TGATAACATGGCTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGACACGACTCCTA
1 AGGGATGATAACATGGTTCCTACGTGATGAGGATGGCTGGTTATCTA-GGGTGACACG-CTCCTA
* * * * *
597741 CGCGATGAGGAGGTATGATCGGTGAATGACACAGTTCCTACGTGATGAGGATGACATGTCATCTT
64 CGTGATGAGGAGGTATGGTCGGGGAATGACACGGTTCCTACGTGATGAGGATGACATGCCATCTT
597806 T
129 T
* * * * *
597807 AGGGATAATAACATGATTCCTACGTGATAAGGATAGCTGGTTATCTATGGGTGACATGGCTCCTA
1 AGGGATGATAACATGGTTCCTACGTGATGAGGATGGCTGGTTATCTA-GGGTGACA-CGCTCCTA
* * * * *
597872 CGTGATGAGGAGGTTTAGTCGGGGGATGACACGGTTCCTACGTGATGAGGATGGCAAGCCATCTT
64 CGTGATGAGGAGGTATGGTCGGGGAATGACACGGTTCCTACGTGATGAGGATGACATGCCATCTT
597937 T
129 T
* * *
597938 AGGGATGATAACACGGTTCCTACATGATGAGGATGGCTGGTTATC-AGGCGTGACACAGCTCTTA
1 AGGGATGATAACATGGTTCCTACGTGATGAGGATGGCTGGTTATCTAGG-GTGACAC-GCTCCTA
* * * * *
598002 CGTGATGAGGAGGTCTGGTTGGGGAATGACATGGTTCCTACGCGATGAGGACGACATGCCATCTT
64 CGTGATGAGGAGGTATGGTCGGGGAATGACACGGTTCCTACGTGATGAGGATGACATGCCATCTT
598067 T
129 T
598068 AGGGAT
1 AGGGAT
598074 AATGGTTTCA
Statistics
Matches: 227, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
129 2 0.01
130 80 0.35
131 144 0.63
132 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (129 bp):
AGGGATGATAACATGGTTCCTACGTGATGAGGATGGCTGGTTATCTAGGGTGACACGCTCCTACG
TGATGAGGAGGTATGGTCGGGGAATGACACGGTTCCTACGTGATGAGGATGACATGCCATCTTT
Found at i:598380 original size:66 final size:66
Alignment explanation
Indices: 598207--598379 Score: 246
Period size: 66 Copynumber: 2.6 Consensus size: 66
598197 AAAAAAAAAA
*
598207 TTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATT
1 TTTCTCAAAAGAAATTGTCTCAA-AGAGACAAAATTTTTTTTCCAAAGAAACAAACTCAAAGATT
598272 TT
65 TT
* * *
598274 TTTCTCAAGAA-AAA-TGTCTCAAAAGAGACAAAACTTTTTTTCCAGAGAAACAGACTCAAAGA-
1 TTTCTCAA-AAGAAATTGTCTC-AAAGAGACAAAATTTTTTTTCCAAAGAAACAAACTCAAAGAT
598336 TTT
64 TTT
598339 TTTCTCAAAAGAAATTGTCT-AAAGAGACAAAATTTGTTTTT
1 TTTCTCAAAAGAAATTGTCTCAAAGAGACAAAATTT-TTTTT
598380 TAAGAAAATT
Statistics
Matches: 96, Mismatches: 5, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
64 16 0.17
65 19 0.20
66 46 0.48
67 13 0.14
68 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (66 bp):
TTTCTCAAAAGAAATTGTCTCAAAGAGACAAAATTTTTTTTCCAAAGAAACAAACTCAAAGATTT
T
Found at i:604299 original size:30 final size:30
Alignment explanation
Indices: 604263--604496 Score: 213
Period size: 30 Copynumber: 7.8 Consensus size: 30
604253 CCGGAATGGG
* * *
604263 AAAAACAGAAACTTAAAGGACCAAGATAGC
1 AAAAATAGAAACTTAAAGGACTAAAATAGC
* * * **
604293 ACAAACAGTAACTTAAAAAACTAAAATAGC
1 AAAAATAGAAACTTAAAGGACTAAAATAGC
* *
604323 AAAAATAGAAACTTAAAGGATTAAAATAGA
1 AAAAATAGAAACTTAAAGGACTAAAATAGC
*
604353 AAAAATAGAAACTTAAAGGACTAAAATAGA
1 AAAAATAGAAACTTAAAGGACTAAAATAGC
* *
604383 AAAAATGGAAACTTAATGGACTAAAATAGC
1 AAAAATAGAAACTTAAAGGACTAAAATAGC
* * * *
604413 AATAATAGAAA-TATAAGGGACCAATATAGC
1 AAAAATAGAAACT-TAAAGGACTAAAATAGC
* * * * *
604443 AAAAATATACATTTAAAGGACTGAAATAAC
1 AAAAATAGAAACTTAAAGGACTAAAATAGC
* *
604473 AAAGTATA-AAA-TTAAGGGACTAAA
1 AAA-AATAGAAACTTAAAGGACTAAA
604497 CAGTAAATAA
Statistics
Matches: 167, Mismatches: 34, Indels: 7
0.80 0.16 0.03
Matches are distributed among these distances:
29 12 0.07
30 151 0.90
31 4 0.02
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.18
Consensus pattern (30 bp):
AAAAATAGAAACTTAAAGGACTAAAATAGC
Found at i:605974 original size:3 final size:3
Alignment explanation
Indices: 605962--606012 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
605952 TAATCAAAAT
*
605962 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA -AA TAT TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
606006 TAA TAA T
1 TAA TAA T
606013 TTTTGTAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:609956 original size:3 final size:3
Alignment explanation
Indices: 609950--610019 Score: 90
Period size: 3 Copynumber: 23.7 Consensus size: 3
609940 TTCATTTGAA
* *
609950 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT TAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
609995 TAT TAG TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
610020 ATAAATATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 3 0.05
3 54 0.93
4 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:611265 original size:17 final size:17
Alignment explanation
Indices: 611233--611280 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
611223 TTTAACACTA
*
611233 TATTTTTAAT-TTATTT
1 TATTTATAATATTATTT
611249 TATTT-TAATCATTA-TT
1 TATTTATAAT-ATTATTT
611265 TATTTATAATATTATT
1 TATTTATAATATTATT
611281 ACTTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.14
16 16 0.57
17 8 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTATAATATTATTT
Found at i:611656 original size:2 final size:2
Alignment explanation
Indices: 611649--611708 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
611639 TGTTATTTAA
611649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
611691 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
611709 TCTTTAAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:614676 original size:23 final size:21
Alignment explanation
Indices: 614630--614707 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 21
614620 TTCTAGGCTA
*
614630 GGTATCGATACCCCCTTGCATG
1 GGTACCGATACCCCCTTG-ATG
614652 GGTACCGATACCCCCTTTGAGTG
1 GGTACCGATACCCCC-TTGA-TG
*
614675 GGTATCGATACCCCCTTGA-G
1 GGTACCGATACCCCCTTGATG
614695 GGTACCGATACCC
1 GGTACCGATACCC
614708 TCCACGGGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.25
22 19 0.37
23 19 0.37
ACGTcount: A:0.19, C:0.32, G:0.24, T:0.24
Consensus pattern (21 bp):
GGTACCGATACCCCCTTGATG
Found at i:617404 original size:21 final size:21
Alignment explanation
Indices: 617378--617417 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
617368 ACCAGATTGT
*
617378 CCAGAGTGTACCGATACCCCC
1 CCAGAGGGTACCGATACCCCC
617399 CCAGAGGGTACCGATACCC
1 CCAGAGGGTACCGATACCC
617418 ACATATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.40, G:0.23, T:0.12
Consensus pattern (21 bp):
CCAGAGGGTACCGATACCCCC
Found at i:624474 original size:16 final size:16
Alignment explanation
Indices: 624453--624483 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
624443 AGGTGTTTAC
624453 AAAATACACTTGAGAG
1 AAAATACACTTGAGAG
624469 AAAATACACTTGAGA
1 AAAATACACTTGAGA
624484 TAGAACTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.16, T:0.19
Consensus pattern (16 bp):
AAAATACACTTGAGAG
Found at i:626762 original size:38 final size:38
Alignment explanation
Indices: 626713--626824 Score: 206
Period size: 38 Copynumber: 2.9 Consensus size: 38
626703 AGGGTACGAC
*
626713 AAATTCATATTCTACTGTAACATTGGTTGTAAATTACA
1 AAATGCATATTCTACTGTAACATTGGTTGTAAATTACA
*
626751 AAATGCGTATTCTACTGTAACATTGGTTGTAAATTACA
1 AAATGCATATTCTACTGTAACATTGGTTGTAAATTACA
626789 AAATGCATATTCTACTGTAACATTGGTTGTAAATTA
1 AAATGCATATTCTACTGTAACATTGGTTGTAAATTA
626825 ATAGTGAGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 71 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (38 bp):
AAATGCATATTCTACTGTAACATTGGTTGTAAATTACA
Found at i:627969 original size:110 final size:108
Alignment explanation
Indices: 627846--628066 Score: 297
Period size: 112 Copynumber: 2.0 Consensus size: 108
627836 TTATGACACT
*
627846 ATGGGAATGCTCGGCGTCTTCAAGTAATT-GG-C-CT-GTGGGATATCTCGGCGTCTTCTGCATG
1 ATGGGAATGCTCGGCGTCTTCAAGCAATTGGGACTCTGGTGGGATATCTCGGCGTCTTCTGCA--
627907 CTACAAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
64 -T---AGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
* *
627956 ATGGGAATGCTCGGTGTCTTCAAGCAATTGGGATCTCTCGGAGTGGGATCTCTCGGCGTCTTCTG
1 ATGGGAATGCTCGGCGTCTTCAAGCAATTGGGA-CTCT--G-GTGGGATATCTCGGCGTCTTCTG
628021 CATAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCT
62 CATAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCT
628067 AGCGGGAATC
Statistics
Matches: 100, Mismatches: 3, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
110 27 0.27
111 2 0.02
112 43 0.43
113 1 0.01
114 2 0.02
115 1 0.01
118 24 0.24
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (108 bp):
ATGGGAATGCTCGGCGTCTTCAAGCAATTGGGACTCTGGTGGGATATCTCGGCGTCTTCTGCATA
GGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
Found at i:628344 original size:18 final size:18
Alignment explanation
Indices: 628321--628367 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
628311 CTTTGTGTCC
628321 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
628339 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
628357 GAAGCGTGAGA
1 GAAGCGTGAGA
628368 CTAATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (18 bp):
GAAGCGTGAGATTCGTCT
Found at i:631754 original size:8 final size:8
Alignment explanation
Indices: 631730--632412 Score: 161
Period size: 8 Copynumber: 92.5 Consensus size: 8
631720 TATTTAATAA
631730 TAATTATT
1 TAATTATT
631738 TAA--ATT
1 TAATTATT
631744 TAATTATT
1 TAATTATT
*
631752 TAA--CTT
1 TAATTATT
*
631758 TAATGATT
1 TAATTATT
*
631766 TAA-TA-A
1 TAATTATT
631772 TAATTATT
1 TAATTATT
*
631780 TAA--CTT
1 TAATTATT
*
631786 TAATGATT
1 TAATTATT
*
631794 TAA-TA-A
1 TAATTATT
631800 TAATTATT
1 TAATTATT
*
631808 TAA--CTT
1 TAATTATT
*
631814 TAATGATT
1 TAATTATT
*
631822 TAA-TA-A
1 TAATTATT
631828 TAATTATT
1 TAATTATT
*
631836 TAA--CTT
1 TAATTATT
*
631842 TAATGATT
1 TAATTATT
*
631850 TAA-TA-A
1 TAATTATT
631856 TAATTACTT
1 TAATTA-TT
*
631865 TAATGATT
1 TAATTATT
631873 TAA-T-TT
1 TAATTATT
*
631879 TAATGATT
1 TAATTATT
*
631887 TAATGATT
1 TAATTATT
*
631895 TAA--CTT
1 TAATTATT
*
631901 TAATGATT
1 TAATTATT
*
631909 TAA-TA-A
1 TAATTATT
*
631915 TAATTACCT
1 TAATTA-TT
*
631924 TAATGATT
1 TAATTATT
*
631932 TAA--CTT
1 TAATTATT
*
631938 TAATGATT
1 TAATTATT
*
631946 TAA-TA-A
1 TAATTATT
631952 TAATTACTT
1 TAATTA-TT
*
631961 TAATGATT
1 TAATTATT
*
631969 TAA--CTT
1 TAATTATT
*
631975 TAATGATT
1 TAATTATT
*
631983 TAA-TA-A
1 TAATTATT
631989 TAATTACTT
1 TAATTA-TT
*
631998 TAATGATT
1 TAATTATT
*
632006 TAA--CTT
1 TAATTATT
*
632012 TAATGATT
1 TAATTATT
*
632020 TAA-TA-A
1 TAATTATT
632026 TAATTACTT
1 TAATTA-TT
*
632035 TAATGATT
1 TAATTATT
*
632043 TAA--CTT
1 TAATTATT
*
632049 TAATGATT
1 TAATTATT
*
632057 TAA-TA-A
1 TAATTATT
632063 TAATTACTT
1 TAATTA-TT
*
632072 TAATGATT
1 TAATTATT
*
632080 TAA--CTT
1 TAATTATT
*
632086 TAATGATT
1 TAATTATT
*
632094 TAA-TA-A
1 TAATTATT
632100 TAATTACTT
1 TAATTA-TT
*
632109 TAATGATT
1 TAATTATT
*
632117 TAATGATT
1 TAATTATT
*
632125 TAATGATT
1 TAATTATT
*
632133 TAATGATT
1 TAATTATT
*
632141 TAATGATT
1 TAATTATT
*
632149 TAATGATT
1 TAATTATT
*
632157 TAA--CTT
1 TAATTATT
*
632163 TAATGATT
1 TAATTATT
*
632171 TAA-TA-A
1 TAATTATT
632177 TAATTACTT
1 TAATTA-TT
*
632186 TAATGATT
1 TAATTATT
*
632194 TAATGATT
1 TAATTATT
*
632202 TAATGATT
1 TAATTATT
*
632210 TAA-TA-A
1 TAATTATT
632216 TAATTATTT
1 TAATTA-TT
*
632225 TAATGATT
1 TAATTATT
*
632233 TAATGATT
1 TAATTATT
*
632241 TAATGATT
1 TAATTATT
*
632249 TAA-TA-A
1 TAATTATT
632255 TAATTACTT
1 TAATTA-TT
*
632264 TAATGATT
1 TAATTATT
632272 TAA-T-TT
1 TAATTATT
*
632278 TAATAATT
1 TAATTATT
*
632286 TAA-TA-A
1 TAATTATT
*
632292 TAATTACT
1 TAATTATT
632300 TAA-T-TT
1 TAATTATT
*
632306 TAATGATT
1 TAATTATT
*
632314 TAATGATT
1 TAATTATT
*
632322 TAATGATT
1 TAATTATT
*
632330 TAA-TA-A
1 TAATTATT
632336 TAATTACTT
1 TAATTA-TT
*
632345 TAATGATT
1 TAATTATT
632353 TAA-T-TT
1 TAATTATT
*
632359 TAATAATT
1 TAATTATT
*
632367 TAA-TA-A
1 TAATTATT
*
632373 TAATTACT
1 TAATTATT
632381 TAA-T-TT
1 TAATTATT
*
632387 TAATGATT
1 TAATTATT
632395 TAA-T-TT
1 TAATTATT
*
632401 TAATGATT
1 TAATTATT
632409 TAAT
1 TAAT
632413 AATAATTACT
Statistics
Matches: 502, Mismatches: 94, Indels: 158
0.67 0.12 0.21
Matches are distributed among these distances:
6 137 0.27
7 50 0.10
8 260 0.52
9 55 0.11
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (8 bp):
TAATTATT
Found at i:631875 original size:37 final size:37
Alignment explanation
Indices: 631742--632423 Score: 796
Period size: 37 Copynumber: 18.1 Consensus size: 37
631732 ATTATTTAAA
*
631742 TTTAATTATTTAACTTTAATGATTTAATAATAATTA-
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
* * * *
631778 TTTAA--CTTTAATGATTTAAT-A-ATAAT--TATTTAAC
1 TTTAATGATTTAA--CTTTAATGATTTAATAATAATT-AC
* * * *
631812 TTTAATGATTTAA-TAATAATTATTTAACT-TTAATGA-
1 TTTAATGATTTAACT-TTAATGATTTAA-TAATAATTAC
* ** *
631848 TTTAATAATAATT-ACTTTAATGATTTAATTTTAATGA-
1 TTTAATGAT--TTAACTTTAATGATTTAATAATAATTAC
631885 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
*
631922 CTTAATGATTTAACTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
631959 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
631996 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
632033 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
632070 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
* * *
632107 TTTAATGATTTAATGATTTAATGATTTAATGATTTAATGA-
1 TTTAATGATTTAA--CTTTAATGATTTAAT-A-ATAATTAC
632147 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
* *
632184 TTTAATGATTTAATGATTTAATGATTTAATAATAATTAT
1 TTTAATGATTTAA--CTTTAATGATTTAATAATAATTAC
*
632223 TTTAATGATTTAATGATTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAA--CTTTAATGATTTAATAATAATTAC
* *
632262 TTTAATGATTTAATTTTAATAATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
*
632299 TTAATTTTAATGATTTAATGATTTAATGATTTAATAATAATTAC
1 -----TTTAATGATTTAA--CTTTAATGATTTAATAATAATTAC
* *
632343 TTTAATGATTTAATTTTAATAATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
*
632380 TTAATTTTAATGATTTAATTTTAATGATTTAATAATAATTAC
1 -----TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
632422 TT
1 TT
632424 GACTTTAATG
Statistics
Matches: 576, Mismatches: 34, Indels: 71
0.85 0.05 0.10
Matches are distributed among these distances:
32 4 0.01
33 2 0.00
34 18 0.03
35 4 0.01
36 54 0.09
37 284 0.49
38 20 0.03
39 100 0.17
40 14 0.02
41 5 0.01
42 49 0.09
44 22 0.04
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (37 bp):
TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
Found at i:631882 original size:14 final size:14
Alignment explanation
Indices: 631730--632412 Score: 371
Period size: 14 Copynumber: 49.9 Consensus size: 14
631720 TATTTAATAA
* *
631730 TAATTATTTAAATT
1 TAATGATTTAATTT
* *
631744 TAATTATTTAACTT
1 TAATGATTTAATTT
**
631758 TAATGATTTAATAA
1 TAATGATTTAATTT
* *
631772 TAATTATTTAACTT
1 TAATGATTTAATTT
**
631786 TAATGATTTAATAA
1 TAATGATTTAATTT
* *
631800 TAATTATTTAACTT
1 TAATGATTTAATTT
**
631814 TAATGATTTAATAA
1 TAATGATTTAATTT
* *
631828 TAATTATTTAACTT
1 TAATGATTTAATTT
**
631842 TAATGATTTAATAA
1 TAATGATTTAATTT
*
631856 TAATTACTTTAATGATT
1 TAATGA-TTTAAT--TT
631873 TAAT--TTTAATGATT
1 TAATGATTTAAT--TT
*
631887 TAATGATTTAACTT
1 TAATGATTTAATTT
631901 TAATGATTTAA---
1 TAATGATTTAATTT
* **
631912 TAAT-AATT-ACCT
1 TAATGATTTAATTT
*
631924 TAATGATTTAACTT
1 TAATGATTTAATTT
631938 TAATGATTTAA---
1 TAATGATTTAATTT
* *
631949 TAAT-AATT-ACTT
1 TAATGATTTAATTT
*
631961 TAATGATTTAACTT
1 TAATGATTTAATTT
631975 TAATGATTTAA---
1 TAATGATTTAATTT
* *
631986 TAAT-AATT-ACTT
1 TAATGATTTAATTT
*
631998 TAATGATTTAACTT
1 TAATGATTTAATTT
632012 TAATGATTTAA---
1 TAATGATTTAATTT
* *
632023 TAAT-AATT-ACTT
1 TAATGATTTAATTT
*
632035 TAATGATTTAACTT
1 TAATGATTTAATTT
632049 TAATGATTTAA---
1 TAATGATTTAATTT
* *
632060 TAAT-AATT-ACTT
1 TAATGATTTAATTT
*
632072 TAATGATTTAACTT
1 TAATGATTTAATTT
**
632086 TAATGATTTAATAA
1 TAATGATTTAATTT
*
632100 TAATTACTTTAATGATT
1 TAATGA-TTTAAT--TT
632117 TAATGATTTAATGATT
1 TAATGATTTAAT--TT
632133 TAATGATTTAATGATT
1 TAATGATTTAAT--TT
*
632149 TAATGATTTAACTT
1 TAATGATTTAATTT
**
632163 TAATGATTTAATAA
1 TAATGATTTAATTT
*
632177 TAATTACTTTAATGATT
1 TAATGA-TTTAAT--TT
632194 TAATGATTTAATGATT
1 TAATGATTTAAT--TT
*
632210 TAATAATAATT-ATTT
1 TAATGAT--TTAATTT
632225 TAATGATTTAATGATT
1 TAATGATTTAAT--TT
632241 TAATGATTTAA---
1 TAATGATTTAATTT
* *
632252 TAAT-AATT-ACTT
1 TAATGATTTAATTT
632264 TAATGATTTAATTT
1 TAATGATTTAATTT
* **
632278 TAATAATTTAATAA
1 TAATGATTTAATTT
* *
632292 TAATTACTTAATTT
1 TAATGATTTAATTT
632306 TAATGATTTAATGATT
1 TAATGATTTAAT--TT
632322 TAATGATTTAA---
1 TAATGATTTAATTT
* *
632333 TAAT-AATT-ACTT
1 TAATGATTTAATTT
632345 TAATGATTTAATTT
1 TAATGATTTAATTT
* **
632359 TAATAATTTAATAA
1 TAATGATTTAATTT
* *
632373 TAATTACTTAATTT
1 TAATGATTTAATTT
632387 TAATGATTTAATTT
1 TAATGATTTAATTT
632401 TAATGATTTAAT
1 TAATGATTTAAT
632413 AATAATTACT
Statistics
Matches: 531, Mismatches: 85, Indels: 106
0.74 0.12 0.15
Matches are distributed among these distances:
9 7 0.01
10 21 0.04
11 28 0.05
12 28 0.05
13 23 0.04
14 296 0.56
15 26 0.05
16 84 0.16
17 16 0.03
18 2 0.00
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (14 bp):
TAATGATTTAATTT
Found at i:632323 original size:81 final size:80
Alignment explanation
Indices: 632147--632423 Score: 451
Period size: 81 Copynumber: 3.5 Consensus size: 80
632137 GATTTAATGA
* *
632147 TTTAATGATTTAA-CTTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTT
1 TTTAATGATTTAATATTTAATGATTTAATAATAATTACTTTAATGATTTAAT--TTTAATAATTT
632211 AATAAT-A--A-TT-AT
64 AATAATAATTACTTAAT
632223 TTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATTTA
1 TTTAATGATTTAAT-ATTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATTTA
632288 ATAATAATTACTTAAT
65 ATAATAATTACTTAAT
632304 TTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATTTA
1 TTTAATGATTTAAT-ATTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATTTA
632369 ATAATAATTACTTAAT
65 ATAATAATTACTTAAT
632385 TTTAATGATTTAAT-TTTAATGATTTAATAATAATTACTT
1 TTTAATGATTTAATATTTAATGATTTAATAATAATTACTT
632424 GACTTTAATG
Statistics
Matches: 192, Mismatches: 2, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
76 29 0.15
77 1 0.01
78 37 0.19
79 26 0.14
80 2 0.01
81 97 0.51
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (80 bp):
TTTAATGATTTAATATTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATTTAA
TAATAATTACTTAAT
Done.