Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 2 of 77
Found at i:178301 original size:23 final size:23
Alignment explanation
Indices: 178274--178322 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
178264 TTGTTAAAAC
178274 ATTTTAAATTATATTATTTTTAT
1 ATTTTAAATTATATTATTTTTAT
* *
178297 ATTTTTATTTATATTATTTTTAT
1 ATTTTAAATTATATTATTTTTAT
178320 ATT
1 ATT
178323 ATATTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTTAAATTATATTATTTTTAT
Found at i:178324 original size:16 final size:15
Alignment explanation
Indices: 178287--178328 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
178277 TTAAATTATA
*
178287 TTATTTTTA-TATTT
1 TTATTTATATTATTT
178301 TTATTTATATTATTT
1 TTATTTATATTATTT
178316 TTATATTATATTA
1 TTAT-TTATATTA
178329 ATATATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.32
15 9 0.36
16 8 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTATATTATTT
Found at i:178332 original size:11 final size:11
Alignment explanation
Indices: 178282--178332 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
178272 ACATTTTAAA
*
178282 TTATATTATTT
1 TTATATTATAT
*
178293 TTATATTTTTAT
1 TTATA-TTATAT
*
178305 TTATATTATTT
1 TTATATTATAT
178316 TTATATTATAT
1 TTATATTATAT
*
178327 TAATAT
1 TTATAT
178333 ATCATATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATATTATAT
Found at i:179529 original size:21 final size:23
Alignment explanation
Indices: 179471--179534 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
179461 TTTATTTTTA
* *
179471 ATATAAAATATAATTAAATATGT
1 ATATAAAAAATAAATAAATATGT
*
179494 ATATAATTAAA-AAATAAATATG-
1 ATATAA-AAAATAAATAAATATGT
179516 A-ATAAAAAATAAATAAATA
1 ATATAAAAAATAAATAAATA
179535 AATCAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 3 0.09
21 13 0.37
22 1 0.03
23 16 0.46
24 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (23 bp):
ATATAAAAAATAAATAAATATGT
Found at i:184535 original size:2 final size:2
Alignment explanation
Indices: 184530--184591 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
184520 CACACATACT
* * * * *
184530 TA TA TA TA TA TA TA TA TA TG TG TG TG TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
184572 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
184592 AACATGTTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (2 bp):
TA
Found at i:188473 original size:29 final size:31
Alignment explanation
Indices: 188426--188496 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 31
188416 AAATAATTAT
*
188426 TTAAATTTTT-ATTATTTTATTATAAT-CAA
1 TTAAATTTTTAAATATTTTATTATAATCCAA
* *
188455 TTAAATTTTTAAATA-TTTATTTTCATCCAA
1 TTAAATTTTTAAATATTTTATTATAATCCAA
188485 TTAAATTTTTAA
1 TTAAATTTTTAA
188497 TTCGATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.51
30 18 0.49
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (31 bp):
TTAAATTTTTAAATATTTTATTATAATCCAA
Found at i:194074 original size:1 final size:1
Alignment explanation
Indices: 194068--194094 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
194058 CATGATACAG
194068 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
194095 GTCATGGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:196621 original size:3 final size:3
Alignment explanation
Indices: 196613--196663 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
196603 TTTTTAAATT
196613 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
196660 TTA T
1 TTA T
196664 GCAAAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:196806 original size:17 final size:17
Alignment explanation
Indices: 196784--196830 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
196774 TATTAAATAT
*
196784 AAAACACAAATATAAAC
1 AAAACACAAATAAAAAC
*
196801 AAAACA-AAACAAAAAAC
1 AAAACACAAA-TAAAAAC
196818 AAAA-ACAAATAAA
1 AAAACACAAATAAA
196831 CAAATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAACACAAATAAAAAC
Found at i:196824 original size:13 final size:13
Alignment explanation
Indices: 196801--196834 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
196791 AAATATAAAC
196801 AAAAC-AAAACAA
1 AAAACAAAAACAA
196813 AAAACAAAAACAA
1 AAAACAAAAACAA
196826 ATAAACAAA
1 A-AAACAAA
196835 TAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 8 0.40
14 7 0.35
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAACAAAAACAA
Found at i:196831 original size:8 final size:8
Alignment explanation
Indices: 196807--196847 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
196797 AAACAAAACA
196807 AAACAAA-
1 AAACAAAT
196814 AAAC-AA-
1 AAACAAAT
196820 AAACAAAT
1 AAACAAAT
196828 AAACAAAT
1 AAACAAAT
*
196836 AAATAAAT
1 AAACAAAT
196844 AAAC
1 AAAC
196848 TTTTCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 6 0.20
7 6 0.20
8 18 0.60
ACGTcount: A:0.78, C:0.12, G:0.00, T:0.10
Consensus pattern (8 bp):
AAACAAAT
Found at i:200066 original size:2 final size:2
Alignment explanation
Indices: 200059--200090 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
200049 GTCATTTGGG
200059 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
200091 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:201121 original size:18 final size:19
Alignment explanation
Indices: 201098--201137 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
201088 TTCTTTTTCC
201098 TTTC-TTATA-TTTAATATT
1 TTTCTTTATATTTTAAT-TT
201116 TTTCTTTATATTTTAATTT
1 TTTCTTTATATTTTAATTT
201135 TTT
1 TTT
201138 GTAGAGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTTTATATTTTAATTT
Found at i:202198 original size:18 final size:18
Alignment explanation
Indices: 202160--202203 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
202150 TCAATCCCAC
* * *
202160 ATTTAAAAATTATAAATA
1 ATTTAAAAAATAAAAAAA
202178 ATTTAAAAAATAAAAAAA
1 ATTTAAAAAATAAAAAAA
*
202196 ATTGAAAA
1 ATTTAAAA
202204 CAAAAAAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
ATTTAAAAAATAAAAAAA
Found at i:202847 original size:122 final size:122
Alignment explanation
Indices: 202621--202840 Score: 296
Period size: 122 Copynumber: 1.8 Consensus size: 122
202611 ATCACACAAT
* *
202621 ATATATGAAGCAACCAATAAATATTTTTGCATAATGATTTACATAGCTAAAATTTTACCATTCAT
1 ATATATGAAGCAACCAATAAATATTTTTGAATAATGATTCACATAGCTAAAATTTTACCATTCAT
* **
202686 CAATTTGTATCATGCTATAATTATTTAAATGTACGTATATTTGATGTACTTCACAGA
66 CAATTTATATCATGCTATAATTATTTAAACATACGTATATTTGATGTACTTCACAGA
* * * * * * * *
202743 ATATATGGAGCAGCCAATAAATATTTTTTAATCATGATTCACATGGCTAAAATTTTGCTATTTAT
1 ATATATGAAGCAACCAATAAATATTTTTGAATAATGATTCACATAGCTAAAATTTTACCATTCAT
* * *
202808 CAATTTATCTCATGCTATCATTGTTTAAACATA
66 CAATTTATATCATGCTATAATTATTTAAACATA
202841 TTTATATATA
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
122 82 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (122 bp):
ATATATGAAGCAACCAATAAATATTTTTGAATAATGATTCACATAGCTAAAATTTTACCATTCAT
CAATTTATATCATGCTATAATTATTTAAACATACGTATATTTGATGTACTTCACAGA
Found at i:208707 original size:128 final size:128
Alignment explanation
Indices: 208479--208736 Score: 516
Period size: 128 Copynumber: 2.0 Consensus size: 128
208469 CCAAGGCAGG
208479 GAAACATTGAAGCATATGAATGAATGCAGCCGGATATAGTACCCTAGAATAAGATTTTCCTTATG
1 GAAACATTGAAGCATATGAATGAATGCAGCCGGATATAGTACCCTAGAATAAGATTTTCCTTATG
208544 ATATTATTCTAGGTAATTACCTGCCTATTGCTCATGTAGTTGAATTACCAAAGTATAGTCTTA
66 ATATTATTCTAGGTAATTACCTGCCTATTGCTCATGTAGTTGAATTACCAAAGTATAGTCTTA
208607 GAAACATTGAAGCATATGAATGAATGCAGCCGGATATAGTACCCTAGAATAAGATTTTCCTTATG
1 GAAACATTGAAGCATATGAATGAATGCAGCCGGATATAGTACCCTAGAATAAGATTTTCCTTATG
208672 ATATTATTCTAGGTAATTACCTGCCTATTGCTCATGTAGTTGAATTACCAAAGTATAGTCTTA
66 ATATTATTCTAGGTAATTACCTGCCTATTGCTCATGTAGTTGAATTACCAAAGTATAGTCTTA
208735 GA
1 GA
208737 GCCACCTAAT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 130 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (128 bp):
GAAACATTGAAGCATATGAATGAATGCAGCCGGATATAGTACCCTAGAATAAGATTTTCCTTATG
ATATTATTCTAGGTAATTACCTGCCTATTGCTCATGTAGTTGAATTACCAAAGTATAGTCTTA
Found at i:221044 original size:18 final size:18
Alignment explanation
Indices: 221021--221057 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
221011 GAATATTTAT
221021 ATATATATATATATAATAAA
1 ATATA-ATATA-ATAATAAA
221041 ATATAATATAATAATAA
1 ATATAATATAATAATAA
221058 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATAATATAATAATAAA
Found at i:221584 original size:18 final size:19
Alignment explanation
Indices: 221561--221599 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
221551 TTCTTACAAT
221561 TAAATAATA-TTAATATTA
1 TAAATAATATTTAATATTA
*
221579 TAAATAATATTTTATATTA
1 TAAATAATATTTAATATTA
221598 TA
1 TA
221600 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATAATATTTAATATTA
Found at i:228406 original size:144 final size:143
Alignment explanation
Indices: 228079--228563 Score: 535
Period size: 144 Copynumber: 3.3 Consensus size: 143
228069 TTAAAACACA
* * * *
228079 AAAAATCATGAAATATTATAAAATTAAGATTTGAAAAGTTTCATGAAAATCCGAGCTCA-AAAAT
1 AAAAATCATGAAATATTATAAAATTAAAATCTGAAAAGTTTCATGAAAATCTGAGCTCAGGAAA-
** * * * * * * * * *
228143 GTCAAATTACAAAAATACCCTTATAGAGGTAATTTGGTAAATTCACACTTCTGTGAGGTATTGTT
65 GTCAAATTATGAAAATACTCTTATA-AGGTATTTTGATAATTTCA-AATT-TTTCAGGTACTGCT
*
228208 GTGATTTCAAATGCACC
127 GTGATTTCAAATGCATC
* * * * ** *
228225 AAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTTATGAAAATCTAAGCTTGGGAACG
1 AAAAATCATGAAATATTATAAAATTAAAATCTGAAAAGTTTCATGAAAATCTGAGCTCAGGAAAG
228290 TCAAATTATGAAAATACTCTTATAATGGTATTTTGATAATTTCAAATTTTTCAGGGTACT-CTGT
66 TCAAATTATGAAAATACTCTTATAA-GGTATTTTGATAATTTCAAATTTTTCA-GGTACTGCTGT
* *
228354 GATTTCAAATACATT
129 GATTTCAAATGCATC
* *
228369 AAAAATCATGAAATATTATAAAATTAAAATCTAAAAAGTTTCATGAAAATTTGAGCTCAGGAAAG
1 AAAAATCATGAAATATTATAAAATTAAAATCTGAAAAGTTTCATGAAAATCTGAGCTCAGGAAAG
* * * ** * * *
228434 GCAAATTATGAAAATATTCTTATAAAAGTATTTCAATAATTTCACACTTTTCAAGATACTGCTGT
66 TCAAATTATGAAAATACTCTTAT-AAGGTATTTTGATAATTTCAAATTTTTC-AGGTACTGCTGT
228499 GATTTCAAATGCATC
129 GATTTCAAATGCATC
* *
228514 AAAAATCATAAATATATTATGAAATTAAAATCTGAAAAGTTTCAT-AAAAT
1 AAAAATCATGAA-ATATTATAAAATTAAAATCTGAAAAGTTTCATGAAAAT
228564 TCGAACTCGA
Statistics
Matches: 287, Mismatches: 45, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
144 121 0.42
145 45 0.16
146 119 0.41
147 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (143 bp):
AAAAATCATGAAATATTATAAAATTAAAATCTGAAAAGTTTCATGAAAATCTGAGCTCAGGAAAG
TCAAATTATGAAAATACTCTTATAAGGTATTTTGATAATTTCAAATTTTTCAGGTACTGCTGTGA
TTTCAAATGCATC
Found at i:229395 original size:106 final size:105
Alignment explanation
Indices: 229202--229506 Score: 323
Period size: 106 Copynumber: 2.9 Consensus size: 105
229192 CCACAAACAA
* * * * *
229202 AAGTCTTACAAATCTCAAAAATCTTTGAATGCTCCA-CGTAATAGAGGCGTTTAAACTTTGAAAA
1 AAGTCATACAAATCTTAAAAATCTTTGAATGCTCCATC-CAATAGAGGCATTGAAACTTTGAAAA
* *
229266 TTTAAAATATTTTG-TCCGGAGGTCTTGAAGATTATGC-CTAG
65 TTTAAAATGTTTTGCT-AGGAGGTCTTGAAGATTATGCTC-AG
* * * *
229307 AGGTCATACAAAAT-TTAAAAATCTTTGAATGCTCCATCCAATCAAAAGCATTGAAACTTTAAAA
1 AAGTCATAC-AAATCTTAAAAATCTTTGAATGCTCCATCCAAT-AGAGGCATTGAAACTTTGAAA
* * *
229371 ATTTAAAATGTTTTGCTAGAAGGTCTTGGAGATTATGCTCGG
64 ATTTAAAATGTTTTGCTAGGAGGTCTTGAAGATTATGCTCAG
** * * * *
229413 AAGTGTTACAAATCTTAAAAATCTTTAAATGCT-CTTCCTAATTAGAGGCAATGAAAATTTGAAA
1 AAGTCATACAAATCTTAAAAATCTTTGAATGCTCCATCC-AA-TAGAGGCATTGAAACTTTGAAA
*
229477 ATTTAAAATGTTTTGCTTGGAGGTCTTGAA
64 ATTTAAAATGTTTTGCTAGGAGGTCTTGAA
229507 AATCTCAAAA
Statistics
Matches: 165, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
105 39 0.24
106 123 0.75
107 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (105 bp):
AAGTCATACAAATCTTAAAAATCTTTGAATGCTCCATCCAATAGAGGCATTGAAACTTTGAAAAT
TTAAAATGTTTTGCTAGGAGGTCTTGAAGATTATGCTCAG
Found at i:229552 original size:189 final size:188
Alignment explanation
Indices: 229324--229680 Score: 461
Period size: 189 Copynumber: 1.9 Consensus size: 188
229314 ACAAAATTTA
* * *
229324 AAAATCTTTGAATGCTCCATCCAATCAAAAGCATTGAAACTTTAAAAATTTAAAATGTTTTGCTA
1 AAAATCTTTGAATGCTCCATCCAATCAAAAGCATTGAAACTATAAAAATTTAAAATATTTTACTA
* * * * *
229389 GAAGGTCTTGGAGATTATGCTCGGAAGTGTT-ACAAATCTTAAAAATCTTTAAATGCTCTTCCTA
66 GAAGGTCTTGGAGATTATGCCCAGAAGTCTTGA-AAATCTCAAAAATCTTTAAATGCTCATCCTA
* *
229453 ATTAGAGGCAATGAAAATTTGAAAATT-TAAAATGTTTTGCTTGGAGGTCTTGAAAATCTC
130 A-TAAAGGCAATGAAAATTT-AAAATTATAAAATATTTTGCTTGGAGGTCTTGAAAATCTC
* * *
229513 AAAATCTTTTGAATGCT-CATCGTAAT-AGAGGCATTGAAACTATAAAAATTTAAAATATTTTAC
1 AAAATC-TTTGAATGCTCCATC-CAATCAAAAGCATTGAAACTATAAAAATTTAAAATATTTTAC
* * * * *
229576 TCGAAGGTCTTGGAGATTATGCCCAGAGGTCTTGAAAATCTCAAAATTCTTTGAATGCTCATCGT
64 TAGAAGGTCTTGGAGATTATGCCCAGAAGTCTTGAAAATCTCAAAAATCTTTAAATGCTCATCCT
* *
229641 AATAAAGGCATTGAAACTTTAAAATTATAAAATATTTTGC
129 AATAAAGGCAATGAAAATTTAAAATTATAAAATATTTTGC
229681 CCAAAGTTCT
Statistics
Matches: 144, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
187 6 0.04
188 27 0.19
189 97 0.67
190 14 0.10
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (188 bp):
AAAATCTTTGAATGCTCCATCCAATCAAAAGCATTGAAACTATAAAAATTTAAAATATTTTACTA
GAAGGTCTTGGAGATTATGCCCAGAAGTCTTGAAAATCTCAAAAATCTTTAAATGCTCATCCTAA
TAAAGGCAATGAAAATTTAAAATTATAAAATATTTTGCTTGGAGGTCTTGAAAATCTC
Found at i:229562 original size:83 final size:83
Alignment explanation
Indices: 229430--229587 Score: 201
Period size: 83 Copynumber: 1.9 Consensus size: 83
229420 ACAAATCTTA
* * * * * *
229430 AAAATCTTTAAATGCTCTTCCTAATTAGAGGCAATGAAAATTTGAAAATTTAAAATGTTTTGCTT
1 AAAATCTTTAAATGCTCATCCTAATTAGAGGCAATGAAAATATAAAAATTTAAAATATTTTACTC
*
229495 GGAGGTCTTGAAAATCTC
66 GAAGGTCTTGAAAATCTC
* * * *
229513 AAAATCTTTTGAATGCTCATCGTAA-TAGAGGCATTGAAACTATAAAAATTTAAAATATTTTACT
1 AAAATC-TTTAAATGCTCATCCTAATTAGAGGCAATGAAAATATAAAAATTTAAAATATTTTACT
229577 CGAAGGTCTTG
65 CGAAGGTCTTG
229588 GAGATTATGC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
83 48 0.76
84 15 0.24
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (83 bp):
AAAATCTTTAAATGCTCATCCTAATTAGAGGCAATGAAAATATAAAAATTTAAAATATTTTACTC
GAAGGTCTTGAAAATCTC
Found at i:229692 original size:105 final size:105
Alignment explanation
Indices: 229496--229694 Score: 312
Period size: 105 Copynumber: 1.9 Consensus size: 105
229486 GTTTTGCTTG
*
229496 GAGGTCTTGAAAATCTCAAAATCTTTTGAATGCTCATCGTAATAGAGGCATTGAAACTATAAAAA
1 GAGGTCTTGAAAATCTCAAAATCTTTTGAATGCTCATCGTAATAAAGGCATTGAAACTATAAAAA
* *
229561 TTTAAAATATTTTACTCGAAGGTCTTGGAGATTATGCCCA
66 TTTAAAATATTTTACCCAAAGGTCTTGGAGATTATGCCCA
*
229601 GAGGTCTTGAAAATCTCAAAAT-TCTTTGAATGCTCATCGTAATAAAGGCATTGAAACT-TTAAA
1 GAGGTCTTGAAAATCTCAAAATCT-TTTGAATGCTCATCGTAATAAAGGCATTGAAACTATAAAA
* *
229664 ATTATAAAATATTTTGCCCAAAGTTCTTGGA
65 ATT-TAAAATATTTTACCCAAAGGTCTTGGA
229695 AATATATCTG
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
104 8 0.09
105 78 0.91
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (105 bp):
GAGGTCTTGAAAATCTCAAAATCTTTTGAATGCTCATCGTAATAAAGGCATTGAAACTATAAAAA
TTTAAAATATTTTACCCAAAGGTCTTGGAGATTATGCCCA
Found at i:230006 original size:18 final size:18
Alignment explanation
Indices: 229980--230022 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
229970 AAATGATGCT
* * *
229980 AATGGAAATATCAATATG
1 AATGCAAATATCAAAATA
*
229998 AATGCAAATGTCAAAATA
1 AATGCAAATATCAAAATA
230016 AATGCAA
1 AATGCAA
230023 GAATGCAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (18 bp):
AATGCAAATATCAAAATA
Found at i:231172 original size:82 final size:82
Alignment explanation
Indices: 231016--231173 Score: 187
Period size: 82 Copynumber: 1.9 Consensus size: 82
231006 TTGTAAATTG
* * **
231016 ATGATTACTATCTGGAATACTTATGGACGGCATGATTGGCAATTCAATTTTTCACTAGTGGGCAT
1 ATGATTACTATCTGGAATACTTATGGACGGCATGATTGACAATTCAAATTTTCACTAGTAAGCAT
231081 ATTTCTAAGAAGGCTTT
66 ATTTCTAAGAAGGCTTT
* * * * *
231098 ATGATTACTATTTGGAATATTTATGGATGTG-GTGATTGATAATTCAAAATTTTCACT-GATAAG
1 ATGATTACTATCTGGAATACTTATGGACG-GCATGATTGACAATTC-AAATTTTCACTAG-TAAG
231161 CATATTT-TAAGAA
63 CATATTTCTAAGAA
231174 AGGATCGATA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
82 44 0.69
83 20 0.31
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (82 bp):
ATGATTACTATCTGGAATACTTATGGACGGCATGATTGACAATTCAAATTTTCACTAGTAAGCAT
ATTTCTAAGAAGGCTTT
Found at i:232203 original size:21 final size:21
Alignment explanation
Indices: 232179--232231 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
232169 TCGAAGTGCA
232179 TTTCTTTCTTTCTTCGCTC-TT
1 TTTCTTTCTTTCTTC-CTCATT
* *
232200 TTTCTTTTTTTTTTCCTCATT
1 TTTCTTTCTTTCTTCCTCATT
232221 TTT-TTTGCTTT
1 TTTCTTT-CTTT
232232 ATCTTATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTCTTTCTTTCTTCCTCATT
Found at i:234040 original size:3 final size:3
Alignment explanation
Indices: 234026--234209 Score: 69
Period size: 3 Copynumber: 58.3 Consensus size: 3
234016 TTTTATCTGG
* * * * *
234026 TAT TAT TTT TAT TAT TAT TTT TTT TCT TTT GTAT T-T TAT GTAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT
* *
234071 TGT TAT TATT TAT TAT TAT TAT TAT TAT TAT GTAT TAA TA- TAT ATAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT
* * *
234118 CT-T TATT TATT TATT TATT TAT T-T TTT TGT TAA TAT T-T ATAT GTAT
1 -TAT TA-T TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT -TAT -TAT
234164 T-T TATT TAT ATAGT TAT ATATT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TA-T TAT -TA-T TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT
234209 T
1 T
234210 TTGTAATATT
Statistics
Matches: 147, Mismatches: 14, Indels: 40
0.73 0.07 0.20
Matches are distributed among these distances:
2 14 0.10
3 86 0.59
4 45 0.31
5 2 0.01
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:234043 original size:12 final size:12
Alignment explanation
Indices: 234026--234211 Score: 80
Period size: 12 Copynumber: 14.8 Consensus size: 12
234016 TTTTATCTGG
234026 TATTATTTTTAT
1 TATTATTTTTAT
*
234038 TATTATTTTTTT
1 TATTATTTTTAT
*
234050 TCTT-TTGTATT-T
1 TATTATT-T-TTAT
*
234062 TATGTA-TTTTGT
1 TAT-TATTTTTAT
234074 TATTATTTATTAT
1 TATTATTT-TTAT
*
234087 TATTATTATTAT
1 TATTATTTTTAT
**
234099 TATGTATTAATA-
1 TAT-TATTTTTAT
*
234111 TATATATCTTTATT
1 TAT-TATTTTTA-T
*
234125 TATT-TATTTATT
1 TATTATTTTTA-T
*
234137 TATT-TTTTTGT
1 TATTATTTTTAT
* *
234148 TAATATTTATAT
1 TATTATTTTTAT
234160 GTATT-TTATTTAT
1 -TATTATT-TTTAT
234173 ATAGTTATATATTTAT
1 -TA-TTAT-T-TTTAT
234189 TATTATATTATTAT
1 TATTAT-TT-TTAT
234203 TATTATTTT
1 TATTATTTT
234212 GTAATATTTT
Statistics
Matches: 138, Mismatches: 19, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
11 10 0.07
12 63 0.46
13 34 0.25
14 21 0.15
15 3 0.02
16 7 0.05
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (12 bp):
TATTATTTTTAT
Found at i:234126 original size:4 final size:4
Alignment explanation
Indices: 234119--234189 Score: 52
Period size: 4 Copynumber: 16.5 Consensus size: 4
234109 TATATATATC
* *
234119 TTTA TTTA TTTA TTTA TTTA TTTT TTTG TTAATA TTTA TATGTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA T-T-TA -TTTA
* * *
234168 TTTA TATA GTTA TATA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TT
234190 ATTATATTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
4 43 0.81
5 3 0.06
6 6 0.11
7 1 0.02
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:234236 original size:104 final size:107
Alignment explanation
Indices: 234055--234252 Score: 257
Period size: 104 Copynumber: 1.9 Consensus size: 107
234045 TTTTTTCTTT
* *
234055 TGTATTTTATGTATTTTGTTATTATTTATTATTATTATTATTATTATGTATTAATATATATATCT
1 TGTATTTTATGTATATAGTTATTATTTATTATTATTATTATTATTATGTATTAATATATATATCT
234120 TTATTTATTTA-TTTA-TTTATTT-TTTTGTTAATATTTATA
66 TTATTTATTTATTTTATTTTATTTATTTTGTTAATATTTATA
* * * *
234159 TGTATTTTATTTATATAGTTATATATTTATTATTA-TATTATTATTAT-TATT-TTGTA-ATATT
1 TGTATTTTATGTATATAGTTAT-TATTTATTATTATTATTATTATTATGTATTAATATATATATC
234220 TTTGGATTTATCTTATTTTATTTTATTTATTTT
65 TTT--ATTTAT-TTATTTTATTTTATTTATTTT
234253 TTTGTAATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
101 7 0.09
102 3 0.04
103 10 0.12
104 34 0.42
105 16 0.20
106 7 0.09
107 4 0.05
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (107 bp):
TGTATTTTATGTATATAGTTATTATTTATTATTATTATTATTATTATGTATTAATATATATATCT
TTATTTATTTATTTTATTTTATTTATTTTGTTAATATTTATA
Found at i:234282 original size:113 final size:104
Alignment explanation
Indices: 234055--234257 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 104
234045 TTTTTTCTTT
* * * **
234055 TGTATTTTATGTATTTTGTTATTATTTATTATTATTATTATTATTATGTATTAATATATATATCT
1 TGTATTTTATTTATATAGTTATTATTTATTATTATTATTATTATTATGTATTAATATATATAGAT
234120 TTATTTATTTATTTATTTATTTTTTTGTTAATATTTATA
66 TTATTTATTTATTTATTTATTTTTTTGTTAATATTTATA
* * *
234159 TGTATTTTATTTATATAGTTATATATTTATTATTATATTATTATTATTAT-TTTGTAATATTTTT
1 TGTATTTTATTTATATAGTTAT-TATTTATTA-T-TATTATTATTATTATGTAT-TAATATATAT
*
234223 GGATTTATCTTATTTTATTTTATTTATTTTTTTGT
62 AGATTTAT-TTA-TTTA-TTTATTTATTTTTTTGT
234258 AATTATCTGT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
104 19 0.23
105 9 0.11
106 3 0.04
107 28 0.34
108 3 0.04
109 4 0.05
110 17 0.20
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (104 bp):
TGTATTTTATTTATATAGTTATTATTTATTATTATTATTATTATTATGTATTAATATATATAGAT
TTATTTATTTATTTATTTATTTTTTTGTTAATATTTATA
Found at i:235166 original size:13 final size:13
Alignment explanation
Indices: 235149--235264 Score: 52
Period size: 14 Copynumber: 8.0 Consensus size: 13
235139 TTTTTTTAGA
235149 ATTTTTTTTATTT
1 ATTTTTTTTATTT
* *
235162 GTTTTATTTATTT
1 ATTTTTTTTATTT
*
235175 ATTTTTATTTATTAG
1 ATTTTT-TTTATT-T
***
235190 ATTAGATTTATTT
1 ATTTTTTTTATTT
235203 AATATTTTTTTACCTTT
1 -AT-TTTTTTTA--TTT
235220 ATCTTATTTTTATTTT
1 AT-TT-TTTTTA-TTT
*
235236 ACTTTTCTTTTTTTT
1 A-TTTT-TTTTATTT
*
235251 ATCTTTATTTATTT
1 AT-TTTTTTTATTT
235265 TCACTTTTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
13 15 0.20
14 21 0.28
15 16 0.21
16 14 0.18
17 10 0.13
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (13 bp):
ATTTTTTTTATTT
Found at i:235182 original size:14 final size:14
Alignment explanation
Indices: 235149--235187 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
235139 TTTTTTTAGA
235149 ATTTTT-TTTATTT
1 ATTTTTATTTATTT
*
235162 -GTTTTATTTATTT
1 ATTTTTATTTATTT
235175 ATTTTTATTTATT
1 ATTTTTATTTATT
235188 AGATTAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 11 0.50
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
ATTTTTATTTATTT
Found at i:235255 original size:31 final size:31
Alignment explanation
Indices: 235217--235277 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
235207 TTTTTTTACC
* *
235217 TTTATCTTATTTTTATTTT-ACTTTTCTTTTT
1 TTTATCTT-TATTTATTTTCACTTTTATTTTT
235248 TTTATCTTTATTTATTTTCACTTTTATTTT
1 TTTATCTTTATTTATTTTCACTTTTATTTT
235278 GTTCTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTATCTTTATTTATTTTCACTTTTATTTTT
Found at i:235273 original size:16 final size:15
Alignment explanation
Indices: 235228--235276 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
235218 TTATCTTATT
*
235228 TTTATTTTACTTTTC
1 TTTATTTTACTTTTA
*
235243 TTTTTTTTA-TCTTTA
1 TTTATTTTACT-TTTA
235258 TTTATTTTCACTTTTA
1 TTTATTTT-ACTTTTA
235274 TTT
1 TTT
235277 TGTTCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.04
15 18 0.64
16 8 0.29
17 1 0.04
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTACTTTTA
Found at i:235273 original size:37 final size:36
Alignment explanation
Indices: 235207--235277 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
235197 TTATTTAATA
*
235207 TTTTTTTACCTTTATCTTATTTTTATTTTACTTTTCT
1 TTTTTTTACCTTTATCTTATTTTCATTTTA-TTTTCT
*
235244 TTTTTTTATCTTTAT-TTATTTTCACTTTTATTTT
1 TTTTTTTACCTTTATCTTATTTTCA-TTTTATTTT
235278 GTTCTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (36 bp):
TTTTTTTACCTTTATCTTATTTTCATTTTATTTTCT
Found at i:235285 original size:22 final size:22
Alignment explanation
Indices: 235247--235288 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
235237 CTTTTCTTTT
235247 TTTTATCTTTATTTATTTTCAC
1 TTTTATCTTTATTTATTTTCAC
*
235269 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTATT-TATTTTC
235289 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTATTTATTTTCAC
Found at i:235368 original size:58 final size:58
Alignment explanation
Indices: 235299--235689 Score: 536
Period size: 58 Copynumber: 6.7 Consensus size: 58
235289 TTTAAATAAA
**
235299 AAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
235357 AAAAAAATATTTTTGGGGAAAAATTGAAAGTATCAATTTTTCTTAAGAATAAATTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
235415 -AAAAAATA-TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
235471 AAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTCAAAATTTTC
1 -AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTTC
* * * * *
235532 -GAAAAATAGTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTTC
* *
235591 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
1 -AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * **
235650 AAAAAAGTATATTTGGGGAAATTTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
235690 TCCTGCACAA
Statistics
Matches: 297, Mismatches: 28, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
56 45 0.15
57 8 0.03
58 99 0.33
59 90 0.30
60 3 0.01
61 52 0.18
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (58 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:243731 original size:9 final size:9
Alignment explanation
Indices: 243711--243789 Score: 78
Period size: 8 Copynumber: 9.1 Consensus size: 9
243701 TACTATGCTT
243711 AAAAAAAT-
1 AAAAAAATG
243719 -AAAAAA-G
1 AAAAAAATG
*
243726 GAAAAAATG
1 AAAAAAATG
243735 -AAAAAATG
1 AAAAAAATG
243743 AAAAAAAAT-
1 -AAAAAAATG
*
243752 AAAAAAATA
1 AAAAAAATG
243761 AAAAAAATG
1 AAAAAAATG
*
243770 AAAAAAGTG
1 AAAAAAATG
243779 AAAAAGAATG
1 AAAAA-AATG
243789 A
1 A
243790 CTCAAGGCGA
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
7 6 0.10
8 22 0.36
9 22 0.36
10 11 0.18
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:243740 original size:18 final size:18
Alignment explanation
Indices: 243711--243789 Score: 94
Period size: 17 Copynumber: 4.6 Consensus size: 18
243701 TACTATGCTT
243711 AAAAAAAT-AAAAAA-G-
1 AAAAAAATGAAAAAATGA
*
243726 GAAAAAATGAAAAAATGA
1 AAAAAAATGAAAAAATGA
*
243744 AAAAAAATAAAAAAAT-A
1 AAAAAAATGAAAAAATGA
243761 AAAAAAATGAAAAAAGTGA
1 AAAAAAATGAAAAAA-TGA
*
243780 AAAAGAATGA
1 AAAAAAATGA
243790 CTCAAGGCGA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
15 7 0.13
16 6 0.11
17 16 0.30
18 15 0.28
19 10 0.19
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (18 bp):
AAAAAAATGAAAAAATGA
Found at i:244837 original size:41 final size:40
Alignment explanation
Indices: 244789--245050 Score: 337
Period size: 41 Copynumber: 6.4 Consensus size: 40
244779 ATGATTGTCA
244789 AGGAGCAATTTACTTTCCAAAGTTCCGT-TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAG-T-CGTGTGCCTCTGTTTAG
* * ** *
244830 ATGAGCAATTTATTTTTTAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAG
*
244871 AGGAGCAATTTGCTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAG
* * *
244912 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAA
1 AGGAGCAATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAG
* *
244953 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCTTTTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAG
* *
244994 AGGAGCAATTTATTTTTCAAAGTCGTAGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAG
245035 AGGAGCAATTTACTTT
1 AGGAGCAATTTACTTT
245051 TTCAAAGAGG
Statistics
Matches: 193, Mismatches: 26, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 190 0.98
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (40 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGTGCCTCTGTTTAG
Found at i:244926 original size:82 final size:82
Alignment explanation
Indices: 244789--245050 Score: 420
Period size: 82 Copynumber: 3.2 Consensus size: 82
244779 ATGATTGTCA
* *
244789 AGGAGCAATTTACTTTCCAAAGTTCCGT--TGCCTCTGTTTAGATGAGCAATTTATTTTTTAAAG
1 AGGAGCAATTTACTTTCCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAG
*
244852 TTGTGGTGCCTCTGTTTAG
64 TCGTGGTGCCTCTGTTTAG
*
244871 AGGAGCAATTTGCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTC
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTC
*
244936 GTGGTGCCTCTGTTTAA
66 GTGGTGCCTCTGTTTAG
* *
244953 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCTTTTGTTTAGAGGAGCAATTTATTTTTCAAAGTC
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTC
*
245018 GTAGTGCCTCTGTTTAG
66 GTGGTGCCTCTGTTTAG
245035 AGGAGCAATTTACTTT
1 AGGAGCAATTTACTTT
245051 TTCAAAGAGG
Statistics
Matches: 168, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
80 3 0.02
81 1 0.01
82 164 0.98
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (82 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTC
GTGGTGCCTCTGTTTAG
Found at i:245015 original size:123 final size:123
Alignment explanation
Indices: 244789--245057 Score: 371
Period size: 123 Copynumber: 2.2 Consensus size: 123
244779 ATGATTGTCA
* * * * * ** *
244789 AGGAGCAATTTACTTTCCAAAGTTCCGTTGCCTCTGTTTAGATGAGCAATTTATTTTTTAAAGTT
1 AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAAAGGAGCAATTTACTTTCCAAAGTC
* *
244854 GTGGTGCCTCTGTTTAGAGGAGCAATTTGCTTTCCAAAGTCGTGGTGCCTCTGTTTAG
66 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTAGTGCCTCTGTTTAG
244912 AGGAGCAATTTATTTTTCAAAG-T-CGTGGTGCCTCTGTTTAAAGGAGCAATTTACTTTCCAAAG
1 AGGAGCAATTTATTTTTCAAAGTTCCGT--TGCCTCTGTTTAAAGGAGCAATTTACTTTCCAAAG
* * * *
244975 TCGTGGTGCTTTTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTAGTGCCTCTGTTTAG
64 TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTAGTGCCTCTGTTTAG
245035 AGGAGCAATTTACTTTTTCAAAG
1 AGGAGCAATTTA-TTTTTCAAAG
245058 AGGAGCAATT
Statistics
Matches: 129, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
121 3 0.02
122 1 0.01
123 115 0.89
124 10 0.08
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (123 bp):
AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAAAGGAGCAATTTACTTTCCAAAGTC
GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTAGTGCCTCTGTTTAG
Found at i:245063 original size:23 final size:23
Alignment explanation
Indices: 245033--245080 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
245023 GCCTCTGTTT
245033 AGAGGAGCAATTTACTTTTTCAA
1 AGAGGAGCAATTTACTTTTTCAA
245056 AGAGGAGCAATTTACTTTTTCAA
1 AGAGGAGCAATTTACTTTTTCAA
245079 AG
1 AG
245081 TCATGGTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
AGAGGAGCAATTTACTTTTTCAA
Found at i:245092 original size:65 final size:64
Alignment explanation
Indices: 244992--245115 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 64
244982 GCTTTTGTTT
*
244992 AGAGGAGCAATTTATTTTTCAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAA
1 AGAGGAGCAATTTATTTTTCAAAGTCATAGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAA
* *
245056 AGAGGAGCAATTTACTTTTTCAAAGTCATGGTGCCTCTGTTTAGATGAGCAATTTACTTT
1 AGAGGAGCAATTTA-TTTTTCAAAGTCATAGTGCCTCTGTTTAGAGGAGCAATTTACTTT
245116 CCAAAAGTCG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
64 14 0.25
65 42 0.75
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (64 bp):
AGAGGAGCAATTTATTTTTCAAAGTCATAGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAA
Found at i:245123 original size:42 final size:42
Alignment explanation
Indices: 245060--245190 Score: 167
Period size: 42 Copynumber: 3.1 Consensus size: 42
245050 TTTCAAAGAG
* *
245060 GAGCAATTTACTTTTTC-AAAGTCATGGTGCCTCTGTTTAGAT
1 GAGCAATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAT
245102 GAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAT
1 GAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAT
* * * *
245144 GAGCAATTTATGTTTCTCAAAA-TCGTTGAGCCTCTGTTTAGAG
1 GAGCAATTTA-CTTTC-CAAAAGTCGTGGTGCCTCTGTTTAGAT
245187 GAGC
1 GAGC
245191 TTTGGTAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
41 4 0.05
42 45 0.56
43 26 0.32
44 5 0.06
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (42 bp):
GAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAT
Found at i:245203 original size:1 final size:1
Alignment explanation
Indices: 245197--245273 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
245187 GAGCTTTGGT
* * * * * * * * *
245197 AAAAAAAAAAACAAAAAAACAAAAAAACACAAAAACAAAACAAAAAAAAAATAAAAAACACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
245262 AAAAACAAAAAA
1 AAAAAAAAAAAA
245274 TGACAATGTT
Statistics
Matches: 56, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:245273 original size:8 final size:8
Alignment explanation
Indices: 245197--245264 Score: 86
Period size: 8 Copynumber: 8.5 Consensus size: 8
245187 GAGCTTTGGT
245197 AAAA-AAA
1 AAAACAAA
245204 AAAACAAA
1 AAAACAAA
245212 AAAACAAA
1 AAAACAAA
*
245220 AAAACACA
1 AAAACAAA
245228 AAAACAAA
1 AAAACAAA
245236 ACAAA-AAA
1 A-AAACAAA
*
245244 AAAATAAA
1 AAAACAAA
245252 AAACACAAA
1 AAA-ACAAA
245261 AAAA
1 AAAA
245265 AACAAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.13
8 37 0.69
9 10 0.19
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.01
Consensus pattern (8 bp):
AAAACAAA
Found at i:245279 original size:10 final size:10
Alignment explanation
Indices: 245197--245273 Score: 95
Period size: 10 Copynumber: 7.6 Consensus size: 10
245187 GAGCTTTGGT
245197 AAAAAAAAA-
1 AAAAAAAAAC
245206 AACAAAAAAAC
1 AA-AAAAAAAC
*
245217 AAAAAAACAC
1 AAAAAAAAAC
245227 AAAAACAAAAC
1 AAAAA-AAAAC
245238 AAAAAAAAA-
1 AAAAAAAAAC
*
245247 ATAAAAAACAC
1 A-AAAAAAAAC
245258 AAAAAAAAAC
1 AAAAAAAAAC
245268 AAAAAA
1 AAAAAA
245274 TGACAATGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
9 3 0.05
10 44 0.75
11 12 0.20
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:245451 original size:3 final size:3
Alignment explanation
Indices: 245437--245597 Score: 57
Period size: 3 Copynumber: 51.3 Consensus size: 3
245427 TTTTATCTGG
* * * * *
245437 TAT TAT TTT TAT TAT TTT TTT TCT TTT GTAT T-T TAT ATAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT
*
245482 TATT TAT TAT TAT TAT TAT TAT GTAT TAA TA- TAT ATAT CT-T TATT
1 TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT -TAT TA-T
* * * *
245527 TAT TTT TTT TGT TAA TAT T-T ATAT GTAT T-T TATT TAT ATAGT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TA-T TAT -TA-T TAT
245572 ATATT TAT TAT TA- TAT TAT TAT TAT T
1 -TA-T TAT TAT TAT TAT TAT TAT TAT T
245598 TTGTAATATT
Statistics
Matches: 125, Mismatches: 14, Indels: 38
0.71 0.08 0.21
Matches are distributed among these distances:
2 12 0.10
3 78 0.62
4 33 0.26
5 2 0.02
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:245607 original size:31 final size:32
Alignment explanation
Indices: 245477--245608 Score: 91
Period size: 31 Copynumber: 4.1 Consensus size: 32
245467 TTTTATATAT
*
245477 TTTATTATTTATTATTATTATTATTATGTATTAATA
1 TTTATTA-TTA-TATTATTATTATT-T-TGTTAATA
245513 TATATATCT-TTAT-TTATT-TT-TTTTGTTAATA
1 T-T-TAT-TATTATATTATTATTATTTTGTTAATA
* * *
245544 TTTA-TA-TGTATT-TTATTTATATAGTTATATA
1 TTTATTATTATATTATTA-TTATTTTGTTA-ATA
245575 TTTATTATTATATTATTATTATTTTG-TAATA
1 TTTATTATTATATTATTATTATTTTGTTAATA
245606 TTT
1 TTT
245609 TTGGATTTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 29
0.68 0.06 0.26
Matches are distributed among these distances:
27 5 0.06
28 2 0.03
29 4 0.05
30 7 0.09
31 21 0.27
32 5 0.06
33 13 0.17
34 5 0.06
35 5 0.06
36 2 0.03
37 4 0.05
38 3 0.04
39 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (32 bp):
TTTATTATTATATTATTATTATTTTGTTAATA
Found at i:246568 original size:13 final size:13
Alignment explanation
Indices: 246552--246593 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
246542 TTTTTTTGGA
246552 ATTTTTTTTATTT
1 ATTTTTTTTATTT
*
246565 ATTTGTTTTATTT
1 ATTTTTTTTATTT
*
246578 A-TTTATTTATTT
1 ATTTTTTTTATTT
246590 ATTT
1 ATTT
246594 ATTAGATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
ATTTTTTTTATTT
Found at i:246573 original size:17 final size:17
Alignment explanation
Indices: 246553--246596 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
246543 TTTTTTGGAA
*
246553 TTTTTTTTATTTATTTG
1 TTTTATTTATTTATTTG
246570 TTTTATTTATTTATTT-
1 TTTTATTTATTTATTTG
*
246586 ATTTATTTATT
1 TTTTATTTATT
246597 AGATTAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTATTTATTTATTTG
Found at i:246612 original size:4 final size:4
Alignment explanation
Indices: 246558--246596 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
246548 TGGAATTTTT
*
246558 TTTA TTTA TTTGT TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TT
246597 AGATTAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:246667 original size:18 final size:18
Alignment explanation
Indices: 246625--246682 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 18
246615 ATTTTTTATC
*
246625 TTTATCTTATTTTTATTTT
1 TTTATCTT-TCTTTATTTT
*
246644 TGTTTTACTTTTCTTTATTTT
1 T-TTAT-C-TTTCTTTATTTT
246665 TTTATCTTTCTTTATTTT
1 TTTATCTTTCTTTATTTT
246683 CACTTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 12 0.36
19 2 0.06
20 6 0.18
21 11 0.33
22 2 0.06
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTATCTTTCTTTATTTT
Found at i:246702 original size:22 final size:22
Alignment explanation
Indices: 246664--246705 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
246654 TTCTTTATTT
246664 TTTTATCTTTCTTTATTTTCAC
1 TTTTATCTTTCTTTATTTTCAC
*
246686 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTCTT-TATTTTC
246706 TTTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTCTTTATTTTCAC
Found at i:246779 original size:59 final size:59
Alignment explanation
Indices: 246715--247223 Score: 716
Period size: 59 Copynumber: 8.7 Consensus size: 59
246705 CTTTAAATTA
* *
246715 AAAAAATATATTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
246774 AAAAAA-ATATTTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAATATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
246832 -AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*** *
246889 AAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
1 AAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
246948 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTT-
1 AAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTTC
* *
247008 GAAAAATAT-TTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
247065 AAAAAA-AGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
1 AAAAAATA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTTC
*
247126 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTC
1 AAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
247183 TAAAAAA-GTATTTTTGAGGAAAATTTGAAAGTATCAATTTT
1 -AAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
247224 TCCTGCACAA
Statistics
Matches: 410, Mismatches: 27, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
56 14 0.03
57 58 0.14
58 125 0.30
59 145 0.35
60 50 0.12
61 18 0.04
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.36
Consensus pattern (59 bp):
AAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:246785 original size:58 final size:58
Alignment explanation
Indices: 246714--247223 Score: 744
Period size: 58 Copynumber: 8.7 Consensus size: 58
246704 TCTTTAAATT
*
246714 AAAAAAATATATTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAATAT-TTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
246774 AAAAAAATATTTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
246832 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
** *
246889 AAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
1 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
246948 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTT-
1 -AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTTC
*
247008 -GAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
247065 AAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
1 AAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTTC
*
247126 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
247183 TAAAAAAGTATTTTTGAGGAAAATTTGAAAGTATCAATTTT
1 -AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
247224 TCCTGCACAA
Statistics
Matches: 412, Mismatches: 23, Indels: 32
0.88 0.05 0.07
Matches are distributed among these distances:
56 13 0.03
57 53 0.13
58 134 0.33
59 130 0.32
60 63 0.15
61 19 0.05
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:246836 original size:117 final size:118
Alignment explanation
Indices: 246715--247223 Score: 731
Period size: 117 Copynumber: 4.3 Consensus size: 118
246705 CTTTAAATTA
246715 AAAAAATATATTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-AAATTTTCAAAA
1 AAAAAATATATTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATCAAATTTTCAAAA
246778 AAATATTTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
65 AAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
246832 AAAAAATAT-TTTTGG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTCAAAAA
1 AAAAAATATATTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTTCAAAAA
** *
246894 AGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
66 A-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
246948 AAAAAAAATATTTTTGG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTT--GA
1 AAAAAATATA-TTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTTCAAA
247010 AAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
64 AAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
247065 AAAAAA-AGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAA
1 AAAAAATA-TATTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAA-TTTTCAAA
*
247129 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTC
64 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
247183 TAAAAAAGTAT-TTTT-GAGGAAAATTTGAAAGTATCAATTTT
1 -AAAAAA-TATATTTTGGAGGAAAAGTTGAAAGTATCAATTTT
247224 TCCTGCACAA
Statistics
Matches: 359, Mismatches: 16, Indels: 33
0.88 0.04 0.08
Matches are distributed among these distances:
115 52 0.14
116 67 0.19
117 101 0.28
118 72 0.20
119 58 0.16
120 8 0.02
121 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.36
Consensus pattern (118 bp):
AAAAAATATATTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTTCAAAAA
AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:247062 original size:176 final size:172
Alignment explanation
Indices: 246724--247223 Score: 793
Period size: 176 Copynumber: 2.8 Consensus size: 172
246714 AAAAAAATAT
* * *
246724 ATTTTGGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAAAATATTTTTT
1 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATATTTTTG
246789 GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAATATTTTTGGGGAAAAG
66 GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT-AAAAAATATTTTT-GGGAAAAG
*
246854 TTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGG
129 TTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGG
*
246898 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAATATTTTT
1 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC-AAAAAAATATTTTT
* *
246963 GGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTGAAAAATATTTTTAGGGAAA
65 GGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTTAAAAAATATTTTT-GGGAAA
247028 AGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGG
127 AGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGG
* *
247074 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAAAATATTTT
1 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTTCAAAAAAATATTTT
* *
247139 TGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTCTAAAAAAGTATTTTTGAGGAA
64 TGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT-TAAAAAA-TATTTTTG-GGAA
*
247204 AATTTGAAAGTATCAATTTT
126 AAGTTGAAAGTATCAATTTT
247224 TCCTGCACAA
Statistics
Matches: 302, Mismatches: 16, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
174 47 0.16
175 54 0.18
176 110 0.36
177 87 0.29
178 4 0.01
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (172 bp):
ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATATTTTTG
GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTAAAAAATATTTTTGGGAAAAGTT
GAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGG
Found at i:251245 original size:3 final size:3
Alignment explanation
Indices: 251237--251277 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
251227 ATACTATTTG
251237 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
251278 AACATGATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:255474 original size:170 final size:170
Alignment explanation
Indices: 255279--255622 Score: 625
Period size: 170 Copynumber: 2.0 Consensus size: 170
255269 AAATACCATT
* * *
255279 TTATCTCTAATGCAAAGTTTTCGATATTTAGGCCATTTTCTTAGAAATAAATGTTTTCATACTCA
1 TTATCTCTAATGCAAAATTTTCGATATTTAGGCCATTTTCTTAGAAATAAATGATTCCATACTCA
*
255344 TTTTTGGGATTTTAAAAGATCAAAAATCATGAAATATTATAAAATTGAGATCTAAAAAGTTTCAT
66 TTTTTGAGATTTTAAAAGATCAAAAATCATGAAATATTATAAAATTGAGATCTAAAAAGTTTCAT
* *
255409 GAAAATTCAAGCTCAAAAAAGTCAAATTACGAAAATATCC
131 GAAAATCCAAGCTCAAAAAAGTCAAATTACGAAAATACCC
255449 TTATCTCTAATGCAAAATTTTCGATATTTAGGCCATTTTCTTAGAAATAAATGATTCCATACTCA
1 TTATCTCTAATGCAAAATTTTCGATATTTAGGCCATTTTCTTAGAAATAAATGATTCCATACTCA
255514 TTTTTGAGATTTTAAAAGATCAAAAATCATGAAATATTATAAAATTGAGATCTAAAAAGTTTCAT
66 TTTTTGAGATTTTAAAAGATCAAAAATCATGAAATATTATAAAATTGAGATCTAAAAAGTTTCAT
*
255579 GAAAATCCAAGCTCAAAAAAGTTAAATTACGAAAATACCC
131 GAAAATCCAAGCTCAAAAAAGTCAAATTACGAAAATACCC
255619 TTAT
1 TTAT
255623 AGAGGTATTT
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 167 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (170 bp):
TTATCTCTAATGCAAAATTTTCGATATTTAGGCCATTTTCTTAGAAATAAATGATTCCATACTCA
TTTTTGAGATTTTAAAAGATCAAAAATCATGAAATATTATAAAATTGAGATCTAAAAAGTTTCAT
GAAAATCCAAGCTCAAAAAAGTCAAATTACGAAAATACCC
Found at i:256146 original size:144 final size:144
Alignment explanation
Indices: 255535--256307 Score: 837
Period size: 145 Copynumber: 5.3 Consensus size: 144
255525 TTAAAAGATC
* * * ** *
255535 AAAAATCATGAAATATTATAAAATTGAGATCTAAAAAGTTTCATGAAAATCCAAGCTCAAAAAAG
1 AAAAATTATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCTGAGCTC-AGAAAG
* * *
255600 TTAAATTACGAAAATACCCTTATAGAGG-TATTTTAGTAATTTCACACTTTTCAGGGTACTACTG
65 GTAAATTACGAAAATACTCTTATA-AGGATATTTTAGTAATTTCACACTTTTCAAGGTACTACTG
**
255664 TGATTTCAAATAG-ACC
129 TGATTTCAAAT-GCATA
* * * * *
255680 AAAAATTATGAAATATTATGAAATTAAGATTTGAACAA-TTTCATAAAAATCTGAGCTCGGGAAG
1 AAAAATTATGAAATATTATGAAATTAAGATCT-AAAAAGTTTCATGAAAATCTGAGCTCAGAAAG
* * * * * * * * * * *
255744 GTCAAATTATGAAAAAATTATTGT-CGAGATATTCTAGTAATTTCACATTTTTTAGGGTATCGA-
65 GT-AAATTACGAAAATACTCTTATAAG-GATATTTTAGTAATTTCACACTTTTCAAGGTA-CTAC
*
255807 TATGATTTCAAATGCATA
127 TGTGATTTCAAATGCATA
*
255825 AAAAATTATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCTGAACTCGAGAAAG
1 AAAAATTATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCTGAGCTC-AGAAAG
* * * * * * **
255890 GTAAATTACGAAAATACTTTTAT-AGGAGTATTTTGGTAATTTTACATTTTTCGAGGTATTGTTG
65 GTAAATTACGAAAATACTCTTATAAGGA-TATTTTAGTAATTTCACACTTTTCAAGGTACTACTG
**
255954 TGATTTCAAATGCACC
129 TGATTTCAAATGCATA
* * * *
255970 AAAAATTATGAAATATTATGAAATCAAGATCTAAAAAATTTTATGAAAATTTGAGCTCAGAAAGG
1 AAAAATTATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCTGAGCTCAGAAAGG
* * * * * *
256035 TCAAATTATGAAAATACTCCTATAAGGATATTATAATAA-TTCATACTTTTCAAGGTACCACTGT
66 T-AAATTACGAAAATACTCTTATAAGGATATTTTAGTAATTTCACACTTTTCAAGGTACTACTGT
256099 GATTTCAAATGCATA
130 GATTTCAAATGCATA
* * * *
256114 AAAAATCATAAAATATTATGAAATTAAAATCTAAAAAGTTTCATGAAAAT-TCGAGCTCGAAAAA
1 AAAAATTATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCT-GAGCTC-AGAAA
* * *
256178 AGTAAATTACGAAAATACTCTTATAAGGGTATTTT-GATAATTTCACACTTCTCAA-GTACTACT
64 GGTAAATTACGAAAATACTCTTATAAGGATATTTTAG-TAATTTCACACTTTTCAAGGTACTACT
*
256241 GTGATTTCAAATGCATT
128 GTGATTTCAAATGCATA
*
256258 AAAAATTATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATGAAAAT
1 AAAAATTATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAAT
256308 TCAAACTCGA
Statistics
Matches: 520, Mismatches: 92, Indels: 33
0.81 0.14 0.05
Matches are distributed among these distances:
143 2 0.00
144 200 0.38
145 302 0.58
146 16 0.03
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (144 bp):
AAAAATTATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCTGAGCTCAGAAAGG
TAAATTACGAAAATACTCTTATAAGGATATTTTAGTAATTTCACACTTTTCAAGGTACTACTGTG
ATTTCAAATGCATA
Found at i:258748 original size:2 final size:2
Alignment explanation
Indices: 258741--258774 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
258731 TTCATATTTT
*
258741 TA TA TA TA AA TGA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
258775 GAAATAGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:272632 original size:14 final size:15
Alignment explanation
Indices: 272580--272636 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 15
272570 GGTTCACTTA
272580 TATTTGTTTAAGTTAGTT
1 TATTTGTTTAA---AGTT
272598 TATATTCGTTTAAAGTT
1 TAT-TT-GTTTAAAGTT
272615 TATTTGTTTAAA-TT
1 TATTTGTTTAAAGTT
272629 TATTTGTT
1 TATTTGTT
272637 ATAGTTCGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 10 0.27
15 7 0.19
16 2 0.05
17 7 0.19
18 3 0.08
19 2 0.05
20 6 0.16
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.61
Consensus pattern (15 bp):
TATTTGTTTAAAGTT
Found at i:272669 original size:23 final size:21
Alignment explanation
Indices: 272628--272672 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
272618 TTGTTTAAAT
*
272628 TTATTTGTTATAGTTCGTTTA
1 TTATTTATTATAGTTCGTTTA
272649 TTATTTATTAATATGTTCGTTTA
1 TTATTTATT-ATA-GTTCGTTTA
272672 T
1 T
272673 ATAATATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
23 10 0.48
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.62
Consensus pattern (21 bp):
TTATTTATTATAGTTCGTTTA
Found at i:272679 original size:17 final size:16
Alignment explanation
Indices: 272652--272683 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
272642 TCGTTTATTA
272652 TTTATTAATATGTTCG
1 TTTATTAATATGTTCG
272668 TTTATATAATATGTTC
1 TTTAT-TAATATGTTC
272684 ATGAACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.56
Consensus pattern (16 bp):
TTTATTAATATGTTCG
Found at i:277821 original size:9 final size:8
Alignment explanation
Indices: 277805--277845 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 8
277795 TTTTGATAAA
277805 AAAAAAAT
1 AAAAAAAT
277813 AAAACAAAT
1 AAAA-AAAT
277822 AAATAAAAT
1 AAA-AAAAT
277831 AAAATAAAT
1 AAAA-AAAT
277840 AAAAAA
1 AAAAAA
277846 TACCAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.23
9 22 0.73
10 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:277831 original size:18 final size:18
Alignment explanation
Indices: 277808--277842 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
277798 TGATAAAAAA
277808 AAAATAAAACAAATAAAT
1 AAAATAAAACAAATAAAT
*
277826 AAAATAAAATAAATAAA
1 AAAATAAAACAAATAAA
277843 AAATACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAATAAAACAAATAAAT
Found at i:279213 original size:41 final size:39
Alignment explanation
Indices: 278942--279244 Score: 277
Period size: 41 Copynumber: 7.4 Consensus size: 39
278932 GCAACAAAAT
* *
278942 TTTGAAAAATAAAATGGCTCCCCTGAATAGAGGCAACGAAC
1 TTTGGAAAAT-AAATGGCTCCTCTGAATAGAGGCAACG-AC
* * * *
278983 TTTGGGGAAATAAATGACTCATCTGAATAAAGGCAACGAAC
1 TTT-GGAAAATAAATGGCTCCTCTGAATAGAGGCAACG-AC
* *
279024 TTTGGGAAAATAAATTGTTCCTCTGAATAGAGGCAACGAAC
1 TTT-GGAAAATAAATGGCTCCTCTGAATAGAGGCAACG-AC
** * *
279065 TTTTAAAAATCAAATGGCTCCTCTAAATAGAGGCAACAAAAC
1 TTTGGAAAAT-AAATGGCTCCTCTGAATAGAGGCAAC--GAC
* *
279107 TTTGGAAAATAAATAGCTCATCTGAATAGAGGCAACGAAC
1 TTTGGAAAATAAATGGCTCCTCTGAATAGAGGCAACG-AC
*
279147 TTTTGAGAAAATAAATGGCTCCTCT-AATCAGAGGTTCAATGAC
1 -TTTG-GAAAATAAATGGCTCCTCTGAAT-AGAGG--CAACGAC
*
279190 TTTGGAAAATAAATGGCTCCTCT-AATCAAAGGTTCAACGAC
1 TTTGGAAAATAAATGGCTCCTCTGAAT-AGAGG--CAACGAC
*
279231 TTTGAAAAATAAAT
1 TTTGGAAAATAAAT
279245 AAATTCTCTA
Statistics
Matches: 222, Mismatches: 30, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
40 7 0.03
41 168 0.76
42 41 0.18
43 2 0.01
44 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (39 bp):
TTTGGAAAATAAATGGCTCCTCTGAATAGAGGCAACGAC
Found at i:279235 original size:83 final size:81
Alignment explanation
Indices: 278930--279448 Score: 365
Period size: 82 Copynumber: 6.3 Consensus size: 81
278920 TTCTAAGCAA
* * * * **
278930 AGGCAACAAAATTTTGAAAAATAAAATGGCTCCCCTGAATAGAGGCAACGAACTTTGGGGAAATA
1 AGGCAACAAAACTTTGGAAAAT-AAATAGCTCCTCTGAATAGAGGCAACGAACTTT-GAAAAATA
* * * *
278995 AATGACTCATCTGAATAA
64 AATGGCTCCTCTAAATAG
* * * *
279013 AGGCAAC-GAACTTTGGGAAAATAAATTGTTCCTCTGAATAGAGGCAACGAACTTTTAAAAATCA
1 AGGCAACAAAACTTT-GGAAAATAAATAGCTCCTCTGAATAGAGGCAACGAACTTTGAAAAAT-A
279077 AATGGCTCCTCTAAATAG
64 AATGGCTCCTCTAAATAG
*
279095 AGGCAACAAAACTTTGGAAAATAAATAGCTCATCTGAATAGAGGCAACGAACTTTTGAGAAAATA
1 AGGCAACAAAACTTTGGAAAATAAATAGCTCCTCTGAATAGAGGCAACGAAC-TTTGA-AAAATA
279160 AATGGCTCCTCT-AATCAG
64 AATGGCTCCTCTAAAT-AG
** * * *
279178 AGG-TTCAATGACTTTGGAAAATAAATGGCTCCTCT-AATCAAAGGTTCAACG-ACTTTGAAAAA
1 AGGCAACAA-AACTTTGGAAAATAAATAGCTCCTCTGAAT-AGAGG--CAACGAACTTTGAAAAA
*** * **
279240 TAAATAAATTCTCTAAGCAG
62 TAAATGGCTCCTCTAAATAG
* * ** ** ** * * *
279260 AAGCACCATGAC-TTCAAAAATAAAT-GCTTTTCTAAACAGAGGCACCAC-AACTTTGAAAAGTA
1 AGGCAACAAAACTTTGGAAAATAAATAGCTCCTCTGAATAGAGGCA--ACGAACTTTGAAAAATA
* *
279322 AATTGCTTCTCTAAATAG
64 AATGGCTCCTCTAAATAG
* * * * * * *
279340 AGGTAACCACAATTTTGGAAAATAAATTGCTCCCCTAAACAGAGGCACCACG-ACTTTGAAAAAT
1 AGGCAA-CAAAACTTTGGAAAATAAATAGCTCCTCTGAATAGAGGCA--ACGAACTTTGAAAAAT
* * *
279404 AAATTGCTCCTCTTAACAG
63 AAATGGCTCCTCTAAATAG
* *
279423 AGGCAATAAAACTTT-GAAAAAAAATA
1 AGGCAACAAAACTTTGGAAAATAAATA
279449 ATTTGCTCCT
Statistics
Matches: 349, Mismatches: 67, Indels: 42
0.76 0.15 0.09
Matches are distributed among these distances:
78 2 0.01
80 40 0.11
81 29 0.08
82 138 0.40
83 128 0.37
84 7 0.02
85 5 0.01
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (81 bp):
AGGCAACAAAACTTTGGAAAATAAATAGCTCCTCTGAATAGAGGCAACGAACTTTGAAAAATAAA
TGGCTCCTCTAAATAG
Found at i:279366 original size:42 final size:41
Alignment explanation
Indices: 279021--279427 Score: 261
Period size: 41 Copynumber: 9.9 Consensus size: 41
279011 AAAGGCAACG
* * *
279021 AACTTTGGGAAAATAAATTGTTCCTCTGAATAGAGGCA--AC
1 AACTTT-GGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
** * * * *
279061 GAACTTTTAAAAATCAAATGGCTCCTCTAAATAGAGGCAACAA
1 -AACTTTGGAAAAT-AAATTGCTCCTCTAAACAGAGGCACCAC
* * * *
279104 AACTTTGGAAAATAAATAGCTCATCTGAATAGAGGCA--AC
1 AACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
* * ** * *
279143 GAACTTTTGAGAAAATAAATGGCTCCTCTAATCAGAGGTTCAAT
1 -AAC-TTTG-GAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
* * * * ** *
279187 GACTTTGGAAAATAAATGGCTCCTCTAATCAAAGGTTCAAC
1 AACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
* * *** * * * *
279228 GACTTTGAAAAATAAATAAATTCTCTAAGCAGAAGCACCAT
1 AACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
* ** **
279269 GAC-TTCAAAAATAAA-TGCTTTTCTAAACAGAGGCACCAC
1 AACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
* * *
279308 AACTTT-GAAAAGTAAATTGCTTCTCTAAATAGAGGTAACCAC
1 AACTTTGGAAAA-TAAATTGCTCCTCTAAACAGAGG-CACCAC
* *
279350 AATTTTGGAAAATAAATTGCTCCCCTAAACAGAGGCACCAC
1 AACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
* * *
279391 GACTTTGAAAAATAAATTGCTCCTCTTAACAGAGGCA
1 AACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCA
279428 ATAAAACTTT
Statistics
Matches: 295, Mismatches: 58, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
39 24 0.08
40 25 0.08
41 169 0.57
42 68 0.23
43 8 0.03
44 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (41 bp):
AACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
Found at i:280070 original size:22 final size:21
Alignment explanation
Indices: 280023--280081 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
280013 GGTTTCACTC
*
280023 CTCAAAGATTTTCATTTTGAAA
1 CTCAAAGATTCTCA-TTTGAAA
**
280045 CTCAAAGATTCTCATTTGAGTT
1 CTCAAAGATTCTCATTTGA-AA
*
280067 CTCAAAAATTCTCAT
1 CTCAAAGATTCTCAT
280082 CGTGACTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAA
Found at i:281142 original size:13 final size:13
Alignment explanation
Indices: 281109--281142 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
281099 GTTTTCCTCA
*
281109 TTTCATCTTTTTT
1 TTTCATTTTTTTT
281122 TTTC-TTTTTTTT
1 TTTCATTTTTTTT
281134 TTTCATTTT
1 TTTCATTTT
281143 CCCCTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCATTTTTTTT
Found at i:287705 original size:14 final size:14
Alignment explanation
Indices: 287651--287694 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
287641 TTATTTTGAT
*
287651 ATAAAA-AAAACAA
1 ATAAAATAAAATAA
*
287664 GTAAAAT-AAATAA
1 ATAAAATAAAATAA
287677 ATAAAATAAAATAA
1 ATAAAATAAAATAA
287691 ATAA
1 ATAA
287695 TAAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (14 bp):
ATAAAATAAAATAA
Found at i:287709 original size:17 final size:18
Alignment explanation
Indices: 287665--287701 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
287655 AAAAAACAAG
287665 TAAAATAAATAAATAAAA
1 TAAAATAAATAAATAAAA
287683 TAAAATAAAT-AATAAAA
1 TAAAATAAATAAATAAAA
287700 TA
1 TA
287702 TAAAAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAATAAATAAATAAAA
Found at i:293288 original size:22 final size:21
Alignment explanation
Indices: 293262--293302 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
293252 GAGAGACGGG
293262 GAGA-AAAAAAGAAAAAAAAA
1 GAGAGAAAAAAGAAAAAAAAA
*
293282 GAGAGAAAAAAGAAAATAAAA
1 GAGAGAAAAAAGAAAAAAAAA
293303 TTTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
GAGAGAAAAAAGAAAAAAAAA
Found at i:297719 original size:64 final size:63
Alignment explanation
Indices: 297601--297724 Score: 158
Period size: 64 Copynumber: 2.0 Consensus size: 63
297591 ATATTGTATC
** * * * *
297601 TTTAATTGAGATTTAACTTTAATATTAGATTTTGAATTGAGCATATGATCAAAAAACTTATTTA
1 TTTAATTGAGATTTAACTCAAATATTAGATCTTGAATTGAACATATAAT-AAAAAAATTATTTA
* * *
297665 TTTAATTGAGATTTGACTCAAATTTTAGATCTTGAATTGAACATTTAATAAAAAAATTAT
1 TTTAATTGAGATTTAACTCAAATATTAGATCTTGAATTGAACATATAATAAAAAAATTAT
297725 GTACAGATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
63 10 0.20
64 41 0.80
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.43
Consensus pattern (63 bp):
TTTAATTGAGATTTAACTCAAATATTAGATCTTGAATTGAACATATAATAAAAAAATTATTTA
Found at i:297947 original size:2 final size:2
Alignment explanation
Indices: 297940--297968 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
297930 AATAAAGATG
297940 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 A
297969 AAACACTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:301036 original size:2 final size:2
Alignment explanation
Indices: 301031--301057 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
301021 CTCTCTCTCT
301031 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
301058 GCGCGGGCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:307131 original size:94 final size:94
Alignment explanation
Indices: 307019--307207 Score: 272
Period size: 94 Copynumber: 2.0 Consensus size: 94
307009 CTATGGAGTG
* * *
307019 TTTTATCCTCATATTCCTTTTGATTTTTCAGATTTTTCTTCATTTTCAAGTTTT-AGTAGGTTTA
1 TTTTATCCTCATATTCCTTTTGATTTTTCAAAATATTCTTCATTTTCAA-TTTTCAGTAGGTTTA
* *
307083 GGTCAACACTTCCTTTTTATATTTTTGTTT
65 GGCCAACAATTCCTTTTTATATTTTTGTTT
* * *
307113 TTTTATCCTCTTATTCCTTTTGATTTTTCAAAATATTCTTCCTTTTTAATTTTCAGTAGGTTTAG
1 TTTTATCCTCATATTCCTTTTGATTTTTCAAAATATTCTTCATTTTCAATTTTCAGTAGGTTTAG
* *
307178 GCCAACAATTCTTTTTTATTTTTTTGTTT
66 GCCAACAATTCCTTTTTATATTTTTGTTT
307207 T
1 T
307208 CTTCTTTTCA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 4 0.05
94 80 0.95
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (94 bp):
TTTTATCCTCATATTCCTTTTGATTTTTCAAAATATTCTTCATTTTCAATTTTCAGTAGGTTTAG
GCCAACAATTCCTTTTTATATTTTTGTTT
Found at i:307832 original size:204 final size:204
Alignment explanation
Indices: 307482--307888 Score: 751
Period size: 204 Copynumber: 2.0 Consensus size: 204
307472 TTAAGGGTTG
* *
307482 AAGGGTGGGCGGAGTTTGGGAAGAAATGCTAGGTTCGTGCCACAATACTCTTTCTTGTAACCAAA
1 AAGGGTGGGCGGAGTTTGGGAAGAAATGCTAGGTTCATGCCACAATACTCTTTCTAGTAACCAAA
307547 GAAAAAATGATAATGCTTTTCATATTAATTCAATTCCTTGTACTTGACCAAACTGAAATCAAAAC
66 GAAAAAATGATAATGCTTTTCATATTAATTCAATTCCTTGTACTTGACCAAACTGAAATCAAAAC
* *
307612 ATGAAACAAGGAAACCAATATGAAGTAAAACCCATTTCCTCTAGTTATGTTGCTTTGACTCTTCA
131 ATGAAACAAGGAAACCAATATGAAGTAAAACCCATTTCCTCTAGCTATGTTGCATTGACTCTTCA
307677 TTTTCCATT
196 TTTTCCATT
*
307686 AAGGGTGGGTGGAGTTTGGGAAGAAATGCTAGGTTCATGCCACAATACTCTTTCTAGTAACCAAA
1 AAGGGTGGGCGGAGTTTGGGAAGAAATGCTAGGTTCATGCCACAATACTCTTTCTAGTAACCAAA
307751 GAAAAAATGATAATGCTTTTCATATTAATTCAATTCCTTGTACTTGACCAAACTGAAATCAAAAC
66 GAAAAAATGATAATGCTTTTCATATTAATTCAATTCCTTGTACTTGACCAAACTGAAATCAAAAC
* *
307816 ATGAAACAAGGAAACCAATATTAAGTAAAATCCATTTCCTCTAGCTATGTTGCATTGACTCTTCA
131 ATGAAACAAGGAAACCAATATGAAGTAAAACCCATTTCCTCTAGCTATGTTGCATTGACTCTTCA
307881 TTTTCCAT
196 TTTTCCAT
307889 GAAGTGTCCA
Statistics
Matches: 196, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
204 196 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (204 bp):
AAGGGTGGGCGGAGTTTGGGAAGAAATGCTAGGTTCATGCCACAATACTCTTTCTAGTAACCAAA
GAAAAAATGATAATGCTTTTCATATTAATTCAATTCCTTGTACTTGACCAAACTGAAATCAAAAC
ATGAAACAAGGAAACCAATATGAAGTAAAACCCATTTCCTCTAGCTATGTTGCATTGACTCTTCA
TTTTCCATT
Found at i:318014 original size:3 final size:3
Alignment explanation
Indices: 318006--318033 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
317996 TTTTACAGCC
318006 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
318034 CATAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:324941 original size:10 final size:10
Alignment explanation
Indices: 324928--324971 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
324918 TGAAACTGAA
324928 TTATATATTT
1 TTATATATTT
324938 TTAT-TAGTTT
1 TTATATA-TTT
324948 TTATATATTT
1 TTATATATTT
*
324958 TT-TAAATTT
1 TTATATATTT
324967 TTATA
1 TTATA
324972 AAATAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 10 0.33
10 18 0.60
11 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
TTATATATTT
Found at i:326554 original size:106 final size:106
Alignment explanation
Indices: 326435--326656 Score: 336
Period size: 106 Copynumber: 2.1 Consensus size: 106
326425 GCAAAATTAC
* * * *
326435 TACTTACTGAAATTCCATTAAAAAAATATTTAAATTTGACTTATTTATTATCAATTTAAATTTAA
1 TACTTACTAAAATTCCATTAAAAAAATATTTAAATTTAACTTAATTATTATCAATTCAAATTTAA
* *
326500 ATTATTCAGATAATGAATTAAGTTAAATTTAAATTTTGTAA
66 ATTATTCAAATAATAAATTAAGTTAAATTTAAATTTTGTAA
* *
326541 TACTTATTAAAATTTCATTAAAAAAATATTTAAATTTAACTTAATTATTATCAATTCAAATTTAA
1 TACTTACTAAAATTCCATTAAAAAAATATTTAAATTTAACTTAATTATTATCAATTCAAATTTAA
**
326606 ATTATTCAAATAATAAATTAAGTTAAATTTAAAAAATTGTAA
66 ATTATTCAAATAATAAATTAAGTTAAATTT-AAATTTTGTAA
326648 TACTCTACT
1 TACT-TACT
326657 TTATTGACCT
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
106 87 0.84
107 13 0.13
108 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (106 bp):
TACTTACTAAAATTCCATTAAAAAAATATTTAAATTTAACTTAATTATTATCAATTCAAATTTAA
ATTATTCAAATAATAAATTAAGTTAAATTTAAATTTTGTAA
Found at i:329959 original size:15 final size:15
Alignment explanation
Indices: 329939--329968 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
329929 TAATTTTTAA
329939 ATATAAAAAAAATTT
1 ATATAAAAAAAATTT
*
329954 ATATAAAAAATATTT
1 ATATAAAAAAAATTT
329969 TTTTATTGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAAAAAAAATTT
Found at i:338547 original size:5 final size:5
Alignment explanation
Indices: 338537--338563 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
338527 GGGTCTGGGG
338537 ATCCC ATCCC ATCCC ATCCC ATCCC AT
1 ATCCC ATCCC ATCCC ATCCC ATCCC AT
338564 TTTCTAGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.56, G:0.00, T:0.22
Consensus pattern (5 bp):
ATCCC
Found at i:348564 original size:76 final size:81
Alignment explanation
Indices: 348462--348680 Score: 209
Period size: 83 Copynumber: 2.7 Consensus size: 81
348452 TTTAAGATTA
* * *
348462 AAAAAAAAAAGCATAATTTATATTAAAAATAAATTATAAGAA-A-TTTTTCAAAATT-TAAAA-T
1 AAAATAAAAATCATAATTTATATT-AAAATAAATTATAA-AATATTTTTTAAAAATTATAAAATT
348523 T-T-TATGTTAAATTTTT
64 TATATATGTTAAATTTTT
* * * *
348539 AAGATAAAAAT-ATAATTTATGTTAAAATATATTCTAAAATTATTTTTTAAAAATTATAAAATTT
1 AAAATAAAAATCATAATTTATATTAAAATAAATTATAAAA-TATTTTTTAAAAATTATAAAATTT
*
348603 CAATATATGTTATATTTTT
65 --ATATATGTTAAATTTTT
* * *
348622 AAAATAAAAATCATAATTTATATTGATAATATATCATAAAAAATTATTTTTTAAAAATT
1 AAAATAAAAATCATAATTTATATT-AAAATAAAT--TATAAAA-TATTTTTTAAAAATT
348681 TTATATTTAA
Statistics
Matches: 116, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
74 2 0.02
75 12 0.10
76 12 0.10
77 19 0.16
78 5 0.04
79 2 0.02
82 1 0.01
83 23 0.20
84 11 0.09
85 8 0.07
87 21 0.18
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (81 bp):
AAAATAAAAATCATAATTTATATTAAAATAAATTATAAAATATTTTTTAAAAATTATAAAATTTA
TATATGTTAAATTTTT
Found at i:348678 original size:87 final size:83
Alignment explanation
Indices: 348525--348680 Score: 224
Period size: 83 Copynumber: 1.8 Consensus size: 83
348515 TTTAAAATTT
* *
348525 TATGTTAAATTTTTAAGATAAAAATATAATTTATGTTAAAATATATTCTAAAATTATTTTTTAAA
1 TATGTTAAATTTTTAAAATAAAAATATAATTTATATTAAAATATATTCTAAAATTATTTTTTAAA
348590 AATTATAAAATTTCAATA
66 AATTATAAAATTTCAATA
* *
348608 TATGTTATATTTTTAAAATAAAAATCATAATTTATATTGATAATATA-TCATAAAAAATTATTTT
1 TATGTTAAATTTTTAAAATAAAAAT-ATAATTTATATT-AAAATATATTC-T--AAAATTATTTT
348672 TTAAAAATT
61 TTAAAAATT
348681 TTATATTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
83 23 0.36
84 13 0.20
85 8 0.12
87 20 0.31
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (83 bp):
TATGTTAAATTTTTAAAATAAAAATATAATTTATATTAAAATATATTCTAAAATTATTTTTTAAA
AATTATAAAATTTCAATA
Found at i:348709 original size:87 final size:83
Alignment explanation
Indices: 348535--348710 Score: 203
Period size: 87 Copynumber: 2.1 Consensus size: 83
348525 TATGTTAAAT
* *
348535 TTTTAAGATAAAAATATAATTTATGTTAAAATATATTCTAAAATTATTTTTTAAAAATTATAAAA
1 TTTTAAAATAAAAATATAATTTATATTAAAATATATTCTAAAATTATTTTTTAAAAATTATAAAA
* * * *
348600 TTTCAATATATGTTATAT
66 TTTAAAAATATATTATAC
*
348618 TTTTAAAATAAAAATCATAATTTATATTGATAATATA-TCATAAAAAATTATTTTTTAAAAATT-
1 TTTTAAAATAAAAAT-ATAATTTATATT-AAAATATATTC-T--AAAATTATTTTTTAAAAATTA
* *
348681 TTATATTTAAAAATATATTATAAC
61 TAAAATTTAAAAATATATTAT-AC
348705 TTTTAA
1 TTTTAA
348711 GCCATTTCGA
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
83 14 0.18
84 13 0.17
85 8 0.10
86 16 0.21
87 27 0.35
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (83 bp):
TTTTAAAATAAAAATATAATTTATATTAAAATATATTCTAAAATTATTTTTTAAAAATTATAAAA
TTTAAAAATATATTATAC
Found at i:348746 original size:21 final size:21
Alignment explanation
Indices: 348720--348760 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
348710 AGCCATTTCG
348720 AATTTGAATTG-ATTTAGAGTC
1 AATTTGAATTGAATTT-GAGTC
*
348741 AATTTGATTTGAATTTGAGT
1 AATTTGAATTGAATTTGAGT
348761 TATTTTCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (21 bp):
AATTTGAATTGAATTTGAGTC
Found at i:352507 original size:2 final size:2
Alignment explanation
Indices: 352500--352524 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
352490 AAATAAATGC
352500 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
352525 CCAGATTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:355562 original size:3 final size:3
Alignment explanation
Indices: 355554--355585 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
355544 CAAAATTAGT
355554 ATA ATA ATA ATA ATA ATA ATA ATA ATCA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA A
355586 CTATATGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:355645 original size:21 final size:21
Alignment explanation
Indices: 355606--355646 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
355596 CGTTAATAAA
*
355606 TAATTAAAAATTTATTTTTTG
1 TAATTAAAAATTTAATTTTTG
*
355627 TAATT-AAAATTTAAATTTTG
1 TAATTAAAAATTTAATTTTTG
355647 ATAACTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
TAATTAAAAATTTAATTTTTG
Found at i:357080 original size:17 final size:17
Alignment explanation
Indices: 357055--357089 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
357045 TATAATTTTT
* *
357055 AATATTAAAAAGTAAAA
1 AATAATAAAAAATAAAA
357072 AATAATAAAAAATAAAA
1 AATAATAAAAAATAAAA
357089 A
1 A
357090 TTTTAGTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AATAATAAAAAATAAAA
Found at i:358318 original size:22 final size:24
Alignment explanation
Indices: 358275--358325 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
358265 ATATTAAATA
358275 TATTTTTATCAGAATTTATCATAT
1 TATTTTTATCAGAATTTATCATAT
*
358299 TATTTTTAT-A-AATTTTTCATAT
1 TATTTTTATCAGAATTTATCATAT
*
358321 CATTT
1 TATTT
358326 AGCTCAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.60
23 1 0.04
24 9 0.36
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTTTTATCAGAATTTATCATAT
Found at i:360983 original size:3 final size:3
Alignment explanation
Indices: 360975--360999 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
360965 GCTATGGCTT
360975 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
361000 ATGTGGAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:368360 original size:16 final size:16
Alignment explanation
Indices: 368339--368371 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
368329 TGGGGATAGT
368339 TTCTTTCCTATAGGTC
1 TTCTTTCCTATAGGTC
368355 TTCTTTCCTATAGGTC
1 TTCTTTCCTATAGGTC
368371 T
1 T
368372 GCCATATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.52
Consensus pattern (16 bp):
TTCTTTCCTATAGGTC
Found at i:369156 original size:20 final size:19
Alignment explanation
Indices: 369127--369166 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
369117 ACAAAATAAG
369127 AAAGTGAATTTTAAATTTT
1 AAAGTGAATTTTAAATTTT
369146 AAAGATGAATTTTAAATTTT
1 AAAG-TGAATTTTAAATTTT
369166 A
1 A
369167 TATTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (19 bp):
AAAGTGAATTTTAAATTTT
Found at i:378986 original size:22 final size:23
Alignment explanation
Indices: 378936--378989 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
378926 TTTTTTAAAT
*
378936 AATTAAAAAAATTTAAATTGATA
1 AATTAATAAAATTTAAATTGATA
378959 AATTAATAAAATTT-AATGTGA-A
1 AATTAATAAAATTTAAAT-TGATA
378981 AATTAATAA
1 AATTAATAA
378990 TATATAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (23 bp):
AATTAATAAAATTTAAATTGATA
Found at i:379083 original size:14 final size:14
Alignment explanation
Indices: 379059--379095 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
379049 TATTAATATT
379059 TTTAT-TAAAAATA
1 TTTATCTAAAAATA
379072 TTTATCTAAAAATA
1 TTTATCTAAAAATA
*
379086 TATATC-AAAA
1 TTTATCTAAAA
379096 TTTATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTATCTAAAAATA
Found at i:379165 original size:19 final size:19
Alignment explanation
Indices: 379125--379166 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
379115 TAAAAAGATT
* *
379125 TTTTAATTTATATTTTTGA
1 TTTTAATTTATATTTATAA
379144 TTTTAATTT-TATTTAATAA
1 TTTTAATTTATATTT-ATAA
379163 TTTT
1 TTTT
379167 TAATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTAATTTATATTTATAA
Found at i:384210 original size:11 final size:10
Alignment explanation
Indices: 384192--384243 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 10
384182 AATAATGGAT
384192 GAAAAAAAAA
1 GAAAAAAAAA
384202 GAGAAAAAAAA
1 GA-AAAAAAAA
384213 GAAAAAATAAA
1 GAAAAAA-AAA
*
384224 AAAATGAAAAAA
1 GAAA--AAAAAA
384236 TGAAAAAA
1 -GAAAAAA
384244 TGAGAAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 7 0.20
11 19 0.54
12 3 0.09
13 6 0.17
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:384217 original size:8 final size:8
Alignment explanation
Indices: 384206--384305 Score: 98
Period size: 8 Copynumber: 12.5 Consensus size: 8
384196 AAAAAAGAGA
*
384206 AAAAAAAG
1 AAAAAATG
*
384214 AAAAAATA
1 AAAAAATG
384222 AAAAAATG
1 AAAAAATG
384230 AAAAAATG
1 AAAAAATG
384238 AAAAAATG
1 AAAAAATG
*
384246 -AGAAATG
1 AAAAAATG
*
384253 GAAAAATG
1 AAAAAATG
*
384261 -AAAAAGG
1 AAAAAATG
384268 AAAAAATG
1 AAAAAATG
384276 AAAAAAATG
1 -AAAAAATG
*
384285 -TAAAATG
1 AAAAAATG
384292 AGAGAAAATG
1 A-A-AAAATG
384302 AAAA
1 AAAA
384306 CTCAAATTGA
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
7 18 0.23
8 43 0.56
9 9 0.12
10 7 0.09
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:384217 original size:16 final size:16
Alignment explanation
Indices: 384193--384243 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
384183 ATAATGGATG
*
384193 AAAAA-AAAAGAGAAA
1 AAAAAGAAAAAAGAAA
*
384208 AAAAAGAAAAAATAAA
1 AAAAAGAAAAAAGAAA
*
384224 AAAATGAAAAAATGAAA
1 AAAAAGAAAAAA-GAAA
384241 AAA
1 AAA
384244 TGAGAAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 5 0.17
16 19 0.63
17 6 0.20
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAA
Found at i:384251 original size:15 final size:15
Alignment explanation
Indices: 384215--384280 Score: 87
Period size: 15 Copynumber: 4.3 Consensus size: 15
384205 AAAAAAAAGA
*
384215 AAAAATAAAAAAATG
1 AAAAATGAAAAAATG
384230 AAAAAATGAAAAAATG
1 -AAAAATGAAAAAATG
* *
384246 AGAAATGGAAAAATG
1 AAAAATGAAAAAATG
*
384261 AAAAAGGAAAAAATG
1 AAAAATGAAAAAATG
384276 AAAAA
1 AAAAA
384281 AATGTAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 30 0.68
16 14 0.32
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (15 bp):
AAAAATGAAAAAATG
Found at i:385109 original size:12 final size:12
Alignment explanation
Indices: 385074--385112 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
385064 AGTTAAAGAA
*
385074 AAATCAAAATAA
1 AAATCAAAATAG
385086 AAATCAAAATAG
1 AAATCAAAATAG
*
385098 AAATCAGAATAG
1 AAATCAAAATAG
385110 AAA
1 AAA
385113 GGAAGGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (12 bp):
AAATCAAAATAG
Found at i:385231 original size:27 final size:27
Alignment explanation
Indices: 385201--385289 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
385191 ATTTTTAAGG
385201 AAAATTGATACTTTCAACTTTTCCCTA
1 AAAATTGATACTTTCAACTTTTCCCTA
** * * * *
385228 AAAA-T-ATTTTTTGGAAATTTATTCTTAA
1 AAAATTGATACTTT-CAACTTT-TCCCT-A
385256 GGAAAATTGATACTTTCAACTTTTCCCTA
1 --AAAATTGATACTTTCAACTTTTCCCTA
385285 AAAAT
1 AAAAT
385290 ATATTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
25 5 0.12
26 6 0.14
27 12 0.28
28 1 0.02
29 1 0.02
30 7 0.16
31 6 0.14
32 5 0.12
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTCCCTA
Found at i:385231 original size:57 final size:58
Alignment explanation
Indices: 385144--385709 Score: 736
Period size: 57 Copynumber: 9.7 Consensus size: 58
385134 TTGTGTAGGA
385144 AAAATTGATACTTTCAACTTTT-CCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
*
385201 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTGGAAATTTATTCTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
* * * * *
385258 AAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAATTTATTTCTGAGA
1 AAAATTGATACTTTCAACTTTTCCCTCAAAA-ATATTTTTTGGAAATTTATTTTTAAGG
*
385317 AAAATTGATACTTTCAACTTTTCCC-CAAAAATATTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
* * * **
385374 AAAATTGATACTTTCAACTTTTCCTTAAAAAATATTTTTTTTGAAACTTTGATTTCCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAATA-TTTTTTGGAAA-TTT-ATTTTTAAGG
* * *
385435 AAAATTGATACTTTCAACCTTT-CCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAA---TATTTTTTGGAAATTTATTTTTAAGG
*
385495 AAAATTGATACTTTCAACTTTTCCC-CAAAAATATTTTTTGGAAATTTATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
* *
385552 AAAATTGATACTTTCAACTTTT-CCTCAAAAATATTTTTTTTTGAAACTTTGA-TCTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAATA--TTTTTTGGAAA-TTT-ATTTTTAAGG
* * * * * *
385612 AAAATTGATACTTTCAACTTTT-CCTCAAAAATCTCTTTTTTGAAAATGTGTTTCTAAAG
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAA--TATTTTTTGGAAATTTATTTTTAAGG
385671 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTCCCTCAAAAATATTTTTT
385710 TTTGGAAAAT
Statistics
Matches: 447, Mismatches: 42, Indels: 40
0.84 0.08 0.08
Matches are distributed among these distances:
56 2 0.00
57 184 0.41
58 18 0.04
59 100 0.22
60 97 0.22
61 35 0.08
62 10 0.02
63 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGG
Found at i:385580 original size:117 final size:115
Alignment explanation
Indices: 385144--385729 Score: 777
Period size: 116 Copynumber: 5.0 Consensus size: 115
385134 TTGTGTAGGA
*
385144 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATTGA
* * *
385209 TACTTTCAACTTTTCCCTAAAAA--TATTTTTTGGAAATTTATTCTTAAGG
66 TACTTTCAACTTTTCCC-AAAAATTTTTTTTTTGAAAATTTATTTTTAAGG
* * * *
385258 AAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAATTTATTTCTGAGAAAAATT
1 AAAATTGATACTTTCAACTTTT-CCTCAAAA-ATATTTTTTGGAAATTTATTTCTAAGGAAAATT
*
385323 GATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGAAAATTTATTTTTAAGG
64 GATACTTTCAACTTTT-CCCAAAAATTTTTTTTTTGAAAATTTATTTTTAAGG
* * *
385374 AAAATTGATACTTTCAACTTTTCCTTAAAAAATATTTTTTTTGAAACTTTGATTTCCAAGGAAAA
1 AAAATTGATACTTTCAACTTTTCC-TCAAAAATA-TTTTTTGGAAA-TTT-ATTTCTAAGGAAAA
*
385439 TTGATACTTTCAACCTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGG
62 TTGATACTTTCAACTTTTCC-CAAAAAT-TTTTTTTTTGAAAATTTATTTTTAAGG
*
385495 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATTGA
* *
385560 TACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGA-TCTTAAGG
66 TACTTTCAACTTTTCC-CAAAAAT-TTTTTTTTTGAAAATTT-ATTTTTAAGG
* * * * *
385612 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTCTTTTTTGAAAATGTGTTTCTAAAGAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGGAAATTTATTTCTAAGGAAAATT
385677 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAAATTTGATTTTTA
64 GATACTTTCAACTTTTCCC-AAAAAT-TTTTTTTTT-GAAAATTT-ATTTTTA
385730 TTTGAAGAAA
Statistics
Matches: 427, Mismatches: 28, Indels: 27
0.89 0.06 0.06
Matches are distributed among these distances:
114 22 0.05
115 12 0.03
116 113 0.26
117 101 0.24
118 39 0.09
119 71 0.17
120 16 0.04
121 53 0.12
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (115 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATTGA
TACTTTCAACTTTTCCCAAAAATTTTTTTTTTGAAAATTTATTTTTAAGG
Found at i:385766 original size:10 final size:10
Alignment explanation
Indices: 385744--385876 Score: 57
Period size: 10 Copynumber: 13.2 Consensus size: 10
385734 AAGAAAATAG
385744 AATAATAAAA
1 AATAATAAAA
385754 AAT-ATAAATA
1 AATAATAAA-A
385764 AATAATAAAA
1 AATAATAAAA
385774 AATAA-AGAAA
1 AATAATA-AAA
* *
385784 AGTAA-AACA
1 AATAATAAAA
385793 AA-AAT-AAA
1 AATAATAAAA
385801 AATAA-AACTAA
1 AATAATAA--AA
* *
385812 GATAAAAAAA
1 AATAATAAAA
*
385822 AATATTAAATA
1 AATAATAAA-A
*
385833 AACCTAATATAA
1 AA--TAATAAAA
*
385845 TA-AATAAAA
1 AATAATAAAA
385854 AATAAATAAATA
1 AAT-AATAAA-A
*
385866 AACAA-AAAA
1 AATAATAAAA
385875 AA
1 AA
385877 AAAACCTGGA
Statistics
Matches: 94, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
8 6 0.06
9 22 0.23
10 32 0.34
11 22 0.23
12 7 0.07
13 5 0.05
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (10 bp):
AATAATAAAA
Found at i:385769 original size:20 final size:21
Alignment explanation
Indices: 385738--385777 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
385728 TATTTGAAGA
385738 AAATAGAATAATAAAAAATAT
1 AAATAGAATAATAAAAAATAT
385759 AAATA-AATAATAAAAAATA
1 AAATAGAATAATAAAAAATA
385778 AAGAAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (21 bp):
AAATAGAATAATAAAAAATAT
Found at i:385801 original size:17 final size:17
Alignment explanation
Indices: 385759--385823 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
385749 TAAAAAATAT
385759 AAATAAATAATAAAA-AA
1 AAATAAA-AATAAAACAA
* *
385776 TAAAGAAAAGTAAAACAA
1 -AAATAAAAATAAAACAA
*
385794 AAATAAAAATAAAACTA
1 AAATAAAAATAAAACAA
*
385811 AGATAAAAA-AAAA
1 AAATAAAAATAAAA
385824 TATTAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 4 0.10
17 28 0.70
18 8 0.20
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (17 bp):
AAATAAAAATAAAACAA
Found at i:385807 original size:11 final size:11
Alignment explanation
Indices: 385751--385879 Score: 58
Period size: 11 Copynumber: 11.5 Consensus size: 11
385741 TAGAATAATA
385751 AAAAATATAAAT
1 AAAAATA-AAAT
385763 AAATAATAAAA-
1 AAA-AATAAAAT
*
385774 AATAAAGAAAAGT
1 AA-AAATAAAA-T
385787 AAAACA-AAAAT
1 AAAA-ATAAAAT
385798 AAAAATAAAACT
1 AAAAATAAAA-T
*
385810 -AAGATAAAA-
1 AAAAATAAAAT
385819 AAAAATATTAAAT
1 AAAAATA--AAAT
** *
385832 AAACCTAATAT
1 AAAAATAAAAT
385843 AATAAATAAAA-
1 AA-AAATAAAAT
385854 AATAAAT-AAAT
1 AA-AAATAAAAT
385865 AAACAA-AAAA-
1 AAA-AATAAAAT
385875 AAAAA
1 AAAAA
385880 ACCTGGAGCG
Statistics
Matches: 93, Mismatches: 9, Indels: 33
0.69 0.07 0.24
Matches are distributed among these distances:
9 2 0.02
10 13 0.14
11 44 0.47
12 22 0.24
13 12 0.13
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:385817 original size:28 final size:28
Alignment explanation
Indices: 385786--385863 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
385776 TAAAGAAAAG
385786 TAAAACAAAAATA-AAAATAAAACTAAGA
1 TAAAA-AAAAATATAAAATAAAACTAAGA
* * *
385814 TAAAAAAAAATATTAAATAAACCTAATA
1 TAAAAAAAAATATAAAATAAAACTAAGA
*
385842 TAATAAATAAAAAAT-AAATAAA
1 TAA-AAA-AAAATATAAAATAAA
385864 TAAACAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
27 7 0.16
28 20 0.47
29 10 0.23
30 6 0.14
ACGTcount: A:0.73, C:0.05, G:0.01, T:0.21
Consensus pattern (28 bp):
TAAAAAAAAATATAAAATAAAACTAAGA
Found at i:386725 original size:3 final size:3
Alignment explanation
Indices: 386719--386757 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
386709 TTATAAAAAA
386719 AAT AAT AAAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
386758 TAACTATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:386844 original size:11 final size:10
Alignment explanation
Indices: 386822--386869 Score: 78
Period size: 11 Copynumber: 4.6 Consensus size: 10
386812 ATAGATATAC
386822 AAAAAAGAAA
1 AAAAAAGAAA
386832 AAAAAAGAGAA
1 AAAAAAGA-AA
386843 AAAAAAGAAA
1 AAAAAAGAAA
386853 AAAGAAAGAAA
1 AAA-AAAGAAA
386864 AAAAAA
1 AAAAAA
386870 CATACAGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 16 0.44
11 20 0.56
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:386848 original size:21 final size:21
Alignment explanation
Indices: 386822--386869 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
386812 ATAGATATAC
386822 AAAAAAGAAAAAA-AAAGAGAA
1 AAAAAAGAAAAAAGAAAGA-AA
386843 AAAAAAGAAAAAAGAAAGAAA
1 AAAAAAGAAAAAAGAAAGAAA
386864 AAAAAA
1 AAAAAA
386870 CATACAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAAGAAAGAAA
Found at i:387075 original size:10 final size:10
Alignment explanation
Indices: 387060--387095 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
387050 TGTATATATA
387060 TTTTTTTGTG
1 TTTTTTTGTG
*
387070 TTTTTTTTTG
1 TTTTTTTGTG
387080 TTTTTTTG-G
1 TTTTTTTGTG
387089 TTTTTTT
1 TTTTTTT
387096 ATCAAAGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTG
Found at i:387172 original size:43 final size:41
Alignment explanation
Indices: 387125--387610 Score: 712
Period size: 41 Copynumber: 11.5 Consensus size: 41
387115 AAGGCTCAAA
*
387125 GACTTTGAAAAACATAAATTGCTCCTCTAAACAGAGGCACCAC
1 GACTTTG-AAAA-GTAAATTGCTCCTCTAAACAGAGGCACCAC
*
387168 GACTTTGGAAAGAGTAAATTGCTCCTCTAAATAGAGGCACCAC
1 GACTTT-GAAA-AGTAAATTGCTCCTCTAAACAGAGGCACCAC
387211 GACTTTGGAAAGAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GACTTT-GAAA-AGTAAATTGCTCCTCTAAACAGAGGCACCAC
387254 GACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC
1 GAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-C-C-AC
387298 TTTGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 ---GAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
387343 GACTTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCAC
1 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
387384 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
387425 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
387466 GACTTTGAAAAGAGTAAATTGCTCCTCTAAACAGAGGTACCAC
1 GACTTTG-AAA-AGTAAATTGCTCCTCTAAACAGAGGCACCAC
* *
387509 AACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
387550 GACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCA--AC
1 GAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
387589 GAAC-TTGGAAAGTAAATTGCTC
1 G-ACTTTGAAAAGTAAATTGCTC
387611 TTTGACAATC
Statistics
Matches: 418, Mismatches: 10, Indels: 34
0.90 0.02 0.07
Matches are distributed among these distances:
38 3 0.01
39 17 0.04
40 2 0.00
41 213 0.51
42 15 0.04
43 120 0.29
44 7 0.02
45 2 0.00
46 1 0.00
47 9 0.02
48 29 0.07
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
Done.