Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 55 of 150
Found at i:16561293 original size:22 final size:22
Alignment explanation
Indices: 16561165--16561294 Score: 141
Period size: 22 Copynumber: 6.1 Consensus size: 22
16561155 TAATTAAGTT
*
16561165 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
16561187 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
16561209 ATGTAAGTTATG--TAAT-TT-
1 ATGTAAGTTATGTATAATATTA
*
16561227 ATGTATA-TTAAT-TAATTAA-GTT-
1 ATGTA-AGTT-ATGT-A-TAATATTA
*
16561249 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
16561271 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
16561293 AT
1 AT
16561295 TCATTAAGTT
Statistics
Matches: 94, Mismatches: 3, Indels: 22
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.07
19 5 0.05
20 7 0.07
21 6 0.06
22 69 0.73
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:16561305 original size:351 final size:349
Alignment explanation
Indices: 16560637--16561360 Score: 947
Period size: 351 Copynumber: 2.1 Consensus size: 349
16560627 TATGTAAGTT
*
16560637 ATTTAT-TATGAAAATTAA-GTAAGTTATGTAATTTACGAATAATTAAAAAAATGTAAGTTATGT
1 ATTTATGTAT-AATATTAATGTAAGTTATGTAATTTACGAATAATTAAAAAAATGTAAGTTATGT
16560700 AAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAAAAAATGTAAGTTA
65 AA--TATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAAAAAATGTAAGTTA
16560765 TGTAAGTTGTAAGTTATGTAAGTTATGTATAAAATTAATTAACTAAGTTATGTAATTTATGTATA
128 TGTAAGTTGTAAGTTATGTAAGTTATGTATAAAATTAATTAACTAAGTTATGTAATTTATGTATA
16560830 ATATTAATGTAAGTTATGTAATTTATGTATATTAATTAAGTTATGTAATTTATGTATAATATTAA
193 ATATTAATGTAAGTTATGTAA-TTA--TATATTAATTAAGTTATGTAATTTATGTATAATATTAA
*
16560895 TGTAAGTTATGTAATTTATGAATAATTAAAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAA
255 TGTAAGTTATGTAATTTATGAATAATTAAAAAAAATGTAAGATATGTAAGTTGTAAGTTATGTAA
16560960 GTTATGTATAATATTAATTAACTAAGTTATGTA
320 GTTATGTATAATATTAA-T--CTAAGTTATGTA
* * **
16560993 ATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTAT-ATT-AATTAAT-TAAGTTATGT-
1 ATTTATGTATAATATTAATGTAAGTTATGTAATTTACGAATAATTAAAAAAATGTAAGTTATGTA
* * * *
16561054 A-ATTTATGTAT-AATATTAATGTAAGTTATGTAATTTATGAATTATTAATAAAATGTAAGTTAT
66 ATATTTAT-TATGAAAATTAA-GTAAGTTATGTAATTTACGAATAATTAAAAAAATGTAAGTTAT
* *
16561117 GTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAA
129 GTAAGTTGTAAGTTATGTAAGTTATGTATAAAATTAATTAACTAAGTTATGTAATTTATGTATAA
*
16561182 TATTAATGTAAGTTATGT-A-TA-ATATTAATGTAAGTTATGTAATTTATGTATATTAATTAAT-
194 TATTAATGTAAGTTATGTAATTATATATTAAT-TAAGTTATGTAATTTATGTATAAT-ATTAATG
* *** *
16561243 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA-ATAT-TAA-TTCATTAAGTT
257 TAAGTTATGTAATTTATGAAT-A-ATTAA---AAAAAATGTA-AGATATGTAAGTT--GTAAGTT
* *
16561305 ATGTAATTTATGTATAATATTAATGTAAGTTATGTA
314 ATGTAAGTTATGTATAATATTAATCTAAGTTATGTA
* *
16561341 ATCTATGTATATTAATTAAT
1 ATTTATGTATAAT-ATTAAT
16561361 TAAATGATAT
Statistics
Matches: 331, Mismatches: 22, Indels: 37
0.85 0.06 0.09
Matches are distributed among these distances:
345 8 0.02
346 43 0.13
347 7 0.02
348 29 0.09
349 8 0.02
350 18 0.05
351 162 0.49
352 1 0.00
353 1 0.00
354 10 0.03
355 5 0.02
356 16 0.05
357 23 0.07
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (349 bp):
ATTTATGTATAATATTAATGTAAGTTATGTAATTTACGAATAATTAAAAAAATGTAAGTTATGTA
ATATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAAAAAATGTAAGTTATGT
AAGTTGTAAGTTATGTAAGTTATGTATAAAATTAATTAACTAAGTTATGTAATTTATGTATAATA
TTAATGTAAGTTATGTAATTATATATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAG
TTATGTAATTTATGAATAATTAAAAAAAATGTAAGATATGTAAGTTGTAAGTTATGTAAGTTATG
TATAATATTAATCTAAGTTATGTA
Found at i:16561306 original size:56 final size:56
Alignment explanation
Indices: 16561231--16561340 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
16561221 TAATTTATGT
16561231 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
1 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
*
16561287 ATATTAATTCATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTA
1 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTA
16561341 ATCTATGTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (56 bp):
ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
Found at i:16565551 original size:14 final size:14
Alignment explanation
Indices: 16565532--16565599 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
16565522 ATGACCGTTG
16565532 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
16565546 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
16565561 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
16565574 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
16565587 AAACCTTAAATCT
1 AAACCCTAAATCT
16565600 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:16565555 original size:15 final size:15
Alignment explanation
Indices: 16565535--16565572 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
16565525 ACCGTTGAAA
16565535 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
16565550 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
16565565 CCCTAAAT
1 CCCTAAAT
16565573 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:16566144 original size:41 final size:40
Alignment explanation
Indices: 16566080--16566319 Score: 178
Period size: 41 Copynumber: 5.9 Consensus size: 40
16566070 TTTTGTTACT
* **
16566080 ATTAGCGGCGCTTTGGCAAAAACGCCGCTAAAGGTAAATAC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAAA-AC
* * * **
16566121 ATTAGCGGCGCTTAGCTACAAACGCCGCTGAAGACAAGAGA-
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAA-A-AC
* * * * ** *
16566162 ATTAGTGGCGCTCAGTTAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT-AAAAC
* * * * *
16566203 ATTAGCGGCGCTTATATAAAAACGCCGCCAAAGGCCAGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-TAAAAC
**** *
16566244 ATTAGCGGCG-TTCAGATAAAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTT-AGATAAAAACGCCGCTAAAG-GTAAAAC
16566285 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT
16566320 TTAAAAAATT
Statistics
Matches: 161, Mismatches: 31, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.01
41 155 0.96
42 4 0.02
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (40 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAAAAC
Found at i:16566318 original size:82 final size:82
Alignment explanation
Indices: 16566120--16566318 Score: 290
Period size: 82 Copynumber: 2.4 Consensus size: 82
16566110 AAGGTAAATA
* * * * * *
16566120 CATTAGCGGCGCTTAGCTACAAACGCCGCTGAAGACAAGAGAATTAGTGGCGCTCAGTTAAAAAC
1 CATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCAAGAGAATTAGCGGCGCTCAGATAAAAAC
*
16566185 GCCGCTAAAGATCCGAG
66 GCCGCTAAAGACCCGAG
* * * * *
16566202 CATTAGCGGCGCTTATATAAAAACGCCGCCAAAGGCCAGAGCATTAGCGGCGTTCAGATAAAAAC
1 CATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCAAGAGAATTAGCGGCGCTCAGATAAAAAC
16566267 GCCGCTAAAGACCCGAG
66 GCCGCTAAAGACCCGAG
16566284 CATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
1 CATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
16566319 TTTAAAAAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (82 bp):
CATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCAAGAGAATTAGCGGCGCTCAGATAAAAAC
GCCGCTAAAGACCCGAG
Found at i:16566465 original size:40 final size:40
Alignment explanation
Indices: 16566377--16566473 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 40
16566367 CGCTTTATAT
* **
16566377 AAAA-CGCCGCTAATTC-CTATTTTTAGCGGCGCTTCCGG
1 AAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGG
* * *
16566415 AAAATTGCCGCTGATGCTCTACCTTTAGCGGCGCTT-TGG
1 AAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGG
*
16566454 CTAAATCGCCGCTAATGCTC
1 -AAAATCGCCGCTAATGCTC
16566474 GATTTTTTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
38 4 0.09
39 11 0.23
40 32 0.68
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (40 bp):
AAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGG
Found at i:16570219 original size:22 final size:22
Alignment explanation
Indices: 16570194--16570236 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
16570184 ATGTCTATGC
16570194 TTGATTTGCTTATGAGAAACTG
1 TTGATTTGCTTATGAGAAACTG
16570216 TTGATTTGCTTATGAGAAACT
1 TTGATTTGCTTATGAGAAACT
16570237 TACATCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (22 bp):
TTGATTTGCTTATGAGAAACTG
Found at i:16582571 original size:21 final size:20
Alignment explanation
Indices: 16582547--16582588 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
16582537 ATTAATTAAT
16582547 ATAATAATAAAATTAAATATC
1 ATAATAATAAAATTAAA-ATC
* *
16582568 ATAATGATAAGATTAAAATC
1 ATAATAATAAAATTAAAATC
16582588 A
1 A
16582589 ATTGTGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAATAATAAAATTAAAATC
Found at i:16588228 original size:103 final size:104
Alignment explanation
Indices: 16587891--16588261 Score: 602
Period size: 105 Copynumber: 3.6 Consensus size: 104
16587881 TGTATATAAA
** * * *
16587891 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
** *
16587955 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCTCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
16587995 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
16588060 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
16588100 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
16588165 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
16588203 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
16588262 ATAACGGCTA
Statistics
Matches: 252, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
103 87 0.35
104 69 0.27
105 95 0.38
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:16589793 original size:30 final size:30
Alignment explanation
Indices: 16589759--16589818 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
16589749 AAGAAAAAGT
16589759 TAGAAAATTTAGACTGTAGGGGTCACACGG
1 TAGAAAATTTAGACTGTAGGGGTCACACGG
16589789 TAGAAAATTTAGACTGTAGGGGTCACACGG
1 TAGAAAATTTAGACTGTAGGGGTCACACGG
16589819 CCTTGTGGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.23
Consensus pattern (30 bp):
TAGAAAATTTAGACTGTAGGGGTCACACGG
Found at i:16590812 original size:38 final size:38
Alignment explanation
Indices: 16590756--16590872 Score: 137
Period size: 38 Copynumber: 3.1 Consensus size: 38
16590746 AACTTTTAAT
* * *
16590756 ACACCGGCACTAAACCTGCTGGGCACAAAGCCTGAATA
1 ACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATA
* *
16590794 ACACCGGCAATAAGCCTGCTAGGCACGAAGCCAGAATA
1 ACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATA
* * * *
16590832 ACACCGGCACA-AAGCCTACTAGGTAGAAAACCTGAATA
1 ACACCGGCA-ATAAGCCTGCTAGGCACAAAGCCTGAATA
16590870 ACA
1 ACA
16590873 ATATAATTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
38 66 0.99
39 1 0.01
ACGTcount: A:0.38, C:0.29, G:0.21, T:0.12
Consensus pattern (38 bp):
ACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATA
Found at i:16593980 original size:17 final size:17
Alignment explanation
Indices: 16593960--16593998 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
16593950 TTAATTCGTC
16593960 TATTTATTTTTC-TTATT
1 TATTTA-TTTTCATTATT
16593977 TATTTATTTTCATTATT
1 TATTTATTTTCATTATT
16593994 TATTT
1 TATTT
16593999 TTATCTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTATTTTCATTATT
Found at i:16593982 original size:30 final size:30
Alignment explanation
Indices: 16593942--16594000 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
16593932 CCTCATTGGT
*
16593942 TTATTGATTTA-ATTCGTCTATTTATTTTTC
1 TTATTGATTTATATTCAT-TATTTATTTTTC
* *
16593972 TTATTTATTTATTTTCATTATTTATTTTT
1 TTATTGATTTATATTCATTATTTATTTTT
16594001 ATCTCAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.69
Consensus pattern (30 bp):
TTATTGATTTATATTCATTATTTATTTTTC
Found at i:16595352 original size:137 final size:135
Alignment explanation
Indices: 16595157--16595565 Score: 514
Period size: 137 Copynumber: 3.0 Consensus size: 135
16595147 AAAATTATAT
* * * * *
16595157 TCTTTCCAACAGAATATTAATTTTCATATCTTTTATATTTTGATTGAAATTATTTAATATAATTG
1 TCTTTCCAAAAAAATATTAATTTCCAT-T-TTTTATATTTTGACTGAAATTAATTAATATAA-TG
16595222 TTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATT
63 TTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATT
16595287 AATTACAC
128 AATTACAC
* * *
16595295 TCTTTCTAAAATAATATTAATTTCCATTTTTTAATATTTTGACCGAAATTAATTAATATAAATGT
1 TCTTTCCAAAAAAATATTAATTTCCATTTTTT-ATATTTTGACTGAAATTAATTAATAT-AATGT
** * * * * *
16595360 TTATATTAATAAATTTAGTAAACTATAT-CAACTAGTATTTTGTATGAATAAAATCCATATATTA
64 TTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTA
** *
16595424 ATTGTAT
129 ATTACAC
* * *
16595431 TTTTTCCAAAAAAATATTAATTTCTATTTCTTTTATATTTTGACTGAAATTAATTAATATAACGT
1 TCTTTCCAAAAAAATATTAATTTCCA-TT-TTTTATATTTTGACTGAAATTAATTAATATAATG-
* * * *
16595496 TTTATATTAATAAATTCGATAAAATATATACAATTGATATTTTGTATAAATCAAACTCATATATT
63 TTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATT
16595561 AATTA
128 AATTA
16595566 TACCTATGTT
Statistics
Matches: 230, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
136 65 0.28
137 104 0.45
138 61 0.27
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.46
Consensus pattern (135 bp):
TCTTTCCAAAAAAATATTAATTTCCATTTTTTATATTTTGACTGAAATTAATTAATATAATGTTT
ATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
TACAC
Found at i:16599062 original size:24 final size:24
Alignment explanation
Indices: 16598999--16599050 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16598989 TTTCTAGAAG
* * *
16598999 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16599023 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16599047 ATTT
1 ATTT
16599051 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:16606802 original size:45 final size:45
Alignment explanation
Indices: 16606752--16606982 Score: 383
Period size: 45 Copynumber: 5.1 Consensus size: 45
16606742 TAAGACTACA
16606752 AGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAACTTACG
1 AGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAACTTACG
*
16606797 AGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAACCTACG
1 AGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAACTTACG
*
16606842 AGCAGTGGGGCCGGTACATTCAGCTCTCAATTCATTCAACTTACG
1 AGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAACTTACG
* *
16606887 AGCAGTGGGGCTGGTACATTCAACTCTCCATTCATTCAACTTACG
1 AGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAACTTACG
* * *
16606932 AGCAGTGGGGCTGGTACATTCACCTCTCATTTCATT-AAGCCTACG
1 AGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAA-CTTACG
16606977 AGCAGT
1 AGCAGT
16606983 AGGACTGCCA
Statistics
Matches: 175, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 2 0.01
45 173 0.99
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (45 bp):
AGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAACTTACG
Found at i:16608143 original size:27 final size:27
Alignment explanation
Indices: 16608124--16608197 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
16608114 AAGAATATAA
*
16608124 GGGGTTTGTTGATGATGAAGGCGGTAG
1 GGGGTTTGGTGATGATGAAGGCGGTAG
16608151 GGGGTTTGGTGATGATGAAGGCGGTAG
1 GGGGTTTGGTGATGATGAAGGCGGTAG
16608178 GGGGTTTGGTGATGATGAAG
1 GGGGTTTGGTGATGATGAAG
16608198 TGTTAGTAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.19, C:0.03, G:0.50, T:0.28
Consensus pattern (27 bp):
GGGGTTTGGTGATGATGAAGGCGGTAG
Found at i:16611424 original size:41 final size:40
Alignment explanation
Indices: 16611361--16611450 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 40
16611351 TTTTTATACA
*
16611361 TATTA-TTATATGTTATTAAACTTTT-ATATCATTATATAT
1 TATTATTTATATATTATTAAACTTTTCATATCA-TATATAT
* *
16611400 TATTATTTATATTATTATTAAACTTTTCATTTTATATATAT
1 TATTATTTATA-TATTATTAAACTTTTCATATCATATATAT
16611441 TACTTATTTA
1 TA-TTATTTA
16611451 GACTAATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 5 0.11
40 5 0.11
41 23 0.52
42 11 0.25
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (40 bp):
TATTATTTATATATTATTAAACTTTTCATATCATATATAT
Found at i:16611442 original size:38 final size:35
Alignment explanation
Indices: 16611352--16611447 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 35
16611342 TATTTTGATT
* *
16611352 TTTTATACATATTATTATATGTTATTAAACTTTTA
1 TTTTATATATATTATTATATATTATTAAACTTTTA
16611387 TATCATTATATATTATTATTTATATTATTATTAAACTTTTCA
1 T-T--TTATATA-TATTA-TTATA-TATTATTAAACTTTT-A
16611429 TTTTATATATATTACTTAT
1 TTTTATATATATTA-TTAT
16611448 TTAGACTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
35 1 0.02
36 1 0.02
38 15 0.29
39 12 0.24
40 5 0.10
41 15 0.29
42 2 0.04
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTTATATATATTATTATATATTATTAAACTTTTA
Found at i:16616137 original size:3 final size:3
Alignment explanation
Indices: 16616120--16616179 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
16616110 TAATTACTCA
* * * * *
16616120 ATT ATT -TT AATT ATT ATT GTT ATT ATT ATT AAT GTT ATT ATA ACT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
16616165 ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT
16616180 TATATTAGTT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:16616576 original size:28 final size:27
Alignment explanation
Indices: 16616522--16616583 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
16616512 ACCGTATTTT
16616522 TAATTTATTTCAAATTTTCATTTATATA
1 TAATTTATTTCAAATTTT-ATTTATATA
* *
16616550 TTATTTATTTTAAA-TTTATTTTAATATA
1 TAATTTATTTCAAATTTTA-TTT-ATATA
16616578 TAATTT
1 TAATTT
16616584 CCTTTCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 6 0.21
28 22 0.76
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATTTATTTCAAATTTTATTTATATA
Found at i:16623510 original size:44 final size:44
Alignment explanation
Indices: 16622427--16623497 Score: 1504
Period size: 44 Copynumber: 24.4 Consensus size: 44
16622417 GGTGAAACTA
* * *
16622427 TAAATCCTAGCTCCCTGAACAGCAGTGGAACAGGTGGAAGA--C
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * **
16622469 TAAAGTCCTAGCTCCCTGAACAGCAGTGGCATAGGCAGAAGATTG
1 TAAA-TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* *
16622514 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGAAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * *
16622558 TAAATACTAGCTCCCTGATCAGCAGTGGAATAGGTGGAAGACTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * * * **
16622602 -AAAGTTCTAGCTCCCTGAACAGTAGTGGAATACGCAGAAGATTG
1 TAAA-TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* *
16622646 TAAATCCTAACTCCCTGACCAGCAGTGGAATAGGTGGAAGATTA
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * *
16622690 TAAATCCTAGAC-CTCTGAACAGCAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAG-CTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* **
16622734 TAAATCCTAGCTCCCTGACTAGCAGTGGAATAGGCAGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* *
16622778 TAAATCCTAGCTCCCTGACC-GACCGTAGAATAGGTGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAG-CAGTGGAATAGGTGGAAGATTG
* * * * *
16622822 TAAGTCCTAGATCCCTGAACACCAGTGGAATAGGTTGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
** * * *
16622866 TATGTCCTAGCTCCCTGAACATCAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
*
16622910 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGAAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * *
16622954 TAAATCCTAGCTCCCTGAACAACAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
16622998 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
16623042 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * *
16623086 TAAATCCTAGCTCCCTGAACAACAGTGGAATAGGTGGAAGACTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * *
16623130 TAAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGTTGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* *
16623174 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
*
16623218 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGAAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * *
16623262 TAAATCCTAGCTCCCTGAACAACAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
*
16623306 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
16623350 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * *
16623394 TAAATCCTAGCTCACTGAACAGCAGTGGAATAGGTGGAAGACTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
* * **
16623438 TAAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
*
16623482 TAAGTCCTAGCTCCCT
1 TAAATCCTAGCTCCCT
16623498 ATGCAACAGT
Statistics
Matches: 920, Mismatches: 100, Indels: 16
0.89 0.10 0.02
Matches are distributed among these distances:
42 4 0.00
43 38 0.04
44 870 0.95
45 8 0.01
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (44 bp):
TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
Found at i:16623540 original size:44 final size:41
Alignment explanation
Indices: 16623492--16623631 Score: 100
Period size: 44 Copynumber: 3.2 Consensus size: 41
16623482 TAAGTCCTAG
16623492 CTCCCTATGCAACAGTGGAGTATGTTGAAAATTACAGATCTTAT
1 CTCCCTA-GCAACAGTGGAGTA-GTTGAAAATTACAG-TCTTAT
** * * *** * *
16623536 CTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCCCAGCCTTGT
1 CTCCCT-AGCAACAGTGGAGTAG-TTGAAAATTACAGTCTTAT
*
16623579 CTCCCTGAGCAACAGTGGAGTAGGTTAAAAAAATTACAGCTCTTAT
1 CTCCCT-AGCAACAGTGGAGTA-GTT--GAAAATTACAG-TCTTAT
16623625 CTCCCTA
1 CTCCCTA
16623632 AGCAGTAGTG
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
43 25 0.36
44 27 0.39
45 8 0.11
46 10 0.14
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (41 bp):
CTCCCTAGCAACAGTGGAGTAGTTGAAAATTACAGTCTTAT
Found at i:16623596 original size:43 final size:43
Alignment explanation
Indices: 16623535--16623696 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 43
16623525 ACAGATCTTA
* *
16623535 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCCCAGCCTTG
1 TCTCCCTAAGCAGCAGTGGAGCAGATTGAAGACCACAGCCTTG
* * * * * * ** *
16623578 TCTCCCTGAGCAACAGTGGAGTAGGTTAAAAAAATTACAGCTCTTA
1 TCTCCCTAAGCAGCAGTGGAGCAGATT--GAAGACCACAGC-CTTG
* * *
16623624 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCTCAGCCTTG
1 TCTCCCTAAGCAGCAGTGGAGCAGATTGAAGACCACAGCCTTG
* * * *
16623667 TCTCCGTGAGCAGCAGTGGAGTAGGTTGAA
1 TCTCCCTAAGCAGCAGTGGAGCAGATTGAA
16623697 AATAACAGAT
Statistics
Matches: 87, Mismatches: 29, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
43 49 0.56
44 7 0.08
45 7 0.08
46 24 0.28
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (43 bp):
TCTCCCTAAGCAGCAGTGGAGCAGATTGAAGACCACAGCCTTG
Found at i:16623629 original size:89 final size:88
Alignment explanation
Indices: 16623492--16623709 Score: 316
Period size: 89 Copynumber: 2.5 Consensus size: 88
16623482 TAAGTCCTAG
* *
16623492 CTCCCT-ATGCAACAGTGGAGTATGTT-GAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
1 CTCCCTGA-GCAACAGTGGAGTAGGTTAAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
*
16623555 GCAGATTGAAGACCCCAGCCTTGT
65 GCAGATCGAAGACCCCAGCCTTGT
*
16623579 CTCCCTGAGCAACAGTGGAGTAGGTTAAAAAAATTACAGCTCTTATCTCCCTAAGCAGTAGTGGA
1 CTCCCTGAGCAACAGTGGAGTAGGTT-AAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
*
16623644 GCAGATCGAAGACCTCAGCCTTGT
65 GCAGATCGAAGACCCCAGCCTTGT
* * * *
16623668 CTCCGTGAGCAGCAGTGGAGTAGGTT-GAAAATAACAGATCTT
1 CTCCCTGAGCAACAGTGGAGTAGGTTAAAAAATTACAGATCTT
16623710 GTCTTCCTGT
Statistics
Matches: 118, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
87 36 0.31
88 1 0.01
89 81 0.69
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (88 bp):
CTCCCTGAGCAACAGTGGAGTAGGTTAAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
CAGATCGAAGACCCCAGCCTTGT
Found at i:16625130 original size:3 final size:3
Alignment explanation
Indices: 16625113--16625172 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
16625103 TAATTACTCA
* * * * *
16625113 ATT ATT -TT CATT ATT ATT GTT ATT ATT ATT AAT GTT ATT ATA ACT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
16625158 ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT
16625173 TATATTAGTT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:16625194 original size:16 final size:18
Alignment explanation
Indices: 16625157--16625194 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
16625147 TTATTATAAC
*
16625157 TATTAGTATTATTATTTA
1 TATTAGTATTATTATGTA
16625175 TATTAGT-TTA-TATGTA
1 TATTAGTATTATTATGTA
16625191 TATT
1 TATT
16625195 TACCTATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 3 0.16
18 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
TATTAGTATTATTATGTA
Found at i:16625569 original size:28 final size:27
Alignment explanation
Indices: 16625515--16625576 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
16625505 ACCGTATTTT
16625515 TAATTTATTTCAAATTTTCATTTATATA
1 TAATTTATTTCAAATTTT-ATTTATATA
* *
16625543 TTATTTATTTTAAA-TTTATTTTAATATA
1 TAATTTATTTCAAATTTTA-TTT-ATATA
16625571 TAATTT
1 TAATTT
16625577 CCTTTCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 6 0.21
28 22 0.76
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATTTATTTCAAATTTTATTTATATA
Found at i:16632782 original size:2 final size:2
Alignment explanation
Indices: 16632775--16632801 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16632765 GGGTAACCTA
16632775 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 A
16632802 GCTTGGATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16634182 original size:17 final size:20
Alignment explanation
Indices: 16634160--16634198 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
16634150 GCCCTACATC
16634160 AATAATT-GAT-TAGG-TAA
1 AATAATTGGATCTAGGCTAA
16634177 AATAATTGGATCTAGGCTAA
1 AATAATTGGATCTAGGCTAA
16634197 AA
1 AA
16634199 GAACTTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 4 0.21
20 5 0.26
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (20 bp):
AATAATTGGATCTAGGCTAA
Found at i:16645410 original size:32 final size:32
Alignment explanation
Indices: 16645367--16645437 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
16645357 TTTGATTCGT
*
16645367 TGTAATGGAATAGAGCTGTAATGGAATAGAGG
1 TGTAATAGAATAGAGCTGTAATGGAATAGAGG
*
16645399 TGTAATAGAATATAGCTGTAATGGAATAGAGG
1 TGTAATAGAATAGAGCTGTAATGGAATAGAGG
*
16645431 CGTAATA
1 TGTAATA
16645438 ATATTCTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.04, G:0.30, T:0.27
Consensus pattern (32 bp):
TGTAATAGAATAGAGCTGTAATGGAATAGAGG
Found at i:16645436 original size:16 final size:16
Alignment explanation
Indices: 16645367--16645429 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
16645357 TTTGATTCGT
16645367 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
*
16645383 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGC
* *
16645399 TGTAATAGAATATAGC
1 TGTAATGGAATAGAGC
16645415 TGTAATGGAATAGAG
1 TGTAATGGAATAGAG
16645430 GCGTAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.27
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:16645736 original size:120 final size:120
Alignment explanation
Indices: 16645599--16645962 Score: 656
Period size: 120 Copynumber: 3.0 Consensus size: 120
16645589 TTAATCATAT
*
16645599 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTGATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
16645664 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
16645719 TTTAACATAATTATTATTAAATATAATTTATTAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
16645784 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
16645839 TCTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
** *
16645904 AAATATTCTTATATGTGTTTACTAAAATCATAATATATAATATTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
16645959 TTTA
1 TTTA
16645963 TAATCTACTT
Statistics
Matches: 233, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 233 1.00
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:16647421 original size:49 final size:49
Alignment explanation
Indices: 16647349--16647452 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
16647339 AGAAAAAAAC
* *
16647349 AAATTAAAATTAAGTTTAATATCATGAATCAAAA-AGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGA-TCAACACTTTATA
16647398 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGATCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGATCAACACTTTATA
16647447 AAATTA
1 AAATTA
16647453 TAACACATGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 51 0.98
50 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.32
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGATCAACACTTTATA
Found at i:16649969 original size:73 final size:75
Alignment explanation
Indices: 16649887--16650059 Score: 323
Period size: 73 Copynumber: 2.3 Consensus size: 75
16649877 TTTTTATTTT
*
16649887 AACAAATGCATTATTTAATAAATTGGAATATTAAAAATAAAAAAT-ATCCAAACTTTA-TTGAAT
1 AACAAATGCATTATTTAGTAAATTGGAATATTAAAAATAAAAAATAATCCAAACTTTACTTGAAT
16649950 TACAAAAATA
66 TACAAAAATA
16649960 AACAAATGCATTATTTAGTAAATTGGAATATTAAAAATAAAAAATAATCCAAACTTTACTTGAAT
1 AACAAATGCATTATTTAGTAAATTGGAATATTAAAAATAAAAAATAATCCAAACTTTACTTGAAT
16650025 TACAAAAATA
66 TACAAAAATA
16650035 AACAAATGCATTATTTAGTAAATTG
1 AACAAATGCATTATTTAGTAAATTG
16650060 AAAAAAAATT
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
73 44 0.45
74 12 0.12
75 41 0.42
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.32
Consensus pattern (75 bp):
AACAAATGCATTATTTAGTAAATTGGAATATTAAAAATAAAAAATAATCCAAACTTTACTTGAAT
TACAAAAATA
Found at i:16651215 original size:21 final size:21
Alignment explanation
Indices: 16651190--16651258 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 21
16651180 ACAGAAACGT
16651190 AAAACATCAACTTAATACAGA
1 AAAACATCAACTTAATACAGA
16651211 AAAACATCAACTTAATACAGAAA
1 AAAACATCAACTTAATACAG--A
*
16651234 CCAAAACATGAACTTAATACAGA
1 --AAAACATCAACTTAATACAGA
16651257 AA
1 AA
16651259 CCAAAACATG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
21 22 0.51
23 2 0.05
25 19 0.44
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.17
Consensus pattern (21 bp):
AAAACATCAACTTAATACAGA
Found at i:16651271 original size:25 final size:25
Alignment explanation
Indices: 16651180--16651267 Score: 121
Period size: 25 Copynumber: 3.6 Consensus size: 25
16651170 TAATCCATAA
*
16651180 ACAGAAACGTAAAACATCAACTTAAT
1 ACAGAAAC-CAAAACATCAACTTAAT
16651206 ACAG--A--AAAACATCAACTTAAT
1 ACAGAAACCAAAACATCAACTTAAT
*
16651227 ACAGAAACCAAAACATGAACTTAAT
1 ACAGAAACCAAAACATCAACTTAAT
16651252 ACAGAAACCAAAACAT
1 ACAGAAACCAAAACAT
16651268 GAACATTATA
Statistics
Matches: 57, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
21 20 0.35
23 1 0.02
24 1 0.02
25 31 0.54
26 4 0.07
ACGTcount: A:0.57, C:0.20, G:0.07, T:0.16
Consensus pattern (25 bp):
ACAGAAACCAAAACATCAACTTAAT
Found at i:16658877 original size:5 final size:5
Alignment explanation
Indices: 16658869--16658895 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
16658859 TTCAAATCTG
16658869 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
16658896 TTATAAAAAC
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:16659888 original size:19 final size:19
Alignment explanation
Indices: 16659864--16659900 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16659854 AGCACTTAAA
16659864 ATTTATACATTTTATTTTT
1 ATTTATACATTTTATTTTT
*
16659883 ATTTATATATTTTATTTT
1 ATTTATACATTTTATTTT
16659901 ATCAATCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTATACATTTTATTTTT
Found at i:16659895 original size:13 final size:14
Alignment explanation
Indices: 16659879--16659937 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 14
16659869 TACATTTTAT
16659879 TTTTATTTATAT-A
1 TTTTATTTATATCA
16659892 TTTTATTT-TATCA
1 TTTTATTTATATCA
* * *
16659905 ATCTA-CTATATCA
1 TTTTATTTATATCA
16659918 -TTTATTTATA-CA
1 TTTTATTTATATCA
16659930 TTTTATTT
1 TTTTATTT
16659938 TATTTTATCC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
12 9 0.24
13 28 0.76
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTATTTATATCA
Found at i:16660147 original size:16 final size:15
Alignment explanation
Indices: 16660126--16660155 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16660116 TCATCTACTT
16660126 ATTTATTTATTCATTC
1 ATTTATTTA-TCATTC
16660142 ATTTATTTATCATT
1 ATTTATTTATCATT
16660156 TTAACGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTATTTATCATTC
Found at i:16660869 original size:16 final size:17
Alignment explanation
Indices: 16660843--16660875 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16660833 CGACTCCATT
*
16660843 TTTATTTTTAATAAAAG
1 TTTATTTTTAAAAAAAG
16660860 TTTA-TTTTAAAAAAAG
1 TTTATTTTTAAAAAAAG
16660876 ATTTCGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TTTATTTTTAAAAAAAG
Found at i:16661239 original size:29 final size:30
Alignment explanation
Indices: 16661174--16661240 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
16661164 GAGCATTTAG
* **
16661174 TAATATTTTTTTAAAAATTGAGGGGTTTAA
1 TAATAATTTTTTAAAAATTGAGGGGCCTAA
16661204 T--TGAATTTTTT-AAAATTGAGGGGCCTAA
1 TAAT-AATTTTTTAAAAATTGAGGGGCCTAA
16661232 TAATAATTT
1 TAATAATTT
16661241 CTACAATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
28 17 0.55
29 12 0.39
30 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (30 bp):
TAATAATTTTTTAAAAATTGAGGGGCCTAA
Found at i:16661634 original size:10 final size:10
Alignment explanation
Indices: 16661619--16661674 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
16661609 TTTTAATTTT
16661619 ATATTTTTAA
1 ATATTTTTAA
**
16661629 ATATTTTTTG
1 ATATTTTTAA
16661639 AT-TTTTTAA
1 ATATTTTTAA
*
16661648 ATATTTTT-T
1 ATATTTTTAA
16661657 ATAATTTTTAA
1 AT-ATTTTTAA
16661668 ATATTTT
1 ATATTTT
16661675 AAGGTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 9 0.24
10 26 0.70
11 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:16661644 original size:19 final size:19
Alignment explanation
Indices: 16661615--16661674 Score: 95
Period size: 19 Copynumber: 3.1 Consensus size: 19
16661605 ATTTTTTTAA
16661615 TTTTATATTTTTAAATATT
1 TTTTATATTTTTAAATATT
16661634 TTTTGAT-TTTTTAAATATT
1 TTTT-ATATTTTTAAATATT
16661653 TTTTATAATTTTTAAATATT
1 TTTTAT-ATTTTTAAATATT
16661673 TT
1 TT
16661675 AAGGTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.05
19 20 0.53
20 16 0.42
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTATATTTTTAAATATT
Found at i:16661683 original size:19 final size:19
Alignment explanation
Indices: 16661622--16661684 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
16661612 TAATTTTATA
*
16661622 TTTTTAAATATTTTTTGAT
1 TTTTTAAATATTTTTAGAT
* *
16661641 TTTTTAAATATTTTTTATAA
1 TTTTTAAATA-TTTTTAGAT
* *
16661661 TTTTTAAATATTTTAAGGT
1 TTTTTAAATATTTTTAGAT
16661680 TTTTT
1 TTTTT
16661685 TGGATGATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTAAATATTTTTAGAT
Found at i:16663551 original size:23 final size:23
Alignment explanation
Indices: 16663516--16663566 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
16663506 GGATAGTGAG
*
16663516 TGTAATATACCGAAAATTACTAC
1 TGTAATACACCGAAAATTACTAC
*
16663539 TGTAATACCCCGAAAATTACTAC
1 TGTAATACACCGAAAATTACTAC
*
16663562 AGTAA
1 TGTAA
16663567 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACACCGAAAATTACTAC
Found at i:16666370 original size:32 final size:32
Alignment explanation
Indices: 16666334--16666477 Score: 182
Period size: 32 Copynumber: 4.5 Consensus size: 32
16666324 AGCGCGGTTC
* *
16666334 TGTGAAATGATAACAAATATCACCTTTCATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
* * *
16666366 TGTGAAATGATAACAAGT-TACGACTTAAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTAATTT
* * * *
16666398 TATGAAATAATAACAATTAACAACTTTAATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
16666430 TGTGAAATGATAACAAATATCAACTTTAATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
*
16666462 TGTTAAATGATAACAA
1 TGTGAAATGATAACAA
16666478 TATTCCTCTA
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
31 1 0.01
32 93 0.99
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTAATTT
Found at i:16674859 original size:229 final size:228
Alignment explanation
Indices: 16674594--16675243 Score: 749
Period size: 230 Copynumber: 2.8 Consensus size: 228
16674584 ATTAAAGCAG
* * * *
16674594 AACGCAGGGTTCGGTGTTGATCAATTGTTGCTTTAGCGGCGCTAATCTAGAAACGCCGCCAAAGA
1 AACGCAGCGTTCGGTGTTAATCAATTGTCGCTTTAGCGGCGCTAATCTAAAAACGCCGCCAAAGA
* * * *
16674659 TCGGTATTAACGGCGCTTATATACTAAACGCCACAGAAAGTTAACCGAAATGCATCGTTTGGCCT
66 TCGGTATTAACGGCGCTTA-AGA-TAAACGCCGCAGAAAGTTAACCAAAACGCATCGTTTGGCCT
* * * *
16674724 CGAGGTATAGTGGCATTTAGCGGCGCTTTAGTTA-C-AACGCCACTAAAGATCTTCATTAGCGGC
129 TGATGTATGGTGGCATTTAGCGGCGCTTTA-TAACCGAACGCCACTAAAGATCTTCATTAGCGGC
* *
16674787 GATTTCACCATAGCGCCGCAAAAG-AAGTTAAAACTA
193 GATTTCACCAAAACGCCGC-AAAGTAAGTTAAAACTA
* * * * *
16674823 AACGCAGCGTTCGGTGTTCATCAATTGTGGCTTTAGCGGCGC-AAACATAAAAACGCCGCTAAAA
1 AACGCAGCGTTCGGTGTTAATCAATTGTCGCTTTAGCGGCGCTAATC-TAAAAACGCCGCCAAAG
* *
16674887 ATCGATATTAACGGCGCTTACCAGATAAACGCCGCAGAAAGCTAACCAAAACGCATCGTTTGGCC
65 ATCGGTATTAACGGCGCTTA--AGATAAACGCCGCAGAAAGTTAACCAAAACGCATCGTTTGGCC
*
16674952 TTGATGTATGGTGGCATTTAGCGGCGCTTT-TAACCTGAACGCCACTAAAGATCTTCATTAACGG
128 TTGATGTATGGTGGCATTTAGCGGCGCTTTATAACC-GAACGCCACTAAAGATCTTCATTAGCGG
* *** ** **
16675016 CGTTTTCGTTAAAACGCCGCCGAGTCTGTTAAAACTA
192 CGATTTCACCAAAACGCCGCAAAGTAAGTTAAAACTA
* * * * * * * * *
16675053 AATGCAGCGTTTGGTTTTAATGAATTG-CGATTCCAGTGGCGCTAAT-AAAAAATCGCCGCGAAA
1 AACGCAGCGTTCGGTGTTAATCAATTGTCGCTT-TAGCGGCGCTAATCTAAAAA-CGCCGCCAAA
* * *
16675116 GATCAGAATTAACGGTGCTTAACGAATAAACGCCGCAGAAAGTTAACCAAAACGCATCGTTTGGC
64 GATCGGTATTAACGGCGCTTAA-G-ATAAACGCCGCAGAAAGTTAACCAAAACGCATCGTTTGGC
*
16675181 CTTGATTTATGGTGGCATTTAGCGGCGCTTTA-AACCGAACGCCACTAAAGATCTTCATTAGCG
127 CTTGATGTATGGTGGCATTTAGCGGCGCTTTATAACCGAACGCCACTAAAGATCTTCATTAGCG
16675244 CAAAATATGT
Statistics
Matches: 360, Mismatches: 49, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
227 2 0.01
228 5 0.01
229 172 0.48
230 179 0.50
231 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (228 bp):
AACGCAGCGTTCGGTGTTAATCAATTGTCGCTTTAGCGGCGCTAATCTAAAAACGCCGCCAAAGA
TCGGTATTAACGGCGCTTAAGATAAACGCCGCAGAAAGTTAACCAAAACGCATCGTTTGGCCTTG
ATGTATGGTGGCATTTAGCGGCGCTTTATAACCGAACGCCACTAAAGATCTTCATTAGCGGCGAT
TTCACCAAAACGCCGCAAAGTAAGTTAAAACTA
Found at i:16674993 original size:115 final size:113
Alignment explanation
Indices: 16674645--16675233 Score: 308
Period size: 115 Copynumber: 5.1 Consensus size: 113
16674635 CTAATCTAGA
* * * * * *
16674645 AACGCCGCCAAAGATCGGTATTAACGGCGCTTATA-TACTAAACGCCACAGAAAGTTAACCGAAA
1 AACGCCACTAAAGATCGATATTAACGGCGCTTA-ACGA-TAAACGCCGCAGAAAGTTAACCAAAA
* * * * *
16674709 TGCATCGTTTGGCCTCGAGGTATAGTGGCATTTAGCGGCGCTTTAGTTA-C-
64 CGCATCGTTTGGCCTTGATGTATGGTGGCATTTAGCGGCGCTTT--TAACCG
* * * * * * * * *
16674759 AACGCCACTAAAGATC-TTCATTAGCGGCGATTTCACCAT-AGCGCCGCAAAAGAAGTTAAAACT
1 AACGCCACTAAAGATCGAT-ATTAACGGCG-CTTAACGATAAACGCCGC-AGA-AAGTT-AACCA
* * ** * ** * *** *
16674822 AAACGCAGCGTTCGGTGTTCATCAATTGTGGC-TTTAGCGGCGCAAACATAA--A
61 AAACGCATCGTTTGGCCTTGATGTATGGTGGCATTTAGCGGCGC--TTTTAACCG
* * * *
16674874 AACGCCGCTAAAAATCGATATTAACGGCGCTTACCAGATAAACGCCGCAGAAAGCTAACCAAAAC
1 AACGCCACTAAAGATCGATATTAACGGCGCTTAAC-GATAAACGCCGCAGAAAGTTAACCAAAAC
16674939 GCATCGTTTGGCCTTGATGTATGGTGGCATTTAGCGGCGCTTTTAACCTG
65 GCATCGTTTGGCCTTGATGTATGGTGGCATTTAGCGGCGCTTTTAACC-G
* ** * *** * *
16674989 AACGCCACTAAAGATC-TTCATTAACGGCG-TTTTCGTTAAAACGCCGCCGAGTCTGTTAAAACT
1 AACGCCACTAAAGATCGAT-ATTAACGGCGCTTAACGAT-AAACGCCG-C-AGAAAGTT-AACCA
* * ** * * * * ** **
16675052 AAATGCAGCGTTTGGTTTTAATGAAT--T-GCGATTCCAGTGGCGCTAATAA-AA
61 AAACGCATCGTTTGGCCTTGATGTATGGTGGC-ATT-TAGCGGCGCTTTTAACCG
* * *
16675103 AATCGCCGCGAAAGATCAGA-ATTAACGGTGCTTAACGAATAAACGCCGCAGAAAGTTAACCAAA
1 AA-CGCCACTAAAGATC-GATATTAACGGCGCTTAACG-ATAAACGCCGCAGAAAGTTAACCAAA
* *
16675167 ACGCATCGTTTGGCCTTGATTTATGGTGGCATTTAGCGGCGCTTTAAACCG
63 ACGCATCGTTTGGCCTTGATGTATGGTGGCATTTAGCGGCGCTTTTAACCG
16675218 AACGCCACTAAAGATC
1 AACGCCACTAAAGATC
16675234 TTCATTAGCG
Statistics
Matches: 339, Mismatches: 104, Indels: 64
0.67 0.21 0.13
Matches are distributed among these distances:
112 3 0.01
113 58 0.17
114 88 0.26
115 105 0.31
116 61 0.18
117 24 0.07
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (113 bp):
AACGCCACTAAAGATCGATATTAACGGCGCTTAACGATAAACGCCGCAGAAAGTTAACCAAAACG
CATCGTTTGGCCTTGATGTATGGTGGCATTTAGCGGCGCTTTTAACCG
Found at i:16675623 original size:189 final size:191
Alignment explanation
Indices: 16675250--16675631 Score: 447
Period size: 190 Copynumber: 2.0 Consensus size: 191
16675240 AGCGCAAAAT
*
16675250 ATGTTAAAACTAAACGCAACGTTCGATTTTGATAAATTCTGGATTTCACGGCGCTAATTGAAAAA
1 ATGTTAAAACTAAACGCAACGTTCGATTTTGATAAATTCTGGATTTCACGGCGCTAAATGAAAAA
**
16675315 CGCCGCTAAAGATCGGTATTAACGACGCTTAACTAGTAAACGCCGCAAAAAGTTAACCAAAACGC
66 CGCCGCTAAAGATCGGTATTAACGACGCTTAACTAAAAAACGCCGCAAAAAGTTAACCAAAACGC
* *
16675380 ATCGTTTGGCCGTGAGGTATAGTGGCATTTAGCGGCGCTTTACCTAAAAACGCCACTAGAG
131 ATCGTTTGGCCGAGAGGTATAGTGGCATTTAGCGGCGCTTTACCTAAAAACGCCACTAAAG
* * * *
16675441 ATGTTAAAACTAAACGCAGCGTTCG-TTGTTGAT-CATTGTGGCA-TTCGCGGCGCTAACAT-AA
1 ATGTTAAAACTAAACGCAACGTTCGATT-TTGATAAATTCTGG-ATTTCACGGCGCTAA-ATGAA
* * * * ** * * **
16675502 AATCGCCGCTAAATATCGGTATTAACGGCGCTTGAC-AAAAAACGCCGCAAGTATTTAACCTAGG
63 AAACGCCGCTAAAGATCGGTATTAACGACGCTTAACTAAAAAACGCCGCAAAAAGTTAACCAAAA
** * *
16675566 CGCATCGTTTTGGTGGAGAGGTATA-TGGTCA-TTAGTGGCGCTTTTA-TTAAAAACGCCACTAA
128 CGCATCG-TTTGGCCGAGAGGTATAGTGG-CATTTAGCGGCGC-TTTACCTAAAAACGCCACTAA
16675628 AG
190 AG
16675630 AT
1 AT
16675632 CATCATTAGC
Statistics
Matches: 162, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
189 57 0.35
190 74 0.46
191 31 0.19
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (191 bp):
ATGTTAAAACTAAACGCAACGTTCGATTTTGATAAATTCTGGATTTCACGGCGCTAAATGAAAAA
CGCCGCTAAAGATCGGTATTAACGACGCTTAACTAAAAAACGCCGCAAAAAGTTAACCAAAACGC
ATCGTTTGGCCGAGAGGTATAGTGGCATTTAGCGGCGCTTTACCTAAAAACGCCACTAAAG
Found at i:16676112 original size:15 final size:16
Alignment explanation
Indices: 16676078--16676114 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
16676068 AAGGATTTAG
16676078 GGTATATTTGGGGATT
1 GGTATATTTGGGGATT
*
16676094 -GTAT-TTTGGGGTTT
1 GGTATATTTGGGGATT
16676108 GGTATAT
1 GGTATAT
16676115 ATTGTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 9 0.50
15 8 0.44
16 1 0.06
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (16 bp):
GGTATATTTGGGGATT
Found at i:16678969 original size:43 final size:42
Alignment explanation
Indices: 16678908--16679163 Score: 160
Period size: 43 Copynumber: 5.6 Consensus size: 42
16678898 CCCATTTATA
*
16678908 ATACAT-ACATTACATAACTTATTAATATATTTATGGATAAATG
1 ATACATAAC-TTACATAACTTATTAATATATTTAT-AATAAATG
* *
16678951 ATACATAACTTACATAACTTATTAATACATATCATTTTTAATACACAACTT
1 ATACATAACTTACATAACTTA-T--TA-ATAT-ATTTATAAT--A-AA-TG
* * * **
16679002 ATATA-ATAC-GACATAACTTATTAATATATATATTTTAAAATG
1 ATACATA-ACTTACATAACTTATTAATATATTTATAAT-AAATG
* *
16679044 ATACATAACTTACATAACTTATTAATACATAACTTATATAATACATA
1 ATACATAACTTACATAACTTATTAAT--AT-A-TT-TATAATAAATG
* * *
16679091 ACTTACATAA-TACGACATAACTTATTAATATATTTATGGAGAAATG
1 A--TACATAACT--TACATAACTTATTAATATATTTAT-AATAAATG
16679137 ATACATAACTTACATAACTTATTAATA
1 ATACATAACTTACATAACTTATTAATA
16679164 CATAACATTT
Statistics
Matches: 165, Mismatches: 24, Indels: 48
0.70 0.10 0.20
Matches are distributed among these distances:
42 7 0.04
43 52 0.32
44 11 0.07
45 11 0.07
46 14 0.08
47 14 0.08
48 12 0.07
49 9 0.05
50 28 0.17
51 7 0.04
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (42 bp):
ATACATAACTTACATAACTTATTAATATATTTATAATAAATG
Found at i:16679059 original size:9 final size:9
Alignment explanation
Indices: 16679045--16679100 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
16679035 TTTAAAATGA
16679045 TACATAACT
1 TACATAACT
16679054 TACATAACT
1 TACATAACT
*
16679063 TA-TTAA--
1 TACATAACT
16679069 TACATAACT
1 TACATAACT
*
16679078 TATATAA--
1 TACATAACT
16679085 TACATAACT
1 TACATAACT
16679094 TACATAA
1 TACATAA
16679101 TACGACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 2 0.05
7 9 0.24
8 3 0.08
9 24 0.63
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:16679066 original size:93 final size:93
Alignment explanation
Indices: 16678919--16679203 Score: 466
Period size: 93 Copynumber: 3.1 Consensus size: 93
16678909 TACATACATT
* *
16678919 ACATAACTTATTAATATATTTATGGATAAATGATACATAACTTACATAACTTATTAATACATATC
1 ACATAACTTATTAATATATTTATGGAGAAATGATACATAACTTACATAACTTATTAATACATAAC
* *
16678984 ATTTTTAATACACAACTTATATAATACG
66 ATTTTTAATACATAACTTACATAATACG
* **
16679012 ACATAACTTATTAATATATATATTTTA-AAATGATACATAACTTACATAACTTATTAATACATAA
1 ACATAACTTATTAATATATTTA-TGGAGAAATGATACATAACTTACATAACTTATTAATACATAA
*
16679076 C-TTATATAATACATAACTTACATAATACG
65 CATT-TTTAATACATAACTTACATAATACG
16679105 ACATAACTTATTAATATATTTATGGAGAAATGATACATAACTTACATAACTTATTAATACATAAC
1 ACATAACTTATTAATATATTTATGGAGAAATGATACATAACTTACATAACTTATTAATACATAAC
16679170 ATTTTTAATACATAACTTACATAATACG
66 ATTTTTAATACATAACTTACATAATACG
16679198 ACATAA
1 ACATAA
16679204 TAACATAAAT
Statistics
Matches: 177, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
92 4 0.02
93 169 0.95
94 4 0.02
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (93 bp):
ACATAACTTATTAATATATTTATGGAGAAATGATACATAACTTACATAACTTATTAATACATAAC
ATTTTTAATACATAACTTACATAATACG
Found at i:16679087 original size:16 final size:16
Alignment explanation
Indices: 16679054--16679103 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
16679044 ATACATAACT
16679054 TACATAACTTAT-TAA
1 TACATAACTTATATAA
16679069 TACATAACTTATATAA
1 TACATAACTTATATAA
*
16679085 TACATAACTTACATAA
1 TACATAACTTATATAA
16679101 TAC
1 TAC
16679104 GACATAACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (16 bp):
TACATAACTTATATAA
Found at i:16679089 original size:31 final size:31
Alignment explanation
Indices: 16678961--16679095 Score: 88
Period size: 31 Copynumber: 4.4 Consensus size: 31
16678951 ATACATAACT
* *
16678961 TACATAACTTATTAATACATATCATT-TTTAA
1 TACATAACTTATTAATACATAAC-TTATATAA
*
16678992 TACACAACTTATATAATACGACATAACTTAT-TAA
1 TACATAACTTAT-TAAT---ACATAACTTATATAA
* * *
16679026 TATATATA-TT-TTAA-A-ATGA--TACATAA
1 TACATA-ACTTATTAATACATAACTTATATAA
16679052 CTTACATAACTTATTAATACATAACTTATATAA
1 --TACATAACTTATTAATACATAACTTATATAA
16679085 TACATAACTTA
1 TACATAACTTA
16679096 CATAATACGA
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
25 2 0.03
26 3 0.04
27 4 0.05
28 8 0.10
29 4 0.05
30 1 0.01
31 25 0.31
32 7 0.09
33 7 0.09
34 11 0.14
35 8 0.10
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.39
Consensus pattern (31 bp):
TACATAACTTATTAATACATAACTTATATAA
Found at i:16679099 original size:40 final size:43
Alignment explanation
Indices: 16679012--16679100 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 43
16679002 ATATAATACG
* * *
16679012 ACATAACTTATTAATATATATATTTTAAAATGATACATAACTT
1 ACATAACTTATTAATACATATATCTTAAAATAATACATAACTT
*
16679055 ACATAACTTATTAATACATA-A-CTT-ATATAATACATAACTT
1 ACATAACTTATTAATACATATATCTTAAAATAATACATAACTT
16679095 ACATAA
1 ACATAA
16679101 TACGACATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 20 0.48
41 2 0.05
42 1 0.02
43 19 0.45
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.38
Consensus pattern (43 bp):
ACATAACTTATTAATACATATATCTTAAAATAATACATAACTT
Found at i:16679109 original size:50 final size:49
Alignment explanation
Indices: 16678962--16679203 Score: 192
Period size: 50 Copynumber: 5.1 Consensus size: 49
16678952 TACATAACTT
* * * *
16678962 ACATAACTTATTAATACATATCATTTTTAATACACAACTTATATAATACG
1 ACATAACTTATTAATACATAAC-TTTATAATACATAACTTACATAATACG
* * *
16679012 ACATAACTTATTAATATATATA-TTT-TAA-A-ATGA--TACAT-A-ACTT
1 ACATAACTTATTAATACATA-ACTTTATAATACATAACTTACATAATAC-G
16679055 ACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACG
1 ACATAACTTATTAATACATAACTT-TATAATACATAACTTACATAATACG
* * * * *
16679105 ACATAACTTATTAAT--AT-A-TTTATGGAGAAATGA--TACAT-A-ACTT
1 ACATAACTTATTAATACATAACTTTAT-AATACATAACTTACATAATAC-G
*
16679148 ACATAACTTATTAATACATAACATTTTTAATACATAACTTACATAATACG
1 ACATAACTTATTAATACATAAC-TTTATAATACATAACTTACATAATACG
16679198 ACATAA
1 ACATAA
16679204 TAACATAAAT
Statistics
Matches: 150, Mismatches: 20, Indels: 44
0.70 0.09 0.21
Matches are distributed among these distances:
42 5 0.03
43 38 0.25
44 10 0.07
45 8 0.05
46 11 0.07
47 10 0.07
48 9 0.06
49 13 0.09
50 42 0.28
51 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (49 bp):
ACATAACTTATTAATACATAACTTTATAATACATAACTTACATAATACG
Found at i:16679196 original size:16 final size:15
Alignment explanation
Indices: 16679147--16679188 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
16679137 ATACATAACT
16679147 TACATAACTTATTAA
1 TACATAACTTATTAA
*
16679162 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
16679178 TACATAACTTA
1 TACATAACTTA
16679189 CATAATACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:16682213 original size:21 final size:21
Alignment explanation
Indices: 16682187--16682258 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
16682177 CTACAACTTA
* * *
16682187 AAGCAGACGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
*
16682208 AAGCAGAGGCTGCAACGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
16682229 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
16682250 AAGCAGAGG
1 AAGCAGAGG
16682259 TTCAAAAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.36, C:0.19, G:0.42, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:16689911 original size:18 final size:18
Alignment explanation
Indices: 16689868--16689911 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
16689858 ACCCAATCCA
* *
16689868 AACCCAAGTATTCAACCC
1 AACCCAATTACTCAACCC
16689886 AACCCAATTACTCAACCC
1 AACCCAATTACTCAACCC
16689904 AACCCAAT
1 AACCCAAT
16689912 CATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.41, G:0.02, T:0.16
Consensus pattern (18 bp):
AACCCAATTACTCAACCC
Found at i:16693139 original size:16 final size:16
Alignment explanation
Indices: 16693095--16693144 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
16693085 CATGTTTTCG
16693095 TAAAATTTT-AATTTA
1 TAAAATTTTAAATTTA
* *
16693110 -GACATTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
16693126 TAAAATTTTAAATTAA
1 TAAAATTTTAAATTTA
16693142 TAA
1 TAA
16693145 TAAAATTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:16694103 original size:9 final size:9
Alignment explanation
Indices: 16694091--16694115 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16694081 TTAATTTTTT
16694091 AAAATTAAA
1 AAAATTAAA
16694100 AAAATTAAA
1 AAAATTAAA
16694109 AAAATTA
1 AAAATTA
16694116 TTTTCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:16696346 original size:262 final size:263
Alignment explanation
Indices: 16695687--16696473 Score: 1058
Period size: 262 Copynumber: 3.0 Consensus size: 263
16695677 CGAGTGGCCC
16695687 TAGAGAATATATATTACGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
1 TAGAGAATATATATTACGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
* * *
16695752 TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTAATTTATCGTCAGCCA
66 TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTT-ATTTATCGCCTGCTA
* * * * * * * *
16695817 ATTTATCAAATCCCTATGAGGA-TACTGAGACTTGAGGAGTTTCATTTCACTACTTCGCAATTAT
130 GTTTATCAAATCTCTAT-AAGATTAATGAGATTTAAGGAGTTTCGTTTCACTACTTCACAATTAT
* * * * * **
16695881 A-TACCTGATATATAATGTTGCATCCT-G-CAAATCTGAAAAATTCAAGT-TTTTTTTTAATATG
194 ACT-CTTGATAAATAATGTTGCATCCTAGTAAAAT-TG-AAAA-TAAAATCAATTTTTTAATATG
16695942 ATACACTCT
255 ATACACTCT
* * * * *
16695951 TAGAGAATATATATAACGTAACGGCGAGGTGAGGTGGCACCACGTTGTGGCAGTTGCTTTTGATG
1 TAGAGAATATATATTACGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
* * * *
16696016 TGCTGGAAGA-TACACAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATTGCCTG-TCA
66 TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATCGCCTGCT-A
* *
16696079 GTTTATCAAATCTCTATAAGATTAATGAGATTTAAGGAGTTTCGTTTCACTATTTCACAATTACA
130 GTTTATCAAATCTCTATAAGATTAATGAGATTTAAGGAGTTTCGTTTCACTACTTCACAATTATA
* * * *
16696144 CTCTTGATAAATAATGCTGTAT-CTAGTAAAATTGAAAATAAAATCAATTTTTTAATATAATATA
195 CTCTTGATAAATAATGTTGCATCCTAGTAAAATTGAAAATAAAATCAATTTTTTAATATGATACA
16696208 CTCT
260 CTCT
16696212 TAGAGAATATATATTACGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
1 TAGAGAATATATATTACGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
16696277 TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATCGCCTGCTAG
66 TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATCGCCTGCTAG
* * * * *
16696342 TTTATCAAATCTCTATAA-AGTTAATGAGATTTAAGAAGTTTTGTTTCATTACTTCAGAGTTATA
131 TTTATCAAATCTCTATAAGA-TTAATGAGATTTAAGGAGTTTCGTTTCACTACTTCACAATTATA
*
16696406 CTCTTGATAAAATAATGTTGCATCCCA-TAAAATTG-AAA-AAAATCAATTTTTTAATATGATAC
195 CTCTTGAT-AAATAATGTTGCATCCTAGTAAAATTGAAAATAAAATCAATTTTTTAATATGATAC
16696468 ACTCT
259 ACTCT
16696473 T
1 T
16696474 TGTGAAAGTT
Statistics
Matches: 458, Mismatches: 54, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
260 4 0.01
261 125 0.27
262 196 0.43
263 63 0.14
264 70 0.15
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (263 bp):
TAGAGAATATATATTACGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATCGCCTGCTAG
TTTATCAAATCTCTATAAGATTAATGAGATTTAAGGAGTTTCGTTTCACTACTTCACAATTATAC
TCTTGATAAATAATGTTGCATCCTAGTAAAATTGAAAATAAAATCAATTTTTTAATATGATACAC
TCT
Found at i:16697497 original size:64 final size:63
Alignment explanation
Indices: 16697394--16697522 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 63
16697384 TTATCAAACT
*
16697394 CTCAACTTTTGTCAGTTCTAATCCTTACAATAGTACCAATGTTACTACTTTTCTCATTCATTAG
1 CTCAACTTTTGTCACTTCTAATCCTTACAATAGTACCAATGTTACTAC-TTTCTCATTCATTAG
* *
16697458 CTCAACTTTTGTCACTTGTAATCCTTACAATAGTGCCAATGTTACTACTTTCTCATTCATTAG
1 CTCAACTTTTGTCACTTCTAATCCTTACAATAGTACCAATGTTACTACTTTCTCATTCATTAG
16697521 CT
1 CT
16697523 TTCTGCATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 17 0.27
64 45 0.73
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.42
Consensus pattern (63 bp):
CTCAACTTTTGTCACTTCTAATCCTTACAATAGTACCAATGTTACTACTTTCTCATTCATTAG
Found at i:16699749 original size:27 final size:27
Alignment explanation
Indices: 16699697--16699749 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
16699687 ACCACTAAAA
*
16699697 ATAATAGAAAATACAAATTTTAAAATT
1 ATAATAGAAAATACAAATTATAAAATT
* *
16699724 ATAATATATAATA-AAATTATATAAAT
1 ATAATAGAAAATACAAATTATA-AAAT
16699750 AATTTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
ATAATAGAAAATACAAATTATAAAATT
Found at i:16699930 original size:24 final size:24
Alignment explanation
Indices: 16699898--16699945 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16699888 GGAGAATGAC
16699898 AAATCATATTTTTCTTCCTGATTT
1 AAATCATATTTTTCTTCCTGATTT
16699922 AAATCATATTTTTCTTCCTGATTT
1 AAATCATATTTTTCTTCCTGATTT
16699946 TTTGCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.54
Consensus pattern (24 bp):
AAATCATATTTTTCTTCCTGATTT
Found at i:16702951 original size:273 final size:269
Alignment explanation
Indices: 16702459--16703005 Score: 830
Period size: 273 Copynumber: 2.0 Consensus size: 269
16702449 AGTATAATAA
*
16702459 AAATATGTGAGACCCATTATAATAAGAATATATATAATATTTGTCCAGTTAATGTATTTATTAGA
1 AAATATGTGAGACCCATTATAATAAGAATATATATAATATTTGTCCAGTTAATGTACTTATTAGA
* *
16702524 TTAAAAATACTTTTAAAAAAAATTAATTTTAATTATAAATTAATAAATATATGTGTGACCGAAAT
66 TTAAAAATACTTTTAAAAAAAATTAAATTAAATTATAAATTAATAAATATATGTGTGACCGAAAT
* * * * *
16702589 TCTTATTAAATAAAATAAGACATTGTCTGCAAGTTAAGTTAAACAAAATATATTTTCTTTCTAGA
131 ACTTATTAAATAAAATAAGACATTATCTGCAAATCAAGTTAAACAAAATATATTTTCTTTCTAAA
* * **
16702654 AGATTTAGTATTTATTAGTATAATATATTTTACA-TTATTAGCATAATTTATTTGACCTATGAAT
196 AGATTTAGTATATATTAATATAATATATTTTACATTTATTAGCATAATTTATTTGACCTACAAAT
16702718 TTAATCTAT
261 TTAATCTAT
*
16702727 AAATATGTGAGACCCATTATAATAAGAATATATATATGTAATATTTGTCTAGTTAATGTACTTAT
1 AAATATGTGAGACCCATTATAATAAG-A-ATATATA--TAATATTTGTCCAGTTAATGTACTTAT
16702792 TAGATTAAAAAAATA-TTTTAAAAAAAATTAAATTAAATTATAAATTAATAAATATATGTGTGAC
62 TAGATT--AAAAATACTTTTAAAAAAAATTAAATTAAATTATAAATTAATAAATATATGTGTGAC
* * *
16702856 TC-AAATACTTATTAAATAAAATAAGAGATTATTTGTAAATCAAGTTAAACAAAATATATTTTCT
125 -CGAAATACTTATTAAATAAAATAAGACATTATCTGCAAATCAAGTTAAACAAAATATATTTTCT
** *
16702920 TTCTAAAAGATTTAGTATATATTAATATAATATATTTTGTATTTATTAGTATAATTTATTTGACC
189 TTCTAAAAGATTTAGTATATATTAATATAATATATTTTACATTTATTAGCATAATTTATTTGACC
*
16702985 TACAAATTTAGTCTAT
254 TACAAATTTAATCTAT
16703001 AAATA
1 AAATA
16703006 GACACTTTTA
Statistics
Matches: 251, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
268 26 0.10
269 1 0.00
270 7 0.03
272 31 0.12
273 138 0.55
274 48 0.19
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (269 bp):
AAATATGTGAGACCCATTATAATAAGAATATATATAATATTTGTCCAGTTAATGTACTTATTAGA
TTAAAAATACTTTTAAAAAAAATTAAATTAAATTATAAATTAATAAATATATGTGTGACCGAAAT
ACTTATTAAATAAAATAAGACATTATCTGCAAATCAAGTTAAACAAAATATATTTTCTTTCTAAA
AGATTTAGTATATATTAATATAATATATTTTACATTTATTAGCATAATTTATTTGACCTACAAAT
TTAATCTAT
Found at i:16702961 original size:24 final size:24
Alignment explanation
Indices: 16702929--16702980 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
16702919 TTTCTAAAAG
16702929 ATTTAGTATATATTAATATAATAT
1 ATTTAGTATATATTAATATAATAT
* * * *
16702953 ATTTTGTATTTATTAGTATAATTT
1 ATTTAGTATATATTAATATAATAT
16702977 ATTT
1 ATTT
16702981 GACCTACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (24 bp):
ATTTAGTATATATTAATATAATAT
Found at i:16709075 original size:13 final size:13
Alignment explanation
Indices: 16709035--16709077 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
16709025 ATCAATAATT
16709035 AAAAATGAAA-AA
1 AAAAATGAAAGAA
*
16709047 AAATAATCATAAGAA
1 AAA-AATGA-AAGAA
16709062 AAAAATGAAAGAA
1 AAAAATGAAAGAA
16709075 AAA
1 AAA
16709078 CTAAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.12
13 12 0.46
14 6 0.23
15 5 0.19
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAATGAAAGAA
Found at i:16709199 original size:6 final size:7
Alignment explanation
Indices: 16709179--16709228 Score: 66
Period size: 7 Copynumber: 7.1 Consensus size: 7
16709169 TCGAAATTTG
16709179 ATTAAAA
1 ATTAAAA
16709186 ATTAAAA
1 ATTAAAA
16709193 ATTAAAA
1 ATTAAAA
16709200 ATTAAAA
1 ATTAAAA
*
16709207 AATAGAAA
1 ATTA-AAA
*
16709215 AGT-AAA
1 ATTAAAA
16709221 ATTAAAA
1 ATTAAAA
16709228 A
1 A
16709229 GAAAAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 5 0.13
7 28 0.74
8 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (7 bp):
ATTAAAA
Found at i:16709934 original size:11 final size:11
Alignment explanation
Indices: 16709920--16709967 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
16709910 ATTGCTGTTA
16709920 TGTTGCTATTT
1 TGTTGCTATTT
*
16709931 TGTTGCTATTA
1 TGTTGCTATTT
*
16709942 TGTTGCTCTTT
1 TGTTGCTATTT
** *
16709953 TACTACTATTT
1 TGTTGCTATTT
16709964 TGTT
1 TGTT
16709968 ATTATATTGC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.60
Consensus pattern (11 bp):
TGTTGCTATTT
Found at i:16709937 original size:22 final size:22
Alignment explanation
Indices: 16709911--16709953 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16709901 TTGTTGTTTA
*
16709911 TTGCTGTTATGTTGCTATTTTG
1 TTGCTATTATGTTGCTATTTTG
*
16709933 TTGCTATTATGTTGCTCTTTT
1 TTGCTATTATGTTGCTATTTT
16709954 ACTACTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.12, G:0.19, T:0.60
Consensus pattern (22 bp):
TTGCTATTATGTTGCTATTTTG
Found at i:16709961 original size:22 final size:22
Alignment explanation
Indices: 16709917--16709967 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
16709907 TTTATTGCTG
** *
16709917 TTATGTTGCTATTTTGTTGCTA
1 TTATGTTGCTATTTTACTACTA
*
16709939 TTATGTTGCTCTTTTACTACTA
1 TTATGTTGCTATTTTACTACTA
*
16709961 TTTTGTT
1 TTATGTT
16709968 ATTATATTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.61
Consensus pattern (22 bp):
TTATGTTGCTATTTTACTACTA
Found at i:16710942 original size:17 final size:17
Alignment explanation
Indices: 16710920--16710960 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
16710910 GTCACTTGCT
16710920 CGTGTGTGACACACGAC
1 CGTGTGTGACACACGAC
16710937 CGTGTGTGACACACGAC
1 CGTGTGTGACACACGAC
16710954 CGTGTGT
1 CGTGTGT
16710961 TAGACTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.22
Consensus pattern (17 bp):
CGTGTGTGACACACGAC
Found at i:16714723 original size:37 final size:37
Alignment explanation
Indices: 16714672--16714764 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
16714662 TACACAAGTT
* ** *
16714672 ATCCAACCGA-AACACGCTAGTTGCTCATAAGGGCTA
1 ATCCAACCGATAACACGCCAAATGCTCATAAGAGCTA
*
16714708 ATCCACCCGATAACACGCCAAATGCTCATAAGAGCTA
1 ATCCAACCGATAACACGCCAAATGCTCATAAGAGCTA
* *
16714745 ATCCATCCGATAACATGCCA
1 ATCCAACCGATAACACGCCA
16714765 GATCAAGATA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 9 0.18
37 40 0.82
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.18
Consensus pattern (37 bp):
ATCCAACCGATAACACGCCAAATGCTCATAAGAGCTA
Found at i:16719067 original size:27 final size:26
Alignment explanation
Indices: 16719001--16719091 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 26
16718991 TTTGAGATCC
* * **
16719001 CTACAAAGGCTTTCATTTTAAATACA
1 CTACAAAGGCTTCCATTTCAAATATG
*
16719027 CTTCAAAGGCTTCCATTTCATAA-ATGG
1 CTACAAAGGCTTCCATTTCA-AATAT-G
*
16719054 CTACAAAGGTTTCCATTTCAAATATG
1 CTACAAAGGCTTCCATTTCAAATATG
16719080 CTACAAAGGCTT
1 CTACAAAGGCTT
16719092 TTATTTCTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
26 32 0.59
27 22 0.41
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (26 bp):
CTACAAAGGCTTCCATTTCAAATATG
Found at i:16719269 original size:23 final size:23
Alignment explanation
Indices: 16719237--16719289 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
16719227 ACCCACCAGT
*
16719237 CATGGTCTTAAAGGATATAGTGC
1 CATGGCCTTAAAGGATATAGTGC
* * *
16719260 CATGGCCTTACATGATATGGTGC
1 CATGGCCTTAAAGGATATAGTGC
16719283 CATGGCC
1 CATGGCC
16719290 ATGGGCTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (23 bp):
CATGGCCTTAAAGGATATAGTGC
Found at i:16723548 original size:40 final size:40
Alignment explanation
Indices: 16723430--16723555 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
16723420 GTAGACAAGC
* *
16723430 TGCCAGTAATGTGGTCGAGCCACCAGTAATGCAGATAAAC
1 TGCCAGTAATGTGGTCAAGCCACCAGTAATGCAGATAAAA
* * * * ** * * *
16723470 TGCTAGTAGTGTAGACAAGCTGCCAGTATTGTATATAAAA
1 TGCCAGTAATGTGGTCAAGCCACCAGTAATGCAGATAAAA
* * * *
16723510 TTCCAGTAATATGGTCAAGCCACCAGTAATACAGATAAAC
1 TGCCAGTAATGTGGTCAAGCCACCAGTAATGCAGATAAAA
16723550 TGCCAG
1 TGCCAG
16723556 AAGTGCAGAC
Statistics
Matches: 61, Mismatches: 25, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCAGTAATGTGGTCAAGCCACCAGTAATGCAGATAAAA
Found at i:16723555 original size:20 final size:21
Alignment explanation
Indices: 16723532--16723577 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
16723522 GGTCAAGCCA
*
16723532 CCAGTAA-TACAGATAAACTG
1 CCAGTAAGTACAGACAAACTG
* *
16723552 CCAG-AAGTGCAGACAAGCTG
1 CCAGTAAGTACAGACAAACTG
16723572 CCAGTA
1 CCAGTA
16723578 CTTCCTCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.10
20 18 0.86
21 1 0.05
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (21 bp):
CCAGTAAGTACAGACAAACTG
Found at i:16723576 original size:40 final size:39
Alignment explanation
Indices: 16723452--16723577 Score: 101
Period size: 40 Copynumber: 3.2 Consensus size: 39
16723442 GGTCGAGCCA
* *
16723452 CCAGTAATGCAGATAAACTGCTAGTAGTGTAGACAAGCTG
1 CCAGTAATGCAGATAAACTGCCAGAAGTG-AGACAAGCTG
* * * * * * * **
16723492 CCAGTATTGTATATAAAATTCCAGTAATATG-GTCAAGCCA
1 CCAGTAATGCAGATAAACTGCCAG-AA-GTGAGACAAGCTG
*
16723532 CCAGTAATACAGATAAACTGCCAGAAGTGCAGACAAGCTG
1 CCAGTAATGCAGATAAACTGCCAGAAGTG-AGACAAGCTG
16723572 CCAGTA
1 CCAGTA
16723578 CTTCCTCCTT
Statistics
Matches: 61, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 54 0.89
41 1 0.02
42 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (39 bp):
CCAGTAATGCAGATAAACTGCCAGAAGTGAGACAAGCTG
Found at i:16723862 original size:37 final size:37
Alignment explanation
Indices: 16723821--16723906 Score: 154
Period size: 37 Copynumber: 2.3 Consensus size: 37
16723811 GAGAATGAGA
* *
16723821 ACAACATGCTTTTCAAATCAGTAATAAACATAGCCAT
1 ACAACATGCTTTTCAAATCAGTAATAAAAATAACCAT
16723858 ACAACATGCTTTTCAAATCAGTAATAAAAATAACCAT
1 ACAACATGCTTTTCAAATCAGTAATAAAAATAACCAT
16723895 ACAACATGCTTT
1 ACAACATGCTTT
16723907 CACAAAGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (37 bp):
ACAACATGCTTTTCAAATCAGTAATAAAAATAACCAT
Found at i:16734620 original size:44 final size:44
Alignment explanation
Indices: 16734549--16734666 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
16734539 ACTTGATGCG
* * * *
16734549 ATCTGCTCTACTGCAACATCAGAGAGATAAGATCTATTACTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCACTTTCA
* * * **
16734593 ATCTGCTCCACTACAACTTTAGGGAGATATGATTATCGGTTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCACTTTCA
* *
16734637 ATTTGCTCCACTGTAACTTCAGGGAGATAA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAA
16734667 AATTTGCCCT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
43 6 0.10
44 53 0.90
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCACTTTCA
Found at i:16734816 original size:128 final size:128
Alignment explanation
Indices: 16734661--16735787 Score: 1594
Period size: 128 Copynumber: 8.8 Consensus size: 128
16734651 AACTTCAGGG
* * * * * *
16734661 AGATAAAATTTGCCCTCTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGAGCTATAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * *
16734726 ACCTATTCCACTACTGAGCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * *
16734789 AGATAAGATTCACCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAATATCTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * * *
16734854 ACCTACTCCACTGCTGGCTAGGGATATTGGACTTGTGGCTTAAATCTGTTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * *
16734917 AGATAAGATTTGCC-ACTTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTGTAATTTTC
1 AGATAAGATTCGCCGTC-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCC
* ** * *
16734981 AACCTATTCCACTACTGACCAGGGACGTAGGACTTGTGGCTTGAATCTGCTTCCTTACATTTGA
65 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * *
16735045 AGATAAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGGGAGACAAGATTTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * * *
16735110 ACCTACTCCATTGCTAACCAAGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
*
16735173 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGATACAAGATCTGTAATTTCCC
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-CC
* * *
16735238 AACCTATTACATTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGTTTCCTTACACTTGA
65 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * * *
16735302 AGATAAGATTTGTCG-CTTTCGATCTGCTCTGTTACTACTTAGGGAGACAAGATCTGTAATTTCC
1 AGATAAGATTCGCCGTC-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-C
* * *
16735366 CAACCTATTCCACTGCTGACGAGGGACATAGGACTTGTGGCTTAAATTTGCTTCCTTACACTTGA
64 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * *
16735431 AGATAAGATTCGCCGTCTTCAATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTGTAATTTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * *
16735496 ACCTACTCCACTGCTGGCTAGGGATATAGGATTTGTGGCTTAAATCTGCTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * *
16735559 AGATAAGATTCACC-ACTTTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTTC
1 AGATAAGATTCGCCGTC-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCC
*
16735623 AACCTATTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
65 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * *
16735687 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTACTTAGGGAGGCAAGATTTGTATTTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * *
16735752 ACCTACTCCACTGTTGACTAGGGAGATAGGACTTGT
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGT
16735788 AATCTTCAAC
Statistics
Matches: 889, Mismatches: 103, Indels: 14
0.88 0.10 0.01
Matches are distributed among these distances:
127 2 0.00
128 654 0.74
129 232 0.26
130 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (128 bp):
AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
Found at i:16735798 original size:44 final size:44
Alignment explanation
Indices: 16735750--16735861 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
16735740 TTGTATTTTC
* * * *
16735750 CAACCTACTCCACTGTTGACT-AGGGAGATAGGACTTGTAATCTT
1 CAACCTATTCCACTGCTG-CTCAGGAAGATAGGACTTGCAATCTT
* * **
16735794 CAACCTATTCCACTGCTGGTCAGGAAGCTAGGTTTTGCAATCTT
1 CAACCTATTCCACTGCTGCTCAGGAAGATAGGACTTGCAATCTT
*
16735838 CAACCTATTCCACTGCTGGTCAGG
1 CAACCTATTCCACTGCTGCTCAGG
16735862 GAGCTAGGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
43 1 0.02
44 58 0.98
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (44 bp):
CAACCTATTCCACTGCTGCTCAGGAAGATAGGACTTGCAATCTT
Found at i:16735867 original size:44 final size:44
Alignment explanation
Indices: 16735788--16735874 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
16735778 TAGGACTTGT
16735788 AATCTTCAACCTATTCCACTGCTGGTCAGGAAGCTAGGTTTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGAAGCTAGGTTTTGC
*
16735832 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAGGTTTTG
1 AATCTTCAACCTATTCCACTGCTGGTCAGGAAGCTAGGTTTTG
16735875 TGGTTTCACC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGGTCAGGAAGCTAGGTTTTGC
Found at i:16738033 original size:6 final size:6
Alignment explanation
Indices: 16738024--16738136 Score: 105
Period size: 6 Copynumber: 19.7 Consensus size: 6
16738014 TTTTTCTCCT
16738024 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA --TTGA TTTTGA -TTT--
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
* * * * * *
16738067 TTTTGC TTTTGA CTTTGA TTTTTA TTTTTA TTTT-- TTTTGTT TTTTGTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTG-A TTTTG-A
16738115 TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTT
16738137 TTTATTGAAT
Statistics
Matches: 94, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
4 11 0.12
5 3 0.03
6 68 0.72
7 12 0.13
ACGTcount: A:0.12, C:0.02, G:0.13, T:0.73
Consensus pattern (6 bp):
TTTTGA
Found at i:16738093 original size:27 final size:25
Alignment explanation
Indices: 16738026--16738128 Score: 81
Period size: 27 Copynumber: 4.1 Consensus size: 25
16738016 TTTCTCCTTT
16738026 TTGATTTTGATTTTGATTTTGATTTTGA
1 TTGATTTTGA-TTT--TTTTGATTTTGA
*
16738054 TTGATTTTGATTTTTTTGCTTTTGA
1 TTGATTTTGATTTTTTTGATTTTGA
* **
16738079 CTTTGATTTTTATTTTTATTTTTTTTG-
1 --TTGATTTTGATTTTT-TTGATTTTGA
16738106 TT--TTTTG--TTTTTTGATTTTGA
1 TTGATTTTGATTTTTTTGATTTTGA
16738127 TT
1 TT
16738129 TTGATTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
20 7 0.11
21 6 0.09
23 4 0.06
25 13 0.20
27 17 0.27
28 17 0.27
ACGTcount: A:0.13, C:0.02, G:0.14, T:0.72
Consensus pattern (25 bp):
TTGATTTTGATTTTTTTGATTTTGA
Found at i:16738109 original size:14 final size:15
Alignment explanation
Indices: 16738023--16738130 Score: 57
Period size: 16 Copynumber: 7.1 Consensus size: 15
16738013 CTTTTTCTCC
16738023 TTTTTGATTTTGATTT
1 TTTTTGATTTT-ATTT
*
16738039 TGATTTTGATTTTGATTG
1 T--TTTTGATTTT-ATTT
*
16738057 ATTTTGATTTT-TTT
1 TTTTTGATTTTATTT
* *
16738071 GCTTTTGACTTTGA-TT
1 -TTTTTGA-TTTTATTT
*
16738087 TTTAT--TTTTATTT
1 TTTTTGATTTTATTT
16738100 TTTTTG-TTTT-TTGT
1 TTTTTGATTTTATT-T
16738114 TTTTTGATTTTGATTT
1 TTTTTGATTTT-ATTT
16738130 T
1 T
16738131 GATTTTTTTA
Statistics
Matches: 72, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
12 4 0.06
13 8 0.11
14 13 0.18
15 13 0.18
16 18 0.25
17 2 0.03
18 14 0.19
ACGTcount: A:0.12, C:0.02, G:0.13, T:0.73
Consensus pattern (15 bp):
TTTTTGATTTTATTT
Found at i:16738138 original size:43 final size:43
Alignment explanation
Indices: 16738023--16738137 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
16738013 CTTTTTCTCC
* *
16738023 TTTTTGATTTTGATTTTGATTTTGATTTTGATTGATTTTGATT
1 TTTTTGCTTTTGATTTTGATTTTGATTTTTATTGATTTTGATT
* * **
16738066 TTTTTGCTTTTGACTTTGATTTTTATTTTTATTTTTTTTG--T
1 TTTTTGCTTTTGATTTTGATTTTGATTTTTATTGATTTTGATT
*
16738107 TTTTTGTTTTTTGATTTTGATTTTGATTTTT
1 TTTTTG-CTTTTGATTTTGATTTTGATTTTT
16738138 TTATTGAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 7 0.11
42 21 0.34
43 34 0.55
ACGTcount: A:0.12, C:0.02, G:0.13, T:0.73
Consensus pattern (43 bp):
TTTTTGCTTTTGATTTTGATTTTGATTTTTATTGATTTTGATT
Found at i:16739387 original size:2 final size:2
Alignment explanation
Indices: 16739380--16739407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16739370 ATGTAAAAAG
16739380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16739408 GAAAACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16739723 original size:3 final size:3
Alignment explanation
Indices: 16739715--16739751 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
16739705 AAGATGAAAC
*
16739715 TAA TAA TAA TTAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
16739752 CACTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:16740592 original size:17 final size:18
Alignment explanation
Indices: 16740570--16740608 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
16740560 TTTATAACCG
*
16740570 AAAATAAAAAAGAAAAT-
1 AAAATAAAAAACAAAATC
16740587 AAAATAAAAAACAAAATC
1 AAAATAAAAAACAAAATC
16740605 AAAA
1 AAAA
16740609 GAAATCTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (18 bp):
AAAATAAAAAACAAAATC
Found at i:16741523 original size:84 final size:85
Alignment explanation
Indices: 16741382--16741543 Score: 281
Period size: 84 Copynumber: 1.9 Consensus size: 85
16741372 GCAAGACTTG
** **
16741382 ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACTG
1 ATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAA
16741447 CTT-AGGGAGATAAGATCTA
66 CTTCAGGGAGATAAGATCTA
16741466 ATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAA
1 ATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAA
16741531 CTTCAGGGAGATA
66 CTTCAGGGAGATA
16741544 GGATTATCGA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 64 0.88
85 9 0.12
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (85 bp):
ATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAA
CTTCAGGGAGATAAGATCTA
Found at i:16741542 original size:44 final size:44
Alignment explanation
Indices: 16741391--16741543 Score: 170
Period size: 44 Copynumber: 3.6 Consensus size: 44
16741381 GATGCGATCT
* *
16741391 GCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCC
1 GCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCC
** * ***
16741435 GCTCCACTACTGCTT-AGGGAGATAAGATCTA--A-TGCGATCC
1 GCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCC
* * *
16741475 ACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCC
1 GCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCC
*
16741519 GCTCCACTACAACTTCAGGGAGATA
1 GCTCCACTACAACTTCAGAGAGATA
16741544 GGATTATCGA
Statistics
Matches: 84, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
40 15 0.18
41 16 0.19
43 16 0.19
44 37 0.44
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (44 bp):
GCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCC
Found at i:16741975 original size:129 final size:130
Alignment explanation
Indices: 16741558--16742793 Score: 1947
Period size: 129 Copynumber: 9.6 Consensus size: 130
16741548 TATCGACTTC
* * * * *
16741558 AATCTGCTTCCTTACCCTTGAAGATAAGATTCACC-ATCTTCGATGTGCTCCGCTACTACTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
*
16741622 GAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* * *
16741686 AATCTACTTCCTTACACTTGAAGATAAGATTCGCTG-TCTCCGATCTGCTCCGCTACTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
* * ** * *
16741750 GAGACCAGATCTGTAATTT-CCAACCTATTTCACTATTAACCAGGGAGATAGGACTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* **
16741814 AATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGCT-TTCGATCTGCTCTACTACTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
*
16741878 GAGACAAGATTTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* * * *
16741943 AATCTGCTTCCTTAGACTTGAAGATAATATTTGCCGCT-TTCGATCTGCTCCGCTGCTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
*
16742007 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGTGATATAGGACTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* *
16742072 AATCTGCTTCCTTACACTTGAAGATAAGATTTGCCG-TCTTCGATCTGCTCCGCTATTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
*
16742136 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTTCTGACCAGGGATATAGGACTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* * *
16742201 AATATGCTTCCTTACACTTGAAGATAAGATTTGCCGCT-TTCGATCTGCTCCACTACTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
* * * * *
16742265 GAGATAAGATCTGTAATTTCCCAACTTATTCCACTGCTGACTAGTGATATAGGGCTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* * *
16742330 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCC-ATCTTCGATCTGCTCTGCTATTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
*
16742394 GAGACAAGATCTGTAATTTCCCAACCTATTTCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* *
16742459 AATCTGCTTCCTTACACTTGAAGATAAGATTCACCGCT-TTCGATTTGCTCCGCTACTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
16742523 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
** * * *
16742588 AATCTATTTCCTTACACTTGAAGATAAGATTTGTCGCT-TTCGATCTGCTCCGCTACAGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
**
16742652 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTTTTGACCAGGGATATAGGACTTGTGGCTTA
66 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
*
16742717 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCG-TCTTCGATCTACTCCGCTACTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
16742781 GAGACAAGATCTG
66 GAGACAAGATCTG
16742794 CTATATTCAC
Statistics
Matches: 1019, Mismatches: 81, Indels: 15
0.91 0.07 0.01
Matches are distributed among these distances:
128 190 0.19
129 827 0.81
130 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (130 bp):
AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTCTTCGATCTGCTCCGCTACTGCTTAGG
GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
Found at i:16749558 original size:3 final size:3
Alignment explanation
Indices: 16749550--16749592 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
16749540 AAGATGAAAC
* *
16749550 TAA TAA TAA TTAA TAG TAA CAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16749593 CACTAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16750439 original size:17 final size:18
Alignment explanation
Indices: 16750413--16750451 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
16750403 TTTATAGCCG
*
16750413 AAAATAAAAAAGAAAAT-
1 AAAATAAAAAACAAAATC
*
16750430 AAAATCAAAAACAAAATC
1 AAAATAAAAAACAAAATC
16750448 AAAA
1 AAAA
16750452 GAAATCTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.10
Consensus pattern (18 bp):
AAAATAAAAAACAAAATC
Found at i:16762700 original size:7 final size:6
Alignment explanation
Indices: 16762672--16762702 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
16762662 CATTAGAACC
16762672 TTTTTA TTTTTA TTTTTA TTTTTA GTTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA
16762703 ACCCTTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:16769905 original size:12 final size:11
Alignment explanation
Indices: 16769859--16769908 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
16769849 GTAGGCAACT
16769859 TTTTTTTTGCG
1 TTTTTTTTGCG
16769870 ATTTTTTTTGCG
1 -TTTTTTTTGCG
*
16769882 --CTTTTTGC-
1 TTTTTTTTGCG
16769890 TTTTTTTTGCTG
1 TTTTTTTTGC-G
16769902 TTTTTTT
1 TTTTTTT
16769909 AGCTTCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 7 0.22
10 7 0.22
12 18 0.56
ACGTcount: A:0.02, C:0.10, G:0.14, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGCG
Found at i:16773088 original size:46 final size:46
Alignment explanation
Indices: 16773036--16773125 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
16773026 ATAAAAGACA
16773036 TCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGAACC
1 TCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGAACC
*
16773082 TCGACCCACTATCAAGGATGATAGGAACCTTGGTATATGATGAA
1 TCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGAA
16773126 TGCCACACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (46 bp):
TCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGAACC
Found at i:16777303 original size:27 final size:27
Alignment explanation
Indices: 16777263--16777331 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
16777253 TTTAAGAGAT
* *
16777263 CGCCATAAATGCTTTCATTTCATGATT-
1 CGCCACAAAGGCTTTCATTTCAT-ATTA
*
16777290 TGCCACAAAGGCTTTCATTTCATATTA
1 CGCCACAAAGGCTTTCATTTCATATTA
16777317 CGCCACAAAGGCTTT
1 CGCCACAAAGGCTTT
16777332 TTTTCTCTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 3 0.08
27 34 0.92
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.35
Consensus pattern (27 bp):
CGCCACAAAGGCTTTCATTTCATATTA
Found at i:16780279 original size:10 final size:10
Alignment explanation
Indices: 16780264--16780300 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
16780254 GCTGCTGCCG
16780264 GAAAAAGAGA
1 GAAAAAGAGA
16780274 GAAAAAGAGA
1 GAAAAAGAGA
*
16780284 GAAAGAGAAGA
1 GAAAAAG-AGA
16780295 GAAAAA
1 GAAAAA
16780301 AAGGTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAAGAGA
Found at i:16780524 original size:39 final size:38
Alignment explanation
Indices: 16780462--16780595 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 38
16780452 TAGATGTTAC
*
16780462 TTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGG
1 TTAGTATTATT-TTAGT--AAAACTAATATTATTGTTATGG
16780503 TTAGTTATTATTTTAGTAAAACCCTAATTATTATTGTTA--G
1 TTAG-TATTATTTTAGTAAAA--CTAA-TATTATTGTTATGG
* *
16780543 TTAGTATTATTTTGAGTATAAAACTATTATTGTTGTTATTGTG
1 TTAGTATTATTTT-AG--TAAAACTAATATTATTGTTA-TG-G
16780586 TTAGTTATTA
1 TTAG-TATTA
16780596 GGATTAGTGG
Statistics
Matches: 78, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
39 23 0.29
40 10 0.13
41 13 0.17
42 22 0.28
43 5 0.06
44 5 0.06
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.51
Consensus pattern (38 bp):
TTAGTATTATTTTAGTAAAACTAATATTATTGTTATGG
Found at i:16783366 original size:116 final size:115
Alignment explanation
Indices: 16783158--16783367 Score: 298
Period size: 116 Copynumber: 1.8 Consensus size: 115
16783148 CTTTTTTCTA
* *
16783158 AAAAAATTTAGTAAAAAACTCTTATTTCGGCCATTTGTTCGTATTTTTTCCCGAATTTTATTACT
1 AAAAAATTTAGTAAAAAACTCTTACTTCGGCCATTTATTCGTATTTTTTCCCGAATTTTATTACT
**
16783223 TTCAAAAAAATATATTGTTTTTGAATTTTTAAAAATTATTTCTGAATTTTT
66 TT-AAAAAAATATATAATTTTTGAATTTTTAAAAATTATTTCTGAATTTTT
* * * *
16783274 AAAAAATTTAGTAAAAGACTCTTACTTCGGCCCTTTATTTGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAATTTAGTAAAAAACTCTTACTTCGGCCATTTATTCGTA-TTTTTTC-CCGAATTTTATTA
16783339 CTTT-AAAAAATATCATAATTTTT-AATTTT
64 CTTTAAAAAAATAT-ATAATTTTTGAATTTT
16783368 ATAATTTTAC
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
116 53 0.64
117 14 0.17
118 16 0.19
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (115 bp):
AAAAAATTTAGTAAAAAACTCTTACTTCGGCCATTTATTCGTATTTTTTCCCGAATTTTATTACT
TTAAAAAAATATATAATTTTTGAATTTTTAAAAATTATTTCTGAATTTTT
Found at i:16783544 original size:160 final size:153
Alignment explanation
Indices: 16783269--16783746 Score: 518
Period size: 158 Copynumber: 3.1 Consensus size: 153
16783259 TATTTCTGAA
* * * * ** * *
16783269 TTTTTAAA-AAATTTAGTAAAAGACTCTTACTTCGGCCCTTTATTTGTATTTTTTTCTCCGCATT
1 TTTTTAAATAAATTTAGTAAAAAACCCTTACTTCAGCCATTTGCTAGTATTATTTTCT-CGCATT
*
16783333 TTATTACTTTAAAAAATATCATAATTTTTAATTTTATAATTTTACATTATTTCAGTACATTATGT
65 TTATTACTTTAAAAAATATCATAATTTTTAATTTTATTATTTTACATTATTTCAGTACATTATGT
16783398 TGGAAATTTATTAATTTAGTGTGT
130 TGGAAATTTATTAATTTAGTGTGT
* * * *
16783422 TTTTTAAATTAATTTAGTGTAAAAAAAACCCTTA-TTACTGCCCTTTGCTCGTATTATTTTCTCG
1 TTTTTAAATAAATTTA--GT--AAAAAACCCTTACTT-CAGCCATTTGCTAGTATTATTTTCTCG
* * * *
16783486 GATTTTATTACTTTCAATAAAAATAT-ATTATTTTTGTATTTTATTATTTTATATTATTTCAGTA
61 CATTTTATTACTTT--A-AAAAATATCATAATTTTT-AATTTTATTATTTTACATTATTTCAGTA
* * * * * *
16783550 CATTTTTTTGAAATATTTTTATTAA-TTATTTCTGAA
122 CATTATGTTGGAA-A--TTTATTAATTTA-GTGTG-T
* * *
16783586 TTTTTAAA-AAATTTAGTAAAAGACTCTTACTTCAGCCATTTGTTAGTATTATTTTC-CGCATTT
1 TTTTTAAATAAATTTAGTAAAAAACCCTTACTTCAGCCATTTGCTAGTATTATTTTCTCGCATTT
* *
16783649 TATTACTTTAAAAAATATCATAATTTTTAATTTTATTATTTTAGATTATTTTAGTACATTATGTT
66 TATTACTTTAAAAAATATCATAATTTTTAATTTTATTATTTTACATTATTTCAGTACATTATGTT
*
16783714 TGAAATTTATTAATTTAGTGTGT
131 GGAAATTTATTAATTTAGTGTGT
16783737 TTTTTAAATA
1 TTTTTAAATA
16783747 TACCATTTTT
Statistics
Matches: 268, Mismatches: 38, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
151 8 0.03
152 12 0.04
153 11 0.04
154 7 0.03
155 42 0.16
156 11 0.04
157 17 0.06
158 45 0.17
159 39 0.15
160 45 0.17
161 3 0.01
162 3 0.01
163 17 0.06
164 8 0.03
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (153 bp):
TTTTTAAATAAATTTAGTAAAAAACCCTTACTTCAGCCATTTGCTAGTATTATTTTCTCGCATTT
TATTACTTTAAAAAATATCATAATTTTTAATTTTATTATTTTACATTATTTCAGTACATTATGTT
GGAAATTTATTAATTTAGTGTGT
Found at i:16784012 original size:10 final size:10
Alignment explanation
Indices: 16783997--16784137 Score: 60
Period size: 10 Copynumber: 14.0 Consensus size: 10
16783987 AAATTACCTT
16783997 TTTTTCTTTC
1 TTTTTCTTTC
*
16784007 TTTTTCCTTC
1 TTTTTCTTTC
* **
16784017 CTTCCCTCTTC
1 TTTTTCT-TTC
*
16784028 TTCTTC-TTC
1 TTTTTCTTTC
*
16784037 TTCCTT-TTT-
1 TT-TTTCTTTC
16784046 TTTTTCTTCTC
1 TTTTTCTT-TC
* *
16784057 CTTTCCTTT-
1 TTTTTCTTTC
* *
16784066 TCTTTCCTTC
1 TTTTTCTTTC
16784076 TTTTTCTTTC
1 TTTTTCTTTC
*
16784086 TTTCCTCTCCTCTC
1 TTT--T-T-CTTTC
*
16784100 CTTTTCTTTC
1 TTTTTCTTTC
16784110 TTTTTCTTTC
1 TTTTTCTTTC
16784120 --TTTCTTTC
1 TTTTTCTTTC
*
16784128 TTCTTCTTTC
1 TTTTTCTTTC
16784138 CCTCTCCTTC
Statistics
Matches: 95, Mismatches: 23, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
8 10 0.11
9 14 0.15
10 50 0.53
11 12 0.13
12 2 0.02
13 1 0.01
14 6 0.06
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:16784052 original size:24 final size:24
Alignment explanation
Indices: 16784025--16784133 Score: 66
Period size: 24 Copynumber: 4.6 Consensus size: 24
16784015 TCCTTCCCTC
*
16784025 TTCTTCTTCTTCTTCCTTTTTTTT
1 TTCTTCTTCTTCTTCCTTTTTCTT
*
16784049 TTCTTC-TCCT-TTCC-TTTTCTT
1 TTCTTCTTCTTCTTCCTTTTTCTT
* * * * *
16784070 TCCTTCTTTTTCTTTCTTTCCTCTC
1 TTCTTCTTCTTCTTCCTTT-TTCTT
* * *
16784095 CTCTCCTT-TTCTTTCTTTTTC-T
1 TTCTTCTTCTTCTTCCTTTTTCTT
16784117 TTCTTTCTTTCTTCTTC
1 TTC-TTC-TTCTTCTTC
16784134 TTTCCCTCTC
Statistics
Matches: 62, Mismatches: 16, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
21 11 0.18
22 8 0.13
23 10 0.16
24 20 0.32
25 13 0.21
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TTCTTCTTCTTCTTCCTTTTTCTT
Found at i:16784066 original size:18 final size:19
Alignment explanation
Indices: 16784031--16784138 Score: 82
Period size: 18 Copynumber: 5.7 Consensus size: 19
16784021 CCTCTTCTTC
*
16784031 TTCTTCTTCCTTT--TTTTT
1 TTCTTC-TCCTTTCCTTTCT
16784049 TTCTTCTCCTTTCCTTTTCT
1 TTCTTCTCCTTTCC-TTTCT
*
16784069 TTCCTTCT--TTTTCTTTCT
1 TT-CTTCTCCTTTCCTTTCT
* *
16784087 TTCCTCTCCTCTCCTTTTCT
1 TTCTTCTCCTTTCC-TTTCT
* *
16784107 TTCTTTTTCTTT-CTTTCT
1 TTCTTCTCCTTTCCTTTCT
*
16784125 TTCTTCTTCTTTCC
1 TTCTTCTCCTTTCC
16784139 CTCTCCTTCT
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
17 10 0.14
18 29 0.40
19 9 0.12
20 19 0.26
21 5 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TTCTTCTCCTTTCCTTTCT
Found at i:16784103 original size:38 final size:36
Alignment explanation
Indices: 16783997--16784127 Score: 113
Period size: 38 Copynumber: 3.4 Consensus size: 36
16783987 AAATTACCTT
*
16783997 TTTTTCTTTCTTTTTCCT-TCCTTCCCTCTTCTTCTTCTTC
1 TTTTTCTTTC--TTTCCTCTCCTT-CCTTTTC-T-TTCTTC
* *
16784037 TTCCTTT-TTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTC
1 TT--TTTCTTTCTTTCCTCTCC-TTCCTTTTCTTT-CTTC
*
16784076 TTTTTCTTTCTTTCCTCTCCTCTCCTTTTCTTTCTTT
1 TTTTTCTTTCTTTCCTCTCCT-TCCTTTTCTTTCTTC
16784113 TTCTTTCTTTCTTTC
1 TT-TTTCTTTCTTTC
16784128 TTCTTCTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
37 9 0.12
38 37 0.48
39 12 0.16
40 11 0.14
41 5 0.06
42 3 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTTTCTTTCTTTCCTCTCCTTCCTTTTCTTTCTTC
Found at i:16784111 original size:34 final size:34
Alignment explanation
Indices: 16783998--16784136 Score: 131
Period size: 34 Copynumber: 4.1 Consensus size: 34
16783988 AATTACCTTT
* * *
16783998 TTTTCTTTCTTTTTCCTTCCTTCC-CTCTTCTTC
1 TTTTCTTTCTTTTTCTTTCTTTCCTCTCCTCTTC
* * * *
16784031 TTCTTCTTCCTTTTTTTTTTCTTCTCCTTTCCTTTTC
1 TT-TTCTTTC-TTTTTCTTTCTT-TCCTCTCCTCTTC
* *
16784068 -TTTCCTTCTTTTTCTTTCTTTCCTCTCCTCTCC
1 TTTTCTTTCTTTTTCTTTCTTTCCTCTCCTCTTC
* *
16784101 TTTTCTTTCTTTTTCTTTCTTT-CTTTCTTCTTC
1 TTTTCTTTCTTTTTCTTTCTTTCCTCTCCTCTTC
16784134 TTT
1 TTT
16784137 CCCTCTCCTT
Statistics
Matches: 84, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
33 23 0.27
34 37 0.44
35 14 0.17
36 4 0.05
37 6 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (34 bp):
TTTTCTTTCTTTTTCTTTCTTTCCTCTCCTCTTC
Found at i:16788727 original size:51 final size:51
Alignment explanation
Indices: 16788651--16788765 Score: 194
Period size: 51 Copynumber: 2.3 Consensus size: 51
16788641 ACTTCTGATC
* *
16788651 AGTGACAAGTGATAAGTGGCAGCTTTAGCTACACTTCTCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGATCAGGGACA
* *
16788702 AGTGACAAGTGATAAGTGGTAGCTTTAGCTATACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGATCAGGGACA
16788753 AGTGACAAGTGAT
1 AGTGACAAGTGAT
16788766 TAATGTGATC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGATCAGGGACA
Found at i:16790218 original size:43 final size:42
Alignment explanation
Indices: 16790152--16790308 Score: 145
Period size: 43 Copynumber: 3.7 Consensus size: 42
16790142 AGTTTGTACA
* * **
16790152 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAAACAAGGTCTTACATGTAATCAAAT-ACG
* * *
16790195 ATGCCACTGTCCCAAACAAGGTCTTACACGTAATCATATACG
1 ATGCCAATGTCCCAAACAAGGTCTTACATGTAATCAAATACG
* * *
16790237 ATGCCAATGTCCCAGACATGGTCTTACATCTAAATCTTAAAT-CG
1 ATGCCAATGTCCCAAACAAGGTCTTACATGT-AATC--AAATACG
* * **
16790281 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAAACAAGGTCTTACA
16790309 CAAAATCATA
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
42 29 0.30
43 36 0.38
44 28 0.29
45 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAAACAAGGTCTTACATGTAATCAAATACG
Found at i:16790316 original size:86 final size:84
Alignment explanation
Indices: 16790152--16790320 Score: 207
Period size: 86 Copynumber: 2.0 Consensus size: 84
16790142 AGTTTGTACA
* *
16790152 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCACTGTCCCAAACAAGGT
1 ATGCCAACGTCCCAGACATGGTCTTACATCTAATCAAAT-ACGATGCCACTGTCCCAAACAAGGT
**
16790217 CTTACACGTAATCATATACG
65 CTTACACAAAATCATATACG
* * **
16790237 ATGCCAATGTCCCAGACATGGTCTTACATCTAAATCTTAAAT-CGATGCCAAC-GTCCCAGACGT
1 ATGCCAACGTCCCAGACATGGTCTTACATCT-AATC--AAATACGATGCC-ACTGTCCCAAACAA
16790300 GGTCTTACACAAAATCATATA
62 GGTCTTACACAAAATCATATA
16790321 TCAGAATCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
85 28 0.39
86 38 0.53
87 2 0.03
88 4 0.06
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACATCTAATCAAATACGATGCCACTGTCCCAAACAAGGTC
TTACACAAAATCATATACG
Found at i:16790954 original size:15 final size:13
Alignment explanation
Indices: 16790926--16790952 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16790916 TACAAACGAT
16790926 AAAATTTTCACAC
1 AAAATTTTCACAC
16790939 AAAATTTTCACAC
1 AAAATTTTCACAC
16790952 A
1 A
16790953 CACAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:16801570 original size:125 final size:125
Alignment explanation
Indices: 16801348--16801760 Score: 646
Period size: 125 Copynumber: 3.3 Consensus size: 125
16801338 TTTTATTAAG
* * *
16801348 GAAATCGCTCCCACGTGGACTCGTTTTTGATATAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* * * * *
16801413 GTTTTTGAGCAAAGAGTATAAAAAACGCTTCAAGCAGGATGTTTTATAAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
* *
16801473 GAAATCGCTCCCATGTGGACGCGCTTTTGCTATAATAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* *
16801538 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
* * *
16801598 GAAATCGCTCCCACGTGGACGTGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTAAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* *
16801663 GTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAGGGTGCTTTATCAGAAGAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
* * *
16801723 GAAATCGCTCTCACGTGGACGTGCTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAG
16801761 CATGTTTGGG
Statistics
Matches: 266, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 266 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
Found at i:16802771 original size:49 final size:49
Alignment explanation
Indices: 16802716--16802833 Score: 227
Period size: 49 Copynumber: 2.4 Consensus size: 49
16802706 GAATATCAAT
16802716 TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAAC
1 TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAAC
*
16802765 TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAATTAAAC
1 TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAAC
16802814 TATTTTGTATTTTATTACAT
1 TATTTTGTATTTTATTACAT
16802834 TAATATAAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (49 bp):
TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAAC
Done.