Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 125 of 135
Found at i:41055091 original size:89 final size:90
Alignment explanation
Indices: 41054983--41055314 Score: 320
Period size: 89 Copynumber: 3.7 Consensus size: 90
41054973 AAGAAATCAT
* * * * ** *
41054983 ATTTTGACCCTTAAGCTTCTTCAAAATTACATGTTGACCCTCAAATTTTTTTAAAATTAAATTTT
1 ATTTTGACCCCTAAACTTCTTCAAAATTACATTTTGACCCTCAAAATTTTCCAAAATTACATTTT
*
41055048 AACCTCTAAATTTTTCAAAAATTAC
66 AACCTCTAAATTTTTCTAAAATTAC
*
41055073 A-TTTGACCCCTAAACTTC-TCTAAAATTACATTTTGACCCTTAAAATTTTCCAAAATTACATTT
1 ATTTTGACCCCTAAACTTCTTC-AAAATTACATTTTGACCCTCAAAATTTTCCAAAATTACATTT
* *
41055136 TGACC-CTTAAATTTTTCTATAATTAC
65 TAACCTC-TAAATTTTTCTAAAATTAC
* * * * *
41055162 ATTTTAACCTCTAAACTT-TTCCAAAATTATATTTTGACCC-CTAAACTTTTCCAAAATTGCATT
1 ATTTTGACCCCTAAACTTCTT-CAAAATTACATTTTGACCCTC-AAAATTTTCCAAAATTACATT
* * * *
41055225 TTAATCTCTAAACTTCTCTAAAATTAT
64 TTAACCTCTAAATTTTTCTAAAATTAC
* * * * * * *
41055252 ATTTTGA-TCCTAAACTTC-TCTAAAATCACATTTTGTCTCT-AAACTTTACCAAAATTGCATTT
1 ATTTTGACCCCTAAACTTCTTC-AAAATTACATTTTGACCCTCAAAATTTTCCAAAATTACATTT
41055314 T
65 T
41055315 GACCCCAAAC
Statistics
Matches: 201, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
88 26 0.13
89 96 0.48
90 77 0.38
91 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (90 bp):
ATTTTGACCCCTAAACTTCTTCAAAATTACATTTTGACCCTCAAAATTTTCCAAAATTACATTTT
AACCTCTAAATTTTTCTAAAATTAC
Found at i:41055226 original size:30 final size:30
Alignment explanation
Indices: 41054983--41055402 Score: 304
Period size: 30 Copynumber: 14.2 Consensus size: 30
41054973 AAGAAATCAT
* *
41054983 ATTTTGACCCTTAAGCTTCTT-CAAAATTAC
1 ATTTTGACCCCTAAACTT-TTCCAAAATTAC
* * ** *
41055013 ATGTTGA-CCCTCAAATTTTTTTAAAATTAA
1 ATTTTGACCCCT-AAACTTTTCCAAAATTAC
* * * *
41055043 ATTTTAACCTCTAAATTTTTCAAAAATTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* *
41055073 A-TTTGACCCCTAAACTTCTCTAAAATTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* *
41055102 ATTTTGACCCTTAAAATTTTCCAAAATTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* * * *
41055132 ATTTTGACCCTTAAATTTTTCTATAATTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* * *
41055162 ATTTTAACCTCTAAACTTTTCCAAAATTAT
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
*
41055192 ATTTTGACCCCTAAACTTTTCCAAAATTGC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* * * * * *
41055222 ATTTTAATCTCTAAACTTCTCTAAAATTAT
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* * * *
41055252 ATTTTGA-TCCTAAACTTCTCTAAAATCAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
* * * *
41055281 ATTTTG-TCTCTAAACTTTACCAAAATTGC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
**
41055310 ATTTTGACCCC-AAACTTCTT-CAAAATCGC
1 ATTTTGACCCCTAAACTT-TTCCAAAATTAC
*** * *
41055339 ATTTT-AATGCT-GAGTTTTCCCAAAATTAC
1 ATTTTGACCCCTAAACTTTT-CCAAAATTAC
* *
41055368 ATTTTCA-CCCTAAACTTTT-CAAATTTAC
1 ATTTTGACCCCTAAACTTTTCCAAAATTAC
*
41055396 GTTTTGA
1 ATTTTGA
41055403 TCCTGTATTC
Statistics
Matches: 306, Mismatches: 72, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
27 2 0.01
28 18 0.06
29 107 0.35
30 176 0.58
31 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
ATTTTGACCCCTAAACTTTTCCAAAATTAC
Found at i:41060900 original size:30 final size:29
Alignment explanation
Indices: 41060865--41061084 Score: 185
Period size: 30 Copynumber: 7.4 Consensus size: 29
41060855 ATACGGGATC
*
41060865 AAAATGTAATTTTAGAAAAGTCTGAGGGT
1 AAAATGTAATTTTAGAAAAGTTTGAGGGT
* *
41060894 AAAAATGTGATTTTAGAAGAGTTTG-GGGT
1 -AAAATGTAATTTTAGAAAAGTTTGAGGGT
* * * *
41060923 CAAAATGTGATTTTGGAAAGGTTTAAGGGT
1 -AAAATGTAATTTTAGAAAAGTTTGAGGGT
* *
41060953 CAAAGTGTAATTTT-GAAAAAGTTTAAGGGT
1 -AAAATGTAATTTTAG-AAAAGTTTGAGGGT
*
41060983 AAAATGTAATTTTAGAAAA-TTTTAGGGGT
1 AAAATGTAATTTTAGAAAAGTTTGA-GGGT
* * * *
41061012 TAAATGTAATTTTGGAAAAATTCGAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTGAGGG-T
* * * *
41061042 AAAATATAATTTTGGAGAAGTTTAGAGGTT
1 AAAATGTAATTTTAGAAAAGTTT-GAGGGT
*
41061072 AAAATGTGATTTT
1 AAAATGTAATTTT
41061085 GGGAAGTTTG
Statistics
Matches: 158, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.03
29 65 0.41
30 85 0.54
31 4 0.03
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTGAGGGT
Found at i:41061100 original size:29 final size:29
Alignment explanation
Indices: 41060865--41061100 Score: 174
Period size: 29 Copynumber: 8.0 Consensus size: 29
41060855 ATACGGGATC
* * *
41060865 AAAATGTAATTTTAGAAAAGTCT-GAGGGTA
1 AAAATGTAATTTT-GGAAAGTTTAG-GGGTT
* * *
41060895 AAAATGTGATTTTAGAAGAGTTT-GGGGTC
1 AAAATGTAATTTTGGAA-AGTTTAGGGGTT
* * *
41060924 AAAATGTGATTTTGGAAAGGTTTAAGGGTC
1 AAAATGTAATTTTGGAAA-GTTTAGGGGTT
* * *
41060954 AAAGTGTAATTTTGAAAAAGTTTAAGGG-T
1 AAAATGTAATTTTG-GAAAGTTTAGGGGTT
* *
41060983 AAAATGTAATTTTAGAAAATTTTAGGGGTT
1 AAAATGTAATTTT-GGAAAGTTTAGGGGTT
** *
41061013 -AAATGTAATTTTGGAAAAATTCGAGGGTT
1 AAAATGTAATTTTGGAAAGTTTAG-GGGTT
* *
41061042 AAAATATAATTTTGGAGAAGTTTAGAGGTT
1 AAAATGTAATTTTGGA-AAGTTTAGGGGTT
* * *
41061072 AAAATGTGATTTTGGGAAGTTTGGGGGTT
1 AAAATGTAATTTTGGAAAGTTTAGGGGTT
41061101 GCTTGCGCAA
Statistics
Matches: 169, Mismatches: 28, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
28 8 0.05
29 77 0.46
30 76 0.45
31 8 0.05
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGTTTAGGGGTT
Found at i:41061100 original size:59 final size:58
Alignment explanation
Indices: 41060865--41061100 Score: 176
Period size: 59 Copynumber: 4.0 Consensus size: 58
41060855 ATACGGGATC
* * * * * *
41060865 AAAATGTAATTTTAGAAAAGTCT-GAGGGTAAAAATGTGATTTTAGAAGAGTTTG-GGGTC
1 AAAATGTAATTTT-GGAAAGTTTAGA-GGTTAAAATGTAATTTTGGAA-AGTTTGAGGGTT
* * * * *
41060924 AAAATGTGATTTTGGAAAGGTTTA-AGGGTCAAAGTGTAATTTTGAAAAAGTTTAAGGG-T
1 AAAATGTAATTTTGGAAA-GTTTAGA-GGTTAAAATGTAATTTTG-GAAAGTTTGAGGGTT
* * * * *
41060983 AAAATGTAATTTTAGAAAATTTTAGGGGTT-AAATGTAATTTTGGAAAAATTCGAGGGTT
1 AAAATGTAATTTT-GGAAAGTTTAGAGGTTAAAATGTAATTTTGG-AAAGTTTGAGGGTT
* * * *
41061042 AAAATATAATTTTGGAGAAGTTTAGAGGTTAAAATGTGATTTTGGGAAGTTTGGGGGTT
1 AAAATGTAATTTTGGA-AAGTTTAGAGGTTAAAATGTAATTTTGGAAAGTTTGAGGGTT
41061101 GCTTGCGCAA
Statistics
Matches: 138, Mismatches: 29, Indels: 20
0.74 0.16 0.11
Matches are distributed among these distances:
58 27 0.20
59 89 0.64
60 22 0.16
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAGTTTAGAGGTTAAAATGTAATTTTGGAAAGTTTGAGGGTT
Found at i:41062361 original size:11 final size:11
Alignment explanation
Indices: 41062341--41062380 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
41062331 GTAAAATAAA
*
41062341 AATTTTAAATT
1 AATTTAAAATT
41062352 AATTTAAAATTT
1 AATTTAAAA-TT
41062364 AATTTAAAATT
1 AATTTAAAATT
*
41062375 TATTTA
1 AATTTA
41062381 GGTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:41062367 original size:12 final size:12
Alignment explanation
Indices: 41062341--41062380 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
41062331 GTAAAATAAA
*
41062341 AATTTTAAA-TT
1 AATTTAAAATTT
41062352 AATTTAAAATTT
1 AATTTAAAATTT
41062364 AATTTAAAATTT
1 AATTTAAAATTT
41062376 -ATTTA
1 AATTTA
41062381 GGTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 13 0.48
12 14 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAAAATTT
Found at i:41062914 original size:124 final size:124
Alignment explanation
Indices: 41062654--41062916 Score: 355
Period size: 124 Copynumber: 2.1 Consensus size: 124
41062644 ATGGATTTGG
* * * *
41062654 TTTACTTCTCTGCATCTCGTCAAAAAGATGACCACTTTATTGCTTCGACCTATTTCTCTATATCT
1 TTTACTTCTCTGTATCTCATCAAAAAGATGACCACTTTATTGCTTCGACCCAATTCTCTATATCT
* * * * * * *
41062719 CATTAGGAAGATGGGGTTTGGAAGTTTTACTCATATTGAGCTTCGCTTCATTAAATTGG
66 CATCAAGAAGATAGGATTTGAAAGTTTTACTCACATTGAGCTTCGCTTCATTAAATTGA
* * * * *
41062778 TCTACTTTTCTGTATCTCATCAAGAAGATGACCACTTTATTGCTTCGACCCAATTCTTTGTATCT
1 TTTACTTCTCTGTATCTCATCAAAAAGATGACCACTTTATTGCTTCGACCCAATTCTCTATATCT
* *
41062843 CATCAAGAATATAGGATTTGAAAGTTTTACTCACATTGAGCTTCGCTTCATTGAATTGA
66 CATCAAGAAGATAGGATTTGAAAGTTTTACTCACATTGAGCTTCGCTTCATTAAATTGA
*
41062902 TTTACTCCTCTGTAT
1 TTTACTTCTCTGTAT
41062917 TTCACCAGGA
Statistics
Matches: 118, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
124 118 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (124 bp):
TTTACTTCTCTGTATCTCATCAAAAAGATGACCACTTTATTGCTTCGACCCAATTCTCTATATCT
CATCAAGAAGATAGGATTTGAAAGTTTTACTCACATTGAGCTTCGCTTCATTAAATTGA
Found at i:41063241 original size:78 final size:76
Alignment explanation
Indices: 41063117--41063402 Score: 274
Period size: 78 Copynumber: 3.7 Consensus size: 76
41063107 GCCCCTATCG
* * * * *
41063117 CGGGGTAAGAGATTGGCTGACGGTGATCTGCC-CAATGATCGAGGTAAAAAATCAAAAAGTTACA
1 CGGGGTAAGAGATT-GCTGATGGTGATCTGCCTCAA-GCTCGGGGTAAAAGATCAAAAAGTT-CT
*
41063181 ATCTGCC-CTAAGCT
63 ATCTGCCTC-AGGCT
* ** *
41063195 CGGGGTAAGAGATTAGCTTATGGTGA-CTTGCCTCAAGCTCGGGGTAAAAGATCGAATGACTTCT
1 CGGGGTAAGAGATT-GCTGATGGTGATC-TGCCTCAAGCTCGGGGTAAAAGATC-AAAAAGTTCT
41063259 ATCTGCCTCAGGCT
63 ATCTGCCTCAGGCT
* * * * **
41063273 TGGGGTAGGAGATTGGTTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGCTTCTA
1 CGGGGTAAGAGATT-GCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCAAAAAG-TTCTA
41063338 TCTGCCTCAGGCT
64 TCTGCCTCAGGCT
* * * *
41063351 CGGGGTAAGAGATTGACTGATGGTGATTTGCC-CAGGCTTGAGGTAAAAGATC
1 CGGGGTAAGAGATTG-CTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATC
41063403 GGATGACTGT
Statistics
Matches: 173, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
77 20 0.12
78 143 0.83
79 10 0.06
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (76 bp):
CGGGGTAAGAGATTGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCAAAAAGTTCTATC
TGCCTCAGGCT
Found at i:41063266 original size:39 final size:38
Alignment explanation
Indices: 41063231--41063655 Score: 232
Period size: 39 Copynumber: 10.9 Consensus size: 38
41063221 CTTGCCTCAA
*
41063231 GCTCGGGGTAAAAGATCGAATGACTTCTATCTGCCTCAG
1 GCTCGGGGTAAAAGATCGGATGACTTCTATCTGCC-CAG
* ** * * ** *
41063270 GCTTGGGGTAGGAGATTGGTTGA-TGGTGATCTGCCTCAA
1 GCTCGGGGTAAAAGATCGGATGACTTCT-ATCTGCC-CAG
* *
41063309 GCTCGGGGTAAAAGATCGAATGGCTTCTATCTGCCTCAG
1 GCTCGGGGTAAAAGATCGGATGACTTCTATCTGCC-CAG
* * ** *
41063348 GCTCGGGGTAAGAGAT-TGACTGA-TGGTGATTTGCCCAG
1 GCTCGGGGTAAAAGATCGGA-TGACTTCT-ATCTGCCCAG
* * * *
41063386 GCTTGAGGTAAAAGATCGGATGACTGT-GATCTGTCCCAT
1 GCTCGGGGTAAAAGATCGGATGACT-TCTATCTG-CCCAG
* * * * * * * *
41063425 GATCAGGGTAAGAGATCGAATGGCTGCAATCTATCCCAG
1 GCTCGGGGTAAAAGATCGGATGACTTCTATCT-GCCCAG
* ** *
41063464 GCTCGGGGTAAAAGATTGGATGGTTTCAATCTGCCCTAG
1 GCTCGGGGTAAAAGATCGGATGACTTCTATCTGCCC-AG
* * ** * * **
41063503 GCTCGAGATAAGCGATTGGTTGA-TGATGATCTGCCCCAG
1 GCTCGGGGTAAAAGATCGGATGACTTCT-ATCTG-CCCAG
* * *
41063542 GCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAA
1 GCTCGGGGTAAAAGATCGGATGACTTCTATCTG-CCCAG
* * * **
41063581 GCTCGAGGTAAAAGATTGGCTGA-TAGTAATCTGCCCCAG
1 GCTCGGGGTAAAAGATCGGATGACTTCT-ATCTG-CCCAG
*
41063620 GCTCGGGGTAAAAGATCGGATGACTTCAATCTGCCC
1 GCTCGGGGTAAAAGATCGGATGACTTCTATCTGCCC
41063656 TAAGCTTGGG
Statistics
Matches: 283, Mismatches: 87, Indels: 33
0.70 0.22 0.08
Matches are distributed among these distances:
38 36 0.13
39 240 0.85
40 7 0.02
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (38 bp):
GCTCGGGGTAAAAGATCGGATGACTTCTATCTGCCCAG
Found at i:41063541 original size:78 final size:78
Alignment explanation
Indices: 41063179--41063677 Score: 359
Period size: 78 Copynumber: 6.4 Consensus size: 78
41063169 CAAAAAGTTA
* * * * * * * *
41063179 CAATCTGCCCTAAGCTCGGGGTAAGAGATTAGCTTATGGTGA-CTTGCCTCAAGCTCGGGGTAAA
1 CAATCTGCCCTAAGCTCGAGATAAGAGATTGGCTGATAGTAATC-TGCCCCAGGCTCGGGGTAAA
* *
41063243 AGATCGAATGACTT
65 AGATCGGATGGCTT
* * * * * * * * * * *
41063257 CTATCTG-CCTCAGGCTTGGGGTAGGAGATTGGTTGATGGTGATCTGCCTCAAGCTCGGGGTAAA
1 CAATCTGCCCT-AAGCTCGAGATAAGAGATTGGCTGATAGTAATCTGCCCCAGGCTCGGGGTAAA
*
41063321 AGATCGAATGGCTT
65 AGATCGGATGGCTT
* * * * * * * * * *
41063335 CTATCTG-CCTCAGGCTCGGGGTAAGAGATTGACTGATGGTGATTTG-CCCAGGCTTGAGGTAAA
1 CAATCTGCCCT-AAGCTCGAGATAAGAGATTGGCTGATAGTAATCTGCCCCAGGCTCGGGGTAAA
*
41063398 AGATCGGATGACTGT
65 AGATCGGATGGCT-T
* * * * * ** * * **
41063413 -GATCTGTCCC-ATGATC-AGGGTAAGAGATCGAATGGCT-GCAATCTATCCCAGGCTCGGGGTA
1 CAATCTG-CCCTAAGCTCGA-GATAAGAGATTGGCT-GATAGTAATCTGCCCCAGGCTCGGGGTA
* *
41063474 AAAGATTGGATGGTTT
63 AAAGATCGGATGGCTT
* * * *
41063490 CAATCTGCCCTAGGCTCGAGATAAGCGATTGGTTGAT-GATGATCTGCCCCAGGCTCGGGGTAAA
1 CAATCTGCCCTAAGCTCGAGATAAGAGATTGGCTGATAG-TAATCTGCCCCAGGCTCGGGGTAAA
41063554 AGATCGGATGGCTT
65 AGATCGGATGGCTT
* * *
41063568 CAATCTGCCCCAAGCTCGAGGTAAAAGATTGGCTGATAGTAATCTGCCCCAGGCTCGGGGTAAAA
1 CAATCTGCCCTAAGCTCGAGATAAGAGATTGGCTGATAGTAATCTGCCCCAGGCTCGGGGTAAAA
*
41063633 GATCGGATGACTT
66 GATCGGATGGCTT
* *
41063646 CAATCTGCCCTAAGCTTGGGATAAGAGATTGG
1 CAATCTGCCCTAAGCTCGAGATAAGAGATTGG
41063678 AATCTTCAAT
Statistics
Matches: 345, Mismatches: 63, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
77 60 0.17
78 280 0.81
79 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (78 bp):
CAATCTGCCCTAAGCTCGAGATAAGAGATTGGCTGATAGTAATCTGCCCCAGGCTCGGGGTAAAA
GATCGGATGGCTT
Found at i:41063652 original size:117 final size:116
Alignment explanation
Indices: 41063295--41063661 Score: 380
Period size: 117 Copynumber: 3.1 Consensus size: 116
41063285 TTGGTTGATG
* * * *
41063295 GTGATCTGCCTCAAGCTCGGGGTAAAAGATCGAATGGCTTCTATCTGCCTCAGGCTCGGGGTAAG
1 GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTTCAATCTGCCCCAGGCTCGGGGTAAA
* * * *
41063360 AGATTGACTGATGGTGATTTG-CCCAGGCTTGAGGTAAAAGATCGGATGACT
66 AGATTGGCTGAT-GTAATCTGCCCCAGGCTCGAGGTAAAAGATCGGATGACT
* * * * * * **
41063411 GTGATCTGTCCCATGATCAGGGTAAGAGATCGAATGGCTGCAATCTATCCCAGGCTCGGGGTAAA
1 GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTTCAATCTGCCCCAGGCTCGGGGTAAA
* * * * * ** * *
41063476 AGATTGGATGGTTTCAATCTGCCCTAGGCTCGAGATAAGCGATTGGTTGA-T
66 AGATTGGCTGATGT-AATCTGCCCCAGGCTCGAGGTAAAAGATCGGATGACT
* * * *
41063527 GATGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAAGCTCGAGGTAA
1 G-TGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTTCAATCTGCCCCAGGCTCGGGGTAA
*
41063592 AAGATTGGCTGATAGTAATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGACT
65 AAGATTGGCTGAT-GTAATCTGCCCCAGGCTCGAGGTAAAAGATCGGATGACT
* *
41063645 -TCAATCTGCCCTAAGCT
1 GT-GATCTGCCCCAAGCT
41063662 TGGGATAAGA
Statistics
Matches: 196, Mismatches: 49, Indels: 11
0.77 0.19 0.04
Matches are distributed among these distances:
115 1 0.01
116 69 0.35
117 124 0.63
118 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (116 bp):
GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTTCAATCTGCCCCAGGCTCGGGGTAAA
AGATTGGCTGATGTAATCTGCCCCAGGCTCGAGGTAAAAGATCGGATGACT
Found at i:41072576 original size:30 final size:30
Alignment explanation
Indices: 41072483--41072774 Score: 301
Period size: 30 Copynumber: 9.9 Consensus size: 30
41072473 GGAGAATATG
** * *
41072483 GGGTCAAAACATAATTTTAGAAAAGTTTGA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * **
41072513 GAG---AAATGTGATTTTGGAGGAGTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * * *
41072540 -GGTCAAAATGTGATTTTGGAAGACTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* *
41072569 GGGTCAAAGTGTAATTTTGGAAAAGTTTAT
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
*
41072599 GGGTCAAAATGTAATTTTAGAAAAGTTT-A
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* *
41072628 GCGGTTAAAATGTAATTTTGGAGAAGTTTAA
1 G-GGTCAAAATGTAATTTTGGAAAAGTTTAA
* * *
41072659 GAGTTAAAATGTAATTTTGGAAAATTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
*
41072689 GGGTTAAAATGTAATTTT-GAAAAGTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* *
41072718 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* *
41072748 GGGTCAAAATGTGATTTT-GAGAAGTTT
1 GGGTCAAAATGTAATTTTGGAAAAGTTT
41072775 GGGGGTTGCC
Statistics
Matches: 223, Mismatches: 32, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
26 1 0.00
27 17 0.08
29 58 0.26
30 145 0.65
31 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTAA
Found at i:41074066 original size:11 final size:12
Alignment explanation
Indices: 41074012--41074063 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
41074002 ATTTTGGATT
*
41074012 TTTAATGTAAAA
1 TTTAATTTAAAA
* *
41074024 TTGACATTTTAAA
1 TTTA-ATTTAAAA
*
41074037 -TTAAATTAAAA
1 TTTAATTTAAAA
41074048 TTTAATTTAAAA
1 TTTAATTTAAAA
41074060 TTTA
1 TTTA
41074064 TTTGGTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
11 6 0.19
12 19 0.61
13 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (12 bp):
TTTAATTTAAAA
Found at i:41079849 original size:20 final size:20
Alignment explanation
Indices: 41079826--41079874 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
41079816 TTTATTTTAG
*
41079826 ATTTTTTTATCGT-ACTAAT
1 ATTTTTTTATAGTAACTAAT
*
41079845 AATTTTTTTATAGTAATTAAT
1 -ATTTTTTTATAGTAACTAAT
41079866 ATTTTTTTA
1 ATTTTTTTA
41079875 AAATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (20 bp):
ATTTTTTTATAGTAACTAAT
Found at i:41083805 original size:23 final size:24
Alignment explanation
Indices: 41083777--41083825 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
41083767 CATTATAGCA
*
41083777 ATAACATAATT-GACAATAATCAT
1 ATAACAAAATTGGACAATAATCAT
**
41083800 ATAACAAAATTGGACTGTAATCAT
1 ATAACAAAATTGGACAATAATCAT
41083824 AT
1 AT
41083826 CTATTCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (24 bp):
ATAACAAAATTGGACAATAATCAT
Found at i:41084346 original size:22 final size:22
Alignment explanation
Indices: 41084303--41084347 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41084293 TATGACTTTT
* *
41084303 AATTTTCTTAATATTTTAATTA
1 AATTTTCTTAAAATTCTAATTA
* *
41084325 AATTTTTTTAAAATTCTCATTA
1 AATTTTCTTAAAATTCTAATTA
41084347 A
1 A
41084348 TCTCACAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTTCTTAAAATTCTAATTA
Found at i:41084616 original size:30 final size:28
Alignment explanation
Indices: 41084582--41084648 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
41084572 ACAATTGGAC
**
41084582 CTAAATTTTGAAATTTAAAACATAAAAAAA
1 CTAAATTTT-AAAAATAAAA-ATAAAAAAA
* *
41084612 CTAAATTCTTAAAAATAAAAATATAAAGA
1 CTAAATT-TTAAAAATAAAAATAAAAAAA
41084641 CTAAATTT
1 CTAAATTT
41084649 CAAATTTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 14 0.44
30 15 0.47
31 2 0.06
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.31
Consensus pattern (28 bp):
CTAAATTTTAAAAATAAAAATAAAAAAA
Found at i:41084771 original size:60 final size:60
Alignment explanation
Indices: 41084698--41084819 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
41084688 ATCATCAAAA
41084698 TTTTCCATTAAATACCATTTTTTAATAATTTAATTTTTAATCTATTTATTGTATCTATTT
1 TTTTCCATTAAATACCATTTTTTAATAATTTAATTTTTAATCTATTTATTGTATCTATTT
41084758 TTTTCCATTAAATACCATTTTTTAATAATTTAATTTTTAATCTATTTATTGTATCTATTT
1 TTTTCCATTAAATACCATTTTTTAATAATTTAATTTTTAATCTATTTATTGTATCTATTT
41084818 TT
1 TT
41084820 ACGGTTTATG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.59
Consensus pattern (60 bp):
TTTTCCATTAAATACCATTTTTTAATAATTTAATTTTTAATCTATTTATTGTATCTATTT
Found at i:41093893 original size:16 final size:17
Alignment explanation
Indices: 41093861--41093893 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41093851 TATATATGTA
41093861 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
41093878 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
41093894 GTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:41094073 original size:19 final size:19
Alignment explanation
Indices: 41094046--41094082 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41094036 ATGTTTTACT
* *
41094046 TTTAGTTTTTTTATTAATG
1 TTTAATTTTTTCATTAATG
41094065 TTTAATTTTTTCATTAAT
1 TTTAATTTTTTCATTAAT
41094083 ATTAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTAATTTTTTCATTAATG
Found at i:41094087 original size:18 final size:19
Alignment explanation
Indices: 41094051--41094089 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41094041 TTACTTTTAG
* *
41094051 TTTTTTTATTAATGTTTAA
1 TTTTTTCATTAATGATTAA
41094070 TTTTTTCATTAAT-ATTAA
1 TTTTTTCATTAATGATTAA
41094088 TT
1 TT
41094090 AAAAAGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTTTCATTAATGATTAA
Found at i:41094217 original size:22 final size:22
Alignment explanation
Indices: 41094192--41094244 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
41094182 CTTAGGGTTG
41094192 GGTTTGGGTGGTATTGGATTTA
1 GGTTTGGGTGGTATTGGATTTA
* * *
41094214 GGTTTGGTTGGTATTGGGTTTG
1 GGTTTGGGTGGTATTGGATTTA
41094236 GGTTTGGGT
1 GGTTTGGGT
41094245 TTGGGTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.08, C:0.00, G:0.45, T:0.47
Consensus pattern (22 bp):
GGTTTGGGTGGTATTGGATTTA
Found at i:41094236 original size:6 final size:6
Alignment explanation
Indices: 41094227--41094263 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
41094217 TTGGTTGGTA
41094227 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT T
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT T
41094264 AAAATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (6 bp):
TTGGGT
Found at i:41095092 original size:7 final size:7
Alignment explanation
Indices: 41095076--41095104 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
41095066 TTTAACTAAT
41095076 ATAA-TA
1 ATAATTA
41095082 ATAATTA
1 ATAATTA
41095089 ATAATTA
1 ATAATTA
41095096 ATAATTA
1 ATAATTA
41095103 AT
1 AT
41095105 GTATTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATAATTA
Found at i:41097336 original size:3 final size:3
Alignment explanation
Indices: 41097324--41097359 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
41097314 ATTGGTAAAT
41097324 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41097360 AATCTAGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:41098103 original size:88 final size:89
Alignment explanation
Indices: 41097993--41098178 Score: 252
Period size: 89 Copynumber: 2.1 Consensus size: 89
41097983 AAAAGTTCTT
* * *
41097993 AAACTTTTTTCAAAAAACCAATTAAGTTCCTAT-TTTTTT-TT-TACTCAATTGGGTACTTGAAC
1 AAACTTTTTTAAAAAAACCAATTAAG-TCCT-TGTTTTTTATTCCACTCAATTGAGTACTTGAAC
* *
41098055 TTTCAAAATGCATAAAAAATGTCCTC
64 TTTCAAAATGCATAAAAAAGGCCCTC
* * *
41098081 ATACTTTTTTAAAAAAAGCAATTAAGTCCTTGTTTTTTATTCCATTCAATTGAGTACTTGAACTT
1 AAACTTTTTTAAAAAAACCAATTAAGTCCTTGTTTTTTATTCCACTCAATTGAGTACTTGAACTT
*
41098146 TCAAAATGCATCAAAAAGGCCCTC
66 TCAAAATGCATAAAAAAGGCCCTC
41098170 AAACTTTTT
1 AAACTTTTT
41098179 AACCCTCTCA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
86 1 0.01
87 10 0.12
88 25 0.29
89 49 0.58
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (89 bp):
AAACTTTTTTAAAAAAACCAATTAAGTCCTTGTTTTTTATTCCACTCAATTGAGTACTTGAACTT
TCAAAATGCATAAAAAAGGCCCTC
Found at i:41098347 original size:19 final size:20
Alignment explanation
Indices: 41098325--41098369 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
41098315 TTATAAAAAC
41098325 TAAAAATCAATAAAATTT-A
1 TAAAAATCAATAAAATTTAA
* * *
41098344 TAAAAATTATTAAATTTTAA
1 TAAAAATCAATAAAATTTAA
41098364 TAAAAA
1 TAAAAA
41098370 ATTAGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATCAATAAAATTTAA
Found at i:41098387 original size:21 final size:21
Alignment explanation
Indices: 41098363--41098412 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
41098353 TTAAATTTTA
41098363 ATAAAAAATTAGAAAAAAAAT
1 ATAAAAAATTAGAAAAAAAAT
* *
41098384 AT-AAAAA-TCGTAAAAAAAT
1 ATAAAAAATTAGAAAAAAAAT
41098403 ATAAAAAATT
1 ATAAAAAATT
41098413 GTAAACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 10 0.40
21 3 0.12
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (21 bp):
ATAAAAAATTAGAAAAAAAAT
Found at i:41098416 original size:20 final size:20
Alignment explanation
Indices: 41098363--41098417 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
41098353 TTAAATTTTA
*
41098363 ATAAAAAATTAGAAAAAAAAT
1 ATAAAAAATT-GTAAAAAAAT
*
41098384 AT-AAAAATCGTAAAAAAAT
1 ATAAAAAATTGTAAAAAAAT
41098403 ATAAAAAATTGTAAA
1 ATAAAAAATTGTAAA
41098418 CTTTTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.37
20 17 0.57
21 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (20 bp):
ATAAAAAATTGTAAAAAAAT
Found at i:41098458 original size:20 final size:20
Alignment explanation
Indices: 41098325--41098448 Score: 60
Period size: 20 Copynumber: 6.2 Consensus size: 20
41098315 TTATAAAAAC
41098325 TAAAAATCA-ATAAAAT-TTA
1 TAAAAATCATA-AAAATATTA
* * *
41098344 TAAAAATTAT-TAAATTTTAA
1 TAAAAATCATAAAAATATT-A
* * * *
41098364 TAAAAAATTAGAAAAAAAATA
1 T-AAAAATCATAAAAATATTA
* *
41098385 TAAAAATCGTAAAAA-AATA
1 TAAAAATCATAAAAATATTA
** * *
41098404 TAAAAAATTGT-AAACTTTTA
1 T-AAAAATCATAAAAATATTA
41098424 TAAAAATCATAAAAATATTA
1 TAAAAATCATAAAAATATTA
41098444 TAAAA
1 TAAAA
41098449 TGCATCAAAA
Statistics
Matches: 79, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
18 4 0.05
19 25 0.32
20 36 0.46
21 10 0.13
22 4 0.05
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAAATCATAAAAATATTA
Found at i:41098756 original size:20 final size:20
Alignment explanation
Indices: 41098678--41098761 Score: 59
Period size: 20 Copynumber: 4.3 Consensus size: 20
41098668 TTCTTACGAC
*
41098678 TTTATT-AAATTTTATAATT
1 TTTATTAAAATTTAATAATT
* **
41098697 TTTTTCTAATTTTTAAT-ATT
1 TTTAT-TAAAATTTAATAATT
* **
41098717 TTTA--AATATTTTCTATATT
1 TTTATTAAAATTTAATA-ATT
41098736 TTTATTAAAATTTAATAATT
1 TTTATTAAAATTTAATAATT
41098756 TTTATT
1 TTTATT
41098762 GATTTTTATT
Statistics
Matches: 48, Mismatches: 11, Indels: 11
0.69 0.16 0.16
Matches are distributed among these distances:
17 7 0.15
19 11 0.23
20 16 0.33
21 14 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTAAAATTTAATAATT
Found at i:41098769 original size:20 final size:19
Alignment explanation
Indices: 41098678--41098769 Score: 66
Period size: 19 Copynumber: 4.7 Consensus size: 19
41098668 TTCTTACGAC
41098678 TTTATTAAATTTTATAAT-TT
1 TTTATT-AATTTT-TAATATT
41098698 TTT-TCTAATTTTTAATATT
1 TTTAT-TAATTTTTAATATT
*
41098717 TTTA--AATATTTTCTATATT
1 TTTATTAAT-TTTT-AATATT
**
41098736 TTTATTAAAATTTAATAATT
1 TTTATTAATTTTTAAT-ATT
*
41098756 TTTATTGATTTTTA
1 TTTATTAATTTTTA
41098770 TTTTTATCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
17 3 0.05
18 8 0.14
19 23 0.40
20 21 0.37
21 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTATTAATTTTTAATATT
Found at i:41103346 original size:2 final size:2
Alignment explanation
Indices: 41103339--41103372 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41103329 CAGACATGCT
41103339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41103373 CCTTTATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41104085 original size:3 final size:3
Alignment explanation
Indices: 41104077--41104108 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41104067 TTCTGCAAAA
41104077 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
41104109 ATGGTCGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:41112383 original size:21 final size:21
Alignment explanation
Indices: 41112331--41112391 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
41112321 TTGTTTAGAT
41112331 AATT-ATGT-TTATTTTTTTA
1 AATTAATGTATTATTTTTTTA
41112350 AATTAA-G-AGTTATTTTTTTA
1 AATTAATGTA-TTATTTTTTTA
*
41112370 ATTTAATGTATTATTTATTTTA
1 AATTAATGTATTATTT-TTTTA
41112392 TCATTTTCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 5 0.14
20 17 0.49
21 7 0.20
22 6 0.17
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
AATTAATGTATTATTTTTTTA
Found at i:41118685 original size:31 final size:31
Alignment explanation
Indices: 41118618--41118688 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
41118608 CATGAGTCAT
*
41118618 AATTTTAATTTCTATATTTTTCGAATTGGTA
1 AATTTTAATTTCTATATTTTTCAAATTGGTA
* *
41118649 AATTTTAATTTTTATATTTATT-AAATT-TTA
1 AATTTTAATTTCTATATTT-TTCAAATTGGTA
41118679 ATATTTTAAT
1 A-ATTTTAAT
41118689 CTCGATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.09
31 30 0.86
32 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (31 bp):
AATTTTAATTTCTATATTTTTCAAATTGGTA
Found at i:41129238 original size:56 final size:56
Alignment explanation
Indices: 41129120--41129227 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
41129110 AACCTAATGG
*
41129120 GATATTATAAGATATTATTATGAGATATTATCTCTTAACAATTTGATTTCTAATAA
1 GATATTATAAGATATTATTATGAGATATTATCTCTTAACAATTTGATTCCTAATAA
* * *
41129176 GATATTATAGGATATTATTATGAGATATTATCTTTTAGCAATTTGATTCCTA
1 GATATTATAAGATATTATTATGAGATATTATCTCTTAACAATTTGATTCCTA
41129228 CGTAACTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (56 bp):
GATATTATAAGATATTATTATGAGATATTATCTCTTAACAATTTGATTCCTAATAA
Found at i:41130643 original size:16 final size:17
Alignment explanation
Indices: 41130612--41130644 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41130602 TTTTTATCAA
41130612 ATAATTGTAATTTAAATT
1 ATAATTGT-ATTTAAATT
41130630 ATAATTGT-TTTAAAT
1 ATAATTGTATTTAAAT
41130645 GAGTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
ATAATTGTATTTAAATT
Found at i:41131065 original size:29 final size:30
Alignment explanation
Indices: 41131033--41131099 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
41131023 TTAAAATTTT
*
41131033 ATGTATAAAATTGCACA-AAATCAAAGTTC
1 ATGTATAAAATTGCACATAAACCAAAGTTC
* *
41131062 ATGTATACAATTGCACATTAAACCATAGTTC
1 ATGTATAAAATTGCACA-TAAACCAAAGTTC
41131093 ATGTATA
1 ATGTATA
41131100 GTCTTAGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 16 0.48
31 17 0.52
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (30 bp):
ATGTATAAAATTGCACATAAACCAAAGTTC
Found at i:41135022 original size:21 final size:19
Alignment explanation
Indices: 41134984--41135022 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
41134974 TGCAAATAAT
*
41134984 AATTATTTGACTTAAACTC
1 AATTATTTGACATAAACTC
41135003 AATTATTTGAAACATAAACT
1 AATTATTTG--ACATAAACT
41135023 TATCCAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (19 bp):
AATTATTTGACATAAACTC
Found at i:41146130 original size:21 final size:21
Alignment explanation
Indices: 41146068--41146130 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
41146058 TTGAGACATC
*
41146068 GAAGTATAAATAGTTAATAAG
1 GAAGCATAAATAGTTAATAAG
* *
41146089 GAAGGCATAATTA-TT-CT---
1 GAA-GCATAAATAGTTAATAAG
41146106 GAAGCATAAATAGTTAATAAG
1 GAAGCATAAATAGTTAATAAG
41146127 GAAG
1 GAAG
41146131 ACCAGTCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 12
0.65 0.10 0.25
Matches are distributed among these distances:
16 8 0.26
17 5 0.16
18 1 0.03
20 1 0.03
21 9 0.29
22 7 0.23
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.27
Consensus pattern (21 bp):
GAAGCATAAATAGTTAATAAG
Found at i:41148288 original size:21 final size:21
Alignment explanation
Indices: 41148262--41148305 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
41148252 TGATGATTAC
41148262 TTAGGTACAAAGCAATTTCTT
1 TTAGGTACAAAGCAATTTCTT
41148283 TTAGGTACAAAGCAATTTCTT
1 TTAGGTACAAAGCAATTTCTT
41148304 TT
1 TT
41148306 TATCATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (21 bp):
TTAGGTACAAAGCAATTTCTT
Found at i:41151301 original size:6 final size:6
Alignment explanation
Indices: 41151292--41151337 Score: 56
Period size: 6 Copynumber: 7.0 Consensus size: 6
41151282 GACATTGGAC
41151292 TTTTAA TTTTAAA TGTTTAGTA TTTTAA TTTTAA TTTTAA TTTTAA
1 TTTTAA TTTT-AA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA
41151338 GTAAATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 23 0.64
7 4 0.11
8 7 0.19
9 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (6 bp):
TTTTAA
Found at i:41151361 original size:30 final size:31
Alignment explanation
Indices: 41151322--41151380 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
41151312 TATTTTAATT
* *
41151322 TTAATTTTAATTTTAAG-TAAATTTAAATAA
1 TTAAATTTAAATTTAAGATAAATTTAAATAA
41151352 TTAAATTTAAATTTAAGATAAATTTAAAT
1 TTAAATTTAAATTTAAGATAAATTTAAAT
41151381 CAAAAGTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
TTAAATTTAAATTTAAGATAAATTTAAATAA
Found at i:41151730 original size:38 final size:38
Alignment explanation
Indices: 41151679--41152035 Score: 160
Period size: 38 Copynumber: 9.4 Consensus size: 38
41151669 CTATCCAACT
41151679 TTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTC
1 TTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTC
* * * *
41151717 TTACTTCAGTTTC-AGA-GAT--AAAGA-ATTGCTATCCAAC
1 TTACTTCAATTTCAAGAGGATGGGAAGAGA-T-CT-TGC-TC
41151754 TTTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTC
1 -TTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTC
* ** * * **
41151793 TTACTTCAGTTTC-AGA-GATAAAGACGTAATATCCAGCT-
1 TTACTTCAATTTCAAGAGGAT-GGGAAG--AGATCTTGCTC
* *
41151831 TTACTTCAATTTC-AGAAGGATAGGAAAAGATCTTGCTC
1 TTACTTCAATTTCAAG-AGGATGGGAAGAGATCTTGCTC
* * *
41151869 TTACTTCAATTT-TAGA-GAT--AAAGACG-TGCTATCCATC
1 TTACTTCAATTTCAAGAGGATGGGAAGA-GAT-CT-TGC-TC
* *
41151906 TCTACTTCAATTTCAAGCA-GATAGGAAAAGATCTTGCTC
1 T-TACTTCAATTTCAAG-AGGATGGGAAGAGATCTTGCTC
* * *
41151945 TTACTTCAATTTC-AGA-GAT--AAAGACG-TGTTATCCATC
1 TTACTTCAATTTCAAGAGGATGGGAAGA-GAT-CT-TGC-TC
* * * * *
41151982 TCTACTTCAATTTCAAGCGGATAGGAAAAGATCCTGTTC
1 T-TACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTC
41152021 TTACTTCAATTTCAA
1 TTACTTCAATTTCAA
41152036 AGATAAAAAC
Statistics
Matches: 242, Mismatches: 40, Indels: 74
0.68 0.11 0.21
Matches are distributed among these distances:
33 1 0.00
34 13 0.05
35 7 0.03
36 19 0.08
37 26 0.11
38 113 0.47
39 25 0.10
40 18 0.07
41 6 0.02
42 13 0.05
43 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (38 bp):
TTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTC
Found at i:41151747 original size:76 final size:76
Alignment explanation
Indices: 41151654--41152414 Score: 776
Period size: 76 Copynumber: 9.8 Consensus size: 76
41151644 GCTTCTTTAG
* * * *
41151654 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
41151719 ACTTCAGTTTC
66 ACTTCAATTTC
* * * * *
41151730 AGAGATAAAGAATTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
41151795 ACTTCAGTTTC
66 ACTTCAATTTC
* ** * *
41151806 AGAGATAAAGACGTAATATCCAGCTTTACTTCAATTTC-AGAAGGATAGGAAAAGATCTTGCTCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAG-AGGATAGGAAAAGATCTTGCTCT
*
41151870 TACTTCAATTTT
65 TACTTCAATTTC
* * *
41151882 AGAGATAAAGACGTGCTATCCATCTCTACTTCAATTTCAAGCA-GATAGGAAAAGATCTTGCTCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAG-AGGATAGGAAAAGATCTTGCTCT
41151946 TACTTCAATTTC
65 TACTTCAATTTC
* * * * *
41151958 AGAGATAAAGACGTGTTATCCATCTCTACTTCAATTTCAAGCGGATAGGAAAAGATCCTGTTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
41152023 ACTTCAATTTC
66 ACTTCAATTTC
* * ** * *
41152034 AAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTCAAAAGGATAGGAAAAGATCTTGCTCCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
41152099 ACTTCAATTTC
66 ACTTCAATTTC
* * *
41152110 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAAGAAAAGATCTTGTTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
41152175 ACTTCAATATCTC
66 ACTTCAAT-T-TC
**** ** * ** ** **
41152188 TCTTACTTCA-ATTTCAGAGATAAAGACT-TGTTGTCCAACTCTACTTCAATTTCAAGAGGATAG
1 AGAGA-TAAAGACTT--GTTATCCA-ACTCTACT-T-CAA---T--TTC-A-----AGAGGATAG
41152251 GAAAAGATCTTGCTCTTACTTCAATTTC
49 GAAAAGATCTTGCTCTTACTTCAATTTC
* * * * * *
41152279 AGAGATAAAGACTTGTTGTCCCACTCTACTTCAATTTCAAGTGGATTGGAAATGATCTTTGCTCC
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATC-TTGCTCT
41152344 TACTTCAATTTC
65 TACTTCAATTTC
* * * *
41152356 AGAGATGAAGACTTGTTATCC-ACTCTACTTCAATTTCAAGCGGATTGGAAATGATCTTG
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
41152415 TTTGGTCTGA
Statistics
Matches: 584, Mismatches: 76, Indels: 51
0.82 0.11 0.07
Matches are distributed among these distances:
75 5 0.01
76 456 0.78
77 41 0.07
78 6 0.01
79 2 0.00
80 5 0.01
81 5 0.01
82 6 0.01
84 1 0.00
85 1 0.00
87 6 0.01
88 5 0.01
89 4 0.01
90 2 0.00
91 6 0.01
92 1 0.00
93 32 0.05
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:41152066 original size:228 final size:226
Alignment explanation
Indices: 41151654--41152414 Score: 932
Period size: 228 Copynumber: 3.3 Consensus size: 226
41151644 GCTTCTTTAG
* * *
41151654 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTCTT
1 AGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
* * * * * *
41151719 ACTTCAGTTTCAGAGATAAAGAATTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAGAG
66 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAG
* ** * * *
41151784 ATCTTGCTCTTACTTCAGTTTCAGAGATAAAGACGTAATATCCAGCTTTACTTCAATTTCAGAAG
131 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGAC-TTGTGTCCAACTCTACTTCAATTTCA-AAG
* *
41151849 GATAGGAAAAGATCTTGCTCTTACTTCAATTTT
194 GATAGGAAAAGATCTTGCTCCTACTTCAATTTC
* *
41151882 AGAGATAAAGACGTGCTATCCATCTCTACTTCAATTTCAAGCA-GATAGGAAAAGATCTTGCTCT
1 AGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCAAG-AGGATAGGAAAAGATCTTGCTCT
* * *
41151946 TACTTCAATTTCAGAGATAAAGACGTGTTATCCATCTCTACTTCAATTTCAAGCGGATAGGAAAA
65 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAA
* * * *
41152011 GATCCTGTTCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTCAAAA
130 GATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGT-GTCCAACTCTACTTCAATTTC-AAA
41152076 GGATAGGAAAAGATCTTGCTCCTACTTCAATTTC
193 GGATAGGAAAAGATCTTGCTCCTACTTCAATTTC
* * *
41152110 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAAGAAAAGATCTTGTTCTT
1 AGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG-----
*
41152175 ACTTCAATATCTCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTT
61 ------------CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTT
*
41152240 CAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCCACTC
114 CAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTG-TGTCCAACTC
* * *
41152305 TACTTCAATTTCAAGTGGATTGGAAATGATCTTTGCTCCTACTTCAATTTC
178 TACTTCAATTTCAA-AGGATAGGAAAAGATC-TTGCTCCTACTTCAATTTC
* * * * *
41152356 AGAGATGAAGACTTGTTATCC-ACTCTACTTCAATTTCAAGCGGATTGGAAATGATCTTG
1 AGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
41152415 TTTGGTCTGA
Statistics
Matches: 460, Mismatches: 49, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
227 3 0.01
228 248 0.54
229 2 0.00
244 2 0.00
245 166 0.36
246 39 0.08
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (226 bp):
AGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAG
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTGTCCAACTCTACTTCAATTTCAAAGGA
TAGGAAAAGATCTTGCTCCTACTTCAATTTC
Found at i:41152257 original size:93 final size:93
Alignment explanation
Indices: 41152098--41152275 Score: 338
Period size: 93 Copynumber: 1.9 Consensus size: 93
41152088 ATCTTGCTCC
41152098 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAAGAAAA
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAAGAAAA
*
41152163 GATCTTGTTCTTACTTCAATATCTCTCT
66 GATCTTGCTCTTACTTCAATATCTCTCT
*
41152191 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAA
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAAGAAAA
41152256 GATCTTGCTCTTACTTCAAT
66 GATCTTGCTCTTACTTCAAT
41152276 TTCAGAGATA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (93 bp):
TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAAGAAAA
GATCTTGCTCTTACTTCAATATCTCTCT
Found at i:41152298 original size:169 final size:170
Alignment explanation
Indices: 41152019--41152352 Score: 553
Period size: 169 Copynumber: 2.0 Consensus size: 170
41152009 AAGATCCTGT
41152019 TCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTCAAAAGGATAGGA
1 TCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTCAAAAGGATAGGA
41152084 AAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCA
66 AAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCA
* *
41152149 AGAGGATAAGAAAAGATC-TTGTTCTTACTTCAATATCTC
131 AGAGGATAAGAAAAGATCTTTGCTCCTACTTCAATATCTC
* * * *
41152188 TCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGA
1 TCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTCAAAAGGATAGGA
* *
41152253 AAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCCACTCTACTTCAATTTCA
66 AAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCA
* ** *
41152318 AGTGGATTGGAAATGATCTTTGCTCCTACTTCAAT
131 AGAGGATAAGAAAAGATCTTTGCTCCTACTTCAAT
41152353 TTCAGAGATG
Statistics
Matches: 152, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
169 138 0.91
170 14 0.09
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (170 bp):
TCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTCAAAAGGATAGGA
AAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCA
AGAGGATAAGAAAAGATCTTTGCTCCTACTTCAATATCTC
Found at i:41152383 original size:245 final size:245
Alignment explanation
Indices: 41151942--41152416 Score: 754
Period size: 245 Copynumber: 1.9 Consensus size: 245
41151932 AAAGATCTTG
* *
41151942 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCATCTCTACTTCAATTTCAAGCGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
*
41152007 AAAAGATCCTGTTCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTC
66 AAAAGATCCTGCTCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTC
*
41152072 AAAAGGATAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCT
131 AAAAGGATAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCT
41152137 ACTTCAATTTCAAGAGGATAAGAAAAGATCTTGTTCTTACTTCAATATCT
196 ACTTCAATTTCAAGAGGATAAGAAAAGATCTTGTTCTTACTTCAATATCT
* *
41152187 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
* * * * *
41152252 AAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCCACTCTACTTCAATTTC
66 AAAAGATCCTGCTCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTC
** * * *
41152317 AAGTGGATTGGAAATGATCTTTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCC-ACTC
131 AAAAGGATAGGAAAAGATC-TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTC
* ** *
41152381 TACTTCAATTTCAAGCGGATTGGAAATGATCTTGTT
195 TACTTCAATTTCAAGAGGATAAGAAAAGATCTTGTT
41152417 TGGTCTGATT
Statistics
Matches: 209, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
245 171 0.82
246 38 0.18
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (245 bp):
CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
AAAAGATCCTGCTCTTACTTCAATTTCAAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTC
AAAAGGATAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCT
ACTTCAATTTCAAGAGGATAAGAAAAGATCTTGTTCTTACTTCAATATCT
Found at i:41164160 original size:30 final size:29
Alignment explanation
Indices: 41164081--41164367 Score: 211
Period size: 30 Copynumber: 9.6 Consensus size: 29
41164071 TGGTGAAATC
** *
41164081 GGGGTTAAAAATGGGATTTAGGAAAG-TTT
1 GGGGTT-AAAATGTAATTTTGGAAAGTTTT
*
41164110 GAGGG-TAAAATGGTAATTTTTGAAAGTTTT
1 G-GGGTTAAAAT-GTAATTTTGGAAAGTTTT
* * *
41164140 GGGGTAAAAATGTATTTTTTTTGAAA-TTTT
1 GGGGTTAAAATGTA--ATTTTGGAAAGTTTT
* * *
41164170 GGGGTCAAAATATGATTTTGGAAAAGTTTT
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTT
* * * * *
41164200 GAGGTCAAAAAGTAATTTTGGAAAACTTTA
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTT
* **
41164230 AGGGTTAAAATGTAATTTTGGAAAAGTTAA
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTT
* *
41164260 AGGGTTAAAATGTAATTTCTAGAAAGTTTT
1 GGGGTTAAAATGTAATTT-TGGAAAGTTTT
*
41164290 GGGGTTAAAATATAATTTTGGAAAAGTTTT
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTT
* *
41164320 AGGGTTAAAATGTAATTTTCAGAAAGTTTT
1 GGGGTTAAAATGTAATTTT-GGAAAGTTTT
** * *
41164350 AAGGTCAACATGTAATTT
1 GGGGTTAAAATGTAATTT
41164368 CTAGATAATT
Statistics
Matches: 212, Mismatches: 35, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
28 10 0.05
29 23 0.11
30 167 0.79
31 12 0.06
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (29 bp):
GGGGTTAAAATGTAATTTTGGAAAGTTTT
Found at i:41164164 original size:31 final size:31
Alignment explanation
Indices: 41164126--41164188 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 31
41164116 AAAATGGTAA
41164126 TTTTTGAAAGTTTTGGGGT-AAAA-ATGTATTT
1 TTTTTGAAA-TTTTGGGGTCAAAATATG-ATTT
41164157 TTTTTGAAATTTTGGGGTCAAAATATGATTT
1 TTTTTGAAATTTTGGGGTCAAAATATGATTT
41164188 T
1 T
41164189 GGAAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 9 0.30
31 18 0.60
32 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.49
Consensus pattern (31 bp):
TTTTTGAAATTTTGGGGTCAAAATATGATTT
Found at i:41164584 original size:161 final size:162
Alignment explanation
Indices: 41164402--41164773 Score: 380
Period size: 162 Copynumber: 2.3 Consensus size: 162
41164392 GCAATAAAAC
* * * * * *
41164402 CAAAAACAGGACACGTGGCAGCCCCACAG-GCA-TCCAGA-AGTCAAAGGATTAGTTTGA-ATAT
1 CAAAAAAAGGACACGTGGCAGCCCC-CAGTGCAGT-CAAACAGTCAAAGGACTAATTT-ATAAAC
* *
41164463 CTTG-AAAATTTTTTGGACCAATTTTGTAATT-AAATAAAAGTTAATTTAAGGACTAAATTAAAA
63 CTTGAAAAATTATTAGG-CCAATTTTGTAATTAAAAT-AAAGTTAATTTAAGGACTAAATTAAAA
* * *
41164526 TAAACCAAAAAAGTCAGGGACTAAATGCATAAATAAG
126 CAAACCAAAAAAGTCAGGGACTAAATACAGAAATAAG
* * * **
41164563 C-CAGAAAGTGACACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGGACTAATTTATAAACCT
1 CAAAAAAAG-GACACGTGGCAGCCCCCAGTGCAGTCAAACAGTCAAAGGACTAATTTATAAACCT
* * * *
41164627 TGAAAAATTATTAGGCTAATTTTGTAATTAAAATAAAGTTGATTTAGGGATTAAATTAAAACAAA
65 TGAAAAATTATTAGGCCAATTTTGTAATTAAAATAAAGTTAATTTAAGGACTAAATTAAAACAAA
** * *
41164692 TTAAAAATGTCAGGGACTAAATATAGAAATAAG
130 CCAAAAAAGTCAGGGACTAAATACAGAAATAAG
* ** * *
41164725 CAAAAAAAGGACACGTGGCAGCCTCTGGTCCAGTCAAACGGTCAAAGGA
1 CAAAAAAAGGACACGTGGCAGCCCCCAGTGCAGTCAAACAGTCAAAGGA
41164774 TTAAATTGAA
Statistics
Matches: 175, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
160 5 0.03
161 23 0.13
162 128 0.73
163 19 0.11
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.24
Consensus pattern (162 bp):
CAAAAAAAGGACACGTGGCAGCCCCCAGTGCAGTCAAACAGTCAAAGGACTAATTTATAAACCTT
GAAAAATTATTAGGCCAATTTTGTAATTAAAATAAAGTTAATTTAAGGACTAAATTAAAACAAAC
CAAAAAAGTCAGGGACTAAATACAGAAATAAG
Found at i:41164608 original size:162 final size:162
Alignment explanation
Indices: 41164440--41164777 Score: 423
Period size: 162 Copynumber: 2.1 Consensus size: 162
41164430 GGCATCCAGA
* * * * *
41164440 AGTCAAAGGATTAGTTTGA-ATATCTTG-AAAATTTTTTGGACCAATTTTGTAATT-AAATAAAA
1 AGTCAAAGGATTAATTT-ATAAACCTTGAAAAATTATTAGG-CCAATTTTGTAATTAAAAT-AAA
* * * *
41164502 GTTAATTTAAGGACTAAATTAAAATAAACCAAAAAAGTCAGGGACTAAATGCATAAATAAGC-CA
63 GTTAATTTAAGGACTAAATTAAAACAAACCAAAAAAGTCAGGGACTAAATACAGAAATAAGCAAA
* *
41164566 GAAAGTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
128 AAAAG-GACACGTGGCAGCCTCTGGTCCAGTCAAAC
* *
41164602 AGTCAAAGGACTAATTTATAAACCTTGAAAAATTATTAGGCTAATTTTGTAATTAAAATAAAGTT
1 AGTCAAAGGATTAATTTATAAACCTTGAAAAATTATTAGGCCAATTTTGTAATTAAAATAAAGTT
* * * ** * *
41164667 GATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATATAGAAATAAGCAAAAAA
66 AATTTAAGGACTAAATTAAAACAAACCAAAAAAGTCAGGGACTAAATACAGAAATAAGCAAAAAA
41164732 AGGACACGTGGCAGCCTCTGGTCCAGTCAAAC
131 AGGACACGTGGCAGCCTCTGGTCCAGTCAAAC
*
41164764 GGTCAAAGGATTAA
1 AGTCAAAGGATTAA
41164778 ATTGAAAACT
Statistics
Matches: 150, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
161 1 0.01
162 130 0.87
163 19 0.13
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (162 bp):
AGTCAAAGGATTAATTTATAAACCTTGAAAAATTATTAGGCCAATTTTGTAATTAAAATAAAGTT
AATTTAAGGACTAAATTAAAACAAACCAAAAAAGTCAGGGACTAAATACAGAAATAAGCAAAAAA
AGGACACGTGGCAGCCTCTGGTCCAGTCAAAC
Found at i:41166281 original size:6 final size:6
Alignment explanation
Indices: 41166265--41166332 Score: 79
Period size: 6 Copynumber: 11.3 Consensus size: 6
41166255 TTTAATTTTT
*
41166265 ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
41166314 GA--TAA ATTTAA ATTTAA AT
1 -ATTTAA ATTTAA ATTTAA AT
41166333 AAAATCAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 39 0.72
7 1 0.02
8 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:41166305 original size:31 final size:31
Alignment explanation
Indices: 41166267--41166326 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
41166257 TAATTTTTAT
41166267 TTAAATTTAAATTTAA-AGTAAATTTAAATAA
1 TTAAATTTAAATTTAAGA-TAAATTTAAATAA
41166298 TTAAATTTAAATTTAAGATAAATTTAAAT
1 TTAAATTTAAATTTAAGATAAATTTAAAT
41166327 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (31 bp):
TTAAATTTAAATTTAAGATAAATTTAAATAA
Found at i:41166337 original size:11 final size:11
Alignment explanation
Indices: 41166265--41166332 Score: 63
Period size: 11 Copynumber: 6.2 Consensus size: 11
41166255 TTTAATTTTT
41166265 ATTTAAATTTAA
1 ATTTAAA-TTAA
*
41166277 ATTTAAAGTAA
1 ATTTAAATTAA
41166288 ATTTAAA-T-A
1 ATTTAAATTAA
41166297 A-TTAAATTTAA
1 ATTTAAA-TTAA
41166308 ATTTAAGA-TAA
1 ATTTAA-ATTAA
41166319 ATTTAAATTTAA
1 ATTTAAA-TTAA
41166331 AT
1 AT
41166333 AAAATCAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
8 5 0.10
9 2 0.04
10 3 0.06
11 21 0.44
12 16 0.33
13 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:41166337 original size:17 final size:16
Alignment explanation
Indices: 41166268--41166335 Score: 95
Period size: 17 Copynumber: 4.2 Consensus size: 16
41166258 AATTTTTATT
41166268 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
41166284 GTAAATTTAAA--TAAT
1 -TAAATTTAAATTTAAA
41166299 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAA-A
41166316 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
41166332 TAAA
1 TAAA
41166336 ATCAATTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
15 3 0.07
16 8 0.17
17 25 0.54
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:41166632 original size:3 final size:3
Alignment explanation
Indices: 41166624--41166662 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
41166614 CCCCAAATTT
41166624 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41166663 GACCCTCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41170665 original size:19 final size:20
Alignment explanation
Indices: 41170622--41170667 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
41170612 TAGCATTTAA
41170622 TATTTAATATTTAAGATATT
1 TATTTAATATTTAAGATATT
*
41170642 T-TTTATTATTTAA-AT-TT
1 TATTTAATATTTAAGATATT
41170659 GTATTTAAT
1 -TATTTAAT
41170668 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 3 0.14
19 16 0.73
20 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TATTTAATATTTAAGATATT
Found at i:41175930 original size:4 final size:4
Alignment explanation
Indices: 41175921--41175979 Score: 84
Period size: 4 Copynumber: 14.5 Consensus size: 4
41175911 TATTTTTATT
*
41175921 TTTA TTTA TTTA TTTA TTTA TTT- TCTA TCTTA TTTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA -TTTA TTTA TTTA TTTA
41175970 TTTA TTTA TT
1 TTTA TTTA TT
41175980 GTCCAGGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
3 2 0.04
4 42 0.84
5 5 0.10
6 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:41178295 original size:22 final size:23
Alignment explanation
Indices: 41178250--41178310 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
41178240 TTCGACTTCC
* *
41178250 CTATTTTCTATT-TCTTTAAGTT
1 CTATTTTCTTTTATTTTTAAGTT
41178272 CTATTTTCTTTTATTTTTAA-TT
1 CTATTTTCTTTTATTTTTAAGTT
*
41178294 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
41178311 CCTTAGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.40
22 15 0.43
23 6 0.17
ACGTcount: A:0.15, C:0.11, G:0.03, T:0.70
Consensus pattern (23 bp):
CTATTTTCTTTTATTTTTAAGTT
Found at i:41182827 original size:18 final size:17
Alignment explanation
Indices: 41182804--41182837 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
41182794 AATTATTTGA
41182804 ATTCTTCTTCTTCTTTTT
1 ATTCTTCTTCTT-TTTTT
41182822 ATTCTTCTTCTTTTTT
1 ATTCTTCTTCTTTTTT
41182838 ATCGTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTCTTCTTCTTTTTTT
Found at i:41182828 original size:15 final size:15
Alignment explanation
Indices: 41182808--41182836 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41182798 ATTTGAATTC
41182808 TTCTTCTTCTTTTTA
1 TTCTTCTTCTTTTTA
41182823 TTCTTCTTCTTTTT
1 TTCTTCTTCTTTTT
41182837 TATCGTCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTCTTCTTTTTA
Found at i:41184170 original size:21 final size:21
Alignment explanation
Indices: 41184144--41184190 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
41184134 AAGCCCTTTT
41184144 AAAATTATTAAAAAAATCA-TA
1 AAAATTA-TAAAAAAATCATTA
*
41184165 AAAATTATAAAAAAATTATTA
1 AAAATTATAAAAAAATCATTA
41184186 AAAAT
1 AAAAT
41184191 ATGTTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATTATAAAAAAATCATTA
Found at i:41184181 original size:11 final size:12
Alignment explanation
Indices: 41184144--41184189 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
41184134 AAGCCCTTTT
41184144 AAAATTATTAAA
1 AAAATTATTAAA
*
41184156 AAAATCA-T--A
1 AAAATTATTAAA
41184165 AAAATTA-TAAA
1 AAAATTATTAAA
41184176 AAAATTATTAAA
1 AAAATTATTAAA
41184188 AA
1 AA
41184190 TATGTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 8 0.28
11 9 0.31
12 12 0.41
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATTATTAAA
Found at i:41184329 original size:13 final size:12
Alignment explanation
Indices: 41184303--41184336 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
41184293 GATATTTTTT
41184303 TAAATATTTGTTA
1 TAAAT-TTTGTTA
41184316 TAAATTTTGTTTA
1 TAAATTTTG-TTA
41184329 TAAATTTT
1 TAAATTTT
41184337 ATGATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (12 bp):
TAAATTTTGTTA
Found at i:41186260 original size:12 final size:13
Alignment explanation
Indices: 41186243--41186277 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
41186233 TATTGTGAGG
41186243 TATGTGTATGT-A
1 TATGTGTATGTGA
41186255 TATGTGTATGTGA
1 TATGTGTATGTGA
41186268 T-TGTGTATGT
1 TATGTGTATGT
41186278 TCTTATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 20 0.91
13 2 0.09
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (13 bp):
TATGTGTATGTGA
Found at i:41191009 original size:21 final size:21
Alignment explanation
Indices: 41190985--41191030 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
41190975 ATTTGGCTCG
41190985 ACTCAAACTTT-ATTTCATTCA
1 ACTCAAA-TTTCATTTCATTCA
41191006 ACTCAAATTTCATTTCATTCA
1 ACTCAAATTTCATTTCATTCA
41191027 ACTC
1 ACTC
41191031 GATTCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (21 bp):
ACTCAAATTTCATTTCATTCA
Found at i:41201078 original size:15 final size:14
Alignment explanation
Indices: 41201042--41201092 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
41201032 ATATATATTA
**
41201042 AAATTAATAAAAAT
1 AAATTAATAAATTT
41201056 AAATTTAATAATATTT
1 AAA-TTAATAA-ATTT
41201072 AAATTAATTAAATTT
1 AAATTAA-TAAATTT
41201087 AAATTA
1 AAATTA
41201093 TTACCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 3 0.09
15 21 0.66
16 8 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTAATAAATTT
Found at i:41205698 original size:18 final size:19
Alignment explanation
Indices: 41205666--41205719 Score: 85
Period size: 18 Copynumber: 2.9 Consensus size: 19
41205656 AAAAAAGCAA
*
41205666 AAGCTCAAGTAAACAATAT
1 AAGCTCAAGTAAACAACAT
41205685 AAGCTCAA-TAAACAACAT
1 AAGCTCAAGTAAACAACAT
41205703 AAGCTCAAGT-AACAACA
1 AAGCTCAAGTAAACAACA
41205720 ATAACACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 24 0.73
19 9 0.27
ACGTcount: A:0.54, C:0.20, G:0.09, T:0.17
Consensus pattern (19 bp):
AAGCTCAAGTAAACAACAT
Found at i:41206592 original size:23 final size:23
Alignment explanation
Indices: 41206548--41206593 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41206538 AAAAAAAAAT
**
41206548 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCGAATAACTCGAA
*
41206571 TAACTCGATTCGAATAATTCGAA
1 TAACTCGATTCGAATAACTCGAA
41206594 ATTCAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTCGAA
Found at i:41208064 original size:3 final size:3
Alignment explanation
Indices: 41208058--41208100 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
41208048 TTCAAAGCAA
41208058 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
41208101 TACTTGACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41208203 original size:30 final size:28
Alignment explanation
Indices: 41208159--41208226 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 28
41208149 ATTTTAGAAT
** *
41208159 TTTTTTAAAATTTTAACTTTTTTATATA
1 TTTTTTAAAATTTTAAAATTTGTATATA
*
41208187 TATTTTTAGAATTTTTAAAATTTGTATATA
1 T-TTTTTA-AAATTTTAAAATTTGTATATA
*
41208217 TTTTTAAAAA
1 TTTTTTAAAA
41208227 AATAAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.09
29 11 0.34
30 18 0.56
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTTTAAAATTTTAAAATTTGTATATA
Found at i:41208263 original size:19 final size:19
Alignment explanation
Indices: 41208239--41208275 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
41208229 TAAATTTTAA
41208239 AATA-TTTATAAATATTTTG
1 AATATTTTA-AAATATTTTG
41208258 AATATTTTAAAATATTTT
1 AATATTTTAAAATATTTT
41208276 TTTGTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
AATATTTTAAAATATTTTG
Found at i:41208275 original size:10 final size:10
Alignment explanation
Indices: 41208232--41208275 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
41208222 AAAAAAATAA
41208232 ATTTTAAAAT
1 ATTTTAAAAT
41208242 A-TTTATAAAT
1 ATTTTA-AAAT
*
41208252 ATTTT-GAAT
1 ATTTTAAAAT
41208261 ATTTTAAAAT
1 ATTTTAAAAT
41208271 ATTTT
1 ATTTT
41208276 TTTGTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 12 0.41
10 14 0.48
11 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:41219090 original size:7 final size:7
Alignment explanation
Indices: 41219078--41219102 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41219068 GATTTATTGA
41219078 TAAAATT
1 TAAAATT
41219085 TAAAATT
1 TAAAATT
41219092 TAAAATT
1 TAAAATT
41219099 TAAA
1 TAAA
41219103 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAAATT
Found at i:41222388 original size:18 final size:18
Alignment explanation
Indices: 41222365--41222401 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41222355 TTTGTGATCA
41222365 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
41222383 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
41222401 A
1 A
41222402 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:41225262 original size:18 final size:18
Alignment explanation
Indices: 41225239--41225273 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41225229 TGTTTCAACT
*
41225239 TTCCATGGTTTTCTTTTC
1 TTCCATAGTTTTCTTTTC
41225257 TTCCATAGTTTTCTTTT
1 TTCCATAGTTTTCTTTT
41225274 TTATGTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.20, G:0.09, T:0.63
Consensus pattern (18 bp):
TTCCATAGTTTTCTTTTC
Found at i:41244401 original size:165 final size:167
Alignment explanation
Indices: 41243921--41244588 Score: 1236
Period size: 165 Copynumber: 4.0 Consensus size: 167
41243911 TTTTATATCA
41243921 TCCATTTCCTCTTTGCTTTTGCCGTAATTACCCCCCATCTCCACCCATTTCTTCTTTTCATTTTC
1 TCCATTTCCTCTTTGCTTTTGCCGTAATTA-CCCCCATCTCCACCCA-TTCTTCTTTTCATTTTC
* *
41243986 CTCATCACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTCTATTTTT
64 TTCATCACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTCCATTTTT
41244051 CTTAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
129 CTTAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
41244090 TCCATTTCCTCTTTGCTTTTGCCGTAATTACCCCCATCTCCACCCATTTCTTCTTTTCATTTTCT
1 TCCATTTCCTCTTTGCTTTTGCCGTAATTACCCCCATCTCCACCCA-TTCTTCTTTTCATTTTCT
41244155 TCATCACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTCCATTTTTC
65 TCATCACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTCCATTTTTC
41244220 TTAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
130 TTAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
*
41244258 TCCATTTCCTCTTTGCTTTTACCGTAATTACCCCCATCTCCACCCA-T-TTCTTTTCATTTTCTT
1 TCCATTTCCTCTTTGCTTTTGCCGTAATTACCCCCATCTCCACCCATTCTTCTTTTCATTTTCTT
*
41244321 CATTACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTCCATTTTTCT
66 CATCACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTCCATTTTTCT
41244386 TAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
131 TAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
41244423 TCCATTTCCTCTTTGCTTTTGCCGTAATTACCCCCATCTCCACCCA-T-TTCTTTTCATTTTCTT
1 TCCATTTCCTCTTTGCTTTTGCCGTAATTACCCCCATCTCCACCCATTCTTCTTTTCATTTTCTT
*
41244486 CATCACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTTCATTTTTCT
66 CATCACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTCCATTTTTCT
41244551 TAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
131 TAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
41244588 T
1 T
41244589 AGCTACCTTA
Statistics
Matches: 492, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
165 280 0.57
166 1 0.00
168 181 0.37
169 30 0.06
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (167 bp):
TCCATTTCCTCTTTGCTTTTGCCGTAATTACCCCCATCTCCACCCATTCTTCTTTTCATTTTCTT
CATCACTTCTTCACCATTTCTTCTTAAATTTCTAAGGCATCCAAGCTTCAATCTTCCATTTTTCT
TAGGAATTTCTTTAAGAAAATCATAAGATTAAGCTAT
Found at i:41245927 original size:6 final size:6
Alignment explanation
Indices: 41245918--41245956 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
41245908 TGATCAAAAT
* * *
41245918 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
41245957 TATGAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:41248408 original size:110 final size:111
Alignment explanation
Indices: 41248041--41248468 Score: 412
Period size: 110 Copynumber: 3.9 Consensus size: 111
41248031 GTTACTTGCT
* * * *
41248041 CATGGATATGTGGATATGACCTCGAAACATGAAAAATGTTAGAAAATTTGA-TGATATTCAG-GC
1 CATGGATATGAGGATATGACCTTGAAACATGAAAAATG-TAGAAAATTTGACTAATATTC-GCAC
* * **
41248104 -C-TCCATCGTATCTGACACTTACAAGTAGGTTACTAGGTTTAATACGACA
64 ACATAC-TCGTATCGGACACTTACAAGTAGGTTACTAGGTTTAAT--GTGA
* **
41248153 CATGGATATGTA-GTTATGA-CTTGTAAACATGAAAAAATGTA-AAAA--AAACTAATGGCATTC
1 CATGGATATG-AGGATATGACCTTG-AAACATG-AAAAATGTAGAAAATTTGACTAAT---ATTC
* * * ** *
41248213 GGACCCATACTCATATTTGACACTTACAAGTAGATTACTAGGTTTAATGTGA
60 GCACACATACTCGTATCGGACACTTACAAGTAGGTTACTAGGTTTAATGTGA
* * *
41248265 -ATGGATATGCGAATATGACCTTGAAACATGAAAAATTTAGAAAATTTGACT-ATATTCGCACAC
1 CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTAGAAAATTTGACTAATATTCGCACAC
* * *
41248328 ATATTTGTATCGGACACTTACAAGTAGGTTACTAGGCTTAATGTGA
66 ATACTCGTATCGGACACTTACAAGTAGGTTACTAGGTTTAATGTGA
* ** *
41248374 CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTAAAAAATCGGACT-ATATTCGCACAT
1 CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTAGAAAATTTGACTAATATTCGCACAC
* *
41248438 ATACTTGTATCGGACCCTTACAAGTAGGTTA
66 ATACTCGTATCGGACACTTACAAGTAGGTTA
41248469 ATTTTGTGTA
Statistics
Matches: 263, Mismatches: 37, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
109 48 0.18
110 96 0.37
111 32 0.12
112 34 0.13
113 15 0.06
114 36 0.14
115 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (111 bp):
CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTAGAAAATTTGACTAATATTCGCACAC
ATACTCGTATCGGACACTTACAAGTAGGTTACTAGGTTTAATGTGA
Found at i:41253532 original size:23 final size:23
Alignment explanation
Indices: 41253498--41253548 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
41253488 ACGGGTGTGC
* *
41253498 ATGTATTTGTTTTCGAGCTTTGA
1 ATGTATTCGTTTTCGAGCTTTAA
41253521 ATGTATTCGTTTTCGAGCTTTAA
1 ATGTATTCGTTTTCGAGCTTTAA
41253544 ATGTA
1 ATGTA
41253549 ATGAGCTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.49
Consensus pattern (23 bp):
ATGTATTCGTTTTCGAGCTTTAA
Found at i:41256788 original size:3 final size:3
Alignment explanation
Indices: 41256782--41256808 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41256772 CAACAACAAC
41256782 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
41256809 TAGCATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41257651 original size:3 final size:3
Alignment explanation
Indices: 41257643--41257679 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
41257633 CGAAGATGTT
41257643 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
41257680 TTGATATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41261540 original size:34 final size:32
Alignment explanation
Indices: 41261479--41261541 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
41261469 ACGGAGTAGA
* **
41261479 GTAGATTTTTTTTTTTAAATTTCAGGTTGGGG
1 GTAGATTTTTTTTCTTAAAGGTCAGGTTGGGG
41261511 GTAGATTTTTTTTCCTTAAAGGTCGAGGTTG
1 GTAGATTTTTTTT-CTTAAAGGTC-AGGTTG
41261542 TATTAAGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 13 0.50
33 7 0.27
34 6 0.23
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.49
Consensus pattern (32 bp):
GTAGATTTTTTTTCTTAAAGGTCAGGTTGGGG
Found at i:41264272 original size:22 final size:22
Alignment explanation
Indices: 41264247--41264289 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41264237 TGTGAGTTCT
**
41264247 GTTCAAATTTATTTTAATTTAA
1 GTTCAAATACATTTTAATTTAA
*
41264269 GTTCGAATACATTTTAATTTA
1 GTTCAAATACATTTTAATTTA
41264290 TAATCTATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (22 bp):
GTTCAAATACATTTTAATTTAA
Found at i:41289387 original size:17 final size:19
Alignment explanation
Indices: 41289367--41289413 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
41289357 ATTTCAAAAT
41289367 TTTATTTTAATAT-AT-CA
1 TTTATTTTAATATAATACA
*
41289384 TTTA--TAAATATAATACA
1 TTTATTTTAATATAATACA
41289401 TTTATTTTAATAT
1 TTTATTTTAATAT
41289414 GAAAGAGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 6 0.25
16 2 0.08
17 10 0.42
19 6 0.25
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATTTTAATATAATACA
Found at i:41306562 original size:28 final size:28
Alignment explanation
Indices: 41306531--41306592 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
41306521 AAAATAAGGT
*
41306531 TTTTGGA-TGCTCGGGGGTAAAATGGTAA
1 TTTTGGACT-CTCGGGGGCAAAATGGTAA
41306559 TTTTGGACTCTCGGGGGCAAAATGGTAA
1 TTTTGGACTCTCGGGGGCAAAATGGTAA
41306587 TTTTGG
1 TTTTGG
41306593 GAAAATTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.23, C:0.10, G:0.34, T:0.34
Consensus pattern (28 bp):
TTTTGGACTCTCGGGGGCAAAATGGTAA
Found at i:41306612 original size:59 final size:60
Alignment explanation
Indices: 41306549--41306685 Score: 134
Period size: 59 Copynumber: 2.3 Consensus size: 60
41306539 GCTCGGGGGT
* ** * * * *
41306549 AAAATGGTAATTTTGGACTCTCGGGGGCAAAATGGT-AATTTTGGGAAAATTTGGGGTTA
1 AAAATGGTAATTTTGGACACTCAAGGGCAAAATGGTAAATTTTGAGAAAAATTGGGATCA
* * * * *
41306608 AAAATGAT-ATTTTAGACACTTAAGGGTAAAATGGTAAATTTTTAGAAAAATTGGGATCA
1 AAAATGGTAATTTTGGACACTCAAGGGCAAAATGGTAAATTTTGAGAAAAATTGGGATCA
* *
41306667 AAAATGGGATTTTTGGACA
1 AAAATGGTAATTTTGGACA
41306686 TCCGTCAAAT
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
58 21 0.35
59 31 0.52
60 8 0.13
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (60 bp):
AAAATGGTAATTTTGGACACTCAAGGGCAAAATGGTAAATTTTGAGAAAAATTGGGATCA
Found at i:41306842 original size:31 final size:30
Alignment explanation
Indices: 41306778--41306921 Score: 137
Period size: 30 Copynumber: 4.8 Consensus size: 30
41306768 GTTCGAGGGT
* ***
41306778 AAAAATATAATTTTTGA-AAGTTTTGGGATC
1 AAAAATATAATTTTAGAGAAGTTTCAAGA-C
*
41306808 AAAAATATAATTTTGGAGAAGTTTCAGAGAC
1 AAAAATATAATTTTAGAGAAGTTTCA-AGAC
* * **
41306839 AAAAATGTAATTTTGGAGAAGTTTCAAGGT
1 AAAAATATAATTTTAGAGAAGTTTCAAGAC
* **
41306869 TAAAATATAATTTTAGAGAAGTTTCAAGGT
1 AAAAATATAATTTTAGAGAAGTTTCAAGAC
* *
41306899 TAAAATGTAATTTTAGAGAAGTT
1 AAAAATATAATTTTAGAGAAGTT
41306922 CGATGGTCAA
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
30 67 0.66
31 32 0.32
32 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (30 bp):
AAAAATATAATTTTAGAGAAGTTTCAAGAC
Found at i:41306934 original size:60 final size:61
Alignment explanation
Indices: 41306809--41306942 Score: 173
Period size: 60 Copynumber: 2.2 Consensus size: 61
41306799 TTTGGGATCA
* * *
41306809 AAAATATAATTTTGGAGAAGTTTCAGAGACAAAAATGTAATTTTGGAGAAGTTTCAAGGTT
1 AAAATATAATTTTAGAGAAGTTTCAGAGACAAAAATGTAATTTTAGAGAAGTTTCAAGGTC
*** *
41306870 AAAATATAATTTTAGAGAAGTTTCA-AGGTTAAAATGTAATTTTAGAGAAG-TTCGATGGTC
1 AAAATATAATTTTAGAGAAGTTTCAGAGACAAAAATGTAATTTTAGAGAAGTTTC-AAGGTC
*
41306930 AAAATAAAATTTT
1 AAAATATAATTTT
41306943 TGGACAGTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 3 0.05
60 37 0.58
61 24 0.38
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (61 bp):
AAAATATAATTTTAGAGAAGTTTCAGAGACAAAAATGTAATTTTAGAGAAGTTTCAAGGTC
Found at i:41306942 original size:30 final size:30
Alignment explanation
Indices: 41306809--41306921 Score: 154
Period size: 30 Copynumber: 3.7 Consensus size: 30
41306799 TTTGGGATCA
* ***
41306809 AAAATATAATTTTGGAGAAGTTTCAGAGACA
1 AAAATATAATTTTAGAGAAGTTTCA-AGGTT
* *
41306840 AAAATGTAATTTTGGAGAAGTTTCAAGGTT
1 AAAATATAATTTTAGAGAAGTTTCAAGGTT
41306870 AAAATATAATTTTAGAGAAGTTTCAAGGTT
1 AAAATATAATTTTAGAGAAGTTTCAAGGTT
*
41306900 AAAATGTAATTTTAGAGAAGTT
1 AAAATATAATTTTAGAGAAGTT
41306922 CGATGGTCAA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
30 51 0.68
31 24 0.32
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (30 bp):
AAAATATAATTTTAGAGAAGTTTCAAGGTT
Found at i:41309489 original size:22 final size:22
Alignment explanation
Indices: 41309464--41309509 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
41309454 TATATATATG
41309464 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
41309486 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
41309508 AT
1 AT
41309510 TATATGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (22 bp):
ATGAACAATGTATATGTGAAAT
Found at i:41309673 original size:12 final size:12
Alignment explanation
Indices: 41309656--41309680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41309646 TTTGTGATCA
41309656 AAATTGAAAGTG
1 AAATTGAAAGTG
41309668 AAATTGAAAGTG
1 AAATTGAAAGTG
41309680 A
1 A
41309681 TATGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:41311636 original size:17 final size:16
Alignment explanation
Indices: 41311615--41311692 Score: 84
Period size: 17 Copynumber: 4.7 Consensus size: 16
41311605 TGGACATTTT
*
41311615 ATTAAATTTATAATAAT
1 ATTAAATTTA-AATAAA
*
41311632 ATTAAATTTAAATTAA
1 ATTAAATTTAAATAAA
*
41311648 ATTCAAATTTAATTAAA
1 ATT-AAATTTAAATAAA
*
41311665 ATTGAATTTAAAATAAA
1 ATTAAATTT-AAATAAA
*
41311682 AATAAATTTAA
1 ATTAAATTTAA
41311693 TTTCAAAGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 14 0.27
17 37 0.73
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTAAATTTAAATAAA
Found at i:41311648 original size:11 final size:11
Alignment explanation
Indices: 41311632--41311695 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
41311622 TTATAATAAT
41311632 ATTAAATTTAA
1 ATTAAATTTAA
*
41311643 ATTAAATTCAA
1 ATTAAATTTAA
* *
41311654 ATTTAATTAAA
1 ATTAAATTTAA
*
41311665 ATTGAATTTAA
1 ATTAAATTTAA
* **
41311676 AATAAAAATAA
1 ATTAAATTTAA
*
41311687 ATTTAATTT
1 ATTAAATTT
41311696 CAAAGTAAAA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:41311688 original size:22 final size:23
Alignment explanation
Indices: 41311663--41311707 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
41311653 AATTTAATTA
41311663 AAATTGAATTT-AAAATAAAAAT
1 AAATTGAATTTCAAAATAAAAAT
* *
41311685 AAATTTAATTTCAAAGTAAAAAT
1 AAATTGAATTTCAAAATAAAAAT
41311708 GGTTTGGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATTGAATTTCAAAATAAAAAT
Found at i:41312072 original size:92 final size:92
Alignment explanation
Indices: 41311959--41312864 Score: 1587
Period size: 92 Copynumber: 9.8 Consensus size: 92
41311949 GATATTGAGG
* * *
41311959 CTTCATCTTGCTCTTACTACAACTTTAGAGAGATGAAGACTTGCTATCCAACTTTACTACAACAT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
41312024 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* * * *
41312051 CTTCACCTTGCTTTTATTACAACTTCAGAGAGATAAAGATTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
41312116 CAAGAGGATAGGAATTGATATTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
41312143 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
41312208 CAAGAGGATAGGAGTTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
41312235 CTTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
41312300 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
41312327 CTTTATCTTGCTCTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
* *
41312392 CAAGAGGATAGGAATTGATATTTAAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
41312419 CTTCATCTTGCTCTTACTACAACTTCAGAGGGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
41312484 CAAGAGGATAGGAAATGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
41312511 CTTCATCTTGCTCTTACTACAACTTCAGAGGGATAAAAACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
41312576 CAAGAGGATAGGAAATGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
41312603 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
41312668 CAAGAGGATAGGAGTTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
41312695 CTTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAAATT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
* *
41312760 CAAGAGGATAAGAATTGATGTCTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
41312787 CTTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
41312852 CAAGAGGATAGGA
66 CAAGAGGATAGGA
41312865 TTATATTATA
Statistics
Matches: 779, Mismatches: 35, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 779 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (92 bp):
CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
CAAGAGGATAGGAATTGATGTTTGAAA
Found at i:41312626 original size:52 final size:50
Alignment explanation
Indices: 41312564--41312818 Score: 158
Period size: 52 Copynumber: 5.4 Consensus size: 50
41312554 CTATCCAACT
41312564 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGAAACTTCATCTTGCTC
1 TTACTACAACTTCAAGAGGATA-GAAATGATGTTTGAAACTT-ATCTTGCTC
* ***
41312616 TTACTACAACTTC-AGAGAGAT--AAA-GA--CTTG---C-TATCCAACT-
1 TTACTACAACTTCAAGAG-GATAGAAATGATGTTTGAAACTTATCTTGCTC
**
41312656 TTACTACAACTTCAAGAGGATAGGAGTTGATGTTTGAAACTTTATCTTGCTC
1 TTACTACAACTTCAAGAGGATA-GAAATGATGTTTGAAAC-TTATCTTGCTC
* ***
41312708 TTACTACAACTTC-AGAGAGAT--AAA-GA--CTTG---C-TATCCAACT-
1 TTACTACAACTTCAAGAG-GATAGAAATGATGTTTGAAACTTATCTTGCTC
* * *
41312748 TTACTACAAATTCAAGAGGATAAGAATTGATGTCTGAAACTTTATCTTGCTC
1 TTACTACAACTTCAAGAGGAT-AGAAATGATGTTTGAAAC-TTATCTTGCTC
41312800 TTACTACAACTTCAGAGAG
1 TTACTACAACTTCA-AGAG
41312819 ATAAAGACTT
Statistics
Matches: 150, Mismatches: 24, Indels: 57
0.65 0.10 0.25
Matches are distributed among these distances:
40 31 0.21
41 19 0.13
42 1 0.01
43 5 0.03
44 4 0.03
46 11 0.07
48 4 0.03
49 6 0.04
51 20 0.13
52 45 0.30
53 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (50 bp):
TTACTACAACTTCAAGAGGATAGAAATGATGTTTGAAACTTATCTTGCTC
Found at i:41324193 original size:59 final size:59
Alignment explanation
Indices: 41324096--41324525 Score: 501
Period size: 59 Copynumber: 7.3 Consensus size: 59
41324086 TTAGATGCTC
* * *
41324096 GGGGTGAAATGGTAA-TTTTGGTAAAATTGAGGTTAAAAATGAGATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCA
* * * * * * *
41324154 GGGGTAAAATGGTAAATTTTAGTGAAAACGAAGTTAAAAATGATATTTTAGAAAGTTCT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCA
* * * * **
41324213 GGGGCAAAATGGTAATTTTTAGTGAAATTGGGGTTAAAAAT-AGGATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGA-GATTTTGGAAAGTTCA
** *
41324272 GGGGTAAAATAATAATTTTTGGTAAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTC-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCA
*
41324330 GGGGATAAAATGGTAATTTTTGGTGAAATC-AGGCTTAAAAATGGGATTTTGGAAAGTTCA
1 GGGG-TAAAATGGTAATTTTTGGTGAAATCGAGG-TTAAAAATGAGATTTTGGAAAGTTCA
* * * * * * *
41324390 AGGGTAAAATGATAACTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAGAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCA
* * * **
41324449 GGGGTAAAATGGTGATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCA
41324508 GGGGTCAAAAT-GTAATTT
1 GGGGT-AAAATGGTAATTT
41324526 CTGGACAGTT
Statistics
Matches: 320, Mismatches: 44, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
58 22 0.07
59 287 0.90
60 11 0.03
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCA
Found at i:41324272 original size:29 final size:29
Alignment explanation
Indices: 41324242--41324510 Score: 95
Period size: 29 Copynumber: 9.1 Consensus size: 29
41324232 TAGTGAAATT
*
41324242 GGGGTTAAAAATAGGATTTTGGAAAGTTTG
1 GGGGTTAAAAATAGGATTTTGGAAAG-TTC
* *
41324272 GGGGTAAAATAATA--ATTTTTGGTAAA-ATC
1 GGGGTTAAA-AATAGGA-TTTTGG-AAAGTTC
*
41324301 GAGGTTAAAAAT-GAGATTTTGGAAAGTTC
1 GGGGTTAAAAATAG-GATTTTGGAAAGTTC
*
41324330 GGGGAT-AAAAT-GGTAATTTTTGGTGAAA--TC
1 GGGGTTAAAAATAGG--A-TTTT-G-GAAAGTTC
* * *
41324360 AGGCTTAAAAATGGGATTTTGGAAAGTTC
1 GGGGTTAAAAATAGGATTTTGGAAAGTTC
*
41324389 AAGGG-TAAAATGATA--ACTTTTGGTGAAA--TC
1 -GGGGTTAAAA--ATAGGA-TTTT-G-GAAAGTTC
* * *
41324419 GGGGTTAAAAATGGGATTTTGGAGAGTTTA
1 GGGGTTAAAAATAGGATTTTGGAAAG-TTC
*
41324449 GGGG-T-AAAATGGTGATTTTTGGTGAAA--TC
1 GGGGTTAAAAATAG-GA-TTTT-G-GAAAGTTC
* *
41324478 GGGGTTAAAAATGGGATTTTGGAAAGTTT
1 GGGGTTAAAAATAGGATTTTGGAAAGTTC
41324507 GGGG
1 GGGG
41324511 GTCAAAATGT
Statistics
Matches: 183, Mismatches: 20, Indels: 73
0.66 0.07 0.26
Matches are distributed among these distances:
27 12 0.07
28 24 0.13
29 58 0.32
30 52 0.28
31 24 0.13
32 13 0.07
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (29 bp):
GGGGTTAAAAATAGGATTTTGGAAAGTTC
Found at i:41324320 original size:30 final size:30
Alignment explanation
Indices: 41324286--41324438 Score: 79
Period size: 30 Copynumber: 5.2 Consensus size: 30
41324276 TAAAATAATA
41324286 ATTTTTGGTAAAATCGAGGTTAAAAATGAG
1 ATTTTTGGTAAAATCGAGGTTAAAAATGAG
* * *
41324316 A-TTTTGG-AAAGTTCGGGGAT-AAAATG-G
1 ATTTTTGGTAAA-ATCGAGGTTAAAAATGAG
* *
41324343 TAATTTTTGGTGAAATC-AGGCTTAAAAATGGG
1 --ATTTTTGGTAAAATCGAGG-TTAAAAATGAG
* * * *
41324375 A-TTTTGG-AAAGTTCAAGGGT-AAAATGATA
1 ATTTTTGGTAAA-ATCGAGGTTAAAAATGA-G
* * * *
41324404 ACTTTTGGTGAAATCGGGGTTAAAAATGGG
1 ATTTTTGGTAAAATCGAGGTTAAAAATGAG
41324434 ATTTT
1 ATTTT
41324439 GGAGAGTTTA
Statistics
Matches: 89, Mismatches: 20, Indels: 28
0.65 0.15 0.20
Matches are distributed among these distances:
27 1 0.01
28 17 0.19
29 25 0.28
30 29 0.33
31 16 0.18
32 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (30 bp):
ATTTTTGGTAAAATCGAGGTTAAAAATGAG
Found at i:41324453 original size:30 final size:30
Alignment explanation
Indices: 41324419--41324517 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
41324409 TGGTGAAATC
41324419 GGGGTTAAAAATGGGATTTTGGAGAGTTTA
1 GGGGTTAAAAATGGGATTTTGGAGAGTTTA
* ** *
41324449 GGGG-T-AAAATGGTGATTTTTGGTGA-AATC
1 GGGGTTAAAAATGG-GA-TTTTGGAGAGTTTA
* *
41324478 GGGGTTAAAAATGGGATTTTGGAAAGTTTG
1 GGGGTTAAAAATGGGATTTTGGAGAGTTTA
*
41324508 GGGGTCAAAA
1 GGGGTTAAAA
41324518 TGTAATTTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
28 7 0.13
29 15 0.28
30 25 0.46
31 7 0.13
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.31
Consensus pattern (30 bp):
GGGGTTAAAAATGGGATTTTGGAGAGTTTA
Found at i:41324868 original size:32 final size:33
Alignment explanation
Indices: 41324806--41324869 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
41324796 TTATCGGGTC
*
41324806 AAATTAAAAATAATTAAAAGTATGAAAAGGACT
1 AAATTAAAAATAATTAAAAGAATGAAAAGGACT
*
41324839 AAATT-AAAATAATTAAAA-AATGCAGAAGGAC
1 AAATTAAAAATAATTAAAAGAATG-AAAAGGAC
41324870 CAAACGCGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 3 0.11
32 20 0.71
33 5 0.18
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (33 bp):
AAATTAAAAATAATTAAAAGAATGAAAAGGACT
Found at i:41326207 original size:6 final size:6
Alignment explanation
Indices: 41326198--41326255 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
41326188 TTTTAATATT
* * *
41326198 AATTTA AA-TTA AATTTA GATTTA AA-GTA AATTTA AATTTA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
41326243 AATTTA AATTTA A
1 AATTTA AATTTA A
41326256 CAATAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 13 0.30
6 30 0.70
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:41326212 original size:11 final size:11
Alignment explanation
Indices: 41326189--41326252 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
41326179 ATTTGGGTTT
41326189 TTTAATATT-AA
1 TTTAA-ATTAAA
41326200 TTTAAATTAAA
1 TTTAAATTAAA
*
41326211 TTTAGATTTAAA
1 TTTA-AATTAAA
*
41326223 -GTAAATTTAAA
1 TTTAAA-TTAAA
*
41326234 TTTAAAATAAA
1 TTTAAATTAAA
41326245 TTTAAATT
1 TTTAAATT
41326253 TAACAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
10 4 0.09
11 29 0.67
12 10 0.23
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:41326221 original size:17 final size:17
Alignment explanation
Indices: 41326198--41326265 Score: 100
Period size: 17 Copynumber: 3.9 Consensus size: 17
41326188 TTTTAATATT
*
41326198 AATTTAAATTAAATTTA
1 AATTTAAAATAAATTTA
* *
41326215 GATTTAAAGTAAATTTA
1 AATTTAAAATAAATTTA
41326232 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
41326249 AATTTAACAATAAATTT
1 AATTTAA-AATAAATTT
41326266 TAATCTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
17 37 0.80
18 9 0.20
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:41327014 original size:201 final size:200
Alignment explanation
Indices: 41326672--41327082 Score: 671
Period size: 201 Copynumber: 2.0 Consensus size: 200
41326662 TGCAATCATC
* * * * *
41326672 TGTTTTAATTCGCTTCTCTGGATCTTCTCAGGAAGACGAATCTGGTCCACTTCCCTGTGTCTCAT
1 TGTTTTGATTCGCTTCTCTAGATCTCCTCAGAAAGACGAATCTGGTCCACTTCCCTGTGCCTCAT
**
41326737 CAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCTGGAAGCTGGGTTCGAA
66 CAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTGGGTTCGAA
41326802 GATTTGCTCGTG-TTGAGCACTAAGTTAGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
131 GATTTGCTCGTGTTTGAGCACTAAGTTAGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
41326866 TCGCT
196 TCGCT
* *
41326871 TGTTTTGATTCGCTTCTCTAGATCTCCTCAGAAAAGACGAATTTGGTCCACTTCTCTGTGCCTCA
1 TGTTTTGATTCGCTTCTCTAGATCTCCTCAG-AAAGACGAATCTGGTCCACTTCCCTGTGCCTCA
41326936 TCAGGAAGCTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTGGGTTCG
65 TCAGGAAGCTAACC-TTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTGGGTTCG
* * * * *
41327001 AAGATTTGCTCGTGTTTGAGCGCTGAGTTGGTGTTCTTCTTTGTATCTCATCAGGAAGATGACTG
129 AAGATTTGCTCGTGTTTGAGCACTAAGTTAGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCG
41327066 CCTCGCT
194 CCTCGCT
41327073 TGTTTTGATT
1 TGTTTTGATT
41327083 GAACTACTCC
Statistics
Matches: 195, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
199 28 0.14
200 43 0.22
201 62 0.32
202 62 0.32
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (200 bp):
TGTTTTGATTCGCTTCTCTAGATCTCCTCAGAAAGACGAATCTGGTCCACTTCCCTGTGCCTCAT
CAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCAAGAAGCTGGGTTCGAA
GATTTGCTCGTGTTTGAGCACTAAGTTAGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
TCGCT
Found at i:41338591 original size:59 final size:59
Alignment explanation
Indices: 41338449--41338755 Score: 424
Period size: 59 Copynumber: 5.3 Consensus size: 59
41338439 TTGGATGCCC
* *
41338449 GGGGTGAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTCT-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT-TG
* * * * *
41338507 AGGG-AAAATGGTAATTTTTGGTGAAATTGTGGTTAAAAATGGGATTTTAGAAATTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTG
* * *
41338565 GGGGTAAAATAGTAATTTTTGGTGAAATTGGGGTTAAAAATGAGATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTG
* * *
41338624 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAGAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTG
* * * *
41338683 AGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTT-AAAATGGGATTTTGGAGAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTG
41338741 GGGGTAAAATGGTAA
1 GGGGTAAAATGGTAA
41338756 AGTTTGGGGG
Statistics
Matches: 223, Mismatches: 23, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
57 10 0.04
58 77 0.35
59 136 0.61
ACGTcount: A:0.33, C:0.02, G:0.32, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTG
Found at i:41338603 original size:30 final size:30
Alignment explanation
Indices: 41338511--41338722 Score: 90
Period size: 30 Copynumber: 7.2 Consensus size: 30
41338501 AGTTCTAGGG
* *
41338511 AAAATGGTAATTTTTGGTGAAATTGTGGTT
1 AAAATAGTAATTTTTGGTGAAATTGGGGTT
** * *
41338541 AAAA-ATGGGA-TTTT--AGAAATTTTGGGGGT
1 AAAATA-GTAATTTTTGGTGAAA--TTGGGGTT
41338570 AAAATAGTAATTTTTGGTGAAATTGGGGTT
1 AAAATAGTAATTTTTGGTGAAATTGGGGTT
*
41338600 AAAA-A-TGAGA-TTTT-G-GAAAGTTTGGGGGT
1 AAAATAGT-A-ATTTTTGGTGAAA--TTGGGGTT
* * *
41338629 AAAATGGTAATTTTTGGTAAAATCGGGGTT
1 AAAATAGTAATTTTTGGTGAAATTGGGGTT
** * *
41338659 AAAA-ATGGGA-TTTTGGAG-AGTTCGAGGG-T
1 AAAATA-GTAATTTTTGGTGAAATT-G-GGGTT
* * *
41338688 AAAATGGTAATTTTTGGTAAAATCGGGGTT
1 AAAATAGTAATTTTTGGTGAAATTGGGGTT
41338718 AAAAT
1 AAAAT
41338723 GGGATTTTGG
Statistics
Matches: 130, Mismatches: 29, Indels: 46
0.63 0.14 0.22
Matches are distributed among these distances:
27 8 0.06
28 4 0.03
29 51 0.39
30 56 0.43
31 4 0.03
32 7 0.05
ACGTcount: A:0.34, C:0.01, G:0.29, T:0.35
Consensus pattern (30 bp):
AAAATAGTAATTTTTGGTGAAATTGGGGTT
Found at i:41338723 original size:30 final size:30
Alignment explanation
Indices: 41338576--41338724 Score: 116
Period size: 30 Copynumber: 5.0 Consensus size: 30
41338566 GGGTAAAATA
* *
41338576 GTAATTTTTGGTGAAATTGGGGTTAAAAAT-
1 GTAATTTTTGGTAAAATCGGGGTT-AAAATG
* * *
41338606 G-AGA-TTTTGG-AAAGTTTGGGGGTAAAATG
1 GTA-ATTTTTGGTAAA-ATCGGGGTTAAAATG
41338635 GTAATTTTTGGTAAAATCGGGGTTAAAAATG
1 GTAATTTTTGGTAAAATCGGGGTT-AAAATG
* **
41338666 G-GA-TTTTGG-AGAGTTCGAGGG-TAAAATG
1 GTAATTTTTGGTA-AAATCG-GGGTTAAAATG
41338694 GTAATTTTTGGTAAAATCGGGGTTAAAATG
1 GTAATTTTTGGTAAAATCGGGGTTAAAATG
41338724 G
1 G
41338725 GATTTTGGAG
Statistics
Matches: 94, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
28 15 0.16
29 31 0.33
30 37 0.39
31 11 0.12
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (30 bp):
GTAATTTTTGGTAAAATCGGGGTTAAAATG
Found at i:41338748 original size:28 final size:27
Alignment explanation
Indices: 41338601--41338752 Score: 92
Period size: 30 Copynumber: 5.3 Consensus size: 27
41338591 ATTGGGGTTA
* * *
41338601 AAAATGAGATTTTGGAAAGTTTGGGGGT
1 AAAATGGGATTTTGGAGAG-TTCGGGGT
* **
41338629 AAAATGGTAATTTTTGGTA-AAATCGGGGTT
1 AAAATGG-GA-TTTTGG-AGAGTTCGGGG-T
41338659 AAAAATGGGATTTTGGAGAGTTCGAGGGT
1 -AAAATGGGATTTTGGAGAGTTCG-GGGT
* **
41338688 AAAATGGTAATTTTTGGTA-AAATCGGGGTT
1 AAAATGG-GA-TTTTGG-AGAGTTCGGGG-T
*
41338718 AAAATGGGATTTTGGAGAGTTTAGGGGT
1 AAAATGGGATTTTGGAGAG-TTCGGGGT
41338746 AAAATGG
1 AAAATGG
41338753 TAAAGTTTGG
Statistics
Matches: 96, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
27 1 0.01
28 29 0.30
29 27 0.28
30 30 0.31
31 9 0.09
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.32
Consensus pattern (27 bp):
AAAATGGGATTTTGGAGAGTTCGGGGT
Found at i:41338777 original size:138 final size:139
Alignment explanation
Indices: 41338616--41338890 Score: 412
Period size: 138 Copynumber: 2.0 Consensus size: 139
41338606 GAGATTTTGG
* *
41338616 AAAGTTTGGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAGAGTT
1 AAAGTTTGGGGGTAAAATAGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT
* * * * * *
41338681 C-GAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTT-AAAATGGGATTTTGGAGAGTTTAGGG
66 CAG-GGGTAAAATAGTAA-TTTTGGTAAAATCAGAGTTAAAAATGGGAGTTTGAAAAGTTTAGGG
41338744 G-TAAAATGGT
129 GTTAAAATGGT
*
41338754 AAAGTTTGGGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT
1 AAAGTTTGGGGGTAAAATAGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT
* *
41338819 CAGGGGTAAAATAGTAATTTTGGTGAAATCAGAGTTAAAAATGGGAGTTTGAAAAGTTTGGGGGT
66 CAGGGGTAAAATAGTAATTTTGGTAAAATCAGAGTTAAAAATGGGAGTTTGAAAAGTTTAGGGGT
41338884 TAAAATG
131 TAAAATG
41338891 TAATTTTTGG
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
137 16 0.13
138 99 0.80
139 8 0.07
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (139 bp):
AAAGTTTGGGGGTAAAATAGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT
CAGGGGTAAAATAGTAATTTTGGTAAAATCAGAGTTAAAAATGGGAGTTTGAAAAGTTTAGGGGT
TAAAATGGT
Found at i:41338778 original size:79 final size:80
Alignment explanation
Indices: 41338684--41338835 Score: 252
Period size: 80 Copynumber: 1.9 Consensus size: 80
41338674 GAGAGTTCGA
* * *
41338684 GGGTAAAATGGTAATTTTTGGTAAAATCGGGGTT-AAAATGGGATTTTGGAGAGTTTAGGGGTAA
1 GGGTAAAATAGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAA
*
41338748 AATGGTAAAGTTTGG
66 AATAGTAAAGTTTGG
*
41338763 GGGTAAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAA
1 GGGTAAAATAGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAA
41338828 AATAGTAA
66 AATAGTAA
41338836 TTTTGGTGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 32 0.48
80 35 0.52
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (80 bp):
GGGTAAAATAGTAATTTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAA
AATAGTAAAGTTTGG
Found at i:41338783 original size:21 final size:21
Alignment explanation
Indices: 41338735--41338776 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41338725 GATTTTGGAG
* *
41338735 AGTTTAGGGGTAAAATGGTAA
1 AGTTTGGGGGTAAAATAGTAA
41338756 AGTTTGGGGGTAAAATAGTAA
1 AGTTTGGGGGTAAAATAGTAA
41338777 TTTTTGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (21 bp):
AGTTTGGGGGTAAAATAGTAA
Found at i:41338795 original size:29 final size:29
Alignment explanation
Indices: 41338762--41338850 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 29
41338752 GTAAAGTTTG
41338762 GGGGTAAAATAGTAATTTTTGGTGAAATC-
1 GGGGTAAAATAGTAA-TTTTGGTGAAATCA
**
41338791 GGGGTTAAAA-ATGGGATTTT-G-GAAAGTTCA
1 GGGG-TAAAATA-GTAATTTTGGTGAAA--TCA
41338821 GGGGTAAAATAGTAATTTTGGTGAAATCA
1 GGGGTAAAATAGTAATTTTGGTGAAATCA
41338850 G
1 G
41338851 AGTTAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
27 4 0.08
28 1 0.02
29 26 0.54
30 13 0.27
31 4 0.08
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.31
Consensus pattern (29 bp):
GGGGTAAAATAGTAATTTTGGTGAAATCA
Found at i:41338825 original size:59 final size:59
Alignment explanation
Indices: 41338762--41338900 Score: 201
Period size: 58 Copynumber: 2.4 Consensus size: 59
41338752 GTAAAGTTTG
* * * *
41338762 GGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
1 GGGGTAAAATAGTAATTTTTGGTGAAATCAGAGTTAAAAATGGGAGTTTGAAAAGTTCA
**
41338821 GGGGTAAAATAGTAA-TTTTGGTGAAATCAGAGTTAAAAATGGGAGTTTGAAAAGTTTG
1 GGGGTAAAATAGTAATTTTTGGTGAAATCAGAGTTAAAAATGGGAGTTTGAAAAGTTCA
41338879 GGGGTTAAAAT-GTAATTTTTGG
1 GGGG-TAAAATAGTAATTTTTGG
41338901 AGAGTTGAAG
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
58 45 0.62
59 27 0.38
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATAGTAATTTTTGGTGAAATCAGAGTTAAAAATGGGAGTTTGAAAAGTTCA
Found at i:41340338 original size:10 final size:10
Alignment explanation
Indices: 41340306--41340339 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
41340296 CCTTCTTCCG
*
41340306 TTTTGTTTCC
1 TTTTGTTTCA
41340316 TTTTGTTTCA
1 TTTTGTTTCA
*
41340326 TTTTGTTTTA
1 TTTTGTTTCA
41340336 TTTT
1 TTTT
41340340 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.76
Consensus pattern (10 bp):
TTTTGTTTCA
Done.