Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 761 of 770
Found at i:241563755 original size:29 final size:30
Alignment explanation
Indices: 241563713--241563772 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
241563703 TAATGAAGAG
241563713 TCACTTCAGTGGCTAATGTGGCA-GCTAGA
1 TCACTTCAGTGGCTAATGTGGCACGCTAGA
241563742 TCACTTCAGTGGCTAATGTGGCACGCTAGA
1 TCACTTCAGTGGCTAATGTGGCACGCTAGA
241563772 T
1 T
241563773 TCGAGTCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (30 bp):
TCACTTCAGTGGCTAATGTGGCACGCTAGA
Found at i:241566274 original size:29 final size:29
Alignment explanation
Indices: 241566246--241566347 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
241566236 CCTCCGAGCT
** * * *
241566246 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
241566275 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
241566304 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
241566333 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
241566348 GATCTCGTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:241575294 original size:79 final size:82
Alignment explanation
Indices: 241575154--241575338 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
241575144 TCGAATGATG
* * *
241575154 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
241575218 CGTGCGAGTTAATA-AA
66 CGTGCGAGTCAATATAA
* **
241575234 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
241575296 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATATAA
**
241575314 -CCGGGCTTTGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
241575339 AGCGAGTCGT
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATATAA
Found at i:241575346 original size:40 final size:40
Alignment explanation
Indices: 241575155--241575346 Score: 151
Period size: 40 Copynumber: 4.8 Consensus size: 40
241575145 CGAATGATGT
* * * * *
241575155 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC
** * * * * *
241575195 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC
* * *
241575235 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
*
241575274 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC
* *
241575314 CCGGGCTT-TGTCCCGAAGGCATTTGAGCGAGTC
1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC
241575347 GTTATATCCG
Statistics
Matches: 126, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
39 33 0.26
40 82 0.65
41 11 0.09
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
Found at i:241583312 original size:79 final size:82
Alignment explanation
Indices: 241583172--241583356 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
241583162 TCGAATGATG
* * *
241583172 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
241583236 CGTGCGAGTTAATA-AA
66 CGTGCGAGTCAATATAA
* **
241583252 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
241583314 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATATAA
**
241583332 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
241583357 AGCGAGTCGT
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATATAA
Found at i:241583364 original size:40 final size:40
Alignment explanation
Indices: 241583173--241583364 Score: 151
Period size: 40 Copynumber: 4.8 Consensus size: 40
241583163 CGAATGATGT
* * * * *
241583173 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC
** * * * * *
241583213 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC
* * *
241583253 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
*
241583292 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC
* *
241583332 CCGGGCTT-CGTCCCGAAGGCATTTGAGCGAGTC
1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC
241583365 GTTATATCCG
Statistics
Matches: 126, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
39 33 0.26
40 82 0.65
41 11 0.09
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
Found at i:241586407 original size:43 final size:44
Alignment explanation
Indices: 241586326--241586432 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 44
241586316 AAATAATTTT
* * **
241586326 TAAAAGGTCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCTGC
1 TAAAAGGTCATATTCTATAGCAACGTTTGTGAGAAAAGCGCTGC
* * * *
241586370 TAAAAGGTC-TATTCTATAGCAACGTTTGTGGGGAAAGCGCGGT
1 TAAAAGGTCATATTCTATAGCAACGTTTGTGAGAAAAGCGCTGC
* *
241586413 TAAAA-ATCATGTTCTATAGC
1 TAAAAGGTCATATTCTATAGC
241586433 GGTGTTTCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 2 0.04
43 41 0.79
44 9 0.17
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (44 bp):
TAAAAGGTCATATTCTATAGCAACGTTTGTGAGAAAAGCGCTGC
Found at i:241588569 original size:79 final size:79
Alignment explanation
Indices: 241588438--241588619 Score: 246
Period size: 79 Copynumber: 2.3 Consensus size: 79
241588428 TATTCGAATG
*
241588438 ATATCCGGGCTAAGTCCCGAAGGCTTTGTGTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGTAAGTGACTATATCCGGACTAAG-TCCCGAAGGCA
*
241588502 TTTATGCGAGTTA-C
65 TTTATGCGAGTGATC
* *
241588516 TATATCCGGGCCAA-ACCCGAAGGCATTTGTGCT-AGTGACTATATCCGGGCTAAGTCCCGAAGG
1 -ATATCCGGGCTAAGACCCGAAGGC-TTTGTG-TAAGTGACTATATCCGGACTAAGTCCCGAAGG
* *
241588579 CATTTGTGCTAGTGATC
63 CATTTATGCGAGTGATC
241588596 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
241588620 CTTGAACGAG
Statistics
Matches: 91, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
78 10 0.11
79 69 0.76
80 12 0.13
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGTAAGTGACTATATCCGGACTAAGTCCCGAAGGCAT
TTATGCGAGTGATC
Found at i:241588583 original size:40 final size:40
Alignment explanation
Indices: 241588438--241588619 Score: 239
Period size: 40 Copynumber: 4.6 Consensus size: 40
241588428 TATTCGAATG
241588438 ATATCCGGGCTAAGTCCCGAAGGC-TTTGTG-TAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACT
* * * *
241588477 ATATCCGGACTAAGAT-CCGAAGGCATTTATGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGTGACT
* *
241588517 ATATCCGGGCCAA-ACCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
241588556 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-T
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
241588595 CATATCCGGGCTAAGACCCGAAGGC
1 -ATATCCGGGCTAAGTCCCGAAGGC
241588620 CTTGAACGAG
Statistics
Matches: 124, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
39 55 0.44
40 69 0.56
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:241596635 original size:40 final size:40
Alignment explanation
Indices: 241596535--241596717 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 40
241596525 TATTCGAATG
* * * *
241596535 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGTTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCT-AGTGACT
* * * *
241596576 ATAT-CGGACTAAGATCCGAAGGCATTTATGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * *
241596615 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
*
241596655 ATATCC-GGCTAAGTCCCGAAGGCATTTATGCTAGTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
241596693 CATATCCGGGCTAAGACCCGAAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
241596718 CTTGTGCGAG
Statistics
Matches: 117, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 42 0.36
40 70 0.60
41 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:241596680 original size:79 final size:78
Alignment explanation
Indices: 241596535--241596754 Score: 248
Period size: 79 Copynumber: 2.8 Consensus size: 78
241596525 TATTCGAATG
* *
241596535 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGTTAAGTGACTATAT-CGGACTAAGAT-CCGAAGG
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCT-AGTGACTATATCCGG-CTAAG-TCCCGAAGG
*
241596598 CATTTATGCGAGTTA-C
62 CATTTATGCGAGTGATC
* * *
241596614 TATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACTATATCCGGCTAAGTCCCGAAGGCA
1 -ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGACTATATCCGGCTAAGTCCCGAAGGCA
*
241596679 TTTATGCTAGTGATC
64 TTTATGCGAGTGATC
* * ** * *
241596694 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCCGGTTAAATCCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGACTATATCCGGCTAAGTCCCGAAGG
241596755 TACGTGATTC
Statistics
Matches: 120, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
78 31 0.26
79 57 0.47
80 32 0.27
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (78 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGACTATATCCGGCTAAGTCCCGAAGGCATT
TATGCGAGTGATC
Found at i:241596737 original size:39 final size:40
Alignment explanation
Indices: 241596535--241596740 Score: 204
Period size: 40 Copynumber: 5.2 Consensus size: 40
241596525 TATTCGAATG
* * **
241596535 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGTTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTG-CGAGTGACT
* * * *
241596576 ATAT-CGGACTAAGATCCGAAGGCATTTATGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * *
241596615 ATATCCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * *
241596655 ATATCC-GGCTAAGTCCCGAAGGCATTTATGCTAGTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* **
241596693 CATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 -ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
241596733 ATATCCGG
1 ATATCCGG
241596741 TTAAATCCCG
Statistics
Matches: 135, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
38 1 0.01
39 59 0.44
40 71 0.53
41 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
Found at i:241599782 original size:30 final size:31
Alignment explanation
Indices: 241599746--241599808 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
241599736 CCTTTTCATA
241599746 TTTCATA-TTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
241599776 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
241599807 TT
1 TT
241599809 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:241600047 original size:24 final size:24
Alignment explanation
Indices: 241600000--241600141 Score: 204
Period size: 23 Copynumber: 6.0 Consensus size: 24
241599990 GCTTTATCAT
*
241600000 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
241600025 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
241600050 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
241600073 ATAACT-GGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
241600095 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
241600119 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
241600142 GCACTTCCTC
Statistics
Matches: 109, Mismatches: 1, Indels: 15
0.87 0.01 0.12
Matches are distributed among these distances:
22 18 0.17
23 30 0.28
24 30 0.28
25 25 0.23
26 6 0.06
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:241600213 original size:9 final size:9
Alignment explanation
Indices: 241600199--241600255 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
241600189 ATCTCGTGTG
241600199 CATATCATA
1 CATATCATA
*
241600208 CATATCATGTG
1 CATATCA--TA
241600219 CATATCATA
1 CATATCATA
* *
241600228 CATGTCATGTG
1 CATATCA--TA
241600239 CATATCATA
1 CATATCATA
241600248 CATATCAT
1 CATATCAT
241600256 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:241600218 original size:20 final size:20
Alignment explanation
Indices: 241600195--241600257 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
241600185 GAACATCTCG
241600195 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
241600215 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
241600235 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
241600255 TGT
1 TGT
241600258 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:241600321 original size:25 final size:25
Alignment explanation
Indices: 241600293--241600340 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
241600283 ATATATAAAC
* * *
241600293 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
241600318 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
241600341 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:241601583 original size:27 final size:26
Alignment explanation
Indices: 241601484--241601576 Score: 143
Period size: 27 Copynumber: 3.5 Consensus size: 26
241601474 GGGCATATTC
*
241601484 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACC-TACAGGGGCT-TTACG
241601511 GTCACTTTACCTACAGGGGCTTTACG
1 GTCACTTTACCTACAGGGGCTTTACG
241601537 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTA-CCTACAGGGGCTTTACG
241601564 GTCACTTTACCTA
1 GTCACTTTACCTA
241601577 ATAGGGGTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
26 26 0.41
27 37 0.59
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (26 bp):
GTCACTTTACCTACAGGGGCTTTACG
Found at i:241601733 original size:56 final size:54
Alignment explanation
Indices: 241601608--241601826 Score: 170
Period size: 54 Copynumber: 3.9 Consensus size: 54
241601598 CATCCTACAA
* * * * * * *
241601608 GGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTAAAAATCAAGGGTATTTCTGTAATTTTGTAAACCAG
* * * * *
241601662 TGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCTGTAACTTTGTAAATCAG
1 GGGTATTT-TGGTAA-TTTTA-AAAATCAAGGGTATTTCTGTAATTTTGTAAACCAG
** * ***
241601718 GGGTATTTTGGTAATTTTAAAAATTGAGGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTAAAAATCAAGGGTATTTCTGTAATTTTGTAAACCAG
* * *
241601772 TGGTATTTTGGTAATTTTACAAACTAATTTAGGGGTATTTCTGTAATTTTGTAAA
1 GGGTATTTTGGTAATTTT--AAA--AA-TCAAGGGTATTTCTGTAATTTTGTAAA
241601827 TCGAGGGTAA
Statistics
Matches: 126, Mismatches: 30, Indels: 13
0.75 0.18 0.08
Matches are distributed among these distances:
54 52 0.41
55 10 0.08
56 41 0.33
58 2 0.02
59 21 0.17
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTAAAAATCAAGGGTATTTCTGTAATTTTGTAAACCAG
Found at i:241601793 original size:27 final size:26
Alignment explanation
Indices: 241601607--241601795 Score: 94
Period size: 27 Copynumber: 7.0 Consensus size: 26
241601597 TCATCCTACA
* * *
241601607 AGGGTGTTTTGGTAAATCTACAAACC
1 AGGGTATTTTGGTAATTTTACAAACC
** **
241601633 AAGGGTATTTCAGTAATTTTGTAAACC
1 -AGGGTATTTTGGTAATTTTACAAACC
* * * *
241601660 AATGGTATTTCT-ATAATTTTTAGAAAGTCA
1 -AGGGTATTT-TGGTAA-TTTTACAAA--CC
* ** *
241601690 AGGGTATTTCT-GTAACTTTGTAAATC
1 AGGGTATTT-TGGTAATTTTACAAACC
* **
241601716 AGGGGTATTTTGGTAATTTTAAAAATTG
1 A-GGGTATTTTGGTAATTTTACAAA-CC
* *
241601744 AGGGTATTTCGGTAATTTCACAAACC
1 AGGGTATTTTGGTAATTTTACAAACC
241601770 AGTGGTATTTTGGTAATTTTACAAAC
1 AG-GGTATTTTGGTAATTTTACAAAC
241601796 TAATTTAGGG
Statistics
Matches: 123, Mismatches: 31, Indels: 16
0.72 0.18 0.09
Matches are distributed among these distances:
26 4 0.03
27 90 0.73
28 15 0.12
29 13 0.11
30 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACC
Found at i:241601844 original size:27 final size:27
Alignment explanation
Indices: 241601814--241602079 Score: 170
Period size: 27 Copynumber: 9.8 Consensus size: 27
241601804 GGGTATTTCT
*
241601814 GTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATA
* *
241601841 GTAATTCTATAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATA
* *
241601868 GTAATTCTATAAATCGACGGT-AAA-A
1 GTAATTCTGTAAATCGAGGGTAAAATA
* * **
241601893 CTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATA
* *
241601920 GTAATTCTGTAAGTCGAGGGTAAAACGA
1 GTAATTCTGTAAATCGAGGGTAAAA-TA
* *
241601948 GGGTAAATTAAT-TATGTAATCG-GGGTAAAATG
1 --GT-AATT-CTGTA---AATCGAGGGTAAAATA
* * *
241601980 GTAATTATGTAAATCAAGGGGTAAAACA
1 GTAATTCTGTAAATCGA-GGGTAAAATA
* * **
241602008 GTAATTCTATAAATCAAGGGT-AAACG
1 GTAATTCTGTAAATCGAGGGTAAAATA
* * **
241602034 GTACTTCTATAAATC--GGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATA
*
241602059 GTAATTATGTAAATCG-GGGTA
1 GTAATTCTGTAAATCGAGGGTA
241602080 CTTTGGTAAT
Statistics
Matches: 195, Mismatches: 29, Indels: 31
0.76 0.11 0.12
Matches are distributed among these distances:
24 4 0.02
25 35 0.18
26 33 0.17
27 69 0.35
28 25 0.13
29 6 0.03
30 4 0.02
31 6 0.03
32 1 0.01
33 8 0.04
34 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATA
Found at i:241601906 original size:79 final size:77
Alignment explanation
Indices: 241601815--241602079 Score: 255
Period size: 79 Copynumber: 3.3 Consensus size: 77
241601805 GGTATTTCTG
* * *
241601815 TAATTTTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATAA
1 TAATTATGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAA
241601880 ATCGACGGTAAAAC
66 ATCG--GGTAAAAC
* * * * *
241601894 TAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGAGGGTAAATTAA
1 TAATTATGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAAC-A--GT-AATT--
* * *
241601959 TTATGTAATCGGGGTAAAATGG
60 CTAT-AAATC-GGGTAAAA--C
* * *
241601981 TAATTATGTAAATCAAGGGGTAAAACAGTAATTCTATAAATCAAGGGT-AAACGGTACTTCTATA
1 TAATTATGTAAATCGA-GGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATA
241602045 AATCGGGTAAAAC
65 AATCGGGTAAAAC
241602058 GGTAATTATGTAAATCG-GGGTA
1 --TAATTATGTAAATCGAGGGTA
241602080 CTTTGGTAAT
Statistics
Matches: 152, Mismatches: 21, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
77 5 0.03
79 68 0.45
80 5 0.03
81 3 0.02
82 2 0.01
83 7 0.05
84 2 0.01
85 10 0.07
86 4 0.03
87 19 0.12
88 27 0.18
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (77 bp):
TAATTATGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAA
ATCGGGTAAAAC
Found at i:241601987 original size:25 final size:26
Alignment explanation
Indices: 241601956--241602079 Score: 128
Period size: 26 Copynumber: 4.8 Consensus size: 26
241601946 GAGGGTAAAT
*
241601956 TAATTATGT-AATCGGGGTAAAATGG
1 TAATTATGTAAATCGGGGTAAAACGG
*
241601981 TAATTATGTAAATCAAGGGGTAAAACAG
1 TAATTATGTAAATC--GGGGTAAAACGG
* * *
241602009 TAATTCTATAAATCAAGGGT-AAACGG
1 TAATTATGTAAATC-GGGGTAAAACGG
* * *
241602035 TACTTCTATAAATC-GGGTAAAACGG
1 TAATTATGTAAATCGGGGTAAAACGG
241602060 TAATTATGTAAATCGGGGTA
1 TAATTATGTAAATCGGGGTA
241602080 CTTTGGTAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
24 4 0.05
25 26 0.31
26 27 0.32
27 5 0.06
28 22 0.26
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (26 bp):
TAATTATGTAAATCGGGGTAAAACGG
Found at i:241601996 original size:139 final size:139
Alignment explanation
Indices: 241601815--241602079 Score: 349
Period size: 139 Copynumber: 1.9 Consensus size: 139
241601805 GGTATTTCTG
* * *
241601815 TAATTTTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCAA-GGGTAAAATAGTAATTCTATA
1 TAATTATGTAAATCGAGGGTAAAATAGTAATTATATAAATCAAGGGGTAAAACAGTAATTCTATA
* * * * *
241601879 AATCGACGGTAAAAC-TAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAA
66 AATCAACGGT-AAACGTAATTCTATAAATC--GGGTAAAACGGTAATTATGTAAATCG-GGGTAA
241601943 AACGAGGGTAAAT
127 AACGAGGGTAAAT
* *
241601956 TAATTATGT-AATCG-GGGTAAAATGGTAATTATGTAAATCAAGGGGTAAAACAGTAATTCTATA
1 TAATTATGTAAATCGAGGGTAAAATAGTAATTATATAAATCAAGGGGTAAAACAGTAATTCTATA
* *
241602019 AATCAAGGGTAAACGGTACTTCTATAAATCGGGTAAAACGGTAATTATGTAAATCGGGGTA
66 AATCAACGGTAAAC-GTAATTCTATAAATCGGGTAAAACGGTAATTATGTAAATCGGGGTA
241602080 CTTTGGTAAT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
138 5 0.05
139 52 0.48
140 33 0.30
141 19 0.17
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (139 bp):
TAATTATGTAAATCGAGGGTAAAATAGTAATTATATAAATCAAGGGGTAAAACAGTAATTCTATA
AATCAACGGTAAACGTAATTCTATAAATCGGGTAAAACGGTAATTATGTAAATCGGGGTAAAACG
AGGGTAAAT
Found at i:241602011 original size:28 final size:25
Alignment explanation
Indices: 241601956--241602076 Score: 111
Period size: 25 Copynumber: 4.7 Consensus size: 25
241601946 GAGGGTAAAT
*
241601956 TAATTATGT-AATCGGGGTAAAATGG
1 TAATTATGTAAATC-GGGTAAAACGG
*
241601981 TAATTATGTAAATCAAGGGGTAAAACAG
1 TAATTATGTAAATC---GGGTAAAACGG
* *
241602009 TAATTCTATAAATCAAGGGT-AAACGG
1 TAATTATGTAAATC--GGGTAAAACGG
* * *
241602035 TACTTCTATAAATCGGGTAAAACGG
1 TAATTATGTAAATCGGGTAAAACGG
241602060 TAATTATGTAAATCGGG
1 TAATTATGTAAATCGGG
241602077 GTACTTTGGT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
24 4 0.05
25 29 0.35
26 22 0.27
27 5 0.06
28 22 0.27
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (25 bp):
TAATTATGTAAATCGGGTAAAACGG
Found at i:241602041 original size:26 final size:27
Alignment explanation
Indices: 241601970--241602073 Score: 115
Period size: 28 Copynumber: 3.9 Consensus size: 27
241601960 TATGTAATCG
* * *
241601970 GGGTAAAATGGTAATTATGTAAATCAA
1 GGGTAAAACGGTAATTCTATAAATCAA
*
241601997 GGGGTAAAACAGTAATTCTATAAATCAA
1 -GGGTAAAACGGTAATTCTATAAATCAA
*
241602025 GGGT-AAACGGTACTTCTATAAATC--
1 GGGTAAAACGGTAATTCTATAAATCAA
* *
241602049 GGGTAAAACGGTAATTATGTAAATC
1 GGGTAAAACGGTAATTCTATAAATC
241602074 GGGGTACTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
24 4 0.06
25 17 0.26
26 18 0.27
27 4 0.06
28 23 0.35
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (27 bp):
GGGTAAAACGGTAATTCTATAAATCAA
Found at i:241604687 original size:30 final size:30
Alignment explanation
Indices: 241604638--241604699 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
241604628 CCTTTTCATA
241604638 TTTCATATTCATAACACT-GGCCGAAGCCT
1 TTTCATATTCATAACACTGGGCCGAAGCCT
**
241604667 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATA-TTCATAACACTGGGCCGAAGCCT
241604698 TT
1 TT
241604700 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
30 9 0.31
31 13 0.45
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (30 bp):
TTTCATATTCATAACACTGGGCCGAAGCCT
Found at i:241604935 original size:24 final size:23
Alignment explanation
Indices: 241604902--241605028 Score: 168
Period size: 24 Copynumber: 5.4 Consensus size: 23
241604892 CTGGAGGCCT
241604902 AGCCTCTTTTAATAACTGGGGCA-A
1 AGCC-CTTTTAATAACT-GGGCATA
241604926 AGCCCTTTTTAATAACTGGGCATA
1 AGCCC-TTTTAATAACTGGGCATA
*
241604950 AGCCC-TTTAATAACTGGGCGTA
1 AGCCCTTTTAATAACTGGGCATA
*
241604972 AGCCCTTTTAATAACTATGGCATA
1 AGCCCTTTTAATAACT-GGGCATA
*
241604996 AACCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACT-GGGCATA
241605020 AGCCCTTTT
1 AGCCCTTTT
241605029 GCACTTCCTC
Statistics
Matches: 92, Mismatches: 7, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.23
23 16 0.17
24 55 0.60
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (23 bp):
AGCCCTTTTAATAACTGGGCATA
Found at i:241604962 original size:46 final size:48
Alignment explanation
Indices: 241604907--241605028 Score: 171
Period size: 46 Copynumber: 2.6 Consensus size: 48
241604897 GGCCTAGCCT
*
241604907 CTTTTAATAACTGGGGCAAAGCCCTTTTTAATAACT-GGGCATAAGCC
1 CTTTTAATAACTGGGGCAAAGCCCTTTTTAATAACTAGGGCATAAACC
* *
241604954 C-TTTAATAACT-GGGCGTAAGCCC-TTTTAATAACTATGGCATAAACC
1 CTTTTAATAACTGGGGC-AAAGCCCTTTTTAATAACTAGGGCATAAACC
241605000 CTTTTAATAACTGGGGCATAAGCCCTTTT
1 CTTTTAATAACTGGGGCA-AAGCCCTTTT
241605029 GCACTTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
45 15 0.23
46 26 0.40
47 11 0.17
48 10 0.15
49 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (48 bp):
CTTTTAATAACTGGGGCAAAGCCCTTTTTAATAACTAGGGCATAAACC
Found at i:241605100 original size:9 final size:9
Alignment explanation
Indices: 241605086--241605142 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
241605076 ATCTCGTGTG
241605086 CATATCATA
1 CATATCATA
*
241605095 CATATCATGTG
1 CATATCA--TA
241605106 CATATCATA
1 CATATCATA
* *
241605115 CATGTCATGTG
1 CATATCA--TA
241605126 CATATCATA
1 CATATCATA
241605135 CATATCAT
1 CATATCAT
241605143 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:241605105 original size:20 final size:20
Alignment explanation
Indices: 241605082--241605144 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
241605072 GAACATCTCG
241605082 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
241605102 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
241605122 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
241605142 TGT
1 TGT
241605145 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:241605209 original size:25 final size:25
Alignment explanation
Indices: 241605181--241605228 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
241605171 ATATATAAAC
* * *
241605181 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
241605206 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
241605229 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:241606405 original size:27 final size:27
Alignment explanation
Indices: 241606370--241606453 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
241606360 GGGCATATTC
*
241606370 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCATACAGGGGCT-TTACG
* *
241606397 GTCACTTTACCTTATAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
*
241606424 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
241606451 GTC
1 GTC
241606454 TTTACCTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGCTTTACG
Found at i:241606615 original size:26 final size:24
Alignment explanation
Indices: 241606575--241606673 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 24
241606565 TAGAAAGTCA
241606575 AGGGTATTTCT-GTAACTTTGTAAATC
1 AGGGTATTT-TGGTAA-TTT-TAAATC
*
241606601 AGGGTATTTTGGTAATTTTAAAATTG
1 AGGGTATTTTGGTAATTTT-AAA-TC
* * *
241606627 AGGGTATTTCGGTAATTTCACAAACC
1 AGGGTATTTTGGTAATTT--TAAATC
241606653 AGTGGTATTTTGGTAATTTTA
1 AG-GGTATTTTGGTAATTTTA
241606674 CAAACTAACT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
24 1 0.02
25 8 0.13
26 33 0.55
27 18 0.30
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.42
Consensus pattern (24 bp):
AGGGTATTTTGGTAATTTTAAATC
Found at i:241606667 original size:27 final size:26
Alignment explanation
Indices: 241606492--241606678 Score: 101
Period size: 27 Copynumber: 7.0 Consensus size: 26
241606482 TCATCCTACA
* * *
241606492 AGGGTGTTTTGGTAAATCTACAAACC
1 AGGGTATTTTGGTAATTTTACAAACC
** **
241606518 AAGGGTATTTCAGTAATTTTGTAAACC
1 -AGGGTATTTTGGTAATTTTACAAACC
* * * *
241606545 AATGGTATTTCT-ATAATTTTTAGAAAGTCA
1 -AGGGTATTT-TGGTAA-TTTTACAAA--CC
* ** *
241606575 AGGGTATTTCT-GTAACTTTGTAAATC
1 AGGGTATTT-TGGTAATTTTACAAACC
**
241606601 AGGGTATTTTGGTAATTTTA-AAATTG
1 AGGGTATTTTGGTAATTTTACAAA-CC
* *
241606627 AGGGTATTTCGGTAATTTCACAAACC
1 AGGGTATTTTGGTAATTTTACAAACC
241606653 AGTGGTATTTTGGTAATTTTACAAAC
1 AG-GGTATTTTGGTAATTTTACAAAC
241606679 TAACTTAAGG
Statistics
Matches: 123, Mismatches: 29, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
25 4 0.03
26 37 0.30
27 55 0.45
28 13 0.11
29 13 0.11
30 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACC
Found at i:241606728 original size:27 final size:27
Alignment explanation
Indices: 241606696--241606964 Score: 226
Period size: 27 Copynumber: 9.8 Consensus size: 27
241606686 AGGGTATTTT
* *
241606696 GTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACA
* * *
241606723 GTAATTCTATAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACA
*
241606750 GTAATTCTATAAATCGA-GGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACA
* *
241606776 ATAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACA
*
241606803 GTAATTCTGTAAGTCGAGGGTAAAACGGGGGTAAA
1 GTAATTCTGTAAATCGAGGGTAAAAC--------A
* **
241606838 TGGTAATTATGTAAATCG-GGGTAAAATG
1 --GTAATTCTGTAAATCGAGGGTAAAACA
*
241606866 GTAATTCTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACA
* *
241606893 GTAATTCTAT-AA---AGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACA
* * *
241606916 GTACTTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACA
* *
241606943 GTAATTATGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
241606965 CTTTGGTAAT
Statistics
Matches: 200, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
23 19 0.09
24 2 0.01
26 38 0.19
27 118 0.59
35 1 0.00
36 8 0.04
37 14 0.07
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACA
Found at i:241606781 original size:53 final size:54
Alignment explanation
Indices: 241606696--241606941 Score: 189
Period size: 53 Copynumber: 4.5 Consensus size: 54
241606686 AGGGTATTTT
* * * *
241606696 GTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACAATAATTCTATAAATCAAGGGTAAAACA
* * * *
241606750 GTAATTCTATAAATCGA-GGTAAAACAATAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACAATAATTCTATAAATCAAGGGTAAAACA
* * * * **
241606803 GTAATTCTGTAAGTCGAGGGTAAAACGGGGGTAAATGGTAATTATGTAAATC-GGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAAC-------AA---TAATTCTATAAATCAAGGGTAAAACA
* * *
241606866 GTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTAT--A--AAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACAATAATTCTATAAATCAAGGGTAAAACA
* *
241606916 GTACTTCTATAAATCGAGGGTAAAAC
1 GTAATTCTGTAAATCGAGGGTAAAAC
241606942 GGTAATTATG
Statistics
Matches: 156, Mismatches: 24, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
50 32 0.21
51 1 0.01
53 52 0.33
54 23 0.15
56 1 0.01
61 2 0.01
63 32 0.21
64 13 0.08
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAACAATAATTCTATAAATCAAGGGTAAAACA
Found at i:241606911 original size:23 final size:23
Alignment explanation
Indices: 241606881--241606928 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
241606871 TCTGTAAATC
241606881 AAGGGTAAAACAGTAATTCTATA
1 AAGGGTAAAACAGTAATTCTATA
* *
241606904 AAGGGTAAAACGGTACTTCTATA
1 AAGGGTAAAACAGTAATTCTATA
241606927 AA
1 AA
241606929 TCGAGGGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (23 bp):
AAGGGTAAAACAGTAATTCTATA
Found at i:241612428 original size:60 final size:61
Alignment explanation
Indices: 241612355--241612497 Score: 270
Period size: 61 Copynumber: 2.4 Consensus size: 61
241612345 AGTGTTGTTA
241612355 GAATTACCAGTCTAGGCTAAATCCCT-TATAACGACAAACACCCTTATTGAGATCGGATCT
1 GAATTACCAGTCTAGGCTAAATCCCTGTATAACGACAAACACCCTTATTGAGATCGGATCT
241612415 GAATTACCAGTCTAGGCTAAATCCCTGTATAACGACAAACACCCTTATTGAGATCGGATCT
1 GAATTACCAGTCTAGGCTAAATCCCTGTATAACGACAAACACCCTTATTGAGATCGGATCT
*
241612476 GAATTACCAGTCCAGGCTAAAT
1 GAATTACCAGTCTAGGCTAAAT
241612498 TCAGACCCTA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
60 26 0.32
61 55 0.68
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (61 bp):
GAATTACCAGTCTAGGCTAAATCCCTGTATAACGACAAACACCCTTATTGAGATCGGATCT
Found at i:241613987 original size:39 final size:40
Alignment explanation
Indices: 241613843--241614064 Score: 264
Period size: 40 Copynumber: 5.7 Consensus size: 40
241613833 GCTACTCGTT
* *
241613843 CAAATGCCTTCGGGA-CATAG-CCGG-TTATAGTAACTCACA
1 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCA
**
241613882 -AAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
241613921 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
241613961 CAAATGCCTTC-GATCTTAGTCCGGA-TTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
* * *
241613999 CAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAAC-TCGCA
*
241614040 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTC-GGATCTTAGTCCGGA
241614065 CATCATTCGA
Statistics
Matches: 166, Mismatches: 9, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
38 41 0.25
39 46 0.28
40 68 0.41
41 11 0.07
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
Found at i:241613990 original size:78 final size:78
Alignment explanation
Indices: 241613843--241614064 Score: 258
Period size: 78 Copynumber: 2.8 Consensus size: 78
241613833 GCTACTCGTT
* *
241613843 CAAATGCCTTCGGGA-CATAG-CCGG-TTATAGTAACTCACA-AAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCACAAATGCCTTC--GACTTAACCC
241613904 GGATTTAGTAACTCGCA
62 GGATTTAGTAACTCGCA
**
241613921 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCACAAATGCCTTCGATCTTAGTCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCACAAATGCCTTCGA-CTTAACCCGGA
241613986 -TTAGTAACTCGCA
65 TTTAGTAACTCGCA
* * * *
241613999 CAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAAC-TCGCACAAATGCCTTC--GACTTAACCCG
241614063 GA
63 GA
241614065 CATCATTCGA
Statistics
Matches: 128, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
77 3 0.02
78 69 0.54
79 42 0.33
80 14 0.11
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCACAAATGCCTTCGACTTAACCCGGAT
TTAGTAACTCGCA
Found at i:241622004 original size:78 final size:77
Alignment explanation
Indices: 241621887--241622104 Score: 293
Period size: 77 Copynumber: 2.8 Consensus size: 77
241621877 GCTACTCGTT
* * *
241621887 CAAATGCCTTCGGGA-CATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTC--GATCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGACTTAGCCCG
241621951 GATTTAGTAACTCGCA
63 GA-TTAGTAACTCGCA
*
241621967 CAAATGCCTTCGATCTTAGCCCGGAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGATCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGA-CTTAGCCCGGA
241622031 TTAGTAACTCGCA
65 TTAGTAACTCGCA
* * *
241622044 CAAATGCCTTCGGTCTTAGTCCGGATATAGT--CACGCACAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGATCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGA
241622105 CATCATTCGA
Statistics
Matches: 127, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
74 10 0.08
75 9 0.07
76 9 0.07
77 40 0.31
78 38 0.30
79 10 0.08
80 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGATCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGAT
TAGTAACTCGCA
Found at i:241622021 original size:39 final size:38
Alignment explanation
Indices: 241621887--241622104 Score: 282
Period size: 39 Copynumber: 5.7 Consensus size: 38
241621877 GCTACTCGTT
* *
241621887 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGAT-TAGTAACTCGCA
*
241621927 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGA-TTAGTAACTCGCA
241621967 CAAATGCCTTC-GATCTTAGCCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTAGTAACTCGCA
*
241622005 CAAATGCCTTCGGATCTTAGTCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTAGTAACTCGCA
* * *
241622044 CAAATGCCTTCGGTCTTAGTCCGGATATAGT--CACGCA
1 CAAATGCCTTCGGACTTAGCCCGGAT-TAGTAACTCGCA
241622081 CAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGA
241622105 CATCATTCGA
Statistics
Matches: 165, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
36 18 0.11
37 9 0.05
38 38 0.23
39 53 0.32
40 46 0.28
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:241629038 original size:46 final size:46
Alignment explanation
Indices: 241628988--241629157 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 46
241628978 TTGAGCATCT
* *
241628988 GAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * * *
241629034 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCC
*
241629081 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * *
241629126 CAAGCTTGTTGAGTTGAGTCTGAGTTCACTTA
1 GAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
241629158 GGGTCGGGTT
Statistics
Matches: 102, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
45 7 0.07
46 52 0.51
47 29 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
Found at i:241629141 original size:93 final size:93
Alignment explanation
Indices: 241628982--241629152 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
241628972 GGATGGTTGA
* * * *
241628982 GCATCTGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAACTCGTTGAGT
241629047 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
241629075 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTTGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAA-CTCGTTGAG
*
241629139 TTGAGTCTGAGTTC
65 TTGAGTCCGAGTTC
241629153 ACTTAGGGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 4 0.06
93 66 0.94
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:241630776 original size:33 final size:34
Alignment explanation
Indices: 241630713--241630783 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
241630703 CGTACGAACC
* * *
241630713 CAAATGTACGACTTCCCCTACCTCCCCCAATTCCT
1 CAAACGTACGAC-TCCCCGACCTCCACCAATTCCT
241630748 CAAACGTACGAC-CCCCGACCTCCACCAATTCCT
1 CAAACGTACGACTCCCCGACCTCCACCAATTCCT
241630781 CAA
1 CAA
241630784 GCCTATGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 22 0.67
35 11 0.33
ACGTcount: A:0.27, C:0.46, G:0.07, T:0.20
Consensus pattern (34 bp):
CAAACGTACGACTCCCCGACCTCCACCAATTCCT
Found at i:241635833 original size:45 final size:46
Alignment explanation
Indices: 241635783--241635910 Score: 156
Period size: 45 Copynumber: 2.8 Consensus size: 46
241635773 ATGGTTGAGC
241635783 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA--GATGCAACTAG
* * * *
241635829 -TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGAGATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCAACTA-G
241635874 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAG
241635911 GGCGGGTTAC
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 6 0.09
43 1 0.01
44 2 0.03
45 29 0.42
47 28 0.41
48 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCAACTAG
Found at i:241648114 original size:29 final size:28
Alignment explanation
Indices: 241648014--241648117 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
241648004 GTGACGAGAT
*
241648014 TGGCACTAAGTGTGC-AAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAA-CTT-AAATATA
* * *
241648043 TGGCACTAAGTGTGCGAGCTCAACTTTATA
1 TGGCACTAAGTGTGCGAACTTAA--ATATA
* *
241648073 TGGCACTATGTGTGCGAACTTAAATCACA
1 TGGCACTAAGTGTGCGAACTTAAAT-ATA
241648102 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
241648118 TGATCGAGTC
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
28 3 0.05
29 34 0.56
30 24 0.39
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAACTTAAATATA
Found at i:241652982 original size:123 final size:123
Alignment explanation
Indices: 241652763--241653101 Score: 597
Period size: 123 Copynumber: 2.8 Consensus size: 123
241652753 GAATTATGTG
*
241652763 AAATGAAATATGGATGTGTAATGATTATTGACATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
*
241652828 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
241652886 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
241652951 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
* * * * *
241653009 AAATGAAATATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
* *
241653074 GCTAAGTCCCGAAGACATTTATGCTAGT
66 GCTAAGTCCCGAAGGCAATTATGCTAGT
241653102 AATTATATCC
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 207 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (123 bp):
AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
Found at i:241653125 original size:40 final size:40
Alignment explanation
Indices: 241653070--241653313 Score: 301
Period size: 40 Copynumber: 6.1 Consensus size: 40
241653060 TGAATGATAC
* * * * **
241653070 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * *
241653110 CCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT
*
241653150 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
*
241653190 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* *
241653230 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * ** *
241653270 CCGGGCTAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
241653310 CCGG
1 CCGG
241653314 TTGTATTCCG
Statistics
Matches: 182, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
40 180 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
Found at i:241660426 original size:122 final size:122
Alignment explanation
Indices: 241660156--241660488 Score: 553
Period size: 122 Copynumber: 2.7 Consensus size: 122
241660146 GAATTATGTG
*
241660156 AAATGAAATATGGATGTGTAATGATTATTGACATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
241660221 GCTAAGTCCCGAAGGCAATTATTGCTAGATATGTTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATTGCTAGATATGTTTGTGTTTGAGCCTTAGTAACGA
241660278 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
*
241660343 GCTAAGTCCCGAAGGCAATTA-TGCTAGTGTTATGTTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATTGCTA--GATATGTTTGTGTTTGAGCCTTAGTAACGA
* * * * *
241660401 AAATGAAATATGGATGTGTAA-GATTATTGATTTATGTGTGCATGAGCAATTGAATGATACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
* *
241660465 GCTAAGTCCCGAAGACATTTATTG
66 GCTAAGTCCCGAAGGCAATTATTG
241660489 TGACAACCCG
Statistics
Matches: 199, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
121 5 0.03
122 142 0.71
123 52 0.26
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (122 bp):
AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
GCTAAGTCCCGAAGGCAATTATTGCTAGATATGTTTGTGTTTGAGCCTTAGTAACGA
Found at i:241661851 original size:41 final size:41
Alignment explanation
Indices: 241661806--241661923 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
241661796 TGAAAGATAA
241661806 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
241661847 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
241661877 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
241661918 ATGTAG
1 ATGTAG
241661924 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:241661862 original size:71 final size:71
Alignment explanation
Indices: 241661774--241661937 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
241661764 GAGATGTATC
241661774 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
241661839 AGGACA
66 AGGACA
241661845 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
241661910 AGGACA
66 AGGACA
241661916 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
241661938 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:241666393 original size:24 final size:24
Alignment explanation
Indices: 241666345--241666394 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
241666335 TTATTATTTT
*
241666345 TTATATGTTATTTTTTAAATAATA
1 TTATATGTTATTTTTTAAACAATA
241666369 TTATATGTTA-TTTTTAAACACATA
1 TTATATGTTATTTTTTAAACA-ATA
241666393 TT
1 TT
241666395 TAATTTCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (24 bp):
TTATATGTTATTTTTTAAACAATA
Found at i:241669665 original size:47 final size:47
Alignment explanation
Indices: 241669601--241669711 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
241669591 GACATTGAGT
*
241669601 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
241669648 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
241669695 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
241669712 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:241680064 original size:28 final size:28
Alignment explanation
Indices: 241680032--241680130 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
241680022 GCAATAAGCC
*
241680032 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
241680060 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
241680088 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
241680117 CGCACACTTAGTGC
1 CGCACACTTAGTGC
241680131 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:241687682 original size:28 final size:28
Alignment explanation
Indices: 241687650--241687748 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
241687640 GCAATAAGCC
*
241687650 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
241687678 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
241687706 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
241687735 CGCACACTTAGTGC
1 CGCACACTTAGTGC
241687749 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:241691448 original size:40 final size:40
Alignment explanation
Indices: 241691403--241691532 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
241691393 CGGAATACAA
241691403 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
241691443 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
241691483 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
241691523 CCGGATATAA
1 CCGGATATAA
241691533 TTTCCAGCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.04
40 75 0.96
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:241699438 original size:40 final size:40
Alignment explanation
Indices: 241699393--241699522 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
241699383 CGGAATACAA
241699393 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
241699433 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
241699473 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
241699513 CCGGATATAA
1 CCGGATATAA
241699523 TTTCCAGCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.04
40 75 0.96
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:241704442 original size:40 final size:40
Alignment explanation
Indices: 241704393--241704560 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 40
241704383 TCTTCGGAAT
* * *
241704393 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* * *** *
241704432 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
241704472 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
241704512 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC
241704552 TTAGCCCGG
1 TTAGCCCGG
241704561 GTATCATTCA
Statistics
Matches: 107, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 103 0.96
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
Found at i:241712737 original size:40 final size:40
Alignment explanation
Indices: 241712688--241712855 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 40
241712678 TCTTCGGAAT
* * *
241712688 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* * *** *
241712727 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
241712767 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
241712807 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC
241712847 TTAGCCCGG
1 TTAGCCCGG
241712856 GTATCATTCA
Statistics
Matches: 107, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 103 0.96
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
Found at i:241718084 original size:39 final size:39
Alignment explanation
Indices: 241718003--241718192 Score: 161
Period size: 39 Copynumber: 4.8 Consensus size: 39
241717993 TTGAATGATG
* ** * * *
241718003 TCCGGGCTAAGTCCCGAAGGC-TTTGTGTAAGTGACTATA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGTTAATAAA
*
241718042 TCCGGACT-AGATCCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCGAAGGCATTCGTGCGAGTTAATAAA
* * *
241718081 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
* * *
241718120 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGTTAATA-AA
** * *
241718161 -CCGGGCTTTGTCCCGAAGGCATTTGAGCGAGT
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGT
241718193 CGTTATATCC
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
38 10 0.08
39 61 0.48
40 53 0.42
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
Found at i:241718149 original size:40 final size:39
Alignment explanation
Indices: 241718054--241718192 Score: 174
Period size: 40 Copynumber: 3.5 Consensus size: 39
241718044 CGGACTAGAT
* *
241718054 CCGAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAG-C
1 CCGAAGGCATTCGTGCGAGTTACTAAA-CCGGGTTAAGTC
*
241718093 CCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-CCGGGTTAAGTC
*
241718133 CCGAAGGCATTCGTGCGAGTTACTATAACCGGGCTT-TGTC
1 CCGAAGGCATTCGTGCGAGTTACTA-AACCGGG-TTAAGTC
* *
241718173 CCGAAGGCATTTGAGCGAGT
1 CCGAAGGCATTCGTGCGAGT
241718193 CGTTATATCC
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.38
40 51 0.57
41 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTACTAAACCGGGTTAAGTC
Found at i:241718149 original size:79 final size:80
Alignment explanation
Indices: 241718003--241718192 Score: 228
Period size: 78 Copynumber: 2.4 Consensus size: 80
241717993 TTGAATGATG
** * *
241718003 TCCGGGCTAAGTCCCGAAGGC-TTTGTGTAAGTGACTATATCCGGACTAGATCCGAAGGCATTCG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAACCCGGACTAGATCCGAAGGCATTCG
241718067 TGCGAGTTAATA-AA
66 TGCGAGTTAATATAA
* **
241718081 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTA-AGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAACCCGGACTAGA-T-CCGAAGGCATT
*
241718144 CGTGCGAGTTACTATAA
64 CGTGCGAGTTAATATAA
** *
241718161 -CCGGGCTTTGTCCCGAAGGCATTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
241718193 CGTTATATCC
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
77 10 0.10
78 32 0.33
79 32 0.33
80 22 0.23
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAACCCGGACTAGATCCGAAGGCATTCG
TGCGAGTTAATATAA
Found at i:241718216 original size:79 final size:79
Alignment explanation
Indices: 241718053--241718218 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
241718043 CCGGACTAGA
* *
241718053 TCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAGCCCGAAGGCATTTGAGCGAGTCACTA
*
241718118 AACCCGGGTTAAGT
66 AACCCGGGTTAAAT
* * ** **
241718132 CCCGAAGGCATTCGTGCGAGTTACTATAA-CCGGGCTTTGTCCCGAAGGCATTTGAGCGAGTCGT
1 TCCGAAGGCATTCGTGCGAGTTAATA-AATCCGGGCTAAG-CCCGAAGGCATTTGAGCGAGTCAC
* *
241718196 TATATCC-GGTTAAAT
64 TAAACCCGGGTTAAAT
241718211 TCCGAAGG
1 TCCGAAGG
241718219 TACGTGATTC
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
79 46 0.63
80 27 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAGCCCGAAGGCATTTGAGCGAGTCACTA
AACCCGGGTTAAAT
Found at i:241726051 original size:39 final size:39
Alignment explanation
Indices: 241725996--241726133 Score: 181
Period size: 39 Copynumber: 3.5 Consensus size: 39
241725986 GGACTAAGAT
* *
241725996 CCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAG-C
1 CCGAAGGCATTCGTGCGAGTTACTAAA-CCGGGTTAAGTC
*
241726035 CCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-CCGGGTTAAGTC
*
241726075 CCGAAGGCATTCGTGCGAGTTACTATAACCGGGTT-TGTC
1 CCGAAGGCATTCGTGCGAGTTACTA-AACCGGGTTAAGTC
* *
241726114 CCGAAGGCATTTGAGCGAGT
1 CCGAAGGCATTCGTGCGAGT
241726134 CGTTATATCC
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 55 0.62
40 32 0.36
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTACTAAACCGGGTTAAGTC
Found at i:241732114 original size:30 final size:30
Alignment explanation
Indices: 241732080--241732140 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
241732070 TCCTTAACTC
241732080 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
241732110 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
241732140 A
1 A
241732141 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:241736126 original size:30 final size:30
Alignment explanation
Indices: 241736092--241736152 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
241736082 TCCTTAACTC
241736092 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
241736122 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
241736152 A
1 A
241736153 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:241756723 original size:29 final size:29
Alignment explanation
Indices: 241756691--241756791 Score: 116
Period size: 29 Copynumber: 3.5 Consensus size: 29
241756681 ATAGTGAATC
*
241756691 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
241756720 CGCACACTTAGTGCTATATA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AACT
* * * *
241756748 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATA-TATTTTCAACT
241756778 CGCACACTTAGTGC
1 CGCACACTTAGTGC
241756792 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 20 0.33
29 21 0.34
30 17 0.28
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAACT
Found at i:241756784 original size:30 final size:29
Alignment explanation
Indices: 241756690--241756791 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
241756680 TATAGTGAAT
* * *
241756690 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
241756719 TCGCACACTTAGTGCTATATAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
241756747 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
241756777 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
241756792 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:241764589 original size:30 final size:30
Alignment explanation
Indices: 241764534--241764693 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
241764524 ATAGTGAATC
241764534 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
241764563 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
241764593 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
241764622 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
241764650 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
241764680 CGCACACTTAGTGC
1 CGCACACTTAGTGC
241764694 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:241764626 original size:59 final size:57
Alignment explanation
Indices: 241764534--241764693 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
241764524 ATAGTGAATC
*
241764534 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
241764593 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
241764650 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
241764694 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:241769467 original size:40 final size:40
Alignment explanation
Indices: 241769361--241769544 Score: 147
Period size: 40 Copynumber: 4.6 Consensus size: 40
241769351 TGCTGGAAAT
* * * * * **
241769361 TATAACCGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
*
241769401 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * *
241769441 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATC-G
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * * * * *
241769479 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC
1 T-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * *
241769520 CATATCCGGGCTATGTCCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC
241769545 GTTTGAACGA
Statistics
Matches: 115, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 29 0.25
40 85 0.74
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
Found at i:241777541 original size:40 final size:39
Alignment explanation
Indices: 241777446--241777615 Score: 130
Period size: 39 Copynumber: 4.3 Consensus size: 39
241777436 TGCTGGAAAT
* * * * **
241777446 TATAACCGGGTTAAGACCCGAAGGCAATGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTCAC
*
241777485 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTCAC
* * *
241777525 TCTATCCGGGCTAAGA-CCGAAGGCATTTGTGC-AATC-G
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGAGTCAC
* * * * * *
241777562 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC
1 T-ATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTCAC
*
241777603 CATATCCGGGCTA
1 TATATCCGGGCTA
241777616 TGTCCGAAGG
Statistics
Matches: 103, Mismatches: 21, Indels: 13
0.75 0.15 0.09
Matches are distributed among these distances:
37 1 0.01
38 17 0.17
39 49 0.48
40 36 0.35
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTCAC
Found at i:241777596 original size:78 final size:78
Alignment explanation
Indices: 241777486--241777631 Score: 177
Period size: 78 Copynumber: 1.9 Consensus size: 78
241777476 GCTAGTGGCT
*
241777486 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTC-TATCCGGGCTAAGACCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA-CCATATCCGGGCTAAGACCGAAGGCA
241777550 TTTGTGCAATCGTG
65 TTTGTGCAATCGTG
* * * * * * * * * *
241777564 ATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTACCATATCCGGGCTATGTCCGAAGGCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCACCATATCCGGGCTAAGACCGAAGGCAT
241777629 TTG
66 TTG
241777632 AACGAGTAGC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
77 1 0.02
78 55 0.98
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (78 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCACCATATCCGGGCTAAGACCGAAGGCAT
TTGTGCAATCGTG
Found at i:241782284 original size:40 final size:40
Alignment explanation
Indices: 241782228--241782445 Score: 253
Period size: 40 Copynumber: 5.5 Consensus size: 40
241782218 CATGAGCATT
* * * *
241782228 TGATTGATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
1 TGATT-ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
241782269 TGATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
1 TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
241782309 TTG-TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 -TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
241782349 TTG-TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAG
1 -TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* ** * * * **
241782389 TTACCAAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTG
1 TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
241782429 TGGTTATATCC-GGCTAA
1 TGATTATATCCGGGCTAA
241782446 ATTCCGAAGA
Statistics
Matches: 154, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
39 6 0.04
40 141 0.92
41 7 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
Found at i:241790500 original size:40 final size:40
Alignment explanation
Indices: 241790444--241790660 Score: 244
Period size: 40 Copynumber: 5.5 Consensus size: 40
241790434 CATGAGCATT
* * * *
241790444 TGATTGATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
1 TGATT-ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
241790485 TGATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
1 TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
241790525 TTG-TTATAT-CGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 -TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
241790564 TTG-TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAG
1 -TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* ** * * * **
241790604 TTACCAAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTG
1 TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
241790644 TGGTTATATCC-GGCTAA
1 TGATTATATCCGGGCTAA
241790661 ATTCCGAAGA
Statistics
Matches: 152, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
39 44 0.29
40 101 0.66
41 7 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
Found at i:241790669 original size:79 final size:80
Alignment explanation
Indices: 241790454--241790660 Score: 274
Period size: 79 Copynumber: 2.6 Consensus size: 80
241790444 TGATTGATAC
* * *
241790454 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
* *** *
241790519 TGCGAGTTGTTATAT
66 TGCAAGTTACCAAAT
* * *
241790534 -CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
241790598 TGCAAGTTACCAAAT
66 TGCAAGTTACCAAAT
* * *
241790613 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAA
241790661 ATTCCGAAGA
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
79 74 0.67
80 36 0.33
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAAT
Found at i:241794033 original size:30 final size:30
Alignment explanation
Indices: 241793997--241794071 Score: 78
Period size: 38 Copynumber: 2.2 Consensus size: 30
241793987 CAATTGTGCA
241793997 AATTGTGATATCCGGGCTAAGCCCGAAGGC
1 AATTGTGATATCCGGGCTAAGCCCGAAGGC
241794027 AATTGTGCGAGTATGATATCCGGGCTAAGCCCGAAGGC
1 AA-T-T----G--TGATATCCGGGCTAAGCCCGAAGGC
241794065 AATTGTG
1 AATTGTG
241794072 CAAATTGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
30 4 0.11
31 1 0.03
32 2 0.05
36 2 0.05
37 1 0.03
38 27 0.73
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (30 bp):
AATTGTGATATCCGGGCTAAGCCCGAAGGC
Found at i:241794050 original size:77 final size:78
Alignment explanation
Indices: 241793963--241794113 Score: 268
Period size: 77 Copynumber: 1.9 Consensus size: 78
241793953 AATGTTCGAG
241793963 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
241794027 AATTGTGCGAGTA
66 AATTGTGCGAGTA
*
241794040 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
**
241794105 CTTTGTGCG
66 AATTGTGCG
241794114 GGTTACCATA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 54 0.77
78 16 0.23
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (78 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTA
Found at i:241794053 original size:38 final size:39
Alignment explanation
Indices: 241793962--241794104 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
241793952 GAATGTTCGA
241793962 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
241794001 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGC-GAGT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
241794039 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
241794078 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
241794105 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:241801923 original size:78 final size:78
Alignment explanation
Indices: 241801834--241802014 Score: 265
Period size: 78 Copynumber: 2.3 Consensus size: 78
241801824 AATGTTCGAG
241801834 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATAT-CGGGCTAAGTCCCGAAGGC
241801898 AATTGTGCGAGTTA
65 AATTGTGCGAGTTA
* *
241801912 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCGGGTTAAGTCCCGAAGGCC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCGGGCTAAGTCCCGAAGGCA
* *
241801977 TTTGTGCGGGTTA
66 ATTGTGCGAGTTA
** * * *
241801990 CCATAACCGGGCTATGTCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGC
241802015 GTTTGAACGA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
77 8 0.09
78 85 0.91
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.24
Consensus pattern (78 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCGGGCTAAGTCCCGAAGGCA
ATTGTGCGAGTTA
Found at i:241801983 original size:39 final size:39
Alignment explanation
Indices: 241801833--241801975 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
241801823 GAATGTTCGA
241801833 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
241801872 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
241801911 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
241801950 GTGATAT-CGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
241801976 CTTTGTGCGG
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 8 0.08
39 88 0.92
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:241810119 original size:44 final size:44
Alignment explanation
Indices: 241810056--241810230 Score: 210
Period size: 44 Copynumber: 3.9 Consensus size: 44
241810046 TGTAACCCGC
* *
241810056 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATTCGCAT
* *
241810100 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATTCGC-A--T
* *
241810146 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGG--ATTCGCAT
*
241810193 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAT
241810231 GCTCAACCAT
Statistics
Matches: 111, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
43 1 0.01
44 39 0.35
45 2 0.02
46 31 0.28
47 31 0.28
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (44 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATTCGCAT
Found at i:241810220 original size:93 final size:91
Alignment explanation
Indices: 241810063--241810232 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 91
241810053 CGCCCATAAG
*
241810063 CGAACTCGGACTCAACTCAACGAGCTCGGGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 CGAACTCGGACTCAACTCAACGAGCTCGGATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
241810128 GAGTTCGGATGCCTAGTTACATCTCA
66 GAGTTCGGATGCCTAGTTACATCTCA
*
241810154 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG--ATTCGCATCCATAAGTGAACTCGGACTCAACTCA
241810219 ACGAGTTCGGATGC
64 ACGAGTTCGGATGC
241810233 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 28 0.37
93 47 0.63
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (91 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCA
Found at i:241817649 original size:46 final size:45
Alignment explanation
Indices: 241817591--241817765 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 45
241817581 TGTAACCCGC
*
241817591 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCAT
* *
241817637 CCATAAGTGAACTCGGACTCAACTCAACGAG-TCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCAT
* * *
241817686 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCAT
*
241817728 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGC
241817766 TCAACCATCC
Statistics
Matches: 110, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 5 0.05
43 1 0.01
44 3 0.03
45 33 0.30
46 53 0.48
47 7 0.06
48 2 0.02
49 3 0.03
50 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCAT
Found at i:241820332 original size:38 final size:40
Alignment explanation
Indices: 241820264--241820450 Score: 131
Period size: 38 Copynumber: 4.8 Consensus size: 40
241820254 CAGATTTGGT
* * * *
241820264 AACTTGCACAAATGCCTTCGGGTCTTTAGCCTGGATATAAC
1 AACTCGCACGAATGCCATCGGGTC-TTAGCCCGGATATAAC
* * ***
241820305 AACTCGCACGAATGCCATC-GG-CTTAGCCCGAATTTGGT
1 AACTCGCACGAATGCCATCGGGTCTTAGCCCGGATATAAC
* *
241820343 AACTTGCACAGAATG-CTTCGGGTCTTAGCCCGGATATAAC
1 AACTCGCAC-GAATGCCATCGGGTCTTAGCCCGGATATAAC
*
241820383 AACTCGCACGAATG-CTTC-GGTCTTA---CGGATATAATC
1 AACTCGCACGAATGCCATCGGGTCTTAGCCCGGATATAA-C
* ** * *
241820419 -ACTAGCATAAATGCCTTCGGGACTTAGCCCGG
1 AACTCGCACGAATGCCATCGGGTCTTAGCCCGG
241820451 GTATCATTCA
Statistics
Matches: 116, Mismatches: 21, Indels: 19
0.74 0.13 0.12
Matches are distributed among these distances:
35 19 0.16
36 5 0.04
37 6 0.05
38 28 0.24
39 17 0.15
40 25 0.22
41 16 0.14
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
AACTCGCACGAATGCCATCGGGTCTTAGCCCGGATATAAC
Found at i:241820340 original size:79 final size:79
Alignment explanation
Indices: 241820209--241820397 Score: 253
Period size: 79 Copynumber: 2.4 Consensus size: 79
241820199 TTCTTCGGAA
* ** *
241820209 TTTAGCCGGATATAACCACAAGCAC-AATTGCCTTCGGGCTTAACCCAGATTTGGTAACTTGCAC
1 TTTAGCCGGATATAACAACTCGCACGAA-TGCCATCGGGCTTAACCCAGATTTGGTAACTTGCAC
241820273 A-AATGCCTTCGGGTC
65 AGAATG-CTTCGGGTC
*
241820288 TTTAGCCTGGATATAACAACTCGCACGAATGCCATC-GGCTTAGCCC-GAATTTGGTAACTTGCA
1 TTTAGCC-GGATATAACAACTCGCACGAATGCCATCGGGCTTAACCCAG-ATTTGGTAACTTGCA
241820351 CAGAATGCTTCGGGTC
64 CAGAATGCTTCGGGTC
241820367 -TTAGCCCGGATATAACAACTCGCACGAATGC
1 TTTAG-CCGGATATAACAACTCGCACGAATGC
241820398 TTCGGTCTTA
Statistics
Matches: 100, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
78 29 0.29
79 44 0.44
80 25 0.25
81 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (79 bp):
TTTAGCCGGATATAACAACTCGCACGAATGCCATCGGGCTTAACCCAGATTTGGTAACTTGCACA
GAATGCTTCGGGTC
Found at i:241828399 original size:69 final size:74
Alignment explanation
Indices: 241828307--241828488 Score: 241
Period size: 69 Copynumber: 2.5 Consensus size: 74
241828297 ACCCATTTGG
241828307 TAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCG-C-AATGCCTTC-GGTC-
1 TAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAAC-ACTCGACGAATGCCTTCGGGTCT
241828368 TAGCCC-G-A
65 TAGCCCGGAA
241828376 TAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACACTCGCACGAATGCCTTCGGGTCT
1 TAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACACTCG-ACGAATGCCTTCGGGTCT
241828441 TAGCCCGGATA
65 TAGCCCGGA-A
* * *
241828452 TAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGG
1 T-A--ACTTGCACAAATGCCTTCGGGTCTTAGCCCGG
241828489 GTATCATTCA
Statistics
Matches: 99, Mismatches: 3, Indels: 12
0.87 0.03 0.11
Matches are distributed among these distances:
68 5 0.05
69 41 0.41
70 1 0.01
71 9 0.09
72 4 0.04
73 6 0.06
74 1 0.01
76 2 0.02
77 1 0.01
79 29 0.29
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (74 bp):
TAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACACTCGACGAATGCCTTCGGGTCTT
AGCCCGGAA
Found at i:241828430 original size:39 final size:39
Alignment explanation
Indices: 241828313--241828488 Score: 219
Period size: 39 Copynumber: 4.7 Consensus size: 39
241828303 TTGGTAACTT
241828313 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAAC-ACTC
*
241828353 G--C-AATGCCTTC-GGTC-TAGCCC-G--AT-A-ACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACACTC
241828382 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACACTC
* *
241828421 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAA-CACTC
* *
241828461 GCATAAATGCCTTCGGGACTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
241828489 GTATCATTCA
Statistics
Matches: 118, Mismatches: 7, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
29 4 0.03
31 2 0.02
32 11 0.09
33 4 0.03
34 7 0.06
35 7 0.06
36 4 0.03
37 11 0.09
38 2 0.02
39 36 0.31
40 30 0.25
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (39 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACACTC
Found at i:241828483 original size:40 final size:39
Alignment explanation
Indices: 241828255--241828488 Score: 217
Period size: 39 Copynumber: 6.2 Consensus size: 39
241828245 TTCTTCGAAT
* *
241828255 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTC
* * * *
241828294 TTAACCC--ATTTGGTA-ACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAT--AACACTAGCACAAATGCCTTCGGGTC
*
241828332 TTAGCCCGGATATAACAACT--CGC-AATGCCTTC-GGTC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTC
*
241828368 -TAGCCC-G--AT-A-ACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTC
* *
241828401 TTAGCCCGGATATAACACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTC
* *
241828440 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTC
241828480 TTAGCCCGG
1 TTAGCCCGG
241828489 GTATCATTCA
Statistics
Matches: 160, Mismatches: 17, Indels: 35
0.75 0.08 0.17
Matches are distributed among these distances:
29 3 0.02
31 3 0.02
32 11 0.07
33 4 0.03
34 7 0.04
35 7 0.04
36 4 0.03
37 11 0.07
38 33 0.21
39 39 0.24
40 38 0.24
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (39 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTC
Found at i:241833814 original size:40 final size:40
Alignment explanation
Indices: 241833759--241833968 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
241833749 AACATTGGAA
241833759 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
241833799 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
241833839 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
241833879 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
241833918 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
241833959 CTATATCCGG
1 ATATATCCGG
241833969 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:241841871 original size:40 final size:40
Alignment explanation
Indices: 241841816--241842065 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
241841806 AACATTGGAA
241841816 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
241841856 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
241841896 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
241841936 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
241841976 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
241842015 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
241842056 CTATATCCGG
1 ATATATCCGG
241842066 TTAAATCCCG
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 189 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:241846451 original size:46 final size:46
Alignment explanation
Indices: 241846396--241846576 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
241846386 TAGGATGGTT
241846396 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
241846442 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
241846488 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
241846535 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
241846577 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:241846557 original size:93 final size:93
Alignment explanation
Indices: 241846398--241846568 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
241846388 GGATGGTTGA
* *
241846398 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
241846463 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
241846491 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
241846556 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
241846569 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:241849546 original size:15 final size:15
Alignment explanation
Indices: 241849526--241849594 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
241849516 GTATCTTGGG
241849526 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
241849541 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
241849556 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
241849571 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
241849586 TTTCTTTAT
1 TTTCTTTAT
241849595 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:241849595 original size:30 final size:30
Alignment explanation
Indices: 241849517--241849604 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
241849507 CATAGTATCG
* * * *
241849517 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
241849547 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
241849577 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
241849605 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:241852016 original size:46 final size:46
Alignment explanation
Indices: 241851966--241852141 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
241851956 GATGGTTGCA
241851966 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
241852012 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
241852059 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
241852105 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
241852142 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:241852122 original size:93 final size:93
Alignment explanation
Indices: 241851963--241852133 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
241851953 TAGGATGGTT
* *
241851963 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
241852028 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
241852056 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
241852121 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
241852134 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:241854739 original size:31 final size:31
Alignment explanation
Indices: 241854701--241854771 Score: 135
Period size: 30 Copynumber: 2.3 Consensus size: 31
241854691 AAGAAAAATT
241854701 TTGAAGAAAAAACAGTCAAAATAAGCTCCAC
1 TTGAAGAAAAAACAGTCAAAATAAGCTCCAC
241854732 TTGAAG-AAAAACAGTCAAAATAAGCTCCAC
1 TTGAAGAAAAAACAGTCAAAATAAGCTCCAC
241854762 TTGAAGAAAA
1 TTGAAGAAAA
241854772 GACTGTTTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 30 0.77
31 9 0.23
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (31 bp):
TTGAAGAAAAAACAGTCAAAATAAGCTCCAC
Found at i:241859048 original size:40 final size:40
Alignment explanation
Indices: 241859003--241859169 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
241858993 CGGAATATAA
241859003 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
241859043 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
241859083 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
241859123 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
241859162 CCGGATAT
1 CCGGATAT
241859170 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:241860009 original size:17 final size:19
Alignment explanation
Indices: 241859986--241860031 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
241859976 AAGAAGCATG
241859986 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
241860004 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
241860022 AATCATGCTC
1 AATCATGCTC
241860032 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:241867045 original size:40 final size:41
Alignment explanation
Indices: 241867000--241867166 Score: 164
Period size: 40 Copynumber: 4.2 Consensus size: 41
241866990 CGGAATATAA
*
241867000 CCGGATATAATCAAGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
241867040 CCGGATAGAAT-AACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
241867080 CCGGATGT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
241867120 CCGGATATAAT-TTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
241867159 CCGGATAT
1 CCGGATAT
241867167 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
39 17 0.16
40 87 0.83
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (41 bp):
CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:241868012 original size:17 final size:19
Alignment explanation
Indices: 241867989--241868034 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
241867979 AAGAAGCATG
241867989 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
241868007 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
241868025 AATCATGCTC
1 AATCATGCTC
241868035 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:241872012 original size:27 final size:28
Alignment explanation
Indices: 241871955--241872024 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
241871945 AAATTTGTAC
**
241871955 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
241871983 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
241872010 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
241872025 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:241879868 original size:26 final size:28
Alignment explanation
Indices: 241879814--241879882 Score: 97
Period size: 26 Copynumber: 2.5 Consensus size: 28
241879804 AAATTTGTAC
**
241879814 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
241879842 AGCACTATGTGTGCG-AGCTGATT-TAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
241879868 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
241879883 GATTCACTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 17 0.46
27 6 0.16
28 14 0.38
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:241884673 original size:25 final size:25
Alignment explanation
Indices: 241884645--241884723 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
241884635 ACTCGGCCCT
*
241884645 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACATTCACATTC
** * *
241884670 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACATTC-ACATTC
*
241884692 ATCACATATATACACCTTCACATTC
1 ATCACATATATACACATTCACATTC
241884717 ATCACAT
1 ATCACAT
241884724 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACATTCACATTC
Found at i:241884769 original size:49 final size:49
Alignment explanation
Indices: 241884595--241884848 Score: 376
Period size: 47 Copynumber: 5.3 Consensus size: 49
241884585 CCCTTCGGGA
* * * * * * *
241884595 CTTATCACAT-T-TATACACTTCCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
241884642 CCTATCACATATAT--ACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241884689 CTTATCACATATATACAC-C-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241884736 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241884785 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241884834 CTTATCACATATATA
1 CTTATCACATATATA
241884849 TATCTCATAC
Statistics
Matches: 193, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
47 95 0.49
48 3 0.02
49 95 0.49
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:241888994 original size:40 final size:40
Alignment explanation
Indices: 241888899--241889169 Score: 436
Period size: 40 Copynumber: 6.8 Consensus size: 40
241888889 CCAGCATGAT
* * *
241888899 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
241888939 TG-TCTTCGGGACTTAGTCCGGTTGCATTACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
241888978 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
241889018 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
241889058 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
241889098 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
241889138 TGCTCTTCGGGATTTAGCCCGGATATATCACT
1 TGCTCTTCGGAACTTAGTCCGGATACATCACT
241889170 CCAATTCTCA
Statistics
Matches: 217, Mismatches: 13, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
39 34 0.16
40 183 0.84
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:241891369 original size:25 final size:25
Alignment explanation
Indices: 241891341--241891419 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
241891331 ACTCGGCCCT
*
241891341 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACATTCACATTC
** * *
241891366 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACATTC-ACATTC
*
241891388 ATCACATATATACACCTTCACATTC
1 ATCACATATATACACATTCACATTC
241891413 ATCACAT
1 ATCACAT
241891420 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACATTCACATTC
Found at i:241891465 original size:49 final size:49
Alignment explanation
Indices: 241891291--241891591 Score: 440
Period size: 47 Copynumber: 6.3 Consensus size: 49
241891281 CCCTTCGGGA
* * * * * * *
241891291 CTTATCACAT-T-TATACACTTCCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
241891338 CCTATCACATATAT--ACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241891385 CTTATCACATATATACAC-C-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241891432 CTTATCACATATATACACACTTTCACATTCATCACATCGGCC---AGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241891478 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241891527 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
241891576 CTTATCACAATATATA
1 CTTATCAC-ATATATA
241891592 TCTCATACAT
Statistics
Matches: 236, Mismatches: 8, Indels: 17
0.90 0.03 0.07
Matches are distributed among these distances:
46 46 0.19
47 95 0.40
48 3 0.01
49 85 0.36
50 7 0.03
ACGTcount: A:0.30, C:0.32, G:0.08, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:241891524 original size:95 final size:95
Alignment explanation
Indices: 241891291--241891591 Score: 416
Period size: 95 Copynumber: 3.2 Consensus size: 95
241891281 CCCTTCGGGA
* * * * * * * *
241891291 CTTATCACAT-T-TATACACTTCCACATCCATCACGTTGGCCACTCGGCCCTATCACATATAT--
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
241891352 ACACTTTCACATTCATCACATTGGCCATTCGGC
66 ACACTTTCACATTCATCACATCGGCCA---GGC
241891385 CTTATCACATATATACAC-C-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
241891448 ACACTTTCACATTCATCACATCGGCCAGGC
66 ACACTTTCACATTCATCACATCGGCCAGGC
241891478 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
241891543 ACACTTTCACATTCATCACATCGGCCATTAGGC
66 ACACTTTCACATTCATCACATCGGCC---AGGC
241891576 CTTATCACAATATATA
1 CTTATCAC-ATATATA
241891592 TCTCATACAT
Statistics
Matches: 188, Mismatches: 9, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
93 21 0.11
94 46 0.24
95 72 0.38
96 30 0.16
98 12 0.06
99 7 0.04
ACGTcount: A:0.30, C:0.32, G:0.08, T:0.31
Consensus pattern (95 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACACTTTCACATTCATCACATCGGCCAGGC
Found at i:241896615 original size:28 final size:28
Alignment explanation
Indices: 241896518--241896615 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
241896508 ATTGGTTTCG
* * * *
241896518 GCACTAAGTGTGCGGGTTCAAATGGTATA
1 GCACTAAGTGTGCGAGTTCGACT-ATATA
* * * *
241896547 G-GCTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTCGACTATATA
241896574 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTCGACTATAT-A
241896602 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
241896616 GGCTTATTAC
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 6 0.11
28 49 0.88
29 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTCGACTATATA
Found at i:241898041 original size:36 final size:36
Alignment explanation
Indices: 241897994--241898066 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
241897984 TAAGTGGCTT
241897994 GAAGTCTGTTAACACCTCGTGTTCGACTCCGGCGAC
1 GAAGTCTGTTAACACCTCGTGTTCGACTCCGGCGAC
241898030 GAAGTCTGTTAACACCTCGTGTTCGACTCCGGCGAC
1 GAAGTCTGTTAACACCTCGTGTTCGACTCCGGCGAC
241898066 G
1 G
241898067 GTCTCGGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.25
Consensus pattern (36 bp):
GAAGTCTGTTAACACCTCGTGTTCGACTCCGGCGAC
Found at i:241904224 original size:28 final size:28
Alignment explanation
Indices: 241904151--241904224 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
241904141 GTTCAAATTG
* * *
241904151 TATAGCACTAAGTGTGCAAGTTTGATTA
1 TATAGCACTAAGTGTGCGAGTTCGACTA
241904179 TATAGCACTAAGTGTGCGAGTTCGACTA
1 TATAGCACTAAGTGTGCGAGTTCGACTA
241904207 T-TAAGCACTAAGTGTGCG
1 TAT-AGCACTAAGTGTGCG
241904225 GGCTTATTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 1 0.02
28 41 0.98
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (28 bp):
TATAGCACTAAGTGTGCGAGTTCGACTA
Found at i:241909804 original size:40 final size:39
Alignment explanation
Indices: 241909639--241909822 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
241909629 AAATTGAATG
* * *
241909639 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
241909679 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
241909719 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
241909759 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
241909798 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
241909823 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:241909847 original size:80 final size:81
Alignment explanation
Indices: 241909679--241909867 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
241909669 GCTGGAAATT
* * * *
241909679 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
241909744 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
241909760 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
241909823 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
241909839 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
241909868 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:241924248 original size:39 final size:39
Alignment explanation
Indices: 241924197--241924273 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
241924187 AAAAAAAAGT
241924197 GTCCCTCTTTCTTCATAGCTCTTGGCCGAATGTTCTAAA
1 GTCCCTCTTTCTTCATAGCTCTTGGCCGAATGTTCTAAA
241924236 GTCCCTCTTTCTTCATAGCTCTTGGCCGAATGTTCTAA
1 GTCCCTCTTTCTTCATAGCTCTTGGCCGAATGTTCTAA
241924274 GGAAGAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.39
Consensus pattern (39 bp):
GTCCCTCTTTCTTCATAGCTCTTGGCCGAATGTTCTAAA
Found at i:241925657 original size:40 final size:39
Alignment explanation
Indices: 241925604--241925783 Score: 224
Period size: 40 Copynumber: 4.6 Consensus size: 39
241925594 AATGATGTCC
* *
241925604 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-ATCCG
*
241925644 GACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-TCCG
241925684 GGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AATCCG
* *
241925722 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATCCG
*
241925762 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
241925784 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 8, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
38 24 0.19
39 23 0.19
40 69 0.56
41 8 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCCG
Found at i:241925744 original size:78 final size:80
Alignment explanation
Indices: 241925604--241925781 Score: 238
Period size: 78 Copynumber: 2.2 Consensus size: 80
241925594 AATGATGTCC
* *
241925604 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTGTGC
*
241925669 GAGTTACTA-ATTCCG
66 GAGTTACTATA-ACCG
* * **
241925684 GGCTAAG-CCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTG
1 GGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTG
241925746 CGAGTTACTATAACCG
65 CGAGTTACTATAACCG
*
241925762 GGCTATGTCCCGAAGGCATT
1 GGCTAAGTCCCGAAGGCATT
241925782 TGAACGAGTA
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
77 1 0.01
78 51 0.59
79 28 0.32
80 7 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTGTGC
GAGTTACTATAACCG
Done.