Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 49 of 438
Found at i:12313505 original size:76 final size:78
Alignment explanation
Indices: 12313379--12313601 Score: 308
Period size: 76 Copynumber: 2.8 Consensus size: 78
12313369 TTGATGATAC
* * * * *
12313379 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATATCCAGGGCTAAGACCCGAAGCATTT
1 CCGGGTTAAGACCCGAA-GCATTTGTGCGAGTTG-CTATATCC-GGGCTAAGACCCGAAGCATTT
12313443 GTGCGAGTTGCTATAT
63 GTGCGAGTTGCTATAT
12313459 CCGGGTTAAGACCC-AAGCATTTGTGCGAGTTG-TATATCCGGGCTAAGACCCGAAGCATTTGTG
1 CCGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGCATTTGTG
12313522 CGAGTTGCTATAT
66 CGAGTTGCTATAT
* * * *
12313535 CTGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGT
1 CCGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAA-GCATTTGT
12313600 GC
65 GC
12313602 TTGTGGTTAT
Statistics
Matches: 131, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
76 50 0.38
77 25 0.19
78 31 0.24
79 13 0.10
80 12 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (78 bp):
CCGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGCATTTGTG
CGAGTTGCTATAT
Found at i:12313545 original size:39 final size:39
Alignment explanation
Indices: 12313379--12313601 Score: 299
Period size: 39 Copynumber: 5.7 Consensus size: 39
12313369 TTGATGATAC
* * * * *
12313379 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGTTAAGACCCGAA-GCATTTGTGCGAGTTG-CTATAT
*
12313419 CCAGGGCTAAGACCCGAAGCATTTGTGCGAGTTGCTATAT
1 CC-GGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATAT
12313459 CCGGGTTAAGACCC-AAGCATTTGTGCGAGTTG-TATAT
1 CCGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATAT
*
12313496 CCGGGCTAAGACCCGAAGCATTTGTGCGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATAT
* *
12313535 CTGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATAC
1 CCGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATAT
*
12313574 CCGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGTTAAGACCCGAA-GCATTTGTGC
12313602 TTGTGGTTAT
Statistics
Matches: 167, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
37 18 0.11
38 36 0.22
39 68 0.41
40 29 0.17
41 16 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGTTAAGACCCGAAGCATTTGTGCGAGTTGCTATAT
Found at i:12313561 original size:115 final size:119
Alignment explanation
Indices: 12313379--12313601 Score: 330
Period size: 115 Copynumber: 1.9 Consensus size: 119
12313369 TTGATGATAC
* * *
12313379 CCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGATTATATCCAGGGCTAAGACCCGAAGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATATCCAGGGCTAAGACCCGAAGCATTTG
* *
12313444 TGCGAGTTGCTATATCCGGGTTAAGACCC-AA-GCATTTGTGCGAGTTGTATAT
66 TGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTTGTATAT
* * *
12313496 CCGGGCTAAGACCCGAA-GCATTTGTGCGAGTTG-CTATAT-CTGGGTTAAGACCCGAAGCATTT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATATCCAGGGCTAAGACCCGAAGCATTT
12313558 GTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
65 GTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
12313602 TTGTGGTTAT
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
115 50 0.53
116 18 0.19
117 27 0.28
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (119 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATATCCAGGGCTAAGACCCGAAGCATTTG
TGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTTGTATAT
Found at i:12319802 original size:40 final size:40
Alignment explanation
Indices: 12319747--12319974 Score: 314
Period size: 40 Copynumber: 5.7 Consensus size: 40
12319737 TGAATGATAC
* * * *
12319747 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
12319787 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * *
12319827 CCGGGTTAAGCCCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
12319867 CCGGGCTAAAACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * *
12319907 CTGGGTTAAGACCCGAAAGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
12319947 CCGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGCTAAGACCCGAAGGCATTTGTGC
12319975 TTGTGGTTAT
Statistics
Matches: 168, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 166 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:12319962 original size:120 final size:120
Alignment explanation
Indices: 12319747--12319995 Score: 349
Period size: 120 Copynumber: 2.1 Consensus size: 120
12319737 TGAATGATAC
** * * *
12319747 CCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAAACCCGAAGGCATTTATGCGAGTGACTATATCCGGGCTAAGACCCGAAAGCATTTG
* * * *
12319812 TGCGAGTTGCTATATCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGTTGTTATAT
66 TGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
* * *
12319867 CCGGGCTAAAACCCGAAGGCATTTGTGCGAGTTG-CTATATCTGGGTTAAGACCCGAAAGCATTT
1 CCGGGCTAAAACCCGAAGGCATTTATGCGAG-TGACTATATCCGGGCTAAGACCCGAAAGCATTT
**
12319931 GTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
65 GTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
12319987 CC-GGCTAAA
1 CCGGGCTAAA
12319996 TTCCGAAGAA
Statistics
Matches: 114, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
119 7 0.06
120 105 0.92
121 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
CCGGGCTAAAACCCGAAGGCATTTATGCGAGTGACTATATCCGGGCTAAGACCCGAAAGCATTTG
TGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
Found at i:12323219 original size:89 final size:89
Alignment explanation
Indices: 12323100--12323521 Score: 378
Period size: 89 Copynumber: 4.8 Consensus size: 89
12323090 ATTAACATGG
* * *
12323100 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAACATAGTGAATCTAATCTCCCTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACATAGCGAATCTTATCTCCCTGAAG
**
12323165 TTGCAGTAGAGCAGGTTGAAGTTA
66 TTGCAGTAGAGCAGGTTGAAGCCA
* ** *
12323189 CAAATCGTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACATAGTAAATCTAATCTCCCTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACATAGCGAATCTTATCTCCCTGAAG
* * *
12323254 TTGTAGTGGAGC-GGATT-AACACCA
66 TTGCAGTAGAGCAGG-TTGAA-GCCA
* * * ** * * * * *
12323278 CAAAACTTATCTTCCTAAAGTTGCAGTAAAGTAGGTTGAA-GTGGCGAATCTTATCTCCCTAAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACATAGCGAATCTTATCTCCCTGAAG
* * *
12323342 TTACAGTGGAGCAGATTGAAGCCA
66 TTGCAGTAGAGCAGGTTGAAGCCA
* * * * * * * *
12323366 CTAATCTTATCTCCCTAAAGTTAC-GATGGAGCAGATT-AAAACCA-CAAACCTTATCTCCTTGA
1 CAAATCTTATCTCCCTGAAGTTGCAG-TGGAGCAGATTGAACA-TAGCGAATCTTATCTCCCTGA
*
12323428 AGTTACAGTAGAGCAGGTTGAA---A
64 AGTTGCAGTAGAGCAGGTTGAAGCCA
* * * * * *
12323451 CAAATATCATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATA-CGAATCTTATTTCTCTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACATAGCGAATCTTATCTCCCTGAAG
12323515 TTGCAGT
66 TTGCAGT
12323522 GGAATAGATT
Statistics
Matches: 267, Mismatches: 57, Indels: 22
0.77 0.16 0.06
Matches are distributed among these distances:
85 52 0.19
86 4 0.01
87 3 0.01
88 98 0.37
89 110 0.41
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (89 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACATAGCGAATCTTATCTCCCTGAAG
TTGCAGTAGAGCAGGTTGAAGCCA
Found at i:12323221 original size:44 final size:44
Alignment explanation
Indices: 12323100--12323524 Score: 342
Period size: 44 Copynumber: 9.7 Consensus size: 44
12323090 ATTAACATGG
* *
12323100 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAACATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
** * * * *
12323144 GTGAATCTAATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* *
12323189 CAAATCGTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * * *
12323233 GTAAATCTAATCTCCCTGAAGTTGTAGTGGAGCGGATT-AACACCA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TA
* * * ** * * *
12323278 CAAAACTTATCTTCCTAAAGTTGCAGTAAAGTAGGTTGAAG-TGG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-A
* * * **
12323322 CGAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTGAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * * * *
12323366 CTAATCTTATCTCCCTAAAGTTAC-GATGGAGCAGATT-AAAACCA
1 CAAATCTTATCTCCCTGAAGTTGCAG-TGGAGCAGATTGAAGA-TA
* * * * *
12323410 CAAACCTTATCTCCTTGAAGTTACAGTAGAGCAGGTTG-A-A-A
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * *
12323451 CAAATATCATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
* * *
12323495 CGAATCTTATTTCTCTGAAGTTGCAGTGGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGA
12323525 ATAGATTGTA
Statistics
Matches: 300, Mismatches: 68, Indels: 25
0.76 0.17 0.06
Matches are distributed among these distances:
41 31 0.10
42 1 0.00
43 5 0.02
44 191 0.64
45 72 0.24
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
Found at i:12323343 original size:133 final size:131
Alignment explanation
Indices: 12323102--12323524 Score: 414
Period size: 133 Copynumber: 3.2 Consensus size: 131
12323092 TAACATGGCA
* * * * * * *
12323102 AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATT-GAA-CATAGTGAATCTAATCTCCCTGAAG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCACA---AAACTTATCTTCCTGAAG
*
12323165 TTGCAGTAGAGCAGGTTGAAGTTACAAATCGTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAC
63 TTGCAGTAGAGCAGGTTGAAG-TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAC
12323230 ATAGT
127 ATAGT
* * * *
12323235 AAATCTAATCTCCCTGAAGTTGTAGTGGAGCGGATTAACACCACAAAACTTATCTTCCTAAAGTT
1 -AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCACAAAACTTATCTTCCTGAAGTT
* * * * * *
12323300 GCAGTAAAGTAGGTTGAAGTGGCGAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTGAAGC-
65 GCAGTAGAGCAGGTTGAAGT-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-CA
* *
12323364 CACT
128 TAGT
* *
12323368 AATCTTATCTCCCTAAAG-T-TACGATGGAGCAGATTAAAACCACAAACCTTATC-TCCTTGAAG
1 AATCTTATCTCCCTGAAGTTGTA-G-TGGAGCAGATTAAAACCACAAAACTTATCTTCC-TGAAG
* * * * *
12323430 TTACAGTAGAGCAGGTTGAA--ACAAATATCATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGA
63 TTGCAGTAGAGCAGGTTGAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACA
12323493 TACG-
128 TA-GT
* * *
12323497 AATCTTATTTCTCTGAAGTTGCAGTGGA
1 AATCTTATCTCCCTGAAGTTGTAGTGGA
12323525 ATAGATTGTA
Statistics
Matches: 235, Mismatches: 43, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
129 54 0.23
130 4 0.02
131 6 0.03
132 64 0.27
133 71 0.30
134 32 0.14
135 1 0.00
136 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (131 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCACAAAACTTATCTTCCTGAAGTTG
CAGTAGAGCAGGTTGAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAACATAG
T
Found at i:12326168 original size:33 final size:33
Alignment explanation
Indices: 12326126--12326203 Score: 138
Period size: 33 Copynumber: 2.3 Consensus size: 33
12326116 ACAAAAACTA
12326126 CATATTCATTTAATATAATAATTTAGCATGAAC
1 CATATTCATTTAATATAATAATTTAGCATGAAC
12326159 CATATTCATTTAATATAATAATTTAGCATGAAC
1 CATATTCATTTAATATAATAATTTAGCATGAAC
*
12326192 CAATATTGATTT
1 C-ATATTCATTT
12326204 TTTCTTGGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 34 0.79
34 9 0.21
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (33 bp):
CATATTCATTTAATATAATAATTTAGCATGAAC
Found at i:12329220 original size:229 final size:229
Alignment explanation
Indices: 12328814--12329259 Score: 856
Period size: 229 Copynumber: 1.9 Consensus size: 229
12328804 ATAGTGTGGC
*
12328814 AGCCTAAATCCAAAAAAATAAGGAACCAAAAGTTGGTACATTAGGTATACGACTTATACATTATG
1 AGCCCAAATCCAAAAAAATAAGGAACCAAAAGTTGGTACATTAGGTATACGACTTATACATTATG
12328879 TAGCATCATTCAAAATAGAGGAATTCATAGCCCAAGACATGCGTAAATGATATCTTCTCATTGGC
66 TAGCATCATTCAAAATAGAGGAATTCATAGCCCAAGACATGCGTAAATGATATCTTCTCATTGGC
*
12328944 ATTACATGATAGATGAAAAGTAAACGTGGTCACGAGTTGTTTTTCTTTTTGATAAATGACTTAAT
131 ATTACATGATAGATGAAAAGTAAACGTGGTCACGAGATGTTTTTCTTTTTGATAAATGACTTAAT
12329009 TACTATATGATAGTAATTGACTGATGTAAGTAAA
196 TACTATATGATAGTAATTGACTGATGTAAGTAAA
*
12329043 AGCCCAAATCCAAATAAATAAGGAACCAAAAGTTGGTACATTAGGTATACGACTTATACATTATG
1 AGCCCAAATCCAAAAAAATAAGGAACCAAAAGTTGGTACATTAGGTATACGACTTATACATTATG
*
12329108 TAGCATCATTCACAATAGAGGAATTCATAGCCCAAGACATGCGTAAATGATATCTTCTCATTGGC
66 TAGCATCATTCAAAATAGAGGAATTCATAGCCCAAGACATGCGTAAATGATATCTTCTCATTGGC
12329173 ATTACATGATAGATGAAAAGTAAACGTGGTCACGAGATGTTTTTCTTTTTGATAAATGACTTAAT
131 ATTACATGATAGATGAAAAGTAAACGTGGTCACGAGATGTTTTTCTTTTTGATAAATGACTTAAT
12329238 TACTATATGATAGTAATTGACT
196 TACTATATGATAGTAATTGACT
12329260 TTTCATGAAG
Statistics
Matches: 213, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
229 213 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (229 bp):
AGCCCAAATCCAAAAAAATAAGGAACCAAAAGTTGGTACATTAGGTATACGACTTATACATTATG
TAGCATCATTCAAAATAGAGGAATTCATAGCCCAAGACATGCGTAAATGATATCTTCTCATTGGC
ATTACATGATAGATGAAAAGTAAACGTGGTCACGAGATGTTTTTCTTTTTGATAAATGACTTAAT
TACTATATGATAGTAATTGACTGATGTAAGTAAA
Found at i:12329610 original size:10 final size:10
Alignment explanation
Indices: 12329595--12329620 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12329585 ATATTGAATC
12329595 AAATGAATAG
1 AAATGAATAG
12329605 AAATGAATAG
1 AAATGAATAG
12329615 AAATGA
1 AAATGA
12329621 TAAAGTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (10 bp):
AAATGAATAG
Found at i:12341239 original size:46 final size:46
Alignment explanation
Indices: 12341186--12341443 Score: 232
Period size: 46 Copynumber: 5.5 Consensus size: 46
12341176 ATTGTTGGCT
*
12341186 AGTGTAAGA-CATGTCTGGGACATGCATCAGCCACATTATGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCAG-CACATTACGATAGCC
* *
12341232 AGTGTAAGACCATGTCTGGGACATGGCATCAG--CATTGAGACGAAAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCAGCACATT---ACGATAGCC
* *
12341280 AGTGTAAGA-CATGTCTGGGACATGCATCAGCCTCGA-GACG-TAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCAG-CAC-ATTACGAT-AGCC
** * *
12341326 AGTGTAAGA-CATGTCTGGGACATGCATCAGCTACAAGATGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCAGC-ACATTACGATAGCC
12341372 AGTGTAAGACCATGTCTGGGACATGGCATC-G-AC-TTGA-GATATGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCAGCACATT-ACG--AT-AGCC
12341419 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
12341444 GTATCTGCAC
Statistics
Matches: 181, Mismatches: 12, Indels: 38
0.78 0.05 0.16
Matches are distributed among these distances:
44 1 0.01
45 9 0.05
46 71 0.39
47 71 0.39
48 27 0.15
49 1 0.01
50 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCAGCACATTACGATAGCC
Found at i:12341438 original size:140 final size:140
Alignment explanation
Indices: 12341186--12341443 Score: 405
Period size: 140 Copynumber: 1.8 Consensus size: 140
12341176 ATTGTTGGCT
**
12341186 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGATAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGATAGCCAGTGTAAGACCATGTCTGG
*
12341251 GACATGGCATCAGCATTGAGACGAAAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA
66 GACATGGCATCAGCATTGAGACGAAAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA
12341316 GACGTAAGCC
131 GACGTAAGCC
* *
12341326 AGTGTAAGACATGTCTGGGACATGCATCAGCTACAAGATGATAGTCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGATAGCCAGTGTAAGACCATGTCTGG
* *
12341391 GACATGGCATC-G-ACTTGAGA-TATGAGCCAGTGTAAGACCATGTCTGGGACATG
66 GACATGGCATCAGCA-TTGAGACGA-AAGCCAGTGTAAGA-CATGTCTGGGACATG
12341444 GTATCTGCAC
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
138 2 0.02
139 19 0.18
140 87 0.81
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGATAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCAGCATTGAGACGAAAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA
GACGTAAGCC
Found at i:12341444 original size:47 final size:47
Alignment explanation
Indices: 12341186--12341444 Score: 270
Period size: 47 Copynumber: 5.6 Consensus size: 47
12341176 ATTGTTGGCT
*
12341186 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGC-C-ACATTATGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCTCGAGA-TAT-A-AGCC
* * *
12341232 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGACGA-AAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGC-TCGAGA-TATAAGCC
**
12341280 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGACGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CTCGAGATATAAGCC
* *
12341326 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTACAAGATGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCT-CGAGAT-ATAAGCC
* *
12341372 AGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGATATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CTCGAGATATAAGCC
12341419 AGTGTAAGACCATGTCTGGGACATGG
1 AGTGTAAGACCATGTCTGGGACATGG
12341445 TATCTGCACT
Statistics
Matches: 184, Mismatches: 16, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
45 2 0.01
46 73 0.40
47 78 0.42
48 27 0.15
49 1 0.01
51 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCTCGAGATATAAGCC
Found at i:12342583 original size:20 final size:21
Alignment explanation
Indices: 12342545--12342583 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12342535 TTGAGTTGGT
12342545 CACAAGGGCGTGTTGCCCTTC
1 CACAAGGGCGTGTTGCCCTTC
*
12342566 CACACGGGCGTG-TGCCCT
1 CACAAGGGCGTGTTGCCCT
12342584 GTTTTAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.36, G:0.31, T:0.21
Consensus pattern (21 bp):
CACAAGGGCGTGTTGCCCTTC
Found at i:12348345 original size:24 final size:24
Alignment explanation
Indices: 12348300--12348346 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12348290 TTTCTCAAAA
* *
12348300 TTTTAAATATATTTTTTTATAAAC
1 TTTTAAATATATTATTTGATAAAC
12348324 TTTTAAATA-ATCTATTTGATAAA
1 TTTTAAATATAT-TATTTGATAAA
12348347 ATTGAACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTAAATATATTATTTGATAAAC
Found at i:12363348 original size:2 final size:2
Alignment explanation
Indices: 12363341--12363365 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12363331 AATCATCTAC
12363341 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12363366 GGCTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12364698 original size:24 final size:26
Alignment explanation
Indices: 12364656--12364710 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
12364646 GTATCCTTTC
* *
12364656 TTTTCTTTTCTGAATTTTTCGTTCTT
1 TTTTATTTTCTGAATTTTTCGCTCTT
*
12364682 TTTTATTTT-TGAA-TTTTCGCTGTT
1 TTTTATTTTCTGAATTTTTCGCTCTT
12364706 TTTTA
1 TTTTA
12364711 ACTTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 14 0.54
25 4 0.15
26 8 0.31
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (26 bp):
TTTTATTTTCTGAATTTTTCGCTCTT
Found at i:12364723 original size:25 final size:25
Alignment explanation
Indices: 12364668--12364723 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
12364658 TTCTTTTCTG
* ** *
12364668 AATTTTTCGTTCTTTTTTATTTTTG
1 AATTTTTCGCTCTTTTTTAACTTTA
*
12364693 AA-TTTTCGCTGTTTTTTAACTTTA
1 AATTTTTCGCTCTTTTTTAACTTTA
12364717 AATTTTT
1 AATTTTT
12364724 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.66
Consensus pattern (25 bp):
AATTTTTCGCTCTTTTTTAACTTTA
Found at i:12374060 original size:20 final size:20
Alignment explanation
Indices: 12374037--12374088 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
12374027 CACCATTGCT
*
12374037 AAGCACGCCAAACCACCGCC
1 AAGCACGCCAAACCACCGAC
**
12374057 AAGCATACCAAACCACCGAC
1 AAGCACGCCAAACCACCGAC
* *
12374077 GAGCACGTCAAA
1 AAGCACGCCAAA
12374089 TTTAACTATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.40, G:0.15, T:0.04
Consensus pattern (20 bp):
AAGCACGCCAAACCACCGAC
Found at i:12388408 original size:10 final size:10
Alignment explanation
Indices: 12388381--12388423 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
12388371 TTAAATTCTA
*
12388381 AAAGATAAAT
1 AAAGATAATT
12388391 ACAA-ATAATT
1 A-AAGATAATT
12388401 AAAGATAATT
1 AAAGATAATT
12388411 AAAGATAATT
1 AAAGATAATT
12388421 AAA
1 AAA
12388424 AATGAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.87
11 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (10 bp):
AAAGATAATT
Found at i:12390393 original size:3 final size:3
Alignment explanation
Indices: 12390375--12390442 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
12390365 GCATCCAAAA
* * *
12390375 AAT AA- AAT AAT AAAT AAT AA- AAT AAA AAT AAA AAGA AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
12390420 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
12390443 ATAAAAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 47 0.82
4 6 0.11
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:12390404 original size:6 final size:6
Alignment explanation
Indices: 12390372--12390457 Score: 68
Period size: 6 Copynumber: 14.0 Consensus size: 6
12390362 TTAGCATCCA
* *
12390372 AAAAAT -AAAAT AATAAAT AATAAAAT AAAAAT AAAAAG AAATAAT AATAAT
1 AAAAAT AAAAAT AA-AAAT -A-AAAAT AAAAAT AAAAAT AAA-AAT AAAAAT
* * * *
12390423 AATAAT AATAAT AATAAT AAATA- AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
12390458 TGGGTTGCCT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
5 9 0.13
6 44 0.65
7 9 0.13
8 5 0.07
9 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:12397266 original size:14 final size:16
Alignment explanation
Indices: 12397230--12397262 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12397220 TCTCATAGCT
12397230 AAAGAGAGACTCCAAA
1 AAAGAGAGACTCCAAA
*
12397246 AAAGAGAGACTCTAAA
1 AAAGAGAGACTCCAAA
12397262 A
1 A
12397263 GAGAAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.15, G:0.18, T:0.09
Consensus pattern (16 bp):
AAAGAGAGACTCCAAA
Found at i:12398294 original size:13 final size:13
Alignment explanation
Indices: 12398276--12398301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12398266 CCTAAACATA
12398276 ATTTTTCGAAAAT
1 ATTTTTCGAAAAT
12398289 ATTTTTCGAAAAT
1 ATTTTTCGAAAAT
12398302 CACAAGTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTTTTCGAAAAT
Found at i:12399333 original size:24 final size:22
Alignment explanation
Indices: 12399289--12399334 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
12399279 AGGTAGCAAA
*
12399289 TAAAAAAAATTCAAGTACTAAT
1 TAAAAAAAATTCAAATACTAAT
*
12399311 TAAAAAAAAGTGTCAAATTCTAAT
1 TAAAAAAAA-T-TCAAATACTAAT
12399335 GCTAATAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.28
Consensus pattern (22 bp):
TAAAAAAAATTCAAATACTAAT
Found at i:12400061 original size:29 final size:29
Alignment explanation
Indices: 12400028--12400083 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
12400018 AAAAAAGGAA
12400028 AACATAATTTCTCTTTTTAAATGTTGAGC
1 AACATAATTTCTCTTTTTAAATGTTGAGC
12400057 AACATAATTTCTCTTTTTAAATGTTGA
1 AACATAATTTCTCTTTTTAAATGTTGA
12400084 ACATGCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.46
Consensus pattern (29 bp):
AACATAATTTCTCTTTTTAAATGTTGAGC
Found at i:12406412 original size:2 final size:2
Alignment explanation
Indices: 12406400--12406447 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
12406390 ATCTTCAAAT
*
12406400 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12406442 TA TA TA
1 TA TA TA
12406448 AACCCACATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12407891 original size:30 final size:30
Alignment explanation
Indices: 12407857--12407918 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
12407847 ACTTATTTTA
12407857 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
12407887 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
12407917 TT
1 TT
12407919 ACTTGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:12424716 original size:12 final size:12
Alignment explanation
Indices: 12424689--12424727 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
12424679 ATGCAAATGA
12424689 AATAATTTAA-T
1 AATAATTTAATT
12424700 AATAATTTAATT
1 AATAATTTAATT
12424712 AATAATATT-ATT
1 AATAAT-TTAATT
12424724 AATA
1 AATA
12424728 TAACAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.38
12 14 0.54
13 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATAATTTAATT
Found at i:12428819 original size:76 final size:76
Alignment explanation
Indices: 12428663--12428803 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 76
12428653 GAATGTCCGG
* * * *
12428663 AGTAAGTAGATTGTGCCCAACGCTCATCAGTTTAACCGAAGTAGTAATTGTGTCCAACACTCATC
1 AGTAAGTAGATTGCGCCCAACACTCATCAGTTTAACCGAAGTAATAATTGTGCCCAACACTCATC
12428728 GAAATGTCTAA
66 GAAATGTCTAA
* * ** ** *
12428739 AGTAAGTAGATTGCGCGCAACACTTATTGGTTTAATTGAAGTAATAATTGTGCCCAGCA-TCATC
1 AGTAAGTAGATTGCGCCCAACACTCATCAGTTTAACCGAAGTAATAATTGTGCCCAACACTCATC
12428803 G
66 G
12428804 CATATGGTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
75 6 0.11
76 48 0.89
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (76 bp):
AGTAAGTAGATTGCGCCCAACACTCATCAGTTTAACCGAAGTAATAATTGTGCCCAACACTCATC
GAAATGTCTAA
Found at i:12430513 original size:41 final size:42
Alignment explanation
Indices: 12430444--12430522 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
12430434 GTGTCTTCAC
12430444 CCGTGTAACTCACTGAGATGCCCCACACG-CTCATGTGTTGAG
1 CCGTGTAACTCACTGAGATGCCCCACACGCCT-ATGTGTTGAG
* * *
12430486 CCGTGTAACTTA-TGAGTTGCCCTACACGCCTATGTGT
1 CCGTGTAACTCACTGAGATGCCCCACACGCCTATGTGT
12430523 CAGGCCGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 20 0.61
42 13 0.39
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (42 bp):
CCGTGTAACTCACTGAGATGCCCCACACGCCTATGTGTTGAG
Found at i:12430530 original size:41 final size:42
Alignment explanation
Indices: 12430444--12430532 Score: 103
Period size: 41 Copynumber: 2.1 Consensus size: 42
12430434 GTGTCTTCAC
*
12430444 CCGTGTAACTCACTGAGATGCCCCACACGCTCATGTGTTGAG
1 CCGTGTAACTCACTGAGATGCCCCACACGCTCATGTGTAGAG
* * *
12430486 CCGTGTAACTTA-TGAGTTGCCCTACACGC-CTATGTGTCAG-G
1 CCGTGTAACTCACTGAGATGCCCCACACGCTC-ATGTGT-AGAG
12430527 CCGTGT
1 CCGTGT
12430533 GCTTGGCAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 1 0.02
41 28 0.68
42 12 0.29
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.27
Consensus pattern (42 bp):
CCGTGTAACTCACTGAGATGCCCCACACGCTCATGTGTAGAG
Found at i:12431304 original size:40 final size:40
Alignment explanation
Indices: 12431246--12431424 Score: 193
Period size: 40 Copynumber: 4.5 Consensus size: 40
12431236 TTAGGATTAC
* *
12431246 CAAAGTACCAACAGGGGCACGTATGTGCATTCAGTGG-TAT
1 CAAAGTACAAATAGGGGCACGTATGTGCATTCAG-GGATAT
* *
12431286 CAAAGTACAAATAAGGGCACGTATGTGCATTCAGAGG-TAC
1 CAAAGTACAAATAGGGGCACGTATGTGCATTCAG-GGATAT
* * *
12431326 CGAAGTACAAATAGGGGCACTTATGT-TATTCAGGGATAT
1 CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGGATAT
** * * * *
12431365 TGAAGTACAAGTAAGGGCACATATGTGCATTTAGGGATAT
1 CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGGATAT
*
12431405 CAAAGTACAAACAGGGGCAC
1 CAAAGTACAAATAGGGGCAC
12431425 ACATGTACAT
Statistics
Matches: 116, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
38 2 0.02
39 30 0.26
40 84 0.72
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (40 bp):
CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGGATAT
Found at i:12431380 original size:79 final size:80
Alignment explanation
Indices: 12431243--12431424 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
12431233 GATTTAGGAT
* *
12431243 TACCAAAGTACCAACAGGGGCACGTATGTGCATTCAGTGGTATCAAAGTACAAATAAGGGCACGT
1 TACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGTGGTATCAAAGTACAAATAAGGGCACAT
12431308 ATGTGCATTCAGAGG-
66 ATGTGCATTCAG-GGA
* * * * ** *
12431323 TACCGAAGTACAAATAGGGGCACTTATGT-TATTCAG-GGATATTGAAGTACAAGTAAGGGCACA
1 TACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGTGG-TATCAAAGTACAAATAAGGGCACA
*
12431386 TATGTGCATTTAGGGA
65 TATGTGCATTCAGGGA
*
12431402 TATCAAAGTACAAACAGGGGCAC
1 TACCAAAGTACAAACAGGGGCAC
12431425 ACATGTACAT
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 4 0.05
79 58 0.67
80 25 0.29
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (80 bp):
TACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGTGGTATCAAAGTACAAATAAGGGCACAT
ATGTGCATTCAGGGA
Found at i:12433586 original size:25 final size:25
Alignment explanation
Indices: 12433557--12433608 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
12433547 AAAGTTGTGG
12433557 TTCCTAAAATAGGATTGATTGTGAT
1 TTCCTAAAATAGGATTGATTGTGAT
*
12433582 TTCCTAAAATATGATTGATTGTGAT
1 TTCCTAAAATAGGATTGATTGTGAT
12433607 TT
1 TT
12433609 AGGCTAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (25 bp):
TTCCTAAAATAGGATTGATTGTGAT
Found at i:12443613 original size:3 final size:3
Alignment explanation
Indices: 12443583--12443672 Score: 119
Period size: 3 Copynumber: 28.7 Consensus size: 3
12443573 GTACTATTCG
*
12443583 TAA TAA -AA TATA TAAA TAAA TGA TAA TAA TAA TAGA TAAA TAA TAA
1 TAA TAA TAA TA-A T-AA T-AA TAA TAA TAA TAA TA-A T-AA TAA TAA
12443629 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12443673 TATGTACAAG
Statistics
Matches: 80, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
2 2 0.03
3 64 0.80
4 12 0.15
5 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12443766 original size:11 final size:11
Alignment explanation
Indices: 12443747--12443807 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
12443737 ATGGATGAAT
*
12443747 AAATAATAATA
1 AAATGATAATA
12443758 AAATGATAATA
1 AAATGATAATA
*
12443769 AAA-GACAATA
1 AAATGATAATA
*
12443779 AAATAATAATA
1 AAATGATAATA
12443790 ATAATTGTATAATA
1 A-AA-TG-ATAATA
12443804 AAAT
1 AAAT
12443808 AAATAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
10 9 0.22
11 19 0.46
12 3 0.07
13 3 0.07
14 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (11 bp):
AAATGATAATA
Found at i:12443770 original size:21 final size:21
Alignment explanation
Indices: 12443735--12443794 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
12443725 GGTAATACAC
12443735 AAATGGATGAATAAATAATAATA
1 AAAT-GAT-AATAAATAATAATA
*
12443758 AAATGATAATAAA-AGACAATA
1 AAATGATAATAAATA-ATAATA
*
12443779 AAATAATAAT-AATAAT
1 AAATGATAATAAATAAT
12443795 TGTATAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 4 0.12
21 21 0.66
22 3 0.09
23 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (21 bp):
AAATGATAATAAATAATAATA
Found at i:12444654 original size:20 final size:20
Alignment explanation
Indices: 12444618--12444659 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12444608 ATAAGTATAT
* *
12444618 ATATGCTATGTTGAAAATAA
1 ATATGCAATGTTGAAAAAAA
12444638 ATATGCAATG-TGTAAAAAAA
1 ATATGCAATGTTG-AAAAAAA
12444658 AT
1 AT
12444660 GAAAATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (20 bp):
ATATGCAATGTTGAAAAAAA
Found at i:12445838 original size:24 final size:25
Alignment explanation
Indices: 12445774--12445828 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
12445764 TAATTTATTT
12445774 TTATTTAAA-ATAAATAAATTAATA
1 TTATTTAAATATAAATAAATTAATA
*
12445798 TTATTTAAATATAAATAGATTAA-A
1 TTATTTAAATATAAATAAATTAATA
12445822 TTATTTA
1 TTATTTA
12445829 TTTGTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TTATTTAAATATAAATAAATTAATA
Found at i:12446468 original size:16 final size:16
Alignment explanation
Indices: 12446447--12446478 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12446437 GAAAGCTAGA
12446447 AAAAAATTTAGGAGGG
1 AAAAAATTTAGGAGGG
12446463 AAAAAATTTAGGAGGG
1 AAAAAATTTAGGAGGG
12446479 TCGGATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (16 bp):
AAAAAATTTAGGAGGG
Found at i:12446682 original size:2 final size:2
Alignment explanation
Indices: 12446675--12446700 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12446665 GCTTCACCCC
12446675 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
12446701 AACTATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12446727 original size:24 final size:24
Alignment explanation
Indices: 12446700--12446759 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
12446690 ATATATATAT
*
12446700 AAACTATTCATATTTTTTTGAGAA
1 AAACTATTCATATATTTTTGAGAA
*
12446724 AAACTATT-AAATATTTTTGAGAA
1 AAACTATTCATATATTTTTGAGAA
*
12446747 AAATTTATTCATA
1 AAA-CTATTCATA
12446760 CTTAAGAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 16 0.53
24 12 0.40
25 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (24 bp):
AAACTATTCATATATTTTTGAGAA
Found at i:12466868 original size:23 final size:22
Alignment explanation
Indices: 12466832--12466876 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
12466822 ATTTGATAAT
12466832 ATGTTTTGATATAACAAATTAAA
1 ATGTTTTGATATAA-AAATTAAA
*
12466855 ATGTTTTGGA-ATAAAAGTTAAA
1 ATGTTTT-GATATAAAAATTAAA
12466877 GTTGAACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 11 0.55
24 2 0.10
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (22 bp):
ATGTTTTGATATAAAAATTAAA
Found at i:12470201 original size:44 final size:43
Alignment explanation
Indices: 12470153--12470253 Score: 118
Period size: 41 Copynumber: 2.4 Consensus size: 43
12470143 AGAACAATTC
* *
12470153 CGCACACTTAGTGCCATCTCA-ATTAGTCGAAGCTAAGTCGATAT
1 CGCACACTTAGTGCCA-CTCATA-TAGCCGAAGCTAAGTCGAAAT
* **
12470197 CGCACACTTAGTG-C-CTCATATAGCCGAAGCTAGGTTTAAAT
1 CGCACACTTAGTGCCACTCATATAGCCGAAGCTAAGTCGAAAT
12470238 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
12470254 AATACTATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
41 33 0.67
42 2 0.04
43 1 0.02
44 13 0.27
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (43 bp):
CGCACACTTAGTGCCACTCATATAGCCGAAGCTAAGTCGAAAT
Found at i:12472782 original size:22 final size:22
Alignment explanation
Indices: 12472742--12472783 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12472732 AATCAATTAC
*
12472742 AAAAAGTATCAATATCTTTTCA
1 AAAAAGTATCAATACCTTTTCA
**
12472764 AAAAAGTATGGATACCTTTT
1 AAAAAGTATCAATACCTTTT
12472784 ACTAGGTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (22 bp):
AAAAAGTATCAATACCTTTTCA
Found at i:12476574 original size:29 final size:27
Alignment explanation
Indices: 12476536--12476614 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 27
12476526 TTTAAATTTA
*
12476536 TTAATATTATAATATAGAGAATATAAAAAC
1 TTAA-ATTATAATA-AAAGAAT-TAAAAAC
* *
12476566 TTAAATTATAATAAAAGTATTATAAAC
1 TTAAATTATAATAAAAGAATTAAAAAC
*
12476593 TTAAATTATAATAAAAGTATTA
1 TTAAATTATAATAAAAGAATTA
12476615 TAAATAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 28 0.61
28 5 0.11
29 9 0.20
30 4 0.09
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (27 bp):
TTAAATTATAATAAAAGAATTAAAAAC
Found at i:12476600 original size:27 final size:27
Alignment explanation
Indices: 12476562--12476618 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
12476552 GAGAATATAA
12476562 AAACTTAAATTATAATAAAAGTATTAT
1 AAACTTAAATTATAATAAAAGTATTAT
12476589 AAACTTAAATTATAATAAAAGTATTAT
1 AAACTTAAATTATAATAAAAGTATTAT
12476616 AAA
1 AAA
12476619 TAATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (27 bp):
AAACTTAAATTATAATAAAAGTATTAT
Found at i:12482863 original size:19 final size:21
Alignment explanation
Indices: 12482839--12482889 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
12482829 TAAGAAAAGC
12482839 ATTTAAAATTATA-T-AAAAT
1 ATTTAAAATTATATTAAAAAT
12482858 ATTTAAAATT-TATTAAAAAT
1 ATTTAAAATTATATTAAAAAT
**
12482878 ATAGAAAATTAT
1 ATTTAAAATTAT
12482890 CAAAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 13 0.48
21 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTAAAATTATATTAAAAAT
Found at i:12482894 original size:19 final size:19
Alignment explanation
Indices: 12482843--12482923 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 19
12482833 AAAAGCATTT
*
12482843 AAAATTAT-ATAAAATATTTA
1 AAAATTATCA-AAAATA-TAA
* * *
12482863 AAATTTATTAAAAATATAG
1 AAAATTATCAAAAATATAA
12482882 AAAATTATC-AAAATCA-AA
1 AAAATTATCAAAAAT-ATAA
12482900 AAAATTA-CAAAAATTATAA
1 AAAATTATCAAAAA-TATAA
12482919 AAAAT
1 AAAAT
12482924 CTTAAATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 1 0.02
18 18 0.36
19 17 0.34
20 13 0.26
21 1 0.02
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAATTATCAAAAATATAA
Found at i:12483036 original size:16 final size:16
Alignment explanation
Indices: 12483015--12483046 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12483005 TATAATTTTT
12483015 TATAAAATTGTAAAAA
1 TATAAAATTGTAAAAA
12483031 TATAAAATTGTAAAAA
1 TATAAAATTGTAAAAA
12483047 GTATTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
TATAAAATTGTAAAAA
Found at i:12483059 original size:55 final size:57
Alignment explanation
Indices: 12482951--12483064 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 57
12482941 AGTTTGTAAT
*
12482951 ATTTTTTATAGAAATGGTAAAAAAATTATAAAATATATAATAATATAGAAAAATTATA
1 ATTTTTTATAGAAATGGT-AAAAAATTATAAAATATATAAAAATATAGAAAAATTATA
* * *
12483009 ATTTTTTATA-AAATTGT-AAAAA-TATAAAAT-TGTAAAAAGTATTATAAAAATTATA
1 ATTTTTTATAGAAATGGTAAAAAATTATAAAATATATAAAAA-TA-TAGAAAAATTATA
12483064 A
1 A
12483065 AATCAAGTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
53 6 0.12
54 10 0.20
55 18 0.36
57 6 0.12
58 10 0.20
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (57 bp):
ATTTTTTATAGAAATGGTAAAAAATTATAAAATATATAAAAATATAGAAAAATTATA
Found at i:12483175 original size:4 final size:4
Alignment explanation
Indices: 12483166--12483215 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
12483156 TGGGGAGTAT
12483166 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
12483214 TA
1 TA
12483216 TTCACTATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:12483621 original size:10 final size:10
Alignment explanation
Indices: 12483590--12483654 Score: 73
Period size: 9 Copynumber: 6.7 Consensus size: 10
12483580 TTCCTATATA
12483590 TTTTATAAA-
1 TTTTATAAAT
*
12483599 TTTTAT-GAT
1 TTTTATAAAT
12483608 TTTTATAAAT
1 TTTTATAAAT
12483618 TTTTAT-AAT
1 TTTTATAAAT
*
12483627 TTTTATAAAA
1 TTTTATAAAT
*
12483637 TTTTACAAAT
1 TTTTATAAAT
12483647 TCTTTATA
1 T-TTTATA
12483655 TATTATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
8 1 0.02
9 21 0.46
10 19 0.41
11 5 0.11
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:12483623 original size:19 final size:18
Alignment explanation
Indices: 12483590--12483641 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 18
12483580 TTCCTATATA
*
12483590 TTTTATAAATTTTATGAT
1 TTTTATAAATTTTATAAT
12483608 TTTTATAAATTTTTATAAT
1 TTTTATAAA-TTTTATAAT
12483627 TTTTATAAAATTTTA
1 TTTTAT-AAATTTTA
12483642 CAAATTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 9 0.29
19 19 0.61
20 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATAAATTTTATAAT
Found at i:12485734 original size:14 final size:14
Alignment explanation
Indices: 12485699--12485741 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
12485689 TTAATATTAA
*
12485699 ATAAGTAATAAATG
1 ATAAATAATAAATG
*
12485713 TAATAAATGATAAATG
1 --ATAAATAATAAATG
12485729 ATAAATAATAAAT
1 ATAAATAATAAAT
12485742 AAAAGTAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (14 bp):
ATAAATAATAAATG
Found at i:12492536 original size:27 final size:27
Alignment explanation
Indices: 12492506--12492557 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
12492496 TTCTCTCATC
12492506 TAATCTCTTCTTAGATCTCGTATTCCG
1 TAATCTCTTCTTAGATCTCGTATTCCG
12492533 TAATCTCTTCTTAGATCTCGTATTC
1 TAATCTCTTCTTAGATCTCGTATTC
12492558 AGATCTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (27 bp):
TAATCTCTTCTTAGATCTCGTATTCCG
Found at i:12492945 original size:5 final size:5
Alignment explanation
Indices: 12492932--12492962 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
12492922 AAGTGATCAT
*
12492932 GGGCT GGGCC GGGCC GGGCC GGGCC GGGCC G
1 GGGCC GGGCC GGGCC GGGCC GGGCC GGGCC G
12492963 AGTTCGGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.35, G:0.61, T:0.03
Consensus pattern (5 bp):
GGGCC
Found at i:12502340 original size:30 final size:31
Alignment explanation
Indices: 12502295--12502353 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
12502285 CAACGATTCA
* *
12502295 ACTCTTTTTTGAAAGG-ATGATGTCAAATTAG
1 ACTCTTTTTTAAAAGGTA-GAGGTCAAATTAG
12502326 ACTC-TTTTTAAAAGGTAGAGGTCAAATT
1 ACTCTTTTTTAAAAGGTAGAGGTCAAATT
12502354 TAACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (31 bp):
ACTCTTTTTTAAAAGGTAGAGGTCAAATTAG
Found at i:12509462 original size:14 final size:14
Alignment explanation
Indices: 12509443--12509474 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
12509433 ATACCAATAA
12509443 TTTGATCACTTGAT
1 TTTGATCACTTGAT
12509457 TTTGATCACTTGAT
1 TTTGATCACTTGAT
12509471 TTTG
1 TTTG
12509475 GCATTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.53
Consensus pattern (14 bp):
TTTGATCACTTGAT
Found at i:12512862 original size:20 final size:20
Alignment explanation
Indices: 12512837--12512897 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 20
12512827 TTGACTTATT
12512837 TTGAAACATTTTTAACTTGA
1 TTGAAACATTTTTAACTTGA
* **
12512857 TTGAAA-ATCTTTAACTCAA
1 TTGAAACATTTTTAACTTGA
12512876 TTGAAATCA-TTTTAACTTGA
1 TTGAAA-CATTTTTAACTTGA
12512896 TT
1 TT
12512898 TTATCATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 16 0.48
20 16 0.48
21 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (20 bp):
TTGAAACATTTTTAACTTGA
Found at i:12512871 original size:19 final size:19
Alignment explanation
Indices: 12512837--12512897 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
12512827 TTGACTTATT
*
12512837 TTGAAACATTTTTAACTTGA
1 TTGAAA-ATCTTTAACTTGA
**
12512857 TTGAAAATCTTTAACTCAA
1 TTGAAAATCTTTAACTTGA
12512876 TTG-AAATCATTTTAACTTGA
1 TTGAAAATC--TTTAACTTGA
12512896 TT
1 TT
12512898 TTATCATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 16 0.47
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (19 bp):
TTGAAAATCTTTAACTTGA
Found at i:12522871 original size:20 final size:20
Alignment explanation
Indices: 12522846--12522885 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12522836 TTAAAATCTC
*
12522846 TTTTTATATATATATATATT
1 TTTTTATAAATATATATATT
*
12522866 TTTTTATAAATATATTTATT
1 TTTTTATAAATATATATATT
12522886 GTATAAGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTATAAATATATATATT
Found at i:12522873 original size:18 final size:18
Alignment explanation
Indices: 12522846--12522880 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12522836 TTAAAATCTC
*
12522846 TTTTTATATATATATATA
1 TTTTTATATAAATATATA
*
12522864 TTTTTTTATAAATATAT
1 TTTTTATATAAATATAT
12522881 TTATTGTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTATATAAATATATA
Found at i:12525970 original size:27 final size:28
Alignment explanation
Indices: 12525933--12525985 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
12525923 GAACTCGAAT
*
12525933 TTGAATCTTGAACTCC-AAACCTTGAAAC
1 TTGAATCTTGAAC-CCTAAACATTGAAAC
12525961 TTGAA-CTTGAACCCTAAACATTGAA
1 TTGAATCTTGAACCCTAAACATTGAA
12525986 CTCAAATCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.09
27 16 0.70
28 5 0.22
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (28 bp):
TTGAATCTTGAACCCTAAACATTGAAAC
Found at i:12531876 original size:31 final size:31
Alignment explanation
Indices: 12531786--12531877 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
12531776 AATAATTTTA
* *
12531786 AGGGGAGGAGAGATTTTGTCAAGCAGCACCT
1 AGGGGAGGAGAGCTTTTGTCAAGCGGCACCT
* *
12531817 AAGGGAGGAGGGCTTTTGTCATA-CGGCACCT
1 AGGGGAGGAGAGCTTTTGTCA-AGCGGCACCT
** *
12531848 AGGGGAGGAGAGCCGTTGTCAAGTGGCACC
1 AGGGGAGGAGAGCTTTTGTCAAGCGGCACC
12531878 ACTGCTAGTA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
30 1 0.02
31 48 0.96
32 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.18
Consensus pattern (31 bp):
AGGGGAGGAGAGCTTTTGTCAAGCGGCACCT
Found at i:12532161 original size:52 final size:53
Alignment explanation
Indices: 12532082--12532188 Score: 207
Period size: 52 Copynumber: 2.0 Consensus size: 53
12532072 GTTAGGAAAG
12532082 AAAGGAAATTGTTGTGTTTTTTTTAATATTATTTACTTGTTTGTTATTTACTT
1 AAAGGAAATTGTTGTGTTTTTTTTAATATTATTTACTTGTTTGTTATTTACTT
12532135 AAAGGAAATTGTTGTG-TTTTTTTAATATTATTTACTTGTTTGTTATTTACTT
1 AAAGGAAATTGTTGTGTTTTTTTTAATATTATTTACTTGTTTGTTATTTACTT
12532187 AA
1 AA
12532189 CTAGTATAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 38 0.70
53 16 0.30
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (53 bp):
AAAGGAAATTGTTGTGTTTTTTTTAATATTATTTACTTGTTTGTTATTTACTT
Found at i:12534014 original size:21 final size:21
Alignment explanation
Indices: 12533988--12534028 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
12533978 TGGGTGGATT
12533988 AGCTCTTACGAGCTTCTGTTA
1 AGCTCTTACGAGCTTCTGTTA
*
12534009 AGCTCTTATGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
12534029 CAACTTCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTGTTA
Found at i:12547984 original size:48 final size:46
Alignment explanation
Indices: 12547885--12547982 Score: 108
Period size: 47 Copynumber: 2.0 Consensus size: 46
12547875 AATTAAATTT
* * *
12547885 AAATATGTAAAATTAAAATATTATTTTAATATAATAATTTCATATAA
1 AAATATATAAAATTAAAATATTATTTT-ATATAAAAATTTCAAATAA
*
12547932 AAATATATAAATTTAAAATCATATATATTT-TATAAAAATTTCAAAGTAA
1 AAATATATAAAATTAAAAT-AT-TAT-TTTATATAAAAATTTCAAA-TAA
12547981 AA
1 AA
12547983 TAAAATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
47 17 0.40
48 15 0.35
49 8 0.19
50 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (46 bp):
AAATATATAAAATTAAAATATTATTTTATATAAAAATTTCAAATAA
Found at i:12548156 original size:19 final size:19
Alignment explanation
Indices: 12548089--12548157 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
12548079 ATAGATTTTT
* * *
12548089 AATTTTTTATATATATTTT
1 AATTTTTTAAATTTATTTA
* *
12548108 AA-TTTCTAAAATTACTTTA
1 AATTTTTTAAATTTA-TTTA
*
12548127 AATTATTTTAAATTTATTTC
1 AATT-TTTTAAATTTATTTA
12548147 AATTTTTTAAA
1 AATTTTTTAAA
12548158 ATTTTTTTGG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 8 0.21
19 14 0.36
20 8 0.21
21 9 0.23
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTTTAAATTTATTTA
Found at i:12548159 original size:20 final size:22
Alignment explanation
Indices: 12548109--12548161 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
12548099 ATATATTTTA
12548109 ATTTCTAAAA-TTACTTTAAATT
1 ATTT-TAAAATTTACTTTAAATT
*
12548131 ATTTT-AAATTTA-TTTCAATT
1 ATTTTAAAATTTACTTTAAATT
12548151 -TTTTAAAATTT
1 ATTTTAAAATTT
12548162 TTTTGGAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 4 0.14
22 4 0.14
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTAAAATTTACTTTAAATT
Found at i:12560226 original size:5 final size:5
Alignment explanation
Indices: 12560216--12560293 Score: 60
Period size: 5 Copynumber: 16.6 Consensus size: 5
12560206 TAAGTTGAAG
* * * *
12560216 AAAAT AAAAT AAAA- AAAAT AAAA- ACAACT AAAAC AAAAT -TAA- AAAAG
1 AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT
*
12560263 AAAAT AAAA- AAAAT AATA- AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
12560294 CTCAATGATA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
4 16 0.28
5 40 0.70
6 1 0.02
ACGTcount: A:0.81, C:0.04, G:0.01, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:12560235 original size:9 final size:9
Alignment explanation
Indices: 12560216--12560289 Score: 67
Period size: 9 Copynumber: 7.4 Consensus size: 9
12560206 TAAGTTGAAG
12560216 AAAATAAAAT
1 AAAA-AAAAT
12560226 AAAAAAAAT
1 AAAAAAAAT
*
12560235 AAAAACAACT
1 AAAAA-AAAT
12560245 AAAACAAAATT
1 AAAA-AAAA-T
12560256 AAAAAAGAAAAT
1 --AAAA-AAAAT
12560268 AAAAAAAAT
1 AAAAAAAAT
*
12560277 AATAAAAAT
1 AAAAAAAAT
12560286 AAAA
1 AAAA
12560290 TAAACTCAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
9 26 0.48
10 17 0.31
11 2 0.04
12 1 0.02
13 8 0.15
ACGTcount: A:0.81, C:0.04, G:0.01, T:0.14
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:12560395 original size:6 final size:6
Alignment explanation
Indices: 12560358--12560396 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
12560348 GAAAAAGAAA
*
12560358 AAAAAT AGAAAT AGCAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT A--AAAAT AAAAAT AAAAAT AAAAAT A
12560397 TATATAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 24 0.83
8 5 0.17
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:12560403 original size:18 final size:18
Alignment explanation
Indices: 12560382--12560434 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
12560372 CAAAATAAAA
12560382 ATAAAAATAAAAATATAT
1 ATAAAAATAAAAATATAT
*
12560400 AT-AAATTAAAAA-ATAT
1 ATAAAAATAAAAATATAT
12560416 ATAAAAAATTAAAAATATA
1 AT-AAAAA-TAAAAATATA
12560435 ACAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
18 5 0.17
19 6 0.21
20 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAATAAAAATATAT
Found at i:12560410 original size:16 final size:16
Alignment explanation
Indices: 12560378--12560434 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
12560368 ATAGCAAAAT
12560378 AAAAATA-A-AAATAA
1 AAAAATATATAAATAA
* *
12560392 AAATATATATAAATTA
1 AAAAATATATAAATAA
*
12560408 AAAAATATATAAAAAA
1 AAAAATATATAAATAA
12560424 TTAAAAATATA
1 --AAAAATATA
12560435 ACAATTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 6 0.18
15 1 0.03
16 18 0.53
18 9 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATATATAAATAA
Found at i:12560460 original size:36 final size:36
Alignment explanation
Indices: 12560373--12560461 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 36
12560363 TAGAAATAGC
*
12560373 AAAATAAAAATAAAAATAAAAATATATATAAATTAAA
1 AAAAT-AAAATAAAATTAAAAATATATATAAATTAAA
* *
12560410 AAATATATAA-AAAATTAAAAATATA-A-CAATTAATA
1 AAA-ATAAAATAAAATTAAAAATATATATAAATTAA-A
12560445 ATAAATAAAATAAAATT
1 A-AAATAAAATAAAATT
12560462 GGGGTGATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
34 6 0.14
35 8 0.18
36 22 0.50
37 6 0.14
38 2 0.05
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (36 bp):
AAAATAAAATAAAATTAAAAATATATATAAATTAAA
Found at i:12564876 original size:12 final size:12
Alignment explanation
Indices: 12564859--12564884 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12564849 TTTTGCTCCC
12564859 AAATGCTTTTCT
1 AAATGCTTTTCT
12564871 AAATGCTTTTCT
1 AAATGCTTTTCT
12564883 AA
1 AA
12564885 GGATAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (12 bp):
AAATGCTTTTCT
Found at i:12567726 original size:86 final size:86
Alignment explanation
Indices: 12567578--12567937 Score: 381
Period size: 86 Copynumber: 4.2 Consensus size: 86
12567568 TTATGTGAAA
* * * * * * *
12567578 AAACGCCGCTATAGAACATGACTTTTAG-CG-GCACTTTTCCTATAAACACCG-TTAAAGAACAT
1 AAACGCCGCTAAAGAACATGACCTTTAGTAGTGC-TTTTTCC-AAAAACGCCGCTAAAAG-ACAT
* * * ** *
12567640 GACCTTTAGCGATACTTTTTTTAA
63 GACCTTTAGCGGTTCTTTCTCCAC
* *
12567664 AAACTCCGCTAAAGAACATGACCTTTAGTAGTGCTTTTTCCAAAAACGCCACTAAAAGACATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGTAGTGCTTTTTCCAAAAACGCCGCTAAAAGACATGAC
12567729 CTTTAGCGGTTCTTTCTCCAC
66 CTTTAGCGGTTCTTTCTCCAC
* * *
12567750 AAACGCCACTAAAGAACATGACCTTTAGTAGTGCTTTTTCTAAAAATGCCGCTAAAAGACATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGTAGTGCTTTTTCCAAAAACGCCGCTAAAAGACATGAC
12567815 CTTTAGCGGTTCTTTCTCCAC
66 CTTTAGCGGTTCTTTCTCCAC
* * * * *
12567836 AAACGCCGCTAAAGAACCA-GACTTTTA--ACTGCGCTTTTCCAAAAAGGCCGCTAAAAAACATG
1 AAACGCCGCTAAAGAA-CATGACCTTTAGTAGTGC-TTTTTCCAAAAACGCCGCTAAAAGACATG
** * *
12567898 ACCTTTAGCGGCGCTCTCTCTAC
64 ACCTTTAGCGGTTCTTTCTCCAC
*
12567921 AAATGCCGCTAAAGAAC
1 AAACGCCGCTAAAGAAC
12567938 TTAACTTTTA
Statistics
Matches: 237, Mismatches: 32, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
84 5 0.02
85 59 0.25
86 157 0.66
87 14 0.06
88 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.27
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGACCTTTAGTAGTGCTTTTTCCAAAAACGCCGCTAAAAGACATGAC
CTTTAGCGGTTCTTTCTCCAC
Found at i:12567932 original size:43 final size:43
Alignment explanation
Indices: 12567576--12567977 Score: 281
Period size: 43 Copynumber: 9.4 Consensus size: 43
12567566 ATTTATGTGA
* * * **
12567576 AAAAACGCCGCTATAGAACATGACTTTTAGCGGCACTTT-TCC
1 AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
* * * * * * * **
12567618 TATAAACACCGTTAAAGAACATGACCTTTAGCGATACTTTTTTT
1 -AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
* * ** *
12567662 AAAAACTCCGCTAAAGAACATGACCTTTAGTAGTGCTTTTTCC
1 AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
* * *
12567705 AAAAACGCCACTAAAAGACATGACCTTTAGCGGTTCTTTCTCC
1 AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
* * * ** * *
12567748 ACAAACGCCACTAAAGAACATGACCTTTAGTAGTGCTTTTTCT
1 AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
* * *
12567791 AAAAATGCCGCTAAAAGACATGACCTTTAGCGGTTCTTTCTCC
1 AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
* * * * * *
12567834 ACAAACGCCGCTAAAGAACCA-GACTTTTAACTGCGCTTT-TCC
1 AAAAACGCCGCTAAA-AAACATGACCTTTAGCGGTGCTTTCTCC
* * * *
12567876 AAAAAGGCCGCTAAAAAACATGACCTTTAGCGGCGCTCTCTCT
1 AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
* * * * * * * **
12567919 ACAAATGCCGCTAAAGAACTTAACTTTTAGCCGCACTTTC-CC
1 AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
*
12567961 AAAAAACGCCACTAAAA
1 -AAAAACGCCGCTAAAA
12567978 GTCATATTCT
Statistics
Matches: 279, Mismatches: 75, Indels: 10
0.77 0.21 0.03
Matches are distributed among these distances:
41 4 0.01
42 31 0.11
43 240 0.86
44 4 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCTAAAAAACATGACCTTTAGCGGTGCTTTCTCC
Found at i:12567945 original size:85 final size:83
Alignment explanation
Indices: 12567578--12567978 Score: 318
Period size: 86 Copynumber: 4.7 Consensus size: 83
12567568 TTATGTGAAA
* * * * * * *
12567578 AAACGCCGCTATAGAACATGACTTTTAGCGGCACTTTTCCTATAAACACCG-TTAAAGAACATGA
1 AAACGCCGCTAAAGAAC-TAACTTTTAACTGC-CTTTTCC-AAAAACGCCGCTAAAAG-ACATGA
* * * ** *
12567642 CCTTTAGCGATACTTTTTTTAA
62 CCTTTAGCGGTTCTTTCTCCAC
* * * * * *
12567664 AAACTCCGCTAAAGAACATGACCTTTAGTAGTGCTTTTTCCAAAAACGCCACTAAAAGACATGAC
1 AAACGCCGCTAAAGAAC-TAACTTTTA--ACTGCCTTTTCCAAAAACGCCGCTAAAAGACATGAC
12567729 CTTTAGCGGTTCTTTCTCCAC
63 CTTTAGCGGTTCTTTCTCCAC
* * * * * * *
12567750 AAACGCCACTAAAGAACATGACCTTTAGTAGTGCTTTTTCTAAAAATGCCGCTAAAAGACATGAC
1 AAACGCCGCTAAAGAAC-TAACTTTTA--ACTGCCTTTTCCAAAAACGCCGCTAAAAGACATGAC
12567815 CTTTAGCGGTTCTTTCTCCAC
63 CTTTAGCGGTTCTTTCTCCAC
* * *
12567836 AAACGCCGCTAAAGAACCAGACTTTTAACTGCGCTTTTCCAAAAAGGCCGCTAAAAAACATGACC
1 AAACGCCGCTAAAGAACTA-ACTTTTAACTGC-CTTTTCCAAAAACGCCGCTAAAAGACATGACC
** * *
12567901 TTTAGCGGCGCTCTCTCTAC
64 TTTAGCGGTTCTTTCTCCAC
* * * * *
12567921 AAATGCCGCTAAAGAACTTAACTTTTAGCCGCACTTTCCCAAAAAACGCCACTAAAAG
1 AAACGCCGCTAAAGAAC-TAACTTTTAACTGC-CTTTTCC-AAAAACGCCGCTAAAAG
12567979 TCATATTCTT
Statistics
Matches: 264, Mismatches: 44, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
84 4 0.02
85 76 0.29
86 171 0.65
87 11 0.04
88 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (83 bp):
AAACGCCGCTAAAGAACTAACTTTTAACTGCCTTTTCCAAAAACGCCGCTAAAAGACATGACCTT
TAGCGGTTCTTTCTCCAC
Found at i:12567958 original size:128 final size:129
Alignment explanation
Indices: 12567740--12567976 Score: 273
Period size: 128 Copynumber: 1.8 Consensus size: 129
12567730 TTTAGCGGTT
* * * * * *
12567740 CTTTCTCCACAAACGCCACTAAAGAACATGACCTTTAGTAGTGCTTTTTCTAAAAATGCCGCTAA
1 CTTTCTCCAAAAACGCCACTAAAAAACATGACCTTTAGCAGCGCTCTCTCTAAAAATGCCGCTAA
* * ** * *
12567805 AAGACATGACCTTTAGCGGTTCTTTCTCC-ACAAACGCCGCTAAAGAACCAGACTTTTAACTGCG
66 AAGACATAACCTTTAGCCGCACTTTC-CCAAAAAACGCCACTAAAGAACCAGACTTTTAACTGCG
* * * *
12567869 CTTT-TCCAAAAAGGCCGCTAAAAAACATGACCTTTAGCGGCGCTCTCTCTACAAATGCCGCT-A
1 CTTTCTCCAAAAACGCCACTAAAAAACATGACCTTTAGCAGCGCTCTCTCTAAAAATGCCGCTAA
* *
12567932 AAGAACTTAACTTTTAGCCGCACTTTCCCAAAAAACGCCACTAAA
66 AAG-ACATAACCTTTAGCCGCACTTTCCCAAAAAACGCCACTAAA
12567977 AGTCATATTC
Statistics
Matches: 88, Mismatches: 18, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
127 6 0.07
128 78 0.89
129 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.25
Consensus pattern (129 bp):
CTTTCTCCAAAAACGCCACTAAAAAACATGACCTTTAGCAGCGCTCTCTCTAAAAATGCCGCTAA
AAGACATAACCTTTAGCCGCACTTTCCCAAAAAACGCCACTAAAGAACCAGACTTTTAACTGCG
Found at i:12568688 original size:23 final size:23
Alignment explanation
Indices: 12568642--12569033 Score: 291
Period size: 23 Copynumber: 17.2 Consensus size: 23
12568632 ACATAAACTA
*
12568642 AATTT-CAGCAAC-TAAACAATTC
1 AATTTACAGC-ACTTAAACACTTC
* *
12568664 AATTTGCAGTACTTAGAA-ACTTC
1 AATTTACAGCACTTA-AACACTTC
* *
12568687 AATTTACAACATTTAAACACTTC
1 AATTTACAGCACTTAAACACTTC
*
12568710 AATTTACAGCACTTTAACACTTC
1 AATTTACAGCACTTAAACACTTC
*
12568733 AATTTACAGCATTTAAACACTTC
1 AATTTACAGCACTTAAACACTTC
* *
12568756 AATTTGCAGCACTTTAACA-TCTC
1 AATTTACAGCACTTAAACACT-TC
* * * * * *
12568779 AATTAACAACATTTATACTCCTC
1 AATTTACAGCACTTAAACACTTC
* *
12568802 AA-TTATAGCGA-TAAAACA-TATC
1 AATTTACAGC-ACTTAAACACT-TC
*
12568824 AATTTCCAGCAAC-TAAACACTTC
1 AATTTACAGC-ACTTAAACACTTC
* * *
12568847 ATTTTGCAGTACTTAAACACTTC
1 AATTTACAGCACTTAAACACTTC
* * *
12568870 AATTTACAACATTTAAGCACTTC
1 AATTTACAGCACTTAAACACTTC
* *
12568893 AATTTACAACATTTAAACACTTC
1 AATTTACAGCACTTAAACACTTC
*
12568916 AATTTACAGCA-TTTAACACTTC
1 AATTTACAGCACTTAAACACTTC
** * *
12568938 AATTTGTAGCACTTTAACCCTTC
1 AATTTACAGCACTTAAACACTTC
*
12568961 AATTTACAGCATTTAAACACTTC
1 AATTTACAGCACTTAAACACTTC
* * *
12568984 AATTTGCTGCACTTTAACA-TCTC
1 AATTTACAGCACTTAAACACT-TC
* * * * *
12569007 AATTAACAACATTTATACACCTC
1 AATTTACAGCACTTAAACACTTC
12569030 AATT
1 AATT
12569034 ATAGCGATAA
Statistics
Matches: 290, Mismatches: 65, Indels: 29
0.76 0.17 0.08
Matches are distributed among these distances:
22 44 0.15
23 243 0.84
24 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (23 bp):
AATTTACAGCACTTAAACACTTC
Found at i:12568704 original size:46 final size:45
Alignment explanation
Indices: 12568654--12569033 Score: 324
Period size: 46 Copynumber: 8.3 Consensus size: 45
12568644 TTTCAGCAAC
* * *
12568654 TAAACAATTCAATTTGCAGTACTTAGAAACTTCAATTTACAACATT
1 TAAACACTTCAATTTGCAGCACTTA-AAACTTCAATTTACAGCATT
* *
12568700 TAAACACTTCAATTTACAGCACTTTAACACTTCAATTTACAGCATT
1 TAAACACTTCAATTTGCAGCAC-TTAAAACTTCAATTTACAGCATT
* * *
12568746 TAAACACTTCAATTTGCAGCACTT-TAACATCTCAATTAACAACATT
1 TAAACACTTCAATTTGCAGCACTTAAAAC-T-TCAATTTACAGCATT
* * * * **
12568792 TATACTCCTCAATTAT--AGCGA--TAAAACATATCAATTTCCAGCAAC
1 TAAACACTTCAATT-TGCAGC-ACTTAAAAC-T-TCAATTTACAGCATT
* * *
12568837 TAAACACTTCATTTTGCAGTACTTAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTGCAGCACTTAAA-ACTTCAATTTACAGCATT
* * * *
12568883 TAAGCACTTCAATTTACAACATTTAAACACTTCAATTTACAGCATT
1 TAAACACTTCAATTTGCAGCACTTAAA-ACTTCAATTTACAGCATT
* **
12568929 T-AACACTTCAATTTGTAGCACTTTAACCCTTCAATTTACAGCATT
1 TAAACACTTCAATTTGCAGCAC-TTAAAACTTCAATTTACAGCATT
* * * *
12568974 TAAACACTTCAATTTGCTGCACTT-TAACATCTCAATTAACAACATT
1 TAAACACTTCAATTTGCAGCACTTAAAAC-T-TCAATTTACAGCATT
* *
12569020 TATACACCTCAATT
1 TAAACACTTCAATT
12569034 ATAGCGATAA
Statistics
Matches: 267, Mismatches: 52, Indels: 30
0.77 0.15 0.09
Matches are distributed among these distances:
44 5 0.02
45 68 0.25
46 183 0.69
47 9 0.03
48 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (45 bp):
TAAACACTTCAATTTGCAGCACTTAAAACTTCAATTTACAGCATT
Found at i:12568872 original size:91 final size:91
Alignment explanation
Indices: 12568642--12568988 Score: 355
Period size: 91 Copynumber: 3.8 Consensus size: 91
12568632 ACATAAACTA
*
12568642 AATTTCAGCAACTAAACAATTCAATTTGCAGTACTTAGAA-ACTTCAATTTACAACATTTAAACA
1 AATTTCAGCAACTAAACACTTCAATTTGCAGTACTTA-AACACTTCAATTTACAACATTTAAACA
* **
12568706 CTTCAATTTACAGCACTTTAACACTTC
65 CCTCAATTTACAGCACTAAAACACTTC
** * * * *
12568733 AATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACATTTATAC
1 AATTT-CAGCAACTAAACACTTCAATTTGCAGTACTTAAACACT-TCAATTTACAACATTTAAAC
* *
12568797 TCCTCAA-TTATAGCGA-TAAAACA-TATC
64 ACCTCAATTTACAGC-ACTAAAACACT-TC
* *
12568824 AATTTCCAGCAACTAAACACTTCATTTTGCAGTACTTAAACACTTCAATTTACAACATTTAAGCA
1 AATTT-CAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACA
* * * *
12568889 CTTCAATTTACAACATTTAAACACTTC
65 CCTCAATTTACAGCACTAAAACACTTC
* * * * * * *
12568916 AATTTACAGC-ATTTAACACTTCAATTTGTAGCACTTTAACCCTTCAATTTACAGCATTTAAACA
1 AATTT-CAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACA
*
12568980 CTTCAATTT
65 CCTCAATTT
12568989 GCTGCACTTT
Statistics
Matches: 211, Mismatches: 36, Indels: 18
0.80 0.14 0.07
Matches are distributed among these distances:
90 1 0.00
91 134 0.64
92 75 0.36
93 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (91 bp):
AATTTCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACAC
CTCAATTTACAGCACTAAAACACTTC
Found at i:12569032 original size:137 final size:135
Alignment explanation
Indices: 12568683--12569033 Score: 379
Period size: 137 Copynumber: 2.6 Consensus size: 135
12568673 TACTTAGAAA
* * *
12568683 CTTCAATTTACAACATTTAAACACTTCAATTTACAGCACTTTAACACTTCAATTTACAGCATTTA
1 CTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACATTT-
* * *
12568748 AACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACTCCTCAATTATAGCGA
65 AACACTTCAATTTACAACACTTTAACATCTCAATTAACAACATTTATACACCTCAATTATAGCGA
12568813 TAAAAC
130 TAAAAC
* * ** * * *
12568819 ATATCAATTTCCAGCAACTAAACACTTCATTTTGCAGTACTTAAACACTTCAATTTACAACATTT
1 CT-TCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACATTT
* * * *
12568884 AAGCACTTCAATTTACAACA-TTTAAACA-CTTCAATTTACAGCATTTA-ACACTTCAATTTGTA
65 AA-CACTTCAATTTACAACACTTT-AACATC-TCAATTAACAACATTTATACACCTCAA-TTATA
* *
12568946 GC-ACTTTAACC
126 GCGA--TAAAAC
* *
12568957 CTTCAATTTACAGCATTTAAACACTTCAATTTGCTGCACTTTAACA-TCTCAATTAACAACATTT
1 CTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACACT-TCAATTTACAACATTT
*
12569021 ATACACCTCAATT
65 A-ACACTTCAATT
12569034 ATAGCGATAA
Statistics
Matches: 177, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
136 16 0.09
137 155 0.88
138 6 0.03
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (135 bp):
CTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTA
ACACTTCAATTTACAACACTTTAACATCTCAATTAACAACATTTATACACCTCAATTATAGCGAT
AAAAC
Found at i:12569062 original size:114 final size:114
Alignment explanation
Indices: 12568708--12569075 Score: 444
Period size: 114 Copynumber: 3.2 Consensus size: 114
12568698 TTTAAACACT
12568708 TCAATTTAC-AGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTA
1 TCAATTT-CTAGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTA
* *
12568772 ACATCTCAATTAACAACATTTATACTCCTCAATTATAGCGATAAAACATA
65 ACATCTCAATTAACAACATTTATACACCTCAATTATAGCGATAAAACATC
* * * * * * * *
12568822 TCAATTTCCAGCAAC-TAAACACTTCATTTTGCAGTACTTAAACACTTCAATTTACAACA-TTTA
1 TCAATTTCTAGC-ACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTA
* * * * **
12568885 AGCA-CTTCAATTTACAACATTTAAACACTTCAATTTACAGC-ATTTAACA-C
65 A-CATC-TCAATTAACAACATTTATACACCTCAA-TTATAGCGATAAAACATC
* * *
12568935 TTCAATTTGTAGCACTTTAACCCTTCAATTTACAGCATTTAAACACTTCAATTTGCTGCACTTTA
1 -TCAATTTCTAGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTA
12569000 ACATCTCAATTAACAACATTTATACACCTCAATTATAGCGATAAAACATC
65 ACATCTCAATTAACAACATTTATACACCTCAATTATAGCGATAAAACATC
*
12569050 TCAATTTCTAGCAAC-TAAACACTTCA
1 TCAATTTCTAGC-ACTTTAACACTTCA
12569076 TTAGTGATGC
Statistics
Matches: 207, Mismatches: 35, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
113 15 0.07
114 175 0.85
115 17 0.08
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (114 bp):
TCAATTTCTAGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAA
CATCTCAATTAACAACATTTATACACCTCAATTATAGCGATAAAACATC
Found at i:12569956 original size:5 final size:5
Alignment explanation
Indices: 12569946--12569976 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
12569936 CAATATTAGT
12569946 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
12569977 AAATAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:12573697 original size:40 final size:40
Alignment explanation
Indices: 12573633--12573753 Score: 136
Period size: 40 Copynumber: 3.0 Consensus size: 40
12573623 GCGACATTTC
* * *
12573633 AAAAAGCGTCGCTAATGGTCGACCTATTGCTG-CTTTTTTT
1 AAAAAGCGCCGCTAATGGTCGACCTATAG-TGACGTTTTTT
* *
12573673 AAAAAGCGCCGCTAGTGGTTGACCTATAGTGACGTTTTTT
1 AAAAAGCGCCGCTAATGGTCGACCTATAGTGACGTTTTTT
* * * * *
12573713 GAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTT
1 AAAAAGCGCCGCTAATGGTCGACCTATAGTGACGTTTTTT
12573753 A
1 A
12573754 TCCAAACGCC
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 2 0.03
40 65 0.97
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (40 bp):
AAAAAGCGCCGCTAATGGTCGACCTATAGTGACGTTTTTT
Found at i:12576468 original size:30 final size:30
Alignment explanation
Indices: 12576434--12576516 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 30
12576424 CTCTCCACCA
* * *
12576434 CCACCTCCACCACCACACAATCCAGTTTCT
1 CCACCACCACCACCCCACCATCCAGTTTCT
*
12576464 CCACCGCCACC-CCCCACCATCCAGTTTCT
1 CCACCACCACCACCCCACCATCCAGTTTCT
12576493 CCACCACCACCACCCCACCATCCA
1 CCACCACCACCACCCCACCATCCA
12576517 ATCACTCCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 26 0.54
30 22 0.46
ACGTcount: A:0.24, C:0.58, G:0.04, T:0.14
Consensus pattern (30 bp):
CCACCACCACCACCCCACCATCCAGTTTCT
Found at i:12576525 original size:30 final size:30
Alignment explanation
Indices: 12576434--12576533 Score: 130
Period size: 30 Copynumber: 3.4 Consensus size: 30
12576424 CTCTCCACCA
* * *
12576434 CCACCTCCACCACCACACAATCCAGTTTCT
1 CCACCGCCACCACCCCACCATCCAGTTTCT
12576464 CCACCGCCACC-CCCCACCATCCAGTTTCT
1 CCACCGCCACCACCCCACCATCCAGTTTCT
* * **
12576493 CCACCACCACCACCCCACCATCCAATCACT
1 CCACCGCCACCACCCCACCATCCAGTTTCT
12576523 CCACCGCCACC
1 CCACCGCCACC
12576534 TCATGTACAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 26 0.43
30 35 0.57
ACGTcount: A:0.24, C:0.58, G:0.04, T:0.14
Consensus pattern (30 bp):
CCACCGCCACCACCCCACCATCCAGTTTCT
Found at i:12576562 original size:24 final size:24
Alignment explanation
Indices: 12576521--12576579 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
12576511 CATCCAATCA
* *
12576521 CTCCACCGCCACCTCATGTACATC
1 CTCCACCACCACCCCATGTACATC
* * *
12576545 CTCCACCACCTCCCCATGTGCGTC
1 CTCCACCACCACCCCATGTACATC
*
12576569 CACCACCACCA
1 CTCCACCACCA
12576580 GCACCACTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.54, G:0.08, T:0.17
Consensus pattern (24 bp):
CTCCACCACCACCCCATGTACATC
Found at i:12587643 original size:18 final size:18
Alignment explanation
Indices: 12587620--12587694 Score: 105
Period size: 18 Copynumber: 4.2 Consensus size: 18
12587610 CCCAACTACT
12587620 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
**
12587638 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
* * *
12587656 GTATATGTAAATAGTGCC
1 GTATACGTGAATAGTACC
12587674 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
12587692 GTA
1 GTA
12587695 AACGGTCGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:12590127 original size:15 final size:15
Alignment explanation
Indices: 12590109--12590138 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12590099 CCAAATGATG
12590109 ATGCCAAATAAACTT
1 ATGCCAAATAAACTT
12590124 ATGCCAAATAAACTT
1 ATGCCAAATAAACTT
12590139 GCCCAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
ATGCCAAATAAACTT
Found at i:12600136 original size:17 final size:17
Alignment explanation
Indices: 12600111--12600153 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
12600101 ATTTTCGTAA
*
12600111 AAAAAATAAATCTTTTT
1 AAAATATAAATCTTTTT
12600128 AAAATATAAATCTTTTT
1 AAAATATAAATCTTTTT
12600145 AAAATATAA
1 AAAATATAA
12600154 GTTAAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATAAATCTTTTT
Found at i:12607206 original size:6 final size:6
Alignment explanation
Indices: 12607186--12607251 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
12607176 ATAGGAAAAC
*
12607186 AAAATA AACATA AAAA-A AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
12607233 AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA A
12607252 TCAGACTCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
5 5 0.09
6 52 0.91
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:12617111 original size:27 final size:27
Alignment explanation
Indices: 12617080--12617132 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
12617070 TTTTGGATTC
12617080 ACAAACTCTGTAACACCGAATTTCTTT
1 ACAAACTCTGTAACACCGAATTTCTTT
12617107 ACAAACTCTGTAACACCGAATTTCTT
1 ACAAACTCTGTAACACCGAATTTCTT
12617133 GGCTGCAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (27 bp):
ACAAACTCTGTAACACCGAATTTCTTT
Found at i:12617854 original size:23 final size:22
Alignment explanation
Indices: 12617811--12617871 Score: 56
Period size: 25 Copynumber: 2.7 Consensus size: 22
12617801 AATAAAAAAC
12617811 TTTAAAA-AATAAAAATTCAAATACA
1 TTTAAAACAA-AAAAA-TCAAAT--A
12617836 TTTAAAACAAAAAAA-CAAATA
1 TTTAAAACAAAAAAATCAAATA
12617857 -TTAAAACAAATAAAA
1 TTTAAAACAAA-AAAA
12617872 AACAAGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 10 0.29
21 5 0.15
23 5 0.15
25 12 0.35
26 2 0.06
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (22 bp):
TTTAAAACAAAAAAATCAAATA
Found at i:12618084 original size:11 final size:11
Alignment explanation
Indices: 12618070--12618123 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
12618060 AACACGACAA
*
12618070 AAAATAGCAGC
1 AAAACAGCAGC
* *
12618081 AAAATAGCACC
1 AAAACAGCAGC
*
12618092 AAAACAGCACC
1 AAAACAGCAGC
* *
12618103 CAAACAACAGC
1 AAAACAGCAGC
12618114 AAAACAGCAG
1 AAAACAGCAG
12618124 TGAGCTAGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.56, C:0.28, G:0.13, T:0.04
Consensus pattern (11 bp):
AAAACAGCAGC
Found at i:12619968 original size:24 final size:22
Alignment explanation
Indices: 12619928--12619973 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
12619918 GTAATTGAGT
*
12619928 TTTAATTTTTTTTAATTTGGCA
1 TTTAATTTTTTTCAATTTGGCA
12619950 TTTAATTTTTTTCCCAATTTGGCA
1 TTTAATTTTTTT--CAATTTGGCA
12619974 CATGAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.59
Consensus pattern (22 bp):
TTTAATTTTTTTCAATTTGGCA
Found at i:12623780 original size:6 final size:6
Alignment explanation
Indices: 12623769--12623813 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
12623759 ATATAAAGAG
** *
12623769 AAAAAT AAAAAT AAGGAT AAAAAT AAAAAT AAAAAT AAACAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
12623814 GAATCATCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:12633792 original size:32 final size:32
Alignment explanation
Indices: 12633754--12633816 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
12633744 TCATAAACTT
* * *
12633754 ATAAATTAATTACTTGAATTTAGTAACTCATG
1 ATAAATTAATTAATTGAATTGAATAACTCATG
*
12633786 ATAAATTAATTAATTTAATTGAATAACTCAT
1 ATAAATTAATTAATTGAATTGAATAACTCAT
12633817 ATTGATTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTGAATAACTCATG
Found at i:12636859 original size:3 final size:3
Alignment explanation
Indices: 12636851--12636882 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12636841 TATTCTTTTA
12636851 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12636883 GAAGTTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12637655 original size:55 final size:55
Alignment explanation
Indices: 12637596--12637706 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
12637586 TTACAATTAA
12637596 TTAAAAAAATCAAAAGTTAATTTGAATTTTAAATTAAGCTTTTAACATTCTTTGT
1 TTAAAAAAATCAAAAGTTAATTTGAATTTTAAATTAAGCTTTTAACATTCTTTGT
12637651 TTAAAAAAATCAAAAGTTAATTTGAATTTTAAATTAAGCTTTTAACATTCTTTGT
1 TTAAAAAAATCAAAAGTTAATTTGAATTTTAAATTAAGCTTTTAACATTCTTTGT
12637706 T
1 T
12637707 CACTGTCAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (55 bp):
TTAAAAAAATCAAAAGTTAATTTGAATTTTAAATTAAGCTTTTAACATTCTTTGT
Found at i:12650456 original size:12 final size:12
Alignment explanation
Indices: 12650428--12650502 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
12650418 TATAAAGTTC
12650428 AAAATAGGAAA-A
1 AAAATA-GAAATA
12650440 CAAAATAGAAATA
1 -AAAATAGAAATA
*
12650453 AAAA-GGAAAATA
1 AAAATAG-AAATA
* *
12650465 AGAATAAAAATA
1 AAAATAGAAATA
12650477 AAAATA-AAATA
1 AAAATAGAAATA
*
12650488 AAAGATAAAAATA
1 AAA-ATAGAAATA
12650501 AA
1 AA
12650503 GATAAACATA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
11 9 0.17
12 29 0.56
13 14 0.27
ACGTcount: A:0.76, C:0.01, G:0.09, T:0.13
Consensus pattern (12 bp):
AAAATAGAAATA
Found at i:12650470 original size:6 final size:6
Alignment explanation
Indices: 12650441--12650525 Score: 82
Period size: 6 Copynumber: 14.2 Consensus size: 6
12650431 ATAGGAAAAC
* ** *
12650441 AAAATA GAAATA AAAAGG AAAATA AGAATA AAAATA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * **
12650488 AAAGATA AAAATA AAGATA AACATA ATCATA AAAATA A
1 AAA-ATA AAAATA AAAATA AAAATA AAAATA AAAATA A
12650526 TCAGACTCAA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
5 5 0.08
6 53 0.83
7 6 0.09
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:12656479 original size:13 final size:13
Alignment explanation
Indices: 12656463--12656495 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12656453 TTTAATTAAA
*
12656463 TTAGTTAATTAGT
1 TTAGATAATTAGT
12656476 TTAGATAATTAGT
1 TTAGATAATTAGT
12656489 TTA-ATAA
1 TTAGATAA
12656496 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:12661787 original size:6 final size:6
Alignment explanation
Indices: 12661776--12661854 Score: 58
Period size: 6 Copynumber: 13.3 Consensus size: 6
12661766 AATCCTCCTA
*
12661776 TTTTAT TTTTA- -TTTAT TCTTAT TTTTAT TTTCT-T TCATTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT T--TTTAT TTTTAT
* * * *
12661823 TCTTAT TTTTCT TTTGAT TTTTAT TTTCAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
12661855 CAATTTTCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
6 44 0.77
7 3 0.05
8 2 0.04
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:12661817 original size:26 final size:26
Alignment explanation
Indices: 12661786--12661836 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
12661776 TTTTATTTTT
*
12661786 ATTTATTCTTATTTTTA-TTTTCTTTC
1 ATTTATT-TTATTCTTATTTTTCTTTC
12661812 ATTTATTTTATTCTTATTTTTCTTT
1 ATTTATTTTATTCTTATTTTTCTTT
12661837 TGATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (26 bp):
ATTTATTTTATTCTTATTTTTCTTTC
Found at i:12664659 original size:13 final size:13
Alignment explanation
Indices: 12664643--12664675 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12664633 TTTAATTAAA
*
12664643 TTAGTTAATTAGT
1 TTAGATAATTAGT
12664656 TTAGATAATTAGT
1 TTAGATAATTAGT
12664669 TTA-ATAA
1 TTAGATAA
12664676 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:12672152 original size:5 final size:5
Alignment explanation
Indices: 12672142--12672181 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
12672132 TTGGTGTGAA
12672142 AAAAT AAAAT -AAAT AAAAT AAAAT -AAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
12672182 GAACACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 12 0.36
5 21 0.64
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:12672157 original size:9 final size:9
Alignment explanation
Indices: 12672143--12672181 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
12672133 TGGTGTGAAA
12672143 AAATAAAAT
1 AAATAAAAT
12672152 AAATAAAAT
1 AAATAAAAT
12672161 AAA-ATAAAT
1 AAATA-AAAT
12672170 AAATAAAAT
1 AAATAAAAT
12672179 AAA
1 AAA
12672182 GAACACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 1 0.04
9 26 0.93
10 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:12672161 original size:14 final size:14
Alignment explanation
Indices: 12672142--12672181 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
12672132 TTGGTGTGAA
12672142 AAAATAAAATAAAT
1 AAAATAAAATAAAT
12672156 AAAATAAAATAAAT
1 AAAATAAAATAAAT
12672170 -AAATAAAATAAA
1 AAAATAAAATAAA
12672182 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:12679818 original size:11 final size:9
Alignment explanation
Indices: 12679790--12679952 Score: 82
Period size: 10 Copynumber: 17.1 Consensus size: 9
12679780 TGATATGAAC
*
12679790 TTATACAAA
1 TTATAAAAA
12679799 TTATTAAAAA
1 TTA-TAAAAA
12679809 GTTATAAAAA
1 -TTATAAAAA
12679819 TTATAAAAA
1 TTATAAAAA
*
12679828 TCTA-ATAAA
1 T-TATAAAAA
12679837 TTAT-AAAA
1 TTATAAAAA
12679845 TTAATAAAACA
1 TT-ATAAAA-A
*
12679856 -TATTTAAAA
1 TTA-TAAAAA
12679865 TT-TAAAAA
1 TTATAAAAA
*
12679873 TATATTAAAA
1 T-TATAAAAA
12679883 TTCAATAAAAA
1 TT--ATAAAAA
*
12679894 TCATAAAAAA
1 TTAT-AAAAA
*
12679904 ATATAAAAA
1 TTATAAAAA
* *
12679913 GTATTAAAAG
1 TTA-TAAAAA
* * *
12679923 TGATATGAAC
1 TTATA-AAAA
12679933 TTATAAAAA
1 TTATAAAAA
12679942 TTATAATAAA
1 TTATAA-AAA
12679952 T
1 T
12679953 AAATAAACAA
Statistics
Matches: 118, Mismatches: 19, Indels: 33
0.69 0.11 0.19
Matches are distributed among these distances:
8 13 0.11
9 43 0.36
10 51 0.43
11 11 0.09
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:12679827 original size:19 final size:18
Alignment explanation
Indices: 12679790--12679952 Score: 82
Period size: 19 Copynumber: 8.6 Consensus size: 18
12679780 TGATATGAAC
*
12679790 TTATACAAATTATTAAAAA
1 TTATAAAAATTA-TAAAAA
12679809 GTTATAAAAATTATAAAAA
1 -TTATAAAAATTATAAAAA
*
12679828 TCTA-ATAAATTAT-AAAA
1 T-TATAAAAATTATAAAAA
*
12679845 TTAATAAAACA-TATTTAAAA
1 TT-ATAAAA-ATTA-TAAAAA
*
12679865 TT-TAAAAATATATTAAAA
1 TTATAAAAAT-TATAAAAA
*
12679883 TTCAATAAAAATCATAAAAAA
1 TT--ATAAAAATTAT-AAAAA
* * *
12679904 ATATAAAAAGTATTAAAAG
1 TTATAAAAATTA-TAAAAA
* * *
12679923 TGATATGAACTTATAAAAA
1 TTATA-AAAATTATAAAAA
12679942 TTATAATAAAT
1 TTATAA-AAAT
12679953 AAATAAACAA
Statistics
Matches: 110, Mismatches: 18, Indels: 31
0.69 0.11 0.19
Matches are distributed among these distances:
16 1 0.01
17 7 0.06
18 27 0.25
19 39 0.35
20 24 0.22
21 12 0.11
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (18 bp):
TTATAAAAATTATAAAAA
Found at i:12679837 original size:18 final size:16
Alignment explanation
Indices: 12679816--12679852 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
12679806 AAAGTTATAA
12679816 AAATTATAAAAATCTAAT
1 AAATTAT-AAAAT-TAAT
12679834 AAATTATAAAATTAAT
1 AAATTATAAAATTAAT
12679850 AAA
1 AAA
12679853 ACATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 5 0.26
18 7 0.37
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAATTAAT
Found at i:12679880 original size:18 final size:17
Alignment explanation
Indices: 12679796--12679884 Score: 65
Period size: 18 Copynumber: 4.8 Consensus size: 17
12679786 GAACTTATAC
12679796 AAATTATTAAAAAGTTATAA
1 AAATTATT-AAAA-TT-TAA
* *
12679816 AAATTATAAAAATCTAA
1 AAATTATTAAAATTTAA
12679833 TAAATTA-TAAAATTAATAA
1 -AAATTATTAAAATT--TAA
12679852 AACA-TATTTAAAATTTAA
1 AA-ATTA-TTAAAATTTAA
12679870 AAATATATTAAAATT
1 AAAT-TATTAAAATT
12679885 CAATAAAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
17 9 0.16
18 24 0.42
19 10 0.18
20 14 0.25
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (17 bp):
AAATTATTAAAATTTAA
Found at i:12680541 original size:19 final size:19
Alignment explanation
Indices: 12680340--12680544 Score: 84
Period size: 19 Copynumber: 10.9 Consensus size: 19
12680330 GTCCAGTTAA
*
12680340 AATTTTTTATAAGTTTATAT
1 AATTTTTTATAA-TTTTTAT
* *
12680360 CAA-TTTTAATGTATTTTTAT
1 -AATTTTTTAT-AATTTTTAT
* *
12680380 AA-TTTTTACATTTTTTAT
1 AATTTTTTATAATTTTTAT
* * * * *
12680398 TATTTTTGAGAATTATAAT
1 AATTTTTTATAATTTTTAT
**
12680417 ACATTTTTTAT--TTTAAAT
1 A-ATTTTTTATAATTTTTAT
*
12680435 AA-GTTTTATTAA-TTTTAT
1 AATTTTTTA-TAATTTTTAT
* *
12680453 AATTTATTAGAATTTTTAT
1 AATTTTTTATAATTTTTAT
* * *
12680472 -A-TTGTTACAATATTTAT
1 AATTTTTTATAATTTTTAT
* *
12680489 ATTTTTTTATAATTTTAAT
1 AATTTTTTATAATTTTTAT
* * *
12680508 AAGTTTATATCATTTTTAT
1 AATTTTTTATAATTTTTAT
* *
12680527 TATTTTTTATGATTTTTA
1 AATTTTTTATAATTTTTA
12680545 ATCATGTTTA
Statistics
Matches: 133, Mismatches: 41, Indels: 22
0.68 0.21 0.11
Matches are distributed among these distances:
16 5 0.04
17 15 0.11
18 23 0.17
19 68 0.51
20 19 0.14
21 3 0.02
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.61
Consensus pattern (19 bp):
AATTTTTTATAATTTTTAT
Found at i:12683879 original size:20 final size:20
Alignment explanation
Indices: 12683854--12683894 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12683844 TGCCTTCGAC
12683854 ATTGACGGAGGAAGAGAAGA
1 ATTGACGGAGGAAGAGAAGA
12683874 ATTGACGGAGGAAGAGAAGA
1 ATTGACGGAGGAAGAGAAGA
12683894 A
1 A
12683895 GCGTAAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.39, T:0.10
Consensus pattern (20 bp):
ATTGACGGAGGAAGAGAAGA
Done.