Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 198 of 290
Found at i:68293460 original size:18 final size:18
Alignment explanation
Indices: 68293437--68293472 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
68293427 ACAAGTACGT
68293437 CGCTCTTTAAATTGACAA
1 CGCTCTTTAAATTGACAA
68293455 CGCTCTTTAAATTGACAA
1 CGCTCTTTAAATTGACAA
68293473 ATGTTAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (18 bp):
CGCTCTTTAAATTGACAA
Found at i:68295181 original size:38 final size:38
Alignment explanation
Indices: 68295138--68295276 Score: 199
Period size: 38 Copynumber: 3.7 Consensus size: 38
68295128 CTTAAAAACT
* *
68295138 CGCAGGCTTTATGCTGGAATTATATCCGGGTTAAATCC
1 CGCAGGCTTCATGCTGGTATTATATCCGGGTTAAATCC
* *
68295176 CGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATTC
1 CGCAGGCTTCATGCTGGTATTATATCCGGGTTAAATCC
* *
68295214 CGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCT
1 CGCAGGCTTCATGCTGGTATTATATCCGGGTTAAATCC
*
68295252 CGCAGGCCT-AGTGCTGGTATTATAT
1 CGCAGGCTTCA-TGCTGGTATTATAT
68295277 GTAACACCCC
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 92 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (38 bp):
CGCAGGCTTCATGCTGGTATTATATCCGGGTTAAATCC
Found at i:68316966 original size:56 final size:55
Alignment explanation
Indices: 68316879--68317040 Score: 254
Period size: 56 Copynumber: 2.9 Consensus size: 55
68316869 ACATGTAATA
* *
68316879 ACATATCGATGCC-ACTGTCTCAAACAGGGTCTTACTCACACACATATATCGGAGTC
1 ACATATCGATGCCAAC-GTAT-AAACATGGTCTTACTCACACACATATATCGGAGTC
68316935 ACATATCGATGCCAACGTATAAAACATGGTCTTACTCACACACATATATCGGAGTC
1 ACATATCGATGCCAACGTAT-AAACATGGTCTTACTCACACACATATATCGGAGTC
* *
68316991 ACATATCGATGCCAACGTATAAACGTGGTCTTACTTACACACATATATCG
1 ACATATCGATGCCAACGTATAAACATGGTCTTACTCACACACATATATCG
68317041 ATGCCATGGT
Statistics
Matches: 100, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
55 28 0.28
56 70 0.70
57 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (55 bp):
ACATATCGATGCCAACGTATAAACATGGTCTTACTCACACACATATATCGGAGTC
Found at i:68319336 original size:41 final size:42
Alignment explanation
Indices: 68319291--68319405 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
68319281 ATATGAGTTA
68319291 TCGTGTAAGACCACGTCTGGGACATTGGCATC-TATTTGATT
1 TCGTGTAAGACCACGTCTGGGACATTGGCATCATATTTGATT
* * *
68319332 TCGTGTAAGACC-CTATCTGGGATAGTGGCATCGATATTTGATT
1 TCGTGTAAGACCAC-GTCTGGGACATTGGCATC-ATATTTGATT
* * * *
68319375 ACATATAAGACCACGTCTGGGACGTTGGCAT
1 TCGTGTAAGACCACGTCTGGGACATTGGCAT
68319406 TGTACGAGCT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
40 1 0.02
41 27 0.45
43 31 0.52
44 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
TCGTGTAAGACCACGTCTGGGACATTGGCATCATATTTGATT
Found at i:68320891 original size:27 final size:27
Alignment explanation
Indices: 68320861--68321038 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
68320851 ATATTGAGTC
* * * *
68320861 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
68320888 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
68320915 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
68320943 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
68320970 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
68320997 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
68321024 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
68321039 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:68321000 original size:82 final size:81
Alignment explanation
Indices: 68320882--68321037 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
68320872 TGCTATATAA
* *
68320882 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
68320947 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
68320964 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
68321028 CACTTAGTGC
65 CACTTAGTGC
68321038 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:68329081 original size:27 final size:27
Alignment explanation
Indices: 68329051--68329228 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
68329041 ATATTGAGTC
* * * *
68329051 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
68329078 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
68329105 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
68329133 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
68329160 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
68329187 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
68329214 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
68329229 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:68329190 original size:82 final size:81
Alignment explanation
Indices: 68329072--68329227 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
68329062 TGCTATATAA
* *
68329072 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
68329137 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
68329154 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
68329218 CACTTAGTGC
65 CACTTAGTGC
68329228 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:68333252 original size:28 final size:28
Alignment explanation
Indices: 68333212--68333301 Score: 139
Period size: 28 Copynumber: 3.3 Consensus size: 28
68333202 GGAGGAAGCG
*
68333212 TTCTGGTGGCTATGCCACAAATATATGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
68333240 TTCTGGTGGCTATGCCACAAATATCTG-
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
68333267 TTCTGGTGGCTCTGCCAC-AATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
68333294 ATCTGGTG
1 TTCTGGTG
68333302 ACTCTATCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
26 8 0.14
27 24 0.41
28 26 0.45
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (28 bp):
TTCTGGTGGCTATGCCACAAATATCTGT
Found at i:68333282 original size:27 final size:26
Alignment explanation
Indices: 68333211--68333325 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
68333201 TGGAGGAAGC
*
68333211 GTTCTGGTGGCTATGCCACAAATATAT
1 GTTCTGGTGGCTATGCCAC-AATATCT
68333238 GTTTCTGGTGGCTATGCCACAAATATCT
1 G-TTCTGGTGGCTATGCCAC-AATATCT
*
68333266 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * **
68333292 GTATCTGGTGACTCTATCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
68333319 GTTCTGG
1 GTTCTGG
68333326 CAGCCATGCT
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
26 14 0.17
27 41 0.51
28 26 0.32
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:68343601 original size:46 final size:47
Alignment explanation
Indices: 68343534--68343706 Score: 178
Period size: 46 Copynumber: 3.7 Consensus size: 47
68343524 TGTAACTCGC
* ** *
68343534 CCATAAGAGAACTTGGACTCAACTCAACGAGCTCGAG-CGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGAGACGTTCGCAT
* * *
68343580 CCATAAGTGAACTCAGACTCAACCCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC-GA-GAC--GTTCGCAT
* * *
68343630 --TTCA-CGAACTCAGACTCAACTCAACGAGTTCG-GACGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGAGACGTTCGCAT
68343673 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC
68343707 AGATGCCCAA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 56 0.54
47 27 0.26
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (47 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGAGACGTTCGCAT
Found at i:68346342 original size:30 final size:31
Alignment explanation
Indices: 68346308--68346551 Score: 207
Period size: 30 Copynumber: 8.1 Consensus size: 31
68346298 AGCTTCAGTT
*
68346308 ATCGAATTATGAAAAGGGAT-GGTGACGACC
1 ATCGAATTATGAAAAGGGATAGCTGACGACC
* * *
68346338 ATCGAAATATGAAAAGGGATAGCT-TCGACT
1 ATCGAATTATGAAAAGGGATAGCTGACGACC
* * * * ***
68346368 ATCAAAATATGAAAAGGGTTAGCTTA-GGTT
1 ATCGAATTATGAAAAGGGATAGCTGACGACC
* *
68346398 ATCTAATTATGAAAAGGGAT-GGTGACGACC
1 ATCGAATTATGAAAAGGGATAGCTGACGACC
* *
68346428 ATCGAATTATGAAAAGGGATAGCT-TCGACT
1 ATCGAATTATGAAAAGGGATAGCTGACGACC
* * *
68346458 ATCGAATAATGAAAAGGGAT-GGTGACAACC
1 ATCGAATTATGAAAAGGGATAGCTGACGACC
* * *
68346488 ATTGAATTAATGAAAAGGGATAGCT-TCGACT
1 ATCGAATT-ATGAAAAGGGATAGCTGACGACC
* * *
68346519 ATCGAACTATGAAAAGGGAT-GGTGACAACC
1 ATCGAATTATGAAAAGGGATAGCTGACGACC
68346549 ATC
1 ATC
68346552 TTGATTCCAC
Statistics
Matches: 168, Mismatches: 38, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
29 7 0.04
30 134 0.80
31 25 0.15
32 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (31 bp):
ATCGAATTATGAAAAGGGATAGCTGACGACC
Found at i:68346415 original size:90 final size:90
Alignment explanation
Indices: 68346264--68346475 Score: 313
Period size: 90 Copynumber: 2.3 Consensus size: 90
68346254 GACGATAAAT
* *
68346264 GATAGCTTCTG-CTATCGAATTATGAAAAAGGTATAGCTTCAGTTATCGAATTATGAAAAGGGAT
1 GATAGCTTC-GACTATC-AAATATGAAAAGGGTATAGCTTCAGTTATCGAATTATGAAAAGGGAT
68346328 GGTGACGACCATCGAAATATGAAAAGG
64 GGTGACGACCATCGAAATATGAAAAGG
*
68346355 GATAGCTTCGACTATCAAAATATGAAAAGGGT-TAGCTT-AGGTTATCTAATTATGAAAAGGGAT
1 GATAGCTTCGACTATC-AAATATGAAAAGGGTATAGCTTCA-GTTATCGAATTATGAAAAGGGAT
*
68346418 GGTGACGACCATCGAATTATGAAAAGG
64 GGTGACGACCATCGAAATATGAAAAGG
*
68346445 GATAGCTTCGACTATCGAATAATGAAAAGGG
1 GATAGCTTCGACTATCAAAT-ATGAAAAGGG
68346476 ATGGTGACAA
Statistics
Matches: 112, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
89 4 0.04
90 81 0.72
91 27 0.24
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.26
Consensus pattern (90 bp):
GATAGCTTCGACTATCAAATATGAAAAGGGTATAGCTTCAGTTATCGAATTATGAAAAGGGATGG
TGACGACCATCGAAATATGAAAAGG
Found at i:68346496 original size:90 final size:91
Alignment explanation
Indices: 68346311--68346538 Score: 268
Period size: 90 Copynumber: 2.5 Consensus size: 91
68346301 TTCAGTTATC
68346311 GAATTATGAAAAGGGATGGTGACGACCATCGAAATATGAAAAGGGATAGCTTCGACTATCAAAAT
1 GAATTATGAAAAGGGATGGTGACGACCATCGAAATATGAAAAGGGATAGCTTCGACTATCAAAAT
* * ****
68346376 ATGAAAAGGGTTAGCTTAGGTTATCT
66 ATGAAAAGGGATAGCTGAAACCATCT
* *
68346402 -AATTATGAAAAGGGATGGTGACGACCATCGAATTATGAAAAGGGATAGCTTCGACTATC-GAAT
1 GAATTATGAAAAGGGATGGTGACGACCATCGAAATATGAAAAGGGATAGCTTCGACTATCAAAAT
*
68346465 AATGAAAAGGGAT-GGTGACAACCAT-T
66 -ATGAAAAGGGATAGCTGA-AACCATCT
* * * *
68346491 GAATTAATGAAAAGGGATAGCT-TCGACTATCGAACTATGAAAAGGGAT
1 GAATT-ATGAAAAGGGAT-GGTGACGACCATCGAAATATGAAAAGGGAT
68346539 GGTGACAACC
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
89 7 0.06
90 75 0.63
91 35 0.29
92 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.24
Consensus pattern (91 bp):
GAATTATGAAAAGGGATGGTGACGACCATCGAAATATGAAAAGGGATAGCTTCGACTATCAAAAT
ATGAAAAGGGATAGCTGAAACCATCT
Found at i:68346531 original size:61 final size:59
Alignment explanation
Indices: 68346308--68346551 Score: 267
Period size: 60 Copynumber: 4.1 Consensus size: 59
68346298 AGCTTCAGTT
* * * * * * *
68346308 ATCGAATTATGAAAAGGGAT-GGTGACGACCATCGAAATATGAAAAGGGATAGCT-TCGACT
1 ATCGAATTATGAAAAGGGATAGCT-TCGACTATCG-AATATGAAAAGGGAT-GGTGACAACC
* * * * ** * *
68346368 ATCAAAATATGAAAAGGGTTAGCTTAGGTTATCTAATTATGAAAAGGGATGGTGACGACC
1 ATCGAATTATGAAAAGGGATAGCTTCGACTATCGAA-TATGAAAAGGGATGGTGACAACC
68346428 ATCGAATTATGAAAAGGGATAGCTTCGACTATCGAATAATGAAAAGGGATGGTGACAACC
1 ATCGAATTATGAAAAGGGATAGCTTCGACTATCGAAT-ATGAAAAGGGATGGTGACAACC
*
68346488 ATTGAATTAATGAAAAGGGATAGCTTCGACTATCGAACTATGAAAAGGGATGGTGACAACC
1 ATCGAATT-ATGAAAAGGGATAGCTTCGACTATCGAA-TATGAAAAGGGATGGTGACAACC
68346549 ATC
1 ATC
68346552 TTGATTCCAC
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
59 5 0.03
60 95 0.61
61 54 0.35
62 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (59 bp):
ATCGAATTATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATGGTGACAACC
Found at i:68352287 original size:27 final size:26
Alignment explanation
Indices: 68352239--68352298 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
68352229 GCGAAGCTGC
*
68352239 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
68352266 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
68352292 CAGATAT
1 CAGATAT
68352299 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:68353297 original size:27 final size:27
Alignment explanation
Indices: 68353264--68353524 Score: 351
Period size: 27 Copynumber: 9.7 Consensus size: 27
68353254 TTAGTTTACC
*
68353264 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
* *
68353291 AATTTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
* * *
68353318 AAATCACCAAAATACCCCTAGTTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
*
68353345 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGGTTTATA
* *
68353372 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
*
68353399 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
* * *
68353426 AAATCACCAAAATACCCCTAGTTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
*
68353453 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGGTTTATA
* * * *
68353480 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCTTGGTTTATA
*
68353507 AAATTACTAAAATACCCT
1 AAATTACCAAAATACCCT
68353525 CGACCTGTAA
Statistics
Matches: 201, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 201 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGGTTTATA
Found at i:68353329 original size:54 final size:54
Alignment explanation
Indices: 68353257--68353524 Score: 401
Period size: 54 Copynumber: 5.0 Consensus size: 54
68353247 GAATACTTTA
* * *
68353257 GTTTACCAAATTACCAAAATACCCTTGGTTTGTAAATTTACTAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTG
* * * * *
68353311 GTTTATAAAATCACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTG
68353365 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTG
* * * * *
68353419 GTTTATAAAATCACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTG
* *
68353473 GTTTACAAAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCT
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCT
68353525 CGACCTGTAA
Statistics
Matches: 189, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 189 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (54 bp):
GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTG
Found at i:68353446 original size:108 final size:108
Alignment explanation
Indices: 68353257--68353524 Score: 491
Period size: 108 Copynumber: 2.5 Consensus size: 108
68353247 GAATACTTTA
* * *
68353257 GTTTACCAAATTACCAAAATACCCTTGGTTTGTAAATTTACTAAAATACCCTTGGTTTATAAAAT
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAAT
68353322 CACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTG
66 CACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTG
68353365 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAAT
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAAT
68353430 CACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTG
66 CACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTG
* *
68353473 GTTTACAAAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCT
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCT
68353525 CGACCTGTAA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 155 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (108 bp):
GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAAT
CACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTG
Found at i:68353576 original size:27 final size:27
Alignment explanation
Indices: 68353264--68353577 Score: 186
Period size: 27 Copynumber: 11.6 Consensus size: 27
68353254 TTAGTTTACC
* **
68353264 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGACTTGTA
* * * ** *
68353291 AATTTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGACTTGTA
* * * *
68353318 AAATCACCAAAATACCC-CTAGTTTATA
1 AAATTACCAAAATACCCTCGA-CTTGTA
* ** **
68353345 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGACTTGTA
**
68353372 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GACTTGTA
* * ** *
68353399 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGACTTGTA
* * * *
68353426 AAATCACCAAAATACCC-CTAGTTTATA
1 AAATTACCAAAATACCCTCGA-CTTGTA
* ** **
68353453 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGACTTGTA
* *
68353480 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GACTTGTA
* *
68353507 AAATTACTAAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGACTTGTA
**
68353534 AAATTATTAAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGACTTGTA
* *
68353561 AAATTTCCAAAGTACCC
1 AAATTACCAAAATACCC
68353578 CTAATTTATA
Statistics
Matches: 234, Mismatches: 45, Indels: 16
0.79 0.15 0.05
Matches are distributed among these distances:
27 233 1.00
28 1 0.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGACTTGTA
Found at i:68353649 original size:27 final size:27
Alignment explanation
Indices: 68353619--68353861 Score: 290
Period size: 27 Copynumber: 9.0 Consensus size: 27
68353609 TTTACAAAAT
* *
68353619 TACCGAAATACCCTTGTAAGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
* ** *
68353646 TACCAAAATACCATTGTAGGATAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
68353673 TACCGAAATACCCCTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
* *
68353700 TACCGAAATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
** * *
68353727 TACTAAAATACCCCTGTAAGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
*
68353754 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
* *
68353781 TACCGAAATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
** *
68353808 TATTGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
* * *
68353835 TACCGAGATACCCTTGTGGGGTA-AAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
68353861 T
1 T
68353862 TACCATTTTA
Statistics
Matches: 185, Mismatches: 31, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
26 3 0.02
27 182 0.98
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (27 bp):
TACCGAAATACCCCTGTAGGGTAGAAA
Found at i:68353877 original size:81 final size:81
Alignment explanation
Indices: 68353619--68353861 Score: 344
Period size: 81 Copynumber: 3.0 Consensus size: 81
68353609 TTTACAAAAT
* * * * * ** * *
68353619 TACCGAAATACCCTTGTAAGGTAGAAATACCAAAATACCATTGTAGGATAGAAATACCGAAATAC
1 TACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAAATAC
*
68353684 CCCTGTAGGGTAGAAA
66 CCTTGTAGGGTAGAAA
*
68353700 TACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATAC
1 TACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAAATAC
68353765 CCTTGTAGGGTAGAAA
66 CCTTGTAGGGTAGAAA
* * *
68353781 TACCGAAATACCCCTATAGGGTAGAATTATTGAAATACCCCTGTAGGGTAGAATTACCGAGATAC
1 TACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAAATAC
*
68353846 CCTTGTGGGGTA-AAA
66 CCTTGTAGGGTAGAAA
68353861 T
1 T
68353862 TACCATTTTA
Statistics
Matches: 146, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
80 4 0.03
81 142 0.97
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (81 bp):
TACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAAATAC
CCTTGTAGGGTAGAAA
Found at i:68354099 original size:27 final size:26
Alignment explanation
Indices: 68354055--68354106 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
68354045 CTCGCTGCAA
*
68354055 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
68354082 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
68354107 GCAGCCTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:68362564 original size:30 final size:30
Alignment explanation
Indices: 68362530--68362590 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
68362520 TCCTTAACTC
68362530 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
68362560 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
68362590 A
1 A
68362591 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:68363760 original size:636 final size:636
Alignment explanation
Indices: 68362542--68363815 Score: 2476
Period size: 636 Copynumber: 2.0 Consensus size: 636
68362532 ACTTTGGAAA
68362542 AATTACAATTTTGCCCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAC
1 AATTACAATTTTGCCCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAC
68362607 TTCATCCCTTATTCTTATGTTTTATGACATGCTGATCACTTTTCCCTTCTATGGCAACATCAAAT
66 TTCATCCCTTATTCTTATGTTTTATGACATGCTGATCACTTTTCCCTTCTATGGCAACATCAAAT
68362672 TCTCACTCTAACATATACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTTACTCGTTTT
131 TCTCACTCTAACATATACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTTACTCGTTTT
68362737 CACTCAAAACCGAGTAGCACAAGTTGTCTAACATAATTTAAAACCTCATATTCTATCATAAAACA
196 CACTCAAAACCGAGTAGCACAAGTTGTCTAACATAATTTAAAACCTCATATTCTATCATAAAACA
68362802 CCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGCTTAAATTATTGCT
261 CCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGCTTAAATTATTGCT
*
68362867 AGAATAAGCTTAATCAAATTACCGGGATTCCAAAAACGTAAAGAACTTGAAAAACGGGGTTAGAA
326 AGAATAAGCTTAATCAAATTACCGGGATTCAAAAAACGTAAAGAACTTGAAAAACGGGGTTAGAA
68362932 CGGACTTACTATTGAGCTTGGAAAGCTTGAAAACCCTAGCCATGGCTTCCCCCATGCTAATTTTG
391 CGGACTTACTATTGAGCTTGGAAAGCTTGAAAACCCTAGCCATGGCTTCCCCCATGCTAATTTTG
68362997 GCCTCCATGAGAAAGATGAGTCAATTTTGGATTTATTTCCCTTTTTATTTCTTTTCATTACCCAA
456 GCCTCCATGAGAAAGATGAGTCAATTTTGGATTTATTTCCCTTTTTATTTCTTTTCATTACCCAA
68363062 TCCTTACTAAACTTTCAAAAATTCCATGCATGTCCAATTTTTGTCCATCACTTAGAAATTGGTCA
521 TCCTTACTAAACTTTCAAAAATTCCATGCATGTCCAATTTTTGTCCATCACTTAGAAATTGGTCA
68363127 AATTGCTATTTAAGACCTCTTAATTAATATTTCAAAGCAATTTCATACTAG
586 AATTGCTATTTAAGACCTCTTAATTAATATTTCAAAGCAATTTCATACTAG
* *
68363178 AATTAGAATTTTGCCCTTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAC
1 AATTACAATTTTGCCCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAC
68363243 TTCATCCCTTATTCTTATGTTTTATGACATGCTGATCACTTTTCCCTTCTATGGCAACATCAAAT
66 TTCATCCCTTATTCTTATGTTTTATGACATGCTGATCACTTTTCCCTTCTATGGCAACATCAAAT
68363308 TCTCACTCTAACATATACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTTACTCGTTTT
131 TCTCACTCTAACATATACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTTACTCGTTTT
* *
68363373 CACTCAAAACCGAGTAGCACAAGTTGTCTAACATAATTTAAAACCTCATATTCTATTATAAAATA
196 CACTCAAAACCGAGTAGCACAAGTTGTCTAACATAATTTAAAACCTCATATTCTATCATAAAACA
*
68363438 GCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGCTTAAATTATTGCT
261 CCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGCTTAAATTATTGCT
* *
68363503 AGAATAAGCTTAATCAAATTACCGGGATTCAAAAAACGTAAAGAACTTGAAAAATGGGGTTATAA
326 AGAATAAGCTTAATCAAATTACCGGGATTCAAAAAACGTAAAGAACTTGAAAAACGGGGTTAGAA
68363568 CGGACTTACTATTGAGCTTGGAAAGCTTGAAAACCCTAGCCATGGCTTCCCCCATGCTAATTTTG
391 CGGACTTACTATTGAGCTTGGAAAGCTTGAAAACCCTAGCCATGGCTTCCCCCATGCTAATTTTG
68363633 GCCTCCATGAGAAAGATGAGTCAATTTTGGATTTATTTCCCTTTTTATTTCTTTTCATTACCCAA
456 GCCTCCATGAGAAAGATGAGTCAATTTTGGATTTATTTCCCTTTTTATTTCTTTTCATTACCCAA
68363698 TCCTTACTAAACTTTCAAAAATTCCATGCATGTCCAATTTTTGTCCATCACTTAGAAATTGGTCA
521 TCCTTACTAAACTTTCAAAAATTCCATGCATGTCCAATTTTTGTCCATCACTTAGAAATTGGTCA
68363763 AATTGCTATTTAAGACCTCTTAATTAATATTTCAAAGCAATTTCATACTAG
586 AATTGCTATTTAAGACCTCTTAATTAATATTTCAAAGCAATTTCATACTAG
68363814 AA
1 AA
68363816 ACTTCTAGAA
Statistics
Matches: 630, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
636 630 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (636 bp):
AATTACAATTTTGCCCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAC
TTCATCCCTTATTCTTATGTTTTATGACATGCTGATCACTTTTCCCTTCTATGGCAACATCAAAT
TCTCACTCTAACATATACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTTACTCGTTTT
CACTCAAAACCGAGTAGCACAAGTTGTCTAACATAATTTAAAACCTCATATTCTATCATAAAACA
CCAAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTAGCTTAAATTATTGCT
AGAATAAGCTTAATCAAATTACCGGGATTCAAAAAACGTAAAGAACTTGAAAAACGGGGTTAGAA
CGGACTTACTATTGAGCTTGGAAAGCTTGAAAACCCTAGCCATGGCTTCCCCCATGCTAATTTTG
GCCTCCATGAGAAAGATGAGTCAATTTTGGATTTATTTCCCTTTTTATTTCTTTTCATTACCCAA
TCCTTACTAAACTTTCAAAAATTCCATGCATGTCCAATTTTTGTCCATCACTTAGAAATTGGTCA
AATTGCTATTTAAGACCTCTTAATTAATATTTCAAAGCAATTTCATACTAG
Found at i:68370037 original size:41 final size:40
Alignment explanation
Indices: 68369971--68370049 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 40
68369961 CAGGGGTTTC
68369971 CACACGGCCTGACACATGCCTATGTC-CATGGCCCATGTCCCT
1 CACACGGCCTGACACA-GCCTATGTCTCA--GCCCATGTCCCT
68370013 CACACGGCCATGACAC-GCCTATGTCTCAGCCCATGTC
1 CACACGGCC-TGACACAGCCTATGTCTCAGCCCATGTC
68370050 TAAAAACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
40 9 0.26
41 9 0.26
42 11 0.31
43 6 0.17
ACGTcount: A:0.20, C:0.41, G:0.19, T:0.20
Consensus pattern (40 bp):
CACACGGCCTGACACAGCCTATGTCTCAGCCCATGTCCCT
Found at i:68376948 original size:50 final size:49
Alignment explanation
Indices: 68376839--68377070 Score: 266
Period size: 49 Copynumber: 4.7 Consensus size: 49
68376829 CTGGTACGCA
* * *
68376839 TAGTAGCCTGCAGTTAGTACTACACATGCGACCAATTATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGATACACG
**
68376888 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCTGATACACG
* * * * *
68376938 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCTGATACACG
* * * * * * *
68376989 TAGTAGCTTGCACTTATTACTACATATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGATACACG
* *
68377038 TAGTAACCTGCACTTAGCACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
68377071 CCACAATAGA
Statistics
Matches: 152, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
49 67 0.44
50 50 0.33
51 35 0.23
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGATACACG
Found at i:68377347 original size:27 final size:27
Alignment explanation
Indices: 68377317--68377370 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
68377307 TCATACAACC
* *
68377317 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
68377344 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
68377371 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:68379868 original size:15 final size:15
Alignment explanation
Indices: 68379844--68379892 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
68379834 AATCGAATAA
68379844 AGAAATCCAAGATTG
1 AGAAATCCAAGATTG
* **
68379859 AGAAAACCAA-ATAA
1 AGAAATCCAAGATTG
68379873 AGAAATCCAAGATTG
1 AGAAATCCAAGATTG
68379888 AGAAA
1 AGAAA
68379893 CCCAGAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.14
Consensus pattern (15 bp):
AGAAATCCAAGATTG
Found at i:68379871 original size:29 final size:29
Alignment explanation
Indices: 68379829--68379909 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
68379819 TAAAGATAAC
* *
68379829 GAGAAAATCGAATAAAGAAATCCAAGATT
1 GAGAAAACCAAATAAAGAAATCCAAGATT
68379858 GAGAAAACCAAATAAAGAAATCCAAGATT
1 GAGAAAACCAAATAAAGAAATCCAAGATT
*
68379887 GAGAAACCCAGAATAAAGAAATC
1 GAGAAAACCA-AATAAAGAAATC
68379910 TAGAATAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 36 0.75
30 12 0.25
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.14
Consensus pattern (29 bp):
GAGAAAACCAAATAAAGAAATCCAAGATT
Found at i:68379906 original size:15 final size:15
Alignment explanation
Indices: 68379888--68379926 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
68379878 TCCAAGATTG
68379888 AGAAACCCAGAATAA
1 AGAAACCCAGAATAA
* *
68379903 AGAAATCTAGAATAA
1 AGAAACCCAGAATAA
68379918 AGAAACCCA
1 AGAAACCCA
68379927 AGATACGATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.59, C:0.18, G:0.13, T:0.10
Consensus pattern (15 bp):
AGAAACCCAGAATAA
Found at i:68382967 original size:46 final size:47
Alignment explanation
Indices: 68382900--68383158 Score: 198
Period size: 46 Copynumber: 5.6 Consensus size: 47
68382890 TGTAACCCGC
*
68382900 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGAG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCAT
* * *
68382946 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GA-GAC--GTTCGCAT
* * *
68382996 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCG-GACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCAT
* * * * * *
68383039 CCATACGTGAACTCAGACTCAACTCAACGAGCTCGAATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCG-A-GAC--GTTCGCAT
* * **
68383089 --TTCA-CGAACTTAGACTCAACTCAACGAGTTCG-GACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCAT
* *
68383132 CCATAAGTGAACTCGGACTCAAATCAA
1 CCATAAGCGAACTCGGACTCAACTCAA
68383159 TGATCGGATA
Statistics
Matches: 163, Mismatches: 32, Indels: 36
0.71 0.14 0.16
Matches are distributed among these distances:
42 5 0.03
43 6 0.04
44 4 0.02
45 3 0.02
46 74 0.45
47 53 0.33
48 4 0.02
49 3 0.02
50 6 0.04
51 5 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (47 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCAT
Found at i:68383015 original size:93 final size:93
Alignment explanation
Indices: 68382907--68383158 Score: 400
Period size: 93 Copynumber: 2.7 Consensus size: 93
68382897 CGCCCATAAG
*
68382907 CGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGTTCGGA-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
*
68382971 AACGAGTTC-AGATGCCTAGTTACATTTCA
65 AACGAGCTCGA-ATGCCTAGTTACATTTCA
* * *
68383000 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATACGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
68383065 ACGAGCTCGAATGCCTAGTTACATTTCA
66 ACGAGCTCGAATGCCTAGTTACATTTCA
** *
68383093 CGAACTTAGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAAATCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
68383158 A
66 A
68383159 TGATCGGATA
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
93 143 0.98
94 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGAATGCCTAGTTACATTTCA
Found at i:68383022 original size:47 final size:47
Alignment explanation
Indices: 68382954--68383119 Score: 171
Period size: 47 Copynumber: 3.6 Consensus size: 47
68382944 ATCCATAAGT
*
68382954 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
1 GAACTCAGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
* * * * * **
68383001 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCA-TACGT
1 GAACTCAGACTCAACTCAACGAGTTC--AGATGC-CTAGTTACATTTCAC
*
68383047 GAACTCAGACTCAACTCAACGAGCTC-GAATGCCTAGTTACATTTCAC
1 GAACTCAGACTCAACTCAACGAGTTCAG-ATGCCTAGTTACATTTCAC
*
68383094 GAACTTAGACTCAACTCAACGAGTTC
1 GAACTCAGACTCAACTCAACGAGTTC
68383120 GGACGTTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 29 0.31
47 55 0.58
49 5 0.05
50 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (47 bp):
GAACTCAGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:68393843 original size:25 final size:24
Alignment explanation
Indices: 68393801--68393848 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
68393791 GCTTTATCAT
*
68393801 ATAACTGGAGGCCTAGCCTCTTTTA
1 ATAACTGGAGGCATAGCC-CTTTTA
68393826 ATAACTGG-GGCATAAGCCCTTTT
1 ATAACTGGAGGCAT-AGCCCTTTT
68393849 GCACTTCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (24 bp):
ATAACTGGAGGCATAGCCCTTTTA
Found at i:68393923 original size:20 final size:20
Alignment explanation
Indices: 68393898--68393964 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
68393888 TTATGAATAC
68393898 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
68393918 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
68393938 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
68393958 ACCATGT
1 ATCATGT
68393965 TAATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:68393929 original size:11 final size:11
Alignment explanation
Indices: 68393898--68393953 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
68393888 TTATGAATAC
68393898 ATCATGTGCAT
1 ATCATGTGCAT
*
68393909 ATCA--TACAT
1 ATCATGTGCAT
68393918 ATCATGTGCAT
1 ATCATGTGCAT
*
68393929 ATCA--TACAT
1 ATCATGTGCAT
*
68393938 GTCATGTGCAT
1 ATCATGTGCAT
68393949 ATCAT
1 ATCAT
68393954 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:68394027 original size:25 final size:25
Alignment explanation
Indices: 68393999--68394047 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
68393989 TCATATTTAA
* * *
68393999 ACCTAGGGGTATAATGGTCATTTTT
1 ACCTAGGGGCAAAACGGTCATTTTT
68394024 ACCTAGGGGCAAAACGGTCATTTT
1 ACCTAGGGGCAAAACGGTCATTTT
68394048 CATATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (25 bp):
ACCTAGGGGCAAAACGGTCATTTTT
Found at i:68397647 original size:16 final size:16
Alignment explanation
Indices: 68397622--68397654 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
68397612 ACCGTATTCT
*
68397622 ATATTTTATAGTAGCA
1 ATATTCTATAGTAGCA
68397638 ATATTCTATAGTAGCA
1 ATATTCTATAGTAGCA
68397654 A
1 A
68397655 AGGAATAAGA
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:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
ATATTCTATAGTAGCA
Found at i:68399422 original size:48 final size:47
Alignment explanation
Indices: 68399306--68399568 Score: 237
Period size: 48 Copynumber: 5.5 Consensus size: 47
68399296 AAGTGGTCAC
* * * * * **
68399306 ATCATGGCCCAAAGCCAACTCAA-TATATCTCGCACTCAAAGTGCTAAT
1 ATCATGGCCCGAATCCAAATCAAGTA-A-CTCGCACCCGAAGTGCCGAT
* * * *
68399354 ATCATGGCCC-ATAACCAAATC-AGTGAATCTCGCACCCTAGGTTCCGAT
1 ATCATGGCCCGA-ATCCAAATCAAGT-AA-CTCGCACCCGAAGTGCCGAT
* * *
68399402 ATCATGGCCCGAATCAAAATCAAAGTAACTCACACCCGAAGTACCGAT
1 ATCATGGCCCGAATCCAAATC-AAGTAACTCGCACCCGAAGTGCCGAT
*
68399450 ATCATGGCCCGAAGT-CAAATCAAAGTAACTCGCACCTGAAGTGCCGAT
1 ATCATGGCCCGAA-TCCAAATC-AAGTAACTCGCACCCGAAGTGCCGAT
* *
68399498 ATCATGGCCCGAAGCCAAATCAAAGTAACTCGCACCCGAAGTGCGGAT
1 ATCATGGCCCGAATCCAAATC-AAGTAACTCGCACCCGAAGTGCCGAT
* **
68399546 ATCATGGCCTGAAGGCAAATCAA
1 ATCATGGCCCGAATCCAAATCAA
68399569 TATATCACCT
Statistics
Matches: 184, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
47 4 0.02
48 172 0.93
49 5 0.03
50 3 0.02
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.19
Consensus pattern (47 bp):
ATCATGGCCCGAATCCAAATCAAGTAACTCGCACCCGAAGTGCCGAT
Found at i:68403373 original size:23 final size:22
Alignment explanation
Indices: 68403321--68403373 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
68403311 TCCACGTCTT
*
68403321 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
68403343 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
68403366 TTTCTTTT
1 TTTCTTTT
68403374 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:68405760 original size:22 final size:23
Alignment explanation
Indices: 68405735--68405794 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
68405725 TGGACTGAAT
68405735 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
68405757 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
68405779 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
68405795 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:68405762 original size:4 final size:4
Alignment explanation
Indices: 68405744--68405777 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
68405734 TATAAAAATT
68405744 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
68405778 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:68411158 original size:48 final size:48
Alignment explanation
Indices: 68411096--68411368 Score: 293
Period size: 48 Copynumber: 5.7 Consensus size: 48
68411086 CTTGCACACT
* * * * * *
68411096 AAGTGCTCACATCATGACCCGAAGCCAACTCAATA-TATCTCGCACCCA
1 AAGTGCTGATATCATGGCCCGAAGCCAAATCAA-AGTAACTCGCACCCG
* * * *
68411144 AAGTGCTAATATCATTGCCCGTAGCCAAATC--AGTGAAGCTTGCACCCG
1 AAGTGCTGATATCATGGCCCGAAGCCAAATCAAAGT-AA-CTCGCACCCG
* * *
68411192 AGGTGCCGATATCATGGCCTGAAGCCAAATCAAAGTAACTCGCACCCG
1 AAGTGCTGATATCATGGCCCGAAGCCAAATCAAAGTAACTCGCACCCG
* *
68411240 AAGTGATGATATCATGGCCCGAAGCCAAATCAAAGTAACTCGCACCCA
1 AAGTGCTGATATCATGGCCCGAAGCCAAATCAAAGTAACTCGCACCCG
* * * *
68411288 AAGTGCCGATATCATGGCCCAAAGCCAAATCAAAGTAACTCGCAGCTG
1 AAGTGCTGATATCATGGCCCGAAGCCAAATCAAAGTAACTCGCACCCG
* *
68411336 AAGTG-TCAATATCATGGCCCAAAGCCAAATCAA
1 AAGTGCT-GATATCATGGCCCGAAGCCAAATCAA
68411369 TATATCTCCT
Statistics
Matches: 190, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
45 1 0.01
46 1 0.01
47 1 0.01
48 182 0.96
49 2 0.01
50 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (48 bp):
AAGTGCTGATATCATGGCCCGAAGCCAAATCAAAGTAACTCGCACCCG
Found at i:68411361 original size:144 final size:144
Alignment explanation
Indices: 68411106--68411368 Score: 334
Period size: 144 Copynumber: 1.8 Consensus size: 144
68411096 AAGTGCTCAC
* * * * **
68411106 ATCATGACCCGAAGCCAACTCAATATATCTCGCACCCAAAGTGCTAATATCATTGCCCGTAGCCA
1 ATCATGACCCGAAGCCAAATCAATATAACTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCCA
* * * **
68411171 AATCAGTGAAGCTTGCACCCGAGGTGCCGATATCATGGCCTGAAGCCAAATCAAAGTAACTCGCA
66 AATCAGTGAAGCTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAAAGTAACTCGCA
68411236 CCCGAAGTGATGAT
131 CCCGAAGTGATGAT
* *
68411250 ATCATGGCCCGAAGCCAAATCAA-AGTAACTCGCACCCAAAGTGCCGATATCATGGCCCAAAGCC
1 ATCATGACCCGAAGCCAAATCAATA-TAACTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCC
* * *
68411314 AAATCAAAGT-AA-CTCGCAGCTGAAGTGTCAATATCATGGCCCAAAGCCAAATCAA
65 AAATC--AGTGAAGCTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAA
68411369 TATATCTCCT
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
143 1 0.01
144 94 0.94
145 2 0.02
146 3 0.03
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.18
Consensus pattern (144 bp):
ATCATGACCCGAAGCCAAATCAATATAACTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCCA
AATCAGTGAAGCTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAAAGTAACTCGCA
CCCGAAGTGATGAT
Found at i:68414309 original size:25 final size:23
Alignment explanation
Indices: 68414277--68414348 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 23
68414267 AATTCTTTTT
68414277 AAAAATTTAAATTTGTTTGTTTAAG
1 AAAAATTTAAATTT-TTT-TTTAAG
*
68414302 AATAATTT-AA--TTTTTTTAAG
1 AAAAATTTAAATTTTTTTTTAAG
68414322 AAAAATTTAAATTTTACTTTTTAAG
1 AAAAATTTAAATTTT--TTTTTAAG
68414347 AA
1 AA
68414349 TACCAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 13 0.32
21 5 0.12
22 1 0.03
23 2 0.05
24 2 0.05
25 17 0.43
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (23 bp):
AAAAATTTAAATTTTTTTTTAAG
Found at i:68414321 original size:20 final size:21
Alignment explanation
Indices: 68414277--68414336 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 21
68414267 AATTCTTTTT
68414277 AAAAATTTAAATTTGTTTGTTTAAG
1 AAAAATTTAAA--T-TTT-TTTAAG
*
68414302 AATAATTT-AATTTTTTTAAG
1 AAAAATTTAAATTTTTTTAAG
68414322 AAAAATTTAAATTTT
1 AAAAATTTAAATTTT
68414337 ACTTTTTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 13 0.41
21 9 0.28
22 1 0.03
24 2 0.06
25 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
AAAAATTTAAATTTTTTTAAG
Found at i:68414951 original size:86 final size:85
Alignment explanation
Indices: 68414836--68415005 Score: 200
Period size: 86 Copynumber: 2.0 Consensus size: 85
68414826 TTTTACTTTA
* * *
68414836 CACTCATTTGGGTAGTTCAACTTTCAAAATATATCAAAAA-AGTCCTCAAATC-TTTTCAAAGAA
1 CACTCAATTGGGTACTTCAACTTTCAAAATATATCAAAAAGA-CCCTCAAA-CATTTTCAAA-AA
*
68414899 AAACAATTAAGCCCCTTTTTTTT
63 AAACAATTAAGCCCCTGTTTTTT
* * * * * *
68414922 CACTCAATTGGGTACTTGAATTTTTAAAATGTATCAAAAAGACCCTCAAACATTTTCAAAAATAG
1 CACTCAATTGGGTACTTCAACTTTCAAAATATATCAAAAAGACCCTCAAACATTTTCAAAAAAAA
*
68414987 TAATTAAGCCCCTGTTTTT
66 CAATTAAGCCCCTGTTTTT
68415006 ATTTAAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
85 21 0.30
86 49 0.69
87 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (85 bp):
CACTCAATTGGGTACTTCAACTTTCAAAATATATCAAAAAGACCCTCAAACATTTTCAAAAAAAA
CAATTAAGCCCCTGTTTTTT
Found at i:68415397 original size:19 final size:19
Alignment explanation
Indices: 68415344--68415403 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
68415334 TCTAAATTTT
*
68415344 AATTTTTTATATTTTTATTAA
1 AATTTTTTAT-TTTTT-CTAA
** *
68415365 AATTTAATAATTTTTCTAA
1 AATTTTTTATTTTTTCTAA
68415384 AATTTTTTATTTTTTTCTAA
1 AATTTTTTA-TTTTTTCTAA
68415404 TTTTTAATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 10 0.32
20 14 0.45
21 7 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTTATTTTTTCTAA
Found at i:68415398 original size:20 final size:20
Alignment explanation
Indices: 68415344--68415403 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
68415334 TCTAAATTTT
68415344 AATTTTTTATATTTTTAT-TAA
1 AATTTTTTAT-TTTTT-TCTAA
** *
68415365 AATTTAATA-ATTTTTCTAA
1 AATTTTTTATTTTTTTCTAA
68415384 AATTTTTTATTTTTTTCTAA
1 AATTTTTTATTTTTTTCTAA
68415404 TTTTTAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 9 0.29
21 7 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
AATTTTTTATTTTTTTCTAA
Found at i:68416573 original size:12 final size:12
Alignment explanation
Indices: 68416556--68416580 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68416546 CAGCCGGCAG
68416556 AGGCTTGTCCAT
1 AGGCTTGTCCAT
68416568 AGGCTTGTCCAT
1 AGGCTTGTCCAT
68416580 A
1 A
68416581 TCTCTGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (12 bp):
AGGCTTGTCCAT
Found at i:68417106 original size:58 final size:58
Alignment explanation
Indices: 68417024--68417141 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
68417014 TCCAAGAATC
*
68417024 TCACTCTTGCACTTAACCAAGCTATAGCATTCTTTGATGCACAAAAGTGTAAGAATTT
1 TCACTCTTGCACTTAACCAAGCTATAACATTCTTTGATGCACAAAAGTGTAAGAATTT
*
68417082 TCACTCTTGCATTTAACCAAGCTATAACATTCTTTGATGCACAAAAGTGTAAGAATTT
1 TCACTCTTGCACTTAACCAAGCTATAACATTCTTTGATGCACAAAAGTGTAAGAATTT
68417140 TC
1 TC
68417142 CTTTGTGAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (58 bp):
TCACTCTTGCACTTAACCAAGCTATAACATTCTTTGATGCACAAAAGTGTAAGAATTT
Found at i:68419423 original size:48 final size:48
Alignment explanation
Indices: 68419352--68419449 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
68419342 TTTTCAACGC
68419352 AAGAATGAGGTAAAAGACAAGGCAAACAGCACATTCTTTGAAACTCCT
1 AAGAATGAGGTAAAAGACAAGGCAAACAGCACATTCTTTGAAACTCCT
68419400 AAGAATGAGGTAAAAGACAAGGCAAACAGCACATTCTTTGAAACTCCT
1 AAGAATGAGGTAAAAGACAAGGCAAACAGCACATTCTTTGAAACTCCT
68419448 AA
1 AA
68419450 TTTCTGATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (48 bp):
AAGAATGAGGTAAAAGACAAGGCAAACAGCACATTCTTTGAAACTCCT
Found at i:68425967 original size:27 final size:26
Alignment explanation
Indices: 68425911--68425968 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
68425901 TGAAGAAGAT
*** *
68425911 AAGAAGAGAGAAAAATAAAGGGGAAT
1 AAGAAGAGAGAAAAATAAAGAAAAAA
*
68425937 AAGAAGAGAAGGAAAATAAAGAAAAAA
1 AAGAAGAG-AGAAAAATAAAGAAAAAA
68425964 AAGAA
1 AAGAA
68425969 AATAATTTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (26 bp):
AAGAAGAGAGAAAAATAAAGAAAAAA
Found at i:68429193 original size:43 final size:43
Alignment explanation
Indices: 68429136--68429242 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
68429126 GATTAACGAG
* *
68429136 ATGTGTTTATGTGTAAGACCATGTCTGGGACACTGGCATCATT
1 ATGTGATTACGTGTAAGACCATGTCTGGGACACTGGCATCATT
* * *
68429179 ATGTGATTACGTGTAACACCATGTCTGGGACATTGGCATCGTT
1 ATGTGATTACGTGTAAGACCATGTCTGGGACACTGGCATCATT
* *
68429222 AT-TTATTTCGTGTAAGACCAT
1 ATGTGATTACGTGTAAGACCAT
68429243 AGCTAGGCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 16 0.29
43 40 0.71
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGTCTGGGACACTGGCATCATT
Found at i:68431662 original size:46 final size:45
Alignment explanation
Indices: 68431609--68431970 Score: 270
Period size: 46 Copynumber: 7.8 Consensus size: 45
68431599 TATTTGGGCA
*
68431609 TCCGAACTCGTTGAGTTGTGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
68431655 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
68431702 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *** * *
68431748 TTCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
68431795 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *** * *
68431841 TTCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
68431888 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
68431934 -CTCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
68431971 GTGGGTTACA
Statistics
Matches: 246, Mismatches: 48, Indels: 44
0.73 0.14 0.13
Matches are distributed among these distances:
43 3 0.01
44 9 0.04
45 4 0.02
46 123 0.50
47 92 0.37
48 3 0.01
49 9 0.04
50 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:68431718 original size:47 final size:47
Alignment explanation
Indices: 68431655--68431916 Score: 261
Period size: 47 Copynumber: 5.6 Consensus size: 47
68431645 GATGCGAATG
68431655 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAGGCA
* * *** * *
68431702 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCA
*
68431746 TGTTCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAGGCA
1 --TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAGGCA
* * *** * *
68431795 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCA
*
68431839 TGTTCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAGGCA
1 --TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAGGCA
*
68431888 TCCGAGCTCGTTGAGTTGAGTCTGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTC
68431917 ACTTATGGAT
Statistics
Matches: 168, Mismatches: 33, Indels: 28
0.73 0.14 0.12
Matches are distributed among these distances:
43 2 0.01
44 6 0.04
45 2 0.01
46 60 0.36
47 88 0.52
48 2 0.01
49 6 0.04
50 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAGGCA
Found at i:68431764 original size:93 final size:93
Alignment explanation
Indices: 68431605--68431963 Score: 637
Period size: 93 Copynumber: 3.9 Consensus size: 93
68431595 AGGATATTTG
* * *
68431605 GGCATCCGAACTCGTTGAGTTGTGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
68431670 TTGAGTCTGAGTTCGAGAGATGTAACTA
66 TTGAGTCTGAGTTCGAGAGATGTAACTA
68431698 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
68431763 TTGAGTCTGAGTTCGAGAGATGTAACTA
66 TTGAGTCTGAGTTCGAGAGATGTAACTA
68431791 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
68431856 TTGAGTCTGAGTTCGAGAGATGTAACTA
66 TTGAGTCTGAGTTCGAGAGATGTAACTA
* * * * *
68431884 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCTCGAGCTCATTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
*
68431949 TTGAGTCCGAGTTCG
66 TTGAGTCTGAGTTCG
68431964 CTTATGGGTG
Statistics
Matches: 257, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 257 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
TTGAGTCTGAGTTCGAGAGATGTAACTA
Found at i:68433471 original size:46 final size:46
Alignment explanation
Indices: 68433399--68433694 Score: 538
Period size: 46 Copynumber: 6.4 Consensus size: 46
68433389 TCGGGATTAC
*
68433399 TCTTACACATTTCTTATCAGGCTGCCATGGTATCTTTCAACCATGG
1 TCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
*
68433445 TCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGG
1 TCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
*
68433491 CCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
1 TCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
*
68433537 TCTTACATATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
1 TCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
*
68433583 TCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGG
1 TCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
*
68433629 CCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
1 TCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
68433675 TCTTACACATTTCATATCAG
1 TCTTACACATTTCATATCAG
68433695 AGAGCACACT
Statistics
Matches: 239, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 239 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.36
Consensus pattern (46 bp):
TCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGG
Found at i:68441452 original size:27 final size:26
Alignment explanation
Indices: 68441417--68441528 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
68441407 AGCATGGCTG
* *
68441417 CCAGAACAGATAATGTGATAGAGTCA
1 CCAGAACAGATAATGTGGTAGAGCCA
*
68441443 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGTAGAGCCA
*
68441471 CCAGAACAGAAATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGTAGAGCCA
* * *
68441498 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGTAGAGCCA
68441525 CCAG
1 CCAG
68441529 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.08
27 51 0.70
28 16 0.22
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGTAGAGCCA
Found at i:68441509 original size:54 final size:54
Alignment explanation
Indices: 68441417--68441528 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
68441407 AGCATGGCTG
* *
68441417 CCAGAACAGATAATGTGATAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGATAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
68441471 CCAGAACAGAAATATGTGGTAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGATAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
68441525 CCAG
1 CCAG
68441529 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGATAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:68445338 original size:16 final size:16
Alignment explanation
Indices: 68445288--68445338 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
68445278 AAGTTTTGTT
68445288 AAATG-ATTTTAGCTAA
1 AAATGCATTTTAGCT-A
* *
68445304 AAATGCATTTGATG-AA
1 AAATGCATTTTA-GCTA
68445320 AAATGCATTTTAGCTA
1 AAATGCATTTTAGCTA
68445336 AAA
1 AAA
68445339 ACTGCGTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 1 0.04
16 21 0.75
17 5 0.18
18 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (16 bp):
AAATGCATTTTAGCTA
Found at i:68447468 original size:40 final size:40
Alignment explanation
Indices: 68447398--68447560 Score: 159
Period size: 40 Copynumber: 4.1 Consensus size: 40
68447388 CGGGGTTTAT
** * *
68447398 CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAAC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
68447437 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * **
68447477 CCGGATATAGTCGCTAGCACAAATGCCTTCGGATCTTAGT
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
68447517 CCGGATGTAGTCACTTAGCACAAAAGCCTTCAGGTACTT-AC
1 CCGGATATAGTCAC-TAGCACAAATGCCTTCGGGT-CTTAAC
68447558 CCG
1 CCG
68447561 ATCCGCTGTC
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
39 15 0.15
40 62 0.62
41 20 0.20
42 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:68447698 original size:28 final size:28
Alignment explanation
Indices: 68447635--68448292 Score: 1237
Period size: 28 Copynumber: 23.5 Consensus size: 28
68447625 ATATTAAGTC
* *
68447635 CGCACACTCAGTGCTATATAATCAA-CT
1 CGCACACTTAGTGCTACATAATCAAGCT
* *
68447662 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAGCT
*
68447690 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAGCT
* **
68447718 CGGACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447746 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447774 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447802 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447830 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447858 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447886 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447914 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447942 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447970 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68447998 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448026 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448054 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448082 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448110 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448138 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448166 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448194 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448222 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448250 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
68448278 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
68448293 GTACAATTTA
Statistics
Matches: 623, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
27 24 0.04
28 599 0.96
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAGCT
Found at i:68449487 original size:9 final size:9
Alignment explanation
Indices: 68449473--68449499 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
68449463 CTACCATGCA
68449473 TTACATACC
1 TTACATACC
68449482 TTACATACC
1 TTACATACC
68449491 TTACATACC
1 TTACATACC
68449500 ATGCATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (9 bp):
TTACATACC
Found at i:68449510 original size:14 final size:14
Alignment explanation
Indices: 68449491--68449538 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
68449481 CTTACATACC
68449491 TTACATACCATGCA
1 TTACATACCATGCA
68449505 TTACATACCATGCA
1 TTACATACCATGCA
68449519 TTACATACCATGCA
1 TTACATACCATGCA
*
68449533 TCACAT
1 TTACAT
68449539 TCAAACATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (14 bp):
TTACATACCATGCA
Found at i:68449531 original size:28 final size:30
Alignment explanation
Indices: 68449464--68449538 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 30
68449454 TTCCAAAAGC
*
68449464 TACCATGCATTACATACCTTACATACCTTACA
1 TACCATGCATTACATACC-T-CATACATTACA
*
68449496 TACCATGCATTACATA-C-CATGCATTACA
1 TACCATGCATTACATACCTCATACATTACA
*
68449524 TACCATGCATCACAT
1 TACCATGCATTACAT
68449539 TCAAACATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 23 0.57
31 1 0.03
32 16 0.40
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (30 bp):
TACCATGCATTACATACCTCATACATTACA
Found at i:68451069 original size:23 final size:24
Alignment explanation
Indices: 68451026--68451070 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
68451016 TTTAGTTAAT
68451026 TTGTTTTTTATTTATATAAATTTG
1 TTGTTTTTTATTTATATAAATTTG
68451050 TTGTTTTTTATTTATA-AAATT
1 TTGTTTTTTATTTATATAAATT
68451071 GGCATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (24 bp):
TTGTTTTTTATTTATATAAATTTG
Found at i:68453684 original size:22 final size:22
Alignment explanation
Indices: 68453648--68453697 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
68453638 AATTGAACAT
* *
68453648 ATGCA-TGTGCGAACCTCTTCC
1 ATGCATTGTGCAAACCTCATCC
*
68453669 ATGCATTGTGCAAACCTCATCT
1 ATGCATTGTGCAAACCTCATCC
68453691 ATGCATT
1 ATGCATT
68453698 CTACGAACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (22 bp):
ATGCATTGTGCAAACCTCATCC
Found at i:68468625 original size:19 final size:19
Alignment explanation
Indices: 68468601--68468917 Score: 616
Period size: 19 Copynumber: 16.6 Consensus size: 19
68468591 AATAGCCCAT
68468601 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468620 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468639 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468658 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468677 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468696 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468715 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468734 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468753 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468772 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468791 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468810 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468829 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468848 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468867 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468886 TTAGATATGATATGCAATC
1 TTAGATATGATATGCAATC
68468905 TTGAAGATATGAT
1 TT--AGATATGAT
68468918 CTTGTAATCT
Statistics
Matches: 296, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
19 287 0.97
21 9 0.03
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
TTAGATATGATATGCAATC
Found at i:68474492 original size:13 final size:12
Alignment explanation
Indices: 68474474--68474527 Score: 60
Period size: 11 Copynumber: 4.7 Consensus size: 12
68474464 CTTCTATTTC
68474474 AAAGAAAAGGAAA
1 AAAGAAAA-GAAA
68474487 AAAGAAAAG-AA
1 AAAGAAAAGAAA
*
68474498 AAAGAGAA-AAA
1 AAAGAAAAGAAA
*
68474509 ATA-AAAAGAAA
1 AAAGAAAAGAAA
68474520 AAAGAAAA
1 AAAGAAAA
68474528 AATGGAGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 3 0.09
11 18 0.53
12 5 0.15
13 8 0.24
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:68474505 original size:8 final size:7
Alignment explanation
Indices: 68474474--68474529 Score: 57
Period size: 7 Copynumber: 8.4 Consensus size: 7
68474464 CTTCTATTTC
68474474 AAAG-AA
1 AAAGAAA
*
68474480 AAGGAAA
1 AAAGAAA
68474487 AAAG--A
1 AAAGAAA
68474492 AAAGAAA
1 AAAGAAA
68474499 AAGAGAAA
1 AA-AGAAA
*
68474507 AAA-TAA
1 AAAGAAA
68474513 AAAGAAA
1 AAAGAAA
68474520 AAAGAAA
1 AAAGAAA
68474527 AAA
1 AAA
68474530 TGGAGAGCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
5 5 0.12
6 8 0.20
7 21 0.51
8 7 0.17
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:68474514 original size:15 final size:14
Alignment explanation
Indices: 68474474--68474529 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
68474464 CTTCTATTTC
*
68474474 AAAG-AAAAGGAAA
1 AAAGAAAAAGAAAA
68474487 AAAG-AAAAGAAAA
1 AAAGAAAAAGAAAA
* *
68474500 AGAGAAAAA-ATAA
1 AAAGAAAAAGAAAA
68474513 AAAGAAAAAAGAAAA
1 AAAG-AAAAAGAAAA
68474528 AA
1 AA
68474530 TGGAGAGCCC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 21 0.60
14 9 0.26
15 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAGAAAA
Found at i:68474530 original size:20 final size:20
Alignment explanation
Indices: 68474474--68474530 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
68474464 CTTCTATTTC
* *
68474474 AAAG-AAAAGGAAAAAA-GA
1 AAAGAAAAAAGAAAAAATAA
68474492 AAAGAAAAAGAGAAAAAATAA
1 AAAGAAAAA-AGAAAAAATAA
68474513 AAAGAAAAAAGAAAAAAT
1 AAAGAAAAAAGAAAAAAT
68474531 GGAGAGCCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 16 0.47
21 10 0.29
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAGAAAAAAGAAAAAATAA
Found at i:68475620 original size:84 final size:84
Alignment explanation
Indices: 68475479--68476172 Score: 1089
Period size: 84 Copynumber: 8.3 Consensus size: 84
68475469 AAATTCAGCA
* *
68475479 CCTTAAT-CCCTAAGCAGTAGGGTAACAGGTTAAATTTGTAGATCTTATCTCCTTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
* *
68475543 GAAGTAGATCGAAGACTCG
66 GGAGCAGATCGAAGACTCG
*
68475562 CCTTAATCCCCTAAGCAGTAAGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
68475627 GGAGCAGATCGAAGACTCG
66 GGAGCAGATCGAAGACTCG
*
68475646 CCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
68475711 GGAGCAGATCGAAGACTCG
66 GGAGCAGATCGAAGACTCG
*
68475730 CCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
68475795 GGAGCAGATCGAAGACTCG
66 GGAGCAGATCGAAGACTCG
*
68475814 CCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
*
68475879 GGAGCAGATCGAAGACTCA
66 GGAGCAGATCGAAGACTCG
* * * *
68475898 CCTTAATCCCCAAAGCAGTAGGGTAATAGGTT-CA----CAGATCTTATCTCCCTAAGCAGTAGC
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
68475958 GGAGCAGATCGACGACGACTCG
66 GGAGCAGATCGA--A-GACTCG
* *
68475980 CCTTAATCCCCTAAGCAGTAGTGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGTAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
* *
68476045 GGAGCAGATTGAAGACCCG
66 GGAGCAGATCGAAGACTCG
* *
68476064 CCTTAATCCCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTA--TCCCTAAGCAGTAGC
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
*
68476127 GGAGCAGATCGAAGACAATGCA
66 GGAGCAGATCGAAGAC--T-CG
*
68476149 CCTTAACCCCCTAAGCAGTAGGGT
1 CCTTAATCCCCTAAGCAGTAGGGT
68476173 CCAAGATGAT
Statistics
Matches: 568, Mismatches: 31, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
79 37 0.07
81 1 0.00
82 62 0.11
83 9 0.02
84 400 0.70
85 24 0.04
87 35 0.06
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (84 bp):
CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGACTCG
Found at i:68476117 original size:41 final size:41
Alignment explanation
Indices: 68475988--68476125 Score: 111
Period size: 41 Copynumber: 3.3 Consensus size: 41
68475978 CGCCTTAATC
*
68475988 CCCTAAGCAGTAGTGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTA--T
* * * * *** * *
68476031 CCCTAAGTAGTAGTGG-AGCAGATTGAA-GACCCG-CCTTAAT
1 CCCTAAGCAGTAG-GGTAACAGGTTAAATTTGCAGATCTT-AT
*
68476071 CCCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTAT
1 -CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTAT
68476113 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
68476126 CGGAGCAGAT
Statistics
Matches: 70, Mismatches: 19, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
40 3 0.04
41 36 0.51
42 7 0.10
43 23 0.33
44 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (41 bp):
CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTAT
Found at i:68476971 original size:19 final size:19
Alignment explanation
Indices: 68476947--68477043 Score: 146
Period size: 19 Copynumber: 5.2 Consensus size: 19
68476937 AATCTTTAAG
*
68476947 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
68476966 GATATGCAATCTTAGA-AT
1 GATATGCAATCTTAGATAT
68476984 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
68477001 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
68477020 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
68477041 GAT
1 GAT
68477044 CTTGTAATCT
Statistics
Matches: 72, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
16 10 0.14
17 6 0.08
18 5 0.07
19 42 0.58
21 9 0.12
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:68476993 original size:35 final size:37
Alignment explanation
Indices: 68476947--68477043 Score: 135
Period size: 35 Copynumber: 2.6 Consensus size: 37
68476937 AATCTTTAAG
*
68476947 GATATGCAATCTTAGATGTGATATGCAATCTTAGA-AT
1 GATA-GCAATCTTAGATATGATATGCAATCTTAGATAT
68476984 GATA-CAATCTTAGATATGATATGCAATCTTAGATAT
1 GATAGCAATCTTAGATATGATATGCAATCTTAGATAT
68477020 GATATGCAATCTTGAAGATATGAT
1 GATA-GCAATCTT--AGATATGAT
68477044 CTTGTAATCT
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
35 28 0.52
36 6 0.11
37 4 0.07
38 7 0.13
40 9 0.17
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (37 bp):
GATAGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:68477088 original size:55 final size:54
Alignment explanation
Indices: 68477027--68477141 Score: 221
Period size: 55 Copynumber: 2.1 Consensus size: 54
68477017 TATGATATGC
68477027 AATCTTGAAGATATGATCTTGTAATCTTGGAGATTTAATTTGTAGATATCCTTT
1 AATCTTGAAGATATGATCTTGTAATCTTGGAGATTTAATTTGTAGATATCCTTT
68477081 AAATCTTGAAGATATGATCTTGTAATCTTGGAGATTTAATTTGTAGATATCCTTT
1 -AATCTTGAAGATATGATCTTGTAATCTTGGAGATTTAATTTGTAGATATCCTTT
68477136 AATCTT
1 AATCTT
68477142 AACCGTTGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 6 0.10
55 54 0.90
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (54 bp):
AATCTTGAAGATATGATCTTGTAATCTTGGAGATTTAATTTGTAGATATCCTTT
Found at i:68478691 original size:16 final size:17
Alignment explanation
Indices: 68478652--68478702 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
68478642 AGCTTAATAT
68478652 TATTATATTATTAATAAA
1 TATT-TATTATTAATAAA
* *
68478670 TTTTTATTTTTAA-AAA
1 TATTTATTATTAATAAA
**
68478686 TATTTAAAATTAATAAA
1 TATTTATTATTAATAAA
68478703 ATACTATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
16 12 0.46
17 11 0.42
18 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTATTATTAATAAA
Found at i:68482903 original size:29 final size:28
Alignment explanation
Indices: 68482869--68482946 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
68482859 TTATGAGATT
68482869 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
68482899 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
68482926 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
68482947 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:68483212 original size:173 final size:174
Alignment explanation
Indices: 68482899--68483225 Score: 584
Period size: 173 Copynumber: 1.9 Consensus size: 174
68482889 AAATTGTACA
* *
68482899 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
68482964 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTATATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
68483029 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
68483073 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
68483138 TGTGC-AACCCAATATATATTTTATATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTATATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
68483202 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
68483226 ACCTTGAGTT
Statistics
Matches: 146, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
173 82 0.56
174 64 0.44
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTATATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:68484154 original size:62 final size:62
Alignment explanation
Indices: 68484057--68484178 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 62
68484047 AAAAATTAGT
*
68484057 AGGAATGGAACTAAATAGTGAATAAATTATGTAATCGAAGCTCGATGAGTCTATTTTCATGC
1 AGGAATGAAACTAAATAGTGAATAAATTATGTAATCGAAGCTCGATGAGTCTATTTTCATGC
* *
68484119 AGGAATGAAATTAATTAGTGAATAAATTATGTAATCGAAGCTCGATGAGTCTATTTTCAT
1 AGGAATGAAACTAAATAGTGAATAAATTATGTAATCGAAGCTCGATGAGTCTATTTTCAT
68484179 ATAAAAGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (62 bp):
AGGAATGAAACTAAATAGTGAATAAATTATGTAATCGAAGCTCGATGAGTCTATTTTCATGC
Found at i:68487815 original size:40 final size:40
Alignment explanation
Indices: 68487723--68487833 Score: 134
Period size: 40 Copynumber: 2.7 Consensus size: 40
68487713 GGGTTTAAAT
* *
68487723 CCGAGCTTGGTTTCGAAGGGCCTTTGAGCCAGTGCTAATAA
1 CCGAACTTAGTTTCGAAGGG-CTTTGAGCCAGTGCTAATAA
*
68487764 CCGAACTTAGTTTCGAAGGGCTTTAGAGCCAGTG-TCATAA
1 CCGAACTTAGTTTCGAAGGGCTTT-GAGCCAGTGCTAATAA
* * *
68487804 CCGGACTTAGTTCCGAAGGGCCTTCGAGCC
1 CCGAACTTAGTTTCGAAGGG-CTTTGAGCC
68487834 TTGGTCTCGA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
40 32 0.52
41 30 0.48
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAACTTAGTTTCGAAGGGCTTTGAGCCAGTGCTAATAA
Found at i:68493644 original size:79 final size:81
Alignment explanation
Indices: 68493508--68493692 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
68493498 TTGAATGATG
* *
68493508 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
68493572 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * ** **
68493587 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
68493649 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
68493667 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
68493693 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:68493706 original size:40 final size:40
Alignment explanation
Indices: 68493509--68493692 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
68493499 TGAATGATGT
* * * *
68493509 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
68493549 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
68493589 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTATTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
68493627 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
68493668 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
68493693 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:68493714 original size:79 final size:79
Alignment explanation
Indices: 68493561--68493725 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
68493551 GGACTAAGAT
* * ** *
68493561 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTATTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
68493626 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
68493640 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
68493703 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
68493719 CCGAAGG
1 CCGAAGG
68493726 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:68502329 original size:16 final size:17
Alignment explanation
Indices: 68502290--68502345 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
68502280 AGCTTAATAT
68502290 TATTATATTATTAATAAA
1 TATT-TATTATTAATAAA
* *
68502308 TTTTTATTTTTAA-AAA
1 TATTTATTATTAATAAA
**
68502324 TATTTAAAATTAATAAAA
1 TATTTATTATTAAT-AAA
68502342 TATT
1 TATT
68502346 ATAATTTTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 12 0.40
17 8 0.27
18 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTATTATTAATAAA
Found at i:68505316 original size:26 final size:27
Alignment explanation
Indices: 68505287--68505339 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
68505277 GCCCCCTAAC
68505287 TGAT-AAATGACTATTATGCCCCTATG
1 TGATAAAATGACTATTATGCCCCTATG
* *
68505313 TGATAAAATGACTGTTATGCCCTTATG
1 TGATAAAATGACTATTATGCCCCTATG
68505340 AATTGTATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (27 bp):
TGATAAAATGACTATTATGCCCCTATG
Found at i:68505726 original size:40 final size:40
Alignment explanation
Indices: 68505671--68505786 Score: 142
Period size: 40 Copynumber: 2.9 Consensus size: 40
68505661 TTTTTCATAC
**
68505671 AGATCGAGCATTAGCGGTGTTTTTTGAAAAACGCCACTAT
1 AGATCGAGCATTAGCGACGTTTTTTGAAAAACGCCACTAT
* * * *
68505711 AGATCGAGCATTAGCGACGTTTCTTCAAAAACACCGCTAT
1 AGATCGAGCATTAGCGACGTTTTTTGAAAAACGCCACTAT
* * * *
68505751 AGGTCGACCATTAGCGACGCTTTCTGAAAAACGCCA
1 AGATCGAGCATTAGCGACGTTTTTTGAAAAACGCCA
68505787 AAAGTTAAGC
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (40 bp):
AGATCGAGCATTAGCGACGTTTTTTGAAAAACGCCACTAT
Found at i:68505884 original size:40 final size:40
Alignment explanation
Indices: 68505829--68505937 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
68505819 AGCTTTAGTG
*
68505829 GCATTAGCGGCGCTTTTTGGAAAACGCCAATACAGGTCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCAATACAGGTCGA
* ** * *
68505869 GCATTAGTGGCGCTTTTTGAAAAACGCCGCTATAGGTTGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCAATACAGGTCGA
* * *
68505909 CCATTAGCAGTGCTTTTTGAAAAACGCCA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCA
68505938 CAAAAAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCAATACAGGTCGA
Found at i:68506039 original size:35 final size:35
Alignment explanation
Indices: 68505997--68506066 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
68505987 ATTAGCGGCA
** * *
68505997 TTTTTGAAAAATGCCGCTGTAGATTGAGCATTAGC
1 TTTTTGAAAAACACCGCTATAGATCGAGCATTAGC
68506032 TTTTTGAAAAACACCGCTATAGATCGAGCATTAGC
1 TTTTTGAAAAACACCGCTATAGATCGAGCATTAGC
68506067 GACGCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAAACACCGCTATAGATCGAGCATTAGC
Found at i:68506094 original size:150 final size:152
Alignment explanation
Indices: 68505678--68506084 Score: 427
Period size: 151 Copynumber: 2.7 Consensus size: 152
68505668 TACAGATCGA
* * * * *
68505678 GCATTAGCGGTGTTTTTTGAAAAACGCCACTATAGATCGAGCATTAGCGACGTTTCTTCAAAAAC
1 GCATTAGCGGCGATTTTTGAAAAACGCCAATACAGATCGAGCATTAG-G-C-TTT-TTGAAAAAC
* * * *
68505743 ACCGCTATAGGTCGACCATTAGC-GACGCTTTCTGAAAAAC-GC-C---AAAAGTTAAGCACAAC
62 ACCGCTATAGATCGACCATTAGCAG-CGCTTTTTGAAAAACACCACAAAAAAAATTAAGCACAAC
68505802 GTCGTCGTTTTATGTTGAGCTTTAGTG
126 GTCGTCGTTTTATGTTGAGCTTTAGTG
* * *
68505829 GCATTAGCGGCGCTTTTTGGAAAACGCCAATACAGGTCGAGCATTAGTGGCGCTTTTTGAAAAAC
1 GCATTAGCGGCGATTTTTGAAAAACGCCAATACAGATCGAGCATTA---G-GCTTTTTGAAAAAC
* * * * * *
68505894 GCCGCTATAGGTTGACCATTAGCAGTGCTTTTTGAAAAACGCCACAAAAAAAATTAAGTACAACG
62 ACCGCTATAGATCGACCATTAGCAGCGCTTTTTGAAAAACACCACAAAAAAAATTAAGCACAACG
*
68505959 TCGTTGTTTTATGTTGAGCTTTAGTG
127 TCGTCGTTTTATGTTGAGCTTTAGTG
* ** ** *
68505985 GCATTAGCGGC-ATTTTTGAAAAATGCCGCTGTAGATTGAGCATTA-GCTTTTTGAAAAACACCG
1 GCATTAGCGGCGATTTTTGAAAAACGCCAATACAGATCGAGCATTAGGCTTTTTGAAAAACACCG
*
68506048 CTATAGATCGAGCATTAGC-GACGCTTTTTGAAAAACA
66 CTATAGATCGACCATTAGCAG-CGCTTTTTGAAAAACA
68506085 TCGTAAAAAA
Statistics
Matches: 216, Mismatches: 30, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
149 1 0.00
150 47 0.22
151 82 0.38
152 5 0.02
153 2 0.01
154 3 0.01
155 25 0.12
156 51 0.24
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (152 bp):
GCATTAGCGGCGATTTTTGAAAAACGCCAATACAGATCGAGCATTAGGCTTTTTGAAAAACACCG
CTATAGATCGACCATTAGCAGCGCTTTTTGAAAAACACCACAAAAAAAATTAAGCACAACGTCGT
CGTTTTATGTTGAGCTTTAGTG
Found at i:68506482 original size:22 final size:21
Alignment explanation
Indices: 68506453--68506508 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
68506443 AGTTACTATT
*
68506453 TTATGGTTTATTGATTATGGA
1 TTATGGTTTATGGATTATGGA
* *
68506474 TTATGGGTTTAAGGATTATGGT
1 TTAT-GGTTTATGGATTATGGA
68506496 TTATGGTTTATGG
1 TTATGGTTTATGG
68506509 TTAAGGGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (21 bp):
TTATGGTTTATGGATTATGGA
Found at i:68506496 original size:14 final size:14
Alignment explanation
Indices: 68506471--68506528 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
68506461 TATTGATTAT
68506471 GGATTATGGGTTTAA
1 GGATTAT-GGTTTAA
*
68506486 GGATTATGGTTTAT
1 GGATTATGGTTTAA
*
68506500 GGTTTATGG-TTAA
1 GGATTATGGTTTAA
* **
68506513 GGGTTGGGGTTTAA
1 GGATTATGGTTTAA
68506527 GG
1 GG
68506529 TTTAGGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 9 0.25
14 20 0.56
15 7 0.19
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (14 bp):
GGATTATGGTTTAA
Found at i:68506509 original size:7 final size:7
Alignment explanation
Indices: 68506452--68506510 Score: 64
Period size: 7 Copynumber: 8.3 Consensus size: 7
68506442 GAGTTACTAT
68506452 TTTATGG
1 TTTATGG
*
68506459 TTTATTG
1 TTTATGG
*
68506466 ATTATGG
1 TTTATGG
*
68506473 ATTATGGG
1 TTTAT-GG
*
68506481 TTTAAGG
1 TTTATGG
*
68506488 ATTATGG
1 TTTATGG
68506495 TTTATGG
1 TTTATGG
68506502 TTTATGG
1 TTTATGG
68506509 TT
1 TT
68506511 AAGGGTTGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 38 0.88
8 5 0.12
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (7 bp):
TTTATGG
Found at i:68506566 original size:21 final size:21
Alignment explanation
Indices: 68506507--68506564 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
68506497 TATGGTTTAT
* * *
68506507 GGTTAAGGGTTGGGGTTTAAG
1 GGTTAGGGGTTAGGGGTTAAG
* *
68506528 GTTTAGGTGTTAGGGGTTAAG
1 GGTTAGGGGTTAGGGGTTAAG
68506549 GGTTAGGGGTTTAGGG
1 GGTTAGGGG-TTAGGG
68506565 TTTATGTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.34
Consensus pattern (21 bp):
GGTTAGGGGTTAGGGGTTAAG
Found at i:68506567 original size:7 final size:7
Alignment explanation
Indices: 68506478--68506592 Score: 56
Period size: 7 Copynumber: 16.4 Consensus size: 7
68506468 TATGGATTAT
68506478 GGGTTTA
1 GGGTTTA
* *
68506485 AGGATTA
1 GGGTTTA
*
68506492 TGGTTTA
1 GGGTTTA
*
68506499 TGGTTTA
1 GGGTTTA
* *
68506506 TGGTTAA
1 GGGTTTA
*
68506513 GGG-TTG
1 GGGTTTA
68506519 GGGTTTA
1 GGGTTTA
*
68506526 AGGTTTA
1 GGGTTTA
68506533 -GGTGTTA
1 GGGT-TTA
*
68506540 GGGGTTAA
1 -GGGTTTA
68506548 GGG-TTA
1 GGGTTTA
68506554 GGGGTTTA
1 -GGGTTTA
68506562 GGGTTTA
1 GGGTTTA
* *
68506569 TGTTTTA
1 GGGTTTA
* *
68506576 TGATTTA
1 GGGTTTA
*
68506583 AGGTTTA
1 GGGTTTA
68506590 GGG
1 GGG
68506593 GATAGGAGTC
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
6 9 0.11
7 67 0.80
8 5 0.06
9 3 0.04
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:68507004 original size:40 final size:40
Alignment explanation
Indices: 68506960--68507043 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
68506950 AAAATTATAA
* * *
68506960 AAAAGTAAAGCATTAGC-AGCATTTATGATAAAAACGCTGC
1 AAAAGGAAAGCAATAGCGA-CATTTATGATAAAAACGCCGC
*
68507000 AAAAGGCAAGCAATAGCGACATTTATGATAAAAACGCCGC
1 AAAAGGAAAGCAATAGCGACATTTATGATAAAAACGCCGC
68507040 AAAA
1 AAAA
68507044 AATTAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.48, C:0.17, G:0.18, T:0.18
Consensus pattern (40 bp):
AAAAGGAAAGCAATAGCGACATTTATGATAAAAACGCCGC
Found at i:68507251 original size:18 final size:18
Alignment explanation
Indices: 68507214--68507267 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
68507204 CTCTCCCCCC
** *
68507214 ATTCCCTTTTTTTTCCCA
1 ATTCCCTTTTCATTCTCA
* *
68507232 ATTTCTTTTTCATTCTCA
1 ATTCCCTTTTCATTCTCA
*
68507250 ATTCCCTTTTCTTTCTCA
1 ATTCCCTTTTCATTCTCA
68507268 GCTTTTCTCA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.30, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTCCCTTTTCATTCTCA
Found at i:68513991 original size:29 final size:28
Alignment explanation
Indices: 68513957--68514034 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
68513947 TTATGAGATT
68513957 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
68513987 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
68514014 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
68514035 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:68514311 original size:173 final size:174
Alignment explanation
Indices: 68513987--68514313 Score: 548
Period size: 173 Copynumber: 1.9 Consensus size: 174
68513977 AAATTGTACA
* * *
68513987 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGCGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* * *
68514052 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
68514117 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
68514161 GCACTAAGTGCGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGCGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
68514226 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
68514290 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
68514314 ACCTTGAGTT
Statistics
Matches: 142, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
173 79 0.56
174 63 0.44
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGCGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:68528834 original size:8 final size:8
Alignment explanation
Indices: 68528821--68528846 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
68528811 ATATTGCATG
68528821 AATTGTGT
1 AATTGTGT
68528829 AATTGTGT
1 AATTGTGT
68528837 AATTGTGT
1 AATTGTGT
68528845 AA
1 AA
68528847 GTATGTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (8 bp):
AATTGTGT
Found at i:68546368 original size:43 final size:43
Alignment explanation
Indices: 68546302--68546387 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
68546292 AAATGAGATA
68546302 CCTTGAACAAACATCATTAAGGTAGAATTATTCGATGTTTGGG
1 CCTTGAACAAACATCATTAAGGTAGAATTATTCGATGTTTGGG
*
68546345 CCTTGAACAAACATCATTGAGGTAGAATTATTCGATGTTTGGG
1 CCTTGAACAAACATCATTAAGGTAGAATTATTCGATGTTTGGG
68546388 GTATTGACTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (43 bp):
CCTTGAACAAACATCATTAAGGTAGAATTATTCGATGTTTGGG
Found at i:68547757 original size:15 final size:15
Alignment explanation
Indices: 68547726--68547754 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
68547716 TTAGTTTAAA
68547726 ATTTAATCATATTTT
1 ATTTAATCATATTTT
68547741 ATTTAATCA-ATTTT
1 ATTTAATCATATTTT
68547755 TATCTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTAATCATATTTT
Found at i:68548185 original size:18 final size:18
Alignment explanation
Indices: 68548143--68548191 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
68548133 CCCGTGCCTA
*
68548143 GTGCTGCTTGCTCCTATT
1 GTGCTGCTTGCTCCTATG
* *
68548161 CTACTGCTTGCTCCTATG
1 GTGCTGCTTGCTCCTATG
*
68548179 GTGCTGCCTGCTC
1 GTGCTGCTTGCTC
68548192 GTACGCACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.06, C:0.33, G:0.22, T:0.39
Consensus pattern (18 bp):
GTGCTGCTTGCTCCTATG
Found at i:68548373 original size:26 final size:25
Alignment explanation
Indices: 68548344--68548392 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
68548334 TTTTTCTCCT
* *
68548344 AAATTTTAATTTTATTTAATTATTTA
1 AAATTTCAA-TTTATTGAATTATTTA
68548370 AAATTTCAATTTATTGAATTATT
1 AAATTTCAATTTATTGAATTATT
68548393 AATAGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AAATTTCAATTTATTGAATTATTTA
Found at i:68554003 original size:31 final size:31
Alignment explanation
Indices: 68553967--68554045 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
68553957 TTTAACGGTT
68553967 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
68553998 ACTGGGTCGAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
68554029 ACTGGGCTGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
68554046 ATTGTAAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:68554116 original size:42 final size:42
Alignment explanation
Indices: 68554069--68554160 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
68554059 TGGCCCATAG
* ** *
68554069 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
68554111 GCCCATTTCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
68554153 GCCCATTT
1 GCCCATTT
68554161 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:68554382 original size:26 final size:26
Alignment explanation
Indices: 68554298--68554428 Score: 180
Period size: 26 Copynumber: 5.2 Consensus size: 26
68554288 GGCCTAGACT
68554298 CTTTT-AAT-AACTGGGGCA-AAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
** **
68554321 CTTTTCGGTAAACTGGGGCA-AAGAT
1 CTTTTCAATAAACTGGGGCATAAGCC
68554346 CTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
**
68554372 CTTTTTGATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
68554398 CTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
68554424 CTTTT
1 CTTTT
68554429 GCACTTCCTC
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
23 5 0.05
24 1 0.01
25 31 0.33
26 56 0.60
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (26 bp):
CTTTTCAATAAACTGGGGCATAAGCC
Found at i:68554507 original size:20 final size:20
Alignment explanation
Indices: 68554478--68554564 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
68554468 TTATGAATAC
68554478 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
68554498 ATCATCTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
68554518 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
68554538 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
68554558 ATCATGT
1 ATCATGT
68554565 ATATCATATC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:68555334 original size:27 final size:27
Alignment explanation
Indices: 68555273--68555336 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
68555263 GGTGTATTCA
68555273 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* * *
68555300 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
68555327 TCTTTTTACC
1 TCATTTTACC
68555337 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:68555398 original size:27 final size:27
Alignment explanation
Indices: 68555368--68555520 Score: 148
Period size: 27 Copynumber: 5.7 Consensus size: 27
68555358 TTCATCCTAC
* * *
68555368 AAGGGTGTTTTGGTAAATCTACAAATT
1 AAGGGTATTTTGGTAATTTTACAAATT
** *
68555395 AAGGGTATTTCT-GTAATTTTGTAAATC
1 AAGGGTATTT-TGGTAATTTTACAAATT
*
68555422 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTGGTAATTTTACAAATT
* * *
68555449 AAGGGTATTTCGGTAATTTCACAAA-C
1 AAGGGTATTTTGGTAATTTTACAAATT
* *
68555475 CAGTGGTATTTTGGTAATTTTACAAACT
1 AAG-GGTATTTTGGTAATTTTACAAATT
* *
68555503 AGGGGTGTTTTGGTAATT
1 AAGGGTATTTTGGTAATT
68555521 CTACCCTATA
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 3 0.03
27 96 0.95
28 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAATT
Found at i:68555436 original size:54 final size:54
Alignment explanation
Indices: 68555370--68555520 Score: 185
Period size: 54 Copynumber: 2.8 Consensus size: 54
68555360 CATCCTACAA
* * * * *** *
68555370 GGGTGTTTTGGTAAATCTACAAATTAAGGGTATTTCTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAG
68555424 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAG
* * * * *
68555478 TGGTATTTTGGTAATTTTACAAACTAGGGGTGTTTTGGTAATT
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATT
68555521 CTACCCTATA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAG
Found at i:68555590 original size:27 final size:27
Alignment explanation
Indices: 68555559--68555643 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
68555549 CACAATCGAA
* * *
68555559 GGTAAAACGGTAATTTTGTAAATCAAG
1 GGTAAAACAGTAATTCTATAAATCAAG
*
68555586 GGTAAAACAGTAATTCTATAAATCGAG
1 GGTAAAACAGTAATTCTATAAATCAAG
* * *
68555613 GGTAAAACAATAATTCTATAAAGCGAG
1 GGTAAAACAGTAATTCTATAAATCAAG
68555640 GGTA
1 GGTA
68555644 CTTTAGTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (27 bp):
GGTAAAACAGTAATTCTATAAATCAAG
Found at i:68555653 original size:27 final size:27
Alignment explanation
Indices: 68555594--68555834 Score: 121
Period size: 27 Copynumber: 8.9 Consensus size: 27
68555584 AGGGTAAAAC
* ****
68555594 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTATAAAGCGAGGGTATTTT
* *
68555621 AATAATTCTATAAAGCGAGGGTACTTT
1 AGTAATTCTATAAAGCGAGGGTATTTT
* *
68555648 AGTAATT-TTTACAAGTCGAAGGTATTTT
1 AGTAATTCTATA-AAG-CGAGGGTATTTT
* * *
68555676 AGTAATTTTACAAAGCAGGGGGTATTTT
1 AGTAATTCTATAAAGC-GAGGGTATTTT
* * *
68555704 AGTAATTTTACAAA-CCAGGGGTATTTT
1 AGTAATTCTATAAAGCGA-GGGTATTTT
* * *
68555731 AGTAATTTTACAAA-CCAGGGGTATTTT
1 AGTAATTCTATAAAGCGA-GGGTATTTT
* * ** *
68555758 GGTAATTTTATTGATCGAGGGTATTTT
1 AGTAATTCTATAAAGCGAGGGTATTTT
* * * * *
68555785 GGTAATTTTGTAAA-CTAAGGGTATTTC
1 AGTAATTCTATAAAGC-GAGGGTATTTT
* * *
68555812 AGTAATTTTGTAAATCGAGGGTA
1 AGTAATTCTATAAAGCGAGGGTA
68555835 AAATGGTAAT
Statistics
Matches: 178, Mismatches: 28, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
26 4 0.02
27 126 0.71
28 46 0.26
29 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.37
Consensus pattern (27 bp):
AGTAATTCTATAAAGCGAGGGTATTTT
Found at i:68555676 original size:28 final size:26
Alignment explanation
Indices: 68555633--68555820 Score: 151
Period size: 27 Copynumber: 6.9 Consensus size: 26
68555623 TAATTCTATA
*
68555633 AAGCGAGGGTACTTTAGTAATTTTTAC
1 AAGCGAGGGTATTTTAGTAA-TTTTAC
*
68555660 AAGTCGAAGGTATTTTAGTAATTTTAC
1 AAG-CGAGGGTATTTTAGTAATTTTAC
*
68555687 AAAGCAGGGGGTATTTTAGTAATTTTAC
1 -AAGC-GAGGGTATTTTAGTAATTTTAC
* *
68555715 AAACCAGGGGTATTTTAGTAATTTTAC
1 AAGCGA-GGGTATTTTAGTAATTTTAC
* * * *
68555742 AAACCAGGGGTATTTTGGTAATTTTATT
1 AAGCGA-GGGTATTTTAGTAATTTTA-C
* * * **
68555770 GATCGAGGGTATTTTGGTAATTTTGT
1 AAGCGAGGGTATTTTAGTAATTTTAC
* * *
68555796 AAACTAAGGGTATTTCAGTAATTTT
1 AAGC-GAGGGTATTTTAGTAATTTT
68555821 GTAAATCGAG
Statistics
Matches: 137, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.02
27 93 0.68
28 41 0.30
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (26 bp):
AAGCGAGGGTATTTTAGTAATTTTAC
Found at i:68555780 original size:54 final size:54
Alignment explanation
Indices: 68555396--68555834 Score: 208
Period size: 54 Copynumber: 8.1 Consensus size: 54
68555386 CTACAAATTA
** * * * **
68555396 AGGGTATTTCT-GTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTA
1 AGGGTATTT-TAGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTATAAATCG
** * * * * *
68555450 AGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAA-CT
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTATAAATCG
* * * ** * * * *
68555503 AGGGGTGTTTTGGTAATTCTACCCTA-TAGGGGTATTTCAGTAATTTCA-CAATCG
1 A-GGGTATTTTAGTAATTTTA-CAAACCAGGGGTATTTTAGTAATTTTATAAATCG
* ***** ** * * **** *
68555557 AAGGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCG
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTATAAATCG
**** * * * * *
68555611 AGGGTAAAACAATAATTCTATAAAGC-GAGGGTACTTTAGTAATTTT-TACAAGTCG
1 AGGGTATTTTAGTAATTTTACAAACCAG-GGGTATTTTAGTAATTTTATA-AA-TCG
* * * *
68555666 AAGGTATTTTAGTAATTTTACAAAGCAGGGGGTATTTTAGTAATTTTACAAA-CC
1 AGGGTATTTTAGTAATTTTACAAACCA-GGGGTATTTTAGTAATTTTATAAATCG
* **
68555720 AGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATTGATCG
1 A-GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTATAAATCG
* ** * * * *
68555775 AGGGTATTTTGGTAATTTTGTAAACTAAGGGTATTTCAGTAATTTTGTAAATCG
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTATAAATCG
68555829 AGGGTA
1 AGGGTA
68555835 AAATGGTAAT
Statistics
Matches: 291, Mismatches: 80, Indels: 28
0.73 0.20 0.07
Matches are distributed among these distances:
52 1 0.00
53 31 0.11
54 189 0.65
55 49 0.17
56 19 0.07
57 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.37
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTATAAATCG
Found at i:68555842 original size:54 final size:54
Alignment explanation
Indices: 68555784--68555906 Score: 138
Period size: 54 Copynumber: 2.3 Consensus size: 54
68555774 GAGGGTATTT
* *** * *
68555784 TGGTAATTTTGTAAACTAAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAACTAAGGGTAAGACAGTAATTCTATAAATCGAGGGTAAAA
* * * *
68555838 TGGTAATTCTGTCAATTGAGGGTAAGACGGTAATTCTATAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAACTAAGGGTAAGACAGTAATTCTATAAATCGAGGGTAAAA
* *
68555892 AGGTAATTCTATAAA
1 TGGTAATTCTGTAAA
68555907 TCGAGGGTAA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (54 bp):
TGGTAATTCTGTAAACTAAGGGTAAGACAGTAATTCTATAAATCGAGGGTAAAA
Found at i:68555842 original size:81 final size:81
Alignment explanation
Indices: 68555695--68555845 Score: 178
Period size: 81 Copynumber: 1.9 Consensus size: 81
68555685 ACAAAGCAGG
* * ***
68555695 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGG
1 GGGTATTTTAGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTACAAACCAGGGGTAAAATGG
68555760 TAATTTTATTGATCGA
66 TAATTTTATTGATCGA
* ** * ** *
68555776 GGGTATTTTGGTAATTTTGTAAACTAAGGGTATTTCAGTAATTTTGTAAATC-GAGGGTAAAATG
1 GGGTATTTTAGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTACAAACCAG-GGGTAAAATG
68555840 GTAATT
65 GTAATT
68555846 CTGTCAATTG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
80 1 0.02
81 56 0.98
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (81 bp):
GGGTATTTTAGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTACAAACCAGGGGTAAAATGG
TAATTTTATTGATCGA
Done.