Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 27 of 59
Found at i:9974146 original size:40 final size:38
Alignment explanation
Indices: 9974081--9974158 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 38
9974071 GAATGTTGAT
*
9974081 ATGTTTATGATATTTAACTGCTATAAACTAAAGTCTGCTG
1 ATGTTTATGATATTTAACTGCTAT-AAC-AAAATCTGCTG
* *
9974121 ATGTTT-TGATATTTTGACTGTTATAACAAAATCTGCTG
1 ATGTTTATGATA-TTTAACTGCTATAACAAAATCTGCTG
9974159 CTAATATGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 10 0.29
39 8 0.24
40 16 0.47
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (38 bp):
ATGTTTATGATATTTAACTGCTATAACAAAATCTGCTG
Found at i:9976045 original size:61 final size:61
Alignment explanation
Indices: 9975755--9976044 Score: 427
Period size: 61 Copynumber: 4.8 Consensus size: 61
9975745 CAGCTCATGT
* * * * *
9975755 GCATCATTACTGACATGTGCACTACCTACTCCGCACATGCACGATTGTGAATATCACGACA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTGAATATCACGACA
* *
9975816 GCATCATTACCGGCATATGCACTGCCCACTCCACACATGCACGGTTGTGAATATCACGACA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTGAATATCACGACA
*
9975877 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTGAATATCACCACA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTGAATATCACGACA
** * * * * * *
9975938 GCATCATTACCCACATATGCACTACCCACTCCACACATGCACGGTTATAAATATCACTACA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTGAATATCACGACA
*
9975999 GCATCATTACCGGCATGTGCACTGCCCACCCCGCACATGCACGGTT
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTT
9976045 ACATCAATTA
Statistics
Matches: 205, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 205 1.00
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.22
Consensus pattern (61 bp):
GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTGAATATCACGACA
Found at i:9989200 original size:15 final size:14
Alignment explanation
Indices: 9989165--9989205 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
9989155 AATCAAATTT
9989165 TTCATTT-TTTTCC
1 TTCATTTCTTTTCC
9989178 TTCATTTCTTTTCC
1 TTCATTTCTTTTCC
*
9989192 TTTCCTTTCTTTTC
1 -TTCATTTCTTTTC
9989206 TTACTTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 12 0.48
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (14 bp):
TTCATTTCTTTTCC
Found at i:9990157 original size:39 final size:39
Alignment explanation
Indices: 9990099--9990190 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 39
9990089 ATGCTGGTAG
* * *
9990099 TGTGCAGTGTAGGAGAGCACACG-TCGATGATATATGCCA
1 TGTGCGGTGTGGGAAAGCACACGAT-GATGATATATGCCA
* *
9990138 TGTGCGGTGTGGGAAAGCACATGATGATGATATTTGCCA
1 TGTGCGGTGTGGGAAAGCACACGATGATGATATATGCCA
*
9990177 TGTACGGTGTGGGA
1 TGTGCGGTGTGGGA
9990191 GTGCACATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (39 bp):
TGTGCGGTGTGGGAAAGCACACGATGATGATATATGCCA
Found at i:9990197 original size:39 final size:38
Alignment explanation
Indices: 9990124--9990236 Score: 140
Period size: 39 Copynumber: 3.0 Consensus size: 38
9990114 AGCACACGTC
* **
9990124 GATGATATATGCCATGTGCGGTGTGGGAAAGCACATGA
1 GATGATATTTGCCATGTGCGGTGTGGGAGTGCACATGA
*
9990162 TGATGATATTTGCCATGTACGGTGTGGGAGTGCACATGA
1 -GATGATATTTGCCATGTGCGGTGTGGGAGTGCACATGA
* * *
9990201 G--GATATTAGCTATGTGCGATGTGGGAGTGCACATGA
1 GATGATATTTGCCATGTGCGGTGTGGGAGTGCACATGA
9990237 ACTGAGTTGA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 31 0.47
38 1 0.02
39 34 0.52
ACGTcount: A:0.26, C:0.12, G:0.35, T:0.27
Consensus pattern (38 bp):
GATGATATTTGCCATGTGCGGTGTGGGAGTGCACATGA
Found at i:9990224 original size:36 final size:38
Alignment explanation
Indices: 9990134--9990236 Score: 129
Period size: 36 Copynumber: 2.7 Consensus size: 38
9990124 GATGATATAT
** *
9990134 GCCATGTGCGGTGTGGGAAAGCACATGATGATGATATTT
1 GCCATGTGCGGTGTGGGAGTGCACATGATGA-GATATTA
*
9990173 GCCATGTACGGTGTGGGAGTGCACATGA-G-GATATTA
1 GCCATGTGCGGTGTGGGAGTGCACATGATGAGATATTA
* *
9990209 GCTATGTGCGATGTGGGAGTGCACATGA
1 GCCATGTGCGGTGTGGGAGTGCACATGA
9990237 ACTGAGTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
36 31 0.54
38 1 0.02
39 25 0.44
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (38 bp):
GCCATGTGCGGTGTGGGAGTGCACATGATGAGATATTA
Found at i:9994361 original size:74 final size:72
Alignment explanation
Indices: 9994267--9994472 Score: 245
Period size: 72 Copynumber: 2.8 Consensus size: 72
9994257 TAACCGTGCG
* * * * *
9994267 TGTGCGGTGTGGGAGTGCACATGATGGTGA-T-GGTGGGTGTAGTGTGGGAATGCACACGATGAT
1 TGTGTGGTGTGGGAGTGCACATGATGGT-ATTAGCTAGGTGCAGTGTGCGAATG--CAC-ATGAT
9994330 GATATTTGCCA
62 GATATTTGCCA
* * *
9994341 TGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTATGTGCGGTGTGCGAGTGCACATGATGATA
1 TGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTAGGTGCAGTGTGCGAATGCACATGATGATA
**
9994406 TTTTTCA
66 TTTGCCA
* * *
9994413 TGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTATGTGCGGTGTGCGAGTGCACATGA
1 TGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTAGGTGCAGTGTGCGAATGCACATGA
9994473 GATGAGTTAC
Statistics
Matches: 120, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
72 74 0.62
73 4 0.03
74 28 0.23
75 14 0.12
ACGTcount: A:0.19, C:0.11, G:0.38, T:0.31
Consensus pattern (72 bp):
TGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTAGGTGCAGTGTGCGAATGCACATGATGATA
TTTGCCA
Found at i:9994380 original size:36 final size:35
Alignment explanation
Indices: 9994267--9994472 Score: 198
Period size: 36 Copynumber: 5.7 Consensus size: 35
9994257 TAACCGTGCG
* *
9994267 TGTGCGGTGTGGGAGTGCACATGATGGTGA-TGGTG
1 TGTGCGGTGTGGGAGTGCACATGATGGT-ATTGCTA
* ** * * *
9994302 GGTGTAGTGTGGGAATGCACACGATGATGATATTTGCCA
1 TGTGCGGTGTGGGAGTG--CAC-ATGATGGTA-TTGCTA
*
9994341 TGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTA
1 TGTGCGGTGTGGGAGTGCACATGATGGTATT-GCTA
* * **
9994377 TGTGCGGTGTGCGAGTGCACATGATGATATTTTTCA
1 TGTGCGGTGTGGGAGTGCACATGATGGTATTGCT-A
*
9994413 TGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTA
1 TGTGCGGTGTGGGAGTGCACATGATGGTATT-GCTA
*
9994449 TGTGCGGTGTGCGAGTGCACATGA
1 TGTGCGGTGTGGGAGTGCACATGA
9994473 GATGAGTTAC
Statistics
Matches: 138, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
35 16 0.12
36 91 0.66
37 8 0.06
38 7 0.05
39 16 0.12
ACGTcount: A:0.19, C:0.11, G:0.38, T:0.31
Consensus pattern (35 bp):
TGTGCGGTGTGGGAGTGCACATGATGGTATTGCTA
Found at i:9994421 original size:72 final size:72
Alignment explanation
Indices: 9994325--9994472 Score: 278
Period size: 72 Copynumber: 2.1 Consensus size: 72
9994315 AATGCACACG
9994325 ATGATGATATTTGCCATGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTATGTGCGGTGTGCG
1 ATGATGATATTTGCCATGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTATGTGCGGTGTGCG
9994390 AGTGCAC
66 AGTGCAC
**
9994397 ATGATGATATTTTTCATGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTATGTGCGGTGTGCG
1 ATGATGATATTTGCCATGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTATGTGCGGTGTGCG
9994462 AGTGCAC
66 AGTGCAC
9994469 ATGA
1 ATGA
9994473 GATGAGTTAC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.20, C:0.11, G:0.35, T:0.33
Consensus pattern (72 bp):
ATGATGATATTTGCCATGTGTGGTGTGGGAGTGCACATGATGGTATTAGCTATGTGCGGTGTGCG
AGTGCAC
Found at i:9994569 original size:2 final size:2
Alignment explanation
Indices: 9994562--9994606 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
9994552 TTGAAATGTC
* * *
9994562 TA TA TA TA TA TT TA TG TA TA TA TA TA TA TA TA TA TA -A TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9994603 TA TA
1 TA TA
9994607 CATAAGTTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9995513 original size:14 final size:14
Alignment explanation
Indices: 9995494--9995535 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
9995484 CAAAAGGAGG
9995494 GAAGAAAGGAGAAA
1 GAAGAAAGGAGAAA
*
9995508 GAAGAAAAGAGAAA
1 GAAGAAAGGAGAAA
* *
9995522 GAAGGAAGAAGAAA
1 GAAGAAAGGAGAAA
9995536 AAGGCTTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GAAGAAAGGAGAAA
Found at i:9995522 original size:21 final size:21
Alignment explanation
Indices: 9995496--9995536 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9995486 AAAGGAGGGA
*
9995496 AGAAAGGAGAAAGAAGAAAAG
1 AGAAAGAAGAAAGAAGAAAAG
*
9995517 AGAAAGAAGGAAGAAGAAAA
1 AGAAAGAAGAAAGAAGAAAA
9995537 AGGCTTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (21 bp):
AGAAAGAAGAAAGAAGAAAAG
Found at i:9996424 original size:2 final size:2
Alignment explanation
Indices: 9996417--9996484 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
9996407 TGTTTTGAAA
*
9996417 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9996459 AT AT AT AT AT AT A- AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9996485 ACAATGTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9999757 original size:92 final size:92
Alignment explanation
Indices: 9999525--9999758 Score: 308
Period size: 92 Copynumber: 2.5 Consensus size: 92
9999515 AATTAAAGCT
* * * *
9999525 CTTGCCTTATATGGTAAGTTGGTTGTAATTTTTTTCCTTACACGGAAACCTAGGATTTACTTACC
1 CTTGCCTTATATAGTAAGTTGGCTGTAATTTTTTT-CTTACAAGGAAACCCAGGATTTACTTACC
*
9999590 ATGAATTAATGATTTACTCTTTTTGGCC
65 ATGAATCAATGATTTACTCTTTTTGGCC
* ** * *
9999618 CTTGCCTTGTATAGTAAGTTGGCTGTACCTTTTTCCTCACAAGGAAACCCAGGATTTACTTACCA
1 CTTGCCTTATATAGTAAGTTGGCTGTAATTTTTTTCTTACAAGGAAACCCAGGATTTACTTACCA
* **
9999683 TGCATCGGTG-TCTTACTCTTTTTGGCC
66 TGAATCAATGAT-TTACTCTTTTTGGCC
* *
9999710 CTTGCCTTATATAGTAAGTTGGCTGTAATTTTTTTCTTGCAAAGAAACC
1 CTTGCCTTATATAGTAAGTTGGCTGTAATTTTTTTCTTACAAGGAAACC
9999759 TATGATNCAG
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
91 1 0.01
92 90 0.75
93 29 0.24
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (92 bp):
CTTGCCTTATATAGTAAGTTGGCTGTAATTTTTTTCTTACAAGGAAACCCAGGATTTACTTACCA
TGAATCAATGATTTACTCTTTTTGGCC
Found at i:10001569 original size:25 final size:27
Alignment explanation
Indices: 10001541--10001629 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 27
10001531 GTGGTCGCAA
10001541 CCACGTAT-ATCAA-CTCGTGGCCTAG
1 CCACGTATAATCAAGCTCGTGGCCTAG
*
10001566 CCACGTATAAT-AAGCT-GTGGCCTTG
1 CCACGTATAATCAAGCTCGTGGCCTAG
* * *
10001591 CTACGTATAATCACAGATCGTGGCTTAG
1 CCACGTATAATCA-AGCTCGTGGCCTAG
*
10001619 CCACGTCTAAT
1 CCACGTATAAT
10001630 AGCCTGTTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
25 28 0.54
26 5 0.10
27 3 0.06
28 16 0.31
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (27 bp):
CCACGTATAATCAAGCTCGTGGCCTAG
Found at i:10005326 original size:2 final size:2
Alignment explanation
Indices: 10005319--10005348 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
10005309 AAATACTTAC
10005319 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
10005349 CACAAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10007498 original size:24 final size:19
Alignment explanation
Indices: 10007467--10007518 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
10007457 GATTTATTTT
10007467 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
10007486 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
10007505 AATATTATTTTATT
1 AATATTATTTTATT
10007519 CCAAAATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTAATAA
Found at i:10009564 original size:45 final size:45
Alignment explanation
Indices: 10009508--10009596 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
10009498 AGAAAAAGAG
10009508 AGAAAAGTGGGAAAGGCTCGGGTTGTGAAGATTCAAGAGAAACCA
1 AGAAAAGTGGGAAAGGCTCGGGTTGTGAAGATTCAAGAGAAACCA
10009553 AGAAAAGTGGGAAAGGCTCGGGTTGTGAAGATTCAAGAGAAACC
1 AGAAAAGTGGGAAAGGCTCGGGTTGTGAAGATTCAAGAGAAACC
10009597 GTGAGGTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.11, G:0.34, T:0.16
Consensus pattern (45 bp):
AGAAAAGTGGGAAAGGCTCGGGTTGTGAAGATTCAAGAGAAACCA
Found at i:10010848 original size:2 final size:2
Alignment explanation
Indices: 10010841--10010889 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
10010831 ATTGTTTTAG
10010841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10010883 AT AT AT A
1 AT AT AT A
10010890 CTCTCTTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10014198 original size:73 final size:72
Alignment explanation
Indices: 10014128--10014345 Score: 276
Period size: 72 Copynumber: 3.0 Consensus size: 72
10014118 TTGAGAATTG
* * * ** *
10014128 ATCTCTTCTCTTTAAAAGATTTATTCTTCTTAATGCATAATGCTTCTTTTTTGCTTTTGGAGGTC
1 ATCTCTTCTCTTCAAAAGATTGATTCTTCATAACACAAAATGCTTC-TTTTTGCTTTTGGAGGTC
10014193 GAGAATCA
65 GAGAATCA
* *
10014201 ATCTCTTCTCTTCAAGAGATTGATTCTTCATAACACAAAATGCTTCTTTTTGCTTTTGGAAG-CT
1 ATCTCTTCTCTTCAAAAGATTGATTCTTCATAACACAAAATGCTTCTTTTTGCTTTTGGAGGTC-
*
10014265 GAAAATCA
65 GAGAATCA
* * * ** *
10014273 ATCTCTTTTCTTCAAGAGATTGATTCTTCATAACACAAAATGCTTCCTTTCACTTTTGGAGGTTG
1 ATCTCTTCTCTTCAAAAGATTGATTCTTCATAACACAAAATGCTTCTTTTTGCTTTTGGAGGTCG
10014338 AGAATCA
66 AGAATCA
10014345 A
1 A
10014346 CCTCCTTTTC
Statistics
Matches: 127, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
71 1 0.01
72 87 0.69
73 39 0.31
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (72 bp):
ATCTCTTCTCTTCAAAAGATTGATTCTTCATAACACAAAATGCTTCTTTTTGCTTTTGGAGGTCG
AGAATCA
Found at i:10014370 original size:72 final size:71
Alignment explanation
Indices: 10014196--10014371 Score: 194
Period size: 72 Copynumber: 2.4 Consensus size: 71
10014186 GGAGGTCGAG
* * * * **
10014196 AATCAATCTCTTCTCTTCAAGAGATTGATTCTTCATAACACAAAATGCTTCTTTTTGCTTTTGGA
1 AATCAACCTCTTTTCTTC-AGAGATCGATTCTTCATAACACAAAATGCTTCCTTTCACTTTTGGA
10014261 AGCTGAA
65 AGCTGAA
* *
10014268 AATCAATCTCTTTTCTTCAAGAGATTGATTCTTCATAACACAAAATGCTTCCTTTCACTTTTGGA
1 AATCAACCTCTTTTCTTC-AGAGATCGATTCTTCATAACACAAAATGCTTCCTTTCACTTTTGGA
* * *
10014333 GGTTGAG
65 AGCTGAA
10014340 AATCAACCTCCTTTTCCATTC-GA-ATCGATTCT
1 AATCAACCT-CTTTT-C-TTCAGAGATCGATTCT
10014372 CCCTAAGCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
72 81 0.88
73 7 0.08
74 1 0.01
75 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (71 bp):
AATCAACCTCTTTTCTTCAGAGATCGATTCTTCATAACACAAAATGCTTCCTTTCACTTTTGGAA
GCTGAA
Found at i:10035968 original size:35 final size:36
Alignment explanation
Indices: 10035929--10035999 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
10035919 CAACCATTAC
*
10035929 AAGTGAAGCACTACTTCACGCAAAACAACTA-AATA
1 AAGTGAAGCACTACTTCACACAAAACAACTAGAATA
** *
10035964 AAGTGAATTACTACTTCACATAAAACAACTAGAATA
1 AAGTGAAGCACTACTTCACACAAAACAACTAGAATA
10036000 TGTGGAGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.21
Consensus pattern (36 bp):
AAGTGAAGCACTACTTCACACAAAACAACTAGAATA
Found at i:10036276 original size:29 final size:29
Alignment explanation
Indices: 10036239--10036325 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
10036229 TACCTTGTTT
* * *
10036239 TCTTGTACCTGTTTA-CATACAGCTTCTTC
1 TCTTATACCTGTTCATC-TACAACTTCTTC
*
10036268 TCTTATACCTATTCATCTACAACTTCTTC
1 TCTTATACCTGTTCATCTACAACTTCTTC
10036297 TCTTATACCTGTTCA-CGTACAAC-TCTTC
1 TCTTATACCTGTTCATC-TACAACTTCTTC
10036325 T
1 T
10036326 TTGTTAAGTC
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.14
29 43 0.84
30 1 0.02
ACGTcount: A:0.21, C:0.30, G:0.06, T:0.44
Consensus pattern (29 bp):
TCTTATACCTGTTCATCTACAACTTCTTC
Found at i:10037188 original size:99 final size:102
Alignment explanation
Indices: 10037011--10037199 Score: 240
Period size: 99 Copynumber: 1.9 Consensus size: 102
10037001 AAAATTCATA
* * * * *
10037011 TTTAGTTGCTAGCTTTATCACTTATATTTTTGCTGTAATTATATTATACTATTAGTCGCAAGCTT
1 TTTAGCTGCAAGCTTTACCACTCATATTTTGGCTGTAATTATATTATACTATTAGTCGCAAGCTT
**
10037076 TATTGCTCATTCTTTAACCATAATTCATTACTTTTAC
66 TATCACTCATTCTTTAACCATAATTCATTACTTTTAC
* * * * *
10037113 TTTAGCTGCAAGCTTTACCACTCATATTTTGGCTGTGA-TAT-TT-TTCTATTGGTCGTAAGTTT
1 TTTAGCTGCAAGCTTTACCACTCATATTTTGGCTGTAATTATATTATACTATTAGTCGCAAGCTT
*
10037175 TATCACTCATTCTTTGACCATAATT
66 TATCACTCATTCTTTAACCATAATT
10037200 TATCATTCAT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
99 37 0.50
100 2 0.03
101 3 0.04
102 32 0.43
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (102 bp):
TTTAGCTGCAAGCTTTACCACTCATATTTTGGCTGTAATTATATTATACTATTAGTCGCAAGCTT
TATCACTCATTCTTTAACCATAATTCATTACTTTTAC
Found at i:10038579 original size:18 final size:20
Alignment explanation
Indices: 10038545--10038585 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
10038535 AAAAATAATC
10038545 AAAATGAGAAAATGAAAA-A
1 AAAATGAGAAAATGAAAACA
10038564 AAAATGCAG-AAA-GAAAACA
1 AAAATG-AGAAAATGAAAACA
10038583 AAA
1 AAA
10038586 GACAAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.25
19 13 0.65
20 2 0.10
ACGTcount: A:0.73, C:0.05, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAATGAGAAAATGAAAACA
Found at i:10040471 original size:21 final size:22
Alignment explanation
Indices: 10040446--10040486 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
10040436 CCTAGGTGGA
10040446 AAAATTCAAGGAAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
10040467 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
10040487 AAAAAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:10040492 original size:22 final size:21
Alignment explanation
Indices: 10040445--10040492 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
10040435 CCCTAGGTGG
*
10040445 AAAAATTCAAGGAAAAAGTGT
1 AAAAATTCAAGGAAAAAGTGA
*
10040466 GAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAA-AAGTGA
10040488 AAAAA
1 AAAAA
10040493 GATAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGA
Found at i:10045363 original size:29 final size:29
Alignment explanation
Indices: 10045324--10045379 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
10045314 TTTTACCTTA
* * *
10045324 TTCTCTTGTACTTGTTCATGTATAGCTTC
1 TTCTCTTGTACTTATTCACGTACAGCTTC
10045353 TTCTCTTGTACTTATTCACGTACAGCT
1 TTCTCTTGTACTTATTCACGTACAGCT
10045380 CTTATTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.23, G:0.12, T:0.48
Consensus pattern (29 bp):
TTCTCTTGTACTTATTCACGTACAGCTTC
Found at i:10048451 original size:20 final size:20
Alignment explanation
Indices: 10048434--10048471 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10048424 CCTCAAATCT
*
10048434 TACTCCAATGAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
10048454 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
10048472 GGGGCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:10049560 original size:25 final size:24
Alignment explanation
Indices: 10049522--10049568 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
10049512 TATAGGATTA
10049522 GTAATAATAATATAACAATAAATTT
1 GTAATAATAATATAACAA-AAATTT
*
10049547 GTAA-AATAATTATATCAAAAAT
1 GTAATAATAA-TATAACAAAAAT
10049569 AAATTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (24 bp):
GTAATAATAATATAACAAAAATTT
Found at i:10051725 original size:29 final size:28
Alignment explanation
Indices: 10051666--10051731 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
10051656 ATGTCTATGG
* * *
10051666 GTAATTTTTCAGTTTTTGGGATAAAAAT
1 GTAATTTTTCACTTTTAGGGACAAAAAT
* *
10051694 GTAATTTTTCACTTTATAGGGGCAAAAGT
1 GTAATTTTTCACTTT-TAGGGACAAAAAT
10051723 GTAATTTTT
1 GTAATTTTT
10051732 AAAAATTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (28 bp):
GTAATTTTTCACTTTTAGGGACAAAAAT
Found at i:10052903 original size:13 final size:13
Alignment explanation
Indices: 10052885--10052909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10052875 GGAAAATGAG
10052885 ATTTTATAAAATA
1 ATTTTATAAAATA
10052898 ATTTTATAAAAT
1 ATTTTATAAAAT
10052910 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:10054415 original size:2 final size:2
Alignment explanation
Indices: 10054408--10054458 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
10054398 AATGTTATGA
* * *
10054408 AT AT AT AT AT AT AT AT AT AT AT TT GT AT AA AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
10054449 AT AC AT AT AT
1 AT AT AT AT AT
10054459 TTAATTTATG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10054642 original size:2 final size:2
Alignment explanation
Indices: 10054635--10054660 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10054625 ATTAATTTTG
10054635 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
10054661 AGGAATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10056512 original size:24 final size:25
Alignment explanation
Indices: 10056485--10056543 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
10056475 GTGGTCGCAA
* *
10056485 CCACGTATATCAATTCGTGGCCTT-
1 CCACGTATAACAACTCGTGGCCTTG
* *
10056509 CCACATGTAACAACTCGTGGCCTTG
1 CCACGTATAACAACTCGTGGCCTTG
10056534 CCACGTATAA
1 CCACGTATAA
10056544 TCACAGATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (25 bp):
CCACGTATAACAACTCGTGGCCTTG
Found at i:10059795 original size:20 final size:20
Alignment explanation
Indices: 10059770--10059815 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
10059760 ATTTGTCCCC
10059770 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
10059790 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
10059810 ATTTGA
1 ATTTGA
10059816 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:10065622 original size:260 final size:259
Alignment explanation
Indices: 10065161--10065677 Score: 953
Period size: 260 Copynumber: 2.0 Consensus size: 259
10065151 TGATTTTCTT
10065161 GGGACATGTGGTGTCCGGAGTTGGAATTTATGTCGATCCTAAGAAGATTAAGGCAATCTTGCAAT
1 GGGACATGTGGTGTCCGGAGTTGGAATTTATGTCGATCCTAAGAAGATTAAGGCAATCTTGCAAT
*
10065226 GGGAGCAATCGAGAACGGTAACTGAGATTCGTAGTTTCATTGGCTTAGTTGGTTATTATCGGAGA
66 GGGAGCAATCGAGAACGGTAACTGAGATTCGTAGTTTCATTGGCTTAGTTGGTTATTACCGGAGA
* * *
10065291 TTTGTTTAGGGATTTTTTTTTATAGCAGCTCCTCTGACTCGTTAGACTCGTAAAGGAGTTAAGTA
131 TTTATTTAGGGATTTTCTTTGATAGCAGCTCCTCTGACTCGTTAGACTCGTAAAGGAGTTAAGTA
*
10065356 TGAGTGCGATGATGTTTGTGAGAATCGATTCCAGGAGCTAAAGAACCGGTTAATCTCCGCTCCC
196 TGAGTGCGATGATGTTTGTGAGAATCGATTCCAGGAGCTAAAGAACCGGTTAACCTCCGCTCCC
*
10065420 NGGGACATGTGGTGTCCGGAGTTGGAATTTATGTCGATCCTAAGAAGATTGAGGCAATCTTGCAA
1 -GGGACATGTGGTGTCCGGAGTTGGAATTTATGTCGATCCTAAGAAGATTAAGGCAATCTTGCAA
10065485 TGGGAGCAATCGAGAACGGTAACTGAGATTCGTAGTTTCATTGGCTTAGTTGGTTATTACCGGAG
65 TGGGAGCAATCGAGAACGGTAACTGAGATTCGTAGTTTCATTGGCTTAGTTGGTTATTACCGGAG
10065550 ATTTATTTAGGGATTTTCTTTGATAGCAGCTCCTCTGACTCGTTAGACTCGTAAAGGAGTTAAGT
130 ATTTATTTAGGGATTTTCTTTGATAGCAGCTCCTCTGACTCGTTAGACTCGTAAAGGAGTTAAGT
* *
10065615 ATGAGTGCGATGATGTTTGTGAGAATTGATTTCAGGAGCTAAAGAACCGGTTAACCTCCGCTC
195 ATGAGTGCGATGATGTTTGTGAGAATCGATTCCAGGAGCTAAAGAACCGGTTAACCTCCGCTC
10065678 TCATTTCGTC
Statistics
Matches: 249, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
260 249 1.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (259 bp):
GGGACATGTGGTGTCCGGAGTTGGAATTTATGTCGATCCTAAGAAGATTAAGGCAATCTTGCAAT
GGGAGCAATCGAGAACGGTAACTGAGATTCGTAGTTTCATTGGCTTAGTTGGTTATTACCGGAGA
TTTATTTAGGGATTTTCTTTGATAGCAGCTCCTCTGACTCGTTAGACTCGTAAAGGAGTTAAGTA
TGAGTGCGATGATGTTTGTGAGAATCGATTCCAGGAGCTAAAGAACCGGTTAACCTCCGCTCCC
Found at i:10067609 original size:20 final size:20
Alignment explanation
Indices: 10067584--10067629 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
10067574 TTTTGACCCC
10067584 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
10067604 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
10067624 ATTTGA
1 ATTTGA
10067630 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:10086781 original size:10 final size:10
Alignment explanation
Indices: 10086762--10086808 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
10086752 AAAAAAAGCG
*
10086762 TTTTCATTTT
1 TTTTCTTTTT
10086772 TTTTCTTTTT
1 TTTTCTTTTT
*
10086782 CTTTC-TTTT
1 TTTTCTTTTT
* *
10086791 TTGTCTTTTG
1 TTTTCTTTTT
10086801 TTTTCTTT
1 TTTTCTTT
10086809 GTTTAGACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:10086792 original size:19 final size:19
Alignment explanation
Indices: 10086761--10086808 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
10086751 GAAAAAAAGC
*
10086761 GTTTTCATTTTTTTTCTTTT
1 GTTTTC-TTTTTTGTCTTTT
10086781 -TCTTTCTTTTTTGTCTTTT
1 GT-TTTCTTTTTTGTCTTTT
10086800 GTTTTCTTT
1 GTTTTCTTT
10086809 GTTTAGACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.79
Consensus pattern (19 bp):
GTTTTCTTTTTTGTCTTTT
Found at i:10102404 original size:15 final size:15
Alignment explanation
Indices: 10102367--10102407 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
10102357 AATTTCGGCA
10102367 TTATAATTATAACTAT
1 TTATAATTA-AACTAT
*
10102383 TTATAATTAAACTCT
1 TTATAATTAAACTAT
*
10102398 TTTTAATTAA
1 TTATAATTAA
10102408 GTTTATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATAATTAAACTAT
Found at i:10116149 original size:35 final size:35
Alignment explanation
Indices: 10116100--10116369 Score: 267
Period size: 35 Copynumber: 7.7 Consensus size: 35
10116090 TCCTTTATAA
** *
10116100 GCCCAATTAACTTAATTATTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTAAATAATTTAATTAATTAG
*
10116136 GCCCAATAACTTAATTAAATAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * * * *
10116171 GCCCAACAATTTAATTAAACAATTATAATCAACTAG
1 GCCCAATAACTTAATTAAATAATT-TAATTAATTAG
* * *
10116207 GCCCAATGACTTAATTAAACAAATTTAATCAATTAG
1 GCCCAATAACTTAATTAAA-TAATTTAATTAATTAG
* ***
10116243 GCTCAATAACTTAATTGTTTAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * * *
10116278 ACCCACTGACTTAATTAAATAATTTAATTAATTAT
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * *
10116313 GCCCAATGATTTAATTAAACAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* *
10116348 GCACAAT---TTAATTAAACAATTT
1 GCCCAATAACTTAATTAAATAATTT
10116370 TAATCAAGTG
Statistics
Matches: 196, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
32 15 0.08
35 123 0.63
36 54 0.28
37 4 0.02
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAATAATTTAATTAATTAG
Found at i:10116241 original size:107 final size:105
Alignment explanation
Indices: 10116121--10116369 Score: 301
Period size: 107 Copynumber: 2.4 Consensus size: 105
10116111 TTAATTATTT
* *
10116121 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTA-AGCCCAAC-AATTTA
1 AATTTAATCAATTAGGCACAATAACTTAATTAAATAATTTAATTAATTAGA-CCC-ACTAACTTA
10116184 ATTAAACAATTATAATCAACTAGGCCCAATGACTTAATTAAAC
64 ATTAAACAATT-TAATCAACTAGGCCCAATGACTTAATTAAAC
* *** *
10116227 AAATTTAATCAATTAGGCTCAATAACTTAATTGTTTAATTTAATTAATTAGACCCACTGACTTAA
1 -AATTTAATCAATTAGGCACAATAACTTAATTAAATAATTTAATTAATTAGACCCACTAACTTAA
* * * * *
10116292 TTAAATAATTTAATTAATTATGCCCAATGATTTAATTAAAC
65 TTAAACAATTTAATCAACTAGGCCCAATGACTTAATTAAAC
* *
10116333 AATTTAATTAATTAGGCACAAT---TTAATTAAACAATTT
1 AATTTAATCAATTAGGCACAATAACTTAATTAAATAATTT
10116370 TAATCAAGTG
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
102 11 0.09
105 20 0.16
106 29 0.24
107 62 0.50
108 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (105 bp):
AATTTAATCAATTAGGCACAATAACTTAATTAAATAATTTAATTAATTAGACCCACTAACTTAAT
TAAACAATTTAATCAACTAGGCCCAATGACTTAATTAAAC
Found at i:10116264 original size:142 final size:138
Alignment explanation
Indices: 10116107--10116376 Score: 396
Period size: 142 Copynumber: 1.9 Consensus size: 138
10116097 TAAGCCCAAT
*
10116107 TAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAG
1 TAACTTAATTATTTAATTTAATCAATTAGACCCAATAACTTAATTAAATAATTTAATTAATTAAG
*
10116172 CCCAACAATTTAATTAAACAATTATAATCAACTAGGCCCAATGACTTAATTAAACAAATTTAATC
66 CCCAACAATTTAATTAAACAATT-TAATCAACTAGGCACAAT---TTAATTAAACAAATTTAATC
10116237 AATTAGGCTCAA
127 AATTAGGCTCAA
* * * * *
10116249 TAACTTAATTGTTTAATTTAATTAATTAGACCCACTGACTTAATTAAATAATTTAATTAATTATG
1 TAACTTAATTATTTAATTTAATCAATTAGACCCAATAACTTAATTAAATAATTTAATTAATTAAG
** * * *
10116314 CCCAATGATTTAATTAAACAATTTAATTAATTAGGCACAATTTAATTAAACAATTTTAATCAA
66 CCCAACAATTTAATTAAACAATTTAATCAACTAGGCACAATTTAATTAAACAAATTTAATCAA
10116377 GTGCTTGAGA
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
138 21 0.18
141 15 0.13
142 80 0.69
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (138 bp):
TAACTTAATTATTTAATTTAATCAATTAGACCCAATAACTTAATTAAATAATTTAATTAATTAAG
CCCAACAATTTAATTAAACAATTTAATCAACTAGGCACAATTTAATTAAACAAATTTAATCAATT
AGGCTCAA
Found at i:10120529 original size:2 final size:2
Alignment explanation
Indices: 10120517--10120582 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
10120507 ACCATATACC
*
10120517 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10120559 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
10120583 NNNNNNNNNN
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10133397 original size:2 final size:2
Alignment explanation
Indices: 10133390--10133414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10133380 ATAATCATGT
10133390 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
10133415 TTCATACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10138460 original size:49 final size:49
Alignment explanation
Indices: 10138388--10138482 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
10138378 ACATTCGTTT
*
10138388 TCTTCATGGCATATTTCTAACTTCGTGATCAGAGGTACTAGAAATAAAA
1 TCTTCATGGCACATTTCTAACTTCGTGATCAGAGGTACTAGAAATAAAA
10138437 TCTTCATGGCACATTTCTAACTTCGTGATCAGAGGTACTAGAAATA
1 TCTTCATGGCACATTTCTAACTTCGTGATCAGAGGTACTAGAAATA
10138483 TGAGTACGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (49 bp):
TCTTCATGGCACATTTCTAACTTCGTGATCAGAGGTACTAGAAATAAAA
Found at i:10144266 original size:19 final size:20
Alignment explanation
Indices: 10144229--10144267 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
10144219 TCAATAGCTG
*
10144229 AAAAAAATTTTGAACTAAAT
1 AAAAAAATTTTGAAATAAAT
*
10144249 AAAAACATTTT-AAATAAAT
1 AAAAAAATTTTGAAATAAAT
10144268 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAAAAATTTTGAAATAAAT
Found at i:10145204 original size:29 final size:29
Alignment explanation
Indices: 10145172--10145235 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
10145162 AACCACTAAT
* *
10145172 TATAAAAACTTATTTAATTAAAATAAAAA
1 TATAAAAACTTAGTTAAATAAAATAAAAA
* * *
10145201 TATAAGAGCTTAGTTAAATATAATAAAAA
1 TATAAAAACTTAGTTAAATAAAATAAAAA
10145230 -ATAAAA
1 TATAAAA
10145236 GCTTCTTTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (29 bp):
TATAAAAACTTAGTTAAATAAAATAAAAA
Found at i:10145563 original size:30 final size:30
Alignment explanation
Indices: 10145528--10145584 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
10145518 AATCAAGTCC
10145528 TTATATGTTTATTTTGAGTCAAATAAGTGT
1 TTATATGTTTATTTTGAGTCAAATAAGTGT
*
10145558 TTATATTTTTATTTTGAGTCAAATAAG
1 TTATATGTTTATTTTGAGTCAAATAAG
10145585 CCCATATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.51
Consensus pattern (30 bp):
TTATATGTTTATTTTGAGTCAAATAAGTGT
Found at i:10145725 original size:33 final size:33
Alignment explanation
Indices: 10145648--10145725 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
10145638 CGTAGTGCTG
*
10145648 ACGTGATATGTTAATATATTATAATTAATAATA
1 ACGTGATATGCTAATATATTATAATTAATAATA
** * *
10145681 ATATGATATGCTAATATATTATAATTGATGATA
1 ACGTGATATGCTAATATATTATAATTAATAATA
*
10145714 ACGTGACATGCT
1 ACGTGATATGCT
10145726 GACGTATCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (33 bp):
ACGTGATATGCTAATATATTATAATTAATAATA
Found at i:10146335 original size:15 final size:17
Alignment explanation
Indices: 10146308--10146340 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10146298 TTTTTGAGCA
10146308 TCTATATTCTTAT-TTT
1 TCTATATTCTTATATTT
10146324 TCTATA-TCTTATATTT
1 TCTATATTCTTATATTT
10146340 T
1 T
10146341 AAAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (17 bp):
TCTATATTCTTATATTT
Found at i:10155930 original size:23 final size:23
Alignment explanation
Indices: 10155851--10155956 Score: 83
Period size: 23 Copynumber: 4.7 Consensus size: 23
10155841 ATATATTGTG
* *
10155851 AACATGGTGTGTAACAAATTT-TG
1 AACATGGTGTGTAAC-ATTTTCTA
* * *
10155874 AAC-TTGTGTGTAAGATTTTC-G
1 AACATGGTGTGTAACATTTTCTA
**
10155895 AACATGGCATGTAACATTTTCTA
1 AACATGGTGTGTAACATTTTCTA
*
10155918 AACATGGTGTGTAACATTTTTTA
1 AACATGGTGTGTAACATTTTCTA
* * *
10155941 AAAATAGCGTGTAACA
1 AACATGGTGTGTAACA
10155957 ACATGATTGA
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
21 8 0.12
22 22 0.33
23 36 0.55
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (23 bp):
AACATGGTGTGTAACATTTTCTA
Found at i:10159872 original size:86 final size:86
Alignment explanation
Indices: 10159725--10160418 Score: 840
Period size: 86 Copynumber: 8.1 Consensus size: 86
10159715 TGGTAGTTGT
* * ** * * * *
10159725 GGTGACACGACATGGGCCAATTGTGGTGACACATTGAGTGTATGTAGACTTCTGGCTTGACACAC
1 GGTGACACGGCATAGGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACGC
* * *
10159790 TAACTTATTGCAATCTTGTGG
66 TGACTTGTTGCAGTCTTGTGG
* * *
10159811 GGTGACACAGCATAGGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTTTGGTATGACACGC
1 GGTGACACGGCATAGGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACGC
*
10159876 TGACTTGTTGCAGTTTTGTGG
66 TGACTTGTTGCAGTCTTGTGG
* * * * *
10159897 GGTGACACGGCACTA-GCCAATTGTGGTGACACGTTGAGTGCATGTAGACTTGTGACGTGACACG
1 GGTGACACGGCA-TAGGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACG
*
10159961 CTGACTTGTCGCAGTCTTGTGG
65 CTGACTTGTTGCAGTCTTGTGG
** * *
10159983 GGTGACATAGCA-AGGGCCAATTGTGGTGAAACGCTGAGTGCATGCAAACTTCTGGCATGACACG
1 GGTGACACGGCATA-GGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACG
* * * *
10160047 TTGACTTGTTACAATATTGTGG
65 CTGACTTGTTGCAGTCTTGTGG
* * *
10160069 GGTGACACGGCATGGGCCAATTGTGGTGACACGCTGAGTGCCTGCAGACTTTTGGCATGACACGC
1 GGTGACACGGCATAGGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACGC
**
10160134 TGACTTGTTGTTGTCTTGT-G
66 TGACTTGTTGCAGTCTTGTGG
* * * * **
10160154 GGTGACACGGCA-AGGGCCAATTATGGTGACATGATGAGTGCATGCAGACTTTTGGTGTGACACG
1 GGTGACACGGCATA-GGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACG
*
10160218 CTGACTTGTTGCAGTATTGTGG
65 CTGACTTGTTGCAGTCTTGTGG
** * * *
10160240 GGTGACACGGCACGGGCCAATTGTGGTGACACGCTGAGTGCATGCAAACTTCTAGCATGACACAC
1 GGTGACACGGCATAGGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACGC
10160305 TGACTTGTTGCAGTCTTGTGG
66 TGACTTGTTGCAGTCTTGTGG
* * * * * *
10160326 GGTGACACGCCAT-GCCCTAATTGTGGTGACACGCTGAGTGCATGCAGATTTCTGACGTGACATG
1 GGTGACACGGCATAGGCC-AATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACG
*
10160390 CTGACTTGTTGCAGTATTGTGG
65 CTGACTTGTTGCAGTCTTGTGG
10160412 GGTGACA
1 GGTGACA
10160419 AGCCATGCCC
Statistics
Matches: 517, Mismatches: 83, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
84 1 0.00
85 77 0.15
86 437 0.85
87 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.28
Consensus pattern (86 bp):
GGTGACACGGCATAGGCCAATTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCATGACACGC
TGACTTGTTGCAGTCTTGTGG
Found at i:10160352 original size:343 final size:344
Alignment explanation
Indices: 10159725--10160418 Score: 955
Period size: 343 Copynumber: 2.0 Consensus size: 344
10159715 TGGTAGTTGT
* * * *
10159725 GGTGACACGACATGGGCCAATTGTGGTGACACATTGAGTGTATGTAGACTTCTGGCTTGACACAC
1 GGTGACACGACATGGGCCAATTGTGGTGACACACTGAGTGCATGCAGACTTCTGGCATGACACAC
* *
10159790 TAACTTATTGCAATCTTGTGGGGTGACACAGCATAGGCCAATTGTGGTGACACGCTGAGTGCATG
66 TAACTTATTGCAATCTTGTGGGGTGACACAGCATAGGCCAATTATGGTGACACGATGAGTGCATG
* *
10159855 CAGACTTTTGGTATGACACGCTGACTTGTTGCAGTTTTGTGGGGTGACACGGCACTAGCCAATTG
131 CAGACTTTTGGTATGACACGCTGACTTGTTGCAGTATTGTGGGGTGACACGGCACGAGCCAATTG
* * * * * *
10159920 TGGTGACACGTTGAGTGCATGTAGACTTGTGACGTGACACGCTGACTTGTCGCAGTCTTGTGGGG
196 TGGTGACACGCTGAGTGCATGCAAACTTCTGACATGACACACTGACTTGTCGCAGTCTTGTGGGG
* * *
10159985 TGACATAGCAAGGGCCAATTGTGGTGAAACGCTGAGTGCATGCAAACTTCTGGCATGACACGTTG
261 TGACATAGCAAGGCCCAATTGTGGTGAAACGCTGAGTGCATGCAAACTTCTGACATGACACGCTG
10160050 ACTTGTTACAATATTGTGG
326 ACTTGTTACAATATTGTGG
* * * * *
10160069 GGTGACACGGCATGGGCCAATTGTGGTGACACGCTGAGTGCCTGCAGACTTTTGGCATGACACGC
1 GGTGACACGACATGGGCCAATTGTGGTGACACACTGAGTGCATGCAGACTTCTGGCATGACACAC
* * *** * *
10160134 TGACTTGTTGTTGTCTTGT-GGGTGACACGGCA-AGGGCCAATTATGGTGACATGATGAGTGCAT
66 TAACTTATTGCAATCTTGTGGGGTGACACAGCATA-GGCCAATTATGGTGACACGATGAGTGCAT
* *
10160197 GCAGACTTTTGGTGTGACACGCTGACTTGTTGCAGTATTGTGGGGTGACACGGCACGGGCCAATT
130 GCAGACTTTTGGTATGACACGCTGACTTGTTGCAGTATTGTGGGGTGACACGGCACGAGCCAATT
*
10160262 GTGGTGACACGCTGAGTGCATGCAAACTTCT-AGCATGACACACTGACTTGTTGCAGTCTTGTGG
195 GTGGTGACACGCTGAGTGCATGCAAACTTCTGA-CATGACACACTGACTTGTCGCAGTCTTGTGG
* * * * * * * *
10160326 GGTGACA-CGCCATGCCCTAATTGTGGTGACACGCTGAGTGCATGCAGATTTCTGACGTGACATG
259 GGTGACATAGCAAGGCCC-AATTGTGGTGAAACGCTGAGTGCATGCAAACTTCTGACATGACACG
* *
10160390 CTGACTTGTTGCAGTATTGTGG
323 CTGACTTGTTACAATATTGTGG
10160412 GGTGACA
1 GGTGACA
10160419 AGCCATGCCC
Statistics
Matches: 305, Mismatches: 42, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
342 8 0.03
343 227 0.74
344 70 0.23
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.28
Consensus pattern (344 bp):
GGTGACACGACATGGGCCAATTGTGGTGACACACTGAGTGCATGCAGACTTCTGGCATGACACAC
TAACTTATTGCAATCTTGTGGGGTGACACAGCATAGGCCAATTATGGTGACACGATGAGTGCATG
CAGACTTTTGGTATGACACGCTGACTTGTTGCAGTATTGTGGGGTGACACGGCACGAGCCAATTG
TGGTGACACGCTGAGTGCATGCAAACTTCTGACATGACACACTGACTTGTCGCAGTCTTGTGGGG
TGACATAGCAAGGCCCAATTGTGGTGAAACGCTGAGTGCATGCAAACTTCTGACATGACACGCTG
ACTTGTTACAATATTGTGG
Found at i:10162024 original size:81 final size:81
Alignment explanation
Indices: 10161837--10162008 Score: 256
Period size: 81 Copynumber: 2.1 Consensus size: 81
10161827 AGAAGATGCT
* *
10161837 CTCCTTCAACCACGAGCGAGTGAAGGTCCCCCTCCCCTTCCACAAATGCATCGATAACCGAATCA
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCCTCCCCTTCCACAAATGCATCGATAACCAAATCA
10161902 GCCTCAAGAACATGGA
66 GCCTCAAGAACATGGA
* * * * * *
10161918 CTTCTTTAGCCACGAGCGAGTGAAGGTCCCCCTCCTC-TCTCACAGATGCATTGATAACTAAATC
1 CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCCTCCCCTTC-CACAAATGCATCGATAACCAAATC
10161982 AGCCTCAAGAACATGGA
65 AGCCTCAAGAACATGGA
10161999 CTCCTTCAGC
1 CTCCTTCAGC
10162009 ATCATTTGAT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 2 0.03
81 78 0.98
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (81 bp):
CTCCTTCAGCCACGAGCGAGTGAAGGTCCCCCTCCCCTTCCACAAATGCATCGATAACCAAATCA
GCCTCAAGAACATGGA
Found at i:10164329 original size:31 final size:31
Alignment explanation
Indices: 10164289--10164366 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
10164279 AAATGTTGTT
*
10164289 ACACG-CATGCATATCAAGTAAAATATTGTA
1 ACACGCCATGCATATCAAGTAAAATATCGTA
* * * * *
10164319 ACATGTCATGCATATCAAGTTAAATGTCGTG
1 ACACGCCATGCATATCAAGTAAAATATCGTA
10164350 ACACGCCATGCATATCA
1 ACACGCCATGCATATCA
10164367 GTGTTGTGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 4 0.10
31 36 0.90
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (31 bp):
ACACGCCATGCATATCAAGTAAAATATCGTA
Found at i:10164538 original size:20 final size:20
Alignment explanation
Indices: 10164513--10164561 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
10164503 TTAACCCACA
*
10164513 ACACGCTAAGAACAGTCGTG
1 ACACGCTAAGAACAGCCGTG
10164533 ACACGCTAAGAACAGCCGTG
1 ACACGCTAAGAACAGCCGTG
*
10164553 ACACACTAA
1 ACACGCTAA
10164562 AAACCCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.29, G:0.20, T:0.12
Consensus pattern (20 bp):
ACACGCTAAGAACAGCCGTG
Found at i:10165191 original size:104 final size:104
Alignment explanation
Indices: 10164998--10165448 Score: 289
Period size: 104 Copynumber: 4.5 Consensus size: 104
10164988 CACACCATGG
* * *
10164998 CGTGTCACAAATTCCCT-CCATGGCTTGTCACACACTCTAAACCCTGCCGCATCACACCCATGTC
1 CGTGTCACAGATT-CCTACCATGGCATGTCACACACTCTAAACCCTGCCGCATCACACCCATATC
* * * *
10165062 ACACATTATCACCGTGTTGTTTCACACATTCTGACCCTAC
65 ACACATTATCACCGTGCTGTCTCACACATTATCACCCTAC
* * ** **
10165102 CGTGTCGCACG-TT-CTGACCATGGCATGTCACACACTCTAAACGCTGCCGTGTCACACCTGTAT
1 CGTGTCACA-GATTCCT-ACCATGGCATGTCACACACTCTAAACCCTGCCGCATCACACCCATAT
* * * * *
10165165 CACATATTCTCACTGTGCTGTCTCACACATTATCACCTTGC
64 CACACATTATCACCGTGCTGTCTCACACATTATCACCCTAC
* * * **
10165206 CGTGTCATAGATTCCTTCCATGGCGTGTCACACACTCTAAA-----CC-C-T---A-CCATGCCA
1 CGTGTCACAGATTCCTACCATGGCATGTCACACACTCTAAACCCTGCCGCATCACACCCATATCA
* * * * *
10165260 CACATTATCACCATGCCGTTTCACACATTATAATCCT-C
66 CACATTATCACCGTGCTGTCTCACACATTATCACCCTAC
* * * * ** * *
10165298 CTATGTCACACG--T-CTAACCATGGCGTGTCACACACTCTAAACCCCGTCGTGTCACACCCCTG
1 C-GTGTCACA-GATTCCT-ACCATGGCATGTCACACACTCTAAACCCTGCCGCATCACACCCATA
* * *
10165360 T--CACATTTTCACCGTGCTGTCTCACACATTATCATCTTGA-
63 TCACACATTATCACCGTGCTGTCTCACACATTATCACCCT-AC
* ** *
10165400 CGTGTCACATATTCCCT-CCATGGTGTGTCACACACTCTAAACCTTGCCG
1 CGTGTCACAGATT-CCTACCATGGCATGTCACACACTCTAAACCCTGCCG
10165449 TGTCACATAT
Statistics
Matches: 267, Mismatches: 55, Indels: 52
0.71 0.15 0.14
Matches are distributed among these distances:
91 2 0.01
92 27 0.10
93 38 0.14
94 2 0.01
97 2 0.01
99 3 0.01
101 38 0.14
102 33 0.12
103 5 0.02
104 115 0.43
105 2 0.01
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (104 bp):
CGTGTCACAGATTCCTACCATGGCATGTCACACACTCTAAACCCTGCCGCATCACACCCATATCA
CACATTATCACCGTGCTGTCTCACACATTATCACCCTAC
Found at i:10165284 original size:47 final size:46
Alignment explanation
Indices: 10165223--10165341 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 46
10165213 TAGATTCCTT
10165223 CCATGGCGTGTCACACACTCTAAACCCTACC-ATGCCACACAT-TATCA
1 CCATGGCGTGTCACACACTCTAAACCCT-CCTATGCCACACATCTA--A
* * * * *
10165270 CCATGCCGTTTCACACA-T-TATAATCCTCCTATGTCACACGTCTAA
1 CCATGGCGTGTCACACACTCTA-AACCCTCCTATGCCACACATCTAA
10165315 CCATGGCGTGTCACACACTCTAAACCC
1 CCATGGCGTGTCACACACTCTAAACCC
10165342 CGTCGTGTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
45 20 0.34
46 20 0.34
47 19 0.32
ACGTcount: A:0.28, C:0.37, G:0.11, T:0.24
Consensus pattern (46 bp):
CCATGGCGTGTCACACACTCTAAACCCTCCTATGCCACACATCTAA
Found at i:10165340 original size:24 final size:24
Alignment explanation
Indices: 10165304--10165354 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
10165294 CCTCCTATGT
*
10165304 CACACGTCTAACCATGGCGTGTCA
1 CACACGTCTAACCACGGCGTGTCA
* *
10165328 CACAC-TCTAAACCCCGTCGTGTCA
1 CACACGTCT-AACCACGGCGTGTCA
10165352 CAC
1 CAC
10165355 CCCTGTCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (24 bp):
CACACGTCTAACCACGGCGTGTCA
Found at i:10165430 original size:194 final size:197
Alignment explanation
Indices: 10165055--10165482 Score: 540
Period size: 194 Copynumber: 2.2 Consensus size: 197
10165045 CGCATCACAC
* ** * * * * *
10165055 CCATGTCACACATTATCACCGTGTTGTTTCACACATTCTGACCCTACCGTGTCGCACGTTCTGAC
1 CCATGTCACACATTATCACCATGACGTTTCACACATTATAACCCTACCATGTCACACGTTCTAAC
* * ** *
10165120 CATGGCATGTCACACACTCTAAACGCTGCCGTGTCACACCTGTATCACATATTCTCACTGTGCTG
66 CATGGCATGTCACACACTCTAAACCCCGCCGTGTCACACCCCTATCACATATTCTCACCGTGCTG
* * *
10165185 TCTCACACATTATCACCTTGCCGTGTCATAGATTCCTTCCATGGCGTGTCACACACTCTAAACCC
131 TCTCACACATTATCACCTTGACGTGTCACAGATTCCCTCCATGGCGTGTCACACACTCTAAACCC
10165250 TA
196 TA
* * *
10165252 CCATGCCACACATTATCACCATGCCGTTTCACACATTATAATCCT-CCTATGTCACACG-TCTAA
1 CCATGTCACACATTATCACCATGACGTTTCACACATTATAACCCTACC-ATGTCACACGTTCTAA
* * *
10165315 CCATGGCGTGTCACACACTCTAAACCCCGTCGTGTCACACCCCTGTCACAT-TT-TCACCGTGCT
65 CCATGGCATGTCACACACTCTAAACCCCGCCGTGTCACACCCCTATCACATATTCTCACCGTGCT
* * *
10165378 GTCTCACACATTATCATCTTGACGTGTCACATATTCCCTCCATGGTGTGTCACACACTCTAAACC
130 GTCTCACACATTATCACCTTGACGTGTCACAGATTCCCTCCATGGCGTGTCACACACTCTAAACC
* *
10165443 TTG
195 CTA
* * * *
10165446 CCGTGTCACATATTCTCACCATGACGTGTCACACATT
1 CCATGTCACACATTATCACCATGACGTTTCACACATT
10165483 CCCACCATGT
Statistics
Matches: 198, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
194 100 0.51
195 2 0.01
196 50 0.25
197 46 0.23
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (197 bp):
CCATGTCACACATTATCACCATGACGTTTCACACATTATAACCCTACCATGTCACACGTTCTAAC
CATGGCATGTCACACACTCTAAACCCCGCCGTGTCACACCCCTATCACATATTCTCACCGTGCTG
TCTCACACATTATCACCTTGACGTGTCACAGATTCCCTCCATGGCGTGTCACACACTCTAAACCC
TA
Found at i:10165524 original size:21 final size:23
Alignment explanation
Indices: 10165400--10165524 Score: 117
Period size: 23 Copynumber: 5.4 Consensus size: 23
10165390 ATCATCTTGA
* *
10165400 CGTGTCACATATTCCCTCCATGGT
1 CGTGTCACACATTCCCACCAT-GT
* ** * *
10165424 -GTGTCACACACTCTAAACCTTGC
1 CGTGTCACACATTC-CCACCATGT
* * *
10165447 CGTGTCACATATTCTCACCATGA
1 CGTGTCACACATTCCCACCATGT
10165470 CGTGTCACACATTCCCACCATGT
1 CGTGTCACACATTCCCACCATGT
*
10165493 TGTGTCACACATTCCCACCATGT
1 CGTGTCACACATTCCCACCATGT
*
10165516 CGTTTCACA
1 CGTGTCACA
10165525 AACTCTAAAC
Statistics
Matches: 80, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
23 66 0.82
24 14 0.17
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.30
Consensus pattern (23 bp):
CGTGTCACACATTCCCACCATGT
Found at i:10167444 original size:22 final size:22
Alignment explanation
Indices: 10167405--10167452 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
10167395 AATAACTTAT
**
10167405 TTTATTTTGGTTTAAAAA-ATAA
1 TTTATTTTAATTTAAAAATAT-A
*
10167427 TTTATTTTAATTTTAAAATATA
1 TTTATTTTAATTTAAAAATATA
10167449 TTTA
1 TTTA
10167453 AAACATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTATTTTAATTTAAAAATATA
Found at i:10167481 original size:8 final size:8
Alignment explanation
Indices: 10167450--10167516 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
10167440 TAAAATATAT
*
10167450 TTAAAACA
1 TTAAAATA
10167458 TTAAAATA
1 TTAAAATA
10167466 TT-AAATA
1 TTAAAATA
*
10167473 TTAATATA
1 TTAAAATA
10167481 TTTAAAATAA
1 -TTAAAAT-A
*
10167491 TTTAAAATG
1 -TTAAAATA
* *
10167500 TTAATATT
1 TTAAAATA
10167508 TTAAAATA
1 TTAAAATA
10167516 T
1 T
10167517 ATTTAAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 7 0.15
8 26 0.54
9 6 0.12
10 9 0.19
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (8 bp):
TTAAAATA
Found at i:10167503 original size:27 final size:27
Alignment explanation
Indices: 10167468--10167525 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
10167458 TTAAAATATT
10167468 AAATATTAATATATTTAAAATA-ATTTA
1 AAATATTAATAT-TTTAAAATATATTTA
*
10167495 AAATGTTAATATTTTAAAATATATTTA
1 AAATATTAATATTTTAAAATATATTTA
10167522 AAAT
1 AAAT
10167526 TAAACTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
AAATATTAATATTTTAAAATATATTTA
Found at i:10167520 original size:12 final size:11
Alignment explanation
Indices: 10167475--10167525 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 11
10167465 ATTAAATATT
10167475 AATATATTTAA
1 AATATATTTAA
10167486 AATA-ATTTAA
1 AATATATTTAA
10167496 AATGTTAATATTTTAA
1 AA---T-ATA-TTTAA
10167512 AATATATTTAA
1 AATATATTTAA
10167523 AAT
1 AAT
10167526 TAAACTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
10 8 0.24
11 12 0.35
12 3 0.09
13 2 0.06
14 1 0.03
15 1 0.03
16 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
AATATATTTAA
Found at i:10168243 original size:30 final size:30
Alignment explanation
Indices: 10168186--10168241 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
10168176 AGAACTTTCC
10168186 CTTTTTTTTTATTTGATCTGATTTGTGTTG
1 CTTTTTTTTTATTTGATCTGATTTGTGTTG
* *
10168216 CTTTTTTTTTTTTTTA-CTG-TTTGTGT
1 CTTTTTTTTTATTTGATCTGATTTGTGT
10168242 GTGTGGGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 3 0.12
30 14 0.58
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (30 bp):
CTTTTTTTTTATTTGATCTGATTTGTGTTG
Found at i:10168370 original size:5 final size:5
Alignment explanation
Indices: 10168360--10168384 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10168350 ATCAAAGACA
10168360 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
10168385 CACAAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:10171531 original size:15 final size:16
Alignment explanation
Indices: 10171511--10171553 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
10171501 ACATAAAATT
*
10171511 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
10171526 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
10171543 AAAATAACTAA
1 AAAATAACTAA
10171554 AAATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:10172897 original size:17 final size:17
Alignment explanation
Indices: 10172868--10172902 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
10172858 GACATATCTT
10172868 AAAATAAAGCTAACTAAA
1 AAAATAAAGCTAAC-AAA
10172886 AAAATAAA-CTAACAAA
1 AAAATAAAGCTAACAAA
10172902 A
1 A
10172903 TTCTAAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAATAAAGCTAACAAA
Found at i:10174842 original size:9 final size:9
Alignment explanation
Indices: 10174828--10174890 Score: 60
Period size: 9 Copynumber: 7.0 Consensus size: 9
10174818 CACTGACTTC
10174828 TTATTTTTT
1 TTATTTTTT
10174837 TTA-TTTTT
1 TTATTTTTT
10174845 TTA--TTTT
1 TTATTTTTT
*
10174852 TAATTTTTT
1 TTATTTTTT
*
10174861 TAATTTTTGAT
1 TTATTTTT--T
10174872 TTGATTTTTT
1 TT-ATTTTTT
10174882 TTATTTTTT
1 TTATTTTTT
10174891 GATTTAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
7 6 0.13
8 8 0.17
9 22 0.47
10 3 0.06
11 2 0.04
12 6 0.13
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (9 bp):
TTATTTTTT
Found at i:10174845 original size:8 final size:8
Alignment explanation
Indices: 10174832--10174895 Score: 53
Period size: 8 Copynumber: 8.4 Consensus size: 8
10174822 GACTTCTTAT
10174832 TTTTTTTA
1 TTTTTTTA
10174840 TTTTTTTA
1 TTTTTTTA
*
10174848 -TTTTTAA
1 TTTTTTTA
10174855 TTTTTTTA
1 TTTTTTTA
* *
10174863 ATTTTTGA
1 TTTTTTTA
**
10174871 -TTTGAT-
1 TTTTTTTA
10174877 TTTTTTTA
1 TTTTTTTA
*
10174885 TTTTTTGA
1 TTTTTTTA
10174893 TTT
1 TTT
10174896 AATTACTTGC
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
7 13 0.30
8 30 0.70
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:10174878 original size:21 final size:22
Alignment explanation
Indices: 10174830--10174895 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
10174820 CTGACTTCTT
* * *
10174830 ATTTTTTTTATTTTTTTATTTTT
1 ATTTTTTTTAATTTTTGA-TTTG
*
10174853 AATTTTTTTAATTTTTGATTTG
1 ATTTTTTTTAATTTTTGATTTG
*
10174875 ATTTTTTTTATTTTTTGATTT
1 ATTTTTTTTAATTTTTGATTT
10174896 AATTACTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 22 0.59
23 15 0.41
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (22 bp):
ATTTTTTTTAATTTTTGATTTG
Found at i:10195394 original size:74 final size:72
Alignment explanation
Indices: 10195236--10195400 Score: 190
Period size: 74 Copynumber: 2.3 Consensus size: 72
10195226 TTCAGACAAA
* * *
10195236 ATGCTCTTAGTCGACTAACATGTGTCTTAGTCGATTAAGTCGTCTTTGTCTCTAAACCCAGTTTC
1 ATGCTCTTAGTTGACTAACATGTGTCTTAGTCGATTAAGTCGTCTCTGTCTCTAAACCCAATTTC
10195301 TGGCAAT
66 TGGCAAT
* * * * **
10195308 AAGCTCTTAGTTGACTAAC-TGTGCTTCTTAGTTGATTAAGTGGTCTCTGTCT-TGCAATCTGAA
1 ATGCTCTTAGTTGACTAACATGTG--TCTTAGTCGATTAAGTCGTCTCTGTCTCT--AAACCCAA
*
10195371 TTTCTGGCAGT
62 TTTCTGGCAAT
10195382 ATGCTCTTAGTTGACTAAC
1 ATGCTCTTAGTTGACTAAC
10195401 CACGTATCTT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
71 4 0.05
72 18 0.23
73 24 0.31
74 32 0.41
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (72 bp):
ATGCTCTTAGTTGACTAACATGTGTCTTAGTCGATTAAGTCGTCTCTGTCTCTAAACCCAATTTC
TGGCAAT
Found at i:10197649 original size:46 final size:46
Alignment explanation
Indices: 10197598--10197776 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 46
10197588 TAATGTTGTG
* *
10197598 TGATGATGATGACCCGACTATGTGCGAGTAGGGAGTGCGCATAAGC
1 TGATGATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATGAGC
* * * *
10197644 ---CGATGATGACCCAACTATGTGCTAGTAGGGAGTGCACATGAGT
1 TGATGATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATGAGC
10197687 TGATGATGATGACCC-AGCTATGTGCGAGTAGGGAGTGCACATGAGC
1 TGATGATGATGACCCGA-CTATGTGCGAGTAGGGAGTGCACATGAGC
* * * *
10197733 TAATGATGATGACCTGGCTATGTGTGAGTAGGGAGTGCACATGA
1 TGATGATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATGA
10197777 CGATGAATGA
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
43 37 0.32
45 1 0.01
46 77 0.67
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (46 bp):
TGATGATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATGAGC
Found at i:10197692 original size:89 final size:90
Alignment explanation
Indices: 10197598--10197776 Score: 247
Period size: 89 Copynumber: 2.0 Consensus size: 90
10197588 TAATGTTGTG
*
10197598 TGATGATGATGACCC-GACTATGTGCGAGTAGGGAGTGCGCATAAGC-CGATGATGACCCAACTA
1 TGATGATGATGACCCAG-CTATGTGCGAGTAGGGAGTGCACATAAGCACGATGATGACCCAACTA
10197661 TGTGCT-AGTAGGGAGTGCACATGAGT
65 TGTG-TGAGTAGGGAGTGCACATGAGT
* * ***
10197687 TGATGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTAATGATGATGACCTGGCT
1 TGATGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGC--ACGATGATGACCCAACT
10197752 ATGTGTGAGTAGGGAGTGCACATGA
64 ATGTGTGAGTAGGGAGTGCACATGA
10197777 CGATGAATGA
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
89 42 0.53
90 1 0.01
91 1 0.01
92 35 0.44
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (90 bp):
TGATGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCACGATGATGACCCAACTAT
GTGTGAGTAGGGAGTGCACATGAGT
Found at i:10204149 original size:18 final size:18
Alignment explanation
Indices: 10204107--10204159 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
10204097 TTAATATGTT
*
10204107 AATATTATTTTATTAATAA
1 AATATTATTTTATT-CTAA
10204126 AATATTATTTTATTCTAA
1 AATATTATTTTATTCTAA
* *
10204144 AGTATTCTTTTCATTC
1 AATATTATTTT-ATTC
10204160 ATTACTGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.55
Consensus pattern (18 bp):
AATATTATTTTATTCTAA
Found at i:10211850 original size:21 final size:21
Alignment explanation
Indices: 10211824--10211872 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
10211814 TGGTAAGGGA
10211824 AGCAAAAGTTGAAAAAGAAGC
1 AGCAAAAGTTGAAAAAGAAGC
10211845 AGCAAAAGTTGAAAAAGAAGC
1 AGCAAAAGTTGAAAAAGAAGC
10211866 AGCAAAA
1 AGCAAAA
10211873 AGCAAAACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.22, T:0.08
Consensus pattern (21 bp):
AGCAAAAGTTGAAAAAGAAGC
Found at i:10212441 original size:82 final size:82
Alignment explanation
Indices: 10212335--10212500 Score: 269
Period size: 82 Copynumber: 2.0 Consensus size: 82
10212325 AGTTTTTCTG
* * *
10212335 ATTTTTTTTATTAACTGCTAATGGTTAGTGCTTGGATGTTGATAACATTTTGTTATGCTATTTTA
1 ATTTTATTTATTAACTACTAATGGTTAGTGCTTGGATGTTGATAACATTTTGTTATGCTATTTAA
* *
10212400 GTTGGCTTGTTGGTGAC
66 GCTGGCTTGTTGATGAC
* *
10212417 ATTTTATTTATTAACTATTAATGGTTAGTGCTTGGATGTTGATAACTTTTTGTTATGCTATTTAA
1 ATTTTATTTATTAACTACTAATGGTTAGTGCTTGGATGTTGATAACATTTTGTTATGCTATTTAA
10212482 GCTGGCTTGTTGATGAC
66 GCTGGCTTGTTGATGAC
10212499 AT
1 AT
10212501 ATGGGTTTAG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.49
Consensus pattern (82 bp):
ATTTTATTTATTAACTACTAATGGTTAGTGCTTGGATGTTGATAACATTTTGTTATGCTATTTAA
GCTGGCTTGTTGATGAC
Found at i:10217194 original size:21 final size:21
Alignment explanation
Indices: 10217170--10217210 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10217160 GACAAAATAC
* *
10217170 TCTTAGTTAATTAAGTGCCTT
1 TCTTAGTCAACTAAGTGCCTT
10217191 TCTTAGTCAACTAAGTGCCT
1 TCTTAGTCAACTAAGTGCCT
10217211 ACGGTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (21 bp):
TCTTAGTCAACTAAGTGCCTT
Found at i:10220392 original size:18 final size:19
Alignment explanation
Indices: 10220369--10220407 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
10220359 AATGTTTGAA
10220369 AAATGAA-ACTTCAAAAAG
1 AAATGAATACTTCAAAAAG
*
10220387 AAATGAATACTTCAAGAAG
1 AAATGAATACTTCAAAAAG
10220406 AA
1 AA
10220408 TTCCACTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (19 bp):
AAATGAATACTTCAAAAAG
Found at i:10227805 original size:31 final size:31
Alignment explanation
Indices: 10227723--10227902 Score: 189
Period size: 31 Copynumber: 5.8 Consensus size: 31
10227713 CACGACATTG
* * *
10227723 GTTATAAGCATGGCGTGTTACAACATTTAAC
1 GTTATATGCATGGCGTGTTACAACATTTTAT
* ** *
10227754 GTTATATGCATTGCAAGTTACAACATTTAAT
1 GTTATATGCATGGCGTGTTACAACATTTTAT
* **
10227785 GTTATATGCATGGCGTGTTACCACATTTTCC
1 GTTATATGCATGGCGTGTTACAACATTTTAT
** * * *
10227816 ACTATATTCATGGCGTGATACCACATTTTAT
1 GTTATATGCATGGCGTGTTACAACATTTTAT
*
10227847 GTTATTTGCATGGCGTGTTACAACATTTTAT
1 GTTATATGCATGGCGTGTTACAACATTTTAT
* *
10227878 ATTATTTGCATGGCGTGTTAGCAAC
1 GTTATATGCATGGCGTGTTA-CAAC
10227903 TCTTCACTTT
Statistics
Matches: 123, Mismatches: 25, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
31 119 0.97
32 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (31 bp):
GTTATATGCATGGCGTGTTACAACATTTTAT
Found at i:10228332 original size:3 final size:3
Alignment explanation
Indices: 10228326--10228373 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
10228316 ATATTTGATG
* * * *
10228326 TTA TTA TTA TTA TTA TTA TTA TT- TTG TTA TAA TTA TTT TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10228373 T
1 T
10228374 AGATTTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:10228447 original size:18 final size:18
Alignment explanation
Indices: 10228424--10228462 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
10228414 ATTTTTTTAT
*
10228424 TTAATCGTGTTAAATGTG
1 TTAATCGTGTTAAACGTG
10228442 TTAATCGTGTTAAACGTG
1 TTAATCGTGTTAAACGTG
10228460 TTA
1 TTA
10228463 TTAATCGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.44
Consensus pattern (18 bp):
TTAATCGTGTTAAACGTG
Found at i:10229084 original size:31 final size:31
Alignment explanation
Indices: 10229017--10229122 Score: 169
Period size: 31 Copynumber: 3.5 Consensus size: 31
10229007 AATAAGGAAT
10229017 AAATGTTGTGACACGCCATGCATAACAAG-A
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
10229047 AAATGTTGTGACACGCCATGCATAATAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
10229078 AAATGTTGTGACACGCCATGCATAACAAATC
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
10229109 AAATGTTGTCACAC
1 AAATGTTGTGACAC
10229123 TAACACGCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 28 0.40
31 42 0.60
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:10230143 original size:35 final size:34
Alignment explanation
Indices: 10230066--10230147 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 34
10230056 TATATAAAAG
*
10230066 AAAAAAAATTCTTGTTATAAAATTAATTGTGTATAGGC
1 AAAAAAAATT-ATG-TATAAAATTAATTGTGTATA--C
*
10230104 -AAAAACATTATGTATAAAA-TATATTGTGTATAC
1 AAAAAAAATTATGTATAAAATTA-ATTGTGTATAC
10230137 AAAAAAAATTA
1 AAAAAAAATTA
10230148 ATTCTGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
33 1 0.03
34 11 0.28
35 17 0.44
36 2 0.05
37 8 0.21
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (34 bp):
AAAAAAAATTATGTATAAAATTAATTGTGTATAC
Found at i:10230204 original size:31 final size:30
Alignment explanation
Indices: 10230166--10230244 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 30
10230156 TACAATGAAT
10230166 TGTATAAAATAAATTGTATACAAAAAAATTA
1 TGTATAAAATAAATTGTATA-AAAAAAATTA
* * *
10230197 TGTATAAAATTAATTGTATAAAAATAATTC
1 TGTATAAAATAAATTGTATAAAAAAAATTA
*
10230227 TATATAAAA-AAA-TGTATA
1 TGTATAAAATAAATTGTATA
10230245 GACAATGGGC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.14
29 2 0.05
30 16 0.37
31 19 0.44
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (30 bp):
TGTATAAAATAAATTGTATAAAAAAAATTA
Found at i:10230212 original size:45 final size:48
Alignment explanation
Indices: 10230114--10230239 Score: 143
Period size: 45 Copynumber: 2.6 Consensus size: 48
10230104 AAAAACATTA
* *
10230114 TGTATAAAATATATTGTGTATACAAAAAAAATTAATTCTGTATACAATGAAT
1 TGTATAAAATATAAT-TGTATAC-AAAAAAATTAA-T-TGTATAAAATGAAT
*
10230166 TGTATAAAATA-AATTGTATACAAAAAAATT-A-TGTATAAAATTAAT
1 TGTATAAAATATAATTGTATACAAAAAAATTAATTGTATAAAATGAAT
* *
10230211 TGTATAAAA-ATAATTCTATATAAAAAAAT
1 TGTATAAAATATAATTGTATACAAAAAAAT
10230240 GTATAGACAA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
44 1 0.01
45 37 0.54
48 1 0.01
49 9 0.13
50 7 0.10
51 2 0.03
52 11 0.16
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (48 bp):
TGTATAAAATATAATTGTATACAAAAAAATTAATTGTATAAAATGAAT
Found at i:10230217 original size:14 final size:14
Alignment explanation
Indices: 10230141--10230230 Score: 72
Period size: 14 Copynumber: 6.1 Consensus size: 14
10230131 GTATACAAAA
10230141 AAAATTAATTCTGTAT
1 AAAATTAA-T-TGTAT
* *
10230157 ACAATGAATTGTAT
1 AAAATTAATTGTAT
*
10230171 AAAATAAATTGTAT
1 AAAATTAATTGTAT
**
10230185 ACAAAAAAATTATGTAT
1 A-AAATTAA-T-TGTAT
10230202 AAAATTAATTGTAT
1 AAAATTAATTGTAT
* *
10230216 AAAAATAATTCTAT
1 AAAATTAATTGTAT
10230230 A
1 A
10230231 TAAAAAAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
14 36 0.58
15 8 0.13
16 12 0.19
17 6 0.10
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAATTAATTGTAT
Found at i:10230244 original size:14 final size:15
Alignment explanation
Indices: 10230168--10230244 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 15
10230158 CAATGAATTG
10230168 TATAAAATAAATTGTA
1 TATAAAATAAA-TGTA
*
10230184 TACAAAA-AAAT-TA
1 TATAAAATAAATGTA
*
10230197 TGTATAAAATTAATTGTA
1 --TATAAAA-TAAATGTA
* *
10230215 TA-AAAATAATTCTA
1 TATAAAATAAATGTA
10230229 TATAAAA-AAATGTA
1 TATAAAATAAATGTA
10230243 TA
1 TA
10230245 GACAATGGGC
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 2 0.04
14 17 0.35
15 17 0.35
16 8 0.16
17 3 0.06
18 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (15 bp):
TATAAAATAAATGTA
Found at i:10233302 original size:18 final size:17
Alignment explanation
Indices: 10233269--10233331 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
10233259 TGTACATTTT
10233269 TTTTGTATACAAAATTA
1 TTTTGTATACAAAATTA
10233286 TTTT-TATAC--AATTA
1 TTTTGTATACAAAATTA
* * *
10233300 ATTT-TATACATAATTT
1 TTTTGTATACAAAATTA
*
10233316 TTTTGTATACACAATT
1 TTTTGTATACAAAATT
10233332 TATTCTATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 13 0.33
16 12 0.31
17 14 0.36
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTTGTATACAAAATTA
Found at i:10233341 original size:47 final size:47
Alignment explanation
Indices: 10233266--10233442 Score: 214
Period size: 47 Copynumber: 3.6 Consensus size: 47
10233256 GTCTGTACAT
*
10233266 TTTTTTTGTATACA-AAATTATTTTTATACAATTAATTTTATACATAA
1 TTTTTTTGTATACACAATTTA-TTTTATACAATTAATTTTATACATAA
* * *
10233313 TTTTTTTGTATACACAATTTATTCTATACAATTCATTATATACAGAATTAA
1 TTTTTTTGTATACACAATTTATTTTATACAATTAATTTTATAC---A-TAA
10233364 TTCTTTTTGTATACACAATATT-TTTTATACAATTAATTTTATACATAA
1 TT-TTTTTGTATACACAAT-TTATTTTATACAATTAATTTTATACATAA
*
10233412 TTTTTTTGCCTATACACAATTAATTTTATAC
1 TTTTTTTG--TATACACAATTTATTTTATAC
10233443 TAAGAATTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
47 39 0.35
48 11 0.10
49 19 0.17
50 1 0.01
51 5 0.04
52 35 0.31
53 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.51
Consensus pattern (47 bp):
TTTTTTTGTATACACAATTTATTTTATACAATTAATTTTATACATAA
Found at i:10233744 original size:85 final size:87
Alignment explanation
Indices: 10233631--10233840 Score: 209
Period size: 85 Copynumber: 2.4 Consensus size: 87
10233621 TAACACTCAA
* * * *
10233631 CGTGTCA-GCCCATAAATTTGCTTCCACTCAGCGTGTCAAAACAATTGGGTCGTGC-CGTGTCAC
1 CGTGTCACG-CCATAAATCTACTTCCACTCAGCGTGTCAAAACAATTGGGCCGT-CACATGTCAC
* * *
10233694 GCCA-TA-ATCTACA-GATACTCAG-
64 CCCACGATAT-TACACCA-ACTCAGC
* * *
10233716 CGTGTGACGCCATAAATCTACTTCCACTC-GATGTGTCATAACAATTGGGCCGTCACATGTCACC
1 CGTGTCACGCCATAAATCTACTTCCACTCAG-CGTGTCAAAACAATTGGGCCGTCACATGTCACC
*
10233780 CCACGATATTACACCAAGTCAGC
65 CCACGATATTACACCAACTCAGC
* *
10233803 CGTGTCACGCCATAAATCTACTTGCACTCAGCATGTCA
1 CGTGTCACGCCATAAATCTACTTCCACTCAGCGTGTCA
10233841 CGACTGTGAC
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
84 2 0.02
85 53 0.52
86 11 0.11
87 35 0.34
88 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (87 bp):
CGTGTCACGCCATAAATCTACTTCCACTCAGCGTGTCAAAACAATTGGGCCGTCACATGTCACCC
CACGATATTACACCAACTCAGC
Found at i:10234473 original size:31 final size:31
Alignment explanation
Indices: 10234430--10234536 Score: 144
Period size: 31 Copynumber: 3.5 Consensus size: 31
10234420 TGACGTGTCA
* *
10234430 GTGTGACAACATTTTACTTGATATGCA-GAAC
1 GTGTCACAACATTTTACTTGTTATGCACG-AC
*
10234461 GTGTAACAACATTTTACTTGTTATGCACGAC
1 GTGTCACAACATTTTACTTGTTATGCACGAC
* * *
10234492 GTGTCACAACATTTTGCTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCACGAC
10234523 GTGTCACAACATTT
1 GTGTCACAACATTT
10234537 ATTCTTTATT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
31 68 0.99
32 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (31 bp):
GTGTCACAACATTTTACTTGTTATGCACGAC
Found at i:10235941 original size:16 final size:18
Alignment explanation
Indices: 10235910--10235942 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
10235900 CACAAACTCA
10235910 TGTGAATGCTATTGTAAT
1 TGTGAATGCTATTGTAAT
10235928 TGTGAA-GC-ATTGTAA
1 TGTGAATGCTATTGTAA
10235943 ATCTCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (18 bp):
TGTGAATGCTATTGTAAT
Found at i:10236406 original size:31 final size:31
Alignment explanation
Indices: 10236353--10236595 Score: 288
Period size: 31 Copynumber: 7.8 Consensus size: 31
10236343 TTTGTCAATC
* *
10236353 ATGTTGTTACACGCCATACATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
** *
10236384 ATGTAATAACACGTCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* * * * *
10236415 ATGTTCTAACACGTCATACAAATAACATAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
10236446 ATGTTCTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
10236477 ATGTAGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* * **
10236508 ATATAGTAACACGCCATGCATATAACGTTCA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* * * **
10236539 ATGTTATAACACACTATGCATATAACGTTCA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
10236570 ATGTTGTAACACGCAATGCATATAAC
1 ATGTTGTAACACGCCATGCATATAAC
10236596 CAATGTCGTG
Statistics
Matches: 185, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 185 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:10238213 original size:23 final size:23
Alignment explanation
Indices: 10238185--10238237 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
10238175 CATACAAATT
10238185 ATGAATGATAACATAAAACCTCA
1 ATGAATGATAACATAAAACCTCA
* *
10238208 ATGAATGATAATATAACACCTCA
1 ATGAATGATAACATAAAACCTCA
10238231 ATGAATG
1 ATGAATG
10238238 TAAAAACCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (23 bp):
ATGAATGATAACATAAAACCTCA
Found at i:10243067 original size:15 final size:15
Alignment explanation
Indices: 10243047--10243081 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10243037 TCTTGAAACG
*
10243047 AAACCTATAATTTCT
1 AAACCTATAATTTCC
*
10243062 AAACCTATACTTTCC
1 AAACCTATAATTTCC
10243077 AAACC
1 AAACC
10243082 CAGCCCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACCTATAATTTCC
Found at i:10249880 original size:35 final size:34
Alignment explanation
Indices: 10249840--10249924 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 34
10249830 CACCTATTTC
*
10249840 AAAAAATAAAAAAATAAATGATAAT-GAAATATAATT
1 AAAAAATAAAAAAA-AAAT-AAAATAGAAATA-AATT
*
10249876 AAAAAA-ACCAAAAAAAATAAAATAAGAAATAAATT
1 AAAAAATA-AAAAAAAAATAAAAT-AGAAATAAATT
10249911 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
10249925 GGAATGAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
34 4 0.10
35 20 0.48
36 18 0.43
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (34 bp):
AAAAAATAAAAAAAAAATAAAATAGAAATAAATT
Found at i:10249905 original size:12 final size:12
Alignment explanation
Indices: 10249887--10249921 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
10249877 AAAAAACCAA
10249887 AAAAAATAAAAT
1 AAAAAATAAAAT
* *
10249899 AAGAAATAAATT
1 AAAAAATAAAAT
10249911 AAAAAATAAAA
1 AAAAAATAAAA
10249922 AAAGGAATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:10250387 original size:22 final size:23
Alignment explanation
Indices: 10250347--10250389 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10250337 ATGGGTGAGG
10250347 GTTTTTGAGGGAATGTTTGGGTA
1 GTTTTTGAGGGAATGTTTGGGTA
10250370 GTTTTTAGAGGG-AT-TTTGGG
1 GTTTTT-GAGGGAATGTTTGGG
10250390 GAGGGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 8 0.42
24 5 0.26
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (23 bp):
GTTTTTGAGGGAATGTTTGGGTA
Found at i:10251370 original size:15 final size:16
Alignment explanation
Indices: 10251350--10251379 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10251340 TAGACAAATA
10251350 AAAAAAATAA-AAAAC
1 AAAAAAATAATAAAAC
10251365 AAAAAAATAATAAAA
1 AAAAAAATAATAAAA
10251380 ATAGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAATAATAAAAC
Found at i:10264138 original size:62 final size:62
Alignment explanation
Indices: 10263983--10264644 Score: 892
Period size: 62 Copynumber: 10.7 Consensus size: 62
10263973 CATTTGTGAA
* * * *
10263983 TTAAATCGAACCTG-TTT-TGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAA-TTT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
*
10264042 TTAAATCGAACCTG-TTTGTGAGATGGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
*
10264103 TTAAATCGAACCTATTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
* * * * *
10264165 TTAAATCGAACTTGTTTTCTGAAATAGGTCGAGCCTAAGTCAAGTCTAGGAATTTCAATTCT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
* * *
10264227 TTAAATCGAACTTGTTTTGTGAGATAGGTCCAGCCTAGGTCAAGTCTAAGAATTTCAATTTTT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAA-TTTT
* * *
10264290 TTGAAAATCGAACCCGTTTTGTGAGATGGGTCGAGCCTAGGTCAAGTCTAGGAATTTTAATTTTT
1 TT--AAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAA---TT
10264355 TT
61 TT
* * * *
10264357 TTAAATTGAACCTGTTTTGTGAGATAGGTCCAACCTAGGTCAAGTATAGGAATTTCAATTTTTT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAA--TTTT
* * *
10264421 TTAAATCGAACTTGTTTTGTGAGATGGGTCGAGCCTAGGTCAAGTCTAGGAATTTTAATTTT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
** *
10264483 TTTTATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTCT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
* * *
10264545 TTAAGTCGAACCTG--TTGTGAGATAGGTCGAGCCTAGATCAAGTCTACGAATTTCAA-TTT
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
* * *
10264604 TTAAGTCGAACCTG-TTT-TGAGATAGGTCGAGTCTAGATCAA
1 TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAA
10264645 ATTTAGAAAT
Statistics
Matches: 542, Mismatches: 52, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
59 56 0.10
60 76 0.14
61 16 0.03
62 226 0.42
63 5 0.01
64 57 0.11
65 99 0.18
67 7 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (62 bp):
TTAAATCGAACCTGTTTTGTGAGATAGGTCGAGCCTAGGTCAAGTCTAGGAATTTCAATTTT
Found at i:10264925 original size:8 final size:8
Alignment explanation
Indices: 10264912--10265005 Score: 71
Period size: 8 Copynumber: 10.8 Consensus size: 8
10264902 TACCTATTTC
10264912 AAAAAATA
1 AAAAAATA
10264920 AAAAAATA
1 AAAAAATA
*
10264928 AATGATAATGA
1 AA--AAAAT-A
*
10264939 AATATAATTA
1 AA-A-AAATA
10264949 AAAAAACTA
1 AAAAAA-TA
10264958 AAAAAATA
1 AAAAAATA
10264966 AAAAAATA
1 AAAAAATA
*
10264974 AAATAAAGA
1 AAA-AAATA
* *
10264983 AATAAATT
1 AAAAAATA
10264991 AAAAAATA
1 AAAAAATA
10264999 GAAAAAA
1 -AAAAAA
10265006 AATAGAATGA
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
8 34 0.50
9 21 0.31
10 8 0.12
11 5 0.07
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (8 bp):
AAAAAATA
Found at i:10264966 original size:21 final size:21
Alignment explanation
Indices: 10264942--10265006 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
10264932 ATAATGAAAT
*
10264942 ATAATTAAAAAAACTAAAAAA
1 ATAATTAAAAAAAATAAAAAA
* *
10264963 ATAA-AAAAATAAAATAAAGAA
1 ATAATTAAAA-AAAATAAAAAA
* *
10264984 ATAAATTAAAAAATAGAAAAAA
1 AT-AATTAAAAAAAATAAAAAA
10265006 A
1 A
10265007 ATAGAATGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 4 0.12
21 15 0.44
22 11 0.32
23 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (21 bp):
ATAATTAAAAAAAATAAAAAA
Found at i:10264978 original size:13 final size:13
Alignment explanation
Indices: 10264914--10264996 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 13
10264904 CCTATTTCAA
10264914 AAAATAAAAAAAT
1 AAAATAAAAAAAT
**
10264927 AAATGATAATGAAAT
1 AAA--ATAAAAAAAT
*
10264942 ATAATTAAAAAAACT
1 A-AAATAAAAAAA-T
10264957 AAAAAAATAAAAAAAT
1 ---AAAATAAAAAAAT
*
10264973 AAAATAAAGAAAT
1 AAAATAAAAAAAT
*
10264986 AAATTAAAAAA
1 AAAATAAAAAA
10264997 TAGAAAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
13 24 0.44
14 6 0.11
15 10 0.19
16 3 0.06
17 10 0.19
18 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:10265005 original size:44 final size:45
Alignment explanation
Indices: 10264912--10265009 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 45
10264902 TACCTATTTC
* *
10264912 AAAAAATAAAAAAATAAATGATAATGAAATATAATTAAAAAAACTA
1 AAAAAATAAAAAAATAAA-GATAAAGAAATATAATTAAAAAAACAA
*
10264958 AAAAAATAAAAAAATAAA-ATAAAGAAATA-AATTAAAAAATAGAA
1 AAAAAATAAAAAAATAAAGATAAAGAAATATAATTAAAAAA-ACAA
10265002 AAAAAATA
1 AAAAAATA
10265010 GAATGAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
43 10 0.21
44 20 0.42
46 18 0.38
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (45 bp):
AAAAAATAAAAAAATAAAGATAAAGAAATATAATTAAAAAAACAA
Found at i:10270263 original size:25 final size:25
Alignment explanation
Indices: 10270225--10270282 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
10270215 ATAAAGTTCT
*
10270225 TATAATTATCATGATTCCTAATTCC
1 TATAATTATCATGATCCCTAATTCC
* *
10270250 TATAATTATGATGATCCCTAATTTC
1 TATAATTATCATGATCCCTAATTCC
10270275 TATAATTA
1 TATAATTA
10270283 CTTTAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (25 bp):
TATAATTATCATGATCCCTAATTCC
Found at i:10271628 original size:35 final size:35
Alignment explanation
Indices: 10271584--10271655 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
10271574 GATAGTGGCA
10271584 AAGGAGTCACCTATGAATGATGTTAAGAATTTGAG
1 AAGGAGTCACCTATGAATGATGTTAAGAATTTGAG
10271619 AAGGAGTCACCTATGAATGATGTTAAGAATTTGAG
1 AAGGAGTCACCTATGAATGATGTTAAGAATTTGAG
10271654 AA
1 AA
10271656 TATAGTGCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (35 bp):
AAGGAGTCACCTATGAATGATGTTAAGAATTTGAG
Found at i:10272828 original size:49 final size:50
Alignment explanation
Indices: 10272772--10272873 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 50
10272762 ACTTTACATA
* * *
10272772 TTGTCTTAATTGAGACAAAAGTTGTCTCAATTTAGATAAG-GTAAATGTG
1 TTGTCTTAATTAAGACAAAAGTTATCTCAATTTAGACAAGAGTAAATGTG
* * * * *
10272821 TTGTCTTAATTAAGATAAGAGTTATTTTAATTTAGACAAGAGTATATGTG
1 TTGTCTTAATTAAGACAAAAGTTATCTCAATTTAGACAAGAGTAAATGTG
10272871 TTG
1 TTG
10272874 ATTTAAGACA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 33 0.75
50 11 0.25
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (50 bp):
TTGTCTTAATTAAGACAAAAGTTATCTCAATTTAGACAAGAGTAAATGTG
Found at i:10272883 original size:25 final size:22
Alignment explanation
Indices: 10272826--10272887 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
10272816 ATGTGTTGTC
*
10272826 TTAA-TTAAGATAAGAGTTATT
1 TTAATTTAAGACAAGAGTTATT
10272847 TTAATTT-AGACAAGAGTATATGT
1 TTAATTTAAGACAAGAGT-TAT-T
*
10272870 GTTGATTTAAGACAAGAG
1 -TTAATTTAAGACAAGAG
10272888 ATGTCTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 13 0.38
22 5 0.15
23 1 0.03
24 6 0.18
25 9 0.26
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (22 bp):
TTAATTTAAGACAAGAGTTATT
Found at i:10277926 original size:33 final size:34
Alignment explanation
Indices: 10277889--10277968 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
10277879 CATATACACA
10277889 TCAAAATCAGCAATTAAGCTGCTCTATTTCT-CT
1 TCAAAATCAGCAATTAAGCTGCTCTATTTCTCCT
* * * *
10277922 TCAAAATCAACAGTTAAGCTGTTCTATTTTTCCT
1 TCAAAATCAGCAATTAAGCTGCTCTATTTCTCCT
10277956 TCAAAAATCAGCA
1 TC-AAAATCAGCA
10277969 GCCAAAGCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 27 0.68
34 4 0.10
35 9 0.22
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.35
Consensus pattern (34 bp):
TCAAAATCAGCAATTAAGCTGCTCTATTTCTCCT
Found at i:10278126 original size:21 final size:23
Alignment explanation
Indices: 10278092--10278133 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
10278082 AGCCAAAGCT
10278092 GTTCCTTCCATCCT-CAAAATCA
1 GTTCCTTCCATCCTCCAAAATCA
*
10278114 GTTCTTTCC-TCCTCCAAAAT
1 GTTCCTTCCATCCTCCAAAAT
10278134 TTGCAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.24, C:0.36, G:0.05, T:0.36
Consensus pattern (23 bp):
GTTCCTTCCATCCTCCAAAATCA
Found at i:10278753 original size:114 final size:113
Alignment explanation
Indices: 10278553--10278776 Score: 376
Period size: 114 Copynumber: 2.0 Consensus size: 113
10278543 ATAATCCTTC
* * * *
10278553 AATCTTTATATTTTAAATTCAATCCTTTTAATACGTCTAAAAATTTCAATTTTCATCTATCTTCC
1 AATCTTTATATTTCAAACTCAATCCTTTTAATAAGTCTAAAAATTTCAATTTTCATCTATCGTCC
*
10278618 TTCCTCTGTACGTGTACTACCAAATTATCAAAATTGCACTTCAACNTTT
66 TTCCTCTGTACGTGTACTACCAAATTATCAAAATTGCACTGCAAC-TTT
* *
10278667 AATCTTTATATTTCAAACTCGATCCTTTTAATAAGTCTAAAAATTTCAATTTTTATCTATCGTCC
1 AATCTTTATATTTCAAACTCAATCCTTTTAATAAGTCTAAAAATTTCAATTTTCATCTATCGTCC
10278732 TTCCTCTGTACGTGTACTACCAAATTATCAAAATTGCACTGCAAC
66 TTCCTCTGTACGTGTACTACCAAATTATCAAAATTGCACTGCAAC
10278777 GCGGTATTAC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.41
Consensus pattern (113 bp):
AATCTTTATATTTCAAACTCAATCCTTTTAATAAGTCTAAAAATTTCAATTTTCATCTATCGTCC
TTCCTCTGTACGTGTACTACCAAATTATCAAAATTGCACTGCAACTTT
Found at i:10286122 original size:2 final size:2
Alignment explanation
Indices: 10286115--10286157 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10286105 ACGTACGTAG
10286115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10286157 T
1 T
10286158 CCAAATTTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10290449 original size:31 final size:31
Alignment explanation
Indices: 10290381--10290458 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
10290371 ATTTATCAAG
* *
10290381 TATTTTT-TATAATTTAGTCCCTCAATATTT
1 TATTTTTGTTTAATTTAGTCCCTCAATATTA
*
10290411 TAATTTTGTTTAATTTAGTCCCT--ATACTATA
1 TATTTTTGTTTAATTTAGTCCCTCAATA-T-TA
*
10290442 TATTTTTGTTCAATTTA
1 TATTTTTGTTTAATTTA
10290459 ACCCCTATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 3 0.08
30 7 0.17
31 30 0.75
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (31 bp):
TATTTTTGTTTAATTTAGTCCCTCAATATTA
Found at i:10294079 original size:126 final size:124
Alignment explanation
Indices: 10293868--10294100 Score: 283
Period size: 126 Copynumber: 1.9 Consensus size: 124
10293858 ACAAAAATTT
* *
10293868 AAATTTAATTTTTTATTTATAATTAATTGACACATGAACTCAACTAGGTTATTAACACGTAAACA
1 AAATTTAAATTTTTATTAATAATTAATTGACACATGAACTCAACTAGGTTATTAACACGTAAACA
* * * **
10293933 AAATATCTTTTCCAGGTCAAATTTGTTTTTTGTTAAAAGTTGATATGATCATTGAGTACA
66 AAATATCCTTTACA-GTCAAATCTGTTTTCCGTTAAAAGTTGATATGATCATTGAGTACA
* * * *
10293993 AAATTTAAATTTTTA-TAATAATTAATTGACACGTGAACT-TACTTTAAGGTTATTAATATGTAA
1 AAATTTAAATTTTTATTAATAATTAATTGACACATGAACTCAAC--T-AGGTTATTAACACGTAA
*
10294056 TCAAAATAACTCCTTTACA-TCAAATCTGTTTTCCGTTAAAAGTTG
63 ACAAAAT-A-TCCTTTACAGTCAAATCTGTTTTCCGTTAAAAGTTG
10294101 GTATATCTAA
Statistics
Matches: 91, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
123 2 0.02
124 22 0.24
125 15 0.16
126 44 0.48
127 1 0.01
128 7 0.08
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (124 bp):
AAATTTAAATTTTTATTAATAATTAATTGACACATGAACTCAACTAGGTTATTAACACGTAAACA
AAATATCCTTTACAGTCAAATCTGTTTTCCGTTAAAAGTTGATATGATCATTGAGTACA
Found at i:10294306 original size:27 final size:27
Alignment explanation
Indices: 10294275--10294328 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
10294265 AGGAGAAGAA
10294275 GGATGAAGACACCAGCAGA-GGAGGTTG
1 GGATGAAGACACCAGCA-ACGGAGGTTG
*
10294302 GGATGAAGTCACCAGCAACGGAGGTTG
1 GGATGAAGACACCAGCAACGGAGGTTG
10294329 CCGACATCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.31, C:0.17, G:0.39, T:0.13
Consensus pattern (27 bp):
GGATGAAGACACCAGCAACGGAGGTTG
Found at i:10304883 original size:36 final size:36
Alignment explanation
Indices: 10304836--10304943 Score: 189
Period size: 36 Copynumber: 3.0 Consensus size: 36
10304826 CATCTCTACT
* *
10304836 CTTTTGTAAATCATTTTTGAACACTGACATTCCACA
1 CTTTTGTAAATCATTTTTGCACACTAACATTCCACA
10304872 CTTTTGTAAATCATTTTTGCACACTAACATTCCACA
1 CTTTTGTAAATCATTTTTGCACACTAACATTCCACA
*
10304908 CTTTTGCAAATCATTTTTGCACACTAACATTCCACA
1 CTTTTGTAAATCATTTTTGCACACTAACATTCCACA
10304944 AGCTTGGGAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (36 bp):
CTTTTGTAAATCATTTTTGCACACTAACATTCCACA
Done.