Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002223.1 Hibiscus syriacus cultivar Beakdansim tig00004523_pilon, whole genome shotgun sequence
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: 139199
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:385 original size:21 final size:21
Alignment explanation
Indices: 359--414 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
349 TCTTTAAAGA
359 GTGCATCGGTACACATTGAAT
1 GTGCATCGGTACACATTGAAT
380 GTGCATCGGTACACATTGAAT
1 GTGCATCGGTACACATTGAAT
401 GTGCAT-GGATACAC
1 GTGCATCGG-TACAC
415 TTTGCCCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 2 0.06
21 32 0.94
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (21 bp):
GTGCATCGGTACACATTGAAT
Found at i:1459 original size:41 final size:41
Alignment explanation
Indices: 1400--1496 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
1390 AGTTGATCCA
1400 TTCCACTGTCACTCAGGGAAGATTGAATCAAGGAAGACTTG
1 TTCCACTGTCACTCAGGGAAGATTGAATCAAGGAAGACTTG
* * *
1441 TTCCACTGTCACTTAGGGAAGATTGAATCGAGGCAGACTTG
1 TTCCACTGTCACTCAGGGAAGATTGAATCAAGGAAGACTTG
1482 TTCCACTGTCACTCA
1 TTCCACTGTCACTCA
1497 AGCAATATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (41 bp):
TTCCACTGTCACTCAGGGAAGATTGAATCAAGGAAGACTTG
Found at i:1571 original size:175 final size:175
Alignment explanation
Indices: 1276--1635 Score: 537
Period size: 175 Copynumber: 2.1 Consensus size: 175
1266 TTCTACTATA
* * * *
1276 ACTCAGGGAAGATTGAATCGAGGCAGATTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
1 ACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGCAATATCAAATCTTGAA
* * * *
1341 AGAGATGGATCTATTCCGCTTATTCTAGAGGAAATATCAAATCTGGGGGAGTTGATCCATTCCAC
66 AAAGAGGGATCTATTCCACTTATTCTAGAGGAAATATCAAATCTGGGGGAGTTGATACATTCCAC
1406 TGTCACTCAGGGAAGATTGAATCAAGGA-AGACT-TGTTCCACTGTC
131 TGTCACTCAGGGAAGATTGAATCAA-GATAGA-TATGTTCCACTGTC
*
1451 ACTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGCAATATCAAATCTTGAA
1 ACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGCAATATCAAATCTTGAA
* * *
1516 AAAGAGGGATCTGTTCCACTTATTCT-GAAGGGAATATCAGATCTGGGGGAGTTGATACATTCCA
66 AAAGAGGGATCTATTCCACTTATTCTAG-AGGAAATATCAAATCTGGGGGAGTTGATACATTCCA
* * *
1580 CTGTCACTCAGGGAATATTGAATCGAGATAGATATTTTCCACTGTC
130 CTGTCACTCAGGGAAGATTGAATCAAGATAGATATGTTCCACTGTC
1626 ACTCAGGGAA
1 ACTCAGGGAA
1636 TATCAAATCT
Statistics
Matches: 166, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
174 4 0.02
175 162 0.98
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (175 bp):
ACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGCAATATCAAATCTTGAA
AAAGAGGGATCTATTCCACTTATTCTAGAGGAAATATCAAATCTGGGGGAGTTGATACATTCCAC
TGTCACTCAGGGAAGATTGAATCAAGATAGATATGTTCCACTGTC
Found at i:1582 original size:134 final size:134
Alignment explanation
Indices: 1441--3481 Score: 2234
Period size: 134 Copynumber: 15.2 Consensus size: 134
1431 GGAAGACTTG
* * *
1441 TTCCACTGTCACTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGCAATATC
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * *
1506 AAATCTTGAAAAAGAGGGATCTGTTCCACTTATTCTGAAGGGAATATCAGATCTGGGGGAGTTGA
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTGA
*
1571 TACA
131 TCCA
* ** *
1575 TTCCACTGTCACTCAGGGAATATTGAATCGAGATAGA-TATTTTCCACTGTCACTCAGGGAATAT
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACT-TGTTCCACTGTCACTCAGGGAATAT
* * * * *
1639 CAAATCTTGAAAGAGA-GGATATGTTTCGCTTCTTCTGGAGAGAATATCAGATTTGGAGGAGTTG
65 CAAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTG
*
1703 ATACA
130 ATCCA
* * * * *
1708 TTCCACTATCACTCAGGGGAGATTGAATTGAGGAAGACTTGTTCCACTGTCACTTAGGGAATATC
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * * *
1773 AAATCTTGAAAGAAATGGATATGTTCCGCTTCTTCTGGAGGTAATATCAGATCT-AGGGACGTTG
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGA-GTTG
1837 ATCCA
130 ATCCA
* * * **
1842 TTCCACTGCCACTCAGGGAATATTTAATCGAGGCAGACTTGTTCCACTACCACTCAGGGAATATC
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * * *
1907 AAATCTTGTAAGAGAGGGATCTAG-TCCACTTCTTCTGGAGGGAATATAAGATCT-AGGGACATT
66 AAATCTTGAAAGAGAGGGATCT-GTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGA-GTT
*
1970 AATCCA
129 GATCCA
* * * * * *
1976 TTCCATTGTCACTCAAGGAAGATTGAATCGAGGCAGACATGTTCCACTATCACTTAGGGAATATT
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * * * *
2041 AAATCTTGAAAGAGAGAGATCTGTTCAGCTTCGTCTGGAGGAAATATCATATC-GGAGGACGTTG
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGA-GTTG
2105 ATCCA
130 ATCCA
* * * * *
2110 TTCCACTATCAATTAAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGGAATATC
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * * * * *
2175 AAATCTAGAAATAGAGGGATCTGTTCCACTTTTTTTGGAGGGAAAATCAGATTTGGGGGAGTTGA
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTGA
2240 TCCA
131 TCCA
* * * * * * * *
2244 TTCTACTATTATTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCAATATCACTCAGAGAATATT
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * * * **
2309 AAATCTTGAAAGAGAGGGGTTTGTTCCGCTTCTTTTGGAAGGAATATCAGATATATTGGGAGTTG
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCT-GGGGGAGTTG
*
2374 ATCAA
130 ATCCA
* *
2379 TTCTACTGTCACTCAGGGAAGA-TGAATCGAGGCAGACTTGCTCCACTGTCACTC-GAGGAATAT
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAG-GGAATAT
* * * *
2442 CAAATCTTGAAAAAGAGGGATCTGTTCTGCTTCTTCTAGAGGGAATATCATATCTGGGGGAGTTG
65 CAAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTG
2507 ATCCA
130 ATCCA
* * * * * * *
2512 TTCCAATGTCACTCAGGAAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTAAGAGAATATC
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * * ***
2577 AAATCTTGAAAGAGAGAGATTTGTTCCTCTTCTTCTGGAAGGAATATCAGATCTATAGGAGTTGA
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTGA
2642 TCCA
131 TCCA
* * * * *
2646 TTCCACTGTCACTCAGGGAATATTGAATTGAGGGAGACTTG-TCTCACTTTCACTCAGGTAATAT
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTC-CACTGTCACTCAGGGAATAT
* * * * *** * * *
2710 CAAATCTTGAAAAAGAGGTATATATTTTACTTCTTCTAGAGGGAATATCATATTTGGGGGAGTTG
65 CAAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTG
2775 ATCCA
130 ATCCA
* * * * * * * *
2780 TTCCAATGTCACTGAGGAAAGATTGAATCGAGGTAGAATTATTCCACTATCACTCAGGGAATATT
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * * *
2845 AAATCTTGAAAGATAGGGATATGTTACGCTTCTTCTGGAGGGAATATAAGATCT-GAGGACGTTG
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGA-GTTG
2909 ATCCA
130 ATCCA
* ** * * *
2914 TTCCATTAACACTTAAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATT
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * *
2979 AAATCTTGAAAGAGATGGATCTGTTCCGCTTCTTCTAGAGGGAATATCAGATCT-GAGGACGTTG
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGA-GTTG
3043 ATCCA
130 ATCCA
* * * * * *
3048 TTCCACTGTCACTTAAGGAAGATTGAATCGATGTAGACTTGTTCTACTGTCACTCAAGGAATATC
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * ** * * * * *
3113 AAATCTAGAAATAGAGGGATTTGTTCCATTTGTTTTGGAGGAAATATCAAATCTAGGGGAGTTGA
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTGA
3178 TCCA
131 TCCA
* * * * * **
3182 TTCTACTATTATTCAGGGAAGATTGAATCGAGGCAGACATGTTCCACTGTCACTTGGGGAATATC
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * ** * * * *
3247 AAATCTTGAAAAAAAAAGATATTTTCTGCTTCTTCTGGAGGGAATATCAGATCTGAGGGAGTTGA
66 AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTGA
3312 TCCA
131 TCCA
* * * * * * * *
3316 TTCCAATGTCACTCAAGAAAGATTTAATCGAGGTAAACTTGTTCCACTGTCAATTAGGGAATATC
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
* * * *** * * *
3381 AAAAT-TTGAAAAAGAGGTATTTGTTTTTCTTCCTCCGGAGGGAATATTAGATCTGGGGGAGTTG
66 -AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTG
*
3445 ATTCA
130 ATCCA
3450 TTCCACTGTCACTCAGGGAAGATTGAATCGAG
1 TTCCACTGTCACTCAGGGAAGATTGAATCGAG
3482 TTTGACTTGC
Statistics
Matches: 1591, Mismatches: 299, Indels: 34
0.83 0.16 0.02
Matches are distributed among these distances:
133 157 0.10
134 1386 0.87
135 48 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (134 bp):
TTCCACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATC
AAATCTTGAAAGAGAGGGATCTGTTCCGCTTCTTCTGGAGGGAATATCAGATCTGGGGGAGTTGA
TCCA
Found at i:7418 original size:7 final size:7
Alignment explanation
Indices: 7408--7434 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
7398 TAAATAATAC
7408 ATATTTA
1 ATATTTA
7415 ATATTTA
1 ATATTTA
7422 ATATTTA
1 ATATTTA
7429 ATATTT
1 ATATTT
7435 TTAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:8725 original size:131 final size:131
Alignment explanation
Indices: 8484--8850 Score: 556
Period size: 131 Copynumber: 2.8 Consensus size: 131
8474 TAATATTAAC
* *
8484 AGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAA
* * *
8549 TCATTTATTACTCCAATCGAAATGAAGATATATCACTATTTCGTCTTAAAATTCAATATTGATTC
66 TCATTTATTACTTCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAATATTGATTC
8614 G
131 G
** * * *
8615 ATTGAAAACGAAAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAG
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAA
* *
8680 TCATTTATTACTTCAATCTAAATGAAGAGATATCATTATTCCGTCTTAAAATTCAATATTGATTC
66 TCATTTATTACTTCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAATATTGATTC
8745 G
131 G
* * *
8746 AGAGAAAACGGTAATATCTAATTATTTTCAATCGAGAATAAATGACCACTCATACCTTAAAGCAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAA
* * *
8811 TCGTTTATTAC-TCAAACCGAAATGAAGAGATATTACTATT
66 TCATTTATTACTTC-AATCGAAATGAAGAGATATCACTATT
8851 TTCAATATTG
Statistics
Matches: 210, Mismatches: 25, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
130 2 0.01
131 208 0.99
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (131 bp):
AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAA
TCATTTATTACTTCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAATATTGATTC
G
Found at i:11452 original size:2 final size:2
Alignment explanation
Indices: 11445--11470 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11435 AGTCCATCTC
11445 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
11471 TGTGTGTGTG
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):
AT
Found at i:12424 original size:21 final size:21
Alignment explanation
Indices: 12399--12491 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
12389 ATTAAGGGTA
12399 GTATCGATACCGGTTGAAGGG
1 GTATCGATACCGGTTGAAGGG
12420 GTATCGATACCGGTTGAAGGG
1 GTATCGATACCGGTTGAAGGG
* *
12441 GTATCGATA-CTGTATG--GGTA
1 GTATCGATACCGGT-TGAAGG-G
*
12461 GTATCGATACCAGTTGAAGGG
1 GTATCGATACCGGTTGAAGGG
12482 GTATCGATAC
1 GTATCGATAC
12492 TATATGGGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.03
20 14 0.22
21 45 0.71
22 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.27
Consensus pattern (21 bp):
GTATCGATACCGGTTGAAGGG
Found at i:12466 original size:20 final size:20
Alignment explanation
Indices: 12441--12511 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
12431 GGTTGAAGGG
12441 GTATCGATACTGTATGGGTA
1 GTATCGATACTGTATGGGTA
* *
12461 GTATCGATACCAGT-TGAAGG-G
1 GTATCGATA-CTGTATG--GGTA
*
12482 GTATCGATACTATATGGGTA
1 GTATCGATACTGTATGGGTA
12502 GTATCGATAC
1 GTATCGATAC
12512 CAGAAGGATG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 2 0.05
20 23 0.56
21 14 0.34
22 2 0.05
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (20 bp):
GTATCGATACTGTATGGGTA
Found at i:12470 original size:41 final size:41
Alignment explanation
Indices: 12420--12514 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
12410 GGTTGAAGGG
* *
12420 GTATCGATACCGGTTGAAGGGGTATCGATACTGTATGGGTA
1 GTATCGATACCAGTTGAAGGGGTATCGATACTATATGGGTA
12461 GTATCGATACCAGTTGAAGGGGTATCGATACTATATGGGTA
1 GTATCGATACCAGTTGAAGGGGTATCGATACTATATGGGTA
12502 GTATCGATACCAG
1 GTATCGATACCAG
12515 AAGGATGGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (41 bp):
GTATCGATACCAGTTGAAGGGGTATCGATACTATATGGGTA
Found at i:12554 original size:20 final size:20
Alignment explanation
Indices: 12481--12554 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
12471 CAGTTGAAGG
* * *
12481 GGTATCGATACTATATGGGT
1 GGTATCGATACCATAAGGAT
* *
12501 AGTATCGATACCAGAAGGAT
1 GGTATCGATACCATAAGGAT
*
12521 GGTATCAATACCATAAGGAT
1 GGTATCGATACCATAAGGAT
12541 GGTATCGATACCAT
1 GGTATCGATACCAT
12555 TTTCAAGATG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCATAAGGAT
Found at i:13844 original size:40 final size:41
Alignment explanation
Indices: 13665--13881 Score: 247
Period size: 41 Copynumber: 5.3 Consensus size: 41
13655 GACAATTCTA
* * *
13665 TAGCGGAGTTTGTATAAAAATGCCACCAAAGTACGAGTCTT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * *
13706 TAGTGGCATTTGTATAAAAATGCCACTAAAGTACGAGTCTT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * * * *
13747 TAGCGGCGTTTGTATAAAACCGCCAATAAAGTATGACTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * * *
13788 TAGCGGCATTGGTATAAAAACGCCACTAAAGTA-TAGGCTT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * * *
13828 TAGCGGCGTTTATATAAAAACACCACTAAAGTACAAGTATT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
*
13869 TAGCAGCGTTTGT
1 TAGCGGCGTTTGT
13882 TCTAAAAATG
Statistics
Matches: 146, Mismatches: 29, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
40 32 0.22
41 114 0.78
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (41 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
Found at i:13871 original size:122 final size:123
Alignment explanation
Indices: 13661--13881 Score: 302
Period size: 122 Copynumber: 1.8 Consensus size: 123
13651 GCCAGACAAT
* * * * *
13661 TCTATAGCGGAGTTTGTATAAAAATGCCACCAAAGTACGAGTCTTTAGTGGCATTTGTATAAAAA
1 TCTATAGCGGAGTTGGTATAAAAACGCCACCAAAGTACGAGGCTTTAGCGGCATTTATATAAAAA
** * * *
13726 TGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAACCGCCAATAAAGTATGAC
66 CACCACTAAAGTACAAGTATTTAGCAGCGTTTGTATAAAACCGCCAATAAAGTATGAC
* * *
13784 TCTATAGCGGCA-TTGGTATAAAAACGCCACTAAAGTA-TAGGCTTTAGCGGCGTTTATATAAAA
1 TCTATAGCGG-AGTTGGTATAAAAACGCCACCAAAGTACGAGGCTTTAGCGGCATTTATATAAAA
13847 ACACCACTAAAGTACAAGTATTTAGCAGCGTTTGT
65 ACACCACTAAAGTACAAGTATTTAGCAGCGTTTGT
13882 TCTAAAAATG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
122 51 0.61
123 32 0.38
124 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (123 bp):
TCTATAGCGGAGTTGGTATAAAAACGCCACCAAAGTACGAGGCTTTAGCGGCATTTATATAAAAA
CACCACTAAAGTACAAGTATTTAGCAGCGTTTGTATAAAACCGCCAATAAAGTATGAC
Found at i:14139 original size:7 final size:7
Alignment explanation
Indices: 14125--14169 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
14115 TTTTCTTCTC
14125 TCTCTTT
1 TCTCTTT
*
14132 TTTCTTT
1 TCTCTTT
*
14139 T-TC-AT
1 TCTCTTT
14144 T-TCTTT
1 TCTCTTT
14150 TCTCTTT
1 TCTCTTT
14157 TCTCTTT
1 TCTCTTT
14164 TCTCTT
1 TCTCTT
14170 CTATTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.12
6 4 0.12
7 25 0.76
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (7 bp):
TCTCTTT
Found at i:14670 original size:19 final size:19
Alignment explanation
Indices: 14646--14687 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
14636 TTCTTGCTTC
*
14646 GAGCATGCCCTAATTATTA
1 GAGCATGCCCCAATTATTA
*
14665 GAGCATGCCCCAATTATTC
1 GAGCATGCCCCAATTATTA
14684 GAGC
1 GAGC
14688 CTCTCTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (19 bp):
GAGCATGCCCCAATTATTA
Found at i:15736 original size:18 final size:18
Alignment explanation
Indices: 15713--15750 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
15703 CATTTGATGA
15713 TGCTTGGTGTCCTTAAAT
1 TGCTTGGTGTCCTTAAAT
15731 TGCTTGGTGTCCTTAAAT
1 TGCTTGGTGTCCTTAAAT
15749 TG
1 TG
15751 TTTGTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (18 bp):
TGCTTGGTGTCCTTAAAT
Found at i:15915 original size:20 final size:20
Alignment explanation
Indices: 15890--15935 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
15880 TCATAGGAAA
15890 TCTTCAATCAACTTCAAATT
1 TCTTCAATCAACTTCAAATT
*
15910 TCTTCAATCAGCTTCAAATT
1 TCTTCAATCAACTTCAAATT
15930 TCTTCA
1 TCTTCA
15936 TTCATTGGTT
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:0.30, C:0.26, G:0.02, T:0.41
Consensus pattern (20 bp):
TCTTCAATCAACTTCAAATT
Found at i:17781 original size:131 final size:130
Alignment explanation
Indices: 17535--17901 Score: 554
Period size: 131 Copynumber: 2.8 Consensus size: 130
17525 AAAAATGTAA
*
17535 GAGAGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * ** *
17600 GTATTTTATCACTCCAATCGAAATGAAGAGATATCACTGTTTCGTATTAAACTTCAATGTTGATT
66 ATA-TTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTATTAAAAATCAATATTGATT
17665 C
130 C
* * * *
17666 GAGTGAAAACGATAATATCTAATGATTTCCAATCGTGAATAAATGACCTCTCATGCCTTAAAGTA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
17731 ATCATTTATTACTCCAATCGAAATGAAGAAATATCACTATTCCGTCTTAAAAATCAATATTGATT
66 AT-ATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTATTAAAAATCAATATTGATT
17796 C
130 C
17797 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
17862 ATATTTTTTACTCCAACCGAAACGAAGAGATATTACTATT
66 ATATTTATTACTCCAATCGAAATGAAGAGATATCACTATT
17902 TTCAATATCG
Statistics
Matches: 212, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
130 33 0.16
131 178 0.84
132 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (130 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
ATATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTATTAAAAATCAATATTGATTC
Found at i:18581 original size:28 final size:29
Alignment explanation
Indices: 18499--18581 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 29
18489 TAAAATTACA
*
18499 AAAATAAAAATAAATAAAACATGGGGACCAAATT
1 AAAAT-AAAATAAA-AAAACAT--AG-CCAAATT
***
18533 AAAATAAAATAAAATTGCATAGCCAAATT
1 AAAATAAAATAAAAAAACATAGCCAAATT
*
18562 -AAATTAAATAAAAAAACATA
1 AAAATAAAATAAAAAAACATA
18582 TTACAGTTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
28 16 0.39
29 7 0.17
30 1 0.02
32 4 0.10
33 8 0.20
34 5 0.12
ACGTcount: A:0.64, C:0.08, G:0.07, T:0.20
Consensus pattern (29 bp):
AAAATAAAATAAAAAAACATAGCCAAATT
Found at i:19528 original size:9 final size:10
Alignment explanation
Indices: 19512--19537 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19502 GTGTTTATAA
19512 CTTTTTTTTT
1 CTTTTTTTTT
19522 CTTTTTTTTT
1 CTTTTTTTTT
19532 CTTTTT
1 CTTTTT
19538 AATAAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:21453 original size:60 final size:60
Alignment explanation
Indices: 21379--21564 Score: 194
Period size: 60 Copynumber: 3.1 Consensus size: 60
21369 TTTGGATGAA
* * * * * *
21379 TTTGGGGATAAAATTGGAAGATTTAAAAGTTTGAGGACTAATTTAGAATGAGGGTCGTAG
1 TTTGAGGATGAAATTGGAAGATTTAAAAGTTTAAGGACTAATTTAAAATGAGGATCATAG
* ** *
21439 TTTGAGGATGAAATTGGAATG-TTTAAAAGTTTAAGGAATAATTTAAAATGATTATTATAG
1 TTTGAGGATGAAATTGGAA-GATTTAAAAGTTTAAGGACTAATTTAAAATGAGGATCATAG
* * * * * * **
21499 TTTGAGGATGAAATTAGAATATTCAAAAGCTTAAGGACCAATTTAAAATAAAAATCATAG
1 TTTGAGGATGAAATTGGAAGATTTAAAAGTTTAAGGACTAATTTAAAATGAGGATCATAG
21559 TTTGAG
1 TTTGAG
21565 AACACATGAT
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
60 103 0.99
61 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (60 bp):
TTTGAGGATGAAATTGGAAGATTTAAAAGTTTAAGGACTAATTTAAAATGAGGATCATAG
Found at i:24261 original size:22 final size:21
Alignment explanation
Indices: 24236--24278 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
24226 ATTGATAACC
*
24236 CTAAACCACAATCCCATAACTT
1 CTAAACCACAAACCC-TAACTT
*
24258 CTAAACCATAAACCCTAACTT
1 CTAAACCACAAACCCTAACTT
24279 AAAACCCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (21 bp):
CTAAACCACAAACCCTAACTT
Found at i:25488 original size:11 final size:11
Alignment explanation
Indices: 25451--25480 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
25441 AACTCTTTCT
25451 TTTTCTTTTTTA
1 TTTT-TTTTTTA
25463 TTTTTTTTTTA
1 TTTTTTTTTTA
25474 TTTTTTT
1 TTTTTTT
25481 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.07, C:0.03, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:32207 original size:2 final size:2
Alignment explanation
Indices: 32195--32253 Score: 102
Period size: 2 Copynumber: 29.5 Consensus size: 2
32185 ATAGTTTAAA
32195 AT AT A- 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
32236 AT AT AT AT AT AGT AT AT A
1 AT AT AT AT AT A-T AT AT A
32254 GTTTGGAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 52 0.95
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32297 original size:8 final size:8
Alignment explanation
Indices: 32191--32299 Score: 55
Period size: 8 Copynumber: 13.1 Consensus size: 8
32181 TAATATAGTT
32191 TAAA-ATA
1 TAAATATA
32198 TAATATATA
1 TAA-ATATA
*
32207 TATATATA
1 TAAATATA
*
32215 TATATATA
1 TAAATATA
*
32223 TATATATA
1 TAAATATA
*
32231 TATATATA
1 TAAATATA
*
32239 TATATATA
1 TAAATATA
* *
32247 GTATATAGTT
1 -TAAATA-TA
32257 TGGAAA-AT-
1 T--AAATATA
32265 TATAATATA
1 TA-AATATA
32274 T-AATATA
1 TAAATATA
32281 GTAATATATA
1 -TAA-ATATA
32291 TAAATATA
1 TAAATATA
32299 T
1 T
32300 TATAATATGG
Statistics
Matches: 87, Mismatches: 3, Indels: 23
0.77 0.03 0.20
Matches are distributed among these distances:
6 1 0.01
7 11 0.13
8 48 0.55
9 18 0.21
10 7 0.08
11 2 0.02
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (8 bp):
TAAATATA
Found at i:33192 original size:3 final size:3
Alignment explanation
Indices: 33184--33283 Score: 89
Period size: 3 Copynumber: 33.0 Consensus size: 3
33174 CCGGTCTTAC
* * *
33184 TTA TTA TTA ATA TTA TTA -TA TTA TTA ATA TTA TTA TATA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
33229 TATA TTA -TA CTA TTA TTA -TA TATG TTA TTA TTA TATA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA
*
33275 GTA TTA TTA
1 TTA TTA TTA
33284 AATAATATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
2 6 0.08
3 62 0.78
4 11 0.14
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:33282 original size:15 final size:14
Alignment explanation
Indices: 33184--33283 Score: 93
Period size: 13 Copynumber: 7.2 Consensus size: 14
33174 CCGGTCTTAC
33184 TTATTATTAATATTA
1 TTATTATT-ATATTA
*
33199 TTA-TATTATTAATA
1 TTATTATTA-TATTA
*
33213 TTATTA-TATATAA
1 TTATTATTATATTA
*
33226 TTATATATTATACTA
1 TTAT-TATTATATTA
*
33241 TTATTA-TATA-TG
1 TTATTATTATATTA
33253 TTATTATTATA-TA
1 TTATTATTATATTA
33266 TTATTATTAGTATTA
1 TTATTATTA-TATTA
33281 TTA
1 TTA
33284 AATAATATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
12 7 0.10
13 26 0.37
14 19 0.27
15 19 0.27
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:42065 original size:20 final size:20
Alignment explanation
Indices: 42002--42055 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
41992 TCTAGAAAAA
*
42002 TAAATCCTCCGAGTAATTCG
1 TAAATCCTCCGGGTAATTCG
*
42022 TAAATCCTCTGGGTAATTCG
1 TAAATCCTCCGGGTAATTCG
42042 TAAATCCTCCGGGT
1 TAAATCCTCCGGGT
42056 TATCTGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (20 bp):
TAAATCCTCCGGGTAATTCG
Found at i:42164 original size:139 final size:139
Alignment explanation
Indices: 41897--42169 Score: 404
Period size: 139 Copynumber: 2.0 Consensus size: 139
41887 ATTTCCCACG
* * **
41897 AATTTGTAAATCCTCTGGGTCATATGTAAAACCTCGGGGTAGGATGTTTTCACATGAAAATGAGA
1 AATTCGTAAATCCTCCGGGTCATATGTAAAACCTCAAGGTAGGATGTTTTCACATGAAAATGAGA
* * *
41962 TAGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAATAAATCCTCCGAGTAATTCGTAAAT
66 TAGCGATTTTCAAAGCTTCTCATTTAATGTTCTAGAAAAATAAATCCTCCGAGTAATTAGTAAAA
42027 CCTCTGGGT
131 CCTCTGGGT
* * * *
42036 AATTCGTAAATCCTCCGGGTTATCTGTAAAACCTCAAGGTATGATGTTTTCGCATGAAAATGAGA
1 AATTCGTAAATCCTCCGGGTCATATGTAAAACCTCAAGGTAGGATGTTTTCACATGAAAATGAGA
* * *
42101 TAGCGATTTTCAAAGCTTCTCATTTAATGTTCTAGAAAATTAAATCCTCTGGGTGAA-TAGTAAA
66 TAGCGATTTTCAAAGCTTCTCATTTAATGTTCTAGAAAAATAAATCCTCCGAGT-AATTAGTAAA
42165 ACCTC
130 ACCTC
42170 CAGGTCATCT
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
139 117 0.98
140 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (139 bp):
AATTCGTAAATCCTCCGGGTCATATGTAAAACCTCAAGGTAGGATGTTTTCACATGAAAATGAGA
TAGCGATTTTCAAAGCTTCTCATTTAATGTTCTAGAAAAATAAATCCTCCGAGTAATTAGTAAAA
CCTCTGGGT
Found at i:42345 original size:3 final size:3
Alignment explanation
Indices: 42337--42413 Score: 59
Period size: 3 Copynumber: 25.0 Consensus size: 3
42327 TCGATCTTAC
* * *
42337 TTA TTA TTA TTA TTA ATA TTA TTA TATA TAA TTA TATA TTA -TA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA TTA
* *
42383 TTG TTA -TA TATG TTA TTA TTA TATA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA
42414 AATAATATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
2 4 0.07
3 44 0.75
4 11 0.19
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:42528 original size:16 final size:16
Alignment explanation
Indices: 42509--42550 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
42499 ACCCAAGCAG
*
42509 ATCCAGGCCCAGATTA
1 ATCCAGACCCAGATTA
*
42525 ATCCAGACCCAGATTG
1 ATCCAGACCCAGATTA
42541 ATCCAGACCC
1 ATCCAGACCC
42551 GGGAATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.17
Consensus pattern (16 bp):
ATCCAGACCCAGATTA
Found at i:45755 original size:17 final size:17
Alignment explanation
Indices: 45714--45756 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
45704 TTACCTACCC
45714 AAAGCCCAAACCAAACG
1 AAAGCCCAAACCAAACG
*
45731 AAACCCCAAACCCAAACG
1 AAAGCCCAAA-CCAAACG
45749 -AAGCCCAA
1 AAAGCCCAA
45757 TTAATATCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.51, C:0.40, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAGCCCAAACCAAACG
Found at i:73048 original size:149 final size:149
Alignment explanation
Indices: 72778--73048 Score: 339
Period size: 149 Copynumber: 1.8 Consensus size: 149
72768 TTTCTCTGGA
*
72778 CTACCTACCAAGGAGACAAGACAGACATCTATCTGCTGAGGTAACAAGCTGGACTCGAGACGATT
1 CTACCTACCAAGGAGACAAGACAGACATCTATCTGCTGAGGTAACAAGCTGGACTCAAGACGATT
* * * * * **
72843 CGATACTGAGACCAATAGTTGAAGATAACGATCCAGCTCGAATGATTTCTGGAAGTAGTAGATTT
66 CGACACTGAGACCAACAGTTGAAGATAACGAACCAGCTCGAAAGACTTCTAAAAGTAGTAGATTT
72908 TGTAACATCAAGGGAAAGC
131 TGTAACATCAAGGGAAAGC
** * * * * *
72927 CTACCTACCAAGGAGATGAGCCAGACATCTATCTGTTGAGGTAACAAGTTGGATTCAAGAATG-T
1 CTACCTACCAAGGAGACAAGACAGACATCTATCTGCTGAGGTAACAAGCTGGACTCAAG-ACGAT
** * *
72991 TCGACGTTGA-AGCCAACAGTTGCAGATCACGAACCAGCTCGAAAGACTTCTAAAAGTA
65 TCGACACTGAGA-CCAACAGTTGAAGATAACGAACCAGCTCGAAAGACTTCTAAAAGTA
73049 AGAGATGAAG
Statistics
Matches: 101, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
148 1 0.01
149 98 0.97
150 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (149 bp):
CTACCTACCAAGGAGACAAGACAGACATCTATCTGCTGAGGTAACAAGCTGGACTCAAGACGATT
CGACACTGAGACCAACAGTTGAAGATAACGAACCAGCTCGAAAGACTTCTAAAAGTAGTAGATTT
TGTAACATCAAGGGAAAGC
Found at i:76427 original size:5 final size:5
Alignment explanation
Indices: 76426--76482 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
76416 AAAAAAAGAA
* * * *
76426 AAAAT AAAAT AAAAG AAAAT AAAAT AAAAGA AAAGAA AAAAG AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAA-AT AAAAT AAAAT AAAAT
76478 AAAAT
1 AAAAT
76483 TTTTGAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
5 37 0.82
6 7 0.16
7 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (5 bp):
AAAAT
Found at i:76444 original size:15 final size:15
Alignment explanation
Indices: 76426--76481 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
76416 AAAAAAAGAA
76426 AAAATAAAATAAAAG
1 AAAATAAAATAAAAG
76441 AAAATAAAATAAAAG
1 AAAATAAAATAAAAG
*
76456 -AAA-AGAA-AAAAG
1 AAAATAAAATAAAAG
76468 AAAATAAAATAAAA
1 AAAATAAAATAAAA
76482 TTTTTGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 5 0.14
13 6 0.17
14 6 0.17
15 19 0.53
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (15 bp):
AAAATAAAATAAAAG
Found at i:76455 original size:32 final size:32
Alignment explanation
Indices: 76411--76482 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
76401 TGAAAGGGAG
* *
76411 AAATGAAA-AAAAGAAAA-AATAAAATAAAAGA
1 AAATAAAATAAAAGAAAAGAA-AAAAGAAAAGA
*
76442 AAATAAAATAAAAGAAAAGAAAAAAGAAAATA
1 AAATAAAATAAAAGAAAAGAAAAAAGAAAAGA
76474 AAATAAAAT
1 AAATAAAAT
76483 TTTTGAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 7 0.19
32 27 0.75
33 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (32 bp):
AAATAAAATAAAAGAAAAGAAAAAAGAAAAGA
Found at i:76472 original size:37 final size:36
Alignment explanation
Indices: 76411--76482 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
76401 TGAAAGGGAG
* *
76411 AAATGAAAAAAAGAAAAAATAAAATAAAAGAAAATA
1 AAATAAAAAAAAGAAAAAAGAAAATAAAAGAAAATA
*
76447 AAATAAAAGAAAAGAAAAAAGAAAATAAAATAAAAT
1 AAATAAAA-AAAAGAAAAAAGAAAATAAAAGAAAAT
76483 TTTTGAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (36 bp):
AAATAAAAAAAAGAAAAAAGAAAATAAAAGAAAATA
Found at i:79976 original size:23 final size:24
Alignment explanation
Indices: 79932--79982 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
79922 AAATTTTGAA
* *
79932 AAAAGATTTAAAGCTTTCAAAAAT
1 AAAAGATTGAAAGCTTTCAAAAAG
* *
79956 AAAA-ATTGAAAGTTTTGAAAAAG
1 AAAAGATTGAAAGCTTTCAAAAAG
79979 AAAA
1 AAAA
79983 TTTTAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (24 bp):
AAAAGATTGAAAGCTTTCAAAAAG
Found at i:81211 original size:19 final size:20
Alignment explanation
Indices: 81187--81224 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
81177 ATTGAATTTA
*
81187 TTCAAAAA-ATTTCAATGTT
1 TTCAAAAATAATTCAATGTT
81206 TTCAAAAATAATTCAATGT
1 TTCAAAAATAATTCAATGT
81225 CCTTAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (20 bp):
TTCAAAAATAATTCAATGTT
Found at i:83403 original size:20 final size:19
Alignment explanation
Indices: 83362--83410 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
83352 AATGATTTTC
* * *
83362 TTTTAAAAGCTAAAATGGA
1 TTTTAAAAACCAAAATGAA
83381 TTTTAAAAACCAAAATGAAA
1 TTTTAAAAACCAAAATG-AA
83401 TTTTGAAAAA
1 TTTT-AAAAA
83411 AGATTTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.60
20 5 0.20
21 5 0.20
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (19 bp):
TTTTAAAAACCAAAATGAA
Found at i:83452 original size:23 final size:24
Alignment explanation
Indices: 83408--83458 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
83398 AAATTTTGAA
* *
83408 AAAAGATTTAAAGCTTTCAAAAAT
1 AAAAGATTGAAAGCTTTCAAAAAG
* *
83432 AAAA-ATTGAAAGTTTTGAAAAAG
1 AAAAGATTGAAAGCTTTCAAAAAG
83455 AAAA
1 AAAA
83459 TTTTGATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (24 bp):
AAAAGATTGAAAGCTTTCAAAAAG
Found at i:84687 original size:19 final size:20
Alignment explanation
Indices: 84663--84700 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
84653 ATTGAATTTA
*
84663 TTCAAAAA-ATTTCAATGTT
1 TTCAAAAATAATTCAATGTT
84682 TTCAAAAATAATTCAATGT
1 TTCAAAAATAATTCAATGT
84701 CCTTAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (20 bp):
TTCAAAAATAATTCAATGTT
Found at i:89522 original size:17 final size:17
Alignment explanation
Indices: 89500--89542 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
89490 CAAGTGAAAC
89500 CCTAAAATTAGACCGCA
1 CCTAAAATTAGACCGCA
*
89517 CCTAAAATTGGACCGCA
1 CCTAAAATTAGACCGCA
89534 CCTAAAATT
1 CCTAAAATT
89543 TGAGAACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.21
Consensus pattern (17 bp):
CCTAAAATTAGACCGCA
Found at i:89700 original size:15 final size:15
Alignment explanation
Indices: 89676--89706 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
89666 GTTTGGTAAT
89676 TTTTAATTTATTTCA
1 TTTTAATTTATTTCA
*
89691 TTTTATTTTATTTCA
1 TTTTAATTTATTTCA
89706 T
1 T
89707 GTATTTGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATTTATTTCA
Found at i:90937 original size:19 final size:19
Alignment explanation
Indices: 90913--90949 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
90903 TGCCACGTGT
90913 GGTAAGGCGCGCCCCCTGG
1 GGTAAGGCGCGCCCCCTGG
90932 GGTAAGGCGCGCCCCCTG
1 GGTAAGGCGCGCCCCCTG
90950 CACTGCGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.38, G:0.41, T:0.11
Consensus pattern (19 bp):
GGTAAGGCGCGCCCCCTGG
Found at i:95073 original size:3 final size:3
Alignment explanation
Indices: 95067--95101 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
95057 ATCACCATCA
* *
95067 TCG TCG TCG TCG TCG TCG TCA TCG TCA TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
95102 CTGAGTAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.06, C:0.34, G:0.26, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:97180 original size:21 final size:20
Alignment explanation
Indices: 97094--97251 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
97084 AAATGACCAA
**
97094 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
97113 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
97133 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
97153 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
97174 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
97195 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
97215 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
97236 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
97252 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:97244 original size:20 final size:20
Alignment explanation
Indices: 97219--97412 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
97209 GATTTTCAAT
* *
97219 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
97239 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
97259 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
97279 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
97299 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
97319 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
97339 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
97359 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
97380 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
97400 AATCGCAACGCGA
1 AATCGCAACGCGA
97413 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:97264 original size:40 final size:39
Alignment explanation
Indices: 97219--97412 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
97209 GATTTTCAAT
* ** *
97219 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
97259 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
97299 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
97339 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
97380 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
97413 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:97302 original size:60 final size:60
Alignment explanation
Indices: 97219--97411 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
97209 GATTTTCAAT
* ** * *
97219 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
97279 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
97339 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
97400 AATCGCAACGCG
1 AATCGCAACGCG
97412 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:97833 original size:33 final size:33
Alignment explanation
Indices: 97794--97864 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
97784 TTCACTTAGA
*
97794 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
97827 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
97860 TTTCA
1 TTTCA
97865 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:98004 original size:14 final size:14
Alignment explanation
Indices: 97985--98039 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
97975 AGAATGACTG
97985 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
97999 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
98018 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
98032 TCGCAACG
1 TCGCAACG
98040 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:98022 original size:33 final size:33
Alignment explanation
Indices: 97985--98055 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
97975 AGAATGACTG
**
97985 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
98018 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
98051 TCGCA
1 TCGCA
98056 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:98073 original size:19 final size:19
Alignment explanation
Indices: 98051--98148 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
98041 GAAACCAAAA
*
98051 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
98070 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
98084 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
98103 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
98117 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
98136 TCGCGTTGCGATT
1 TCGCGTTGCGATT
98149 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:98092 original size:14 final size:14
Alignment explanation
Indices: 98073--98162 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
98063 TTTCATTTCG
98073 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
98087 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
98106 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
98120 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
98137 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
98153 CGTTGCGATT
1 CGTTGCGATT
98163 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:98098 original size:33 final size:33
Alignment explanation
Indices: 98056--98170 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
98046 CAAAATCGCA
98056 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
98089 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
98122 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
98155 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
98171 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:100072 original size:92 final size:93
Alignment explanation
Indices: 99866--100243 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
99856 TAGATTGCTT
*
99866 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
99931 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
99959 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
100023 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
100051 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
100114 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
100142 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
100207 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
100235 AGTAAATTT
1 AGTAAATTT
100244 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 91 0.32
92 91 0.32
93 100 0.35
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:100327 original size:19 final size:19
Alignment explanation
Indices: 100287--100415 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
100277 TAGTTTACTT
* *
100287 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
100307 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
100326 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
100345 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
100359 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
100378 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
100392 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
100411 TCGCA
1 TCGCA
100416 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:100366 original size:33 final size:32
Alignment explanation
Indices: 100323--100415 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
100313 CGCGAAACCA
**
100323 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
100355 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
100388 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
100416 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:100413 original size:52 final size:52
Alignment explanation
Indices: 100287--100415 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
100277 TAGTTTACTT
**
100287 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
100339 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
100392 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
100416 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:100433 original size:19 final size:19
Alignment explanation
Indices: 100411--100545 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
100401 GAAACCAAAA
*
100411 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
100430 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
100446 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
100463 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
100479 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
100496 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
100515 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
100535 TCGTGTTGCGA
1 TCGCGTTGCGA
100546 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:100452 original size:14 final size:14
Alignment explanation
Indices: 100433--100489 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
100423 TTTCATTTCG
100433 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
100447 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
100464 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
100480 CGTTGCGATT
1 CGTTGCGATT
100490 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:100458 original size:33 final size:33
Alignment explanation
Indices: 100416--100508 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
100406 CAAAATCGCA
*
100416 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
100449 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
100482 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
100509 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:102459 original size:14 final size:14
Alignment explanation
Indices: 102440--102475 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
102430 ATTGTTTAAT
102440 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
102454 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
102468 TGATTTGT
1 TGATTTGT
102476 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:102650 original size:20 final size:19
Alignment explanation
Indices: 102582--102664 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
102572 AAAAATGACT
102582 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
102601 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
102615 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
102634 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
102654 ATCGCAATGCG
1 ATCGCAATGCG
102665 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:102717 original size:19 final size:19
Alignment explanation
Indices: 102693--102966 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
102683 GATTATCTCG
102693 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
102712 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
102731 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
102745 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
102764 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
102783 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
102802 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
102821 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
102840 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
102854 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
102873 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
102892 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
102906 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
102926 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
102940 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
102959 TTGCGATT
1 TTGCGATT
102967 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 3 0.01
19 137 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:102733 original size:52 final size:52
Alignment explanation
Indices: 102671--102938 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
102661 TGCGTTTATA
*
102671 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
102723 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
102775 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
102832 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
102884 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
102937 AT
1 AT
102939 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 131 0.63
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:102822 original size:109 final size:105
Alignment explanation
Indices: 102671--102938 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
102661 TGCGTTTATA
102671 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
102735 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
102775 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
102840 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
102884 ATTTCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
102939 GTTGGGATTT
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 29 0.19
105 19 0.12
106 4 0.03
107 6 0.04
108 2 0.01
109 95 0.61
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:105267 original size:12 final size:12
Alignment explanation
Indices: 105250--105274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105240 TCTTCGGGGA
105250 CTTTTTCTTCTT
1 CTTTTTCTTCTT
105262 CTTTTTCTTCTT
1 CTTTTTCTTCTT
105274 C
1 C
105275 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:105483 original size:24 final size:24
Alignment explanation
Indices: 105449--105495 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
105439 CTGAAACATC
105449 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
105473 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
105496 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:106199 original size:20 final size:20
Alignment explanation
Indices: 106171--106560 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
106161 AAATTTCAGT
* * * *
106171 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
106191 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
106211 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
106231 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
106251 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
106271 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
106291 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
106311 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
106331 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
106351 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
106371 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
106391 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
106412 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
106432 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
106452 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
106472 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
106492 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
106512 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
106532 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
106552 GTTGCGATT
1 GTTGCGATT
106561 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:108787 original size:6 final size:6
Alignment explanation
Indices: 108776--108818 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
108766 GGAGCCAAGA
108776 GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT G
1 GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT G
108819 GTTATTCCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.51, T:0.16
Consensus pattern (6 bp):
GAAGGT
Found at i:109639 original size:2 final size:2
Alignment explanation
Indices: 109634--109664 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
109624 ATTTTTTAGG
109634 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
109665 AAAATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:110477 original size:16 final size:16
Alignment explanation
Indices: 110438--110477 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
110428 AAAATATTAC
*
110438 TTCAAATCTTTCAAAG
1 TTCAAATTTTTCAAAG
110454 TTCAAATTTTTCAAAG
1 TTCAAATTTTTCAAAG
110470 TTCAAATT
1 TTCAAATT
110478 CAATCCTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (16 bp):
TTCAAATTTTTCAAAG
Found at i:118554 original size:21 final size:21
Alignment explanation
Indices: 118528--118567 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
118518 CAGAACCCCA
*
118528 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
118549 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
118568 TCAAATGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:125386 original size:24 final size:24
Alignment explanation
Indices: 125333--125387 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
125323 TAGAGCTTGG
* *
125333 TATGAAAGACTGTCAAATTTTTTG
1 TATGAAAGACTGTCAAATTGTTTA
*
125357 TATGAAAGATTGTCAAATTGTTTA
1 TATGAAAGACTGTCAAATTGTTTA
*
125381 TTTGAAA
1 TATGAAA
125388 AATATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.42
Consensus pattern (24 bp):
TATGAAAGACTGTCAAATTGTTTA
Found at i:126713 original size:21 final size:22
Alignment explanation
Indices: 126700--126757 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
126690 CCCTTGCATG
126700 GGTACCGATTCCCCTTTGAATA
1 GGTACCGATTCCCCTTTGAATA
*
126722 GGTACTGATTCCCCTTTGAATA
1 GGTACCGATTCCCCTTTGAATA
126744 GGTACCGATTCCCC
1 GGTACCGATTCCCC
126758 CTTAAGGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (22 bp):
GGTACCGATTCCCCTTTGAATA
Found at i:126713 original size:22 final size:22
Alignment explanation
Indices: 126683--126760 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
126673 CGCTAGAAAT
* * *
126683 CGATACCCCCTTGCATGGGTAC
1 CGATTCCCCCTTGAATAGGTAC
*
126705 CGATTCCCCTTTGAATAGGTAC
1 CGATTCCCCCTTGAATAGGTAC
* *
126727 TGATTCCCCTTTGAATAGGTAC
1 CGATTCCCCCTTGAATAGGTAC
126749 CGATTCCCCCTT
1 CGATTCCCCCTT
126761 AAGGGAATCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.19, C:0.32, G:0.18, T:0.31
Consensus pattern (22 bp):
CGATTCCCCCTTGAATAGGTAC
Found at i:127262 original size:13 final size:13
Alignment explanation
Indices: 127244--127281 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
127234 TATATATTAA
127244 TTTTCAAACATTG
1 TTTTCAAACATTG
*
127257 TTTTCAAACATAG
1 TTTTCAAACATTG
127270 TTTTCAAA-ATTG
1 TTTTCAAACATTG
127282 CCCATTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:134373 original size:3 final size:3
Alignment explanation
Indices: 134365--134394 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
134355 GAATTGGGTT
134365 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
134395 CTATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:136700 original size:81 final size:79
Alignment explanation
Indices: 136565--136724 Score: 248
Period size: 81 Copynumber: 2.0 Consensus size: 79
136555 AGCCCAACAG
* *
136565 CTCAATATCCTCTGTAGTATTCTGACTCGAATCTCTTCCTACGAGGCTTGTCTGTGCAGTTGATT
1 CTCAATATCCTCTGTAGTATTCTGACCCAAATCTCTTCCTACGAGGCTTGTCTGTGCAGTTGATT
*
136630 TATTGTGATGCCTGGA
66 CA-T-TGATGCCTGGA
* * *
136646 CTCAATATCGTCTGTAGTATTCTGACCCAAATCTCTTTCTGCGAGGCTTGTCTGTGCAGTTGATT
1 CTCAATATCCTCTGTAGTATTCTGACCCAAATCTCTTCCTACGAGGCTTGTCTGTGCAGTTGATT
136711 CATTGATGCCTGGA
66 CATTGATGCCTGGA
136725 GTCGTCCATT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
79 11 0.15
80 1 0.01
81 61 0.84
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (79 bp):
CTCAATATCCTCTGTAGTATTCTGACCCAAATCTCTTCCTACGAGGCTTGTCTGTGCAGTTGATT
CATTGATGCCTGGA
Done.