Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 96 of 410
Found at i:28176830 original size:40 final size:40
Alignment explanation
Indices: 28176771--28176912 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
28176761 AAATTGAATG
* * *
28176771 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
28176811 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
28176851 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
28176891 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
28176913 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:28176913 original size:40 final size:39
Alignment explanation
Indices: 28176810--28176938 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
28176800 TGCTGGAAAT
* * *
28176810 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
28176850 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
28176890 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
28176930 TATATCCGG
1 TATATCCGG
28176939 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:28190525 original size:26 final size:26
Alignment explanation
Indices: 28190496--28190603 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28190486 TGGTACAAAT
28190496 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28190522 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28190548 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28190574 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28190600 TGAT
1 TGAT
28190604 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28194121 original size:40 final size:40
Alignment explanation
Indices: 28194027--28194211 Score: 246
Period size: 40 Copynumber: 4.6 Consensus size: 40
28194017 TATTCGAATG
* *
28194027 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
28194068 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
*
28194108 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
28194148 ATATCCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
28194188 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
28194212 CTTGTGCAAG
Statistics
Matches: 124, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.76
41 29 0.23
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:28196113 original size:40 final size:40
Alignment explanation
Indices: 28196068--28196197 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
28196058 CGGAATACAA
28196068 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
28196108 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * * *
28196148 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
28196188 CCGGATATAA
1 CCGGATATAA
28196198 TTTCCAGCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:28205497 original size:40 final size:41
Alignment explanation
Indices: 28205403--28205623 Score: 246
Period size: 40 Copynumber: 5.6 Consensus size: 41
28205393 TATTCGAATG
*
28205403 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTA-GTGACT
* * * *
28205444 ATAACCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAG-TGACT
*
28205484 ATATCCGGGCTAAGA-CCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
* *
28205524 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
* * *
28205564 ATATCCGGGCTAAGA-CCCGAAGGC-CTTGTGCAAGT-AGTT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGA-CT
28205603 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGATCCCGAAG
28205624 ATTACTTGAG
Statistics
Matches: 154, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
37 1 0.01
38 14 0.09
39 15 0.10
40 94 0.61
41 29 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (41 bp):
ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
Found at i:28212593 original size:41 final size:41
Alignment explanation
Indices: 28212548--28212665 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
28212538 TGAAAGATAA
28212548 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
28212589 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
28212619 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
28212660 ATGTAG
1 ATGTAG
28212666 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:28212604 original size:71 final size:71
Alignment explanation
Indices: 28212516--28212684 Score: 329
Period size: 71 Copynumber: 2.4 Consensus size: 71
28212506 GAGATGTATC
28212516 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
28212581 AGGACA
66 AGGACA
28212587 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
28212652 AGGACA
66 AGGACA
*
28212658 CCATGTAGACAAGAGAGCTACGAGAAA
1 CCATGTAGACAAGAGAGCTACGTGAAA
28212685 ATCGGTTAGG
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 97 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:28214961 original size:26 final size:26
Alignment explanation
Indices: 28214932--28215039 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
28214922 TGGTACAAAT
28214932 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28214958 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28214984 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28215010 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28215036 TGAT
1 TGAT
28215040 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28219383 original size:46 final size:46
Alignment explanation
Indices: 28219330--28219505 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
28219320 TATTTGGGCA
*
28219330 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28219376 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
28219421 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28219469 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28219506 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 27 0.25
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28219485 original size:93 final size:93
Alignment explanation
Indices: 28219326--28219498 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
28219316 GGGATATTTG
*
28219326 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
28219391 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* ** *
28219419 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
28219484 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
28219499 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:28221518 original size:13 final size:15
Alignment explanation
Indices: 28221485--28221517 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28221475 CATAGCCTGG
28221485 CACACGGGCGTCTAA
1 CACACGGGCGTCTAA
28221500 CACACGGGCGTCTAA
1 CACACGGGCGTCTAA
28221515 CAC
1 CAC
28221518 GACCGTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.36, G:0.24, T:0.12
Consensus pattern (15 bp):
CACACGGGCGTCTAA
Found at i:28222305 original size:36 final size:36
Alignment explanation
Indices: 28222247--28222316 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
28222237 AGAGGAGCAC
*
28222247 ATCAGTTAGAATAGATCTGAAAGGCTGT-TGAACTGA
1 ATCAGTCAGAATAGATCTGAAAGGCT-TCTGAACTGA
*
28222283 ATCAGTCAGAATAGGT-TCGAAAGGCTTCTGAACT
1 ATCAGTCAGAATAGATCT-GAAAGGCTTCTGAACT
28222317 AATTATAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (36 bp):
ATCAGTCAGAATAGATCTGAAAGGCTTCTGAACTGA
Found at i:28228523 original size:18 final size:18
Alignment explanation
Indices: 28228500--28228536 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28228490 AATAAAAGAC
28228500 TTAATTTGCACATTTTAT
1 TTAATTTGCACATTTTAT
28228518 TTAATTTGCACATTTTAT
1 TTAATTTGCACATTTTAT
28228536 T
1 T
28228537 AACTTAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (18 bp):
TTAATTTGCACATTTTAT
Found at i:28235229 original size:40 final size:40
Alignment explanation
Indices: 28235174--28235383 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
28235164 AACATTGGAA
28235174 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28235214 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28235254 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
28235294 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
28235333 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
28235374 CTATATCCGG
1 ATATATCCGG
28235384 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:28243364 original size:40 final size:40
Alignment explanation
Indices: 28243309--28243518 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
28243299 AACATTGGAA
28243309 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28243349 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28243389 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
28243429 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
28243468 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
28243509 CTATATCCGG
1 ATATATCCGG
28243519 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:28245288 original size:12 final size:12
Alignment explanation
Indices: 28245271--28245296 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28245261 AAGCTGCTGG
28245271 ATTCGGTCCTGC
1 ATTCGGTCCTGC
28245283 ATTCGGTCCTGC
1 ATTCGGTCCTGC
28245295 AT
1 AT
28245297 AACGAGTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.35
Consensus pattern (12 bp):
ATTCGGTCCTGC
Found at i:28255636 original size:40 final size:39
Alignment explanation
Indices: 28255591--28255756 Score: 174
Period size: 40 Copynumber: 4.2 Consensus size: 39
28255581 CGGAATATAA
28255591 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28255631 CCGGATAGAATCTC-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTGCACAAATGCCTTCGGGTCTTAGC
** * *
28255669 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
28255709 CCGGATATAATTTC-CAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAA--TCACTGCACAAATGCCTTCGGGTCTTAGC
28255749 CCGGATAT
1 CCGGATAT
28255757 CATTCAATTT
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
38 33 0.31
40 70 0.67
41 1 0.01
42 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (39 bp):
CCGGATATAATCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:28259024 original size:14 final size:13
Alignment explanation
Indices: 28259002--28259046 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
28258992 CGCCGAGGTA
28259002 TTTTTAATTTCTG
1 TTTTTAATTTCTG
28259015 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
* *
28259029 CTTTTAATTTCTA
1 TTTTTAATTTCTG
28259042 TTTTT
1 TTTTT
28259047 CAAAAATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:28259037 original size:13 final size:13
Alignment explanation
Indices: 28259003--28259040 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
28258993 GCCGAGGTAT
*
28259003 TTTTAATTTCTGT
1 TTTTAATTTCTGC
28259016 TTTTCAATTTCTGC
1 TTTT-AATTTCTGC
28259030 TTTTAATTTCT
1 TTTTAATTTCT
28259041 ATTTTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.16, C:0.13, G:0.05, T:0.66
Consensus pattern (13 bp):
TTTTAATTTCTGC
Found at i:28259111 original size:100 final size:97
Alignment explanation
Indices: 28258943--28259310 Score: 409
Period size: 100 Copynumber: 3.8 Consensus size: 97
28258933 CAATTTATGC
* * * * *
28258943 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCACGCCGAGGTATTTTTA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
*
28259008 ATTTCTGTTTTTCAATTTCTGCTTTTAATTTCTA
66 ATTTCTGTTTTTCAATTTATGC--TTAATTTCTA
* *
28259042 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTAAGGTATTTTC
1 -TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* * *
28259107 AATTTCTGTTTTTCAATTTTTGCCTTACAAATTCTGC
65 AATTTCTGTTTTTCAATTTATG-CTT--AATTTCT-A
*
28259144 TTTTC--AAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
*
28259207 ATTT-TCGTTTTTTTAATTTATG-----TTTCTA
66 ATTTCT-G-TTTTTCAATTTATGCTTAATTTCTA
* * *
28259235 ----AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
* *
28259296 ATTTTTGTTTGTCAA
66 ATTTCTGTTTTTCAA
28259311 AACTCAACTC
Statistics
Matches: 238, Mismatches: 21, Indels: 30
0.82 0.07 0.10
Matches are distributed among these distances:
88 6 0.03
89 60 0.25
90 1 0.00
92 4 0.02
98 1 0.00
99 62 0.26
100 92 0.39
101 12 0.05
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (97 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
ATTTCTGTTTTTCAATTTATGCTTAATTTCTA
Found at i:28259412 original size:148 final size:147
Alignment explanation
Indices: 28259216--28259826 Score: 773
Period size: 148 Copynumber: 4.1 Consensus size: 147
28259206 AATTTTCGTT
* * * * *
28259216 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * * *
28259280 CGCTGAGGTAATTTCAATTTTTGTTTGTC-AAAACTCAACTCATATTACAAGAGGCGAGTTGAGC
66 CGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAAC
*
28259344 CTCAAGACACGTTGAGGTA
131 CTCAAG--ACGCTGAGGTA
* *
28259363 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
28259428 CGCTGAGGTAATTTCAATTTCTGTTTTTC-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGC
66 CGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAAC
*
28259492 CTCAAGACACGTTGAGGTA
131 CTCAAG--ACGCTGAGGTA
* * * *
28259511 TTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * *
28259576 CGTTGAGGTATTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAA
66 CGCTGAGGTAATTTCAATTTCTGTTTTTC-AAAAAATCAACTCATATTACGAGAGGTGAGTTGAA
28259641 CCTCAAGACGCTGAGGTA
130 CCTCAAGACGCTGAGGTA
* * * *
28259659 ATTTCAATTTTTATTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
** * * * *
28259722 CATTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGA
66 CGCTGAGGTAATTTCAATTTCTGTTTTTC--AAAAAATCAACTCATATTACGAGAGGTGAGTTGA
*
28259787 ACCTCAAGACGCTGAGGTG
129 ACCTCAAGACGCTGAGGTA
* * *
28259806 TTTTCCATTTCTATTCTTCAA
1 TTTTCAATTTCTGTTTTTCAA
28259827 TTTCAGTGTT
Statistics
Matches: 416, Mismatches: 42, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
146 68 0.16
147 80 0.19
148 230 0.55
150 38 0.09
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (147 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAAC
CTCAAGACGCTGAGGTA
Found at i:28259428 original size:75 final size:75
Alignment explanation
Indices: 28259216--28259826 Score: 785
Period size: 73 Copynumber: 8.3 Consensus size: 75
28259206 AATTTTCGTT
* * * * *
28259216 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
28259280 CGCTGAGGTA
66 CGCTGAGGTA
* * * * * * *
28259290 ATTTCAATTTTTGTTTGTC--AAAACTCAACTCATATTACAAGAGGCGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
28259353 CGTTGAGGTA
66 CGCTGAGGTA
* *
28259363 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
28259428 CGCTGAGGTA
66 CGCTGAGGTA
* *
28259438 ATTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
28259501 CGTTGAGGTA
66 CGCTGAGGTA
* * * *
28259511 TTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
28259576 CGTTGAGGTA
66 CGCTGAGGTA
* * *
28259586 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
28259649 CGCTGAGGTA
66 CGCTGAGGTA
* * * *
28259659 ATTTCAATTTTTATTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
**
28259722 CATTGAGGTA
66 CGCTGAGGTA
* * *
28259732 TTTTCAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
*
28259795 ACGCTGAGGTG
65 ACGCTGAGGTA
* * *
28259806 TTTTCCATTTCTATTCTTCAA
1 TTTTCAATTTCTGTTTTTCAA
28259827 TTTCAGTGTT
Statistics
Matches: 468, Mismatches: 59, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
71 39 0.08
73 180 0.38
74 37 0.08
75 173 0.37
76 39 0.08
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGCTGAGGTA
Found at i:28259933 original size:15 final size:14
Alignment explanation
Indices: 28259897--28259929 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28259887 CACTGAGGTA
28259897 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
28259911 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
28259925 TTTTC
1 TTTTC
28259930 CAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:28260025 original size:90 final size:88
Alignment explanation
Indices: 28259732--28260311 Score: 409
Period size: 92 Copynumber: 6.5 Consensus size: 88
28259722 CATTGAGGTA
* * * *
28259732 TTTTCAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA--AG
1 TTTTCAATTTATGT-TTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCAC
* * *
28259795 ACGCTGAGGTGTTTTCCATTTCTAT
64 ACGCTGAGGTATTTTCAATTTCTTT
* * * * *
28259820 TCTTCAATTTCA-GTGTTTCAAAAAAAATCAGCTCAT-TTGCGAGTGGTGAGTTGAGCCTTGACT
1 TTTTCAATTT-ATGT-TTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCA-G
* * *
28259883 CACACACTGAGGTATTTTCAAATTCTGT
61 CACACGCTGAGGTATTTTCAATTTCTTT
* * *
28259911 TTTTCAAATTT-TGTTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGAC
1 TTTTC-AATTTATG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCAC
*
28259975 ACGCTGAGATATTTTCAATTTCTTTT
64 ACGCTGAGGTATTTTCAATTTC-TTT
* *
28260001 TTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTTAGATCA
1 TTTTCAATTTATGTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--CA
* * *
28260066 CACGCCGAGGTATTTTTAATTGATTTTT
63 CACGCTGAGGTATTTTCAATT--TCTTT
* * * * *
28260094 ATTTTTATTTTATGCTTTGC--AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTC
1 -TTTTCAATTTATG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AG-C
** * ** *
28260157 ACATACCGAGGTATTTTCAAAATCTGT
62 ACACGCTGAGGTATTTTCAATTTCTTT
* * * * ** *
28260184 TTTACAAATTT-TGTTTT---AATAATCAACTCATATTGCGAGAAGTGAGTTGAGTCTTGGCTCA
1 TTTTC-AATTTATGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCACA
*
28260245 CGTGCTGAGCTATTTTCAATTT-TTGT
65 C--GCTGAGGTATTTTCAATTTCTT-T
* * *
28260271 TTTT-AATGTT-TAGTTTT--AAAGAGTCAATTCATATTGCGAGA
1 TTTTCAAT-TTAT-GTTTTCAAAAAAATCAACTCATATTGCGAGA
28260312 AATGAGTTAA
Statistics
Matches: 400, Mismatches: 66, Indels: 52
0.77 0.13 0.10
Matches are distributed among these distances:
85 6 0.01
86 6 0.01
87 75 0.19
88 57 0.14
89 34 0.09
90 72 0.18
91 49 0.12
92 81 0.20
93 4 0.01
94 13 0.03
95 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (88 bp):
TTTTCAATTTATGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCACAC
GCTGAGGTATTTTCAATTTCTTT
Found at i:28260259 original size:87 final size:86
Alignment explanation
Indices: 28260115--28260341 Score: 217
Period size: 87 Copynumber: 2.6 Consensus size: 86
28260105 ATGCTTTGCA
* * * *
28260115 AAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAAT
28260180 CTGTTTTACAAAT-TTT-GTTTT
66 CTGTTTT--AAATGTTTAGTTTT
* * * * * **
28260201 AATAATCAACTCATATTGCGAGAAGTGAGTTGAGTCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AA-AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
* *
28260266 TTTGTTTTTAATGTTTAGTTTT
65 TCTGTTTTAAATGTTTAGTTTT
* * * * *
28260288 AAAGAGTCAATTCATATTGCGAGAAATGAGTTAAG-CTCAGGATCACATGCCGAG
1 AAA-A-TCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGCTCACATACCGAG
28260342 TAAAGAATAA
Statistics
Matches: 115, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
85 3 0.03
86 6 0.05
87 68 0.59
88 38 0.33
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (86 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAAT
CTGTTTTAAATGTTTAGTTTT
Found at i:28261556 original size:18 final size:18
Alignment explanation
Indices: 28261533--28261586 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
28261523 CCACCACCAA
28261533 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
28261551 CTCCACCA-CCA-A----
1 CTCCACTAGCCACACTTG
28261563 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
28261581 CTCCAC
1 CTCCAC
28261587 CACCTACTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 1 0.04
16 1 0.04
17 3 0.11
18 13 0.46
ACGTcount: A:0.24, C:0.50, G:0.07, T:0.19
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:28261559 original size:30 final size:30
Alignment explanation
Indices: 28261523--28261621 Score: 180
Period size: 30 Copynumber: 3.3 Consensus size: 30
28261513 CTAGCCTTTG
28261523 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
28261553 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
28261583 CCACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
28261613 CCACCACCA
1 CCACCACCA
28261622 CATGTACCTA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:28262154 original size:24 final size:24
Alignment explanation
Indices: 28262106--28262237 Score: 74
Period size: 25 Copynumber: 5.5 Consensus size: 24
28262096 TTTTTTTTGT
*
28262106 TATTAT-TATATTTCTTAATATTA
1 TATTATGTATATTTCTTAATAATA
*
28262129 TATTATGTATATATTCTT-TTAATA
1 TATTATGTATAT-TTCTTAATAATA
* * **
28262153 TATTAGGTATA-TTCTAAATTCTA
1 TATTATGTATATTTCTTAATAATA
* * *
28262176 TATTACGTATATATATATT-ATACTA
1 TATTATGTATAT-T-TCTTAATAATA
* * * *
28262201 TTTTATGTATATATCTTTAATACTT
1 TATTATGTATATTTC-TTAATAATA
*
28262226 TATTATTTATAT
1 TATTATGTATAT
28262238 ATATATTTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
22 4 0.05
23 20 0.24
24 21 0.25
25 36 0.43
26 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TATTATGTATATTTCTTAATAATA
Found at i:28262201 original size:25 final size:26
Alignment explanation
Indices: 28262120--28262244 Score: 93
Period size: 25 Copynumber: 5.1 Consensus size: 26
28262110 ATTATATTTC
* *
28262120 TTAATATTATATTATGTATATAT-TC
1 TTAATACTATATTATGTATATATATA
* * * *
28262145 TT-TTAATATATTAGGTATAT-TCTA
1 TTAATACTATATTATGTATATATATA
* *
28262169 --AATTCTATATTACGTATATATATA
1 TTAATACTATATTATGTATATATATA
* *
28262193 TT-ATACTATTTTATGTATATATCT-
1 TTAATACTATATTATGTATATATATA
* *
28262217 TTAATACTTTATTATTTATATATATA
1 TTAATACTATATTATGTATATATATA
28262243 TT
1 TT
28262245 TTTTTCTACA
Statistics
Matches: 76, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
23 15 0.20
24 21 0.28
25 38 0.50
26 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (26 bp):
TTAATACTATATTATGTATATATATA
Found at i:28262313 original size:25 final size:24
Alignment explanation
Indices: 28262263--28262325 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
28262253 CATGTTATCT
*
28262263 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
28262289 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
**
28262314 TACATATTTTTT
1 TATGTATTTTTT
28262326 TTTATCTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.15
25 21 0.64
26 7 0.21
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:28262414 original size:25 final size:24
Alignment explanation
Indices: 28262386--28262441 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28262376 GTTATATTTT
*
28262386 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
28262411 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
28262434 CACTATTA
1 CACTATTA
28262442 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:28263399 original size:39 final size:39
Alignment explanation
Indices: 28263299--28263402 Score: 127
Period size: 39 Copynumber: 2.7 Consensus size: 39
28263289 GTTTATAAAA
* * **
28263299 TAATTATATGAGTATTGGGAAATATGCTTGAATGTTATG
1 TAATTATATGAGTATTGCGATATATGCTTGAACATTATG
* * *
28263338 TGATCATATGAGTATTGCGATATGTGCTTGAACATTATG
1 TAATTATATGAGTATTGCGATATATGCTTGAACATTATG
**
28263377 TAATTATATGAGTATTATGATATATG
1 TAATTATATGAGTATTGCGATATATG
28263403 TTTAAATGTT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (39 bp):
TAATTATATGAGTATTGCGATATATGCTTGAACATTATG
Found at i:28263438 original size:78 final size:78
Alignment explanation
Indices: 28263299--28263443 Score: 175
Period size: 78 Copynumber: 1.9 Consensus size: 78
28263289 GTTTATAAAA
* * * *
28263299 TAATTATATGAGTATTGGGAAATATGCTTGAATGTTATGTGATCATATGAGTATTGCGATATGTG
1 TAATTATATGAGTATTAGGAAATATGCTTAAATGTTATATGATCATATGAGTATTGCGATATATG
28263364 CTTGAACATTATG
66 CTTGAACATTATG
* * * * * * *
28263377 TAATTATATGAGTATTATGATATATGTTTAAATGTTATATGGTTATATGTGTAATT-TGATATAT
1 TAATTATATGAGTATTAGGAAATATGCTTAAATGTTATATGATCATATGAGT-ATTGCGATATAT
28263441 GCT
65 GCT
28263444 CAAAAGTGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
78 52 0.95
79 3 0.05
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.44
Consensus pattern (78 bp):
TAATTATATGAGTATTAGGAAATATGCTTAAATGTTATATGATCATATGAGTATTGCGATATATG
CTTGAACATTATG
Found at i:28266126 original size:7 final size:7
Alignment explanation
Indices: 28266116--28266179 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
28266106 TTTACCCTTC
*
28266116 TTTTTTT
1 TTTTTTA
*
28266123 TTTTTTC
1 TTTTTTA
28266130 TTTTTT-
1 TTTTTTA
28266136 TTGTTTTA
1 TT-TTTTA
28266144 TTTTTTA
1 TTTTTTA
28266151 TTTTATTAA
1 TTTT-TT-A
28266160 TTTTTT-
1 TTTTTTA
*
28266166 TCTTTTA
1 TTTTTTA
28266173 TTGTTTT
1 TT-TTTT
28266180 TACTTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
6 7 0.15
7 26 0.54
8 10 0.21
9 5 0.10
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:28266135 original size:13 final size:13
Alignment explanation
Indices: 28266117--28266180 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 13
28266107 TTACCCTTCT
*
28266117 TTTTTTTTTTTTC
1 TTTTTTTTTTTTA
28266130 TTTTTTTTGTTTTA
1 TTTTTTTT-TTTTA
28266144 TTTTTTATTTTATTAA
1 TTTTTT-TTTT-TT-A
*
28266160 TTTTTTTCTTTTA
1 TTTTTTTTTTTTA
28266173 TTGTTTTT
1 TT-TTTTT
28266181 ACTTTAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 11 0.25
14 19 0.43
15 7 0.16
16 7 0.16
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTTTA
Found at i:28266142 original size:17 final size:17
Alignment explanation
Indices: 28266116--28266180 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 17
28266106 TTTACCCTTC
28266116 TTTTTT-TTTTTTTCTT
1 TTTTTTGTTTTTTTCTT
*
28266132 TTTTTTGTTTTATTTTTT
1 TTTTTTGTTTT-TTTCTT
*
28266150 ATTTTATTAATTTTTTTC-T
1 -TTTT-TT-GTTTTTTTCTT
*
28266169 TTTATTGTTTTT
1 TTTTTTGTTTTT
28266181 ACTTTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 11 0.28
17 6 0.15
18 8 0.21
19 5 0.13
20 5 0.13
21 4 0.10
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTGTTTTTTTCTT
Found at i:28267507 original size:3 final size:3
Alignment explanation
Indices: 28267499--28267526 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28267489 AATTTGATTC
28267499 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28267527 TGTGAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28268371 original size:73 final size:74
Alignment explanation
Indices: 28268278--28268434 Score: 298
Period size: 73 Copynumber: 2.1 Consensus size: 74
28268268 AAAGATTTCT
*
28268278 TGATTTTTTTATTTAAGAGTAATAGATATATACTTTAAGGTCACAAATTTTATATTAATTATTTT
1 TGATTTATTTATTTAAGAGTAATAGATATATACTTTAAGGTCACAAATTTTATATTAATTATTTT
28268343 TAGGTATAA
66 TAGGTATAA
28268352 TGATTTATTT-TTTAAGAGTAATAGATATATACTTTAAGGTCACAAATTTTATATTAATTATTTT
1 TGATTTATTTATTTAAGAGTAATAGATATATACTTTAAGGTCACAAATTTTATATTAATTATTTT
28268416 TAGGTATAA
66 TAGGTATAA
28268425 TGATTTATTT
1 TGATTTATTT
28268435 GACCCTTTAA
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 73 0.89
74 9 0.11
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.50
Consensus pattern (74 bp):
TGATTTATTTATTTAAGAGTAATAGATATATACTTTAAGGTCACAAATTTTATATTAATTATTTT
TAGGTATAA
Found at i:28272429 original size:29 final size:29
Alignment explanation
Indices: 28272387--28272450 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
28272377 ATTTATTTCT
*
28272387 ATATAAAAGATAAAAATACCTTCAAAATA
1 ATATAAAAGATAAAAACACCTTCAAAATA
* *
28272416 ATATAAAAGATAAAAACACTTTTAAAATA
1 ATATAAAAGATAAAAACACCTTCAAAATA
28272445 ATATAA
1 ATATAA
28272451 CTTACTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (29 bp):
ATATAAAAGATAAAAACACCTTCAAAATA
Found at i:28274791 original size:2 final size:2
Alignment explanation
Indices: 28274784--28274811 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28274774 TGTTGAGGTG
28274784 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
28274812 GTTTTACGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28277426 original size:2 final size:2
Alignment explanation
Indices: 28277419--28277444 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28277409 CTAACTACAA
28277419 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
28277445 TTTCTGGTTC
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:28288114 original size:28 final size:28
Alignment explanation
Indices: 28288082--28288165 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
28288072 AACTGTGATC
28288082 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
28288110 ACGTGTGTCA--AAT-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
28288132 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
28288160 ACGTGT
1 ACGTGT
28288166 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 1 0.02
22 8 0.19
23 3 0.07
24 3 0.07
25 6 0.14
26 3 0.07
27 3 0.07
28 14 0.33
29 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:28288205 original size:49 final size:49
Alignment explanation
Indices: 28288034--28288267 Score: 279
Period size: 49 Copynumber: 4.7 Consensus size: 49
28288024 TGAGGTTGCA
* * * * *
28288034 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACG
** * **
28288085 TGTGTAGTACTAAGTGCAGGCTACTACGTGTGTCAAATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
*
28288135 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * * *
28288184 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * *
28288233 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
28288268 AATAGCTTTG
Statistics
Matches: 156, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
49 82 0.53
50 43 0.28
51 31 0.20
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:28288210 original size:99 final size:100
Alignment explanation
Indices: 28288032--28288266 Score: 321
Period size: 99 Copynumber: 2.4 Consensus size: 100
28288022 TGTGAGGTTG
*
28288032 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAGTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAACTGTGATCACGTGTGTAGTACTA
* **
28288097 AGTGCAGGCTACTACGTGTGTCAAATGGTTAGGTCA
66 AGTGCAGGCTACTACGTGTATCAAATAATT-GGTCA
* * * * *
28288133 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACGTGTGTAGTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAACTGTGATCACGTGTGTAGTACTA
* * *
28288196 AGTGTAGGCTACTACGTGTATCAGATAATTGGTCG
66 AGTGCAGGCTACTACGTGTATCAAATAATTGGTCA
* *
28288231 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACC
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACC
28288267 AAATAGCTTT
Statistics
Matches: 118, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
98 36 0.31
99 44 0.37
100 1 0.01
101 37 0.31
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (100 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAACTGTGATCACGTGTGTAGTACTA
AGTGCAGGCTACTACGTGTATCAAATAATTGGTCA
Found at i:28295504 original size:40 final size:40
Alignment explanation
Indices: 28295443--28295606 Score: 213
Period size: 40 Copynumber: 4.1 Consensus size: 40
28295433 CGGAATTTAG
* ** *
28295443 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* *
28295483 CCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
*
28295523 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* * * *
28295563 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGGCTTAGC
1 CCGGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAAC
28295603 CCGG
1 CCGG
28295607 GTATCATTCA
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
40 110 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
Found at i:28303367 original size:40 final size:40
Alignment explanation
Indices: 28303306--28303469 Score: 204
Period size: 40 Copynumber: 4.1 Consensus size: 40
28303296 CGGAATTTAG
* ** *
28303306 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* *
28303346 CCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* *
28303386 CCGGATATAACAACTCACACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* * * *
28303426 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGGCTTAGC
1 CCGGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAAC
28303466 CCGG
1 CCGG
28303470 GTATCATTCA
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 108 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
Found at i:28303693 original size:27 final size:27
Alignment explanation
Indices: 28303663--28303717 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
28303653 CGCCATAATA
28303663 TGACAAATCATTTCAATATAATTCAAG
1 TGACAAATCATTTCAATATAATTCAAG
28303690 TGACAAATCATTTCAATATAATTCAAG
1 TGACAAATCATTTCAATATAATTCAAG
28303717 T
1 T
28303718 AGGGTCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.35
Consensus pattern (27 bp):
TGACAAATCATTTCAATATAATTCAAG
Found at i:28305317 original size:37 final size:36
Alignment explanation
Indices: 28305255--28305334 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 36
28305245 GGAAACATAT
* * *
28305255 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTCTG
1 TCCGGGTAAGACCCGATGACCACGTGTGG-GATTCTA
* *
28305292 TCCGGGTAAGACCCGATGGCCACGTGTGGGATTTTA
1 TCCGGGTAAGACCCGATGACCACGTGTGGGATTCTA
28305328 TCCGGGT
1 TCCGGGT
28305335 TAAAACCCCG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
36 12 0.32
37 26 0.68
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (36 bp):
TCCGGGTAAGACCCGATGACCACGTGTGGGATTCTA
Found at i:28307688 original size:40 final size:40
Alignment explanation
Indices: 28307577--28307883 Score: 356
Period size: 40 Copynumber: 7.7 Consensus size: 40
28307567 CGGATGATAA
* *
28307577 CCGGGCTAAGTCCCGAA-GGCAATT-GTGCGAGTTACTA-ATT
1 CCGGGCTAAGTCCCGAAGGGC-ATTCGTGCTAGTGA-TATA-T
*
28307617 CCGGGCTAAG-CCCGAA-GGCAATCGTGCTAGTGATATAT
1 CCGGGCTAAGTCCCGAAGGGCATTCGTGCTAGTGATATAT
* *
28307655 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGGGCATTCGTGCTAGTGATATAT
* ** *
28307695 CCGGACTAAGTCCCGAAGGGCATTCGTGCCGGTGTTATAT
1 CCGGGCTAAGTCCCGAAGGGCATTCGTGCTAGTGATATAT
* * *
28307735 CCGGGCTAAGTCCCGGAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGGGCATTCGTGCTAGTGATATAT
** *
28307775 CCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTTATAT
1 CCGGGCTAAGTCCCGAAGGGCATTCGTGCTAGTGATATAT
* * * *
28307815 CCGGGCTAAATCCCGAAGGGTATTCGTGC-CGATGTTATAT
1 CCGGGCTAAGTCCCGAAGGGCATTCGTGCTAG-TGATATAT
*
28307855 CCGGGCTAAATCCCGAAGGGCATTCGTGC
1 CCGGGCTAAGTCCCGAAGGGCATTCGTGC
28307884 CGGTGATGTG
Statistics
Matches: 233, Mismatches: 29, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
38 15 0.06
39 25 0.11
40 193 0.83
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGGCATTCGTGCTAGTGATATAT
Found at i:28307755 original size:80 final size:80
Alignment explanation
Indices: 28307577--28307888 Score: 402
Period size: 80 Copynumber: 3.9 Consensus size: 80
28307567 CGGATGATAA
* * *
28307577 CCGGGCTAAGTCCCGAAG-GCAATT-GTGCGAGTTACT-AATTCCGGGCTAAG-CCCGAA-GGCA
1 CCGGGCTAAGTCCCGAAGAGC-ATTCGTGCTAGTGA-TGTA-TCCGGGCTAAGTCCCGAAGGGCA
* ** *
28307637 ATCGTGCTAGTGATATAT
63 TTCGTGCCGGTGTTATAT
*
28307655 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCCGAAGGGCATTC
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGGGCATTC
28307720 GTGCCGGTGTTATAT
66 GTGCCGGTGTTATAT
*
28307735 CCGGGCTAAGTCCCGGAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGGGCATTC
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGGGCATTC
28307800 GTGCCGGTGTTATAT
66 GTGCCGGTGTTATAT
* * * * * * *
28307815 CCGGGCTAAATCCCGAAGGGTATTCGTGC-CGATGTTATATCCGGGCTAAATCCCGAAGGGCATT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAG-TGATGTATCCGGGCTAAGTCCCGAAGGGCATT
28307879 CGTGCCGGTG
65 CGTGCCGGTG
28307889 ATGTGTATTC
Statistics
Matches: 210, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
78 32 0.15
79 18 0.09
80 160 0.76
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGGGCATTC
GTGCCGGTGTTATAT
Found at i:28307798 original size:120 final size:119
Alignment explanation
Indices: 28307616--28307892 Score: 394
Period size: 120 Copynumber: 2.3 Consensus size: 119
28307606 AGTTACTAAT
* *
28307616 TCCGGGCTAAG-CCCGAAGGCAATCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTC
* * * *
28307680 GTGCTAGTGATGTATCCGGACTAAGTCCCGAAGGGCATTCGTGCCGGTGTTATA
66 GTGCCAGTGATATATCCGGACTAAATCCCGAAGGGCATTCGTGCCGATGTTATA
* *
28307734 TCCGGGCTAAGTCCCGGAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGGGCATT
1 TCCGGGCTAAGTCCCGAAG-GCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
* * * *
28307799 CGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGTATTCGTGCCGATGTTATA
65 CGTGCCAGTGATATATCCGGACTAAATCCCGAAGGGCATTCGTGCCGATGTTATA
* **
28307854 TCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGATGT
1 TCCGGGCTAAGTCCCGAA-GGCATTCGTGCTAGTGATGT
28307893 GTATTCGGGC
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
118 11 0.08
119 6 0.04
120 122 0.87
121 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.25
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTC
GTGCCAGTGATATATCCGGACTAAATCCCGAAGGGCATTCGTGCCGATGTTATA
Found at i:28314880 original size:30 final size:30
Alignment explanation
Indices: 28314844--28314904 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
28314834 CCAATAGCTA
*
28314844 TCTTCCCTAGCATAAATAAAATCAAGTCTT
1 TCTTCCCTAGCATAAAGAAAATCAAGTCTT
28314874 TCTTCCCTAGCATAAAGAAAATCAAGTCTT
1 TCTTCCCTAGCATAAAGAAAATCAAGTCTT
28314904 T
1 T
28314905 TACGAGTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (30 bp):
TCTTCCCTAGCATAAAGAAAATCAAGTCTT
Found at i:28316718 original size:27 final size:28
Alignment explanation
Indices: 28316640--28316755 Score: 114
Period size: 27 Copynumber: 4.2 Consensus size: 28
28316630 CAGCATGGCT
* * * *
28316640 ACCAGATACAGA-AAATGTGACAGAGTC
1 ACCAGATACAGATATATGTGGCAGTGCC
*
28316667 ACCAGATACAGATATGTTGTGGCAGTGCC
1 ACCAGATACAGATAT-ATGTGGCAGTGCC
*
28316696 ACCAGA-ACAGATATATGTGGCAGGGCC
1 ACCAGATACAGATATATGTGGCAGTGCC
*
28316723 ACCAGA-ACAGATAATTTGTGGCA-TAGCC
1 ACCAGATACAGAT-ATATGTGGCAGT-GCC
28316751 ACCAG
1 ACCAG
28316756 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
27 35 0.46
28 26 0.34
29 15 0.20
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (28 bp):
ACCAGATACAGATATATGTGGCAGTGCC
Found at i:28316742 original size:55 final size:56
Alignment explanation
Indices: 28316640--28316755 Score: 141
Period size: 55 Copynumber: 2.1 Consensus size: 56
28316630 CAGCATGGCT
*
28316640 ACCAGATACAGAAAATGTGACAGAGTCACCAGATACAGATATGTTGTGGCAGT-GCC
1 ACCAGATACAGAAAATGTGACAGAGCCACCAGATACAGATATGTTGTGGCA-TAGCC
* * *
28316696 ACCAGA-ACAGATATATGTGGCAGGGCCACCAGA-ACAGATAAT-TTGTGGCATAGCC
1 ACCAGATACAGA-AAATGTGACAGAGCCACCAGATACAGAT-ATGTTGTGGCATAGCC
28316751 ACCAG
1 ACCAG
28316756 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
54 1 0.02
55 27 0.51
56 25 0.47
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (56 bp):
ACCAGATACAGAAAATGTGACAGAGCCACCAGATACAGATATGTTGTGGCATAGCC
Found at i:28316751 original size:28 final size:26
Alignment explanation
Indices: 28316666--28316755 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 26
28316656 GTGACAGAGT
28316666 CACCAGATACAGATATGTTGTGGCAGTGC
1 CACCAGA-ACAGATAT-TTGTGGCA-TGC
* *
28316695 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCA-TGC
28316722 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGAT-ATTTGTGGCAT-GC
28316750 CACCAG
1 CACCAG
28316756 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (26 bp):
CACCAGAACAGATATTTGTGGCATGC
Found at i:28316908 original size:28 final size:28
Alignment explanation
Indices: 28316861--28316925 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
28316851 AAATTAACCC
*
28316861 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
*
28316889 TAGGGGTATA-AGGGTAATTTTGCATAGA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
28316917 TAGGGGTAT
1 TAGGGGTAT
28316926 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:28324507 original size:27 final size:27
Alignment explanation
Indices: 28324455--28324544 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
28324445 GTGACAGAGT
28324455 CACCAGATACAGATATGTTGTGGCAGTGC
1 CACCAGA-ACAGATAT-TTGTGGCAGTGC
* *
28324484 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
28324511 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
28324539 CACCAG
1 CACCAG
28324545 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:28324697 original size:28 final size:28
Alignment explanation
Indices: 28324653--28324714 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
28324643 TTAATCCTAT
*
28324653 GGGTATAGAGGTCATTTTGCATACATAG
1 GGGTATAGAGGTAATTTTGCATACATAG
*
28324681 GGGTATA-ATGGTAATTTTGCATAGATAG
1 GGGTATAGA-GGTAATTTTGCATACATAG
28324709 GGGTAT
1 GGGTAT
28324715 TCTAGTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.29, C:0.06, G:0.31, T:0.34
Consensus pattern (28 bp):
GGGTATAGAGGTAATTTTGCATACATAG
Found at i:28332825 original size:40 final size:40
Alignment explanation
Indices: 28332766--28332934 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
28332756 CGGGACTTTA
* * *
28332766 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
28332806 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
28332846 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
28332886 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
28332926 CCCGGATAT
1 CCCGGATAT
28332935 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:28333783 original size:17 final size:19
Alignment explanation
Indices: 28333760--28333805 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28333750 AAGAAGCATG
28333760 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
28333778 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
28333796 AATCATGCTC
1 AATCATGCTC
28333806 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:28342242 original size:40 final size:39
Alignment explanation
Indices: 28342197--28342404 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
28342187 CGGAATACAA
*
28342197 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28342237 CCGGATACAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28342277 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28342317 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
28342357 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
28342397 CCGGATAT
1 CCGGATAT
28342405 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:28342337 original size:80 final size:80
Alignment explanation
Indices: 28342197--28342403 Score: 245
Period size: 80 Copynumber: 2.6 Consensus size: 80
28342187 CGGAATACAA
* * *
28342197 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATACAACGACTTGCACAAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATACAACGACTAGCACAAATG
*
28342262 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* ** * *
28342277 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTC-ACTAGCACAATT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATACA-ACGACTAGCACAAAT
*
28342341 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
28342357 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
28342404 TCATTCAATT
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
80 106 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATACAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:28349531 original size:40 final size:39
Alignment explanation
Indices: 28349486--28349693 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
28349476 CGGAATACAA
*
28349486 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28349526 CCGGATACAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28349566 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28349606 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
28349646 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
28349686 CCGGATAT
1 CCGGATAT
28349694 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:28349626 original size:80 final size:80
Alignment explanation
Indices: 28349486--28349692 Score: 245
Period size: 80 Copynumber: 2.6 Consensus size: 80
28349476 CGGAATACAA
* * *
28349486 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATACAACGACTTGCACAAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATACAACGACTAGCACAAATG
*
28349551 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* ** * *
28349566 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTC-ACTAGCACAATT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATACA-ACGACTAGCACAAAT
*
28349630 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
28349646 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
28349693 TCATTCAATT
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
80 106 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATACAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:28354063 original size:26 final size:26
Alignment explanation
Indices: 28354034--28354093 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
28354024 GCCCTTTGAA
* * *
28354034 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
28354060 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
28354088 CCATTC
1 TCATTC
28354094 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:28354079 original size:28 final size:28
Alignment explanation
Indices: 28354048--28354119 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
28354038 TCGATATTTT
*
28354048 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
28354076 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* *
28354104 GTACACTGAGTGCCAT
1 GCACACTAAGTGCCAT
28354120 ATTTGATTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:28363718 original size:47 final size:47
Alignment explanation
Indices: 28363667--28363954 Score: 459
Period size: 47 Copynumber: 6.1 Consensus size: 47
28363657 TTACGATTTT
28363667 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28363714 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28363761 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
28363808 ATATGATGAATATGAACATGCATATATGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
28363855 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
28363902 ATATGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28363949 ATGTGA
1 ATGTGA
28363955 AATATGTATG
Statistics
Matches: 222, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 222 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:28363720 original size:22 final size:22
Alignment explanation
Indices: 28363692--28363767 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
28363682 ACATGCATAT
28363692 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
28363714 ATGTGATGAATGTG-AGCAT-G-CA
1 ATGTGAT-AA-G-GCCGAATGGCCA
28363736 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
28363761 ATGTGAT
1 ATGTGAT
28363768 GAATGTGAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 16 0.39
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:28363788 original size:23 final size:23
Alignment explanation
Indices: 28363714--28363788 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
28363704 CGAATGGCCA
28363714 ATGTGATGAATGTGAGCATGCAT
1 ATGTGATGAATGTGAGCATGCAT
* * *
28363737 ATGTG-TGATAAG-GCCGAATGGCCA-
1 ATGTGATGA-ATGTG-AGCAT-G-CAT
28363761 ATGTGATGAATGTGAGCATGCAT
1 ATGTGATGAATGTGAGCATGCAT
28363784 ATGTG
1 ATGTG
28363789 TGATAAGGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 6 0.15
23 16 0.41
24 11 0.28
25 6 0.15
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGTGATGAATGTGAGCATGCAT
Found at i:28363989 original size:48 final size:48
Alignment explanation
Indices: 28363924--28364058 Score: 234
Period size: 48 Copynumber: 2.8 Consensus size: 48
28363914 TGAACATGCA
* * *
28363924 TATATGTGATAAGGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
*
28363972 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGGTATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
28364020 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
28364059 GGCAATGTGC
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 83 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
Found at i:28364313 original size:37 final size:37
Alignment explanation
Indices: 28364205--28364313 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
28364195 GGAAATATAT
* *
28364205 TCCGGGTAAGACCCGATGACTACGTGTAGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
28364242 TCTGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
28364279 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
28364314 CGTCTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:28366354 original size:57 final size:58
Alignment explanation
Indices: 28366281--28366403 Score: 140
Period size: 58 Copynumber: 2.1 Consensus size: 58
28366271 CTAGTCTAGA
** * * *
28366281 CTAAATCCTTTTTGTAATATATGTTCAAAAGAG-CTAAATTAGGATTACCAGTCCAAG
1 CTAAATCCTAATTGTAACATATGCTCAAAAGAGACTAAATCAGGATTACCAGTCCAAG
* * * * * *
28366338 CTAAATCCTAATTGTAACATATGCTCGATAGGGATTATATCAGGATTACCAGTCCAGG
1 CTAAATCCTAATTGTAACATATGCTCAAAAGAGACTAAATCAGGATTACCAGTCCAAG
28366396 CTAAATCC
1 CTAAATCC
28366404 CATCAGCAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
57 26 0.48
58 28 0.52
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (58 bp):
CTAAATCCTAATTGTAACATATGCTCAAAAGAGACTAAATCAGGATTACCAGTCCAAG
Found at i:28382639 original size:27 final size:27
Alignment explanation
Indices: 28382599--28382710 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
28382589 AGGAAGCGTC
*
28382599 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
28382626 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
28382653 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
28382681 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
28382707 CTGG
1 CTGG
28382711 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:28382705 original size:54 final size:54
Alignment explanation
Indices: 28382599--28382710 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
28382589 AGGAAGCGTC
* *
28382599 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
28382653 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
28382707 CTGG
1 CTGG
28382711 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:28388460 original size:27 final size:27
Alignment explanation
Indices: 28388442--28388626 Score: 221
Period size: 27 Copynumber: 6.9 Consensus size: 27
28388432 CTCAATTTGT
*
28388442 AGAATTACCATTTTACCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTAC
* *
28388469 AGAATTACCGTTTCACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
* * * *
28388496 AAAATTACCGTTTTATCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTAC
*
28388523 AGAATTACCATTTTACCCTTGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
28388550 AGAATTACCGTTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
* *
28388577 AAAATTACCATTTTACCCTC-AGTTTAA
1 AGAATTACCATTTTACCCTCGA-TTTAC
* * *
28388604 AAAATTATCGTTTTA-CCTCGATT
1 AGAATTACCATTTTACCCTCGATT
28388627 GTGAAATTAC
Statistics
Matches: 137, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.05
27 130 0.95
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (27 bp):
AGAATTACCATTTTACCCTCGATTTAC
Found at i:28388502 original size:54 final size:54
Alignment explanation
Indices: 28388444--28388626 Score: 253
Period size: 54 Copynumber: 3.4 Consensus size: 54
28388434 CAATTTGTAG
* * *
28388444 AATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTACAA
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAA
* * *
28388498 AATTACCGTTTTATCCTCGATTTATAGAATTACCATTTTACCCTTGATTTACAG
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAA
* * *
28388552 AATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTC-AGTTTAAAA
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGA-TTTACAA
*
28388606 AATTATCGTTTTA-CCTCGATT
1 AATTACCGTTTTACCCTCGATT
28388627 GTGAAATTAC
Statistics
Matches: 115, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
53 9 0.08
54 106 0.92
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (54 bp):
AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAA
Found at i:28388547 original size:81 final size:81
Alignment explanation
Indices: 28388430--28388626 Score: 279
Period size: 81 Copynumber: 2.4 Consensus size: 81
28388420 TACTGAAATG
* *
28388430 CCCTCAATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTA
1 CCCTCAATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTA
*
28388495 CAAAATTACCGTTTTA
66 CAAAATTACCATTTTA
* * * *
28388511 TCCTCGATTTATAGAATTACCATTTTACCCTTGATTTACAGAATTACCGTTTTACCCTCGATTTA
1 CCCTCAATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTA
28388576 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * * * *
28388592 CCCTCAGTTTAAAAAATTATCGTTTTA-CCTCGATT
1 CCCTCAATTTATAGAATTACCATTTTACCCTCGATT
28388627 GTGAAATTAC
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 7 0.07
81 94 0.93
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (81 bp):
CCCTCAATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTA
CAAAATTACCATTTTA
Found at i:28388688 original size:27 final size:27
Alignment explanation
Indices: 28388658--28388808 Score: 155
Period size: 27 Copynumber: 5.6 Consensus size: 27
28388648 TGTAGGATAG
28388658 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
28388685 AATTACCAAAATACCCCTAATTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
** * * *
28388712 AATTACTGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * *
28388739 AATTACCGAAGTA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
**
28388766 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
28388793 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
28388809 TTGACTTTCT
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
26 5 0.05
27 93 0.91
28 4 0.04
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:28388743 original size:81 final size:81
Alignment explanation
Indices: 28388658--28388807 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 81
28388648 TGTAGGATAG
* ** *
28388658 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACTGAA
1 AATTACCAAAATACCCTC-AATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAA
28388722 ATACCACTGGTTTGTGA
65 ATACCACTGGTTTGTGA
* * *
28388739 AATTACCGAAGTACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAA
1 AATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAA
28388804 TACC
66 TACC
28388808 CTTGACTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 60 0.98
82 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAA
TACCACTGGTTTGTGA
Found at i:28388809 original size:54 final size:55
Alignment explanation
Indices: 28388658--28388809 Score: 177
Period size: 54 Copynumber: 2.8 Consensus size: 55
28388648 TGTAGGATAG
28388658 AATTACCAAAATACCCCT-AGTTTGTAAAATTACCA-AAATACCC-CTAATTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAAAATTA-CAGAAATACCCTCTAATTTGTAA
** * * * * *
28388712 AATTACTGAAATACCACTGGTTTGTGAAATTACCGAAGTACCCTC-AATTTGTAA
1 AATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCTCTAATTTGTAA
**
28388766 AATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCT
1 AATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCT
28388810 TGACTTTCTA
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
53 1 0.01
54 77 0.97
55 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.29
Consensus pattern (55 bp):
AATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCTCTAATTTGTAA
Found at i:28388871 original size:27 final size:27
Alignment explanation
Indices: 28388710--28388871 Score: 87
Period size: 27 Copynumber: 5.9 Consensus size: 27
28388700 CCTAATTTGT
**
28388710 AAAATTACTGAAATACCAC-TGGTTTGT
1 AAAATTACTGAAATACC-CTTGGTTTAC
* * * *** **
28388737 GAAATTACCGAAGTACCCTCAATTTGT
1 AAAATTACTGAAATACCCTTGGTTTAC
** * *
28388764 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
28388791 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
* *
28388818 TAAAAATTA-TAGAAATACCATTAGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
*
28388847 AAAGTTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
28388872 GTAGATTTAC
Statistics
Matches: 103, Mismatches: 25, Indels: 14
0.73 0.18 0.10
Matches are distributed among these distances:
26 1 0.01
27 77 0.75
28 7 0.07
29 18 0.17
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:28388989 original size:27 final size:26
Alignment explanation
Indices: 28388912--28388989 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
28388902 AAATGACTAA
* *
28388912 AATACCCCTAATAGGTAAAAAGACCGT
1 AATACCCCTTAT-GGTAAAATGACCGT
* *
28388939 AA-AGCCCCTATAGGGTAAAGTGACCGT
1 AATA-CCCCT-TATGGTAAAATGACCGT
28388966 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCT-TATGGTAAAATGAC
28388990 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 38 0.93
28 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (26 bp):
AATACCCCTTATGGTAAAATGACCGT
Found at i:28389830 original size:25 final size:24
Alignment explanation
Indices: 28389793--28389861 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
28389783 AGGAAGTGCT
*
28389793 AAAA-GGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
28389816 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
28389841 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
28389862 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.12
25 36 0.88
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:28389874 original size:24 final size:23
Alignment explanation
Indices: 28389793--28389888 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 23
28389783 AGGAAGTGCT
* *
28389793 AAAA-GGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAG-TTATC
28389816 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAG-TTATC
*
28389841 AGAAAGGGCTTTGCCCCAGTTATT
1 A-AAAGGGCTTTGCCCCAGTTATC
**
28389865 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTTTGCC-CCAGTTAT
28389889 ATGATAAAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
23 4 0.06
24 17 0.27
25 42 0.67
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCCAGTTATC
Found at i:28390068 original size:42 final size:42
Alignment explanation
Indices: 28390009--28390142 Score: 232
Period size: 42 Copynumber: 3.2 Consensus size: 42
28389999 TAGTCTCCCC
28390009 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
* *
28390051 AAATGGGCTTGCATACATTCATTGGCATTACATATGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
* *
28390093 AAATGAGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
28390135 AAATGGGC
1 AAATGGGC
28390143 CTAAGGGCCA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
Found at i:28390212 original size:31 final size:31
Alignment explanation
Indices: 28390166--28390267 Score: 143
Period size: 31 Copynumber: 3.3 Consensus size: 31
28390156 CATTTACAGT
*
28390166 AAAGGCTT-CAGCCCAGTGATATCATTTATGA
1 AAAGGCTTCCA-CCCAGTGATATGATTTATGA
*
28390197 AAAGGTTTCCACCCAGTGATATGATTTATGA
1 AAAGGCTTCCACCCAGTGATATGATTTATGA
** *
28390228 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCCACCCAGTGATATGATTTATGA
28390259 AAAGGCTTC
1 AAAGGCTTC
28390268 AGCCTAGTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 62 0.97
32 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCCACCCAGTGATATGATTTATGA
Found at i:28398241 original size:27 final size:27
Alignment explanation
Indices: 28398061--28398237 Score: 228
Period size: 27 Copynumber: 6.6 Consensus size: 27
28398051 CTTTAATCAA
* * *
28398061 TAAAATGATTGTTTTGCCGTTATGTGG
1 TAAAATGACTGTTTTGCCCTTATATGG
*
28398088 TAAAATGATTGTTTTGCCCTTATATGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* *
28398115 TAAAATGACTATTTTGCCTTTATATGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* * * * *
28398142 TAAGATGACCGTTTCGCCATTATGTGG
1 TAAAATGACTGTTTTGCCCTTATATGG
28398169 TAAAATGACTGTTTTGCCCTTATATGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* *
28398196 TAAAATGACTATTTTACCCTTATATGG
1 TAAAATGACTGTTTTGCCCTTATATGG
*
28398223 TAAAATGATTGTTTT
1 TAAAATGACTGTTTT
28398238 ACCCCTATGT
Statistics
Matches: 130, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 130 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATATGG
Found at i:28398248 original size:81 final size:81
Alignment explanation
Indices: 28398061--28398237 Score: 282
Period size: 81 Copynumber: 2.2 Consensus size: 81
28398051 CTTTAATCAA
* *
28398061 TAAAATGATTGTTTTGCCGTTATGTGGTAAAATGATTGTTTTGCCCTTATATGGTAAAATGACTA
1 TAAAATGATTGTTTTGCCATTATGTGGTAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTA
* *
28398126 TTTTGCCTTTATATGG
66 TTTTACCCTTATATGG
* ** *
28398142 TAAGATGACCGTTTCGCCATTATGTGGTAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTA
1 TAAAATGATTGTTTTGCCATTATGTGGTAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTA
28398207 TTTTACCCTTATATGG
66 TTTTACCCTTATATGG
28398223 TAAAATGATTGTTTT
1 TAAAATGATTGTTTT
28398238 ACCCCTATGT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (81 bp):
TAAAATGATTGTTTTGCCATTATGTGGTAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTA
TTTTACCCTTATATGG
Found at i:28400415 original size:28 final size:28
Alignment explanation
Indices: 28400375--28400455 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 28
28400365 TGGGAAGTAG
** *
28400375 TTGGGCCTGATGGGCCATATGAATGTGA
1 TTGGGCCAAATGGGCCATATGAATGAGA
* * *
28400403 TTGGGCCAAATGGGCCATGTCAACGAGA
1 TTGGGCCAAATGGGCCATATGAATGAGA
* *
28400431 TTGGGCCTAAATTGGCCAAATGAAT
1 TTGGGCC-AAATGGGCCATATGAAT
28400456 AAGTGTGTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
28 29 0.71
29 12 0.29
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (28 bp):
TTGGGCCAAATGGGCCATATGAATGAGA
Found at i:28400784 original size:27 final size:27
Alignment explanation
Indices: 28400754--28401065 Score: 330
Period size: 27 Copynumber: 11.6 Consensus size: 27
28400744 TAATAAAGAG
28400754 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
28400781 AAATTACCGAAATACCCTCGA-TTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* *
28400807 AAATTACTGAAATACCCTCAATTTTTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
28400834 AAATTA-TCGAAAATACCTTCGA-TTGTG
1 AAATTACT-G-AAATACCCTCGATTTGTA
* * *
28400861 AAATTACTAAAATACCCTTGATTTTTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * **
28400888 AAATTACTAAAATACCTTTAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
28400915 AAATTA-TCGAAACACCCTCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
*
28400942 AAATTA-TCGAAATACCCTCAATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* *
28400969 AAATTACCGAAATACCTTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
28400996 AAATTA-TCGAAATACCCTCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* ** * *
28401023 AAACTACCAAAACACCCCCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
28401050 AAATTATTGAAATACC
1 AAATTACTGAAATACC
28401066 TTGTAGTGTA
Statistics
Matches: 236, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
26 35 0.15
27 190 0.81
28 11 0.05
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:28400901 original size:81 final size:81
Alignment explanation
Indices: 28400754--28401067 Score: 400
Period size: 81 Copynumber: 3.9 Consensus size: 81
28400744 TAATAAAGAG
* *
28400754 AAATTA-CTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGA-TTGTGAAATTACTGA
1 AAATTATC-GAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACTGA
* *
28400817 AATACCCTCAATTTTTA
65 AATACCTTCAATTTGTA
* * * * * *
28400834 AAATTATCGAAAATACCTTCGA-TTGTGAAATTACTAAAATACCCTTGATTTTTAAAATTACTAA
1 AAATTATCG-AAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACTGA
*
28400898 AATACCTTTAATTTGTA
65 AATACCTTCAATTTGTA
* * * * *
28400915 AAATTATCGAAACACCCTCGATTTGTAAAATTATCGAAATACCCTCAATTTGTAAAATTACCGAA
1 AAATTATCGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACTGAA
*
28400980 ATACCTTCGATTTGTA
66 ATACCTTCAATTTGTA
* * * *
28400996 AAATTATCGAAATACCCTCGATTTGTAAAACTACCAAAACACCCCCGATTTGTAAAATTATTGAA
1 AAATTATCGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACTGAA
28401061 ATACCTT
66 ATACCTT
28401068 GTAGTGTAAA
Statistics
Matches: 197, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
80 39 0.20
81 158 0.80
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (81 bp):
AAATTATCGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACTGAA
ATACCTTCAATTTGTA
Found at i:28401087 original size:26 final size:27
Alignment explanation
Indices: 28401046--28401106 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
28401036 ACCCCCGATT
**
28401046 TGTAAAATTATTGAAAT-ACCTTGTAG
1 TGTAAAATTACGGAAATGACCTTGTAG
*
28401072 TGTAAAATTACGGAAATGCCCTTGTAG
1 TGTAAAATTACGGAAATGACCTTGTAG
28401099 TGTAAAAT
1 TGTAAAAT
28401107 GACTGGCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 15 0.48
27 16 0.52
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (27 bp):
TGTAAAATTACGGAAATGACCTTGTAG
Found at i:28404724 original size:27 final size:27
Alignment explanation
Indices: 28404694--28404927 Score: 297
Period size: 27 Copynumber: 8.7 Consensus size: 27
28404684 CCTTAATCGA
* *
28404694 TAAAATGACTATTTTGCCCTTATACGG
1 TAAAATGACTGTTTTGCCCTTATATGG
28404721 TAAAATGACTGTTTTGCCCTTATATGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* * **
28404748 TAAGATGACTGTTTTGCCCTTATGTCA
1 TAAAATGACTGTTTTGCCCTTATATGG
* *
28404775 TAAAATGATTGTTTTGCCCTTATGTGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* *
28404802 TAAAATGACTATTTTTCCCTTATATGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* * * *
28404829 TAAGATGACTGTTTTTCCCTTATGTCG
1 TAAAATGACTGTTTTGCCCTTATATGG
* *
28404856 TAAAATGACTGTATTGCCCTTATTTGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* *
28404883 TAAAATGACTATTTTTCCCTTATATGG
1 TAAAATGACTGTTTTGCCCTTATATGG
*
28404910 TAAGATGACTGTTTTGCC
1 TAAAATGACTGTTTTGCC
28404928 TCTATGTGAT
Statistics
Matches: 177, Mismatches: 30, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 177 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATATGG
Found at i:28404934 original size:81 final size:81
Alignment explanation
Indices: 28404693--28404927 Score: 380
Period size: 81 Copynumber: 2.9 Consensus size: 81
28404683 CCCTTAATCG
* * * *
28404693 ATAAAATGACTATTTTGCCCTTATACGGTAAAATGACTGTTTTGCCCTTATATGGTAAGATGACT
1 ATAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTATTTTTCCCTTATATGGTAAGATGACT
28404758 GTTTTGCCCTTATGTC
66 GTTTTGCCCTTATGTC
* *
28404774 ATAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTATTTTTCCCTTATATGGTAAGATGACT
1 ATAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTATTTTTCCCTTATATGGTAAGATGACT
*
28404839 GTTTTTCCCTTATGTC
66 GTTTTGCCCTTATGTC
* * *
28404855 GTAAAATGACTGTATTGCCCTTATTTGGTAAAATGACTATTTTTCCCTTATATGGTAAGATGACT
1 ATAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTATTTTTCCCTTATATGGTAAGATGACT
28404920 GTTTTGCC
66 GTTTTGCC
28404928 TCTATGTGAT
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 142 1.00
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.42
Consensus pattern (81 bp):
ATAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTATTTTTCCCTTATATGGTAAGATGACT
GTTTTGCCCTTATGTC
Found at i:28407253 original size:37 final size:37
Alignment explanation
Indices: 28407203--28407276 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
28407193 TTCATCTTTT
28407203 GATGTGACGGCAATATCGATTCGACCCTTCACACGTA
1 GATGTGACGGCAATATCGATTCGACCCTTCACACGTA
28407240 GATGTGACGGCAATATCGATTCGACCCTTCACACGTA
1 GATGTGACGGCAATATCGATTCGACCCTTCACACGTA
28407277 ATTTGCCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (37 bp):
GATGTGACGGCAATATCGATTCGACCCTTCACACGTA
Found at i:28419878 original size:41 final size:41
Alignment explanation
Indices: 28419833--28419950 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
28419823 TGAAAGATAA
28419833 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
28419874 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
28419904 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
28419945 ATGTAG
1 ATGTAG
28419951 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:28419889 original size:71 final size:71
Alignment explanation
Indices: 28419801--28419964 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
28419791 GAGATGTATC
28419801 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
28419866 AGGACA
66 AGGACA
28419872 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
28419937 AGGACA
66 AGGACA
28419943 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
28419965 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:28424307 original size:40 final size:39
Alignment explanation
Indices: 28424132--28424353 Score: 240
Period size: 39 Copynumber: 5.8 Consensus size: 39
28424122 CGAATGGTGT
* * * * *
28424132 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACCAAA
* *
28424172 TCCGGGTCAATTCCCGAAGGCATTTGTGCGAGTTACCAAA
1 -CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAA
*
28424212 CTGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACC---
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAA
*
28424247 CTGGGTTAAGT--CGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACC-AAA
* *
28424285 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAA
* * * *
28424324 TCGGGCTAATTCCCGAAGGCAATTGTGCGA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGA
28424354 ATCACTATAA
Statistics
Matches: 157, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
34 23 0.15
35 11 0.07
38 34 0.22
39 36 0.23
40 29 0.18
41 24 0.15
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAA
Found at i:28424352 original size:113 final size:113
Alignment explanation
Indices: 28424145--28424353 Score: 278
Period size: 112 Copynumber: 1.8 Consensus size: 113
28424135 GGCTAAGTCC
* * * * *
28424145 CGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCATTTGTGCGAGTTACCA
1 CGAAGGCATTTGTGCTAAGTGACCAAAACCGGGTCAAGTCCCGAAGGCATTCGTGCGAGTTACCA
* *
28424210 AACTGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACCCTGGGTTAAGT
66 AACTGGGCTAAGTCCGAAGGCAATTGTGCGAGTTACCCTGGGTTAAGT
* * * *
28424258 CGAAGGCATTTGTGC-GAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTA
1 CGAAGGCATTTGTGCTAAGTGACCAAAACCGGGTCAAGTCCCGAAGGCATTCGTGCGAGTTACCA
*
28424322 AA-TCGGGCTAATTCCCGAAGGCAATTGTGCGA
66 AACT-GGGCTAAGT-CCGAAGGCAATTGTGCGA
28424354 ATCACTATAA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
111 1 0.01
112 50 0.61
113 31 0.38
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (113 bp):
CGAAGGCATTTGTGCTAAGTGACCAAAACCGGGTCAAGTCCCGAAGGCATTCGTGCGAGTTACCA
AACTGGGCTAAGTCCGAAGGCAATTGTGCGAGTTACCCTGGGTTAAGT
Found at i:28424379 original size:39 final size:40
Alignment explanation
Indices: 28424282--28424385 Score: 108
Period size: 39 Copynumber: 2.6 Consensus size: 40
28424272 CGAGTTACCA
* * * *
28424282 AAACCGGGTTAAGTCCCGAAGGC-ATTCGTGCGAGTTACT
1 AAACCGGGCTAATTCCCGAAGGCAATTCGTGCGAATCACT
*
28424321 AAATCGGGCTAATTCCCGAAGGCAATT-GTGCGAATCACT
1 AAACCGGGCTAATTCCCGAAGGCAATTCGTGCGAATCACT
*
28424360 ATAACCGGGC-AATGT-CCGAAGACAAT
1 A-AACCGGGCTAAT-TCCCGAAGGCAAT
28424386 CGAGCGAGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 44 0.80
40 11 0.20
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (40 bp):
AAACCGGGCTAATTCCCGAAGGCAATTCGTGCGAATCACT
Found at i:28432379 original size:39 final size:38
Alignment explanation
Indices: 28432335--28432463 Score: 132
Period size: 40 Copynumber: 3.3 Consensus size: 38
28432325 CGGAATATAA
28432335 CCGGATATAACATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAT-TGCACAAATGCCTTCGGGTCTTAGC
* ** *
28432374 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAT-T-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
28432414 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACA-TTGCACAAATGCCTTCGGGTCTTAGC
28432454 CCGGATATAA
1 CCGGATATAA
28432464 TTTCCAGCAT
Statistics
Matches: 71, Mismatches: 16, Indels: 6
0.76 0.17 0.06
Matches are distributed among these distances:
39 11 0.15
40 59 0.83
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (38 bp):
CCGGATATAACATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:28432478 original size:40 final size:40
Alignment explanation
Indices: 28432350--28432500 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
28432340 TATAACATGT
* * *
28432350 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
28432390 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
28432430 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* * *
28432470 GCATAATTGTCTTCGGG-ATTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
28432501 CATTCAATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 14 0.16
40 74 0.82
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:28432484 original size:80 final size:79
Alignment explanation
Indices: 28432350--28432498 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 79
28432340 TATAACATGT
* *
28432350 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-ATTAGCC
28432415 CGGATGTAGCCACTA
65 CGGATGTAGCCACTA
* * * * *
28432430 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTAGC
28432493 CCGGAT
64 CCGGAT
28432499 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
79 14 0.23
80 46 0.77
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTAGCCC
GGATGTAGCCACTA
Found at i:28440361 original size:40 final size:40
Alignment explanation
Indices: 28440316--28440446 Score: 174
Period size: 40 Copynumber: 3.3 Consensus size: 40
28440306 CGGAATATAA
28440316 CCGGATATAATAACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATAAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * *
28440356 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATAACTAGCACAAATGCCTTCGGGTCTTAGC
*** * *
28440396 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATAACTAGCACAAATGCCTTCGGGTCTTAGC
28440436 CCGGATATAAT
1 CCGGATATAAT
28440447 TTCCAGCTCT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 1 0.01
40 77 0.99
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAATAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28444886 original size:31 final size:32
Alignment explanation
Indices: 28444850--28444939 Score: 105
Period size: 31 Copynumber: 2.8 Consensus size: 32
28444840 AAAAAAATTC
28444850 AAAAAAAAGTCAAAATAGTGAAAAAAAG-AGA
1 AAAAAAAAGTCAAAATAGTGAAAAAAAGTAGA
* * * *
28444881 GAAAAAAATTCAAAAT--TAAAAAAAAAGTTGA
1 AAAAAAAAGTCAAAATAGT-GAAAAAAAGTAGA
28444912 AAAAAAAAGTCGAAAATAGTGAAAAAAA
1 AAAAAAAAGTC-AAAATAGTGAAAAAAA
28444940 AAGAAAGAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
29 1 0.02
30 8 0.17
31 25 0.53
32 5 0.11
33 7 0.15
34 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (32 bp):
AAAAAAAAGTCAAAATAGTGAAAAAAAGTAGA
Found at i:28444927 original size:12 final size:13
Alignment explanation
Indices: 28444898--28444927 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28444888 ATTCAAAATT
*
28444898 AAAAAAAAAGTTG
1 AAAAAAAAAGTCG
28444911 AAAAAAAAAGTCG
1 AAAAAAAAAGTCG
28444924 AAAA
1 AAAA
28444928 TAGTGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAGTCG
Found at i:28446013 original size:13 final size:12
Alignment explanation
Indices: 28445982--28446013 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28445972 TTGAGAGAAC
*
28445982 TTGAAAAGGCCT
1 TTGAAAAAGCCT
28445994 TTGAAAAAGCCT
1 TTGAAAAAGCCT
28446006 TTGAAAAA
1 TTGAAAAA
28446014 CAAAAAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:28450702 original size:28 final size:28
Alignment explanation
Indices: 28450662--28450753 Score: 175
Period size: 28 Copynumber: 3.3 Consensus size: 28
28450652 CGAGCGTGTG
28450662 GGCCCATTTGGACCGAGAATGGGCTTTA
1 GGCCCATTTGGACCGAGAATGGGCTTTA
28450690 GGCCCATTTGGACCGAGAATGGGCTTTA
1 GGCCCATTTGGACCGAGAATGGGCTTTA
*
28450718 GGCCCATTTGGACTGAGAATGGGCTTTA
1 GGCCCATTTGGACCGAGAATGGGCTTTA
28450746 GGCCCATT
1 GGCCCATT
28450754 CGTATTGTTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.26
Consensus pattern (28 bp):
GGCCCATTTGGACCGAGAATGGGCTTTA
Found at i:28450849 original size:27 final size:27
Alignment explanation
Indices: 28450817--28450889 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
28450807 CTCGACTTGT
*
28450817 AAAATTACCAAAGTACCCCCAATTTAC
1 AAAATTACCAAAATACCCCCAATTTAC
* *** * *
28450844 AGAATTACCATTTTACCCTCGATTTAC
1 AAAATTACCAAAATACCCCCAATTTAC
28450871 AAAATTACCAAAATACCCC
1 AAAATTACCAAAATACCCC
28450890 TGTAAGGTAG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.41, C:0.29, G:0.04, T:0.26
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCCAATTTAC
Found at i:28450903 original size:27 final size:27
Alignment explanation
Indices: 28450881--28451104 Score: 295
Period size: 27 Copynumber: 8.3 Consensus size: 27
28450871 AAAATTACCA
28450881 AAATACCCCTGTAAGGTAGAATTACTG
1 AAATACCCCTGTAAGGTAGAATTACTG
*
28450908 AAATACCCCTGTAAGGTAGAATTACCG
1 AAATACCCCTGTAAGGTAGAATTACTG
* *
28450935 AAATACCCCCGTAGGGTAGAATTACTG
1 AAATACCCCTGTAAGGTAGAATTACTG
* *
28450962 AAATACCCCTATAAGGTAGAATTACCG
1 AAATACCCCTGTAAGGTAGAATTACTG
* * * *
28450989 AAATACCCTTGTAGGGTAAAATTACTA
1 AAATACCCCTGTAAGGTAGAATTACTG
* *
28451016 AAATATCCCTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAAGGTAGAATTACTG
* * * *
28451043 AAATACCCTTGTAGGGTAGAAATACTA
1 AAATACCCCTGTAAGGTAGAATTACTG
*
28451070 AAATACCCCTGTAAGGTAGAATTACCG
1 AAATACCCCTGTAAGGTAGAATTACTG
*
28451097 AGATACCC
1 AAATACCC
28451105 TCGTGGGGTA
Statistics
Matches: 169, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 169 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (27 bp):
AAATACCCCTGTAAGGTAGAATTACTG
Found at i:28450942 original size:81 final size:81
Alignment explanation
Indices: 28450881--28451121 Score: 331
Period size: 81 Copynumber: 3.0 Consensus size: 81
28450871 AAAATTACCA
*
28450881 AAATACCCCTGTAAGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCCG
1 AAATACCCCTGTAAGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCTCG
28450946 TAGGGTAGAATTACTG
66 TAGGGTAGAATTACTG
* * * * * **
28450962 AAATACCCCTATAAGGTAGAATTACCGAAATACCCTTGTAGGGTAAAATTACTAAAATATCCCT-
1 AAATACCCCTGTAAGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA-CCCTC
28451026 GTAGGGTAGAATTACTG
65 GTAGGGTAGAATTACTG
* * * * *
28451043 AAATACCCTTGTAGGGTAGAAATACTAAAATACCCCTGTAAGGTAGAATTACCGAGATACCCTCG
1 AAATACCCCTGTAAGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCTCG
* *
28451108 TGGGGTAAAATTAC
66 TAGGGTAGAATTAC
28451122 CATTTTGCCC
Statistics
Matches: 136, Mismatches: 22, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
80 4 0.03
81 129 0.95
82 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (81 bp):
AAATACCCCTGTAAGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCTCG
TAGGGTAGAATTACTG
Found at i:28451133 original size:54 final size:54
Alignment explanation
Indices: 28450873--28451121 Score: 331
Period size: 54 Copynumber: 4.6 Consensus size: 54
28450863 CGATTTACAA
* * * *
28450873 AATTACCAAAATACCC-CTGTAAGGTAGAATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCTC-GTAGGGTAAAATTACTAAAATACCCCTGTAAGGTAG
* * * *
28450927 AATTACCGAAATACCCCCGTAGGGTAGAATTACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCTCGTAGGGTAAAATTACTAAAATACCCCTGTAAGGTAG
* * *
28450981 AATTACCGAAATACCCTTGTAGGGTAAAATTACTAAAATATCCCTGTAGGGTAG
1 AATTACCGAAATACCCTCGTAGGGTAAAATTACTAAAATACCCCTGTAAGGTAG
* *
28451035 AATTACTGAAATACCCTTGTAGGGTAGAAA-TACTAAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCTCGTAGGGTA-AAATTACTAAAATACCCCTGTAAGGTAG
* *
28451089 AATTACCGAGATACCCTCGTGGGGTAAAATTAC
1 AATTACCGAAATACCCTCGTAGGGTAAAATTAC
28451122 CATTTTGCCC
Statistics
Matches: 175, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
53 3 0.02
54 168 0.96
55 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (54 bp):
AATTACCGAAATACCCTCGTAGGGTAAAATTACTAAAATACCCCTGTAAGGTAG
Found at i:28453947 original size:30 final size:31
Alignment explanation
Indices: 28453891--28453948 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
28453881 TGCCAAAGTT
*
28453891 CAAAAAACAAGCAAATTGGGCTAAATTGGAA
1 CAAAAAACAAGCAAAATGGGCTAAATTGGAA
28453922 CAAAAAACAAG-AAAATGGGAC-AAATTG
1 CAAAAAACAAGCAAAATGGG-CTAAATTG
28453949 AAAAGTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.55, C:0.12, G:0.19, T:0.14
Consensus pattern (31 bp):
CAAAAAACAAGCAAAATGGGCTAAATTGGAA
Found at i:28462130 original size:48 final size:48
Alignment explanation
Indices: 28462069--28462398 Score: 333
Period size: 48 Copynumber: 6.8 Consensus size: 48
28462059 GGGTACATGT
* * **
28462069 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGATATTGTTATGA
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACATCATTATGA
* * * * * * *
28462117 GAGCTAGTGTAAGACCATGTCTGGGACATAGCATCAACCTCAATATGT
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACATCATTATGA
* * *
28462165 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGA
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACATCATTATGA
* * * * *
28462213 GCGCTAGTGTAAGACCATGTTTGGGACATGGCATC-AGCCTCAATATGT
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGA-CATCATTATGA
* * *
28462261 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAGT-GTTAT-A
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACA-TCATTATGA
* * * *
28462308 TGTGTCAGTGTAAGACCATGTTTGGGACATGGCATCGGCACCGATGTATGA
1 -GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACATC-AT-TATGA
* **
28462359 AAGCCAGTGTAAGACCATGTCCGGGACATGGCATCGACAT
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACAT
28462399 TTTAACCTTT
Statistics
Matches: 225, Mismatches: 49, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
48 186 0.83
49 2 0.01
50 36 0.16
51 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACATCATTATGA
Found at i:28462229 original size:96 final size:96
Alignment explanation
Indices: 28462065--28462343 Score: 445
Period size: 96 Copynumber: 2.9 Consensus size: 96
28462055 GTTAGGGTAC
**
28462065 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGATATTGTTATGAGAGCTAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAG
* *
28462130 ACCATGTCTGGGACATAGCATCAACCTCAAT
66 ACCATGTTTGGGACATGGCATCAACCTCAAT
* *
28462161 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGAGCGCTAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAG
*
28462226 ACCATGTTTGGGACATGGCATCAGCCTCAAT
66 ACCATGTTTGGGACATGGCATCAACCTCAAT
* *
28462257 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAGTGTTAT-ATGTG-TCAGTGTA
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGA-GAGCT-AGTGTA
28462320 AGACCATGTTTGGGACATGGCATC
64 AGACCATGTTTGGGACATGGCATC
28462344 GGCACCGATG
Statistics
Matches: 171, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
95 2 0.01
96 169 0.99
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (96 bp):
ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAG
ACCATGTTTGGGACATGGCATCAACCTCAAT
Found at i:28465819 original size:44 final size:44
Alignment explanation
Indices: 28465754--28465849 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
28465744 GGGTTCGTGA
* *
28465754 TATGTATG-AAGCATCCGAGCTCGTTGAGTTGGTCCGAGTTTAT
1 TATGGATGCAAGCATCCGAGCTCGTTGAGTTGGTCCGAGTTCAT
*
28465797 TATGGATGCAAGCATTCGAGCTCGTTGAGTTGGTCCGAGTTCAT
1 TATGGATGCAAGCATCCGAGCTCGTTGAGTTGGTCCGAGTTCAT
28465841 TATGGATGC
1 TATGGATGC
28465850 GATACATGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 7 0.14
44 42 0.86
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (44 bp):
TATGGATGCAAGCATCCGAGCTCGTTGAGTTGGTCCGAGTTCAT
Found at i:28470661 original size:40 final size:39
Alignment explanation
Indices: 28470616--28470823 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
28470606 CGGAATACAA
*
28470616 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28470656 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28470696 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28470736 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
28470776 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
28470816 CCGGATAT
1 CCGGATAT
28470824 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:28470756 original size:80 final size:81
Alignment explanation
Indices: 28470616--28470821 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
28470606 CGGAATACAA
* * *
28470616 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
28470680 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
28470696 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
28470759 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
** * ** * *
28470776 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
28470822 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
80 104 0.96
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:28478731 original size:40 final size:39
Alignment explanation
Indices: 28478686--28478893 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
28478676 CGGAATACAA
*
28478686 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28478726 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
28478766 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28478806 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
28478846 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
28478886 CCGGATAT
1 CCGGATAT
28478894 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Done.