Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 88 of 362
Found at i:27974306 original size:43 final size:42
Alignment explanation
Indices: 27974259--27974421 Score: 116
Period size: 43 Copynumber: 3.8 Consensus size: 42
27974249 TGTGATTACA
*
27974259 TGTAAGACCATTTCTGGGACATCGGCATTGTATTGCGATTAAG
1 TGTAAGACCATTTCTGGGACAT-GGCATCGTATTGCGATTAAG
* * * * **
27974302 TGTAAGATCATGTCTGGGACCTTGGCATCGTTAAT-CGATTTCG
1 TGTAAGACCATTTCTGGGA-CATGGCATCG-TATTGCGATTAAG
* * * * *
27974345 TATAAGACCCTTTCTAGGACAGTGGCATCG-ATATGTGA-TAACA
1 TGTAAGACCATTTCTGGGACA-TGGCATCGTAT-TGCGATTAA-G
* * *
27974388 TGTAAGACCATATCTGGGATATGGCATTGTATTG
1 TGTAAGACCATTTCTGGGACATGGCATCGTATTG
27974422 GCTTATGTGA
Statistics
Matches: 89, Mismatches: 24, Indels: 15
0.70 0.19 0.12
Matches are distributed among these distances:
41 1 0.01
42 12 0.13
43 71 0.80
44 5 0.06
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATTTCTGGGACATGGCATCGTATTGCGATTAAG
Found at i:27977785 original size:46 final size:46
Alignment explanation
Indices: 27977732--27977857 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
27977722 TATTTGGGCA
*
27977732 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
27977778 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
27977824 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
27977858 CGGGCGGGTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:27984685 original size:13 final size:13
Alignment explanation
Indices: 27984667--27984706 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
27984657 GGATCAAATG
27984667 GTCTAGCCTATGT
1 GTCTAGCCTATGT
27984680 GTCTAGCCTATGT
1 GTCTAGCCTATGT
27984693 GTCTAGCCTATGT
1 GTCTAGCCTATGT
27984706 G
1 G
27984707 CCCTTCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (13 bp):
GTCTAGCCTATGT
Found at i:27984912 original size:13 final size:13
Alignment explanation
Indices: 27984894--27984926 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
27984884 ACCTTGTGTC
27984894 ACACACGACTGAG
1 ACACACGACTGAG
27984907 ACACACGACTGAG
1 ACACACGACTGAG
27984920 ACACACG
1 ACACACG
27984927 CCTGTGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.33, G:0.21, T:0.06
Consensus pattern (13 bp):
ACACACGACTGAG
Found at i:27987514 original size:21 final size:21
Alignment explanation
Indices: 27987488--27987530 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27987478 ATCTCATGAA
27987488 ACATTCAAGCATGAAATGCAC
1 ACATTCAAGCATGAAATGCAC
*
27987509 ACATTCAAGCATGACATGCAC
1 ACATTCAAGCATGAAATGCAC
27987530 A
1 A
27987531 ATTAGTAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.19
Consensus pattern (21 bp):
ACATTCAAGCATGAAATGCAC
Found at i:27988525 original size:15 final size:15
Alignment explanation
Indices: 27988505--27988535 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27988495 AAGAACATGC
27988505 ATTTTTAAGTATATT
1 ATTTTTAAGTATATT
27988520 ATTTTTAAGTATATT
1 ATTTTTAAGTATATT
27988535 A
1 A
27988536 AGAGTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTTTTAAGTATATT
Found at i:27996387 original size:15 final size:15
Alignment explanation
Indices: 27996367--27996395 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27996357 AGAACATGCA
27996367 TTTTAAGTATATTAT
1 TTTTAAGTATATTAT
27996382 TTTTAAGTATATTA
1 TTTTAAGTATATTA
27996396 AGAGTTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTTAAGTATATTAT
Found at i:28002014 original size:27 final size:27
Alignment explanation
Indices: 28001982--28002034 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
28001972 GTATCATAAC
28001982 TTCATCACCACCACTTCTCAATCGTTT
1 TTCATCACCACCACTTCTCAATCGTTT
28002009 TTCATCACCACCACTTCTCAATCGTT
1 TTCATCACCACCACTTCTCAATCGTT
28002035 CCCCTCTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.36
Consensus pattern (27 bp):
TTCATCACCACCACTTCTCAATCGTTT
Found at i:28005692 original size:34 final size:34
Alignment explanation
Indices: 28005644--28005710 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
28005634 AGGTAAAGCA
*
28005644 ATCAAGAAGGTTAATGCAACCTCTGGAACTAACC
1 ATCAAGAAGGTTAATGCAACCTATGGAACTAACC
*
28005678 ATCAGGAAGGTTAATGCAACCTATGGAACTAAC
1 ATCAAGAAGGTTAATGCAACCTATGGAACTAAC
28005711 ACTTATCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (34 bp):
ATCAAGAAGGTTAATGCAACCTATGGAACTAACC
Found at i:28006779 original size:15 final size:17
Alignment explanation
Indices: 28006745--28006782 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
28006735 GTAAAATAAC
28006745 TTTTAACATATTTTAAT
1 TTTTAACATATTTTAAT
*
28006762 TTTTAA-AT-TTTTACT
1 TTTTAACATATTTTAAT
28006777 TTTTAA
1 TTTTAA
28006783 TATAGCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAACATATTTTAAT
Found at i:28011664 original size:6 final size:7
Alignment explanation
Indices: 28011625--28011652 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28011615 TTTATAAGTA
28011625 AAAAAAT
1 AAAAAAT
28011632 AAAAAAT
1 AAAAAAT
28011639 AAAAAAT
1 AAAAAAT
28011646 AAAAAAT
1 AAAAAAT
28011653 TTATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:28011795 original size:8 final size:8
Alignment explanation
Indices: 28011782--28011853 Score: 65
Period size: 8 Copynumber: 8.4 Consensus size: 8
28011772 CAAAATATGA
28011782 TTTTATAT
1 TTTTATAT
28011790 TTTTATAAT
1 TTTTAT-AT
*
28011799 TTTATATTGT
1 TTT-TA-TAT
28011809 TTTTATACT
1 TTTTATA-T
*
28011818 TTTTGTAAT
1 TTTTAT-AT
28011827 TGTTT-TAT
1 T-TTTATAT
28011835 TTTTATAT
1 TTTTATAT
28011843 TTTTATAT
1 TTTTATAT
28011851 TTT
1 TTT
28011854 CACTGAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
7 3 0.06
8 24 0.44
9 16 0.30
10 10 0.19
11 1 0.02
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.72
Consensus pattern (8 bp):
TTTTATAT
Found at i:28014696 original size:12 final size:12
Alignment explanation
Indices: 28014674--28014732 Score: 75
Period size: 12 Copynumber: 4.9 Consensus size: 12
28014664 ACAAAAAAAT
28014674 TGAAGTAAATAAG
1 TGAA-TAAATAAG
28014687 TGAATAAATAAG
1 TGAATAAATAAG
28014699 TGAATAAATAAG
1 TGAATAAATAAG
* *
28014711 TGAGTGAATAAG
1 TGAATAAATAAG
*
28014723 T-AAAAAATAA
1 TGAATAAATAA
28014733 TTAAGAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
11 6 0.15
12 31 0.76
13 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.24
Consensus pattern (12 bp):
TGAATAAATAAG
Found at i:28015104 original size:9 final size:9
Alignment explanation
Indices: 28015090--28015122 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
28015080 TCGAGTTGAT
28015090 TCGATTAAC
1 TCGATTAAC
*
28015099 TCGATTAAT
1 TCGATTAAC
28015108 TCGATTAAC
1 TCGATTAAC
28015117 TCGATT
1 TCGATT
28015123 CGAATAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (9 bp):
TCGATTAAC
Found at i:28015111 original size:18 final size:18
Alignment explanation
Indices: 28015088--28015122 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
28015078 ATTCGAGTTG
28015088 ATTCGATTAACTCGATTA
1 ATTCGATTAACTCGATTA
28015106 ATTCGATTAACTCGATT
1 ATTCGATTAACTCGATT
28015123 CGAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (18 bp):
ATTCGATTAACTCGATTA
Found at i:28033954 original size:68 final size:67
Alignment explanation
Indices: 28033908--28034065 Score: 280
Period size: 68 Copynumber: 2.3 Consensus size: 67
28033898 ATACTATATA
28033908 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
28033973 AAT
65 AAT
28033976 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
28034041 AAT
65 AAT
* *
28034044 GTAGCTAGGTCGCATGAGTGAT
1 GTAGCTAGGTCACATGTGTGAT
28034066 TGCAAGTGAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 88 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (67 bp):
GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGGAGAGATAA
AT
Found at i:28034139 original size:66 final size:67
Alignment explanation
Indices: 28033942--28034139 Score: 185
Period size: 68 Copynumber: 2.9 Consensus size: 67
28033932 GGGATGTATC
* * *
28033942 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGA-TAC--GGGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGAGTACAAGTGA
* *
28034004 TGTATC-
62 AGGA-CA
* *
28034010 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTGCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGAGTACAAGTGA
28034075 AGGACA
62 AGGACA
28034081 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTG-GTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGAGTAC-AAGTG
28034140 TTCACCATGT
Statistics
Matches: 116, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
65 2 0.02
66 22 0.19
67 9 0.08
68 54 0.47
69 2 0.02
70 1 0.01
71 26 0.22
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.21
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGAGTACAAGTGAAGGA
CA
Found at i:28037587 original size:42 final size:43
Alignment explanation
Indices: 28037528--28037608 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
28037518 TGAGTTTACA
*
28037528 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATTTTG
1 TGTAAGACCATAGCTGGGATATTGGCATCGATATGAGATTTTG
* *
28037570 TGTAAGACCATAGCTGGGCTATTGGCATCGATTTGAGAT
1 TGTAAGACCATAGCTGGGATATTGGCATCGATATGAGAT
28037609 CCCATATAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 19 0.54
43 16 0.46
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATAGCTGGGATATTGGCATCGATATGAGATTTTG
Found at i:28037619 original size:43 final size:42
Alignment explanation
Indices: 28037530--28037636 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 42
28037520 AGTTTACATG
* **** *
28037530 TAAGACCATATCTGGGATATGGCATCGATATGAGATTTTGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATGAGATCCCATA
* *
28037572 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGATCCCATA
1 TAAGACCATAGCTGGGATA-TGGCATCGATATGAGATCCCATA
**
28037615 TAAGACCATATTTGGGATATGG
1 TAAGACCATAGCTGGGATATGG
28037637 TATTGGTATG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 20 0.38
43 33 0.62
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (42 bp):
TAAGACCATAGCTGGGATATGGCATCGATATGAGATCCCATA
Found at i:28044902 original size:43 final size:42
Alignment explanation
Indices: 28044809--28044907 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 42
28044799 TTTGAGTATA
* * **
28044809 CATGTAAGACCATATCTGGGGTATGGCATCGATATGAGATTT
1 CATGTAAGACCATAGCTGGGCTATGGCATCGATATGAGATCC
* * *
28044851 CTTTTAAGACCATAGCTGGGCTATTGGCATCGATTTGAGATCC
1 CATGTAAGACCATAGCTGGGCTA-TGGCATCGATATGAGATCC
28044894 CATGTAAGACCATA
1 CATGTAAGACCATA
28044908 TCCGGGATGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 19 0.40
43 28 0.60
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
CATGTAAGACCATAGCTGGGCTATGGCATCGATATGAGATCC
Found at i:28045020 original size:20 final size:20
Alignment explanation
Indices: 28044995--28045037 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28044985 CCATGTTAAA
**
28044995 GTTATGAAAGATTATGGTAT
1 GTTATGAAAGACAATGGTAT
*
28045015 GTTATGGAAGACAATGGTAT
1 GTTATGAAAGACAATGGTAT
28045035 GTT
1 GTT
28045038 GCAAGTTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (20 bp):
GTTATGAAAGACAATGGTAT
Found at i:28065379 original size:17 final size:17
Alignment explanation
Indices: 28065359--28065394 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28065349 TATTTTGCCT
28065359 GCCAGACAATACTATTC
1 GCCAGACAATACTATTC
* *
28065376 GCCATACAATACTGTTC
1 GCCAGACAATACTATTC
28065393 GC
1 GC
28065395 AGGGCAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.25
Consensus pattern (17 bp):
GCCAGACAATACTATTC
Found at i:28069007 original size:20 final size:19
Alignment explanation
Indices: 28068978--28069016 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
28068968 TATTTTTTTG
*
28068978 TAATAGTTGTGTTTCCAAAA
1 TAATAATTGT-TTTCCAAAA
*
28068998 TAATAATTGTTTTTCAAAA
1 TAATAATTGTTTTCCAAAA
28069017 CACGTGTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (19 bp):
TAATAATTGTTTTCCAAAA
Found at i:28069317 original size:13 final size:13
Alignment explanation
Indices: 28069299--28069323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28069289 TATTAATTAA
28069299 ATAATAAAATATT
1 ATAATAAAATATT
28069312 ATAATAAAATAT
1 ATAATAAAATAT
28069324 GTTAAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAAAATATT
Found at i:28077152 original size:26 final size:26
Alignment explanation
Indices: 28077119--28077174 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
28077109 TTACTAAGTA
28077119 TTTTACATACTTACTCGGGTTACTAC
1 TTTTACATACTTACTCGGGTTACTAC
28077145 TTTTACATACTTACTCGGGTTACTAC
1 TTTTACATACTTACTCGGGTTACTAC
28077171 TTTT
1 TTTT
28077175 TTTATAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (26 bp):
TTTTACATACTTACTCGGGTTACTAC
Found at i:28082440 original size:15 final size:15
Alignment explanation
Indices: 28082420--28082449 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28082410 TTAATCTAAC
28082420 TTTAATTTTATTAAA
1 TTTAATTTTATTAAA
28082435 TTTAATTTTATTAAA
1 TTTAATTTTATTAAA
28082450 GTTGTAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAATTTTATTAAA
Found at i:28083576 original size:28 final size:28
Alignment explanation
Indices: 28083517--28083576 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
28083507 AGGCCGTGTG
* **
28083517 AGCCACACGGCAAGGACATGTGCGTATG
1 AGCCACACAGCAAGGACATGTGCGTAAC
*
28083545 AGCCACACAAGCAAGGACATG-GTGTAAC
1 AGCCACAC-AGCAAGGACATGTGCGTAAC
28083573 AGCC
1 AGCC
28083577 CCATTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.33, C:0.27, G:0.28, T:0.12
Consensus pattern (28 bp):
AGCCACACAGCAAGGACATGTGCGTAAC
Found at i:28097061 original size:42 final size:42
Alignment explanation
Indices: 28097006--28097123 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
28096996 TGCTTTAGAA
* *
28097006 CCACACAGCCAAGGACATGGGCATGTGCCCAGGCCGTGTGAG
1 CCACACAGGCAAGGACATGGGCATGTGCCCAGGCCGTGTAAG
* * *
28097048 CCACACGGGCAAGGACATGAGCGTGTGCCCAGGCCGTGTAAG
1 CCACACAGGCAAGGACATGGGCATGTGCCCAGGCCGTGTAAG
* * *
28097090 CCACACAAGCAAGGACATGGACATTTGCCCAGGC
1 CCACACAGGCAAGGACATGGGCATGTGCCCAGGC
28097124 TATGTAACTC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.26, C:0.31, G:0.31, T:0.12
Consensus pattern (42 bp):
CCACACAGGCAAGGACATGGGCATGTGCCCAGGCCGTGTAAG
Found at i:28098209 original size:15 final size:15
Alignment explanation
Indices: 28098189--28098218 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28098179 TTAATTGCGA
28098189 TGTTTTGCTCTGTTC
1 TGTTTTGCTCTGTTC
*
28098204 TGTTTTGCTTTGTTC
1 TGTTTTGCTCTGTTC
28098219 CGCTGTACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.20, T:0.63
Consensus pattern (15 bp):
TGTTTTGCTCTGTTC
Found at i:28101925 original size:38 final size:37
Alignment explanation
Indices: 28101877--28102141 Score: 341
Period size: 38 Copynumber: 7.0 Consensus size: 37
28101867 TTGTTTGACA
**
28101877 ATTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCA
1 ATTCG-TTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
28101915 ATTCAGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
1 ATTC-GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* *
28101953 TTTTGGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
1 -ATTCGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* * *
28101991 TTTCGATTGGATCAGCTCTTATGAGCTTTTGTTTGGCG
1 ATTCG-TTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* *
28102029 ATTCGATTGGATTAGCTCTTTTGAGCTTCTGTTTGGTG
1 ATTCG-TTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* * *
28102067 ATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTG
1 A-TTCGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* *
28102105 TTTCGGTTGGATCAGCTCTTATGAGCTTCTGTCTGGT
1 ATTC-GTTGGATCAGCTCTTATGAGCTTCTGTTTGGT
28102142 CTGTTCGGTT
Statistics
Matches: 200, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
37 6 0.03
38 188 0.94
39 6 0.03
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (37 bp):
ATTCGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
Found at i:28102080 original size:114 final size:114
Alignment explanation
Indices: 28101878--28102136 Score: 421
Period size: 114 Copynumber: 2.3 Consensus size: 114
28101868 TGTTTGACAA
28101878 TTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCAATTCAGTTGGATCAGCTCTTATGAGCTT
1 TTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCAATTCAGTTGGATCAGCTCTTATGAGCTT
* * * *
28101943 CTGTTTGGTGTTTTGGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGT
66 CTGTTTGGTGATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTGT
* * * *
28101992 TTCGATTGGATCAGCTCTTATGAGCTTTTGTTTGGCGATTC-GATTGGATTAGCTCTTTTGAGCT
1 TTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCAATTCAG-TTGGATCAGCTCTTATGAGCT
28102056 TCTGTTTGGTGATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTGT
65 TCTGTTTGGTGATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTGT
*
28102106 TTCGGTTGGATCAGCTCTTATGAGCTTCTGT
1 TTCGATTGGATCAGCTCTTATGAGCTTCTGT
28102137 CTGGTCTGTT
Statistics
Matches: 134, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 1 0.01
114 133 0.99
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.44
Consensus pattern (114 bp):
TTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCAATTCAGTTGGATCAGCTCTTATGAGCTT
CTGTTTGGTGATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTGT
Found at i:28107808 original size:3 final size:3
Alignment explanation
Indices: 28107800--28107824 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28107790 AACACATTTT
28107800 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
28107825 TCCTACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:28108003 original size:21 final size:21
Alignment explanation
Indices: 28107960--28108004 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
28107950 CACATAATCG
**
28107960 CATTTCATTTTGTTAGATTCA
1 CATTTCATTTTGTTAGAGCCA
28107981 CATTTCATTTTGTTAGAGCCA
1 CATTTCATTTTGTTAGAGCCA
28108002 CAT
1 CAT
28108005 ATCACTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (21 bp):
CATTTCATTTTGTTAGAGCCA
Found at i:28112613 original size:21 final size:21
Alignment explanation
Indices: 28112555--28112621 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
28112545 ATGTCTCAAA
* *
28112555 ACATCACTTCAAAGTCTTAAG
1 ACATCTCTTCAAAGTCTTGAG
* *
28112576 AC-TCATTCTT-GATGTCTTGAG
1 ACATC--TCTTCAAAGTCTTGAG
*
28112597 ACATCTCTTCAAAGTCTTGAA
1 ACATCTCTTCAAAGTCTTGAG
28112618 ACAT
1 ACAT
28112622 TTTGTCTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 6 0.17
21 24 0.69
22 5 0.14
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (21 bp):
ACATCTCTTCAAAGTCTTGAG
Found at i:28124241 original size:72 final size:72
Alignment explanation
Indices: 28124155--28124315 Score: 200
Period size: 72 Copynumber: 2.2 Consensus size: 72
28124145 TGTGGGTCCA
** * *
28124155 GGTACTGACTTTGTGTATAAACTAGTGAGTAACTCGCTGAG-TGAGCA-TATCATGTTAATGCTT
1 GGTACTGACTTTGTGTATAAACTAGTGAGTAACTCAATGAGCGGA-CATTA-CATGATAATGCTT
28124218 TGGGGCCCG
64 TGGGGCCCG
* *
28124227 GGTACTGACTTTGTGTATAAACTTGTGAGTAGCTCAATGAGCGGACATTACATGATAATGCTTTG
1 GGTACTGACTTTGTGTATAAACTAGTGAGTAACTCAATGAGCGGACATTACATGATAATGCTTTG
**
28124292 GGGTTCG
66 GGGCCCG
**
28124299 GGTGTTGACTTTGTGTA
1 GGTACTGACTTTGTGTA
28124316 CAGACCCGTG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 73 0.95
73 4 0.05
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (72 bp):
GGTACTGACTTTGTGTATAAACTAGTGAGTAACTCAATGAGCGGACATTACATGATAATGCTTTG
GGGCCCG
Found at i:28130065 original size:68 final size:64
Alignment explanation
Indices: 28130000--28130207 Score: 197
Period size: 67 Copynumber: 3.2 Consensus size: 64
28129990 CATCATGTGT
*
28130000 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
28130065 TAG
62 TAG
* * * * * * *
28130068 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGT
28130133 AG
63 AG
* * * * *
28130135 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATATA-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
28130197 TACAAGAGAGC
1 -ACAAGAGAGC
28130208 CGAACTATAT
Statistics
Matches: 116, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.16
64 21 0.18
65 11 0.09
66 18 0.16
67 31 0.27
68 15 0.13
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
Found at i:28140197 original size:23 final size:23
Alignment explanation
Indices: 28140171--28140217 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
28140161 AATTTTCGCC
28140171 TTCAAATTACTTAAAGTTGGTGA
1 TTCAAATTACTTAAAGTTGGTGA
*
28140194 TTCAAATTGCTTAAAGTTGGTGA
1 TTCAAATTACTTAAAGTTGGTGA
28140217 T
1 T
28140218 CTCTCAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (23 bp):
TTCAAATTACTTAAAGTTGGTGA
Found at i:28144663 original size:13 final size:13
Alignment explanation
Indices: 28144647--28144682 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
28144637 ATTTTTCGTG
28144647 AAAATTTCATTCA
1 AAAATTTCATTCA
28144660 AAAATTTCATTCA
1 AAAATTTCATTCA
28144673 AAAATTTCAT
1 AAAATTTCAT
28144683 CGATTGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATTTCATTCA
Found at i:28147801 original size:43 final size:43
Alignment explanation
Indices: 28147717--28147798 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
28147707 GTATCGTACA
* * *
28147717 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAAACACATATCG
*
28147760 ATGCCACTGTCCCAGACATGGTCTTAC-T-CAAACACATAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAAACACATAT
28147799 ATCAGAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 9 0.26
42 1 0.03
43 25 0.71
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGCAAACACATATCG
Found at i:28166581 original size:30 final size:30
Alignment explanation
Indices: 28166547--28166611 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
28166537 CCAGTCTGAG
* *
28166547 ACTATGAAAGATGGAATTCTACAAAGGTGC
1 ACTATGAAAGATAGAATTCCACAAAGGTGC
*
28166577 ACTATGATAGATAGAATTCCACAAAGGTGC
1 ACTATGAAAGATAGAATTCCACAAAGGTGC
28166607 ACTAT
1 ACTAT
28166612 CTTAAAGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (30 bp):
ACTATGAAAGATAGAATTCCACAAAGGTGC
Found at i:28169945 original size:33 final size:33
Alignment explanation
Indices: 28169903--28169969 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
28169893 ATCCATATGA
*
28169903 AAATAGACTCATTAAGCTTCAATTTCATAACTT
1 AAATAGACTCATCAAGCTTCAATTTCATAACTT
*
28169936 AAATAGACTCATCAAGCTTTAATTTCATAACTT
1 AAATAGACTCATCAAGCTTCAATTTCATAACTT
28169969 A
1 A
28169970 CTCATCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (33 bp):
AAATAGACTCATCAAGCTTCAATTTCATAACTT
Found at i:28180481 original size:59 final size:60
Alignment explanation
Indices: 28180414--28180537 Score: 205
Period size: 59 Copynumber: 2.0 Consensus size: 60
28180404 ATTATGTTCC
28180414 TAATGCTTATCATAAGCCTAAACGACATTATC-CCTGACTTATTGTATTTATCCATGATA
1 TAATGCTTATCATAAGCCTAAACGACATTATCACCTGACTTATTGTATTTATCCATGATA
*
28180473 TAATGCTTATCATAAGCCTAAACGTCATTATCAATTCCTGACTTATTGTATTTATCCATGATA
1 TAATGCTTATCATAAGCCTAAACGACATTATC-A--CCTGACTTATTGTATTTATCCATGATA
28180536 TA
1 TA
28180538 GGTATATTCA
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
59 31 0.52
63 29 0.48
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (60 bp):
TAATGCTTATCATAAGCCTAAACGACATTATCACCTGACTTATTGTATTTATCCATGATA
Found at i:28181960 original size:24 final size:25
Alignment explanation
Indices: 28181933--28181984 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
28181923 CTCACCACAA
28181933 CTCGCATGAGCTTACCAAT-TTTAG
1 CTCGCATGAGCTTACCAATATTTAG
*
28181957 CTCGTATGAGCTTACCAATATTTAG
1 CTCGCATGAGCTTACCAATATTTAG
28181982 CTC
1 CTC
28181985 AGAAAAGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (25 bp):
CTCGCATGAGCTTACCAATATTTAG
Found at i:28181993 original size:25 final size:24
Alignment explanation
Indices: 28181941--28181997 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
28181931 AACTCGCATG
**
28181941 AGCTTACCAATTTTAGCTCGTATG
1 AGCTTACCAATTTTAGCTCGTAAA
28181965 AGCTTACCAATATTTAGCTCAG-AAA
1 AGCTTACCAAT-TTTAGCTC-GTAAA
28181990 AGCTTACC
1 AGCTTACC
28181998 GTTTATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 11 0.38
25 17 0.59
26 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (24 bp):
AGCTTACCAATTTTAGCTCGTAAA
Found at i:28191048 original size:79 final size:80
Alignment explanation
Indices: 28190950--28191132 Score: 239
Period size: 79 Copynumber: 2.3 Consensus size: 80
28190940 TACTCGTTCA
* *
28190950 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
28191013 ATTTAGTAAC-TCGCACC
64 ATATAGTAACTTAGCA-C
**
28191030 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
*
28191094 ATAGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
28191109 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28191133 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:28191132 original size:40 final size:40
Alignment explanation
Indices: 28190948--28191132 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
28190938 GCTACTCGTT
* *
28190948 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28190988 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
28191028 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * *
28191067 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
28191108 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28191133 CATCATTCGA
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 81 0.64
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:28195088 original size:37 final size:37
Alignment explanation
Indices: 28195035--28195137 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
28195025 CGAATAGTCC
*
28195035 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
28195072 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
28195109 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
28195138 ATATATTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:28195335 original size:48 final size:48
Alignment explanation
Indices: 28195277--28195769 Score: 828
Period size: 48 Copynumber: 10.3 Consensus size: 48
28195267 ATATACACAC
*
28195277 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
28195325 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACGTATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
28195373 ATCTCATTCATATTTCACACTAGCCATTCGGTTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
28195421 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* **
28195469 ATCTCATATATATTTCACGTTAGCCATTCGGCTTTA-CACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
**
28195516 ATCTCATACATATTTCACGTTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
28195564 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
28195612 ATCTCATAGATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
28195660 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCATATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
28195708 ATCTCATACATA-TTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
28195755 ATCTCATACATATTT
1 ATCTCATACATATTT
28195770 ATCTTGTACA
Statistics
Matches: 423, Mismatches: 20, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 91 0.22
48 332 0.78
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:28195530 original size:191 final size:192
Alignment explanation
Indices: 28195277--28195769 Score: 830
Period size: 191 Copynumber: 2.6 Consensus size: 192
28195267 ATATACACAC
* *
28195277 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
* * * *
28195342 CACTAGCCATTCGGCTTTACCACGTATACATATCTCATTCATATTTCACACTAGCCATTCGGTTT
66 CATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTT
*
28195407 TACCACATATACATATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
131 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
**
28195469 ATCTCATATATATTTCACGTTAGCCATTCGGCTTTA-CACATATACATATCTCATACATATTTCA
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
* *
28195533 CGTTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTT
66 CATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTT
* *
28195598 TACCACATATACATATCTCATAGATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
131 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
28195660 ATCTCAT-TCATATTTCACACTAGCCATTCGGCTTTACCATATATACATATCTCATACATA-TTC
1 ATCTCATAT-ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
28195723 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTT
65 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTT
28195770 ATCTTGTACA
Statistics
Matches: 282, Mismatches: 17, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
190 1 0.00
191 227 0.80
192 54 0.19
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (192 bp):
ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
CATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTT
TACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:28199347 original size:39 final size:40
Alignment explanation
Indices: 28199270--28199395 Score: 179
Period size: 39 Copynumber: 3.2 Consensus size: 40
28199260 CCTTCGGAGT
* *
28199270 TTAG-CCGGATATAGCT-ACTAGCTC-AATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
* *
28199308 TTAGCCCGGTTATAGTAACTCGCACAAATG-CTTCAGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
28199347 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
28199387 TTAGCCCGG
1 TTAGCCCGG
28199396 GTATCAATCC
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
38 5 0.06
39 52 0.67
40 21 0.27
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:28207579 original size:40 final size:40
Alignment explanation
Indices: 28207511--28207678 Score: 259
Period size: 40 Copynumber: 4.2 Consensus size: 40
28207501 CCTTCGGAGT
* *
28207511 TTAG-CCGGATATAGCT-ACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
* *
28207550 TTAGCCCGGCTATAGTAACTCGCAAAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
28207590 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCAGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
28207630 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
28207670 TTAGCCCGG
1 TTAGCCCGG
28207679 GTATCAATCC
Statistics
Matches: 118, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 5 0.04
40 113 0.96
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:28210732 original size:2 final size:2
Alignment explanation
Indices: 28210725--28210754 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28210715 ACTAATAGAC
28210725 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28210755 ATGGAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28215956 original size:11 final size:11
Alignment explanation
Indices: 28215920--28215973 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
28215910 TATTTTACAG
28215920 GTTGTTTTTGGT
1 GTTG-TTTTGGT
* *
28215932 GCTATTTTGGGT
1 GTTGTTTT-GGT
28215944 GTTGTTTTGGT
1 GTTGTTTTGGT
*
28215955 GTTGTTTTGAT
1 GTTGTTTTGGT
28215966 GTTGTTTT
1 GTTGTTTT
28215974 TAATGTTCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
11 25 0.69
12 11 0.31
ACGTcount: A:0.04, C:0.02, G:0.31, T:0.63
Consensus pattern (11 bp):
GTTGTTTTGGT
Found at i:28215974 original size:23 final size:24
Alignment explanation
Indices: 28215920--28215974 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
28215910 TATTTTACAG
*
28215920 GTTGTTTTTGGTGCTATTTTGGGT
1 GTTGTTTTTGGTGCTATTTTGGAT
* *
28215944 GTTG-TTTTGGTGTTGTTTT-GAT
1 GTTGTTTTTGGTGCTATTTTGGAT
28215966 GTTGTTTTT
1 GTTGTTTTT
28215975 AATGTTCTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.22
23 17 0.63
24 4 0.15
ACGTcount: A:0.04, C:0.02, G:0.31, T:0.64
Consensus pattern (24 bp):
GTTGTTTTTGGTGCTATTTTGGAT
Found at i:28219373 original size:20 final size:20
Alignment explanation
Indices: 28219348--28219468 Score: 76
Period size: 20 Copynumber: 6.1 Consensus size: 20
28219338 TAAATGTTTT
*
28219348 CAGGGGTACCAATGTACAAA
1 CAGGGGCACCAATGTACAAA
**
28219368 CAGGGGCACGTATG-AGCAAA
1 CAGGGGCACCAATGTA-CAAA
*
28219388 CA--GGCATGCCAAAGTACAAA
1 CAGGGGCA--CCAATGTACAAA
*
28219408 C-GGGGCACGC-ATGTGCAAA
1 CAGGGGCAC-CAATGTACAAA
* *
28219427 CAAGGGTACCGAA-GTACAAA
1 CAGGGGCACC-AATGTACAAA
28219447 CAGGGGCA-CATATGTACAAA
1 CAGGGGCACCA-ATGTACAAA
28219467 CA
1 CA
28219469 AAGGTACCGA
Statistics
Matches: 76, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
18 5 0.07
19 13 0.17
20 52 0.68
21 6 0.08
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (20 bp):
CAGGGGCACCAATGTACAAA
Found at i:28219405 original size:40 final size:39
Alignment explanation
Indices: 28219354--28219468 Score: 126
Period size: 39 Copynumber: 2.9 Consensus size: 39
28219344 TTTTCAGGGG
*
28219354 TACCAATGTACAAACAGGGGCACGTATGAGCAAACAGGCA
1 TACCAAAGTACAAACAGGGGCACGTATGAGCAAACAGG-A
* * * *
28219394 TGCCAAAGTACAAAC-GGGGCACGCATGTGCAAACAAGGG
1 TACCAAAGTACAAACAGGGGCACGTATGAGCAAAC-AGGA
* *
28219433 TACCGAAGTACAAACAGGGGCACATATGTA-CAAACA
1 TACCAAAGTACAAACAGGGGCACGTATG-AGCAAACA
28219469 AAGGTACCGA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
39 31 0.50
40 31 0.50
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (39 bp):
TACCAAAGTACAAACAGGGGCACGTATGAGCAAACAGGA
Found at i:28219426 original size:39 final size:40
Alignment explanation
Indices: 28219354--28219455 Score: 127
Period size: 39 Copynumber: 2.6 Consensus size: 40
28219344 TTTTCAGGGG
* *
28219354 TACCAATGTACAAACAGGGGCACGTATGAGCAAAC-AGGCA
1 TACCAAAGTACAAACAGGGGCACGCATGAGCAAACAAGG-A
* * *
28219394 TGCCAAAGTACAAAC-GGGGCACGCATGTGCAAACAAGGG
1 TACCAAAGTACAAACAGGGGCACGCATGAGCAAACAAGGA
*
28219433 TACCGAAGTACAAACAGGGGCAC
1 TACCAAAGTACAAACAGGGGCAC
28219456 ATATGTACAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 30 0.57
40 23 0.43
ACGTcount: A:0.38, C:0.24, G:0.27, T:0.11
Consensus pattern (40 bp):
TACCAAAGTACAAACAGGGGCACGCATGAGCAAACAAGGA
Found at i:28219469 original size:40 final size:40
Alignment explanation
Indices: 28219351--28219488 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
28219341 ATGTTTTCAG
28219351 GGGTACC-AATGTACAAACAGGGGCACGTATG-AGCAAAC-A
1 GGGTACCGAA-GTACAAACAGGGGCACGTATGTA-CAAACAA
* * * * *
28219390 GGCATGCCAAAGTACAAAC-GGGGCACGCATGTGCAAACAA
1 GG-GTACCGAAGTACAAACAGGGGCACGTATGTACAAACAA
*
28219430 GGGTACCGAAGTACAAACAGGGGCACATATGTACAAACAA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTACAAACAA
* *
28219470 AGGTACCGAAGAACAAACA
1 GGGTACCGAAGTACAAACA
28219489 TTCAACAATT
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
39 31 0.38
40 49 0.60
41 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.11
Consensus pattern (40 bp):
GGGTACCGAAGTACAAACAGGGGCACGTATGTACAAACAA
Found at i:28230395 original size:20 final size:20
Alignment explanation
Indices: 28230370--28230415 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
28230360 TATCGACATG
*
28230370 CAAACAGGGGTACCGAAGTA
1 CAAACAGGGGTACCAAAGTA
*
28230390 CAAACAGGGGTCCCAAAGTA
1 CAAACAGGGGTACCAAAGTA
*
28230410 AAAACA
1 CAAACA
28230416 TTCAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.24, T:0.09
Consensus pattern (20 bp):
CAAACAGGGGTACCAAAGTA
Found at i:28234254 original size:29 final size:30
Alignment explanation
Indices: 28234216--28234296 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
28234206 AACTTTGATT
28234216 AAAATAACAAAACAATCACTAAAC-TTAAA
1 AAAATAACAAAACAATCACTAAACTTTAAA
* ** * **
28234245 AAAATTACAATTCAGTCACTAAACTTTAGG
1 AAAATAACAAAACAATCACTAAACTTTAAA
*
28234275 AAAATAACAAACCAATCACTAA
1 AAAATAACAAAACAATCACTAA
28234297 CATTATCGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 20 0.49
30 21 0.51
ACGTcount: A:0.57, C:0.19, G:0.04, T:0.21
Consensus pattern (30 bp):
AAAATAACAAAACAATCACTAAACTTTAAA
Found at i:28236053 original size:38 final size:38
Alignment explanation
Indices: 28236006--28236082 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
28235996 TCAATGCATA
* * *
28236006 TGCTCTGTGTTGTCATGAATTCTCACTATTGATGTTAG
1 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
28236044 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
1 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
28236082 T
1 T
28236083 ATTAACATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (38 bp):
TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
Found at i:28238180 original size:9 final size:9
Alignment explanation
Indices: 28238168--28238192 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28238158 ATTATATAAG
28238168 ATTATTATC
1 ATTATTATC
28238177 ATTATTATC
1 ATTATTATC
28238186 ATTATTA
1 ATTATTA
28238193 GGTAGCGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATTATC
Found at i:28249727 original size:31 final size:31
Alignment explanation
Indices: 28249691--28249754 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
28249681 ATTGAGTTAG
*
28249691 AATCCAGTTGATGAGTAATACCAACTTAATA
1 AATCCAGTTGATGAATAATACCAACTTAATA
28249722 AATCCAGTTGATGAATAATACCAACTTAATA
1 AATCCAGTTGATGAATAATACCAACTTAATA
28249753 AA
1 AA
28249755 GAACTTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (31 bp):
AATCCAGTTGATGAATAATACCAACTTAATA
Found at i:28256817 original size:16 final size:17
Alignment explanation
Indices: 28256796--28256830 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
28256786 ACTATTTAAT
28256796 ATATAAATT-AAAAACA
1 ATATAAATTAAAAAACA
28256812 ATATAAATTAAAAAACA
1 ATATAAATTAAAAAACA
28256829 AT
1 AT
28256831 CACTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ATATAAATTAAAAAACA
Found at i:28257821 original size:5 final size:5
Alignment explanation
Indices: 28257811--28257869 Score: 75
Period size: 5 Copynumber: 11.2 Consensus size: 5
28257801 AATTATGTTT
28257811 TTATA TTATA TTATTA TTATATA TTATA TTATA TTATA TTATA TTATTA
1 TTATA TTATA TTA-TA -T-TATA TTATA TTATA TTATA TTATA TTA-TA
28257860 TTATA -TATA T
1 TTATA TTATA T
28257870 GACAAAGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.08
5 32 0.65
6 8 0.16
7 3 0.06
8 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:28257827 original size:3 final size:3
Alignment explanation
Indices: 28257814--28257863 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
28257804 TATGTTTTTA
28257814 TAT TA- TAT TAT TAT TAT ATAT TA- TAT TA- TAT TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
28257855 TAT TAT TAT
1 TAT TAT TAT
28257864 ATATATGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 10 0.24
3 28 0.68
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:28257835 original size:10 final size:10
Alignment explanation
Indices: 28257814--28257867 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 10
28257804 TATGTTTTTA
28257814 TATTATATTAT
1 TATTATA-TAT
28257825 TATTATATAT
1 TATTATATAT
28257835 TA-TATTATATT
1 TATTA-TATA-T
28257846 ATATTATATTAT
1 -TATTATA-TAT
28257858 TATTATATAT
1 TATTATATAT
28257868 ATGACAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.05
10 12 0.32
11 15 0.39
12 5 0.13
13 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTATATAT
Found at i:28257935 original size:40 final size:40
Alignment explanation
Indices: 28257878--28257973 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
28257868 ATGACAAAGA
28257878 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
28257919 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
28257959 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
28257974 AAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:28259380 original size:41 final size:39
Alignment explanation
Indices: 28259333--28259469 Score: 111
Period size: 39 Copynumber: 3.5 Consensus size: 39
28259323 CGACCTTGAG
28259333 TCGATGAGACACTGGGTGTCATACTATTACTTCGGATAGAT-
1 TCGATGAGACACTGGGTGTCA-ACTATTACTTCGGAT-G-TC
** ** *
28259374 TCGATGAGGTACTGGGTACCAAC--TTACTTCGGGGTGTC
1 TCGATGAGACACTGGGTGTCAACTATTACTTC-GGATGTC
* * *
28259412 TCCGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 T-CGATGAGACACTGGGTGTCAACTATTACTTCGGA-TGTC
*
28259453 -CGATGAGGCACTGGGTG
1 TCGATGAGACACTGGGTG
28259470 CCATTCTGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
37 1 0.01
38 9 0.12
39 37 0.49
40 3 0.04
41 26 0.34
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAACTATTACTTCGGATGTC
Found at i:28260912 original size:15 final size:15
Alignment explanation
Indices: 28260889--28260923 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28260879 ATATCCATGG
* *
28260889 CCATTAAACCTTAAA
1 CCATAAAACCCTAAA
28260904 CCATAAAACCCTAAA
1 CCATAAAACCCTAAA
28260919 CCATA
1 CCATA
28260924 GACCTTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (15 bp):
CCATAAAACCCTAAA
Found at i:28261148 original size:38 final size:39
Alignment explanation
Indices: 28261070--28261149 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 39
28261060 TTTTTGGGGG
* **
28261070 TTTAAGGTTTTAGGGGTTATAGTTTAGTATTTAGGGTTT
1 TTTAAGGTTTTAGGGGTTATAGATTAGTATTTAGAATTT
* *
28261109 TTTAAGG-TTTAGGGGTTATAGATTAGTGTTTATAATTT
1 TTTAAGGTTTTAGGGGTTATAGATTAGTATTTAGAATTT
28261147 TTT
1 TTT
28261150 GGGGGGTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (39 bp):
TTTAAGGTTTTAGGGGTTATAGATTAGTATTTAGAATTT
Found at i:28263423 original size:40 final size:40
Alignment explanation
Indices: 28263386--28263571 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
28263376 GCTACTCGTT
* *
28263386 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
28263426 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28263466 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
28263506 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28263547 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28263572 CATCATTCAA
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28270954 original size:78 final size:81
Alignment explanation
Indices: 28270811--28270994 Score: 252
Period size: 78 Copynumber: 2.3 Consensus size: 81
28270801 GCTACTCGTT
* *
28270811 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
28270876 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
**
28270891 CAAATGCCTTCGGGACTTA-CCCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
28270953 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
28270970 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28270995 CATCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
77 3 0.03
78 52 0.56
79 20 0.22
80 18 0.19
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:28270994 original size:40 final size:40
Alignment explanation
Indices: 28270792--28270994 Score: 254
Period size: 40 Copynumber: 5.1 Consensus size: 40
28270782 CGGAATTTAA
** *
28270792 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28270832 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28270872 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTA-C
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28270911 CCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
28270950 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28270990 CCGGA
1 CCGGA
28270995 CATCATTCAA
Statistics
Matches: 145, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
37 3 0.02
38 27 0.19
39 14 0.10
40 90 0.62
41 11 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28273510 original size:35 final size:35
Alignment explanation
Indices: 28273393--28273510 Score: 139
Period size: 35 Copynumber: 3.3 Consensus size: 35
28273383 AGTCCAACTA
* * *
28273393 AAACACACCAGATGCTCATAAGAGCCAATCCAAACG
1 AAACACACCA-AAGCTCATAAGAGCTAATCCAACCG
**
28273429 AAACACACCAATA-CTCATAAGAGCTAATTTAACCG
1 AAACACACCAA-AGCTCATAAGAGCTAATCCAACCG
* * *
28273464 GAACACACCAAAGCTCAGAAGAGCTAGTCCAACCG
1 AAACACACCAAAGCTCATAAGAGCTAATCCAACCG
28273499 AAACACACCAAA
1 AAACACACCAAA
28273511 CAGAGAGTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.01
35 58 0.84
36 10 0.14
ACGTcount: A:0.46, C:0.30, G:0.13, T:0.12
Consensus pattern (35 bp):
AAACACACCAAAGCTCATAAGAGCTAATCCAACCG
Found at i:28275926 original size:26 final size:30
Alignment explanation
Indices: 28275869--28275929 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 30
28275859 GCTATAAAGT
28275869 TTGGGTTTCAAAATTATATTTTGGAAAGAA
1 TTGGGTTTCAAAATTATATTTTGGAAAGAA
* *
28275899 TTGGTTTTC-AAA-TAT-TTTTGGATA-AA
1 TTGGGTTTCAAAATTATATTTTGGAAAGAA
28275925 TTGGG
1 TTGGG
28275930 AAGTATGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 6 0.21
27 8 0.29
28 3 0.11
29 3 0.11
30 8 0.29
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (30 bp):
TTGGGTTTCAAAATTATATTTTGGAAAGAA
Found at i:28278718 original size:21 final size:21
Alignment explanation
Indices: 28278692--28278733 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28278682 GCAGGGGAAG
28278692 GAAAGAAAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
*
28278713 GAAAGAAAGAAAAAGGGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
28278734 TCAAAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAAGAGAAAA
Found at i:28280936 original size:46 final size:46
Alignment explanation
Indices: 28280663--28280926 Score: 395
Period size: 46 Copynumber: 5.7 Consensus size: 46
28280653 AGTGTGCTCT
28280663 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28280709 CTGATATGAAATGTGTAAGACCATGGTTAAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28280755 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28280801 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *** *
28280847 GTGACATGAAATGAACAAAACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
28280893 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGA
28280927 CGCTATGGCA
Statistics
Matches: 202, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 201 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:28283121 original size:11 final size:11
Alignment explanation
Indices: 28283105--28283146 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
28283095 TTATATACTA
28283105 AATAAAATATT
1 AATAAAATATT
28283116 AATAAAATATCT
1 AATAAAATAT-T
*
28283128 CATTAAAATATT
1 -AATAAAATATT
28283140 AATAAAA
1 AATAAAA
28283147 CAATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.59
12 2 0.07
13 9 0.33
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:28288313 original size:18 final size:18
Alignment explanation
Indices: 28288290--28288325 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28288280 TAACATATAA
28288290 AAGTATATAATACATACC
1 AAGTATATAATACATACC
28288308 AAGTATATAATACATACC
1 AAGTATATAATACATACC
28288326 TGACCAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (18 bp):
AAGTATATAATACATACC
Found at i:28288713 original size:39 final size:39
Alignment explanation
Indices: 28288458--28288691 Score: 364
Period size: 39 Copynumber: 6.0 Consensus size: 39
28288448 AAAAAGCATG
* * *
28288458 CGGGACTTTAAGCCCGGATATAATACCAGCATAAA-GCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACAAATGCCTT
*
28288498 CGGGACTTTAGCCCGGATATAACACCAGCATAAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACAAATGCCTT
28288538 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
*
28288577 CGGGACTTAGCTCGGATATAACACCAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
28288616 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
* *
28288655 CGGGACTTAGCCCGGATATAATACCAGCATAAA-GCCT
1 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCT
28288692 GCGGACCTCA
Statistics
Matches: 186, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
38 4 0.02
39 163 0.88
40 19 0.10
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
Found at i:28295968 original size:26 final size:26
Alignment explanation
Indices: 28295938--28295993 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
28295928 TGAAATTCCC
28295938 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28295964 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28295990 ATCA
1 ATCA
28295994 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28311506 original size:6 final size:6
Alignment explanation
Indices: 28311495--28311520 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28311485 AATTTACTAG
28311495 TTTTGA TTTTGA TTTTGA TTTTGA TT
1 TTTTGA TTTTGA TTTTGA TTTTGA TT
28311521 GTTCATGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:28313085 original size:43 final size:43
Alignment explanation
Indices: 28313025--28313115 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
28313015 CTTTGAGTTC
* * *
28313025 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
28313067 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
28313110 ATTACC
1 ATTACC
28313116 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:28313855 original size:43 final size:43
Alignment explanation
Indices: 28313775--28313856 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
28313765 ATAATTATTT
* * * *
28313775 TTAAAGGTTATGTTTTTTAGCGGCTTTTGTGGAAAAAATACAG
1 TTAAAAGTCATGTTTTATAGCGGCTTTTATGGAAAAAATACAG
*
28313818 TTAAAAGTCATGTTTTATAGCGG-TGTTTATGGGAAAAAT
1 TTAAAAGTCATGTTTTATAGCGGCT-TTTATGGAAAAAAT
28313857 GCCACTAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 32 0.97
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (43 bp):
TTAAAAGTCATGTTTTATAGCGGCTTTTATGGAAAAAATACAG
Found at i:28314710 original size:21 final size:21
Alignment explanation
Indices: 28314686--28314729 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
28314676 ACTTGTTATT
28314686 ACCCTTTGAACCTTGAAACTA
1 ACCCTTTGAACCTTGAAACTA
*
28314707 ACCCTTTGAATCTTGAAACTA
1 ACCCTTTGAACCTTGAAACTA
28314728 AC
1 AC
28314730 TTTTGGCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (21 bp):
ACCCTTTGAACCTTGAAACTA
Found at i:28320749 original size:27 final size:27
Alignment explanation
Indices: 28320698--28320770 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
28320688 AAACATAAAA
28320698 TTAAATTAAA-AAAAATTATTGTTAA-
1 TTAAATTAAATAAAAATTATTGTTAAG
28320723 TATATAATTAAATACAAAATTA-T-TTAAG
1 T-TA-AATTAAATA-AAAATTATTGTTAAG
28320751 TTAAATTAAATGAATAAATT
1 TTAAATTAAAT-AA-AAATT
28320771 TTTAAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
25 1 0.02
26 11 0.27
27 19 0.46
28 3 0.07
29 7 0.17
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (27 bp):
TTAAATTAAATAAAAATTATTGTTAAG
Found at i:28321766 original size:20 final size:20
Alignment explanation
Indices: 28321743--28321823 Score: 58
Period size: 21 Copynumber: 4.0 Consensus size: 20
28321733 AGGGAGCAAG
*
28321743 TTTTTCACTTGAGTTAAAAA
1 TTTTTCACTCGAGTTAAAAA
* *
28321763 -TTTTCAATCGA-TTCAAAAC
1 TTTTTCACTCGAGTT-AAAAA
* * *
28321782 TGTTTCACTCGATTTTAAAA
1 TTTTTCACTCGAGTTAAAAA
* *
28321802 TTGTTTCACTTGAGATAAAAA
1 TT-TTTCACTCGAGTTAAAAA
28321823 T
1 T
28321824 ACTTGAAGTG
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
18 2 0.04
19 13 0.29
20 13 0.29
21 17 0.38
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTTCACTCGAGTTAAAAA
Found at i:28321806 original size:21 final size:20
Alignment explanation
Indices: 28321745--28321811 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 20
28321735 GGAGCAAGTT
* *
28321745 TTTCACTTGAGTTAAAAAT-
1 TTTCACTCGATTTAAAAATG
* * *
28321764 TTTCAATCGATTCAAAACTG
1 TTTCACTCGATTTAAAAATG
*
28321784 TTTCACTCGATTTTAAAATTG
1 TTTCACTCGA-TTTAAAAATG
28321805 TTTCACT
1 TTTCACT
28321812 TGAGATAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 14 0.37
20 9 0.24
21 15 0.39
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.43
Consensus pattern (20 bp):
TTTCACTCGATTTAAAAATG
Found at i:28321932 original size:14 final size:15
Alignment explanation
Indices: 28321897--28321926 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28321887 GAGACTTCAA
28321897 AAAACTTTTTACTTT
1 AAAACTTTTTACTTT
28321912 AAAACTTTTTACTTT
1 AAAACTTTTTACTTT
28321927 GAACTTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAACTTTTTACTTT
Found at i:28324057 original size:20 final size:20
Alignment explanation
Indices: 28324012--28324062 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
28324002 CACTTATAGA
**
28324012 TAAGTATCGATATTTTTTCT
1 TAAGTATCGATAAATTTTCT
* *
28324032 TTAGTATCGATAAATTTTGT
1 TAAGTATCGATAAATTTTCT
*
28324052 TAAGTACCGAT
1 TAAGTATCGAT
28324063 TTGAAAGTGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TAAGTATCGATAAATTTTCT
Found at i:28345224 original size:42 final size:43
Alignment explanation
Indices: 28345156--28345267 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 43
28345146 CACAAGGCCA
*
28345156 AGACACACGCCTATGT-TCTAGGCCGTGTAGCACACACGGCTG
1 AGACACACGCCTATGTCTCTAGCCCGTGTAGCACACACGGCTG
*
28345198 AGACACACGCCTATGTCTCTA-CCCGTGTAGCACACATGGCTG
1 AGACACACGCCTATGTCTCTAGCCCGTGTAGCACACACGGCTG
* * *
28345240 AGACACACACCTGTGTCTCT-GCTCGTGT
1 AGACACACGCCTATGTCTCTAGCCCGTGT
28345268 GCTTAATTCT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
42 59 0.94
43 4 0.06
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.22
Consensus pattern (43 bp):
AGACACACGCCTATGTCTCTAGCCCGTGTAGCACACACGGCTG
Found at i:28361924 original size:22 final size:22
Alignment explanation
Indices: 28361895--28361951 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
28361885 AATCAACATA
28361895 GCACAGAGCCATATTTAGGTTG
1 GCACAGAGCCATATTTAGGTTG
*
28361917 GCATAGAGCCATATTTAGGTTG
1 GCACAGAGCCATATTTAGGTTG
28361939 GCACAGAGCCATA
1 GCACAGAGCCATA
28361952 ATTTGATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
GCACAGAGCCATATTTAGGTTG
Found at i:28362336 original size:27 final size:27
Alignment explanation
Indices: 28362306--28362367 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
28362296 CAAAACAGTC
*
28362306 ATTTTACCCTACAACG-GTATTTCGACA
1 ATTTTACACTACAA-GAGTATTTCGACA
*
28362333 ATTTTACACTACAAGAGTATTTCGGCA
1 ATTTTACACTACAAGAGTATTTCGACA
28362360 ATTTTACA
1 ATTTTACA
28362368 AATTTAGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (27 bp):
ATTTTACACTACAAGAGTATTTCGACA
Found at i:28362379 original size:27 final size:27
Alignment explanation
Indices: 28362349--28362557 Score: 208
Period size: 27 Copynumber: 7.8 Consensus size: 27
28362339 CACTACAAGA
* *
28362349 GTATTTCGGCAATTTTACAAATTTAGG
1 GTATTTCAGTAATTTTACAAATTTAGG
* * *
28362376 GTATTTTAGTAATTTTATAAATTTGGG
1 GTATTTCAGTAATTTTACAAATTTAGG
* ***
28362403 GTATTTCAATAATTTTACAAATCGGGG
1 GTATTTCAGTAATTTTACAAATTTAGG
** * *
28362430 GTATTTTGGTAATTTTACAAATTAAAG
1 GTATTTCAGTAATTTTACAAATTTAGG
* *
28362457 GTATTT-GGATAATTTTACAAATTGAGG
1 GTATTTCAG-TAATTTTACAAATTTAGG
* *
28362484 GTATTTTAGTAATTTTACAAA-TCAGG
1 GTATTTCAGTAATTTTACAAATTTAGG
* *
28362510 GTATTTCGGTAATTTTATAAA-TTAGGG
1 GTATTTCAGTAATTTTACAAATTTA-GG
28362537 GTATTTCAGTAATTTTACAAA
1 GTATTTCAGTAATTTTACAAA
28362558 CTGGAGTCTT
Statistics
Matches: 152, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
26 26 0.17
27 125 0.82
28 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATTTAGG
Found at i:28362390 original size:54 final size:54
Alignment explanation
Indices: 28362344--28362557 Score: 245
Period size: 54 Copynumber: 4.0 Consensus size: 54
28362334 TTTTACACTA
* * * *
28362344 CAAGAGTATTTCGGCAATTTTACAAATTTAGGGTATTTTAGTAATTTTATAAAT
1 CAAGGGTATTTCGGTAATTTTACAAATTGAGGGTATTTTAGTAATTTTACAAAT
*** ** * * *
28362398 TTGGGGTATTTCAATAATTTTACAAATCGGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCGGTAATTTTACAAATTGAGGGTATTTTAGTAATTTTACAAAT
* *
28362452 TAAAGGTATTT-GGATAATTTTACAAATTGAGGGTATTTTAGTAATTTTACAAAT
1 CAAGGGTATTTCGG-TAATTTTACAAATTGAGGGTATTTTAGTAATTTTACAAAT
* *
28362506 C-AGGGTATTTCGGTAATTTTATAAATT-AGGGGTATTTCAGTAATTTTACAAA
1 CAAGGGTATTTCGGTAATTTTACAAATTGA-GGGTATTTTAGTAATTTTACAAA
28362558 CTGGAGTCTT
Statistics
Matches: 133, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
52 1 0.01
53 43 0.32
54 89 0.67
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.42
Consensus pattern (54 bp):
CAAGGGTATTTCGGTAATTTTACAAATTGAGGGTATTTTAGTAATTTTACAAAT
Found at i:28362444 original size:81 final size:80
Alignment explanation
Indices: 28362349--28362557 Score: 262
Period size: 81 Copynumber: 2.6 Consensus size: 80
28362339 CACTACAAGA
* *
28362349 GTATTTCGGCAATTTTACAAATTTAGGGTATTTTAGTAATTTTATAAATTTG-GGGTATTTCAAT
1 GTATTTCGGTAATTTTACAAATTTAGGGTATTTTAGTAATTTTACAAA-TTGAGGGTATTTCAAT
*
28362413 AATTTTACAAATCGGGG
65 AATTTTACAAATC-AGG
* * * * * *
28362430 GTATTTTGGTAATTTTACAAATTAAAGGTA-TTTGGATAATTTTACAAATTGAGGGTATTTTAGT
1 GTATTTCGGTAATTTTACAAATTTAGGGTATTTTAG-TAATTTTACAAATTGAGGGTATTTCAAT
28362494 AATTTTACAAATCAGG
65 AATTTTACAAATCAGG
* *
28362510 GTATTTCGGTAATTTTATAAA-TTAGGGGTATTTCAGTAATTTTACAAA
1 GTATTTCGGTAATTTTACAAATTTA-GGGTATTTTAGTAATTTTACAAA
28362558 CTGGAGTCTT
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
79 2 0.02
80 44 0.40
81 63 0.58
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (80 bp):
GTATTTCGGTAATTTTACAAATTTAGGGTATTTTAGTAATTTTACAAATTGAGGGTATTTCAATA
ATTTTACAAATCAGG
Found at i:28370487 original size:14 final size:14
Alignment explanation
Indices: 28370468--28370497 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28370458 CAAAAACACA
28370468 TTCTTTTCTTTTCT
1 TTCTTTTCTTTTCT
*
28370482 TTCTTTTTTTTTCT
1 TTCTTTTCTTTTCT
28370496 TT
1 TT
28370498 TTTGGGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTCTTTTCT
Found at i:28373731 original size:25 final size:26
Alignment explanation
Indices: 28373696--28373746 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
28373686 ATTGTAGAAT
28373696 AATTAAATTATTTGTTTCACTAATGA
1 AATTAAATTATTTGTTTCACTAATGA
28373722 AATT-AATTATTTGTTTCACTAATGA
1 AATTAAATTATTTGTTTCACTAATGA
28373747 TATTTTAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (26 bp):
AATTAAATTATTTGTTTCACTAATGA
Found at i:28374570 original size:36 final size:36
Alignment explanation
Indices: 28374521--28374599 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
28374511 ATTCCAACTA
*
28374521 AAACACACCAGATGCTCATAAGAGCTAATCCATCTG
1 AAACACACCAGATGCTCATAAGAGCCAATCCATCTG
* * * *
28374557 AAACACACTAGATGCTCATACGAGCCAGTCCATTTG
1 AAACACACCAGATGCTCATAAGAGCCAATCCATCTG
28374593 ATAACAC
1 A-AACAC
28374600 CCAATAGCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 32 0.86
37 5 0.14
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (36 bp):
AAACACACCAGATGCTCATAAGAGCCAATCCATCTG
Found at i:28376366 original size:38 final size:38
Alignment explanation
Indices: 28376283--28376366 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
28376273 TGCATCTGGT
28376283 ATGTTATCAAATAGAATAACTCTTATGAGAAAACTGAC
1 ATGTTATCAAATAGAATAACTCTTATGAGAAAACTGAC
* * * * *
28376321 ATATTATCAGATGGAATAGCTCTTATGAGAAATCT-AGC
1 ATGTTATCAAATAGAATAACTCTTATGAGAAAACTGA-C
28376359 ATGTTATC
1 ATGTTATC
28376367 GATTGGTTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 1 0.03
38 38 0.97
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (38 bp):
ATGTTATCAAATAGAATAACTCTTATGAGAAAACTGAC
Found at i:28381055 original size:47 final size:47
Alignment explanation
Indices: 28381004--28381461 Score: 736
Period size: 47 Copynumber: 9.7 Consensus size: 47
28380994 CTTCCACTTC
* * * *
28381004 CATCACATTGACCATTCGGCCTTATCATATATATATACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
28381051 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
*
28381098 CATCACATTGGCCATTCGGCCTTATCACATATACATACACCTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCAC--ATACATACACTTTCACATT
* * *
28381147 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
28381194 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
*
28381241 CATCACATTGGCCATTCGGCCTGATCACATACATACACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
*
28381288 CATCACATTGGCCATTCGGCCTTATCACATATACATACACCTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCAC--ATACATACACTTTCACATT
* * * * *
28381337 CATCACATTGGCTATTCGGCTTTATCATATATATATACTTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
*
28381384 CATCACATTGGCCATTCGGCCTTATCACATACATACACCTTCACATT
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
28381431 CATCACATTGGCCATTCGGCCTTATCACATA
1 CATCACATTGGCCATTCGGCCTTATCACATA
28381462 TACATATCTT
Statistics
Matches: 380, Mismatches: 27, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
47 292 0.77
49 88 0.23
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATT
Found at i:28381262 original size:143 final size:141
Alignment explanation
Indices: 28381004--28381463 Score: 776
Period size: 143 Copynumber: 3.2 Consensus size: 141
28380994 CTTCCACTTC
*
28381004 CATCACATTGACCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
28381069 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATACAT
28381134 ACACCTTCACATT
129 ACACCTTCACATT
28381147 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
*
28381212 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTGATCACATACATAC
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACATAC
*
28381277 ACTTTCACATT
131 ACCTTCACATT
* * * *
28381288 CATCACATTGGCCATTCGGCCTTATCACATATACATACACCTTCACATTCATCACATTGGCTATT
1 CATCACATTGGCCATTCGGCCTTAT--CATATATATATACTTTCACATTCATCACATTGGCCATT
* * * *
28381353 CGGCTTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACAT
64 CGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACAT
28381418 ACACCTTCACATT
129 ACACCTTCACATT
*
28381431 CATCACATTGGCCATTCGGCCTTATCACATATA
1 CATCACATTGGCCATTCGGCCTTATCATATATA
28381464 CATATCTTGT
Statistics
Matches: 300, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
141 49 0.16
143 251 0.84
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (141 bp):
CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACATAC
ACCTTCACATT
Found at i:28381320 original size:190 final size:190
Alignment explanation
Indices: 28381004--28381461 Score: 844
Period size: 190 Copynumber: 2.4 Consensus size: 190
28380994 CTTCCACTTC
* * * *
28381004 CATCACATTGACCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCG
28381069 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
28381134 ACACCTTCACATTCATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATT
131 ACACCTTCACATTCATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATT
28381194 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCG
*
28381259 GCCTGATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
* *
28381324 ACACCTTCACATTCATCACATTGGCTATTCGGCTTTATCATATATATATACTTTCACATT
131 ACACCTTCACATTCATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATT
*
28381384 CATCACATTGGCCATTCGGCCTTATCACATACATACACCTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCG
28381449 GCCTTATCACATA
66 GCCTTATCACATA
28381462 TACATATCTT
Statistics
Matches: 259, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
190 259 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (190 bp):
CATCACATTGGCCATTCGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCG
GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
ACACCTTCACATTCATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATT
Found at i:28385733 original size:27 final size:28
Alignment explanation
Indices: 28385649--28385746 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
28385639 CATGAGATTG
* * * *
28385649 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
28385678 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
28385706 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28385733 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
28385747 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28385757 original size:27 final size:27
Alignment explanation
Indices: 28385677--28385759 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
28385667 TAAATTGTAC
* *
28385677 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
28385705 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
28385732 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
28385759 A
1 A
28385760 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:28385760 original size:29 final size:27
Alignment explanation
Indices: 28385649--28385760 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
28385639 CATGAGATTG
** * *
28385649 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
28385678 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
28385706 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
28385733 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
28385761 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:28388699 original size:130 final size:130
Alignment explanation
Indices: 28388466--28388725 Score: 511
Period size: 130 Copynumber: 2.0 Consensus size: 130
28388456 TAGCTAGTGT
28388466 GGGCAATAATCGTCACGAGAAACCTGAATGCCCCCAATGCGGAAGACGACACCTAGGTGAATGTT
1 GGGCAATAATCGTCACGAGAAACCTGAATGCCCCCAATGCGGAAGACGACACCTAGGTGAATGTT
*
28388531 GGGGTAAGTCTACTAACAGGGCCTGTTACGGATGCGGCTCGAAGGACCACTTCATTAGAGATTGC
66 GGGGTAAGTCTACTAACAGAGCCTGTTACGGATGCGGCTCGAAGGACCACTTCATTAGAGATTGC
28388596 GGGCAATAATCGTCACGAGAAACCTGAATGCCCCCAATGCGGAAGACGACACCTAGGTGAATGTT
1 GGGCAATAATCGTCACGAGAAACCTGAATGCCCCCAATGCGGAAGACGACACCTAGGTGAATGTT
28388661 GGGGTAAGTCTACTAACAGAGCCTGTTACGGATGCGGCTCGAAGGACCACTTCATTAGAGATTGC
66 GGGGTAAGTCTACTAACAGAGCCTGTTACGGATGCGGCTCGAAGGACCACTTCATTAGAGATTGC
28388726 ACGGAGCTTG
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (130 bp):
GGGCAATAATCGTCACGAGAAACCTGAATGCCCCCAATGCGGAAGACGACACCTAGGTGAATGTT
GGGGTAAGTCTACTAACAGAGCCTGTTACGGATGCGGCTCGAAGGACCACTTCATTAGAGATTGC
Found at i:28389053 original size:83 final size:83
Alignment explanation
Indices: 28388914--28389080 Score: 316
Period size: 83 Copynumber: 2.0 Consensus size: 83
28388904 AGGCATCCTC
*
28388914 TCCTGATGTCATCACTGGTACTTTCACCCTCTTTGATACCAATGTGATTGCATTGATTGACCCTA
1 TCCTGACGTCATCACTGGTACTTTCACCCTCTTTGATACCAATGTGATTGCATTGATTGACCCTA
28388979 GCTCTACTCATTCATATG
66 GCTCTACTCATTCATATG
*
28388997 TCCTGACGTCATCACTGGTACTTTCACCCTCTTTGATACCAATGTGATTGCATTGATTGACCCTG
1 TCCTGACGTCATCACTGGTACTTTCACCCTCTTTGATACCAATGTGATTGCATTGATTGACCCTA
28389062 GCTCTACTCATTCATATG
66 GCTCTACTCATTCATATG
28389080 T
1 T
28389081 ATGTGAAACC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (83 bp):
TCCTGACGTCATCACTGGTACTTTCACCCTCTTTGATACCAATGTGATTGCATTGATTGACCCTA
GCTCTACTCATTCATATG
Found at i:28394144 original size:27 final size:28
Alignment explanation
Indices: 28394060--28394157 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
28394050 CATGAGATTG
* * * *
28394060 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
28394089 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
28394117 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28394144 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
28394158 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28394168 original size:27 final size:27
Alignment explanation
Indices: 28394088--28394170 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
28394078 TAAATTGTAC
* *
28394088 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
28394116 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
28394143 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
28394170 A
1 A
28394171 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:28394171 original size:29 final size:27
Alignment explanation
Indices: 28394060--28394171 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
28394050 CATGAGATTG
** * *
28394060 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
28394089 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
28394117 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
28394144 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
28394172 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:28397998 original size:15 final size:16
Alignment explanation
Indices: 28397978--28398015 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28397968 TAATTTGGTT
*
28397978 AATAAACAAAA-ATTA
1 AATAAACAAAAGATGA
28397993 AATAAA-AAAAGATGA
1 AATAAACAAAAGATGA
28398008 AATAAACA
1 AATAAACA
28398016 TCATCTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (16 bp):
AATAAACAAAAGATGA
Found at i:28399032 original size:25 final size:25
Alignment explanation
Indices: 28398986--28399055 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
28398976 GTGGATTCTC
* *
28398986 CATAGCTCATGTGACCAATTACAGT
1 CATAGCTCATGTGAACATTTACAGT
* * *
28399011 TATAGCTCGTGTGAACATTTACCGT
1 CATAGCTCATGTGAACATTTACAGT
* *
28399036 CAGAGCTCATGTGAGCATTT
1 CATAGCTCATGTGAACATTT
28399056 TCCTACATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (25 bp):
CATAGCTCATGTGAACATTTACAGT
Found at i:28401408 original size:23 final size:23
Alignment explanation
Indices: 28401365--28401408 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
28401355 AAAGGGTTTG
*
28401365 TATTATTTTAGTAAATTTTTTCA
1 TATTATTTTAGTAAATATTTTCA
*
28401388 TATTA-TTTGGTAAATAATTTT
1 TATTATTTTAGTAAAT-ATTTT
28401409 TTTTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
TATTATTTTAGTAAATATTTTCA
Found at i:28405684 original size:16 final size:16
Alignment explanation
Indices: 28405665--28405695 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28405655 AAACAGCTTA
28405665 TTTAAAAATATTTTTG
1 TTTAAAAATATTTTTG
*
28405681 TTTAAAAGTATTTTT
1 TTTAAAAATATTTTT
28405696 TTCTCCTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTAAAAATATTTTTG
Found at i:28408024 original size:19 final size:19
Alignment explanation
Indices: 28407977--28408013 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28407967 TTTCTAAAAG
*
28407977 AATACCCAAATTTGTAACT
1 AATACCAAAATTTGTAACT
28407996 AATACCAAAATTTGTAAC
1 AATACCAAAATTTGTAAC
28408014 GTGATACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (19 bp):
AATACCAAAATTTGTAACT
Found at i:28408025 original size:20 final size:19
Alignment explanation
Indices: 28407984--28408025 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28407974 AAGAATACCC
*
28407984 AAATTTGTAACTAATACCA
1 AAATTTGTAACTAATACAA
*
28408003 AAATTTGTAACGTGATACAA
1 AAATTTGTAAC-TAATACAA
28408023 AAA
1 AAA
28408026 ACTCTACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (19 bp):
AAATTTGTAACTAATACAA
Found at i:28408092 original size:18 final size:19
Alignment explanation
Indices: 28408071--28408110 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28408061 CAAAAATTGT
28408071 TAAT-GATAACAAAATTTC
1 TAATCGATAACAAAATTTC
* *
28408089 TAATCGATTACAATATTTC
1 TAATCGATAACAAAATTTC
28408108 TAA
1 TAA
28408111 CGTGATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATCGATAACAAAATTTC
Found at i:28409536 original size:28 final size:28
Alignment explanation
Indices: 28409482--28409537 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
28409472 TACAGGGTTT
28409482 TCACACGGCCTGACACACACCCATGTCCC
1 TCACACGGCCTGA-ACACACCCATGTCCC
*
28409511 TCACACGGCCATG-ACACACCCGTGTCC
1 TCACACGGCC-TGAACACACCCATGTCC
28409538 TATCTCGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 13 0.52
29 10 0.40
30 2 0.08
ACGTcount: A:0.23, C:0.46, G:0.16, T:0.14
Consensus pattern (28 bp):
TCACACGGCCTGAACACACCCATGTCCC
Done.