Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 31
Found at i:3904309 original size:75 final size:75
Alignment explanation
Indices: 3904159--3904367 Score: 267
Period size: 75 Copynumber: 2.8 Consensus size: 75
3904149 CAAAGTCAAA
* * * **
3904159 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
3904224 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* *
3904236 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
3904301 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
3904311 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
3904368 TGTACAACGG
Statistics
Matches: 117, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 85 0.73
76 6 0.05
77 26 0.22
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:3907002 original size:84 final size:81
Alignment explanation
Indices: 3906914--3907113 Score: 202
Period size: 82 Copynumber: 2.4 Consensus size: 81
3906904 CGCTACAATT
* * * * * * *
3906914 CTAATTTTTTGCGGCGTTTATTGGAAAAACGCTACTATAGGTGAACCCTATTATGATGTTTTTTA
1 CTAATTTTTTGTGGCGTTT-TTGAAAAAACGCCACTATAGATGAA-CCTATTACGACG-TTTGTA
* * *
3906979 TAAAAATGCCGCTAAAGTA
63 TAAAAACGACACTAAAGTA
* * * * *
3906998 CTAATTTATTGTGGCGTTCGTCGAAAAAACGCCACTATAGATGGACCTATTACGACGTTTGTATG
1 CTAATTTTTTGTGGCGTT-TTTGAAAAAACGCCACTATAGATGAACCTATTACGACGTTTGTATA
3907063 AAAACGACACTAAAGTA
65 AAAACGACACTAAAGTA
* *
3907080 CTACTCTTTTGTGGCGTTCTTTGAAAAAACGCCA
1 CTAATTTTTTGTGGCGTT-TTTGAAAAAACGCCA
3907114 TTACATATGT
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
82 49 0.52
83 10 0.11
84 36 0.38
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (81 bp):
CTAATTTTTTGTGGCGTTTTTGAAAAAACGCCACTATAGATGAACCTATTACGACGTTTGTATAA
AAACGACACTAAAGTA
Found at i:3907149 original size:82 final size:83
Alignment explanation
Indices: 3906972--3907172 Score: 221
Period size: 82 Copynumber: 2.5 Consensus size: 83
3906962 TATTATGATG
* * * *
3906972 TTTTTTATAAAAATGCCGCTAAAGTACTAAT-TTATTGTGGCGTTCGTCGAAAAAACGCCACTAT
1 TTTTATATAAAAACGCCGCTAAAGTACTACTCTTATTGTGGCGTTCGTCGAAAAAACGCCACTAC
3907036 AGATGGACCTATTACGAC
66 AGATGGACCTATTACGAC
* * * * * * * *
3907054 GTTTGTATGAAAACGACACTAAAGTACTACTCTT-TTGTGGCGTTCTTTGAAAAAACGCCATTAC
1 TTTTATATAAAAACGCCGCTAAAGTACTACTCTTATTGTGGCGTTCGTCGAAAAAACGCCACTAC
* * *
3907118 ATATGTACCTATTGCTG-C
66 AGATGGACCTATTAC-GAC
*
3907136 TTTTATATAAAAACGCCGCTAAATTACTACTC-TATTG
1 TTTTATATAAAAACGCCGCTAAAGTACTACTCTTATTG
3907173 CGGTGTTTGT
Statistics
Matches: 96, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
81 1 0.01
82 92 0.96
83 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (83 bp):
TTTTATATAAAAACGCCGCTAAAGTACTACTCTTATTGTGGCGTTCGTCGAAAAAACGCCACTAC
AGATGGACCTATTACGAC
Found at i:3920710 original size:18 final size:18
Alignment explanation
Indices: 3920687--3920729 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3920677 TTGAAGGTAG
* *
3920687 CAACAAGGTTTGCTAGCT
1 CAACAAGGTGTGCAAGCT
3920705 CAACAAGGTGTGCAAGCT
1 CAACAAGGTGTGCAAGCT
3920723 CAACAAG
1 CAACAAG
3920730 TCTCTATACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (18 bp):
CAACAAGGTGTGCAAGCT
Found at i:3926997 original size:6 final size:6
Alignment explanation
Indices: 3926988--3927013 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3926978 TATTATTTAG
3926988 TTATAA TTATAA TTATAA TTATAA TT
1 TTATAA TTATAA TTATAA TTATAA TT
3927014 TTCTTATTTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:3930770 original size:19 final size:20
Alignment explanation
Indices: 3930738--3930775 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3930728 ACTACTATAT
3930738 TACTTGCATCGA-TTGTGTA
1 TACTTGCATCGATTTGTGTA
3930757 TACTTGCA-CAGATTTGTGT
1 TACTTGCATC-GATTTGTGT
3930776 GCCACAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 10 0.59
20 6 0.35
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (20 bp):
TACTTGCATCGATTTGTGTA
Found at i:3950450 original size:26 final size:26
Alignment explanation
Indices: 3950414--3950467 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
3950404 ACCGAAGTGT
3950414 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
*
3950440 TAATACACATAAGGTCGTGCTCACCA
1 TAATACACATAAGGTCGTGCCCACCA
3950466 TA
1 TA
3950468 TGCACTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:3958000 original size:26 final size:26
Alignment explanation
Indices: 3957960--3958039 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
3957950 ACCAAATTGC
3957960 TAATACACATAAGGTCATGCCCACTA
1 TAATACACATAAGGTCATGCCCACTA
* * *
3957986 TAATACACATTAGGT-AGTTCCCACCA
1 TAATACACATAAGGTCA-TGCCCACTA
*
3958012 TAATACACATAAGGTCGTGCCCACTA
1 TAATACACATAAGGTCATGCCCACTA
3958038 TA
1 TA
3958040 TTCACTTAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
25 1 0.02
26 44 0.98
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.25
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACTA
Found at i:3962575 original size:22 final size:23
Alignment explanation
Indices: 3962506--3962589 Score: 143
Period size: 23 Copynumber: 3.7 Consensus size: 23
3962496 TTCCCTGTGG
3962506 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
3962529 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
3962552 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
3962574 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
3962590 TCTACCAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 16 0.27
23 43 0.73
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:3966409 original size:21 final size:21
Alignment explanation
Indices: 3966385--3966424 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3966375 AATACTATTT
3966385 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTGAAACA
3966406 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
3966425 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAACA
Found at i:3968739 original size:19 final size:18
Alignment explanation
Indices: 3968717--3968762 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
3968707 AACTGATTAC
3968717 AAAAATATACCAATTGTT
1 AAAAATATACCAATTGTT
*
3968735 AAAAAGATACCAATTGTT
1 AAAAATATACCAATTGTT
*
3968753 GGAAAATATA
1 -AAAAATATA
3968763 TGAAAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAAATATACCAATTGTT
Found at i:3971104 original size:21 final size:21
Alignment explanation
Indices: 3971078--3971118 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3971068 TCATAACATG
*
3971078 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACACCTTCATA
*
3971099 GGGTATCGGTGCACCTTCAT
1 GGGTATCGGTACACCTTCAT
3971119 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (21 bp):
GGGTATCGGTACACCTTCATA
Found at i:3971319 original size:36 final size:37
Alignment explanation
Indices: 3971250--3971319 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
3971240 CAGTCATAGG
* *
3971250 TGTATGGATACACCTGAAGGGGGTATCGGTACACCAA
1 TGTATGGATACACCTCAAGGGGGTATCGATACACCAA
3971287 TGTATGGATACA-CTCATA-GGGGTATCGATACAC
1 TGTATGGATACACCTCA-AGGGGGTATCGATACAC
3971320 ATTTGTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 17 0.57
37 13 0.43
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (37 bp):
TGTATGGATACACCTCAAGGGGGTATCGATACACCAA
Found at i:3971700 original size:2 final size:2
Alignment explanation
Indices: 3971693--3971719 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3971683 ACCTTGGCAC
3971693 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3971720 CAAAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3974311 original size:16 final size:16
Alignment explanation
Indices: 3974290--3974344 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
3974280 GGAAACAAAA
3974290 AAAAGAAAAAAACAAT
1 AAAAGAAAAAAACAAT
3974306 AAAAGAAAATAGAA-AA-
1 AAAAGAAAA-A-AACAAT
* *
3974322 GAAAGAAACGAAACAAT
1 AAAAGAAA-AAAACAAT
3974339 AAAAGA
1 AAAAGA
3974345 GTGAAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
15 2 0.06
16 19 0.61
17 8 0.26
18 2 0.06
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (16 bp):
AAAAGAAAAAAACAAT
Found at i:3979011 original size:2 final size:2
Alignment explanation
Indices: 3979004--3979056 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
3978994 GCAACTCATT
3979004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3979045 TA TA T- TA TA TA T
1 TA TA TA TA TA TA T
3979057 TTTTAAATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3983668 original size:43 final size:43
Alignment explanation
Indices: 3983589--3983691 Score: 107
Period size: 43 Copynumber: 2.4 Consensus size: 43
3983579 CCTCCGAATA
* * * * ** *
3983589 GATCCCAAACAGAAACATGATGGAGATTTTTTCATCCTTAGAG
1 GATCCCATACAGAAACATAAGGGAGATTATGCCATCCGTAGAG
*
3983632 GATCCCATACAGAAACATAAGGGGGATTATGCCATCCGTAGAG
1 GATCCCATACAGAAACATAAGGGAGATTATGCCATCCGTAGAG
* **
3983675 GATTCCATGTAGAAACA
1 GATCCCATACAGAAACA
3983692 GGACGAAGAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (43 bp):
GATCCCATACAGAAACATAAGGGAGATTATGCCATCCGTAGAG
Found at i:3985838 original size:21 final size:21
Alignment explanation
Indices: 3985812--3985851 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3985802 ACATGTTAAG
3985812 GAATGAA-TTCATAAAATTTGA
1 GAATGAACTT-ATAAAATTTGA
3985833 GAATGAACTTATAAAATTT
1 GAATGAACTTATAAAATTT
3985852 CAGGGATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATGAACTTATAAAATTTGA
Found at i:3991894 original size:223 final size:220
Alignment explanation
Indices: 3991470--3991956 Score: 641
Period size: 223 Copynumber: 2.2 Consensus size: 220
3991460 TATTCATATA
* *
3991470 TGAATAAAA-ATATTTTTTTATTATTTCGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGTCG
1 TGAATAAAATA-ATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGAGTCG
** * *
3991534 GGTCGGGTGAAACTTTATTTTTTTCGGGTCGGGTCTAGTTCGGGTTTAGGGTGAAAAATATCCAA
65 GGTCGGGT---ACTTTATTTTTTAAGGGTCGAGTCGAGTTCGGGTTTAGGGTGAAAAATATCCAA
* * *
3991599 CCCGAAAATATATATAATTTTACCTTATATATTTAAGAATAATTATAATAATATCCCTCTATATA
127 CCCCAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATATCCCTCTATATA
3991664 A-TTTTTTTCAATTAAGTCACTGTTTTTAT
192 ATTTTTTTTCAATTAAGTCACTG-TTTTAT
*
3991693 TGAATAAAATAATTTTTTTATTATTTCGGGTCGGGTTGGGTTTCTAATTCATATATTCGAGTCGG
1 TGAATAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGAGTCGG
* * * *
3991758 GTCGGGT-CTTT-TTTTTTAAGTGT-GATATTCGGGTTCGGGTTTAGGGTG-AAAATA-CCTGAC
66 GTCGGGTACTTTATTTTTTAAGGGTCG--AGTCGAGTTCGGGTTTAGGGTGAAAAATATCC--AA
*
3991818 CTGGCCCAAAAAATATATAATTTTA-CTTATATATTTAGGAATAATTACAATAATA-CCCTCTAT
127 C---CCCAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATATCCCTC--T
3991881 ATATAATTTTTTTTTCAATTAAGTCACTGTTTTAT
187 ATATAA-TTTTTTTTCAATTAAGTCACTGTTTTAT
3991916 TGAATAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGT
1 TGAATAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGT
3991957 CGAAACTTTA
Statistics
Matches: 236, Mismatches: 16, Indels: 24
0.86 0.06 0.09
Matches are distributed among these distances:
217 3 0.01
218 15 0.06
219 24 0.10
220 5 0.02
221 28 0.12
222 26 0.11
223 113 0.48
224 22 0.09
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (220 bp):
TGAATAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGAGTCGG
GTCGGGTACTTTATTTTTTAAGGGTCGAGTCGAGTTCGGGTTTAGGGTGAAAAATATCCAACCCC
AAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATATCCCTCTATATAATTT
TTTTTCAATTAAGTCACTGTTTTAT
Found at i:3992315 original size:16 final size:17
Alignment explanation
Indices: 3992294--3992336 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
3992284 GGAATTGGAT
*
3992294 TTCAATTCC-TGACAGA
1 TTCAATTCCTTCACAGA
3992310 TTCAATTCCTTCACAGA
1 TTCAATTCCTTCACAGA
3992327 TTCTAATTCC
1 TTC-AATTCC
3992337 CTCAAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 9 0.38
18 6 0.25
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (17 bp):
TTCAATTCCTTCACAGA
Found at i:3993534 original size:20 final size:20
Alignment explanation
Indices: 3993509--3993546 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3993499 AAATAAGCAC
3993509 AGAACCGG-TAGAGAACCGGA
1 AGAACCGGCT-GAGAACCGGA
3993529 AGAACCGGCTGAGAACCG
1 AGAACCGGCTGAGAACCG
3993547 ATAAATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.37, C:0.24, G:0.34, T:0.05
Consensus pattern (20 bp):
AGAACCGGCTGAGAACCGGA
Found at i:3993544 original size:31 final size:31
Alignment explanation
Indices: 3993509--3993574 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3993499 AAATAAGCAC
* * **
3993509 AGAACCGGTAGAGAACCGGAAGAACCGGCTG
1 AGAACCGATAAAGAACCGGAAGAACCAACTG
* *
3993540 AGAACCGATAAATAACTGGAAGAACCAACTG
1 AGAACCGATAAAGAACCGGAAGAACCAACTG
3993571 AGAA
1 AGAA
3993575 TCAGAAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.20, G:0.27, T:0.09
Consensus pattern (31 bp):
AGAACCGATAAAGAACCGGAAGAACCAACTG
Found at i:3997891 original size:11 final size:11
Alignment explanation
Indices: 3997871--3997957 Score: 93
Period size: 11 Copynumber: 7.8 Consensus size: 11
3997861 GGATTGGGTC
*
3997871 AATCGCGCTTG
1 AATCGAGCTTG
3997882 AATCGAGCTTG
1 AATCGAGCTTG
**
3997893 AATCGAGCTCAA
1 AATCGAGCT-TG
*
3997905 AATCGAGCTTA
1 AATCGAGCTTG
* *
3997916 AATCAAGCTTC
1 AATCGAGCTTG
3997927 AATCGAGCTTG
1 AATCGAGCTTG
* *
3997938 AATCAAGCTTC
1 AATCGAGCTTG
3997949 AATCGAGCT
1 AATCGAGCT
3997958 CGAGTCAAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
11 55 0.86
12 9 0.14
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (11 bp):
AATCGAGCTTG
Found at i:3997925 original size:34 final size:34
Alignment explanation
Indices: 3997871--3997935 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
3997861 GGATTGGGTC
* * * *
3997871 AATCGCGCTTGAATCGAGCTTGAATCGAGCTCAA
1 AATCGAGCTTAAATCAAGCTTCAATCGAGCTCAA
3997905 AATCGAGCTTAAATCAAGCTTCAATCGAGCT
1 AATCGAGCTTAAATCAAGCTTCAATCGAGCT
3997936 TGAATCAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (34 bp):
AATCGAGCTTAAATCAAGCTTCAATCGAGCTCAA
Found at i:3997933 original size:22 final size:22
Alignment explanation
Indices: 3997877--3997966 Score: 110
Period size: 22 Copynumber: 4.0 Consensus size: 22
3997867 GGTCAATCGC
* *
3997877 GCTTGAATCGAGCTTGAATCGA
1 GCTTCAATCGAGCTTGAATCAA
*
3997899 GC-TCAAAATCGAGCTTAAATCAA
1 GCTTC--AATCGAGCTTGAATCAA
3997922 GCTTCAATCGAGCTTGAATCAA
1 GCTTCAATCGAGCTTGAATCAA
* *
3997944 GCTTCAATCGAGCTCGAGTCAA
1 GCTTCAATCGAGCTTGAATCAA
3997966 G
1 G
3997967 TTTTATTCGA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.02
22 39 0.66
23 17 0.29
24 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (22 bp):
GCTTCAATCGAGCTTGAATCAA
Found at i:3998193 original size:16 final size:16
Alignment explanation
Indices: 3998169--3998216 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
3998159 AGTCTCCAAC
*
3998169 GTTTATGTTCGTTTAT
1 GTTTGTGTTCGTTTAT
*
3998185 GTTTGTGTTCATTTAT
1 GTTTGTGTTCGTTTAT
*
3998201 GTTCGTGTTCGTTTAT
1 GTTTGTGTTCGTTTAT
3998217 TTATTAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.10, C:0.08, G:0.21, T:0.60
Consensus pattern (16 bp):
GTTTGTGTTCGTTTAT
Found at i:4000103 original size:423 final size:428
Alignment explanation
Indices: 3999328--4000196 Score: 1444
Period size: 423 Copynumber: 2.0 Consensus size: 428
3999318 ACAATATTTT
3999328 ACTAAATAGTTATTTTAACTCTTATTCTCAATTAAGGCGTAATGAAAAAAAACATAATATTAAAA
1 ACTAAATAGTTATTTTAACTCTTATTCTCAATTAAGGCGTAATGAAAAAAAACATAATATTAAAA
* *
3999393 ATATTTCTGACGTTTTACTAAATATTCATTTTAGTTTTTTATTTTATTTTTTAGATTATTTGGTA
66 ATATTTCTAACGTGTTACTAAATATTCATTTTAG--TTTTATTTTATTTTTTAGATTATTTGGTA
3999458 TCTAACATTTTATTTCTAAGTAAATAAACTTATAACGTCTGACTAAATATTTACTTTAGTCTTTA
129 TCTAACATTTTATTTCTAAGTAAATAAACTTATAACGTCTGACTAAATATTTACTTTAGTCTTTA
*
3999523 TTCTTACTTTTTAAAATATTTTAGCCTCCAAAGTTTCATTTCATGACAAAATTCCACGTATTTTA
194 TTCTTACTTTTTAAAATATTTTAGCCTCCAAAGTTTCATTTCATGACAAAATTCCAAGTATTTTA
* * *
3999588 GAGCGTTAATTGTTTTTTGACTAATGATTTTCATCCGTTGAGGAATCTTTTTGCCCCAAAACTAA
259 GAGCGTTAATTGTTTTTTGACCAACGATTTTCATCCGTTGAGGAATCTTTCTGCCCCAAAACTAA
*
3999653 ATGTTAGAGGTCAAAATACTCTAAAAAGAAATATAAGTCAAAATGACTATTTAATCAAACATTAG
324 AAGTTAGAGGTCAAAATACTCTAAAAAGAAATATAAGTCAAAATGACTATTTAATCAAACATTAG
*
3999718 AGATATTTTTTGACATAATGACAAAAACTTGTAACGTTTA
389 AGATATTTTTTGACATAATGACAAAAACCTGTAACGTTTA
*
3999758 ACTATATAGTTATTTTAACTCTTATTCTCAATTAAGGCGTAATG-AAAAAAACATAATATTAAAA
1 ACTAAATAGTTATTTTAACTCTTATTCTCAATTAAGGCGTAATGAAAAAAAACATAATATTAAAA
*
3999822 ATATTTCTAACGTGTTACTAAATATTTATTTTAG-TTT-TTTTA-TTTTTA-ATTATTTGGTATC
66 ATATTTCTAACGTGTTACTAAATATTCATTTTAGTTTTATTTTATTTTTTAGATTATTTGGTATC
* * * *
3999883 TAACATTTTATTTTTAAGTAAAATAAATTTATAATGTCTGACTAAATATTTATTTTAGTCTTTAT
131 TAACATTTTATTTCTAAGT-AAATAAACTTATAACGTCTGACTAAATATTTACTTTAGTCTTTAT
*
3999948 TCTTAC-TTTTAGAATATTTTAGCCTCCAAAGTTTCATTTCATGACAAAATTCCAAGTATTTTAG
195 TCTTACTTTTTAAAATATTTTAGCCTCCAAAGTTTCATTTCATGACAAAATTCCAAGTATTTTAG
* * *
4000012 AGCGTTGATTGTTTTTTGACCAACGATTTTCATCCGTTGAGGAATCTTTCTGTCCCAAAATTAAA
260 AGCGTTAATTGTTTTTTGACCAACGATTTTCATCCGTTGAGGAATCTTTCTGCCCCAAAACTAAA
* * * * * *
4000077 AGTTAGAGGTCAAAATATTCTAAAAAGGAATATAAGTCGAAATGATTATTTAGTCAAACGTTAGA
325 AGTTAGAGGTCAAAATACTCTAAAAAGAAATATAAGTCAAAATGACTATTTAATCAAACATTAGA
*
4000142 GGTATTTTTTGACATAATGACAAAAACCTGTAACGTTTA
390 GATATTTTTTGACATAATGACAAAAACCTGTAACGTTTA
4000181 ACTAAATAGTTATTTT
1 ACTAAATAGTTATTTT
4000197 GATTTCTATA
Statistics
Matches: 412, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
423 256 0.62
424 54 0.13
425 5 0.01
426 3 0.01
429 51 0.12
430 43 0.10
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (428 bp):
ACTAAATAGTTATTTTAACTCTTATTCTCAATTAAGGCGTAATGAAAAAAAACATAATATTAAAA
ATATTTCTAACGTGTTACTAAATATTCATTTTAGTTTTATTTTATTTTTTAGATTATTTGGTATC
TAACATTTTATTTCTAAGTAAATAAACTTATAACGTCTGACTAAATATTTACTTTAGTCTTTATT
CTTACTTTTTAAAATATTTTAGCCTCCAAAGTTTCATTTCATGACAAAATTCCAAGTATTTTAGA
GCGTTAATTGTTTTTTGACCAACGATTTTCATCCGTTGAGGAATCTTTCTGCCCCAAAACTAAAA
GTTAGAGGTCAAAATACTCTAAAAAGAAATATAAGTCAAAATGACTATTTAATCAAACATTAGAG
ATATTTTTTGACATAATGACAAAAACCTGTAACGTTTA
Found at i:4001999 original size:70 final size:72
Alignment explanation
Indices: 4001897--4002036 Score: 221
Period size: 70 Copynumber: 2.0 Consensus size: 72
4001887 GATGCAAAAT
*
4001897 TGGATAAACAAAAAAAAATATACGAAAAATATTTAAATTATGCGAGAATTTAAAATTTTAAAAAG
1 TGGATAAACAAAAAAAAATATAC-AAAAATATTTAAATTATACGAGAATTTAAAATTTTAAAAAG
4001962 TACAACTA
65 TACAACTA
* * *
4001970 TGGATAAAC-AAAAAATATATA-AAAAATATTTAAATTATACGATAATTTGAAATTTTAAAAAGT
1 TGGATAAACAAAAAAAAATATACAAAAATATTTAAATTATACGAGAATTTAAAATTTTAAAAAGT
4002033 ACAA
66 ACAA
4002037 AATGTATCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 43 0.68
72 11 0.17
73 9 0.14
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (72 bp):
TGGATAAACAAAAAAAAATATACAAAAATATTTAAATTATACGAGAATTTAAAATTTTAAAAAGT
ACAACTA
Found at i:4010482 original size:13 final size:13
Alignment explanation
Indices: 4010439--4010485 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
4010429 AATTTGTGAA
*
4010439 TTGTGTCTCAAAG
1 TTGTTTCTCAAAG
*
4010452 TTGTCTCTCAAAG
1 TTGTTTCTCAAAG
4010465 TTGTTTCTCAAAG
1 TTGTTTCTCAAAG
4010478 TTGTTTCT
1 TTGTTTCT
4010486 AAGATTGTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (13 bp):
TTGTTTCTCAAAG
Found at i:4010678 original size:35 final size:35
Alignment explanation
Indices: 4010630--4010701 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
4010620 TAAACTAAAA
*
4010630 AATAAGTCCATTCACCAAGTGATATGACTTATTAT
1 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
*
4010665 AATAAGTCTATTCACCAAGTGACATGACTTATTAT
1 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
4010700 AA
1 AA
4010702 ATAGCATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (35 bp):
AATAAGTCCATTCACCAAGTGACATGACTTATTAT
Found at i:4013846 original size:13 final size:13
Alignment explanation
Indices: 4013828--4013878 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
4013818 CAACTTTGTG
4013828 AATTGTGTCTCAA
1 AATTGTGTCTCAA
*
4013841 AATTGTTTCTCAA
1 AATTGTGTCTCAA
* *
4013854 AGTTGTTTCT-AA
1 AATTGTGTCTCAA
* *
4013866 GATTGTGCCTCAA
1 AATTGTGTCTCAA
4013879 CCATTATAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (13 bp):
AATTGTGTCTCAA
Found at i:4017692 original size:69 final size:68
Alignment explanation
Indices: 4017609--4017745 Score: 265
Period size: 69 Copynumber: 2.0 Consensus size: 68
4017599 AATCTCAATG
4017609 CTCAAACTCAACACCTCGCCAGGATTCACTCAAATCACTCAATGTGTTTTGAGTATAGAAACGCT
1 CTCAAACTCAACACCTCGCCAGGATTCACTCAAATCACTCAATGTGTTTTGAGTATAGAAACGCT
4017674 CAA
66 CAA
4017677 CTCATAACTCAACACCTCGCCAGGATTCACTCAAATCACTCAATGTGTTTTGAGTATAGAAACGC
1 CTCA-AACTCAACACCTCGCCAGGATTCACTCAAATCACTCAATGTGTTTTGAGTATAGAAACGC
4017742 TCAA
65 TCAA
4017746 TGTCAGAACC
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 4 0.06
69 64 0.94
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (68 bp):
CTCAAACTCAACACCTCGCCAGGATTCACTCAAATCACTCAATGTGTTTTGAGTATAGAAACGCT
CAA
Found at i:4018029 original size:21 final size:20
Alignment explanation
Indices: 4018005--4018044 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4017995 AATGCATTGA
4018005 TTTTTTCCTTTTCACATTTTG
1 TTTTTTCCTTTTC-CATTTTG
**
4018026 TTTTTTTGTTTTCCATTTT
1 TTTTTTCCTTTTCCATTTT
4018045 TTCCATGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTCCTTTTCCATTTTG
Found at i:4020691 original size:30 final size:31
Alignment explanation
Indices: 4020657--4020719 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
4020647 AGGGTAAATT
* *
4020657 AAAATT-TTAAAAGTACATAGAGT-AAATAGG
1 AAAATTATGAAAA-TACAGAGAGTGAAATAGG
4020687 AAAATTATGAAAATACAGAGAGTGAAATAGG
1 AAAATTATGAAAATACAGAGAGTGAAATAGG
4020718 AA
1 AA
4020720 GAGTAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (31 bp):
AAAATTATGAAAATACAGAGAGTGAAATAGG
Found at i:4021057 original size:35 final size:36
Alignment explanation
Indices: 4020998--4021074 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 36
4020988 AACACAATCA
* *
4020998 TCAATTACATTCTAATCCCTAAATTCC-AAAATACT
1 TCAATTACATTATAAACCCTAAATTCCAAAAATACT
4021033 TCAATTACATTATAAA-CCTCAAATTCCAAAAATACT
1 TCAATTACATTATAAACCCT-AAATTCCAAAAATACT
*
4021069 TTAATT
1 TCAATT
4021075 GCATGCCCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 3 0.08
35 21 0.57
36 13 0.35
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (36 bp):
TCAATTACATTATAAACCCTAAATTCCAAAAATACT
Found at i:4021799 original size:148 final size:143
Alignment explanation
Indices: 4021529--4021810 Score: 440
Period size: 148 Copynumber: 1.9 Consensus size: 143
4021519 TTTAAACTAG
* * **
4021529 AATCAAATATCATTATAGTATTATAAATATTTATAATTAAATTTAAATAGAAACTTGAAAATTCA
1 AATCAAATATCATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTAAAAAATTCA
*
4021594 ATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAAC
66 ATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAATTTCGAGTCAACTATTTTATAAAC
4021659 TGAACTGAATTAT
131 TGAACTGAATTAT
*
4021672 AATCAAATAAT-ATTATAATATGATAAATATTTATAATTAAATTTAAATATAAACTCAAAAATTC
1 AATCAAAT-ATCATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACT--AAAA---
*
4021736 AATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAATTTCGAGTCAAGTATTTT
60 AATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAATTTCGAGTCAACTATTTT
4021801 ATAAACTGAA
125 ATAAACTGAA
4021811 TTGAGTATTT
Statistics
Matches: 126, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
143 49 0.39
144 2 0.02
145 2 0.02
148 73 0.58
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (143 bp):
AATCAAATATCATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTAAAAAATTCA
ATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAATTTCGAGTCAACTATTTTATAAAC
TGAACTGAATTAT
Found at i:4022027 original size:35 final size:35
Alignment explanation
Indices: 4021988--4022065 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
4021978 GGGATTGGGC
* *
4021988 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTAAAATATTTTGGAATTTGAGGTTTAGA
* * *
4022023 ATGTAATTAAAATATTTTGGATTTTGGGGTTTATA
1 ATGTAATTAAAATATTTTGGAATTTGAGGTTTAGA
*
4022058 ATATAATT
1 ATGTAATT
4022066 TATGATTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (35 bp):
ATGTAATTAAAATATTTTGGAATTTGAGGTTTAGA
Found at i:4027220 original size:70 final size:70
Alignment explanation
Indices: 4027107--4027249 Score: 241
Period size: 70 Copynumber: 2.0 Consensus size: 70
4027097 AGTTCTCAGA
* *
4027107 CAACATCTATAATTCAATTTTGCTTTTTGAGGTCTAAAATCTAAATGTCAACTATTCAACATACC
1 CAACATCTATAATTCAATTTTGCTTTTTGAAGTCTAAAATCTAAACGTCAACTATTCAACATACC
*
4027172 ACATG
66 ACAGG
* *
4027177 CAACATCTATAATTCAATTTTTCTTTTTGAAGTCTAAAATCTAAACGTCAACTATTCAACATACT
1 CAACATCTATAATTCAATTTTGCTTTTTGAAGTCTAAAATCTAAACGTCAACTATTCAACATACC
4027242 ACAGG
66 ACAGG
4027247 CAA
1 CAA
4027250 GAAGGAAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (70 bp):
CAACATCTATAATTCAATTTTGCTTTTTGAAGTCTAAAATCTAAACGTCAACTATTCAACATACC
ACAGG
Found at i:4028143 original size:20 final size:20
Alignment explanation
Indices: 4028118--4028155 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4028108 TTTTTGCCTA
* *
4028118 AAAAGGTTGAAAATAAAAGG
1 AAAAGGTAGAAAAGAAAAGG
4028138 AAAAGGTAGAAAAGAAAA
1 AAAAGGTAGAAAAGAAAA
4028156 ATAATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.11
Consensus pattern (20 bp):
AAAAGGTAGAAAAGAAAAGG
Found at i:4034020 original size:35 final size:35
Alignment explanation
Indices: 4033981--4034060 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
4033971 AACACAATCA
**
4033981 TCAATTACATTCTAAACC-CTAAAATCCAAAATGTT
1 TCAATTACATTCTAAACCTC-AAAATCCAAAATACT
*
4034016 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCTCAAAATCCAAAATACT
4034051 TCAATTACAT
1 TCAATTACAT
4034061 ACCTAATCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 40 0.98
36 1 0.02
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAAATCCAAAATACT
Found at i:4034500 original size:143 final size:145
Alignment explanation
Indices: 4034237--4034515 Score: 402
Period size: 143 Copynumber: 1.9 Consensus size: 145
4034227 TCAATTCAGT
* * *
4034237 TTATAAAATATTTGACTCGAATTTTTTTCAATTTGAGTTTATAAAATTTAAATCAATTCGAATTG
1 TTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAA-T-G-ATCG
** * * *
4034302 AATTGAATTTTTTAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAAT-ATTATTT
63 AATTGAATTTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATGA-TATTT
4034366 GATTCTAATTCAGTTCAAC
127 GATTCTAATTCAGTTCAAC
* * *
4034385 TTATAAAATAGTTGGCTTGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAA-G-TCGAAT
1 TTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAATGATCGAAT
4034448 TGAATTTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATGATATTTGATT
66 TGAATTTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATGATATTTGATT
4034513 CTA
131 CTA
4034516 GTTTAAATAG
Statistics
Matches: 119, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
143 66 0.55
144 1 0.01
145 1 0.01
148 51 0.43
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (145 bp):
TTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAATGATCGAAT
TGAATTTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATGATATTTGATT
CTAATTCAGTTCAAC
Found at i:4035087 original size:35 final size:36
Alignment explanation
Indices: 4035020--4035098 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 36
4035010 GGGTTTGGGC
* *
4035020 ATGTAATTGAAGTGTTTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTGATTTTAGAATTTGAGGTTTAGA
*
4035056 ATGTAATTGAAGT-ATTTTAGAATTTGGGGTTTAGA
1 ATGTAATTGAAGTGATTTTAGAATTTGAGGTTTAGA
4035091 ATGTAATT
1 ATGTAATT
4035099 AATGACTGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 27 0.68
36 13 0.32
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.44
Consensus pattern (36 bp):
ATGTAATTGAAGTGATTTTAGAATTTGAGGTTTAGA
Found at i:4037463 original size:8 final size:8
Alignment explanation
Indices: 4037452--4037478 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4037442 TCTCTCCCTT
4037452 CTCTCTCC
1 CTCTCTCC
4037460 CTCTCTCC
1 CTCTCTCC
4037468 CTCTCTCC
1 CTCTCTCC
4037476 CTC
1 CTC
4037479 ATCCGGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (8 bp):
CTCTCTCC
Found at i:4038410 original size:39 final size:37
Alignment explanation
Indices: 4038338--4038714 Score: 305
Period size: 38 Copynumber: 10.1 Consensus size: 37
4038328 TTTAAAATAT
* * *
4038338 TATA-TATTTTCAAAAAGGTTTTCCAAAATTATATGTTA
1 TATATTATTTTC-AAAATGTTTT-CAAAACTATATATTA
*
4038376 TATATTTATTTTCAAAATGTTTTAAAAAACTATATATTA
1 TATA-TTATTTTCAAAATGTTTT-CAAAACTATATATTA
* *
4038415 TATATGTGTTTTCAAAATGTTTTCAAAACCATATATTA
1 TATAT-TATTTTCAAAATGTTTTCAAAACTATATATTA
*
4038453 TATA-TATTTTCAAAATGTTTGCAAAAC-------TA
1 TATATTATTTTCAAAATGTTTTCAAAACTATATATTA
* *
4038482 TATA-TATTTTCAAAAATATTTTTAAAACTATATATTA
1 TATATTATTTTC-AAAATGTTTTCAAAACTATATATTA
* *
4038519 TATA-CATTTTCAACAATATTTTCAAAAACTATATATTATA
1 TATATTATTTTCAA-AATGTTTTC-AAAACTATATA-T-TA
* * *
4038559 TATATATATTTTCAAATTTTTTTCAAAAATTATATATTA
1 TATAT-TATTTTCAAAATGTTTTC-AAAACTATATATTA
4038598 TATA-TATTTTCAAAATGTTTTCAAAAACTATATATTA
1 TATATTATTTTCAAAATGTTTTC-AAAACTATATATTA
* *** *
4038635 TATATATGTTTTCAAAAAAAATTT-AAAACTATATAATA
1 TATAT-TATTTTC-AAAATGTTTTCAAAACTATATATTA
* * *
4038673 TATA-TATATTCGAAAACCGTTTTCAAAACTATACATTA
1 TATATTATTTTC-AAAA-TGTTTTCAAAACTATATATTA
4038711 TATA
1 TATA
4038715 AAAAAAAACT
Statistics
Matches: 282, Mismatches: 35, Indels: 44
0.78 0.10 0.12
Matches are distributed among these distances:
29 13 0.05
30 13 0.05
36 32 0.11
37 57 0.20
38 66 0.23
39 54 0.19
40 21 0.07
41 18 0.06
42 8 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
TATATTATTTTCAAAATGTTTTCAAAACTATATATTA
Found at i:4038493 original size:29 final size:30
Alignment explanation
Indices: 4038451--4038516 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
4038441 AACCATATAT
*
4038451 TATATATATTTTC-AAAATGTTTGCAAAAC
1 TATATATATTTTCAAAAATATTTGCAAAAC
**
4038480 TATATATATTTTCAAAAATATTTTTAAAAC
1 TATATATATTTTCAAAAATATTTGCAAAAC
4038510 TATATAT
1 TATATAT
4038517 TATATACATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (30 bp):
TATATATATTTTCAAAAATATTTGCAAAAC
Found at i:4038511 original size:104 final size:104
Alignment explanation
Indices: 4038376--4038563 Score: 265
Period size: 104 Copynumber: 1.8 Consensus size: 104
4038366 TTATATGTTA
* * ** *
4038376 TATATTTATTTTCAAAATGTTTTAAAAAACTATATATTATATATGTGTTTTCAA-AATGTTTTC-
1 TATATATATTTTCAAAATATTTTAAAAAACTATATATTATATA--CATTTTCAACAATATTTTCA
4038439 AAAACCATATATTATATATATTTTCAAAATGTTTGCAAAAC
64 AAAACCATATATTATATATATTTTCAAAATGTTTGCAAAAC
*
4038480 TATATATATTTTCAAAAATATTTT-TAAAACTATATATTATATACATTTTCAACAATATTTTCAA
1 TATATATATTTTC-AAAATATTTTAAAAAACTATATATTATATACATTTTCAACAATATTTTCAA
*
4038544 AAACTATATATTATATATAT
65 AAACCATATATTATATATAT
4038564 ATATTTTCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
102 7 0.09
103 8 0.11
104 50 0.68
105 9 0.12
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (104 bp):
TATATATATTTTCAAAATATTTTAAAAAACTATATATTATATACATTTTCAACAATATTTTCAAA
AACCATATATTATATATATTTTCAAAATGTTTGCAAAAC
Found at i:4038701 original size:38 final size:37
Alignment explanation
Indices: 4038480--4038714 Score: 163
Period size: 37 Copynumber: 6.2 Consensus size: 37
4038470 TTTGCAAAAC
* * * *
4038480 TATATATATTTTCAAAAATATTTT-TAAAACTATATAT
1 TATATATATATTC-AAAATGTTTTCAAAAACTATATAA
* * *
4038517 TATATACATTTTCAACAATATTTTCAAAAACTATATATTA
1 TATATATATATTCAA-AATGTTTTCAAAAACTATATA--A
* * * *
4038557 TATATATATATTTTCAAATTTTTTTCAAAAATTATATAT
1 TATATATATA--TTCAAAATGTTTTCAAAAACTATATAA
*
4038596 TATATATATTTTCAAAATGTTTTCAAAAACTATATATTA
1 TATATATATATTCAAAATGTTTTCAAAAACTATATA--A
* * ***
4038635 TATATATGTTTTCAAAAAAAATTT--AAAACTATATAA
1 TATATATATATTC-AAAATGTTTTCAAAAACTATATAA
* * *
4038671 TATATATATATTCGAAAACCGTTTTC-AAAACTATACAT
1 TATATATATATTC-AAAA-TGTTTTCAAAAACTATATAA
4038709 TATATA
1 TATATA
4038715 AAAAAAAACT
Statistics
Matches: 161, Mismatches: 26, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
36 18 0.11
37 46 0.29
38 38 0.24
39 21 0.13
40 15 0.09
41 18 0.11
42 5 0.03
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (37 bp):
TATATATATATTCAAAATGTTTTCAAAAACTATATAA
Found at i:4046962 original size:39 final size:40
Alignment explanation
Indices: 4046894--4046983 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 40
4046884 AAATATTATA
* * *
4046894 TATTTTCAAAATGATTTTCCAAAATTATATGTTATATATT
1 TATTTTCAAAATGATTTTCAAAAACTATATATTATATATT
* *
4046934 TATTTTTAAAAT-ATTTTCAAAAACTATATATTATATATG
1 TATTTTCAAAATGATTTTCAAAAACTATATATTATATATT
*
4046973 TGTTTTCAAAA
1 TATTTTCAAAA
4046984 CCATATATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 32 0.74
40 11 0.26
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (40 bp):
TATTTTCAAAATGATTTTCAAAAACTATATATTATATATT
Found at i:4046995 original size:25 final size:27
Alignment explanation
Indices: 4046944--4047008 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 27
4046934 TATTTTTAAA
*
4046944 ATATTTTCAAAAACTATATATTATATAT
1 ATATTTTC-AAAACCATATATTATATAT
* *
4046972 GTGTTTTCAAAACCATATA-T-TATAT
1 ATATTTTCAAAACCATATATTATATAT
4046997 ATATTTTCAAAA
1 ATATTTTCAAAA
4047009 TGTTTTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 15 0.47
26 1 0.03
27 10 0.31
28 6 0.19
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (27 bp):
ATATTTTCAAAACCATATATTATATAT
Found at i:4046998 original size:68 final size:65
Alignment explanation
Indices: 4046928--4047118 Score: 224
Period size: 68 Copynumber: 2.9 Consensus size: 65
4046918 TTATATGTTA
* * * *
4046928 TATATTTATTTTTAAAATATTTTCAAAAACTATATAT-TATATATGTGTTTTCAAAACCATATAT
1 TATATATATTTTAAAAATATTTTCAAAAACTATATATATATATATATATTTTCAAAACCATATAT
* * * * *
4046992 TATATATATTTTCAAAATGTTTTC-AAAACTATATATATATTTTCAAAAATATTTTCAAAACTAT
1 TATATATATTTTAAAAATATTTTCAAAAACTATATATATA---T-ATATATATTTTCAAAACCAT
4047056 ATAT
62 ATAT
*
4047060 TATATACATTTTCAAAAATATTTTCAAAAACTATATTATATATATATATATTTTCAAAA
1 TATATATATTTT-AAAAATATTTTCAAAAACTATA-TATATATATATATATTTTCAAAA
4047119 TGTTTTCAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
63 12 0.11
64 23 0.22
67 15 0.14
68 31 0.29
69 10 0.09
70 9 0.08
71 6 0.06
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (65 bp):
TATATATATTTTAAAAATATTTTCAAAAACTATATATATATATATATATTTTCAAAACCATATAT
Found at i:4047001 original size:36 final size:35
Alignment explanation
Indices: 4046973--4047166 Score: 162
Period size: 41 Copynumber: 5.3 Consensus size: 35
4046963 ATTATATATG
*
4046973 TGTTTTCAAAACCATATATTATATATATTTTCAAAA
1 TGTTTTCAAAACCATATA-TATATATATTATCAAAA
4047009 TGTTTTCAAAA-C-TATATATATAT-TT-TCAAAAA
1 TGTTTTCAAAACCATATATATATATATTATC-AAAA
* * * *
4047041 TATTTTCAAAACTATATATTATATACATTTTCAAAAA
1 TGTTTTCAAAACCATATA-TATATATATTATC-AAAA
* *
4047078 TATTTTCAAAAACTATATTATATATATATATATTTTCAAAA
1 TGTTTTC-AAAACCATA-TATATATATAT-TA---TCAAAA
* * *
4047119 TGTTTTCAAAAACTATATATTATATATATTTTTAAAA
1 TGTTTTC-AAAACCATATA-TATATATATTATCAAAA
4047156 TGTTTTCAAAA
1 TGTTTTCAAAA
4047167 TGTTTTCAAA
Statistics
Matches: 137, Mismatches: 8, Indels: 26
0.80 0.05 0.15
Matches are distributed among these distances:
31 2 0.01
32 16 0.12
33 7 0.05
34 8 0.06
35 7 0.05
36 17 0.12
37 26 0.19
38 17 0.12
39 3 0.02
40 3 0.02
41 29 0.21
42 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (35 bp):
TGTTTTCAAAACCATATATATATATATTATCAAAA
Found at i:4047071 original size:37 final size:37
Alignment explanation
Indices: 4046975--4047305 Score: 284
Period size: 38 Copynumber: 8.6 Consensus size: 37
4046965 TATATATGTG
* *
4046975 TTTTCAAAACCATATATTATATATATTTTC-AAAATG
1 TTTTCAAAACTATATATTATATATATTTTCAAAAATA
4047011 TTTTCAAAAC----TA-TATATATATTTTCAAAAATA
1 TTTTCAAAACTATATATTATATATATTTTCAAAAATA
*
4047043 TTTTCAAAACTATATATTATATACATTTTCAAAAATA
1 TTTTCAAAACTATATATTATATATATTTTCAAAAATA
*
4047080 TTTTCAAAAACTATATTATATATATATATATTTTC-AAAATG
1 TTTTC-AAAAC--TA-TATAT-TATATATATTTTCAAAAATA
* *
4047121 TTTTCAAAAACTATATATTATATATATTTTTAAAATGTTTTCAAAATG
1 TTTTC-AAAACTATATATTATATATA-TTTT--CA-------AAAATA
* *
4047169 TTTTCAAAAATTATATATTATATATATTTTTAAAAATA
1 TTTTC-AAAACTATATATTATATATATTTTCAAAAATA
*
4047207 TTTTCAAAAACTAAATATTATATATATGTTTTCAAAAA-A
1 TTTTC-AAAACTATATATTATATATA--TTTTCAAAAATA
* * ***
4047246 -TTTCAAAGCTATATAATATATATATTTTCGAAAACCG
1 TTTTCAAAACTATATATTATATATATTTTC-AAAAATA
4047283 TTTTCAAAACTATATATTATATA
1 TTTTCAAAACTATATATTATATA
4047306 AAAAACTTTG
Statistics
Matches: 250, Mismatches: 18, Indels: 52
0.78 0.06 0.16
Matches are distributed among these distances:
31 13 0.05
32 17 0.07
35 5 0.02
36 16 0.06
37 49 0.20
38 67 0.27
39 3 0.01
40 11 0.04
41 21 0.08
42 12 0.05
45 1 0.00
47 4 0.02
48 31 0.12
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (37 bp):
TTTTCAAAACTATATATTATATATATTTTCAAAAATA
Found at i:4047161 original size:11 final size:11
Alignment explanation
Indices: 4047147--4047177 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4047137 ATTATATATA
*
4047147 TTTTTAAAATG
1 TTTTCAAAATG
4047158 TTTTCAAAATG
1 TTTTCAAAATG
4047169 TTTTCAAAA
1 TTTTCAAAA
4047178 ATTATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (11 bp):
TTTTCAAAATG
Found at i:4047166 original size:48 final size:49
Alignment explanation
Indices: 4047107--4047215 Score: 193
Period size: 48 Copynumber: 2.2 Consensus size: 49
4047097 ATATATATAT
4047107 ATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTT-AAA
1 ATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTAAAA
* *
4047155 ATGTTTTCAAAATGTTTTCAAAAATTATATATTATATATATTTTTAAAA
1 ATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTAAAA
4047204 ATATTTTCAAAA
1 ATATTTTCAAAA
4047216 ACTAAATATT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
48 43 0.75
49 14 0.25
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (49 bp):
ATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTAAAA
Found at i:4048542 original size:44 final size:43
Alignment explanation
Indices: 4048484--4048571 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 43
4048474 TTATAATTTA
* * *
4048484 TTTTTTTAATATTTG-TA-TAAGTGTTCAATTTTTTGTCAATATT
1 TTTTTTTAACATTTGTTATTAAGGGCTCAATTTTTT-T-AATATT
4048527 TTTTTTCTAACATTTGTTATTAAGGGCTCAATTTTTTTAATATT
1 TTTTTT-TAACATTTGTTATTAAGGGCTCAATTTTTTTAATATT
4048571 T
1 T
4048572 ATTATTAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
43 6 0.15
44 15 0.38
45 3 0.08
46 15 0.38
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (43 bp):
TTTTTTTAACATTTGTTATTAAGGGCTCAATTTTTTTAATATT
Found at i:4048562 original size:30 final size:30
Alignment explanation
Indices: 4048528--4048607 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
4048518 GTCAATATTT
*
4048528 TTTTTCTAACATTTGTTATTAAGGG-CTCAA
1 TTTTTCTAATATTTGTTATTAAGGGCCT-AA
* *
4048558 TTTTTTTAATATTTATTATTAAGGGCCTAA
1 TTTTTCTAATATTTGTTATTAAGGGCCTAA
4048588 TTTTTC-AATATTTGTTATTA
1 TTTTTCTAATATTTGTTATTA
4048608 GAGACATGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 13 0.30
30 29 0.66
31 2 0.05
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.54
Consensus pattern (30 bp):
TTTTTCTAATATTTGTTATTAAGGGCCTAA
Found at i:4048605 original size:29 final size:30
Alignment explanation
Indices: 4048527--4048607 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
4048517 TGTCAATATT
*
4048527 TTTTTTCTAACATTTGTTATTAAGGGCTCAA
1 TTTTTTC-AATATTTGTTATTAAGGGCTCAA
* *
4048558 TTTTTTTAATATTTATTATTAAGGGC-CTAA
1 TTTTTTCAATATTTGTTATTAAGGGCTC-AA
4048588 -TTTTTCAATATTTGTTATTA
1 TTTTTTCAATATTTGTTATTA
4048608 GAGACATGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 19 0.43
30 19 0.43
31 6 0.14
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.54
Consensus pattern (30 bp):
TTTTTTCAATATTTGTTATTAAGGGCTCAA
Found at i:4048685 original size:30 final size:29
Alignment explanation
Indices: 4048650--4048721 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
4048640 AATATTTATT
4048650 TTTTATTATGAGTACAATTTTTTCAATACA
1 TTTTATTATGAGTACAATTTTTTCAATA-A
* * *
4048680 TTTTATTA-GAGGTCCATTTTTTTCAATAT
1 TTTTATTATGA-GTACAATTTTTTCAATAA
4048709 TTGTTATTATGAG
1 TT-TTATTATGAG
4048722 CATACTCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 4 0.11
30 30 0.83
31 2 0.06
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (29 bp):
TTTTATTATGAGTACAATTTTTTCAATAA
Found at i:4051296 original size:15 final size:15
Alignment explanation
Indices: 4051276--4051309 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
4051266 GTGTTTTGAA
4051276 TCTTCGAGACTTTGT
1 TCTTCGAGACTTTGT
4051291 TCTTCGAGACTTTGT
1 TCTTCGAGACTTTGT
4051306 TCTT
1 TCTT
4051310 TTAATAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.50
Consensus pattern (15 bp):
TCTTCGAGACTTTGT
Found at i:4053851 original size:60 final size:60
Alignment explanation
Indices: 4053729--4053856 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
4053719 ATAGTCGGAT
* * * * * * *
4053729 GATCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACTCCCTATAGTTGGGG
1 GATCATTTTATAACTTTTAATAGTCGAGCGACTCAACAAAACAACTCCATATAATCGAGG
* *
4053789 GATCATTTTATAACTTTTAATAGTATGA-CGACTCAACAAAACAA-TATCATATAATCGAGG
1 GATCATTTTATAACTTTTAATAGT-CGAGCGACTCAACAAAACAACT-CCATATAATCGAGG
4053849 GATCATTT
1 GATCATTT
4053857 GTGTACTCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 1 0.02
60 54 0.95
61 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTCGAGCGACTCAACAAAACAACTCCATATAATCGAGG
Found at i:4055894 original size:42 final size:41
Alignment explanation
Indices: 4055837--4055956 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 41
4055827 TTTTGAAGTT
4055837 AAAATAAATAATTTAG-ATAGTTATGGTGAAATAATTTTAAAA
1 AAAAT-AATAATTTAGAAT-GTTATGGTGAAATAATTTTAAAA
4055879 AATAATAATAATTTAGAATGTTATGGTGAAATAA-TTTAAAA
1 AA-AATAATAATTTAGAATGTTATGGTGAAATAATTTTAAAA
* ** *
4055920 AAATTAGGAATTTAGAATGTTAAGGGTGAAATAATTT
1 AAAATAATAATTTAGAATGTT-ATGGTGAAATAATTT
4055957 GGGAATTATG
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
40 16 0.23
41 20 0.29
42 29 0.41
43 5 0.07
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (41 bp):
AAAATAATAATTTAGAATGTTATGGTGAAATAATTTTAAAA
Found at i:4055948 original size:41 final size:41
Alignment explanation
Indices: 4055846--4055956 Score: 136
Period size: 41 Copynumber: 2.7 Consensus size: 41
4055836 TAAAATAAAT
* *
4055846 AATTTAG-ATAGTTATGGTGAAATAATTTTAAAAAATAATAAT
1 AATTTAGAAT-GTTAGGGTGAAATAA-TTTAAAAAATAATAAG
* * *
4055888 AATTTAGAATGTTATGGTGAAATAATTTAAAAAA-ATTAGG
1 AATTTAGAATGTTAGGGTGAAATAATTTAAAAAATAATAAG
4055928 AATTTAGAATGTTAAGGGTGAAATAATTT
1 AATTTAGAATGTT-AGGGTGAAATAATTT
4055957 GGGAATTATG
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
40 16 0.25
41 23 0.37
42 22 0.35
43 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (41 bp):
AATTTAGAATGTTAGGGTGAAATAATTTAAAAAATAATAAG
Found at i:4057216 original size:60 final size:60
Alignment explanation
Indices: 4057105--4057247 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
4057095 ATTTGAGATA
* * *
4057105 AAATTGAAATGTTCAAAAAGTTTGAGGATCAAACTAGAGTGAAGATTATAGTTTGGGGATG
1 AAATTGAAATGTT-AAAAAGTTTGAGGATCAAACTAGACTGAAGATCATAGTTTAGGGATG
* * **
4057166 GAATTCAAATGTTAAAAAGTTTGAGGA-CTAATTTAGACTGATAG-TCATAGTTTAGGGATG
1 AAATTGAAATGTTAAAAAGTTTGAGGATC-AAACTAGACTGA-AGATCATAGTTTAGGGATG
*
4057226 AAATTGGAATGCTT-AAAAGTTT
1 AAATTGAAATG-TTAAAAAGTTT
4057248 AGAGAACATT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
59 1 0.01
60 53 0.77
61 15 0.22
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (60 bp):
AAATTGAAATGTTAAAAAGTTTGAGGATCAAACTAGACTGAAGATCATAGTTTAGGGATG
Found at i:4058346 original size:2 final size:2
Alignment explanation
Indices: 4058341--4058382 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4058331 ATACTATTCA
4058341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4058383 GCGGGTTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4063286 original size:25 final size:26
Alignment explanation
Indices: 4063250--4063298 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
4063240 TAGTTTGAGG
4063250 TTTTTTTAAAATAT-T-TATTTATGA
1 TTTTTTTAAAATATCTATATTTATGA
*
4063274 TTTTATTTCAAATATCTATATTTAT
1 TTTT-TTTAAAATATCTATATTTAT
4063299 TATGTGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 1 0.05
27 7 0.33
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTTTTAAAATATCTATATTTATGA
Found at i:4068056 original size:28 final size:26
Alignment explanation
Indices: 4068025--4068083 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
4068015 TGAAGTGAGA
*
4068025 AATGACCTAAAATACCCCTAAGCCTCGG
1 AATGA-CT-AAATACCCCTAAGCATCGG
* * *
4068053 AATGACTGAATACCCTTAAGCATTGG
1 AATGACTAAATACCCCTAAGCATCGG
4068079 AATGA
1 AATGA
4068084 ATAGATCTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 20 0.74
27 2 0.07
28 5 0.19
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (26 bp):
AATGACTAAATACCCCTAAGCATCGG
Found at i:4069245 original size:96 final size:96
Alignment explanation
Indices: 4069092--4069323 Score: 313
Period size: 96 Copynumber: 2.4 Consensus size: 96
4069082 CTTGAGTAGG
*
4069092 CTCTGAGGCCCTAAGACATTTCCTTGGGTAGGCTCTAAGGCCCCAAGGTATTTCCTTGGGCAGAC
1 CTCTGAGGCCCCAAGACATTTCCTTGGGTAGGCTCTAAGGCCCCAAGGTATTTCCTTGGGCAGAC
*
4069157 TCTGAGGCCCCAAGGCATTTCC-TTGGGCAGA
66 TCTGAGGCCCCAAGGCA-CTCCATTGGGCAGA
* *
4069188 CTCTGAGGCCCCAAGGCATTTCCTTGGGTAGGCTCTAAGGCCCCAAGGTATTTCCTTGGGTAGAC
1 CTCTGAGGCCCCAAGACATTTCCTTGGGTAGGCTCTAAGGCCCCAAGGTATTTCCTTGGGCAGAC
* * * * *
4069253 TCTTAGGCCCTAAGGTACTCCATTGGGTAGG
66 TCTGAGGCCCCAAGGCACTCCATTGGGCAGA
* * * * *
4069284 CTCTTAGGCCCCAAGATATTCCCTTAGGTTGGCTCCTAAG
1 CTCTGAGGCCCCAAGACATTTCCTTGGGTAGGCT-CTAAG
4069324 CACAATGGGT
Statistics
Matches: 119, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
95 3 0.03
96 111 0.93
97 5 0.04
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (96 bp):
CTCTGAGGCCCCAAGACATTTCCTTGGGTAGGCTCTAAGGCCCCAAGGTATTTCCTTGGGCAGAC
TCTGAGGCCCCAAGGCACTCCATTGGGCAGA
Found at i:4069318 original size:32 final size:32
Alignment explanation
Indices: 4069081--4069318 Score: 271
Period size: 32 Copynumber: 7.4 Consensus size: 32
4069071 ACTAAGGTGA
* * **
4069081 CCTTGAGTAGGCTCTGAGGCCCTAAGACATTT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGTATTT
*
4069113 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGTATTT
* * *
4069145 CCTTGGGCAGACTCTGAGGCCCCAAGGCATTT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGTATTT
* * *
4069177 CCTTGGGCAGACTCTGAGGCCCCAAGGCATTT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGTATTT
*
4069209 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGTATTT
* * * *
4069241 CCTTGGGTAGACTCTTAGGCCCTAAGGTA-CT
1 CCTTGGGTAGGCTCTGAGGCCCCAAGGTATTT
* * *
4069272 CCATTGGGTAGGCTCTTAGGCCCCAAGATATTC
1 CC-TTGGGTAGGCTCTGAGGCCCCAAGGTATTT
* *
4069305 CCTTAGGTTGGCTC
1 CCTTGGGTAGGCTC
4069319 CTAAGCACAA
Statistics
Matches: 180, Mismatches: 24, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
31 3 0.02
32 175 0.97
33 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTGAGGCCCCAAGGTATTT
Found at i:4070515 original size:2 final size:2
Alignment explanation
Indices: 4070508--4070540 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4070498 TATTGTACAT
*
4070508 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4070541 CATCCCTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4070722 original size:29 final size:29
Alignment explanation
Indices: 4070680--4070798 Score: 202
Period size: 29 Copynumber: 4.1 Consensus size: 29
4070670 AGTCCATTAT
* *
4070680 TCTTTTACTCAACAGTGTTTAACCTTTCA
1 TCTTTTACTCAACAATATTTAACCTTTCA
*
4070709 TCTTTTACTCAACAGTATTTAACCTTTCA
1 TCTTTTACTCAACAATATTTAACCTTTCA
4070738 TCTTTTACTCAACAATATTTAACCTTTCA
1 TCTTTTACTCAACAATATTTAACCTTTCA
*
4070767 TCTTTTACTCAACAATATTTAACCATTCA
1 TCTTTTACTCAACAATATTTAACCTTTCA
4070796 TCT
1 TCT
4070799 AACTGGCATA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 87 1.00
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.45
Consensus pattern (29 bp):
TCTTTTACTCAACAATATTTAACCTTTCA
Found at i:4071153 original size:45 final size:43
Alignment explanation
Indices: 4071098--4071548 Score: 209
Period size: 45 Copynumber: 11.2 Consensus size: 43
4071088 TTTTAGGTTG
4071098 ATAATGCACCCATATGCATTTCAACGTTGGCATCTTGTCATGCCA
1 ATAATGCACCCATATGCATTTCAAC-TTGGCATCTT-TCATGCCA
**
4071143 ATAATGCACCCATATGCA-TT--A-TT---AT-TTT-ATGCTG
1 ATAATGCACCCATATGCATTTCAACTTGGCATCTTTCATGCCA
* *
4071177 ATAATGCACGCATATGCATTTCAGCTATGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACT-TGGCAT-CTTTCATGCCA
* **
4071222 ATAATGCACACATATGCA-TT--A-TT--C-T-TTT-ATGCTG
1 ATAATGCACCCATATGCATTTCAACTTGGCATCTTTCATGCCA
* * * *
4071256 ATAATGCACCCGTACGCATTTCAGCTATGACATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACT-TGGCAT-CTTTCATGCCA
**
4071301 ATAATGCACCCATATGCA-TT--A-TT--C-T-TTT-ATGCTG
1 ATAATGCACCCATATGCATTTCAACTTGGCATCTTTCATGCCA
* * * * *
4071335 ATAATGCACCCATATACATTTTAGCTATGACATCCTTTCATGCAA
1 ATAATGCACCCATATGCATTTCAACT-TGGCAT-CTTTCATGCCA
**
4071380 ATAATGCACCCATATGCA-TT--A-TT--C-T-TTT-ATGCTG
1 ATAATGCACCCATATGCATTTCAACTTGGCATCTTTCATGCCA
* **
4071414 ATAATGCACACCCATATGCATTTCAGCTATAACATCATTTCATGCCA
1 ATAATG--CACCCATATGCATTTCAACT-TGGCATC-TTTCATGCCA
**
4071461 ATAATGCACCCATATGCA-TT--A-TT--C-T-TTT-ATGCTG
1 ATAATGCACCCATATGCATTTCAACTTGGCATCTTTCATGCCA
* * *
4071495 ATAATGCATCCATATGCATTTCAGCTATGACATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACT-TGGCAT-CTTTCATGCCA
4071540 ATAATGCAC
1 ATAATGCAC
4071549 ACACAGTGCC
Statistics
Matches: 309, Mismatches: 40, Indels: 114
0.67 0.09 0.25
Matches are distributed among these distances:
34 92 0.30
35 21 0.07
36 14 0.05
37 8 0.03
38 8 0.03
39 4 0.01
40 7 0.02
41 8 0.03
42 6 0.02
43 1 0.00
44 23 0.07
45 104 0.34
46 3 0.01
47 10 0.03
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (43 bp):
ATAATGCACCCATATGCATTTCAACTTGGCATCTTTCATGCCA
Found at i:4071181 original size:34 final size:34
Alignment explanation
Indices: 4071143--4071514 Score: 168
Period size: 34 Copynumber: 9.6 Consensus size: 34
4071133 TGTCATGCCA
4071143 ATAATGCACCCATATGCATTATTATTTTATGCTG
1 ATAATGCACCCATATGCATTATTATTTTATGCTG
* **
4071177 ATAATGCACGCATATGCATTTCAGCTATGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCA-TT-A--T-T---AT--TTT-ATGCTG
* *
4071222 ATAATGCACACATATGCATTATTCTTTTATGCTG
1 ATAATGCACCCATATGCATTATTATTTTATGCTG
* * **
4071256 ATAATGCACCCGTACGCATTTCAGCTATGACATCCTTTCATGCCA
1 ATAATGCACCCATATGCA-TT-A--T-T---AT--TTT-ATGCTG
*
4071301 ATAATGCACCCATATGCATTATTCTTTTATGCTG
1 ATAATGCACCCATATGCATTATTATTTTATGCTG
* **
4071335 ATAATGCACCCATATACATTTTAGCTATGACATCCTTTCATGCAA
1 ATAATGCACCCATATGCA--TTA--T-T---AT--TTT-ATGCTG
*
4071380 ATAATGCACCCATATGCATTATTCTTTTATGCTG
1 ATAATGCACCCATATGCATTATTATTTTATGCTG
**
4071414 ATAATGCACACCCATATGCATTTCAGCTATAACATCATTTCATGCCA
1 ATAATG--CACCCATATGCA-TT-A--T-T---AT--TTT-ATGCTG
*
4071461 ATAATGCACCCATATGCATTATTCTTTTATGCTG
1 ATAATGCACCCATATGCATTATTATTTTATGCTG
*
4071495 ATAATGCATCCATATGCATT
1 ATAATGCACCCATATGCATT
4071515 TCAGCTATGA
Statistics
Matches: 259, Mismatches: 33, Indels: 92
0.67 0.09 0.24
Matches are distributed among these distances:
34 90 0.35
35 16 0.06
36 17 0.07
37 6 0.02
38 4 0.02
39 3 0.01
40 5 0.02
41 5 0.02
42 4 0.02
43 6 0.02
44 16 0.06
45 74 0.29
46 3 0.01
47 10 0.04
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (34 bp):
ATAATGCACCCATATGCATTATTATTTTATGCTG
Found at i:4071181 original size:79 final size:79
Alignment explanation
Indices: 4071084--4071548 Score: 736
Period size: 79 Copynumber: 5.9 Consensus size: 79
4071074 CAATTATAGC
* * * *
4071084 ATTCTTTTAGGTTGATAATGCACCCATATGCATTTCAACGT-TGGCAT-CTTGTCATGCCAATAA
1 ATTCTTTTATGCTGATAATGCACCCATATGCATTTCAGC-TATGACATCCTT-TCATGCCAATAA
4071147 TGCACCCATATGCATT
64 TGCACCCATATGCATT
* * *
4071163 ATTATTTTATGCTGATAATGCACGCATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATG
1 ATTCTTTTATGCTGATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
*
4071228 CACACATATGCATT
66 CACCCATATGCATT
* *
4071242 ATTCTTTTATGCTGATAATGCACCCGTACGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
1 ATTCTTTTATGCTGATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
4071307 CACCCATATGCATT
66 CACCCATATGCATT
* * *
4071321 ATTCTTTTATGCTGATAATGCACCCATATACATTTTAGCTATGACATCCTTTCATGCAAATAATG
1 ATTCTTTTATGCTGATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
4071386 CACCCATATGCATT
66 CACCCATATGCATT
* *
4071400 ATTCTTTTATGCTGATAATGCACACCCATATGCATTTCAGCTATAACATCATTTCATGCCAATAA
1 ATTCTTTTATGCTGATAATG--CACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAA
4071465 TGCACCCATATGCATT
64 TGCACCCATATGCATT
*
4071481 ATTCTTTTATGCTGATAATGCATCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
1 ATTCTTTTATGCTGATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
4071546 CAC
66 CAC
4071549 ACACAGTGCC
Statistics
Matches: 357, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
78 1 0.00
79 279 0.78
80 3 0.01
81 74 0.21
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (79 bp):
ATTCTTTTATGCTGATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
CACCCATATGCATT
Found at i:4071502 original size:239 final size:237
Alignment explanation
Indices: 4071084--4071548 Score: 736
Period size: 239 Copynumber: 2.0 Consensus size: 237
4071074 CAATTATAGC
* * * *
4071084 ATTCTTTTAGGTTGATAATGCACCCATATGCATTTCAACGTTGGCATCTTGTCATGCCAATAATG
1 ATTCTTTTAGGCTGATAATGCACCCATATACATTTCAACGTTGACATCTTGTCATGCAAATAATG
* ** *
4071149 CACCCATATGCATTATTATTTTATGCTGATAATGCACGCATATGCATTTCAGCTATGGCATCCTT
66 CACCCATATGCATTATTATTTTATGCTGATAATGCACCCATATGCATTTCAGCTATAACATCATT
*
4071214 TCATGCCAATAATGCACACATATGCATTATTCTTTTATGCTGATAATGCACCCGTACGCATTTCA
131 TCATGCCAATAATGCACACATATGCATTATTCTTTTATGCTGATAATGCACCCATACGCATTTCA
4071279 GCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
196 GCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
* * *
4071321 ATTCTTTTATGCTGATAATGCACCCATATACATTTTAGC-TATGACATCCTT-TCATGCAAATAA
1 ATTCTTTTAGGCTGATAATGCACCCATATACATTTCAACGT-TGACAT-CTTGTCATGCAAATAA
*
4071384 TGCACCCATATGCATTATTCTTTTATGCTGATAATGCACACCCATATGCATTTCAGCTATAACAT
64 TGCACCCATATGCATTATTATTTTATGCTGATAATG--CACCCATATGCATTTCAGCTATAACAT
* * *
4071449 CATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGATAATGCATCCATATGCAT
127 CATTTCATGCCAATAATGCACACATATGCATTATTCTTTTATGCTGATAATGCACCCATACGCAT
4071514 TTCAGCTATGACATCCTTTCATGCCAATAATGCAC
192 TTCAGCTATGACATCCTTTCATGCCAATAATGCAC
4071549 ACACAGTGCC
Statistics
Matches: 208, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
236 1 0.00
237 85 0.41
238 3 0.01
239 119 0.57
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (237 bp):
ATTCTTTTAGGCTGATAATGCACCCATATACATTTCAACGTTGACATCTTGTCATGCAAATAATG
CACCCATATGCATTATTATTTTATGCTGATAATGCACCCATATGCATTTCAGCTATAACATCATT
TCATGCCAATAATGCACACATATGCATTATTCTTTTATGCTGATAATGCACCCATACGCATTTCA
GCTATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
Found at i:4072009 original size:20 final size:20
Alignment explanation
Indices: 4071984--4072037 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
4071974 TGTTCTTCAT
4071984 TATCGATACCCCTACCATGG
1 TATCGATACCCCTACCATGG
** *
4072004 TATCGATACTACTATACTATGG
1 TATCGATAC--CCCTACCATGG
4072026 TATCGATACCCC
1 TATCGATACCCC
4072038 CTTCCGGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.30
Consensus pattern (20 bp):
TATCGATACCCCTACCATGG
Found at i:4074475 original size:2 final size:2
Alignment explanation
Indices: 4074468--4074563 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
4074458 TACAAAAACC
4074468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4074510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4074552 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4074564 TAACAGATTA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4077723 original size:16 final size:16
Alignment explanation
Indices: 4077702--4077757 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 16
4077692 TTTTCCTCTC
4077702 ATTTTTCATTTCATTTT
1 ATTTTTCA-TTCATTTT
4077719 ATTTTTCATTCATTTTTT
1 ATTTTTCATTCA--TTTT
*
4077737 AATTTTCATTC-TTTT
1 ATTTTTCATTCATTTT
*
4077752 CTTTTT
1 ATTTTT
4077758 TCCTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 8 0.24
18 14 0.41
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTCATTCATTTT
Found at i:4077735 original size:29 final size:30
Alignment explanation
Indices: 4077687--4077746 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
4077677 ACCCCCTTTA
* *
4077687 TTTATTTTTCCTCTCATTTTTCA-TTTCAT
1 TTTATTTTTCATCTCATTTTTAATTTTCAT
4077716 TTTATTTTTCAT-TCATTTTTTAATTTTCAT
1 TTTATTTTTCATCTCA-TTTTTAATTTTCAT
4077746 T
1 T
4077747 CTTTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 17 0.63
30 7 0.26
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTATTTTTCATCTCATTTTTAATTTTCAT
Found at i:4077736 original size:18 final size:18
Alignment explanation
Indices: 4077702--4077751 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
4077692 TTTTCCTCTC
4077702 ATTTTTCATTTCA--TTTT
1 ATTTTTCA-TTCATTTTTT
4077719 ATTTTTCATTCATTTTTT
1 ATTTTTCATTCATTTTTT
*
4077737 AATTTTCATTC-TTTT
1 ATTTTTCATTCATTTT
4077752 CTTTTTTCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 4 0.13
17 12 0.40
18 14 0.47
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTCATTCATTTTTT
Found at i:4077758 original size:16 final size:16
Alignment explanation
Indices: 4077720--4077775 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
4077710 TTTCATTTTA
4077720 TTTTTCATTCATTTT-T
1 TTTTTCATTC-TTTTCT
4077736 TAATTTTCATTCTTTTCT
1 T--TTTTCATTCTTTTCT
* *
4077754 TTTTTCCTTTTTTTCT
1 TTTTTCATTCTTTTCT
4077770 TTTTTC
1 TTTTTC
4077776 CACTTTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 20 0.57
17 4 0.11
18 11 0.31
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCATTCTTTTCT
Found at i:4077782 original size:16 final size:16
Alignment explanation
Indices: 4077748--4077782 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4077738 ATTTTCATTC
**
4077748 TTTTCTTTTTTCCTTT
1 TTTTCTTTTTTCCACT
4077764 TTTTCTTTTTTCCACT
1 TTTTCTTTTTTCCACT
4077780 TTT
1 TTT
4077783 GTTTTATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTTCCACT
Found at i:4081275 original size:15 final size:16
Alignment explanation
Indices: 4081242--4081279 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
4081232 TAAGATAAGT
*
4081242 AAAATGAAATAATATAA
1 AAAAT-AAATAATAGAA
4081259 AAAATAAATAAT-GAA
1 AAAATAAATAATAGAA
4081274 AAAATA
1 AAAATA
4081280 CATGGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 7 0.35
17 5 0.25
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (16 bp):
AAAATAAATAATAGAA
Found at i:4091452 original size:3 final size:3
Alignment explanation
Indices: 4091444--4091507 Score: 83
Period size: 3 Copynumber: 20.3 Consensus size: 3
4091434 GCATGTAAAT
* *
4091444 TAA TAA TAA TAA TAA TTAT TAA TAA TAA TTAT TAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA -TAA TAA TAA TAA -TAA TAA
4091492 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
4091508 TATTATTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
3 47 0.87
4 7 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:4091466 original size:16 final size:16
Alignment explanation
Indices: 4091441--4091509 Score: 104
Period size: 16 Copynumber: 4.3 Consensus size: 16
4091431 CATGCATGTA
4091441 AATTAATAATAATAAT
1 AATTAATAATAATAAT
*
4091457 AATTATTAATAATAAT
1 AATTAATAATAATAAT
*
4091473 TATTAATAATAATTAAT
1 AATTAATAATAA-TAAT
4091490 AA-TAATAATAATAAT
1 AATTAATAATAATAAT
4091505 AATTA
1 AATTA
4091510 TTATTATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.13
16 36 0.77
17 5 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAATAATAATAAT
Found at i:4091468 original size:13 final size:13
Alignment explanation
Indices: 4091450--4091515 Score: 98
Period size: 13 Copynumber: 5.2 Consensus size: 13
4091440 AAATTAATAA
4091450 TAATAATAATTAT
1 TAATAATAATTAT
4091463 TAATAATAATTAT
1 TAATAATAATTAT
*
4091476 TAATAATAATTAA
1 TAATAATAATTAT
*
4091489 TAATAATAA-TAA
1 TAATAATAATTAT
*
4091501 TAATAATTATTAT
1 TAATAATAATTAT
4091514 TA
1 TA
4091516 TTATAATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
12 11 0.22
13 38 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATAATTAT
Found at i:4093702 original size:21 final size:20
Alignment explanation
Indices: 4093656--4093702 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
4093646 ATATTAAATT
4093656 ATTAAACTAAAAGGGAATAA
1 ATTAAACTAAAAGGGAATAA
* **
4093676 ACTAAACATAAAAGGGGCTAA
1 ATTAAAC-TAAAAGGGAATAA
4093697 ATTAAA
1 ATTAAA
4093703 ACAAATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (20 bp):
ATTAAACTAAAAGGGAATAA
Found at i:4096494 original size:25 final size:25
Alignment explanation
Indices: 4096436--4096495 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
4096426 GATATTTTAA
*
4096436 AATAAAAATAATATAAAATTTCAACT
1 AATAAAAA-AATATAAAATTTCAAAT
*
4096462 -TTATAAAAAATATAAAATTT-AAAT
1 AATA-AAAAAATATAAAATTTCAAAT
*
4096486 AATACAAAAA
1 AATAAAAAAA
4096496 CCATACATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
24 8 0.29
25 16 0.57
26 4 0.14
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (25 bp):
AATAAAAAAATATAAAATTTCAAAT
Found at i:4097415 original size:19 final size:20
Alignment explanation
Indices: 4097375--4097418 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4097365 ATTTTAAGTA
*
4097375 ATAATATTTTTAAGACGGTT
1 ATAATATTTTTAAGACGATT
4097395 ATAATATTTTCT-A-ACGATT
1 ATAATATTTT-TAAGACGATT
4097414 ATAAT
1 ATAAT
4097419 GGATTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 11 0.50
21 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (20 bp):
ATAATATTTTTAAGACGATT
Found at i:4101874 original size:23 final size:23
Alignment explanation
Indices: 4101839--4101892 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
4101829 TAACTACCAG
* * *
4101839 AACGAATATAATAAATGAACATA
1 AACGAACACAATAAACGAACATA
4101862 AACGAACACAATAAACGAACATA
1 AACGAACACAATAAACGAACATA
*
4101885 AACAAACA
1 AACGAACA
4101893 ACACAAACAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.63, C:0.17, G:0.07, T:0.13
Consensus pattern (23 bp):
AACGAACACAATAAACGAACATA
Found at i:4101895 original size:13 final size:14
Alignment explanation
Indices: 4101861--4101901 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
4101851 AAATGAACAT
*
4101861 AAACGAACAC-AAT
1 AAACGAACACAAAC
*
4101874 AAACGAACATAAAC
1 AAACGAACACAAAC
4101888 AAAC-AACACAAAC
1 AAACGAACACAAAC
4101901 A
1 A
4101902 CAAAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.66, C:0.24, G:0.05, T:0.05
Consensus pattern (14 bp):
AAACGAACACAAAC
Found at i:4101900 original size:23 final size:23
Alignment explanation
Indices: 4101855--4101900 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4101845 TATAATAAAT
* *
4101855 GAACATAAACGAACACAATAAAC
1 GAACATAAACAAACACAACAAAC
4101878 GAACATAAACAAACA-ACACAAAC
1 GAACATAAACAAACACA-ACAAAC
4101901 ACAAAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.63, C:0.24, G:0.07, T:0.07
Consensus pattern (23 bp):
GAACATAAACAAACACAACAAAC
Found at i:4102181 original size:24 final size:26
Alignment explanation
Indices: 4102152--4102203 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
4102142 GCCCTCTGTT
*
4102152 CGAACATAAATGAACATA-AAT-GAA
1 CGAACATAAACGAACATATAATCGAA
4102176 CGAACATAAACGAACATATAATCGAA
1 CGAACATAAACGAACATATAATCGAA
4102202 CG
1 CG
4102204 TTCATGAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (26 bp):
CGAACATAAACGAACATATAATCGAA
Found at i:4104193 original size:12 final size:12
Alignment explanation
Indices: 4104172--4104206 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4104162 CTTCCATTAG
4104172 CTGCTGCTGCTA
1 CTGCTGCTGCTA
*
4104184 CTGCTACTGCTA
1 CTGCTGCTGCTA
*
4104196 CGGCTGCTGCT
1 CTGCTGCTGCT
4104207 GTGGTGGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.34, G:0.26, T:0.31
Consensus pattern (12 bp):
CTGCTGCTGCTA
Found at i:4111594 original size:14 final size:15
Alignment explanation
Indices: 4111565--4111639 Score: 50
Period size: 15 Copynumber: 5.2 Consensus size: 15
4111555 AAATAATTAA
4111565 AATTATATATTTTAT
1 AATTATATATTTTAT
*
4111580 AATTGTATA-TTTAT
1 AATTATATATTTTAT
* *
4111594 AATCAT-T-TATTAT
1 AATTATATATTTTAT
* * *
4111607 -ATTTTAAATTATTAA
1 AATTATATATT-TTAT
*
4111622 AATAATATATTTTAT
1 AATTATATATTTTAT
4111637 AAT
1 AAT
4111640 AATTTACTAT
Statistics
Matches: 42, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
12 3 0.07
13 5 0.12
14 10 0.24
15 17 0.40
16 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (15 bp):
AATTATATATTTTAT
Found at i:4111645 original size:43 final size:42
Alignment explanation
Indices: 4111585--4111677 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 42
4111575 TTTATAATTG
* * *
4111585 TATA-TTTATAATCATTTATTATATTTTAAATTATTAAAATAA
1 TATATTTTATAATAATTTACTATATTTTAAATAATT-AAATAA
*
4111627 TATATTTTATAATAATTTACTATATTTTTAATAATTAAATAA
1 TATATTTTATAATAATTTACTATATTTTAAATAATTAAATAA
4111669 TATATTTTA
1 TATATTTTA
4111678 ACATTATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 19 0.41
43 27 0.59
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (42 bp):
TATATTTTATAATAATTTACTATATTTTAAATAATTAAATAA
Found at i:4111672 original size:22 final size:22
Alignment explanation
Indices: 4111604--4111676 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 22
4111594 AATCATTTAT
* *
4111604 TATATTTTAAATTATTAAAATAA
1 TATATTTTTAATAATT-AAATAA
*
4111627 TATATTTTATAATAATT---TAC
1 TATATTTT-TAATAATTAAATAA
4111647 TATATTTTTAATAATTAAATAA
1 TATATTTTTAATAATTAAATAA
4111669 TATATTTT
1 TATATTTT
4111677 AACATTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 8 0.19
20 10 0.24
22 10 0.24
23 8 0.19
24 6 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATTTTTAATAATTAAATAA
Found at i:4111687 original size:22 final size:22
Alignment explanation
Indices: 4111604--4111693 Score: 78
Period size: 23 Copynumber: 4.1 Consensus size: 22
4111594 AATCATTTAT
4111604 TATATTTTAAATTATTAAAATAA
1 TATATTTTAAATTATT-AAATAA
* *
4111627 TATATTTTATAATAATT---TAC
1 TATATTTTA-AATTATTAAATAA
* *
4111647 TATATTTTTAATAATTAAATAA
1 TATATTTTAAATTATTAAATAA
* *
4111669 TATATTTTAACATTATAAAAAAA
1 TATATTTTAA-ATTATTAAATAA
4111692 TA
1 TA
4111694 AAAATATTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
19 7 0.13
20 10 0.19
22 11 0.20
23 20 0.37
24 6 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTTTAAATTATTAAATAA
Found at i:4115047 original size:16 final size:16
Alignment explanation
Indices: 4115028--4115075 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
4115018 TTCTTGTCTT
4115028 CTAAGACTCTTATC-A
1 CTAAGACTCTTATCTA
**
4115043 GCTAAGAAACTTATCTA
1 -CTAAGACTCTTATCTA
*
4115060 CAAAGACTCTTATCTA
1 CTAAGACTCTTATCTA
4115076 ATCAGATAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (16 bp):
CTAAGACTCTTATCTA
Found at i:4144590 original size:28 final size:28
Alignment explanation
Indices: 4144544--4144613 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
4144534 ATTTTTTTGA
** *
4144544 AAAAAACCCGACCTGAATATCACA-CTT
1 AAAAAACCCGACCCAAATATCAAATCTT
* *
4144571 ACAAAAACCCGACCCAAATATTAAATTTT
1 A-AAAAACCCGACCCAAATATCAAATCTT
4144600 AAAAAACCCGACCC
1 AAAAAACCCGACCC
4144614 GAACCCAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.03
28 32 0.89
29 3 0.08
ACGTcount: A:0.47, C:0.30, G:0.06, T:0.17
Consensus pattern (28 bp):
AAAAAACCCGACCCAAATATCAAATCTT
Found at i:4144643 original size:32 final size:33
Alignment explanation
Indices: 4144600--4144686 Score: 117
Period size: 31 Copynumber: 2.7 Consensus size: 33
4144590 ATTAAATTTT
*
4144600 AAAAAACCCGACCCGAA-CCCAAATTTTTTTAA
1 AAAAAATCCGACCCGAATCCCAAATTTTTTTAA
*
4144632 AAAAAATCCGA-CC-AATCCCAAATTTTTTTTA
1 AAAAAATCCGACCCGAATCCCAAATTTTTTTAA
* *
4144663 GAAAAATCCGACCCGAATACCAAA
1 AAAAAATCCGACCCGAATCCCAAA
4144687 AGATTGATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 2 0.04
31 26 0.54
32 12 0.25
33 8 0.17
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.22
Consensus pattern (33 bp):
AAAAAATCCGACCCGAATCCCAAATTTTTTTAA
Found at i:4144896 original size:26 final size:26
Alignment explanation
Indices: 4144852--4144901 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
4144842 ATTGGATTCT
* ** *
4144852 AATTCCCTCTAATTTTAAGGGATTTC
1 AATTCCCCCTAATACTAAGAGATTTC
4144878 AATTCCCCCTAATACTAAGAGATT
1 AATTCCCCCTAATACTAAGAGATT
4144902 CCAACGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (26 bp):
AATTCCCCCTAATACTAAGAGATTTC
Found at i:4145762 original size:18 final size:18
Alignment explanation
Indices: 4145739--4145774 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4145729 TCTCCTGCTC
4145739 TTTTTTATAATATAAAAG
1 TTTTTTATAATATAAAAG
*
4145757 TTTTTTATTATATAAAAG
1 TTTTTTATAATATAAAAG
4145775 ATGTAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTTTTATAATATAAAAG
Found at i:4147507 original size:19 final size:17
Alignment explanation
Indices: 4147479--4147523 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
4147469 CGTAATTAAA
*
4147479 TTTTAAATTTTTATATAAT
1 TTTTATATTTTT-TAT-AT
4147498 TTTTATATTTTTTATAT
1 TTTTATATTTTTTATAT
*
4147515 TTTTTTATT
1 TTTTATATT
4147524 AATGATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.42
18 3 0.12
19 11 0.46
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATATTTTTTATAT
Found at i:4147509 original size:9 final size:9
Alignment explanation
Indices: 4147479--4147523 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
4147469 CGTAATTAAA
*
4147479 TTTTAAATT
1 TTTTATATT
*
4147488 TTTATATAAT
1 TTT-TATATT
4147498 TTTTATATT
1 TTTTATATT
4147507 TTTTATATT
1 TTTTATATT
4147516 TTTT-TATT
1 TTTTATATT
4147524 AATGATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
8 4 0.12
9 21 0.66
10 7 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATATT
Found at i:4149348 original size:16 final size:15
Alignment explanation
Indices: 4149327--4149360 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
4149317 TTGAGGTTAG
*
4149327 GTAATTCACAATTCGT
1 GTAATTAACAATTC-T
4149343 GTAATTAACAATTCT
1 GTAATTAACAATTCT
4149358 GTA
1 GTA
4149361 CAAAGCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (15 bp):
GTAATTAACAATTCT
Found at i:4152757 original size:17 final size:15
Alignment explanation
Indices: 4152737--4152772 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
4152727 TTCAAAGATA
4152737 TATTTAATTTATAATT
1 TATTTAATTTA-AATT
4152753 CTATTTAATTTAAATT
1 -TATTTAATTTAAATT
4152769 TATT
1 TATT
4152773 ACAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTAATTTAAATT
Found at i:4153171 original size:14 final size:15
Alignment explanation
Indices: 4153141--4153173 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4153131 AATAGAATAA
4153141 ATAAATAAATATTAT
1 ATAAATAAATATTAT
*
4153156 ATAAATATAT-TTAT
1 ATAAATAAATATTAT
4153170 ATAA
1 ATAA
4153174 CTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATAAATATTAT
Found at i:4153261 original size:15 final size:14
Alignment explanation
Indices: 4153231--4153290 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
4153221 TATTAAACGT
4153231 AATAATAAAA-TAA
1 AATAATAAAATTAA
4153244 AATAATAATAATTAA
1 AATAATAA-AATTAA
4153259 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
4153274 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
4153289 AA
1 AA
4153291 ACTAATGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:4154574 original size:3 final size:3
Alignment explanation
Indices: 4154566--4154650 Score: 84
Period size: 3 Copynumber: 28.0 Consensus size: 3
4154556 TCTGTTTGTA
* *
4154566 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT ATAT ATAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT
* **
4154611 AAT ATTT AAT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4154651 TTAAGTAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
2 3 0.04
3 57 0.83
4 9 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:4154592 original size:22 final size:21
Alignment explanation
Indices: 4154567--4154650 Score: 95
Period size: 22 Copynumber: 4.0 Consensus size: 21
4154557 CTGTTTGTAA
4154567 ATAATAATTATTTAATAATAAT
1 ATAATAA-TATTTAATAATAAT
*
4154589 ATAAT-ATATAT-ATAAT-A-
1 ATAATAATATTTAATAATAAT
4154606 ATAATAATATTTAATAATAAT
1 ATAATAATATTTAATAATAAT
4154627 AATAATAATAATTTTAATAATAAT
1 -ATAATAAT-A-TTTAATAATAAT
4154651 TTAAGTAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.09
18 6 0.11
19 10 0.19
20 5 0.09
21 1 0.02
22 13 0.25
23 1 0.02
24 12 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATAATATTTAATAATAAT
Found at i:4154603 original size:19 final size:19
Alignment explanation
Indices: 4154566--4154650 Score: 102
Period size: 19 Copynumber: 4.5 Consensus size: 19
4154556 TCTGTTTGTA
*
4154566 AATAATAATTATTTAATAAT
1 AATAATAA-TATATAATAAT
4154586 AAT-ATAATATATATATAAT
1 AATAATAATATATA-ATAAT
*
4154605 AATAATAATATTTAATAAT
1 AATAATAATATATAATAAT
**
4154624 AATAATAATA-ATAATTTT
1 AATAATAATATATAATAAT
4154642 AATAATAAT
1 AATAATAAT
4154651 TTAAGTAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
18 19 0.33
19 27 0.47
20 12 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAATAATATATAATAAT
Found at i:4154607 original size:25 final size:24
Alignment explanation
Indices: 4154579--4154650 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 24
4154569 AATAATTATT
4154579 TAATAATAATA-TAATATATATATAA
1 TAATAATAATATTAATA-ATA-ATAA
4154604 TAATAATAATATTTAATAATAATAA
1 TAATAATAATA-TTAATAATAATAA
*
4154629 TAATAATAATTTTAATAATAAT
1 TAATAATAATATTAATAATAAT
4154651 TTAAGTAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
24 11 0.25
25 25 0.57
26 3 0.07
27 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATAATAATATTAATAATAATAA
Found at i:4154896 original size:76 final size:76
Alignment explanation
Indices: 4154804--4155289 Score: 875
Period size: 76 Copynumber: 6.4 Consensus size: 76
4154794 GAGGTCTTAA
* * *
4154804 AAACATCATGCACTGCAGGACTTACGGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4154869 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4154880 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4154945 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4154956 AAACATCATGCACTGCAGGACTTACTGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4155021 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
4155032 AAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4155097 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4155108 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4155172 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4155183 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAAACTCCCG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGCTCCCG
4155248 AAGGCTTTTTGG
65 AAGGCTTTTTGG
4155260 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
4155290 TGGGAAATAG
Statistics
Matches: 396, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
75 73 0.18
76 270 0.68
77 53 0.13
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:4156157 original size:22 final size:22
Alignment explanation
Indices: 4156132--4156187 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
4156122 GATAAAGCTT
*
4156132 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
4156154 TCATCTTTAAAAAAGGGAATCTA
1 TCATCTTT-GAAAAGAGAATCTA
4156177 TCATCTTTGAA
1 TCATCTTTGAA
4156188 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:4158152 original size:114 final size:113
Alignment explanation
Indices: 4157952--4158285 Score: 551
Period size: 114 Copynumber: 2.9 Consensus size: 113
4157942 GATCATGCAG
* * * * *
4157952 TTCATCTTTCAATTCCAATGATTGGTTCTGGGATTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACC-AAACAGATCAGATAACTCAAAGA
4158017 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAACAAA
65 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAACAAA
4158066 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAA-CAGATCAGATAACTCAAAGA
** *
4158131 ACACTTCCAGAAGATGCTATTGGGTTTTCTTATTTCTACTATGAACAAA
65 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAACAAA
*
4158180 TTTATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAAC-AGATCAGATAACTCAAAGA
*
4158245 ACACTTGCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
65 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
4158286 CGAGAACGTG
Statistics
Matches: 205, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
113 3 0.01
114 202 0.99
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (113 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAACAAA
Found at i:4165418 original size:15 final size:15
Alignment explanation
Indices: 4165368--4165419 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
4165358 AAAATACCTG
*
4165368 AATAAAATAAATA--
1 AATAAAATAAAAAGT
4165381 AATAAAATAAAAAGT
1 AATAAAATAAAAAGT
*
4165396 -ATAAAAATAATAAGT
1 AAT-AAAATAAAAAGT
4165411 AATAAAATA
1 AATAAAATA
4165420 TTTGAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 12 0.36
14 2 0.06
15 17 0.52
16 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (15 bp):
AATAAAATAAAAAGT
Found at i:4165890 original size:17 final size:15
Alignment explanation
Indices: 4165870--4165905 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
4165860 TTCAAAGATA
4165870 TATTTAATTTATAATT
1 TATTTAATTTA-AATT
4165886 CTATTTAATTTAAATT
1 -TATTTAATTTAAATT
4165902 TATT
1 TATT
4165906 ACTATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTAATTTAAATT
Found at i:4167185 original size:3 final size:3
Alignment explanation
Indices: 4167177--4167251 Score: 64
Period size: 3 Copynumber: 24.0 Consensus size: 3
4167167 CCTGTTTGTA
* *
4167177 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT ATAT ATAT ATAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT A-AT A-AT AAT
*
4167224 AAT ATTT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT
4167252 TTAAGTAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
2 3 0.05
3 43 0.68
4 17 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:4167238 original size:16 final size:16
Alignment explanation
Indices: 4167190--4167251 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
4167180 AATAATTATT
4167190 TAATA-ATAAT-ATAA
1 TAATATATAATAATAA
4167204 TATATATATATATATATAA
1 TA-ATATATA-ATA-ATAA
*
4167223 TAATATTTAATAATAA
1 TAATATATAATAATAA
4167239 TAATA-ATAATAAT
1 TAATATATAATAAT
4167252 TTAAGTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 10 0.24
16 12 0.29
17 5 0.12
18 6 0.15
19 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATATAATAATAA
Found at i:4167249 original size:22 final size:22
Alignment explanation
Indices: 4167177--4167255 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
4167167 CCTGTTTGTA
4167177 AATAATAATTATTTAATAATAAT
1 AATAATAA-TATTTAATAATAAT
*
4167200 -ATAAT-ATATAT-AT-AT-AT
1 AATAATAATATTTAATAATAAT
4167217 ATATAATAATATTTAATAATAAT
1 A-ATAATAATATTTAATAATAAT
4167240 AATAATAATAATTTAA
1 AATAATAAT-ATTTAA
4167256 GTAAAATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
17 2 0.04
18 2 0.04
19 7 0.15
20 9 0.19
21 3 0.06
22 15 0.32
23 9 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATAATATTTAATAATAAT
Done.