Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 116 of 295
Found at i:39876550 original size:18 final size:18
Alignment explanation
Indices: 39876487--39876564 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
39876477 TTATTTACTC
*
39876487 TTATTTTTA-TTTTA-TT
1 TTATTTTAATTTTTATTT
*
39876503 TTATTTTTATTTTTATTT
1 TTATTTTAATTTTTATTT
* *
39876521 TTCTTTTGATTTTTATTT
1 TTATTTTAATTTTTATTT
*
39876539 TTATTTCAA-TTTTATTATT
1 TTATTTTAATTTTTA-T-TT
39876558 TTATTTT
1 TTATTTT
39876565 GAAAGACATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
16 9 0.17
17 10 0.19
18 25 0.48
19 8 0.15
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (18 bp):
TTATTTTAATTTTTATTT
Found at i:39880575 original size:19 final size:20
Alignment explanation
Indices: 39880551--39880588 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39880541 GGTACCACCA
39880551 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39880570 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39880589 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39880929 original size:93 final size:93
Alignment explanation
Indices: 39880818--39880988 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
39880808 GCCCTTAATT
* *
39880818 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
39880883 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CAAGTTCGGATGCCTAGTTACATCTCAC
* * * *
39880911 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
39880976 CAAGTTCGGATGC
66 CAAGTTCGGATGC
39880989 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CAAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39880985 original size:46 final size:45
Alignment explanation
Indices: 39880817--39880985 Score: 180
Period size: 46 Copynumber: 3.7 Consensus size: 45
39880807 CGCCCTTAAT
* * * * *
39880817 TGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCAT-AA
* * *
39880863 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAA
*
39880910 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAA
*
39880955 GTGAACTCGGACTCAACTCAACAAGTTCGGA
1 -TGAACTCGGACTCAACTCAACGAGTTCGGA
39880986 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 55 0.54
47 30 0.29
48 1 0.01
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAA
Found at i:39887494 original size:19 final size:20
Alignment explanation
Indices: 39887470--39887507 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39887460 GGTATCACCA
39887470 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39887489 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39887508 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39887803 original size:46 final size:46
Alignment explanation
Indices: 39887736--39887857 Score: 156
Period size: 46 Copynumber: 2.7 Consensus size: 46
39887726 CGCCCCTAAG
* * *
39887736 TGAACTCGGACTCAAGTCAACGAGCTC-GAGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGCTCGGA-CATTCACATCCATAAA
* * * *
39887782 TGAACTCGGACTCAACTCAACGAGTTTGGACATTTACATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAA
*
39887828 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGCTCGGA
39887858 TGCTCAACCA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 65 0.97
47 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAA
Found at i:39888314 original size:30 final size:30
Alignment explanation
Indices: 39888280--39888340 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
39888270 ATTTAATACG
*
39888280 AACTTTAAGAAAATTACACTTTTGCCCCTA
1 AACTTTAACAAAATTACACTTTTGCCCCTA
* *
39888310 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTAACAAAATTACACTTTTGCCCCTA
39888340 A
1 A
39888341 GCTCGGGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (30 bp):
AACTTTAACAAAATTACACTTTTGCCCCTA
Found at i:39896499 original size:47 final size:47
Alignment explanation
Indices: 39896052--39896479 Score: 750
Period size: 47 Copynumber: 9.1 Consensus size: 47
39896042 GATTCTATGA
* *
39896052 GATGAATGTGAACATGCATATGTGTGATAAGG-CGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
39896098 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
* *
39896145 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
*
39896192 GATGAATGTGAACATGCAAATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
39896239 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
* *
39896286 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
39896333 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
*
39896380 GATGAATGTGAACATGCAAATATGAGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
* **
39896427 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
39896474 GATGAA
1 GATGAA
39896480 CGTGGAAGTG
Statistics
Matches: 366, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
46 30 0.08
47 336 0.92
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (47 bp):
GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
Found at i:39897816 original size:40 final size:40
Alignment explanation
Indices: 39897772--39898129 Score: 482
Period size: 40 Copynumber: 8.9 Consensus size: 40
39897762 CGAGAGTTAA
* * * *
39897772 ATATCCGGGCTAGGTCCCGAAGAGCATTCGAGCTGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
* *
39897812 ATATCCGGGCTAGGTCCCGAAGAGCATTCGTGCCGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
** * * * *
39897852 ATATCCGGGAAAAATCCCGAAGAGCATTCGAGCTGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
* * * * *
39897892 ATATCCAGGCTAGGTCCCGAAGAGCATTCGAGCTGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
*
39897932 ATATCCGGGCTAAGTCTCGAAGGGCATTCGTGCCGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
* *
39897972 ATATCCGGGCAAAATCCCGAAGGGCATTCGTGCCGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
* *
39898012 ATATCCGGGCAAAATCCCGAAGGGCATTCGTGCCGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
* * *
39898052 ATATCCGGGCTAAATCCCGAAGGGTATTCGTGCCGATGTT
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
*
39898092 ATATCCGGGCTAAGTCCTGAAGGGCATTCGTGCCGGTG
1 ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTG
39898130 ATGTGTATTC
Statistics
Matches: 289, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 289 1.00
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTT
Found at i:39902129 original size:22 final size:22
Alignment explanation
Indices: 39902102--39902223 Score: 63
Period size: 22 Copynumber: 5.3 Consensus size: 22
39902092 CATGCATATG
39902102 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
39902124 TGTGATGAATG-TGAACAT-GCAAATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
39902149 TGTGATAAGGCCGAGTGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
39902171 TGTGATGAATG-TGAACAT-GCAAATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
39902196 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
39902218 TGTGAT
1 TGTGAT
39902224 GAATGTGAAC
Statistics
Matches: 72, Mismatches: 14, Indels: 28
0.63 0.12 0.25
Matches are distributed among these distances:
22 22 0.31
23 17 0.24
24 17 0.24
25 16 0.22
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.24
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:39902293 original size:47 final size:47
Alignment explanation
Indices: 39902080--39902273 Score: 325
Period size: 47 Copynumber: 4.1 Consensus size: 47
39902070 GATTCTATGA
* *
39902080 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
*
39902127 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAGTGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
39902174 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
* * **
39902221 GATGAATGTGAACATGCATATATGTGAGAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
39902268 GATGAA
1 GATGAA
39902274 CGTGGAAGTG
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 139 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.24
Consensus pattern (47 bp):
GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
Found at i:39905806 original size:34 final size:34
Alignment explanation
Indices: 39905764--39905843 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
39905754 TTGTTTGCAT
*
39905764 ACTG-TACTGATATGGGCTAAGGCCCAAACTACC
1 ACTGTTACTGAAATGGGCTAAGGCCCAAACTACC
* * *
39905797 ACTGTTACTGAAATGGGCTCAGGCCCAGACTACT
1 ACTGTTACTGAAATGGGCTAAGGCCCAAACTACC
39905831 ACTGTTACTGAAA
1 ACTGTTACTGAAA
39905844 AAAGGGCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 4 0.10
34 38 0.90
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (34 bp):
ACTGTTACTGAAATGGGCTAAGGCCCAAACTACC
Found at i:39906659 original size:31 final size:31
Alignment explanation
Indices: 39906624--39906688 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
39906614 TGAAATAATA
*
39906624 GTATTGATATGTTATT-TCTGAGACTACTTAG
1 GTATTGAAATGTTATTAT-TGAGACTACTTAG
* *
39906655 GTATTGAAATGTTCTTATTGATACTACTTAG
1 GTATTGAAATGTTATTATTGAGACTACTTAG
39906686 GTA
1 GTA
39906689 GTATTGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (31 bp):
GTATTGAAATGTTATTATTGAGACTACTTAG
Found at i:39906693 original size:34 final size:33
Alignment explanation
Indices: 39906622--39906697 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 33
39906612 ACTGAAATAA
*
39906622 TAGTATTGATATGTTATTTCTGAGACTACTTAG
1 TAGTATTGAAATGTTATTTCTGAGACTACTTAG
* *
39906655 --GTATTGAAATGTTCTTAT-TGATACTACTTAGG
1 TAGTATTGAAATGTTATT-TCTGAGACTACTTA-G
39906687 TAGTATTGAAA
1 TAGTATTGAAA
39906698 CCATCTAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
31 25 0.69
32 2 0.06
34 9 0.25
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.43
Consensus pattern (33 bp):
TAGTATTGAAATGTTATTTCTGAGACTACTTAG
Found at i:39908410 original size:45 final size:45
Alignment explanation
Indices: 39908341--39908431 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
39908331 GGGCGCATAG
*
39908341 TAGCCCCTATGCTATACACGCAGGTGGAAATAAGATGTACAGAGA
1 TAGCCCCTATGCTATACACCCAGGTGGAAATAAGATGTACAGAGA
39908386 TAGCCCCTATGCTATACACCCAGGTGGAAATAAGATGTACAGAGA
1 TAGCCCCTATGCTATACACCCAGGTGGAAATAAGATGTACAGAGA
39908431 T
1 T
39908432 CTTTGTGAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (45 bp):
TAGCCCCTATGCTATACACCCAGGTGGAAATAAGATGTACAGAGA
Found at i:39926569 original size:42 final size:42
Alignment explanation
Indices: 39926497--39926614 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
39926487 CAGAAAACAT
* * ** ***
39926497 ATACAATGCCAACGTCCCAGACGCGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACAAAATCAA
* * *
39926539 ATTCGATGCCACTGTCCTAGACA-GGTTCTTACACAAAATCAA
1 ATACGATGCCAATGTCCCAGACATGG-TCTTACACAAAATCAA
39926581 ATACGATGCCAATGTCCCAGACATGGTCTTACAC
1 ATACGATGCCAATGTCCCAGACATGGTCTTACAC
39926615 GCAAAATAGA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 58 0.94
43 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACATGGTCTTACACAAAATCAA
Found at i:39926668 original size:44 final size:44
Alignment explanation
Indices: 39926537--39926657 Score: 115
Period size: 44 Copynumber: 2.8 Consensus size: 44
39926527 ACATGTAATC
* * *
39926537 AAATTCGATGCCACTGTCCTAGACA-GGTTCTTACA--CAAAAT-C
1 AAATT-GATGCCAATGTCCCAGACATGG-TCTTACACGCAAAATAG
*
39926579 AAATACGATGCCAATGTCCCAGACATGGTCTTACACGCAAAATAG
1 AAAT-TGATGCCAATGTCCCAGACATGGTCTTACACGCAAAATAG
* * **
39926624 AAATTGATGTCAATGTCTCAGATGTGGTCTTACA
1 AAATTGATGCCAATGTCCCAGACATGGTCTTACA
39926658 TGTAGAATAG
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
42 28 0.43
43 2 0.03
44 31 0.48
45 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (44 bp):
AAATTGATGCCAATGTCCCAGACATGGTCTTACACGCAAAATAG
Found at i:39928641 original size:33 final size:33
Alignment explanation
Indices: 39928604--39928681 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
39928594 TGGCCCTGCC
* *
39928604 ATGGTCTTACATTCATAGTGTCATAACCCAG-T
1 ATGGTCTTACATTCAGAATGTCATAACCCAGCT
* *
39928636 GATGGTCTTATCA-TCGGAATGTCATAGCCCAGCT
1 -ATGGTCTTA-CATTCAGAATGTCATAACCCAGCT
39928670 ATGGTCTTACAT
1 ATGGTCTTACAT
39928682 ATAAATAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 2 0.05
33 33 0.87
34 3 0.08
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (33 bp):
ATGGTCTTACATTCAGAATGTCATAACCCAGCT
Found at i:39943921 original size:25 final size:25
Alignment explanation
Indices: 39943902--39943984 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
39943892 CAGCTCGCAT
39943902 GAGCTTACCGTTATTTAGCTCAAAG
1 GAGCTTACCGTTATTTAGCTCAAAG
**
39943927 GAGCTTACCAATATTTAGCTCATAAG
1 GAGCTTACCGTTATTTAGCTCA-AAG
* * **
39943953 G-GCTTACTGTTATTCAGCTCGGAG
1 GAGCTTACCGTTATTTAGCTCAAAG
39943977 GAGCTTAC
1 GAGCTTAC
39943985 TGTTTACAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 3 0.06
25 41 0.85
26 4 0.08
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGTTATTTAGCTCAAAG
Found at i:39943988 original size:25 final size:25
Alignment explanation
Indices: 39943892--39943984 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
39943882 TGCCAATAAC
* *
39943892 CAGCTCGCATGAGCTTACCGTTATT
1 CAGCTCGAAGGAGCTTACCGTTATT
* * **
39943917 TAGCTCAAAGGAGCTTACCAATATT
1 CAGCTCGAAGGAGCTTACCGTTATT
* * *
39943942 TAGCTCATAAGG-GCTTACTGTTATT
1 CAGCTC-GAAGGAGCTTACCGTTATT
*
39943967 CAGCTCGGAGGAGCTTAC
1 CAGCTCGAAGGAGCTTAC
39943985 TGTTTACAGC
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
24 3 0.06
25 46 0.87
26 4 0.08
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (25 bp):
CAGCTCGAAGGAGCTTACCGTTATT
Found at i:39953219 original size:16 final size:16
Alignment explanation
Indices: 39953198--39953240 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
39953188 TCTCAGAAGA
*
39953198 ATAAAGAATACAAAAC
1 ATAAAGAAAACAAAAC
39953214 ATAAAGAAAACAAAAC
1 ATAAAGAAAACAAAAC
39953230 ATAAAGAAAAC
1 ATAAAGAAAAC
39953241 CCAAAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.72, C:0.12, G:0.07, T:0.09
Consensus pattern (16 bp):
ATAAAGAAAACAAAAC
Found at i:39956313 original size:42 final size:43
Alignment explanation
Indices: 39956216--39956339 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
39956206 GATACTCGGT
* * *
39956216 CTAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTC
1 CTAGACATGGTCTTACACGAAATCAAATATCGATGCCACTGTC
* * * *
39956259 CCAAACAGGGTCTTACACGAAATCAAATA-CGATGTCGA-TGTC
1 CTAGACATGGTCTTACACGAAATCAAATATCGATG-CCACTGTC
*
39956301 CTAGACATGGTCTTACACATAAATCATAA-ATCGATGCCA
1 CTAGACATGGTCTTACAC-GAAATCA-AATATCGATGCCA
39956340 ACGTCCCAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
42 24 0.37
43 34 0.52
44 7 0.11
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (43 bp):
CTAGACATGGTCTTACACGAAATCAAATATCGATGCCACTGTC
Found at i:39958348 original size:24 final size:24
Alignment explanation
Indices: 39958321--39958366 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39958311 TATGGAGTGT
*
39958321 ATCATGGAGAGATATTA-GGAGAAA
1 ATCAAGGAGAGAT-TTATGGAGAAA
*
39958345 ATCAAGGAGTGATTTATGGAGA
1 ATCAAGGAGAGATTTATGGAGA
39958367 GATTTAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.41, C:0.04, G:0.30, T:0.24
Consensus pattern (24 bp):
ATCAAGGAGAGATTTATGGAGAAA
Found at i:39959721 original size:27 final size:26
Alignment explanation
Indices: 39959685--39959903 Score: 161
Period size: 27 Copynumber: 8.2 Consensus size: 26
39959675 GGTCGTTAAG
*
39959685 ACCCCGATTTGTAAAATTACCGAAAT
1 ACCCCAATTTGTAAAATTACCGAAAT
*
39959711 ACTCCCAATTTATAAAATTACCGAAAT
1 AC-CCCAATTTGTAAAATTACCGAAAT
**
39959738 ACCCACAATTTGTAAAATTATTGAAAT
1 ACCC-CAATTTGTAAAATTACCGAAAT
* ** *
39959765 ACCATCGGTTTGTAAAATTATCGAAAT
1 ACC-CCAATTTGTAAAATTACCGAAAT
**
39959792 ACCCCTAGA-TTGTAAAATTACTTAAAT
1 ACCCC-A-ATTTGTAAAATTACCGAAAT
* ***
39959819 ACCTCCTATTTGTAAAATTATTAAAAT
1 ACC-CCAATTTGTAAAATTACCGAAAT
** * *
39959846 ACCCCCGGTTGGTAAAATTACCAAAAT
1 A-CCCCAATTTGTAAAATTACCGAAAT
** * *
39959873 ACCCTTATAATGTAAAATTATCGAAAT
1 ACCCCAAT-TTGTAAAATTACCGAAAT
39959900 ACCC
1 ACCC
39959904 TTGTAGGGTA
Statistics
Matches: 154, Mismatches: 30, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
26 10 0.06
27 140 0.91
28 4 0.03
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (26 bp):
ACCCCAATTTGTAAAATTACCGAAAT
Found at i:39959830 original size:81 final size:80
Alignment explanation
Indices: 39959692--39959903 Score: 248
Period size: 81 Copynumber: 2.6 Consensus size: 80
39959682 AAGACCCCGA
*
39959692 TTTGTAAAATTACCGAAATACTCCC-AATTTATAAAATTACCGAAATACCCACAATTTGTAAAAT
1 TTTGTAAAATTACCGAAATAC-CCCTAA-TTGTAAAATTACCGAAATACCCACAATTTGTAAAAT
* *
39959756 TATTGAAATACCATCGG
64 TATTAAAATACCACCGG
* ** *
39959773 TTTGTAAAATTATCGAAATACCCCTAGATTGTAAAATTACTTAAATACCTC-CTATTTGTAAAAT
1 TTTGTAAAATTACCGAAATACCCCTA-ATTGTAAAATTACCGAAATACC-CACAATTTGTAAAAT
*
39959837 TATTAAAATACCCCCGG
64 TATTAAAATACCACCGG
* * * * *
39959854 TTGGTAAAATTACCAAAATACCCTTATAATGTAAAATTATCGAAATACCC
1 TTTGTAAAATTACCGAAATACCCCTA-ATTGTAAAATTACCGAAATACCC
39959904 TTGTAGGGTA
Statistics
Matches: 111, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
80 4 0.04
81 105 0.95
82 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.32
Consensus pattern (80 bp):
TTTGTAAAATTACCGAAATACCCCTAATTGTAAAATTACCGAAATACCCACAATTTGTAAAATTA
TTAAAATACCACCGG
Found at i:39959839 original size:54 final size:53
Alignment explanation
Indices: 39959685--39959903 Score: 180
Period size: 54 Copynumber: 4.1 Consensus size: 53
39959675 GGTCGTTAAG
* * * *
39959685 ACCCC-GATTTGTAAAATTACCGAAATA-CTCCCAATTTATAAAATTACCGAAAT
1 ACCCCAGA-TTGTAAAATTACCTAAATACCT-CCTATTTGTAAAATTATCGAAAT
* **
39959738 ACCCACA-ATTTGTAAAATTA-TTGAAATACCAT-CGGTTTGTAAAATTATCGAAAT
1 ACCC-CAGA-TTGTAAAATTACCT-AAATACC-TCCTATTTGTAAAATTATCGAAAT
* **
39959792 ACCCCTAGATTGTAAAATTACTTAAATACCTCCTATTTGTAAAATTATTAAAAT
1 ACCCC-AGATTGTAAAATTACCTAAATACCTCCTATTTGTAAAATTATCGAAAT
* * * * *
39959846 ACCCCCGGTTGGTAAAATTACCAAAATACC-CTTATAATGTAAAATTATCGAAAT
1 ACCCCAGATT-GTAAAATTACCTAAATACCTCCTAT-TTGTAAAATTATCGAAAT
39959900 ACCC
1 ACCC
39959904 TTGTAGGGTA
Statistics
Matches: 137, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
53 13 0.09
54 119 0.87
55 4 0.03
56 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (53 bp):
ACCCCAGATTGTAAAATTACCTAAATACCTCCTATTTGTAAAATTATCGAAAT
Found at i:39959914 original size:27 final size:27
Alignment explanation
Indices: 39959856--39959917 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
39959846 ACCCCCGGTT
39959856 GGTAAAATTACCAAAATACCCTTATAA
1 GGTAAAATTACCAAAATACCCTTATAA
* * * * *
39959883 TGTAAAATTATCGAAATACCCTTGTAG
1 GGTAAAATTACCAAAATACCCTTATAA
39959910 GGTAAAAT
1 GGTAAAAT
39959918 GATTGTCTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (27 bp):
GGTAAAATTACCAAAATACCCTTATAA
Found at i:39959951 original size:24 final size:26
Alignment explanation
Indices: 39959902--39959951 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
39959892 ATCGAAATAC
* *
39959902 CCTTGTAGGGTAAAATGATTGTCTTG
1 CCTTGTAGGGTAAAATGACTGACTTG
39959928 CCTTGT-GGGT-AAATGACTGACTTG
1 CCTTGTAGGGTAAAATGACTGACTTG
39959952 GATTATGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 4 0.18
26 6 0.27
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (26 bp):
CCTTGTAGGGTAAAATGACTGACTTG
Found at i:39967314 original size:43 final size:43
Alignment explanation
Indices: 39967256--39967378 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
39967246 ATTGCCAACA
* *
39967256 TCCCGGACATGGTCTTACATGTAATCAAATATCGAT-GCCACTG
1 TCCCAGACATGGTCTTACACGTAATCAAATATCGATAGCCA-TG
* * * *
39967299 TCCCAGACAAGGTCTTACACGAAATCAAATA-CGATATCGATG
1 TCCCAGACATGGTCTTACACGTAATCAAATATCGATAGCCATG
*
39967341 TCCCAGACATGATCTTACACGTAAATCATAA-ATCGATA
1 TCCCAGACATGGTCTTACACGT-AATCA-AATATCGATA
39967379 CCAACGTCCT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
42 25 0.37
43 35 0.52
44 7 0.10
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCAAATATCGATAGCCATG
Found at i:39972910 original size:93 final size:93
Alignment explanation
Indices: 39972802--39972972 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
39972792 GCCCCTAAGT
* *** * * *
39972802 GAACTCGGACTCAACTCAACGAGCTCAGGTGTTCGCATCCATAAGTGAACTCGGACTCAGCTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCAATAAGTGAACTCGAACTCAACTCAA
*
39972867 CGAGTTTGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
39972895 GAACTCAGACTCAACTCAACGAGTTCAGACATTCGCATCAATAAGTGAACTCGAACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCAATAAGTGAACTCGAACTCAACTCAA
39972960 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39972973 TCAACCATCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCAATAAGTGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:39978582 original size:27 final size:26
Alignment explanation
Indices: 39978551--39978615 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 26
39978541 GTTTAACATC
*
39978551 CCATTGGACTATCCTGAGTTTAATGT
1 CCATTGGACTATCCCGAGTTTAATGT
*
39978577 CTCATTGGACTATCCCGTGTTTAATGT
1 C-CATTGGACTATCCCGAGTTTAATGT
39978604 CCTATTGGACTA
1 CC-ATTGGACTA
39978616 ACTATGATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (26 bp):
CCATTGGACTATCCCGAGTTTAATGT
Found at i:39981168 original size:48 final size:48
Alignment explanation
Indices: 39981116--39981229 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 48
39981106 CATCCCAAAT
* *
39981116 ATGGTCTTACATGGGATCACAT-GTCGATGCCAATGCCATGTCCTAGAC
1 ATGGTCTTACATGGGATCACATAAT-GATGCCAAAGCCATGTCCTAGAC
*** * *
39981164 ATGGTCTTATGGGGGATCTCATAATGATGCCAAAGTCATGTCCTAGAC
1 ATGGTCTTACATGGGATCACATAATGATGCCAAAGCCATGTCCTAGAC
39981212 ATGGTCTTACATGGGATC
1 ATGGTCTTACATGGGATC
39981230 GTACATAACC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 54 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (48 bp):
ATGGTCTTACATGGGATCACATAATGATGCCAAAGCCATGTCCTAGAC
Found at i:39983630 original size:47 final size:45
Alignment explanation
Indices: 39983577--39983677 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 45
39983567 TGTCATAGCG
* * *
39983577 TCTTTCAACCATAGTCCTAGTCCTGTTTCTATCATGATGCCATAACA
1 TCTTTCAACCATAGTCCTACTCAT-CTT-TATCATGATGCCATAACA
* * * * *
39983624 TCTTTCAGCTATGGTCTTACTCATCTTTATCATGATGTCATAACA
1 TCTTTCAACCATAGTCCTACTCATCTTTATCATGATGCCATAACA
39983669 TCTTTCAAC
1 TCTTTCAAC
39983678 TAGGTTTTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
45 25 0.56
46 2 0.04
47 18 0.40
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.40
Consensus pattern (45 bp):
TCTTTCAACCATAGTCCTACTCATCTTTATCATGATGCCATAACA
Found at i:39983657 original size:45 final size:43
Alignment explanation
Indices: 39983606--39983695 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 43
39983596 GTCCTGTTTC
*
39983606 TATCATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTT
1 TATCATGATGCCATAACATCTTTCAACTA-GGTCTTACTCAT-TT
* *
39983651 TATCATGATGTCATAACATCTTTCAACTAGGTTTTACTCATTT
1 TATCATGATGCCATAACATCTTTCAACTAGGTCTTACTCATTT
39983694 TA
1 TA
39983696 GGCAATAGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 4 0.10
44 11 0.26
45 27 0.64
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (43 bp):
TATCATGATGCCATAACATCTTTCAACTAGGTCTTACTCATTT
Found at i:39987219 original size:22 final size:23
Alignment explanation
Indices: 39987144--39987244 Score: 116
Period size: 23 Copynumber: 4.4 Consensus size: 23
39987134 CTGAGCCAAT
*
39987144 AAACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCGAAGAGCTG
* *
39987167 AAACGGTAAGCCCCTAAG-GACTG
1 AAACGGTAAGCTCCGAAGAG-CTG
39987190 AAACGGTAAGCTCCGAAGAGCTG
1 AAACGGTAAGCTCCGAAGAGCTG
* **
39987213 -AACGGTATGCTCATAAGAGCTG
1 AAACGGTAAGCTCCGAAGAGCTG
*
39987235 AAATGGTAAG
1 AAACGGTAAG
39987245 TTCATACAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
22 20 0.31
23 44 0.68
24 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.17
Consensus pattern (23 bp):
AAACGGTAAGCTCCGAAGAGCTG
Found at i:39989915 original size:26 final size:26
Alignment explanation
Indices: 39989875--39989938 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
39989865 CGACGATCTC
39989875 AAAAACATAGAAATCATTAAAAAACGAG
1 AAAAA-AT-GAAATCATTAAAAAACGAG
*
39989903 CAAAAATGAAATCATTAAAAAACGAG
1 AAAAAATGAAATCATTAAAAAACGAG
39989929 AAAAAATGAA
1 AAAAAATGAA
39989939 CTTACAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 28 0.82
27 2 0.06
28 4 0.12
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.14
Consensus pattern (26 bp):
AAAAAATGAAATCATTAAAAAACGAG
Found at i:39991394 original size:85 final size:85
Alignment explanation
Indices: 39991246--39991424 Score: 340
Period size: 85 Copynumber: 2.1 Consensus size: 85
39991236 GGCCAGCCAT
39991246 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTACATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTACATTAT
39991311 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
39991331 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTACATTAT
39991396 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
39991416 GGGCATGGG
1 GAGCATGGG
39991425 CAATAAAATA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTACATTAT
GTAAGGATTAATAAAATAAA
Found at i:39992747 original size:47 final size:47
Alignment explanation
Indices: 39992693--39993099 Score: 588
Period size: 47 Copynumber: 8.6 Consensus size: 47
39992683 TATTTGAATA
*
39992693 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
39992740 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
39992789 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
39992838 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
39992885 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
39992932 AATGTGAACA-TGTGTATGTGTGATAAGGACGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
39992979 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
39993026 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
39993073 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
39993100 TCCTAAAGGG
Statistics
Matches: 342, Mismatches: 14, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 247 0.72
49 93 0.27
50 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:39995593 original size:38 final size:38
Alignment explanation
Indices: 39995529--39995603 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
39995519 AATCCGAGTT
*
39995529 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
39995567 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
39995604 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:39995721 original size:40 final size:40
Alignment explanation
Indices: 39995657--39995897 Score: 322
Period size: 40 Copynumber: 6.0 Consensus size: 40
39995647 AGGTCTCGAC
*
39995657 GATG-ATCCAGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
39995696 GATGTATCGGGGCTAAGTTCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
39995736 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
39995776 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * ** * *
39995816 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * ** * *
39995856 GTTATATCCGGGCTGGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
39995896 GA
1 GA
39995898 CGTGTATTCG
Statistics
Matches: 179, Mismatches: 22, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
39 4 0.02
40 175 0.98
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:39996773 original size:13 final size:13
Alignment explanation
Indices: 39996755--39996781 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39996745 AATGAATACA
39996755 ATTGCTATCGATG
1 ATTGCTATCGATG
39996768 ATTGCTATCGATG
1 ATTGCTATCGATG
39996781 A
1 A
39996782 GCTAATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (13 bp):
ATTGCTATCGATG
Found at i:39997309 original size:85 final size:85
Alignment explanation
Indices: 39997166--39997344 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
39997156 GGCCGGCCAT
39997166 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
39997231 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
39997251 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
39997316 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
39997336 GGGCATGGG
1 GAGCATGGG
39997345 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:39998688 original size:23 final size:23
Alignment explanation
Indices: 39998658--39998705 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
39998648 AATGTGATGA
39998658 ATGTGAAAGTGTATATATATGTG
1 ATGTGAAAGTGTATATATATGTG
39998681 ATGTGAAAGTGTATATATATGTG
1 ATGTGAAAGTGTATATATATGTG
39998704 AT
1 AT
39998706 AAGGCCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (23 bp):
ATGTGAAAGTGTATATATATGTG
Found at i:39998821 original size:47 final size:47
Alignment explanation
Indices: 39998694--39999039 Score: 491
Period size: 47 Copynumber: 7.3 Consensus size: 47
39998684 TGAAAGTGTA
*
39998694 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA-AGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
39998741 TATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 --TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* * * *
39998790 TGTATGTGCGATAAGGCCGAATGGCCAATGTGATGAATGTGAATATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
39998837 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* * *
39998884 TGTATGTGTGATAAGGACGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
39998931 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
* *
39998978 TATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAA-GTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATG
*
39999025 TATAAATGTGATAAG
1 TATATATGTGATAAG
39999040 TCCTAAAGGG
Statistics
Matches: 269, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
46 1 0.00
47 220 0.82
48 3 0.01
49 44 0.16
50 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (47 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
Found at i:40000862 original size:48 final size:48
Alignment explanation
Indices: 40000806--40000901 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
40000796 GAAATTTTTA
40000806 AAATGGACTGCGATAGTAAGCGAATTTAGTCTGTGAACCCCTCGTGTC
1 AAATGGACTGCGATAGTAAGCGAATTTAGTCTGTGAACCCCTCGTGTC
40000854 AAATGGACTGCGATAGTAAGCGAATTTAGTCTGTGAACCCCTCGTGTC
1 AAATGGACTGCGATAGTAAGCGAATTTAGTCTGTGAACCCCTCGTGTC
40000902 CGACTCCAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (48 bp):
AAATGGACTGCGATAGTAAGCGAATTTAGTCTGTGAACCCCTCGTGTC
Found at i:40001193 original size:13 final size:13
Alignment explanation
Indices: 40001175--40001199 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40001165 AATTCTCTCA
40001175 CCACTATGATCAG
1 CCACTATGATCAG
40001188 CCACTATGATCA
1 CCACTATGATCA
40001200 TAGCAAGTAA
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:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (13 bp):
CCACTATGATCAG
Found at i:40013822 original size:47 final size:47
Alignment explanation
Indices: 40013768--40013961 Score: 262
Period size: 47 Copynumber: 4.1 Consensus size: 47
40013758 TTAGGATTTT
** * *
40013768 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
40013815 ATGTGATGAATGTGAACATGCATATATGTGATAACGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
40013862 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGACTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
40013909 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40013956 ATGTGA
1 ATGTGA
40013962 AATATGTATG
Statistics
Matches: 127, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 127 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40013991 original size:48 final size:48
Alignment explanation
Indices: 40013931--40014213 Score: 433
Period size: 48 Copynumber: 5.8 Consensus size: 48
40013921 TGAACATGCA
40013931 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
*
40013979 TATATGTGGTAAAACCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* *
40014027 TATATGTGGTAAAGCCGAATGGCTAATATAAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
*
40014075 TATATGTGGTAAAGCCGAATGGCTATTGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* * *
40014123 CATATGTGGTGAAGCCGAATGG-TCAATGTGAAATATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG--A-A-ATATGTATGAGATATG
* *
40014175 TATATGTGGTAAAGCCGAGTGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
40014214 GGCGATGTGC
Statistics
Matches: 213, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
47 1 0.00
48 168 0.79
49 1 0.00
50 2 0.01
51 1 0.00
52 39 0.18
53 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:40014467 original size:37 final size:37
Alignment explanation
Indices: 40014363--40014467 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
40014353 ATATATTCCA
*
40014363 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
* *
40014400 AGTAAGACCCGATGACTACGAGTGGAGATTTTGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
* *
40014437 GGTAAGACCCGATAACTTCGTGTGGAGATTT
1 GGTAAGACCCGATGACTACGTGTGGAGATTT
40014468 CATCTGAGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (37 bp):
GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
Found at i:40016383 original size:14 final size:16
Alignment explanation
Indices: 40016358--40016390 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40016348 TATTATTTGA
40016358 TTTAATTTTAATT-TT
1 TTTAATTTTAATTCTT
40016373 TTTAA-TTTAATTCTT
1 TTTAATTTTAATTCTT
40016388 TTT
1 TTT
40016391 CCTAAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTAATTTTAATTCTT
Found at i:40016982 original size:29 final size:29
Alignment explanation
Indices: 40016945--40017003 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
40016935 CCGTGTGCCT
* * *
40016945 GGTCATGTGGTAGGTCGTGTGCGACACAC
1 GGTCATGTGGTAGGCCGTATGCAACACAC
*
40016974 GGTCGTGTGGTAGGCCGTATGCAACACAC
1 GGTCATGTGGTAGGCCGTATGCAACACAC
40017003 G
1 G
40017004 ACCTTGTGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.22, G:0.37, T:0.22
Consensus pattern (29 bp):
GGTCATGTGGTAGGCCGTATGCAACACAC
Found at i:40017011 original size:29 final size:29
Alignment explanation
Indices: 40016950--40017011 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
40016940 TGCCTGGTCA
* * * **
40016950 TGTGGTAGGTCGTGTGCGACACACGGTCG
1 TGTGGTAGGCCGTATGCAACACACGACCG
*
40016979 TGTGGTAGGCCGTATGCAACACACGACCT
1 TGTGGTAGGCCGTATGCAACACACGACCG
40017008 TGTG
1 TGTG
40017012 ACGGGTGTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.23, G:0.35, T:0.24
Consensus pattern (29 bp):
TGTGGTAGGCCGTATGCAACACACGACCG
Found at i:40023619 original size:23 final size:24
Alignment explanation
Indices: 40023576--40023629 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
40023566 ATGTATAAAT
40023576 TCAAAATTTTCATTATCTATT-TA
1 TCAAAATTTTCATTATCTATTATA
*
40023599 TCAAAATTTT-ATTGATTTATTATA
1 TCAAAATTTTCATT-ATCTATTATA
*
40023623 TAAAAAT
1 TCAAAAT
40023630 ATATTCTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 16 0.59
24 8 0.30
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (24 bp):
TCAAAATTTTCATTATCTATTATA
Found at i:40024660 original size:3 final size:3
Alignment explanation
Indices: 40024652--40024676 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40024642 TTTCAAAATG
40024652 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
40024677 AAACAAAAGT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40025038 original size:3 final size:3
Alignment explanation
Indices: 40025030--40025056 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40025020 AATTTCACAA
40025030 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
40025057 TAGAGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40030511 original size:46 final size:46
Alignment explanation
Indices: 40030450--40030540 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
40030440 AACCTAGGCC
*
40030450 CTCATGCATATAACATAATGCTCTTGCCATTGGGCGAAGAGGTTAT
1 CTCATGCATACAACATAATGCTCTTGCCATTGGGCGAAGAGGTTAT
*
40030496 CTCATGCCTACAACATAATGCTCTTGCCATTGGGCGAAGAGGTTA
1 CTCATGCATACAACATAATGCTCTTGCCATTGGGCGAAGAGGTTA
40030541 ACTTAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (46 bp):
CTCATGCATACAACATAATGCTCTTGCCATTGGGCGAAGAGGTTAT
Found at i:40033473 original size:24 final size:24
Alignment explanation
Indices: 40033445--40033501 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
40033435 GAGTAGACCC
40033445 ATATTCACAAATCGTGCGAGCATT
1 ATATTCACAAATCGTGCGAGCATT
* *
40033469 ATATTCACAACTCGTGTGAGCATT
1 ATATTCACAAATCGTGCGAGCATT
40033493 ATATTCACA
1 ATATTCACA
40033502 GCTCATGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (24 bp):
ATATTCACAAATCGTGCGAGCATT
Found at i:40033510 original size:24 final size:24
Alignment explanation
Indices: 40033445--40033512 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
40033435 GAGTAGACCC
* * *
40033445 ATATTCACAAATCGTGCGAGCATT
1 ATATTCACAACTCATGTGAGCATT
*
40033469 ATATTCACAACTCGTGTGAGCATT
1 ATATTCACAACTCATGTGAGCATT
*
40033493 ATATTCACAGCTCATGTGAG
1 ATATTCACAACTCATGTGAG
40033513 AATTTCTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (24 bp):
ATATTCACAACTCATGTGAGCATT
Found at i:40046398 original size:37 final size:37
Alignment explanation
Indices: 40046339--40046447 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
40046329 AGCTCAGACG
* *
40046339 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* * *
40046376 AAATCTCCATATGTAGTCATCGGGCCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
40046413 TAATCTCCACACGTAGTCATCGGGTCTTGCCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
40046448 ATATATTTCC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:40046651 original size:50 final size:47
Alignment explanation
Indices: 40046594--40046830 Score: 321
Period size: 50 Copynumber: 4.8 Consensus size: 47
40046584 GCACATCGCC
40046594 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACA-TAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
40046644 TATATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATAG-CCATTCGGCTTTACCACATATACATATCTCA
40046692 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATACATATCTCATA
1 TACATATTTCACA-TAGCCATTCGGCTTTACCAC--ATATACATATCTC--A
* * *
40046744 TATATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATAG-CCATTCGGCTTTACCACATATACATATCTCA
40046792 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACA-TAGCCATTCGGCTTTACCACATATA
40046831 TACATGTTCA
Statistics
Matches: 167, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
48 64 0.38
49 6 0.04
50 65 0.39
51 2 0.01
52 30 0.18
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (47 bp):
TACATATTTCACATAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:40046718 original size:48 final size:49
Alignment explanation
Indices: 40046594--40046830 Score: 347
Period size: 48 Copynumber: 4.8 Consensus size: 49
40046584 GCACATCGCC
*
40046594 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA-A
* *
40046644 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCAA
40046692 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCAC--ATATACATATCTCA-A
* *
40046744 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCAA
40046792 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
40046831 TACATGTTCA
Statistics
Matches: 170, Mismatches: 9, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
48 68 0.40
49 3 0.02
50 66 0.39
51 1 0.01
52 32 0.19
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (49 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAA
Found at i:40046773 original size:100 final size:100
Alignment explanation
Indices: 40046594--40046843 Score: 461
Period size: 100 Copynumber: 2.5 Consensus size: 100
40046584 GCACATCGCC
*
40046594 TACATATTTCACACTAGCCATTCGGCTTTACCAC--ATATACATATCTCATATATATATTTCACA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATACATATCTCATATATATATTTCACA
40046657 TTGACCATTCGGCTTTACCACATATGCATATCTCA
66 TTGACCATTCGGCTTTACCACATATGCATATCTCA
40046692 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATACATATCTCATATATATATTTCACA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATACATATCTCATATATATATTTCACA
40046757 TTGACCATTCGGCTTTACCACATATGCATATCTCA
66 TTGACCATTCGGCTTTACCACATATGCATATCTCA
*
40046792 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATACATGT-TCATAT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATACATATCTCATAT
40046844 TCACCACATT
Statistics
Matches: 148, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
98 33 0.22
99 6 0.04
100 109 0.74
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (100 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATATACATATCTCATATATATATTTCACA
TTGACCATTCGGCTTTACCACATATGCATATCTCA
Found at i:40046860 original size:47 final size:47
Alignment explanation
Indices: 40046752--40046899 Score: 149
Period size: 47 Copynumber: 3.1 Consensus size: 47
40046742 TATATATATT
* * *
40046752 TCACATTGACCATTCGGCTTTACCACATATGCATATC-TCATACATATT--
1 TCACATTGGCCATTCGGCTTTACCACATAT--ATA-CAT-GTTCATATTCA
*
40046800 TCACATTAGCCATTCGGCTTTACCACATATATACATGTTCATATTCA
1 TCACATTGGCCATTCGGCTTTACCACATATATACATGTTCATATTCA
* * * * * *
40046847 CCACATTGGCCATTCGGCCTTATCACACATATACATGCTCACATTCA
1 TCACATTGGCCATTCGGCTTTACCACATATATACATGTTCATATTCA
40046894 TCACAT
1 TCACAT
40046900 AAAATCCTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
45 8 0.09
46 4 0.05
47 45 0.53
48 28 0.33
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCTTTACCACATATATACATGTTCATATTCA
Found at i:40051503 original size:23 final size:23
Alignment explanation
Indices: 40051477--40051524 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
40051467 ATATGTTGGC
*
40051477 TTATTTTAGCATTTTGATTTATT
1 TTATTTTAGCATTTTGATTCATT
40051500 TTATTTTAGCATTTTGATTCATT
1 TTATTTTAGCATTTTGATTCATT
40051523 TT
1 TT
40051525 GTATAACGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (23 bp):
TTATTTTAGCATTTTGATTCATT
Found at i:40054328 original size:18 final size:18
Alignment explanation
Indices: 40054305--40054340 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40054295 TTCGAATTTG
40054305 ACTTATTCAATCTCACAT
1 ACTTATTCAATCTCACAT
40054323 ACTTATTCAATCTCACAT
1 ACTTATTCAATCTCACAT
40054341 TCATTCAAAT
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:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (18 bp):
ACTTATTCAATCTCACAT
Found at i:40060736 original size:23 final size:23
Alignment explanation
Indices: 40060710--40060753 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40060700 TATATCCATA
* *
40060710 CCAAAATCATGCCAAATCATAAG
1 CCAAAATCATACCAAAACATAAG
*
40060733 CCAAAGTCATACCAAAACATA
1 CCAAAATCATACCAAAACATA
40060754 TGTTTCATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.27, G:0.07, T:0.16
Consensus pattern (23 bp):
CCAAAATCATACCAAAACATAAG
Found at i:40061529 original size:42 final size:43
Alignment explanation
Indices: 40061420--40061532 Score: 117
Period size: 43 Copynumber: 2.7 Consensus size: 43
40061410 AGCTCGTACA
* * *
40061420 ATGCCAAC-ATCCCAAATATGGTCTTACATGTAATCAAATGCCG
1 ATGCC-ACTATCCCAAACATGGTCTTACATGAAATCAAATGACG
40061463 ATGCCACTATCCCAAACA-GAGTCTTACATGAAATCAAAT-ACG
1 ATGCCACTATCCCAAACATG-GTCTTACATGAAATCAAATGACG
* * *
40061505 ATGCCGA-TGTCCTAGACATGGTCTTACA
1 ATGCC-ACTATCCCAAACATGGTCTTACA
40061533 CGTAAATCTC
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
42 26 0.43
43 34 0.57
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (43 bp):
ATGCCACTATCCCAAACATGGTCTTACATGAAATCAAATGACG
Found at i:40072356 original size:48 final size:48
Alignment explanation
Indices: 40072283--40072394 Score: 161
Period size: 48 Copynumber: 2.3 Consensus size: 48
40072273 AGTAACGAGA
* *
40072283 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATTGATATATGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATATGT
* * * * *
40072331 GTCAGTGTAAAACCATGTCTGGGACATGGCATCGGCGTTGATATGTTT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATATGT
40072379 GCCAGTGTAAGACCAT
1 GCCAGTGTAAGACCAT
40072395 ATCTAGGATA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATATGT
Found at i:40078402 original size:40 final size:40
Alignment explanation
Indices: 40078018--40078519 Score: 511
Period size: 40 Copynumber: 12.6 Consensus size: 40
40078008 TCGAATGATG
* *
40078018 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TATA
* * * *
40078058 TTCGGACTAAGAT-CCGAAG-GCATTTGTG-TGAGTTACTA-A
1 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGCT-AGTGA-TATA
* * * *
40078097 TTCCGGGCTAAG-CCCGAAG-GCATTGGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TATA
* * * *
40078137 TCCGGGTTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TATA
* * * *
40078177 ACCGGGCTAAGTCCCGAAGAGTATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* *
40078217 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* *
40078257 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* * *
40078297 TCTGGGCTAAGTCCCGAAGAGCATTCATTCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* * *
40078337 TTCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* *
40078377 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* *
40078417 TCCGGGCTAAGTTCCGAAAAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* * * * *
40078457 TCCGTGCTAA-ACCCTGAAGAGCATTCGTGTTGGTGTTATA
1 TCCGGGCTAAGTCCC-GAAGAGCATTCGTGCTAGTGATATA
*
40078497 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCA
40078520 ATCATGCTGG
Statistics
Matches: 400, Mismatches: 52, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
39 35 0.09
40 344 0.86
41 21 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:40086016 original size:20 final size:20
Alignment explanation
Indices: 40085991--40086036 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40085981 ATTGGGCCTT
40085991 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
40086011 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
40086030 GCCCATA
1 GCCCATA
40086037 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:40086045 original size:19 final size:20
Alignment explanation
Indices: 40086003--40086046 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
40085993 CCATATTAAC
** *
40086003 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
40086023 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
40086042 ACAGT
1 ACAGT
40086047 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:40090094 original size:177 final size:176
Alignment explanation
Indices: 40089398--40090080 Score: 833
Period size: 177 Copynumber: 3.9 Consensus size: 176
40089388 ACCACATCAA
* *
40089398 GGAGATAATATCTACAATCTTCAGTC-AGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCG
1 GGAGATAAGATCTTCAATCTTCAGTCTA-CTTCCTTGCTACCTCAGGAAGATAAGACTACAATCG
* * * *
40089462 CCAACCTGTTCTCTTGCTACCTCAAAGAAATAAGGCTGGTGGCTAAAATCTACTCCACTGCTACC
65 CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCACTGCTA--
*
40089527 T-CGA-GAAGATAAGACTCGCCATCTTCGATCTGCTCCACAACTGCTTAG
128 TAC-ATGAAGATAAGACTCGCCATCTTCGATCTACTCCACAACTGCTTAG
* * * *
40089575 GGAAATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTGAGGAAGATAAGACTACAATCGA
1 GGAGATAAGATCTTCAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGC
* * * * * *
40089640 CAACCTGCTCTCTTGCTACCT-A-AGAGATAAGGTTGGTGG-TTAAAATATGCTCCCCTACTA-C
66 CAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTT-AAATCTACTCCACTGCTATA
* * *
40089701 CTTGGGAAGATCAGACTCGCCATCTTCGATCTACTCCGCAACTGCTTAG
130 CAT--GAAGATAAGACTCGCCATCTTCGATCTACTCCACAACTGCTTAG
* * * *
40089750 GGAGATAAGATCTTGAATCTTCAATCTGCTTCCTGGCTACCTCAGGAAGATAAGACTACAATCGC
1 GGAGATAAGATCTTCAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGC
* *
40089815 CAACCTGCTCTCTTTG-TACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCATTGCCGAT
66 CAACCTGCTCTC-TTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCACTG-CTAT
* * *
40089879 ACATAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAG
129 ACATGAAGATAAGACTCGCCATCTTCGATCTACTCCACAACTGCTTAG
* * * * *
40089927 AGAGATAAGATCTTTAATCTTTAGTCTACTTCCTTGCTGCCTTAGGAAGATAAGACTACAATCGC
1 GGAGATAAGATCTTCAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGC
* * * * * *
40089992 CAACCTGTTCTTTTGCTACCTTAGAGAGATAAGGTTGGTGGCTTAAATCTACTCTATTGCTGATA
66 CAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCACTGCT-ATA
* * *
40090057 CATGGAGATAAGATTCACCATCTT
130 CATGAAGATAAGACTCGCCATCTT
40090081 GAGTTTGCTC
Statistics
Matches: 437, Mismatches: 55, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
173 1 0.00
174 1 0.00
175 146 0.33
176 9 0.02
177 274 0.63
178 4 0.01
179 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (176 bp):
GGAGATAAGATCTTCAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGC
CAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCACTGCTATAC
ATGAAGATAAGACTCGCCATCTTCGATCTACTCCACAACTGCTTAG
Found at i:40090510 original size:64 final size:64
Alignment explanation
Indices: 40090409--40090536 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
40090399 TCATGTATCT
40090409 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCACCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCACCTAACTAGATGTG
* *
40090473 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCACCTAACTAGATGTG
40090537 TTATGAAGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCACCTAACTAGATGTG
Found at i:40091646 original size:30 final size:30
Alignment explanation
Indices: 40091612--40091669 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
40091602 AAATTTTGAT
* *
40091612 TGATTCTTTTTTTATTTTTTATTTTTTTTG
1 TGATTCATTTTTTACTTTTTATTTTTTTTG
* * *
40091642 TGATTGATTTTTTCCTTTTTGTTTTTTT
1 TGATTCATTTTTTACTTTTTATTTTTTT
40091670 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.09, C:0.05, G:0.09, T:0.78
Consensus pattern (30 bp):
TGATTCATTTTTTACTTTTTATTTTTTTTG
Found at i:40092229 original size:12 final size:12
Alignment explanation
Indices: 40092212--40092239 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40092202 GTTTTTTTTG
40092212 TTTTTCTTCTTC
1 TTTTTCTTCTTC
40092224 TTTTTCTTCTTC
1 TTTTTCTTCTTC
40092236 TTTT
1 TTTT
40092240 ATTTTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:40092244 original size:28 final size:28
Alignment explanation
Indices: 40092213--40092267 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
40092203 TTTTTTTTGT
*
40092213 TTTTCTTCTTCTTTTTCTTCTTCTTTTA
1 TTTTCTTCTACTTTTTCTTCTTCTTTTA
* * * *
40092241 TTTTTTTGTACTTTTTGTTTTTCTTTT
1 TTTTCTTCTACTTTTTCTTCTTCTTTT
40092268 TGGTTGCCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.78
Consensus pattern (28 bp):
TTTTCTTCTACTTTTTCTTCTTCTTTTA
Found at i:40092266 original size:12 final size:12
Alignment explanation
Indices: 40092206--40092269 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 12
40092196 ACCTTGGTTT
40092206 TTTTTGTTTTTC
1 TTTTTGTTTTTC
* *
40092218 TTCTTCTTTTTC
1 TTTTTGTTTTTC
* * *
40092230 TTCTT-CTTTTA
1 TTTTTGTTTTTC
* *
40092241 TTTTT-TTGTAC
1 TTTTTGTTTTTC
40092252 TTTTTGTTTTTC
1 TTTTTGTTTTTC
40092264 TTTTTG
1 TTTTTG
40092270 GTTGCCTTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
11 15 0.38
12 25 0.62
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.78
Consensus pattern (12 bp):
TTTTTGTTTTTC
Found at i:40108476 original size:44 final size:44
Alignment explanation
Indices: 40108422--40108508 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
40108412 GTCCCATGTG
* *
40108422 ATGATAGGCAAACCTCACATAAATGAGTTTTGGCAAATTTGTAA
1 ATGATAGGCAAACCTCACAAAAATGAGTTTTGGAAAATTTGTAA
*
40108466 ATGATGGGCAAACCTCACAAAAATGAGTTTTGGAAAATTTGTA
1 ATGATAGGCAAACCTCACAAAAATGAGTTTTGGAAAATTTGTA
40108509 CCACCCCAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (44 bp):
ATGATAGGCAAACCTCACAAAAATGAGTTTTGGAAAATTTGTAA
Found at i:40111286 original size:28 final size:28
Alignment explanation
Indices: 40111247--40111317 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
40111237 AACACGATAG
40111247 AAAAGAATAGCCTTTGTGGTGAATCGTA
1 AAAAGAATAGCCTTTGTGGTGAATCGTA
*
40111275 AAAAGAATAGCCTTTGTGGTGAATTGTA
1 AAAAGAATAGCCTTTGTGGTGAATCGTA
40111303 AAAAGGAA-AGCCTTT
1 AAAA-GAATAGCCTTT
40111318 ATGGCAGATC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 38 0.93
29 3 0.07
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (28 bp):
AAAAGAATAGCCTTTGTGGTGAATCGTA
Found at i:40112425 original size:26 final size:26
Alignment explanation
Indices: 40112389--40112457 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
40112379 TTCCATTTTG
40112389 GAAAATATTTTTATTTTTTTATACAA
1 GAAAATATTTTTATTTTTTTATACAA
40112415 GAAAATATTTTTATTTTTTTATACAA
1 GAAAATATTTTTATTTTTTTATACAA
*
40112441 GAAAATATTTTGATTTT
1 GAAAATATTTTTATTTT
40112458 AAAGTGTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (26 bp):
GAAAATATTTTTATTTTTTTATACAA
Found at i:40115172 original size:20 final size:20
Alignment explanation
Indices: 40115147--40115187 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40115137 ACATGTAAAT
40115147 ACGATTTTTGATTATTTATA
1 ACGATTTTTGATTATTTATA
40115167 ACGATTTTTGATTATTTATA
1 ACGATTTTTGATTATTTATA
40115187 A
1 A
40115188 TTTTGTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (20 bp):
ACGATTTTTGATTATTTATA
Found at i:40120068 original size:14 final size:14
Alignment explanation
Indices: 40120049--40120075 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40120039 TCCACATTTT
40120049 ATAAACATACATTA
1 ATAAACATACATTA
40120063 ATAAACATACATT
1 ATAAACATACATT
40120076 TCATACACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAACATACATTA
Found at i:40130661 original size:18 final size:18
Alignment explanation
Indices: 40130634--40130669 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40130624 AAGTTACATC
40130634 GAGTACTTTGTTAGTAAT
1 GAGTACTTTGTTAGTAAT
*
40130652 GAGTATTTTGTTAGTAAT
1 GAGTACTTTGTTAGTAAT
40130670 ATGTTAATAA
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:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (18 bp):
GAGTACTTTGTTAGTAAT
Found at i:40130962 original size:21 final size:19
Alignment explanation
Indices: 40130901--40130964 Score: 51
Period size: 21 Copynumber: 3.3 Consensus size: 19
40130891 TTTTATATGA
* *
40130901 TTAAAT-TTCAAAATAATT
1 TTAAATATTTAAAATAAAT
* *
40130919 TTAAATATTTAATATGTAA-
1 TTAAATATTTAAAAT-AAAT
40130938 TTAATAGTATTTAAAATAAAT
1 TTAA-A-TATTTAAAATAAAT
40130959 TTAAAT
1 TTAAAT
40130965 TTAAATTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
18 6 0.17
19 11 0.31
20 5 0.14
21 13 0.37
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (19 bp):
TTAAATATTTAAAATAAAT
Found at i:40131078 original size:25 final size:25
Alignment explanation
Indices: 40131049--40131096 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40131039 AAGTAAAATT
* *
40131049 TTACTCCCTTTTATAAAATCCCAAA
1 TTACTACCTTTGATAAAATCCCAAA
*
40131074 TTACTACCTTTGATACAATCCCA
1 TTACTACCTTTGATAAAATCCCA
40131097 GAGCTTAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.35
Consensus pattern (25 bp):
TTACTACCTTTGATAAAATCCCAAA
Found at i:40140040 original size:40 final size:40
Alignment explanation
Indices: 40139950--40140169 Score: 241
Period size: 40 Copynumber: 5.5 Consensus size: 40
40139940 ACCCAAGTAT
* ** * *
40139950 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
40139988 CTTTGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* **
40140028 CTTCGGGACTTAGCCCGGATATAATCGTTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
40140068 CTTCGGGTCTTAGCCCGGATATAG-CAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
40140108 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
40140148 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
40140170 CATTCGAATA
Statistics
Matches: 149, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
38 10 0.07
39 18 0.12
40 117 0.79
41 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:40143357 original size:21 final size:21
Alignment explanation
Indices: 40143308--40143359 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
40143298 TGTTGAAAAG
*
40143308 GAAGTTGTTGCTACAGAAGAG
1 GAAGTTGTTGCTACAGAAGAA
40143329 GATA-TTGTTGCTGA-AGAAGAA
1 GA-AGTTGTTGCT-ACAGAAGAA
40143350 GAAGTTGTTG
1 GAAGTTGTTG
40143360 AAAATGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.29
Consensus pattern (21 bp):
GAAGTTGTTGCTACAGAAGAA
Found at i:40143830 original size:17 final size:17
Alignment explanation
Indices: 40143808--40143841 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40143798 GATAAATATA
* *
40143808 TATTGTGATTGCATTTT
1 TATTGTCATTACATTTT
40143825 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
40143842 CATGTTAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:40158977 original size:19 final size:19
Alignment explanation
Indices: 40158943--40158979 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40158933 AGTATTAAAG
40158943 CAAATAAAATATAAATCCC
1 CAAATAAAATATAAATCCC
40158962 CAAATTAAAATA-AAATCC
1 CAAA-TAAAATATAAATCC
40158980 AGAGAGGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (19 bp):
CAAATAAAATATAAATCCC
Found at i:40165605 original size:16 final size:16
Alignment explanation
Indices: 40165586--40165616 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40165576 CTTCTTCACT
40165586 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
40165602 TACTTACTTACTTAA
1 TACTCACTTACTTAA
40165617 TCAAATTTAT
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:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:40165622 original size:20 final size:20
Alignment explanation
Indices: 40165583--40165622 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40165573 AAACTTCTTC
* *
40165583 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
40165603 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
40165623 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:40165998 original size:55 final size:54
Alignment explanation
Indices: 40165852--40166058 Score: 247
Period size: 55 Copynumber: 3.8 Consensus size: 54
40165842 GGTATCCTCT
* * * *
40165852 TGAAACTTACCATTTCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTA
1 TGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
* * *
40165906 TG-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTA
1 TGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTA
* * *
40165959 TAGAAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA
1 T-GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
* * * *
40166014 GGAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTAT
1 TGAAACTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTAT
40166059 TCTTAAATCC
Statistics
Matches: 128, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
52 2 0.02
53 42 0.33
54 13 0.10
55 69 0.54
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (54 bp):
TGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
Found at i:40173744 original size:14 final size:14
Alignment explanation
Indices: 40173725--40173808 Score: 78
Period size: 15 Copynumber: 5.8 Consensus size: 14
40173715 CAAAGATAAC
* *
40173725 AAGAAAACCGAATA
1 AAGAAATCCAAATA
40173739 AAGAAATCCAAGATA
1 AAGAAATCCAA-ATA
* *
40173754 GAGAAACCCAAATA
1 AAGAAATCCAAATA
40173768 AAGAAATCCAGAATA
1 AAGAAATCCA-AATA
* *
40173783 AAGAGATCCAGGATA
1 AAGAAATCCA-AATA
*
40173798 AAGAAACCCAA
1 AAGAAATCCAA
40173809 GATACGATAC
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
14 20 0.35
15 37 0.65
ACGTcount: A:0.58, C:0.17, G:0.15, T:0.10
Consensus pattern (14 bp):
AAGAAATCCAAATA
Found at i:40173764 original size:15 final size:15
Alignment explanation
Indices: 40173736--40173812 Score: 86
Period size: 15 Copynumber: 5.2 Consensus size: 15
40173726 AGAAAACCGA
40173736 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
40173751 ATAGAGAAACCCAA-
1 ATAAAGAAATCCAAG
40173765 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
40173779 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
40173795 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
40173810 ATA
1 ATA
40173813 CGATACTATG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 38 0.76
16 1 0.02
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:40173767 original size:29 final size:29
Alignment explanation
Indices: 40173725--40173812 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
40173715 CAAAGATAAC
*
40173725 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAAACCAAATAAAGAAATCCAAGATA
* *
40173754 GAGAAACCCAAATAAAGAAATCC-AGAATA
1 AAGAAAACCAAATAAAGAAATCCAAG-ATA
* * * *
40173783 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCA-AATAAAGAAATCCAAGATA
40173813 CGATACTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.04
29 30 0.62
30 14 0.29
31 2 0.04
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (29 bp):
AAGAAAACCAAATAAAGAAATCCAAGATA
Found at i:40173792 original size:44 final size:43
Alignment explanation
Indices: 40173725--40173808 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 43
40173715 CAAAGATAAC
*
40173725 AAGAAAACCGAATAAAGAAATCCAAGATAGAGAAACCCAAATA
1 AAGAAAACCGAATAAAGAAATCCAAGATAAAGAAACCCAAATA
* * *
40173768 AAGAAATCCAGAATAAAGAGATCCAGGATAAAGAAACCCAA
1 AAGAAAACC-GAATAAAGAAATCCAAGATAAAGAAACCCAA
40173809 GATACGATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 8 0.22
44 28 0.78
ACGTcount: A:0.58, C:0.17, G:0.15, T:0.10
Consensus pattern (43 bp):
AAGAAAACCGAATAAAGAAATCCAAGATAAAGAAACCCAAATA
Found at i:40176844 original size:93 final size:93
Alignment explanation
Indices: 40176732--40176903 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
40176722 GCCCATAAGT
* *
40176732 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40176797 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
40176825 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40176890 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
40176904 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40176899 original size:46 final size:46
Alignment explanation
Indices: 40176724--40176899 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
40176714 TGTAACCCGC
* * * *
40176724 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
40176770 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
40176820 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
40176863 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40176900 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 2 0.02
46 64 0.58
47 29 0.26
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:40178698 original size:7 final size:7
Alignment explanation
Indices: 40178637--40178729 Score: 80
Period size: 7 Copynumber: 13.1 Consensus size: 7
40178627 TTAAGGGTTG
40178637 GGGTTTA
1 GGGTTTA
*
40178644 AGGTTTA
1 GGGTTTA
40178651 GAGGTTTA
1 G-GGTTTA
*
40178659 GGGGTTA
1 GGGTTTA
*
40178666 GGGGTTA
1 GGGTTTA
40178673 GGGTTTA
1 GGGTTTA
***
40178680 TATTTTA
1 GGGTTTA
*
40178687 -TGTTTA
1 GGGTTTA
40178693 GGGTTTA
1 GGGTTTA
*
40178700 GGATTTA
1 GGGTTTA
*
40178707 GGGGTTA
1 GGGTTTA
40178714 GGGGTTTA
1 -GGGTTTA
40178722 GGGTTTA
1 GGGTTTA
40178729 G
1 G
40178730 ATTAATTAGT
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
6 4 0.06
7 52 0.75
8 13 0.19
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:40178721 original size:15 final size:15
Alignment explanation
Indices: 40178636--40178729 Score: 65
Period size: 15 Copynumber: 6.6 Consensus size: 15
40178626 TTTAAGGGTT
*
40178636 GGGGTTTAAGGTTTA
1 GGGGTTTAGGGTTTA
* *
40178651 GAGGTTTAGGGGTTA
1 GGGGTTTAGGGTTTA
40178666 GGGG-TTAGGGTTTA
1 GGGGTTTAGGGTTTA
*** *
40178680 -TATTTTA-TGTTTA
1 GGGGTTTAGGGTTTA
*
40178693 -GGGTTTAGGATTTA
1 GGGGTTTAGGGTTTA
40178707 GGGG-TTAGGGGTTTA
1 GGGGTTTA-GGGTTTA
40178722 -GGGTTTAG
1 GGGGTTTAG
40178730 ATTAATTAGT
Statistics
Matches: 59, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
13 9 0.15
14 23 0.39
15 27 0.46
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.41
Consensus pattern (15 bp):
GGGGTTTAGGGTTTA
Found at i:40179410 original size:14 final size:13
Alignment explanation
Indices: 40179361--40179412 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
40179351 TTGGTTTTTT
40179361 TATTTATAAAAACCA
1 TATTTATAAAAA--A
40179376 -ATTTATAAAAAA
1 TATTTATAAAAAA
* *
40179388 TAGTAATAAAAAA
1 TATTTATAAAAAA
40179401 TATTTTATAAAA
1 TA-TTTATAAAA
40179413 TCACTTAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 12 0.39
14 18 0.58
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (13 bp):
TATTTATAAAAAA
Found at i:40184210 original size:42 final size:43
Alignment explanation
Indices: 40184164--40184500 Score: 439
Period size: 43 Copynumber: 7.9 Consensus size: 43
40184154 GCATTTTTAA
* *
40184164 GAAAAGCGCCGTTAAAGGTC-TGTTCTATAGTGGCGTTTGTGG
1 GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGG
* *
40184206 GAAAAGCACCACTAAAGGTCATGTTCTATAGCGGCGTTTGTGG
1 GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGG
* * *
40184249 G-AGAGCGCCGTTAAAGGTCATGTTCTATAGCGGCGTTTGTAG
1 GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGG
* * * *
40184291 TAAAAGCGCCACTAAAGGTCTTATTCTATAGCGGCGTTTGT-G
1 GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGG
* * *
40184333 GAAAAGCACCACTAAAGGTCATGTTCTATAGCGACGTTTGTGG
1 GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGG
** * *
40184376 GAAAAATGCCTCTAAAGGTCATGTTCTATAGCGGCATTTGTGG
1 GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGG
* **
40184419 GAAAAGTGCCGCTAAAGGGT-ATGTTCTATATTGGCGTTTGTGG
1 GAAAAGCGCCGCTAAA-GGTCATGTTCTATAGCGGCGTTTGTGG
*
40184462 GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCTGCGTTT
1 GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTT
40184501 TTCTATATAA
Statistics
Matches: 255, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
42 93 0.36
43 159 0.62
44 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (43 bp):
GAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGG
Found at i:40184303 original size:85 final size:85
Alignment explanation
Indices: 40184166--40184500 Score: 440
Period size: 85 Copynumber: 3.9 Consensus size: 85
40184156 ATTTTTAAGA
* * *
40184166 AAAGCGCCGTTAAAGGTC-TGTTCTATAGTGGCGTTTGTGGGAAAAGCACCACTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGT
40184230 TCTATAGCGGCGTTTGTGGG
66 TCTATAGCGGCGTTTGTGGG
* * * * * *
40184250 AGAGCGCCGTTAAAGGTCATGTTCTATAGCGGCGTTTGTAGTAAAAGCGCCACTAAAGGTCTTAT
1 AAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGT
*
40184315 TCTATAGCGGCGTTTGTGGA
66 TCTATAGCGGCGTTTGTGGG
* * * ** *
40184335 AAAGCACCACTAAAGGTCATGTTCTATAGCGACGTTTGTGGGAAAAATGCCTCTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGT
*
40184400 TCTATAGCGGCATTTGTGGG
66 TCTATAGCGGCGTTTGTGGG
* ** *
40184420 AAAAGTGCCGCTAAAGGGT-ATGTTCTATATTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAT
1 -AAAGCGCCGCTAAA-GGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCAT
*
40184484 GTTCTATAGCTGCGTTT
64 GTTCTATAGCGGCGTTT
40184501 TTCTATATAA
Statistics
Matches: 215, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
84 17 0.08
85 130 0.60
86 65 0.30
87 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (85 bp):
AAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGT
TCTATAGCGGCGTTTGTGGG
Found at i:40186942 original size:31 final size:31
Alignment explanation
Indices: 40186907--40186966 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
40186897 TTTCACTCCA
40186907 TTACTAAACCAAATTAATAAACCATTCACCG
1 TTACTAAACCAAATTAATAAACCATTCACCG
40186938 TTACTAAACCAAATTAATAAACCATTCAC
1 TTACTAAACCAAATTAATAAACCATTCAC
40186967 AAAGAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.25, G:0.02, T:0.27
Consensus pattern (31 bp):
TTACTAAACCAAATTAATAAACCATTCACCG
Found at i:40188010 original size:43 final size:43
Alignment explanation
Indices: 40187954--40188110 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 43
40187944 ATATCGTACA
* *
40187954 ATGCCAATGTCCTAAACGTGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCTAAACGTGGTCTTACACGTAATCACATATCG
* * * *
40187997 ATGCCACTATCCTAGACAG-GGTCTTACACG-AATCAAATAT-G
1 ATGCCAATGTCCTAAAC-GTGGTCTTACACGTAATCACATATCG
* * *
40188038 ATGCCAATGTCCCAAACATGGTCTTACACATAATCACATATCG
1 ATGCCAATGTCCTAAACGTGGTCTTACACGTAATCACATATCG
* * * * *
40188081 ATGCGAACGTCCCAGACATGGTCTTACACG
1 ATGCCAATGTCCTAAACGTGGTCTTACACG
40188111 AGAACACATA
Statistics
Matches: 93, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 24 0.26
42 17 0.18
43 51 0.55
44 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCTAAACGTGGTCTTACACGTAATCACATATCG
Found at i:40188098 original size:84 final size:84
Alignment explanation
Indices: 40187954--40188111 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 84
40187944 ATATCGTACA
* * ** * * *
40187954 ATGCCAATGTCCTAAACGTGGTCTTACATGTTATCACATATCGATGCCACTATCCTAGACAGGGT
1 ATGCCAATGTCCCAAACATGGTCTTACACATAATCACATATCGATGCAACTATCCCAGACAGGGT
40188019 CTTACACGAATCAAATATG
66 CTTACACGAATCAAATATG
* *
40188038 ATGCCAATGTCCCAAACATGGTCTTACACATAATCACATATCGATGCGAAC-GTCCCAGACATGG
1 ATGCCAATGTCCCAAACATGGTCTTACACATAATCACATATCGATGC-AACTATCCCAGACAGGG
40188102 TCTTACACGA
65 TCTTACACGA
40188112 GAACACATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 62 0.97
85 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (84 bp):
ATGCCAATGTCCCAAACATGGTCTTACACATAATCACATATCGATGCAACTATCCCAGACAGGGT
CTTACACGAATCAAATATG
Found at i:40190962 original size:95 final size:95
Alignment explanation
Indices: 40190799--40190990 Score: 375
Period size: 95 Copynumber: 2.0 Consensus size: 95
40190789 AGGAAGTGTT
40190799 CAGGAGAGAAAATTAAGGAAAGGATCAAGAGGTTATTAGGGAGAAAAACAAGGAGATGAGAAGGG
1 CAGGAGAGAAAATTAAGGAAAGGATCAAGAGGTTATTAGGGAGAAAAACAAGGAGATGAGAAGGG
40190864 AGAAGTGATGGAGCCGAATGGGGAATTGGG
66 AGAAGTGATGGAGCCGAATGGGGAATTGGG
*
40190894 CAGGAGAGAAAATTAAGGAAAGGATCAAGAGGTTATTAGGGAGAAAAACGAGGAGATGAGAAGGG
1 CAGGAGAGAAAATTAAGGAAAGGATCAAGAGGTTATTAGGGAGAAAAACAAGGAGATGAGAAGGG
40190959 AGAAGTGATGGAGCCGAATGGGGAATTGGG
66 AGAAGTGATGGAGCCGAATGGGGAATTGGG
40190989 CA
1 CA
40190991 TGGGAAAATT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.42, C:0.06, G:0.39, T:0.14
Consensus pattern (95 bp):
CAGGAGAGAAAATTAAGGAAAGGATCAAGAGGTTATTAGGGAGAAAAACAAGGAGATGAGAAGGG
AGAAGTGATGGAGCCGAATGGGGAATTGGG
Found at i:40191924 original size:19 final size:18
Alignment explanation
Indices: 40191900--40191936 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
40191890 AGGATTGGCC
40191900 AAATGGGCCTGTATGGGCT
1 AAATGGGCCTGT-TGGGCT
40191919 AAATGGGCCTGTTGGGCT
1 AAATGGGCCTGTTGGGCT
40191937 GTTGGGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.19, C:0.16, G:0.38, T:0.27
Consensus pattern (18 bp):
AAATGGGCCTGTTGGGCT
Found at i:40192050 original size:29 final size:28
Alignment explanation
Indices: 40192005--40192119 Score: 99
Period size: 29 Copynumber: 4.1 Consensus size: 28
40191995 GTGAGCATGA
*
40192005 ATAT-AATATGATTTGGGCCTAATGGGCC
1 ATATGAATATGAATT-GGCCTAATGGGCC
* * *
40192033 ATATGAATGTGAATTGGGCGTAGTGGGCC
1 ATATGAATATGAATT-GGCCTAATGGGCC
* * *
40192062 ATAAGAATATGAACTGGCCCAGATGGGCC
1 ATATGAATATGAATTGGCCTA-ATGGGCC
* * *
40192091 ATTTGAATAAG-ATTGGCCTAGTGGGCC
1 ATATGAATATGAATTGGCCTAATGGGCC
40192118 AT
1 AT
40192120 GTGCATGTAT
Statistics
Matches: 69, Mismatches: 16, Indels: 5
0.77 0.18 0.06
Matches are distributed among these distances:
27 8 0.12
28 15 0.22
29 46 0.67
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
ATATGAATATGAATTGGCCTAATGGGCC
Found at i:40195894 original size:15 final size:15
Alignment explanation
Indices: 40195871--40195901 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40195861 TCAAAAATTC
40195871 CAATACAAAACATAT
1 CAATACAAAACATAT
*
40195886 CAATCCAAAACATAT
1 CAATACAAAACATAT
40195901 C
1 C
40195902 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:40219983 original size:22 final size:23
Alignment explanation
Indices: 40219958--40220000 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
40219948 TATCCCCACA
*
40219958 TGGAGTGTAG-GGCTGGATGGAG
1 TGGAGTGTAGAGGATGGATGGAG
40219980 TGGAGTGTAGAGGATGGATGG
1 TGGAGTGTAGAGGATGGATGG
40220001 GTAGGATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.21, C:0.02, G:0.53, T:0.23
Consensus pattern (23 bp):
TGGAGTGTAGAGGATGGATGGAG
Found at i:40220080 original size:34 final size:34
Alignment explanation
Indices: 40220032--40220099 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
40220022 TTGTTATTGT
*
40220032 TACTGTATTAGGCTAAGGCCCACACTGATA-TAGA
1 TACTGTAATAGGCTAAGGCCC-CACTGATACTAGA
* * *
40220066 TACTGTAATGGGCTATGGCCCTACTGATACTAGA
1 TACTGTAATAGGCTAAGGCCCCACTGATACTAGA
40220100 CTGTCTCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (34 bp):
TACTGTAATAGGCTAAGGCCCCACTGATACTAGA
Found at i:40225783 original size:47 final size:44
Alignment explanation
Indices: 40225720--40225979 Score: 167
Period size: 47 Copynumber: 5.6 Consensus size: 44
40225710 TTTGTGAGAT
*
40225720 AGTGTAAGTCATGTCTGGGACATGCATCAGCCACATT-ATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-G--ACATTGATGAGAGCC
* *
40225766 AGTGTAAGACCATGTCTGGGACGTGGCATCGACATTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACATT--GATGAGAGCC
* ** *
40225814 AGTGTAAGACATGTCTGGTG-CATGCATCGGC-CCGA-GACGTAAGCT
1 AGTGTAAGACATGTCTGG-GACATGCATCGACATTGATGA-G--AGCC
* *
40225859 AGTGTAAGATATGTCTGGGACATGCATCGAC-TATGA-GATGAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGACAT-TGATGA-GAGCC
* * * *
40225903 AATGTAAGACCATGTTTAGGACATGGTATCGAC-TTGA-GATATGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACATTGATG--A-GAGCC
40225950 AGTGTAAGACTATGTCTGGGACATGGCATC
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATC
40225980 TGCACCTTAC
Statistics
Matches: 174, Mismatches: 24, Indels: 31
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 11 0.06
45 51 0.29
46 29 0.17
47 55 0.32
48 23 0.13
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACATTGATGAGAGCC
Found at i:40225925 original size:45 final size:46
Alignment explanation
Indices: 40225761--40225979 Score: 137
Period size: 45 Copynumber: 4.8 Consensus size: 46
40225751 CACATTATGA
* * *
40225761 GAGCCAGTGTAAGACCATGTCTGGGACGTGGCATCGACATTGAG-AT
1 GAGCCAATGTAAGACCATGTCTAGGACATGGCATCGAC-TTGAGAAT
* * * * ** *
40225807 GAGAGCTAGTGTAAGA-CATGTCT-GGTGCAT-GCATCGGCCCGAGACGT
1 --GAGCCAATGTAAGACCATGTCTAGG-ACATGGCATCGACTTGAGA-AT
* * * * *
40225854 AAGCTAGTGTAAGA-TATGTCTGGGACAT-GCATCGACTATGAG-AT
1 GAGCCAATGTAAGACCATGTCTAGGACATGGCATCGACT-TGAGAAT
* * *
40225898 GAGTCAATGTAAGACCATGTTTAGGACATGGTATCGACTTGAGATAT
1 GAGCCAATGTAAGACCATGTCTAGGACATGGCATCGACTTGAGA-AT
* * *
40225945 GAGCCAGTGTAAGACTATGTCTGGGACATGGCATC
1 GAGCCAATGTAAGACCATGTCTAGGACATGGCATC
40225980 TGCACCTTAC
Statistics
Matches: 134, Mismatches: 28, Indels: 19
0.74 0.15 0.10
Matches are distributed among these distances:
44 11 0.08
45 47 0.35
46 22 0.16
47 41 0.31
48 13 0.10
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (46 bp):
GAGCCAATGTAAGACCATGTCTAGGACATGGCATCGACTTGAGAAT
Found at i:40248545 original size:37 final size:34
Alignment explanation
Indices: 40248495--40248566 Score: 81
Period size: 37 Copynumber: 2.0 Consensus size: 34
40248485 AGTGTGCCAT
* *
40248495 TTTTTCTGACCATCTTTCCTCCTCCTCCTTTCTTTTC
1 TTTTTCTCACCATC-TACCTCCTCCT-C-TTCTTTTC
* *
40248532 TTTTTCTCTCCATCTACCTTCTCCTCTTCTTTTC
1 TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
40248566 T
1 T
40248567 CCATAGCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 9 0.29
35 1 0.03
36 9 0.29
37 12 0.39
ACGTcount: A:0.06, C:0.38, G:0.01, T:0.56
Consensus pattern (34 bp):
TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
Found at i:40254249 original size:12 final size:12
Alignment explanation
Indices: 40254232--40254270 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40254222 CCTAACTATG
*
40254232 TTTAATTAATAC
1 TTTAATTAATAA
40254244 TTTAATTAATAA
1 TTTAATTAATAA
*
40254256 TTAAATTAATTAA
1 TTTAATTAA-TAA
40254269 TT
1 TT
40254271 ATGGATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAATTAATAA
Found at i:40259110 original size:18 final size:16
Alignment explanation
Indices: 40259078--40259115 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
40259068 ATGTCATGCG
40259078 TGATGAATTGTTGATT
1 TGATGAATTGTTGATT
40259094 TGATGAAATTAGTTGATT
1 TGATG-AATT-GTTGATT
40259112 TGAT
1 TGAT
40259116 TTGATATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 4 0.20
18 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (16 bp):
TGATGAATTGTTGATT
Found at i:40261450 original size:39 final size:39
Alignment explanation
Indices: 40261387--40261515 Score: 150
Period size: 40 Copynumber: 3.3 Consensus size: 39
40261377 TACTTTCTGT
* * *
40261387 TTGGCGTGATTCGAGTGTATCAGCTCTTATGAGCTTTTG
1 TTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGCTTTTG
*
40261426 TTGGCGTGTTTCGGGTGGACCAGCTCTTATGAGCTTTTG
1 TTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGCTTTTG
* * * * *
40261465 TTTGGCATATTTTGGTTGGATCAGCTCTTATGAGCTTCTG
1 -TTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGCTTTTG
*
40261505 TCTGGTGTGTT
1 T-TGGCGTGTT
40261516 CGATCTATTT
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
39 36 0.48
40 39 0.52
ACGTcount: A:0.12, C:0.16, G:0.29, T:0.43
Consensus pattern (39 bp):
TTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGCTTTTG
Found at i:40268207 original size:21 final size:21
Alignment explanation
Indices: 40268183--40268222 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40268173 AATGAAAGGA
40268183 AGCCATTTTATCATGAATGAT
1 AGCCATTTTATCATGAATGAT
*
40268204 AGCCATTTTATCATTAATG
1 AGCCATTTTATCATGAATG
40268223 TTATATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (21 bp):
AGCCATTTTATCATGAATGAT
Found at i:40272370 original size:46 final size:45
Alignment explanation
Indices: 40272317--40272492 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 45
40272307 TATTTGGGCA
40272317 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
40272363 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
40272410 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
40272456 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40272493 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 64 0.59
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Done.