Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 90 of 320
Found at i:28649274 original size:151 final size:151
Alignment explanation
Indices: 28648994--28649432 Score: 695
Period size: 151 Copynumber: 2.9 Consensus size: 151
28648984 AAGCTCTCTA
* *
28648994 GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGCC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCC
*
28649059 TGCACTTAGTACTACATACGTGACTTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
66 TGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
28649124 ACACGTGATCGAAGTTAACGG
131 ACACGTGATCGAAGTTAACGG
* * *
28649145 GTACGTATAGTAGCCTGCACTTAGCACTACACATGTGACCTATCAATCTGGAACACGTAGTAGCC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCC
*
28649210 TGTACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
66 TGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
28649275 ACACGTGATCGAAGTTAACGG
131 ACACGTGATCGAAGTTAACGG
* * *
28649296 GTGCGCATAGTAG-CTGCACTTAGTACTACACATATGACCTATCAATCTGGTACACGTAGTAGCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCC
* * * * * *
28649360 TGCACTTAGTACTACACATACG-G-CCTATCAATTTGGTACACGCAGTAGCCTGCACTTAGTACT
66 TGCACTTAGTACTACAC--ACGTGACTTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACT
28649423 ACACACGTGA
129 ACACACGTGA
28649433 CTCATAATGG
Statistics
Matches: 266, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
150 107 0.40
151 156 0.59
152 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (151 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
ACACGTGATCGAAGTTAACGG
Found at i:28669549 original size:49 final size:49
Alignment explanation
Indices: 28669488--28669613 Score: 164
Period size: 49 Copynumber: 2.6 Consensus size: 49
28669478 CATCAAGTCT
* * *
28669488 ATGCCATATCCCAGACAGGTCTTACACTGACTTTCATATAACGAG-GTTG
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATAACG-GTGTCG
* * * *
28669537 ATGCCATGTCCCAGACAGGTCTTACATTGGCTCTCATCTATCGGTGTCG
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATAACGGTGTCG
*
28669586 ATGCCATGTCCCAGATAGGTCTTACACT
1 ATGCCATGTCCCAGACAGGTCTTACACT
28669614 AGCTCTTGTC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
48 1 0.01
49 66 0.99
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATAACGGTGTCG
Found at i:28678192 original size:20 final size:20
Alignment explanation
Indices: 28678167--28678204 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28678157 CCTTGCAACT
28678167 TACCATAATCTTTCACAAAA
1 TACCATAATCTTTCACAAAA
*
28678187 TACCATAGTCTTTCACAA
1 TACCATAATCTTTCACAA
28678205 CTTAAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (20 bp):
TACCATAATCTTTCACAAAA
Found at i:28678412 original size:42 final size:42
Alignment explanation
Indices: 28678291--28678412 Score: 138
Period size: 43 Copynumber: 2.9 Consensus size: 42
28678281 CACCATACCA
* * * **
28678291 ATGCTATATTCCAGATATGGTCTTACATGGGATCTCATAACG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAACG
* * *
28678333 ATGCCAATAGCCCAGCTATGGTCTTACAC-AAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAA-TCTCATAACG
*
28678376 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCA
28678413 ACTAACTCTA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 31 0.47
43 35 0.53
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAACG
Found at i:28679916 original size:30 final size:30
Alignment explanation
Indices: 28679857--28679916 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28679847 TTTTACGAGC
* *
28679857 TTAGGGGCAAAAGTGTAAATATGTGAAAGT
1 TTAGGGGCAAAAGTATAAATATGTCAAAGT
* * *
28679887 TTAGGGGCAAAATTATAATTTTGTCAAAGT
1 TTAGGGGCAAAAGTATAAATATGTCAAAGT
28679917 ATGATTTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (30 bp):
TTAGGGGCAAAAGTATAAATATGTCAAAGT
Found at i:28680396 original size:42 final size:42
Alignment explanation
Indices: 28680327--28680407 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
28680317 TGGCGTTGAT
* * **
28680327 ATGAGATTTCGTGTAAGACCACGTCTGGGACATGGCATCGAA
1 ATGAGATTTCGTATAAAACCAAATCTGGGACATGGCATCGAA
* * *
28680369 ATGAGATTTTGTATAAAACCAAATCTGGGATATGTCATC
1 ATGAGATTTCGTATAAAACCAAATCTGGGACATGGCATC
28680408 AATGTGAGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (42 bp):
ATGAGATTTCGTATAAAACCAAATCTGGGACATGGCATCGAA
Found at i:28684448 original size:17 final size:17
Alignment explanation
Indices: 28684426--28684462 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28684416 GGTTTAACGA
28684426 ATGCTCCTGCAATTTTC
1 ATGCTCCTGCAATTTTC
*
28684443 ATGCTCCTGCAGTTTTC
1 ATGCTCCTGCAATTTTC
28684460 ATG
1 ATG
28684463 GATTTAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41
Consensus pattern (17 bp):
ATGCTCCTGCAATTTTC
Found at i:28689379 original size:48 final size:48
Alignment explanation
Indices: 28689315--28689771 Score: 556
Period size: 48 Copynumber: 9.5 Consensus size: 48
28689305 CATGTCTTAG
* * * *
28689315 ACATTGTCTTACACTGGCTCTCATATCAATACCGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
* * * * * *
28689363 ACATGGTCTTAGACTGGCTCACATATCGAGGCCGATGCCATGTCCCAG
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
* * **
28689411 ACATGGTCTTACACTAGCTCTCATATCAATGCTGATGCCATGTTTGAA
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
* * * * **
28689459 ACATGGTCTTACACTGGCTCACATATCAAGGCTGATGCCATGTCCCTG
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
* * * *
28689507 ACATAGTCTTACACTAGCTCTCATATCAATGCCAATTCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
* * * * *
28689555 ACATGGTGTTACACTAGCTCACATATCGAGGCTGATGCCATGTCCCAA
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
* *
28689603 ACATGGTCTTACACTAGCTCTCATATCAGTGCCGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
* * * *
28689651 ACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATG-TCCTAG
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCC-AA
* *
28689699 ACATGGTCTTACACTAGCTCTCATATCAATGCTGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
*
28689747 ACATGGTCTTACACTGGCTCACATA
1 ACATGGTCTTACACTAGCTCACATA
28689772 ACCCTAGTAC
Statistics
Matches: 341, Mismatches: 66, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
47 3 0.01
48 335 0.98
49 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (48 bp):
ACATGGTCTTACACTAGCTCACATATCAATGCCGATGCCATGTTCCAA
Found at i:28689468 original size:96 final size:96
Alignment explanation
Indices: 28689304--28689771 Score: 738
Period size: 96 Copynumber: 4.9 Consensus size: 96
28689294 GCTGTAGATA
** * * *
28689304 CCATGTCTTAGACATTGTCTTACACTGGCTCTCATATCAATACCGATGCCATGTTCCAAACATGG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACATGG
*
28689369 TCTTAGACTGGCTCACATATCGAGGCCGATG
66 TCTTACACTGGCTCACATATCGAGGCCGATG
* **
28689400 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCTGATGCCATGTTTGAAACATGG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACATGG
* *
28689465 TCTTACACTGGCTCACATATCAAGGCTGATG
66 TCTTACACTGGCTCACATATCGAGGCCGATG
* * * *
28689496 CCATGTCCCTGACATAGTCTTACACTAGCTCTCATATCAATGCCAATTCCATGTTCCAAACATGG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACATGG
* * *
28689561 TGTTACACTAGCTCACATATCGAGGCTGATG
66 TCTTACACTGGCTCACATATCGAGGCCGATG
* *
28689592 CCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAGTGCCGATGCCATGTTCCAAACATGG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACATGG
28689657 TCTTACACTGGCTCACATATCGAGGCCGATG
66 TCTTACACTGGCTCACATATCGAGGCCGATG
* *
28689688 CCATGTCCTAGACATGGTCTTACACTAGCTCTCATATCAATGCTGATGCCATGTTCCAAACATGG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACATGG
28689753 TCTTACACTGGCTCACATA
66 TCTTACACTGGCTCACATA
28689772 ACCCTAGTAC
Statistics
Matches: 338, Mismatches: 34, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 338 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (96 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACATGG
TCTTACACTGGCTCACATATCGAGGCCGATG
Found at i:28694478 original size:42 final size:39
Alignment explanation
Indices: 28694395--28694478 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 39
28694385 AGCATGGGCC
* *
28694395 AAAATTAAAAGAAAAAATAATTAAAACCAAGCAAAAGAA
1 AAAATTAAAAGAAAAAATAAATAAAACCAAGCAAAAAAA
*
28694434 AAAATTAAAAGAAAATTAATTAAATAAAACCAGGCAAAAAAA
1 AAAATTAAAAGAAAA--AA-TAAATAAAACCAAGCAAAAAAA
28694476 AAA
1 AAA
28694479 CACTATGTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 15 0.38
41 2 0.05
42 22 0.56
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (39 bp):
AAAATTAAAAGAAAAAATAAATAAAACCAAGCAAAAAAA
Found at i:28699874 original size:13 final size:13
Alignment explanation
Indices: 28699856--28699888 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28699846 GGCACATGGG
28699856 CGTGTGACACGAC
1 CGTGTGACACGAC
28699869 CGTGTGACACGAC
1 CGTGTGACACGAC
*
28699882 AGTGTGA
1 CGTGTGA
28699889 TCCTACTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.18
Consensus pattern (13 bp):
CGTGTGACACGAC
Found at i:28726571 original size:45 final size:48
Alignment explanation
Indices: 28726458--28726584 Score: 147
Period size: 50 Copynumber: 2.7 Consensus size: 48
28726448 GTAAACTACA
*
28726458 GATGACATGTCCCAGACATGATCTTACACTAGCTCTCACATAACTGTGCC
1 GATGACATGTCCCAGACATGATCTTACACTAG--CACACATAACTGTGCC
* *
28726508 GATGCCATGTCCCAGACATGATCTTACACT-G-ACACAT-CCTGTAGCC
1 GATGACATGTCCCAGACATGATCTTACACTAGCACACATAACTGT-GCC
* *
28726554 GATG-CATGTCCTAGACATG-TCTTATACTAGC
1 GATGACATGTCCCAGACATGATCTTACACTAGC
28726585 TTACGCCCCG
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
44 8 0.12
45 19 0.28
46 12 0.17
49 1 0.01
50 29 0.42
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (48 bp):
GATGACATGTCCCAGACATGATCTTACACTAGCACACATAACTGTGCC
Found at i:28728978 original size:17 final size:17
Alignment explanation
Indices: 28728956--28728990 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28728946 TCTGAATAAG
28728956 CTCATTGTCCTCAGGTA
1 CTCATTGTCCTCAGGTA
28728973 CTCATTGTCCTCAGGTA
1 CTCATTGTCCTCAGGTA
28728990 C
1 C
28728991 ACAAATTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (17 bp):
CTCATTGTCCTCAGGTA
Found at i:28734070 original size:140 final size:140
Alignment explanation
Indices: 28733917--28734223 Score: 515
Period size: 140 Copynumber: 2.2 Consensus size: 140
28733907 ACATCTCGTA
* *
28733917 GTCGATGCATGTCCCAGACATGTCTTATACTGGCTTATGTCCCTAGGCTAATGCATGTCCCAGAC
1 GTCGATGCATGTCCCAGACATGTCTTATACTGGCTTATGTCCCGAGGCTAATGCATGTCCCAAAC
*
28733982 ATGTCTTACACTAGCACTTATCTCAATGCCGATGCCAAGTCCCAGACATGGTCTTACACTGGCTC
66 ATGTCTTACACTAGCACTCATCTCAATGCCGATGCCAAGTCCCAGACATGGTCTTACACTGGCTC
28734047 TCATAATGTG
131 TCATAATGTG
*
28734057 GTCGATGCATGTCCCAGACATGTCTTATACTGGCTTATGTCCCGAGGCTGATGCATGTCCCAAAC
1 GTCGATGCATGTCCCAGACATGTCTTATACTGGCTTATGTCCCGAGGCTAATGCATGTCCCAAAC
* * * * * *
28734122 ATGTCTTACACTAGCTCTCGTCTTAATGTCGATGCCATGTCCCAGACATGGTCTTACATTGGCTC
66 ATGTCTTACACTAGCACTCATCTCAATGCCGATGCCAAGTCCCAGACATGGTCTTACACTGGCTC
28734187 TCATAATGTG
131 TCATAATGTG
*
28734197 GTCGATGCATGTCCAAGACATGTCTTA
1 GTCGATGCATGTCCCAGACATGTCTTA
28734224 CACAAGCTCA
Statistics
Matches: 156, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 156 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (140 bp):
GTCGATGCATGTCCCAGACATGTCTTATACTGGCTTATGTCCCGAGGCTAATGCATGTCCCAAAC
ATGTCTTACACTAGCACTCATCTCAATGCCGATGCCAAGTCCCAGACATGGTCTTACACTGGCTC
TCATAATGTG
Found at i:28734110 original size:94 final size:92
Alignment explanation
Indices: 28733967--28734179 Score: 225
Period size: 94 Copynumber: 2.3 Consensus size: 92
28733957 CCCTAGGCTA
* * *
28733967 ATGCATGTCCCAGACATGTCTTACACTAGCACTTATCTCAATGCCGATGCCAAGTCCCAGACATG
1 ATGCATGTCCCAGACATGTCTTACACTAGCACTTATCCCAAGGCCGATG-CAAGTCCCAAACAT-
* *
28734032 GTCTTACACTGGCTCTCATAAT-GTGGTCG
64 GTCTTACACTAGCTCTCATAATAAT-GTCG
* * * * *
28734061 ATGCATGTCCCAGACATGTCTTATACT-G-GCTTATGTCCCGAGGCTGATGCATGTCCCAAACAT
1 ATGCATGTCCCAGACATGTCTTACACTAGCACTTA--TCCCAAGGCCGATGCAAGTCCCAAACAT
* **
28734124 GTCTTACACTAGCTCTCGTCTTAATGTCG
64 GTCTTACACTAGCTCTCATAATAATGTCG
28734153 ATGCCATGTCCCAGACATGGTCTTACA
1 ATG-CATGTCCCAGACAT-GTCTTACA
28734180 TTGGCTCTCA
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
92 29 0.29
93 28 0.28
94 43 0.43
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (92 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCACTTATCCCAAGGCCGATGCAAGTCCCAAACATGT
CTTACACTAGCTCTCATAATAATGTCG
Found at i:28734156 original size:46 final size:45
Alignment explanation
Indices: 28733774--28734232 Score: 204
Period size: 46 Copynumber: 9.8 Consensus size: 45
28733764 AGTAAAGTGC
* * * * *
28733774 CGATGCCATGTCCTAGACATTGTCTTACACTGGCTATCATC-TTTGAGG
1 CGATG-CATGTCCCAGACA-TGTCTTACACTAGCTCTCATCATAT--GT
* *
28733822 CTGATGCCATATCCCAGACATGGTCTTACACTAGCTCTC-TCATAACCGTGC
1 C-GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCAT-A---TGT
* * * * *
28733873 CAATGCCATATCCCAGACATGGCCTTACACT-GACACATC-TCGTA-GT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTC-TCATCATATGT
* * * *
28733919 CGATGCATGTCCCAGACATGTCTTATACTGGCT-T-ATGTCCCTA-GG
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCA--T-CATATGT
* * * *
28733964 CTAATGCATGTCCCAGACATGTCTTACACTAGCACTTATC-TCAATGC
1 C-GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCAT--ATGT
* * * *
28734011 CGATGCCAAGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCATAT-GT
* * ** *
28734059 CGATGCATGTCCCAGACATGTCTTATACTGGCT-T-ATGTCCCGA-GG
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCA--T-CATATGT
* * *
28734104 CTGATGCATGTCCCAAACATGTCTTACACTAGCTCTCGTCTTAATGT
1 C-GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCAT-ATGT
* * * *
28734151 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAATGTGGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCATAT-GT
* *
28734199 CGATGCATGTCCAAGACATGTCTTACACAAGCTC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTC
28734233 ACACAAATGA
Statistics
Matches: 320, Mismatches: 56, Indels: 72
0.71 0.12 0.16
Matches are distributed among these distances:
42 1 0.00
44 12 0.04
45 24 0.08
46 99 0.31
47 60 0.19
48 51 0.16
49 34 0.11
50 31 0.10
51 7 0.02
53 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCATATGT
Found at i:28739695 original size:24 final size:24
Alignment explanation
Indices: 28739662--28739720 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
28739652 TTTATAGGAA
*
28739662 AAACTAAAAATGGTGAAAAAGACG
1 AAACTAAAAATGGTGAAAAAGAAG
28739686 AAACTGAAAAA-GGTGAAAAAGAAG
1 AAACT-AAAAATGGTGAAAAAGAAG
28739710 AAACTAAAAAT
1 AAACTAAAAAT
28739721 AACTTAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 5 0.16
24 22 0.69
25 5 0.16
ACGTcount: A:0.63, C:0.07, G:0.19, T:0.12
Consensus pattern (24 bp):
AAACTAAAAATGGTGAAAAAGAAG
Found at i:28744890 original size:42 final size:42
Alignment explanation
Indices: 28744834--28744943 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
28744824 GGTGTAGATT
* *
28744834 CACATGGCCAAGACACACGCCCATGTTCTAGGCTATGTAGCA
1 CACACGGCTAAGACACACGCCCATGTTCTAGGCTATGTAGCA
*
28744876 CACACGGCTAAGACACACGCCCGTGTTCTAGGCTATGTAGCA
1 CACACGGCTAAGACACACGCCCATGTTCTAGGCTATGTAGCA
*
28744918 CACACGGCTGAGACACACGCCCATGT
1 CACACGGCTAAGACACACGCCCATGT
28744944 CTCTGCCCGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (42 bp):
CACACGGCTAAGACACACGCCCATGTTCTAGGCTATGTAGCA
Found at i:28747633 original size:93 final size:93
Alignment explanation
Indices: 28747520--28747691 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28747510 CGCCCATAAG
* *
28747520 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28747585 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
28747613 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28747678 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28747692 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28747688 original size:46 final size:46
Alignment explanation
Indices: 28747513--28747688 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28747503 TGTAACCCGC
* * *
28747513 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28747559 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28747609 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28747652 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28747689 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28752492 original size:27 final size:27
Alignment explanation
Indices: 28752462--28752639 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28752452 ATATTGAGTC
* * * *
28752462 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28752489 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28752516 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28752544 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28752571 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28752598 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28752625 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28752640 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28752601 original size:82 final size:81
Alignment explanation
Indices: 28752483--28752638 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28752473 TGCTATATAA
* *
28752483 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28752548 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28752565 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28752629 CACTTAGTGC
65 CACTTAGTGC
28752639 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28758285 original size:27 final size:27
Alignment explanation
Indices: 28758254--28758431 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
28758244 TAAATTGTAC
28758254 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *** *
28758281 TGCACTAAGTGTGCGAAACGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28758307 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28758335 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28758363 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28758390 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28758417 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28758432 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28758395 original size:82 final size:81
Alignment explanation
Indices: 28758255--28758410 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28758245 AAATTGTACA
* *
28758255 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAACGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAAGTGT
28758320 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
*** *
28758336 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGAT-GCACTAAGT
*
28758400 GTGCGAGTTGA
64 GTGCGAATTGA
28758411 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28758422 original size:82 final size:81
Alignment explanation
Indices: 28758251--28758431 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
28758241 GATTAAATTG
* *
28758251 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAACGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAA
28758316 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * *** *
28758332 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGAT-GCACT
* **
28758396 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28758414 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28758432 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28763866 original size:27 final size:27
Alignment explanation
Indices: 28763836--28764013 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28763826 ATATTGAGTC
* * * *
28763836 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28763863 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28763890 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28763918 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28763945 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28763972 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28763999 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28764014 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28763975 original size:82 final size:81
Alignment explanation
Indices: 28763857--28764012 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28763847 TGCTATATAA
* *
28763857 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28763922 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28763939 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28764003 CACTTAGTGC
65 CACTTAGTGC
28764013 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28765911 original size:20 final size:20
Alignment explanation
Indices: 28765883--28765945 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
28765873 ATTCATTTTT
28765883 ATTCGTATAAACTGTAATTC
1 ATTCGTATAAACTGTAATTC
* *
28765903 ATTCATAT-AACTAGTAGTTC
1 ATTCGTATAAACT-GTAATTC
* * *
28765923 ATCCGTATAACCAGTAATTC
1 ATTCGTATAAACTGTAATTC
28765943 ATT
1 ATT
28765946 AGTAATAACA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.12
20 27 0.82
21 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
ATTCGTATAAACTGTAATTC
Found at i:28765980 original size:20 final size:20
Alignment explanation
Indices: 28765957--28766024 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
28765947 GTAATAACAT
*
28765957 TAATTTATCTATATCAATAG
1 TAATTCATCTATATCAATAG
* *
28765977 TAATTCATTTGTATCAATAG
1 TAATTCATCTATATCAATAG
* *
28765997 TAATTCAT-TCATTTCAACAG
1 TAATTCATCT-ATATCAATAG
28766017 TAATTCAT
1 TAATTCAT
28766025 TCATTTCGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (20 bp):
TAATTCATCTATATCAATAG
Found at i:28766001 original size:40 final size:40
Alignment explanation
Indices: 28765896--28766025 Score: 99
Period size: 40 Copynumber: 3.2 Consensus size: 40
28765886 CGTATAAACT
* * *
28765896 GTAATTCATTCA-T-ATAACTAGTAGTTCATCCGTAT-AACCA
1 GTAATTCATT-AGTAATAAC-AGTAATTCATTCATATCAA-CA
* * *
28765936 GTAATTCATTAGTAATAACATTAATTTA-TCTATATCAATA
1 GTAATTCATTAGTAATAACAGTAATTCATTC-ATATCAACA
* * *
28765976 GTAATTCATTTGT-ATCAATAGTAATTCATTCATTTCAACA
1 GTAATTCATTAGTAAT-AACAGTAATTCATTCATATCAACA
28766016 GTAATTCATT
1 GTAATTCATT
28766026 CATTTCGACA
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
39 4 0.06
40 59 0.82
41 9 0.12
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.41
Consensus pattern (40 bp):
GTAATTCATTAGTAATAACAGTAATTCATTCATATCAACA
Found at i:28766025 original size:20 final size:20
Alignment explanation
Indices: 28765970--28766031 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
28765960 TTTATCTATA
** *
28765970 TCAATAGTAATTCATTTGTA
1 TCAATAGTAATTCATTCATT
28765990 TCAATAGTAATTCATTCATT
1 TCAATAGTAATTCATTCATT
*
28766010 TCAACAGTAATTCATTCATT
1 TCAATAGTAATTCATTCATT
28766030 TC
1 TC
28766032 GACATAGCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (20 bp):
TCAATAGTAATTCATTCATT
Found at i:28772817 original size:20 final size:19
Alignment explanation
Indices: 28772777--28772813 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28772767 ATATTTTTAG
28772777 GGACAAAAATCTCTTTTGA
1 GGACAAAAATCTCTTTTGA
28772796 GGACAAAAAATC-CTTTTG
1 GGAC-AAAAATCTCTTTTG
28772814 GAGGGAGAGG
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:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (19 bp):
GGACAAAAATCTCTTTTGA
Found at i:28774168 original size:27 final size:25
Alignment explanation
Indices: 28774138--28774195 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
28774128 AAAGCTCATA
* *
28774138 TGAGCAGACCCATTTTCATAGCTCGTG
1 TGAGCAGACCCATTTACA-A-CTCCTG
* *
28774165 TGAGCATACCGATTTACAACTCCTG
1 TGAGCAGACCCATTTACAACTCCTG
28774190 TGAGCA
1 TGAGCA
28774196 TAATGATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 11 0.41
26 1 0.04
27 15 0.56
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (25 bp):
TGAGCAGACCCATTTACAACTCCTG
Found at i:28774197 original size:25 final size:25
Alignment explanation
Indices: 28774152--28774248 Score: 95
Period size: 25 Copynumber: 3.9 Consensus size: 25
28774142 CAGACCCATT
* *
28774152 TTCATAGCTCGTGTGAGCATACCGA
1 TTCACAGCTCATGTGAGCATACCGA
* * * **
28774177 TTTACAACTCCTGTGAGCATAATGA
1 TTCACAGCTCATGTGAGCATACCGA
* * *
28774202 TTCACAGCTCGTTTCAGCATACCGA
1 TTCACAGCTCATGTGAGCATACCGA
*
28774227 TTCACAGCTCATATGAGCATAC
1 TTCACAGCTCATGTGAGCATAC
28774249 ATGCACAGGA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (25 bp):
TTCACAGCTCATGTGAGCATACCGA
Found at i:28774221 original size:50 final size:50
Alignment explanation
Indices: 28774152--28774247 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
28774142 CAGACCCATT
* * * * *
28774152 TTCATAGCTCGTGTGAGCATACCGATTTACAACTCCTGTGAGCATAATGA
1 TTCACAGCTCGTGTCAGCATACCGATTCACAACTCATATGAGCATAATGA
* *
28774202 TTCACAGCTCGTTTCAGCATACCGATTCACAGCTCATATGAGCATA
1 TTCACAGCTCGTGTCAGCATACCGATTCACAACTCATATGAGCATA
28774248 CATGCACAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (50 bp):
TTCACAGCTCGTGTCAGCATACCGATTCACAACTCATATGAGCATAATGA
Found at i:28780802 original size:40 final size:40
Alignment explanation
Indices: 28780747--28780884 Score: 183
Period size: 40 Copynumber: 3.5 Consensus size: 40
28780737 CGGATGATAA
*
28780747 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-T
* *
28780787 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
*
28780827 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT-AGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATAT
* *
28780867 CC-GGCTAAATCCCAAAGG
1 CCGGGCTAAGTCCCGAAGG
28780885 TACTTGGTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
39 15 0.17
40 73 0.82
41 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
Found at i:28787629 original size:39 final size:40
Alignment explanation
Indices: 28787425--28787647 Score: 191
Period size: 40 Copynumber: 5.6 Consensus size: 40
28787415 TTGAATGCTG
* * * * * *
28787425 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGCTAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * * *
28787465 TCCGGACTAAGAT-CCGAAGGCCTTTGTGTGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
28787505 TTCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* **
28787545 GCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
28787585 TCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
28787624 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28787648 TGAATGAGGA
Statistics
Matches: 151, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
39 33 0.22
40 111 0.74
41 7 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:28787646 original size:79 final size:80
Alignment explanation
Indices: 28787501--28787647 Score: 206
Period size: 79 Copynumber: 1.9 Consensus size: 80
28787491 TGTGAGATAC
* * * * *
28787501 TAAATTCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
28787566 ATTCGTGCGAGTTGT
66 ATTCGTGCGAGTTGT
* * * *
28787581 TAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
28787645 ATT
66 ATT
28787648 TGAATGAGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
79 35 0.60
80 23 0.40
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGTGCGAGTTGT
Found at i:28787667 original size:79 final size:80
Alignment explanation
Indices: 28787500--28787682 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
28787490 GTGTGAGATA
* * * * *
28787500 CTAAATTCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
28787565 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * * *
28787580 TTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
28787644 CATTTGAATGAGGAG
66 CATTCGAACGAGGAG
* *
28787659 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
28787683 TACGTGATTT
Statistics
Matches: 83, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
78 14 0.17
79 46 0.55
80 23 0.28
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:28795470 original size:40 final size:40
Alignment explanation
Indices: 28795372--28795539 Score: 198
Period size: 39 Copynumber: 4.3 Consensus size: 40
28795362 GGACTAAGAT
* * *
28795372 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
28795412 CCG-AGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
28795451 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * * *
28795491 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGT-
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
28795529 CCGAAGGCATT
1 CCGAAGGCATT
28795540 TGAAGAGGAG
Statistics
Matches: 111, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.08
39 57 0.51
40 45 0.41
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:28795478 original size:79 final size:78
Alignment explanation
Indices: 28795360--28795539 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 78
28795350 GCGAATATAT
* * *
28795360 CCGGACTAAGATCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCG-AGGCATTCG
1 CCGGGCTAAG-TCCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCA-TCG
* *
28795424 TGCGAGTTATTAAAG
64 TGCGAGTTACTAAAA
* * ** * *
28795439 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTCCCGAAGGCATGGT
1 CCGGGCTAAGT-CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATCGT
*
28795504 GTGAGTTACTAAAA
65 GCGAGTTACTAAAA
*
28795518 CCGGGCTATGTCCGAAGGCATT
1 CCGGGCTAAGTCCGAAGGCATT
28795540 TGAAGAGGAG
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 12 0.14
79 68 0.80
80 5 0.06
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (78 bp):
CCGGGCTAAGTCCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATCGTG
CGAGTTACTAAAA
Found at i:28812943 original size:30 final size:30
Alignment explanation
Indices: 28812909--28812968 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
28812899 ATCTAATACG
*
28812909 AACTTTTGCAAAATTACATTTTTGCCCCTA
1 AACTTTTGCAAAATTACACTTTTGCCCCTA
*
28812939 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTGCAAAATTACACTTTTGCCCCTA
28812969 GGCTTGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTTGCAAAATTACACTTTTGCCCCTA
Found at i:28813934 original size:14 final size:14
Alignment explanation
Indices: 28813917--28813973 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
28813907 AAGGTTAAAA
*
28813917 GTTTAAGGTTCATG
1 GTTTGAGGTTCATG
*
28813931 GTTTGA-GTTCAAG
1 GTTTGAGGTTCATG
28813944 GTTTGAGGTTC-TG
1 GTTTGAGGTTCATG
*
28813957 AGTTTGGGGTTCATG
1 -GTTTGAGGTTCATG
28813972 GT
1 GT
28813974 AAAATAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 13 0.36
14 21 0.58
15 2 0.06
ACGTcount: A:0.16, C:0.07, G:0.35, T:0.42
Consensus pattern (14 bp):
GTTTGAGGTTCATG
Found at i:28816665 original size:18 final size:18
Alignment explanation
Indices: 28816642--28816678 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28816632 TCAGATTGAG
28816642 TTAACCCAAAAAGATCAT
1 TTAACCCAAAAAGATCAT
28816660 TTAACCCAAAAAGATCAT
1 TTAACCCAAAAAGATCAT
28816678 T
1 T
28816679 CTTTTTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.24
Consensus pattern (18 bp):
TTAACCCAAAAAGATCAT
Found at i:28820813 original size:21 final size:22
Alignment explanation
Indices: 28820775--28820818 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
28820765 TCTCTTATAC
*
28820775 TTTGTTCTTATTTGTTGT-TTG
1 TTTGTTCTTATTTCTTGTATTG
28820796 TTTGTTCGTTA-TTCTTGTATTG
1 TTTGTTC-TTATTTCTTGTATTG
28820818 T
1 T
28820819 ATTTCTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (22 bp):
TTTGTTCTTATTTCTTGTATTG
Found at i:28823054 original size:49 final size:49
Alignment explanation
Indices: 28822982--28823169 Score: 250
Period size: 49 Copynumber: 3.8 Consensus size: 49
28822972 TGAGATCACG
*
28822982 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * * * *
28823031 TGTGTAGTACTAAGTGCAAGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCGCA
*
28823082 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
28823131 TGTGTAGTACTAAGTGCAGGCTATTATGTGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
28823170 GCTTCGGTTA
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 76 0.65
50 2 0.02
51 39 0.33
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:28823148 original size:100 final size:100
Alignment explanation
Indices: 28822975--28823164 Score: 335
Period size: 100 Copynumber: 1.9 Consensus size: 100
28822965 ACTATTGTGA
*
28822975 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
1 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTA
28823040 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
66 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
*
28823075 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTA
1 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTA
* * *
28823140 CTAAGTGCAGGCTATTATGTGTACC
66 CTAAGTGCAAGCTACTATGCGTACC
28823165 AGATAGCTTC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (100 bp):
GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTA
CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
Found at i:28826191 original size:15 final size:15
Alignment explanation
Indices: 28826171--28826235 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
28826161 GTATCTTGGG
28826171 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
28826186 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
28826201 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
28826216 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
28826230 TTTCTT
1 TTTCTT
28826236 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.28
15 27 0.63
16 4 0.09
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:28826203 original size:30 final size:31
Alignment explanation
Indices: 28826167--28826235 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
28826157 TATCGTATCT
28826167 TGGGTTTCTT-TAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCT-TGGATTTCTTTATTC
28826197 TGGGTTT-TTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCTTGGATTTCTTTATTC
*
28826227 -GGTTTTCTT
1 TGGGTTTCTT
28826236 GTTATCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.61
Consensus pattern (31 bp):
TGGGTTTCTTCTATCTTGGATTTCTTTATTC
Found at i:28828870 original size:100 final size:100
Alignment explanation
Indices: 28828697--28828886 Score: 326
Period size: 100 Copynumber: 1.9 Consensus size: 100
28828687 ACTATTGTGA
* **
28828697 GATCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
1 GATCACATATGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTA
28828762 CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
66 CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
* *
28828797 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTA
1 GATCACATATGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTA
*
28828862 CTAAGTGCAGGCTATTATGCGTACC
66 CTAAGTGCAGGCTACTATGCGTACC
28828887 AGATAGCTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (100 bp):
GATCACATATGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTA
CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
Found at i:28828886 original size:49 final size:49
Alignment explanation
Indices: 28828706--28828891 Score: 246
Period size: 49 Copynumber: 3.8 Consensus size: 49
28828696 AGATCACGTA
* **
28828706 TGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCGCATG
* * * * *
28828755 TGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-T-TGGTCGCATG
* *
28828806 TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCGCATG
* *
28828855 TGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATA
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
28828892 GCTTCGGCTA
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 74 0.63
50 2 0.02
51 41 0.35
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCGCATG
Found at i:28832784 original size:49 final size:48
Alignment explanation
Indices: 28832725--28832896 Score: 184
Period size: 48 Copynumber: 3.6 Consensus size: 48
28832715 TGTTGTGTGT
* *
28832725 CAGTGTAAGACCTGTCTGGGACATGGCATCTACATCGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCAACATCAAT-GATGAGAGC
** * * * *
28832774 CAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCAATTATGGGAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCAACATCAATGATGAGAGC
* * * * **
28832822 CAGTGTAAGACCTATCTGGGACATGACGTCAACTTCAATG-TGCTAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCAACATCAATGATGAGAGC
*
28832869 TAGTGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
28832897 GTCAGCATTT
Statistics
Matches: 102, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
47 15 0.15
48 52 0.51
49 35 0.34
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (48 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCAACATCAATGATGAGAGC
Found at i:28836399 original size:56 final size:56
Alignment explanation
Indices: 28836339--28836474 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
28836329 TCCCAGGTAG
* * *
28836339 GGTCTTACTCACACACATATATCGTAATCACATATCGATGCCAATGTATTAAACGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
* *
28836395 GGTCTTACTCGCACACATATAACGGAATCACATATCGATGCCAACGTATTAAACTT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
28836451 GGTCTTACTCGCACACATATATCG
1 GGTCTTACTCGCACACATATATCG
28836475 ATGCCATGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
Found at i:28837054 original size:28 final size:26
Alignment explanation
Indices: 28837011--28837062 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
28837001 TACATTTCAT
**
28837011 TTATTTTACATTTTAGTCCCTCAATTTA
1 TTATTTTACAAATTAG-CCCT-AATTTA
28837039 TTATTTTACAAATTAGCCCTAATT
1 TTATTTTACAAATTAGCCCTAATT
28837063 ACTCAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 4 0.18
28 14 0.64
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (26 bp):
TTATTTTACAAATTAGCCCTAATTTA
Found at i:28837651 original size:14 final size:16
Alignment explanation
Indices: 28837625--28837657 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28837615 TAAAACACAA
28837625 AAATTTCACACAT-AT
1 AAATTTCACACATAAT
28837640 AAATTT-ACACATAAT
1 AAATTTCACACATAAT
28837655 AAA
1 AAA
28837658 CACAGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTTCACACATAAT
Found at i:28853853 original size:23 final size:23
Alignment explanation
Indices: 28853823--28853869 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28853813 TTGTTTCCAT
28853823 AGATTTCATGCTTACCCATATGC
1 AGATTTCATGCTTACCCATATGC
28853846 AGATTTCATGCTTACCCATATGC
1 AGATTTCATGCTTACCCATATGC
28853869 A
1 A
28853870 TTCATTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (23 bp):
AGATTTCATGCTTACCCATATGC
Found at i:28862746 original size:2 final size:2
Alignment explanation
Indices: 28862739--28862776 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28862729 CTCAATATTT
28862739 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28862777 TATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28868503 original size:43 final size:43
Alignment explanation
Indices: 28868455--28868579 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 43
28868445 GCTGGTACTA
*
28868455 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATATG
** *
28868498 TATTCGGGCCTTTATGCCTAGCAGGCTTCGTGCCGGTGATATG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATATG
* *
28868541 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGA
28868580 AATGATATGT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATATG
Found at i:28870843 original size:42 final size:42
Alignment explanation
Indices: 28870797--28871021 Score: 193
Period size: 42 Copynumber: 5.2 Consensus size: 42
28870787 TCCAACTTTA
* * *
28870797 GTCTTACACGAAGTCTCACATCGATGCCATGTCCCAGACATG
1 GTCTTACACGAAATCTCATATCGATGCCATATCCCAGACATG
* * ** * *
28870839 GTCTT-TACGAAATCACATATCGATGCCGCATCCTAGACAAG
1 GTCTTACACGAAATCTCATATCGATGCCATATCCCAGACATG
* * * *
28870880 GTCTTACACGAAATCTCATACCGAAGCCATATCCCAGATATA
1 GTCTTACACGAAATCTCATATCGATGCCATATCCCAGACATG
* * * *
28870922 GTCTTACAAGTAATCTCATATCGATACCGATGCCATATCCCAAATATG
1 GTCTTACACGAAATCTC--AT--AT--CGATGCCATATCCCAGACATG
* *
28870970 GTCTTACAC-AGGATCTCATATCGATGCCATGTCCCAGACATG
1 GTCTTACACGA-AATCTCATATCGATGCCATATCCCAGACATG
*
28871012 GTATTACACG
1 GTCTTACACG
28871022 TATCACAATG
Statistics
Matches: 142, Mismatches: 32, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
41 32 0.23
42 72 0.51
44 4 0.03
46 3 0.02
48 31 0.22
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (42 bp):
GTCTTACACGAAATCTCATATCGATGCCATATCCCAGACATG
Found at i:28870950 original size:48 final size:48
Alignment explanation
Indices: 28870897--28870994 Score: 144
Period size: 48 Copynumber: 2.0 Consensus size: 48
28870887 ACGAAATCTC
*
28870897 ATACCGAAGCCATATCCCAGATATAGTCTTACA-AGTAATCTCATATCG
1 ATACCGAAGCCATATCCCAAATATAGTCTTACACAG-AATCTCATATCG
* * *
28870945 ATACCGATGCCATATCCCAAATATGGTCTTACACAGGATCTCATATCG
1 ATACCGAAGCCATATCCCAAATATAGTCTTACACAGAATCTCATATCG
28870993 AT
1 AT
28870995 GCCATGTCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 43 0.96
49 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (48 bp):
ATACCGAAGCCATATCCCAAATATAGTCTTACACAGAATCTCATATCG
Found at i:28871042 original size:36 final size:37
Alignment explanation
Indices: 28870993--28871065 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
28870983 TCTCATATCG
28870993 ATGCCATGTCCCAGAC-ATGGTATTACACGTA-TCACA
1 ATGCCATGTCCCAG-CTATGGTATTACACGTACTCACA
*
28871029 ATGCCATAG-CCCAGCTATGGTCTTACACGTACTCACA
1 ATGCCAT-GTCCCAGCTATGGTATTACACGTACTCACA
28871066 TGTATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
35 1 0.03
36 26 0.79
37 6 0.18
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (37 bp):
ATGCCATGTCCCAGCTATGGTATTACACGTACTCACA
Found at i:28875299 original size:2 final size:2
Alignment explanation
Indices: 28875294--28875327 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28875284 CATTAAGTGC
28875294 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28875328 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28875422 original size:40 final size:40
Alignment explanation
Indices: 28875336--28875411 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
28875326 CATATATATA
*
28875336 TAGCCGAAGCTATCACAAATCGCACACCAAGAGCCACATT
1 TAGCCGAAGCTATCACAAACCGCACACCAAGAGCCACATT
** * *
28875376 TAGCCGAAGCTATTTCAAACCGCACACTAAGTGCCA
1 TAGCCGAAGCTATCACAAACCGCACACCAAGAGCCA
28875412 TTCTTAGCCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.17
Consensus pattern (40 bp):
TAGCCGAAGCTATCACAAACCGCACACCAAGAGCCACATT
Found at i:28879771 original size:44 final size:44
Alignment explanation
Indices: 28879723--28879824 Score: 177
Period size: 44 Copynumber: 2.3 Consensus size: 44
28879713 AATTGAGTTT
* *
28879723 GCACTAAGTGTGTGGAAATCATTCTAGCATTAGCTAACTTTTAA
1 GCACTAAGTGTGCGGAAATCATTCTAGCATTAGCTAACCTTTAA
*
28879767 GCACTAAGTGTGCGGAAATCGTTCTAGCATTAGCTAACCTTTAA
1 GCACTAAGTGTGCGGAAATCATTCTAGCATTAGCTAACCTTTAA
28879811 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28879825 AATGTTTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
GCACTAAGTGTGCGGAAATCATTCTAGCATTAGCTAACCTTTAA
Found at i:28881310 original size:46 final size:46
Alignment explanation
Indices: 28881157--28881379 Score: 195
Period size: 46 Copynumber: 4.8 Consensus size: 46
28881147 CACTCGTGTT
* * * *
28881157 AGCTAGTGTAAGCCATGTCTGGGACATGCATCGGCAAC-ATTATGAG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGA-GACGAG
* * *
28881203 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAG
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAG
* * * *
28881251 TGCTGGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGACGTA-
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACG-AG
* * *
28881297 AGCTAGTGTAAGACATGTCTGGCACATGCATCGGC-TACGAGATGTG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGACGAG
* * *
28881343 -TC-AGTGTAAGACCATGTTTGGGATATGGCATCGGCAT
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAT
28881380 AGATATACTA
Statistics
Matches: 144, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
44 9 0.06
45 13 0.09
46 69 0.48
47 30 0.21
48 22 0.15
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAG
Found at i:28883760 original size:47 final size:44
Alignment explanation
Indices: 28883692--28883811 Score: 134
Period size: 47 Copynumber: 2.7 Consensus size: 44
28883682 TACTATGAGT
* *
28883692 GCCAGAGTAAGACATGTCTGGGACATGCAACGGCCTCGACAGAGAT-A
1 GCCAGTGTAAGACGTGTCTGGGACATGCAACGG-CT--A-AGAGATGA
* * *
28883739 GCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAGAGATGT
1 GCCAGTGTAAGACGTGTCTGGGACATGCAACGGCTAAGAGATGA
* *
28883783 GCTAGTGTAAGTCGTGTCTGGGACATGCA
1 GCCAGTGTAAGACGTGTCTGGGACATGCA
28883812 TCAGCACGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
43 6 0.09
44 27 0.42
46 2 0.03
47 29 0.45
ACGTcount: A:0.27, C:0.21, G:0.33, T:0.20
Consensus pattern (44 bp):
GCCAGTGTAAGACGTGTCTGGGACATGCAACGGCTAAGAGATGA
Found at i:28887277 original size:42 final size:42
Alignment explanation
Indices: 28887230--28887314 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
28887220 TCACCATGGG
* *
28887230 GTGCTCCAGTGCTTTTTGTGAAAAAGAAGGATGGGTCGATGA
1 GTGCTCCAGTGCTTTTTGTGAAAAAGAAGGACGGGTCAATGA
*
28887272 GTGCTCCAGTGCTTTTTGTGAAAAAGAAGTACGGGTCAATGA
1 GTGCTCCAGTGCTTTTTGTGAAAAAGAAGGACGGGTCAATGA
28887314 G
1 G
28887315 GTTATGTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (42 bp):
GTGCTCCAGTGCTTTTTGTGAAAAAGAAGGACGGGTCAATGA
Found at i:28893636 original size:43 final size:43
Alignment explanation
Indices: 28893570--28893696 Score: 118
Period size: 43 Copynumber: 3.0 Consensus size: 43
28893560 AGATCGTACA
* *
28893570 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
28893613 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATA--G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAATCAAATATCG
* * * * * * * *
28893654 GTGCCGATGTCCCAAACATGGTCGTACACGAAAACACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
28893697 GATCCTGTGT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
41 31 0.45
42 3 0.04
43 34 0.49
44 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
Found at i:28903699 original size:22 final size:22
Alignment explanation
Indices: 28903670--28903717 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
28903660 CTTGATACAA
28903670 ACTCAAAAATATCTCTTTTCAT
1 ACTCAAAAATATCTCTTTTCAT
28903692 -CTCAAAAATATCTCTTTTCAT
1 ACTCAAAAATATCTCTTTTCAT
28903713 ACTCA
1 ACTCA
28903718 GCCACCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (22 bp):
ACTCAAAAATATCTCTTTTCAT
Found at i:28907832 original size:48 final size:48
Alignment explanation
Indices: 28907597--28907879 Score: 201
Period size: 48 Copynumber: 5.9 Consensus size: 48
28907587 AATTGGGTGA
* * **
28907597 TATGTGTGCCAGTGTAAGACCATGTCTCGGACATGGCATCGGCCAAAT
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGT
* * * * * * *
28907645 TATGAGAGCCAGTGTAGGACCATGTTTGGGACATGGCATC-GACATTGA
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCA-CGT
** * * * * *** *
28907693 TATGTTTGCTAGTATAAGGCCATGTCTAGGACATGACATCGGCGTTGA
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGT
* * * * * * *
28907741 TATGTGTGCTAGTGTAAGATCATGTCT-GAGATATAGCAACGGCCACCT
1 TATGTGAGCCAGTGTAAGACCATGTCTAG-GACATGGCATCGGCCACGT
* * *
28907789 TATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGT
* * * * * *
28907837 CATGTGAGCCAGTGTAAAACAATGCCTTGGACATGACATCGGC
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC
28907880 AATTTACCCT
Statistics
Matches: 179, Mismatches: 52, Indels: 8
0.75 0.22 0.03
Matches are distributed among these distances:
47 4 0.02
48 173 0.97
49 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGT
Found at i:28907869 original size:144 final size:144
Alignment explanation
Indices: 28907594--28907879 Score: 349
Period size: 144 Copynumber: 2.0 Consensus size: 144
28907584 GACAATTGGG
* *
28907594 TGATATGTGTGCCAGTGTAAGACCATGTCTCGGACATGGCATCGGCCAAATTATGAGAGCCAGTG
1 TGATATGTGTGCCAGTGTAAGACCATGTCTCGGACATAGCAACGGCCAAATTATGAGAGCCAGTG
* * * * * ** * ** * *
28907659 TAGGACCATGTTTGGGACATGGCATCGACATTGATATGTTTGCTAGTATAAGGCCATGTCTAGGA
66 TAAGACCATGTCTAGGACATGGCATCGACATCGACATGTGAGCCAGTATAAAACAATGCCTAGGA
28907724 CATGACATCGGCGT
131 CATGACATCGGCGT
* * * **
28907738 TGATATGTGTGCTAGTGTAAGATCATGTCT-GAGATATAGCAACGGCCACCTTATGAGAGCCAGT
1 TGATATGTGTGCCAGTGTAAGACCATGTCTCG-GACATAGCAACGGCCAAATTATGAGAGCCAGT
* * * *
28907802 GTAAGACCATGTCTAGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAAACAATGCCTTGG
65 GTAAGACCATGTCTAGGACATGGCATCGACATCGACATGTGAGCCAGTATAAAACAATGCCTAGG
28907867 ACATGACATCGGC
130 ACATGACATCGGC
28907880 AATTTACCCT
Statistics
Matches: 118, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
143 1 0.01
144 117 0.99
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (144 bp):
TGATATGTGTGCCAGTGTAAGACCATGTCTCGGACATAGCAACGGCCAAATTATGAGAGCCAGTG
TAAGACCATGTCTAGGACATGGCATCGACATCGACATGTGAGCCAGTATAAAACAATGCCTAGGA
CATGACATCGGCGT
Found at i:28919620 original size:42 final size:43
Alignment explanation
Indices: 28919519--28919623 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 43
28919509 CTGAGATATT
*
28919519 GTGTAAGACCGTGTCTGGGACACAGGCAATGATTGAGATTTAC
1 GTGTAAGACCATGTCTGGGACACAGGCAATGATTGAGATTTAC
* * *
28919562 GTATAAGACCAAGTCTGGGACATC-GGCATTGTATCT-AG-TTT-C
1 GTGTAAGACCATGTCTGGGACA-CAGGCAATG-AT-TGAGATTTAC
*
28919604 GTGTAAGACCCTGTCTGGGA
1 GTGTAAGACCATGTCTGGGA
28919624 TAAGGCATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
42 18 0.35
43 28 0.54
44 5 0.10
45 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACACAGGCAATGATTGAGATTTAC
Found at i:28920031 original size:25 final size:21
Alignment explanation
Indices: 28919981--28920024 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28919971 CTCTTTGTAG
28919981 CTTACTTTGTGTGATTTCTGC
1 CTTACTTTGTGTGATTTCTGC
28920002 CTTACTTTGTGTGATTTCTGC
1 CTTACTTTGTGTGATTTCTGC
28920023 CT
1 CT
28920025 GTTTTACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.20, G:0.18, T:0.52
Consensus pattern (21 bp):
CTTACTTTGTGTGATTTCTGC
Found at i:28920525 original size:26 final size:26
Alignment explanation
Indices: 28920466--28920525 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
28920456 AGAATCACAC
* *
28920466 GGCCGTGGCATACGGGCGTGTCTGTT
1 GGCCGTGGCACACGGGCGTGTCTATT
* **
28920492 AGTTGTGGCACACGGGCGTGTCTATT
1 GGCCGTGGCACACGGGCGTGTCTATT
28920518 GGCCGTGG
1 GGCCGTGG
28920526 GAATAAGTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.10, C:0.22, G:0.42, T:0.27
Consensus pattern (26 bp):
GGCCGTGGCACACGGGCGTGTCTATT
Found at i:28926198 original size:24 final size:25
Alignment explanation
Indices: 28926168--28926225 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
28926158 CGGACCGTAT
28926168 CTTGATGAATTTGTTG-TTGTATTCA
1 CTTGATGAATTTGTTGATT-TATTCA
*
28926193 -TTGATG-ATTTTTTGATTTATTCA
1 CTTGATGAATTTGTTGATTTATTCA
*
28926216 CATGATGAAT
1 CTTGATGAAT
28926226 CTGAGCATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 13 0.46
24 13 0.46
25 2 0.07
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (25 bp):
CTTGATGAATTTGTTGATTTATTCA
Found at i:28929840 original size:43 final size:42
Alignment explanation
Indices: 28929750--28929842 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
28929740 GATTTACGTA
* * *
28929750 TAAGACCATGTTTGGGACATTGGTATCGTATCTGATTTCATG
1 TAAGACCATGTTTGGGACATAGGCATCGTATCTGATTACATG
*
28929792 TAAGACCCTGTTTGGGAC-TGAGGCATCGATAT-TGAATTACATG
1 TAAGACCATGTTTGGGACAT-AGGCATCG-TATCTG-ATTACATG
28929835 TAAGACCA
1 TAAGACCA
28929843 CGTCCGGGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 1 0.02
42 25 0.58
43 17 0.40
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (42 bp):
TAAGACCATGTTTGGGACATAGGCATCGTATCTGATTACATG
Found at i:28953927 original size:28 final size:27
Alignment explanation
Indices: 28953878--28953932 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
28953868 AGCCATTTTA
* *
28953878 AAAACAAAAGAATATTCAAAAATAAAT
1 AAAACAAAAGAATAATCAAAAAAAAAT
* *
28953905 AAAACAAAATAGATAATCTAAAAAAAAT
1 AAAACAAAAGA-ATAATCAAAAAAAAAT
28953933 TTAAATGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.18
Consensus pattern (27 bp):
AAAACAAAAGAATAATCAAAAAAAAAT
Found at i:28963160 original size:37 final size:37
Alignment explanation
Indices: 28963110--28963183 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
28963100 TTACACTGAC
28963110 ACATCGTGTAGTCGATGAATGTCCCAGACATGTCTTA
1 ACATCGTGTAGTCGATGAATGTCCCAGACATGTCTTA
* *
28963147 ACATCTTGTAGTCGATGCATGTCCCAGACATGTCTTA
1 ACATCGTGTAGTCGATGAATGTCCCAGACATGTCTTA
28963184 CACTGGCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (37 bp):
ACATCGTGTAGTCGATGAATGTCCCAGACATGTCTTA
Found at i:28973755 original size:37 final size:37
Alignment explanation
Indices: 28973705--28973783 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
28973695 TTATTACGAA
* *
28973705 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
28973742 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
28973779 GTCTT
1 GTCTT
28973784 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:28974123 original size:49 final size:47
Alignment explanation
Indices: 28973902--28974173 Score: 402
Period size: 47 Copynumber: 5.7 Consensus size: 47
28973892 CCCTTCGGGA
* * ** * * *
28973902 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28973949 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28973996 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28974043 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28974090 CTTATCAAATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATC--ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28974139 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
28974174 AGAATCCTAA
Statistics
Matches: 207, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
46 1 0.00
47 160 0.77
49 46 0.22
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28985774 original size:38 final size:38
Alignment explanation
Indices: 28985723--28985799 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
28985713 GCACATGCTT
28985723 ATCCAAATACATATCTTTCATAATATCATCATATACTA
1 ATCCAAATACATATCTTTCATAATATCATCATATACTA
28985761 ATCCAAATACATATCTTTCATAATATCATCATATACTA
1 ATCCAAATACATATCTTTCATAATATCATCATATACTA
28985799 A
1 A
28985800 GTCCTCATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (38 bp):
ATCCAAATACATATCTTTCATAATATCATCATATACTA
Found at i:28988007 original size:9 final size:9
Alignment explanation
Indices: 28987993--28988017 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28987983 TTATATATAT
28987993 ATTAAATTA
1 ATTAAATTA
28988002 ATTAAATTA
1 ATTAAATTA
28988011 ATTAAAT
1 ATTAAAT
28988018 ACTTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTAAATTA
Found at i:28991533 original size:8 final size:8
Alignment explanation
Indices: 28991508--28991546 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
28991498 ATAAAAATTG
28991508 ATTTAAAA
1 ATTTAAAA
*
28991516 TATTAAAAAA
1 -ATT-TAAAA
28991526 ATTTAAAA
1 ATTTAAAA
28991534 ATTTAAAA
1 ATTTAAAA
28991542 ATTTA
1 ATTTA
28991547 TGCAAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 17 0.63
9 6 0.22
10 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTTAAAA
Found at i:28993028 original size:4 final size:4
Alignment explanation
Indices: 28993019--28993043 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28993009 CTATGTTACC
28993019 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
28993044 GCAACTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:28998547 original size:14 final size:12
Alignment explanation
Indices: 28998528--28998578 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 12
28998518 TCATAATCTA
28998528 TTTTTCTATTTCAT
1 TTTTTCT-TTTC-T
28998542 TTTTTCTTTTC-
1 TTTTTCTTTTCT
*
28998553 TTTTT-TTTCCT
1 TTTTTCTTTTCT
*
28998564 TTTTCCTTTTCT
1 TTTTTCTTTTCT
28998576 TTT
1 TTT
28998579 ATTCATTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 4 0.12
11 9 0.28
12 8 0.25
13 4 0.12
14 7 0.22
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:28998566 original size:22 final size:22
Alignment explanation
Indices: 28998536--28998578 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28998526 TATTTTTCTA
*
28998536 TTTCATTTTTTCTTTTCTTTTT
1 TTTCATTTTTCCTTTTCTTTTT
*
28998558 TTTCCTTTTTCCTTTTCTTTT
1 TTTCATTTTTCCTTTTCTTTT
28998579 ATTCATTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCATTTTTCCTTTTCTTTTT
Found at i:28999789 original size:19 final size:19
Alignment explanation
Indices: 28999761--28999800 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
28999751 AGTTGCGTCA
28999761 AACTTAGAAATGTTGAATG
1 AACTTAGAAATGTTGAATG
*
28999780 AACTTGGAAATGTTGAATG
1 AACTTAGAAATGTTGAATG
28999799 AA
1 AA
28999801 TTCAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (19 bp):
AACTTAGAAATGTTGAATG
Found at i:29005216 original size:22 final size:24
Alignment explanation
Indices: 29005191--29005245 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
29005181 ATTATTTTTT
29005191 TATTTTTTAAATATTT-AT-ATTA
1 TATTTTTTAAATATTTAATAATTA
*
29005213 TATTATTTT-AATATTTAATAATTT
1 TATT-TTTTAAATATTTAATAATTA
29005237 TATTTTTTA
1 TATTTTTTA
29005246 TTTATTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 11 0.39
23 10 0.36
24 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTTTTAAATATTTAATAATTA
Found at i:29005240 original size:24 final size:23
Alignment explanation
Indices: 29005188--29005263 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
29005178 CATATTATTT
29005188 TTTTATTTTTTAAATATTT-AT-A
1 TTTTATTTTTT-AATATTTAATAA
*
29005210 TTATATTATTTTAATATTTAATAA
1 TTTTATT-TTTTAATATTTAATAA
* * *
29005234 TTTTATTTTTTATTTATTGAAAAA
1 TTTTATTTTTTA-ATATTTAATAA
29005258 TTTTAT
1 TTTTAT
29005264 ATAGTCATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 13 0.29
23 11 0.24
24 21 0.47
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (23 bp):
TTTTATTTTTTAATATTTAATAA
Found at i:29028837 original size:87 final size:87
Alignment explanation
Indices: 29028691--29028871 Score: 292
Period size: 87 Copynumber: 2.1 Consensus size: 87
29028681 GACACGCTCA
*
29028691 TGTCCTCAGCCCGTGTAACTCTTTATTTGTGAAATCAGCAAGTAATTTGAACCACACGGCCAGGC
1 TGTCCTCAGCCCGTATAACTCTTTATTTGTGAAATCAGCAAGTAATTTGAACCACACGGCCAGGC
*
29028756 CACACGCCCGTGTGCTAGG-CTG
66 CACACACCCGTGTGCTAGGTC-G
* * **
29028778 TGTCCTCAGCTCGTATAATTCTTTATTTGTGACGTCAGCAAGTAATTTGAACCACACGGCCAGGC
1 TGTCCTCAGCCCGTATAACTCTTTATTTGTGAAATCAGCAAGTAATTTGAACCACACGGCCAGGC
29028843 CACACACCCGTGTGCTAGGTCG
66 CACACACCCGTGTGCTAGGTCG
29028865 TGTCCTC
1 TGTCCTC
29028872 CACACAACTG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 86 0.99
88 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (87 bp):
TGTCCTCAGCCCGTATAACTCTTTATTTGTGAAATCAGCAAGTAATTTGAACCACACGGCCAGGC
CACACACCCGTGTGCTAGGTCG
Found at i:29031332 original size:31 final size:31
Alignment explanation
Indices: 29031297--29031359 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
29031287 TATTTTAATC
29031297 ATCATATTAACCAATAGATTTCATAATTTAT
1 ATCATATTAACCAATAGATTTCATAATTTAT
29031328 ATCATATTAACCAATAGATTTCATAATTTAT
1 ATCATATTAACCAATAGATTTCATAATTTAT
29031359 A
1 A
29031360 CTTTGGCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.41
Consensus pattern (31 bp):
ATCATATTAACCAATAGATTTCATAATTTAT
Found at i:29034757 original size:13 final size:13
Alignment explanation
Indices: 29034739--29034773 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
29034729 ATTATATGAA
*
29034739 TAATTATTTTATT
1 TAATTATGTTATT
29034752 TAATTATGTTATT
1 TAATTATGTTATT
29034765 TAATTATGT
1 TAATTATGT
29034774 AGGTTCAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TAATTATGTTATT
Found at i:29038700 original size:10 final size:10
Alignment explanation
Indices: 29038687--29038741 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
29038677 AGCTCCAATC
29038687 AGCTCGCTTG
1 AGCTCGCTTG
* *
29038697 AGCTCGATTT
1 AGCTCGCTTG
29038707 AGCTCGCTTG
1 AGCTCGCTTG
* * *
29038717 AGCTTGATTT
1 AGCTCGCTTG
29038727 AGCTCGCTTG
1 AGCTCGCTTG
29038737 AGCTC
1 AGCTC
29038742 AAATTTAGCC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (10 bp):
AGCTCGCTTG
Found at i:29038710 original size:20 final size:20
Alignment explanation
Indices: 29038687--29038741 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
29038677 AGCTCCAATC
29038687 AGCTCGCTTGAGCTCGATTT
1 AGCTCGCTTGAGCTCGATTT
*
29038707 AGCTCGCTTGAGCTTGATTT
1 AGCTCGCTTGAGCTCGATTT
29038727 AGCTCGCTTGAGCTC
1 AGCTCGCTTGAGCTC
29038742 AAATTTAGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (20 bp):
AGCTCGCTTGAGCTCGATTT
Found at i:29038765 original size:40 final size:40
Alignment explanation
Indices: 29038687--29038766 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
29038677 AGCTCCAATC
* * *
29038687 AGCTCGCTTGAGCTCGATTTAGCTCGCTTGAGCTTGATTT
1 AGCTCGCTTGAGCTCAATTTAGCCCGCTTCAGCTTGATTT
*
29038727 AGCTCGCTTGAGCTCAAATTTAGCCCGTTTCAGC-TGATTT
1 AGCTCGCTTGAGCTC-AATTTAGCCCGCTTCAGCTTGATTT
29038767 CTTTTACATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 21 0.60
41 14 0.40
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (40 bp):
AGCTCGCTTGAGCTCAATTTAGCCCGCTTCAGCTTGATTT
Found at i:29038999 original size:13 final size:13
Alignment explanation
Indices: 29038981--29039015 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
29038971 ATTATATGAA
29038981 TAATTATTTTATT
1 TAATTATTTTATT
*
29038994 TAATTATGTTATT
1 TAATTATTTTATT
29039007 TAATTATTT
1 TAATTATTT
29039016 AGGTTCAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TAATTATTTTATT
Found at i:29047211 original size:30 final size:30
Alignment explanation
Indices: 29047177--29047237 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29047167 TCCTTAACTC
29047177 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
29047207 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
29047237 A
1 A
29047238 GGCTCAGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:29051176 original size:67 final size:65
Alignment explanation
Indices: 29051033--29051185 Score: 168
Period size: 67 Copynumber: 2.3 Consensus size: 65
29051023 CTAGCCAGTT
* *
29051033 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGAGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTG--CTACACATGGAACCACGCATGAGACCTAGCTACA
29051098 TA
64 TA
* * * *
29051100 TATCCCGTAGCTCTCTTGTCTACATGGTG-TACACATAGTATCC-C-CATGCGACCTAGCTACAT
1 TATCTCGTAGCTCTCTTGTCTACATGGTGCTACACAT-GGAACCACGCATGAGACCTAGCTACAT
29051162 CA
65 -A
29051164 TAATGTCTCGTAGCTCTCTTGT
1 T-A--TCTCGTAGCTCTCTTGT
29051186 ACACATGATG
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
63 17 0.23
64 8 0.11
65 5 0.07
67 44 0.59
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (65 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGCTACACATGGAACCACGCATGAGACCTAGCTACATA
Found at i:29055946 original size:26 final size:26
Alignment explanation
Indices: 29055917--29055969 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
29055907 TCAAACATGC
*
29055917 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGAT-AATTTAACTCCTAGGGGT
* *
29055943 ATTTCGATAATTTATCTCCTAGGGGT
1 ATTTAGATAATTTAACTCCTAGGGGT
29055969 A
1 A
29055970 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAGATAATTTAACTCCTAGGGGT
Found at i:29057486 original size:26 final size:26
Alignment explanation
Indices: 29057455--29057562 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
29057445 TGAAATGCCC
*
29057455 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
29057481 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
29057507 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
29057533 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29057559 ATCA
1 ATCA
29057563 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29063048 original size:25 final size:27
Alignment explanation
Indices: 29063011--29063063 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
29063001 TCAAACATGC
29063011 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
29063037 ATTTCGGT-AATTTACCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
29063063 A
1 A
29063064 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:29064579 original size:26 final size:26
Alignment explanation
Indices: 29064548--29064655 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
29064538 TGAAATGCCC
*
29064548 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
29064574 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
29064600 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
29064626 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29064652 ATCA
1 ATCA
29064656 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29066652 original size:38 final size:38
Alignment explanation
Indices: 29066554--29066690 Score: 157
Period size: 38 Copynumber: 3.6 Consensus size: 38
29066544 TGAGGTATAA
* * * *
29066554 AACCCGAACATAACACCAGCACGAAGCCTACGGGACTTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTT
* * * *
29066593 AAACTCAGATATAATACCAGCACTAGGCCTGCGGGATTT
1 -AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
* *
29066632 AACCCGGTTATAATACCAGCACGAAGTCTGCGGGATTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
*
29066670 AACCCGGATATAATTCCAGCA
1 AACCCGGATATAATACCAGCA
29066691 TAAAGCCTAT
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
38 51 0.63
39 3 0.04
40 27 0.33
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (38 bp):
AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
Found at i:29072873 original size:24 final size:22
Alignment explanation
Indices: 29072818--29072891 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 22
29072808 ATCTAAATAA
*
29072818 AATCTAAAT-TAAATCAAAC-T
1 AATCCAAATATAAATCAAACAT
* *
29072838 AAGCCAATTATATAATACAAACAT
1 AATCCAAATATA-AAT-CAAACAT
29072862 AATCCAAATATAAATCAAATACAT
1 AATCCAAATATAAATC-AA-ACAT
29072886 AATCCA
1 AATCCA
29072892 GTTTCTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.14
21 2 0.05
22 4 0.09
23 10 0.23
24 21 0.49
ACGTcount: A:0.55, C:0.18, G:0.01, T:0.26
Consensus pattern (22 bp):
AATCCAAATATAAATCAAACAT
Found at i:29094738 original size:29 final size:30
Alignment explanation
Indices: 29094697--29094761 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
29094687 ATTAATAAAA
29094697 ATAAAATTGTAATTTAATCT-CTT-AAAATT
1 ATAAAATTGTAATTTAAT-TACTTAAAAATT
* *
29094726 ATAAAATTTTAATTTAATTATTTAAAAATT
1 ATAAAATTGTAATTTAATTACTTAAAAATT
29094756 ATAAAA
1 ATAAAA
29094762 ATATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 19 0.59
30 12 0.38
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (30 bp):
ATAAAATTGTAATTTAATTACTTAAAAATT
Found at i:29094771 original size:15 final size:15
Alignment explanation
Indices: 29094751--29094783 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29094741 AATTATTTAA
29094751 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
29094766 AAATTATTAAAAATT
1 AAATTATTAAAAATT
29094781 AAA
1 AAA
29094784 ATTTTAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:29095623 original size:45 final size:45
Alignment explanation
Indices: 29095557--29095646 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
29095547 TATGGTTGAA
29095557 ATCGAAAAGCTACATTAGCCACTGGAATAACTCAAAAAAGACTTT
1 ATCGAAAAGCTACATTAGCCACTGGAATAACTCAAAAAAGACTTT
* * *
29095602 ATCGAAAAGCTATATTGGCCACTGGAATGACTCAAAAAAGACTTT
1 ATCGAAAAGCTACATTAGCCACTGGAATAACTCAAAAAAGACTTT
29095647 CTTGATTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (45 bp):
ATCGAAAAGCTACATTAGCCACTGGAATAACTCAAAAAAGACTTT
Found at i:29097383 original size:18 final size:18
Alignment explanation
Indices: 29097360--29097642 Score: 153
Period size: 18 Copynumber: 15.3 Consensus size: 18
29097350 GAATAATTAT
29097360 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
29097378 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
29097396 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
* *
29097414 TTATTCAGTATCGATTAATTGATCGG
1 TTATTCAGTA---A--CA--G-TCAG
* *
29097440 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
29097458 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
29097475 ATATTCAGTAACTATTAAG
1 TTATTCAGTAAC-AGTCAG
*
29097494 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* *
29097511 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
29097530 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
29097548 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
29097566 TTATTCAGTAACAGTC--
1 TTATTCAGTAACAGTCAG
* *
29097582 TAATATCTAGTAACAGTCAA
1 TTAT-TC-AGTAACAGTCAG
* * *
29097602 TTATTCGGTAATAGTCAA
1 TTATTCAGTAACAGTCAG
* *
29097620 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
29097638 TTATT
1 TTATT
29097643 TTATACCTTT
Statistics
Matches: 201, Mismatches: 46, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
16 3 0.01
17 18 0.09
18 143 0.71
19 19 0.09
20 3 0.01
21 2 0.01
23 2 0.01
26 11 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:29097402 original size:36 final size:36
Alignment explanation
Indices: 29097360--29097642 Score: 180
Period size: 36 Copynumber: 7.6 Consensus size: 36
29097350 GAATAATTAT
* *
29097360 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * * * *
29097396 TTATTCAATAATAACCAGTTATTCAGTATCGATTAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* *
29097432 TTGATCGGTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA
1 TT-A-----T-T-CAGTAACAATCAGTTATTCAGTAACAATCA-A
* * * *
29097476 -TATTCAGTAACTATTAAGTTATTCAGTAGCAGTC-A
1 TTATTCAGTAAC-AATCAGTTATTCAGTAACAATCAA
* **
29097511 TTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 TT-ATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * *
29097548 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATC-AA
* * * * *
29097585 -TA-TCTAGTAACAGTCAATTATTCGGTAATAGTCAA
1 TTATTC-AGTAACAATCAGTTATTCAGTAACAATCAA
*
29097620 TTATTCAGTAATAATCAGTTATT
1 TTATTCAGTAACAATCAGTTATT
29097643 TTATACCTTT
Statistics
Matches: 187, Mismatches: 42, Indels: 36
0.71 0.16 0.14
Matches are distributed among these distances:
35 12 0.06
36 128 0.68
37 21 0.11
42 2 0.01
43 5 0.03
44 19 0.10
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (36 bp):
TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
Found at i:29097509 original size:54 final size:54
Alignment explanation
Indices: 29097440--29097642 Score: 193
Period size: 54 Copynumber: 3.8 Consensus size: 54
29097430 AATTGATCGG
* *
29097440 TTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGATATTCAGTAACTATTAA
1 TTATTCAGTAACAGTCAATTATTCAGTAACAATCAGATATTCAGTAACTATCAA
* * *
29097493 GTTATTCAGTAGCAGTC-ATTCATTCAGTGACAATCAGTTATTCAGTAA-TGATCAA
1 -TTATTCAGTAACAGTCAATT-ATTCAGTAACAATCAGATATTCAGTAACT-ATCAA
* * * *
29097548 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA-ATA-TCTAGTAAC-AGTCAA
1 TTATTCAGTAACAGTCAATTATTCAGTAACAATC-AGATATTC-AGTAACTA-TCAA
* * * *
29097602 TTATTCGGTAATAGTCAATTATTCAGTAATAATCAGTTATT
1 TTATTCAGTAACAGTCAATTATTCAGTAACAATCAGATATT
29097643 TTATACCTTT
Statistics
Matches: 121, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
53 7 0.06
54 90 0.74
55 24 0.20
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (54 bp):
TTATTCAGTAACAGTCAATTATTCAGTAACAATCAGATATTCAGTAACTATCAA
Found at i:29097575 original size:72 final size:71
Alignment explanation
Indices: 29097441--29097642 Score: 230
Period size: 72 Copynumber: 2.8 Consensus size: 71
29097431 ATTGATCGGT
* * * * *
29097441 TATCCAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTCAGTAACTATTAAGTTATTCAGTAG
1 TATCTAGTAACAATCAATTATTCAGTAATATCA-ATTATTCAGTAA-TATTCAGTTATTCAGTAA
*
29097505 CAGTC-AT
64 CAGTCTAA
* *
29097512 TCAT-TCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTA
1 T-ATCT-AGTAACAATCAATTATTCAGTAAT-ATCAATTATTCAGTAATATTCAGTTATTCAGTA
29097576 ACAGTCTAA
63 ACAGTCTAA
* * *
29097585 TATCTAGTAACAGTCAATTATTCGGTAATAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCTAGTAACAATCAATTATTCAGTAATA-TCAATTATTCAGTAATATTCAGTTATT
29097643 TTATACCTTT
Statistics
Matches: 111, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
71 2 0.02
72 92 0.83
73 17 0.15
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (71 bp):
TATCTAGTAACAATCAATTATTCAGTAATATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:29098044 original size:45 final size:45
Alignment explanation
Indices: 29097810--29098038 Score: 305
Period size: 45 Copynumber: 5.1 Consensus size: 45
29097800 ATCCGGAATA
* * * * * * *
29097810 GTAACAGTAACAATAATAGTATTCAACACACAAAGTGCTGAATTG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
29097855 GTAACGGTAACAGTAACAATATTCGACACACACAGTGCTGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * *
29097900 GTAATGGTAACAGTAACAATATTCGACACACACAGTACCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * *
29097945 ATAACGGTAACAGTAACAATACTCGATACACAAAGTGCCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
29097990 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTGCCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
29098035 GTAA
1 GTAA
29098039 TAGTAGTAGT
Statistics
Matches: 163, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 163 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (45 bp):
GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
Found at i:29098469 original size:5 final size:5
Alignment explanation
Indices: 29098458--29098504 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
29098448 AATAAATCAT
* * *
29098458 AATTC CATTC CATTC CATTC AATTC AATTC AATTC AATTC AAATTC A
1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC -AATTC A
29098505 CTTTTCCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 34 0.87
6 5 0.13
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTC
Found at i:29099893 original size:9 final size:9
Alignment explanation
Indices: 29099875--29099909 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
29099865 TTTCTTTTTC
*
29099875 ATTTCTTTT
1 ATTTCATTT
29099884 ATTTCATTT
1 ATTTCATTT
29099893 ATTTC-TTT
1 ATTTCATTT
29099901 ATTTCATTT
1 ATTTCATTT
29099910 CTTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTCATTT
Found at i:29099901 original size:17 final size:18
Alignment explanation
Indices: 29099875--29099921 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
29099865 TTTCTTTTTC
29099875 ATTTCTTTTATTTCATTT
1 ATTTCTTTTATTTCATTT
29099893 ATTTC-TTTATTTCATTT
1 ATTTCTTTTATTTCATTT
* *
29099910 CTTTATTTTATT
1 ATTTCTTTTATT
29099922 ATTAAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTCTTTTATTTCATTT
Found at i:29099911 original size:13 final size:13
Alignment explanation
Indices: 29099875--29099917 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
29099865 TTTCTTTTTC
* *
29099875 ATTTCTTTTATTT
1 ATTTCATTTCTTT
29099888 CATTT-ATTTCTTT
1 -ATTTCATTTCTTT
29099901 ATTTCATTTCTTT
1 ATTTCATTTCTTT
29099914 ATTT
1 ATTT
29099918 TATTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTCATTTCTTT
Found at i:29100469 original size:19 final size:19
Alignment explanation
Indices: 29100445--29100491 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
29100435 ATGGCCAAAT
*
29100445 TCATTTTTTCACTTAAAAA
1 TCATTTTTCCACTTAAAAA
29100464 TCATTTTTCCACTTAAAAA
1 TCATTTTTCCACTTAAAAA
29100483 TCATTTTTC
1 TCATTTTTC
29100492 ATTTTGGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (19 bp):
TCATTTTTCCACTTAAAAA
Found at i:29106159 original size:46 final size:46
Alignment explanation
Indices: 29106106--29106195 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
29106096 TAATTCCAAG
*
29106106 AGGAAAAACAACTAAGTTATTGAAAAGTCAAAATAAAATTAATCTA
1 AGGAAAAACAACTAAGTTATTGAAAAGTCAAAAGAAAATTAATCTA
29106152 AGGAAAAACAACTAAGTTATTGAAAAGTCAAAAGAAAATTAATC
1 AGGAAAAACAACTAAGTTATTGAAAAGTCAAAAGAAAATTAATC
29106196 ATTAATCTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.57, C:0.09, G:0.12, T:0.22
Consensus pattern (46 bp):
AGGAAAAACAACTAAGTTATTGAAAAGTCAAAAGAAAATTAATCTA
Found at i:29108471 original size:30 final size:30
Alignment explanation
Indices: 29108437--29108510 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
29108427 TCAAGATTCT
*
29108437 AAATCCTGGTTTCAAGAAAATTACGAAACA
1 AAATCTTGGTTTCAAGAAAATTACGAAACA
29108467 AAATCTTGGTTTCAAGAAAATTACGAAACA
1 AAATCTTGGTTTCAAGAAAATTACGAAACA
29108497 AAATCTTGGTTTCA
1 AAATCTTGGTTTCA
29108511 TACAAACTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (30 bp):
AAATCTTGGTTTCAAGAAAATTACGAAACA
Found at i:29111572 original size:46 final size:46
Alignment explanation
Indices: 29111520--29111642 Score: 219
Period size: 46 Copynumber: 2.7 Consensus size: 46
29111510 GATATTTGGT
29111520 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
29111566 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *
29111612 CGTCCAAACTCATTGAGTTGAGTCCGAGTTC
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC
29111643 GTGAAATGTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Done.