Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 115 of 150
Found at i:35535302 original size:86 final size:86
Alignment explanation
Indices: 35535184--35535347 Score: 240
Period size: 86 Copynumber: 1.9 Consensus size: 86
35535174 CCTCTTTTTT
* * * * *
35535184 TTTTTTGCACTCAGTTGAGTACTTGAATTTTCAAAATCCATCAAAAAGGCCCTCAAACTTCTT-C
1 TTTTTTCCACTCAATTGAGTACTTGAACTTTCAAAATCCATCAAAAAGACCCTCAAAATT-TTCC
35535248 AAAAAAGCAATTAATCCCCTGC
65 AAAAAAGCAATTAATCCCCTGC
* * *
35535270 TTTTTTCCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTTAAAATTTTCCA
1 TTTTTTCCACTCAATTGAGTACTTGAACTTTCAAAATCCATCAAAAAGACCCTCAAAATTTTCCA
35535335 AAAAAGCAATTAA
66 AAAAAGCAATTAA
35535348 GTCCTTACTC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
85 2 0.03
86 67 0.97
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (86 bp):
TTTTTTCCACTCAATTGAGTACTTGAACTTTCAAAATCCATCAAAAAGACCCTCAAAATTTTCCA
AAAAAGCAATTAATCCCCTGC
Found at i:35535758 original size:8 final size:8
Alignment explanation
Indices: 35535721--35535813 Score: 51
Period size: 8 Copynumber: 10.5 Consensus size: 8
35535711 CTTTATAAAA
35535721 TTTTATAAT
1 TTTTAT-AT
35535730 TTTTATAT
1 TTTTATAT
*
35535738 TTCTATAT
1 TTTTATAT
35535746 ATTTTATAT
1 -TTTTATAT
*
35535755 TTTTTTCGAT
1 TTTTAT--AT
*
35535765 TTTTATAAAA
1 TTTTAT--AT
*
35535775 TTTTACAAT
1 TTTTA-TAT
*
35535784 TTTTTTAT
1 TTTTATAT
*
35535792 TTTTTTCGAT
1 TTTTAT--AT
35535802 TTTTATAT
1 TTTTATAT
35535810 TTTT
1 TTTT
35535814 TTCTAATTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
8 28 0.42
9 18 0.27
10 20 0.30
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTTATAT
Found at i:35535768 original size:18 final size:18
Alignment explanation
Indices: 35535747--35535816 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
35535737 TTTCTATATA
35535747 TTTTATATTTTTTTCGAT
1 TTTTATATTTTTTTCGAT
** * *
35535765 TTTTATAAAATTTTACAAT
1 TTTTAT-ATTTTTTTCGAT
*
35535784 TTTTTTATTTTTTTCGAT
1 TTTTATATTTTTTTCGAT
35535802 TTTTATATTTTTTTC
1 TTTTATATTTTTTTC
35535817 TAATTTTTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
18 28 0.68
19 13 0.32
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTATATTTTTTTCGAT
Found at i:35535785 original size:54 final size:55
Alignment explanation
Indices: 35535712--35535836 Score: 155
Period size: 54 Copynumber: 2.3 Consensus size: 55
35535702 TTCTTACGAC
* *
35535712 TTTATAAAATTTTATAATTTTTATATTTCTAT-ATATTTTATATTTTTTTC-GATT
1 TTTATAAAATTTTACAATTTTTATATTTCTATCAT-TTTTATATTTTTTTCTAATT
* * *
35535766 TTTATAAAATTTTACAATTTTTTTATTTTTTTCGATTTTTATATTTTTTTCTAATT
1 TTTATAAAATTTTACAATTTTTATATTTCTATC-ATTTTTATATTTTTTTCTAATT
*
35535822 TTTAATAAATTTTTA
1 TTT-ATAAAATTTTA
35535837 ATATTTGATA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
54 28 0.46
55 15 0.25
56 8 0.13
57 10 0.16
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (55 bp):
TTTATAAAATTTTACAATTTTTATATTTCTATCATTTTTATATTTTTTTCTAATT
Found at i:35535822 original size:37 final size:38
Alignment explanation
Indices: 35535737--35535825 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 38
35535727 AATTTTTATA
35535737 TTTCTATATATTTTATATTTTTTTCGATTTTTATAAAATT
1 TTTCTA-AT-TTTTATATTTTTTTCGATTTTTATAAAATT
* * **
35535777 TTAC-AATTTTTTTATTTTTTTCGATTTTTAT-ATTTT
1 TTTCTAATTTTTATATTTTTTTCGATTTTTATAAAATT
35535813 TTTCTAATTTTTA
1 TTTCTAATTTTTA
35535826 ATAAATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
36 6 0.14
37 30 0.71
38 2 0.05
39 1 0.02
40 3 0.07
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (38 bp):
TTTCTAATTTTTATATTTTTTTCGATTTTTATAAAATT
Found at i:35535823 original size:18 final size:18
Alignment explanation
Indices: 35535746--35535823 Score: 68
Period size: 18 Copynumber: 4.3 Consensus size: 18
35535736 ATTTCTATAT
35535746 ATTTTATATTTTTTTCGA
1 ATTTTATATTTTTTTCGA
* ** *
35535764 TTTTTATAAAATTTTAC-A
1 ATTTTAT-ATTTTTTTCGA
*
35535782 ATTTTTTTATTTTTTTCGA
1 A-TTTTATATTTTTTTCGA
* *
35535801 TTTTTATATTTTTTTCTA
1 ATTTTATATTTTTTTCGA
35535819 ATTTT
1 ATTTT
35535824 TAATAAATTT
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
18 32 0.73
19 12 0.27
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTATATTTTTTTCGA
Found at i:35536063 original size:91 final size:89
Alignment explanation
Indices: 35535910--35536106 Score: 288
Period size: 91 Copynumber: 2.2 Consensus size: 89
35535900 AATTTTAAAT
* * * *
35535910 AAAAGCAGGGGCTTACTTCCTTTTTTTTTAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAG
1 AAAAGAAGGGGCTTAATTCCTTTTTTTTTAAAAAGTTTGAGGGCCTTTTTAATGCATTTTGAAAG
* *
35535975 TTCAAGTACTCAATTGAGTGCAAA
66 TTCAAGTACCCAAATGAGTGCAAA
* *
35535999 AAAAGTAGGGGCTTAATTGCTCTTTTTTTTAAAAAGGTTTGAGGGCCTTTTTAATGCATTTTGAA
1 AAAAGAAGGGGCTTAATTCCT-TTTTTTTTAAAAA-GTTTGAGGGCCTTTTTAATGCATTTTGAA
*
35536064 AGTTTAAGTACCCAAATGAGTGCAAA
64 AGTTCAAGTACCCAAATGAGTGCAAA
35536090 AAAA-AAGGGGCTTAATT
1 AAAAGAAGGGGCTTAATT
35536107 TATTGGTACA
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
89 18 0.19
90 25 0.26
91 54 0.56
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (89 bp):
AAAAGAAGGGGCTTAATTCCTTTTTTTTTAAAAAGTTTGAGGGCCTTTTTAATGCATTTTGAAAG
TTCAAGTACCCAAATGAGTGCAAA
Found at i:35536913 original size:23 final size:23
Alignment explanation
Indices: 35536861--35536914 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
35536851 ACCAAAATGT
*
35536861 AAACTT-ACTAATAGTTAAATAA
1 AAACTTAACTAATAGTTAAAAAA
**
35536883 AATTTTAACTAATAGTTAAAAAA
1 AAACTTAACTAATAGTTAAAAAA
35536906 AAACTTAAC
1 AAACTTAAC
35536915 AATTCAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (23 bp):
AAACTTAACTAATAGTTAAAAAA
Found at i:35537176 original size:21 final size:22
Alignment explanation
Indices: 35537127--35537177 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
35537117 ACCAAAATGT
35537127 AAACTT-ACTAATAGTTAAATA
1 AAACTTAACTAATAGTTAAATA
* *
35537148 AAATTTAATTAATAGTTAAA-A
1 AAACTTAACTAATAGTTAAATA
35537169 AAACTTAAC
1 AAACTTAAC
35537178 AGTTCAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (22 bp):
AAACTTAACTAATAGTTAAATA
Found at i:35537312 original size:266 final size:265
Alignment explanation
Indices: 35536776--35537304 Score: 990
Period size: 263 Copynumber: 2.0 Consensus size: 265
35536766 CTAAGGTTGA
35536776 TTCAATTTTAGGATTAAACCGAGCCTGTGAGTCAAGTCTAGATATACATGCCATATAGGAGAGCA
1 TTCAATTTTAGGATTAAACCGAGCCTGTGAGTCAAGTCTAGATATACATGCCATATAGGAGAGCA
35536841 AAGGTGAGTGACCAAAATGTAAACTTACTAATAGTTAAATAAAATTTTAACTAATAGTTAAAAAA
66 AAGGTGAGTGACCAAAATGTAAACTTACTAATAGTTAAATAAAATTTTAACTAATAGTT-AAAAA
35536906 AAACTTAACAATTCAATGACTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAAATTT
130 AAACTTAACAATTCAATGACTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAAATTT
*
35536971 TCAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCTGATTTTTAGTGGTACTAGA
195 TCAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCCGATTTTTAGTGGTACTAGA
35537036 AAATGT
260 AAATGT
*
35537042 TTCAATTTTAGGATTAAACCGAGCCTGTGAGTCAAGTCTAGATATACATGCCATGTAGGAGAGCA
1 TTCAATTTTAGGATTAAACCGAGCCTGTGAGTCAAGTCTAGATATACATGCCATATAGGAGAGCA
* *
35537107 AAGGTGATTGACCAAAATGTAAACTTACTAATAGTTAAATAAAA-TTTAATTAATAGTT-AAAAA
66 AAGGTGAGTGACCAAAATGTAAACTTACTAATAGTTAAATAAAATTTTAACTAATAGTTAAAAAA
*
35537170 AACTTAACAGTTCAATGACTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAAATTTT
131 AACTTAACAATTCAATGACTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAAATTTT
35537235 CAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCCGATTTTTAGTGGTACTAGAA
196 CAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCCGATTTTTAGTGGTACTAGAA
35537300 AATGT
261 AATGT
35537305 GGTTTCAAAA
Statistics
Matches: 258, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
263 138 0.53
265 13 0.05
266 107 0.41
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (265 bp):
TTCAATTTTAGGATTAAACCGAGCCTGTGAGTCAAGTCTAGATATACATGCCATATAGGAGAGCA
AAGGTGAGTGACCAAAATGTAAACTTACTAATAGTTAAATAAAATTTTAACTAATAGTTAAAAAA
AACTTAACAATTCAATGACTTAAATAAAAGCTTTCGAATAGTTCAATAGCTTAAGTGAAAATTTT
CAATTAGGTTTATTTAAAATAAGAATATTAAATTTGTAATGACCCGATTTTTAGTGGTACTAGAA
AATGT
Found at i:35538415 original size:2 final size:2
Alignment explanation
Indices: 35538408--35538486 Score: 140
Period size: 2 Copynumber: 39.5 Consensus size: 2
35538398 GTTTCCTTTG
35538408 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
35538450 AT AT AT AT AT AT AT AT AT CT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35538487 NNNNNNNNNN
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35547409 original size:19 final size:19
Alignment explanation
Indices: 35547381--35547429 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
35547371 TATAAATTTT
*
35547381 TAAAAGTGAAAATAATATA
1 TAAAATTGAAAATAATATA
*
35547400 TAAAATTGAAAAATGATATA
1 TAAAATTG-AAAATAATATA
35547420 -AAAATTGAAA
1 TAAAATTGAAA
35547430 TTTTGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 14 0.52
20 10 0.37
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (19 bp):
TAAAATTGAAAATAATATA
Found at i:35547479 original size:30 final size:32
Alignment explanation
Indices: 35547436--35547494 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
35547426 GAAATTTTGA
*
35547436 AAAATATATTATTTT-GACTTTT-TAAAATTT
1 AAAATATATTATTTTAGAATTTTATAAAATTT
35547466 AAAATGATA-TATTTTAGAATTTTATAAAA
1 AAAAT-ATATTATTTTAGAATTTTATAAAA
35547495 AAATTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 11 0.44
31 9 0.36
32 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (32 bp):
AAAATATATTATTTTAGAATTTTATAAAATTT
Found at i:35547719 original size:19 final size:19
Alignment explanation
Indices: 35547664--35547721 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
35547654 ATATTTAAAT
* *
35547664 ATTTAATATTATAATTTT-
1 ATTTAATATTTTTATTTTA
*
35547682 -TTTTATATTTTTTACTTTTA
1 ATTTAATA-TTTTTA-TTTTA
35547702 ATTTAATATTTTTATTTTA
1 ATTTAATATTTTTATTTTA
35547721 A
1 A
35547722 ATAAACTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 6 0.19
18 4 0.12
19 10 0.31
20 6 0.19
21 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTAATATTTTTATTTTA
Found at i:35548299 original size:20 final size:18
Alignment explanation
Indices: 35548267--35548305 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
35548257 TAAAAAATTT
35548267 AATTTTTTTATTTTCAAA
1 AATTTTTTTATTTTCAAA
*
35548285 AATTCTTTTTCATTTTTAAA
1 AATT-TTTTT-ATTTTCAAA
35548305 A
1 A
35548306 GGTTTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTTTTTATTTTCAAA
Found at i:35552866 original size:20 final size:20
Alignment explanation
Indices: 35552843--35552912 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
35552833 CTTTACCACT
35552843 TCTCATTTC-CATATCTAAGC
1 TCTCATTTCACATA-CTAAGC
*
35552863 TCTCATGTTTCACGTACTAAGC
1 TCTCA--TTTCACATACTAAGC
* *
35552885 TCTCATGTTTAACGTACTAAGC
1 TCTCA--TTTCACATACTAAGC
35552907 TCTCAT
1 TCTCAT
35552913 GTTTAACGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.13
22 36 0.80
23 3 0.07
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (20 bp):
TCTCATTTCACATACTAAGC
Found at i:35552882 original size:22 final size:22
Alignment explanation
Indices: 35552857--35552935 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
35552847 ATTTCCATAT
*
35552857 CTAAGCTCTCATGTTTCACGTA
1 CTAAGCTCTCATGTTTAACGTA
35552879 CTAAGCTCTCATGTTTAACGTA
1 CTAAGCTCTCATGTTTAACGTA
*
35552901 CTAAGCTCTCATGTTTAACGAA
1 CTAAGCTCTCATGTTTAACGTA
* *
35552923 CTAAACCCTCATG
1 CTAAGCTCTCATG
35552936 GCTTCTTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (22 bp):
CTAAGCTCTCATGTTTAACGTA
Found at i:35561493 original size:25 final size:24
Alignment explanation
Indices: 35561460--35561513 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
35561450 ATATACCCGT
* *
35561460 ATATGGATATTGTAATAATT-TATTA
1 ATATTGATATTAT-ATAATTATA-TA
35561485 ATATTGATATTATATAATTATATA
1 ATATTGATATTATATAATTATATA
35561509 ATATT
1 ATATT
35561514 TAATTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
ATATTGATATTATATAATTATATA
Found at i:35561888 original size:12 final size:13
Alignment explanation
Indices: 35561870--35561909 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
35561860 TAAAAATCAT
35561870 AAAAA-TTATAAA
1 AAAAAGTTATAAA
* *
35561882 CAAAATTTATAAA
1 AAAAAGTTATAAA
35561895 AAAAAGTTATAAA
1 AAAAAGTTATAAA
35561908 AA
1 AA
35561910 TTTTAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (13 bp):
AAAAAGTTATAAA
Found at i:35563600 original size:2 final size:2
Alignment explanation
Indices: 35563593--35563650 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
35563583 CACTTTTGGG
35563593 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35563635 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
35563651 TTCAATCCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35571004 original size:35 final size:35
Alignment explanation
Indices: 35570899--35571026 Score: 114
Period size: 35 Copynumber: 3.6 Consensus size: 35
35570889 GCACATCGTC
* * * *
35570899 AGTCCAACCATAACACGCCAGATGCTCATACGAGCCC
1 AGTCCAACCAAAACACGCCA-ATGCTCACAAGAG-CT
** * *
35570936 A-TCCCTCTAAAACACACCAAATGCTCACAAGAGCT
1 AGTCCAACCAAAACACGCC-AATGCTCACAAGAGCT
* * **
35570971 AGTCCAACCGAAACATGCCAATGCTCATTAGAGCT
1 AGTCCAACCAAAACACGCCAATGCTCACAAGAGCT
35571006 AGTCCAACCAAAACACGCCAA
1 AGTCCAACCAAAACACGCCAA
35571027 ACAGAGAGTA
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
35 35 0.49
36 34 0.48
37 2 0.03
ACGTcount: A:0.38, C:0.34, G:0.13, T:0.15
Consensus pattern (35 bp):
AGTCCAACCAAAACACGCCAATGCTCACAAGAGCT
Found at i:35573782 original size:38 final size:38
Alignment explanation
Indices: 35573739--35573817 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
35573729 AATTCGCCTA
35573739 ATCCACTATCATATTTTTCTAGATTTATTAAAGAATTT
1 ATCCACTATCATATTTTTCTAGATTTATTAAAGAATTT
35573777 ATCCACTATCATATTTTTCTAGATTTATTAAAGAATTT
1 ATCCACTATCATATTTTTCTAGATTTATTAAAGAATTT
35573815 ATC
1 ATC
35573818 TCCTCATCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (38 bp):
ATCCACTATCATATTTTTCTAGATTTATTAAAGAATTT
Found at i:35593118 original size:11 final size:11
Alignment explanation
Indices: 35593095--35593208 Score: 103
Period size: 11 Copynumber: 10.4 Consensus size: 11
35593085 TAAAAATTAA
35593095 AAAAAGTATTTT
1 AAAAA-TATTTT
*
35593107 AAAAATAATTT
1 AAAAATATTTT
35593118 --AAA-A--TT
1 AAAAATATTTT
35593124 AAAAATATTTT
1 AAAAATATTTT
35593135 AAAAATATTTT
1 AAAAATATTTT
35593146 AAAAATATTTT
1 AAAAATATTTT
35593157 AAAAATATTTT
1 AAAAATATTTT
* ** *
35593168 AAAATTAAAAAATA
1 -AAA--AATATTTT
35593182 AAAAAGTATTTT
1 AAAAA-TATTTT
35593194 AAAAATATTTT
1 AAAAATATTTT
35593205 AAAA
1 AAAA
35593209 TTAAAAAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
6 2 0.02
8 4 0.05
9 4 0.05
11 52 0.62
12 15 0.18
13 3 0.04
14 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:35593127 original size:17 final size:17
Alignment explanation
Indices: 35593105--35593138 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35593095 AAAAAGTATT
35593105 TTAAAAATAATTTAAAA
1 TTAAAAATAATTTAAAA
*
35593122 TTAAAAATATTTTAAAA
1 TTAAAAATAATTTAAAA
35593139 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATAATTTAAAA
Found at i:35593162 original size:50 final size:48
Alignment explanation
Indices: 35593095--35593229 Score: 170
Period size: 50 Copynumber: 2.8 Consensus size: 48
35593085 TAAAAATTAA
*
35593095 AAAAAGTATTTTAAAAATAATTTAAAATTAAAAATATTTTAAAAA-TATTTT
1 AAAAA-TATTTTAAAAATAATTTAAAATTAAAAA-A--TAAAAAAGTATTTT
*
35593146 AAAAATATTTTAAAAATATTTTAAAATTAAAAAATAAAAAAGTATTTT
1 AAAAATATTTTAAAAATAATTTAAAATTAAAAAATAAAAAAGTATTTT
*
35593194 AAAAATATTTTAAAATTAA---AAAATTTAAAAAATAAA
1 AAAAATATTTTAAAAATAATTTAAAA-TTAAAAAATAAA
35593230 TATATTTATT
Statistics
Matches: 78, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
45 4 0.05
46 12 0.15
47 6 0.08
48 23 0.29
49 1 0.01
50 27 0.35
51 5 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (48 bp):
AAAAATATTTTAAAAATAATTTAAAATTAAAAAATAAAAAAGTATTTT
Found at i:35593201 original size:37 final size:36
Alignment explanation
Indices: 35593146--35593227 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 36
35593136 AAAATATTTT
35593146 AAAAATATTTTAAAAATATTTTAAAATTAAAAAATA
1 AAAAATATTTTAAAAATATTTTAAAATTAAAAAATA
35593182 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTA
1 AAAAA-TATTTTAAAAATATTTTAAAATTAAAAAA--TA
35593221 AAAAATA
1 AAAAATA
35593228 AATATATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 5 0.12
37 29 0.67
38 2 0.05
39 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (36 bp):
AAAAATATTTTAAAAATATTTTAAAATTAAAAAATA
Found at i:35593237 original size:17 final size:16
Alignment explanation
Indices: 35593195--35593237 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
35593185 AAGTATTTTA
* *
35593195 AAAATATTTTAAAATT
1 AAAATATTTAAAAAAT
*
35593211 AAAAAATTTAAAAAAT
1 AAAATATTTAAAAAAT
35593227 AAATATATTTA
1 AAA-ATATTTA
35593238 TTATATCGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:35596225 original size:21 final size:21
Alignment explanation
Indices: 35596199--35596250 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
35596189 AACACCCACA
*
35596199 ACAACCCCCGCCAGAGCAACC
1 ACAACCCCCGCCAGAACAACC
* **
35596220 ACAACCCTCGCTGGAACAACC
1 ACAACCCCCGCCAGAACAACC
35596241 ACAACCCCCG
1 ACAACCCCCG
35596251 TCGAAAGCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.50, G:0.13, T:0.04
Consensus pattern (21 bp):
ACAACCCCCGCCAGAACAACC
Found at i:35596415 original size:27 final size:28
Alignment explanation
Indices: 35596385--35596455 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 28
35596375 TATTTAATAA
35596385 AATAAAAGTTATTTTTAATA-TTTTAAT
1 AATAAAAGTTATTTTTAATATTTTTAAT
35596412 AAT-AAA-TTATTTTT-ATATTTTTAAT
1 AATAAAAGTTATTTTTAATATTTTTAAT
* * *
35596437 AA-AATAGTTCTTTTGAATA
1 AATAAAAGTTATTTTTAATA
35596456 AAGTAATAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 3 0.08
25 19 0.51
26 9 0.24
27 6 0.16
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (28 bp):
AATAAAAGTTATTTTTAATATTTTTAAT
Found at i:35599685 original size:125 final size:125
Alignment explanation
Indices: 35599418--35599684 Score: 346
Period size: 125 Copynumber: 2.2 Consensus size: 125
35599408 AGCCAAACAG
* * ** *
35599418 GAACTACGGTAGAAAAAGAACGTCCACGTAGGAGTTTTTTCATCAATTTTGCTGACAGTGCATCC
1 GAACTACTGTAGAAAAAAAACGTCCACGTAGGAACTTTTTCATCAATTTTGCTGACACTGCATCC
* *
35599483 TGCTTGAAGCGTTTTTAACACCATTTGTTCAGAATCGTCTTCTCAAAATTATTTTTTCAG
66 TACTTGAAGCGTTTTTAACACCATTTGTTCAGAATCGTCTTCTCAAAATTATTTTTTCAA
* * * * *
35599543 GAACTATTGTGGAAAAAAAGCGTCCACGTGGGAACTTTTTCAGT-AATTTTGCTGATACTGCATC
1 GAACTACTGTAGAAAAAAAACGTCCACGTAGGAACTTTTTCA-TCAATTTTGCTGACACTGCATC
* **
35599607 CTACTTGAAGCGTTTTTTACATTATCTT-TTCAGAATCGTCTTCTCAAAA-T-TTTTTT-AA
65 CTACTTGAAGCGTTTTTAACACCAT-TTGTTCAGAATCGTCTTCTCAAAATTATTTTTTCAA
35599665 GAACTACTGTAGAAAAAAAA
1 GAACTACTGTAGAAAAAAAA
35599685 ACAAAATCCT
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
122 18 0.15
123 6 0.05
124 1 0.01
125 94 0.77
126 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAAAACGTCCACGTAGGAACTTTTTCATCAATTTTGCTGACACTGCATCC
TACTTGAAGCGTTTTTAACACCATTTGTTCAGAATCGTCTTCTCAAAATTATTTTTTCAA
Found at i:35599781 original size:34 final size:34
Alignment explanation
Indices: 35599743--35599872 Score: 147
Period size: 34 Copynumber: 3.8 Consensus size: 34
35599733 CACAAAATTA
35599743 TTTCTTAAAAGCTCTAAACCCTAATTTAATTAAT
1 TTTCTTAAAAGCTCTAAACCCTAATTTAATTAAT
35599777 TTTCTTAAAAGCTCTAAACCCTAATTTAATTAAT
1 TTTCTTAAAAGCTCTAAACCCTAATTTAATTAAT
* * * * *
35599811 TCAT-TTAAAA-CCCAAAAACCTAAGTTAATTAAT
1 T-TTCTTAAAAGCTCTAAACCCTAATTTAATTAAT
* * * *
35599844 TTTTTTAAAAAACTCTAATCCTTAATTTA
1 TTTCTT-AAAAGCTCTAAACCCTAATTTA
35599873 TTCCCTAAAC
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
32 1 0.01
33 22 0.28
34 45 0.56
35 12 0.15
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.40
Consensus pattern (34 bp):
TTTCTTAAAAGCTCTAAACCCTAATTTAATTAAT
Found at i:35599938 original size:33 final size:33
Alignment explanation
Indices: 35599896--35599958 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
35599886 CCTTAAAACC
* * *
35599896 TAACTCTAAATTATTTTAAGAAAACCCTAACTT
1 TAACCCTAAATTACTTTAACAAAACCCTAACTT
*
35599929 TAACCCTAAATTACTTTAACAAAACTCTAA
1 TAACCCTAAATTACTTTAACAAAACCCTAA
35599959 AATCATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (33 bp):
TAACCCTAAATTACTTTAACAAAACCCTAACTT
Found at i:35607292 original size:12 final size:12
Alignment explanation
Indices: 35607275--35607299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35607265 TTGAGAATTT
35607275 TTCCAAAAGAAA
1 TTCCAAAAGAAA
35607287 TTCCAAAAGAAA
1 TTCCAAAAGAAA
35607299 T
1 T
35607300 ATGTTGGCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (12 bp):
TTCCAAAAGAAA
Found at i:35616762 original size:37 final size:37
Alignment explanation
Indices: 35616719--35616849 Score: 142
Period size: 37 Copynumber: 3.5 Consensus size: 37
35616709 CATTATTTTA
35616719 GCGTGTTATCGGGTGGATTAGCTCTAATGAGCATTTG
1 GCGTGTTATCGGGTGGATTAGCTCTAATGAGCATTTG
* * * * *
35616756 GTGTGTT-TACGGTTGGACTAGCTCTTCA-GAGCAATTG
1 GCGTGTTAT-CGGGTGGATTAGCTC-TAATGAGCATTTG
*
35616793 GCGTGTTATCGGGTGGATTAGCTCTTATGAGC-TTCTG
1 GCGTGTTATCGGGTGGATTAGCTCTAATGAGCATT-TG
* *
35616830 GCGTGTTTTCGGATGGATTA
1 GCGTGTTATCGGGTGGATTA
35616850 CTGTGCTAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
36 4 0.05
37 70 0.91
38 3 0.04
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.37
Consensus pattern (37 bp):
GCGTGTTATCGGGTGGATTAGCTCTAATGAGCATTTG
Found at i:35620394 original size:18 final size:16
Alignment explanation
Indices: 35620361--35620408 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
35620351 CTTAAAATAT
*
35620361 ATATTTTAAAAATAAA
1 ATATGTTAAAAATAAA
35620377 ATATGTTAAATAATTAAA
1 ATATGTTAAA-AA-TAAA
*
35620395 AT-TATTAAAAATAA
1 ATATGTTAAAAATAA
35620409 TTAATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 3 0.11
16 11 0.39
17 8 0.29
18 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
ATATGTTAAAAATAAA
Found at i:35620934 original size:38 final size:38
Alignment explanation
Indices: 35620866--35620948 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 38
35620856 TTTTTAAAAT
*
35620866 TTTTTAATTTTAAAATAATTTTAAAATACTTTTTTATTA
1 TTTTTAATTTTAAAATAATTTTAAAATACTTTTTT-TAA
35620905 TTTTTAATTTTAAAAT-ATTTTAAAATACTTTTTTTAA
1 TTTTTAATTTTAAAATAATTTTAAAATACTTTTTTTAA
35620942 TTTTTAA
1 TTTTTAA
35620949 AATAAATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
37 9 0.21
38 18 0.42
39 16 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (38 bp):
TTTTTAATTTTAAAATAATTTTAAAATACTTTTTTTAA
Found at i:35620936 original size:28 final size:29
Alignment explanation
Indices: 35620881--35620952 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
35620871 AATTTTAAAA
** *
35620881 TAATTTTAAAATACTTTTTTATTA-TTTT
1 TAATTTTAAAATACTTTTAAAATATTTTT
35620909 TAATTTTAAAATA-TTTTAAAATACTTTTTT
1 TAATTTTAAAATACTTTTAAAATA--TTTTT
35620939 TAATTTTTAAAATA
1 TAA-TTTTAAAATA
35620953 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.19
28 13 0.35
30 7 0.19
31 10 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
TAATTTTAAAATACTTTTAAAATATTTTT
Found at i:35624305 original size:900 final size:899
Alignment explanation
Indices: 35622513--35624317 Score: 3549
Period size: 900 Copynumber: 2.0 Consensus size: 899
35622503 GGTTTTGCTG
35622513 GTTTCATATATTATATATGTTTAATGATTGTTTTAAAATCAAGTAAACAATAGCAGATACTTAGC
1 GTTTCATATATTATATATGTTTAATGATTGTTTTAAAATCAAGTAAACAATAGCAGATACTTAGC
35622578 TGAATTATTAACAGAGAAAGAGAAGCTGGGACCTTTCACACAAGTTCTTCCTCAGTGCACCGGGC
66 TGAATTATTAACAGAGAAAGAGAAGCTGGGACCTTTCACACAAGTTCTTCCTCAGTGCACCGGGC
35622643 TTTTTAATCAAGGTTATTGAATCTTCTGTTTTCCTTTTCTTTATCCTGCAATATAAAGATTCAAT
131 TTTTTAATCAAGGTTATTGAATCTTCTGTTTTCCTTTTCTTTATCCTGCAATATAAAGATTCAAT
35622708 CACATGTATACAAGTATGAAACACTAATGATTTAAACTAGTAAGGGTTCAATTGATTATCGAGTA
196 CACATGTATACAAGTATGAAACACTAATGATTTAAACTAGTAAGGGTTCAATTGATTATCGAGTA
35622773 ATTCTTGACTGAGTGTAGGGTGTACATAAGAGGCAAAGGTTCTGTCAAGGATTCTGTTAAGGTAA
261 ATTCTTGACTGAGTGTAGGGTGTACATAAGAGGCAAAGGTTCTGTCAAGGATTCTGTTAAGGTAA
35622838 AGTCAACTGTAAATTCTTTTATGATATTCATTTTTTCATCTCTCCTCCCAATACAAGGCCATATT
326 AGTCAACTGTAAATTCTTTTATGATATTCATTTTTTCATCTCTCCTCCCAATACAAGGCCATATT
35622903 GGACTGCAGGTGATGTGAAAATTGCTCGGCTAATCTTATATATACTCTGATCATATGCATCTCCA
391 GGACTGCAGGTGATGTGAAAATTGCTCGGCTAATCTTATATATACTCTGATCATATGCATCTCCA
*
35622968 TTTGCATTTCACATGTTTTATGAAGAACTTTCAGTATTATGATCAATGAAATCATCACTTTTACT
456 TTTGCATTTCACATGCTTTATGAAGAACTTTCAGTATTATGATCAATGAAATCATCACTTTTACT
35623033 AAGAAAAGTACCTTGTGAAAAAAACAGTTATGCAAAATCAAGGTCTGACCTAATTAAAGACGAGA
521 AAGAAAAGTACCTTGTGAAAAAAACAGTTATGCAAAATCAAGGTCTGACCTAATTAAAGACGAGA
35623098 GTTGGCTTTTTTTGTGCGTTTTCTTCTTGAATATAAGAAGACTGAGTTCTCCTTTGATGTTGCTT
586 GTTGGCTTTTTTTGTGCGTTTTCTTCTTGAATATAAGAAGACTGAGTTCTCCTTTGATGTTGCTT
35623163 CACTTGTTATTCATTGACTGCTTACCCATTTTTAACATGTAGGAAGAGAAACTAAAAGATAAACC
651 CACTTGTTATTCATTGACTGCTTACCCATTTTTAACATGTAGGAAGAGAAACTAAAAGATAAACC
35623228 TGGATTCGAACACCTTAATGAGCCATTGCATGTGTTGGTGGAGGCTGAACTTCCCAAAGATGTGA
716 TGGATTCGAACACCTTAATGAGCCATTGCATGTGTTGGTGGAGGCTGAACTTCCCAAAGATGTGA
*
35623293 TAAATTCTCGTTTGGACTACGTTGTTGCCATACTAGAAAATCTTCTGAAACCTGTGGTATGAACA
781 TAAATTCTCGTTTGGACTACGTTGTTGCCATACTAGAAAATCTTCTGAAACCCGTGGTATGAACA
35623358 AAAGCAAAATTTTATTGTTGTTTTTAAAGTTAGTCTTTCCTTTTTTTTTGTATAT
846 AAAGCAAAATTTTATTGTTGTTTTTAAAGTTAGTCTTTCC-TTTTTTTTGTATAT
35623413 GTTTCATATATTATATATGTTTAATGATTGTTTTAAAATCAAGTAAACAATAGCAGATACTTAGC
1 GTTTCATATATTATATATGTTTAATGATTGTTTTAAAATCAAGTAAACAATAGCAGATACTTAGC
35623478 TGAATTATTAACAGAGAAAGAGAAGCTGGGACCTTTCACACAAGTTCTTCCTCAGTGCACCGGGC
66 TGAATTATTAACAGAGAAAGAGAAGCTGGGACCTTTCACACAAGTTCTTCCTCAGTGCACCGGGC
35623543 TTTTTAATCAAGGTTATTGAATCTTCTGTTTTCCTTTTCTTTATCCTGCAATATAAAGATTCAAT
131 TTTTTAATCAAGGTTATTGAATCTTCTGTTTTCCTTTTCTTTATCCTGCAATATAAAGATTCAAT
35623608 CACATGTATACAAGTATGAAACACTAATGATTTAAACTAGTAAGGGTTCAATTGATTATCGAGTA
196 CACATGTATACAAGTATGAAACACTAATGATTTAAACTAGTAAGGGTTCAATTGATTATCGAGTA
35623673 ATTCTTGACTGAGTGTAGGGTGTACATAAGAGGCAAAGGTTCTGTCAAGGATTCTGTTAAGGTAA
261 ATTCTTGACTGAGTGTAGGGTGTACATAAGAGGCAAAGGTTCTGTCAAGGATTCTGTTAAGGTAA
35623738 AGTCAACTGTAAATTCTTTTATGATATTCATTTTTTCATCTCTCCTCCCAATACAAGGCCATATT
326 AGTCAACTGTAAATTCTTTTATGATATTCATTTTTTCATCTCTCCTCCCAATACAAGGCCATATT
35623803 GGACTGCAGGTGATGTGAAAATTGCTCGGCTAATCTTATATATACTCTGATCATATGCATCTCCA
391 GGACTGCAGGTGATGTGAAAATTGCTCGGCTAATCTTATATATACTCTGATCATATGCATCTCCA
*
35623868 TTTGCATTTCACATGCTTTATGAAGAACTTTCAGTATTATGATCAATGAAATGATCACTTTTACT
456 TTTGCATTTCACATGCTTTATGAAGAACTTTCAGTATTATGATCAATGAAATCATCACTTTTACT
35623933 AAGAAAAGTACCTTGTGAAAAAAACAGTTATGCAAAATCAAGGTCTGACCTAATTAAAGACGAGA
521 AAGAAAAGTACCTTGTGAAAAAAACAGTTATGCAAAATCAAGGTCTGACCTAATTAAAGACGAGA
35623998 GTTGGCTTCTTTTTGTGCGTTTTCTTCTTGAATATAAGAAGACTGAGTTCTCCTTTGATGTTGCT
586 GTTGGCTT-TTTTTGTGCGTTTTCTTCTTGAATATAAGAAGACTGAGTTCTCCTTTGATGTTGCT
*
35624063 TCACTTGTTATTCATTGACTGCTTACCCATTTTTAACATGTGGGAAGAGAAACTAAAAGATAAAC
650 TCACTTGTTATTCATTGACTGCTTACCCATTTTTAACATGTAGGAAGAGAAACTAAAAGATAAAC
35624128 CTGGATTCGAACACCTTAATGAGCCATTGCATGTGTTGGTGGAGGCTGAACTTCCCAAAGATGTG
715 CTGGATTCGAACACCTTAATGAGCCATTGCATGTGTTGGTGGAGGCTGAACTTCCCAAAGATGTG
35624193 ATAAATTCTCGTTTGGACTACGTTGTTGCCATACTAGAAAATCTTCTGAAACCCGTGGTATGAAC
780 ATAAATTCTCGTTTGGACTACGTTGTTGCCATACTAGAAAATCTTCTGAAACCCGTGGTATGAAC
35624258 AAAAGCAAAATTTTATTGTTGTTTTTAAAGTTAGTCTTTCC-TTTTTTTGTATAT
845 AAAAGCAAAATTTTATTGTTGTTTTTAAAGTTAGTCTTTCCTTTTTTTTGTATAT
35624312 GTTTCA
1 GTTTCA
35624318 GCTCCTCGAT
Statistics
Matches: 900, Mismatches: 4, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
899 19 0.02
900 591 0.66
901 290 0.32
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (899 bp):
GTTTCATATATTATATATGTTTAATGATTGTTTTAAAATCAAGTAAACAATAGCAGATACTTAGC
TGAATTATTAACAGAGAAAGAGAAGCTGGGACCTTTCACACAAGTTCTTCCTCAGTGCACCGGGC
TTTTTAATCAAGGTTATTGAATCTTCTGTTTTCCTTTTCTTTATCCTGCAATATAAAGATTCAAT
CACATGTATACAAGTATGAAACACTAATGATTTAAACTAGTAAGGGTTCAATTGATTATCGAGTA
ATTCTTGACTGAGTGTAGGGTGTACATAAGAGGCAAAGGTTCTGTCAAGGATTCTGTTAAGGTAA
AGTCAACTGTAAATTCTTTTATGATATTCATTTTTTCATCTCTCCTCCCAATACAAGGCCATATT
GGACTGCAGGTGATGTGAAAATTGCTCGGCTAATCTTATATATACTCTGATCATATGCATCTCCA
TTTGCATTTCACATGCTTTATGAAGAACTTTCAGTATTATGATCAATGAAATCATCACTTTTACT
AAGAAAAGTACCTTGTGAAAAAAACAGTTATGCAAAATCAAGGTCTGACCTAATTAAAGACGAGA
GTTGGCTTTTTTTGTGCGTTTTCTTCTTGAATATAAGAAGACTGAGTTCTCCTTTGATGTTGCTT
CACTTGTTATTCATTGACTGCTTACCCATTTTTAACATGTAGGAAGAGAAACTAAAAGATAAACC
TGGATTCGAACACCTTAATGAGCCATTGCATGTGTTGGTGGAGGCTGAACTTCCCAAAGATGTGA
TAAATTCTCGTTTGGACTACGTTGTTGCCATACTAGAAAATCTTCTGAAACCCGTGGTATGAACA
AAAGCAAAATTTTATTGTTGTTTTTAAAGTTAGTCTTTCCTTTTTTTTGTATAT
Found at i:35625874 original size:29 final size:29
Alignment explanation
Indices: 35625833--35625890 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
35625823 CTGTCTTCTC
*
35625833 CCCCAAATGTTCTTTCCCCTCTGCCGGTT
1 CCCCAAACGTTCTTTCCCCTCTGCCGGTT
* *
35625862 CCCCAAACGTTCTTTTCCCTCTGCTGGTT
1 CCCCAAACGTTCTTTCCCCTCTGCCGGTT
35625891 TTTTGGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.10, C:0.40, G:0.14, T:0.36
Consensus pattern (29 bp):
CCCCAAACGTTCTTTCCCCTCTGCCGGTT
Found at i:35630143 original size:13 final size:13
Alignment explanation
Indices: 35630125--35630187 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
35630115 ACACTCAAAT
35630125 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
35630138 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
35630151 TCTT-AAAAGCAC
1 TTTTCAAAAGCAC
35630163 TTCTT-AAAAGCAC
1 TT-TTCAAAAGCAC
*
35630176 TTCTCAAAAGCA
1 TTTTCAAAAGCA
35630188 ATGAAGAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
12 10 0.22
13 35 0.78
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.29
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:35630159 original size:25 final size:26
Alignment explanation
Indices: 35630128--35630187 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 26
35630118 CTCAAATTTT
35630128 TCAAAAGCACTT-TTCAAAAGCAC-TC
1 TCAAAAGCACTTCTT-AAAAGCACTTC
*
35630153 TTAAAAGCACTTCTTAAAAGCACTTC
1 TCAAAAGCACTTCTTAAAAGCACTTC
35630179 TCAAAAGCA
1 TCAAAAGCA
35630188 ATGAAGAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 19 0.61
26 12 0.39
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (26 bp):
TCAAAAGCACTTCTTAAAAGCACTTC
Found at i:35635316 original size:9 final size:9
Alignment explanation
Indices: 35635284--35635320 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
35635274 TGAATTTTCG
35635284 AATTCGAAT
1 AATTCGAAT
*
35635293 AACTCGAAT
1 AATTCGAAT
35635302 AATTCGAAT
1 AATTCGAAT
*
35635311 AGTTCGAAT
1 AATTCGAAT
35635320 A
1 A
35635321 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:35635713 original size:17 final size:16
Alignment explanation
Indices: 35635679--35635709 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35635669 CCTATTTACT
*
35635679 TTCCCTCAAACTTTTA
1 TTCCCTAAAACTTTTA
35635695 TTCCCTAAAACTTTT
1 TTCCCTAAAACTTTT
35635710 TATTTTCCCC
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:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCCCTAAAACTTTTA
Found at i:35640842 original size:12 final size:13
Alignment explanation
Indices: 35640827--35640861 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
35640817 GAAAAAATGA
35640827 TAAA-AAATAAAG
1 TAAATAAATAAAG
35640839 TAAATAAATAAAG
1 TAAATAAATAAAG
35640852 -AAATAAATAA
1 TAAATAAATAA
35640862 TATATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (13 bp):
TAAATAAATAAAG
Found at i:35640848 original size:4 final size:4
Alignment explanation
Indices: 35640826--35640876 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
35640816 GGAAAAAATG
* *
35640826 ATAA A-AA ATAA AGTAA ATAA ATAA AGAA ATAA ATAA TATAT ATAA TATAA
1 ATAA ATAA ATAA A-TAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA -ATAA
35640876 A
1 A
35640877 AGAAGGTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 3 0.08
4 25 0.64
5 11 0.28
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:35646029 original size:23 final size:25
Alignment explanation
Indices: 35645980--35646029 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
35645970 AAAAAAAATG
*
35645980 TTTTTTAATTGTTTTCTTGCCTCTT
1 TTTTTTAATTGTTTTCTTGCCTATT
* *
35646005 TTTTTTTA-TGTTTTGTTG-CTATT
1 TTTTTTAATTGTTTTCTTGCCTATT
35646028 TT
1 TT
35646030 CTTGTTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 6 0.27
24 9 0.41
25 7 0.32
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.72
Consensus pattern (25 bp):
TTTTTTAATTGTTTTCTTGCCTATT
Found at i:35646234 original size:25 final size:25
Alignment explanation
Indices: 35646206--35646253 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
35646196 GTATTTTTTT
35646206 AAAATTTATTTTCAAT-TTTTTAGGA
1 AAAATTTATTTT-AATGTTTTTAGGA
35646231 AAAATTTATTTTAATGTTTTTAG
1 AAAATTTATTTTAATGTTTTTAG
35646254 TATTTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.54
Consensus pattern (25 bp):
AAAATTTATTTTAATGTTTTTAGGA
Found at i:35652251 original size:10 final size:10
Alignment explanation
Indices: 35652236--35652265 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
35652226 TTTACCTTCT
35652236 TATACATATA
1 TATACATATA
35652246 TATACATATA
1 TATACATATA
*
35652256 TATATATATA
1 TATACATATA
35652266 AGTGACGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TATACATATA
Found at i:35653106 original size:17 final size:17
Alignment explanation
Indices: 35653084--35653116 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35653074 TTATTTTCTA
35653084 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
*
35653101 TATAAGTTTTGTAAAT
1 TATAAGTTTTCTAAAT
35653117 AATTATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:35653162 original size:15 final size:16
Alignment explanation
Indices: 35653125--35653163 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35653115 ATAATTATTC
*
35653125 TAAATTTATTAGTATA
1 TAAATTTAGTAGTATA
*
35653141 AAAATTTAGTAGTAT-
1 TAAATTTAGTAGTATA
35653156 TAAATTTA
1 TAAATTTA
35653164 TAAGTTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (16 bp):
TAAATTTAGTAGTATA
Found at i:35653164 original size:61 final size:61
Alignment explanation
Indices: 35653095--35653243 Score: 169
Period size: 61 Copynumber: 2.5 Consensus size: 61
35653085 ATAAGTTTTC
35653095 TAAATTTATAAGTTTTGTAAATAATTATTCTAAATTTATTAGT-ATAAAAATTTAGT-AGTAT
1 TAAATTTATAAGTTTTGTAAATAATTATTCTAAATTTATTAGTAAT-AAAATTTA-TAAGTAT
* * * * * *
35653156 TAAATTTATAAGTTTTCTAAAAAAGTGTTCTAGATTTATTATTAATAAAATTTATAAGTAT
1 TAAATTTATAAGTTTTGTAAATAATTATTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * * *
35653217 CAATTTTACACG-TTTGTAAATAATTAT
1 TAAATTTATAAGTTTTGTAAATAATTAT
35653244 ATTTTTAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
60 12 0.17
61 58 0.81
62 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (61 bp):
TAAATTTATAAGTTTTGTAAATAATTATTCTAAATTTATTAGTAATAAAATTTATAAGTAT
Found at i:35653479 original size:8 final size:7
Alignment explanation
Indices: 35653466--35653511 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
35653456 TAACGTATAT
35653466 ATAATAAC
1 ATAAT-AC
35653474 ATAATA-
1 ATAATAC
*
35653480 A-ATTAC
1 ATAATAC
35653486 ATAATAC
1 ATAATAC
35653493 ATAATAAC
1 ATAAT-AC
35653501 ATAATAC
1 ATAATAC
35653508 ATAA
1 ATAA
35653512 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:35653499 original size:95 final size:95
Alignment explanation
Indices: 35653387--35653650 Score: 377
Period size: 95 Copynumber: 2.8 Consensus size: 95
35653377 AATCATTTGC
* * * *
35653387 TTACTTAATACATAATAACACAATGCATAA-TTGGTATATAAGCTTGCATAACTTACATAATAAC
1 TTACATAATACATAATAACATAATACATAACTT-ATATATAAGCTTGCATAACTTACATAATAAC
*
35653451 TTCCATAACGTATATATAATAACATAATAAA
65 TTCCATAACGTACATATAATAACATAATAAA
*
35653482 TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGTATAACTTACATAATAACT
1 TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACT
* * *** *
35653547 TTCATAACTTACATATAATCTGATAATACA
66 TCCATAACGTACATATAATAACATAATAAA
* *
35653577 TTACATAATACATATTAACATAATACATAACTTATATTATAATCTTGCATAACTTACATAATAAC
1 TTACATAATACATAATAACATAATACATAACTTATA-TATAAGCTTGCATAACTTACATAATAAC
35653642 TTCCATAAC
65 TTCCATAAC
35653651 TTAATACACC
Statistics
Matches: 151, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
95 115 0.76
96 36 0.24
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.35
Consensus pattern (95 bp):
TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACT
TCCATAACGTACATATAATAACATAATAAA
Found at i:35653504 original size:15 final size:15
Alignment explanation
Indices: 35653466--35653511 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
35653456 TAACGTATAT
35653466 ATAATAACATAAT--
1 ATAATAACATAATAC
*
35653479 A-AATTACATAATAC
1 ATAATAACATAATAC
35653493 ATAATAACATAATAC
1 ATAATAACATAATAC
35653508 ATAA
1 ATAA
35653512 CTTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACATAATAC
Found at i:35653533 original size:21 final size:20
Alignment explanation
Indices: 35653507--35653564 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
35653497 TAACATAATA
*
35653507 CATAACTTATATATAAGCTTGT
1 CATAACTTACATATAA-CTT-T
35653529 -ATAACTTACATAATAACTTT
1 CATAACTTACAT-ATAACTTT
35653549 CATAACTTACATATAA
1 CATAACTTACATATAA
35653565 TCTGATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.15
21 24 0.73
22 4 0.12
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (20 bp):
CATAACTTACATATAACTTT
Found at i:35653627 original size:22 final size:21
Alignment explanation
Indices: 35653602--35653653 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
35653592 TAACATAATA
* * *
35653602 CATAACTTATATTATAATCTTG
1 CATAACTTACATAATAA-CTTC
35653624 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
35653645 CATAACTTA
1 CATAACTTA
35653654 ATACACCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:35653746 original size:9 final size:9
Alignment explanation
Indices: 35653732--35653799 Score: 83
Period size: 9 Copynumber: 8.0 Consensus size: 9
35653722 TAATAACTTT
35653732 CTTACATAA
1 CTTACATAA
*
35653741 CTTACATTA
1 CTTACATAA
35653750 CTTACAGT-A
1 CTTACA-TAA
35653759 CTTACATAA
1 CTTACATAA
35653768 --TACATAA
1 CTTACATAA
35653775 --TACATAA
1 CTTACATAA
35653782 CTTACATAA
1 CTTACATAA
35653791 CTTACATAA
1 CTTACATAA
35653800 TACATAAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
7 14 0.26
8 1 0.02
9 38 0.70
10 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.34
Consensus pattern (9 bp):
CTTACATAA
Found at i:35653773 original size:7 final size:7
Alignment explanation
Indices: 35653761--35653806 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
35653751 TTACAGTACT
35653761 TACATAA
1 TACATAA
35653768 TACATAA
1 TACATAA
35653775 TACATAA
1 TACATAA
35653782 CTTACATAA
1 --TACATAA
35653791 CTTACATAA
1 --TACATAA
35653800 TACATAA
1 TACATAA
35653807 AAATATATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 21 0.57
9 16 0.43
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:35653785 original size:32 final size:33
Alignment explanation
Indices: 35653734--35653806 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 33
35653724 ATAACTTTCT
*
35653734 TACATAACTTACATTACTTACAGT-ACTTACATAA
1 TACATAAC-TACATAACTTACA-TAACTTACATAA
35653768 TACATAA-TACATAACTTACATAACTTACATAA
1 TACATAACTACATAACTTACATAACTTACATAA
35653800 TACATAA
1 TACATAA
35653807 AAATATATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 1 0.03
32 29 0.78
34 7 0.19
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (33 bp):
TACATAACTACATAACTTACATAACTTACATAA
Found at i:35656858 original size:19 final size:19
Alignment explanation
Indices: 35656834--35656872 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
35656824 ATAAGTTGTT
*
35656834 TACAGAATTTTTTTATGAA
1 TACAGAATCTTTTTATGAA
35656853 TACAGAATCTTTTTATGAA
1 TACAGAATCTTTTTATGAA
35656872 T
1 T
35656873 GGTTAAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (19 bp):
TACAGAATCTTTTTATGAA
Found at i:35659373 original size:21 final size:21
Alignment explanation
Indices: 35659337--35659403 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
35659327 AACTTAAAGA
*
35659337 AGAGGCGGCAGCGAGGGAAGC
1 AGAGGCTGCAGCGAGGGAAGC
* *
35659358 AGCGGCTGCAGTGAGGGAAGC
1 AGAGGCTGCAGCGAGGGAAGC
*
35659379 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGGGAAGC
35659400 AGAG
1 AGAG
35659404 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.30, C:0.18, G:0.48, T:0.04
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGGGAAGC
Found at i:35659759 original size:42 final size:42
Alignment explanation
Indices: 35659712--35659874 Score: 265
Period size: 42 Copynumber: 3.9 Consensus size: 42
35659702 ACGTTTTTGT
*
35659712 AAAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
*
35659754 AAAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTA-
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* *
35659795 ATAAAAAACGCCGCTAAAGACCATGTTTTTTAGCGGCGCTTAG
1 A-AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
*
35659838 AGAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
35659875 TTTTTGTTTG
Statistics
Matches: 113, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
41 1 0.01
42 111 0.98
43 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
Found at i:35671693 original size:21 final size:20
Alignment explanation
Indices: 35671667--35671719 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
35671657 ACAAAAAGAT
* *
35671667 TTTTTTTTAATAATTTTTCAA
1 TTTTTTTTAA-AATTTGTAAA
35671688 TTTTTTTTAAAATTTGTAAA
1 TTTTTTTTAAAATTTGTAAA
*
35671708 CTTTTTTTAAAA
1 TTTTTTTTAAAA
35671720 AATTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTTTTAAAATTTGTAAA
Found at i:35671727 original size:20 final size:21
Alignment explanation
Indices: 35671688--35671727 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35671678 AATTTTTCAA
* *
35671688 TTTTTTTTAAAATTTGTAAAC
1 TTTTTTTAAAAAATTGTAAAC
35671709 TTTTTTTAAAAAATT-TAAA
1 TTTTTTTAAAAAATTGTAAA
35671728 AAAATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTTTTAAAAAATTGTAAAC
Found at i:35671753 original size:43 final size:45
Alignment explanation
Indices: 35671706--35671803 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 45
35671696 AAAATTTGTA
35671706 AACTTTTTTTAAAAAATTT-AAAAAAAT-T-TTGTATTTA-TTTTTT
1 AACTTTTTTT-AAAAATTTGAAAAAAATGTATT-TATTTATTTTTTT
* * *
35671749 AAC-TTTTATAGAAATTTGAAAAAAATGTATTTTTTTATTTTTTT
1 AACTTTTTTTAAAAATTTGAAAAAAATGTATTTATTTATTTTTTT
35671793 AATCTTTTTTT
1 AA-CTTTTTTT
35671804 TTCTCATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
41 7 0.16
42 13 0.29
43 9 0.20
44 10 0.22
45 1 0.02
46 5 0.11
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (45 bp):
AACTTTTTTTAAAAATTTGAAAAAAATGTATTTATTTATTTTTTT
Found at i:35671793 original size:44 final size:42
Alignment explanation
Indices: 35671719--35671800 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 42
35671709 TTTTTTTAAA
35671719 AAATTTAAAAAAATTTTGTATTTATTTTTTAA-CTTTTATAG
1 AAATTTAAAAAAATTTTGTATTTATTTTTTAATCTTTTATAG
*
35671760 AAATTTGAAAAAAATGTATT-TTTTTATTTTTTTAATCTTTT
1 AAATTT-AAAAAAAT-T-TTGTATTTA-TTTTTTAATCTTTT
35671801 TTTTTCTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
41 6 0.17
42 8 0.23
43 6 0.17
44 10 0.29
45 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (42 bp):
AAATTTAAAAAAATTTTGTATTTATTTTTTAATCTTTTATAG
Found at i:35672452 original size:21 final size:21
Alignment explanation
Indices: 35672428--35672489 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
35672418 CATTTAATTA
35672428 ATTTTTTAAAATTAAAAAAAT
1 ATTTTTTAAAATTAAAAAAAT
* *
35672449 ATTTTTTAAATCATTTAAATAAT
1 ATTTTTTAAA--ATTAAAAAAAT
**
35672472 -TTTTTTAATTTTAAAAAA
1 ATTTTTTAAAATTAAAAAA
35672490 GTTAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 6 0.18
21 10 0.30
22 8 0.24
23 9 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTTTAAAATTAAAAAAAT
Found at i:35675565 original size:50 final size:50
Alignment explanation
Indices: 35675499--35675618 Score: 195
Period size: 50 Copynumber: 2.4 Consensus size: 50
35675489 AATGAAAAAG
* *
35675499 ATATGATGGTAGCTGTGCATTTCAACTTCTCTGATTTAGTTAGTATAAAT
1 ATATGATAGTACCTGTGCATTTCAACTTCTCTGATTTAGTTAGTATAAAT
**
35675549 ATATGATAGTACCTGTGCATTTTGACTTCTCTGATTTAGTTAGTATAAAT
1 ATATGATAGTACCTGTGCATTTCAACTTCTCTGATTTAGTTAGTATAAAT
*
35675599 ATATGATAGTACCCGTGCAT
1 ATATGATAGTACCTGTGCAT
35675619 CATGTGGAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (50 bp):
ATATGATAGTACCTGTGCATTTCAACTTCTCTGATTTAGTTAGTATAAAT
Found at i:35679943 original size:22 final size:21
Alignment explanation
Indices: 35679918--35679958 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
35679908 TTCTTTATTT
*
35679918 TCTATTCTCTTCTGCTTCTCCC
1 TCTATTCTCCTCT-CTTCTCCC
*
35679940 TCTATTTTCCTCTCTTCTC
1 TCTATTCTCCTCTCTTCTC
35679959 GATCTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.05, C:0.39, G:0.02, T:0.54
Consensus pattern (21 bp):
TCTATTCTCCTCTCTTCTCCC
Found at i:35681481 original size:34 final size:34
Alignment explanation
Indices: 35681439--35681503 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
35681429 TTTTTAATTT
35681439 TAAAATTAAATAAATTAATTATTTTAAGGAAGAA
1 TAAAATTAAATAAATTAATTATTTTAAGGAAGAA
35681473 TAAAATTAAATAAATTAATTATTTTAAGGAA
1 TAAAATTAAATAAATTAATTATTTTAAGGAA
35681504 TAATTTCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (34 bp):
TAAAATTAAATAAATTAATTATTTTAAGGAAGAA
Found at i:35684861 original size:19 final size:19
Alignment explanation
Indices: 35684837--35684918 Score: 76
Period size: 19 Copynumber: 4.2 Consensus size: 19
35684827 TTACAAAAAA
35684837 AAAATTTAAAATAATTTTT
1 AAAATTTAAAATAATTTTT
* * *
35684856 AAAATTCAAAATAATTATA
1 AAAATTTAAAATAATTTTT
*
35684875 AAAATTTTAATATATATTTTT
1 AAAA-TTTAAAATA-ATTTTT
* *
35684896 AAAAATTATAAAT-TTTTTT
1 AAAATTTA-AAATAATTTTT
35684915 AAAA
1 AAAA
35684919 AATTAAAGAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
19 29 0.58
20 10 0.20
21 11 0.22
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATTTAAAATAATTTTT
Found at i:35698753 original size:110 final size:110
Alignment explanation
Indices: 35698560--35698778 Score: 366
Period size: 110 Copynumber: 2.0 Consensus size: 110
35698550 TTAGCACATT
* *
35698560 TTATGTGAGCTTTCCCGCGTATCAGATATTATTCTAAGTGATTCAACGGGCATGCAAAGGGAATG
1 TTATGTAAGCTTTCCCGCGTATCAGATATTATTCTAAGTGATTCAACGGGCATGCAAAGGGAAGG
* *
35698625 AACGGTAAGTGTTCTAATGGTTATGTTATAAACATATGGAAAGGA
66 AACAGTAAGTGTTCTAATGGTTATCTTATAAACATATGGAAAGGA
* * *
35698670 TTATGTAAGCTTTCCTGCGTATCCGATATTATTCTAAGTGATTCAACGGGCATGCATAGGGAAGG
1 TTATGTAAGCTTTCCCGCGTATCAGATATTATTCTAAGTGATTCAACGGGCATGCAAAGGGAAGG
*
35698735 AACAGTAAGTGTTCTAATGGTTATCTTATAAACCTATGGAAAGG
66 AACAGTAAGTGTTCTAATGGTTATCTTATAAACATATGGAAAGG
35698779 TATGAAATGA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 101 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (110 bp):
TTATGTAAGCTTTCCCGCGTATCAGATATTATTCTAAGTGATTCAACGGGCATGCAAAGGGAAGG
AACAGTAAGTGTTCTAATGGTTATCTTATAAACATATGGAAAGGA
Found at i:35702319 original size:25 final size:25
Alignment explanation
Indices: 35702252--35702320 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
35702242 ATAAAATAAT
*
35702252 GGTAAGCTCATACGAGCTGAGAATC
1 GGTAAGCTCATACGAGCTGAAAATC
*
35702277 GATAAGCTC-TCACGAGCT-ACAAATC
1 GGTAAGCTCAT-ACGAGCTGA-AAATC
*
35702302 GGTAAGCTCATACAAGCTG
1 GGTAAGCTCATACGAGCTG
35702321 TGGTGTGTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
24 2 0.06
25 33 0.92
26 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (25 bp):
GGTAAGCTCATACGAGCTGAAAATC
Found at i:35702497 original size:20 final size:20
Alignment explanation
Indices: 35702469--35702510 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
35702459 GCAATTACTC
35702469 AATTCAAAAACACAT-AATTT
1 AATTC-AAAACACATAAATTT
* *
35702489 AATTTAAAACATATAAATTT
1 AATTCAAAACACATAAATTT
35702509 AA
1 AA
35702511 AATTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTCAAAACACATAAATTT
Found at i:35709732 original size:25 final size:25
Alignment explanation
Indices: 35709700--35709769 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
35709690 GATGAAATAA
*
35709700 CGGTAAGCTCATACGAGCTG-AGAAT
1 CGGTAAGCTCATATGAGCTGCA-AAT
35709725 CGGTAAGCTC-TCATGAGCTGCAAAT
1 CGGTAAGCTCAT-ATGAGCTGCAAAT
*
35709750 CGGTAAGCTTATATGAGCTG
1 CGGTAAGCTCATATGAGCTG
35709770 TGGTGTGTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
24 1 0.03
25 37 0.93
26 2 0.05
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (25 bp):
CGGTAAGCTCATATGAGCTGCAAAT
Found at i:35715500 original size:16 final size:17
Alignment explanation
Indices: 35715470--35715505 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35715460 AGTAAAAATG
*
35715470 ATAAAAATTATTTAAAA
1 ATAAAAATCATTTAAAA
*
35715487 ATAAAAATCATTAAAAA
1 ATAAAAATCATTTAAAA
35715504 AT
1 AT
35715506 GTAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAAAATCATTTAAAA
Found at i:35715672 original size:2 final size:2
Alignment explanation
Indices: 35715659--35715688 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
35715649 TAAAAGAGAA
*
35715659 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35715689 TGTAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35720019 original size:21 final size:21
Alignment explanation
Indices: 35719994--35720040 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
35719984 AATAACTCTT
*
35719994 TTATTTTATATAA-ATAAATA
1 TTATTTTATATAATAAAAATA
35720014 TGTA--TTATATAATAAAAATA
1 T-TATTTTATATAATAAAAATA
35720034 TTATTTT
1 TTATTTT
35720041 TTTATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
19 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATTTTATATAATAAAAATA
Found at i:35720432 original size:13 final size:13
Alignment explanation
Indices: 35720402--35720426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35720392 CAATATATTT
35720402 ATTAATTAAAAAC
1 ATTAATTAAAAAC
35720415 ATTAATTAAAAA
1 ATTAATTAAAAA
35720427 ATTTAAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:35720448 original size:22 final size:21
Alignment explanation
Indices: 35720405--35720449 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35720395 TATATTTATT
* *
35720405 AATTAAAAACATTAATTAAAA
1 AATTAAAAACATGAAATAAAA
*
35720426 AATTTAAAACATGAAATAGAAA
1 AATTAAAAACATGAAATA-AAA
35720448 AA
1 AA
35720450 GATTCGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (21 bp):
AATTAAAAACATGAAATAAAA
Found at i:35722765 original size:29 final size:31
Alignment explanation
Indices: 35722733--35722793 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
35722723 AAACTTCTTT
35722733 ACTTTC-CCCCAAAACTTTTACTCCT-TCCC
1 ACTTTCTCCCCAAAACTTTTACTCCTCTCCC
* *
35722762 ACTTTCTCCTCAAAATTTTTACTCCTCTCCC
1 ACTTTCTCCCCAAAACTTTTACTCCTCTCCC
35722793 A
1 A
35722794 TCCCACCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.21
30 17 0.61
31 5 0.18
ACGTcount: A:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (31 bp):
ACTTTCTCCCCAAAACTTTTACTCCTCTCCC
Found at i:35722867 original size:19 final size:20
Alignment explanation
Indices: 35722834--35722871 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35722824 GCTCTTTCAA
35722834 CCCCCAAAACTTTTTACTTT
1 CCCCCAAAACTTTTTACTTT
35722854 CCCCCAAAAC-TTTTACTT
1 CCCCCAAAACTTTTTACTT
35722872 CTCACCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (20 bp):
CCCCCAAAACTTTTTACTTT
Found at i:35738226 original size:43 final size:43
Alignment explanation
Indices: 35738165--35738249 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
35738155 ACCTAATTAG
*
35738165 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAAA
1 GAAAATAATCCCCTTATTCTAATAAACTACTAAAAGATAAAAA
35738208 GAAAATAATCCCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAATCCCCTTATTCTAATAAACTACTAAAAGATAAAA
35738250 TAAAATATTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (43 bp):
GAAAATAATCCCCTTATTCTAATAAACTACTAAAAGATAAAAA
Found at i:35738295 original size:19 final size:19
Alignment explanation
Indices: 35738271--35738317 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
35738261 TAGAATATCT
35738271 ATAAGATTTATCTACCTAA
1 ATAAGATTTATCTACCTAA
*
35738290 ATAAGATTTATCTATCTAA
1 ATAAGATTTATCTACCTAA
35738309 ATAA-ATTTA
1 ATAAGATTTA
35738318 AAATATATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (19 bp):
ATAAGATTTATCTACCTAA
Found at i:35739786 original size:24 final size:24
Alignment explanation
Indices: 35739754--35739800 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
35739744 CTAAATTTAT
*
35739754 AATACTTTCCTTTC-CTTTCTCTTC
1 AATACTTTCC-ATCACTTTCTCTTC
*
35739778 AATATTTTCCATCACTTTCTCTT
1 AATACTTTCCATCACTTTCTCTT
35739801 ATTTCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (24 bp):
AATACTTTCCATCACTTTCTCTTC
Found at i:35746745 original size:16 final size:15
Alignment explanation
Indices: 35746713--35746746 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
35746703 AATAAATTAA
*
35746713 ATTTTATATTGAATT
1 ATTTTATATTAAATT
35746728 ATTTTATATTTAAATT
1 ATTTTATA-TTAAATT
35746744 ATT
1 ATT
35746747 ATGTTCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTATATTAAATT
Found at i:35747174 original size:3 final size:3
Alignment explanation
Indices: 35747168--35747207 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
35747158 ATTTGAAAAT
35747168 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
35747208 ATAAAGTTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35753012 original size:2 final size:2
Alignment explanation
Indices: 35753005--35753030 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35752995 ATTCAATAGG
35753005 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
35753031 GTATGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35758399 original size:18 final size:18
Alignment explanation
Indices: 35758376--35758410 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35758366 ACAAACATTA
35758376 ATTTTAATTATATAATAT
1 ATTTTAATTATATAATAT
*
35758394 ATTTTAATTTTATAATA
1 ATTTTAATTATATAATA
35758411 CGCACAAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTATATAATAT
Found at i:35800641 original size:26 final size:26
Alignment explanation
Indices: 35800612--35800697 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
35800602 ATCAATTCAA
35800612 AACTATCTTCAAACTTCAAACCATTG
1 AACTATCTTCAAACTTCAAACCATTG
* * * * * *
35800638 AACTTTCATCAAACAAGT-ACATCAATTCAA
1 AACTATCTTCAAAC--TTCA-AACCATT--G
35800668 AACTATCTTCAAACTTCAAACCATTG
1 AACTATCTTCAAACTTCAAACCATTG
35800694 AACT
1 AACT
35800698 TTCATCACTA
Statistics
Matches: 42, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
26 16 0.38
27 1 0.02
28 12 0.29
29 1 0.02
30 12 0.29
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.29
Consensus pattern (26 bp):
AACTATCTTCAAACTTCAAACCATTG
Found at i:35800678 original size:56 final size:56
Alignment explanation
Indices: 35800592--35800704 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
35800582 GAAACCTTTG
35800592 AAACAAGTACATCAATTCAAAACTATCTTCAAACTTCAAACCATTGAACTTTCATC
1 AAACAAGTACATCAATTCAAAACTATCTTCAAACTTCAAACCATTGAACTTTCATC
35800648 AAACAAGTACATCAATTCAAAACTATCTTCAAACTTCAAACCATTGAACTTTCATC
1 AAACAAGTACATCAATTCAAAACTATCTTCAAACTTCAAACCATTGAACTTTCATC
35800704 A
1 A
35800705 CTAACTCACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.43, C:0.25, G:0.04, T:0.28
Consensus pattern (56 bp):
AAACAAGTACATCAATTCAAAACTATCTTCAAACTTCAAACCATTGAACTTTCATC
Found at i:35802470 original size:44 final size:43
Alignment explanation
Indices: 35802422--35802504 Score: 130
Period size: 44 Copynumber: 1.9 Consensus size: 43
35802412 AAAATTATCA
* *
35802422 CAACTTTTTTTAACTAATAATTATTTTTAAATGTGTAATTATTT
1 CAACTTTTATTAAATAATAATTATTTTTAAATGTG-AATTATTT
*
35802466 CAACTTTTATTAAATTATAATTATTTTTAAATGTGAATT
1 CAACTTTTATTAAATAATAATTATTTTTAAATGTGAATT
35802505 TAGTAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 4 0.11
44 32 0.89
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (43 bp):
CAACTTTTATTAAATAATAATTATTTTTAAATGTGAATTATTT
Found at i:35807204 original size:25 final size:29
Alignment explanation
Indices: 35807169--35807254 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 29
35807159 CATATTTATG
35807169 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
35807195 -AAAGTCAAAGATATGAGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
35807223 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
35807254 G
1 G
35807255 GCATAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
25 20 0.39
26 2 0.04
27 1 0.02
28 1 0.02
30 21 0.41
31 6 0.12
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:35807231 original size:30 final size:30
Alignment explanation
Indices: 35807167--35807255 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
35807157 TCCATATTTA
35807167 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
35807194 T--AAAGTCAAAGATATGAGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
35807222 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
35807253 TGG
1 TGG
35807256 CATAAAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
25 20 0.38
26 2 0.04
27 2 0.04
28 1 0.02
30 20 0.38
31 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:35809614 original size:3 final size:3
Alignment explanation
Indices: 35809606--35809653 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
35809596 ATTCCCACTC
* * * *
35809606 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA TTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35809654 CTTACCTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:35809630 original size:18 final size:18
Alignment explanation
Indices: 35809607--35809653 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
35809597 TTCCCACTCA
35809607 TAATAATAATAATAATAC
1 TAATAATAATAATAATAC
*
35809625 TAATAATAATATTAATAC
1 TAATAATAATAATAATAC
*
35809643 TAATATTAATA
1 TAATAATAATA
35809654 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAATAATAATAATAC
Found at i:35809655 original size:12 final size:12
Alignment explanation
Indices: 35809606--35809653 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
35809596 ATTCCCACTC
*
35809606 ATAATAATAATA
1 ATAATATTAATA
*
35809618 ATAATACTAATA
1 ATAATATTAATA
35809630 ATAATATTAATA
1 ATAATATTAATA
*
35809642 CTAATATTAATA
1 ATAATATTAATA
35809654 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATATTAATA
Found at i:35810417 original size:3 final size:3
Alignment explanation
Indices: 35810409--35810446 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
35810399 ATTCATTAGT
35810409 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35810447 TTATTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35810451 original size:3 final size:3
Alignment explanation
Indices: 35810445--35810487 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
35810435 ATAATAATAA
35810445 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35810488 TACTTAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:35810610 original size:14 final size:14
Alignment explanation
Indices: 35810591--35810636 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
35810581 TTTTTTTATT
35810591 ATAATAATAATTTA
1 ATAATAATAATTTA
*
35810605 ATAATACTAATTTA
1 ATAATAATAATTTA
35810619 ATAATAATAATTTA
1 ATAATAATAATTTA
35810633 ATAA
1 ATAA
35810637 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:35810646 original size:28 final size:28
Alignment explanation
Indices: 35810581--35810647 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
35810571 TTTGTCAACT
*
35810581 TTTTTTTATTATAATAATAATTTAATAATA
1 TTTTTTTA--ATAATAATAATTTAATAACA
* **
35810611 CTAATTTAATAATAATAATTTAATAACA
1 TTTTTTTAATAATAATAATTTAATAACA
35810639 TTTTTTTAA
1 TTTTTTTAA
35810648 CACATAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 25 0.83
30 5 0.17
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTTTTTAATAATAATAATTTAATAACA
Found at i:35817520 original size:7 final size:7
Alignment explanation
Indices: 35817508--35817537 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
35817498 CTGAAAGGGG
35817508 TTCTTCT
1 TTCTTCT
35817515 TTCTTCT
1 TTCTTCT
35817522 TTCTTCT
1 TTCTTCT
35817529 TTCTTCT
1 TTCTTCT
35817536 TT
1 TT
35817538 TCCCTAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTCT
Found at i:35818143 original size:18 final size:18
Alignment explanation
Indices: 35818120--35818162 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35818110 ACCCAATCTA
**
35818120 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
35818138 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
35818156 AACCCAA
1 AACCCAA
35818163 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:35818289 original size:9 final size:9
Alignment explanation
Indices: 35818269--35818353 Score: 134
Period size: 9 Copynumber: 9.4 Consensus size: 9
35818259 GTAGTGATTC
*
35818269 AATTTGGTT
1 AATTCGGTT
*
35818278 AATTCGGGT
1 AATTCGGTT
35818287 AATTCGGTT
1 AATTCGGTT
*
35818296 AATTCGGGT
1 AATTCGGTT
35818305 AATTCGGTT
1 AATTCGGTT
*
35818314 AATTCGGGT
1 AATTCGGTT
35818323 AATTCGGTT
1 AATTCGGTT
35818332 AATTCGGTT
1 AATTCGGTT
35818341 AATTCGGTT
1 AATTCGGTT
35818350 AATT
1 AATT
35818354 TTTAACCAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:35818295 original size:18 final size:18
Alignment explanation
Indices: 35818269--35818353 Score: 152
Period size: 18 Copynumber: 4.7 Consensus size: 18
35818259 GTAGTGATTC
*
35818269 AATTTGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
35818287 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
35818305 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
35818323 AATTCGGTTAATTCGGTT
1 AATTCGGTTAATTCGGGT
35818341 AATTCGGTTAATT
1 AATTCGGTTAATT
35818354 TTTAACCAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:35819575 original size:25 final size:25
Alignment explanation
Indices: 35819535--35819582 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35819525 TTGTAAATAA
*
35819535 AAATAATATCTCTAGAAATTTTTTG
1 AAATAATATCTCTAGAAAATTTTTG
* *
35819560 AAATAATTTCTTTAGAAAATTTT
1 AAATAATATCTCTAGAAAATTTT
35819583 CTCTTTACAA
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:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (25 bp):
AAATAATATCTCTAGAAAATTTTTG
Found at i:35819727 original size:6 final size:6
Alignment explanation
Indices: 35819716--35819756 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
35819706 AAATATTATC
35819716 AATATA AATATA AATATA AATATTA AAT-TA AAT-TA AATATA
1 AATATA AATATA AATATA AATA-TA AATATA AATATA AATATA
35819757 TCGTATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.30
6 18 0.55
7 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AATATA
Found at i:35822422 original size:43 final size:43
Alignment explanation
Indices: 35822361--35822496 Score: 152
Period size: 43 Copynumber: 3.2 Consensus size: 43
35822351 GTGAAGAAAT
*
35822361 GCCGCTAAAGATCATGACCTTTAACGACGCTTCTACCATAAAC
1 GCCGCTAAAGATCATGACCTTTAACGACGCTTCTACCACAAAC
**
35822404 GCCGCTAAAGATCATGACCTTTAGTGACGCTTCTACCACAAAC
1 GCCGCTAAAGATCATGACCTTTAACGACGCTTCTACCACAAAC
* * * **
35822447 GCCACTATAAAGA--ATGACTTTTAACGGCGCTT-TTTCACAAAC
1 GCCGC--TAAAGATCATGACCTTTAACGACGCTTCTACCACAAAC
*
35822489 GCTGCTAA
1 GCCGCTAA
35822497 CAACATGACT
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.04
42 11 0.14
43 59 0.75
45 6 0.08
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (43 bp):
GCCGCTAAAGATCATGACCTTTAACGACGCTTCTACCACAAAC
Found at i:35822981 original size:29 final size:29
Alignment explanation
Indices: 35822941--35823003 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
35822931 AGAAAATTAA
35822941 AAAAAGTATTTTAAAA-ATATTTTAAAAAT
1 AAAAAGTATTTTAAAATAT-TTTTAAAAAT
35822970 AAAAAGTATTTTAAAATATTTTTAAAAAT
1 AAAAAGTATTTTAAAATATTTTTAAAAAT
35822999 AAAAA
1 AAAAA
35823004 ATATATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATATTTTTAAAAAT
Found at i:35822984 original size:12 final size:11
Alignment explanation
Indices: 35822941--35822999 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
35822931 AGAAAATTAA
35822941 AAAAAGTATTTT
1 AAAAA-TATTTT
35822953 AAAAATATTTT
1 AAAAATATTTT
35822964 AAAAATA----
1 AAAAATATTTT
*
35822971 AAAAGTATTTT
1 AAAAATATTTT
35822982 -AAAATATTTTT
1 AAAAATA-TTTT
35822993 AAAAATA
1 AAAAATA
35823000 AAAAATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 6 0.15
10 5 0.13
11 17 0.44
12 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:35823003 original size:18 final size:18
Alignment explanation
Indices: 35822952--35822985 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35822942 AAAAGTATTT
35822952 TAAAAA-TATTTTAAAAA
1 TAAAAAGTATTTTAAAAA
35822969 TAAAAAGTATTTTAAAA
1 TAAAAAGTATTTTAAAA
35822986 TATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAAAAGTATTTTAAAAA
Found at i:35824694 original size:13 final size:13
Alignment explanation
Indices: 35824673--35824706 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
35824663 GACCCTTTCT
*
35824673 GGAATGTCTGTCA
1 GGAAAGTCTGTCA
35824686 GGAAAGTCTGTCA
1 GGAAAGTCTGTCA
35824699 GGAAAGTC
1 GGAAAGTC
35824707 ATGCACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (13 bp):
GGAAAGTCTGTCA
Found at i:35826396 original size:22 final size:21
Alignment explanation
Indices: 35826371--35826442 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
35826361 TCGTAGTCCC
35826371 TAAACCCATAATCCATAAACCT
1 TAAACCCATAA-CCATAAACCT
**
35826393 TAAA-ATAGTAACACATAAACCT
1 TAAACCCA-TAAC-CATAAACCT
*
35826415 TAAACCC-TACACCATATACCT
1 TAAACCCATA-ACCATAAACCT
35826436 TAAACCC
1 TAAACCC
35826443 TAAACTATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 19 0.46
22 22 0.54
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (21 bp):
TAAACCCATAACCATAAACCT
Found at i:35831424 original size:7 final size:7
Alignment explanation
Indices: 35831412--35831484 Score: 65
Period size: 7 Copynumber: 10.3 Consensus size: 7
35831402 AATTAATCTA
35831412 AACCCCT
1 AACCCCT
35831419 AACCCCT
1 AACCCCT
* *
35831426 AAACCAT
1 AACCCCT
** *
35831433 AAATCAT
1 AACCCCT
35831440 AAACCCCT
1 -AACCCCT
*
35831448 AACCCTT
1 AACCCCT
*
35831455 AACCCTT
1 AACCCCT
35831462 AACCCCT
1 AACCCCT
35831469 AACCCCT
1 AACCCCT
*
35831476 AACCACT
1 AACCCCT
35831483 AA
1 AA
35831485 ACCTTAAACC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
7 52 0.93
8 4 0.07
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCCT
Found at i:35831458 original size:14 final size:14
Alignment explanation
Indices: 35831441--35831505 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
35831431 ATAAATCATA
* *
35831441 AACCCCTAACCCTT
1 AACCCTTAACCCCT
35831455 AACCCTTAACCCCT
1 AACCCTTAACCCCT
* *
35831469 AACCCCTAACCACT
1 AACCCTTAACCCCT
*
35831483 AAACCTTAAACCCC-
1 AACCCTT-AACCCCT
35831497 AACCCTTAA
1 AACCCTTAA
35831506 ACCATAAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 2 0.05
14 35 0.83
15 5 0.12
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCCTTAACCCCT
Found at i:35831458 original size:28 final size:27
Alignment explanation
Indices: 35831406--35831515 Score: 90
Period size: 28 Copynumber: 4.1 Consensus size: 27
35831396 AACACTAATT
*
35831406 AATCTAAACCCCTAACCCCTAAACCATA
1 AATCTAAACCCCTAA-CCCTTAACCATA
35831434 AATCATAAACCCCTAACCCTTAACC---
1 AATC-TAAACCCCTAACCCTTAACCATA
* *
35831459 ---CTTAACCCCTAACCCCTAACCACTA
1 AATCTAAACCCCTAACCCTTAACCA-TA
*
35831484 AACCTTAAACCCC-AACCCTTAAACCATA
1 AATC-TAAACCCCTAACCCTT-AACCATA
35831512 AATC
1 AATC
35831516 ATAATCCCTA
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
21 18 0.27
22 1 0.02
28 24 0.36
29 23 0.35
ACGTcount: A:0.40, C:0.41, G:0.00, T:0.19
Consensus pattern (27 bp):
AATCTAAACCCCTAACCCTTAACCATA
Found at i:35831506 original size:21 final size:22
Alignment explanation
Indices: 35831448--35831513 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
35831438 ATAAACCCCT
* * *
35831448 AACCCTTAACCCTTAACCCCT-
1 AACCCCTAACCCTTAAACCATA
*
35831469 AACCCCTAACCAC-TAAACCTTA
1 AACCCCTAACC-CTTAAACCATA
35831491 AACCCC-AACCCTTAAACCATA
1 AACCCCTAACCCTTAAACCATA
35831512 AA
1 AA
35831514 TCATAATCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 30 0.79
22 7 0.18
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCCTAACCCTTAAACCATA
Found at i:35832936 original size:2 final size:2
Alignment explanation
Indices: 35832931--35832970 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
35832921 TTTTTGCATG
* *
35832931 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35832971 AGAAAGAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35844201 original size:3 final size:3
Alignment explanation
Indices: 35844193--35844234 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
35844183 ATAACTTCTT
35844193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35844235 ACCAAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35848453 original size:8 final size:9
Alignment explanation
Indices: 35848431--35848526 Score: 95
Period size: 9 Copynumber: 10.0 Consensus size: 9
35848421 TGTAGTATTT
35848431 TAAAAATTA
1 TAAAAATTA
35848440 TAAAAATTA
1 TAAAAATTA
35848449 TAAAAAAATTTA
1 T--AAAAA-TTA
35848461 TAAAAATTA
1 TAAAAATTA
*
35848470 TCAAAACTTA
1 T-AAAAATTA
35848480 TAATATAATT-
1 TAA-A-AATTA
*
35848490 TAAAAATATT
1 TAAAAAT-TA
35848500 TAAAAATTA
1 TAAAAATTA
*
35848509 TAAAAATCA
1 TAAAAATTA
35848518 TAAAAATTA
1 TAAAAATTA
35848527 CAACACAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
8 3 0.04
9 35 0.47
10 24 0.32
11 8 0.11
12 4 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Done.