Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold160
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: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 92036 characters in sequence are not A, C, G, or T
File 2 of 30
Found at i:133551 original size:33 final size:33
Alignment explanation
Indices: 133409--133700 Score: 271
Period size: 33 Copynumber: 8.9 Consensus size: 33
133399 TATTGGACTT
* *
133409 AAAGGTGCCACAAAGTTGTGGACTT-ACAGGAA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
* * *
133441 AAAGGGATGCCACGGAGGTGTGGGCTTAAAAGGGAA
1 AAA-GG-TGCCACAGAGTTGTGGACTTAAAA-GGAA
* * * *
133477 AAGGGTGCCACGGAGTCGTGGACTTAAAAAG-A
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
*
133509 AAAGGTGCCACAGAGTTGTAGACTTAAAAGGAA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
* *
133542 CAAGGTGCCACAGAGTTATGGACTTAAAAGGAA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
* * *
133575 AAAGATGCCGCAGAGTTATGGACTTAAAA-G--
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
* *
133605 ---GGTGCCACAGAGTTATGGACTTAAAAAGAA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
* *
133635 AAAGAGTGCCACGGAGTTGTAGG-CTTTAAAAAGAA
1 AAAG-GTGCCACAGAGTTGT-GGAC-TTAAAAGGAA
*
133670 AAAGGT-CTCATAGAGTTGTGGACTTAAAAGG
1 AAAGGTGC-CACAGAGTTGTGGACTTAAAAGG
133701 GTGCCAAAAA
Statistics
Matches: 216, Mismatches: 28, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
27 24 0.11
28 1 0.00
32 31 0.14
33 71 0.33
34 63 0.29
35 20 0.09
36 6 0.03
ACGTcount: A:0.38, C:0.13, G:0.30, T:0.19
Consensus pattern (33 bp):
AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
Found at i:133620 original size:60 final size:60
Alignment explanation
Indices: 133475--133652 Score: 205
Period size: 60 Copynumber: 2.9 Consensus size: 60
133465 CTTAAAAGGG
* ** * *
133475 AAAAGGGTGCCACGGAGTCGTGGACTTAAAAAG-AAAAGGTGCCACAGAGTTGTAGACTT
1 AAAAGGGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGATGCCACAGAGTTATAGACTT
* * *
133534 AAAAGGAACAAGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAGATGCCGCAGAGTTATGGACT
1 AAAA-G-----GGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGATGCCACAGAGTTATAGACT
133599 T
60 T
*
133600 AAAAGGGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGAGTGCCACGGAGTT
1 AAAAGGGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGA-TGCCACAGAGTT
133653 GTAGGCTTTA
Statistics
Matches: 100, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
59 4 0.04
60 35 0.35
61 10 0.10
65 25 0.25
66 26 0.26
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.18
Consensus pattern (60 bp):
AAAAGGGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGATGCCACAGAGTTATAGACTT
Found at i:133671 original size:35 final size:34
Alignment explanation
Indices: 133600--133698 Score: 105
Period size: 34 Copynumber: 2.9 Consensus size: 34
133590 TTATGGACTT
*
133600 AAAAGGGTGCCACAGAGTTATGGACTTAAAAAGA
1 AAAAGAGTGCCACAGAGTTATGGACTTAAAAAGA
* *
133634 AAAAGAGTGCCACGGAGTTGTAGG-CTTTAAAAAGA
1 AAAAGAGTGCCACAGAGTTAT-GGAC-TTAAAAAGA
* *
133669 AAAAG-GT-CTCATAGAGTTGTGGACTTAAAA
1 AAAAGAGTGC-CACAGAGTTATGGACTTAAAA
133699 GGGTGCCAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
33 9 0.16
34 31 0.55
35 16 0.29
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.21
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTATGGACTTAAAAAGA
Found at i:133692 original size:95 final size:93
Alignment explanation
Indices: 133402--133751 Score: 307
Period size: 95 Copynumber: 3.7 Consensus size: 93
133392 TCGGTGATAT
* * * * * *
133402 TGGACTT-AAA-GGTGCCACAAAGTTGTGGACTT-ACAGGAAAAAGGGATGCCACGGAGGTGTGG
1 TGGACTTAAAAGGGTGCCACAAAGTTGTAGACTTAAAAAGAAAAAGAG-TGCCACAGAGTTGT-G
* * *
133464 GCTTAAAAGGGAAAAGGGTGCCACGGAGTCG
64 GCTTAAAA-GGAAAAAGGTGCCACAGAGTTG
* * *
133495 TGGACTTAAAAAGAAAAGGTGCCACAGAGTTGTAGACTTAAAAGGAACAAG-GTGCCACAGAGTT
1 TGGACTT-AAAAG----GGTGCCACAAAGTTGTAGACTTAAAAAGAAAAAGAGTGCCACAGAGTT
* * * *
133559 ATGGACTTAAAAGGAAAAAGATGCCGCAGAGTTA
61 GTGG-CTTAAAAGGAAAAAGGTGCCACAGAGTTG
* * * *
133593 TGGACTTAAAAGGGTGCCACAGAGTTATGGACTTAAAAAGAAAAAGAGTGCCACGGAGTTGTAGG
1 TGGACTTAAAAGGGTGCCACAAAGTTGTAGACTTAAAAAGAAAAAGAGTGCCACAGAGTTGT-GG
* *
133658 CTTTAAAAAGAAAAAGGT-CTCATAGAGTTG
65 C-TTAAAAGGAAAAAGGTGC-CACAGAGTTG
* * * *
133688 TGGACTTAAAAGGGTGCCAAAAAGTTCTAGACTTTGAAAAGAAAAA-AGTGCCACAGAGTCGTGG
1 TGGACTTAAAAGGGTGCCACAAAGTTGTAGAC-TTAAAAAGAAAAAGAGTGCCACAGAGTTGTGG
133752 ACATTGGGAA
Statistics
Matches: 212, Mismatches: 31, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
93 37 0.17
94 17 0.08
95 68 0.32
96 12 0.06
97 5 0.02
98 25 0.12
99 18 0.08
100 21 0.10
101 9 0.04
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.19
Consensus pattern (93 bp):
TGGACTTAAAAGGGTGCCACAAAGTTGTAGACTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGC
TTAAAAGGAAAAAGGTGCCACAGAGTTG
Found at i:133777 original size:30 final size:30
Alignment explanation
Indices: 133736--134043 Score: 244
Period size: 30 Copynumber: 10.0 Consensus size: 30
133726 AAGAAAAAAG
* * *
133736 TGCCACAGAGTCGTGGACATTGGGAAGAGA
1 TGCCACTGAGTCATGGACTTTGGGAAGAGA
* * *
133766 TGCCACTGAGTCGTGAACTTTGAGAAGAGA
1 TGCCACTGAGTCATGGACTTTGGGAAGAGA
* * * *
133796 TTGCCACTAAGTCGTGGACTTTGAAGAAAAGA
1 -TGCCACTGAGTCATGGACTTTG-GGAAGAGA
133828 TGCCACTGAGTCATGGACTTTGGGAAGAGA
1 TGCCACTGAGTCATGGACTTTGGGAAGAGA
* *
133858 TGCCACTGAGTCATGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCATGGACTTTG--G-GAAGAGA
* * *
133891 TGCCACCGAGTCGTGGAC-TTGGAAGAAAAGGA
1 TGCCACTGAGTCATGGACTTTGG--GAAGA-GA
* *
133923 TGCCACTGAGTCATGGAC-TTAGAAGAGAGA
1 TGCCACTGAGTCATGGACTTTGGGA-AGAGA
** *** * *
133953 TGCCACTGAGTTGTGGACTTTAAAAAAAACA
1 TGCCACTGAGTCATGGACTTT-GGGAAGAGA
* *
133984 TGCCACTAAGTCATGGACTTTGGGATA-ATA
1 TGCCACTGAGTCATGGACTTTGGGA-AGAGA
* *
134014 TGCCACTGAGTCATGGACATTGAGAAGAGA
1 TGCCACTGAGTCATGGACTTTGGGAAGAGA
134044 GATTTGAAGA
Statistics
Matches: 229, Mismatches: 37, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.00
30 101 0.44
31 71 0.31
32 35 0.15
33 21 0.09
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.22
Consensus pattern (30 bp):
TGCCACTGAGTCATGGACTTTGGGAAGAGA
Found at i:133801 original size:61 final size:60
Alignment explanation
Indices: 133736--134043 Score: 264
Period size: 61 Copynumber: 5.0 Consensus size: 60
133726 AAGAAAAAAG
* * * *
133736 TGCCACAGAGTCGTGGACATTGGGAAGAGATGCCACTGAGTCGTGAACTTTGAGAAGAGA
1 TGCCACAGAGTCATGGACTTTGGGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA
* * * *
133796 TTGCCACTA-AGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCATGGACTTTGGGAAGAGA
1 -TGCCAC-AGAGTCATGGACTTTG-GGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA
* * * * *
133858 TGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACCGAGTCGTGGACTTGGAAGAAAAGGA
1 TGCCACAGAGTCATGGACTTTG--G-GAAAAGATGCCACTGAGTCGTGGACTTTG-AGAAGA-GA
* * * * * * *
133923 TGCCACTGAGTCATGGAC-TT-AGAAGAGAGATGCCACTGAGTTGTGGACTTTAAAAAAAACA
1 TGCCACAGAGTCATGGACTTTGGGAA-A-AGATGCCACTGAGTCGTGGACTTT-GAGAAGAGA
* * * *
133984 TGCCACTA-AGTCATGGACTTTGGGATAATATGCCACTGAGTCATGGACATTGAGAAGAGA
1 TGCCAC-AGAGTCATGGACTTTGGGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA
134044 GATTTGAAGA
Statistics
Matches: 200, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
60 7 0.04
61 76 0.38
62 64 0.32
63 27 0.14
64 6 0.03
65 20 0.10
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.22
Consensus pattern (60 bp):
TGCCACAGAGTCATGGACTTTGGGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA
Found at i:134017 original size:156 final size:154
Alignment explanation
Indices: 133717--134036 Score: 423
Period size: 156 Copynumber: 2.1 Consensus size: 154
133707 AAAAGTTCTA
* *
133717 GACTTTGAAAAGAAAAAAGTGCCACAGAGTCGTGGACATTGGGAAGAGATGCCACTGAGTCGTGA
1 GACTTTG--AAGAAAAAAGTGCCACAGAGTCGTGGACATTGGGAAAAGATGCCACTGAGTCATGA
* * * * *
133782 ACTTTGAGAAGAGATTGCCACTAAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCATGGACT
64 ACTTTGAGAAGAGAATGCCACTAAGTCGTGGACTTTAAAAAAAACATGCCACTAAGTCATGGACT
133847 TTGGGAAGAGATGCCACTGAGTCATG
129 TTGGGAAGAGATGCCACTGAGTCATG
*
133873 GACTTTGAAGAAAAAAGATGCCACCGAGTCGTGGAC-TTGGAAGAAAAGGATGCCACTGAGTCAT
1 GACTTTGAAGAAAAAAG-TGCCACAGAGTCGTGGACATTGG--GAAAA-GATGCCACTGAGTCAT
* * *
133937 GGAC-TT-AGAAGAGAGATGCCACTGAGTTGTGGACTTTAAAAAAAACATGCCACTAAGTCATGG
62 GAACTTTGAGAAGAGA-ATGCCACTAAGTCGTGGACTTTAAAAAAAACATGCCACTAAGTCATGG
*
134000 ACTTTGGGATA-ATATGCCACTGAGTCATG
126 ACTTTGGGA-AGAGATGCCACTGAGTCATG
*
134029 GACATTGA
1 GACTTTGA
134037 GAAGAGAGAT
Statistics
Matches: 145, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
154 14 0.10
155 25 0.17
156 87 0.60
157 19 0.13
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (154 bp):
GACTTTGAAGAAAAAAGTGCCACAGAGTCGTGGACATTGGGAAAAGATGCCACTGAGTCATGAAC
TTTGAGAAGAGAATGCCACTAAGTCGTGGACTTTAAAAAAAACATGCCACTAAGTCATGGACTTT
GGGAAGAGATGCCACTGAGTCATG
Found at i:134164 original size:8 final size:8
Alignment explanation
Indices: 134141--134186 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
134131 GATGCAAATA
*
134141 ATGATGTT
1 ATGATGTC
*
134149 ATTGATGTT
1 A-TGATGTC
134158 ATGATGTC
1 ATGATGTC
134166 ATGATGTC
1 ATGATGTC
134174 ATGATGTC
1 ATGATGTC
134182 ATGAT
1 ATGAT
134187 TACAACACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
8 28 0.78
9 8 0.22
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (8 bp):
ATGATGTC
Found at i:148909 original size:28 final size:28
Alignment explanation
Indices: 148877--149061 Score: 161
Period size: 28 Copynumber: 6.8 Consensus size: 28
148867 TTTTGGAGAT
*
148877 AATAATGGGGTTAGAGTATCCCCTCGAA
1 AATAACGGGGTTAGAGTATCCCCTCGAA
* *
148905 AATAACGGGGTTGGAGTATCCCCGCGAA
1 AATAACGGGGTTAGAGTATCCCCTCGAA
* *
148933 AATAACGGGGTTGGAGTAT-CCC-CGAT
1 AATAACGGGGTTAGAGTATCCCCTCGAA
** *** * ** *
148959 TGTAA-GAAATCA-A-TAT--TTTAGGAA
1 AATAACGGGGTTAGAGTATCCCCT-CGAA
148983 TAA-AATCGGGGTTAGAGTATCCCCTCGAA
1 -AATAA-CGGGGTTAGAGTATCCCCTCGAA
149012 AATAACGGGGTTAGAGTATCCCCTCGAA
1 AATAACGGGGTTAGAGTATCCCCTCGAA
149040 AATAACGGGGTTAGAGTATCCC
1 AATAACGGGGTTAGAGTATCCC
149062 TGATTATGAG
Statistics
Matches: 123, Mismatches: 24, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
23 3 0.02
24 5 0.04
25 2 0.02
26 9 0.07
27 4 0.03
28 94 0.76
29 5 0.04
30 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTAGAGTATCCCCTCGAA
Found at i:148999 original size:107 final size:107
Alignment explanation
Indices: 148863--149066 Score: 340
Period size: 107 Copynumber: 1.9 Consensus size: 107
148853 TGAGAAATTT
*
148863 AATATTTTGGAGATAATAATGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
1 AATATTTTGGAGATAATAATGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCC
*
148928 GCGAAAATAACGGGGTTGGAGTATCCCCGATTGTAAGAAATC
66 GCGAAAATAACGGGGTTAGAGTATCCCCGATTGTAAGAAATC
148970 AATATTTTAGGA-ATAA-AATCGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCC
1 AATATTTT-GGAGATAATAAT-GGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCC
* *
149033 CCTCGAAAATAACGGGGTTAGAGTATCCCTGATT
64 CCGCGAAAATAACGGGGTTAGAGTATCCCCGATT
149067 ATGAGTGTAG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
106 3 0.03
107 85 0.93
108 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (107 bp):
AATATTTTGGAGATAATAATGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCC
GCGAAAATAACGGGGTTAGAGTATCCCCGATTGTAAGAAATC
Found at i:149412 original size:33 final size:33
Alignment explanation
Indices: 149375--149441 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
149365 TTCAACGATT
149375 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
149408 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
149441 T
1 T
149442 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:149413 original size:13 final size:13
Alignment explanation
Indices: 149395--149419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
149385 CATAAAATGT
149395 TGTATCGATACAA
1 TGTATCGATACAA
149408 TGTATCGATACA
1 TGTATCGATACA
149420 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:149503 original size:13 final size:13
Alignment explanation
Indices: 149485--149509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
149475 ATTACTCACA
149485 TGTATCGATACAT
1 TGTATCGATACAT
149498 TGTATCGATACA
1 TGTATCGATACA
149510 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:149646 original size:52 final size:52
Alignment explanation
Indices: 149518--149638 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
149508 CACTGATCTT
*
149518 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
149570 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
149622 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
149639 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:152724 original size:79 final size:79
Alignment explanation
Indices: 152603--152873 Score: 377
Period size: 79 Copynumber: 3.4 Consensus size: 79
152593 AAGAGAAATC
*
152603 CCCCTCGAATAATAAC-GGG-T-GACGTATCCCTGATTATGAGAAATCAATATTTTAGAAATAAA
1 CCCCTCGAA-AATAACGGGGTTGGA-GTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAA
** *
152665 ACCAGGGTTGGAGTAT
64 GTCGGGGTTGGAGTAT
* * * * * * *
152681 CCCCTCGGAAATAACGAGGTTCGAGTATTCCCGATTGTGAGAAATTAATATTTTTGAAATAAAGT
1 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGT
152746 CGGGGTTGGAGTAT
66 CGGGGTTGGAGTAT
* * *
152760 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATATTTTAGGAATAGAGT
1 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGT
152825 CGGGGTTGGAGTAT
66 CGGGGTTGGAGTAT
152839 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
152874 GATTAACGGG
Statistics
Matches: 170, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
77 6 0.04
78 10 0.06
79 152 0.89
80 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (79 bp):
CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGT
CGGGGTTGGAGTAT
Found at i:152866 original size:107 final size:107
Alignment explanation
Indices: 152746--153115 Score: 471
Period size: 107 Copynumber: 3.5 Consensus size: 107
152736 GAAATAAAGT
152746 CGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATA
1 CGGGGTTGGAGTAT-CCCTCGATAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATA
* *
152810 TTTTAGGAATAGAGTCGGGGTTGGAGTATCCCCTCGAAAATAA
65 TTTTAGGAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAA
* * * * *** *
152853 CGGGGTTGGAGTATCCC-CGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGT
1 CGGGGTTGGAGTATCCCTCGATAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATAT
* * ** *
152917 TTTTGAAAATAAAATCGAAGTTGGAGTATCCCCTCAAAAATAA
66 TTTAG-GAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAA
* *
152960 CGGGGTTGGAGTATCCC-CGCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAACCAATA
1 CGGGGTTGGAGTATCCCTCG-ATAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATA
* *
153024 TTTTAGGAATAAAACCGGGGTTGGAGTATCCCTTCCG-AAATAA
65 TTTTAGGAATAAAATCGGGGTTGGAGTATCCCCT-CGAAAATAA
* * *
153067 CGGGGTTGGAGTATCCCT-GATGATTAACGGGGTTGGGGTATCCCCGATT
1 CGGGGTTGGAGTATCCCTCGATAAATAACGGGGTTGGAGTATCCCCGATT
153116 GTGAAAAATT
Statistics
Matches: 221, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
105 3 0.01
106 67 0.30
107 111 0.50
108 40 0.18
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCTCGATAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATAT
TTTAGGAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAA
Found at i:152888 original size:27 final size:27
Alignment explanation
Indices: 152825--152900 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
152815 GGAATAGAGT
152825 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTAT-CCC-CGATAAATAA
* *
152853 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATAAATAA
152880 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
152901 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 3 0.07
27 28 0.62
28 14 0.31
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:152970 original size:28 final size:28
Alignment explanation
Indices: 152936--153006 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
152926 TAAAATCGAA
* *
152936 GTTGGAGTATCCCCTCAAAAATAACGGG
1 GTTGGAGTATCCCCGCAAAAATAACAGG
152964 GTTGGAGTATCCCCGCAAAAATAACAGG
1 GTTGGAGTATCCCCGCAAAAATAACAGG
152992 GTTGGAGTATCCCCG
1 GTTGGAGTATCCCCG
153007 ATTATGAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.21
Consensus pattern (28 bp):
GTTGGAGTATCCCCGCAAAAATAACAGG
Found at i:153102 original size:27 final size:28
Alignment explanation
Indices: 153039--153110 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
153029 GGAATAAAAC
**
153039 CGGGGTTGGAGTATCCCTTCCGAAATAA
1 CGGGGTTGGAGTATCCCTGACGAAATAA
* *
153067 CGGGGTTGGAGTATCCCTGATG-ATTAA
1 CGGGGTTGGAGTATCCCTGACGAAATAA
*
153094 CGGGGTTGGGGTATCCC
1 CGGGGTTGGAGTATCCC
153111 CGATTGTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 20 0.51
28 19 0.49
ACGTcount: A:0.19, C:0.19, G:0.35, T:0.26
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCTGACGAAATAA
Found at i:153115 original size:214 final size:214
Alignment explanation
Indices: 152746--153163 Score: 703
Period size: 214 Copynumber: 2.0 Consensus size: 214
152736 GAAATAAAGT
* * *
152746 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATAT
1 CGGGGTTGGAGTATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAACCAATAT
* **
152811 TTTAGGAATAGAGTCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGA
66 TTTAGGAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGA
152876 TTAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTTGAAAATAAAATCGAAGTTGG
131 TTAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTTGAAAATAAAATCGAAGTTGG
152941 AGTATCCCCTCAAAAATAA
196 AGTATCCCCTCAAAAATAA
152960 CGGGGTTGGAGTATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAACCAATAT
1 CGGGGTTGGAGTATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAACCAATAT
* *
153025 TTTAGGAATAAAACCGGGGTTGGAGTATCCCTTCCG-AAATAACGGGGTTGGAGTATCCCTGATG
66 TTTAGGAATAAAACCGGGGTTGGAGTATCCCCT-CGAAAATAACGGGGTTGGAGTATCCCCGATG
* * * * *
153089 ATTAACGGGGTTGGGGTATCCCCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATTGGAGTTG
130 ATTAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTTGAAAATAAAATCGAAGTTG
153154 GAGTATCCCC
195 GAGTATCCCC
153164 GATTATAGAA
Statistics
Matches: 190, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
214 188 0.99
215 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (214 bp):
CGGGGTTGGAGTATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAACCAATAT
TTTAGGAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGA
TTAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTTGAAAATAAAATCGAAGTTGG
AGTATCCCCTCAAAAATAA
Found at i:153142 original size:107 final size:106
Alignment explanation
Indices: 152746--153163 Score: 462
Period size: 107 Copynumber: 3.9 Consensus size: 106
152736 GAAATAAAGT
*
152746 CGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATA
1 CGGGGTTGGAGTAT-CCC-CGATAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAACCAATA
* * *
152810 TTTTAGGAATAGAGTCGGGGTTGGAGTATCCCCT-CGAAAATAA
64 TTTTAGGAATAAAATCGGAGTTGGAGTATCCCCTCCG-AAATAA
* * * *** *
152853 CGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTT
1 CGGGGTTGGAGTATCCCCGATAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAACCAATATT
* * * **
152918 TTTGAAAATAAAATCGAAGTTGGAGTATCCCCTCAAAAATAA
66 TTAG-GAATAAAATCGGAGTTGGAGTATCCCCTCCGAAATAA
* * *
152960 CGGGGTTGGAGTATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAACCAATAT
1 CGGGGTTGGAGTATCCCCG-ATAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAACCAATAT
* * *
153025 TTTAGGAATAAAACCGGGGTTGGAGTATCCCTTCCGAAATAA
65 TTTAGGAATAAAATCGGAGTTGGAGTATCCCCTCCGAAATAA
* * * * * **** *
153067 CGGGGTTGGAGTATCCCTGATGATTAACGGGGTTGGGGTATCCCCGATTGTGAAAAATTGGTGTT
1 CGGGGTTGGAGTATCCCCGATAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAACCAATATT
* *
153132 TTTGGAAATAAAATTGGAGTTGGAGTATCCCC
66 TTAGG-AATAAAATCGGAGTTGGAGTATCCCC
153164 GATTATAGAA
Statistics
Matches: 254, Mismatches: 52, Indels: 10
0.80 0.16 0.03
Matches are distributed among these distances:
105 3 0.01
106 80 0.31
107 132 0.52
108 39 0.15
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (106 bp):
CGGGGTTGGAGTATCCCCGATAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAACCAATATT
TTAGGAATAAAATCGGAGTTGGAGTATCCCCTCCGAAATAA
Found at i:155701 original size:21 final size:21
Alignment explanation
Indices: 155675--155715 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
155665 CATGTATCGA
*
155675 TACAAATGTATTGATACATTC
1 TACAAATGTATCGATACATTC
155696 TACAAATGTATCGATACATT
1 TACAAATGTATCGATACATT
155716 TCCTTGGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (21 bp):
TACAAATGTATCGATACATTC
Found at i:156491 original size:40 final size:42
Alignment explanation
Indices: 156447--156546 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 42
156437 GTCCCACCTT
* *
156447 TTGAGGACAAAGGAAAA-CAG-AATGAAATAG-GTCCTGCTCC
1 TTGAGGACAAAGGAAAATAAGAAAAGAAA-AGTGTCCTGCTCC
* *
156487 TTGAGGACAAAGGAAAATAAGAAAAGGAAAGTGTCCTGCTTC
1 TTGAGGACAAAGGAAAATAAGAAAAGAAAAGTGTCCTGCTCC
156529 TTGAGGACAAAGTGAAAA
1 TTGAGGACAAAG-GAAAA
156547 AGAGTATGTC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
40 17 0.33
41 4 0.08
42 26 0.50
43 5 0.10
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.18
Consensus pattern (42 bp):
TTGAGGACAAAGGAAAATAAGAAAAGAAAAGTGTCCTGCTCC
Found at i:156776 original size:61 final size:57
Alignment explanation
Indices: 156683--157333 Score: 747
Period size: 55 Copynumber: 11.4 Consensus size: 57
156673 AAGGAAGTGT
* * * *
156683 GTCCCGCTCTTTGAGGACTGAAAAGTGTCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---AA-GAAAGGC
* * * * *
156744 GTCCTGCTCTTTGAGGATTAGAAGGTGCCACCAAATTGTGTGGGCTTTACAAAGAGAAAGC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---AAGA-AAGGC
* *
156805 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT--GAAAGGC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGC
* * * * *
156860 ATCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGCGTGGGCTTTAAG--AGGC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGC
*
156915 GTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-AG-AAGGC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGC
* * * *
156970 ATCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTCGTGTGGGCTTT--GAAAGGC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGC
* *
157025 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---AAG-AAAGGC
157086 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT--GAAAGGC
1 GTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAAAGGC
* *
157141 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGT
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---AAG-AAAGGC
* *
157202 GTCCTGCTCTTTGAGGACTAGAAATGTGCCACCAACTTATGTGGGCTTT-A-AAAGGC
1 GTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAAAGGC
* * **
157258 GTCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTCATGTGGGCTTT--GAAAGGC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGC
*
157313 GTCCTGCTCTTTAAGGACTGG
1 GTCCTGCTCTTTGAGGACTGG
157334 GCAAAAGGAG
Statistics
Matches: 521, Mismatches: 48, Indels: 48
0.84 0.08 0.08
Matches are distributed among these distances:
54 3 0.01
55 288 0.55
56 34 0.07
57 1 0.00
58 1 0.00
60 8 0.02
61 164 0.31
62 22 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (57 bp):
GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGC
Found at i:156903 original size:116 final size:113
Alignment explanation
Indices: 156683--157331 Score: 743
Period size: 116 Copynumber: 5.7 Consensus size: 113
156673 AAGGAAGTGT
* * *
156683 GTCCCGCTCTTTGAGGACT-GAAAAGTGTCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTC
1 GTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT----A-GAAAGGCGTC
* * *
156747 CTGCTCTTTGAGGATTAGAAGGTGCCACCAAATTGTGTGGGCTTTACAAAGAGAAAGC
60 CTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT---AAGAG-AAGC
* * *
156805 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-GAAAGGCATCCTGTTC
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAGAAAGGCGTCCTGCTC
* *
156869 TTTGAGGACTAGAAAATGCCACCAACTTGCGTGGGCTTTAAGAG--GC
66 TTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGAAGC
* * * *
156915 GTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAG-AAGGCATCCTACTC
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAGAAAGGCGTCCTGCTC
* * *
156979 TTTGAGGACTGGGAAGTGCCACCAACTCGTGTGGGCTTT--GA-AAGGC
66 TTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGAA-GC
*
157025 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCGTCC
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----AG-AAAGGCGTCC
157090 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT--GA-AAGGC
61 TGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGAA-GC
*
157141 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGTGTCC
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----AG-AAAGGCGTCC
* *
157206 TGCTCTTTGAGGACTAGAAATGTGCCACCAACTTATGTGGGCTTTAA-A-AGGC
61 TGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGAAGC
* **
157258 GTCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTCATGTGGGCTTT-GAAAGGCGTCCTGCTC
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAGAAAGGCGTCCTGCTC
*
157322 TTTAAGGACT
66 TTTGAGGACT
157332 GGGCAAAAGG
Statistics
Matches: 474, Mismatches: 38, Indels: 41
0.86 0.07 0.07
Matches are distributed among these distances:
108 2 0.00
110 140 0.30
111 24 0.05
112 1 0.00
113 5 0.01
114 2 0.00
115 3 0.01
116 178 0.38
117 74 0.16
118 2 0.00
122 38 0.08
123 5 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (113 bp):
GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAGAAAGGCGTCCTGCTC
TTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGAAGC
Found at i:156994 original size:27 final size:27
Alignment explanation
Indices: 156964--157045 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
156954 GTGGGCTTTA
156964 GAAGGCATCCTACTCTTTGAGGACTGG
1 GAAGGCATCCTACTCTTTGAGGACTGG
* * *
156991 GAAGTGCCA-CCAACTCGTGTG-GG-CTTTG
1 GAAG-G-CATCCTACTC-TTTGAGGAC-TGG
* *
157019 AAAGGCATCCTGCTCTTTGAGGACTGG
1 GAAGGCATCCTACTCTTTGAGGACTGG
157046 AAAATGCCAC
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
26 5 0.12
27 15 0.38
28 15 0.38
29 5 0.12
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (27 bp):
GAAGGCATCCTACTCTTTGAGGACTGG
Found at i:158408 original size:13 final size:12
Alignment explanation
Indices: 158390--158433 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
158380 AAGCAGATTC
*
158390 TTTTTTTTTCAT
1 TTTTTTTTTTAT
158402 TTTTTTTTTGTAT
1 TTTTTTTTT-TAT
* *
158415 TGTTTTTTTTGT
1 TTTTTTTTTTAT
158427 TTTTTTT
1 TTTTTTT
158434 GTTTGAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.05, C:0.02, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:158431 original size:8 final size:9
Alignment explanation
Indices: 158391--158437 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
158381 AGCAGATTCT
*
158391 TTTTTTTTC
1 TTTTTTTTG
*
158400 ATTTTTTT-
1 TTTTTTTTG
* *
158408 TTTGTATTG
1 TTTTTTTTG
158417 TTTTTTTTG
1 TTTTTTTTG
158426 TTTTTTTTG
1 TTTTTTTTG
158435 TTT
1 TTT
158438 GAAAAAGAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
8 5 0.16
9 26 0.84
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:170525 original size:79 final size:79
Alignment explanation
Indices: 170421--170784 Score: 498
Period size: 79 Copynumber: 4.6 Consensus size: 79
170411 AGATAATAAT
* * *
170421 GGGGCTGGAGTA-CCCCTACGAAAATAACGGGGTTGGAGTATCCCCGATTGTAAGAAATCAATAT
1 GGGGTTGGAGTATCCCCT-CAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
*
170485 TTTAGGAATAAAACC
65 TTTAGAAATAAAACC
*
170500 GGGGTTGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
1 GGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
170565 TTAGAAATAAAACC
66 TTAGAAATAAAACC
* * * *
170579 AGGGTTGGAGTATCCCCT-AAGAAATAACAGGGTTTGAGTATTCCCGATTGTGAGAAATCAATAT
1 GGGGTTGGAGTATCCCCTCAA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
* *
170643 TTTTGAAATAAAGCC
65 TTTAGAAATAAAACC
* * * * * *
170658 GAGGTTGGAGTATCCCCTTAGAAATAACGGGGTTAGAGTATCCCCGATTATGAGAAACCAATATT
1 GGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
* * *
170723 TTAGGAATAGAGCC
66 TTAGAAATAAAACC
* *
170737 GGGGCTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGAT
170785 GATTAACAGG
Statistics
Matches: 255, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
78 2 0.01
79 247 0.97
80 6 0.02
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
TTAGAAATAAAACC
Found at i:170771 original size:107 final size:106
Alignment explanation
Indices: 170660--171027 Score: 436
Period size: 107 Copynumber: 3.4 Consensus size: 106
170650 ATAAAGCCGA
* *
170660 GGTTGGAGTATCCCC-TTAGAAATAACGGGGTTAGAGTATCCCCGATTATGAGAAACCAATATTT
1 GGTTGGAGTATCCCCGAT-G-AATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATATTT
* * *
170724 TAGGAATAGAGCCGGGGCTGGAGTATCCCCTCAGAAATAACGG
64 TAGGAATAAAGCTGGGGTTGGAGTATCCCCTCAGAAATAACGG
* * * * **** * *
170767 GGTTGGAGTATCCCCGATGATTAACAGGGTTGGAGTATCCCCGATTCTGAAAAATTGGTGTTTTT
1 GGTTGGAGTATCCCCGATGAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATATTTTA
** * *
170832 GGAAATAAAATTGGAGTTGGAGTATCCCCTCAAAAATAACGG
66 GG-AATAAAGCTGGGGTTGGAGTATCCCCTCAGAAATAACGG
*
170874 GGTTGGAGTATCCCCGCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATATTT
1 GGTTGGAGTAT-CCC-CGATGAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATATTT
* *
170938 TAGGAATAAAGCTGAGGGTTGGAGTATCCTCTC-GAAAATAACGA
64 TAGGAATAAAGCTG-GGGTTGGAGTATCCCCTCAG-AAATAACGG
* *
170982 GGTTGGAGTATCCCCGATGATTAACGGGGTTGGGGTATCCCCGATT
1 GGTTGGAGTATCCCCGATGAATAACGGGGTTGGAGTATCCCCGATT
171028 GTGAAAAATT
Statistics
Matches: 215, Mismatches: 39, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
106 40 0.19
107 95 0.44
108 77 0.36
109 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (106 bp):
GGTTGGAGTATCCCCGATGAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATATTTTA
GGAATAAAGCTGGGGTTGGAGTATCCCCTCAGAAATAACGG
Found at i:170776 original size:28 final size:27
Alignment explanation
Indices: 170736--170808 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
170726 GGAATAGAGC
*
170736 CGGGGCTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-CATG-AATAA
* *
170764 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCCATGAATAA
*
170791 CAGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
170809 GATTCTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCCATGAATAA
Found at i:170880 original size:28 final size:28
Alignment explanation
Indices: 170847--170917 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
170837 TAAAATTGGA
*
170847 GTTGGAGTATCCCCTCAAAAATAACGGG
1 GTTGGAGTATCCCCGCAAAAATAACGGG
*
170875 GTTGGAGTATCCCCGCGAAAATAACGGG
1 GTTGGAGTATCCCCGCAAAAATAACGGG
170903 GTTGGAGTATCCCCG
1 GTTGGAGTATCCCCG
170918 ATTATGAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.21
Consensus pattern (28 bp):
GTTGGAGTATCCCCGCAAAAATAACGGG
Found at i:170913 original size:214 final size:215
Alignment explanation
Indices: 170660--171075 Score: 678
Period size: 215 Copynumber: 1.9 Consensus size: 215
170650 ATAAAGCCGA
**
170660 GGTTGGAGTATCCCCTTAGAAATAACGGGGTTAGAGTATCCCCGATTATGAGAAACCAATATTTT
1 GGTTGGAGTATCCCCCGAGAAATAACGGGGTTAGAGTATCCCCGATTATGAGAAACCAATATTTT
* *
170725 AGGAATAGAGCCG-GGGCTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCGATGAT
66 AGGAATAAAGCCGAGGGCTGGAGTATCCCCTCGA-AAATAACGAGGTTGGAGTATCCCCGATGAT
170788 TAACAGGGTTGGAGTATCCCCGATTCTGAAAAATTGGTGTTTTTGGAAATAAAATT-GGAGTTGG
130 TAACAGGGTTGGAGTATCCCCGATTCTGAAAAATTGGTGTTTTTGGAAAT-AAATTCGGAGTTGG
170852 AGTATCCCCTCAAAAATAACGG
194 AGTATCCCCTCAAAAATAACGG
*
170874 GGTTGGAGTATCCCCGCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAACCAATATTT
1 GGTTGGAGTATCCCC-CGAGAAATAACGGGGTTAGAGTATCCCCGATTATGAGAAACCAATATTT
* * *
170938 TAGGAATAAAGCTGAGGGTTGGAGTATCCTCTCGAAAATAACGAGGTTGGAGTATCCCCGATGAT
65 TAGGAATAAAGCCGAGGGCTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATGAT
* * *
171003 TAACGGGGTTGGGGTATCCCCGATTGTGAAAAATTGGTGTTTTTGGAAATAAATTCGGAGTTGGA
130 TAACAGGGTTGGAGTATCCCCGATTCTGAAAAATTGGTGTTTTTGGAAATAAATTCGGAGTTGGA
171068 GTATCCCC
195 GTATCCCC
171076 GATTATAGAA
Statistics
Matches: 187, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
214 76 0.41
215 110 0.59
216 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (215 bp):
GGTTGGAGTATCCCCCGAGAAATAACGGGGTTAGAGTATCCCCGATTATGAGAAACCAATATTTT
AGGAATAAAGCCGAGGGCTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATGATT
AACAGGGTTGGAGTATCCCCGATTCTGAAAAATTGGTGTTTTTGGAAATAAATTCGGAGTTGGAG
TATCCCCTCAAAAATAACGG
Found at i:171014 original size:27 final size:27
Alignment explanation
Indices: 170953--171026 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
170943 ATAAAGCTGA
170953 GGGTTGGAGTATCCTCTCGA-AAATAACG
1 GGGTTGGAGTATCC-C-CGATAAATAACG
* * *
170981 AGGTTGGAGTATCCCCGATGATTAACG
1 GGGTTGGAGTATCCCCGATAAATAACG
*
171008 GGGTTGGGGTATCCCCGAT
1 GGGTTGGAGTATCCCCGAT
171027 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 3 0.08
27 24 0.60
28 13 0.32
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGATAAATAACG
Found at i:171054 original size:108 final size:106
Alignment explanation
Indices: 170742--171075 Score: 413
Period size: 107 Copynumber: 3.1 Consensus size: 106
170732 GAGCCGGGGC
*
170742 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACAGGGTTGGAGTATCC
1 TGGAGTATCCCCTCA-AAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCC
* *
170807 CCGATTCTGAAAAATTGGTGTTTTTGGAAATAAAATTGGAGT
65 CCGATTATGAAAAATTGGTGTTTTTGGAAATAAAACTGGAGT
* *
170849 TGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGA-AAATAACGGGGTTGGAGTAT
1 TGGAGTATCCCCTC-AAAATAACGGGGTTGGAGTAT-CCC-CGATGATTAACGGGGTTGGAGTAT
* **** * * * *
170913 CCCCGATTATGAGAAACCAATATTTTAGG-AATAAAGCTGAGGGT
63 CCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAACTG-GAGT
* * *
170957 TGGAGTATCCTCTCGAAAATAACGAGGTTGGAGTATCCCCGATGATTAACGGGGTTGGGGTATCC
1 TGGAGTATCCCCTC-AAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCC
* *
171022 CCGATTGTGAAAAATTGGTGTTTTTGGAAAT-AAATTCGGAGT
65 CCGATTATGAAAAATTGGTGTTTTTGGAAATAAAACT-GGAGT
171064 TGGAGTATCCCC
1 TGGAGTATCCCC
171076 GATTATAGAA
Statistics
Matches: 188, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
106 3 0.02
107 100 0.53
108 82 0.44
109 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (106 bp):
TGGAGTATCCCCTCAAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCC
CGATTATGAAAAATTGGTGTTTTTGGAAATAAAACTGGAGT
Found at i:173599 original size:13 final size:13
Alignment explanation
Indices: 173581--173606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
173571 GCAAAGATCC
173581 ATGTATCGATACA
1 ATGTATCGATACA
173594 ATGTATCGATACA
1 ATGTATCGATACA
173607 TTCTACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:175643 original size:19 final size:19
Alignment explanation
Indices: 175600--175673 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
175590 TGCCAGTTTT
175600 ATGTATCGATACAATTG-TCC
1 ATGTATCGATACAA-TGAT-C
175620 ATGTATCGATACAATGATC
1 ATGTATCGATACAATGATC
*
175639 ATGTATTGATACAATGATC
1 ATGTATCGATACAATGATC
*
175658 ATGTATTGATACAATG
1 ATGTATCGATACAATG
175674 TATCGATACA
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
19 37 0.71
20 15 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACAATGATC
Found at i:177024 original size:30 final size:30
Alignment explanation
Indices: 176988--177057 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
176978 TGCTATTTAT
176988 TCATGAATGCTATTAATGTTTACCTTGATA
1 TCATGAATGCTATTAATGTTTACCTTGATA
177018 TCATGAATGCTATTAATGTTTACCTTGATA
1 TCATGAATGCTATTAATGTTTACCTTGATA
177048 TCATGAATGC
1 TCATGAATGC
177058 ACAGGAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (30 bp):
TCATGAATGCTATTAATGTTTACCTTGATA
Found at i:177659 original size:13 final size:13
Alignment explanation
Indices: 177641--177665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177631 ATATTGCTTA
177641 GTATCGATACATT
1 GTATCGATACATT
177654 GTATCGATACAT
1 GTATCGATACAT
177666 GTTCTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:177682 original size:32 final size:33
Alignment explanation
Indices: 177620--177683 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
177610 CACACTCATA
177620 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
* *
177653 TGTATCGATACATGTT-CTTAGTATTGATACA
1 TGTATCGATACATATTGCTTAGTATCGATACA
177684 CACTTAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTAGTATCGATACAT
Found at i:177768 original size:20 final size:20
Alignment explanation
Indices: 177738--177797 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
177728 ACTCAAAATC
*
177738 GATACATTGTATCGATACAT
1 GATAAATTGTATCGATACAT
*
177758 GATGAATTGTATCGATACAT
1 GATAAATTGTATCGATACAT
* * *
177778 GGTAAAATGTATTGATACAT
1 GATAAATTGTATCGATACAT
177798 TGAGCCCAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (20 bp):
GATAAATTGTATCGATACAT
Found at i:185338 original size:19 final size:19
Alignment explanation
Indices: 185314--185368 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
185304 ACATTATGCT
**
185314 TTGTATTGATACATGTTAA
1 TTGTATTGATACATGACAA
185333 TTGTATTGATACATGGACAA
1 TTGTATTGATACAT-GACAA
*
185353 TTGTATCGATACATGA
1 TTGTATTGATACATGA
185369 AACTGGCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (19 bp):
TTGTATTGATACATGACAA
Found at i:185356 original size:20 final size:20
Alignment explanation
Indices: 185314--185367 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
185304 ACATTATGCT
**
185314 TTGTATTGATACAT-GTTAA
1 TTGTATTGATACATGGACAA
185333 TTGTATTGATACATGGACAA
1 TTGTATTGATACATGGACAA
*
185353 TTGTATCGATACATG
1 TTGTATTGATACATG
185368 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (20 bp):
TTGTATTGATACATGGACAA
Found at i:185438 original size:33 final size:33
Alignment explanation
Indices: 185396--185464 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
185386 CTACCACTAT
*
185396 TTGTATCGATACAT-AGGACAATGTATTGATACA
1 TTGTATCGATACATGAGGA-AATGTATCGATACA
* *
185429 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATGTATCGATACA
185462 TTG
1 TTG
185465 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGAGGAAATGTATCGATACA
Found at i:186729 original size:19 final size:19
Alignment explanation
Indices: 186705--186757 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
186695 TGTCAACGAT
*
186705 TTGTATCGATACGTAAGTG
1 TTGTATCGATACATAAGTG
186724 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
186743 TTGTATCGATACATA
1 TTGTATCGATACATA
186758 TGAAGCTACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:186854 original size:52 final size:52
Alignment explanation
Indices: 186798--186926 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
186788 CACTGATCTT
*
186798 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATAAACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATAAACTATGAAA
* *
186850 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATAAACTATGAAA
186902 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
186927 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATAAACTATGAAA
Found at i:200789 original size:9 final size:9
Alignment explanation
Indices: 200775--200857 Score: 71
Period size: 10 Copynumber: 8.8 Consensus size: 9
200765 CTCTGCCAAA
200775 AAAAAAAAC
1 AAAAAAAAC
*
200784 AAAAAAAAAGA
1 -AAAAAAAA-C
200795 AAAAAAAAGC
1 AAAAAAAA-C
200805 AAAAACCAAA-
1 AAAAA--AAAC
200815 AAAAAAAAC
1 AAAAAAAAC
*
200824 AAACAAAAC
1 AAAAAAAAC
200833 AAAAAAAA-
1 AAAAAAAAC
*
200841 TAAAAAAAC
1 AAAAAAAAC
200850 AACAAAAA
1 AA-AAAAA
200858 GAGTCCGGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
8 10 0.16
9 16 0.26
10 32 0.52
12 3 0.05
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:200817 original size:28 final size:28
Alignment explanation
Indices: 200771--200855 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 28
200761 CATCCTCTGC
*
200771 CAAAAAAAAAAACAAAAAAAAAGAA-AAA
1 CAAAACAAAAAACAAAAAAAAA-AACAAA
*
200799 -AAAAGCAAAAACCAAAAAAAAAAACAAA
1 CAAAA-CAAAAAACAAAAAAAAAAACAAA
200827 CAAAACAAAAAA-AATAAAAAAACAACAAA
1 CAAAACAAAAAACAA-AAAAAAA-AACAAA
200856 AAGAGTCCGG
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
27 8 0.16
28 31 0.63
29 10 0.20
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (28 bp):
CAAAACAAAAAACAAAAAAAAAAACAAA
Found at i:200849 original size:17 final size:16
Alignment explanation
Indices: 200772--200857 Score: 77
Period size: 17 Copynumber: 5.2 Consensus size: 16
200762 ATCCTCTGCC
200772 AAAAAAAAAAACAAAA
1 AAAAAAAAAAACAAAA
200788 AAAAAGAAAAAA-AAAGCA
1 AAAAA-AAAAAACAAA--A
**
200806 AAAACCAAAAA-AAAA
1 AAAAAAAAAAACAAAA
* *
200821 AACAAACAAAACAAAA
1 AAAAAAAAAAACAAAA
200837 AAAATAAAAAAACAACAA
1 AAAA-AAAAAAACAA-AA
200855 AAA
1 AAA
200858 GAGTCCGGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
15 8 0.14
16 15 0.27
17 23 0.41
18 10 0.18
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.01
Consensus pattern (16 bp):
AAAAAAAAAAACAAAA
Found at i:200857 original size:1 final size:1
Alignment explanation
Indices: 200772--200848 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
200762 ATCCTCTGCC
* * ** ** * * *
200772 AAAAAAAAAAACAAAAAAAAAGAAAAAAAAAGCAAAAACCAAAAAAAAAAACAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
200837 AAAATAAAAAAA
1 AAAAAAAAAAAA
200849 CAACAAAAAG
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:200857 original size:40 final size:39
Alignment explanation
Indices: 200772--200857 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
200762 ATCCTCTGCC
*
200772 AAAAAAAAAAACAAAAAAAAAGAAAAAAAAAGCAAAAACC
1 AAAAAAAAAAACAAAAAAAAAGAAAAAAAAA-CAAAAACA
*
200812 AAAAAAAAAAACAAACAAAACAA-AAAAAATAA-AAAAACA
1 AAAAAAAAAAACAAA-AAAA-AAGAAAAAAAAACAAAAACA
*
200851 ACAAAAA
1 AAAAAAA
200858 GAGTCCGGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 12 0.29
40 15 0.37
41 12 0.29
42 2 0.05
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.01
Consensus pattern (39 bp):
AAAAAAAAAAACAAAAAAAAAGAAAAAAAAACAAAAACA
Found at i:202378 original size:58 final size:59
Alignment explanation
Indices: 202295--202588 Score: 361
Period size: 58 Copynumber: 5.1 Consensus size: 59
202285 TCCCTCACCC
202295 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCCTTT
* * *
202354 TTC-AAAGCCCACAAATTAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCC-TT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCCTTT
* *
202411 TTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCAACC---
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCCTTT
* * * *
202467 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACC---
1 TTCAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTTAGTGGCACCCTTT
* * * * * *
202525 TTCAAAAGCCCACAAGTTAGTGGCACCCTTTTCCAAAGCCCACAATTTCGTGGCACCGTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTTAGTGGCACCCTTT
202586 TTC
1 TTC
202589 TTTTTAAAGC
Statistics
Matches: 212, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
56 26 0.12
57 5 0.02
58 175 0.83
59 3 0.01
61 3 0.01
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCCTTT
Found at i:202447 original size:86 final size:86
Alignment explanation
Indices: 202293--202586 Score: 425
Period size: 86 Copynumber: 3.4 Consensus size: 86
202283 CATCCCTCAC
* * * *
202293 CCTTCAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTTAGTGGCACCCTTTTT
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACC---TT
*
202356 C-AAAGCCCACAAATTAGTGGCAA
63 CAAAAGCCCACAAGTTAGTGGCAA
202379 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAA
202444 AAGCCCACAAGTTAGTGGCAA
66 AAGCCCACAAGTTAGTGGCAA
202465 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAA
*
202530 AAGCCCACAAGTTAGTGGCAC
66 AAGCCCACAAGTTAGTGGCAA
* * *
202551 CCTTTTCCAAAGCCCACAATTTC-GTGGCACCGTTTT
1 CC--TTCAAAAGCCCACAA-GTCAGTGGCACCCTTTT
202587 TCTTTTTAAA
Statistics
Matches: 193, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
85 3 0.02
86 137 0.71
88 51 0.26
89 2 0.01
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (86 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAA
AAGCCCACAAGTTAGTGGCAA
Found at i:202579 original size:144 final size:144
Alignment explanation
Indices: 202293--202569 Score: 500
Period size: 144 Copynumber: 1.9 Consensus size: 144
202283 CATCCCTCAC
* *
202293 CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCCTTTTTCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCA
*
202358 AAGCCCACAAATTAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCA
66 AAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCA
202423 CAAGTCAGTGGCAA
131 CAAGTCAGTGGCAA
*
202437 CCTTCAAAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCA
* *
202502 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCCTTTTCCAAAGCCCA
66 AAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCA
202567 CAA
131 CAA
202570 TTTCGTGGCA
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 127 1.00
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.18
Consensus pattern (144 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCA
AAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCA
CAAGTCAGTGGCAA
Found at i:202638 original size:34 final size:34
Alignment explanation
Indices: 202560--202704 Score: 177
Period size: 34 Copynumber: 4.2 Consensus size: 34
202550 CCCTTTTCCA
* * *
202560 AAGCCCACAA-TTTCGTGGCAC-CGTTTTTCTTTTT
1 AAGCCCACAACTCT-GTGGCACTC-TTTTTCCTTCT
* *
202594 AAAGCCCACAACTCTATGGCACTCTTTTTCCTTTT
1 -AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
202629 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
* *
202663 AAGCGCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
*
202697 AAGTCCAC
1 AAGCCCAC
202705 GAGTCCGTGG
Statistics
Matches: 99, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
34 70 0.71
35 26 0.26
36 3 0.03
ACGTcount: A:0.20, C:0.32, G:0.12, T:0.35
Consensus pattern (34 bp):
AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
Found at i:202840 original size:49 final size:49
Alignment explanation
Indices: 202712--203061 Score: 304
Period size: 49 Copynumber: 7.1 Consensus size: 49
202702 CACGAGTCCG
* ** * * *
202712 TGGCACCCTTATCTTTAAGTCCAATGTAACTAGCCTTCACTCAGCACAT
1 TGGCACCCTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
* * *
202761 TGGCA--C----CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATAT
1 TGGCACCCTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
*
202804 TGGCACCCTTATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACAT
1 TGGCACCCTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
* * *
202853 TGGCACCCTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGCACCCTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
* * *
202902 TGGCA-CCTTCATCTTTAAGTCCAATAGCGCTGGCCTTGAATCAACATAT
1 TGGCACCCTT-ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
* * * *
202951 TGACA-CCTTTTCCGTCTTGAGTCCAAT-GCTGCTGGCCTTGAATCAGCACAT
1 TGGCACCCTTAT-C-T-TTAAGTCCAATATC-GCTGGCCTTGAATCAGCACAT
** * * **
203002 TAACATCCTTTTTCTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCGTAT
1 TGGCA-CC-----CTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
203057 TGGCA
1 TGGCA
203062 TCTTTAATAT
Statistics
Matches: 248, Mismatches: 34, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
43 37 0.15
45 1 0.00
47 1 0.00
48 4 0.02
49 131 0.53
50 3 0.01
51 33 0.13
53 1 0.00
55 31 0.12
56 2 0.01
57 1 0.00
58 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (49 bp):
TGGCACCCTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACAT
Found at i:202916 original size:98 final size:99
Alignment explanation
Indices: 202766--203061 Score: 339
Period size: 98 Copynumber: 2.9 Consensus size: 99
202756 CACATTGGCA
* * * *
202766 CCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCCTT-ATCTTTAAGACCAATA
1 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCTTCATCTTTAAGTCCAATA
*
202830 TCGCTGGCCTTGAATCAGCACATTGGCACCCTCAT
66 TCGCTGGCCTTGAATCAGCATATTGGCA-CCTCAT
202865 -CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTCATCTTTAAGTCCAATA
1 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCTTCATCTTTAAGTCCAATA
* * * **
202928 GCGCTGGCCTTGAATCAACATATTGACACCTTTT
66 TCGCTGGCCTTGAATCAGCATATTGGCACCTCAT
* ** *
202962 CCGTCTTGAGTCCAATGCT-GCTGGCCTTGAATCAGCACATTAACATCCTTTTTCTCATCTTTAA
1 CC-T-TTAAGTCCAATG-TAGCTGGCCTTGAATCAGCACATTGGCA-CC---CT-TCATCTTTAA
* *
203026 GTCCAATATCGTTGGCCTTGAATCAGCGTATTGGCA
58 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
203062 TCTTTAATAT
Statistics
Matches: 167, Mismatches: 19, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
97 8 0.05
98 79 0.47
99 1 0.01
100 35 0.21
101 1 0.01
102 1 0.01
105 1 0.01
106 41 0.25
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.32
Consensus pattern (99 bp):
CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCTTCATCTTTAAGTCCAATA
TCGCTGGCCTTGAATCAGCATATTGGCACCTCAT
Found at i:203856 original size:19 final size:18
Alignment explanation
Indices: 203832--203897 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
203822 TGTCAACGAT
203832 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAA-TG
203851 TTGTATCGATAC--AA--
1 TTGTATCGATACATAATG
203865 -TGTATCGATACATAAATG
1 TTGTATCGATACAT-AATG
203883 TTGTATCGATACATA
1 TTGTATCGATACATA
203898 TGAAGCTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.27
16 2 0.05
17 2 0.05
18 1 0.02
19 25 0.61
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (18 bp):
TTGTATCGATACATAATG
Found at i:203869 original size:32 final size:32
Alignment explanation
Indices: 203833--203895 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
203823 GTCAACGATT
*
203833 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
203865 TGTATCGATACATAAATGTTGTATCGATACA
1 TGTATCGATACATAAATGTTGTATCGATACA
203896 TATGAAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTGTATCGATACAA
Found at i:203870 original size:13 final size:13
Alignment explanation
Indices: 203852--203876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
203842 ACATAAGTGT
203852 TGTATCGATACAA
1 TGTATCGATACAA
203865 TGTATCGATACA
1 TGTATCGATACA
203877 TAAATGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:203982 original size:52 final size:52
Alignment explanation
Indices: 203938--204067 Score: 215
Period size: 53 Copynumber: 2.5 Consensus size: 52
203928 CACTGATCTT
203938 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
203990 TGTATCGATACATACTAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGC-AGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
204043 TGTAGCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
204068 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
52 23 0.32
53 49 0.68
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:214779 original size:13 final size:13
Alignment explanation
Indices: 214761--214787 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
214751 ACATTATGCT
214761 TTGTATCGATACA
1 TTGTATCGATACA
214774 TTGTATCGATACA
1 TTGTATCGATACA
214787 T
1 T
214788 GTTAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:214797 original size:19 final size:19
Alignment explanation
Indices: 214773--214828 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
214763 GTATCGATAC
**
214773 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
214792 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
*
214812 ATTCTATCGATACATGA
1 ATTGTATCGATACATGA
214829 AACTGGCAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:214819 original size:20 final size:20
Alignment explanation
Indices: 214777--214827 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
214767 CGATACATTG
** *
214777 TATCGATACAT-GTTAATTG
1 TATCGATACATGGACAATTC
214796 TATCGATACATGGACAATTC
1 TATCGATACATGGACAATTC
214816 TATCGATACATG
1 TATCGATACATG
214828 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTC
Found at i:221037 original size:8 final size:8
Alignment explanation
Indices: 221026--221066 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
221016 AAAATCACCA
221026 AAAAAATT
1 AAAAAATT
221034 AAAAAA-T
1 AAAAAATT
*
221041 AAAAAAAT
1 AAAAAATT
*
221049 AAAAAATA
1 AAAAAATT
221057 AAAAAATT
1 AAAAAATT
221065 AA
1 AA
221067 TCATAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAAATT
Found at i:221044 original size:6 final size:7
Alignment explanation
Indices: 221026--221061 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
221016 AAAATCACCA
221026 AAAAAATT
1 AAAAAA-T
221034 AAAAAAT
1 AAAAAAT
221041 AAAAAAAT
1 -AAAAAAT
221049 AAAAAAT
1 AAAAAAT
221056 AAAAAA
1 AAAAAA
221062 ATTAATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.52
8 13 0.48
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:221044 original size:15 final size:16
Alignment explanation
Indices: 221025--221066 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
221015 GAAAATCACC
221025 AAAAAAATTAAAAAAT
1 AAAAAAATTAAAAAAT
221041 AAAAAAA-TAAAAAAT
1 AAAAAAATTAAAAAAT
221056 AAAAAAATTAA
1 AAAAAAATTAA
221067 TCATAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAAAATTAAAAAAT
Found at i:222481 original size:33 final size:32
Alignment explanation
Indices: 222300--222623 Score: 337
Period size: 32 Copynumber: 10.0 Consensus size: 32
222290 TGGAGTAACT
* * * * *
222300 TTTTCAAAGCCTATACAAGTCGATGGTAACTC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
222332 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * *
222364 TTTTCAAAGCCCACACAAGTCGATGGTAACTC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * * *
222396 TTTTCAAAGCCCACATAAGCCAGTAGCAACCC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * * *
222428 TTTTTAAAGCACATATAAGTCGGTGGCAACCC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* *
222460 TTTTCAAAAGCCTACACAAGTCTGTGGCAACCC
1 TTTTC-AAAGCCCACACAAGTCGGTGGCAACCC
* *
222493 TTTTCAAAAGCCCACACAAGTCAGTGGTAACCC
1 TTTTC-AAAGCCCACACAAGTCGGTGGCAACCC
* * *
222526 ATTTCAAAACCCCATACAAGTCGGT-GCTAACCCC
1 TTTTC-AAAGCCCACACAAGTCGGTGGC-AA-CCC
**
222560 TTTT-AAAGCCCACACAAGTTAGTGGCAACCC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * *
222591 TTTCCAAAGCCCACAAAAGTTGGTGGCAACCC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
222623 T
1 T
222624 CTCAATAGCT
Statistics
Matches: 244, Mismatches: 43, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
31 6 0.02
32 155 0.64
33 77 0.32
34 6 0.02
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (32 bp):
TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
Found at i:222875 original size:58 final size:58
Alignment explanation
Indices: 222724--222875 Score: 223
Period size: 58 Copynumber: 2.6 Consensus size: 58
222714 CCCAATGTTG
* * * *
222724 TTGGCCTTGAATCAATAGATTGGCACTTGTCAAACATTCTTTGTTAAACCTAATGTCA
1 TTGGCCTTGAATCAACAAATTGGCACTTGTCAAACCTTCTTTCTTAAACCTAATGTCA
* * *
222782 TTGGCCTTGAATCAACACATTGGCACTTGTCAAACCTTTTTTCTTAAACTTAATGTCA
1 TTGGCCTTGAATCAACAAATTGGCACTTGTCAAACCTTCTTTCTTAAACCTAATGTCA
* *
222840 TTGGCCTTGAATCAACAAATTGGAACTTTTCAAACC
1 TTGGCCTTGAATCAACAAATTGGCACTTGTCAAACC
222876 ATCTAAGTCT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 85 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (58 bp):
TTGGCCTTGAATCAACAAATTGGCACTTGTCAAACCTTCTTTCTTAAACCTAATGTCA
Found at i:223172 original size:52 final size:51
Alignment explanation
Indices: 223107--223261 Score: 170
Period size: 52 Copynumber: 3.0 Consensus size: 51
223097 TTCTTGAATT
*
223107 AATATCACTAGCCTTGAATCAGCACATTGGTACTCTTCTCATCTTTAAGTCC
1 AATATCACTAGCCTTGAATCA-CACATTGGCACTCTTCTCATCTTTAAGTCC
** * *
223159 AATATTGCTAGCCTTGAATCAACATATTGGCAC-CTTCATCATATTTAAGTCC
1 AATATCACTAGCCTTGAATC-ACACATTGGCACTCTTC-TCATCTTTAAGTCC
* * * *
223211 AATGTCACTAGCCTTAAATTACTACATTGGCACAT-TTATCATCTTTAAGTC
1 AATATCACTAGCCTTGAATCAC-ACATTGGCAC-TCTTCTCATCTTTAAGTC
223262 TAGTGTCGTA
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
51 6 0.07
52 76 0.89
53 3 0.04
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (51 bp):
AATATCACTAGCCTTGAATCACACATTGGCACTCTTCTCATCTTTAAGTCC
Found at i:223280 original size:52 final size:52
Alignment explanation
Indices: 223111--223299 Score: 143
Period size: 52 Copynumber: 3.6 Consensus size: 52
223101 TGAATTAATA
* * * * * *
223111 TCACTAGCCTTGAATC-AGCACATTGGTAC-TCTTCTCATCTTTAAGTCCAATA
1 TCACTAGCCTTAAATCTA-TACATTGGCACAT-TTATCATATTTAAGTCCAATG
** * * * * * *
223163 TTGCTAGCCTTGAATCAACATATTGGCACCTTCATCATATTTAAGTCCAATG
1 TCACTAGCCTTAAATCTATACATTGGCACATTTATCATATTTAAGTCCAATG
* * *
223215 TCACTAGCCTTAAAT-TACTACATTGGCACATTTATCATCTTTAAGTCTAGTG
1 TCACTAGCCTTAAATCTA-TACATTGGCACATTTATCATATTTAAGTCCAATG
* *
223267 TC-GTAGGCTTTAAATCTATACATTGGCACATTT
1 TCACTA-GCCTTAAATCTATACATTGGCACATTT
223300 GTTAAGAAAT
Statistics
Matches: 111, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
51 3 0.03
52 104 0.94
53 4 0.04
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (52 bp):
TCACTAGCCTTAAATCTATACATTGGCACATTTATCATATTTAAGTCCAATG
Found at i:223902 original size:20 final size:21
Alignment explanation
Indices: 223857--223903 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
223847 AATTTATATC
223857 GATACAATAATGTAATGTATTA
1 GATAC-ATAATGTAATGTATTA
223879 -ATACATAA-GTGAATGTA-TA
1 GATACATAATGT-AATGTATTA
223898 GATACA
1 GATACA
223904 GAACCATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.17
20 15 0.65
21 4 0.17
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (21 bp):
GATACATAATGTAATGTATTA
Found at i:224936 original size:20 final size:21
Alignment explanation
Indices: 224911--224949 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
224901 TCTTAACATC
*
224911 CCATGTT-TATGCATTTTATG
1 CCATGTTCCATGCATTTTATG
224931 CCATGTTCCATGCATTTTA
1 CCATGTTCCATGCATTTTA
224950 ACATGTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.46
Consensus pattern (21 bp):
CCATGTTCCATGCATTTTATG
Found at i:227763 original size:20 final size:20
Alignment explanation
Indices: 227715--227769 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
227705 GTTAAAACCC
*
227715 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
227735 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
227755 TGCATTGTATCGATA
1 TGAAATGTATCGATA
227770 TCTGTATCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:227777 original size:12 final size:12
Alignment explanation
Indices: 227760--227798 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
227750 CAGATTGCAT
227760 TGTATCGATATC-
1 TGTATCGATA-CA
227772 TGTATCGATACA
1 TGTATCGATACA
227784 TTGTATCGATACA
1 -TGTATCGATACA
227797 TG
1 TG
227799 ACCAAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 12 0.48
13 12 0.48
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:227790 original size:13 final size:13
Alignment explanation
Indices: 227757--227797 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
227747 ATACAGATTG
227757 CATTGTATCGAT-
1 CATTGTATCGATA
227769 -ATCTGTATCGATA
1 CAT-TGTATCGATA
227782 CATTGTATCGATA
1 CATTGTATCGATA
227795 CAT
1 CAT
227798 GACCAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.08
12 9 0.35
13 13 0.50
14 2 0.08
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:227912 original size:32 final size:33
Alignment explanation
Indices: 227869--227936 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
227859 GTAGCCAAGT
* *
227869 TTGTATCGATACA-C-ACAATATGTATCGATACA
1 TTGTATCGATACACCAAAAAT-TATATCGATACA
*
227901 TTGTATTGATACACCAAAAATTATATCGATACA
1 TTGTATCGATACACCAAAAATTATATCGATACA
227934 TTG
1 TTG
227937 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 12 0.39
33 15 0.48
34 4 0.13
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCAAAAATTATATCGATACA
Found at i:232017 original size:15 final size:15
Alignment explanation
Indices: 231997--232026 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
231987 CTAAATTGAG
231997 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
232012 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
232027 ATTGATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:236543 original size:20 final size:20
Alignment explanation
Indices: 236512--236568 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
236502 GTCAAAACCC
*
236512 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
236532 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
236552 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
236569 TGACCAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:236678 original size:13 final size:13
Alignment explanation
Indices: 236660--236684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
236650 ACACACAATA
236660 TGTATCGATACAT
1 TGTATCGATACAT
236673 TGTATCGATACA
1 TGTATCGATACA
236685 CCAAATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:236681 original size:32 final size:33
Alignment explanation
Indices: 236640--236707 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
236630 GTAGCCAAAT
236640 TTGTATCGATACA-CACAATA-TGTATCGATACA
1 TTGTATCGATACACCA-AATATTGTATCGATACA
236672 TTGTATCGATACACCAAATATTGTATCGATACA
1 TTGTATCGATACACCAAATATTGTATCGATACA
236705 TTG
1 TTG
236708 GCTTGTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 17 0.50
33 17 0.50
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCAAATATTGTATCGATACA
Found at i:241403 original size:21 final size:21
Alignment explanation
Indices: 241374--241415 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
241364 TACTTTGAAT
*
241374 GTAATGTATCGATAT-TCATA
1 GTAATGTATCAATATATCATA
241394 GTAATTGTATCAATATATCATA
1 GTAA-TGTATCAATATATCATA
241416 ATGGGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
GTAATGTATCAATATATCATA
Found at i:245958 original size:17 final size:18
Alignment explanation
Indices: 245936--245973 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
245926 AAAAGAAATG
245936 TTTTGGG-TTATTGAATA
1 TTTTGGGATTATTGAATA
245953 TTTTGGGACTTTATTGAATA
1 TTTTGGGA--TTATTGAATA
245973 T
1 T
245974 CAAATGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
20 11 0.61
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.53
Consensus pattern (18 bp):
TTTTGGGATTATTGAATA
Found at i:246536 original size:20 final size:20
Alignment explanation
Indices: 246511--246548 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
246501 GTATCAATAT
*
246511 ATTGTATCGATACCTGAAGA
1 ATTGTATCGATACATGAAGA
246531 ATTGTATCGATACATGAA
1 ATTGTATCGATACATGAA
246549 ACTAACAGTA
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:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGAAGA
Found at i:257013 original size:166 final size:166
Alignment explanation
Indices: 256657--257078 Score: 538
Period size: 166 Copynumber: 2.5 Consensus size: 166
256647 TTAAGAATCT
* * * * * *
256657 AAATTCTTTAAATATTATCATTTAA-TTACTACTAAATTAGTTTTAAAAAATTCCTTTTATTTCA
1 AAATTCATCAAATATCATCATTTAATTTA-TAATAAATCAGTTTTAAAAAATTCATTTT-TTTCA
*
256721 TGAAG-TTTTCA--TTTTTTCTTAAAATTTTTCGTTTCCAAAAAATTGAGTTTTTTATTTCATAA
64 T-AGGTTTTTCATTTTTTTTCTTAAAATTTTTCGTTTCCAAAAAATTGAGTTTTTTATTTCATAA
256783 AGGTTTTCAAGGGGGATTTTCACCAGTCTAAAATTTTTA
128 AGGTTTTCAAGGGGGATTTTCACCAGTCTAAAATTTTTA
* *
256822 AAATTTATCAAATATCATCATTTAATTTATAATAAATCAGTTTCAAAAAATTCATTTCTTTTCAT
1 AAATTCATCAAATATCATCATTTAATTTATAATAAATCAGTTTTAAAAAATTCATTT-TTTTCAT
* * *
256887 AGGTTTTTCATTTTTTTTCTTGAAATTTCTT-GTTTCTAAAAAATTGAGTTTCTTTATTTTATAA
65 AGGTTTTTCATTTTTTTTCTTAAAATTT-TTCGTTTCCAAAAAATTGAGTTT-TTTATTTCATAA
* *
256951 AGGTTTTC-AGGGGGTTTTTC-TCAGT-TCAAAATTTTTA
128 AGGTTTTCAAGGGGGATTTTCACCAGTCT-AAAATTTTTA
* * *
256988 ATATTCATCAAATATCATCATTTAATTCATAGTAAATCAGTTTTAAAAAATTCATTTATTTTCAT
1 AAATTCATCAAATATCATCATTTAATTTATAATAAATCAGTTTTAAAAAATTCATTT-TTTTCAT
*
257053 -GAGTTTTTCATTTTTTTCCTTAAAAT
65 AG-GTTTTTCATTTTTTTTCTTAAAAT
257079 GCATTTGTTT
Statistics
Matches: 226, Mismatches: 22, Indels: 17
0.85 0.08 0.06
Matches are distributed among these distances:
164 2 0.01
165 59 0.26
166 99 0.44
167 45 0.20
168 21 0.09
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (166 bp):
AAATTCATCAAATATCATCATTTAATTTATAATAAATCAGTTTTAAAAAATTCATTTTTTTCATA
GGTTTTTCATTTTTTTTCTTAAAATTTTTCGTTTCCAAAAAATTGAGTTTTTTATTTCATAAAGG
TTTTCAAGGGGGATTTTCACCAGTCTAAAATTTTTA
Found at i:257151 original size:166 final size:159
Alignment explanation
Indices: 256657--257161 Score: 514
Period size: 166 Copynumber: 3.1 Consensus size: 159
256647 TTAAGAATCT
* * * * * *
256657 AAATTCTTTAAATATTATCATTTAATTACTACTAAATTAGTTTTAAAAAATTCCTTTTATTTCAT
1 AAATTCATCAAATATCATCATTTAATTA-TAATAAATCAGTTTTAAAAAATTCATTTT-TTTCAT
256722 GAAG-TTTTCA-TTTTTTCTTAAAATTTTTCGTTTCCAAAAAATTGAGTTTTTTATTTCATAAAG
64 G-AGTTTTTCATTTTTTTCTTAAAATTTTT-GTTT-CAAAAAATTGAGTTTTTTATTT-ATAAAG
* *
256785 GTTTTCAAGGGGGATTTTCACCAGTCTAAAATTTTTA
125 GTTTT-AA-GGGGATTTTCATCAGTTTAAAATTTTTA
* *
256822 AAATTTATCAAATATCATCATTTAATTTATAATAAATCAGTTTCAAAAAATTCATTTCTTTTCAT
1 AAATTCATCAAATATCATCATTTAA-TTATAATAAATCAGTTTTAAAAAATTCATTT-TTTTCAT
*
256887 -AGGTTTTTCATTTTTTTTCTTGAAATTTCTTGTTTCTAAAAAATTGAGTTTCTTTATTTTATAA
64 GA-GTTTTTCA-TTTTTTTCTTAAAATTT-TTGTTTC-AAAAAATTGAGTTT-TTTA-TTTATAA
* * *
256951 AGGTTTTCAGGGGGTTTTTC-TCAGTTCAAAATTTTTA
123 AGGTTTT-AAGGGGATTTTCATCAGTTTAAAATTTTTA
* *
256988 ATATTCATCAAATATCATCATTTAATTCATAGTAAATCAGTTTTAAAAAATTCATTTATTTTCAT
1 AAATTCATCAAATATCATCATTTAATT-ATAATAAATCAGTTTTAAAAAATTCATTT-TTTTCAT
* * * * * *
257053 GAGTTTTTCATTTTTTTCCTTAAAATGCATTTGTTTCGAAAAATCGAATTTTCTATTCTATAAAT
64 GAGTTTTTCATTTTTTT-CTTAAAAT--TTTTGTTTCAAAAAATTGAGTTTTTTATT-TATAAAG
* * ** * *
257118 GTTTTTAGAAGGATTTTGGTCAGTTTGAAATTTTCA
125 GTTTTAAG-GGGATTTTCATCAGTTTAAAATTTTTA
257154 AAATTCAT
1 AAATTCAT
257162 TTAATGTTCT
Statistics
Matches: 287, Mismatches: 35, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
163 1 0.00
164 4 0.01
165 86 0.30
166 123 0.43
167 50 0.17
168 20 0.07
169 3 0.01
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (159 bp):
AAATTCATCAAATATCATCATTTAATTATAATAAATCAGTTTTAAAAAATTCATTTTTTTCATGA
GTTTTTCATTTTTTTCTTAAAATTTTTGTTTCAAAAAATTGAGTTTTTTATTTATAAAGGTTTTA
AGGGGATTTTCATCAGTTTAAAATTTTTA
Found at i:257192 original size:166 final size:167
Alignment explanation
Indices: 256689--257220 Score: 432
Period size: 166 Copynumber: 3.2 Consensus size: 167
256679 TAATTACTAC
* * * *
256689 TAAATTAGTTTTAAAAAATTCCTTT-TATTTCATGAAG-TTTTCA-TTTTTT-CTTAAAAT-TTT
1 TAAATCAGTTTTAAAAAATTCATTTAT-TTTCATGAGGTTTTTCATTTTTTTCCTTAAAATATCT
* * * * * *
256749 TCGTTTCCAAAAAATTGAGTTT-TTTATT-TCATAAAGGTTTTCAAGGGGGATTTT-CACCAG-T
65 T-GTTTCTAAAAAATCGAATTTCTCTATTCT-ATAAAGGTTTTC-A-GAGGATTTTGC-TCAGTT
* * * ** *
256810 CTAAAATTTTTAAAATTTATCAAATATCATCATTTAATTTATAA
125 C-AAAATTTTCAAAATTCATCAAATATCATCATTAAATCCATAG
* * * * *
256854 TAAATCAGTTTCAAAAAATTCATTTCTTTTCAT-AGGTTTTTCATTTTTTTTCTTGAAATTTCTT
1 TAAATCAGTTTTAAAAAATTCATTTATTTTCATGAGGTTTTTCATTTTTTTCCTTAAAATATCTT
* * * * * * *
256918 GTTTCTAAAAAATTGAGTTTCTTTATTTTATAAAGGTTTTCAGGGGGTTTTTCTCAGTTCAAAAT
66 GTTTCTAAAAAATCGAATTTCTCTATTCTATAAAGGTTTTCAGAGGATTTTGCTCAGTTCAAAAT
* * * *
256983 TTTTAATATTCATCAAATATCATCATTTAATTCATAG
131 TTTCAAAATTCATCAAATATCATCATTAAATCCATAG
257020 TAAATCAGTTTTAAAAAATTCATTTATTTTCATGA-GTTTTTCATTTTTTTCCTTAAAATGCAT-
1 TAAATCAGTTTTAAAAAATTCATTTATTTTCATGAGGTTTTTCATTTTTTTCCTTAAAAT--ATC
* * * * **
257083 TTGTTTC-GAAAAATCGAATTT-TCTATTCTATAAATGTTTTTAGAAGGATTTTGGTCAGTTTGA
64 TTGTTTCTAAAAAATCGAATTTCTCTATTCTATAAAGGTTTTCAG-AGGATTTTGCTCAGTTCAA
** * *
257146 AATTTTCAAAATTCATTTAATGTTC-TCATTAAACTCCA-AT
128 AATTTTCAAAATTCATCAAAT-ATCATCATTAAA-TCCATAG
* *
257186 TAAATCAATTTTGAAAAATTCAATTTA-TTTCATGA
1 TAAATCAGTTTTAAAAAATTC-ATTTATTTTCATGA
257221 AAATTTAATT
Statistics
Matches: 310, Mismatches: 41, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
164 2 0.01
165 52 0.17
166 185 0.60
167 48 0.15
168 22 0.07
169 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.48
Consensus pattern (167 bp):
TAAATCAGTTTTAAAAAATTCATTTATTTTCATGAGGTTTTTCATTTTTTTCCTTAAAATATCTT
GTTTCTAAAAAATCGAATTTCTCTATTCTATAAAGGTTTTCAGAGGATTTTGCTCAGTTCAAAAT
TTTCAAAATTCATCAAATATCATCATTAAATCCATAG
Found at i:257740 original size:10 final size:11
Alignment explanation
Indices: 257709--257742 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
257699 GAGAAATGAG
*
257709 AGAAAAAAAAA
1 AGAAAGAAAAA
257720 AGAAAGAAAAA
1 AGAAAGAAAAA
*
257731 AGAGAGAAAAA
1 AGAAAGAAAAA
257742 A
1 A
257743 TTAAGCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:258968 original size:135 final size:140
Alignment explanation
Indices: 258673--258978 Score: 360
Period size: 135 Copynumber: 2.2 Consensus size: 140
258663 TTCGTGGGGG
* *
258673 GTATGAAAATTTTTAAAACTTTTTGTA-CATTTTTGATTCTCCATTAAGGTACAAAATAAATTTT
1 GTATAAAAATTTTTAAAACTTTTCGTATCATTTTTGATTCTCCATTAAGGTACAAAATAAATTTT
258737 TTGAAAATTAAAATATTAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTTCTATG
66 TTGAAAATT-AAATATT-AAT-AAAATTATTATCTTAATTTTTCAAGATTTCTAATATTTCTATG
* *
258802 GTTTTTCGTTAGG
128 GTTTTCCGTTAGA
* * * * *
258815 GTATAGAAATCTTCAAAACTTTTCGTATC-TTTTCTG-TTCTCCATTAAGGTACGAAATGAATTT
1 GTATAAAAATTTTTAAAACTTTTCGTATCATTTT-TGATTCTCCATTAAGGTACAAAATAAATTT
* * ** * *
258878 TTTGGAAATT-AA-ATT-CT-CCATTATTTTCTTAATTTTTCAAGATTTCTAATA-TTCTTGTGG
65 TTTGAAAATTAAATATTAATAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTTC-TATGG
258938 TTTTCCG-TAGAA
129 TTTTCCGTTAG-A
258950 GTATAAAAATTTTTAAAACTTTTCGTATC
1 GTATAAAAATTTTTAAAACTTTTCGTATC
258979 CCCTAGTTTT
Statistics
Matches: 142, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
134 6 0.04
135 67 0.47
137 1 0.01
139 3 0.02
140 2 0.01
142 60 0.42
143 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (140 bp):
GTATAAAAATTTTTAAAACTTTTCGTATCATTTTTGATTCTCCATTAAGGTACAAAATAAATTTT
TTGAAAATTAAATATTAATAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTTCTATGGTT
TTCCGTTAGA
Found at i:263454 original size:22 final size:22
Alignment explanation
Indices: 263428--263473 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
263418 ATACTTGTTG
*
263428 ATATTGCTTTAAAACATGAAAA
1 ATATTGCTTGAAAACATGAAAA
* *
263450 ATATTGCTTGAAAACTTGCAAA
1 ATATTGCTTGAAAACATGAAAA
263472 AT
1 AT
263474 CTAATTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (22 bp):
ATATTGCTTGAAAACATGAAAA
Found at i:264843 original size:16 final size:18
Alignment explanation
Indices: 264817--264849 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
264807 TAAGATATCA
264817 ATTTAATTTGAG-CAAAC
1 ATTTAATTTGAGACAAAC
264834 ATTT-ATTTGAGACAAA
1 ATTTAATTTGAGACAAA
264850 AATAAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (18 bp):
ATTTAATTTGAGACAAAC
Found at i:264949 original size:20 final size:20
Alignment explanation
Indices: 264924--264962 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
264914 GATATCGGTA
* *
264924 AATTTATTATCTACATAATT
1 AATTTAATATCTAAATAATT
264944 AATTTAATATCTAAATAAT
1 AATTTAATATCTAAATAAT
264963 CTTGTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAATATCTAAATAATT
Found at i:269236 original size:79 final size:79
Alignment explanation
Indices: 269124--269325 Score: 208
Period size: 79 Copynumber: 2.6 Consensus size: 79
269114 AATAACGGGG
* * * * * * * * *
269124 TTGGAGTGTCCCCTTGAAAATAATGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
269188 AAAAAAAAATCAGGA
65 AAAAAAAAACCAGGA
* * *
269203 TTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * * *
269268 GAATAAAGCCGGGG
66 AAAAAAAACCAGGA
**
269282 TTGGAGTATCCCCTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGAT
269326 GAAATAATGA
Statistics
Matches: 101, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 1 0.01
79 100 0.99
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAACCAGGA
Found at i:269498 original size:51 final size:51
Alignment explanation
Indices: 269336--269500 Score: 168
Period size: 52 Copynumber: 3.2 Consensus size: 51
269326 GAAATAATGA
* * * *
269336 GGTTAGAGTATCCTCAATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCTCGATTGTGGAAAATTAGTG-TTTTGGAAATAAAACCGG
* * ** * * * * *
269388 AGTTGGAGTATCCCCGATTAAAGGAGAATTGGTGTTTTGAAAATAAAGCTGG
1 GGTTGGAGTATCCTCGATT-GTGGAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
269440 GGTTGGAGTATCCTCGATTGTGGAAAATCAATGATTTGGAAATAAAACCGG
1 GGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTTGGAAATAAAACCGG
269491 GGTTGGAGTA
1 GGTTGGAGTA
269501 AAAGGTGCCA
Statistics
Matches: 87, Mismatches: 25, Indels: 3
0.76 0.22 0.03
Matches are distributed among these distances:
51 32 0.37
52 46 0.53
53 9 0.10
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:269911 original size:59 final size:59
Alignment explanation
Indices: 269502--270317 Score: 1031
Period size: 59 Copynumber: 14.0 Consensus size: 59
269492 GTTGGAGTAA
* * *** *
269502 AAGGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGTGTCCTATTCTTTGAGGACTAA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-G
* *
269557 AAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTGG
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-G
** * * *
269612 AAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
* * * * * * *
269666 AAAAGTGCCACCAACTCGTGTGGGCTATGAAAAGAAAAAGCATCCTGCTCTTTGAGGATTGG
1 -AAGGTGCCACCAACTTGTGTGGGCT-TTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-G
** * * *
269728 AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGC-T---GCTCTTTAAGGACTG
1 AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
* * *
269784 AAGGTGCCACTAACTTGTGTGGGCTTTGAAAGGAGAAGGCGTCCCGCTCTTTGAGGACTG
1 AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
*
269844 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTG
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
269903 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
* *
269962 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGGGGACTAG
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-G
** * * **
270022 AAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCTTGCTCTTTGAGGACTG
1 AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
* * *
270082 AAGGTGCCACCAACTTGGGTGGGACTTTAAGAGAAAAGGCGTCCCGCTTTTTGAGGACTG
1 AAGGTGCCACCAACTTGTGTGGG-CTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
270142 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
*
270201 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTG
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
*
270260 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACT
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT
270318 AAAAAGCGGA
Statistics
Matches: 689, Mismatches: 56, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.00
55 123 0.18
56 39 0.06
57 13 0.02
59 291 0.42
60 138 0.20
61 83 0.12
62 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (59 bp):
AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
Found at i:270145 original size:298 final size:294
Alignment explanation
Indices: 269543--270322 Score: 1145
Period size: 298 Copynumber: 2.7 Consensus size: 294
269533 GGTGTCCTAT
* * *
269543 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTT
1 TCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTT
** * * *
269603 GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGGGGA
65 GAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
* * * * * * *
269663 CTGAAAAGTGCCACCAACTCGTGTGGGCTATGAAAAGAAAAAGCATCCTGCTCTTTGAGGATTGG
129 CTG-AAGGTGCCACCAACTTGTGTGGGCT-TTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAG
* *
269728 AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCTGCTCTTTAAGGACTGAAGGTGCCA
192 AAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAAAGGCTGCTCTTTAAGGACTGAAGGTGCCA
* * *
269793 CTAACTTGTGTGGGCTTTGAAAGGAGAAGGCGTCCCGC
257 CCAACTTGGGTGGGCTTTGAAAGGAAAAGGCGTCCCGC
*
269831 TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTG
1 TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTG
269896 AGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT
66 AGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT
*
269961 GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGGGGACTAGAAAA
131 GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAA
* *
270026 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCTTGCTCTTTGAGGACTGAAGGTGCCA
196 TGCCACCAACTTGTGTGGGCTTTG-AAAGAAAAAG--GC-TGCTCTTTAAGGACTGAAGGTGCCA
270091 CCAACTTGGGTGGGACTTT--AAGAGAAAAGGCGTCCCGC
257 CCAACTTGGGTGGG-CTTTGAAAG-GAAAAGGCGTCCCGC
*
270129 TTTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTG
1 TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTG
*
270194 AGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACT
66 AGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT
270259 GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAA
131 GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAA
270323 GCGGAAGGAG
Statistics
Matches: 448, Mismatches: 28, Indels: 23
0.90 0.06 0.05
Matches are distributed among these distances:
287 27 0.06
288 12 0.03
291 27 0.06
292 22 0.05
294 57 0.13
295 32 0.07
296 23 0.05
297 8 0.02
298 236 0.53
299 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (294 bp):
TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTG
AGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT
GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAA
TGCCACCAACTTGTGTGGGCTTTGAAAGAAAAAGGCTGCTCTTTAAGGACTGAAGGTGCCACCAA
CTTGGGTGGGCTTTGAAAGGAAAAGGCGTCCCGC
Found at i:271296 original size:1 final size:1
Alignment explanation
Indices: 271286--271378 Score: 78
Period size: 1 Copynumber: 93.0 Consensus size: 1
271276 CTTAAGCAGA
* * * * * * * *
271286 TTTTTCTTTTTTTTTTGTTTTGTTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTTTTTGTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
271351 TTTTGTTGTTTTTTTGTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
271379 AAAAGAATGT
Statistics
Matches: 68, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (1 bp):
T
Found at i:271312 original size:23 final size:21
Alignment explanation
Indices: 271286--271378 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
271276 CTTAAGCAGA
*
271286 TTTTTCTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTGTTTT
* *
271307 GTTTTTTTGTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTGTTTT
*
271328 TTTTGTTTTTTTTTTTGTGTTT
1 TTTTTTTTTTTTTTTTGT-TTT
* * *
271350 TTTTTGTTGTTTTTTTGTGTT
1 TTTTTTTTTTTTTTTTGTTTT
271371 TTTTTTTT
1 TTTTTTTT
271379 AAAAGAATGT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 42 0.70
22 18 0.30
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTTGTTTT
Found at i:271313 original size:13 final size:12
Alignment explanation
Indices: 271286--271378 Score: 102
Period size: 12 Copynumber: 7.8 Consensus size: 12
271276 CTTAAGCAGA
*
271286 TTTTTCTTTT-T
1 TTTTTTTTTTGT
*
271297 TTTTTGTTTTGT
1 TTTTTTTTTTGT
271309 TTTTTTGTTTT-T
1 TTTTTT-TTTTGT
271321 TTGTTTTTTTTGT
1 TT-TTTTTTTTGT
271334 TTTTTTTTTTG-
1 TTTTTTTTTTGT
*
271345 TGTTTTTTTTGT
1 TTTTTTTTTTGT
*
271357 TGTTTTTTTGTGT
1 T-TTTTTTTTTGT
271370 TTTTTTTTT
1 TTTTTTTTT
271379 AAAAGAATGT
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
11 19 0.27
12 30 0.43
13 21 0.30
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:271360 original size:43 final size:43
Alignment explanation
Indices: 271292--271375 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
271282 CAGATTTTTC
*
271292 TTTTTTTTTTGTTTTGTTTTTTTGTTTTTTTGT-TTTTTTTGT
1 TTTTTTTTTTGTTTTGTTTTTGTGTTTTTTTGTGTTTTTTTGT
271334 TTTTTTTTTTGTGTTT-TTTTTGTTGTTTTTTTGTGTTTTTTT
1 TTTTTTTTTTGT-TTTGTTTTTG-TGTTTTTTTGTGTTTTTTT
271376 TTTAAAAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
42 17 0.45
43 14 0.37
44 7 0.18
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (43 bp):
TTTTTTTTTTGTTTTGTTTTTGTGTTTTTTTGTGTTTTTTTGT
Found at i:283858 original size:79 final size:79
Alignment explanation
Indices: 283756--283957 Score: 203
Period size: 79 Copynumber: 2.6 Consensus size: 79
283746 AATAACGGGG
* * * * * *
283756 TTGGAGTGTCCCCT-TGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
*
283819 GAAAAAAAA-ATCAGGA
64 GAAAAAAAAGCT-AGGA
* * * *
283835 TTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * *
283900 TAATAAAGCTGGGG
66 AAAAAAAGCTAGGA
**
283914 TTGGAGTATCCCCTCAGAGGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT
283958 GAAATAACGA
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
78 1 0.01
79 98 0.97
80 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAGCTAGGA
Found at i:283965 original size:28 final size:28
Alignment explanation
Indices: 283910--283980 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
283900 TAATAAAGCT
**
283910 GGGGTTGGAGTATCCCCTCAGAGGTAAC
1 GGGGTTGGAGTATCCCCTCAGAAATAAC
*
283938 GGGGTTGGAGTATCCCC-GATGAAATAAC
1 GGGGTTGGAGTATCCCCTCA-GAAATAAC
* *
283966 GAGGTTAGAGTATCC
1 GGGGTTGGAGTATCC
283981 TCAATTGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCTCAGAAATAAC
Found at i:284032 original size:52 final size:51
Alignment explanation
Indices: 283968--284137 Score: 187
Period size: 52 Copynumber: 3.3 Consensus size: 51
283958 GAAATAACGA
* * * * *
283968 GGTTAGAGTATCCTCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTTGGAAATAAAACCGG
* ** * * * *
284020 AGTTGGAGTATCCCCGATTAAAGGAGAATTGGTGTTTTGAAAATAAAGCTGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAATTGGTGTTTTGGAAATAAAACCGG
* * *
284072 GGTTGGAGTATCCCCGATTGTGGAAAATCGATGATTTGGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAACCGG
284123 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
284138 TCGGAGATAA
Statistics
Matches: 95, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
51 38 0.40
52 47 0.49
53 10 0.11
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAACCGG
Found at i:284131 original size:51 final size:52
Alignment explanation
Indices: 284003--284137 Score: 164
Period size: 51 Copynumber: 2.6 Consensus size: 52
283993 AATTGGTGTT
* * * * * *
284003 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAGAATTGGTGT
1 TTTGGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAATCGATGA
* * * **
284055 TTTGAAAATAAAGCTGGGGTTGGAGTATCCCCGATT-GTGGAAAATCGATGA
1 TTTGGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAATCGATGA
284106 TTTGGAAATAAAACCGGGGTTGGAGTATCCCC
1 TTTGGAAATAAAACCGGGGTTGGAGTATCCCC
284138 TCGGAGATAA
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
51 38 0.55
52 31 0.45
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (52 bp):
TTTGGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAATCGATGA
Found at i:284178 original size:79 final size:80
Alignment explanation
Indices: 284070--284217 Score: 199
Period size: 79 Copynumber: 1.9 Consensus size: 80
284060 AAATAAAGCT
* * * *
284070 GGGGTTGGAGTATCCCCGATTGTGGAAAATCGATG-ATTTGGAAATAAAACCGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTATTTAGAAATAAAACCGGAGTTGGAGTAT
284134 CCCCTCGGAGATAAC
66 CCCCTCGGAGATAAC
** * * * *
284149 GGGGTTGGAGTATCCTTGATTATGAAAAATTGGTGTTTTTAGAAATAAAATCGGAGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTATTTAGAAATAAAACCGGAGTTGGAGTAT
284214 CCCC
66 CCCC
284218 GATTAAAGGA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
79 29 0.50
80 29 0.50
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (80 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTATTTAGAAATAAAACCGGAGTTGGAGTAT
CCCCTCGGAGATAAC
Found at i:284181 original size:183 final size:183
Alignment explanation
Indices: 283937--284322 Score: 574
Period size: 183 Copynumber: 2.1 Consensus size: 183
283927 TCAGAGGTAA
* *
283937 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCTCAATTGTGAAAAATTGGTGT
1 CGGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTAGAGTATCCTCAATTATGAAAAATTGGTGT
* *
284002 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAGAATTGGTGTTTTGAAAATAAA
66 TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAA
* ** * * *
284067 GCTGGGGTTGGAGTATCCCCGATTGTGGAAAATCGATGATTTGGAAATAAAAC
131 ACCAGGGTTGGAGTATCCCCGATTATGGAAAATCAATGATTTAGAAATAAAAC
** * * * **
284120 CGGGGTTGGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATCCTTGATTATGAAAAATTGGTGT
1 CGGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTAGAGTATCCTCAATTATGAAAAATTGGTGT
284185 TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAA
66 TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAA
* * *
284250 ACCAGGGTTGGAGTATCCCCGATTATGGAAAATTAATGTTTTAGAAATAAAAT
131 ACCAGGGTTGGAGTATCCCCGATTATGGAAAATCAATGATTTAGAAATAAAAC
* *
284303 CGGAGTTGGAGTATCTCCGA
1 CGGGGTTGGAGTATCCCCGA
284323 TTATAGAAAA
Statistics
Matches: 179, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
183 179 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (183 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAACGAGGTTAGAGTATCCTCAATTATGAAAAATTGGTGT
TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAA
ACCAGGGTTGGAGTATCCCCGATTATGGAAAATCAATGATTTAGAAATAAAAC
Found at i:284301 original size:51 final size:51
Alignment explanation
Indices: 284152--284385 Score: 274
Period size: 51 Copynumber: 4.5 Consensus size: 51
284142 AGATAACGGG
** * * *
284152 GTTGGAGTATCCTTGATTATGAAAAATTGGTGTTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGA-AAATAAAATCGGA
* * *
284204 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCAGG-
1 GTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTGAAAATAAAATC-GGA
*
284256 GTTGGAGTATCCCCGATTATGGAAAATTAATGTTTT-AGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGA-AAATAAAATCGGA
* * *
284307 GTTGGAGTATCTCCGATTATAGAAAATTAGCGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAATCGGA
* * * *
284358 GTGGGAATATCCCCGATTGTGGAGAATT
1 GTTGGAGTATCCCCGATTATGGAAAATT
284386 GAGAAACTCA
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
50 3 0.02
51 91 0.58
52 44 0.28
53 19 0.12
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:286765 original size:13 final size:13
Alignment explanation
Indices: 286747--286772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
286737 ACAAAGATCC
286747 ATGTATCGATACA
1 ATGTATCGATACA
286760 ATGTATCGATACA
1 ATGTATCGATACA
286773 TGAAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:286784 original size:33 final size:33
Alignment explanation
Indices: 286726--286792 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
286716 AAATTTCCCA
*
286726 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGATCAATGTATCGATAC
286759 AATGTATCGATACATGAA-AT-AATGTATCGATAC
1 AATGTATCGATACA--AAGATCAATGTATCGATAC
286792 A
1 A
286793 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 27 0.87
34 2 0.06
35 2 0.06
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAAAGATCAATGTATCGATAC
Found at i:286836 original size:19 final size:18
Alignment explanation
Indices: 286812--286879 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
286802 CAGTAGCTAA
286812 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
286831 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
286846 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
286863 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
286880 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:286852 original size:13 final size:13
Alignment explanation
Indices: 286834--286858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
286824 ACAATACTTA
286834 TGTATCGATACAT
1 TGTATCGATACAT
286847 TGTATCGATACA
1 TGTATCGATACA
286859 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:286856 original size:32 final size:32
Alignment explanation
Indices: 286815--286877 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
286805 TAGCTAATTA
*
286815 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
286847 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
286878 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:287940 original size:20 final size:21
Alignment explanation
Indices: 287896--287941 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
287886 TTTTACAATT
*
287896 TGTATCGATACAAATAGTAAA
1 TGTATCAATACAAATAGTAAA
* *
287917 TGTATCAATACATA-AGTGAA
1 TGTATCAATACAAATAGTAAA
287937 TGTAT
1 TGTAT
287942 TGATACATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (21 bp):
TGTATCAATACAAATAGTAAA
Found at i:287947 original size:20 final size:21
Alignment explanation
Indices: 287896--287949 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
287886 TTTTACAATT
*
287896 TGTATCGATACAAATAGTAAA
1 TGTATCGATACATATAGTAAA
* *
287917 TGTATCAATACATA-AGTGAA
1 TGTATCGATACATATAGTAAA
*
287937 TGTATTGATACAT
1 TGTATCGATACAT
287950 GCCTAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATATAGTAAA
Found at i:288017 original size:20 final size:20
Alignment explanation
Indices: 287989--288029 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
287979 TGCATCCTGC
287989 TAAGGAAATGTATCGATACA
1 TAAGGAAATGTATCGATACA
*
288009 TAAGTAAATGTATCGATACA
1 TAAGGAAATGTATCGATACA
288029 T
1 T
288030 TTACTGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (20 bp):
TAAGGAAATGTATCGATACA
Found at i:288043 original size:21 final size:20
Alignment explanation
Indices: 288017--288071 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
288007 CATAAGTAAA
**
288017 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTT-CTCAT
* * *
288038 TGTATCAATATATTTTTCAT
1 TGTATCGATACATTTCTCAT
288058 TGTATCGATACATT
1 TGTATCGATACATT
288072 CTGAGTTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:290706 original size:107 final size:107
Alignment explanation
Indices: 290517--290725 Score: 323
Period size: 107 Copynumber: 2.0 Consensus size: 107
290507 TACTTGTCGG
* *
290517 GGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACTGA
1 GGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTCTAAAACACTGA
*
290582 TTTTCCACCATCAAGGATACTCCAATCACGTTATTTCCTAAC
66 TTTTCCACCATCAAGGATACTCCAACCACGTTATTTCCTAAC
* *
290624 GGATACTCCAACCCCATTATTTTTGAGAGGATACTCTAACCCC-AGTTTTATTTCTAAAACA-TC
1 GGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGA-TTTTATTTCTAAAACACT-
* *
290687 GATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTC
64 GATTTTCCACCATCAAGGATACTCCAACCACGTTATTTC
290726 TGAGGGAAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
106 2 0.02
107 91 0.98
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (107 bp):
GGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTCTAAAACACTGA
TTTTCCACCATCAAGGATACTCCAACCACGTTATTTCCTAAC
Found at i:290707 original size:79 final size:79
Alignment explanation
Indices: 290624--290794 Score: 227
Period size: 79 Copynumber: 2.2 Consensus size: 79
290614 ATTTCCTAAC
* * * * *
290624 GGATACTCCAACCCCATTATTTTTGAGAGG-ATACTCTAACCCCAGTTTTATTTCTAAAACATCG
1 GGATACTCCAACCCCATTATTTCTGAG-GGAAAACTCCAACCCCAGTTTTATTTCCAAAACACCG
290688 ATTTTCCACCATCGA
65 ATTTTCCACCATCGA
* **
290703 GGATACTCCAACCCCGTTATTTCTGAGGGAAAACTCCAACCCTGGTTTTATTTCCAAAACACCGA
1 GGATACTCCAACCCCATTATTTCTGAGGGAAAACTCCAACCCCAGTTTTATTTCCAAAACACCGA
* *
290768 TTTTCCACCATGGG
66 TTTTCCACCATCGA
*
290782 GGATACTCTAACC
1 GGATACTCCAACC
290795 TTATTTTCAG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 2 0.03
79 78 0.98
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (79 bp):
GGATACTCCAACCCCATTATTTCTGAGGGAAAACTCCAACCCCAGTTTTATTTCCAAAACACCGA
TTTTCCACCATCGA
Found at i:290919 original size:186 final size:182
Alignment explanation
Indices: 290517--290929 Score: 413
Period size: 186 Copynumber: 2.2 Consensus size: 182
290507 TACTTGTCGG
* * * *
290517 GGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACTGA
1 GGATACTCCAACCTCA-TA-TTTCGAGGGAAAACTCCAACCCCGATTTTATTTCCAAAACACCGA
290582 TTTTCCACCATCAAGGATACTCCAATCACGTTATTTCCTAACGGATACTCCAACCCCATTATTTT
64 TTTTCCACCATCAAGGATACTCCAATCACGTTATTTCCTAACGGATACTCCAACCCCATTATTTT
* * * * **
290647 TGAGAGGATACTCTAACCCCAGTTTTATTTCTAAAACATCGATTTTCCACCATCGA
129 TGAAAGGATACTCCAACCCCAGTTTTATCTCCAAAACATAAATTTT-C-CCATCGA
* * * *
290703 GGATACTCCAACCCCGTTATTTCTGAGGGAAAACTCCAACCCTGGTTTTATTTCCAAAACACCGA
1 GGATACTCCAACCTC-ATATTTC-GAGGGAAAACTCCAACCCCGATTTTATTTCCAAAACACCGA
*** * *
290768 TTTTCCACCATGGGGGATACTCTAA-C-C-TTATTTTCAGC-ATCGGGGATACTCCAACCCCATT
64 TTTTCCACCATCAAGGATACTCCAATCACGTTA-TTTC--CTAAC--GGATACTCCAACCCCATT
* * * * *
290829 GTTTTTGAAAGGATACTCCAATCCCATTTTTATCTCCAAAATATTAAATTTT-TCATCGA
124 ATTTTTGAAAGGATACTCCAACCCCAGTTTTATCTCCAAAACA-TAAATTTTCCCATCGA
* * *
290888 GGAGTGTACTCCAACCTCATACTTCGAGGGAACATTCCAACC
1 GGA---TACTCCAACCTCATATTTCGAGGGAAAACTCCAACC
290930 TTATCTCTTT
Statistics
Matches: 187, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
183 3 0.02
184 5 0.03
185 16 0.09
186 88 0.47
187 58 0.31
188 17 0.09
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (182 bp):
GGATACTCCAACCTCATATTTCGAGGGAAAACTCCAACCCCGATTTTATTTCCAAAACACCGATT
TTCCACCATCAAGGATACTCCAATCACGTTATTTCCTAACGGATACTCCAACCCCATTATTTTTG
AAAGGATACTCCAACCCCAGTTTTATCTCCAAAACATAAATTTTCCCATCGA
Found at i:295892 original size:10 final size:10
Alignment explanation
Indices: 295866--295897 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
295856 AAGATTCATC
295866 TTTAAACAAG
1 TTTAAACAAG
295876 TTT-AACAAG
1 TTTAAACAAG
295885 TTTAAACAAG
1 TTTAAACAAG
295895 TTT
1 TTT
295898 CAAAACCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (10 bp):
TTTAAACAAG
Done.