Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold91
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: 1327174
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 48727 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:275259 original size:127 final size:127
Alignment explanation
Indices: 275104--275429 Score: 376
Period size: 127 Copynumber: 2.5 Consensus size: 127
275094 CTCTTTTTCC
*
275104 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCTGTGGCACTCT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCTGTGGCAC-CT
*
275169 TTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCT-T-T-AAAGCCCACAACTCCGTGGCACT
64 TTTT-TCTTTTCAAAGCCCACGACTCAGTGGCACTCTGTCTCAAAGCCCACAACTCCGTGGCACT
* *
275231 CTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAGCTCTGTGGCACC-T
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCTGTGGCACCTT
* * * * * *
275295 TCTTCTTTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCAAAGTCCACGACTCCGTGGCACT
65 TTTTCTTTTCAAAGCCCACGACTCAGTGGCACTCTGTCTCAAAGCCCACAACTCCGTGGCACT
* * * *
275358 CTTTTTCCTTCTAAG-CCACAACTCTGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGG
1 C--TTT--TT-AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCTGTGG
*
275421 CACCCTTTT
59 CACCTTTTT
275430 AAGCCCATAA
Statistics
Matches: 170, Mismatches: 17, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
124 28 0.16
125 4 0.02
126 2 0.01
127 79 0.46
128 1 0.01
129 3 0.02
131 38 0.22
132 14 0.08
133 1 0.01
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.32
Consensus pattern (127 bp):
CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCTTT
TTTCTTTTCAAAGCCCACGACTCAGTGGCACTCTGTCTCAAAGCCCACAACTCCGTGGCACT
Found at i:275456 original size:27 final size:27
Alignment explanation
Indices: 275397--275450 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
275387 CACTCTTTTT
* *
275397 CCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCAC
*
275424 CCTTTTAAGCCCATAACTCCATGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCAC
275451 TTTTTTCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.41, G:0.13, T:0.22
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCATGGCAC
Found at i:275548 original size:73 final size:71
Alignment explanation
Indices: 275425--275563 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 71
275415 CCGTGGCACC
*
275425 CTTTTAAGCCCATAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTT
1 CTTTTAAGCCCACAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTT
275490 TTTTTT
66 TTTTTT
* * *
275496 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATCT
1 CTTTT-AAGCCCACAACTCCATGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCT
275560 TTTT
63 TTTT
275564 CCCTTCCTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
71 5 0.08
72 21 0.34
73 35 0.57
ACGTcount: A:0.19, C:0.30, G:0.11, T:0.40
Consensus pattern (71 bp):
CTTTTAAGCCCACAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTT
TTTTTT
Found at i:275594 original size:73 final size:71
Alignment explanation
Indices: 275430--275581 Score: 191
Period size: 73 Copynumber: 2.1 Consensus size: 71
275420 GCACCCTTTT
* * ***
275430 AAGCCCATAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCCCT
*
275495 TCTTTTA
66 TC-TCTA
* *
275502 AAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCC
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCTTTTTCC
275566 CTTC-CTA
64 CTTCTCTA
275573 AAGCCCACA
1 AAGCCCACA
275582 CAAGTTGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
71 11 0.16
72 21 0.30
73 38 0.54
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.36
Consensus pattern (71 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCCCT
TCTCTA
Found at i:275609 original size:33 final size:35
Alignment explanation
Indices: 275566--275635 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
275556 ATCTTTTTCC
*
275566 CTTCCTAAAGCCCACACAAGTTGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
275600 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
275634 CT
1 CT
275636 AAGCCCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:275754 original size:49 final size:49
Alignment explanation
Indices: 275635--276385 Score: 951
Period size: 49 Copynumber: 15.7 Consensus size: 49
275625 GCAACCCTTC
* * * *
275635 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTT
* *
275687 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
275736 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * * *
275779 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
275828 TAAGTCCAATGTAGCTGGCCCTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
275871 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
**
275920 TAAGTCCAATGTAGCTGGCCTTGACGCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
275969 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
276012 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* **
276061 TAAGTCCAATGTAGCTAGCCTTGACGCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
276110 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
276158 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
276207 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
276255 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
276298 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
276350 TAAATTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
276386 ACATCCTTTT
Statistics
Matches: 613, Mismatches: 58, Indels: 56
0.84 0.08 0.08
Matches are distributed among these distances:
43 153 0.25
45 2 0.00
47 3 0.00
48 90 0.15
49 290 0.47
50 2 0.00
52 73 0.12
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:275841 original size:92 final size:92
Alignment explanation
Indices: 275684--276341 Score: 800
Period size: 92 Copynumber: 7.0 Consensus size: 92
275674 CATTTTCCAT
* *
275684 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
275749 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * * * *
275776 CTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
*
275841 GCTGGCCCTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
275868 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
**
275933 GCTGGCCTTGACGCAGCACATTGGCACCTTC
66 GCTGGCCTTGAATCAGCACATTGGCA----C
*
275964 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
* *
276023 TCGCTGGCCTTGAATCAGCATATTGGCATCATC
64 TAGCTGGCCTTGAATCAGCACATTGG---CA-C
* **
276056 ATCTTTAAGTCCAATGTAGCTAGCCTTGACGCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
276121 TAGCTGGCCTTGAATCAGCACATTGGCACCTC
64 TAGCTGGCCTTGAATCAGCACATTGGCA---C
*
276153 ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
276218 TAGCTGGCCTTGAATCAGCACATTGGCACCTCAC
64 TAGCTGGCCTTGAATCAGCACATTGG-----CAC
*
276252 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CATCTTTAAGTCCAATATA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
276311 GCTGGCCTTGAATCAGCATATCGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
276338 CTTT
1 CTTT
276342 TCCATCTTTA
Statistics
Matches: 509, Mismatches: 35, Indels: 50
0.86 0.06 0.08
Matches are distributed among these distances:
86 7 0.01
91 40 0.08
92 246 0.48
94 1 0.00
95 4 0.01
96 2 0.00
97 130 0.26
98 76 0.15
99 1 0.00
102 2 0.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (92 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:275921 original size:141 final size:141
Alignment explanation
Indices: 275635--276385 Score: 1003
Period size: 141 Copynumber: 5.3 Consensus size: 141
275625 GCAACCCTTC
* * * *
275635 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTCCAATGTA
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTTTAAGTCCAATGTA
* *
275700 GCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
63 GCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAG
*
275765 CACATTGG---CA-C--CTT
122 CATATTGGCATCATCATCTT
* * * * * *
275779 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* *
275844 GGCCCTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
275909 ATCATCATCTT
131 ATCATCATCTT
**
275920 TAAGTCCAATGTAGCTGGCCTTGACGCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
*
275985 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
276050 ATCATCATCTT
131 ATCATCATCTT
* **
276061 TAAGTCCAATGTAGCTAGCCTTGACGCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* * *
276126 GGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACA
66 GGCCTTGAATCAGCACATTGGCA---C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
* *
276191 TTGGCACCTTCATCTT
126 TTGGCATCATCATCTT
*
276207 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* *
276271 GGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
**
276336 ACCTTTTCCATCTT
131 A--TCAT-CATCTT
* *
276350 TAAATTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
276386 ACATCCTTTT
Statistics
Matches: 555, Mismatches: 38, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
135 37 0.07
138 2 0.00
139 1 0.00
140 39 0.07
141 265 0.48
142 4 0.01
143 40 0.07
144 38 0.07
145 45 0.08
146 84 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (141 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
ATCATCATCTT
Found at i:277313 original size:13 final size:13
Alignment explanation
Indices: 277295--277319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277285 CATAAAATGT
277295 TGTATCGATACAA
1 TGTATCGATACAA
277308 TGTATCGATACA
1 TGTATCGATACA
277320 TATTTTTTTT
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:277317 original size:33 final size:34
Alignment explanation
Indices: 277275--277345 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
277265 TTCAACGATT
277275 TGTATCGATACATA-AAATGTTGTATCGATACAA
1 TGTATCGATACATATAAATGTTGTATCGATACAA
*** *
277308 TGTATCGATACATATTTTTTTTGTATCGATACAA
1 TGTATCGATACATATAAATGTTGTATCGATACAA
277342 TGTA
1 TGTA
277346 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (34 bp):
TGTATCGATACATATAAATGTTGTATCGATACAA
Found at i:277403 original size:13 final size:13
Alignment explanation
Indices: 277385--277409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277375 ATTACTCACA
277385 TGTATCGATACAT
1 TGTATCGATACAT
277398 TGTATCGATACA
1 TGTATCGATACA
277410 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:277546 original size:52 final size:52
Alignment explanation
Indices: 277418--277538 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
277408 CACTGATCTT
*
277418 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
277470 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
277522 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
277539 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:284083 original size:13 final size:13
Alignment explanation
Indices: 284062--284095 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
284052 TAAAAATTAA
*
284062 ATAAAATATATAT
1 ATAATATATATAT
*
284075 ATAATATATATGT
1 ATAATATATATAT
284088 ATAATATA
1 ATAATATA
284096 ATAAAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:284710 original size:56 final size:56
Alignment explanation
Indices: 284639--284765 Score: 211
Period size: 56 Copynumber: 2.3 Consensus size: 56
284629 AAGCTGCTGC
* * *
284639 AAACAGTAGCAATGAAGAATGTAATGAAGACACCAACGTGTTGCAATGAAGAGAAG
1 AAACGGTAGCAATGAAGAAAGTAATGAAGACACCAACGTGCTGCAATGAAGAGAAG
284695 AAACGGTAGCAATGAAGAAAGTAATGAAGACACCAACGTGCTGCAATGAAGAGAAG
1 AAACGGTAGCAATGAAGAAAGTAATGAAGACACCAACGTGCTGCAATGAAGAGAAG
*
284751 AAACGGCAGC-ATGAA
1 AAACGGTAGCAATGAA
284766 ATCAAAGCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 5 0.07
56 62 0.93
ACGTcount: A:0.46, C:0.14, G:0.26, T:0.13
Consensus pattern (56 bp):
AAACGGTAGCAATGAAGAAAGTAATGAAGACACCAACGTGCTGCAATGAAGAGAAG
Found at i:285027 original size:19 final size:19
Alignment explanation
Indices: 284982--285025 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
284972 AAATTGCAGC
284982 AAAAAAAATAGAAGAGAAG
1 AAAAAAAATAGAAGAGAAG
*
285001 AAAAAAAAT-GAAG-GAGG
1 AAAAAAAATAGAAGAGAAG
285018 AAAAAAAA
1 AAAAAAAA
285026 AAGCAAGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.46
18 4 0.17
19 9 0.38
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (19 bp):
AAAAAAAATAGAAGAGAAG
Found at i:285240 original size:20 final size:21
Alignment explanation
Indices: 285215--285253 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
285205 AAAAAAGAAA
285215 ACAGC-AAACATCAAGCAAAG
1 ACAGCAAAACATCAAGCAAAG
285235 ACAGCAAAACATCAAGCAA
1 ACAGCAAAACATCAAGCAA
285254 TAGTAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.26, G:0.13, T:0.05
Consensus pattern (21 bp):
ACAGCAAAACATCAAGCAAAG
Found at i:285339 original size:23 final size:22
Alignment explanation
Indices: 285299--285341 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
285289 CAATAAACAT
*
285299 CAAGAAAGCAGCAACAGCAAAG
1 CAAGAAAGAAGCAACAGCAAAG
*
285321 CAAGAAATGAAGCAGCAGCAA
1 CAAGAAA-GAAGCAACAGCAA
285342 CTTTGCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.53, C:0.21, G:0.23, T:0.02
Consensus pattern (22 bp):
CAAGAAAGAAGCAACAGCAAAG
Found at i:288882 original size:96 final size:96
Alignment explanation
Indices: 288718--288909 Score: 330
Period size: 96 Copynumber: 2.0 Consensus size: 96
288708 AGATCAAAGT
* * * *
288718 TAAGCCAAAACTTAAAACCTTGATAACTAACAAATTCTAAAGAAGCTCCAAGTATAAACTACTTG
1 TAAGCCAAAACTTAAAAACTTGATAACCAACAAATTCTAAAGAAACTCCAAGTATAAACTACATG
288783 AAAAACACTTGGAAAATGGTTTTTGTAGCCC
66 AAAAACACTTGGAAAATGGTTTTTGTAGCCC
* *
288814 TAAGCCCAAACTTAAAAACTTGTTAACCAACAAATTCTAAAGAAACTCCAAGTATAAACTACATG
1 TAAGCCAAAACTTAAAAACTTGATAACCAACAAATTCTAAAGAAACTCCAAGTATAAACTACATG
288879 AAAAACACTTGGAAAATGGTTTTTGTAGCCC
66 AAAAACACTTGGAAAATGGTTTTTGTAGCCC
288910 ATTTACAGCA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (96 bp):
TAAGCCAAAACTTAAAAACTTGATAACCAACAAATTCTAAAGAAACTCCAAGTATAAACTACATG
AAAAACACTTGGAAAATGGTTTTTGTAGCCC
Found at i:291535 original size:14 final size:14
Alignment explanation
Indices: 291516--291558 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
291506 TATATTATAT
*
291516 TTTTTTATAATTTA
1 TTTTTTAAAATTTA
*
291530 TTTTTTAAAAATATA
1 TTTTTT-AAAATTTA
*
291545 TATTTTAAAATTTA
1 TTTTTTAAAATTTA
291559 ATCTTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTTAAAATTTA
Found at i:291548 original size:17 final size:16
Alignment explanation
Indices: 291509--291554 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
291499 GCCTAGCTAT
* *
291509 ATTATATTTTTTTATA
1 ATTATATTTTTTAAAA
291525 ATT-TATTTTTTAAAA
1 ATTATATTTTTTAAAA
*
291540 A-TATATATTTTAAAA
1 ATTATATTTTTTAAAA
291555 TTTAATCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 1 0.04
15 22 0.85
16 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATATTTTTTAAAA
Found at i:293391 original size:127 final size:128
Alignment explanation
Indices: 293162--293414 Score: 418
Period size: 127 Copynumber: 2.0 Consensus size: 128
293152 CTCAAACAAA
* * *
293162 ATGTAAAGGTGTTGAGTTTCTCTCAAGAATGAATCAAGAACATTTCTAATTATCAAGAACAAAAA
1 ATGTAAAGGTATTGAATTTCTCTCAAGAATGAATCAAGAACATTTCCAATTATCAAGAACAAAAA
* *
293227 ATAACAATTGAGAAAAAAATAATCGCAAGGTGCGACAATGGTTTTAT-GTTTCAACTATCTGT
66 ATAACAATTGAGAAAAAAACAATCGCAAGGTGCGACAATGGCTTTATGGTTTCAACTATCTGT
* *
293289 ATGTAAAGGTATTGAATTTCTCTTAAGAATGAATCAAGAACATTTCCAATTATCAAGAATAAAAA
1 ATGTAAAGGTATTGAATTTCTCTCAAGAATGAATCAAGAACATTTCCAATTATCAAGAACAAAAA
* *
293354 ATAACAATTGAGAAAAAAACAATGGCAAGGTGTGACAATGGCTTTATGGTTTCAACTATCT
66 ATAACAATTGAGAAAAAAACAATCGCAAGGTGCGACAATGGCTTTATGGTTTCAACTATCT
293415 TTTTCTTGTG
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
127 103 0.89
128 13 0.11
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (128 bp):
ATGTAAAGGTATTGAATTTCTCTCAAGAATGAATCAAGAACATTTCCAATTATCAAGAACAAAAA
ATAACAATTGAGAAAAAAACAATCGCAAGGTGCGACAATGGCTTTATGGTTTCAACTATCTGT
Found at i:297831 original size:2 final size:2
Alignment explanation
Indices: 297824--297865 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
297814 CTGAAGCCAA
297824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
297866 CCCTTCAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:298600 original size:2 final size:2
Alignment explanation
Indices: 298588--298621 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
298578 ATATTCTAAA
298588 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
298622 AGTTACACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:301894 original size:75 final size:75
Alignment explanation
Indices: 301771--301931 Score: 304
Period size: 75 Copynumber: 2.1 Consensus size: 75
301761 AAGATTCCTA
301771 AGTTTTAATGCATGCTTCACTTCTTCATATTGCTTTCCACTTCTCTCAATTCCATCCCTAAGATT
1 AGTTTTAATGCATGCTTCACTTCTTCATATTGCTTTCCACTTCTCTCAATTCCATCCCTAAGATT
301836 AATCCTACTC
66 AATCCTACTC
301846 AGTTTTAATGCATGCTTCACTTCTTCATATTGCTTTCCACTTCTCTCAATTCCATCCCTAAGATT
1 AGTTTTAATGCATGCTTCACTTCTTCATATTGCTTTCCACTTCTCTCAATTCCATCCCTAAGATT
301911 AATCCTACTC
66 AATCCTACTC
* *
301921 AATTTTGATGC
1 AGTTTTAATGC
301932 TTAGCTCATT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (75 bp):
AGTTTTAATGCATGCTTCACTTCTTCATATTGCTTTCCACTTCTCTCAATTCCATCCCTAAGATT
AATCCTACTC
Found at i:305038 original size:86 final size:86
Alignment explanation
Indices: 304893--305066 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 86
304883 TCATGAAATT
*
304893 CTTAAGTGATTTCTGTTTCACTAACTTCTAAGTAAATAATTTTGGGCTACTCAAATTTAAGAAAC
1 CTTAAGCGATTTCTGTTTCACTAACTTCTAAGTAAATAATTTTGGGCTACTCAAATTTAAGAAAC
304958 TAAATACTAATTGGGTTATGG
66 TAAATACTAATTGGGTTATGG
304979 CTTAAGCGATTTCTGTTTCACTAACTTCTAAGTAAATAATTTTGGGCTACTCAAATTTAAGAAAC
1 CTTAAGCGATTTCTGTTTCACTAACTTCTAAGTAAATAATTTTGGGCTACTCAAATTTAAGAAAC
305044 TAAATACTAATTGGGTTATGG
66 TAAATACTAATTGGGTTATGG
305065 CT
1 CT
305067 GAACCAAATG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (86 bp):
CTTAAGCGATTTCTGTTTCACTAACTTCTAAGTAAATAATTTTGGGCTACTCAAATTTAAGAAAC
TAAATACTAATTGGGTTATGG
Found at i:306257 original size:257 final size:256
Alignment explanation
Indices: 305843--306448 Score: 828
Period size: 257 Copynumber: 2.4 Consensus size: 256
305833 TATTGATAAA
* * *
305843 TGAAGAAAACCAAGCACTAATAGGCACCAAGAAGTGACAACCCTTTATTTTTGCTTCACCTTCCT
1 TGAAGAAAACCAAGCACTAATAGGCACCAAGAAGTGACAGCCCTTTATCTTTCCTTCACCTTCCT
* * * * *
305908 TTTTTTCTTTACA-TTTTGCTTCCCTTTTAACTTGTTTTTGCATGATCTTTTGCTTTTCCTACCA
66 CTTTTTCTTTA-AGTTTTGCTTCCTTTTTAACTTGCTCTTGCACGATCTTTTGCTTTTCCTACCA
* *
305972 AATCTAGCCATTTACGACATGGATACACAAAAATTTCCCCAAAAAGAGCTAGAAATAGCACATGC
130 AATCTAGCCATTTACAACATGAATACAC-AAAA-TTCCCCAAAAAGAGCTAGAAATAGCACA-GC
*
306037 TTTATTC-T-T-TCTCTCCCCCCATTGCCTTTATAACCTAAGCCAATAACAATGAAAGGAGCCCT
192 TTTATTCATATCTCTCTCCCCCCATCGCCTTTATAACCTAAGCCAATAACAATGAAAGGAGCCCT
*
306099 TGAAGAAAACCAAGCACTAATAGGCACCAAGAAGTGACAGCCCTTTATCCTTTCCTTCACCCTCC
1 TGAAGAAAACCAAGCACTAATAGGCACCAAGAAGTGACAGCCCTTTAT-CTTTCCTTCACCTTCC
*
306164 TCTTTTTCTTTAAGTTTTGCTTCCTTTTTAACTTGCTCTTGCACGATCTTTTGCTTTTCCTGCCA
65 TCTTTTTCTTTAAGTTTTGCTTCCTTTTTAACTTGCTCTTGCACGATCTTTTGCTTTTCCTACCA
* * ** **
306229 AATCTAGCTATTTACAACATGAATACACAACATTCTGCAAAAAGAGCTAGAGCTAGCACAGCTTT
130 AATCTAGCCATTTACAACATGAATACACAAAATTCCCCAAAAAGAGCTAGAAATAGCACAGCTTT
* * * * *
306294 ATTCTATATCTCTCTCCCCCCATCGCCTTTATAATCTAGGCCAGTTACAATGAGAGGAGCCCT
195 ATTC-ATATCTCTCTCCCCCCATCGCCTTTATAACCTAAGCCAATAACAATGAAAGGAGCCCT
** * *
306357 CAAAGAAAACCAAGCACTAATAGGCA-AAAGAAGTGACAGTCCTTTATTCTTTCCTTCACCTTCC
1 TGAAGAAAACCAAGCACTAATAGGCACCAAGAAGTGACAGCCCTTTA-TCTTTCCTTCACCTTCC
* *
306421 TCTTTATCTTT-AGATTTTTCTTCCTTTT
65 TCTTTTTCTTTAAG-TTTTGCTTCCTTTT
306449 CTTTATCTTT
Statistics
Matches: 311, Mismatches: 31, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
254 9 0.03
255 24 0.08
256 54 0.17
257 152 0.49
258 72 0.23
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (256 bp):
TGAAGAAAACCAAGCACTAATAGGCACCAAGAAGTGACAGCCCTTTATCTTTCCTTCACCTTCCT
CTTTTTCTTTAAGTTTTGCTTCCTTTTTAACTTGCTCTTGCACGATCTTTTGCTTTTCCTACCAA
ATCTAGCCATTTACAACATGAATACACAAAATTCCCCAAAAAGAGCTAGAAATAGCACAGCTTTA
TTCATATCTCTCTCCCCCCATCGCCTTTATAACCTAAGCCAATAACAATGAAAGGAGCCCT
Found at i:306453 original size:27 final size:27
Alignment explanation
Indices: 306421--306475 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
306411 TTCACCTTCC
306421 TCTTTATCTTTAGATTTTTCTTCCTTT
1 TCTTTATCTTTAGATTTTTCTTCCTTT
306448 TCTTTATCTTTAGATTTTTCTTCCTTT
1 TCTTTATCTTTAGATTTTTCTTCCTTT
306475 T
1 T
306476 TAACTTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.11, C:0.18, G:0.04, T:0.67
Consensus pattern (27 bp):
TCTTTATCTTTAGATTTTTCTTCCTTT
Found at i:313924 original size:1 final size:1
Alignment explanation
Indices: 313918--313945 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
313908 AACCGAAGTG
313918 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
313946 CTAGTTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:315797 original size:109 final size:109
Alignment explanation
Indices: 315601--315825 Score: 414
Period size: 109 Copynumber: 2.1 Consensus size: 109
315591 TTTGAAAGGC
315601 AGAATGAAGCCATAATAAATATTCAAGAGACAGTGACAAATAATGCAAGAAGGCAGCCACGTGAT
1 AGAA-GAAGCCATAATAAATATTCAAGAGACAGTGACAAATAATGCAAGAAGGCAGCCACGTGAT
* *
315666 AATTCTCCACCTACCCATGGAGATTCTAGTAGCCTTCAAAGAGAA
65 AATTCTCCACCTACCCATGGAGATTCTAGTAGCCCTCAAAAAGAA
315711 AGAAGAAGCCATAATAAATATTCAAGAGACAGTGACAAATAATGCAAGAAGGCAGCCACGTGATA
1 AGAAGAAGCCATAATAAATATTCAAGAGACAGTGACAAATAATGCAAGAAGGCAGCCACGTGATA
*
315776 ATTCTCCACCTACCTATGGAGATTCTAGTAGCCCTCAAAAAGAA
66 ATTCTCCACCTACCCATGGAGATTCTAGTAGCCCTCAAAAAGAA
315820 AGAAGA
1 AGAAGA
315826 GATAGGAGAG
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
109 108 0.96
110 4 0.04
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (109 bp):
AGAAGAAGCCATAATAAATATTCAAGAGACAGTGACAAATAATGCAAGAAGGCAGCCACGTGATA
ATTCTCCACCTACCCATGGAGATTCTAGTAGCCCTCAAAAAGAA
Found at i:315843 original size:12 final size:12
Alignment explanation
Indices: 315826--315861 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
315816 AGAAAGAAGA
315826 GATAGGAGAGAT
1 GATAGGAGAGAT
315838 GATAGGAGGAGA-
1 GATAGGA-GAGAT
315850 GATAGGAGAGAT
1 GATAGGAGAGAT
315862 AGTACAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.18
12 14 0.64
13 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:315920 original size:42 final size:42
Alignment explanation
Indices: 315823--315931 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
315813 AAAAGAAAGA
* * * * *
315823 AGAGATAGGAGAGATGATAGGAGGAGAGATAGGAGAGATAGT
1 AGAGATAGGAGGGATGACAGGAGGAAAGATAAGAGAGATAAT
* **
315865 ACAGATAAAAGGGATGA-AGGGAGGAAAGATAAGAGAGATAAT
1 AGAGATAGGAGGGATGACA-GGAGGAAAGATAAGAGAGATAAT
*
315907 AGAGAGAGGAGGGATGACAGGAGGA
1 AGAGATAGGAGGGATGACAGGAGGA
315932 GGAGAGAAGA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 1 0.02
42 52 0.96
43 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.41, T:0.11
Consensus pattern (42 bp):
AGAGATAGGAGGGATGACAGGAGGAAAGATAAGAGAGATAAT
Found at i:326376 original size:41 final size:40
Alignment explanation
Indices: 326277--326377 Score: 94
Period size: 41 Copynumber: 2.5 Consensus size: 40
326267 TAAGAATTCC
* * * * *
326277 ATTATCACTGAGGATAAGTCTTATTCTTTTAACATACGTA
1 ATTATCACTTAGGATAATTCTTATTCTTTGAAAATACATA
* * * * *
326317 GTTATCATTTTCGAATAATTCTTATTCTTTGAAAATATATA
1 ATTATCA-CTTAGGATAATTCTTATTCTTTGAAAATACATA
326358 ATTATCACTATAGGATAATT
1 ATTATCACT-TAGGATAATT
326378 ACTATGTTAT
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
40 7 0.16
41 38 0.84
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (40 bp):
ATTATCACTTAGGATAATTCTTATTCTTTGAAAATACATA
Found at i:327892 original size:41 final size:41
Alignment explanation
Indices: 327835--327920 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
327825 TATCACTTAA
* * *
327835 TAAGATATATAATTATCA-TTCTAGGATAAATCTTATTCTTT
1 TAAGATATATAATTATCACTT-TAGCATAAATATTATACTTT
* *
327876 TAAGATATGTAATTATCACTTTAGCATAATTATTATACTTT
1 TAAGATATATAATTATCACTTTAGCATAAATATTATACTTT
327917 TAAG
1 TAAG
327921 TTAAGCATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.45
Consensus pattern (41 bp):
TAAGATATATAATTATCACTTTAGCATAAATATTATACTTT
Found at i:329687 original size:18 final size:19
Alignment explanation
Indices: 329656--329704 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
329646 TATTTTTAAT
329656 TTTAATTTATTATTATAAA
1 TTTAATTTATTATTATAAA
*
329675 TTTATTTTA-TATTAT-AA
1 TTTAATTTATTATTATAAA
* *
329692 TTAAATTTTTTAT
1 TTTAATTTATTAT
329705 CTAAATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 8 0.32
18 9 0.36
19 8 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTAATTTATTATTATAAA
Found at i:329701 original size:19 final size:20
Alignment explanation
Indices: 329679--329721 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
329669 TATAAATTTA
329679 TTTTATAT-TATAATTAA-AT
1 TTTTATATCTA-AATTAATAT
329698 TTTT-TATCTAAATTAATAT
1 TTTTATATCTAAATTAATAT
329717 TTTTA
1 TTTTA
329722 ATAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATATCTAAATTAATAT
Found at i:329721 original size:18 final size:18
Alignment explanation
Indices: 329660--329721 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
329650 TTTAATTTTA
329660 ATTTATTATTATAAATT--T
1 ATTT-TTATTAT-AATTAAT
329678 ATTTTATATTATAATTAA-
1 ATTTT-TATTATAATTAAT
329696 ATTTTTTATCTA-AATTAAT
1 A-TTTTTAT-TATAATTAAT
329715 ATTTTTA
1 ATTTTTA
329722 ATAATAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 5 0.13
18 26 0.68
19 7 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATTATAATTAAT
Found at i:329728 original size:3 final size:3
Alignment explanation
Indices: 329720--329755 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
329710 TTAATATTTT
329720 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
329756 GCACATGCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:334823 original size:19 final size:19
Alignment explanation
Indices: 334799--334848 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
334789 AGCAATACAT
334799 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
334818 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
334837 TGTATCGATACA
1 TGTATCGATACA
334849 GTTATTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:337538 original size:13 final size:13
Alignment explanation
Indices: 337505--337538 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
337495 TATTCAGTAC
*
337505 CGATACAGTGTAT
1 CGATACATTGTAT
337518 CGATACATTGTAT
1 CGATACATTGTAT
337531 CGATACAT
1 CGATACAT
337539 GGTGAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:338662 original size:14 final size:14
Alignment explanation
Indices: 338643--338670 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
338633 ATAATATTTT
338643 CTTATTATGTTATG
1 CTTATTATGTTATG
338657 CTTATTATGTTATG
1 CTTATTATGTTATG
338671 AAATGCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (14 bp):
CTTATTATGTTATG
Found at i:344108 original size:20 final size:19
Alignment explanation
Indices: 344083--344157 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
344073 AAAAACCCAG
344083 AATGTATCGATACAATGAAT
1 AATGTATCGATACAAT-AAT
* *
344103 AATGTATTGATACAAATAGT
1 AATGTATCGATAC-AATAAT
* * *
344123 AAATATATCGATACATTTACT
1 -AATGTATCGATACA-ATAAT
*
344144 TATGTATCGATACA
1 AATGTATCGATACA
344158 TTTCTTTTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACAATAAT
Found at i:350545 original size:12 final size:13
Alignment explanation
Indices: 350522--350550 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
350512 TTTGACATTA
350522 AAAAAATAATAAT
1 AAAAAATAATAAT
350535 AAAAAAT-ATAAT
1 AAAAAATAATAAT
350547 AAAA
1 AAAA
350551 TAAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:350545 original size:15 final size:14
Alignment explanation
Indices: 350520--350563 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
350510 TATTTGACAT
350520 TAAAAAAATAATAA
1 TAAAAAAATAATAA
350534 TAAAAAATATAATAA
1 TAAAAAA-ATAATAA
* *
350549 AATAAAAAAGAATAA
1 TA-AAAAAATAATAA
350564 AATTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.27
15 14 0.54
16 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAAAAAATAATAA
Found at i:350562 original size:20 final size:21
Alignment explanation
Indices: 350529--350572 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
350519 TTAAAAAAAT
*
350529 AATAATAAAAAATATAA-TAA
1 AATAATAAAAAATAAAATTAA
350549 AATAA-AAAAGAATAAAATTAA
1 AATAATAAAA-AATAAAATTAA
350570 AAT
1 AAT
350573 TTAGTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (21 bp):
AATAATAAAAAATAAAATTAA
Found at i:350720 original size:62 final size:62
Alignment explanation
Indices: 350642--350762 Score: 206
Period size: 62 Copynumber: 2.0 Consensus size: 62
350632 CCAAATTTGG
*
350642 TGGATTTCATGCTTAATTTACTGCCACTTAAGCTTTCTAGGTGTCATTGCATTGCATTGGAT
1 TGGATTTCATGCTTAATTTACTGCCACCTAAGCTTTCTAGGTGTCATTGCATTGCATTGGAT
* * *
350704 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTGTATTG
1 TGGATTTCATGCTTAATTTACTGCCACCTAAGCTTTCTAGGTGTCATTGCATTGCATTG
350763 CATTTCATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (62 bp):
TGGATTTCATGCTTAATTTACTGCCACCTAAGCTTTCTAGGTGTCATTGCATTGCATTGGAT
Found at i:350782 original size:12 final size:12
Alignment explanation
Indices: 350765--350799 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
350755 TTGTATTGCA
350765 TTTCATGCATGC
1 TTTCATGCATGC
350777 TTTCATGCATGC
1 TTTCATGCATGC
*
350789 TTTCACGCATG
1 TTTCATGCATG
350800 GAATCAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (12 bp):
TTTCATGCATGC
Found at i:350969 original size:12 final size:12
Alignment explanation
Indices: 350939--350977 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
350929 AAATCATACA
350939 TTTCATGCATGC
1 TTTCATGCATGC
*
350951 -CTCATGCATGC
1 TTTCATGCATGC
*
350962 TTTCATGCATGT
1 TTTCATGCATGC
350974 TTTC
1 TTTC
350978 GCACTTGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (12 bp):
TTTCATGCATGC
Found at i:369088 original size:20 final size:20
Alignment explanation
Indices: 369062--369117 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
369052 AAAAAGATAG
*
369062 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
369082 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
369102 AATGTATCGATACATT
1 AATGTATCGATACATT
369118 TGGGCATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:373095 original size:79 final size:79
Alignment explanation
Indices: 372964--373132 Score: 212
Period size: 79 Copynumber: 2.1 Consensus size: 79
372954 ACGACGGGGC
* * * * ** * *
372964 TGGAGTACCCCTGATTATGGAAAATCGATGTTCTGGAAATAAAATCGGGGTTGGAGTATCCCTTT
1 TGGAGTATCCCTAATTATAGAAAATCGATGTTCTGAAAATAAAATCAAGGTTGGAGTATCCCCTC
**
373029 GGAAATAACAGGGT
66 AAAAATAACAGGGT
* * *
373043 TGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCAAGGTTGGAGTATCCCCTC
1 TGGAGTATCCCTAATTATAGAAAATCGATGTTCTGAAAATAAAATCAAGGTTGGAGTATCCCCTC
*
373108 AAAAATAACGGGGT
66 AAAAATAACAGGGT
373122 TGGAGTATCCC
1 TGGAGTATCCC
373133 CGCGAAAATA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
TGGAGTATCCCTAATTATAGAAAATCGATGTTCTGAAAATAAAATCAAGGTTGGAGTATCCCCTC
AAAAATAACAGGGT
Found at i:373125 original size:28 final size:28
Alignment explanation
Indices: 373091--373162 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
373081 ATAAAATCAA
*
373091 GGTTGGAGTATCCCCTCAAAAATAACGG
1 GGTTGGAGTATCCCCGCAAAAATAACGG
*
373119 GGTTGGAGTATCCCCGCGAAAATAACGG
1 GGTTGGAGTATCCCCGCAAAAATAACGG
373147 GGTTGGAGTATCCCCG
1 GGTTGGAGTATCCCCG
373163 ATTGTGAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGCAAAAATAACGG
Found at i:373230 original size:28 final size:27
Alignment explanation
Indices: 373197--373269 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
373187 AATAAAGCCA
**
373197 GGGTTGGAGTATCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCGAGG-AATAACG
* * *
373225 GGGTTGGAGTATTCCCGATGATTAACG
1 GGGTTGGAGTATCCCCGAGGAATAACG
*
373252 GGGTTGGAGTGTCCCCGA
1 GGGTTGGAGTATCCCCGA
373270 TTGTGAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.25
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGGAATAACG
Found at i:373298 original size:107 final size:108
Alignment explanation
Indices: 373009--373319 Score: 337
Period size: 107 Copynumber: 2.9 Consensus size: 108
372999 GAAATAAAAT
*** * * ** * *
373009 CGGGGTTGGAGTATCCCTTTGGAAATAACAGGGTTGGAGTATCCCTAATTAT-AGAAAATTGGTG
1 CGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGA-AAAATTAGTG
* *
373073 -TTTTGAAAATAAAATCAAGGTTGGAGTATCCCCTCAAAAATAA
65 TTTTTGGAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAA
* * * *
373116 CGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGT
* ** **
373181 TTTAGG-AATAAAGCCAGGGTTGGAGTATCCCCTCGGAAATAA
66 TTTTGGAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAA
* * * *
373223 CGGGGTTGGAGTAT-TCC-CGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGAAAAATTAGTG
1 CGGGGTTGGAGTATCCCCGCGA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTG
373286 TTTTTGGAAATAAAATC-GGAGTTGGAGTATCCCC
65 TTTTTGGAAATAAAATCAGG-GTTGGAGTATCCCC
373320 GATTATAGAA
Statistics
Matches: 168, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
105 3 0.02
106 45 0.27
107 115 0.68
108 5 0.03
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (108 bp):
CGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGT
TTTTGGAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAA
Found at i:373485 original size:153 final size:154
Alignment explanation
Indices: 373254--373538 Score: 421
Period size: 153 Copynumber: 1.9 Consensus size: 154
373244 GATTAACGGG
* * * * *
373254 GTTGGAGTGTCCCCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
1 GTTGGAGTATCCACGATTGTGAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTACCCC
* *
373319 CGATTATAGAAAATTAGTGTTTT-GAAAATAAAACCGGGGTTAGAGTATCCCCAATTGTGAAAAA
66 CGATTATAGAAAATTAGTGTTTTAG-AAATAAAACCGGGGTTAGAGTACCCCCAATTATGAAAAA
373383 TTGGTGTTTCGAAAATAAAATCGGA
130 TTGGTGTTTCGAAAATAAAATCGGA
* * *
373408 GTTGGAGTATCCACGATTGTGGAAAATTAGTG-TTTTAGAAATAATACCGGGGTTGGAGTACCCC
1 GTTGGAGTATCCACGATTGTGAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTACCCC
* * * *
373472 CGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTTGAGTACCCCCGATTATGAAAAAT
66 CGATTATAGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTAGAGTACCCCCAATTATGAAAAAT
373537 TG
131 TG
373539 AGAAACTTAA
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
153 86 0.74
154 30 0.26
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (154 bp):
GTTGGAGTATCCACGATTGTGAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTACCCC
CGATTATAGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTAGAGTACCCCCAATTATGAAAAAT
TGGTGTTTCGAAAATAAAATCGGA
Found at i:373536 original size:51 final size:51
Alignment explanation
Indices: 373250--373537 Score: 348
Period size: 51 Copynumber: 5.6 Consensus size: 51
373240 CGATGATTAA
* * *
373250 CGGGGTTGGAGTGTCCCCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTG-TTTTAGAAATAAAAC
* *
373302 CGGAGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGA-AAAATTAGTGTTTTAG-AAATAAAAC
* * * * *
373353 CGGGGTTAGAGTATCCCCAATTGTGAAAAATTGGTG-TTTCGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAG-AAATAAAAC
* * * *
373404 CGGAGTTGGAGTATCCACGATTGTGGAAAATTAGTGTTTTAGAAATAATAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
* *
373455 CGGGGTTGGAGTACCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
* * *
373506 CGGGGTTTGAGTACCCCCGATTATGAAAAATT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATT
373538 GAGAAACTTA
Statistics
Matches: 205, Mismatches: 26, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
50 4 0.02
51 165 0.80
52 36 0.18
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
Found at i:375789 original size:20 final size:20
Alignment explanation
Indices: 375764--375814 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
375754 TGCCTGAATG
375764 TATCGATACATTGTAAAATA
1 TATCGATACATTGTAAAATA
*
375784 TATCGATACATTGTAAAATG
1 TATCGATACATTGTAAAATA
375804 TATCGATACAT
1 TATCGATACAT
375815 CTGGGTAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTGTAAAATA
Found at i:375870 original size:13 final size:13
Alignment explanation
Indices: 375852--375877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
375842 ACAAAGATCG
375852 ATGTATCGATACA
1 ATGTATCGATACA
375865 ATGTATCGATACA
1 ATGTATCGATACA
375878 TTTCATTGGC
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:375933 original size:19 final size:21
Alignment explanation
Indices: 375909--375960 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
375899 AGCGATACAC
*
375909 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
375928 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
375949 TGTATCGATACA
1 TGTATCGATACA
375961 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:384018 original size:20 final size:19
Alignment explanation
Indices: 383976--384019 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
383966 GTAGAACGGG
383976 TTTTTCCCATCATGTCTGA
1 TTTTTCCCATCATGTCTGA
383995 TTTTTCCCATCATGTCTGA
1 TTTTTCCCATCATGTCTGA
384014 TTTTTC
1 TTTTTC
384020 TTTGAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.14, C:0.25, G:0.09, T:0.52
Consensus pattern (19 bp):
TTTTTCCCATCATGTCTGA
Found at i:387792 original size:4 final size:4
Alignment explanation
Indices: 387783--387942 Score: 126
Period size: 4 Copynumber: 40.2 Consensus size: 4
387773 GCAGCATATT
* * * * * * * * * *
387783 AAAG AAAG AAAC AAAG GAAG GAGG GAAG GAAG GAAG GAAG GAAG ATAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* * * * *
387831 AAAG AAGG AAAG AAAG AAAG ATAG ATAG ATAG AAAG AAAG AAAG GAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* * * *
387879 ACAG AAAG AAAG AAAG ATAG AAAG AAAG AAAG GAAG AGAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
387927 -AA- AAAG AAAAG AAAG A
1 AAAG AAAG -AAAG AAAG A
387943 TTACCCAACA
Statistics
Matches: 131, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
3 4 0.03
4 123 0.94
5 4 0.03
ACGTcount: A:0.64, C:0.01, G:0.31, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:388660 original size:3 final size:3
Alignment explanation
Indices: 388624--388673 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
388614 ATAAAATCTG
* *
388624 AAT AAT TAT AA- AAT AA- AAT AGT AAAT ATAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT AAT AAT AAT
388669 AAT AA
1 AAT AA
388674 AGATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:388705 original size:13 final size:13
Alignment explanation
Indices: 388687--388731 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 13
388677 TATATATTTT
388687 AATTTAAAAAATA
1 AATTTAAAAAATA
388700 AATTTAAAAAATTA
1 AATTTAAAAAA-TA
388714 ACATCTTAAAAAATA
1 A-AT-TTAAAAAATA
388729 AAT
1 AAT
388732 CATAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.38
14 5 0.17
15 5 0.17
16 8 0.28
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTTAAAAAATA
Found at i:389803 original size:18 final size:18
Alignment explanation
Indices: 389780--389820 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
389770 TTTTATGTTA
389780 AAATATTTTAATAAATTT
1 AAATATTTTAATAAATTT
* *
389798 AAATA-TTTAGTGAATTT
1 AAATATTTTAATAAATTT
389815 AAATAT
1 AAATAT
389821 CATGTAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
AAATATTTTAATAAATTT
Found at i:390315 original size:19 final size:18
Alignment explanation
Indices: 390289--390327 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
390279 ATTTTATAGT
390289 TTTATATTTTATTTAAAA
1 TTTATATTTTATTTAAAA
*
390307 TTTATTATTTTATTTAGAA
1 TTTA-TATTTTATTTAAAA
390326 TT
1 TT
390328 AATTTAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATATTTTATTTAAAA
Found at i:390440 original size:21 final size:21
Alignment explanation
Indices: 390426--390467 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
390416 AATATATATT
390426 AAATATTTAAAAATAATTAAA
1 AAATATTTAAAAATAATTAAA
390447 AAATATTTAAATAAATAATTA
1 AAATATTT-AA-AAATAATTA
390468 CTATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATTTAAAAATAATTAAA
Found at i:390448 original size:11 final size:11
Alignment explanation
Indices: 390434--390467 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
390424 TTAAATATTT
390434 AAAAATAATTA
1 AAAAATAATTA
*
390445 AAAAATATTTA
1 AAAAATAATTA
390456 AATAAATAATTA
1 AA-AAATAATTA
390468 CTATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATAATTA
Found at i:390726 original size:19 final size:18
Alignment explanation
Indices: 390669--390738 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 18
390659 ATATAATACA
*
390669 TATTGAAAT-ATTAAAATT
1 TATTTAAATAATTAAAA-T
* *
390687 TATTTAAATAAATAATTAT
1 TATTTAAATAATTAA-AAT
390706 TATTTAATATAATTAAAAT
1 TATTTAA-ATAATTAAAAT
*
390725 TATATTAAAAAATT
1 TAT-TTAAATAATT
390739 TCCAAAATCC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 8 0.19
19 22 0.52
20 12 0.29
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
TATTTAAATAATTAAAAT
Found at i:391227 original size:22 final size:21
Alignment explanation
Indices: 391188--391237 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
391178 AATATTTTTT
* *
391188 AATTTAAGTTTAAGTTAATTA
1 AATTTAAGGTTAAATTAATTA
391209 AATTTAATGGTTAAATTAATTA
1 AATTTAA-GGTTAAATTAATTA
391231 AATTTAA
1 AATTTAA
391238 ATAAATCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (21 bp):
AATTTAAGGTTAAATTAATTA
Found at i:391318 original size:16 final size:15
Alignment explanation
Indices: 391299--391332 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
391289 TTTATTAATT
391299 TTAAAATTAAATCAAA
1 TTAAAATTAAAT-AAA
*
391315 TTAAATTTAAATAAA
1 TTAAAATTAAATAAA
391330 TTA
1 TTA
391333 TTTAATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAAATTAAATAAA
Found at i:391828 original size:18 final size:18
Alignment explanation
Indices: 391805--391840 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
391795 TAGATTATCC
*
391805 TTTTAAAAAATATTTATA
1 TTTTAAAAAATATGTATA
*
391823 TTTTAAACAATATGTATA
1 TTTTAAAAAATATGTATA
391841 CCATAAGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTAAAAAATATGTATA
Found at i:394172 original size:28 final size:28
Alignment explanation
Indices: 394132--394187 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
394122 TACACAACTC
394132 TTCAACGATGATATTTTAAGGGGTTTTT
1 TTCAACGATGATATTTTAAGGGGTTTTT
394160 TTCAACGATGATATTTTAAGGGGTTTTT
1 TTCAACGATGATATTTTAAGGGGTTTTT
394188 AAGTTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (28 bp):
TTCAACGATGATATTTTAAGGGGTTTTT
Found at i:395096 original size:16 final size:16
Alignment explanation
Indices: 395075--395105 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
395065 TTGATCTCAT
395075 AAATTAAAGTATAGAA
1 AAATTAAAGTATAGAA
395091 AAATTAAAGTATAGA
1 AAATTAAAGTATAGA
395106 GATACTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (16 bp):
AAATTAAAGTATAGAA
Found at i:403107 original size:52 final size:52
Alignment explanation
Indices: 402963--403087 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
402953 ATATGAAAAG
* *
402963 TTGCTTGCATGTATCGATACATTTTATAGTTTATCGATACATCTGGGCAAAT
1 TTGCTTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
*
403015 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCTTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
403067 TTGCTTGCATGTATCGATACA
1 TTGCTTGCATGTATCGATACA
403088 AAGATCAATG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (52 bp):
TTGCTTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
Found at i:403111 original size:13 final size:13
Alignment explanation
Indices: 403093--403118 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
403083 ATACAAAGAT
403093 CAATGTATCGATA
1 CAATGTATCGATA
403106 CAATGTATCGATA
1 CAATGTATCGATA
403119 TATTTGAGTA
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):
CAATGTATCGATA
Found at i:403203 original size:13 final size:13
Alignment explanation
Indices: 403185--403209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
403175 CAAAAAAAAA
403185 TGTATCGATACAT
1 TGTATCGATACAT
403198 TGTATCGATACA
1 TGTATCGATACA
403210 ACACTTTATG
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:405420 original size:34 final size:34
Alignment explanation
Indices: 405361--405430 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
405351 TCGATAGTTT
*
405361 TTCCTCTCCAGCAGCTTCACTTGCTGCTGTCTTC
1 TTCCTCTCCAGCAACTTCACTTGCTGCTGTCTTC
* *
405395 TTCC-CTCGAGCAACTTCACATTGCTGCTGTTTTC
1 TTCCTCTCCAGCAACTTCAC-TTGCTGCTGTCTTC
405429 TT
1 TT
405431 TTCTGTTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 13 0.41
34 19 0.59
ACGTcount: A:0.11, C:0.34, G:0.14, T:0.40
Consensus pattern (34 bp):
TTCCTCTCCAGCAACTTCACTTGCTGCTGTCTTC
Found at i:405682 original size:22 final size:20
Alignment explanation
Indices: 405653--405708 Score: 51
Period size: 22 Copynumber: 2.8 Consensus size: 20
405643 GCTTCGGGCT
405653 GCTA-TTGGTTGCTAGAGCG
1 GCTATTTGGTTGCTAGAGCG
* * * *
405672 GCTACTGTTGGCTACTGGAGCT
1 GCTA-T-TTGGTTGCTAGAGCG
405694 GCTATTTGGTTGCTA
1 GCTATTTGGTTGCTA
405709 AAGATGCTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
19 4 0.15
20 7 0.26
21 1 0.04
22 15 0.56
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.36
Consensus pattern (20 bp):
GCTATTTGGTTGCTAGAGCG
Found at i:405850 original size:22 final size:22
Alignment explanation
Indices: 405789--405858 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
405779 TGGGCTGCTA
* * **
405789 TTGGTTGCCGGAGTGGCAATTG
1 TTGGTTGCTGGAGCGGCTGTTG
*
405811 TTGGTTGCTAGAGCGGCTGTTG
1 TTGGTTGCTGGAGCGGCTGTTG
*
405833 TTGGTTGCTGGAGCGGCTGCTG
1 TTGGTTGCTGGAGCGGCTGTTG
405855 TTGG
1 TTGG
405859 CTTACATTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.09, C:0.14, G:0.43, T:0.34
Consensus pattern (22 bp):
TTGGTTGCTGGAGCGGCTGTTG
Found at i:406522 original size:58 final size:58
Alignment explanation
Indices: 406451--406577 Score: 168
Period size: 58 Copynumber: 2.2 Consensus size: 58
406441 TGCTTTGTTC
* * *
406451 TGCTTCATGTGTTCTTGGCCTTCATCTTTTTCCATG-TTTCTAGCTTTTGCCT-GTGTAT
1 TGCTTCACGTGTTCTTGGCCTTCATCTTCTCCCATGTTTTC-AGCTTTT-CCTCGTGTAT
* *
406509 TGCTTCACGTGTTCTTGGCTTTCATCTTCTCCCATGTTTTGCAGCTTTTTCTCGTGTAT
1 TGCTTCACGTGTTCTTGGCCTTCATCTTCTCCCATGTTTT-CAGCTTTTCCTCGTGTAT
406568 TGCTTCACGT
1 TGCTTCACGT
406578 TACTTTGTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
58 34 0.56
59 26 0.43
60 1 0.02
ACGTcount: A:0.09, C:0.24, G:0.17, T:0.50
Consensus pattern (58 bp):
TGCTTCACGTGTTCTTGGCCTTCATCTTCTCCCATGTTTTCAGCTTTTCCTCGTGTAT
Found at i:406737 original size:9 final size:9
Alignment explanation
Indices: 406725--406781 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
406715 TTTTTTAGGA
406725 TTTTGATTT
1 TTTTGATTT
406734 TTTTGATTT
1 TTTTGATTT
* *
406743 AATTTTTA-GT
1 --TTTTGATTT
*
406753 TTTTGATTA
1 TTTTGATTT
*
406762 TTTTAATTT
1 TTTTGATTT
406771 TTTTGATTT
1 TTTTGATTT
406780 TT
1 TT
406782 AATTTACTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
8 5 0.14
9 26 0.70
10 1 0.03
11 5 0.14
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTGATTT
Found at i:406742 original size:28 final size:27
Alignment explanation
Indices: 406709--406774 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
406699 ATGCATTTCA
*
406709 TGATTTTTTTTTAGGATTTTGATTTTTT
1 TGATTTTTTTTTA-GATTTTGATTATTT
* *
406737 TGATTTAATTTTTAGTTTTTGATTATTT
1 TGATTT-TTTTTTAGATTTTGATTATTT
*
406765 TAATTTTTTT
1 TGATTTTTTT
406775 GATTTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 3 0.09
28 23 0.72
29 6 0.19
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (27 bp):
TGATTTTTTTTTAGATTTTGATTATTT
Found at i:406781 original size:16 final size:18
Alignment explanation
Indices: 406724--406786 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 18
406714 TTTTTTTAGG
*
406724 ATTTTGATTTTTTTGATTT
1 ATTTTAATTTTTTTGA-TT
* *
406743 AATTTTTA-GTTTTTGATT
1 -ATTTTAATTTTTTTGATT
406761 ATTTTAATTTTTTTGA-T
1 ATTTTAATTTTTTTGATT
406778 -TTTTAATTT
1 ATTTTAATTT
406787 ACTTTTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 9 0.24
17 7 0.18
18 9 0.24
19 7 0.18
20 6 0.16
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (18 bp):
ATTTTAATTTTTTTGATT
Found at i:406793 original size:37 final size:37
Alignment explanation
Indices: 406724--406798 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
406714 TTTTTTTAGG
* *
406724 ATTTTGATTTTTTTGATTTAATTTTTA-GTTTTTGATT
1 ATTTTAATTTTTTTGATTTAA-TTTTACTTTTTTGATT
406761 ATTTTAATTTTTTTGATTTTTAA-TTTACTTTTTTGATT
1 ATTTTAATTTTTTTGA--TTTAATTTTACTTTTTTGATT
406799 GACTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 19 0.58
38 9 0.27
39 5 0.15
ACGTcount: A:0.20, C:0.01, G:0.08, T:0.71
Consensus pattern (37 bp):
ATTTTAATTTTTTTGATTTAATTTTACTTTTTTGATT
Found at i:407828 original size:32 final size:32
Alignment explanation
Indices: 407783--407885 Score: 111
Period size: 32 Copynumber: 3.2 Consensus size: 32
407773 CATTGGGCCT
*
407783 AGAAGGAGATGCCACCAACTTGTATGGGCTTTTG
1 AGAAGG-GTTGCCACCAACTTGTATGGGC-TTTG
*
407817 A-AAGGGTTGCCACCAGCTTG-AGTGGGCTTTG
1 AGAAGGGTTGCCACCAACTTGTA-TGGGCTTTG
* * * *
407848 AGAAGGGTTGCCACTAACTTGTGTGGGATTTA
1 AGAAGGGTTGCCACCAACTTGTATGGGCTTTG
407880 AGAAGG
1 AGAAGG
407886 TTTCTCCATT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 6 0.10
32 48 0.81
33 4 0.07
34 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (32 bp):
AGAAGGGTTGCCACCAACTTGTATGGGCTTTG
Found at i:408052 original size:32 final size:32
Alignment explanation
Indices: 408004--408111 Score: 164
Period size: 32 Copynumber: 3.4 Consensus size: 32
407994 ACTAGCTCGA
* * *
408004 GTGGGCTTTGAGAAGGGTTACCACCTACTTGT
1 GTGGGCTTTGAAAAGGGTTGCCACCGACTTGT
*
408036 GTGAGCTTTGAAAAGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAAAGGGTTGCCACCGACTTGT
408068 GTGGGCTTT-AAGAAGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAA-AAGGGTTGCCACCGACTTGT
408100 GTGGGCTTTGAA
1 GTGGGCTTTGAA
408112 GAGGTGCCAC
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 2 0.03
32 65 0.94
33 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (32 bp):
GTGGGCTTTGAAAAGGGTTGCCACCGACTTGT
Found at i:418024 original size:17 final size:17
Alignment explanation
Indices: 418002--418037 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
417992 AAAAGAAGAG
418002 CATAACTAGTACTTCCC
1 CATAACTAGTACTTCCC
*
418019 CATAACTGGTACTTCCC
1 CATAACTAGTACTTCCC
418036 CA
1 CA
418038 CATCTGTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.28
Consensus pattern (17 bp):
CATAACTAGTACTTCCC
Found at i:427367 original size:51 final size:52
Alignment explanation
Indices: 427299--427418 Score: 170
Period size: 51 Copynumber: 2.3 Consensus size: 52
427289 TTTGAAAAGA
*
427299 AAATGTATCGATACATTTTTCATTGTATCCATACATTCTG-GGTTTTGACCC
1 AAATATATCGATACATTTTTCATTGTATCCATACATTCTGCGGTTTTGACCC
* * * * *
427350 AATTATATTGATACATTTTTCATTGTATCGATACATTTTGCGTTTTTGACCC
1 AAATATATCGATACATTTTTCATTGTATCCATACATTCTGCGGTTTTGACCC
*
427402 AAATGTATCGATACATT
1 AAATATATCGATACATT
427419 CAGTTAAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 35 0.59
52 24 0.41
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (52 bp):
AAATATATCGATACATTTTTCATTGTATCCATACATTCTGCGGTTTTGACCC
Found at i:427631 original size:14 final size:14
Alignment explanation
Indices: 427612--427641 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
427602 ATCATTACCT
427612 CATCTTTATCATCA
1 CATCTTTATCATCA
427626 CATCTTTATCATCA
1 CATCTTTATCATCA
427640 CA
1 CA
427642 GTCTAGGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (14 bp):
CATCTTTATCATCA
Found at i:431008 original size:20 final size:20
Alignment explanation
Indices: 430971--431014 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
430961 AGATAAAGAG
*
430971 TTTAAAGTATTTAAAAAATT
1 TTTAAAGTATTTAAAAAATA
**
430991 TTTAAAGTATTTTCAAAATA
1 TTTAAAGTATTTAAAAAATA
431011 TTTA
1 TTTA
431015 TTTTAAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTAAAGTATTTAAAAAATA
Found at i:431454 original size:20 final size:21
Alignment explanation
Indices: 431415--431454 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
431405 AATACATAAA
*
431415 TTTCTTTTTTTCTTTACTTCT
1 TTTCTTTTTCTCTTTACTTCT
*
431436 TTTCTTTTTCT-TTTCCTTC
1 TTTCTTTTTCTCTTTACTTC
431455 CCTTCTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCTTTTTCTCTTTACTTCT
Found at i:432354 original size:144 final size:144
Alignment explanation
Indices: 432235--432503 Score: 373
Period size: 144 Copynumber: 1.9 Consensus size: 144
432225 GATACGATAT
*
432235 GAAAAATAAT-ATGGACA-AAATATAAATAGATAAACGTGTCAAAATTTGTATAAAATAAATTAT
1 GAAAAAT-ATCATGGACATAAA-ATAAATAGA-AAACGTGTCAAAATTTATATAAAATAAATTAT
** * * * *
432298 TAACT-TATCTAAATTTATATAAATATATAATATTTTGCATATGATTATGATATGAAAAAGTAAC
63 TAA-TGTATAAAAATTCATATAAATATATAATATCTTGAATACGATTATGATATGAAAAAGTAAC
*
432362 ATGAACATGACATACCAA
127 ATGAAAATGACATACCAA
* *
432380 GAAAAATATCATGGACATAAAATGAATAGAAAACGTGTTAAAATTTATATAAAATAAATTATTAA
1 GAAAAATATCATGGACATAAAATAAATAGAAAACGTGTCAAAATTTATATAAAATAAATTATTAA
**
432445 TGTATAAAAATTCATATAAATATATAATATCTTGAATACGATTATGATACCAAAAAGTA
66 TGTATAAAAATTCATATAAATATATAATATCTTGAATACGATTATGATATGAAAAAGTA
432504 TAATAATACG
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
143 1 0.01
144 84 0.76
145 22 0.20
146 3 0.03
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (144 bp):
GAAAAATATCATGGACATAAAATAAATAGAAAACGTGTCAAAATTTATATAAAATAAATTATTAA
TGTATAAAAATTCATATAAATATATAATATCTTGAATACGATTATGATATGAAAAAGTAACATGA
AAATGACATACCAA
Found at i:432699 original size:2 final size:2
Alignment explanation
Indices: 432692--432716 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
432682 TGTCAAAATC
432692 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
432717 TTAAAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:432929 original size:29 final size:29
Alignment explanation
Indices: 432897--432987 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
432887 ATATAATAAT
*
432897 AATACTTTAAATGTAATTATAATACAAAA
1 AATACTTTAAATATAATTATAATACAAAA
* * *
432926 AATA-TTTACATAATAATAATATAAATGC-ATA
1 AATACTTTAAAT-ATAAT--TAT-AATACAAAA
*
432957 AATACTTTAAATATAATTATAACACAAAA
1 AATACTTTAAATATAATTATAATACAAAA
432986 AA
1 AA
432988 CCTATACATA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
28 9 0.19
29 15 0.31
31 14 0.29
32 10 0.21
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (29 bp):
AATACTTTAAATATAATTATAATACAAAA
Found at i:435315 original size:6 final size:6
Alignment explanation
Indices: 435306--435337 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
435296 ATGAAAATGC
435306 TCATTG TCATTG TCATTG TCATTG TCATTG TC
1 TCATTG TCATTG TCATTG TCATTG TCATTG TC
435338 TTTCCTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (6 bp):
TCATTG
Found at i:435473 original size:17 final size:17
Alignment explanation
Indices: 435453--435516 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
435443 ATTAAATTTG
435453 ATAATTTTAAAAATAAT
1 ATAATTTTAAAAATAAT
* *
435470 ATAATTATATAATATAA-
1 ATAATTTTA-AAAATAAT
*
435487 ATAA-ATTAAAAAT-AT
1 ATAATTTTAAAAATAAT
*
435502 ATTAATTTTTAAAAT
1 A-TAATTTTAAAAAT
435517 TAATTTATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
14 1 0.03
15 5 0.14
16 5 0.14
17 19 0.53
18 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATTTTAAAAATAAT
Found at i:442897 original size:19 final size:16
Alignment explanation
Indices: 442860--442890 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
442850 TAGAAAAAGT
442860 TATTATTAAAGAGTGC
1 TATTATTAAAGAGTGC
442876 TATTATTAAAGAGTG
1 TATTATTAAAGAGTG
442891 TTGCTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (16 bp):
TATTATTAAAGAGTGC
Found at i:449475 original size:2 final size:2
Alignment explanation
Indices: 449468--449494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
449458 TTTAATTATT
449468 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
449495 CGTTCGGCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:450094 original size:26 final size:23
Alignment explanation
Indices: 450065--450111 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 23
450055 TTACAGCAAT
450065 AAATATAAAATGAAAATAATTATTAA
1 AAATAT-AAAT-AAAAT-ATTATTAA
*
450091 AAATATTAATAAAATATTATT
1 AAATATAAATAAAATATTATT
450112 TACAAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 3 0.15
26 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATATAAATAAAATATTATTAA
Found at i:450228 original size:40 final size:41
Alignment explanation
Indices: 450174--450250 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
450164 TAAAAAATAC
450174 TATTTATATATTTATTTAAATAT-TTTAATTA-ATTAACTAT
1 TATTTATATATTTATTTAAATATATTT-ATTATATTAACTAT
450214 TATTTATATATTTATTTAAATATATTTATTATATTAA
1 TATTTATATATTTATTTAAATATATTTATTATATTAA
450251 ATAAATGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
40 27 0.77
41 8 0.23
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (41 bp):
TATTTATATATTTATTTAAATATATTTATTATATTAACTAT
Found at i:450414 original size:22 final size:22
Alignment explanation
Indices: 450388--450431 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
450378 GGCTATAACT
450388 GCACTGGTAGGGCGCAAACTAA
1 GCACTGGTAGGGCGCAAACTAA
450410 GCACTGGTAGGGCGCAAACTAA
1 GCACTGGTAGGGCGCAAACTAA
450432 ACGCACCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.32, T:0.14
Consensus pattern (22 bp):
GCACTGGTAGGGCGCAAACTAA
Found at i:451261 original size:26 final size:25
Alignment explanation
Indices: 451225--451292 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
451215 TTAACTGTTT
*
451225 TTTTTTAATTTAAAAATAAGATAATA
1 TTTTTAAATTTAAAAATAA-ATAATA
* *
451251 TTTTTAAATTTAAAATTGAATAATA
1 TTTTTAAATTTAAAAATAAATAATA
* *
451276 TTTTTAAAATTCAAAAT
1 TTTTTAAATTTAAAAAT
451293 TATCTTATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 20 0.56
26 16 0.44
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (25 bp):
TTTTTAAATTTAAAAATAAATAATA
Found at i:451265 original size:25 final size:25
Alignment explanation
Indices: 451225--451292 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
451215 TTAACTGTTT
*
451225 TTTTTTAATTTAAAAATA-AGATAATA
1 TTTTTAAATTT-AAAATAGA-ATAATA
*
451251 TTTTTAAATTTAAAATTGAATAATA
1 TTTTTAAATTTAAAATAGAATAATA
*
451276 TTTTTAAAATTCAAAAT
1 TTTTT-AAATTTAAAAT
451293 TATCTTATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (25 bp):
TTTTTAAATTTAAAATAGAATAATA
Found at i:453862 original size:20 final size:21
Alignment explanation
Indices: 453837--453888 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
453827 AGAAAAATTA
453837 TATTGATACATAAGTG-AATG
1 TATTGATACATAAGTGTAATG
**
453857 TATTGATACATACTTGTAATG
1 TATTGATACATAAGTGTAATG
*
453878 TATCGATACAT
1 TATTGATACAT
453889 TTTTCTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
TATTGATACATAAGTGTAATG
Found at i:454369 original size:19 final size:21
Alignment explanation
Indices: 454321--454376 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
454311 AATTTCTACA
454321 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
454342 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
454362 -TTTGTATCGATACAA
1 ATTTGTATCGATACAA
454377 TGTATCGATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 12 0.41
20 3 0.10
21 14 0.48
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:454382 original size:13 final size:13
Alignment explanation
Indices: 454364--454389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
454354 ACATAAGTTT
454364 TGTATCGATACAA
1 TGTATCGATACAA
454377 TGTATCGATACAA
1 TGTATCGATACAA
454390 AACTACTTTG
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):
TGTATCGATACAA
Found at i:454481 original size:20 final size:20
Alignment explanation
Indices: 454416--454490 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
454406 ACCAAGGAAA
* * *
454416 TGTATTGATACATTAATAAA
1 TGTATCGATACATTTATAAT
454436 TGTATCGATACATGCTTCA-AAT
1 TGTATCGATACAT--TT-ATAAT
*
454458 TGTATCGATACATTTATCAT
1 TGTATCGATACATTTATAAT
454478 TGTATCGATACAT
1 TGTATCGATACAT
454491 CTGGGTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 29 0.62
22 16 0.34
23 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTATAAT
Found at i:458383 original size:13 final size:13
Alignment explanation
Indices: 458365--458390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
458355 TACACCAAGT
458365 ATGTATCGATACA
1 ATGTATCGATACA
458378 ATGTATCGATACA
1 ATGTATCGATACA
458391 CAAAAAATTG
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:458388 original size:32 final size:33
Alignment explanation
Indices: 458347--458410 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
458337 TAGCCAAACT
* **
458347 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
458379 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
458411 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:461729 original size:21 final size:21
Alignment explanation
Indices: 461703--461755 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
461693 CATGTTGCAT
461703 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACTTGAAAAAGA
461724 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACTTGAAAAAGA
461745 TGTATCGATAC
1 TGTATCGATAC
461756 AAGCCATTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACTTGAAAAAGA
Found at i:461826 original size:13 final size:13
Alignment explanation
Indices: 461808--461832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
461798 ACACACAGTA
461808 TGTATCGATACAT
1 TGTATCGATACAT
461821 TGTATCGATACA
1 TGTATCGATACA
461833 CCATAAAATG
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:471754 original size:8 final size:8
Alignment explanation
Indices: 471741--471830 Score: 83
Period size: 8 Copynumber: 10.8 Consensus size: 8
471731 ATTCGAACCA
471741 AAAAAAAC
1 AAAAAAAC
471749 AAAAAAAC
1 AAAAAAAC
471757 AAAAAAACC
1 AAAAAAA-C
471766 AAGAAAAA-
1 AA-AAAAAC
*
471774 AACAAAGATAG
1 AA-AAA-A-AC
471785 AAAAAAAC
1 AAAAAAAC
* *
471793 CAAAAACC
1 AAAAAAAC
*
471801 AAAAAAAT
1 AAAAAAAC
471809 AAAAAAAC
1 AAAAAAAC
*
471817 AAACAAAC
1 AAAAAAAC
471825 AAAAAA
1 AAAAAA
471831 GGGGTCCAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
8 51 0.76
9 5 0.07
10 9 0.13
11 2 0.03
ACGTcount: A:0.81, C:0.13, G:0.03, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:471761 original size:17 final size:17
Alignment explanation
Indices: 471739--471830 Score: 73
Period size: 17 Copynumber: 5.4 Consensus size: 17
471729 TCATTCGAAC
471739 CAAAAAAAACAAAAAAA
1 CAAAAAAAACAAAAAAA
*
471756 CAAAAAAACCAAGAAAAA
1 CAAAAAAAACAA-AAAAA
* *
471774 -AACAAAGATAGAAAAAAA
1 CAA-AAA-AAACAAAAAAA
* *
471792 C-CAAAAACCAAAAAAA
1 CAAAAAAAACAAAAAAA
* *
471808 -TAAAAAAACAAACAAA
1 CAAAAAAAACAAAAAAA
471824 CAAAAAA
1 CAAAAAA
471831 GGGGTCCAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
16 20 0.35
17 21 0.37
18 13 0.23
19 3 0.05
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.02
Consensus pattern (17 bp):
CAAAAAAAACAAAAAAA
Found at i:471779 original size:28 final size:28
Alignment explanation
Indices: 471741--471795 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
471731 ATTCGAACCA
471741 AAAAAAACAAAAAAACAAAAAAACCAAG
1 AAAAAAACAAAAAAACAAAAAAACCAAG
* * *
471769 AAAAAAACAAAGATAGAAAAAAACCAA
1 AAAAAAACAAAAAAACAAAAAAACCAA
471796 AAACCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.80, C:0.13, G:0.05, T:0.02
Consensus pattern (28 bp):
AAAAAAACAAAAAAACAAAAAAACCAAG
Found at i:473139 original size:28 final size:28
Alignment explanation
Indices: 473098--473514 Score: 359
Period size: 28 Copynumber: 14.5 Consensus size: 28
473088 CCACAGGTCC
*
473098 TTTCAAAGCCCACAAGTTAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * * *
473126 TTTCAAATCTCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
473154 TTTCAAAGCCCACAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * * *
473182 CTTCAAAAGACCACAAGTCAGTGGCACCC
1 TTTC-AAAGCCCACAAGTCAGTGGCATCT
* * * *
473211 TTTCAAAGCCAACAAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* *
473239 TTTCAAAGCCCATAAGTCAGTGGCATATCA
1 TTTCAAAGCCCACAAGTCAGTGGC--ATCT
* * *
473269 TTTCAAAGCCCACACAAATCAGTGGCACCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCT
* * *
473299 TTCCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * * * *
473327 TTTCAAAACCCATAAGTTAGTGGCAACC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * * * *
473355 TTTCAAAGCTCAGAAGTCAGTGGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
473383 CTTCAAAGCCCATAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
473411 TTTCAAAGCCCCCAAGCCAGTGGCATACCC
1 TTTCAAAGCCCACAAGTCAGTGGCAT--CT
* *
473441 TTTCAAAGCCCATAAGTC-GATGGCATCC
1 TTTCAAAGCCCACAAGTCAG-TGGCATCT
*
473469 TTTCAAAGCCCACACAAGTCGGTGGCAACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCT
473501 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
473515 CAAGTTAGTG
Statistics
Matches: 321, Mismatches: 55, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
28 208 0.65
29 29 0.09
30 56 0.17
31 6 0.02
32 22 0.07
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCT
Found at i:473181 original size:56 final size:56
Alignment explanation
Indices: 473095--473514 Score: 412
Period size: 56 Copynumber: 7.3 Consensus size: 56
473085 AGCCCACAGG
* * * * * *
473095 TCCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAATCTCACAAGTCAATGGCA
1 TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
473151 TCCTTTCAAAGCCCACAAGTCAGTGGCA-TCTCTTCAAAAGACCACAAGTCAGTGGCA
1 TCCTTTCAAAGCCCACAAGTCAGTGGCACCCT-TTC-AAAGCCCACAAGTCAGTGGCA
* * * *
473208 CCCTTTCAAAGCCAACAAGTCAATGGCACCCTTTCAAAGCCCATAAGTCAGTGGCATA
1 TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC--A
* * *
473266 TCATTTCAAAGCCCACACAAATCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCA
1 TCCTTTCAAAG-CC-CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * * * *
473324 CCCTTTCAAAACCCATAAGTTAGTGGCAACCTTTCAAAGCTCAGAAGTCAGTGGTA
1 TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * *
473380 CCCCTTCAAAGCCCATAAGTCAGTGGCACCTTTTCAAAGCCCCCAAGCCAGTGGCA
1 TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
473436 TACCCTTTCAAAGCCCATAAGTC-GATGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAA
1 T--CCTTTCAAAGCCCACAAGTCAG-TGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGC-A
*
473497 CTCTTTTCAAAGCCCACA
1 -TCCTTTCAAAGCCCACA
473515 CAAGTTAGTG
Statistics
Matches: 300, Mismatches: 50, Indels: 24
0.80 0.13 0.06
Matches are distributed among these distances:
55 1 0.00
56 129 0.43
57 48 0.16
58 54 0.18
59 4 0.01
60 62 0.21
61 1 0.00
62 1 0.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (56 bp):
TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:473487 original size:172 final size:171
Alignment explanation
Indices: 473096--473514 Score: 468
Period size: 172 Copynumber: 2.4 Consensus size: 171
473086 GCCCACAGGT
* * * * * *
473096 CCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAATCTCACAAGTCAATGGCATCCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
* * *
473161 GCCCACAAGTCAGTGGCATCTCTTCAAAAGACCACAAGTCAGTGGCACCCTTTCAAAGCCAACAA
66 ACCCACAAGTCAGTGGCACCTCTTCAAAAGACCACAAGTCAGTGGCACCCCTTCAAAGCCAACAA
* * *
473226 GTCAATGGCACCCTTTCAAAGCCCATAAGTCAGTGGCATAT
131 GTCAATGGCACCCTTTCAAAGCCCACAAGCCAGTGGCATAC
* * * *
473267 CATTTCAAAGCCCACACAAATCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCACCCTTTCA
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
* * * * *
473332 AAACCCATAAGTTAGTGGCAACCT-TTC-AAAG-CTCAGAAGTCAGTGGTACCCCTTCAAAGCCC
64 AAACCCACAAGTCAGTGGC-ACCTCTTCAAAAGAC-CACAAGTCAGTGGCACCCCTTCAAAGCCA
* * * *
473394 ATAAGTCAGTGGCACCTTTTCAAAGCCCCCAAGCCAGTGGCATAC
127 ACAAGTCAATGGCACCCTTTCAAAGCCCACAAGCCAGTGGCATAC
* * *
473439 CCTTTCAAAGCCCATAAGTC-GATGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTT
1 CCTTTCAAAGCCCACAAGTCAG-TGGCATCCTTTCAAAG-CC-CACAAGTCAGTGGC-AC-CCTT
*
473503 TCAAAGCCCACA
61 TCAAAACCCACA
473515 CAAGTTAGTG
Statistics
Matches: 205, Mismatches: 34, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
169 1 0.00
170 20 0.10
171 14 0.07
172 91 0.44
173 63 0.31
174 16 0.08
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (171 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
ACCCACAAGTCAGTGGCACCTCTTCAAAAGACCACAAGTCAGTGGCACCCCTTCAAAGCCAACAA
GTCAATGGCACCCTTTCAAAGCCCACAAGCCAGTGGCATAC
Found at i:474505 original size:20 final size:20
Alignment explanation
Indices: 474443--474493 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
474433 TACCCAGATA
474443 TATCGATACATTTTTCAAGG
1 TATCGATACATTTTTCAAGG
474463 TATCGATACATTTTTCAAGG
1 TATCGATACATTTTTCAAGG
474483 TATCGATACAT
1 TATCGATACAT
474494 GTATGAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
TATCGATACATTTTTCAAGG
Found at i:477897 original size:48 final size:48
Alignment explanation
Indices: 477817--477930 Score: 140
Period size: 48 Copynumber: 2.4 Consensus size: 48
477807 CGTCGCGATA
* *
477817 ATCATATATACCTAATTTTGAGATAACAAAAGATAATTATTTATTATT
1 ATCATATATACATAATTTTGAGATAACAAAAGAAAATTATTTATTATT
** *
477865 ATCATATATACATAATTTTGTA-ATAATGAAAGAAAATTATTTGTTATT
1 ATCATATATACATAATTTTG-AGATAACAAAAGAAAATTATTTATTATT
* * *
477913 GTCATATAAACTTAATTT
1 ATCATATATACATAATTT
477931 AAAATCATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 56 0.98
49 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (48 bp):
ATCATATATACATAATTTTGAGATAACAAAAGAAAATTATTTATTATT
Found at i:478104 original size:60 final size:60
Alignment explanation
Indices: 477957--478157 Score: 287
Period size: 60 Copynumber: 3.3 Consensus size: 60
477947 TTCATGATAG
* * * *
477957 ATAATTAAGTTTATATAATAACATA-ACATATTTATCTATTATGAAAACTACATATAATTTT
1 ATAATTAAGTTTATATGATAACATATA-ATATTTATCTATCATGAAACCTAAATATAA-TTT
* * * *
478018 TTAATTAAGTTTATATGATAATATATAATATTTATCAATCATGAAACCAAAATATAATTT
1 ATAATTAAGTTTATATGATAACATATAATATTTATCTATCATGAAACCTAAATATAATTT
478078 ATAATTAAGTTTATATGATAACATATAATATTTATCTATCATGAAACCTAAATATAATTT
1 ATAATTAAGTTTATATGATAACATATAATATTTATCTATCATGAAACCTAAATATAATTT
* *
478138 AAAATTAAGTTCATATGATA
1 ATAATTAAGTTTATATGATA
478158 GCAACAAATA
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
60 77 0.62
61 47 0.38
62 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (60 bp):
ATAATTAAGTTTATATGATAACATATAATATTTATCTATCATGAAACCTAAATATAATTT
Found at i:478202 original size:48 final size:48
Alignment explanation
Indices: 478150--478275 Score: 173
Period size: 48 Copynumber: 2.6 Consensus size: 48
478140 AATTAAGTTC
* * *
478150 ATATGATAGCAACAAATAATTATCTTTCATTAT-TCAGAAATTATGCGT
1 ATATGATAACAACAAATAATTATCTTTCATTATCTC-GAAATTAGGCAT
** *
478198 ATATGATAACAACAAATAATTATCTTTTGTTATCTCGAAATTAGGTAT
1 ATATGATAACAACAAATAATTATCTTTCATTATCTCGAAATTAGGCAT
*
478246 ATATGATAACAACAAATAATTATTTTTCAT
1 ATATGATAACAACAAATAATTATCTTTCAT
478276 GAAGAAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
48 66 0.97
49 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (48 bp):
ATATGATAACAACAAATAATTATCTTTCATTATCTCGAAATTAGGCAT
Found at i:480885 original size:20 final size:19
Alignment explanation
Indices: 480842--480881 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
480832 AATTTAAATA
*
480842 TTTAT-TTTAAAAAATTAT
1 TTTATATTTAAAAAACTAT
*
480860 TTTATATTTAAATAACTAT
1 TTTATATTTAAAAAACTAT
480879 TTT
1 TTT
480882 TATAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATATTTAAAAAACTAT
Done.