Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold313
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: 790584
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 6
Found at i:105358 original size:52 final size:52
Alignment explanation
Indices: 105262--105389 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
105252 CACTGATCTT
*
105262 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACATTATTAAA
* *
105313 TGTATCGATACATGCAGGCAAATTTGCCCCGATATATCGATACATTGTTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACATTATTAAA
105365 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
105390 TCATATTTCG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.26
52 54 0.74
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACATTATTAAA
Found at i:108562 original size:33 final size:33
Alignment explanation
Indices: 108525--108591 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
108515 TTCAACGATT
108525 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
108558 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
108591 T
1 T
108592 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:108563 original size:13 final size:13
Alignment explanation
Indices: 108545--108569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
108535 CATAAAATGT
108545 TGTATCGATACAA
1 TGTATCGATACAA
108558 TGTATCGATACA
1 TGTATCGATACA
108570 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:108745 original size:52 final size:52
Alignment explanation
Indices: 108652--108779 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
108642 CACTGATCTT
108652 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
*
108703 TGTATCGATACATGCAGGCAAATTTGCCCCGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
108755 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
108780 TCATATTTCG
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
51 19 0.25
52 56 0.75
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
Found at i:111499 original size:21 final size:21
Alignment explanation
Indices: 111474--111516 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
111464 CATGTCAGGA
111474 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
111495 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
111516 G
1 G
111517 TCATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GCATCTCGTCATGCAATGAAT
Found at i:116543 original size:30 final size:31
Alignment explanation
Indices: 116509--116589 Score: 110
Period size: 30 Copynumber: 2.6 Consensus size: 31
116499 TACCTTTTTC
116509 AAGTCCACGACTCAGTGGCATTTTGTC-TCA
1 AAGTCCACGACTCAGTGGCATTTTGTCTTCA
* *
116539 AAGTCCACGACTCAGTGGCATTTTTTCTTTA
1 AAGTCCACGACTCAGTGGCATTTTGTCTTCA
* * *
116570 AAGCCCACAACTCCGTGGCA
1 AAGTCCACGACTCAGTGGCA
116590 CCTTGTTCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 26 0.58
31 19 0.42
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (31 bp):
AAGTCCACGACTCAGTGGCATTTTGTCTTCA
Found at i:116634 original size:61 final size:62
Alignment explanation
Indices: 116566--117272 Score: 614
Period size: 61 Copynumber: 10.9 Consensus size: 62
116556 GCATTTTTTC
*
116566 TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACC-CT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTCT
* * *
116627 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACC-CT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAGTCCACAACTCCGTGGCACCTCT
* * * * *
116689 TTTAAAGCCCACAATTCTGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACC-CG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAGTCCACAACTCCGTGGCACCTCT
*
116751 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAG-CTCACAACTCCGTGGCACCTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGTC-CACAACTCCGTGGCACC----
116814 TCT
60 TCT
* **
116817 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAACCCACAACTCCGTGGCACCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT--AAGTCCACAACTCCGTGGCACC--
*
116882 TTTTT
60 --TCT
* *
116887 GTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-CT
1 -TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTC-CTTTT--AAGTCCACAACTCCGTGGCACCT
116951 C-
61 CT
* * * * *
116952 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAG-CCTACAGCTCCATAGCACCTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGTCC-ACAACTCCGTGGCA-C--C-
117016 TCT
60 TCT
* * * * * *
117019 TTTCAAAGCCCACGACTCTGTGGCA-C-TCTT--TTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-CTCT
* * * *
117079 TTCCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACC-
1 TT--T--AAAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCT
117143 CT
61 CT
* * *
117145 TTT-AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAGTCCACAACTCCGTGGCACC-----
117209 TTTCT
60 --TCT
117214 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAGTCCACAACTCCGTGGCA
117273 TCTTTCTCCC
Statistics
Matches: 555, Mismatches: 47, Indels: 78
0.82 0.07 0.11
Matches are distributed among these distances:
60 17 0.03
61 134 0.24
62 96 0.17
63 40 0.07
64 31 0.06
65 2 0.00
66 17 0.03
67 25 0.05
68 48 0.09
69 10 0.02
70 48 0.09
71 85 0.15
72 2 0.00
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (62 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTCT
Found at i:116673 original size:34 final size:33
Alignment explanation
Indices: 116543--117277 Score: 485
Period size: 34 Copynumber: 22.6 Consensus size: 33
116533 GTCTCAAAGT
* * *
116543 CCACGACTCAGTGGCA-TTTTTTCT-TTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
* * *
116574 CCACAACTCCGTGGCACCTTGTTC-CTTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCTC-TTTAAGC
*
116607 CCACAACTCCGTGGCAC-----CCT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* *
116635 CCACAATTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-TCTTTAAGC
*
116669 CCACAACTCCGTGGCAC-----CCT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* * *
116697 CCACAATTCTGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-TCTTTAAGC
116731 CCACAACTCCGTGGCAC------C-CGTTTAAGC
1 CCACAACTCCGTGGCACTTTTTTCTC-TTTAAGC
* *
116758 CCACAACTCCGTGGCACCTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* *
116792 TCACAACTCCGTGGCACCTTTTTCT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* * *
116825 CCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAAC
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTT--AAGC
*
116862 CCACAACTCCGTGGCACCTTTTTT-TGTTTAAAGC
1 CCACAACTCCGTGGCA-CTTTTTTCTCTTT-AAGC
116896 CCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGC
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTT--AAGC
* *
116933 CCACGACTCCGTGGCAC-----TCT-TTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
* * *
116960 CCACAACTCCGTGGCACCTTCTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* * * * * *
116994 CTACAGCTCCATAGCACCTTCTTCT-TTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT--AAGC
* * * *
117028 CCACGACTCTGTGGCAC--TCTT-T-TTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
*
117057 CCACAACTCCGTGGCACTCTTTTTC-CTCCTAAGC
1 CCACAACTCCGTGGCACT-TTTTTCTCT-TTAAGC
*
117091 CCACAACTCTGTGGCACTCTTTTTC-CTTCTAAGC
1 CCACAACTCCGTGGCACT-TTTTTCTCTT-TAAGC
*
117125 CCACAACTCCGTGGCAC-----CCT-TTTAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
* *
117152 CCATAACTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-TCTTTAAGC
*
117186 CCACAACTCCGTGGCACCTTTTTTTTCTTTTAAAGC
1 CCACAACTCCGTGGCA-CTTTTTTCTC-TTT-AAGC
* *
117222 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTTAAGC
117257 CCACAACTCCGTGGCATCTTT
1 CCACAACTCCGTGGCA-CTTT
117278 CTCCCTTCCT
Statistics
Matches: 572, Mismatches: 66, Indels: 128
0.75 0.09 0.17
Matches are distributed among these distances:
26 1 0.00
27 70 0.12
28 43 0.08
29 22 0.04
31 20 0.03
32 16 0.03
33 60 0.10
34 213 0.37
35 43 0.08
36 37 0.06
37 45 0.08
38 2 0.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
Found at i:116762 original size:27 final size:27
Alignment explanation
Indices: 116724--116775 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
116714 TTTTTTCATC
*
116724 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
116751 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
116776 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:116814 original size:95 final size:96
Alignment explanation
Indices: 116566--117244 Score: 614
Period size: 95 Copynumber: 7.0 Consensus size: 96
116556 GCATTTTTTC
* * *
116566 TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCACC-----
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
* **
116625 CT-TTTAAAGCCCACAATTCCGTGGCACTTT
66 CTCTTTAAAGCCCACAACTCCGTGGCACCCT
* * *
116655 TTTCATCTTTAAGTCCACAACTCCGTGGCACC-----C-TTTTAAAGCCCACAATTCTGTGGCAC
1 TTT-A-----AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC
* * *
116714 TTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCCG
60 CTTTTTC-TCTTTAAAGCCCACAACTCCGTGGCACCCT
*
116751 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCTCACAACTCCGTGGCACCTTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
*
116815 CT-TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCT
66 CTCTTTAAAGCCCACAACTCCGTGGCA--------CCCT
*
116853 TTTCAAAACCCACAACTCCGTGGCACCTTTTT-TTGTTTAAAGCCCACAACTCCGTGGCACTCTT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTT-TTTAAAGCCCACAACTCCGTGGCAC-CTT
* *
116917 TTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTC-
63 TTTCTC-TTT-AAAGCCCACAACTCCGTGGCACCCT
* * * * * *
116952 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCTACAGCTCCATAGCACCTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
* * *
117017 CT-TTTCAAAGCCCACGACTCTGTGGCACTCTT
66 CTCTTT-AAAGCCCACAACTCCGTGGCAC-CCT
* ** *
117049 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTCCT-AAGCCCACAACTCTGTGGCACTCTTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTT
117113 TTC-CTTCT-AAGCCCACAACTCCGTGGCACCCT
64 TTCTCTT-TAAAGCCCACAACTCCGTGGCACCCT
* * * *
117145 TTT-AAGCCCATAACTCCGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTTAAAGCCCACAACTCCGTGGCACC-TTT
* *
117208 TTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
64 TTCTC-TTTAAAGCCCACAACTCCGTGGCACCCT
117242 TTT
1 TTT
117245 TCCCTTTTAA
Statistics
Matches: 486, Mismatches: 56, Indels: 88
0.77 0.09 0.14
Matches are distributed among these distances:
89 28 0.06
90 20 0.04
93 3 0.01
94 27 0.06
95 121 0.25
96 30 0.06
97 98 0.20
98 63 0.13
99 6 0.01
100 2 0.00
102 6 0.01
103 2 0.00
104 50 0.10
105 8 0.02
107 3 0.01
108 19 0.04
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (96 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
CTCTTTAAAGCCCACAACTCCGTGGCACCCT
Found at i:117174 original size:27 final size:27
Alignment explanation
Indices: 117115--117168 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
117105 CACTCTTTTT
*
117115 CCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
117142 CCTTTTAAGCCCATAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
117169 TTTTTTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:117283 original size:34 final size:34
Alignment explanation
Indices: 117141--117284 Score: 164
Period size: 36 Copynumber: 4.1 Consensus size: 34
117131 CTCCGTGGCA
*
117141 CCCTTTTAAGCCCATAACTCCGTGGCA-CTTTTT
1 CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* * * *
117174 TCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTT
1 CCCT-TTTAAGCCCACAACTCCGTGGCATC-TTTTT
**
117210 TTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTT-AAGCCCACAACTCCGTGGCA-TCTTTTT
* *
117246 CCCTTTTAAGTCCACAACTCCGTGGCATCTTTCT
1 CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
117280 CCCTT
1 CCCTT
117285 CCTAAAGCCC
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
33 2 0.02
34 32 0.34
35 23 0.24
36 36 0.38
37 1 0.01
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (34 bp):
CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
Found at i:117291 original size:71 final size:70
Alignment explanation
Indices: 117148--117297 Score: 196
Period size: 71 Copynumber: 2.1 Consensus size: 70
117138 GCACCCTTTT
* * **
117148 AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTTTTC
1 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTCTCCC
*
117213 TTTTA
66 TTCTA
* *
117218 AAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATC-TTTCTC
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCTTTTCTC
117281 CCTTCCTA
64 CCTT-CTA
117289 AAGCCCACA
1 AAGCCCACA
117298 CAAGTCGGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
70 29 0.41
71 41 0.59
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (70 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTCTCCC
TTCTA
Found at i:117325 original size:33 final size:35
Alignment explanation
Indices: 117282--117351 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
117272 ATCTTTCTCC
117282 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
117316 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
117350 CT
1 CT
117352 AAGCCCAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:117419 original size:49 final size:49
Alignment explanation
Indices: 117362--118254 Score: 1048
Period size: 49 Copynumber: 18.6 Consensus size: 49
117352 AAGCCCAACA
*
117362 TAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* *
117411 TAGCTGGCCTTGACTCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* * *
117454 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCA--TCTT-CATCTTTAAGTCCAATG
* *
117506 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* *
117555 TAGCTGGCCTTGAATCAGCACATT-G-A----CACCTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* *
117598 TCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* *
117647 TAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTCAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* *
117690 TCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
*
117739 TAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* * *
117782 TCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* * * * *
117831 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* * *
117880 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* ** * * * * *
117929 TAGCTGGCCTTGACTCAGCACATAAGCACCTTCACCATTAAGCCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* *
117978 TAGCTGGCCTTGAATCAGCATATTGGCA-CTTTTATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCATC-TTCATCTTTAAGTCCAATG
* * * *
118027 TAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCATTAAGTCC-ATA
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTT-CATCTTTAAGTCCAATG
* * *
118075 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* * *
118124 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
* * * *
118173 TAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCA--TCTT-CATCTTTAAGTCCAATG
*
118225 TAGCTGGCCTTGAATCAGCACATTGACATC
1 TAGCTGGCCTTGAATCAGCACATTGGCATC
118255 CTTTTTCATC
Statistics
Matches: 718, Mismatches: 92, Indels: 67
0.82 0.10 0.08
Matches are distributed among these distances:
43 152 0.21
44 1 0.00
45 4 0.01
47 3 0.00
48 42 0.06
49 432 0.60
50 4 0.01
51 2 0.00
52 78 0.11
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATG
Found at i:117900 original size:98 final size:98
Alignment explanation
Indices: 117362--118312 Score: 1191
Period size: 92 Copynumber: 9.8 Consensus size: 98
117352 AAGCCCAACA
* * * * *
117362 TAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTC
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATC
* *
117427 AGCACATTGGCA----C--CTTTAAGTCCAATA
66 AGCATATTGGCATCTTCATCTTTAAGTCCAATG
* * * *
117454 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGA
1 TAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CACCTTTAAGTCCAATATAGCTGGCCTTGA
* * *
117519 CTCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
63 ATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
*
117555 TAGCTGGCCTTGAATCAGCACATT-G-A----CACCTTTAAGTCCAATATCGCTGGCCTTGAATC
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATC
117614 AGCATATTGGCATCTTCATCTTTAAGTCCAATG
66 AGCATATTGGCATCTTCATCTTTAAGTCCAATG
*
117647 TAGCTGGCCTTGAATCAGCACATTGGCACCTT---C---AAGTCCAATATCGCTGGCCTTGAATC
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATC
117706 AGCATATTGGCATCTTCATCTTTAAGTCCAATG
66 AGCATATTGGCATCTTCATCTTTAAGTCCAATG
*
117739 TAGCTGGCCTTGAATCAGCACATTGG------CACCTTTAAGTCCAATATCGCTGGCCTTGAATC
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATC
*
117798 AGCATATTGGCATCATCATCTTTAAGTCCAATG
66 AGCATATTGGCATCTTCATCTTTAAGTCCAATG
* *
117831 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATC
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATC
* *
117896 AGCATATTGGCACCTTTATCTTTAAGTCCAATG
66 AGCATATTGGCATCTTCATCTTTAAGTCCAATG
* ** * *
117929 TAGCTGGCCTTGACTCAGCACATAAGCACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATC
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATC
*
117994 AGCATATTGGCA-CTTTTATCTTTAAGTCCAATG
66 AGCATATTGGCATC-TTCATCTTTAAGTCCAATG
* *
118027 TAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCATTAAGTCC-ATATAGCTGGCCTTGAAT
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTT-CACCTTTAAGTCCAATATAGCTGGCCTTGAAT
* *
118090 CAGCATATTGGCACCTTTATCTTTAAGTCCAATG
65 CAGCATATTGGCATCTTCATCTTTAAGTCCAATG
* *
118124 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATC
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATC
* * *
118189 AGCATATCGGCACCTTTTCCATCTTTAAGTTCAATG
66 AGCATATTGGCA--TCTT-CATCTTTAAGTCCAATG
* * * *
118225 TAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTTTAAGCCCAATATCGTTGGCC
1 TAGCTGGCCTTGAATCAGCACATTGGCA-CC---TTCA-C--CTTTAAGTCCAATATAGCTGGCC
* *
118290 ATGAATCAACATATTGGCATCTT
59 TTGAATCAGCATATTGGCATCTT
118313 TATCACTTTT
Statistics
Matches: 776, Mismatches: 41, Indels: 70
0.87 0.05 0.08
Matches are distributed among these distances:
89 1 0.00
92 280 0.36
93 1 0.00
94 3 0.00
95 46 0.06
97 93 0.12
98 226 0.29
99 2 0.00
100 3 0.00
101 76 0.10
102 2 0.00
105 4 0.01
106 3 0.00
108 36 0.05
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (98 bp):
TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATC
AGCATATTGGCATCTTCATCTTTAAGTCCAATG
Found at i:119215 original size:33 final size:33
Alignment explanation
Indices: 119178--119244 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
119168 TTCAACGATT
119178 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
119211 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
119244 T
1 T
119245 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:119216 original size:13 final size:13
Alignment explanation
Indices: 119198--119222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119188 CATAAAATGT
119198 TGTATCGATACAA
1 TGTATCGATACAA
119211 TGTATCGATACA
1 TGTATCGATACA
119223 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:123020 original size:13 final size:13
Alignment explanation
Indices: 123002--123059 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
122992 CAATTTTTTG
123002 TGTATCGATACAT
1 TGTATCGATACAT
123015 TGTATCGATACATATTTT
1 TGTATCGATAC--A---T
123033 GTGTATCGATACAT
1 -TGTATCGATACAT
123047 TGTATCGATACAT
1 TGTATCGATACAT
123060 ATTTTGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.62
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 11 0.28
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:123038 original size:32 final size:32
Alignment explanation
Indices: 122982--123077 Score: 174
Period size: 32 Copynumber: 3.0 Consensus size: 32
122972 TACAAGCCAA
*
122982 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATAC-ATATTTTGTGTATCGATACAT
123015 TGTATCGATACATATTTTGTGTATCGATACAT
1 TGTATCGATACATATTTTGTGTATCGATACAT
123047 TGTATCGATACATATTTTGTGTATCGATACA
1 TGTATCGATACATATTTTGTGTATCGATACA
123078 AGTTTGGCTA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.82
33 11 0.18
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (32 bp):
TGTATCGATACATATTTTGTGTATCGATACAT
Found at i:123039 original size:19 final size:19
Alignment explanation
Indices: 122982--123077 Score: 90
Period size: 19 Copynumber: 5.6 Consensus size: 19
122972 TACAAGCCAA
*
122982 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
123002 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
123015 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
123034 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
123047 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
123066 TGTATCGATACA
1 TGTATCGATACA
123078 AGTTTGGCTA
Statistics
Matches: 63, Mismatches: 1, Indels: 25
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.35
14 2 0.03
15 2 0.03
17 1 0.02
18 2 0.03
19 23 0.37
20 11 0.17
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:123177 original size:20 final size:20
Alignment explanation
Indices: 123129--123184 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
123119 ACATCTTTTT
*
123129 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
*
123149 CATGGATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
123168 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
123185 TAAGGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:127627 original size:92 final size:92
Alignment explanation
Indices: 127429--128080 Score: 1009
Period size: 92 Copynumber: 7.0 Consensus size: 92
127419 GTTAAAGATG
* * **
127429 AAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGACGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATAT
* *
127494 GCTGATTCAAGGCCAGCGATATCGGACATA
63 GCTGATTCAAGGCCAGCGATATTGGACTTA
*
127524 AAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCT
127589 GATTCAAGGCCAGCGATATTGGACTTA
66 GATTCAAGGCCAGCGATATTGGACTTA
* *
127616 AAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCT
* *
127681 GATTCAAGGCCAGCGATATTGGGCTTG
66 GATTCAAGGCCAGCGATATTGGACTTA
* * *
127708 GAGGTGCCAATGCGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCT
*
127773 GATTCAAGGCCAGCTATATTGGACTTA
66 GATTCAAGGCCAGCGATATTGGACTTA
*
127800 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCT
*
127865 GATTCAAGGCCAGCGATATTGGACTTG
66 GATTCAAGGCCAGCGATATTGGACTTA
* *
127892 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCGAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCT
*
127957 GATTTAAGGCCAGCGATATTGGACTTA
66 GATTCAAGGCCAGCGATATTGGACTTA
** * *
127984 AATATGCTAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGC
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGC
* * *
128048 TGATTCAAGGTCAGCTATATTGGGCTTA
65 TGATTCAAGGCCAGCGATATTGGACTTA
128076 GAAGG
1 -AAGG
128081 GTTGCCACCA
Statistics
Matches: 516, Mismatches: 39, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
92 469 0.91
93 2 0.00
95 45 0.09
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTTA
Found at i:128119 original size:33 final size:33
Alignment explanation
Indices: 128075--128400 Score: 411
Period size: 32 Copynumber: 9.9 Consensus size: 33
128065 TATTGGGCTT
128075 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
*
128108 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
*
128141 AG-AGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
*
128173 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTT-G
1 -AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
* * *
128205 AAAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
*
128238 AG--GGGATTGCCATCAACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCAACTTGTGTGGGCTTTAG
*
128270 AGAAAGGTTGCCACCAACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
*
128302 AGAAGGGGATTGCCACCAACTTGTGTGGGCTTTGG
1 AGAA-GGG-TTGCCACCAACTTGTGTGGGCTTTAG
* *
128337 A-AGAGGGATTGCCACCGA-TGTGTGTAGGCTTT--
1 AGA-AGGG-TTGCCACCAACT-TGTGTGGGCTTTAG
128369 AGAAGAGGTTGCCACCAACTTGTGTGGGCTTT
1 AGAAG-GGTTGCCACCAACTTGTGTGGGCTTT
128401 TAGAAGGAAA
Statistics
Matches: 263, Mismatches: 15, Indels: 31
0.85 0.05 0.10
Matches are distributed among these distances:
31 5 0.02
32 109 0.41
33 94 0.36
34 52 0.20
35 3 0.01
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
Found at i:128170 original size:65 final size:64
Alignment explanation
Indices: 128068--128400 Score: 419
Period size: 65 Copynumber: 5.1 Consensus size: 64
128058 TCAGCTATAT
*
128068 TGGGC-TTAGA-AGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCAACTTGTG
*
128131 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAG-AGAAGGTTGCCACCAACTTGTG
* * * *
128196 TGGGCTTT-GAAAAAGGTTGCCACCGACTTGTGTGGGCTTTAGAG-GGGATTGCCATCAACTTGT
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG-TTGCCACCAACTTGT
128259 G
64 G
* *
128260 TGGGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGGCTTT-GAGAAGGGGATTGCCACCAACTT
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA--GG-TTGCCACCAACTT
128324 GTG
62 GTG
* *
128327 TGGGCTTTGGAAGAGGGATTGCCACCGA-TGTGTGTAGGCTTTAGA-AGAGGTTGCCACCAACTT
1 TGGGCTTTAG-AGAGGG-TTGCCACCGACT-TGTGTGGGCTTTAGAGA-AGGTTGCCACCAACTT
128390 GTG
62 GTG
128393 TGGGCTTT
1 TGGGCTTT
128401 TAGAAGGAAA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
63 7 0.03
64 34 0.14
65 112 0.47
66 28 0.12
67 33 0.14
68 23 0.10
69 3 0.01
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.29
Consensus pattern (64 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTG
Found at i:128497 original size:36 final size:35
Alignment explanation
Indices: 128399--129253 Score: 871
Period size: 36 Copynumber: 25.3 Consensus size: 35
128389 TGTGTGGGCT
* * *
128399 TTTAGAAGGAAAAAGAGTGGCGCGG-GTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
* * *
128433 -TTAAAAAGAACAAG-GTGCCACGGGGTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
*
128466 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
**
128502 TTTGAAAA-G---AAG-GTGCCACGGAGTCATGGAC
1 TTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
* *
128533 -TTAAAAGGAACAAG-GTGCCACAGAGTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
* *
128566 TTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
* * *
128602 TTTAAAAGGGAAAAAGAGTGCGACGGAGTTCTGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
* *
128638 TTT----GGAAAGAA-CGTGCCACGGAGTCGTGGAC
1 TTTAAAAGGAAA-AAGAGTGCCACGGAGTTGTGGAC
* * *
128669 -TTAAATGGAACAAG-GTACCACGGAGTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
* *
128702 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTATGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
*
128738 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
* *
128774 -TTAAAAGGAACAAG-GTGCCACAGAGTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
*
128807 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
*
128843 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
*
128879 -TTAAAAGGAACAAG-GTGCCACGGAGTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
*
128912 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
* *
128948 -TTAAAAGGAACAAG-GTGCCACGGATTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
*
128981 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
*
129017 TTT-GAA--AAAAAG-GTGCCACGGAGTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
* * *
129048 -TTAGAAGGAAAAAGAGTGCCACGAAGTTGTGGGC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
*
129082 -TT-AAACG-----G-GTGCCACGGAGTTGTGGAC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
* * *
129109 -TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGC
1 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
*
129143 TTTAAAAAGGAAAAAGA-TGCCACAGAGTTGTGGAC
1 TTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
*
129178 -TTAAAAGGAACAAAGAGTGCCACGGAGTTGTGGGC
1 TTTAAAAGGAA-AAAGAGTGCCACGGAGTTGTGGAC
*
129213 TTTGAAAA-G---AAG-GTGCCACGGAGTCGTGGAC
1 TTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
129244 TTTAAGAAGG
1 TTTAA-AAGG
129254 TATTTGAAGA
Statistics
Matches: 702, Mismatches: 70, Indels: 100
0.81 0.08 0.11
Matches are distributed among these distances:
27 19 0.03
28 4 0.01
29 4 0.01
30 9 0.01
31 79 0.11
32 22 0.03
33 128 0.18
34 103 0.15
35 97 0.14
36 229 0.33
37 8 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (35 bp):
TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
Found at i:128723 original size:69 final size:69
Alignment explanation
Indices: 128650--129253 Score: 735
Period size: 69 Copynumber: 8.9 Consensus size: 69
128640 TGGAAAGAAC
* * * *
128650 GTGCCACGGAGTCGTGGACTTAAATGGAACAAGGTACCACGGAGTTGTGGACTTTAAAAGGGAAA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAA
128715 AAGA
66 AAGA
* * *
128719 GTGCCACGGAGTTATGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAA-GG
1 GTGCCACGGAGTTGTGGGC-TTAAAA-GGAACAAG-GTGCCACGGAGTTGTGGACTTTAAAAGGG
*
128782 AACAAG-
63 AAAAAGA
* * * *
128788 GTGCCACAGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
1 GTGCCACGGAGTTGTGGGC-TTAAAA-GGAACAAG-GTGCCACGGAGTTGTGGACTTTAAAAGGG
128853 AAAAAGA
63 AAAAAGA
128860 GTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAA
128925 AAGA
66 AAGA
*
128929 GTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGGTGCCACGGATTTGTGGACTTTAAAAGGGAAA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAA
128994 AAGA
66 AAGA
* *
128998 GTGCCACGGAGTTGTGGGCTTTGAAA--AA-AAGGTGCCACGGAGTTGTGGAC-TTAGAA-GGAA
1 GTGCCACGGAGTTGTGGGC-TTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAA
129058 AAAGA
65 AAAGA
* * *
129063 GTGCCACGAAGTTGTGGGCTT---A--AAC-GGGTGCCACGGAGTTGTGGAC-TTAGAA-GGAAA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAA
129120 AAGA
66 AAGA
* * * *
129124 GTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGAC-TTAAAA-GGA
1 GTGCCACGGAGTTGTGGGC-TT-AAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGA
129187 ACAAAGA
64 A-AAAGA
** * *
129194 GTGCCACGGAGTTGTGGGCTTTGAA--AAGAAGGTGCCACGGAGTCGTGGACTTTAAGAAGG
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAA-AAGG
129254 TATTTGAAGA
Statistics
Matches: 479, Mismatches: 36, Indels: 40
0.86 0.06 0.07
Matches are distributed among these distances:
61 55 0.11
62 2 0.00
64 2 0.00
65 27 0.06
66 27 0.06
67 25 0.05
68 8 0.02
69 220 0.46
70 53 0.11
71 26 0.05
72 34 0.07
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (69 bp):
GTGCCACGGAGTTGTGGGCTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAA
AAGA
Found at i:128800 original size:105 final size:104
Alignment explanation
Indices: 128406--129221 Score: 895
Period size: 105 Copynumber: 8.0 Consensus size: 104
128396 GCTTTTAGAA
* * * * * *
128406 GGAAAAAGAGTGGCGCGG-GTTGTGGACTTAAAAAGAACAAG-GTGCCACGGGGTTGTGGACTTT
1 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC-TT
* *
128469 AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-
65 AAAA-GGAACAAGAGTGCCACGGAGTTGTGGACTTT-AAAAG
** * * *
128510 -G---AAG-GTGCCACGGAGTCATGGACTTAAAAGGAACAAG-GTGCCACAGAGTTGTGGACTTT
1 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC-TT
* * *
128569 AAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAG
65 AAAA-GGAACAAGAGTGCCACGGAGTTGTGGACTTTAAAAG
* * * * *
128610 GGAAAAAGAGTGCGACGGAGTTCTGGGCTT---TGGAAAGAA-CGTGCCACGGAGTCGTGGACTT
1 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAA-AAGAGTGCCACGGAGTTGTGGACTT
* *
128671 AAATGGAACAAG-GTACCACGGAGTTGTGGACTTTAAAAG
65 AAAAGGAACAAGAGTGCCACGGAGTTGTGGACTTTAAAAG
* *
128710 GGAAAAAGAGTGCCACGGAGTTATGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1 GGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGACT
*
128775 TAAAAGGAACAAG-GTGCCACAGAGTTGTGGACTTTAAAAG
64 TAAAAGGAACAAGAGTGCCACGGAGTTGTGGACTTTAAAAG
*
128815 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1 GGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGACT
128880 TAAAAGGAACAAG-GTGCCACGGAGTTGTGGACTTTAAAAG
64 TAAAAGGAACAAGAGTGCCACGGAGTTGTGGACTTTAAAAG
* *
128920 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAACAAG-GTGCCACGGATTTGTGGACTTT
1 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC-TT
* * *
128984 AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-GAA-
65 AAAA-GGAACAAGAGTGCCACGGAGTTGTGGACTTTAAAAG
* * * *
129023 --AAAAAG-GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTT-
1 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTA
* *
129084 --A--AAC--GGGTGCCACGGAGTTGTGGAC-TTAGAA-
66 AAAGGAACAAGAGTGCCACGGAGTTGTGGACTTTAAAAG
* *
129115 GGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAAGA-TGCCACAGAGTTGTGGACT
1 GGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGACT
*
129179 TAAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG
64 TAAAAGGAAC-AAGAGTGCCACGGAGTTGTGGACTTT-AAAAG
129222 AAGGTGCCAC
Statistics
Matches: 620, Mismatches: 56, Indels: 69
0.83 0.08 0.09
Matches are distributed among these distances:
91 2 0.00
92 22 0.04
94 8 0.01
95 17 0.03
96 19 0.03
97 13 0.02
99 12 0.02
100 160 0.26
101 35 0.06
102 26 0.04
103 33 0.05
104 39 0.06
105 231 0.37
106 3 0.00
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.19
Consensus pattern (104 bp):
GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTA
AAAGGAACAAGAGTGCCACGGAGTTGTGGACTTTAAAAG
Found at i:129171 original size:35 final size:34
Alignment explanation
Indices: 129090--129210 Score: 172
Period size: 35 Copynumber: 3.5 Consensus size: 34
129080 GCTTAAACGG
* *
129090 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGA
1 GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGA
*
129124 GTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAAGA
1 GTGCCACAGAGTTGTGGAC-TT-AAAAGGAAAAAGA
129160 -TGCCACAGAGTTGTGGACTTAAAAGGAACAAAGA
1 GTGCCACAGAGTTGTGGACTTAAAAGGAA-AAAGA
*
129194 GTGCCACGGAGTTGTGG
1 GTGCCACAGAGTTGTGG
129211 GCTTTGAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
33 8 0.10
34 24 0.31
35 34 0.44
36 12 0.15
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (34 bp):
GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGA
Found at i:130220 original size:23 final size:21
Alignment explanation
Indices: 130190--130259 Score: 97
Period size: 23 Copynumber: 3.2 Consensus size: 21
130180 GATTTTTCCC
130190 TTTTCTTTTTTTGTTTGTTTGT
1 TTTTCTTTTTTTGTTTGTTT-T
130212 TTCTTCTTTTTTTGTTTGTTTT
1 TT-TTCTTTTTTTGTTTGTTTT
130234 TTTTC-TTTTTTGTTTTGTTTCT
1 TTTTCTTTTTTTG-TTTGTTT-T
130256 TTTT
1 TTTT
130260 TTGAAAAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.16
21 10 0.22
22 10 0.22
23 18 0.40
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (21 bp):
TTTTCTTTTTTTGTTTGTTTT
Found at i:130227 original size:15 final size:14
Alignment explanation
Indices: 130207--130261 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 14
130197 TTTTTGTTTG
130207 TTTGTTTCTTCTTTT
1 TTTGTTTCTT-TTTT
*
130222 TTTGTTT-GTTTTT
1 TTTGTTTCTTTTTT
* *
130235 TTT-CTT-TTTTGT
1 TTTGTTTCTTTTTT
130247 TTTGTTTCTTTTTT
1 TTTGTTTCTTTTTT
130261 T
1 T
130262 GAAAAGAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
12 9 0.28
13 9 0.28
14 7 0.22
15 7 0.22
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (14 bp):
TTTGTTTCTTTTTT
Found at i:130245 original size:16 final size:17
Alignment explanation
Indices: 130195--130262 Score: 75
Period size: 16 Copynumber: 3.9 Consensus size: 17
130185 TTCCCTTTTC
*
130195 TTTTTTTGTTTGTTTGT
1 TTTTTTTCTTTGTTTGT
*
130212 TTCTTCTTTTTTTGTTTGT
1 TT-TT-TTTCTTTGTTTGT
130231 TTTTTTTCTTT-TTTGT
1 TTTTTTTCTTTGTTTGT
* *
130247 TTTGTTTCTTTTTTTG
1 TTTTTTTCTTTGTTTG
130263 AAAAGAACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
16 15 0.33
17 12 0.27
18 4 0.09
19 14 0.31
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTGTTTGT
Found at i:130519 original size:17 final size:17
Alignment explanation
Indices: 130499--130551 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
130489 CCTTTGCACC
130499 TTTT-TTCTGTGTTTTTG
1 TTTTGTTCTGT-TTTTTG
*
130516 TTTTGTTTTGTTTTTTG
1 TTTTGTTCTGTTTTTTG
130533 TTTTGTT-T-TTTTTGTG
1 TTTTGTTCTGTTTTT-TG
130549 TTT
1 TTT
130552 ACTTTTGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 17 0.52
18 5 0.15
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (17 bp):
TTTTGTTCTGTTTTTTG
Found at i:130527 original size:16 final size:16
Alignment explanation
Indices: 130508--130551 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
130498 CTTTTTTCTG
130508 TGTTTTTGTTTTGTTT
1 TGTTTTTGTTTTGTTT
130524 TGTTTTTTGTTTTGTTT
1 TG-TTTTTGTTTTGTTT
130541 T-TTTTGTGTTT
1 TGTTTT-TGTTT
130552 ACTTTTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.15
16 7 0.27
17 15 0.58
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (16 bp):
TGTTTTTGTTTTGTTT
Found at i:130531 original size:12 final size:12
Alignment explanation
Indices: 130516--130543 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
130506 TGTGTTTTTG
130516 TTTTGTTTTGTT
1 TTTTGTTTTGTT
130528 TTTTGTTTTGTT
1 TTTTGTTTTGTT
130540 TTTT
1 TTTT
130544 TTGTGTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTTGTTTTGTT
Found at i:136658 original size:52 final size:52
Alignment explanation
Indices: 136589--136697 Score: 191
Period size: 52 Copynumber: 2.1 Consensus size: 52
136579 GAAATATGAC
*
136589 AATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGCA
1 AATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATATGGGCA
* *
136641 AATTTGCCTGCATGTATCGATACATTTTATAGTGTATCAATACATCTGGGCA
1 AATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATATGGGCA
136693 AATTT
1 AATTT
136698 TTTCATCCTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (52 bp):
AATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATATGGGCA
Found at i:141276 original size:20 final size:20
Alignment explanation
Indices: 141251--141310 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
141241 CTGCCAATCT
141251 CATGTATCAATACAATTATC
1 CATGTATCAATACAATTATC
** * * *
141271 CATGTATTGACATAATTA-A
1 CATGTATCAATACAATTATC
141290 CATGTATCAATACAATGTATC
1 CATGTATCAATACAAT-TATC
141311 GATACAAAGC
Statistics
Matches: 28, Mismatches: 10, Indels: 3
0.68 0.24 0.07
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (20 bp):
CATGTATCAATACAATTATC
Found at i:144480 original size:104 final size:103
Alignment explanation
Indices: 144129--144531 Score: 467
Period size: 102 Copynumber: 3.9 Consensus size: 103
144119 CAGAGAAATG
** * *
144129 GGGTTGGAGCATCCCTAAAGATAAAATTATGAAAATATTT-AGGAACAAAGAGAAAATTTAATTC
1 GGGTTGGAGTTTCCCTAAAGATAAAATTATGAAAACATTTAAGG-ACAAAGAGAAAATTTGATT-
* * * * * *
144193 TTTTATGAAGAACGTGGTTGGAGTATTTCCTCGAAGTATT
64 TTTTATGAAGAATGAGGTTGAAGTATTCCCTCAAAGTATA
* * * *
144233 GGAATTAGAGTTTCCCTAAAGATAAAATTATGAAAACATTTAGGGATAAAGAGAAAATTTGATTT
1 GG-GTTGGAGTTTCCCTAAAGATAAAATTATGAAAACATTTAAGGACAAAGAGAAAATTTGATTT
*
144298 TTT-TGAAGAATGAGGTTGAAGTA-TCCTCTCAAGGTACTA
65 TTTATGAAGAATGAGGTTGAAGTATTCC-CTCAAAGTA-TA
* *
144337 -GGTTGGAGTTTCCTTGAAGATAAAATTATGAAAACATTTAAGGACAAAGAGAAAATTTGATTTT
1 GGGTTGGAGTTTCCCTAAAGATAAAATTATGAAAACATTTAAGGACAAAGAGAAAATTTGATTTT
* *
144401 TTATGAAGAATG-GGATTGAAGTATTCCCACAAAATAGTA
66 TTATGAAGAATGAGG-TTGAAGTATTCCCTCAAAGTA-TA
* *
144440 GGGTTGGACTTTCCCTAAAGATAAAATTATG-AAACTATTTAAGGACAAAGAGAAATTTTGATTT
1 GGGTTGGAGTTTCCCTAAAGATAAAATTATGAAAAC-ATTTAAGGACAAAGAGAAAATTTGA---
*
144504 TTTTTTATGAAGAATGAGGTTAAAGTAT
62 TTTTTTATGAAGAATGAGGTTGAAGTAT
144532 CTCTTCGAAG
Statistics
Matches: 256, Mismatches: 30, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
102 63 0.25
103 54 0.21
104 61 0.24
105 50 0.20
106 2 0.01
107 24 0.09
108 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (103 bp):
GGGTTGGAGTTTCCCTAAAGATAAAATTATGAAAACATTTAAGGACAAAGAGAAAATTTGATTTT
TTATGAAGAATGAGGTTGAAGTATTCCCTCAAAGTATA
Found at i:144492 original size:206 final size:209
Alignment explanation
Indices: 144146--144532 Score: 527
Period size: 206 Copynumber: 1.9 Consensus size: 209
144136 AGCATCCCTA
*
144146 AAGATAAAATTATGAAAATATTTAGGAACAAAGAGAAAATTTAATTCTTTTATGAAGAACGTGGT
1 AAGATAAAATTATGAAAACATTTAGGAACAAAGAGAAAATTTAATTCTTTTATGAAGAACGTGGT
* * * * * * * *
144211 TGGAGTATTTCCTCGAAGTATTGGAATTAGAGTTTCCCTAAAGATAAAATTATGAAAACATTTAG
66 TGAAGTATTCCCACAAAATATAGGAATTAGACTTTCCCTAAAGATAAAATTATGAAAACATTTAA
* *
144276 GGATAAAGAGAAAATTTGA-TTTTTT-TGAAGAATGAGGTTGAAGTATCCTCTCAAGGTACTAGG
131 GGACAAAGAGAAAATTTGATTTTTTTATGAAGAATGAGGTTAAAGTATCCTCTCAAGGTACTAGG
144339 TTGGAGTTTCCTTG
196 TTGGAGTTTCCTTG
* *
144353 AAGATAAAATTATGAAAACATTTAAGG-ACAAAGAGAAAATTTGATT-TTTTATGAAGAATG-GG
1 AAGATAAAATTATGAAAACATTT-AGGAACAAAGAGAAAATTTAATTCTTTTATGAAGAACGTGG
* *
144415 ATTGAAGTATTCCCACAAAATAGTAGG-GTTGGACTTTCCCTAAAGATAAAATTATG-AAACTAT
65 -TTGAAGTATTCCCACAAAATA-TAGGAATTAGACTTTCCCTAAAGATAAAATTATGAAAAC-AT
*
144478 TTAAGGACAAAGAGAAATTTTGATTTTTTTTTATGAAGAATGAGGTTAAAGTATC
127 TTAAGGACAAAGAGAAAATTTGA--TTTTTTTATGAAGAATGAGGTTAAAGTATC
144533 TCTTCGAAGT
Statistics
Matches: 156, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
205 6 0.04
206 77 0.49
207 43 0.28
208 3 0.02
209 6 0.04
210 21 0.13
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.33
Consensus pattern (209 bp):
AAGATAAAATTATGAAAACATTTAGGAACAAAGAGAAAATTTAATTCTTTTATGAAGAACGTGGT
TGAAGTATTCCCACAAAATATAGGAATTAGACTTTCCCTAAAGATAAAATTATGAAAACATTTAA
GGACAAAGAGAAAATTTGATTTTTTTATGAAGAATGAGGTTAAAGTATCCTCTCAAGGTACTAGG
TTGGAGTTTCCTTG
Found at i:147760 original size:65 final size:65
Alignment explanation
Indices: 147669--147824 Score: 203
Period size: 65 Copynumber: 2.4 Consensus size: 65
147659 TAACCTTACA
* * **
147669 ACACTATCTTTCAAGGCTAATATAGAAACCTCCCTATCTATT-CACGGGCTAAGATAGAACCTCT
1 ACACTATCTTTTAAGGCTAAGATAGAAACCTCCCTATCTATTACAAAGGCTAAGATAGAACCTCT
* *
147733 TC-CTTATCTTTTGCAA-GCTAAGATAG-AACCTCCCTATCTTTTACAAAGGCTAAGATAGAACC
1 ACAC-TATCTTTT--AAGGCTAAGATAGAAACCTCCCTATCTATTACAAAGGCTAAGATAGAACC
147795 TCT
63 TCT
147798 ACACTATCTTTTAAGGCTAAGATAGAA
1 ACACTATCTTTTAAGGCTAAGATAGAA
147825 CCTTTTAATC
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
63 3 0.04
64 33 0.42
65 39 0.50
66 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (65 bp):
ACACTATCTTTTAAGGCTAAGATAGAAACCTCCCTATCTATTACAAAGGCTAAGATAGAACCTCT
Found at i:147763 original size:64 final size:64
Alignment explanation
Indices: 147669--147827 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 64
147659 TAACCTTACA
* * **
147669 ACACTATCTTTCAAGGCTAATATAGAAACCTCCCTATCTATT-CACGGGCTAAGATAGAACCTCT
1 ACACTATCTTTTAAGGCTAAGATAG-AACCTCCCTATCTATTACAAAGGCTAAGATAGAACCTCT
* *
147733 TC-CTTATCTTTTGCAA-GCTAAGATAGAACCTCCCTATCTTTTACAAAGGCTAAGATAGAACCT
1 ACAC-TATCTTTT--AAGGCTAAGATAGAACCTCCCTATCTATTACAAAGGCTAAGATAGAACCT
147796 CT
63 CT
147798 ACACTATCTTTTAAGGCTAAGATAGAACCT
1 ACACTATCTTTTAAGGCTAAGATAGAACCT
147828 TTTAATCACT
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
63 3 0.04
64 38 0.46
65 38 0.46
66 3 0.04
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.30
Consensus pattern (64 bp):
ACACTATCTTTTAAGGCTAAGATAGAACCTCCCTATCTATTACAAAGGCTAAGATAGAACCTCT
Found at i:147790 original size:32 final size:31
Alignment explanation
Indices: 147672--147827 Score: 169
Period size: 32 Copynumber: 4.9 Consensus size: 31
147662 CCTTACAACA
*
147672 CTATC-TTTCAAGGCTAATATAGAAACCTC-C
1 CTATCTTTTCAAGGCTAAGATAG-AACCTCTC
* *
147702 CTATCTATTCACGGGCTAAGATAGAACCTCTTC
1 CTATCTTTTCA-AGGCTAAGATAGAACCTC-TC
147735 CTTATCTTTTGCAA-GCTAAGATAGAACCTC-C
1 C-TATCTTTT-CAAGGCTAAGATAGAACCTCTC
147766 CTATCTTTTACAAAGGCTAAGATAGAACCTCTAC
1 CTATCTTTT-C-AAGGCTAAGATAGAACCTCT-C
147800 ACTATCTTTT-AAGGCTAAGATAGAACCT
1 -CTATCTTTTCAAGGCTAAGATAGAACCT
147828 TTTAATCACT
Statistics
Matches: 109, Mismatches: 6, Indels: 20
0.81 0.04 0.15
Matches are distributed among these distances:
30 14 0.13
31 14 0.13
32 44 0.40
33 18 0.17
34 8 0.07
35 11 0.10
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (31 bp):
CTATCTTTTCAAGGCTAAGATAGAACCTCTC
Found at i:148295 original size:13 final size:13
Alignment explanation
Indices: 148279--148305 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
148269 ACAATTCATC
148279 ATGTATCGATACA
1 ATGTATCGATACA
148292 ATGTATCGATACA
1 ATGTATCGATACA
148305 A
1 A
148306 AGTGAGTTTT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:148502 original size:20 final size:21
Alignment explanation
Indices: 148479--148522 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
148469 GATACTTTGA
148479 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
148499 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTA-GCTTGAAAAAC
148521 AT
1 AT
148523 CTACACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:149174 original size:20 final size:20
Alignment explanation
Indices: 149149--149225 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
149139 TTTTACCCAG
149149 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
*
149169 ATGTATCGATACATGTA-TGA
1 ATGTATCGATACAT-TATTCA
* *
149189 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTATTCA
149209 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
149226 GTCTTTTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.94
21 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTATTCA
Found at i:149209 original size:40 final size:39
Alignment explanation
Indices: 149149--149226 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
149139 TTTTACCCAG
149149 ATGTATCGATACATTATTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTATTCAATGTATCGATACAT-TATGA
* *
149189 ATGTATTGATACATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTATTCAATGTATCGATACATTATG
149227 TCTTTTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTATTCAATGTATCGATACATTATGA
Found at i:157938 original size:13 final size:13
Alignment explanation
Indices: 157920--157945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
157910 AATTTTTTTG
157920 TGTATCGATACAT
1 TGTATCGATACAT
157933 TGTATCGATACAT
1 TGTATCGATACAT
157946 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:163502 original size:21 final size:21
Alignment explanation
Indices: 163476--163552 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
163466 AAAAAATTCA
163476 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
163497 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
163518 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
163539 AATGTATCGATACA
1 AATGTATCGATACA
163553 GGGTCTTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:163612 original size:19 final size:19
Alignment explanation
Indices: 163588--163655 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
163578 AATTCAACAA
163588 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
163607 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
163622 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
163639 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
163656 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:163627 original size:13 final size:13
Alignment explanation
Indices: 163609--163633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
163599 ACATAAGTTT
163609 TGTATCGATACAA
1 TGTATCGATACAA
163622 TGTATCGATACA
1 TGTATCGATACA
163634 TAAGTATTGT
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:163631 original size:32 final size:32
Alignment explanation
Indices: 163590--163652 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
163580 TTCAACAATT
*
163590 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
163622 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
163653 TAATTAGCTA
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:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:166188 original size:27 final size:28
Alignment explanation
Indices: 166158--166231 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 28
166148 TTCTCACAAT
166158 CGGGGATACTCCAACCCCGTTA-ATCAC
1 CGGGGATACTCCAACCCCGTTATATCAC
* * **
166185 CGGGGATACTCCAACCCCATTATTTCTG
1 CGGGGATACTCCAACCCCGTTATATCAC
*
166213 AGGGGATACTCCAACCCCG
1 CGGGGATACTCCAACCCCG
166232 ACTTTATTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.20
Consensus pattern (28 bp):
CGGGGATACTCCAACCCCGTTATATCAC
Found at i:166333 original size:52 final size:51
Alignment explanation
Indices: 166048--166436 Score: 265
Period size: 51 Copynumber: 7.4 Consensus size: 51
166038 CTCAATTCTC
* * * *
166048 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTT
* * * * * *
166098 CTATAATCGGGGATACTGCAACTCCGATTTTATTTCCAAAAAACACCAAATTCT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAACACTAATTTTT
* ** **
166152 CACAATCGGGGATACTCCAACCCCG--TTAATCACCGGGGATACTCCAAC-CCCATTATTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCC----A-A----AACACTAATT-TTT
** * * * *
166210 C-TGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTT
* * *
166258 CACAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTT
* * *
166309 CAACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTT
** *
166361 C-CTTTAATCGGGGATACTCCAATTCCGATTTTATTTCCAAAA-ATATCAATTTTT
1 CAC---AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACA-CT-AATTTTT
*
166415 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
166437 TCGTTATCTC
Statistics
Matches: 265, Mismatches: 49, Indels: 48
0.73 0.14 0.13
Matches are distributed among these distances:
48 6 0.02
49 4 0.02
50 2 0.01
51 75 0.28
52 65 0.25
53 64 0.24
54 13 0.05
55 19 0.07
57 11 0.04
58 6 0.02
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTT
Found at i:166393 original size:53 final size:52
Alignment explanation
Indices: 166214--166436 Score: 243
Period size: 52 Copynumber: 4.3 Consensus size: 52
166204 TTATTTCTGA
** * ***
166214 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTC-ACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCAACAATC
* * *
166265 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCAACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCAACAATC
* ***
166317 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTT-CAACAATC
** * * *
166370 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATATCAATTTTTC-ACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTTCAACAATC
*
166422 GAGGATACTCCAACC
1 GGGGATACTCCAACC
166437 TCGTTATCTC
Statistics
Matches: 144, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
51 38 0.26
52 62 0.43
53 31 0.22
54 13 0.09
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCAACAATC
Found at i:166523 original size:28 final size:28
Alignment explanation
Indices: 166455--166523 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
166445 TCATCGGGGG
*
166455 TACTCCAACCCCATTACTTCCGAGGAGA
1 TACTCCAACCCCGTTACTTCCGAGGAGA
* *
166483 TACTCCAACCCCGTTATTTTCGAAGG-GA
1 TACTCCAACCCCGTTACTTCCG-AGGAGA
*
166511 TACTCCAATCCCG
1 TACTCCAACCCCG
166524 ATTTTTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 33 0.92
29 3 0.08
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.25
Consensus pattern (28 bp):
TACTCCAACCCCGTTACTTCCGAGGAGA
Found at i:168359 original size:7 final size:7
Alignment explanation
Indices: 168344--168428 Score: 59
Period size: 7 Copynumber: 11.9 Consensus size: 7
168334 TCCTTCGTAC
168344 CAAAAAA
1 CAAAAAA
168351 -AATAAAA
1 CAA-AAAA
168358 -AAACAAA
1 CAAA-AAA
*
168365 -AAAAAC
1 CAAAAAA
*
168371 CAAGAAA
1 CAAAAAA
*
168378 TAAAAAA
1 CAAAAAA
*
168385 GAAAAAA
1 CAAAAAA
*
168392 CCAAAAA
1 CAAAAAA
168399 CAAAAAAA
1 C-AAAAAA
168407 CAAAAAA
1 CAAAAAA
168414 CAAACAAA
1 CAAA-AAA
168422 CGAAAAA
1 C-AAAAA
168429 GAGGTCCAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
6 5 0.08
7 43 0.68
8 12 0.19
9 3 0.05
ACGTcount: A:0.81, C:0.13, G:0.04, T:0.02
Consensus pattern (7 bp):
CAAAAAA
Found at i:168367 original size:15 final size:14
Alignment explanation
Indices: 168347--168428 Score: 65
Period size: 15 Copynumber: 5.4 Consensus size: 14
168337 TTCGTACCAA
168347 AAAAAATAAAAAAAC
1 AAAAAA-AAAAAAAC
*
168362 AAAAAAAACCAAGAAAT
1 AAAAAAAA--AA-AAAC
*
168379 AAAAAAGAAAAAACC
1 AAAAAA-AAAAAAAC
*
168394 AAAAACAAAAAAAC
1 AAAAAAAAAAAAAC
*
168408 AAAAAACAAACAAAC
1 AAAAAA-AAAAAAAC
168423 GAAAAA
1 -AAAAA
168429 GAGGTCCAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 14 0.26
15 20 0.37
16 9 0.17
17 9 0.17
18 2 0.04
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:168389 original size:22 final size:22
Alignment explanation
Indices: 168364--168428 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
168354 AAAAAAACAA
* *
168364 AAAAAACCAAGAAA-TAAAAAAG
1 AAAAAACCAA-AAACAAAAAAAC
168386 AAAAAACCAAAAACAAAAAAAC
1 AAAAAACCAAAAACAAAAAAAC
* *
168408 AAAAAACAAACAAACGAAAAA
1 AAAAAACCAA-AAACAAAAAA
168429 GAGGTCCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 3 0.08
22 25 0.68
23 9 0.24
ACGTcount: A:0.80, C:0.14, G:0.05, T:0.02
Consensus pattern (22 bp):
AAAAAACCAAAAACAAAAAAAC
Found at i:169545 original size:20 final size:20
Alignment explanation
Indices: 169501--169558 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
169491 ATTTCAACGA
***
169501 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATATTTT
*
169521 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
169541 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
169559 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:169615 original size:13 final size:13
Alignment explanation
Indices: 169597--169621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169587 ATTACTCAAA
169597 TGTATCGATACAT
1 TGTATCGATACAT
169610 TGTATCGATACA
1 TGTATCGATACA
169622 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:169721 original size:52 final size:52
Alignment explanation
Indices: 169630--169757 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
169620 CACTGATCTT
* *
169630 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATATA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
169681 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
169733 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
169758 TCATATTTCG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 19 0.26
52 51 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:173316 original size:28 final size:28
Alignment explanation
Indices: 173284--173685 Score: 466
Period size: 28 Copynumber: 14.1 Consensus size: 28
173274 CGTTCATGTC
* *
173284 TTCAAAGCCCACAGGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
173312 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
173340 TTCAAAGCCAACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
173368 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
173396 TTGAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
173424 TTCAAAGCCCACAAGCCAGTGGCAT-TT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** * *
173451 CTTCAAAAAACCACAAGTTAATGGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
* * *
173481 TTCAAAGCCCACAAGTCAATGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
173509 TCCAAAGCCCACAAATCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
173537 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
173565 TTCAAAGGCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
*
173595 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
173623 TTCAAAGCCCACACAAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
*
173655 TTCAAAGCCCACACAAGTTAGTGGCA-CCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
173684 TT
1 TT
173686 TTTTTAAAAA
Statistics
Matches: 322, Mismatches: 43, Indels: 17
0.84 0.11 0.04
Matches are distributed among these distances:
27 1 0.00
28 228 0.71
29 26 0.08
30 40 0.12
31 2 0.01
32 25 0.08
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:173538 original size:141 final size:142
Alignment explanation
Indices: 173284--173635 Score: 460
Period size: 141 Copynumber: 2.5 Consensus size: 142
173274 CGTTCATGTC
* ** ** *
173284 TTCAAAGCCCACAGGTTAGTGGCAT--CCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAG
1 TTCAAAGCCCACAAGCCAGTGGCATACCCTTTCAAAAACCACAAGTCAGTGGCATCCTTTCAAAG
* * * * * *
173347 CCAACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTGAAAGCCCACAAGT
66 CCCACAAGTCAATGGCACCCTTCCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGT
*
173412 CAGTGGCATCCT
131 CAGTGGCACCCT
** * *
173424 TTCAAAGCCCACAAGCCAGTGGCAT-TTC-TTCAAAAAACCACAAGTTAATGGCATCCTTTCAAA
1 TTCAAAGCCCACAAGCCAGTGGCATACCCTTTC-AAAAACCACAAGTCAGTGGCATCCTTTCAAA
*
173487 GCCCACAAGTCAATGGTACCCTTCCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAG
65 GCCCACAAGTCAATGGCACCCTTCCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAG
173552 TCAGTGGCACCCT
130 TCAGTGGCACCCT
* * ** *
173565 TTCAAAGGCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
1 TTCAAAGCCCACAAGCCAGTGGCATACCCTTTCAAAAACCACAAGTCAGTGGCATCCTTTCAAAG
173630 CCCACA
66 CCCACA
173636 CAAGTCGGTG
Statistics
Matches: 182, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
140 25 0.14
141 120 0.66
142 34 0.19
143 3 0.02
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.21
Consensus pattern (142 bp):
TTCAAAGCCCACAAGCCAGTGGCATACCCTTTCAAAAACCACAAGTCAGTGGCATCCTTTCAAAG
CCCACAAGTCAATGGCACCCTTCCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGT
CAGTGGCACCCT
Found at i:174543 original size:20 final size:20
Alignment explanation
Indices: 174518--174577 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
174508 ATTTACACAG
*
174518 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
174538 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
*
174558 ATGTATCCATACATTCTATC
1 ATGTATCGATACATT-TATC
174578 TTTTTACCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:174631 original size:20 final size:20
Alignment explanation
Indices: 174608--174645 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
174598 TATATGTATA
174608 AATGTATCAATACATTCTTC
1 AATGTATCAATACATTCTTC
*
174628 AATGTATCGATACATTCT
1 AATGTATCAATACATTCT
174646 ATCTTTTTAT
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:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
AATGTATCAATACATTCTTC
Found at i:174632 original size:71 final size:71
Alignment explanation
Indices: 174515--174673 Score: 205
Period size: 71 Copynumber: 2.2 Consensus size: 71
174505 CATATTTACA
* * * * *
174515 CAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCCATACATTCTATCTT
1 CAGATGTATCGATACATGTATAAATGTATCAATACATGTATCAATGTATCCATACATTCTATCTT
174580 TTTA-C
66 TTTATC
* * *
174585 CTAGATGTATCGATATATGTATAAATGTATCAATACAT-TCTTCAATGTATCGATACATTCTATC
1 C-AGATGTATCGATACATGTATAAATGTATCAATACATGT-ATCAATGTATCCATACATTCTATC
174649 TTTTTATC
64 TTTTTATC
*
174657 CAGATGTATCAATACAT
1 CAGATGTATCGATACAT
174674 TGAATAATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
70 2 0.03
71 72 0.95
72 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (71 bp):
CAGATGTATCGATACATGTATAAATGTATCAATACATGTATCAATGTATCCATACATTCTATCTT
TTTATC
Found at i:174692 original size:71 final size:71
Alignment explanation
Indices: 174557--174693 Score: 188
Period size: 71 Copynumber: 1.9 Consensus size: 71
174547 TACATGTATG
* * * *
174557 AATGTATCCATACATTCTATCTTTTTACCTAGATGTATCGATATATGTATAAATGTATCAATACA
1 AATGTATCCATACATTCTATCTTTTTACCTAGATGTATCAATACATGAATAAATATATCAATACA
174622 TTCTTC
66 TTCTTC
* *
174628 AATGTATCGATACATTCTATCTTTTTATCC-AGATGTATCAATACATTGAAT-AATATATCGATA
1 AATGTATCCATACATTCTATCTTTTTA-CCTAGATGTATCAATACA-TGAATAAATATATCAATA
174691 CAT
64 CAT
174694 CTAGTTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
71 52 0.90
72 6 0.10
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (71 bp):
AATGTATCCATACATTCTATCTTTTTACCTAGATGTATCAATACATGAATAAATATATCAATACA
TTCTTC
Found at i:181610 original size:13 final size:13
Alignment explanation
Indices: 181592--181617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
181582 ACAATTTTTG
181592 TGTATCGATACAT
1 TGTATCGATACAT
181605 TGTATCGATACAT
1 TGTATCGATACAT
181618 ACTTTCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:181614 original size:32 final size:32
Alignment explanation
Indices: 181573--181635 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
181563 TACAAGCCAA
* *
181573 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCTGTATCGATACAT
181605 TGTATCGATACATACTTTCTGTATCGATACA
1 TGTATCGATACATACTTTCTGTATCGATACA
181636 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTCTGTATCGATACAT
Found at i:181682 original size:21 final size:21
Alignment explanation
Indices: 181656--181731 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
181646 CTGCCAAGAA
*
181656 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
181677 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
181697 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
181718 ATGTATCGATACAT
1 ATGTATCGATACAT
181732 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:181702 original size:20 final size:20
Alignment explanation
Indices: 181677--181749 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
181667 CATCTTTTTT
181677 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
181697 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
181718 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
181738 ATGTATCGATAC
1 ATGTATCGATAC
181750 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:181713 original size:41 final size:41
Alignment explanation
Indices: 181656--181749 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
181646 CTGCCAAGAA
*
181656 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
181697 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
181738 ATGTATCGATAC
1 ATGTATCGATAC
181750 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:183453 original size:13 final size:13
Alignment explanation
Indices: 183435--183459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183425 ACTGAAGCAA
183435 TGTATCGATACAT
1 TGTATCGATACAT
183448 TGTATCGATACA
1 TGTATCGATACA
183460 ATCTGGAAAA
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:187012 original size:13 final size:13
Alignment explanation
Indices: 186994--187019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
186984 ACAATTTTTG
186994 TGTATCGATACAT
1 TGTATCGATACAT
187007 TGTATCGATACAT
1 TGTATCGATACAT
187020 ACTTTCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:187016 original size:32 final size:32
Alignment explanation
Indices: 186975--187037 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
186965 TACAAGCCAA
* *
186975 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCTGTATCGATACAT
187007 TGTATCGATACATACTTTCTGTATCGATACA
1 TGTATCGATACATACTTTCTGTATCGATACA
187038 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTCTGTATCGATACAT
Found at i:187084 original size:21 final size:21
Alignment explanation
Indices: 187058--187133 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
187048 CTGCCAAGAA
*
187058 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
187079 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
187099 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
187120 ATGTATCGATACAT
1 ATGTATCGATACAT
187134 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:187104 original size:20 final size:20
Alignment explanation
Indices: 187079--187151 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
187069 CATCTTTTTT
187079 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
187099 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
187120 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
187140 ATGTATCGATAC
1 ATGTATCGATAC
187152 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:187115 original size:41 final size:41
Alignment explanation
Indices: 187058--187151 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
187048 CTGCCAAGAA
*
187058 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
187099 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
187140 ATGTATCGATAC
1 ATGTATCGATAC
187152 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:189799 original size:13 final size:13
Alignment explanation
Indices: 189781--189806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
189771 CAATTTTTGG
189781 TGTATCGATACAT
1 TGTATCGATACAT
189794 TGTATCGATACAT
1 TGTATCGATACAT
189807 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:189818 original size:32 final size:33
Alignment explanation
Indices: 189761--189824 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
189751 TACAAGCCAA
**
189761 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
189794 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
189825 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:189831 original size:19 final size:18
Alignment explanation
Indices: 189761--189831 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
189751 TACAAGCCAA
189761 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
189781 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
189794 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
189813 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
189832 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:189918 original size:20 final size:20
Alignment explanation
Indices: 189865--189920 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
189855 ACATCCTTTT
* *
189865 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGAAA
189885 CATGTATCGATACTTTGAAA
1 CATGTATCGATACTTTGAAA
**
189905 TGTGTATCGATACTTT
1 CATGTATCGATACTTT
189921 TAAGGGTTTT
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:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGAAA
Found at i:190477 original size:39 final size:37
Alignment explanation
Indices: 190429--190521 Score: 91
Period size: 39 Copynumber: 2.5 Consensus size: 37
190419 TTTCTTTCTT
190429 CCTTAAATAAAATAATTTTAACAAGTT-CGTACATTCTCCC
1 CCTT-AATAAAATAATTTTAACAAGTTACG--CATTCT-CC
** * *
190469 CCTTAATAAGGTAATTTTAGCAATTTACGCATTCTCC
1 CCTTAATAAAATAATTTTAACAAGTTACGCATTCTCC
*
190506 CCTTAA-AAAAAAATTT
1 CCTTAATAAAATAATTT
190522 CCACCTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
36 7 0.16
37 8 0.18
38 6 0.13
39 18 0.40
40 6 0.13
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (37 bp):
CCTTAATAAAATAATTTTAACAAGTTACGCATTCTCC
Found at i:192366 original size:13 final size:13
Alignment explanation
Indices: 192348--192373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
192338 ATAATCACCC
192348 TGTATCGATACAA
1 TGTATCGATACAA
192361 TGTATCGATACAA
1 TGTATCGATACAA
192374 AGAAAAATGT
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:198564 original size:13 final size:13
Alignment explanation
Indices: 198546--198571 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
198536 CAATTTTTGG
198546 TGTATCGATACAT
1 TGTATCGATACAT
198559 TGTATCGATACAT
1 TGTATCGATACAT
198572 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:198588 original size:32 final size:33
Alignment explanation
Indices: 198526--198589 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
198516 TACAAGCCAA
**
198526 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
*
198559 TGTATCGATAC-ATACTTGGTGTATTGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
198590 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:198683 original size:20 final size:20
Alignment explanation
Indices: 198630--198685 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
198620 ACATCTTTTT
* *
198630 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGAAA
198650 CATGTATCGATACTTTGAAA
1 CATGTATCGATACTTTGAAA
**
198670 TGTGTATCGATACTTT
1 CATGTATCGATACTTT
198686 TAAAGGTTTT
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:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGAAA
Found at i:199079 original size:64 final size:64
Alignment explanation
Indices: 198985--199144 Score: 214
Period size: 64 Copynumber: 2.5 Consensus size: 64
198975 TAACCTTACA
* * * **
198985 ACACTATCTTTCAAGGCTAAGATAAAAACCTCCTTATCTTTT-CATGGGCTAAGATAGAACCTCT
1 ACACTATCTTTTAAGGCTAAGAT-AGAACCTCCCTATCTTTTACAAAGGCTAAGATAGAACCTCT
* * *
199049 TCCCTATCTTTTGCAGGCTAAGATAGAACCTCCCTATCTTTTACAAAGGCTAAGATAGAACCTCT
1 ACACTATCTTTT-AAGGCTAAGATAGAACCTCCCTATCTTTTACAAAGGCTAAGATAGAACCTCT
*
199114 ACACTATCTTTTAAGGCTAAAATAGAACCTC
1 ACACTATCTTTTAAGGCTAAGATAGAACCTC
199145 TCAATCACTT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 42 0.51
65 40 0.49
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (64 bp):
ACACTATCTTTTAAGGCTAAGATAGAACCTCCCTATCTTTTACAAAGGCTAAGATAGAACCTCT
Found at i:199139 original size:32 final size:31
Alignment explanation
Indices: 198988--199146 Score: 146
Period size: 32 Copynumber: 5.0 Consensus size: 31
198978 CCTTACAACA
* *
198988 CTATC-TTTCAAGGCTAAGATAAAAACCTC-C
1 CTATCTTTTAAAGGCTAAGAT-AGAACCTCTC
* **
199018 TTATCTTTTCATGGGCTAAGATAGAACCTCTTCC
1 CTATCTTTT-AAAGGCTAAGATAGAACCTC-T-C
**
199052 CTATCTTTTGCAGGCTAAGATAGAACCTC-C
1 CTATCTTTTAAAGGCTAAGATAGAACCTCTC
199082 CTATCTTTTACAAAGGCTAAGATAGAACCTCTAC
1 CTATCTTTT--AAAGGCTAAGATAGAACCTCT-C
*
199116 ACTATCTTTT-AAGGCTAAAATAGAACCTCTC
1 -CTATCTTTTAAAGGCTAAGATAGAACCTCTC
199147 AATCACTTGG
Statistics
Matches: 107, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
30 14 0.13
31 11 0.10
32 46 0.43
33 17 0.16
34 10 0.09
35 9 0.08
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (31 bp):
CTATCTTTTAAAGGCTAAGATAGAACCTCTC
Found at i:199600 original size:20 final size:20
Alignment explanation
Indices: 199575--199629 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
199565 GTTGGGCTCA
199575 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
*
199595 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
*
199615 ACGTATCGATACAAT
1 ATGTATCGATACAAT
199630 GTATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:199635 original size:13 final size:13
Alignment explanation
Indices: 199617--199641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
199607 AATTCATCAC
199617 GTATCGATACAAT
1 GTATCGATACAAT
199630 GTATCGATACAA
1 GTATCGATACAA
199642 AGTGAGTTTT
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:199855 original size:20 final size:21
Alignment explanation
Indices: 199830--199870 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
199820 ACTTTGAATA
199830 ATTTTTA-CTTGAAAAACATT
1 ATTTTTACCTTGAAAAACATT
199850 ATTTTTATCCTTGAAAAACAT
1 ATTTTTA-CCTTGAAAAACAT
199871 CTATACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTTTACCTTGAAAAACATT
Found at i:205563 original size:21 final size:21
Alignment explanation
Indices: 205525--205569 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
205515 TTGCAAGTTG
*
205525 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
205547 AAATAATGAA-TTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
205567 AAA
1 AAA
205570 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:207388 original size:15 final size:15
Alignment explanation
Indices: 207368--207398 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
207358 TAAAAATGTC
*
207368 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
207383 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
207398 C
1 C
207399 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:209492 original size:20 final size:20
Alignment explanation
Indices: 209413--209492 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
209403 AATGTCCAAA
*
209413 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
209433 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
209458 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
209478 TTGTATCGATACATT
1 ATGTATCGATACATT
209493 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:209496 original size:13 final size:13
Alignment explanation
Indices: 209478--209516 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
209468 ACATTTTTCT
209478 TTGTATCGATACA
1 TTGTATCGATACA
209491 TTGTATCGATACA
1 TTGTATCGATACA
*
209504 CTGTATCGATACA
1 TTGTATCGATACA
209517 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:209661 original size:21 final size:21
Alignment explanation
Indices: 209637--209683 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
209627 AAATCTTTTG
209637 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
209658 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
209678 CAAAAT
1 CAAAAT
209684 CAGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:209680 original size:20 final size:19
Alignment explanation
Indices: 209639--209681 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
209629 ATCTTTTGCA
209639 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
209659 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
209679 AAA
1 AAA
209682 ATCAGCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:214508 original size:78 final size:78
Alignment explanation
Indices: 214264--214580 Score: 397
Period size: 78 Copynumber: 4.1 Consensus size: 78
214254 GGGATTTAAT
* * *
214264 TATCCCCTCAAAAATAA-GAGGTTGGAGTATCCCTGATGGT-GAGAATGGGGTTTTAGAAATAAA
1 TATCCCCTCAAAAATAACGAGGTTAGAGTATCCCTGATGGTGGAAAATGGTGTTTTAGAAATAAA
*
214327 ATCGGGGTTAGAG
66 ATCGAGGTTAGAG
* * * * *
214340 TATCCCCTCGAAAATAGC-AGGGTTAGAGTATCCTTAATAGTGGAAAATTGGTGTTTTAGAAATA
1 TATCCCCTCAAAAATAACGA-GGTTAGAGTATCCCTGATGGTGGAAAA-TGGTGTTTTAGAAATA
214404 AAATCGAGGTTAGAG
64 AAATCGAGGTTAGAG
* * *
214419 TATCCCTTCAAAAATAACGAGGTTAGAGTATCCCCGATGGTGGAAAATCGTGTTTTAGAAATAAA
1 TATCCCCTCAAAAATAACGAGGTTAGAGTATCCCTGATGGTGGAAAATGGTGTTTTAGAAATAAA
* *
214484 ATCAAGGTTGGAG
66 ATCGAGGTTAGAG
* * * * **
214497 TATCCCCTCAAAAATAACGGGGTTGGAGTATACCTGATGGTGAAAAATTATGTTTTAGAAATAAA
1 TATCCCCTCAAAAATAACGAGGTTAGAGTATCCCTGATGGTGGAAAATGGTGTTTTAGAAATAAA
* *
214562 ACCGAGGTTGGAG
66 ATCGAGGTTAGAG
214575 TATCCC
1 TATCCC
214581 TAATGGTAGA
Statistics
Matches: 207, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
76 16 0.08
77 17 0.08
78 106 0.51
79 67 0.32
80 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (78 bp):
TATCCCCTCAAAAATAACGAGGTTAGAGTATCCCTGATGGTGGAAAATGGTGTTTTAGAAATAAA
ATCGAGGTTAGAG
Found at i:214576 original size:156 final size:155
Alignment explanation
Indices: 214264--214581 Score: 424
Period size: 157 Copynumber: 2.0 Consensus size: 155
214254 GGGATTTAAT
* * * * *
214264 TATCCCCTCAAAAATAAGAGGTTGGAGTATCCCTGATGGTGAGAATGGGGTTTTAGAAATAAAAT
1 TATCCCTTCAAAAATAAGAGGTTAGAGTATCCCCGATGGTGAAAATCGGGTTTTAGAAATAAAAT
** * * * *
214329 CGGGGTTAGAGTATCCCCTCGAAAATAGCAGGGTTAGAGTATCCTTAATAGTGGAAAATTGGTGT
66 CAAGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCTTAATAGTGAAAAATTGATGT
*
214394 TTTAGAAATAAAATCGAGGTTAGAG
131 TTTAGAAATAAAACCGAGGTTAGAG
*
214419 TATCCCTTCAAAAATAACGAGGTTAGAGTATCCCCGATGGTGGAAAATCGTGTTTTAGAAATAAA
1 TATCCCTTCAAAAATAA-GAGGTTAGAGTATCCCCGATGGT-GAAAATCGGGTTTTAGAAATAAA
* * * * *
214484 ATCAAGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATACC-TGATGGTGAAAAATT-A
64 ATCAAGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTAT-CCTTAATAGTGAAAAATTGA
*
214547 TGTTTTAGAAATAAAACCGAGGTTGGAG
128 TGTTTTAGAAATAAAACCGAGGTTAGAG
214575 TATCCCT
1 TATCCCT
214582 AATGGTAGAA
Statistics
Matches: 141, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
155 16 0.11
156 54 0.38
157 69 0.49
158 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (155 bp):
TATCCCTTCAAAAATAAGAGGTTAGAGTATCCCCGATGGTGAAAATCGGGTTTTAGAAATAAAAT
CAAGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCTTAATAGTGAAAAATTGATGT
TTTAGAAATAAAACCGAGGTTAGAG
Found at i:214587 original size:50 final size:51
Alignment explanation
Indices: 214517--214629 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
214507 AAAATAACGG
* * *
214517 GGTTGGAGTATACCTGATGGT-GAAAAAT-TATGTTTTAGAAATAAAACCGA
1 GGTTGGAGTATCCCTAATGGTAG-AAAATCGATGTTTTAGAAATAAAACCGA
* * * *
214567 GGTTGGAGTATCCCTAATGGTAGAAAATCGGTGTTTTAGAAGTAAAACTGG
1 GGTTGGAGTATCCCTAATGGTAGAAAATCGATGTTTTAGAAATAAAACCGA
*
214618 GGTGGGAGTATC
1 GGTTGGAGTATC
214630 GCTTCAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 24 0.45
51 29 0.55
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCTAATGGTAGAAAATCGATGTTTTAGAAATAAAACCGA
Found at i:214626 original size:129 final size:129
Alignment explanation
Indices: 214436--214711 Score: 344
Period size: 129 Copynumber: 2.1 Consensus size: 129
214426 TCAAAAATAA
* ** * *
214436 CGAGGTTAGAGTATCCCCGATGGTGGAAAATCGTGTTTTAGAAATAAAATCAAGGTTGGAGTATC
1 CGAGGTTGGAGTATCCCTAATGGTAGAAAATCGTGTTTTAGAAATAAAATCAAGGTGGGAGTATC
*
214501 CCCTCAAAAATAACGGGGTTG-GAGTATACC-TGATGGTGAAAAATT-ATGTTTTAGAAATAAAA
66 CCCTCAAAAATAACAGGGTTGAG-GTAT-CCATGATGGTGAAAAATTGATGTTTTAGAAATAAAA
214563 C
129 C
* **
214564 CGAGGTTGGAGTATCCCTAATGGTAGAAAATCGGTGTTTTAGAAGTAAAA-CTGGGGTGGGAGTA
1 CGAGGTTGGAGTATCCCTAATGGTAGAAAATC-GTGTTTTAGAAATAAAATC-AAGGTGGGAGTA
* * * * *
214628 TCGCTTCAAAAATAATAGGGTTTAGGTATCCATGATGGTGAAAAATTGATGTTTTAGAAGTAAAA
64 TCCCCTCAAAAATAACAGGGTTGAGGTATCCATGATGGTGAAAAATTGATGTTTTAGAAATAAAA
214693 C
129 C
* *
214694 TGGGGTTGGAGTATCCCT
1 CGAGGTTGGAGTATCCCT
214712 TCGAAAATAA
Statistics
Matches: 127, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
128 31 0.24
129 62 0.49
130 34 0.27
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (129 bp):
CGAGGTTGGAGTATCCCTAATGGTAGAAAATCGTGTTTTAGAAATAAAATCAAGGTGGGAGTATC
CCCTCAAAAATAACAGGGTTGAGGTATCCATGATGGTGAAAAATTGATGTTTTAGAAATAAAAC
Found at i:214673 original size:79 final size:79
Alignment explanation
Indices: 214598--214930 Score: 278
Period size: 79 Copynumber: 4.2 Consensus size: 79
214588 AGAAAATCGG
* * * *
214598 TGTTTTAGAAGTAAAACTGGGGTGGGAGTATCGCTTCAAAAATAATAGGGTTTAG-GTATCCATG
1 TGTTTTAGAAGTAAAACTGGGGTGGGAGTATCCCTTCAAAAATAACAAGG-TTAGAGTATCCACG
*
214662 ATGGTGAAAAATTGA
65 ATGATGAAAAATTGA
* * *
214677 TGTTTTAGAAGTAAAACTGGGGTTGGAGTATCCCTTCGAAAATAACAAGGTTAGAGTATCCCCGA
1 TGTTTTAGAAGTAAAACTGGGGTGGGAGTATCCCTTCAAAAATAACAAGGTTAGAGTATCCACGA
*
214742 TGATGGAAAATTGA
66 TGATGAAAAATTGA
* * * ** ** * * * *
214756 TGTTTTAAAAGTAAAACCGAGGTTTGAGTATCTTTCTCGAAAAA-AACGAGATTGGAGTATCCCC
1 TGTTTTAGAAGTAAAACTGGGGTGGGAGTATCCCT-TC-AAAAATAACAAGGTTAGAGTATCCAC
* * *
214820 GATGGTGAAAAATCGG
64 GATGATGAAAAATTGA
* * * * * * * * *
214836 TATTTTGGAAATAAAACAGGGGTTGAAGTATCTCC-TCAAAAATAACGAGATTAGAGTATCCCCG
1 TGTTTTAGAAGTAAAACTGGGGTGGGAGTATC-CCTTCAAAAATAACAAGGTTAGAGTATCCACG
* *
214900 ATGGTGGAAAATTGA
65 ATGATGAAAAATTGA
*
214915 TATTTTAGGAA-TAAAA
1 TGTTTTA-GAAGTAAAA
214931 AAATCAATGA
Statistics
Matches: 210, Mismatches: 38, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
78 9 0.04
79 139 0.66
80 58 0.28
81 4 0.02
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
TGTTTTAGAAGTAAAACTGGGGTGGGAGTATCCCTTCAAAAATAACAAGGTTAGAGTATCCACGA
TGATGAAAAATTGA
Found at i:220399 original size:51 final size:51
Alignment explanation
Indices: 220239--220409 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
220229 GAAATAACGA
* * *
220239 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTGGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTT-GAAAATAAAATCGG
** * * * * *
220291 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
220344 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
220395 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
220410 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 29 0.30
54 13 0.13
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:220455 original size:27 final size:28
Alignment explanation
Indices: 220392--220467 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
220382 AAAATAAAGT
*
220392 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
220420 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
220447 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
220468 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:222956 original size:13 final size:13
Alignment explanation
Indices: 222938--222963 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
222928 ACAAAGATCC
222938 ATGTATCGATACA
1 ATGTATCGATACA
222951 ATGTATCGATACA
1 ATGTATCGATACA
222964 CAGAAAAATG
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:222959 original size:33 final size:33
Alignment explanation
Indices: 222917--222983 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
222907 AAAATTTCCA
***
222917 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
222950 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
222983 A
1 A
222984 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:223027 original size:19 final size:18
Alignment explanation
Indices: 223003--223070 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
222993 CAGTAGCTAA
223003 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
223022 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
223037 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
223054 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
223071 TTGTTGAATT
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 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:223043 original size:13 final size:13
Alignment explanation
Indices: 223025--223049 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223015 ACAATACTTA
223025 TGTATCGATACAT
1 TGTATCGATACAT
223038 TGTATCGATACA
1 TGTATCGATACA
223050 AAACTTATGT
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:223047 original size:32 final size:32
Alignment explanation
Indices: 223006--223068 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
222996 TAGCTAATTA
*
223006 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
223038 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
223069 AATTGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:223150 original size:21 final size:21
Alignment explanation
Indices: 223126--223182 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
223116 CATTTGTAGG
223126 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
223147 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
223168 ATGTATCGATACATT
1 ATGTATCGATACATT
223183 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:223193 original size:1 final size:1
Alignment explanation
Indices: 223187--223231 Score: 63
Period size: 1 Copynumber: 45.0 Consensus size: 1
223177 TACATTTAAA
***
223187 TTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
223232 CAAACACTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:223219 original size:21 final size:21
Alignment explanation
Indices: 223193--223234 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
223183 TAAATTTTTT
223193 TTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTCAA
223214 TTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTCAA
223235 ACACTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTTTTCAA
Found at i:224050 original size:19 final size:18
Alignment explanation
Indices: 224026--224088 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
224016 AGCGATACAT
224026 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
224045 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
224058 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
224077 TGTATCGATACA
1 TGTATCGATACA
224089 GTTACTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:224059 original size:32 final size:32
Alignment explanation
Indices: 224018--224088 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
224008 AGCTTCGTAG
224018 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
224050 CGATACATTGTATTGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
224082 CGATACA
1 CGATACA
224089 GTTACTTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:224739 original size:61 final size:60
Alignment explanation
Indices: 224604--224792 Score: 204
Period size: 61 Copynumber: 3.1 Consensus size: 60
224594 TGAAGTAGAT
* *
224604 AGGTGCCACCAACTTGTATGGGT-TTT-AAAAGAAAAAGGAAGTGTCTTGCTCTTTGAGGACTAA
1 AGGTGCCACCAACTTGTGT-GGTCTTTAAAAAG-AAAAGG-A---TCCTGCTCTTTGAGGACTAA
224667 A
60 A
*
224668 AAGTGCCACCAACTTGTGTGGTCTTTAAAAAGAAAAGGCATCCTGCTCTTTGAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGTCTTTAAAAAGAAAAGG-ATCCTGCTCTTTGAGGACTAAA
* * * * * * *
224729 AGGTGCCACCAATTTGTGTGGACTTTAAAAGGAAAATG-TCCTACTTTTTAAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGTCTTTAAAAAGAAAAGGATCCTGCTCTTTGAGGACTAAA
224788 AGGTG
1 AGGTG
224793 TTAACTTCAG
Statistics
Matches: 111, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
59 23 0.21
61 53 0.48
63 3 0.03
64 27 0.24
65 5 0.05
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (60 bp):
AGGTGCCACCAACTTGTGTGGTCTTTAAAAAGAAAAGGATCCTGCTCTTTGAGGACTAAA
Found at i:235274 original size:20 final size:19
Alignment explanation
Indices: 235247--235323 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 19
235237 GTAAAAAGAC
235247 AAAATGTATCGATACATTG
1 AAAATGTATCGATACATTG
*
235266 AAGAATGTATCGATACATTC
1 AA-AATGTATCGATACATTG
*
235286 ATACATGTATCGATACATTG
1 A-AAATGTATCGATACATTG
235306 AAAAATGTATCGATACAT
1 -AAAATGTATCGATACAT
235324 CTGGGTAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
19 2 0.04
20 47 0.92
21 2 0.04
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:236560 original size:28 final size:28
Alignment explanation
Indices: 236201--236549 Score: 441
Period size: 28 Copynumber: 12.4 Consensus size: 28
236191 TAAAAAGGGT
* * *
236201 TGCCACCGACTTGCGTGGGCTTTTAAAGGG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGA
236231 TGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
236259 TGCCACTAACTTGTGGTCTTTTG-AAGAGA
1 TGCCACTGACTTGTGGGC-TTTGAAAG-GA
*
236288 TGTCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
236316 TGCCACTGAATTGTAGGCTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
236344 TGCCTCTGACTTGTGGACTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * **
236372 TGCCACTAACTTATCAGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
236400 TGCCACTAACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
236428 TGCCACTAACTTGTGGGCTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
236456 TGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
236484 TGCCACTGACCTGTGGGCTTTG-AAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAAG-GA
* * *
236512 CGCCATTGACTTATGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
236540 TGCCACTGAC
1 TGCCACTGAC
236550 CTACGAGCTT
Statistics
Matches: 278, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
27 3 0.01
28 237 0.85
29 27 0.10
30 11 0.04
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:237835 original size:18 final size:18
Alignment explanation
Indices: 237809--237852 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
237799 TTCTGGAACC
237809 TTTTTTTTGGTTTTTT-T
1 TTTTTTTTGGTTTTTTCT
237826 TTTGTTTTTGGTTTTTTCT
1 TTT-TTTTTGGTTTTTTCT
237845 TTTTTTTT
1 TTTTTTTT
237853 TTCTTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.86
Consensus pattern (18 bp):
TTTTTTTTGGTTTTTTCT
Found at i:240477 original size:28 final size:27
Alignment explanation
Indices: 240437--240492 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
240427 CCTCACCCTG
*
240437 TCAAAAGCCCACAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAACTCAGTGGC-ACCT
* *
240465 TCAAAAGTCCACAACTCTGTGGCACCT
1 TCAAAAGCCCACAACTCAGTGGCACCT
240492 T
1 T
240493 TTTCCTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (27 bp):
TCAAAAGCCCACAACTCAGTGGCACCT
Done.