Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold305
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: 704983
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 3 of 5
Found at i:295682 original size:52 final size:54
Alignment explanation
Indices: 295612--296266 Score: 236
Period size: 55 Copynumber: 11.8 Consensus size: 54
295602 ACATTGGCAC
295612 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * ** * *
295664 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * * * *
295719 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATC--TTTATCACT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCA-T
* * * * * * *
295772 CTTCTCA-TCATCATTTTTAAG-T--CC--AATATC-GC-TGGCCTTGAATCAGCATATTGGCAT
1 CTT-TAAGTC--CA-ATAT-AGCTGGCCTTGA-ATCAGCAT---ATTG--GCACCAT-TT----T
295829 CTTCAT
50 C-TCAT
* *
295835 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG---CA------C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
295878 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * ** * *
295930 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * *
295985 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-----CA--TTT-TC-TCAT
* *
296049 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG---CA-TCT-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * ** * *
296101 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * * *
296156 CTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-----CA---TT-T--TC-TC
296221 AT
53 AT
* *
296223 CTTTAAGTCCAATATTGCTGGTCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
296267 TTCATCATCT
Statistics
Matches: 443, Mismatches: 87, Indels: 137
0.66 0.13 0.21
Matches are distributed among these distances:
43 38 0.09
45 3 0.01
49 33 0.07
50 1 0.00
51 1 0.00
52 87 0.20
53 9 0.02
54 23 0.05
55 112 0.25
56 6 0.01
57 3 0.01
58 2 0.00
59 4 0.01
60 5 0.01
61 3 0.01
62 10 0.02
63 14 0.03
64 12 0.03
66 3 0.01
67 74 0.17
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
Found at i:295747 original size:55 final size:52
Alignment explanation
Indices: 295612--295749 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
295602 ACATTGGCAC
* *
295612 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACATTTTCCAT
* * * *
295664 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA--CATTTTC-CAT
* * * *
295719 CTTTAAGCCCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
295750 ACATATTGGC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 37 0.52
54 6 0.08
55 28 0.39
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACATTTTCCAT
Found at i:295828 original size:266 final size:266
Alignment explanation
Indices: 295349--296135 Score: 1538
Period size: 266 Copynumber: 3.0 Consensus size: 266
295339 GCAACCCCTC
* *
295349 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTTCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATGTA
295414 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
295479 AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCATTTTTAAGTCCAATATCGCTGGCCT
131 AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCATTTTTAAGTCCAATATCGCTGGCCT
295544 TGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
196 TGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
295609 CACCTT
261 CACCTT
295615 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATGTA
295680 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
295745 AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCATTTTTAAGTCCAATATCGCTGGCCT
131 AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCATTTTTAAGTCCAATATCGCTGGCCT
295810 TGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
196 TGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
295875 CACCTT
261 CACCTT
295881 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATGTA
295946 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
*
296011 AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATTTTTAAGTCCAATATCGCTGGCCT
131 AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCATTTTTAAGTCCAATATCGCTGGCCT
*
296076 TGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
196 TGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
296136 GTTGACATCC
Statistics
Matches: 517, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
266 517 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.35
Consensus pattern (266 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCATTTTTAAGTCCAATATCGCTGGCCT
TGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
CACCTT
Found at i:295859 original size:49 final size:49
Alignment explanation
Indices: 295777--296030 Score: 241
Period size: 49 Copynumber: 5.1 Consensus size: 49
295767 TCACTCTTCT
* * *
295777 CATCATCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* *
295826 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
295875 CA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* * * ** *
295918 CACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGA
1 --CATCTT-CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* * * * *
295970 CATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGG
1 CAT-C----T-TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
296025 CATCTT
1 CATCTT
296031 TATCACTTTT
Statistics
Matches: 167, Mismatches: 23, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
43 38 0.23
45 3 0.02
49 47 0.28
50 5 0.03
52 35 0.21
54 1 0.01
55 37 0.22
56 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (49 bp):
CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
Found at i:295896 original size:43 final size:44
Alignment explanation
Indices: 295787--295921 Score: 191
Period size: 43 Copynumber: 3.0 Consensus size: 44
295777 CATCATCATT
*
295787 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----CA-C
* *
295836 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACAC
295879 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACA
295922 TTTTCCATCT
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
43 41 0.51
45 1 0.01
49 38 0.47
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACAC
Found at i:296007 original size:55 final size:55
Alignment explanation
Indices: 295878--296261 Score: 264
Period size: 67 Copynumber: 6.7 Consensus size: 55
295868 ACATTGGCAC
* *
295878 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
295930 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
295985 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
296049 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
296101 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * * *
296156 CTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-C-TTT-T--TC-TC
296221 AT
54 AT
* *
296223 CTTTAAGTCCAATATTGCTGGTCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
296262 GCACCTTCAT
Statistics
Matches: 256, Mismatches: 43, Indels: 52
0.73 0.12 0.15
Matches are distributed among these distances:
49 36 0.14
50 1 0.00
52 42 0.16
54 8 0.03
55 64 0.25
56 2 0.01
57 2 0.01
58 2 0.01
59 1 0.00
61 8 0.03
62 6 0.02
63 5 0.02
64 7 0.03
66 4 0.02
67 68 0.27
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:296168 original size:171 final size:171
Alignment explanation
Indices: 295878--296272 Score: 691
Period size: 171 Copynumber: 2.3 Consensus size: 171
295868 ACATTGGCAC
*
295878 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAAT
295943 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
296008 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
128 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
296052 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
*
296117 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
*
296182 AATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* * *
296223 CTTTAAGTCCAATATTGCTGGTCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
296273 ATCTCTAAAA
Statistics
Matches: 212, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
171 169 0.80
172 5 0.02
174 38 0.18
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (171 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:297070 original size:33 final size:33
Alignment explanation
Indices: 297033--297099 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
297023 TTCAACGATT
297033 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
297066 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
297099 T
1 T
297100 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:297071 original size:13 final size:13
Alignment explanation
Indices: 297053--297077 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
297043 CATAAAATGT
297053 TGTATCGATACAA
1 TGTATCGATACAA
297066 TGTATCGATACA
1 TGTATCGATACA
297078 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:297158 original size:13 final size:13
Alignment explanation
Indices: 297140--297164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
297130 ATTACTCAAA
297140 TGTATCGATACAT
1 TGTATCGATACAT
297153 TGTATCGATACA
1 TGTATCGATACA
297165 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:297266 original size:52 final size:52
Alignment explanation
Indices: 297173--297300 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
297163 CACTGATCTT
*
297173 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
297224 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
297276 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
297301 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:303651 original size:13 final size:13
Alignment explanation
Indices: 303633--303658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
303623 TACACAAAGT
303633 ATGTATCGATACA
1 ATGTATCGATACA
303646 ATGTATCGATACA
1 ATGTATCGATACA
303659 CAAAAAATTA
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:307423 original size:13 final size:13
Alignment explanation
Indices: 307405--307429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
307395 TTTTCCAGAT
307405 TGTATCGATACAA
1 TGTATCGATACAA
307418 TGTATCGATACA
1 TGTATCGATACA
307430 TTGCTTCAGT
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:309514 original size:32 final size:33
Alignment explanation
Indices: 309473--309534 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
309463 TAGCCAAACT
**
309473 TGTATCGATACACAAAGTA-TGTATCGATATAA
1 TGTATCGATACACAAAAAATTGTATCGATATAA
309505 TGTATCGATACACAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAATTGTATCGATA
309535 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATATAA
Found at i:310338 original size:20 final size:20
Alignment explanation
Indices: 310313--310362 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
310303 AACTAGATAT
310313 ATCGATACATTGAATAATGC
1 ATCGATACATTGAATAATGC
310333 ATCGATACATTGAATAATGC
1 ATCGATACATTGAATAATGC
*
310353 ATTGATACAT
1 ATCGATACAT
310363 CTAGATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
ATCGATACATTGAATAATGC
Found at i:310405 original size:20 final size:20
Alignment explanation
Indices: 310379--310430 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
310369 AAAAAGACAG
* *
310379 AATGTATCGATACATTCATA
1 AATGTATCGATACATTAAAA
* *
310399 CATGTATCGATGCATTAAAA
1 AATGTATCGATACATTAAAA
310419 AATGTATCGATA
1 AATGTATCGATA
310431 TATTTGGGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:313787 original size:10 final size:10
Alignment explanation
Indices: 313772--313815 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
313762 CCTTCCTCTT
313772 TTTTTCTTTC
1 TTTTTCTTTC
313782 TTTTTCTTTC
1 TTTTTCTTTC
*
313792 TTTCTTCTCTC
1 TTT-TTCTTTC
**
313803 TTCCTCTTTC
1 TTTTTCTTTC
313813 TTT
1 TTT
313816 CTTTTCTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:313799 original size:21 final size:21
Alignment explanation
Indices: 313775--313834 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
313765 TCCTCTTTTT
*
313775 TTCTTTCTTTTTCTTTCTTTC
1 TTCTTTCTTTCTCTTTCTTTC
* *
313796 TTCTCTCTTCCTCTTTCTTTC
1 TTCTTTCTTTCTCTTTCTTTC
*
313817 TT-TTCTCTTTGT-TTTCTT
1 TTCTT-TCTTTCTCTTTCTT
313835 GTTCCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.72
Consensus pattern (21 bp):
TTCTTTCTTTCTCTTTCTTTC
Found at i:314932 original size:3 final size:3
Alignment explanation
Indices: 314924--314960 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
314914 AAAATTTTAT
314924 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
314961 GTTCCTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:315514 original size:26 final size:25
Alignment explanation
Indices: 315485--315558 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 25
315475 GAATTAATTT
315485 AAATAACTTAATTTATTAATTTAATA
1 AAATAA-TTAATTTATTAATTTAATA
*
315511 AAATTAATT-ATTT-GTAATTTACAT-
1 AAA-TAATTAATTTATTAATTTA-ATA
*
315535 AAA-AATTAA-TTATAAATTTAATA
1 AAATAATTAATTTATTAATTTAATA
315558 A
1 A
315559 CAAAAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
22 8 0.20
23 8 0.20
24 10 0.25
25 6 0.15
26 5 0.12
27 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (25 bp):
AAATAATTAATTTATTAATTTAATA
Found at i:315517 original size:22 final size:22
Alignment explanation
Indices: 315477--315558 Score: 78
Period size: 22 Copynumber: 3.6 Consensus size: 22
315467 ATTTAACAGA
*
315477 ATTAATTTAA-ATAACTTAATTT
1 ATTAATTTAATA-AAATTAATTT
315499 ATTAATTTAATAAAATTAATTAT
1 ATTAATTTAATAAAATTAATT-T
*
315522 TTGTAATTTACATAAAAATTAA-TT
1 AT-TAATTTA-AT-AAAATTAATTT
*
315546 ATAAATTTAATAA
1 ATTAATTTAATAA
315559 CAAAAAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.04
22 20 0.39
23 9 0.18
24 9 0.18
25 3 0.06
26 8 0.16
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (22 bp):
ATTAATTTAATAAAATTAATTT
Found at i:321496 original size:20 final size:20
Alignment explanation
Indices: 321463--321501 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
321453 GTTAATAAAA
321463 TAACATAAAAAAATTTATAT
1 TAACATAAAAAAATTTATAT
321483 TAAC-TAAAACAAATTTATA
1 TAACATAAAA-AAATTTATA
321502 AAATGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
TAACATAAAAAAATTTATAT
Found at i:322206 original size:20 final size:21
Alignment explanation
Indices: 322181--322220 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
322171 ATCTATAATT
322181 TTTTTATTATTAATATTTT-A
1 TTTTTATTATTAATATTTTAA
322201 TTTTTATT-TATAAT-TTTTAA
1 TTTTTATTAT-TAATATTTTAA
322221 AAATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTATTATTAATATTTTAA
Found at i:322259 original size:59 final size:60
Alignment explanation
Indices: 322187--322344 Score: 214
Period size: 59 Copynumber: 2.6 Consensus size: 60
322177 AATTTTTTTA
* *
322187 TTATTAATATTTTATTTTTATTTATAATTTTTAAAAATTATATTTATTATTCATT-AT-TT
1 TTATTAATATTTTATTTTTATTTATAATTTTTAAAAATTACATTTATCATT-ATTAATATT
* *
322246 TTATTAATATTTTATTTTTATTTATAA-TTTTAATAAGTTACATTTATCATTTTTAATATT
1 TTATTAATATTTTATTTTTATTTATAATTTTTAA-AAATTACATTTATCATTATTAATATT
* * *
322306 TAATTAGTATTTAATTTTTATTTATAATTTTTAAAAATT
1 TTATTAATATTTTATTTTTATTTATAATTTTTAAAAATT
322345 TAATATATCA
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
58 8 0.09
59 43 0.49
60 30 0.34
61 6 0.07
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (60 bp):
TTATTAATATTTTATTTTTATTTATAATTTTTAAAAATTACATTTATCATTATTAATATT
Found at i:322262 original size:17 final size:18
Alignment explanation
Indices: 322240--322277 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
322230 TTATTATTCA
322240 TTATTTTTATTAAT-ATT
1 TTATTTTTATTAATAATT
*
322257 TTATTTTTATTTATAATT
1 TTATTTTTATTAATAATT
322275 TTA
1 TTA
322278 ATAAGTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTTATTAATAATT
Found at i:322354 original size:60 final size:61
Alignment explanation
Indices: 322189--322359 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 61
322179 TTTTTTTATT
* * *
322189 ATTAATATTTTATTTTTATTTATAATTTTTAAAAATT-ATAT-TTATTATTCATTATTTTT
1 ATTAATATTTTATTTTTATTTATAATTTTTAAAAATTAATATATCATTATTCAATATTTTA
* * *
322248 ATTAATATTTTATTTTTATTTATAA-TTTTAATAAGTTACATTTATCATT-TTTAATA-TTTA
1 ATTAATATTTTATTTTTATTTATAATTTTTAA-AAATTA-ATATATCATTATTCAATATTTTA
* * *
322308 ATTAGTATTTAATTTTTATTTATAATTTTTAAAAATTTAATATATCAATATT
1 ATTAATATTTTATTTTTATTTATAATTTTTAAAAA-TTAATATATCATTATT
322360 TATAATTTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
58 6 0.06
59 29 0.31
60 36 0.38
61 19 0.20
62 4 0.04
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (61 bp):
ATTAATATTTTATTTTTATTTATAATTTTTAAAAATTAATATATCATTATTCAATATTTTA
Found at i:323503 original size:14 final size:15
Alignment explanation
Indices: 323473--323519 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
323463 AATTTTAAAA
*
323473 TATATTTATTTTTTAT
1 TATATTTA-TATTTAT
323489 TATATTT-TATTTAT
1 TATATTTATATTTAT
*
323503 TTTATTTATATTATAT
1 TATATTTATATT-TAT
323519 T
1 T
323520 TAAATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 12 0.44
15 4 0.15
16 11 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATATTTATATTTAT
Found at i:323505 original size:9 final size:9
Alignment explanation
Indices: 323483--323521 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
323473 TATATTTATT
323483 TTTTATTATA
1 TTTTATT-TA
323493 TTTTATTTA
1 TTTTATTTA
323502 TTTTATTTA
1 TTTTATTTA
323511 TATTATATTTA
1 T-TT-TATTTA
323522 AATAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 12 0.44
10 9 0.33
11 6 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATTTA
Found at i:323514 original size:11 final size:11
Alignment explanation
Indices: 323475--323521 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
323465 TTTTAAAATA
*
323475 TATTTATTTTT
1 TATTTATATTT
323486 TA-TTATATTT
1 TATTTATATTT
323496 TA-TT-TATTT
1 TATTTATATTT
*
323505 TATTTATATTA
1 TATTTATATTT
323516 TATTTA
1 TATTTA
323522 AATAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 7 0.22
10 13 0.41
11 12 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTATATTT
Found at i:325031 original size:16 final size:16
Alignment explanation
Indices: 325004--325060 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
324994 GAGATACGAA
*
325004 ATTAATAAAATTATTTT
1 ATTAA-AAAATTAATTT
325021 ATTAAAAAATTAATTT
1 ATTAAAAAATTAATTT
** *
325037 -TTAAATCATAAATTT
1 ATTAAAAAATTAATTT
*
325052 TTTAAAAAA
1 ATTAAAAAA
325061 ATTCAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.36
16 16 0.48
17 5 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTAAAAAATTAATTT
Found at i:325036 original size:17 final size:17
Alignment explanation
Indices: 325004--325037 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
324994 GAGATACGAA
325004 ATTAATAAAATTATTTT
1 ATTAATAAAATTATTTT
325021 ATTAA-AAAATTAATTTT
1 ATTAATAAAATT-ATTTT
325038 TAAATCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAATAAAATTATTTT
Found at i:326285 original size:24 final size:24
Alignment explanation
Indices: 326258--326322 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 24
326248 ACAGTTTATA
326258 TAAAATTTTTATTTTTAATTTTTT
1 TAAAATTTTTATTTTTAATTTTTT
* *
326282 TAAAGTTATTTA--TTTGATTTTTT
1 TAAAATT-TTTATTTTTAATTTTTT
*
326305 AAATTAATTTTTATTTTT
1 TAA--AATTTTTATTTTT
326323 TGTCTTGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 12 0.38
24 10 0.31
25 7 0.22
26 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
TAAAATTTTTATTTTTAATTTTTT
Found at i:326290 original size:21 final size:19
Alignment explanation
Indices: 326266--326323 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 19
326256 TATAAAATTT
326266 TTATTTTTAATTTTTTTAAA
1 TTATTTTT-ATTTTTTTAAA
326286 GTTATTTATT-TGATTTTTTAAA
1 -TTATTT-TTAT--TTTTTTAAA
326308 TTAATTTTTATTTTTT
1 TT-ATTTTTATTTTTT
326324 GTCTTGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
20 6 0.19
21 10 0.31
22 16 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
TTATTTTTATTTTTTTAAA
Found at i:326305 original size:22 final size:19
Alignment explanation
Indices: 326277--326323 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
326267 TATTTTTAAT
*
326277 TTTTTTAAAGTTATTTATTTGA
1 TTTTTTAAA-TTAATT-TTT-A
326299 TTTTTTAAATTAATTTTTA
1 TTTTTTAAATTAATTTTTA
326318 TTTTTT
1 TTTTTT
326324 GTCTTGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
21 5 0.21
22 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTTTAAATTAATTTTTA
Found at i:326354 original size:21 final size:21
Alignment explanation
Indices: 326298--326356 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
326288 TATTTATTTG
*
326298 ATTTTTTA-AATTA-ATTTTT
1 ATTTTTTATTATTATATTTTT
* *
326317 ATTTTTTGTCT-TGATATTTTT
1 ATTTTTTAT-TATTATATTTTT
326338 ATTTTTTATTATTATATTT
1 ATTTTTTATTATTATATTT
326357 AAAAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 7 0.23
20 3 0.10
21 21 0.68
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (21 bp):
ATTTTTTATTATTATATTTTT
Found at i:330737 original size:11 final size:11
Alignment explanation
Indices: 330731--330759 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
330721 ACTTAAAAAT
330731 AATTTAAATAA
1 AATTTAAATAA
330742 AATTTAAATAA
1 AATTTAAATAA
330753 AATTTAA
1 AATTTAA
330760 TTATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTTAAATAA
Found at i:331000 original size:7 final size:6
Alignment explanation
Indices: 330977--331041 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
330967 TTATTTTTAT
**
330977 TTTAAA -TTAAA TTTAAA TTTTAAA AATAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
331023 -TTAAA TCTAAA ATTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
331042 CAGACTTCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
4 4 0.09
5 10 0.22
6 26 0.57
7 6 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:331008 original size:19 final size:18
Alignment explanation
Indices: 330975--331013 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
330965 TTTTATTTTT
*
330975 ATTTTAAATTAAATTTAA
1 ATTTTAAAATAAATTTAA
330993 ATTTTAAAAATAAATTTAA
1 ATTTT-AAAATAAATTTAA
331012 AT
1 AT
331014 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTAAAATAAATTTAA
Found at i:331015 original size:10 final size:10
Alignment explanation
Indices: 331000--331033 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
330990 TAAATTTTAA
331000 AAATAAATTT
1 AAATAAATTT
331010 AAATAAATTT
1 AAATAAATTT
*
331020 AAATTAAATCT
1 AAA-TAAATTT
331031 AAA
1 AAA
331034 ATTAAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATAAATTT
Found at i:331508 original size:25 final size:27
Alignment explanation
Indices: 331461--331510 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
331451 AATTAAAAAA
331461 ATTAAATATTAAAAATATAATTTTAAT
1 ATTAAATATTAAAAATATAATTTTAAT
*
331488 ATTAAA-A-TAAAAATATTATTTTA
1 ATTAAATATTAAAAATATAATTTTA
331511 TTTAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 1 0.05
27 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATTAAATATTAAAAATATAATTTTAAT
Found at i:331523 original size:26 final size:25
Alignment explanation
Indices: 331465--331523 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
331455 AAAAAAATTA
*
331465 AATATTAAAAATATAATTTTAATATT
1 AATA-TAAAAATATAATTTTAATAAT
* * *
331491 AAAATAAAAATATTATTTTATTTAAT
1 AATATAAAAATATAATTTTA-ATAAT
331517 AATATAA
1 AATATAA
331524 TTTTTAACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATAAAAATATAATTTTAATAAT
Found at i:332465 original size:2 final size:2
Alignment explanation
Indices: 332458--332484 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
332448 AATTTTCATC
332458 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
332485 TTCGTAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:334929 original size:2 final size:2
Alignment explanation
Indices: 334922--334961 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
334912 TTTGGCTTTT
*
334922 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
334962 CACACGGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:335974 original size:16 final size:16
Alignment explanation
Indices: 335943--335973 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
335933 ACAGATATAA
335943 AATTAATTAAATTTTT
1 AATTAATTAAATTTTT
335959 AATTAATT-AATTTTT
1 AATTAATTAAATTTTT
335974 TTATTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTAATTAAATTTTT
Found at i:336976 original size:21 final size:21
Alignment explanation
Indices: 336950--336993 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
336940 GATCAGGATT
336950 CATGTCAAATCTCAATTGTCA
1 CATGTCAAATCTCAATTGTCA
336971 CATGTCAAATCTCAATTGTCA
1 CATGTCAAATCTCAATTGTCA
336992 CA
1 CA
336994 CGGCAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (21 bp):
CATGTCAAATCTCAATTGTCA
Found at i:337000 original size:21 final size:21
Alignment explanation
Indices: 336955--337000 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
336945 GGATTCATGT
* *
336955 CAAATCTCAATTGTCACATGT
1 CAAATCTCAATTGTCACACGG
336976 CAAATCTCAATTGTCACACGG
1 CAAATCTCAATTGTCACACGG
336997 CAAA
1 CAAA
337001 ACCAACCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (21 bp):
CAAATCTCAATTGTCACACGG
Found at i:337998 original size:20 final size:20
Alignment explanation
Indices: 337975--338047 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
337965 ACAATTCAAA
337975 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
337995 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
338016 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
338036 GTATCGATACAT
1 GTATCGATACAT
338048 AAAAAAGATG
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:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:338019 original size:21 final size:21
Alignment explanation
Indices: 337993--338068 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
337983 ACATGTTGCA
337993 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
338014 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
338034 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
338055 ATGTATCGATACAT
1 ATGTATCGATACAT
338069 TTCTTGGCAG
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:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:338026 original size:41 final size:41
Alignment explanation
Indices: 337975--338068 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
337965 ACAATTCAAA
*
337975 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
338016 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
338057 GTATCGATACAT
1 GTATCGATACAT
338069 TTCTTGGCAG
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:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:338125 original size:13 final size:13
Alignment explanation
Indices: 338107--338132 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
338097 TACAACAAGT
338107 ATGTATCGATACA
1 ATGTATCGATACA
338120 ATGTATCGATACA
1 ATGTATCGATACA
338133 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:340377 original size:21 final size:21
Alignment explanation
Indices: 340344--340388 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
340334 TTGCAAGTTG
*
340344 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
340366 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
340386 AAA
1 AAA
340389 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 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:342212 original size:15 final size:15
Alignment explanation
Indices: 342192--342222 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
342182 TAAAAATGTC
*
342192 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
342207 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
342222 C
1 C
342223 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:344316 original size:20 final size:21
Alignment explanation
Indices: 344247--344324 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
344237 AATGTCCAAA
344247 ATGTATCGATACATATTTT-T
1 ATGTATCGATACATATTTTCT
* **
344267 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T--ATTTTCT
344292 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATATTTTCT
*
344312 TTGTATCGATACA
1 ATGTATCGATACA
344325 ATGTATCGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 28 0.61
22 1 0.02
23 1 0.02
24 3 0.07
25 13 0.28
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATATTTTCT
Found at i:344331 original size:13 final size:13
Alignment explanation
Indices: 344313--344350 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
344303 CATTTTTCTT
344313 TGTATCGATACAA
1 TGTATCGATACAA
*
344326 TGTATCGATACAC
1 TGTATCGATACAA
344339 TGTATCGATACA
1 TGTATCGATACA
344351 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:346817 original size:20 final size:20
Alignment explanation
Indices: 346794--346866 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
346784 ACAATTCAAA
346794 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
346814 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
346835 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
346855 GTATCGATACAT
1 GTATCGATACAT
346867 AAAAAAGATG
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:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:346838 original size:21 final size:21
Alignment explanation
Indices: 346812--346887 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
346802 ACATGTTGCA
346812 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
346833 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
346853 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
346874 ATGTATCGATACAT
1 ATGTATCGATACAT
346888 TTCTTGGCAG
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:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:346845 original size:41 final size:41
Alignment explanation
Indices: 346794--346887 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
346784 ACAATTCAAA
*
346794 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
346835 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
346876 GTATCGATACAT
1 GTATCGATACAT
346888 TTCTTGGCAG
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:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:346944 original size:13 final size:13
Alignment explanation
Indices: 346926--346951 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
346916 TACAGCAAGT
346926 ATGTATCGATACA
1 ATGTATCGATACA
346939 ATGTATCGATACA
1 ATGTATCGATACA
346952 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:351447 original size:3 final size:3
Alignment explanation
Indices: 351439--351482 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
351429 AATTCAAGAT
351439 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
351483 GTCCTGCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:352921 original size:25 final size:25
Alignment explanation
Indices: 352887--352939 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
352877 GACTCTTAAT
352887 TCACTTACTTCTATTTATAATTTGA
1 TCACTTACTTCTATTTATAATTTGA
* *
352912 TCACTTACTTTTATTTATACTTTGA
1 TCACTTACTTCTATTTATAATTTGA
352937 TCA
1 TCA
352940 TTCACTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53
Consensus pattern (25 bp):
TCACTTACTTCTATTTATAATTTGA
Found at i:354803 original size:16 final size:17
Alignment explanation
Indices: 354782--354815 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
354772 ATAAGAGCAA
354782 AATTAATTAA-ATTTTT
1 AATTAATTAATATTTTT
354798 AATTAATTAATATTTTT
1 AATTAATTAATATTTTT
354815 A
1 A
354816 TTTTCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTAATTAATATTTTT
Found at i:355354 original size:21 final size:21
Alignment explanation
Indices: 355328--355368 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
355318 CCTTGAAGCC
*
355328 AGTCCATTTGTGTTCATGATT
1 AGTCCATGTGTGTTCATGATT
*
355349 AGTCCATGTGTGTTCTTGAT
1 AGTCCATGTGTGTTCATGAT
355369 ATATACATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.46
Consensus pattern (21 bp):
AGTCCATGTGTGTTCATGATT
Found at i:355601 original size:2 final size:2
Alignment explanation
Indices: 355594--355621 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
355584 ATTTATAGGA
355594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
355622 TTGCTAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:358091 original size:22 final size:22
Alignment explanation
Indices: 358066--358121 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
358056 TTTTATAATT
* **
358066 AAATGTACATATGCTTATAGTA
1 AAATATACATATAATTATAGTA
*
358088 AAATATGCATATAATTATAGTA
1 AAATATACATATAATTATAGTA
* *
358110 ACATTTACATAT
1 AAATATACATAT
358122 TTATTTGTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
AAATATACATATAATTATAGTA
Found at i:361246 original size:16 final size:17
Alignment explanation
Indices: 361209--361246 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
361199 ATCTTTCAAA
*
361209 TAATTTTTTTTAAAATT
1 TAATATTTTTTAAAATT
361226 T-ATATTTTTT-AAATT
1 TAATATTTTTTAAAATT
361241 TAATAT
1 TAATAT
361247 CTATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 12 0.63
17 1 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TAATATTTTTTAAAATT
Found at i:362836 original size:34 final size:34
Alignment explanation
Indices: 362742--362836 Score: 101
Period size: 29 Copynumber: 2.9 Consensus size: 34
362732 GATCTTTCAA
* * *
362742 ATTGTTAACTAAATAAGTGATTTGGTAGTTTGCT
1 ATTGTTAACTAAATTAGTGATTTGATAGTTTGCC
* * *
362776 A-TG---ACTAAA-TGGTGATTTGTTGGTTTGCC
1 ATTGTTAACTAAATTAGTGATTTGATAGTTTGCC
362805 ATTGTTAACTAAATTAGTGATTTGATAGTTTG
1 ATTGTTAACTAAATTAGTGATTTGATAGTTTG
362837 TCAAGGTGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
29 16 0.33
30 8 0.17
33 8 0.17
34 16 0.33
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.44
Consensus pattern (34 bp):
ATTGTTAACTAAATTAGTGATTTGATAGTTTGCC
Found at i:362858 original size:21 final size:21
Alignment explanation
Indices: 362821--362860 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
362811 AACTAAATTA
*
362821 GTGATTTGATAGTTTGTCAAG
1 GTGATTTGATAGGTTGTCAAG
362842 GTGATTT-AGTAGGTTGTCA
1 GTGATTTGA-TAGGTTGTCA
362861 TTATTGACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.42
Consensus pattern (21 bp):
GTGATTTGATAGGTTGTCAAG
Found at i:367984 original size:19 final size:19
Alignment explanation
Indices: 367960--368003 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
367950 CTATATTAAC
367960 TTTTAAATTT-ATTAAATT
1 TTTTAAATTTAATTAAATT
*
367978 ATTTTAATTTTAAATTAAATT
1 -TTTTAAATTT-AATTAAATT
367999 TTTTA
1 TTTTA
368004 TGATCATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 5 0.23
21 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAATTTAATTAAATT
Found at i:374721 original size:18 final size:17
Alignment explanation
Indices: 374698--374739 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
374688 AATAATTTTT
*
374698 ATAAATTTTTAAATCTCA
1 ATAAATTTATAAAT-TCA
*
374716 ATAAATATATAAATTCA
1 ATAAATTTATAAATTCA
374733 ATAAATT
1 ATAAATT
374740 AAAAAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATTTATAAATTCA
Found at i:381471 original size:31 final size:29
Alignment explanation
Indices: 381408--381485 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
381398 TGAATTGCAA
* *
381408 AATTTTTAAAAAGTTTATGAATGGTAAGTAT
1 AATTTTT-AAAAG-TTATGAATGATAAATAT
381439 AATTTTTAAAAGTTATGAATGAATAAAATAT
1 AATTTTTAAAAGTTATGAATG-AT-AAATAT
*
381470 AAATTTTAAAAGTTAT
1 AATTTTTAAAAGTTAT
381486 AGATAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 9 0.21
30 6 0.14
31 27 0.64
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (29 bp):
AATTTTTAAAAGTTATGAATGATAAATAT
Found at i:381502 original size:33 final size:31
Alignment explanation
Indices: 381436--381502 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
381426 GAATGGTAAG
* **
381436 TATAATTTTTAAAAGTTATGAATGAATAAAA
1 TATAAATTTTAAAAGTTATGAAAAAATAAAA
381467 TATAAATTTTAAAAGTTATAGATAAAAATAAAA
1 TATAAATTTTAAAAGTTAT-GA-AAAAATAAAA
381500 TAT
1 TAT
381503 TAATAAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 18 0.58
32 2 0.06
33 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.37
Consensus pattern (31 bp):
TATAAATTTTAAAAGTTATGAAAAAATAAAA
Found at i:384363 original size:19 final size:19
Alignment explanation
Indices: 384339--384384 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
384329 ATTTTTTTAA
* * *
384339 ATTAATGAAAGATTATATT
1 ATTAATAAAAGATAAAATT
384358 ATTAATAAAAGATAAAATT
1 ATTAATAAAAGATAAAATT
384377 ATT-ATAAA
1 ATTAATAAA
384385 TATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTAATAAAAGATAAAATT
Found at i:384622 original size:30 final size:30
Alignment explanation
Indices: 384573--384636 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
384563 GTCTAATTAT
384573 TTAAGGTTATAATCATCTAATTA-TTTAAA
1 TTAAGGTTATAATCATCTAATTATTTTAAA
* *
384602 TTAAGGGTTGTAATCTTCTAATTATTTTAAA
1 TTAA-GGTTATAATCATCTAATTATTTTAAA
384633 TTAA
1 TTAA
384637 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 17 0.55
31 10 0.32
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (30 bp):
TTAAGGTTATAATCATCTAATTATTTTAAA
Found at i:385058 original size:38 final size:39
Alignment explanation
Indices: 384987--385061 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
384977 AATACTAATA
* **
384987 TAATAATATAATTAAAAAATACCAACATCATAATAATCC
1 TAATAATATAATTAAAAAATAACAACAAAATAATAATCC
* *
385026 TAATAATATTATT-AAAAATAATAACAAAATAATAAT
1 TAATAATATAATTAAAAAATAACAACAAAATAATAAT
385062 AATTGTAGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 19 0.61
39 12 0.39
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (39 bp):
TAATAATATAATTAAAAAATAACAACAAAATAATAATCC
Found at i:390553 original size:21 final size:19
Alignment explanation
Indices: 390511--390550 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
390501 GAAAATGGAC
390511 TTATTTTTAAAATATATTT
1 TTATTTTTAAAATATATTT
390530 TTATTTTTGAAAA-ATATTT
1 TTATTTTT-AAAATATATTT
390549 TT
1 TT
390551 TTAAAATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATTTTTAAAATATATTT
Found at i:397206 original size:20 final size:19
Alignment explanation
Indices: 397177--397219 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 19
397167 TTAATAAAAA
397177 TAATATATTAAATATAATTTT
1 TAATATATT-AA-ATAATTTT
397198 TAATA-ATTAAATAATTTT
1 TAATATATTAAATAATTTT
397216 TAAT
1 TAAT
397220 TAATATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.55
19 2 0.09
20 3 0.14
21 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATATTAAATAATTTT
Found at i:397211 original size:38 final size:37
Alignment explanation
Indices: 397089--397211 Score: 97
Period size: 38 Copynumber: 3.2 Consensus size: 37
397079 TATTATTTTT
* * *
397089 ATTAATTAAAAAAATTTATTAATTATATATTTTTAATA
1 ATTAAATAAAAAAATATATTAAATATA-ATTTTTAATA
* ** * * *
397127 TTTTTATGAAAAAAATATAAATAATAAATTATTTTT-A-A
1 ATTAAAT-AAAAAAATAT-ATTAA-ATATAATTTTTAATA
*
397165 ATTTAATAAAAATAATATATTAAATATAATTTTTAATA
1 ATTAAATAAAAA-AATATATTAAATATAATTTTTAATA
397203 ATTAAATAA
1 ATTAAATAA
397212 TTTTTAATTA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
36 9 0.14
37 10 0.16
38 23 0.36
39 10 0.16
40 10 0.16
41 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.46
Consensus pattern (37 bp):
ATTAAATAAAAAAATATATTAAATATAATTTTTAATA
Found at i:397456 original size:3 final size:3
Alignment explanation
Indices: 397450--397479 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
397440 AATATTTATT
397450 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
397480 CAGCGCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:397635 original size:4 final size:4
Alignment explanation
Indices: 397610--397651 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
397600 AAATAACGGA
*
397610 AAAT AAA- AAAT AGAAA AAAT AAAT -AAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
397652 AGGCTGCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 6 0.18
4 24 0.73
5 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:397648 original size:15 final size:16
Alignment explanation
Indices: 397609--397650 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
397599 AAAATAACGG
*
397609 AAAATAAAAAATAGAA
1 AAAATAAATAATAGAA
397625 AAAATAAATAATA-AA
1 AAAATAAATAATAGAA
*
397640 TAAATAAATAA
1 AAAATAAATAA
397651 AAGGCTGCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAATAAATAATAGAA
Found at i:401281 original size:14 final size:14
Alignment explanation
Indices: 401262--401290 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
401252 CAATAATGCA
401262 GGAATAATTTAGGT
1 GGAATAATTTAGGT
401276 GGAATAATTTAGGT
1 GGAATAATTTAGGT
401290 G
1 G
401291 CAGAGTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (14 bp):
GGAATAATTTAGGT
Found at i:405321 original size:17 final size:17
Alignment explanation
Indices: 405299--405333 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
405289 GAATGAACTC
405299 TTTTCAA-CCTAAGCTTT
1 TTTTCAACCCT-AGCTTT
405316 TTTTCAACCCTAGCTTT
1 TTTTCAACCCTAGCTTT
405333 T
1 T
405334 CTAACAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.20, C:0.26, G:0.06, T:0.49
Consensus pattern (17 bp):
TTTTCAACCCTAGCTTT
Found at i:407239 original size:11 final size:11
Alignment explanation
Indices: 407198--407246 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
407188 ATTTTTTTAA
407198 ATAAATAAATT
1 ATAAATAAATT
*
407209 AGATAA-AAATT
1 ATA-AATAAATT
407220 A-AAAT-AATT
1 ATAAATAAATT
407229 ATAAATAAATT
1 ATAAATAAATT
*
407240 ACAAATA
1 ATAAATA
407247 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 7 0.22
10 5 0.16
11 18 0.56
12 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
ATAAATAAATT
Found at i:407788 original size:16 final size:15
Alignment explanation
Indices: 407769--407799 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
407759 TTAATAAAAT
407769 AAATTTAAAATAATTC
1 AAATTTAAAA-AATTC
407785 AAATTTAAAAAATTC
1 AAATTTAAAAAATTC
407800 GAACACGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATTTAAAAAATTC
Found at i:410229 original size:2 final size:2
Alignment explanation
Indices: 410224--410268 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
410214 AAAAAATTAA
*
410224 AT AT AT TT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
410267 AT
1 AT
410269 CTAAAGTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:411816 original size:9 final size:9
Alignment explanation
Indices: 411784--411821 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
411774 TAAAAATATG
411784 AATATTTTT
1 AATATTTTT
411793 -ATA-TTTT
1 AATATTTTT
411800 AATCATTTTT
1 AAT-ATTTTT
411810 AATATTTTT
1 AATATTTTT
411819 AAT
1 AAT
411822 TAAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 4 0.15
8 5 0.19
9 10 0.38
10 7 0.27
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:411958 original size:22 final size:22
Alignment explanation
Indices: 411905--411963 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
411895 GGTTTTAATA
* *
411905 AAAATATTTCAATGATAAAATATT
1 AAAAT-TTT-AATAATAAAAAATT
*
411929 ACAATTTTAATAATAAAAAATT
1 AAAATTTTAATAATAAAAAATT
411951 AAAATTTTTAATA
1 AAAA-TTTTAATA
411964 TTTTACATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.50
23 11 0.37
24 4 0.13
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATTTTAATAATAAAAAATT
Found at i:412049 original size:29 final size:30
Alignment explanation
Indices: 412013--412073 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
412003 ATTTTAAATA
*
412013 TTTTAAAATTTTAATAATAA-ATAGTATTT
1 TTTTAAAATTTTAATAATAATATAGGATTT
*
412042 TTTTAAAATTTTAATATTAATATAGGATTT
1 TTTTAAAATTTTAATAATAATATAGGATTT
412072 TT
1 TT
412074 AATATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (30 bp):
TTTTAAAATTTTAATAATAATATAGGATTT
Found at i:412062 original size:35 final size:34
Alignment explanation
Indices: 411988--412063 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
411978 AATAAATATT
*
411988 TTAATAATAAATACTATTTTAAATATTTTAAAATT
1 TTAATAATAAATACTATTTTAAATATTTT-AAATA
*
412023 TTAATAATAAATAGTATTTTTTTAAA-ATTTT-AATA
1 TTAATAATAAATACTA---TTTTAAATATTTTAAATA
412058 TTAATA
1 TTAATA
412064 TAGGATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
35 24 0.67
37 5 0.14
38 7 0.19
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (34 bp):
TTAATAATAAATACTATTTTAAATATTTTAAATA
Found at i:412073 original size:28 final size:28
Alignment explanation
Indices: 412013--412088 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 28
412003 ATTTTAAATA
*
412013 TTTTAAAATTTTAATAATAAATAGTATTT
1 TTTTAAAATTTTAATAATAAATAGGA-TT
*
412042 TTTTAAAATTTTAATATTAATATAGGA-T
1 TTTTAAAATTTTAATAATAA-ATAGGATT
* *
412070 TTTTAATATTTTATTAATA
1 TTTTAAAATTTTAATAATA
412089 TATAAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.41
29 19 0.46
30 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTTAAAATTTTAATAATAAATAGGATT
Found at i:413039 original size:23 final size:22
Alignment explanation
Indices: 413011--413056 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
413001 TTTACAATTT
413011 TATAATTAATGTTTACATAAAAA
1 TATAATTAATGTTTACA-AAAAA
413034 TATAATTAATGTTTACAAAAAA
1 TATAATTAATGTTTACAAAAAA
413056 T
1 T
413057 TTATAAGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (22 bp):
TATAATTAATGTTTACAAAAAA
Found at i:413438 original size:81 final size:82
Alignment explanation
Indices: 413352--413505 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 82
413342 CCTTTTCTCG
* * *
413352 ACTAATCATCTTAC-TTTAATTTTTTATATTTAAAGATAA-TATAAATATTAGTATATTATATAA
1 ACTAATCATCTTACTTTTAATTTTCTATATTTAAAGATAATTA-AAATATAAGTATATTATAAAA
413415 ATAACTAATTATTCGTTA
65 ATAACTAATTATTCGTTA
* * * * *
413433 ACTAATTATCTTACTTTTAGTTTTCTCTATTTAAAGATAATTAAAATATAATTATTTTATAAAAA
1 ACTAATCATCTTACTTTTAATTTTCTATATTTAAAGATAATTAAAATATAAGTATATTATAAAAA
413498 TAACTAAT
66 TAACTAAT
413506 CACTCATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 13 0.21
82 48 0.76
83 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (82 bp):
ACTAATCATCTTACTTTTAATTTTCTATATTTAAAGATAATTAAAATATAAGTATATTATAAAAA
TAACTAATTATTCGTTA
Found at i:414295 original size:29 final size:29
Alignment explanation
Indices: 414258--414318 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
414248 TTATTTATCT
*
414258 TTTTAATTTACTTTATTTTTAG-TAATTTA
1 TTTTAATTTAC-TTATTTTTAGAAAATTTA
*
414287 TTTTCATTTACTTATTTTTAGAAAATTTA
1 TTTTAATTTACTTATTTTTAGAAAATTTA
414316 TTT
1 TTT
414319 GGTTTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTTAATTTACTTATTTTTAGAAAATTTA
Found at i:414538 original size:15 final size:16
Alignment explanation
Indices: 414506--414542 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
414496 TTAAAAAGTA
414506 AAATTTAAAATAATCT
1 AAATTTAAAATAATCT
414522 AAATTTAAAAT-ATCT
1 AAATTTAAAATAATCT
414537 AAATTT
1 AAATTT
414543 GAATGAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTAAAATAATCT
Found at i:415144 original size:2 final size:2
Alignment explanation
Indices: 415137--415163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
415127 TGAGACTAAC
415137 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
415164 AAAGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:415486 original size:16 final size:16
Alignment explanation
Indices: 415447--415492 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
415437 TAATATATTC
*
415447 AAATTATTTCAAATTT
1 AAATTATTTTAAATTT
415463 -AA-TATTTTAAATTT
1 AAATTATTTTAAATTT
415477 AAATTATTTTAAATTT
1 AAATTATTTTAAATTT
415493 GAGTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 11 0.41
15 4 0.15
16 12 0.44
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:416911 original size:2 final size:2
Alignment explanation
Indices: 416904--416939 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
416894 TCCTACATGC
416904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
416940 CATGGTATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:427460 original size:16 final size:16
Alignment explanation
Indices: 427439--427469 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
427429 AAATGAAATT
427439 TAAAAAATATAAAAAA
1 TAAAAAATATAAAAAA
*
427455 TAAAAAATCTAAAAA
1 TAAAAAATATAAAAA
427470 TTATAACAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAAATATAAAAAA
Found at i:427962 original size:22 final size:22
Alignment explanation
Indices: 427930--427980 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
427920 ATATCAATTT
*
427930 TTTAACATTTTAATTTTAATAAA
1 TTTAA-ATTTTAATATTAATAAA
* *
427953 TTTAAATTTTTATATTAATTAA
1 TTTAAATTTTAATATTAATAAA
427975 -TTAAAT
1 TTTAAAT
427981 AAAAGATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.24
22 14 0.56
23 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAATTTTAATATTAATAAA
Found at i:428383 original size:3 final size:3
Alignment explanation
Indices: 428375--428399 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
428365 AATATAATTT
428375 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
428400 CAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:429323 original size:2 final size:2
Alignment explanation
Indices: 429316--429345 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
429306 AGGTTATTAA
429316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
429346 TAGTTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:429373 original size:76 final size:74
Alignment explanation
Indices: 429252--429400 Score: 237
Period size: 76 Copynumber: 2.0 Consensus size: 74
429242 GGAAGTAAAA
* *
429252 ATATATATATATATAATTTAGTTTTTTTGGTTTTGTTGGATTTTAAGCAAACAAAGGTTATTAAA
1 ATATATATATATATAATTTAGTTTTTTTGGTTTTGTTGGACTTTAAGCAAACAAAGGCTATTAAA
429317 TATATATAT
66 TATATATAT
429326 ATATATATATATATATATATTAG-TTTTTTGGTTTTTGTTGGACTTTAAGCAAACAAAGGCTATT
1 ATATATATATATATA-AT-TTAGTTTTTTTGG-TTTTGTTGGACTTTAAGCAAACAAAGGCTATT
*
429390 AAATATGTATA
63 AAATATATATA
429401 CATGTATGCA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
74 15 0.22
75 10 0.14
76 44 0.64
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (74 bp):
ATATATATATATATAATTTAGTTTTTTTGGTTTTGTTGGACTTTAAGCAAACAAAGGCTATTAAA
TATATATAT
Found at i:434036 original size:23 final size:22
Alignment explanation
Indices: 433992--434038 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
433982 AATAAATTTT
433992 TATTTAAATTTAATTATAAAAA
1 TATTTAAATTTAATTATAAAAA
*
434014 TATTATAAATATTAA-TATTAAAA
1 TATT-TAAAT-TTAATTATAAAAA
434037 TA
1 TA
434039 ATTCATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 14 0.64
24 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTTAAATTTAATTATAAAAA
Found at i:437933 original size:10 final size:10
Alignment explanation
Indices: 437918--437948 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
437908 AATCTCATAT
437918 TCACTATTCA
1 TCACTATTCA
*
437928 TCACTATTTA
1 TCACTATTCA
437938 TCACTATTCA
1 TCACTATTCA
437948 T
1 T
437949 GTATCGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (10 bp):
TCACTATTCA
Found at i:440128 original size:21 final size:21
Alignment explanation
Indices: 440104--440162 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
440094 TAATATTCTT
* *
440104 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
440125 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
440146 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
440163 GTTGCAAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:442546 original size:21 final size:22
Alignment explanation
Indices: 442513--442553 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
442503 CCATGTTAAC
442513 AGCTCATGATTCATGCATTTTG
1 AGCTCATGATTCATGCATTTTG
*
442535 AGCT-ATGTTTCATGCATTT
1 AGCTCATGATTCATGCATTT
442554 ACAGCACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (22 bp):
AGCTCATGATTCATGCATTTTG
Found at i:448380 original size:55 final size:55
Alignment explanation
Indices: 448250--449555 Score: 1286
Period size: 55 Copynumber: 22.7 Consensus size: 55
448240 GCACCTCTTT
*
448250 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATG-C----CTTTT-AAAGCCCACACAAGTTGG
* ** * * * *
448311 TGACACCATTCAGTCCTCAAAGAGCAAGATGCCTTTTAAAGCCCACATAAATCGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* * *
448366 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
*
448421 TGGCA-TTTCTCAGTCCTCAAAGAGCAGGATACCTTTTCCTTTTAAAGCCCACACAAGTTGG
1 TGGCACTTT-TCAGTCCTCAAAGAGCAGG--A----TGCCTTTTAAAGCCCACACAAGTTGG
* * *
448482 TGGCACCTTTT-AGTCCTCAAAGAGCAAGACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGG
1 TGGCA-CTTTTCAGTCCTCAAAGAGC-AG-GA------TGCCTTTTAAAGCCCACACAAGTTGG
* * *
448545 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* *
448600 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTT-AAAGCCCACACAAGTTGG
* *
448656 TGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* ** *
448711 TGGCA-TTTTCCAGTTCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTCGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* * **
448766 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGAGGCCTTTCAAAGCCCACATGAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* * *
448821 TGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACATACGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATG------CCTTTTAAAGCCCACACAAGTTGG
* *
448882 TGGCACCTTTT-AGTCCTCAAAGAGCAGGACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGG
1 TGGCA-CTTTTCAGTCCTCAAAGAGCAGG--A------TGCCTTTTAAAGCCCACACAAGTTGG
* * * * *
448945 TGGCACCTTTCAGTCCTTAAATAGCAGAACGCCTTTTAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* * *
449000 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
449055 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* * * * *
449110 TGGCACCTTCCAGTCCTTAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAATTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCC--T--TTT--AAAGCCCACACAAGTTGG
* * * * *
449171 TGGAACCTTTCAGTCCTCAAAAAGCAGGACGCCTTTCCTTTTCAAAGCCCACATAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGA-----TGCCTTTT-AAAGCCCACACAAGTTGG
*
449232 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCTCACACAAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGATGC-----CTTTT-AAAGCCCACACAAGTTGG
*
449293 TGGCA-TTTTCTAGTCCTCAAAGAGCATGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTC-AGTCCTCAAAGAGCAGGATGC-----CTTTT-AAAGCCCACACAAGTTGG
* *
449354 TGGCACCTTTCAGTCCCCAAAGAGCAGGA--CACTTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGC-CTTTT-AAAGCCCACACAAGTTGG
** *
449409 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* * * *
449464 TGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
* *
449519 TGGCACTTTTTAGTCCTTAAAGAGCAGGATGCACTTT
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGATGC-CTTT
449556 ATTTTCCCCT
Statistics
Matches: 1077, Mismatches: 108, Indels: 125
0.82 0.08 0.10
Matches are distributed among these distances:
54 11 0.01
55 565 0.52
56 78 0.07
57 3 0.00
59 4 0.00
60 5 0.00
61 294 0.27
62 24 0.02
63 89 0.08
64 1 0.00
66 2 0.00
69 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (55 bp):
TGGCACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGG
Found at i:448634 original size:26 final size:26
Alignment explanation
Indices: 448605--448693 Score: 63
Period size: 26 Copynumber: 3.3 Consensus size: 26
448595 GTTGGTGGCA
448605 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
* * * ** *
448631 CCTTTTCAAAGCCCACACAAGTTGGTGG-CA
1 CC-TTTC--AGTCCTCA-AAG-AGCAGGACG
*
448661 CCTTTCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
448687 CCTTTCA
1 CCTTTCA
448694 AAGCCCACAC
Statistics
Matches: 44, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
25 3 0.07
26 12 0.27
27 10 0.23
29 10 0.23
30 6 0.14
31 3 0.07
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:449029 original size:400 final size:398
Alignment explanation
Indices: 448250--449547 Score: 1822
Period size: 400 Copynumber: 3.2 Consensus size: 398
448240 GCACCTCTTT
*
448250 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGAC
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACG-C----C-TTTCAAAGCCCACACAAGTTGGTGGC
* * * *
448315 ACCATTCAGTCCTCAAAGAGCAAGATGCCTTTTAAAGCCCACATAAATCGGTGGCATTTTCCAGT
60 ACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAATCGGTGGCATTTTCCAGT
* *
448380 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCATTTCTCAGTCCTCAAAGAG
125 CCTCAAAGAGCAGGAGGCCTTTCAAAGCCCACATGAGTTGGTGGCA-TTCTCAGTCCTCAAAGAG
*
448445 CAGGATACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAG
189 CAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAG
448510 ACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC
254 ACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC
*
448575 GTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCAA
319 GACTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTT-AA
448640 AGCCCACACAAGTTGG
383 AGCCCACACAAGTTGG
* * *
448656 TGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
448720 CCAGTTCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTCGGTGGCATTTTCCAGTCCTCA
66 -CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAATCGGTGGCATTTTCCAGTCCTCA
448785 AAGAGCAGGAGGCCTTTCAAAGCCCACATGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGA
130 AAGAGCAGGAGGCCTTTCAAAGCCCACATGAGTTGGTGGCA-TTCTCAGTCCTCAAAGAGCAGGA
* * *
448850 TGCCTTTTCCTTTTAAAGCCCACATACGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACC
194 TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACC
* * * *
448915 TTTTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAAATAGCAGAACGCCTT
259 TTTTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGACTT
448980 TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCA
324 TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCA
*
449045 CACGAGTTGG
389 CACAAGTTGG
* *
449055 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * * *
449119 CCAGTCCTTAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAATTGGTGGAACCTTT-CA
65 TCAGTCCTCAAAGAGCAGGACGCC--T--TTT--AAAGCCCACACAAATCGGTGGCA-TTTTCCA
* * * *
449183 GTCCTCAAAAAGCAGGACGCCTTTCCTTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCC
123 GTCCTCAAAGAGCAGGA-G----GCC-TTTCAAAGCCCACATGAGTTGGTGGCATTCT-CAGTCC
* * *
449248 TCAAAGAGCAGGATG-CTTTTTCTTTTCAAAGCTCACACAAGTTGGTGGCA-TTTTCTAGTCCTC
181 TCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTC
* ** * *
449311 AAAGAGCATGA-TGCTTTTT-CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAA
244 AAAGAGCAAGACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
*
449374 AGAGCAGGAC-ACTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGG
309 AGAGCAGGACGACTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGG
* *
449437 ACACCTCTTAAAGCCCACACAAGTTGG
372 ACGCCTTTTAAAGCCCACACAAGTTGG
* * *
449464 TGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* *
449529 TAGTCCTTAAAGAGCAGGA
66 CAGTCCTCAAAGAGCAGGA
449548 TGCACTTTAT
Statistics
Matches: 807, Mismatches: 63, Indels: 41
0.89 0.07 0.05
Matches are distributed among these distances:
398 3 0.00
399 93 0.12
400 327 0.41
401 2 0.00
403 3 0.00
405 39 0.05
406 33 0.04
408 8 0.01
409 186 0.23
410 28 0.03
411 85 0.11
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (398 bp):
TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAATCGGTGGCATTTTCCAGTCCTCAA
AGAGCAGGAGGCCTTTCAAAGCCCACATGAGTTGGTGGCATTCTCAGTCCTCAAAGAGCAGGATG
CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTT
TTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGACTTTT
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACA
CAAGTTGG
Found at i:450389 original size:19 final size:21
Alignment explanation
Indices: 450341--450395 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
450331 AATTTCAATA
*
450341 ATTTGTATCGATACATTCAGT
1 ATTTGTATCGATACATTAAGT
**
450362 AAATGTATCGATACA-TAAGT
1 ATTTGTATCGATACATTAAGT
450382 -TTTGTATCGATACA
1 ATTTGTATCGATACA
450396 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTGTATCGATACATTAAGT
Found at i:452907 original size:52 final size:52
Alignment explanation
Indices: 452840--453226 Score: 264
Period size: 52 Copynumber: 7.4 Consensus size: 52
452830 CCAATTGTTC
* *
452840 ATAATTGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTT
* * ** * * * *
452892 TTAATCGGGAATACTCTGACTCTGATTTTATTTCCAAAAACACAAATTTT-TC
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCTT
* * * * ***** * * *** *
452944 ACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCTGTT
1 ATAATCGGGGATACTCCAACCCCG--ATTTTATTTCCAAAACACCAATTTTCTT
** ** * * ***
452998 A-CCTCCGTGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGA-TTTCTT
1 ATAAT-C--GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTT
* * * *
453051 ATAATCCGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT-TC
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTT
* *
453102 ACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTT-CTT
* *
453155 -TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTT-TC
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCTT
* *
453206 ACAATCGAGGATACTCCAACC
1 ATAATCGGGGATACTCCAACC
453227 TCGTTATTTC
Statistics
Matches: 245, Mismatches: 77, Indels: 26
0.70 0.22 0.07
Matches are distributed among these distances:
51 77 0.31
52 94 0.38
53 41 0.17
54 17 0.07
56 16 0.07
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (52 bp):
ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTT
Found at i:452998 original size:28 final size:30
Alignment explanation
Indices: 452947--453021 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 30
452937 ATTTTTCACA
* * *
452947 ATCGAGGATACTCCAA-CCTCGTTA-TTTC
1 ATCGGGGATACTCCAACCCTCGTTACCTCC
452975 ATCGGGGATACTCCAACCCT-GTTACCTCC
1 ATCGGGGATACTCCAACCCTCGTTACCTCC
*
453004 GT-GGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
453022 CGGCTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 35 0.85
29 6 0.15
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCTCGTTACCTCC
Found at i:453338 original size:106 final size:108
Alignment explanation
Indices: 453160--453363 Score: 272
Period size: 106 Copynumber: 1.9 Consensus size: 108
453150 TCCTTTAATC
*
453160 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
* *
453225 CCTCGTTATTT-CATCGGGGATACTCCAATCCCGTTACCTCCGA
66 CCCCGTTATTTCCA-AGGGGATACTCCAATCCCGTTACCTCCGA
* *** * * *
453268 GGGGATACTCCAAC-CCGGA-TTTATTTCC-AAAATATTGATTTCTCATAATTGGGGATACTCCA
1 GGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAATTTCTCACAATCGAGGATACTCCA
453330 ACCCCGTTATTTCCAAGGGGATACTCCAATCCCG
65 ACCCCGTTATTTCCAAGGGGATACTCCAATCCCG
453364 ATTTTATTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
106 55 0.65
107 13 0.15
108 16 0.19
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (108 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCCAAGGGGATACTCCAATCCCGTTACCTCCGA
Found at i:453349 original size:78 final size:77
Alignment explanation
Indices: 453240--453472 Score: 270
Period size: 79 Copynumber: 2.9 Consensus size: 77
453230 TTATTTCATC
* ** *
453240 GGGGATACTCCAATCCCGTTACCTCCGAGGGGATACTCCAACCCGGATTTATTTCCAAAATATTG
1 GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCC-GATTTATTTCCAAAATATTG
*
453305 ATTTCTCATAATT
65 ATTTCTCATAACT
*
453318 GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAATCCCGATTTTATTTCC-TAATCAT
1 GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAA-CCCGA-TTTATTTCCAAAAT-AT
* * *
453382 CGATTTTTCACAACT
63 TGATTTCTCATAACT
* * * *
453397 GGGGATACTCCAACCTCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTCCAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAA-CCCGAT-TTATTTCCAAAATATT
*
453462 AAATTTCTCAT
64 -GATTTCTCAT
453473 CGGGAAATAT
Statistics
Matches: 130, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
78 43 0.33
79 77 0.59
80 10 0.08
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (77 bp):
GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCGATTTATTTCCAAAATATTGA
TTTCTCATAACT
Found at i:454607 original size:13 final size:13
Alignment explanation
Indices: 454589--454613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
454579 CATAAAGTGT
454589 TGTATCGATACAA
1 TGTATCGATACAA
454602 TGTATCGATACA
1 TGTATCGATACA
454614 TATATATATT
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:454698 original size:13 final size:13
Alignment explanation
Indices: 454680--454704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
454670 ATTACTCAAA
454680 TGTATCGATACAT
1 TGTATCGATACAT
454693 TGTATCGATACA
1 TGTATCGATACA
454705 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:454769 original size:52 final size:52
Alignment explanation
Indices: 454713--454841 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
454703 CACTGATCTT
* *
454713 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
454765 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
454817 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
454842 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:459768 original size:141 final size:141
Alignment explanation
Indices: 459514--459799 Score: 554
Period size: 141 Copynumber: 2.0 Consensus size: 141
459504 AACTCGTCGG
* *
459514 AAAGCCATGGAGAATGATCATTAGGCCTGCATTGAGCGATTAGAGCTTGTGTATAGAGAATCTCA
1 AAAGCCATGGAGAATGATCATCAGGCCCGCATTGAGCGATTAGAGCTTGTGTATAGAGAATCTCA
459579 AGAATAGTCAGCCCAAAGGAATGAAGAACTTCAAGCTCAAATGGCCGAGTTGACAAAACTATTGT
66 AGAATAGTCAGCCCAAAGGAATGAAGAACTTCAAGCTCAAATGGCCGAGTTGACAAAACTATTGT
459644 CCGAAGCTCTA
131 CCGAAGCTCTA
459655 AAAGCCATGGAGAATGATCATCAGGCCCGCATTGAGCGATTAGAGCTTGTGTATAGAGAATCTCA
1 AAAGCCATGGAGAATGATCATCAGGCCCGCATTGAGCGATTAGAGCTTGTGTATAGAGAATCTCA
459720 AGAATAGTCAGCCCAAAGGAATGAAGAACTTCAAGCTCAAATGGCCGAGTTGACAAAACTATTGT
66 AGAATAGTCAGCCCAAAGGAATGAAGAACTTCAAGCTCAAATGGCCGAGTTGACAAAACTATTGT
459785 CCGAAGCTCTA
131 CCGAAGCTCTA
459796 AAAG
1 AAAG
459800 AGAAAGGGCA
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 143 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (141 bp):
AAAGCCATGGAGAATGATCATCAGGCCCGCATTGAGCGATTAGAGCTTGTGTATAGAGAATCTCA
AGAATAGTCAGCCCAAAGGAATGAAGAACTTCAAGCTCAAATGGCCGAGTTGACAAAACTATTGT
CCGAAGCTCTA
Found at i:463509 original size:55 final size:54
Alignment explanation
Indices: 463378--464612 Score: 1200
Period size: 55 Copynumber: 21.5 Consensus size: 54
463368 GCACCTCTTT
463378 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACG-C----CTTTT-AAAGCCCACACAAGTTGG
* * *
463439 TGGCACCTTTT-AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACATAAGTCGG
1 TGGCA--TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * *
463494 TGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCATTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * *
463549 TGGCACTTCTCAGTCCTCATAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGA---C---GCCTTTTAAAGCCCACACAAGTTGG
*
463610 TGGCACCTTTT-AGTCCTCAAAGAGCAGGACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGG
1 TGGCA--TTTTCAGTCCTCAAAGAGCAGGACGCC----T---TTT-AAAGCCCACACAAGTTGG
* * *
463673 TGGCACCTTTCTGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTCG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * * *
463728 TGGCACCTTTCAATCCTCAAAAAGCAGGACGCCTTTTCAAAGCCCACACATGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTT-AAAGCCCACACAAGTTGG
*
463784 TGGCACCTTTCAGTCCTCAAAGAGCAGGACG-CTTTTCAAAGCCCACACAAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTT-AAAGCCCACACAAGTTGG
* * *
463839 TCGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCATTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * * *
463894 TGGCACTTCTCAGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * *
463949 TGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACATAAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGA---C---GCCTTTTAAAGCCCACACAAGTTGG
*
464010 TGGTACCTTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
1 TGG--CATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * *
464065 TGGCACTTTTCAGTCCTCAAAGAACATGACGCCTTTTAAAGCCCACACGAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* *
464120 TGGCATTTTCTAGTCTTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGGTGG
1 TGGCATTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * * * * *
464175 TGGCACCTTCCAGTCCTCAAAGAGCAAGACATCTTTCCTTTGCAAAGCCCAGACAAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGC-AG-GA-C--GCCTTT-TAAAGCCCACACAAGTTGG
** *
464236 TGGCACCTTCTAGTCCTCAAAAAGCAGGACGCCTTTCCCTTTCAAAGCCCACACAAGTTGG
1 TGGCATTTTC-AGTCCTCAAAGAGCAGGACGCC--T---TTT-AAAGCCCACACAAGTTGG
* * *
464297 TAGCATTTTCCAGTCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGG
1 TGGCATTTT-CAGTCCTCAAAGAGCAGGACGC-----CTTTT-AAAGCCCACACAAGTTGG
* *
464358 TGGCATTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGC-----CTTTT-AAAGCCCACACAAGTTGG
* * * *
464419 TGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * *
464474 TGGCATTTTTCAGTCCTCAAAGAGTAGGACACCTCTTAAAGCCCACACAAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* * * *
464529 TGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
* *
464584 TGGCGCTTTTTAGTCCTCAAAGAGCAGGA
1 TGGC-ATTTTCAGTCCTCAAAGAGCAGGA
464613 TGCACTTTAT
Statistics
Matches: 1014, Mismatches: 103, Indels: 120
0.82 0.08 0.10
Matches are distributed among these distances:
53 5 0.00
54 12 0.01
55 544 0.54
56 74 0.07
57 1 0.00
58 6 0.01
59 3 0.00
60 11 0.01
61 288 0.28
62 24 0.02
63 44 0.04
64 1 0.00
66 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (54 bp):
TGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
Found at i:464053 original size:171 final size:168
Alignment explanation
Indices: 463378--464612 Score: 1269
Period size: 171 Copynumber: 7.2 Consensus size: 168
463368 GCACCTCTTT
*
463378 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGC
1 TGGCACTTCTCAGTCCTCAAAGAGCAGGACG-C----C-TTTCAAAGCCCACACAAGTTGGTGGC
* * * * *
463443 ACCTTTTAGTCCTCAAAGAGCAAGA-C---GCCTTTTAAAGCCCACATAAGTCGGTGGCA--TTT
60 A-CTTTCAGTCCTCAAAGAGCAGGAGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* *
463502 TCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGG
124 T--AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* *
463549 TGGCACTTCTCAGTCCTCATAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
1 TGGCACTTCTCAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGC
* * *
463614 ACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGGTGGCAC
60 A-CTTTCAGTCCTCAAAGAGCAGG--AGC-TTTT-CCTTTTAAAGCCCACACAAGTTGGTGGCAC
* *
463679 CTTTCT-GTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTCG
120 CTTT-TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * *
463728 TGGCACCTT-TCAATCCTCAAAAAGCAGGACGCCTTTTCAAAGCCCACACATGTTGGTGGCACCT
1 TGGCA-CTTCTCAGTCCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACAAGTTGGTGGCA-CT
*
463792 TTCAGTCCTCAAAGAGCAGGACGCTTTT-C----AAAGCCCACACAAGTTGGTCGCA--TTTTCC
63 TTCAGTCCTCAAAGAGCAGGA-GCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT--
*
463850 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGG
125 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* *
463894 TGGCACTTCTCAGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCT
1 TGGCACTTCTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTT-T
* *
463959 CAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACATAAGTTGGTGGTACCTTTTAGT
65 CAGTCCTCAAAGAGCAGGA-G-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGT
*
464024 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGG
128 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * * * * *
464065 TGGCACTTTTCAGTCCTCAAAGAACATGACGCCTTTTAAAGCCCACACGAGTTGGTGGCATTTTC
1 TGGCACTTCTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * * **
464130 TAGTCTTCAAAGAGCAGGA-C---GCCTTTTAAAGCCCACACAAGGTGGTGGCACCTTCCAGTCC
66 -AGTCCTCAAAGAGCAGGAGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCC
* * *
464191 TCAAAGAGCAAGACATCTTTCCTTTGCAAAGCCCAGACAAGTTGG
130 TCAAAGAGC-AG-GA-C--GCCTTT-CAAAGCCCACACAAGTTGG
* *
464236 TGGCACCTTCT-AGTCCTCAAAAAGCAGGACGCCTTTCCCTTTCAAAGCCCACACAAGTTGGTAG
1 TGGCA-CTTCTCAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGG
* * * **
464300 CATTTTCCAGTCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATT
59 CACTTT-CAGTCCTCAAAGAGCAGGA-GCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACC
*
464365 TTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGG
121 TTTTAGTCCTCAAAGAGCAGGACGC-----C-TTTCAAAGCCCACACAAGTTGG
* * *
464419 TGGCACCTT-TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 TGGCA-CTTCTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTT
* * * *
464483 TCAGTCCTCAAAGAGTAGGA-C---ACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
64 TCAGTCCTCAAAGAGCAGGAGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTC
* *
464544 CTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGG
129 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * *
464584 TGGCGCTTTTTAGTCCTCAAAGAGCAGGA
1 TGGCACTTCTCAGTCCTCAAAGAGCAGGA
464613 TGCACTTTAT
Statistics
Matches: 918, Mismatches: 85, Indels: 128
0.81 0.08 0.11
Matches are distributed among these distances:
163 1 0.00
164 9 0.01
165 136 0.15
166 101 0.11
167 3 0.00
168 2 0.00
170 9 0.01
171 295 0.32
172 13 0.01
173 6 0.01
174 45 0.05
175 1 0.00
177 93 0.10
178 7 0.01
179 95 0.10
180 3 0.00
181 4 0.00
182 9 0.01
183 83 0.09
184 3 0.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (168 bp):
TGGCACTTCTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
AGTCCTCAAAGAGCAGGAGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCT
CAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
Done.