Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 1 of 295
Found at i:2593 original size:26 final size:27
Alignment explanation
Indices: 2526--2593 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
2516 AAAAATAAGT
* *
2526 AAATTAATCTGTATAATTTCTATTATTA
1 AAATTATTCTATAT-ATTTCTATTATTA
* * *
2554 AAAAT-TTATATATATTTTTATTATTA
1 AAATTATTCTATATATTTCTATTATTA
2580 AAATTATTCT-TATA
1 AAATTATTCTATATA
2594 CATCATTTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
26 20 0.62
27 8 0.25
28 4 0.12
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (27 bp):
AAATTATTCTATATATTTCTATTATTA
Found at i:7493 original size:18 final size:18
Alignment explanation
Indices: 7469--7511 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
7459 GGATGAACCA
7469 GAAGAAGATGATGAAGGG
1 GAAGAAGATGATGAAGGG
* * *
7487 GATGAAGATGGTGAATGG
1 GAAGAAGATGATGAAGGG
7505 GAAGAAG
1 GAAGAAG
7512 CGGATGCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (18 bp):
GAAGAAGATGATGAAGGG
Found at i:10694 original size:4 final size:4
Alignment explanation
Indices: 10685--10780 Score: 120
Period size: 4 Copynumber: 24.0 Consensus size: 4
10675 TTCTTAATAG
* * * *
10685 CATA CATA CATA CATA CATA CATA CATA CATA CATG CATG CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
10733 CACA CATG CACA GATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
10781 TCCACTGTCC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 82 1.00
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (4 bp):
CATA
Found at i:12913 original size:3 final size:3
Alignment explanation
Indices: 12905--12943 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12895 GGACCTACTA
12905 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12944 GAAATACGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18158 original size:24 final size:24
Alignment explanation
Indices: 18131--18177 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
18121 AGCCCACCCT
18131 TCCTTTTCTTTCACCTCTCACCAA
1 TCCTTTTCTTTCACCTCTCACCAA
18155 TCCTTTTCTTTCACCTCTCACCA
1 TCCTTTTCTTTCACCTCTCACCA
18178 CCACTCAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.43, G:0.00, T:0.43
Consensus pattern (24 bp):
TCCTTTTCTTTCACCTCTCACCAA
Found at i:27805 original size:21 final size:22
Alignment explanation
Indices: 27766--27808 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
27756 CAAAGGAAAG
*
27766 AATTAGAAGTAAGAATGCAAAA
1 AATTAGAAGTAAAAATGCAAAA
27788 AATTAGAA-TAAAAATGCAAAA
1 AATTAGAAGTAAAAATGCAAAA
27809 GCTTAATCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.63, C:0.05, G:0.14, T:0.19
Consensus pattern (22 bp):
AATTAGAAGTAAAAATGCAAAA
Found at i:38364 original size:14 final size:14
Alignment explanation
Indices: 38345--38371 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38335 ATGCATCTTT
38345 AATAATAATAATAA
1 AATAATAATAATAA
38359 AATAATAATAATA
1 AATAATAATAATA
38372 TACAATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:42093 original size:122 final size:124
Alignment explanation
Indices: 41889--42608 Score: 1031
Period size: 122 Copynumber: 5.7 Consensus size: 124
41879 AATATCATAC
41889 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACAT-ATATACATATAATTCATGGTG
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAATATACATATAATTCATGGTG
41953 TGAACAA-TAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
66 TGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
*
42011 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACAT-TTATACATATAATTCATGGTG
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAATATACATATAATTCATGGTG
*
42075 TGAACAA-TAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTAATATAACAT
66 TGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
* *
42133 TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATAT--A-A-ACATA-ATATACATATAATTCA
* * ** * *
42198 TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACAT
61 TGGTGTGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
*
42262 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACAT-TTATACATATAATTCATGGTG
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAATATACATATAATTCATGGTG
*
42326 TGAACAA-TAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTAATATAACAT
66 TGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
* *
42384 TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATAT--A-A-ACATA-ATATACATATAATTCA
* * ** * *
42449 TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACAT
61 TGGTGTGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
* * *
42513 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTG-TGATAGACATATACAAATACACATAATTCAT
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGAT-ATA-A-ACATA-ATATACATATAATTCAT
* *
42577 GGTGTGAACAACTAGGAATCTGAAAAGATGGA
62 GGTGTGAACAACTAGGAACCT-TAAAGATGGA
42609 AAATTAGGAG
Statistics
Matches: 539, Mismatches: 43, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
122 237 0.44
123 25 0.05
124 2 0.00
125 6 0.01
126 9 0.02
127 41 0.08
128 59 0.11
129 160 0.30
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (124 bp):
TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAATATACATATAATTCATGGTG
TGAACAACTAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACAT
Found at i:42312 original size:251 final size:251
Alignment explanation
Indices: 41889--42608 Score: 1204
Period size: 251 Copynumber: 2.9 Consensus size: 251
41879 AATATCATAC
* *
41889 TCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATAT--A-A-ACAT--ATATACATATAATTCA
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
* * ** * *
41948 TGGTGTGAACAA-TAGGAACCTTAAAGATGGAGCTTTAGATCAATTTGGGGTGTAATATAACATT
66 TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACATT
42012 CAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATTTATACATATAATTCATGGTGTG
131 CAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATTTATACATATAATTCATGGTGTG
42077 AACAATAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTAATATAACAT
196 AACAATAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTAATATAACAT
42133 TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
42198 TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACATT
66 TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACATT
42263 CAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATTTATACATATAATTCATGGTGTG
131 CAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATTTATACATATAATTCATGGTGTG
42328 AACAATAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTAATATAACAT
196 AACAATAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTAATATAACAT
42384 TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
1 TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
42449 TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACATT
66 TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACATT
* * *
42514 CAATCAAGATGAGCTAGCATGAAAAAGTGTTG-TGATAGACATATACAAATACACATAATTCATG
131 CAATCAAGATGAGCTAGCATGAAAAAGTGTTGAT-ATAAACAT-T---TATACATATAATTCATG
* *
42578 GTGTGAACAACTAGGAATCTGAAAAGATGGA
191 GTGTGAACAA-TAGGAACCT-TAAAGATGGA
42609 AAATTAGGAG
Statistics
Matches: 449, Mismatches: 13, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
244 36 0.08
246 1 0.00
247 1 0.00
248 4 0.01
250 27 0.06
251 337 0.75
252 1 0.00
255 25 0.06
256 8 0.02
257 9 0.02
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (251 bp):
TCAATCAAGATGAGCTAGCATGAAAAAGTGTAGATATAGACACACATACATAAACATATAATTCA
TGGTTTGAACAACTAAGAATGTTAAAGATGTAGCTTTAGGTCAATTTGGGGTGTAATATAACATT
CAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATTTATACATATAATTCATGGTGTG
AACAATAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTAATATAACAT
Found at i:45944 original size:9 final size:9
Alignment explanation
Indices: 45930--46003 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
45920 TTCATTAAAA
*
45930 TTTTATGAT
1 TTTTATAAT
45939 TTTTATAAAT
1 TTTTAT-AAT
45949 TTTTA-AAT
1 TTTTATAAT
*
45957 TTTTAATGAT
1 TTTT-ATAAT
45967 TTTTATAAT
1 TTTTATAAT
45976 TTTT-T-AT
1 TTTTATAAT
* *
45983 TTTTTTTAT
1 TTTTATAAT
*
45992 TTTTATAGT
1 TTTTATAAT
46001 TTT
1 TTT
46004 AGAATTAATC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
7 6 0.11
8 9 0.17
9 26 0.48
10 13 0.24
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (9 bp):
TTTTATAAT
Found at i:45958 original size:18 final size:19
Alignment explanation
Indices: 45930--45979 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
45920 TTCATTAAAA
*
45930 TTTTATGATTTTT-ATAAAT
1 TTTTATAATTTTTAAT-AAT
*
45949 TTTTA-AATTTTTAATGAT
1 TTTTATAATTTTTAATAAT
45967 TTTTATAATTTTT
1 TTTTATAATTTTT
45980 TATTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTAATAAT
Found at i:45980 original size:28 final size:27
Alignment explanation
Indices: 45924--45981 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
45914 ATTTATTTCA
45924 TTAAAATTTTATGATTTTTATAAATTT
1 TTAAAATTTTATGATTTTTATAAATTT
* *
45951 TTAAATTTTTAATGATTTTTATAATTTT
1 TTAAAATTTT-ATGATTTTTATAAATTT
45979 TTA
1 TTA
45982 TTTTTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (27 bp):
TTAAAATTTTATGATTTTTATAAATTT
Found at i:52242 original size:3 final size:3
Alignment explanation
Indices: 52234--52260 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52224 AAAATGAGGA
52234 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
52261 AGAAGCCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54661 original size:12 final size:12
Alignment explanation
Indices: 54622--54654 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
54612 TTTATATTTT
54622 TTTATTTTTATC
1 TTTATTTTTATC
*
54634 TTTATCTTTATC
1 TTTATTTTTATC
54646 TTTATTTTT
1 TTTATTTTT
54655 TTATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTTATC
Found at i:54661 original size:24 final size:24
Alignment explanation
Indices: 54622--54670 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54612 TTTATATTTT
* **
54622 TTTATTTTTATCTTTATCTTTATC
1 TTTATTTTTATATTTAAATTTATC
*
54646 TTTATTTTTTTATTTAAATTTATC
1 TTTATTTTTATATTTAAATTTATC
54670 T
1 T
54671 CTCAATCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTATTTTTATATTTAAATTTATC
Found at i:63267 original size:14 final size:14
Alignment explanation
Indices: 63236--63269 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
63226 ATTAAAATCA
63236 AAATTTCATATATC
1 AAATTTCATATATC
63250 AAATTATCATATAT-
1 AAATT-TCATATATC
63264 AAATTT
1 AAATTT
63270 AAAATGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 10 0.53
15 8 0.42
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTCATATATC
Found at i:64486 original size:23 final size:23
Alignment explanation
Indices: 64442--64486 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
64432 ACCTGAATCT
*
64442 AATTTTAAAAATTATTTGTATAC
1 AATTTTAAAAATTATATGTATAC
64465 AATTTATAAAAATTATAT-TATA
1 AATTT-TAAAAATTATATGTATA
64487 AGAATCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTTTAAAAATTATATGTATAC
Found at i:68370 original size:36 final size:36
Alignment explanation
Indices: 68318--68388 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
68308 AGCTTCTGTG
*
68318 TCATCTTATACAAGACCATCCTCTCCCATTACTCGA
1 TCATCTAATACAAGACCATCCTCTCCCATTACTCGA
* *
68354 TCATCTAATACCAGACCATCCTCTCCTATTACTCG
1 TCATCTAATACAAGACCATCCTCTCCCATTACTCG
68389 CTCGCCATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.37, G:0.06, T:0.31
Consensus pattern (36 bp):
TCATCTAATACAAGACCATCCTCTCCCATTACTCGA
Found at i:71682 original size:2 final size:2
Alignment explanation
Indices: 71675--71709 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
71665 CTTTTAGAAC
*
71675 TA TA TA TA TA TT 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 TA TA TA TA T
71710 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:91556 original size:119 final size:118
Alignment explanation
Indices: 91334--91570 Score: 465
Period size: 119 Copynumber: 2.0 Consensus size: 118
91324 GCGCTTCCTT
91334 AACCTTTATGGTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCTC
1 AACCTTTATGGTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCTC
91399 AACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
66 AACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
91452 AACCTTTATGGTTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCT
1 AACCTTTATGG-TTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCT
91517 CAACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
65 CAACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
91571 TAACAATTTT
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 11 0.09
119 107 0.91
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (118 bp):
AACCTTTATGGTTCCGTACTGGAGATCTTTTCAGCCTTCAGAGCACTCAACCTCTGAATTTTCTC
AACCTTGACAGCACTAGCAGTGCCATTTTTCTCACTCTTGGAAGGCTCTTCAA
Found at i:92522 original size:12 final size:12
Alignment explanation
Indices: 92502--92550 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
92492 CACTGCTAGC
92502 ACATACATGCAT
1 ACATACATGCAT
* *
92514 ACATCCATGTAT
1 ACATACATGCAT
* *
92526 CCATGCATGCAT
1 ACATACATGCAT
*
92538 GCATACATGCAT
1 ACATACATGCAT
92550 A
1 A
92551 TAGTTAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (12 bp):
ACATACATGCAT
Found at i:97490 original size:11 final size:12
Alignment explanation
Indices: 97463--97491 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
97453 AAGGCAAACA
97463 TAAAAAAAAAAG
1 TAAAAAAAAAAG
97475 TAAAAAAAAAAG
1 TAAAAAAAAAAG
97487 -AAAAA
1 TAAAAA
97492 GGGATCTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
TAAAAAAAAAAG
Found at i:108969 original size:25 final size:24
Alignment explanation
Indices: 108941--108998 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
108931 TATTATCAAG
* *
108941 AATTTTATGAAATTATATATTATTA
1 AATTATATGAAATAATA-ATTATTA
*
108966 AATTATATGTAATAATAATTATTTTA
1 AATTATATGAAATAATAATTA--TTA
108992 AATTATA
1 AATTATA
108999 CAAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTATATGAAATAATAATTATTA
Found at i:108991 original size:88 final size:91
Alignment explanation
Indices: 108820--109023 Score: 297
Period size: 88 Copynumber: 2.3 Consensus size: 91
108810 TGATTTTAGT
* *
108820 AAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAAA
1 AAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAAA
* * * *
108885 TTTAATATTAATTATTTTAAATTGTAT
65 TGTAATAATAATTATTTTAAATTATAC
* *
108912 AATTTCATATAAGAAAATTTATTATCAAGAATTTTATGAAA-T-TATAT-ATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAAAT
108974 GTAATAATAATTATTTTAAATTATAC
66 GTAATAATAATTATTTTAAATTATAC
*
109000 AAATTCATATAAGATAATTTATTA
1 AAATTCATATAAGAAAATTTATTA
109024 GTTATAATTA
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
88 58 0.57
89 5 0.05
90 1 0.01
91 24 0.24
92 14 0.14
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
AAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAAAT
GTAATAATAATTATTTTAAATTATAC
Found at i:109065 original size:47 final size:49
Alignment explanation
Indices: 108941--109066 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 49
108931 TATTATCAAG
* *
108941 AATTTTATGAAATTATATATTATTAAATTATATGTAATAATAATTATTTTA
1 AATTTTATCAAATCATATATT-TT-AATTATATGTAATAATAATTATTTTA
* *** * *
108992 AATTATA-CAAATTCATATAAGATAATT-TAT-TAGTTATAATTATTTTA
1 AATTTTATCAAA-TCATATATTTTAATTATATGTAATAATAATTATTTTA
*
109039 AATTTTATTAAATCATATATTTTAATTA
1 AATTTTATCAAATCATATATTTTAATTA
109067 AAATATATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
47 33 0.56
48 6 0.10
49 4 0.07
50 4 0.07
51 12 0.20
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (49 bp):
AATTTTATCAAATCATATATTTTAATTATATGTAATAATAATTATTTTA
Found at i:109147 original size:66 final size:65
Alignment explanation
Indices: 109077--109275 Score: 163
Period size: 66 Copynumber: 3.2 Consensus size: 65
109067 AAATATATTT
109077 AATATTAATTATTTAAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATAAAA
1 AATATTAATTATTTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATAAAA
109142 G
65 G
* * * * **
109143 AATATTAATTA-TTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-AT-ATT
1 AATATTAATTATTTAA-AATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATAAAA
*
109196 T
65 G
* * * *
109197 AATAATAATTATGTT-AATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATAAA
109261 AG
64 AG
*
109263 AATATTGATTATT
1 AATATTAATTATT
109276 AAGAATTTTA
Statistics
Matches: 99, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
54 14 0.14
55 4 0.04
56 7 0.07
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 8 0.08
66 25 0.25
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (65 bp):
AATATTAATTATTTAAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATAAAAG
Found at i:109163 original size:120 final size:120
Alignment explanation
Indices: 109039--109336 Score: 499
Period size: 120 Copynumber: 2.5 Consensus size: 120
109029 AATTATTTTA
* * * *
109039 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
109103 TATAGTATAATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAG
65 TATAGTATAATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAG
*
109159 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* * *
109224 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATAATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAG
109279 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
109337 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 160 0.96
121 7 0.04
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATAATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAG
Found at i:109176 original size:59 final size:59
Alignment explanation
Indices: 109113--109296 Score: 164
Period size: 59 Copynumber: 3.1 Consensus size: 59
109103 TATAGTATAA
*
109113 TATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* * * * * * * *
109172 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 TATATTATGATTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
109231 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
109292 TATAT
1 TATAT
109297 ATTTTAATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
56 6 0.06
57 10 0.11
58 10 0.11
59 19 0.20
60 8 0.09
61 14 0.15
62 9 0.10
63 11 0.12
64 6 0.06
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:109179 original size:61 final size:61
Alignment explanation
Indices: 109112--109299 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
109102 TTATAGTATA
109112 ATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * ** * * * *
109173 ATATATTTTAATTAT-AATATATTTAATAATAATTATGTTAA-T-TT-A-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTA-AATTCATAA-AAGAATATTAATTATTAAGAATTTTATTA-AATT
* *
109232 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAATT
109293 ATATATT
1 ATATATT
109300 TTAATTATAA
Statistics
Matches: 93, Mismatches: 24, Indels: 20
0.68 0.18 0.15
Matches are distributed among these distances:
57 7 0.08
58 10 0.11
59 24 0.26
60 2 0.02
61 31 0.33
62 11 0.12
63 8 0.09
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:109199 original size:15 final size:15
Alignment explanation
Indices: 109164--109215 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
109154 TTAAGAATTT
*
109164 TATTAAATTAT-ATA
1 TATTTAATTATAATA
109178 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
109192 TATTTAATAATAAT-
1 TATTTAATTATAATA
109206 TATGTTAATT
1 TAT-TTAATT
109216 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:109314 original size:16 final size:16
Alignment explanation
Indices: 109293--109334 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
109283 TTATTAAATT
*
109293 ATATATTTTAATTATA
1 ATATATTTTAATAATA
109309 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
109324 AT-TATGTTTAA
1 ATATAT-TTTAA
109335 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:109319 original size:15 final size:15
Alignment explanation
Indices: 109284--109325 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
109274 TTAAGAATTT
*
109284 TATTAAATTAT-ATA
1 TATTTAATTATAATA
109298 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
109312 TATTTAATAATAAT
1 TATTTAATTATAAT
109326 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:109561 original size:45 final size:44
Alignment explanation
Indices: 109480--109570 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 44
109470 ACATCTATTC
*
109480 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
* *
109524 CATTCAACCAAACA-ATTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACACCTCTATTCCATTA
109569 CA
1 CA
109571 CCTCTATTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.38
45 25 0.60
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:109597 original size:16 final size:16
Alignment explanation
Indices: 109549--109585 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
109539 TTGATTTGCT
109549 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
109565 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
109581 ATTAC
1 ATTAC
109586 GTCTCTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:110866 original size:16 final size:16
Alignment explanation
Indices: 110840--110896 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
110830 TTAAAGCCTC
110840 ATTTATTTTTATGTAAT
1 ATTTATTTTTATG-AAT
110857 ATTT-TTTTTATGAAT
1 ATTTATTTTTATGAAT
* *
110872 ATATTAATTATAT-AAT
1 AT-TTATTTTTATGAAT
110888 -TTTATTTTT
1 ATTTATTTTT
110897 CACTCATATC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 6 0.18
15 6 0.18
16 13 0.38
17 9 0.26
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
ATTTATTTTTATGAAT
Found at i:114914 original size:29 final size:31
Alignment explanation
Indices: 114850--114915 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
114840 TTGGAGACAT
* *
114850 ATGAATTTTTGATTTAATGTGTAATTTGATAT
1 ATGAATTTTTAATTTAA-GTGTAATTTGATAC
114882 ATGAA-TTTTAATTTAA-TGTAATTAT-ATAC
1 ATGAATTTTTAATTTAAGTGTAATT-TGATAC
114911 ATGAA
1 ATGAA
114916 ACTTTGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 15 0.48
30 1 0.03
31 10 0.32
32 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (31 bp):
ATGAATTTTTAATTTAAGTGTAATTTGATAC
Found at i:143816 original size:15 final size:17
Alignment explanation
Indices: 143796--143828 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
143786 ACAGATGGAA
143796 AGATAA-TC-AAACACC
1 AGATAACTCAAAACACC
143811 AGATAACTCAAAACACC
1 AGATAACTCAAAACACC
143828 A
1 A
143829 AGATTTGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.55, C:0.27, G:0.06, T:0.12
Consensus pattern (17 bp):
AGATAACTCAAAACACC
Found at i:150358 original size:20 final size:20
Alignment explanation
Indices: 150326--150377 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
150316 AAAAATATAA
150326 ATTTTAGAATTTTTAAAAAT-
1 ATTTT-GAATTTTTAAAAATC
150346 ATTTTGAATTTTTAAAAATC
1 ATTTTGAATTTTTAAAAATC
150366 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
150378 TTTTTGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATC
Found at i:161076 original size:30 final size:30
Alignment explanation
Indices: 161040--161151 Score: 113
Period size: 29 Copynumber: 3.8 Consensus size: 30
161030 ATTTGAGTGC
161040 TTTTGAAAAGGTTTGGCCCTTATTTGACCA
1 TTTTGAAAAGGTTTGGCCCTTATTTGACCA
* *
161070 TTTTGAAAA-GTTT-GACCTTCATTTGATCA
1 TTTTGAAAAGGTTTGGCCCTT-ATTTGACCA
* ** * *
161099 CTTTTGTAAAGGTTAAGCCCTTATATGACTA
1 -TTTTGAAAAGGTTTGGCCCTTATTTGACCA
*
161130 TTTT-AAAAAGTTTGGCCCTTAT
1 TTTTGAAAAGGTTTGGCCCTTAT
161152 ATGAGCTACC
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
28 5 0.08
29 26 0.39
30 21 0.32
31 9 0.14
32 5 0.08
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (30 bp):
TTTTGAAAAGGTTTGGCCCTTATTTGACCA
Found at i:179062 original size:15 final size:15
Alignment explanation
Indices: 179042--179090 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
179032 TCTTTATGTT
179042 TTTTGGTTTTGGATC
1 TTTTGGTTTTGGATC
* *
179057 TTTTGG-TAT-G-TT
1 TTTTGGTTTTGGATC
179069 TTTTGGTTTTGGATC
1 TTTTGGTTTTGGATC
179084 TTTTGGT
1 TTTTGGT
179091 GCCTTCTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
14 3 0.11
15 14 0.52
ACGTcount: A:0.06, C:0.04, G:0.27, T:0.63
Consensus pattern (15 bp):
TTTTGGTTTTGGATC
Found at i:179066 original size:27 final size:27
Alignment explanation
Indices: 179036--179090 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
179026 CACACGTCTT
179036 TATGTTTTTTGGTTTTGGATCTTTTGG
1 TATGTTTTTTGGTTTTGGATCTTTTGG
179063 TATGTTTTTTGGTTTTGGATCTTTTGG
1 TATGTTTTTTGGTTTTGGATCTTTTGG
179090 T
1 T
179091 GCCTTCTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.07, C:0.04, G:0.25, T:0.64
Consensus pattern (27 bp):
TATGTTTTTTGGTTTTGGATCTTTTGG
Found at i:182844 original size:23 final size:23
Alignment explanation
Indices: 182818--182865 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
182808 TTCATTAGCT
182818 AACTTATGTGAAATATTAAAGAA
1 AACTTATGTGAAATATTAAAGAA
182841 AACTTATGTGAAATATTAAAGAA
1 AACTTATGTGAAATATTAAAGAA
182864 AA
1 AA
182866 GAGTATCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (23 bp):
AACTTATGTGAAATATTAAAGAA
Found at i:183784 original size:6 final size:6
Alignment explanation
Indices: 183775--183819 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
183765 TATTTTAATG
183775 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA
183820 TTTTTTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:185605 original size:49 final size:49
Alignment explanation
Indices: 185533--185632 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
185523 TTGTCGTTTT
**
185533 GCTGTCTTGGTTTTCATAGCTATCGGTTGGTGTGATCATCAACCTAAGA
1 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
*
185582 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATGAACCTAAGA
1 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
185631 GC
1 GC
185633 ATTCATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (49 bp):
GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
Found at i:191369 original size:101 final size:101
Alignment explanation
Indices: 191194--191391 Score: 333
Period size: 101 Copynumber: 2.0 Consensus size: 101
191184 TGCAGCTGCT
*
191194 GCTTCTACCAACACTTGAGCTTCTTCGATCTAGAAGCTATCCTCATCTCGACTTAAACCCTCTTA
1 GCTTCTACCAACACTGGAGCTTCTTCGATCTAGAAGCTATCCTCATCTCGACTTAAACCCTCTTA
191259 TGCGATTACACGTGCTGTTTTGCTACCAGATCCGCC
66 TGCGATTACACGTGCTGTTTTGCTACCAGATCCGCC
* * * *
191295 GCTTCTACTAACACTGGAGCTTCTTCGATCTAGAAGCTATTCTCATCTCGACTTAAACTCTCTTG
1 GCTTCTACCAACACTGGAGCTTCTTCGATCTAGAAGCTATCCTCATCTCGACTTAAACCCTCTTA
* *
191360 TGCGATTACATGTGCTGTTTTGTTACCAGATC
66 TGCGATTACACGTGCTGTTTTGCTACCAGATC
191392 GGCCAATGAA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (101 bp):
GCTTCTACCAACACTGGAGCTTCTTCGATCTAGAAGCTATCCTCATCTCGACTTAAACCCTCTTA
TGCGATTACACGTGCTGTTTTGCTACCAGATCCGCC
Found at i:196190 original size:13 final size:13
Alignment explanation
Indices: 196159--196190 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
196149 TACTGAACTA
196159 TTAAGTTTTTTTT
1 TTAAGTTTTTTTT
196172 TT--GTTTTTTTT
1 TTAAGTTTTTTTT
196183 TTAAGTTT
1 TTAAGTTT
196191 GACTACCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (13 bp):
TTAAGTTTTTTTT
Found at i:202622 original size:20 final size:18
Alignment explanation
Indices: 202593--202635 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
202583 TTTTTTTTTA
202593 TTTTTTATTTGCAAG-ATTT
1 TTTTTTATTT-C-AGTATTT
202612 TTTTATTATTTCAGTATTT
1 TTTT-TTATTTCAGTATTT
202631 TTTTT
1 TTTTT
202636 GTTAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.14
19 13 0.59
20 6 0.27
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTTTATTTCAGTATTT
Found at i:205165 original size:13 final size:13
Alignment explanation
Indices: 205147--205172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
205137 CCTCAAATCG
205147 ACTTAATTTTAAT
1 ACTTAATTTTAAT
205160 ACTTAATTTTAAT
1 ACTTAATTTTAAT
205173 GTATATTATT
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:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ACTTAATTTTAAT
Found at i:211991 original size:93 final size:93
Alignment explanation
Indices: 211832--212017 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
211822 ACAATAACTG
211832 TTAGATATTACTCTTTCTAAAACCTAATGCGACAAACATATTATCATATGCGTAAGTCATATCAA
1 TTAGATATTACTCTTTCTAAAACCTAATGCGACAAACATATTATCATATGCGTAAGTCATATCAA
211897 CTTGTTATTTCAACATATTACTCATTAA
66 CTTGTTATTTCAACATATTACTCATTAA
211925 TTAGATATTACTCTTTCTAAAACCTAATGCGACAAACATATTATCATATGCGTAAGTCATATCAA
1 TTAGATATTACTCTTTCTAAAACCTAATGCGACAAACATATTATCATATGCGTAAGTCATATCAA
211990 CTTGTTATTTCAACATATTACTCATTAA
66 CTTGTTATTTCAACATATTACTCATTAA
212018 AAATACAGAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (93 bp):
TTAGATATTACTCTTTCTAAAACCTAATGCGACAAACATATTATCATATGCGTAAGTCATATCAA
CTTGTTATTTCAACATATTACTCATTAA
Found at i:214638 original size:13 final size:13
Alignment explanation
Indices: 214620--214645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
214610 ATTGGAGGAG
214620 AATATGTATATAT
1 AATATGTATATAT
214633 AATATGTATATAT
1 AATATGTATATAT
214646 CATTTGTCCA
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AATATGTATATAT
Found at i:217522 original size:14 final size:14
Alignment explanation
Indices: 217505--217533 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
217495 TCTTATCTTA
217505 AACTATATATATAT
1 AACTATATATATAT
217519 AACTATATATATAT
1 AACTATATATATAT
217533 A
1 A
217534 GTTTGATGTC
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AACTATATATATAT
Found at i:218417 original size:24 final size:24
Alignment explanation
Indices: 218390--218435 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
218380 CATTCCCATG
*
218390 TAAATATTAAAATATAAATTAGTA
1 TAAATATTAAAATAAAAATTAGTA
*
218414 TAAATATTAATATAAAAATTAG
1 TAAATATTAAAATAAAAATTAG
218436 GTATGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAATATTAAAATAAAAATTAGTA
Found at i:219198 original size:13 final size:12
Alignment explanation
Indices: 219175--219204 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
219165 ATCCCACCAG
219175 AAAAAAGAAAAA
1 AAAAAAGAAAAA
219187 AAAAAAGAAAAA
1 AAAAAAGAAAAA
219199 AAAAAA
1 AAAAAA
219205 CCTTGAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:221921 original size:18 final size:18
Alignment explanation
Indices: 221898--221939 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
221888 ATTATTTTTA
* *
221898 TATAAAAATTTAAGTAAT
1 TATAAAAATTAAACTAAT
*
221916 TGTAAAAATTAAACTAAT
1 TATAAAAATTAAACTAAT
221934 TATAAA
1 TATAAA
221940 TTAAATAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
TATAAAAATTAAACTAAT
Found at i:222095 original size:28 final size:30
Alignment explanation
Indices: 222063--222129 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
222053 GTGCCATTAC
*
222063 ATTTTAGAGGCCT-ATTAAAAATTTT-AAA-
1 ATTTTAGAGGACTAATT-AAAATTTTAAAAT
*
222091 ATTTTCGA-GACTAATTAAAATTTTAAAAT
1 ATTTTAGAGGACTAATTAAAATTTTAAAAT
222120 ATTTTAGAGG
1 ATTTTAGAGG
222130 TTTAATGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 11 0.34
28 13 0.41
29 7 0.22
30 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (30 bp):
ATTTTAGAGGACTAATTAAAATTTTAAAAT
Found at i:222499 original size:21 final size:19
Alignment explanation
Indices: 222465--222508 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 19
222455 ATTGATTCGG
222465 AAATTAATAAAAATTAATT
1 AAATTAATAAAAATTAATT
222484 AAATTAAATGAAAAATTAATT
1 AAATT-AAT-AAAAATTAATT
222505 AAAT
1 AAAT
222509 CGATTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.22
20 3 0.13
21 15 0.65
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTAATAAAAATTAATT
Found at i:237385 original size:67 final size:67
Alignment explanation
Indices: 237308--237443 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 67
237298 GGAAATTGCT
* * *
237308 CTGAATTTTAATTATTGCTTGCTTTTTCTTCATACAATTCCTTCTTAACTGCCAACCACGGAAAT
1 CTGAATTTTAATTATTGCTTGCTTCTTCTTCATAAAATTCCTTCTTAACTGCAAACCACGGAAAT
237373 GA
66 GA
*
237375 CTGAATTTTAATTATTGCTTGCTTCTTCTTCATAAAATTCCTTCTTGACTGCAAACCACGGAAAT
1 CTGAATTTTAATTATTGCTTGCTTCTTCTTCATAAAATTCCTTCTTAACTGCAAACCACGGAAAT
237440 GA
66 GA
237442 CT
1 CT
237444 CTGAATTCTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (67 bp):
CTGAATTTTAATTATTGCTTGCTTCTTCTTCATAAAATTCCTTCTTAACTGCAAACCACGGAAAT
GA
Found at i:243878 original size:18 final size:18
Alignment explanation
Indices: 243857--243909 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
243847 AAGTAATATA
*
243857 AAATAATATTATTTGT-AT
1 AAATAATAATATTT-TAAT
*
243875 AAATATTAATATTTTAAT
1 AAATAATAATATTTTAAT
* *
243893 AAATAAGAATACTTTAA
1 AAATAATAATATTTTAA
243910 AAAAAATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 1 0.03
18 28 0.97
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (18 bp):
AAATAATAATATTTTAAT
Found at i:256584 original size:10 final size:10
Alignment explanation
Indices: 256529--256584 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
256519 GTATTCTTAT
*
256529 TTAAATTTAA
1 TTAATTTTAA
*
256539 TTAATATTAA
1 TTAATTTTAA
256549 TTAA--TTAA
1 TTAATTTTAA
*
256557 TTATATTTATTA
1 TTA-ATTT-TAA
256569 TTAATTTTAA
1 TTAATTTTAA
256579 TTAATT
1 TTAATT
256585 ATATTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 7 0.18
9 1 0.03
10 20 0.53
11 5 0.13
12 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:256600 original size:26 final size:27
Alignment explanation
Indices: 256533--256606 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 27
256523 TCTTATTTAA
256533 ATTTAAT-TAATATTAATTAATTAATTAT
1 ATTTAATATAA-ATT-ATTAATTAATTAT
* *
256561 ATTTATTATTAATT-TTAATTAATTAT
1 ATTTAATATAAATTATTAATTAATTAT
256587 ATTTAA-ATAAAATTATTAAT
1 ATTTAATAT-AAATTATTAAT
256607 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 2 0.05
26 21 0.54
27 5 0.13
28 9 0.23
29 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTAATATAAATTATTAATTAATTAT
Found at i:258368 original size:31 final size:32
Alignment explanation
Indices: 258330--258397 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
258320 TTTTTAAGCT
** * *
258330 AAATTTAATCTTCAACCTTTTAGAAAT-AGTG
1 AAATTTAATCACCAACCTTTTAAAAATGAGTC
*
258361 AAATTTAATCACCAATCTTTTAAAAATGAGTC
1 AAATTTAATCACCAACCTTTTAAAAATGAGTC
258393 AAATT
1 AAATT
258398 GATTTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (32 bp):
AAATTTAATCACCAACCTTTTAAAAATGAGTC
Found at i:258518 original size:20 final size:21
Alignment explanation
Indices: 258468--258536 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 21
258458 TACTTCATGC
258468 TATTTTTATGCAATTTTTATAAT
1 TATTTTT-T-CAATTTTTATAAT
* *
258491 T-TTGTTTCAATTTTTAT-TT
1 TATTTTTTCAATTTTTATAAT
*
258510 TATTTTTTCATAAATTTTA-AAT
1 TATTTTTTC--AATTTTTATAAT
258532 TATTT
1 TATTT
258537 ATTAACGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
19 2 0.05
20 16 0.43
21 1 0.03
22 17 0.46
23 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (21 bp):
TATTTTTTCAATTTTTATAAT
Found at i:262914 original size:23 final size:23
Alignment explanation
Indices: 262888--262952 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
262878 ATAAGAATAA
262888 ATTTAATAGAGTTAAC-TTTGACT
1 ATTTAATAGAGTTAACATTT-ACT
* * *
262911 ATTTAA-AAAGATATCATTTACT
1 ATTTAATAGAGTTAACATTTACT
* *
262933 ATTTAATCGAGTTAATATTT
1 ATTTAATAGAGTTAACATTT
262953 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (23 bp):
ATTTAATAGAGTTAACATTTACT
Found at i:263735 original size:6 final size:6
Alignment explanation
Indices: 263726--263786 Score: 86
Period size: 6 Copynumber: 9.8 Consensus size: 6
263716 ACATTCACAA
* *
263726 ATATAC ATATAC ATGTAC ATACATAT ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC AT--ATAC ATATAC ATATAC ATATAC ATATAC
263776 ATATAC ATATA
1 ATATAC ATATA
263787 GACTTACTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
6 45 0.92
8 4 0.08
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:263744 original size:26 final size:25
Alignment explanation
Indices: 263708--263786 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 25
263698 TAGGGTTCAC
*
263708 ATACACATACATTCACAAATATACAT
1 ATACATATACATTCAC-AATATACAT
* * *
263734 ATACATGTACATACATATATATACAT
1 ATACATATACATTCACA-ATATACAT
263760 ATACATATACATAT-AC-ATATACAT
1 ATACATATACAT-TCACAATATACAT
263784 ATA
1 ATA
263787 GACTTACTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
24 11 0.25
25 1 0.02
26 32 0.73
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (25 bp):
ATACATATACATTCACAATATACAT
Found at i:263749 original size:16 final size:16
Alignment explanation
Indices: 263726--263786 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
263716 ACATTCACAA
**
263726 ATATACATATACATGT
1 ATATACATATACATAC
* *
263742 ACATACATATATATAC
1 ATATACATATACATAC
263758 ATATACATATACATATAC
1 ATATACATATAC--ATAC
263776 ATATACATATA
1 ATATACATATA
263787 GACTTACTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
16 22 0.59
18 15 0.41
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (16 bp):
ATATACATATACATAC
Found at i:271043 original size:21 final size:22
Alignment explanation
Indices: 271014--271060 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
271004 CAGAAGGAGT
*
271014 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
271036 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
271057 GAGT
1 GAGT
271061 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:274004 original size:31 final size:32
Alignment explanation
Indices: 273967--274030 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
273957 TTATTATTAT
*
273967 TTTCATTTACA-ATTCAA-TTTTAAATAAAATA
1 TTTCATTTACAGATACAACTTTTAAA-AAAATA
*
273998 TTTCATTTACAGATACAACTTTTTAAAAAATA
1 TTTCATTTACAGATACAACTTTTAAAAAAATA
274030 T
1 T
274031 ATACTCTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 11 0.38
32 12 0.41
33 6 0.21
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTCATTTACAGATACAACTTTTAAAAAAATA
Found at i:276832 original size:21 final size:23
Alignment explanation
Indices: 276808--276850 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
276798 GGGCATGCAT
276808 TTAATTCA-AATATT-ATGGAAA
1 TTAATTCATAATATTAATGGAAA
276829 TTAATTCATTAATATTAATGGA
1 TTAATTCA-TAATATTAATGGA
276851 TTGTTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (23 bp):
TTAATTCATAATATTAATGGAAA
Found at i:279296 original size:35 final size:35
Alignment explanation
Indices: 279250--279322 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
279240 TTGTCTCAAT
279250 CTGATTTTTCATTTGGGTTAAAACATAAATGTAAA
1 CTGATTTTTCATTTGGGTTAAAACATAAATGTAAA
279285 CTGATTTTTCATTTGGGTTAAAACATAAATGTAAA
1 CTGATTTTTCATTTGGGTTAAAACATAAATGTAAA
279320 CTG
1 CTG
279323 TTTATAGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.40
Consensus pattern (35 bp):
CTGATTTTTCATTTGGGTTAAAACATAAATGTAAA
Found at i:284920 original size:35 final size:38
Alignment explanation
Indices: 284857--284928 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
284847 TTTTTTTCAA
* *
284857 TTTAATTAAATTTTATATCAATATTAAAATATTTTATTT
1 TTTAAATAAATTTTATA-CAATATTAAAATATATTATTT
284896 TTTAAATAAATTTT-TA-AATA-TAAAATATATTAT
1 TTTAAATAAATTTTATACAATATTAAAATATATTAT
284929 ATTGGTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 12 0.39
36 4 0.13
38 2 0.06
39 13 0.42
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (38 bp):
TTTAAATAAATTTTATACAATATTAAAATATATTATTT
Found at i:286650 original size:15 final size:16
Alignment explanation
Indices: 286630--286659 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
286620 AATGGTCATT
286630 CCTCTCTT-TTTCTTA
1 CCTCTCTTATTTCTTA
286645 CCTCTCTTATTTCTT
1 CCTCTCTTATTTCTT
286660 CTTTACCACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (16 bp):
CCTCTCTTATTTCTTA
Found at i:288513 original size:31 final size:30
Alignment explanation
Indices: 288459--288519 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
288449 ACCCGATGAT
* * *
288459 TTAAATAAATTTTTTGAATAGTTTAGTGAC
1 TTAAATAAAATTTTTAAAAAGTTTAGTGAC
288489 TTAAATGAAAATTTTTAAAAAGTTTAGTGAC
1 TTAAAT-AAAATTTTTAAAAAGTTTAGTGAC
288520 CATTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (30 bp):
TTAAATAAAATTTTTAAAAAGTTTAGTGAC
Found at i:292825 original size:22 final size:22
Alignment explanation
Indices: 292799--292840 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
292789 AAAATTTTGG
292799 AAAATTATAATTAAACCCCTTA
1 AAAATTATAATTAAACCCCTTA
* *
292821 AAAATTTTAATTATACCCCT
1 AAAATTATAATTAAACCCCT
292841 CATAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATTATAATTAAACCCCTTA
Found at i:292850 original size:22 final size:22
Alignment explanation
Indices: 292799--292852 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
292789 AAAATTTTGG
* *
292799 AAAATTATAATTAAACCCCTTA
1 AAAATTTTAATTAAACCCCTCA
*
292821 AAAATTTTAATTATACCCCTCA
1 AAAATTTTAATTAAACCCCTCA
* *
292843 TAATTTTTAA
1 AAAATTTTAA
292853 AAATCCTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTTTAATTAAACCCCTCA
Found at i:292856 original size:31 final size:30
Alignment explanation
Indices: 292818--292973 Score: 98
Period size: 31 Copynumber: 5.1 Consensus size: 30
292808 ATTAAACCCC
292818 TTAAAAATTTTAATTATACCCCTCATAATTT
1 TTAAAAATTTTAATTATACCCCTCA-AATTT
** * * * *
292849 TTAAAAATCCTCATTAGACCACTCAAAATT
1 TTAAAAATTTTAATTATACCCCTCAAATTT
* ** * *
292879 TTAGAAAATTTGAATTACGCTCTCACAAAATTT
1 TTA-AAAATTTTAATTATAC-CCCTC-AAATTT
* * * * *
292912 TTAGAAATTTTTATCATGCCCCT-TAATTAT
1 TTAAAAATTTTAATTATACCCCTCAAATT-T
* *
292942 TTAAAAACTTTAATTATACCCTTCAAATTT
1 TTAAAAATTTTAATTATACCCCTCAAATTT
292972 TT
1 TT
292974 TGAAAATTCA
Statistics
Matches: 90, Mismatches: 30, Indels: 11
0.69 0.23 0.08
Matches are distributed among these distances:
29 4 0.04
30 28 0.31
31 36 0.40
32 14 0.16
33 8 0.09
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (30 bp):
TTAAAAATTTTAATTATACCCCTCAAATTT
Found at i:295295 original size:84 final size:84
Alignment explanation
Indices: 295188--295348 Score: 198
Period size: 84 Copynumber: 1.9 Consensus size: 84
295178 TTTTGAAGGA
* * * * * * * * *
295188 GGTTAAAGTATAATCTTATCATTGTATTAACATATAATTTTATAATTTCTAAAGGGATTATAAAG
1 GGTTAAAGTACAATCTTACCATTGTAGTAACATAAAAATTCAAAATTTCTAAAGGGACTAAAAAG
295253 AAATTTTACCATCTTAGGG
66 AAATTTTACCATCTTAGGG
* *
295272 GGTTAAAGTACAA-CTTAACCATTGTAGTAACTTAAAAATTCAAAATTTTTAAAGGGACTAAAAA
1 GGTTAAAGTACAATCTT-ACCATTGTAGTAACATAAAAATTCAAAATTTCTAAAGGGACTAAAAA
*
295336 GAAATTTTGCCAT
65 GAAATTTTACCAT
295349 TTGTCACTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
83 3 0.05
84 61 0.95
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (84 bp):
GGTTAAAGTACAATCTTACCATTGTAGTAACATAAAAATTCAAAATTTCTAAAGGGACTAAAAAG
AAATTTTACCATCTTAGGG
Found at i:298334 original size:31 final size:34
Alignment explanation
Indices: 298298--298364 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 34
298288 AAAATCCAAG
* *
298298 ATAGTTGGGTGAC-CAAAAAAAA-TAA-AATTGA
1 ATAGTTGAGTGACAAAAAAAAAACTAATAATTGA
298329 ATAGTTGAGTGACAAAAAAAAAACTAATAATTGA
1 ATAGTTGAGTGACAAAAAAAAAACTAATAATTGA
298363 AT
1 AT
298365 GATTATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 12 0.39
32 8 0.26
33 3 0.10
34 8 0.26
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.24
Consensus pattern (34 bp):
ATAGTTGAGTGACAAAAAAAAAACTAATAATTGA
Found at i:298740 original size:16 final size:17
Alignment explanation
Indices: 298705--298744 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
298695 TTTATACTTT
*
298705 TTTTTAATTTTGATTTA
1 TTTTTAATTTTGATTAA
*
298722 TTTTTAATTTTTA-TAA
1 TTTTTAATTTTGATTAA
298738 TTTTTAA
1 TTTTTAA
298745 ATTAATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTAATTTTGATTAA
Found at i:301285 original size:22 final size:24
Alignment explanation
Indices: 301260--301313 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 24
301250 CCTATTGATA
301260 TTCG-GAAG-TAAGAAAATTTGAC
1 TTCGTGAAGTTAAGAAAATTTGAC
*
301282 TTCGTTTAGAGGTTAAGAAAATTTGAC
1 TTCG--T-GAAGTTAAGAAAATTTGAC
301309 TTCGT
1 TTCGT
301314 TTAGAGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 4 0.15
25 1 0.04
26 3 0.12
27 18 0.69
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (24 bp):
TTCGTGAAGTTAAGAAAATTTGAC
Found at i:301298 original size:27 final size:27
Alignment explanation
Indices: 301268--301323 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
301258 TATTCGGAAG
301268 TAAGAAAATTTGACTTCGTTTAGAGGT
1 TAAGAAAATTTGACTTCGTTTAGAGGT
301295 TAAGAAAATTTGACTTCGTTTAGAGGT
1 TAAGAAAATTTGACTTCGTTTAGAGGT
301322 TA
1 TA
301324 TTAGAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (27 bp):
TAAGAAAATTTGACTTCGTTTAGAGGT
Found at i:303831 original size:35 final size:35
Alignment explanation
Indices: 303785--303854 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
303775 GCGCTATTCA
303785 AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
1 AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
303820 AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
1 AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
303855 TGAATTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.43
Consensus pattern (35 bp):
AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
Found at i:316858 original size:69 final size:71
Alignment explanation
Indices: 316719--316868 Score: 216
Period size: 69 Copynumber: 2.1 Consensus size: 71
316709 ATCAGTAAAA
*
316719 CTAGCTAAATCTTACATTAATTTACGAAACATTAATCGAAAAAACCCCGGAAAAAGTAGTAAATC
1 CTAGCTAAATATTACATTAATTTACGAAACATTAATCGAAAAAACCCCGGAAAAAGTAGTAAATC
316784 GAGCTC
66 GAGCTC
* * * **
316790 GTAGCTAAATATTCCATTAA-TTACCG-AACATTAGTCGATCAAACCCCGG-AAAAGTAGTAAAT
1 CTAGCTAAATATTACATTAATTTA-CGAAACATTAATCGAAAAAACCCCGGAAAAAGTAGTAAAT
316852 CGAGCTC
65 CGAGCTC
316859 CTAGCTAAAT
1 CTAGCTAAAT
316869 CTAGCTAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
69 29 0.41
70 23 0.32
71 19 0.27
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (71 bp):
CTAGCTAAATATTACATTAATTTACGAAACATTAATCGAAAAAACCCCGGAAAAAGTAGTAAATC
GAGCTC
Found at i:320522 original size:15 final size:14
Alignment explanation
Indices: 320488--320581 Score: 61
Period size: 13 Copynumber: 6.5 Consensus size: 14
320478 TAATTAAAAC
*
320488 ATAATAAAAATATA-
1 ATAA-AAAAATTTAT
320502 ATAAAAAAACTTTAT
1 ATAAAAAAA-TTTAT
*
320517 AT-AAAAAATCTAT
1 ATAAAAAAATTTAT
*
320530 -TAAACAAATTTAT
1 ATAAAAAAATTTAT
*
320543 ATAAAAATAAAATTAT
1 AT-AAAA-AAATTTAT
320559 -TAATATTAAAATTTAT
1 ATAA-A--AAAATTTAT
320575 ATAAAAA
1 ATAAAAA
320582 TATAATTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
12 1 0.02
13 18 0.29
14 18 0.29
15 7 0.11
16 15 0.24
17 4 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAAAAATTTAT
Found at i:320541 original size:26 final size:27
Alignment explanation
Indices: 320493--320549 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
320483 AAAACATAAT
320493 AAAAATATAATAAAAAAACTTTATATA
1 AAAAATATAATAAAAAAACTTTATATA
* * *
320520 AAAAATCTATTAAACAAA-TTTATATA
1 AAAAATATAATAAAAAAACTTTATATA
320546 AAAA
1 AAAA
320550 TAAAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAATATAATAAAAAAACTTTATATA
Found at i:320557 original size:26 final size:27
Alignment explanation
Indices: 320491--320557 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
320481 TTAAAACATA
*
320491 ATAAAAATATAA-TAAAAAAACTTTAT
1 ATAAAAATAAAATTAAAAAAACTTTAT
** *
320517 ATAAAAA-ATCTATTAAACAAA-TTTAT
1 ATAAAAATA-AAATTAAAAAAACTTTAT
320543 ATAAAAATAAAATTA
1 ATAAAAATAAAATTA
320558 TTAATATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
25 1 0.03
26 24 0.73
27 8 0.24
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
ATAAAAATAAAATTAAAAAAACTTTAT
Found at i:320574 original size:16 final size:17
Alignment explanation
Indices: 320535--320589 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
320525 TCTATTAAAC
320535 AAATTTATATAAAAATA
1 AAATTTATATAAAAATA
* *
320552 AAA-TTAT-TAATATTA
1 AAATTTATATAAAAATA
320567 AAATTTATATAAAAATA
1 AAATTTATATAAAAATA
*
320584 TAATTT
1 AAATTT
320590 TAAATATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 9 0.29
16 8 0.26
17 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTATATAAAAATA
Found at i:328133 original size:31 final size:31
Alignment explanation
Indices: 328087--328145 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
328077 ATTTGGTCAT
* *
328087 TGAATTATTCGAAAGTTTTCATTTAAGTTGC
1 TGAACTATTCAAAAGTTTTCATTTAAGTTGC
*
328118 TGAACTATTCAAAAGTTTTTATTTAAGT
1 TGAACTATTCAAAAGTTTTCATTTAAGT
328146 CATTGGGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTTGC
Found at i:338986 original size:30 final size:31
Alignment explanation
Indices: 338923--338998 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
338913 TTTGAAAGTT
* * *
338923 AAAATTTTTAAAATTTTAATTAAGTTTGTTC
1 AAAATTTTTAAAATTCTAATTAAGTCTGCTC
* *
338954 AAATTTTTTAAAATTCTCATTAAGTCT-CTC
1 AAAATTTTTAAAATTCTAATTAAGTCTGCTC
*
338984 AAAATTTTTGAAATT
1 AAAATTTTTAAAATT
338999 ATGTATTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 15 0.39
31 23 0.61
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (31 bp):
AAAATTTTTAAAATTCTAATTAAGTCTGCTC
Found at i:343855 original size:31 final size:30
Alignment explanation
Indices: 343790--343888 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 30
343780 AAAAAATTAG
*
343790 AAAATTTTAA-TAAGTTT-GTAAAATTTTTT
1 AAAATTTTAATTAAGTTTCTTAAAA-TTTTT
343819 AAAAATTTTAATTAAGTTTCTTAAAATTTTCT
1 -AAAATTTTAATTAAGTTTCTTAAAATTTT-T
* * ** *
343851 AAAATTCTCATTAAGCCTCTCAAAATTTTT
1 AAAATTTTAATTAAGTTTCTTAAAATTTTT
*
343881 GAAATTTT
1 AAAATTTT
343889 TATCGAACTC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
30 17 0.29
31 35 0.60
32 6 0.10
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (30 bp):
AAAATTTTAATTAAGTTTCTTAAAATTTTT
Found at i:349247 original size:21 final size:21
Alignment explanation
Indices: 349221--349261 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
349211 AGACGAGCAA
* *
349221 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
349242 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
349262 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:360616 original size:134 final size:132
Alignment explanation
Indices: 360458--360702 Score: 427
Period size: 134 Copynumber: 1.8 Consensus size: 132
360448 ATACGAATGA
*
360458 AAATTTGAAGGGATATTCGATTATTTTAAGCAAACGCAAAATTGCAACCCAACACGTTAGGGCAC
1 AAATTTGAAGGGACATTCGATTATTTTAAGCAAACGCAAAATTGCAACCCAACACGTTAGGGCAC
360523 TATTCCGCGAATTGCCAAATATCGAATTTCGCCTTCATTTTAAAGAATTCTTTTAAAAGGCATGA
66 T-TTCCGCGAATTGCCAAATATCGAATTTCGCCTTCATTTTAAAGAATTCTTTTAAAAGGCATGA
360588 GGG
130 GGG
* *
360591 AAATCTTGAAGGGACATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCA
1 AAAT-TTGAAGGGACATTCGATTATTTTAAGCAAACGCAAAATTGCAACCCAACACGTTAGGGCA
* *
360656 CTTTCCGCGAATTGCCAAATATCGGATTTCGCCTTCGTTTTAAAGAA
65 CTTTCCGCGAATTGCCAAATATCGAATTTCGCCTTCATTTTAAAGAA
360703 AATTGTTTTA
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
133 47 0.44
134 59 0.56
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (132 bp):
AAATTTGAAGGGACATTCGATTATTTTAAGCAAACGCAAAATTGCAACCCAACACGTTAGGGCAC
TTTCCGCGAATTGCCAAATATCGAATTTCGCCTTCATTTTAAAGAATTCTTTTAAAAGGCATGAG
GG
Found at i:368159 original size:7 final size:7
Alignment explanation
Indices: 368147--368172 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
368137 TCTTTTTGAA
368147 AAAATTG
1 AAAATTG
368154 AAAATTG
1 AAAATTG
368161 AAAATTG
1 AAAATTG
368168 AAAAT
1 AAAAT
368173 CAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
AAAATTG
Found at i:368178 original size:14 final size:14
Alignment explanation
Indices: 368146--368180 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
368136 ATCTTTTTGA
*
368146 AAAAATTGAAAATT
1 AAAAATTGAAAATC
*
368160 GAAAATTGAAAATC
1 AAAAATTGAAAATC
368174 AAAAATT
1 AAAAATT
368181 TAATATTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26
Consensus pattern (14 bp):
AAAAATTGAAAATC
Found at i:372652 original size:747 final size:753
Alignment explanation
Indices: 371200--372701 Score: 2069
Period size: 747 Copynumber: 2.0 Consensus size: 753
371190 CAATTATGGC
* * *
371200 CACCAACATCCCCTGCTTCTTATCTTGAATGAAGACCAGCTGATCTACAATCAAAGTGGTGTAAC
1 CACCAACATCCCCTGCTTCTTATCTTGAATCAAGACCAGCTGATCGACAATCAAAGGGGTGTAAC
*
371265 TCATTGCTCCAGGTGCGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGTGGACCACTGTGGGT
66 TCATTGCTCCAGGTGCGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCGGACCACTGTGGGT
* * * * *
371330 TTTATCTTCACAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCATCCTTTTCATCACGATCAT
131 TTTATATTCACAAGGTATGTGCCAAGGCACCTTTGGAGCTTAATCACCCTTTTCATCACAACCAT
* *
371395 CCTCTTCTTCTTATGGATTCACATCTTATTACAAAACCGAATTATTCATCAGGGTACATCTGTAA
196 CCTCTTCTTCTTATGG--TCACA---TAATAC--AACC--ATTATTCATCAGGGTACATCTGCAA
** * * * * * *
371460 TTTCTGTGATGAAGAGGATAATAAGTTTGTTTATCACTGCTCTTGTTGTGAATTGGACTTACATA
252 TTTCTGCAATAAACAGGACAACAAGTCTGTTTATCACTGCTCTTCTTGTGAATTGGACTTACATA
*
371525 TTAAATGTGCTATGTTTACATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTACC
317 TTAAATGTGCTATGTTTACATTTAATATTGCTGAGAATAATTTGAAACAGCTTGACCATGTTACC
* * * *
371590 CTTCAACATCCTTTGATTTCCACTGAAAATGGTGATGAACAACTTGAAGATGATAGTAAGTGCTT
382 CTTCAACATCCATTGATTTCCACTGAAAATGGTGATGAAAAACTTAAAGATGATAGTAACTGCTT
* * *
371655 CGGGTGTAGGGAACCATTAGCAAAGTATACACACTTTTCTCCTGACTGTGGATTTAATTTACATG
447 CGGGTGCAGGGAACCATTAGCAAAGTATACACACTTTTCTCCTGACCGTGGATTTAACTTACATG
* * * * * *
371720 AGAAATGCGCCGAGCTTCCTTTCGAACTGAATCTTGTTTGCCATCGCGAACATCCTCTTGTTCTA
512 AGAAATGCACCGAGATTCCTTTCAAACTGAATCATGTGTGCCATCGCGAACATCCTCTTGTCCTA
* *
371785 CAATTTTATAGCGAACGGATCTCTTGCGAGATATGCTGCCGGCGAACAAGGCCAAGAGGATTTGT
577 CAATTTAATAGCGAACGGATCTCTTGCAAGATATGCTGCCGGCGAACAAGGCCAAGAGGATTTGT
* * *
371850 TTATGGTTGTTCTCCTTGTAAGTTCGTTGTTCACATTGAATGTGCATCGCAATCACCATTACAAG
642 TTATGGTTGTTCTCCTTGTAAGTTCGTTGTTCACATTGAATGCGCATCACAATCACCATTAAAAG
*
371915 TTATTAAGAGTACAAATCATGAACATCCATTTACCTTGTTTAACGGG
707 TTATTAAGAGTACAAATCATGAACATCCATTCACCTTGTTTAACGGG
* * * *
371962 CACCAACATCCCCTGTTTCTTATGTTGAATCAAGAGCAGCTGATGGACAATCAAAGGGGTGTAAC
1 CACCAACATCCCCTGCTTCTTATCTTGAATCAAGACCAGCTGATCGACAATCAAAGGGGTGTAAC
* * * *
372027 TGATTGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCGGAGCACTGTGGGT
66 TCATTGCTCCAGGTGCGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCGGACCACTGTGGGT
* *
372092 TTTATATTCATAAGGTATGTGCCAAGGCACCTTTGGAGCTTAATCACCCTTTTCATCTCAACCAT
131 TTTATATTCACAAGGTATGTGCCAAGGCACCTTTGGAGCTTAATCACCCTTTTCATCACAACCAT
* * * *
372157 -C-C-TCTTCTTAT-G-CA-A-AATGC-ACC-TTATTCATCCGGAATGTACATTTGCAATTTTTG
196 CCTCTTCTTCTTATGGTCACATAATACAACCATTATTCATCAGG---GTACATCTGCAATTTCTG
* * * *
372213 CAATAAATCTGG-CCACAAGTCTGTTTATCGCTGCTCTTCTTGTGAATTGGACTTTCATATTAAA
258 CAATAAA-CAGGACAACAAGTCTGTTTATCACTGCTCTTCTTGTGAATTGGACTTACATATTAAA
* * *
372277 TGTGCTTTGTTTACATTTAATATTGCTGAGAATAATTTGAAACAGCTTGAGCATGTTGCCCTTCA
322 TGTGCTATGTTTACATTTAATATTGCTGAGAATAATTTGAAACAGCTTGACCATGTTACCCTTCA
* * ** *
372342 ACATCCATTGA-TTCCGAGTGAAAATGGTGATGAAAAACTTAAAGATGTTTTTAACTGCTTTGGG
387 ACATCCATTGATTTCC-ACTGAAAATGGTGATGAAAAACTTAAAGATGATAGTAACTGCTTCGGG
* * *
372406 TGCCGGGAACCATTAGCAAATTATACACGCTTTTCTCCTTG-CCGTGGATTTAACTTACATGAGA
451 TGCAGGGAACCATTAGCAAAGTATACACACTTTTCTCC-TGACCGTGGATTTAACTTACATGAGA
* * *
372470 AATGCACTGAGATTCCTTTCAAATTGAATCATGTGTGGCATCGC-AAGCATCCTCTTGTCCTACA
515 AATGCACCGAGATTCCTTTCAAACTGAATCATGTGTGCCATCGCGAA-CATCCTCTTGTCCTACA
* * * *
372534 ATTTAATAGCGAACGGCTCTCTTGCAAGATATGCTGCCAGG-TAACAATGCGAAGAGGATTTGTT
579 ATTTAATAGCGAACGGATCTCTTGCAAGATATGCTGCC-GGCGAACAAGGCCAAGAGGATTTGTT
*
372598 TATGGTTGTTCTCCTTGTAAGTTTGTTGTTCACATTGAATGCGCATCACAATCACCATTAAAAGT
643 TATGGTTGTTCTCCTTGTAAGTTCGTTGTTCACATTGAATGCGCATCACAATCACCATTAAAAGT
372663 TATTAAGAGTACAAATCATGAACATCCATTCACCTTGTT
708 TATTAAGAGTACAAATCATGAACATCCATTCACCTTGTT
372702 GTTGAGACAA
Statistics
Matches: 656, Mismatches: 76, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
744 11 0.02
746 6 0.01
747 439 0.67
748 6 0.01
750 3 0.00
754 1 0.00
755 2 0.00
758 1 0.00
759 9 0.01
760 1 0.00
761 1 0.00
762 176 0.27
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (753 bp):
CACCAACATCCCCTGCTTCTTATCTTGAATCAAGACCAGCTGATCGACAATCAAAGGGGTGTAAC
TCATTGCTCCAGGTGCGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCGGACCACTGTGGGT
TTTATATTCACAAGGTATGTGCCAAGGCACCTTTGGAGCTTAATCACCCTTTTCATCACAACCAT
CCTCTTCTTCTTATGGTCACATAATACAACCATTATTCATCAGGGTACATCTGCAATTTCTGCAA
TAAACAGGACAACAAGTCTGTTTATCACTGCTCTTCTTGTGAATTGGACTTACATATTAAATGTG
CTATGTTTACATTTAATATTGCTGAGAATAATTTGAAACAGCTTGACCATGTTACCCTTCAACAT
CCATTGATTTCCACTGAAAATGGTGATGAAAAACTTAAAGATGATAGTAACTGCTTCGGGTGCAG
GGAACCATTAGCAAAGTATACACACTTTTCTCCTGACCGTGGATTTAACTTACATGAGAAATGCA
CCGAGATTCCTTTCAAACTGAATCATGTGTGCCATCGCGAACATCCTCTTGTCCTACAATTTAAT
AGCGAACGGATCTCTTGCAAGATATGCTGCCGGCGAACAAGGCCAAGAGGATTTGTTTATGGTTG
TTCTCCTTGTAAGTTCGTTGTTCACATTGAATGCGCATCACAATCACCATTAAAAGTTATTAAGA
GTACAAATCATGAACATCCATTCACCTTGTTTAACGGG
Found at i:381870 original size:7 final size:7
Alignment explanation
Indices: 381858--381883 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
381848 TCTTTTTGAA
381858 AAAATTG
1 AAAATTG
381865 AAAATTG
1 AAAATTG
381872 AAAATTG
1 AAAATTG
381879 AAAAT
1 AAAAT
381884 CAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
AAAATTG
Found at i:381889 original size:14 final size:14
Alignment explanation
Indices: 381857--381891 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
381847 ATCTTTTTGA
*
381857 AAAAATTGAAAATT
1 AAAAATTGAAAATC
*
381871 GAAAATTGAAAATC
1 AAAAATTGAAAATC
381885 AAAAATT
1 AAAAATT
381892 TAATATTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26
Consensus pattern (14 bp):
AAAAATTGAAAATC
Found at i:385423 original size:15 final size:15
Alignment explanation
Indices: 385403--385434 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
385393 CTCTTGTTCT
385403 ACAATTTTATAGCGA
1 ACAATTTTATAGCGA
385418 ACAATTTTATAGCGA
1 ACAATTTTATAGCGA
385433 AC
1 AC
385435 GGATCTCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (15 bp):
ACAATTTTATAGCGA
Found at i:390158 original size:21 final size:21
Alignment explanation
Indices: 390132--390172 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
390122 ATCTGCTCAA
* *
390132 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
390153 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
390173 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:394284 original size:93 final size:95
Alignment explanation
Indices: 394173--394355 Score: 255
Period size: 93 Copynumber: 1.9 Consensus size: 95
394163 GTTTCAGATA
* **
394173 ATTTCGGGCTCATATTGAACGGTGTTGGATAAT-TTTTTTAGTCAAATCGA-G-TTTAAAGTTTC
1 ATTTCGGGCTCATATTGAACGGTGTTGGATAATCTTGTTTAGTCAAAT-GAGGTTTTAAAACTTC
*
394235 CAAATCATTTTGGTTCAAGTTAGTTTTGATC
65 CAAATCATTTTGATTCAAGTTAGTTTTGATC
* * *
394266 ATTTTGGGCTCATATTGAACGGTGTTGGATTATCTTGTTTAGTCAAATTAGGTTTTAAAACTTCC
1 ATTTCGGGCTCATATTGAACGGTGTTGGATAATCTTGTTTAGTCAAATGAGGTTTTAAAACTTCC
* *
394331 AGATCATTTTGATTCAGGTTAGTTT
66 AAATCATTTTGATTCAAGTTAGTTT
394356 CAAGTTTAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 32 0.41
94 14 0.18
95 32 0.41
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (95 bp):
ATTTCGGGCTCATATTGAACGGTGTTGGATAATCTTGTTTAGTCAAATGAGGTTTTAAAACTTCC
AAATCATTTTGATTCAAGTTAGTTTTGATC
Found at i:394352 original size:95 final size:93
Alignment explanation
Indices: 394173--394355 Score: 251
Period size: 95 Copynumber: 1.9 Consensus size: 93
394163 GTTTCAGATA
* * **
394173 ATTTCGGGCTCATATTGAACGGTGTTGGATAATTTTTTTAGTCAAATCGAGTTTAAAGTTTCCAA
1 ATTTCGGGCTCATATTGAACGGTGTTGGATAATTTGTTTAGTCAAATAGAGTTTAAAACTTCCAA
*
394238 ATCATTTTGGTTCAAGTTAGTTTTGATC
66 ATCATTTTGATTCAAGTTAGTTTTGATC
* *
394266 ATTTTGGGCTCATATTGAACGGTGTTGGATTATCTTGTTTAGTCAAATTAG-GTTTTAAAACTTC
1 ATTTCGGGCTCATATTGAACGGTGTTGGATAAT-TTGTTTAGTCAAA-TAGAG-TTTAAAACTTC
* *
394330 CAGATCATTTTGATTCAGGTTAGTTT
63 CAAATCATTTTGATTCAAGTTAGTTT
394356 CAAGTTTAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 31 0.40
94 13 0.17
95 34 0.44
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (93 bp):
ATTTCGGGCTCATATTGAACGGTGTTGGATAATTTGTTTAGTCAAATAGAGTTTAAAACTTCCAA
ATCATTTTGATTCAAGTTAGTTTTGATC
Found at i:394489 original size:122 final size:124
Alignment explanation
Indices: 394275--394500 Score: 264
Period size: 122 Copynumber: 1.8 Consensus size: 124
394265 CATTTTGGGC
* * *
394275 TCATATTGAACGGTGTTGGATTATCTTGTTTAGTCAAATTAGGTTTTAAAACTTCCAGATCATTT
1 TCATATAGAACGGTGTTGGATTATCTTGTATAATCAAATTAGGTTTTAAAACTTCCAGATCATTT
* * * *
394340 TGATTCAGGTTAGTTTCAAGTTTAAATCAATTTCAATTTCGGATTTGATTATTTCAAGT
66 TGATTCAGGTTAATTCCAAGTTCAAATCAAATTCAATTTCGGATTTGATTATTTCAAGT
* ***
394399 TCATATAGAACGGTGTTGGATTAT-TT-TATAATCAAATTGGGTTTTAAAA-TTTTTGAATCATT
1 TCATATAGAACGGTGTTGGATTATCTTGTATAATCAAATTAGGTTTTAAAACTTCCAG-ATCATT
** *
394461 TTCG-TTCTA-GTTAATTCCCGGTTCAAATCAAATTCGATTT
65 TT-GATTC-AGGTTAATTCCAAGTTCAAATCAAATTCAATTT
394501 TAGATCATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
121 3 0.04
122 55 0.65
123 4 0.05
124 23 0.27
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (124 bp):
TCATATAGAACGGTGTTGGATTATCTTGTATAATCAAATTAGGTTTTAAAACTTCCAGATCATTT
TGATTCAGGTTAATTCCAAGTTCAAATCAAATTCAATTTCGGATTTGATTATTTCAAGT
Found at i:399852 original size:17 final size:18
Alignment explanation
Indices: 399814--399852 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
399804 AATATGTTCT
*
399814 AAATTACATAATATATAA
1 AAATAACATAATATATAA
399832 AAATAACATAATATA-AA
1 AAATAACATAATATATAA
399849 AAAT
1 AAAT
399853 TATAAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAACATAATATATAA
Found at i:402511 original size:13 final size:13
Alignment explanation
Indices: 402495--402520 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
402485 GGGCTTAACA
402495 AAAAAAATGTGAT
1 AAAAAAATGTGAT
402508 AAAAAAATGTGAT
1 AAAAAAATGTGAT
402521 GTACATTTGA
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:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AAAAAAATGTGAT
Found at i:409401 original size:7 final size:7
Alignment explanation
Indices: 409391--409416 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
409381 ACAAAAACCC
409391 AAAACGT
1 AAAACGT
409398 AAAACGT
1 AAAACGT
409405 AAAACGT
1 AAAACGT
409412 AAAAC
1 AAAAC
409417 AAAGAGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAACGT
Found at i:411338 original size:22 final size:22
Alignment explanation
Indices: 411308--411356 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
411298 GTTCAAATTT
*
411308 AAATTTTAAA-TTGATTAATAAA
1 AAATATTAAAGTTGATTAA-AAA
*
411330 AAATATTAAAGTTGGTTAAAAA
1 AAATATTAAAGTTGATTAAAAA
*
411352 TAATA
1 AAATA
411357 AATTTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATATTAAAGTTGATTAAAAA
Found at i:411728 original size:29 final size:29
Alignment explanation
Indices: 411632--411728 Score: 81
Period size: 29 Copynumber: 3.2 Consensus size: 29
411622 TTAAATGTTG
*
411632 ACAATTGAATGAAAATCAAAGTTC-TATAT
1 ACAATTGAAT-CAAATCAAAGTTCATATAT
*
411661 ACACATATGAATCATAATTC-AAGTTTCATGTAT
1 ACA-AT-TGAATCA-AA-TCAAAG-TTCATATAT
* *
411694 ATAATTGCATCAAATCAAAGTTCATATAT
1 ACAATTGAATCAAATCAAAGTTCATATAT
*
411723 CCAATT
1 ACAATT
411729 ACACATTGGA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
29 17 0.31
30 8 0.15
31 16 0.30
32 7 0.13
33 6 0.11
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.34
Consensus pattern (29 bp):
ACAATTGAATCAAATCAAAGTTCATATAT
Found at i:417985 original size:2 final size:2
Alignment explanation
Indices: 417978--418002 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
417968 ATATACGTAC
417978 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 A
418003 AACAATGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:419844 original size:29 final size:29
Alignment explanation
Indices: 419798--419855 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
419788 TTTGATTTTT
*
419798 TTTAATAATATAGAGACTAAATTGATACA
1 TTTAATAATAGAGAGACTAAATTGATACA
* * * *
419827 TTTAATAGTAGAGGGACTAATTTGGTACA
1 TTTAATAATAGAGAGACTAAATTGATACA
419856 ATCTATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (29 bp):
TTTAATAATAGAGAGACTAAATTGATACA
Found at i:421605 original size:25 final size:25
Alignment explanation
Indices: 421571--421618 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
421561 TACGTTAGAT
421571 TAAAGAGCAAACAGGTCCTTGTATG
1 TAAAGAGCAAACAGGTCCTTGTATG
421596 TAAAGAGCAAACAGGTCCTTGTA
1 TAAAGAGCAAACAGGTCCTTGTA
421619 CGTTACCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (25 bp):
TAAAGAGCAAACAGGTCCTTGTATG
Found at i:425042 original size:28 final size:30
Alignment explanation
Indices: 425006--425071 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
424996 CTATTTGAAT
* * *
425006 TAATCAATAACATTA-CAAAATATTAA-AC
1 TAATTAATAACATTATAAAAATATAAATAC
425034 TAATTAATAACATTATAAAAATATAAATAC
1 TAATTAATAACATTATAAAAATATAAATAC
425064 TAAATTAA
1 T-AATTAA
425072 GTTAGAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.44
29 9 0.28
30 3 0.09
31 6 0.19
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATTAATAACATTATAAAAATATAAATAC
Found at i:426605 original size:2 final size:2
Alignment explanation
Indices: 426598--426624 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
426588 CGATCCCTTT
426598 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
426625 TTTTGTTTTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:430618 original size:39 final size:39
Alignment explanation
Indices: 430564--430641 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
430554 AGTTGGTGTT
430564 CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
1 CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
430603 CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
1 CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
430642 AAGAATCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (39 bp):
CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
Found at i:433770 original size:16 final size:17
Alignment explanation
Indices: 433746--433778 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
433736 AACCCTATTG
433746 TTTGCTTTT-TTCTCCA
1 TTTGCTTTTGTTCTCCA
*
433762 TTTGTTTTTGTTCTCCA
1 TTTGCTTTTGTTCTCCA
433779 ATATAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.06, C:0.21, G:0.09, T:0.64
Consensus pattern (17 bp):
TTTGCTTTTGTTCTCCA
Found at i:438342 original size:26 final size:27
Alignment explanation
Indices: 438306--438363 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
438296 GTTGATGTTG
*
438306 TGTTTCCAATATATTCCGGTATATGC-
1 TGTTTCCAATAAATTCCGGTATATGCT
* *
438332 TGTTTCTAATAAATTCCGGTTTATGCT
1 TGTTTCCAATAAATTCCGGTATATGCT
438359 TGTTT
1 TGTTT
438364 TGGTTTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (27 bp):
TGTTTCCAATAAATTCCGGTATATGCT
Found at i:442764 original size:34 final size:35
Alignment explanation
Indices: 442719--442788 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
442709 TGTAAAAGAG
442719 AAAGAAAATAAAAGTTTTCTATTGGTACAATCGGT
1 AAAGAAAATAAAAGTTTTCTATTGGTACAATCGGT
442754 AAAG-AAATAAAAGTTTTCTATTGGTACAATCGGT
1 AAAGAAAATAAAAGTTTTCTATTGGTACAATCGGT
442788 A
1 A
442789 TGAGTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 31 0.89
35 4 0.11
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (35 bp):
AAAGAAAATAAAAGTTTTCTATTGGTACAATCGGT
Found at i:462451 original size:12 final size:13
Alignment explanation
Indices: 462434--462470 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
462424 GAACCGGACA
462434 CGAACCGAA-CTC
1 CGAACCGAAGCTC
462446 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
462458 CGAACCGTAGCTC
1 CGAACCGAAGCTC
462471 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:464663 original size:39 final size:37
Alignment explanation
Indices: 464605--464677 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
464595 TCTCCATTTT
* *
464605 TATATATAATATTAGTTTAAAAAATATGATAATAAAA
1 TATATATAATATTACTTTAAAAAATATAATAATAAAA
* *
464642 TATATATTAATATTTACTTTAACATATATAATAATA
1 TATATA-TAATA-TTACTTTAAAAAATATAATAATA
464678 TCATTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 6 0.20
38 5 0.17
39 19 0.63
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (37 bp):
TATATATAATATTACTTTAAAAAATATAATAATAAAA
Found at i:464692 original size:18 final size:16
Alignment explanation
Indices: 464669--464703 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
464659 TTTAACATAT
464669 ATAATAATATCATTAAAA
1 ATAATAATA--ATTAAAA
464687 ATAATAATAATTAAAA
1 ATAATAATAATTAAAA
464703 A
1 A
464704 CTATTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATAATAATTAAAA
Found at i:474649 original size:20 final size:20
Alignment explanation
Indices: 474612--474652 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
474602 TATATATAAT
*
474612 TAAATTAACTAATGAAATTA
1 TAAATTAAATAATGAAATTA
* *
474632 TAAATTAAATGATTAAATTA
1 TAAATTAAATAATGAAATTA
474652 T
1 T
474653 TTGAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (20 bp):
TAAATTAAATAATGAAATTA
Done.