Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold137
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: 675198
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:214823 original size:22 final size:22
Alignment explanation
Indices: 214795--214851 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
214785 ATATTTTATT
* *
214795 TATATTTAATATAATAATTAAA
1 TATATTTAATAAAATAATAAAA
*
214817 TATATTTAAAAAAATAATAAAA
1 TATATTTAATAAAATAATAAAA
* *
214839 TTTATTAAATAAA
1 TATATTTAATAAA
214852 TTTTACGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATATTTAATAAAATAATAAAA
Found at i:216989 original size:23 final size:25
Alignment explanation
Indices: 216957--217015 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
216947 AATTTAAAGA
* *
216957 ATTTAATATATA-CTATTAT-TGAT
1 ATTTATTATATATCTATTATATAAT
*
216980 ATTTATTATA-ATTTATTATGATAAT
1 ATTTATTATATATCTATTAT-ATAAT
217005 ATTTATTATAT
1 ATTTATTATAT
217016 TTTTAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.03
23 15 0.52
25 13 0.45
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (25 bp):
ATTTATTATATATCTATTATATAAT
Found at i:220473 original size:16 final size:16
Alignment explanation
Indices: 220452--220485 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
220442 TCGGATTATT
220452 TAATTTAAATATAAAA
1 TAATTTAAATATAAAA
* *
220468 TAATTTTAATATCAAA
1 TAATTTAAATATAAAA
220484 TA
1 TA
220486 TGCATTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATTTAAATATAAAA
Found at i:223991 original size:5 final size:5
Alignment explanation
Indices: 223981--224042 Score: 65
Period size: 5 Copynumber: 12.2 Consensus size: 5
223971 AAATACATAT
* *
223981 TTATA TTATA TTATA TTATA TTATA TTAT- GTAT- TTAATA TTTTA TTTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT-ATA TTATA -TTATA
224031 TTATA TTTATA T
1 TTATA -TTATA T
224043 AATCGTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
4 4 0.08
5 34 0.69
6 11 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:224549 original size:26 final size:28
Alignment explanation
Indices: 224520--224593 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 28
224510 ATAATTAAAA
*
224520 TATAATATGATAT-GATATAAA-TATTT
1 TATAATATGATATAAATATAAATTATTT
*
224546 TATAAT-TTATATAAATATAAATTATTT
1 TATAATATGATATAAATATAAATTATTT
*
224573 TA-AATATAATTATAAA-ATAAA
1 TATAATATGA-TATAAATATAAA
224594 AATAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.12
26 16 0.39
27 14 0.34
28 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
TATAATATGATATAAATATAAATTATTT
Found at i:224570 original size:15 final size:15
Alignment explanation
Indices: 224546--224596 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
224536 ATAAATATTT
*
224546 TATAATTTATATAAA
1 TATAAATTATATAAA
*
224561 TATAAATTATTTTAAA
1 TATAAATTA-TATAAA
224577 TAT-AATTATA-AAA
1 TATAAATTATATAAA
*
224590 TAAAAAT
1 TATAAAT
224597 AAATAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 5 0.17
14 4 0.13
15 13 0.43
16 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAATTATATAAA
Found at i:224934 original size:19 final size:19
Alignment explanation
Indices: 224892--224932 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
224882 TTATTTTATT
224892 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
224911 TAAATATTAA-TATAAAA-A
1 TAAAT-TTAATTATAAAATA
224929 TAAA
1 TAAA
224933 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:224940 original size:20 final size:20
Alignment explanation
Indices: 224892--224942 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
224882 TTATTTTATT
224892 TAAA-TTTAATTATAAAATA
1 TAAATTTTAATTATAAAATA
*
224911 TAAATATTAA-TATAAAA-A
1 TAAATTTTAATTATAAAATA
224929 TAAAATTTTTAATT
1 T-AAA-TTTTAATT
224943 TTTATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 9 0.35
21 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATTTTAATTATAAAATA
Found at i:227830 original size:31 final size:32
Alignment explanation
Indices: 227754--227834 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 32
227744 CGCTGGGCAC
*
227754 CGTGGCACCCTTTTTC-AAAGTCCACAACTTT
1 CGTGGCACCCTTTTTCAAAAGCCCACAACTTT
* *
227785 CATTGCACCCTTTTTCAAAAGCCCACAAC-TT
1 CGTGGCACCCTTTTTCAAAAGCCCACAACTTT
* *
227816 CGTGGTACCATTTTTCAAA
1 CGTGGCACCCTTTTTCAAA
227835 GTTTATAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 31 0.74
32 11 0.26
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.32
Consensus pattern (32 bp):
CGTGGCACCCTTTTTCAAAAGCCCACAACTTT
Found at i:227946 original size:29 final size:29
Alignment explanation
Indices: 227875--228322 Score: 214
Period size: 29 Copynumber: 15.2 Consensus size: 29
227865 AGTCCACTTC
* * * *
227875 TCAAAGTTTACAACTTCATGGCACC-CTT
1 TCAAAGTCTACAACTCCGTGGCACCTTTT
* *
227903 TCAAAGTCCATAACTCCGTGGCACCTTTT
1 TCAAAGTCTACAACTCCGTGGCACCTTTT
* *
227932 TCAAGGTCTACAACTCCGTGACATTCC-TTT
1 TCAAAGTCTACAACTCCGTGGCA--CCTTTT
** *
227962 T-AAAGT-TCACAACTTTGT-GCACCATTT
1 TCAAAGTCT-ACAACTCCGTGGCACCTTTT
* * * *
227989 TCAAGGTCCACAACTCCGTAGCACCTTTC
1 TCAAAGTCTACAACTCCGTGGCACCTTTT
228018 TCAAAGT-TCACAACTCCGTGGCACCCTTTT
1 TCAAAGTCT-ACAACTCCGTGGCA-CCTTTT
* * * * * *
228048 T-AAAGTCCATAACTTCATGGTACCTTTC
1 TCAAAGTCTACAACTCCGTGGCACCTTTT
* * ** * *
228076 TCAAAGTCCACAATTTTGTGACA-CTCTT
1 TCAAAGTCTACAACTCCGTGGCACCTTTT
* * **
228104 TCAAAGT-TCACAACTTCGTAGCACCCCTT
1 TCAAAGTCT-ACAACTCCGTGGCACCTTTT
* *
228133 TCAAAGTCTGCAACTCTGTGGCACCTATTT
1 TCAAAGTCTACAACTCCGTGGCACCT-TTT
* * * **
228163 TCTAAAGTCCACAGCTCTGTGGTACTATTTTTT
1 TC-AAAGTCTACAACTCCGTGG--C-ACCTTTT
* * * * *
228196 TAAAAGTCCATAACTTCGTAGCACCAATTTT
1 TCAAAGTCTACAACTCCGTGGCACC--TTTT
* * *
228227 TTAAAGTCTACAACTCTGTGGCACCTCTTC
1 TCAAAGTCTACAACTCCGTGGCACCT-TTT
*
228257 TCGAAATTC-ACAACTCCGTGGCACCATTTT
1 TC-AAAGTCTACAACTCCGTGGCACC-TTTT
* * * *
228287 TCAAAGTTTACAACTCTGTGGTATCTTTTT
1 TCAAAGTCTACAACTCCGTGGCA-CCTTTT
228317 TCAAAG
1 TCAAAG
228323 CCCATATAAA
Statistics
Matches: 314, Mismatches: 79, Indels: 52
0.71 0.18 0.12
Matches are distributed among these distances:
26 2 0.01
27 4 0.01
28 61 0.19
29 118 0.38
30 60 0.19
31 48 0.15
32 14 0.04
33 5 0.02
34 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.33
Consensus pattern (29 bp):
TCAAAGTCTACAACTCCGTGGCACCTTTT
Found at i:227984 original size:57 final size:57
Alignment explanation
Indices: 227923--228128 Score: 170
Period size: 57 Copynumber: 3.6 Consensus size: 57
227913 TAACTCCGTG
* *
227923 GCACCTTTTTCAAGGTCTACAACTCCGT-GACATTCCTTT-T-AAAGTTCACAACTTTGT
1 GCACCATTTTCAAGGTCCACAACTCCGTAG-CA--CCTTTCTCAAAGTTCACAACTTTGT
**
227980 GCACCATTTTCAAGGTCCACAACTCCGTAGCACCTTTCTCAAAGTTCACAACTCCGT
1 GCACCATTTTCAAGGTCCACAACTCCGTAGCACCTTTCTCAAAGTTCACAACTTTGT
* * * * * * * * * *
228037 GGCACCCTTTTTAAAGTCCATAACTTCATGGTACCTTTCTCAAAGTCCACAATTTTGT
1 -GCACCATTTTCAAGGTCCACAACTCCGTAGCACCTTTCTCAAAGTTCACAACTTTGT
* * *
228095 G-A-CACTCTTTCAAAGTTCACAACTTCGTAGCACC
1 GCACCA-T-TTTCAAGGTCCACAACTCCGTAGCACC
228129 CCTTTCAAAG
Statistics
Matches: 120, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
55 6 0.05
56 3 0.03
57 65 0.54
58 46 0.38
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (57 bp):
GCACCATTTTCAAGGTCCACAACTCCGTAGCACCTTTCTCAAAGTTCACAACTTTGT
Found at i:228049 original size:86 final size:86
Alignment explanation
Indices: 227901--228088 Score: 213
Period size: 86 Copynumber: 2.2 Consensus size: 86
227891 CATGGCACCC
* * * *
227901 TTTCAAAGTCCATAACTCCGTGGCACCTTTTTCAAGGTCTACAACTCCGTGACATTCCTTTTAAA
1 TTTCAAAGTCCACAACTCCGTAGCACCTTTCTCAAGGTCTACAACTCCGTGACATCCCTTTTAAA
*
227966 GTTCACAACTTTGTGCACCAT
66 GTCCACAACTTTGTGCACCAT
* * *
227987 TTTCAAGGTCCACAACTCCGTAGCACCTTTCTCAAAGT-TCACAACTCCGTGGCA-CCCTTTTTA
1 TTTCAAAGTCCACAACTCCGTAGCACCTTTCTCAAGGTCT-ACAACTCCGTGACATCCC-TTTTA
* *
228050 AAGTCCATAACTTCATG-GTACC-T
64 AAGTCCACAACTT--TGTGCACCAT
228073 TTCTCAAAGTCCACAA
1 TT-TCAAAGTCCACAA
228089 TTTTGTGACA
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
85 3 0.03
86 65 0.76
87 16 0.19
88 2 0.02
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (86 bp):
TTTCAAAGTCCACAACTCCGTAGCACCTTTCTCAAGGTCTACAACTCCGTGACATCCCTTTTAAA
GTCCACAACTTTGTGCACCAT
Found at i:228088 original size:115 final size:117
Alignment explanation
Indices: 227868--228314 Score: 299
Period size: 115 Copynumber: 3.8 Consensus size: 117
227858 TTTCAAAAGT
* ** * * * * * *
227868 CCACTTCTCAAAGTTTACAACTTCATGGCACCCTT-TCAAAGTCCATAACTCCGTGGCACC-TTT
1 CCACTTTTCAAAGTCCACAACTCCGTAGCACCTTTCTCAAAGTTCACAACTCCGTGGCACCATTT
* * ** ** * *
227931 TTCAAGGTCTACAACTCCGTGACATTCCTTT-T-AAAGTTCACAACTTTGTGCA
66 TT-AAAGTCCACAACTCTATGGTACT-CTTTCTAAAAGTCCACAACTTTGTGCA
* *
227983 CCA-TTTTCAAGGTCCACAACTCCGTAGCACCTTTCTCAAAGTTCACAACTCCGTGGCACCCTTT
1 CCACTTTTCAAAGTCCACAACTCCGTAGCACCTTTCTCAAAGTTCACAACTCCGTGGCACCATTT
* * *
228047 TTAAAGTCCATAACT-TCATGGTAC-CTTTCTCAAAGTCCACAATTTTGTG-A
66 TTAAAGTCCACAACTCT-ATGGTACTCTTTCTAAAAGTCCACAACTTTGTGCA
* * * * *
228097 -CACTCTTTCAAAGTTCACAACTTCGTAGCACCCCTT-TCAAAG-TCTGCAACTCTGTGGCACCT
1 CCACT-TTTCAAAGTCCACAACTCCGTAGCA-CCTTTCTCAAAGTTC-ACAACTCCGTGGCACC-
* * * * * *
228159 ATTTTCTAAAGTCCACAGCTCTGTGGTACTATTTTTTTAAAAGTCCATAACTTCGTAGCA
62 ATTTT-TAAAGTCCACAACTCTATGGTAC--TCTTTCTAAAAGTCCACAACTTTGT-GCA
* * * * *
228219 CCAATTTTTTAAAGTCTACAACTCTGTGGCACCTCTTCTCGAAA-TTCACAACTCCGTGGCACCA
1 CC-ACTTTTCAAAGTCCACAACTCCGTAGCACCT-TTCTC-AAAGTTCACAACTCCGTGGCACCA
** *
228283 TTTTTCAAAGTTTACAACTCTGTGGTA-TCTTT
63 TTTTT-AAAGTCCACAACTCTATGGTACTCTTT
228315 TTTCAAAGCC
Statistics
Matches: 258, Mismatches: 50, Indels: 43
0.74 0.14 0.12
Matches are distributed among these distances:
113 6 0.02
114 28 0.11
115 97 0.38
116 13 0.05
117 18 0.07
118 1 0.00
120 22 0.09
121 1 0.00
122 4 0.02
123 45 0.17
124 18 0.07
125 5 0.02
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (117 bp):
CCACTTTTCAAAGTCCACAACTCCGTAGCACCTTTCTCAAAGTTCACAACTCCGTGGCACCATTT
TTAAAGTCCACAACTCTATGGTACTCTTTCTAAAAGTCCACAACTTTGTGCA
Found at i:228270 original size:30 final size:30
Alignment explanation
Indices: 228236--228307 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
228226 TTTAAAGTCT
228236 ACAACTCTGTGGCACC-TCTTCTCGAAA-TTC
1 ACAACTCTGTGGCACCAT-TTCTC-AAAGTTC
* * *
228266 ACAACTCCGTGGCACCATTTTTCAAAGTTT
1 ACAACTCTGTGGCACCATTTCTCAAAGTTC
228296 ACAACTCTGTGG
1 ACAACTCTGTGG
228308 TATCTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.08
30 32 0.89
31 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (30 bp):
ACAACTCTGTGGCACCATTTCTCAAAGTTC
Found at i:228351 original size:32 final size:32
Alignment explanation
Indices: 228315--228697 Score: 182
Period size: 32 Copynumber: 11.9 Consensus size: 32
228305 TGGTATCTTT
* * *
228315 TTTCAAAGCCCATATAAATTGGTGGTAACCCC
1 TTTCAAAGCCCATACAAGTTGGTGGCAACCCC
* * * **
228347 TTTCAGAGCCGATACAA-TTCGGTGGTAACCTT
1 TTTCAAAGCCCATACAAGTT-GGTGGCAACCCC
* * * **
228379 TTTAAAAAGCCCATATAAGTTAGTAACAA-CCC
1 TTT-CAAAGCCCATACAAGTTGGTGGCAACCCC
* * * *
228411 TTTCAACAATCACAT--AAGTTGATGGCAACCCT
1 TTTC-A-AAGCCCATACAAGTTGGTGGCAACCCC
* * *
228443 TTTCAAAACCCACACAAGTTGGTGACAACCCC
1 TTTCAAAGCCCATACAAGTTGGTGGCAACCCC
** * * *
228475 TTTCAAAAGCTTACACAAGTTGGTGGTAA-CTC
1 TTTC-AAAGCCCATACAAGTTGGTGGCAACCCC
* * * * * ***
228507 TTTCAAAACCCATATAAATTAGTGGCATCATT
1 TTTCAAAGCCCATACAAGTTGGTGGCAACCCC
* *
228539 TTTCAAAGCCCATACAAGTTAGTGGTAACCCC
1 TTTCAAAGCCCATACAAGTTGGTGGCAACCCC
* * ***
228571 TTTCAAAAACCCATACAAGTTGGTGGCATCTTT
1 TTTC-AAAGCCCATACAAGTTGGTGGCAACCCC
* * * * * *
228604 TTTCAAGGCTCACACAAGTTGATGGCAAGCTC
1 TTTCAAAGCCCATACAAGTTGGTGGCAACCCC
* * * * *
228636 TTTCACAGCCCACATAAGTTGGTGACAACCTC
1 TTTCAAAGCCCATACAAGTTGGTGGCAACCCC
* * * *
228668 TTCCAAAGCCTACACAAGTTAGTGGCAACC
1 TTTCAAAGCCCATACAAGTTGGTGGCAACC
228698 TTCTCAAAAG
Statistics
Matches: 257, Mismatches: 83, Indels: 22
0.71 0.23 0.06
Matches are distributed among these distances:
30 5 0.02
31 27 0.11
32 159 0.62
33 64 0.25
34 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (32 bp):
TTTCAAAGCCCATACAAGTTGGTGGCAACCCC
Found at i:228510 original size:96 final size:96
Alignment explanation
Indices: 228410--228701 Score: 259
Period size: 96 Copynumber: 3.0 Consensus size: 96
228400 AGTAACAACC
* *
228410 CTTTCAACAATCACATAAGTTGATGGCAACCCTTTTCAAAACCCACACAAGTTGGTGACAACCCC
1 CTTTCAA-AATCACATAAGTTGATGGCAACACTTTTCAAAGCCCACACAAGTTGGTGACAACCCC
* *
228475 TTTCAAAAGCTTACACAAGTTGGTGGTAAC-T
65 TTTCAAAAGCCTACACAAGTTGGTGGCAACTT
* * * * * * * **
228506 CTTTCAAAACCCATATAAATT-AGTGGCATCATTTTTCAAAGCCCATACAAGTTAGTGGTAACCC
1 CTTTCAAAA-TCACATAAGTTGA-TGGCAACACTTTTCAAAGCCCACACAAGTTGGTGACAACCC
* * * *
228570 CTTTCAAAAACCCATACAAGTTGGTGGCATCTT
64 CTTTCAAAAGCCTACACAAGTTGGTGGCAACTT
* ** * * * * *
228603 TTTTCAAGGCTCACACAAGTTGATGGCAA-GCTCTTTCACAGCCCACATAAGTTGGTGACAACCT
1 CTTTCAA-AATCACATAAGTTGATGGCAACACT-TTTCAAAGCCCACACAAGTTGGTGACAACCC
* *
228667 C-TTCCAAAGCCTACACAAGTTAGTGGCAACCTT
64 CTTTCAAAAGCCTACACAAGTTGGTGGCAA-CTT
228700 CT
1 CT
228702 CAAAAGCCTA
Statistics
Matches: 148, Mismatches: 41, Indels: 13
0.73 0.20 0.06
Matches are distributed among these distances:
95 3 0.02
96 96 0.65
97 48 0.32
98 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (96 bp):
CTTTCAAAATCACATAAGTTGATGGCAACACTTTTCAAAGCCCACACAAGTTGGTGACAACCCCT
TTCAAAAGCCTACACAAGTTGGTGGCAACTT
Found at i:228511 original size:64 final size:64
Alignment explanation
Indices: 228433--228742 Score: 216
Period size: 64 Copynumber: 4.8 Consensus size: 64
228423 CATAAGTTGA
* ** *
228433 TGGCAACC-CTTTTCAAAACCCACACAAGTTGGTGACAACCCCTTTCAAAAGCTTACACAAGTTG
1 TGGCAACCTC-TTTCAAAACCCACACAAGTTGGTGACAACCTCTTTC-AAAGCCCACACAAGTTA
228497 G
64 G
* * * * * * * * * *
228498 TGGTAA-CTCTTTCAAAACCCATATAAATTAGTGGCATCATTTTTCAAAGCCCATACAAGTTAG
1 TGGCAACCTCTTTCAAAACCCACACAAGTTGGTGACAACCTCTTTCAAAGCCCACACAAGTTAG
* * * * * * * * *
228561 TGGTAACCCCTTTCAAAAACCCATACAAGTTGGTGGCATCTTTTTTCAAGGCTCACACAAGTT-G
1 TGGCAACCTCTTTC-AAAACCCACACAAGTTGGTGACAACCTCTTTCAAAGCCCACACAAGTTAG
* * * * * *
228625 ATGGCAAGCTCTTTCACAGCCCACATAAGTTGGTGACAACCTCTTCCAAAGCCTACACAAGTTAG
1 -TGGCAACCTCTTTCAAAACCCACACAAGTTGGTGACAACCTCTTTCAAAGCCCACACAAGTTAG
* * * * * * *
228690 TGGCAACCT-TCTCAAAAGCCTACAAAAGTTAGTGGC-ATCTCTTTCTAAGCCCA
1 TGGCAACCTCTTTCAAAA-CCCACACAAGTTGGTGACAACCTCTTTCAAAGCCCA
228743 ATGTCGTTGG
Statistics
Matches: 190, Mismatches: 49, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
63 38 0.20
64 93 0.49
65 59 0.31
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (64 bp):
TGGCAACCTCTTTCAAAACCCACACAAGTTGGTGACAACCTCTTTCAAAGCCCACACAAGTTAG
Found at i:228835 original size:59 final size:59
Alignment explanation
Indices: 228729--228841 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 59
228719 TAGTGGCATC
* * * *
228729 TCTTTCTAAGCCCAATGTCGTTGGCCTTGAAACAACACATTGGCACTTGTCAAACAATT
1 TCTTTCTAAGCCCAATGTCGCTCGCCTTGAAACAACACATTGACACTTATCAAACAATT
* * * * * *
228788 TCTTTCTAAGTCTAATGTTGCTCGCCTTGAATCAGCATATTGACACTTATCAAA
1 TCTTTCTAAGCCCAATGTCGCTCGCCTTGAAACAACACATTGACACTTATCAAA
228842 TCTTCTTTCT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (59 bp):
TCTTTCTAAGCCCAATGTCGCTCGCCTTGAAACAACACATTGACACTTATCAAACAATT
Found at i:228930 original size:52 final size:52
Alignment explanation
Indices: 228853--229229 Score: 321
Period size: 52 Copynumber: 7.2 Consensus size: 52
228843 CTTCTTTCTC
** * * * *
228853 AAGCCTAATGTCATTGGCCTGGAATCAACACATTAGCACCCTTATCATCTTT
1 AAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTTT
* * * *
228905 AAGCCTAATGTCGTTAGTCTTGAATCAGTATATTGGCACCCTTATCATCTTT
1 AAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTTT
* * * * **
228957 AAGCCTAATGTTGTTGGCCTTGAATCAGCATATTGGCACTATTATCATCTTT
1 AAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTTT
* * * * ** *
229009 AAGTCTGATATCGCTAGCCTTGAATCTCAGCATATTGGCACTTTTATTATCTTT
1 AAGCCTAATGTCGCTAGCCTTGAA--TCAGCACATTGGCACCCTTATCATCTTT
* ** * **
229063 AAGACC-AGTGTCGCT-GTATTGAATCAGCACTTTGGCATCTTTTATCATCTTT
1 AAG-CCTAATGTCGCTAGCCTTGAATCAGCACATTGGCA-CCCTTATCATCTTT
* * * * * *
229115 AAGCCCAATGTCACTGGCCTTCAATCAGCACGTTGGCACCCTTATCATC-TC
1 AAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTTT
* * * * *
229166 AAGCCTGATATCGCTAGCCTTGAATTAGCACATTGGCACCCTCATTATCTTT
1 AAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTTT
229218 AAGTCC-AATGTC
1 AAG-CCTAATGTC
229230 ACCGGCCTTC
Statistics
Matches: 264, Mismatches: 53, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
51 54 0.20
52 148 0.56
53 26 0.10
54 35 0.13
55 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (52 bp):
AAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTTT
Found at i:229117 original size:158 final size:155
Alignment explanation
Indices: 228881--229229 Score: 398
Period size: 158 Copynumber: 2.2 Consensus size: 155
228871 CTGGAATCAA
* * * * * *
228881 CACATTAGCACCCTTATCATCTTTAAG-CCTAATGTCGTTAGTCTTGAATCAGTA-TATTGGCA-
1 CACATTGGCACCCTCATTATCTTTAAGACC-AATGTCGCT-GTATTGAATCAGCACT-TTGGCAT
** * *** * * *
228943 CCCTTATCATCTTTAAGCCTAATGTTGTTGGCCTTGAATCAGCATATTGGCACTATTATCATCTT
63 CTTTTATCATCTTTAAGCCCAATGTCACTGGCCTTCAATCAGCACATTGGCACCATTATCATC-T
* *
229008 TAAGTCTGATATCGCTAGCCTTGAATCTCAG
127 CAAGCCTGATATCGCTAGCCTTGAAT-T-AG
* ** * *
229039 CATATTGGCACTTTTATTATCTTTAAGACCAGTGTCGCTGTATTGAATCAGCACTTTGGCATCTT
1 CACATTGGCACCCTCATTATCTTTAAGACCAATGTCGCTGTATTGAATCAGCACTTTGGCATCTT
* *
229104 TTATCATCTTTAAGCCCAATGTCACTGGCCTTCAATCAGCACGTTGGCACCCTTATCATCTCAAG
66 TTATCATCTTTAAGCCCAATGTCACTGGCCTTCAATCAGCACATTGGCACCATTATCATCTCAAG
229169 CCTGATATCGCTAGCCTTGAATTAG
131 CCTGATATCGCTAGCCTTGAATTAG
*
229194 CACATTGGCACCCTCATTATCTTTAAGTCCAATGTC
1 CACATTGGCACCCTCATTATCTTTAAGACCAATGTC
229230 ACCGGCCTTC
Statistics
Matches: 160, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
155 32 0.20
156 1 0.01
157 43 0.27
158 82 0.51
159 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (155 bp):
CACATTGGCACCCTCATTATCTTTAAGACCAATGTCGCTGTATTGAATCAGCACTTTGGCATCTT
TTATCATCTTTAAGCCCAATGTCACTGGCCTTCAATCAGCACATTGGCACCATTATCATCTCAAG
CCTGATATCGCTAGCCTTGAATTAG
Found at i:230483 original size:20 final size:21
Alignment explanation
Indices: 230441--230484 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
230431 TTCTATGATT
* **
230441 TGTATTGATACAATAAGGTAA
1 TGTATCGATACAATAAGAAAA
230462 TGTATCGATAC-ATAAGAAAA
1 TGTATCGATACAATAAGAAAA
230482 TGT
1 TGT
230485 CATGTATTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAATAAGAAAA
Found at i:232161 original size:154 final size:154
Alignment explanation
Indices: 231877--232177 Score: 458
Period size: 154 Copynumber: 2.0 Consensus size: 154
231867 TGATTCCTTA
* * * *
231877 GTGATAAAGACTTGCTAAAATATGCCATAAGTTTGCCTTCTAAAGTTGGCTCAGCGCCAATGCCA
1 GTGATAAAGACTTGCTAAAATATGCCATAAATCTGCCTTCTAAAGTTAGCTCAGCCCCAATGCCA
* * * *
231942 TTAGAGGAAACATTAATATCCTCTACAAAGAGTTCGTTAAAATTAGGTAAGGCAAGAACTGGAGT
66 CTAGAGGAAACATTAATATCCTCTACAAAAAGTTCGTTAAAATTACGTAAGGCAAGAACTAGAGT
*
232007 TGAAGTCATTGTTGCTTGAAGTTG
131 TAAAGTCATTGTTGCTTGAAGTTG
* * *
232031 GTGATAAAGACTTGCTAAGATATGCCATAAATCTGCCTTTTAGAGTTAGCTCAGCCCCAATGCCA
1 GTGATAAAGACTTGCTAAAATATGCCATAAATCTGCCTTCTAAAGTTAGCTCAGCCCCAATGCCA
* * * *
232096 CTAGAGGAAGCATTAATATCCTTTACAAAAAGTTCGTTGAAATTACGTAAGGCAAGCACTAGAGT
66 CTAGAGGAAACATTAATATCCTCTACAAAAAGTTCGTTAAAATTACGTAAGGCAAGAACTAGAGT
232161 TAAAGTCATTGTTGCTT
131 TAAAGTCATTGTTGCTT
232178 TAAGCCTTTA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
154 131 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (154 bp):
GTGATAAAGACTTGCTAAAATATGCCATAAATCTGCCTTCTAAAGTTAGCTCAGCCCCAATGCCA
CTAGAGGAAACATTAATATCCTCTACAAAAAGTTCGTTAAAATTACGTAAGGCAAGAACTAGAGT
TAAAGTCATTGTTGCTTGAAGTTG
Found at i:234356 original size:13 final size:13
Alignment explanation
Indices: 234336--234386 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
234326 TTTAAAAATA
234336 AAAATTAT-TTTT
1 AAAATTATATTTT
*
234348 AATAATTATAATTT
1 AA-AATTATATTTT
234362 AAAATTATATTTTT
1 AAAATTATA-TTTT
*
234376 AAAATAATATT
1 AAAATTATATT
234387 CATCTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 15 0.45
14 16 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AAAATTATATTTT
Found at i:234696 original size:39 final size:39
Alignment explanation
Indices: 234653--234731 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
234643 TTACAATTAT
234653 TTCTTTTTTTATGCATTGTGCATGTCATTTATATATATA
1 TTCTTTTTTTATGCATTGTGCATGTCATTTATATATATA
*
234692 TTCTTTTTTTATTCATTGTGCATGTCATTTATATATATA
1 TTCTTTTTTTATGCATTGTGCATGTCATTTATATATATA
234731 T
1 T
234732 ATATATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.09, T:0.58
Consensus pattern (39 bp):
TTCTTTTTTTATGCATTGTGCATGTCATTTATATATATA
Found at i:235786 original size:13 final size:13
Alignment explanation
Indices: 235768--235794 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
235758 TTATTTCAAT
235768 TTAAATATAAATA
1 TTAAATATAAATA
235781 TTAAATATAAATA
1 TTAAATATAAATA
235794 T
1 T
235795 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:237549 original size:25 final size:26
Alignment explanation
Indices: 237511--237559 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
237501 TAGATGATTT
**
237511 TTTAAAAATAATATTTTATATTTATA
1 TTTAAAAATAATATTGAATATTTATA
237537 TTTAAAAAT-ATATTGAATATTTA
1 TTTAAAAATAATATTGAATATTTA
237560 AAAACAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTAAAAATAATATTGAATATTTATA
Found at i:239122 original size:6 final size:6
Alignment explanation
Indices: 239111--239152 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
239101 TAATAATACC
239111 ATGAAA ATGAAA ATGAAA ATG-AA ATGAAA ATGAAA ATGAAA A
1 ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA A
239153 GCAAGTTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGAAA
Found at i:239137 original size:17 final size:17
Alignment explanation
Indices: 239115--239151 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
239105 AATACCATGA
239115 AAATGAAAATGAAAATG
1 AAATGAAAATGAAAATG
239132 AAATGAAAATGAAAATG
1 AAATGAAAATGAAAATG
239149 AAA
1 AAA
239152 AGCAAGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (17 bp):
AAATGAAAATGAAAATG
Found at i:246245 original size:16 final size:16
Alignment explanation
Indices: 246221--246268 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
246211 AAATAAATTA
246221 TTAAATTAATTTAAAT
1 TTAAATTAATTTAAAT
*
246237 TTAACTTAATTTAAATT
1 TTAAATTAATTTAAA-T
*
246254 TTAAA-AAATTTAAAT
1 TTAAATTAATTTAAAT
246269 AAAATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 1 0.04
16 22 0.79
17 5 0.18
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATTAATTTAAAT
Found at i:251896 original size:13 final size:14
Alignment explanation
Indices: 251878--251906 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
251868 TCACGTTCAA
251878 TAAATTTTAA-ATT
1 TAAATTTTAATATT
251891 TAAATTTTAATATT
1 TAAATTTTAATATT
251905 TA
1 TA
251907 TAATCTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAATTTTAATATT
Found at i:253963 original size:2 final size:2
Alignment explanation
Indices: 253956--253980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
253946 ATCACATGAA
253956 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
253981 ATGCATAAAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:254110 original size:3 final size:3
Alignment explanation
Indices: 254102--254137 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
254092 CTATACTTAC
254102 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
254138 TTACAACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:257718 original size:21 final size:22
Alignment explanation
Indices: 257680--257725 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
257670 ATCTGTTGAA
* **
257680 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
257701 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
257723 ACT
1 ACT
257726 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:260662 original size:5 final size:5
Alignment explanation
Indices: 260652--260832 Score: 60
Period size: 5 Copynumber: 36.4 Consensus size: 5
260642 AGTTATGGTA
* * *
260652 AATAT AATAT AAGA- AAAAT AAT-T AATAT AATAT AATAT AAAAT -ATGAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT-AT
* * * *
260700 AAAAA AATAT AATATT AATAT -ATA- ATATAT AA-AT TATAT GATATT
1 AATAT AATAT AATA-T AATAT AATAT A-ATAT AATAT AATAT AATA-T
* **
260745 AAATATT AATTAT CAA-AT TATAT AA-AT AA-AT AATAT TTTA- AATAT
1 -AATA-T AA-TAT -AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * * * *
260790 AATTAT AATAA AAAAT AAAAT AAATAT GATAT AAAAT -ATAT AA
1 AA-TAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AA
260833 ATTATCAAAT
Statistics
Matches: 131, Mismatches: 26, Indels: 38
0.67 0.13 0.19
Matches are distributed among these distances:
4 28 0.21
5 74 0.56
6 20 0.15
7 9 0.07
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:260689 original size:33 final size:34
Alignment explanation
Indices: 260652--260728 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
260642 AGTTATGGTA
*
260652 AATATAATATAAGA-AAAATAAT-TAATATAATAT
1 AATATAATATAAGATAAAAAAATATAATATAA-AT
* * *
260685 AATATAAAATATGATAAAAAAATATAATATTAAT
1 AATATAATATAAGATAAAAAAATATAATATAAAT
260719 -ATATAATATA
1 AATATAATATA
260729 TAAATTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 21 0.57
34 9 0.24
35 7 0.19
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (34 bp):
AATATAATATAAGATAAAAAAATATAATATAAAT
Found at i:260743 original size:16 final size:15
Alignment explanation
Indices: 260706--260769 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 15
260696 TGATAAAAAA
260706 ATATAATATT-AA-T
1 ATATAATATTAAATT
260719 ATATAATATATAAATT
1 ATATAATAT-TAAATT
*
260735 ATATGATATTAAA-T
1 ATATAATATTAAATT
*
260749 AT-TAATTATCAAATT
1 ATATAA-TATTAAATT
260764 ATATAA
1 ATATAA
260770 ATAAATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 11 0.26
14 10 0.24
15 9 0.21
16 12 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATAATATTAAATT
Found at i:260750 original size:21 final size:19
Alignment explanation
Indices: 260671--260808 Score: 65
Period size: 21 Copynumber: 7.1 Consensus size: 19
260661 TAAGAAAAAT
260671 AATTA-ATATAATATAATATA
1 AATTATATAT-ATA-AATATA
* * *
260691 AAATATGATAAAAAAATATA
1 AATTAT-ATATATAAATATA
260711 ATATTA-ATATATAATATATA
1 A-ATTATATATATAA-ATATA
*
260731 AATTATATGATATTAAATATT
1 AATTATAT-ATA-TAAATATA
*
260752 AATTATCAAATTATATAA-ATA
1 AATTAT-ATA-TATA-AATATA
* *
260773 AATAATAT-TTTAAATAT-
1 AATTATATATATAAATATA
*
260790 AATTATA-ATA-AAAAATA
1 AATTATATATATAAATATA
260807 AA
1 AA
260809 ATAAATATGA
Statistics
Matches: 90, Mismatches: 15, Indels: 29
0.67 0.11 0.22
Matches are distributed among these distances:
16 5 0.06
17 11 0.12
18 5 0.06
19 10 0.11
20 20 0.22
21 28 0.31
22 11 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
AATTATATATATAAATATA
Found at i:260754 original size:29 final size:29
Alignment explanation
Indices: 260671--260769 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 29
260661 TAAGAAAAAT
* *
260671 AATTAATATAATA-TAATATAAAATATGATAA
1 AATT-ATATAATATTAATATATAAT-T-ATCA
**
260702 AAAAATATAATATTAATATATAATATAT-A
1 AATTATATAATATTAATATATAAT-TATCA
*
260731 AATTATATGATATTAA-ATATTAATTATCA
1 AATTATATAATATTAATATA-TAATTATCA
260760 AATTATATAA
1 AATTATATAA
260770 ATAAATAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
28 6 0.10
29 28 0.48
30 10 0.17
31 14 0.24
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (29 bp):
AATTATATAATATTAATATATAATTATCA
Found at i:260825 original size:21 final size:22
Alignment explanation
Indices: 260783--260834 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
260773 AATAATATTT
*
260783 TAAATATAATTATAATAAAAAA
1 TAAATATAAATATAATAAAAAA
* *
260805 TAAA-ATAAATATGATATAAAA
1 TAAATATAAATATAATAAAAAA
260826 T--ATATAAAT
1 TAAATATAAAT
260835 TATCAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 6 0.23
21 15 0.58
22 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATATAAATATAATAAAAAA
Found at i:261305 original size:50 final size:50
Alignment explanation
Indices: 261251--261399 Score: 199
Period size: 50 Copynumber: 3.0 Consensus size: 50
261241 TACAGACAAT
* * *
261251 AATTACGGTCACCTTTCTCTATTGTCAAAGGTTAGTGAATAATAGTCAAC
1 AATTACGGTCACCTTTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAAC
* * * ** *
261301 AATTACAGCCACCTCTCTCGATTGTCAAAAATTGGTGAAGAATAGTCAAC
1 AATTACGGTCACCTTTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAAC
* *
261351 AATTAGGGTCACATTTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAA
1 AATTACGGTCACCTTTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAA
261400 ATCACTTTGC
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (50 bp):
AATTACGGTCACCTTTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAAC
Found at i:266103 original size:15 final size:15
Alignment explanation
Indices: 266083--266133 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
266073 AGCTAAAAAT
266083 TTTAAAATTTATAAA
1 TTTAAAATTTATAAA
* *
266098 TTTAAAAATCATAAA
1 TTTAAAATTTATAAA
*
266113 TTTAAAGTTT-TAAAA
1 TTTAAAATTTAT-AAA
266128 TTTAAA
1 TTTAAA
266134 TTCAAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 1 0.03
15 29 0.97
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TTTAAAATTTATAAA
Found at i:266239 original size:2 final size:2
Alignment explanation
Indices: 266232--266263 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
266222 CTCTTTAGTT
266232 TA 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
266264 ATGGGTGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:269664 original size:22 final size:22
Alignment explanation
Indices: 269634--269694 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
269624 AAAAATAAAA
*
269634 ATTTTAATTAAACT-TATAAATT
1 ATTTAAATTAAA-TATATAAATT
*
269656 ATTTAAATTAAATATTTAAATT
1 ATTTAAATTAAATATATAAATT
269678 ATTTAAATTAAATATAT
1 ATTTAAATTAAATATAT
269695 TTAAATTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAAATTAAATATATAAATT
Found at i:269697 original size:15 final size:14
Alignment explanation
Indices: 269671--269701 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
269661 AATTAAATAT
269671 TTAAATTATTTAAA
1 TTAAATTATTTAAA
269685 TTAAATATATTTAAA
1 TTAAAT-TATTTAAA
269700 TT
1 TT
269702 TGACTCCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAATTATTTAAA
Found at i:269937 original size:12 final size:13
Alignment explanation
Indices: 269906--269940 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
269896 AAATTACTAC
*
269906 ATTTAATATTTAT
1 ATTTAATATATAT
269919 ATTTAATATATAT
1 ATTTAATATATAT
269932 -TTTAATATA
1 ATTTAATATA
269941 AATAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTAATATATAT
Found at i:270732 original size:14 final size:15
Alignment explanation
Indices: 270686--270736 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
270676 CAATAAATAT
270686 TAATTA-AAATATTAA
1 TAATTATAAA-ATTAA
*
270701 TAA-TAAAAAATTAA
1 TAATTATAAAATTAA
270715 -AATTATAAAA-TAA
1 TAATTATAAAATTAA
270728 TAATTATAA
1 TAATTATAA
270737 TGAAACTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 5 0.16
14 21 0.66
15 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATTATAAAATTAA
Found at i:271198 original size:25 final size:25
Alignment explanation
Indices: 271170--271217 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
271160 TGAACAAAAA
271170 TAAAATAAA-ATAATTTATTTATTTT
1 TAAAATAAATATAATTT-TTTATTTT
*
271195 TAAATTAAATATAATTTTTTATT
1 TAAAATAAATATAATTTTTTATT
271218 ATCAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAAATAAATATAATTTTTTATTTT
Found at i:271227 original size:25 final size:25
Alignment explanation
Indices: 271175--271227 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
271165 AAAAATAAAA
* *
271175 TAAAATAATTTATTTATTTTTAAAT
1 TAAAATAATTTATTTATTATCAAAT
*
271200 TAAATATAATTT-TTTATTATCAATT
1 TAAA-ATAATTTATTTATTATCAAAT
271225 TAA
1 TAA
271228 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TAAAATAATTTATTTATTATCAAAT
Found at i:271271 original size:37 final size:38
Alignment explanation
Indices: 271224--271299 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 38
271214 TATTATCAAT
271224 TTAATTTAAAAATAAAAA-ATTATAGATAAATT-AATTAA
1 TTAATTT-AAAATAAAAATATTATA-ATAAATTAAATTAA
*
271262 TTAA-TTAAAATAAAAATATTTTAATAAATTAAATTAA
1 TTAATTTAAAATAAAAATATTATAATAAATTAAATTAA
271299 T
1 T
271300 CGAATTTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
36 17 0.49
37 14 0.40
38 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (38 bp):
TTAATTTAAAATAAAAATATTATAATAAATTAAATTAA
Found at i:274976 original size:16 final size:15
Alignment explanation
Indices: 274951--274982 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
274941 AAAATTTTGA
274951 TTAATTAATTTAAAT
1 TTAATTAATTTAAAT
274966 TTAATTTAATTTAAAT
1 TTAA-TTAATTTAAAT
274982 T
1 T
274983 GATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATTAATTTAAAT
Found at i:275938 original size:110 final size:109
Alignment explanation
Indices: 275818--276035 Score: 386
Period size: 110 Copynumber: 2.0 Consensus size: 109
275808 AATATTATAC
275818 CCAATTGACTTAAATCTAAAAAAACCCAAACTCAAAAAATGATCTAAAAATTTTAAAACTC-AAA
1 CCAATTGACTTAAATCTAAAAAAACCCAAACTC-AAAAATGATCTAAAAATTTTAAAACTCAAAA
275882 TAATCTTATCTAAAATACCACGTAACTTAAAATCAATTC-ACTCGTA
65 TAATCTTATCTAAAATA--ACGTAACTTAAAATCAATTCAACTCGTA
275928 CCAATTGACTTAAATCTAAAAAAACCCAAACTCAAAAATGATCTAAAAATTTTAAAACTCAAAAT
1 CCAATTGACTTAAATCTAAAAAAACCCAAACTCAAAAATGATCTAAAAATTTTAAAACTCAAAAT
*
275993 AATCTTATCTAAAATAACTTAACTTAAAATCAATTCAACTCGT
66 AATCTTATCTAAAATAACGTAACTTAAAATCAATTCAACTCGT
276036 TTAATTGATA
Statistics
Matches: 105, Mismatches: 1, Indels: 5
0.95 0.01 0.05
Matches are distributed among these distances:
108 19 0.18
109 33 0.31
110 53 0.50
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (109 bp):
CCAATTGACTTAAATCTAAAAAAACCCAAACTCAAAAATGATCTAAAAATTTTAAAACTCAAAAT
AATCTTATCTAAAATAACGTAACTTAAAATCAATTCAACTCGTA
Found at i:279493 original size:2 final size:2
Alignment explanation
Indices: 279486--279523 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
279476 CAATCAACTC
* *
279486 CA CA CA CA CA CA CA CA CT CA CA CA CA CA TA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
279524 AAAGAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.47, G:0.00, T:0.05
Consensus pattern (2 bp):
CA
Found at i:280352 original size:37 final size:36
Alignment explanation
Indices: 280280--280352 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 36
280270 ATTTATGAAT
*
280280 AAATATATATATAAATAATTAATAATAATATAATTA
1 AAATATATATATAAAAAATTAATAATAATATAATTA
* * *
280316 AAATAT-TATTTAAAAAATTGATATATTAATTTAATTA
1 AAATATATATATAAAAAATT-A-ATAATAATATAATTA
280353 TCGATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 11 0.35
36 7 0.23
37 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
AAATATATATATAAAAAATTAATAATAATATAATTA
Found at i:281486 original size:2 final size:2
Alignment explanation
Indices: 281479--281506 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
281469 ATGCATCCAT
281479 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
281507 TATGTATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:282304 original size:23 final size:23
Alignment explanation
Indices: 282261--282304 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
282251 TAATTTAAAT
* *
282261 TATTATATAAATATATTAATTTA
1 TATTATATAAAAATATCAATTTA
282284 TATTATATACAAAATA-CAATT
1 TATTATATA-AAAATATCAATT
282305 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATATAAAAATATCAATTTA
Found at i:284872 original size:12 final size:11
Alignment explanation
Indices: 284845--284884 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
284835 ATCATAATTG
*
284845 ATATATATATAT
1 ATATATAT-TAA
284857 ATATATATTCAA
1 ATATATATT-AA
284869 ATATATATTAA
1 ATATATATTAA
284880 ATATA
1 ATATA
284885 AATATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATATTAA
Found at i:287284 original size:18 final size:18
Alignment explanation
Indices: 287244--287278 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
287234 TGCTGTCACA
*
287244 TATTT-TATTTAATTATC
1 TATTTATATTTAAGTATC
287261 TATTTATATTTAAGTATC
1 TATTTATATTTAAGTATC
287279 GTTTTAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTTATATTTAAGTATC
Found at i:288186 original size:2 final size:2
Alignment explanation
Indices: 288179--288224 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
288169 AATGGATGAC
* * *
288179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT GT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
288221 AT AT
1 AT AT
288225 TTATTTGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:291564 original size:2 final size:2
Alignment explanation
Indices: 291552--291587 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
291542 CTCTTTCCCT
*
291552 TA TA CA 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
291588 GCCAAAAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:293615 original size:29 final size:27
Alignment explanation
Indices: 293572--293651 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 27
293562 TAAAAGCTTA
*
293572 TAAAAAATATATTTATTTTTTAATATT
1 TAAAAAATATATTTATTTTTTAAAATT
293599 TAAAAAATATTTATTTATTTTTTAAAATT
1 TAAAAAATA--TATTTATTTTTTAAAATT
*
293628 TATTTTAAAATATATTTATTTTTT
1 TA---AAAAATATATTTATTTTTT
293652 TAAGTTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
27 9 0.20
29 19 0.41
30 12 0.26
32 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TAAAAAATATATTTATTTTTTAAAATT
Found at i:293631 original size:22 final size:21
Alignment explanation
Indices: 293582--293633 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
293572 TAAAAAATAT
293582 ATTTATTTTTTAATATTTAAA
1 ATTTATTTTTTAATATTTAAA
** * *
293603 AAATATTTATTTATTTTTTAAA
1 ATTTATTT-TTTAATATTTAAA
293625 ATTTATTTT
1 ATTTATTTT
293634 AAAATATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTATTTTTTAATATTTAAA
Found at i:293659 original size:29 final size:29
Alignment explanation
Indices: 293572--293660 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 29
293562 TAAAAGCTTA
293572 TAAAAAATATATTTA-TTTTTTAA-TATT
1 TAAAAAATATATTTATTTTTTTAATTATT
*
293599 TAAAAAATATTTATTTATTTTTTAAAATTTATT
1 TAAAAAATA--TATTTATTTTTT-TAA-TTATT
*
293632 T-TAAAATATATTTATTTTTTTAAGTTATT
1 TAAAAAATATATTTATTTTTTTAA-TTATT
293661 ATTTATAGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 9 0.17
29 13 0.25
30 17 0.33
31 2 0.04
32 6 0.12
33 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (29 bp):
TAAAAAATATATTTATTTTTTTAATTATT
Found at i:294392 original size:17 final size:18
Alignment explanation
Indices: 294372--294421 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
294362 TAATATTTTT
294372 TTAAAAAAAATA-TTAAA
1 TTAAAAAAAATATTTAAA
294389 TTAAAAAATAA-ATTTAAA
1 TTAAAAAA-AATATTTAAA
294407 -TAAAAATAAA-ATTTA
1 TTAAAAA-AAATATTTA
294422 TTGTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 22 0.73
18 8 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAAAAAAATATTTAAA
Found at i:294405 original size:18 final size:17
Alignment explanation
Indices: 294372--294439 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
294362 TAATATTTTT
294372 TTAAAAA-AAATATTAAA
1 TTAAAAATAAAT-TTAAA
294389 TTAAAAAATAAATTTAAA
1 TT-AAAAATAAATTTAAA
*
294407 -TAAAAATAAAATTT-AT
1 TTAAAAAT-AAATTTAAA
294423 TGTAAAAATAAATTTAA
1 T-TAAAAATAAATTTAA
294440 TTTTAATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
16 7 0.16
17 15 0.34
18 18 0.41
19 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (17 bp):
TTAAAAATAAATTTAAA
Found at i:294412 original size:34 final size:34
Alignment explanation
Indices: 294373--294439 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
294363 AATATTTTTT
294373 TAAAAA-AAATATTAAATT-AAAAAATAAATTTAAA
1 TAAAAATAAA-ATT-AATTGAAAAAATAAATTTAAA
* *
294407 TAAAAATAAAATTTATTGTAAAAATAAATTTAA
1 TAAAAATAAAATTAATTGAAAAAATAAATTTAA
294440 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 3 0.10
34 23 0.79
35 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (34 bp):
TAAAAATAAAATTAATTGAAAAAATAAATTTAAA
Found at i:294796 original size:2 final size:2
Alignment explanation
Indices: 294789--294814 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
294779 AATTATTAGA
294789 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
294815 TTAAGAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295023 original size:2 final size:2
Alignment explanation
Indices: 295016--295040 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
295006 CTATAAAATA
295016 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
295041 CATGAAAATT
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:295715 original size:20 final size:21
Alignment explanation
Indices: 295690--295739 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
295680 AATTAATAAA
295690 ATATTAAAAATTATAT-TTTT
1 ATATTAAAAATTATATATTTT
* *
295710 ATATTAATATTTATATATTTT
1 ATATTAAAAATTATATATTTT
295731 ATAATTAAA
1 AT-ATTAAA
295740 TTTAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 14 0.56
21 6 0.24
22 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTAAAAATTATATATTTT
Found at i:295729 original size:22 final size:21
Alignment explanation
Indices: 295700--295743 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
295690 ATATTAAAAA
295700 TTATAT-TTTTAT-ATTAATAT
1 TTATATATTTTATAATTAA-AT
295720 TTATATATTTTATAATTAAAT
1 TTATATATTTTATAATTAAAT
295741 TTA
1 TTA
295744 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATATATTTTATAATTAAAT
Found at i:295755 original size:36 final size:36
Alignment explanation
Indices: 295715--295785 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
295705 TTTTTATATT
295715 AATATTTATATATT-TTATAAT-TAAATTTAAATTAAA
1 AATATTTATA-ATTATTA-AATATAAATTTAAATTAAA
* *
295751 AATATTTTTAATTATTAAATATCAATTTAAATTAA
1 AATATTTATAATTATTAAATATAAATTTAAATTAA
295786 CAAAAAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (36 bp):
AATATTTATAATTATTAAATATAAATTTAAATTAAA
Found at i:298048 original size:15 final size:15
Alignment explanation
Indices: 298028--298060 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
298018 TTTGTCTCAG
298028 TGATGACGACGATGA
1 TGATGACGACGATGA
*
298043 TGATGACGAGGATGA
1 TGATGACGACGATGA
298058 TGA
1 TGA
298061 AGAAGCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.09, G:0.36, T:0.21
Consensus pattern (15 bp):
TGATGACGACGATGA
Found at i:308460 original size:70 final size:70
Alignment explanation
Indices: 308376--308518 Score: 261
Period size: 70 Copynumber: 2.0 Consensus size: 70
308366 ACACAAATTT
*
308376 TTAAAAAATACAGTATTGTAAATCAAAATG-AGATAAACAGGAAAGACCAAAACACTAAGCAAAG
1 TTAAAAAATACAGTATTGTAAATCAAAA-GCAGATAAACAGGAAAGACCAAAAAACTAAGCAAAG
308440 ATCACA
65 ATCACA
308446 TTAAAAAATACAGTATTGTAAATCAAAAGCAGATAAACAGGAAAGACCAAAAAACTAAGCAAAGA
1 TTAAAAAATACAGTATTGTAAATCAAAAGCAGATAAACAGGAAAGACCAAAAAACTAAGCAAAGA
308511 TCACA
66 TCACA
308516 TTA
1 TTA
308519 TCTACTATAG
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 1 0.01
70 70 0.99
ACGTcount: A:0.56, C:0.14, G:0.13, T:0.17
Consensus pattern (70 bp):
TTAAAAAATACAGTATTGTAAATCAAAAGCAGATAAACAGGAAAGACCAAAAAACTAAGCAAAGA
TCACA
Found at i:310911 original size:2 final size:2
Alignment explanation
Indices: 310904--310940 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
310894 TTATGTATTC
310904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
310941 ATAACTAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:311167 original size:22 final size:22
Alignment explanation
Indices: 311131--311178 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
311121 ATAATATTTT
*
311131 AATTTTAATAAAAATCAAATTA
1 AATTTTAATAAAAATCAAATCA
*
311153 AATTTT-ATATAAAATTAAATCA
1 AATTTTAATA-AAAATCAAATCA
311175 AATT
1 AATT
311179 AAATTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTTAATAAAAATCAAATCA
Found at i:311286 original size:19 final size:17
Alignment explanation
Indices: 311259--311302 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
311249 TAAAAAATTT
311259 TATTAATTTATAAGTTAAA
1 TATTAATTT-TAA-TTAAA
* *
311278 TATTTATTTTTATTAAA
1 TATTAATTTTAATTAAA
311295 TATTAATT
1 TATTAATT
311303 AAAATATCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 12 0.55
18 2 0.09
19 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTAATTTTAATTAAA
Found at i:311546 original size:36 final size:36
Alignment explanation
Indices: 311506--311601 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 36
311496 ACAAATATAT
311506 AATTTTGTTTATTAGTTTTTATTATTAGTTACAGGA
1 AATTTTGTTTATTAGTTTTTATTATTAGTTACAGGA
311542 AATTTTTTTTGTTTATTAGTTTTTATTATTAGTTACAGGA
1 AA----TTTTGTTTATTAGTTTTTATTATTAGTTACAGGA
311582 AATTTT-TTTATGTA-TTTTTA
1 AATTTTGTTTAT-TAGTTTTTA
311602 ATATATACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
35 11 0.20
36 8 0.15
40 36 0.65
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.60
Consensus pattern (36 bp):
AATTTTGTTTATTAGTTTTTATTATTAGTTACAGGA
Found at i:311553 original size:40 final size:40
Alignment explanation
Indices: 311508--311590 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
311498 AAATATATAA
311508 TTTTGTTTATTAGTTTTTATTATTAGTTACAGGAAATTTT
1 TTTTGTTTATTAGTTTTTATTATTAGTTACAGGAAATTTT
311548 TTTTGTTTATTAGTTTTTATTATTAGTTACAGGAAATTTT
1 TTTTGTTTATTAGTTTTTATTATTAGTTACAGGAAATTTT
311588 TTT
1 TTT
311591 ATGTATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (40 bp):
TTTTGTTTATTAGTTTTTATTATTAGTTACAGGAAATTTT
Found at i:312557 original size:71 final size:70
Alignment explanation
Indices: 312464--312600 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 70
312454 AATAAATCAT
* *
312464 ATTAATAATAAAAAAATTATAATAACAATTTAGAAATATAATAAATATATATGACTAATTTCATT
1 ATTAATAATAAAAAAATTATAATAACAATTTAAAAATACAATAAATATATATGACTAATTTCATT
312529 AATTA
66 AATTA
* * * *
312534 ATTAATAATAATAATATCTATAATAACAATTTAAAAATACAATAAATATATATGACTATTTTTAT
1 ATTAATAATAAAAAAAT-TATAATAACAATTTAAAAATACAATAAATATATATGACTAATTTCAT
312599 TA
65 TA
312601 GTTTAAAAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 15 0.25
71 45 0.75
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (70 bp):
ATTAATAATAAAAAAATTATAATAACAATTTAAAAATACAATAAATATATATGACTAATTTCATT
AATTA
Found at i:314379 original size:17 final size:17
Alignment explanation
Indices: 314354--314422 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
314344 AAATTAATTA
314354 AATAT-AATATAAAAAT
1 AATATAAATATAAAAAT
314370 AATATAAATATAATACGAAT
1 AATATAAATATAA-A--AAT
*
314390 -ATATAAATATATAAAT
1 AATATAAATATAAAAAT
* *
314406 TATATAAAAATAAAAAT
1 AATATAAATATAAAAAT
314423 CTATTTAGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.18
17 21 0.47
18 2 0.04
19 11 0.24
20 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (17 bp):
AATATAAATATAAAAAT
Found at i:314383 original size:11 final size:11
Alignment explanation
Indices: 314324--314384 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
314314 AAATTGATAC
*
314324 ATAACATAAAT
1 ATAATATAAAT
* *
314335 ATAACATAAAA
1 ATAATATAAAT
314346 ATTAAT-TAAAT
1 A-TAATATAAAT
*
314357 ATAATATAAAA
1 ATAATATAAAT
314368 ATAATATAAAT
1 ATAATATAAAT
314379 ATAATA
1 ATAATA
314385 CGAATATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
10 4 0.09
11 36 0.84
12 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:314383 original size:22 final size:22
Alignment explanation
Indices: 314324--314384 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
314314 AAATTGATAC
* *
314324 ATAACATAAATATAACATAAAA
1 ATAATATAAATATAATATAAAA
314346 ATTAAT-TAAATATAATATAAAA
1 A-TAATATAAATATAATATAAAA
314368 ATAATATAAATATAATA
1 ATAATATAAATATAATA
314385 CGAATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 4 0.11
22 28 0.80
23 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAATATAAATATAATATAAAA
Found at i:314502 original size:15 final size:15
Alignment explanation
Indices: 314460--314514 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
314450 CCCTTTTCCC
* *
314460 TCTCTTTCTCTTTTT
1 TCTCTTTCTCCTTGT
*
314475 TCTCTTTCCCCTTGT
1 TCTCTTTCTCCTTGT
* *
314490 TCTCTTTTTCCTT-C
1 TCTCTTTCTCCTTGT
314504 TCT-TTTCTCCT
1 TCTCTTTCTCCT
314515 AAACCCTAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 7 0.21
14 3 0.09
15 23 0.70
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.64
Consensus pattern (15 bp):
TCTCTTTCTCCTTGT
Found at i:315141 original size:22 final size:23
Alignment explanation
Indices: 315113--315178 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
315103 AAACTTGTTT
* *
315113 TATTTTTTATTTTATTA-TTAAA
1 TATTTTTTATATTAATATTTAAA
*
315135 TA-TTTTTATATTAATATTTATA
1 TATTTTTTATATTAATATTTAAA
315157 TA-TTTTTATAATTAA-ATTTAAA
1 TATTTTTTAT-ATTAATATTTAAA
315179 ATAAAAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.32
22 21 0.55
23 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTTTTATATTAATATTTAAA
Found at i:315152 original size:14 final size:15
Alignment explanation
Indices: 315122--315160 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
315112 TTATTTTTTA
315122 TTTTATTATTAAATAT
1 TTTTA-TATTAAATAT
315138 TTTTATATT-AATAT
1 TTTTATATTAAATAT
*
315152 TTATATATT
1 TTTTATATT
315161 TTTATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 4 0.18
16 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTATATTAAATAT
Found at i:319928 original size:18 final size:18
Alignment explanation
Indices: 319905--319947 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
319895 GGATTTTAAA
319905 AAATTTATTTAGATTATG
1 AAATTTATTTAGATTATG
319923 AAATTTATTTAGATTATG
1 AAATTTATTTAGATTATG
319941 AAATTTA
1 AAATTTA
319948 AAAACTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
AAATTTATTTAGATTATG
Found at i:324200 original size:2 final size:2
Alignment explanation
Indices: 324182--324221 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
324172 TTTTTCAGGA
*
324182 AT AT GAT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
324222 GGCAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:324753 original size:25 final size:23
Alignment explanation
Indices: 324718--324767 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
324708 ATAAATATTT
*
324718 ATATATTTTATTATAAAATTTAAAA
1 ATATATATTATT-T-AAATTTAAAA
*
324743 ATATATATTATTTTAATTTAAAA
1 ATATATATTATTTAAATTTAAAA
324766 AT
1 AT
324768 GTTGTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATATATTATTTAAATTTAAAA
Found at i:330913 original size:26 final size:26
Alignment explanation
Indices: 330877--330929 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
330867 AAAAGAAAAA
* * *
330877 GAGAATATAACTTGTTTAATAAATAT
1 GAGAAGATAACGTGGTTAATAAATAT
*
330903 GAGAAGATAACGTGGTTAATTAATAT
1 GAGAAGATAACGTGGTTAATAAATAT
330929 G
1 G
330930 GTTTAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (26 bp):
GAGAAGATAACGTGGTTAATAAATAT
Found at i:332482 original size:28 final size:28
Alignment explanation
Indices: 332414--332489 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
332404 CTTATATATA
*
332414 TAAAAAATAGTTTATAAATATTAAATTT
1 TAAAAAATAATTTATAAATATTAAATTT
** * *
332442 TAAAATTTAAATTTATTATATATT-ATTTT
1 TAAAAAAT-AATTTA-TAAATATTAAATTT
332471 TAAAAAATAATTATATAAA
1 TAAAAAATAATT-TATAAA
332490 ATAATTAAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
28 13 0.35
29 17 0.46
30 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TAAAAAATAATTTATAAATATTAAATTT
Found at i:333613 original size:14 final size:12
Alignment explanation
Indices: 333585--333626 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
333575 AAATAATAAA
333585 ATATTAATTTTT
1 ATATTAATTTTT
*
333597 ATATTAATATTT
1 ATATTAATTTTT
333609 ATA-T-ATTTTT
1 ATATTAATTTTT
333619 ATAATTAA
1 AT-ATTAA
333627 ATTTAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 15 0.60
13 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:333618 original size:22 final size:21
Alignment explanation
Indices: 333591--333650 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
333581 TAAAATATTA
*
333591 ATTTTTATATTAATATTTATAT
1 ATTTTTATATTAA-ATTTAAAT
333613 ATTTTTATAATTAAATTTAAAT
1 ATTTTTAT-ATTAAATTTAAAT
333635 ATTATTTA-ATTAAATT
1 ATT-TTTATATTAAATT
333651 AATAATAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 8 0.23
22 18 0.51
23 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTTATATTAAATTTAAAT
Found at i:333657 original size:22 final size:22
Alignment explanation
Indices: 333594--333657 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
333584 AATATTAATT
*
333594 TTTATATTAATATTTAT-ATATTT
1 TTTA-ATTAA-ATTTATAATATTA
333617 TTATAATTAAATTTA-AATATTA
1 TT-TAATTAAATTTATAATATTA
*
333639 TTTAATTAAATTAATAATA
1 TTTAATTAAATTTATAATA
333658 ATTTGATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 11 0.31
22 16 0.44
23 7 0.19
24 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATTAAATTTATAATATTA
Found at i:338171 original size:16 final size:17
Alignment explanation
Indices: 338139--338171 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
338129 TCAGAACCAT
338139 TTTCTTGTTTGTTTTCC
1 TTTCTTGTTTGTTTTCC
*
338156 TTTCTT-TTTTTTTTCC
1 TTTCTTGTTTGTTTTCC
338172 CGATTCGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTCTTGTTTGTTTTCC
Found at i:338426 original size:13 final size:13
Alignment explanation
Indices: 338396--338426 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
338386 TAAGAATATT
338396 TAAAGAAAAAATA
1 TAAAGAAAAAATA
338409 T-AAGAAAAAATA
1 TAAAGAAAAAATA
338421 TAAAGA
1 TAAAGA
338427 GCTGGGGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (13 bp):
TAAAGAAAAAATA
Found at i:340772 original size:20 final size:19
Alignment explanation
Indices: 340722--340772 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
340712 ATTATAAAAT
340722 TTAT-ATTTTATAATATAA
1 TTATAATTTTATAATATAA
* * *
340740 CTATATATGTTATAATAATAG
1 TTATA-ATTTTATAAT-ATAA
340761 TTATAATTTTAT
1 TTATAATTTTAT
340773 TTCAAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 3 0.12
20 15 0.60
21 7 0.28
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
TTATAATTTTATAATATAA
Found at i:342182 original size:20 final size:20
Alignment explanation
Indices: 342154--342193 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
342144 AAAAATATTT
*
342154 TTATTTAAAT-TTAATTATAA
1 TTATATAAATATTAA-TATAA
342174 TTATATAAATATTAATATAA
1 TTATATAAATATTAATATAA
342194 AAATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATAAATATTAATATAA
Found at i:342983 original size:22 final size:21
Alignment explanation
Indices: 342953--343026 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 21
342943 TGAACATATT
342953 TATTCAAATTTAATTAATATAAA
1 TATT-AAATTTAATT-ATATAAA
*
342976 TATTAAATTTAATTATTTAAA
1 TATTAAATTTAATTATATAAA
*
342997 -ATTAAA-ATAATT-T-TAAA
1 TATTAAATTTAATTATATAAA
*
343014 TTTTAAA-TTAATT
1 TATTAAATTTAATT
343027 TAACTCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
17 4 0.09
18 11 0.24
19 5 0.11
20 6 0.13
21 6 0.13
22 10 0.22
23 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTAAATTTAATTATATAAA
Found at i:343028 original size:17 final size:16
Alignment explanation
Indices: 342978--343029 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
342968 AATATAAATA
342978 TTAAATTT-AATT-AT
1 TTAAATTTAAATTAAT
* *
342992 TTAAAATTAAAATAATT
1 TTAAATTTAAATTAA-T
343009 TTAAATTTTAAATTAAT
1 TTAAA-TTTAAATTAAT
343026 TTAA
1 TTAA
343030 CTCAAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
16 1 0.03
17 11 0.37
18 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATTTAAATTAAT
Found at i:343414 original size:23 final size:25
Alignment explanation
Indices: 343369--343422 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
343359 ATAGGTGCGG
*
343369 TAATATTTTTGTATTTATATTATAA
1 TAATATATTTGTATTTATATTATAA
*
343394 TAATATATTT-TA-TTATTTTATAA
1 TAATATATTTGTATTTATATTATAA
*
343417 TTATAT
1 TAATAT
343423 TTAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 15 0.58
24 2 0.08
25 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TAATATATTTGTATTTATATTATAA
Found at i:343442 original size:22 final size:23
Alignment explanation
Indices: 343388--343449 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
343378 TGTATTTATA
* ** *
343388 TTATAATAATATATTTTATTATT
1 TTATAATTATATATTAAAATATT
343411 TTATAATTATAT-TTAAAATATT
1 TTATAATTATATATTAAAATATT
**
343433 TTATTTTTATATATTAA
1 TTATAATTATATATTAA
343450 TAATTTATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATAATTATATATTAAAATATT
Found at i:343651 original size:16 final size:16
Alignment explanation
Indices: 343627--343667 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
343617 TATATTATAC
343627 AAAATTTAAAATTAATT
1 AAAA-TTAAAATTAATT
*
343644 AAAATTAAATTTAATT
1 AAAATTAAAATTAATT
*
343660 AAATTTAA
1 AAAATTAA
343668 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTAAAATTAATT
Found at i:343661 original size:20 final size:20
Alignment explanation
Indices: 343636--343689 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
343626 CAAAATTTAA
*
343636 AATTAATTAAAATTAAATTT
1 AATTAATTATAATTAAATTT
*
343656 AATTAAATT-TAATTTAATTT
1 AATT-AATTATAATTAAATTT
*
343676 AAATAATTATAATT
1 AATTAATTATAATT
343690 TTTTTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTAATTATAATTAAATTT
Found at i:343677 original size:16 final size:16
Alignment explanation
Indices: 343628--343679 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
343618 ATATTATACA
* *
343628 AAATTTAAAATTAATTA
1 AAATTT-AATTTAATTT
*
343645 AAATTAAATTTAA-TT
1 AAATTTAATTTAATTT
343660 AAATTTAATTTAATTT
1 AAATTTAATTTAATTT
343676 AAAT
1 AAAT
343680 AATTATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTTAATTTAATTT
Found at i:343723 original size:16 final size:17
Alignment explanation
Indices: 343695--343726 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
343685 TAATTTTTTT
343695 ATAAATATAAAATTAAA
1 ATAAATATAAAATTAAA
343712 ATAAAT-TAAAATTAA
1 ATAAATATAAAATTAA
343727 TATATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAATATAAAATTAAA
Found at i:344894 original size:16 final size:17
Alignment explanation
Indices: 344873--344908 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
344863 ATCATTAACA
*
344873 TTTTTTCTTCTTTT-TT
1 TTTTTTCTTATTTTCTT
344889 TTTTTTCTTATTTTCTT
1 TTTTTTCTTATTTTCTT
344906 TTT
1 TTT
344909 GGGAAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTCTTATTTTCTT
Found at i:349977 original size:16 final size:16
Alignment explanation
Indices: 349956--349993 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
349946 TCGAATCGAT
*
349956 TTAAATTTTATTTTAA
1 TTAAATTTTATTATAA
349972 TTAAATTTTATTATAA
1 TTAAATTTTATTATAA
349988 TATAAA
1 T-TAAA
349994 AATAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATTTTATTATAA
Found at i:352763 original size:2 final size:2
Alignment explanation
Indices: 352756--352792 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
352746 ATAAGGGATC
* *
352756 TA TA TA TA TA TA TG TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
352793 TTATTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:352775 original size:12 final size:12
Alignment explanation
Indices: 352758--352792 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
352748 AAGGGATCTA
352758 TATATATATATG
1 TATATATATATG
352770 TATATATATATG
1 TATATATATATG
352782 TATATATATAT
1 TATATATATAT
352793 TTATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:355321 original size:2 final size:2
Alignment explanation
Indices: 355314--355345 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
355304 TACTGAATGG
355314 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
355346 TTCATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355460 original size:3 final size:3
Alignment explanation
Indices: 355452--355480 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
355442 AATTTAGCAA
355452 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
355481 CTTGAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:370048 original size:2 final size:2
Alignment explanation
Indices: 370041--370083 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
370031 GGTTTTACAT
370041 TA TA TA TA TA TA 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 TA
370083 T
1 T
370084 GTTTGTGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:373577 original size:28 final size:28
Alignment explanation
Indices: 373545--373601 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
373535 CTGAAGAAAG
373545 AATATGTCACACAATAGCTCTACATCTT
1 AATATGTCACACAATAGCTCTACATCTT
373573 AATATGTCACACAATAGCTCTACATCTT
1 AATATGTCACACAATAGCTCTACATCTT
373601 A
1 A
373602 TTAACACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (28 bp):
AATATGTCACACAATAGCTCTACATCTT
Found at i:376822 original size:5 final size:5
Alignment explanation
Indices: 376809--376894 Score: 68
Period size: 5 Copynumber: 16.2 Consensus size: 5
376799 CGATTAAATT
376809 ATATAA ATATA ATATAA ATATA AT-TAA ATATA ATATAAA ATATA ATATA
1 ATAT-A ATATA ATAT-A ATATA ATAT-A ATATA ATAT--A ATATA ATATA
* * *
376858 ATATTA ATATAA ATATA TTAAA ATTTA A-ATA ATATA A
1 ATA-TA ATAT-A ATATA ATATA ATATA ATATA ATATA A
376895 ATTATTATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
4 4 0.06
5 37 0.56
6 20 0.30
7 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:376831 original size:17 final size:17
Alignment explanation
Indices: 376809--376896 Score: 82
Period size: 17 Copynumber: 5.5 Consensus size: 17
376799 CGATTAAATT
376809 ATATAAATAT-AATATA
1 ATATAAATATAAATATA
376825 A-ATATAAT-TAAATATA
1 ATATA-AATATAAATATA
376841 ATATAAA-ATATAATATA
1 ATATAAATATA-AATATA
*
376858 ATATTAATATAAATATA
1 ATATAAATATAAATATA
* *
376875 TTA-AAAT-TTAA-ATA
1 ATATAAATATAAATATA
376889 ATATAAAT
1 ATATAAAT
376897 TATTATTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.08
15 11 0.18
16 18 0.30
17 23 0.38
18 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAAATATAAATATA
Found at i:376855 original size:27 final size:27
Alignment explanation
Indices: 376805--376964 Score: 81
Period size: 26 Copynumber: 6.1 Consensus size: 27
376795 AAAACGATTA
* *
376805 AATTATATA-AATATAATATA-AATAT
1 AATTAAATATAATATAAAATATAATAT
376830 AATTAAATATAATATAAAATATAATAT
1 AATTAAATATAATATAAAATATAATAT
* *
376857 AA-T--AT-TAATAT-AAATATATTAA
1 AATTAAATATAATATAAAATATAATAT
* * *
376879 AATTTAA-ATAATATAAATTATTAT-T
1 AATTAAATATAATATAAAATATAATAT
**
376904 ATATTAAA-ATTAATATTAATTTATAATAT
1 A-ATTAAATA-TAATA-TAAAATATAATAT
* *
376933 -TTTAAATGTAAATATAATAAATATATATAT
1 AATTAAATAT-AATAT-A-AAATATA-ATAT
376963 AA
1 AA
376965 AAATAAGATA
Statistics
Matches: 102, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
22 11 0.11
23 7 0.07
24 2 0.02
25 16 0.16
26 23 0.23
27 19 0.19
28 14 0.14
29 6 0.06
30 4 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (27 bp):
AATTAAATATAATATAAAATATAATAT
Found at i:376888 original size:22 final size:21
Alignment explanation
Indices: 376813--376893 Score: 78
Period size: 22 Copynumber: 3.9 Consensus size: 21
376803 TAAATTATAT
*
376813 AAATATAATATAAATATAATT-
1 AAATTTAATATAAATAT-ATTA
* *
376834 AAATATAATATAAAATATAATA
1 AAATTTAATAT-AAATATATTA
*
376856 TAATATTAATATAAATATATTA
1 AAAT-TTAATATAAATATATTA
376878 AAATTTAA-AT-AATATA
1 AAATTTAATATAAATATA
376894 AATTATTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.12
20 2 0.04
21 17 0.33
22 21 0.40
23 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATTTAATATAAATATATTA
Found at i:378338 original size:26 final size:26
Alignment explanation
Indices: 378289--378337 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
378279 ATACAATAAG
378289 TTTCTTTCTTTATAATATTCTTTTCT
1 TTTCTTTCTTTATAATATTCTTTTCT
378315 TTTCTTT-TTT-TAGATATTCTTTT
1 TTTCTTTCTTTATA-ATATTCTTTT
378338 TTAACTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 2 0.09
25 13 0.59
26 7 0.32
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTCTTTCTTTATAATATTCTTTTCT
Found at i:378556 original size:23 final size:23
Alignment explanation
Indices: 378505--378566 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
378495 ATTAATGAAA
* *
378505 ATTTTTTA-AATTAATATTTATAT
1 ATTTTTTATAATTAA-ACTTAAAT
378528 A-TTTTTATAATTAAACTTAAAT
1 ATTTTTTATAATTAAACTTAAAT
*
378550 ATTTTTTTATTATTAAA
1 A-TTTTTTATAATTAAA
378567 TAGTGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 13 0.39
23 7 0.21
24 13 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTTTATAATTAAACTTAAAT
Found at i:378823 original size:32 final size:33
Alignment explanation
Indices: 378787--378856 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
378777 AAGATTTTTA
* *
378787 TTTAAAT-TTAATTATAAA-ATTAATATAAATAT
1 TTTAAATATT-ATTATAAATAATAAAATAAATAT
* *
378819 TTTAAATATTATTTTAAATAATAAAATAAATTT
1 TTTAAATATTATTATAAATAATAAAATAAATAT
378852 TTTAA
1 TTTAA
378857 TCTATTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
TTTAAATATTATTATAAATAATAAAATAAATAT
Found at i:379084 original size:29 final size:31
Alignment explanation
Indices: 379050--379134 Score: 147
Period size: 29 Copynumber: 2.8 Consensus size: 31
379040 CACAAAATAA
379050 TAAAAAAAAAAGTCAATTAATTACATTG-TT
1 TAAAAAAAAAAGTCAATTAATTACATTGTTT
379080 T-AAAAAAAAAGTCAATTAATTACATTGTTT
1 TAAAAAAAAAAGTCAATTAATTACATTGTTT
379110 TAAAAAAAAAGAGTCAATTAATTAC
1 TAAAAAAAAA-AGTCAATTAATTAC
379135 GGTGAGCATA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
29 26 0.50
30 4 0.08
31 8 0.15
32 14 0.27
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (31 bp):
TAAAAAAAAAAGTCAATTAATTACATTGTTT
Done.