Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009621.1 Hibiscus syriacus cultivar Beakdansim tig00117010_pilon, whole genome shotgun sequence
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: 839111
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 4
Found at i:316 original size:15 final size:15
Alignment explanation
Indices: 298--332 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
288 CTTGATCCTT
298 TTTTTTTATTTATTA
1 TTTTTTTATTTATTA
* *
313 TTTTTTTTTTTTTTA
1 TTTTTTTATTTATTA
328 TTTTT
1 TTTTT
333 CTTCAAGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTATTTATTA
Found at i:3877 original size:9 final size:8
Alignment explanation
Indices: 3848--3877 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3838 TGAAATAAAT
3848 AAATGTAA
1 AAATGTAA
3856 AAATGTAA
1 AAATGTAA
3864 AAATGTAA
1 AAATGTAA
3872 AGAATG
1 A-AATG
3878 ATTGCCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (8 bp):
AAATGTAA
Found at i:11658 original size:20 final size:19
Alignment explanation
Indices: 11619--11670 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
11609 TTTCTTCGAT
11619 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
11638 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
11658 ATTTATAAAATAA
1 A-TTAAAAAATAA
11671 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:11676 original size:120 final size:118
Alignment explanation
Indices: 11528--11764 Score: 314
Period size: 120 Copynumber: 2.0 Consensus size: 118
11518 AAAATATATT
* * * *
11528 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATG-ACTTCTAGG
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGAACATCCAGG
* *
11592 TACCTTAAGACAACTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAAC
66 TACCTTAAGACAACCCTTTCCTTCGATATTAAAAAATAAATAAAT-ATTAAAAC
*
11646 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGAACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGAACATCCA
* *** ** *
11711 GTTGTTTTAAGACTGCCCTTTCCTTCGATATTGAAAAATAAATAAATATTAAAA
64 GGTACCTTAAGACAACCCTTTCCTTCGATATTAAAAAATAAATAAATATTAAAA
11765 TATGATAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
118 10 0.10
119 6 0.06
120 43 0.42
121 43 0.42
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (118 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGAACATCCAGG
TACCTTAAGACAACCCTTTCCTTCGATATTAAAAAATAAATAAATATTAAAAC
Found at i:12841 original size:14 final size:12
Alignment explanation
Indices: 12813--12848 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
12803 TCATTCTCTA
12813 TCTTTTTTTTGT
1 TCTTTTTTTTGT
12825 TCTTTGTTTTTGCT
1 TCTTT-TTTTTG-T
12839 TCTTTTTTTT
1 TCTTTTTTTT
12849 TCTGTTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.23
13 11 0.50
14 6 0.27
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (12 bp):
TCTTTTTTTTGT
Found at i:12849 original size:14 final size:13
Alignment explanation
Indices: 12815--12849 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
12805 ATTCTCTATC
12815 TTTTTTTTGTTCT
1 TTTTTTTTGTTCT
*
12828 TTGTTTTTGCTTCT
1 TTTTTTTTG-TTCT
12842 TTTTTTTT
1 TTTTTTTT
12850 CTGTTGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.83
Consensus pattern (13 bp):
TTTTTTTTGTTCT
Found at i:13309 original size:3 final size:3
Alignment explanation
Indices: 13298--13342 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
13288 TAATTTTAAA
13298 AAT AA- AAT AAT AAT AAT AAT -AT AAAT AAT AAT -AT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT
13342 A
1 A
13343 GAAAATGGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.16
3 27 0.73
4 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:13318 original size:12 final size:12
Alignment explanation
Indices: 13297--13342 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
13287 ATAATTTTAA
13297 AAATAA-AATA-
1 AAATAATAATAT
13307 ATAATAATAATAT
1 A-AATAATAATAT
13320 AAATAATAATAT
1 AAATAATAATAT
13332 AAATAATAATA
1 AAATAATAATA
13343 GAAAATGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 1 0.03
11 5 0.15
12 26 0.79
13 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAATAATAT
Found at i:22287 original size:21 final size:21
Alignment explanation
Indices: 22263--22307 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22253 GATTATAAAA
22263 AAAATTAAAAGTTTAAGTACT
1 AAAATTAAAAGTTTAAGTACT
* * * *
22284 AAAATTGATAGTTTATGTATT
1 AAAATTAAAAGTTTAAGTACT
22305 AAA
1 AAA
22308 TATGTAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (21 bp):
AAAATTAAAAGTTTAAGTACT
Found at i:26009 original size:30 final size:29
Alignment explanation
Indices: 25969--26030 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
25959 TAGACTCCCC
25969 AAACAATACATTTATAGAAGGATTAATATA
1 AAACAATACATTTATAGAA-GATTAATATA
*
25999 AAACAGTACATTTATAGAAGATTAATATA
1 AAACAATACATTTATAGAAGATTAATATA
26028 AAA
1 AAA
26031 ATAAGTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (29 bp):
AAACAATACATTTATAGAAGATTAATATA
Found at i:26831 original size:16 final size:17
Alignment explanation
Indices: 26810--26847 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
26800 TTAAATTGCG
26810 AAATATAAAAAAGAAA-
1 AAATATAAAAAAGAAAT
* *
26826 AAATATTAAAAATAAAT
1 AAATATAAAAAAGAAAT
26843 AAATA
1 AAATA
26848 AAGATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATATAAAAAAGAAAT
Found at i:29133 original size:121 final size:121
Alignment explanation
Indices: 28919--29636 Score: 1123
Period size: 121 Copynumber: 5.9 Consensus size: 121
28909 GTCGATCTGT
* *
28919 TGGGCATGATATCCTTCGTCTTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* * *
28984 TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTTCATTGCTGTTTG
66 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTG
* * *
29040 TGGGCACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCTTTGTGAAGTTAAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* * *
29105 TAGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGGGTTACATTGCTGCTTG
66 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTG
* * * *
29161 TGGGCATGATATCCTTCGTCGTGAAGTTAAAATCATGGATGACTCATTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* * *
29226 TTGAATTGGATATCCTTCATCGTAAAGGTT-AAATCCAAGGGTTGCATTGCTGCTTA
66 TTGAATTGGATATCCTTCGTCGTGAA-GTTGAAATCCAAGGGTTGCATTGCTGCTTG
*
29282 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAATTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* *
29347 TTAAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTG
66 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTG
* * *
29403 TGGACACGATATCCTTCATCGTGAAGTTGAAATCGTGGATAGCTCATTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* * * * *
29468 TTGAATTAGATATCATTCATCGTGAAGTTAAAATCCAAGGGTTGCATTGTTGCTTG
66 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTG
* * *
29524 TGGGCACGATATCATTCTTCGTGAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
*
29589 TTGAATTGGATATCCTTCGTAGTGAAGTTGAAATCCAAGGGTTGCATT
66 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATT
29637 ACTTCGAGTC
Statistics
Matches: 543, Mismatches: 52, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
120 3 0.01
121 537 0.99
122 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (121 bp):
TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTG
Found at i:29753 original size:56 final size:59
Alignment explanation
Indices: 29659--29927 Score: 240
Period size: 64 Copynumber: 4.4 Consensus size: 59
29649 TTATCCTTCG
* * *
29659 CTGTGAAGTTGAAATTGACTTTAAATGAAACTGGAAAGTTGTTTGTTGAGTCCAATAT-A
1 CTGT-AAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATATCA
*
29718 CT-T-AGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTAAGTCCAATATCCTTCA
1 CTGTAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATA----TCA
* * * * * *
29779 CTGTGAAGTTGAAATTGAATCTGAATGGAACTG-AAAGTCGTTTGATGAGTCCATTATCCTTCG
1 CTGT-AAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCA--AT--ATCA
* * * *
29842 CTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTATTGAGTCCAATATTCTTCG
1 CTGT-AAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATA----TCA
29906 CTGTAAAGTTGAAATTGACTCT
1 CTGT-AAGTTGAAATTGACTCT
29928 AAAAGCTACA
Statistics
Matches: 172, Mismatches: 21, Indels: 29
0.77 0.09 0.13
Matches are distributed among these distances:
56 47 0.27
58 1 0.01
59 2 0.01
60 1 0.01
61 3 0.02
62 3 0.02
63 49 0.28
64 64 0.37
65 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (59 bp):
CTGTAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATATCA
Found at i:29795 original size:64 final size:64
Alignment explanation
Indices: 29721--29927 Score: 299
Period size: 64 Copynumber: 3.2 Consensus size: 64
29711 CAATATACTT
* *
29721 AGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTAAGTCCAATATCCTTCACTGTGA
1 AGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATATCCTTCGCTGTGA
* * * * *
29785 AGTTGAAATTGAATCTGAATGGAACTG-AAAGTCGTTTGATGAGTCCATTATCCTTCGCTGTGA
1 AGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATATCCTTCGCTGTGA
* * * * *
29848 AGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTATTGAGTCCAATATTCTTCGCTGTAA
1 AGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATATCCTTCGCTGTGA
29912 AGTTGAAATTGACTCT
1 AGTTGAAATTGACTCT
29928 AAAAGCTACA
Statistics
Matches: 124, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
63 55 0.44
64 69 0.56
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (64 bp):
AGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAGTCCAATATCCTTCGCTGTGA
Found at i:29894 original size:127 final size:120
Alignment explanation
Indices: 29642--29930 Score: 346
Period size: 127 Copynumber: 2.4 Consensus size: 120
29632 GCATTACTTC
* * * * *
29642 GAGTCCATTATCCTTCGCTGTGAAGTTGAAATTGACTTTAAATGAAACTGGAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGAATCTAAATGAAACTGGAAAGTCGTTTGATG
* * *
29707 AGTCCAATATACTTAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTT
66 AGTCCAATATACTTAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTATT
* * * *
29762 AAGTCCAATATCCTTCACTGTGAAGTTGAAATTGAATCTGAATGGAACT-GAAAGTCGTTTGATG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGAATCTAAATGAAACTGGAAAGTCGTTTGATG
* *
29826 AGTCCATTATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTATT
66 AGTCCA--AT--AT-ACT-T--AGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTATT
* * *
29889 GAGTCCAATATTCTTCGCTGTAAAGTTGAAATTGACTCTAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGAATCTAAA
29931 AGCTACAAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
119 19 0.13
120 42 0.30
121 2 0.01
123 1 0.01
124 2 0.01
125 1 0.01
127 74 0.52
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (120 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGAATCTAAATGAAACTGGAAAGTCGTTTGATG
AGTCCAATATACTTAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTATT
Found at i:34540 original size:3 final size:3
Alignment explanation
Indices: 34532--34580 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
34522 ATATTAGATG
34532 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34580 A
1 A
34581 ACAAATATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35237 original size:21 final size:21
Alignment explanation
Indices: 35213--35252 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35203 GTCCTCCTAC
*
35213 TTGACGATAGATAAATGAACT
1 TTGACGACAGATAAATGAACT
35234 TTGACGACAGATAAATGAA
1 TTGACGACAGATAAATGAA
35253 GAATCGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (21 bp):
TTGACGACAGATAAATGAACT
Found at i:37784 original size:25 final size:22
Alignment explanation
Indices: 37768--37816 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 22
37758 TAGTATATTC
37768 ATAAATAGAGTCTATTAATATAT
1 ATAAA-AGAGTCTATTAATATAT
*
37791 ATTAAAGAGTCTATTAATATAAT
1 ATAAAAGAGTCTATTAATAT-AT
37814 ATA
1 ATA
37817 TATAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (22 bp):
ATAAAAGAGTCTATTAATATAT
Found at i:38763 original size:3 final size:3
Alignment explanation
Indices: 38757--38798 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
38747 TTCTCAGATA
38757 TAT 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 TAT
38799 GGTTATGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40511 original size:6 final size:6
Alignment explanation
Indices: 40500--40526 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40490 CCAATTCTAA
40500 CCATAC CCATAC CCATAC CCATAC CCA
1 CCATAC CCATAC CCATAC CCATAC CCA
40527 ACTCTAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
CCATAC
Found at i:50210 original size:198 final size:195
Alignment explanation
Indices: 49904--50474 Score: 624
Period size: 198 Copynumber: 2.9 Consensus size: 195
49894 TTGTGAATCA
* * *
49904 GTTAAGTTATAAGGTTTTAACAC-TTTATATTATAATAACCTATAAGAAATTTGGTTGTGATGGT
1 GTTAAGTTATAAGGCTTTAAC-CGTTTATATTATAATAACCTATAAGAAATTCGGTTGCGATGGT
* * * *
49968 AACGTAATATGTTGCGTATTAA-TTTTTTTAATCGATTAAGTTATAAGG-TTTTAACCACTTATA
65 AACGTAATAGGTTGCG--TTAATTTTTTTTAA-CGGTTAAGTTATAAGGACTTTAACAACTTATA
*
50031 TTATAATAACTTATAAAAAAATTTG-TTACGATGG-AAACGTAATAGGTTGCGCCATGAATTTTT
127 TTATAATAACCTAT-AAAAAATTTGATTACGATGGTAAA-GTAATAGGTTGCGCCATG-A--TTT
50094 TTTAA-CCG
187 TTTAATCCG
* * *
50102 GTTAAGTTATAAGACTTTAGCCGTTTATATTATAATAATCTATAAGAAATTCGGTTGCGATGGTA
1 GTTAAGTTATAAGGCTTTAACCGTTTATATTATAATAACCTATAAGAAATTCGGTTGCGATGGTA
* * *
50167 ACGTAATAGGTTGCAGTTGATTTTTTTTAACAGGTTAAGTTAT-AGGACTTTAATAATTTATATT
66 ACGTAATAGGTTGC-GTTAATTTTTTTTAAC-GGTTAAGTTATAAGGACTTTAACAACTTATATT
* * *
50231 ATAATAACCTATAACAAATTTGATTTCGATGGTAAAGTAATAGGTTGCGCCTTGATTTTTTAATC
129 ATAATAACCTATAAAAAATTTGATTACGATGGTAAAGTAATAGGTTGCGCCATGATTTTTTAATC
50296 CG
194 CG
* * *
50298 GTTAAGTTATAAGGCTTTAACCGTTTATATTATAACAACCTATAAGAGA-TCAGGTTTCG-TAGG
1 GTTAAGTTATAAGGCTTTAACCGTTTATATTATAATAACCTATAAGAAATTC-GGTTGCGAT-GG
* * **
50361 TAACGTAATAGGTTGCTCCTTAATTTTTTTGAACTGGTTAAGTTATAA-GACTTTAATC-GTTTA
64 TAACGTAATAGGTTG--CGTTAATTTTTTTTAAC-GGTTAAGTTATAAGGACTTTAA-CAACTTA
* * * * * ** *
50424 TATTATAGTAACCTGTAAGAAATCTGGTTGTGATGGTAAAGTAATATGTTG
125 TATTATAATAACCTATAAAAAATTTGATTACGATGGTAAAGTAATAGGTTG
50475 TGTCTTATTT
Statistics
Matches: 322, Mismatches: 37, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
195 11 0.03
196 70 0.22
197 97 0.30
198 140 0.43
199 4 0.01
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (195 bp):
GTTAAGTTATAAGGCTTTAACCGTTTATATTATAATAACCTATAAGAAATTCGGTTGCGATGGTA
ACGTAATAGGTTGCGTTAATTTTTTTTAACGGTTAAGTTATAAGGACTTTAACAACTTATATTAT
AATAACCTATAAAAAATTTGATTACGATGGTAAAGTAATAGGTTGCGCCATGATTTTTTAATCCG
Found at i:50430 original size:99 final size:98
Alignment explanation
Indices: 49904--50474 Score: 566
Period size: 98 Copynumber: 5.8 Consensus size: 98
49894 TTGTGAATCA
** *
49904 GTTAAGTTATAAGGTTTTAACAC-TTTATATTATAATAACCTATAAGAAATTTGGTTGT-GATGG
1 GTTAAGTTATAAGACTTTAAC-CGTTTATATTATAATAACCTATAAGAAA-TCGGTT-TCGATGG
* ** *
49967 TAACGTAATATGTTGCGTATTAA-TTTTTTTAATCG
63 TAACGTAATAGGTTGCGCCTTAATTTTTTTTAACCG
* ** ** * * ** * *
50002 ATTAAGTTATAAGGTTTTAACCACTTATATTATAATAACTTATAAAAAAATTTGTTACGATGGAA
1 GTTAAGTTATAAGACTTTAACCGTTTATATTATAATAACCTAT-AAGAAATCGGTTTCGATGGTA
*
50067 ACGTAATAGGTTGCGCCATGAATTTTTTTTAACCG
65 ACGTAATAGGTTGCGCC-TTAATTTTTTTTAACCG
* * *
50102 GTTAAGTTATAAGACTTTAGCCGTTTATATTATAATAATCTATAAGAAATTCGGTTGCGATGGTA
1 GTTAAGTTATAAGACTTTAACCGTTTATATTATAATAACCTATAAGAAA-TCGGTTTCGATGGTA
* *
50167 ACGTAATAGGTTGCAG--TTGATTTTTTTTAACAG
65 ACGTAATAGGTTGC-GCCTTAATTTTTTTTAACCG
* *** * * *
50200 GTTAAGTTATAGGACTTTAATAATTTATATTATAATAACCTATAACAAATTTGATTTCGATGGTA
1 GTTAAGTTATAAGACTTTAACCGTTTATATTATAATAACCTATAAGAAA-TCGGTTTCGATGGTA
* *
50265 AAGTAATAGGTTGCGCCTTGA--TTTTTTAATCCG
65 ACGTAATAGGTTGCGCCTTAATTTTTTTTAA-CCG
* * *
50298 GTTAAGTTATAAGGCTTTAACCGTTTATATTATAACAACCTATAAGAGATCAGGTTTCG-TAGGT
1 GTTAAGTTATAAGACTTTAACCGTTTATATTATAATAACCTATAAGAAATC-GGTTTCGAT-GGT
* * *
50362 AACGTAATAGGTTGCTCCTTAATTTTTTTGAACTG
64 AACGTAATAGGTTGCGCCTTAATTTTTTTTAACCG
* * *
50397 GTTAAGTTATAAGACTTTAATCGTTTATATTATAGTAACCTGTAAGAAATCTGGTTGT-GATGGT
1 GTTAAGTTATAAGACTTTAACCGTTTATATTATAATAACCTATAAGAAATC-GGTT-TCGATGGT
* *
50461 AAAGTAATATGTTG
64 AACGTAATAGGTTG
50475 TGTCTTATTT
Statistics
Matches: 393, Mismatches: 64, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
97 12 0.03
98 216 0.55
99 84 0.21
100 80 0.20
101 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (98 bp):
GTTAAGTTATAAGACTTTAACCGTTTATATTATAATAACCTATAAGAAATCGGTTTCGATGGTAA
CGTAATAGGTTGCGCCTTAATTTTTTTTAACCG
Found at i:50538 original size:20 final size:20
Alignment explanation
Indices: 50513--50550 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
50503 TTTTCAACTA
50513 TTACATAAATACCGATACTT
1 TTACATAAATACCGATACTT
*
50533 TTACATAAATATCGATAC
1 TTACATAAATACCGATAC
50551 CATCGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (20 bp):
TTACATAAATACCGATACTT
Found at i:51250 original size:13 final size:13
Alignment explanation
Indices: 51198--51252 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
51188 GTTTTGAGAA
*
51198 GTATTGCTTTAAT
1 GTATTGCTTCAAT
* *
51211 ATATTTCTTCAAT
1 GTATTGCTTCAAT
* *
51224 ATTTTGCTTCAAT
1 GTATTGCTTCAAT
*
51237 GTATTACTTCAAT
1 GTATTGCTTCAAT
51250 GTA
1 GTA
51253 CATAATTGGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (13 bp):
GTATTGCTTCAAT
Found at i:59780 original size:206 final size:207
Alignment explanation
Indices: 59415--59806 Score: 552
Period size: 206 Copynumber: 1.9 Consensus size: 207
59405 TTTTTCCTTG
* *
59415 TTATGATTAGTGAAAGAAATTGGGGAAAGTTCCAAGACCAAGGGCAAGGAGAAGTCGGCTCTTGG
1 TTATGATTAGTGAAAGAAATTAGAGAAAGTTCCAAGACCAAGGGCAAGGAGAAGTCGGCTCTTGG
* * * * * *
59480 TTTATTTATAGACATTTTTCAACAACTCAAGACTAATACAACACATTTCTAACCTGTCTATACCA
66 TTGATTTAGAGACATTTTTCAACAACTCAAGACTAAGACAACACATATCTAACCTCTATATACCA
*** * * *
59545 CTTGTGAGCCATTAAGTATTCTTGTTTAGCTTGCACTAGTTTATGAGACATATAAGCAGTTATTG
131 CGCATGAGCCACTAAGTATTCTTGTTTAGCTTGCACTAATTTATGAGACACATAAGCAGTTATTG
59610 GTAAATTCTAGT
196 GTAAATTCTAGT
** * * * *
59622 TTATGATTAGTGAAAGAAATTAGAGAAAGTTCCAAGACCAAGGTTAATGAGAAGTTGGGTTTTGG
1 TTATGATTAGTGAAAGAAATTAGAGAAAGTTCCAAGACCAAGGGCAAGGAGAAGTCGGCTCTTGG
**
59687 TTGATTTAGAGACA-TTTTCAACAACTCAAGACTAAGGTAACACATATCTAACCTCTATATACCA
66 TTGATTTAGAGACATTTTTCAACAACTCAAGACTAAGACAACACATATCTAACCTCTATATACCA
* * *
59751 CGCATGAGTCACTAAGTGTTCTTGTTTAGCTTGTACTAATTTATGAGACACATAAG
131 CGCATGAGCCACTAAGTATTCTTGTTTAGCTTGCACTAATTTATGAGACACATAAG
59807 ACTTAAAAAT
Statistics
Matches: 160, Mismatches: 25, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
206 91 0.57
207 69 0.43
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (207 bp):
TTATGATTAGTGAAAGAAATTAGAGAAAGTTCCAAGACCAAGGGCAAGGAGAAGTCGGCTCTTGG
TTGATTTAGAGACATTTTTCAACAACTCAAGACTAAGACAACACATATCTAACCTCTATATACCA
CGCATGAGCCACTAAGTATTCTTGTTTAGCTTGCACTAATTTATGAGACACATAAGCAGTTATTG
GTAAATTCTAGT
Found at i:69257 original size:32 final size:32
Alignment explanation
Indices: 69147--69262 Score: 94
Period size: 32 Copynumber: 3.6 Consensus size: 32
69137 ACTAGTAATG
* * *
69147 TTGCATTCAGATAATGCACAATAG-AGTTAGTG
1 TTGCATTCAAATAATGCACAAGAGTA-TTAGTT
* * * *
69179 TTGCATTTAAATAATGCACAGGAGTGTCA-TT
1 TTGCATTCAAATAATGCACAAGAGTATTAGTT
* *
69210 CTCT-CATTCAGATAATGCATAAGAGTATTAGTT
1 -T-TGCATTCAAATAATGCACAAGAGTATTAGTT
*
69243 TTGCATTTAAATAATGCACA
1 TTGCATTCAAATAATGCACA
69263 GAAGTTACAG
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
31 2 0.03
32 58 0.92
33 3 0.05
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
TTGCATTCAAATAATGCACAAGAGTATTAGTT
Found at i:71483 original size:2 final size:2
Alignment explanation
Indices: 71476--71508 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
71466 GGGTAATCTT
71476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71509 CATTCATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81708 original size:3 final size:3
Alignment explanation
Indices: 81683--81755 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
81673 TTTCATTAAA
* * * **
81683 ATT ATT CTT AATT ATT TTT ATT ATT ATT ATT AAT A-T AAC ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
81728 ATT ATT AAT ATAT ATT ATT ATT -TT ATT A
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT A
81756 CAATAATACA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
2 4 0.07
3 47 0.84
4 5 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:81727 original size:20 final size:19
Alignment explanation
Indices: 81702--81749 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
81692 AATTATTTTT
81702 ATTATTATTATTAATATAAC
1 ATTATTATTATTAATAT-AC
*
81722 ATTATTATTATTAATATAT
1 ATTATTATTATTAATATAC
81741 ATTATTATT
1 ATTATTATT
81750 TTATTACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATTATTATTAATATAC
Found at i:85730 original size:22 final size:22
Alignment explanation
Indices: 85702--85745 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
85692 TCGGGTATGA
85702 CTCAAAAGATGAGACAAAGATC
1 CTCAAAAGATGAGACAAAGATC
85724 CTCAAAAGATGAGACAAAGATC
1 CTCAAAAGATGAGACAAAGATC
85746 AAGTTGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (22 bp):
CTCAAAAGATGAGACAAAGATC
Found at i:88028 original size:17 final size:17
Alignment explanation
Indices: 87991--88029 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
87981 ATTATACTTG
* *
87991 AAAAAAGGGAAAAAAGG
1 AAAAAAAGGAAAAAAGA
*
88008 AAAAAAAGGAAAAATGA
1 AAAAAAAGGAAAAAAGA
88025 AAAAA
1 AAAAA
88030 TTGAACCAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAAAAAGGAAAAAAGA
Found at i:88524 original size:32 final size:32
Alignment explanation
Indices: 88485--88546 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
88475 TCGAGACACA
*
88485 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
88517 AGAAGTATCTCTACAAGATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
88547 TCATTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:90999 original size:75 final size:75
Alignment explanation
Indices: 90911--91050 Score: 199
Period size: 75 Copynumber: 1.9 Consensus size: 75
90901 ATTAACAAAA
* * *
90911 AGCAAATATTGGGGCATACTAAAAGCCCCTCTCAATCAAAATCATGAATGTTGATGTATTTTGAA
1 AGCAAATACTGGGGCATACTAAAAGCCCCTCTCAATCAAAATCAAGAATGTTGATGCATTTTGAA
90976 CATTTATATC
66 CATTTATATC
* * * * * *
90986 AGCAAATGCTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATGAAGAATGTTGATGCATTTTGAA
1 AGCAAATACTGGGGCATACTAAAAGCCCCTCTCAATCAAAATCAAGAATGTTGATGCATTTTGAA
91051 TGCTTGTATT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 56 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (75 bp):
AGCAAATACTGGGGCATACTAAAAGCCCCTCTCAATCAAAATCAAGAATGTTGATGCATTTTGAA
CATTTATATC
Found at i:92471 original size:22 final size:19
Alignment explanation
Indices: 92421--92459 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
92411 TCTATATTAT
92421 TCAAAGATGATAGATTTTC
1 TCAAAGATGATAGATTTTC
92440 TCAAAGATGATAGATTTTC
1 TCAAAGATGATAGATTTTC
92459 T
1 T
92460 TTTTAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
TCAAAGATGATAGATTTTC
Found at i:93162 original size:44 final size:44
Alignment explanation
Indices: 93099--93186 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
93089 AAAGTAAGAA
93099 AATGATTTCCATAGTTTTTTTACTTAGTAAACTATTTCCAACAT
1 AATGATTTCCATAGTTTTTTTACTTAGTAAACTATTTCCAACAT
93143 AATGATTTCCATAGTTTTTTTACTTAGTAAACTATTTCCAACAT
1 AATGATTTCCATAGTTTTTTTACTTAGTAAACTATTTCCAACAT
93187 CTGTAAGTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (44 bp):
AATGATTTCCATAGTTTTTTTACTTAGTAAACTATTTCCAACAT
Found at i:93287 original size:46 final size:46
Alignment explanation
Indices: 93184--93953 Score: 1138
Period size: 46 Copynumber: 16.8 Consensus size: 46
93174 CTATTTCCAA
* * *
93184 CATCTGTAAGTCCTTCAATGTATGATGTTATCAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
*
93231 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
** *
93277 CATCACTAAGTCCTTCAGTGCATGATGTTATC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
93322 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * * *
93368 CATCTGTATGTCCTTCAGTACATGATGTTATC-AAAACCTTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
** *
93413 CATCTGTAAGTCCTTCAGTGCATGATGTTATAAAAAAACCTTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTT-TTCAAAAACCTTCGGGT
* *
93460 CATCTGTAAG-CCATTTAGTGTATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCC-TTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
93505 -ATTCTGTAAGCCCTTCAGTGCATGATGTTATC-AAAACCTTCAGGT
1 CA-TCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
93550 CATCTGTAAGCCCTTCAGTGCATGATATTTTTAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
93596 CATCTGTAAGTCCTTCAGTGCATGATGTTTTTAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
93642 CATCTGTAAGTCCTTCACTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
93688 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
**
93734 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAACCTTCAAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
*
93781 CATATGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
93827 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACTTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
93873 CATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAAACCTTTGAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
93919 CATCTGTAAGCCCTTCAGTGCGTGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
93954 CATTTTCGTC
Statistics
Matches: 668, Mismatches: 46, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.00
45 157 0.24
46 399 0.60
47 111 0.17
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (46 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:94104 original size:24 final size:24
Alignment explanation
Indices: 94072--94118 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
94062 TAATTTTTCA
*
94072 ATTTCATTAAAATTATTCTTAATT
1 ATTTCATTAAAATTATTATTAATT
* **
94096 ATTTTATTATTATTATTATTAAT
1 ATTTCATTAAAATTATTATTAAT
94119 ATAATAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTCATTAAAATTATTATTAATT
Found at i:94107 original size:3 final size:3
Alignment explanation
Indices: 94083--94147 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
94073 TTTCATTAAA
* * * *
94083 ATT ATT CTT AATT ATT -TT ATT ATT ATT ATT ATT AAT A-T AAT AAT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
94127 AAT ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
94148 CAAATAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.85
4 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:95826 original size:18 final size:19
Alignment explanation
Indices: 95793--95828 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
95783 AACTATACTA
95793 ATTTATTTTATTAATATTT
1 ATTTATTTTATTAATATTT
95812 ATTTATTTT-TTAATATT
1 ATTTATTTTATTAATATT
95829 AAGAAAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTATTTTATTAATATTT
Found at i:95831 original size:110 final size:106
Alignment explanation
Indices: 95690--95885 Score: 293
Period size: 110 Copynumber: 1.8 Consensus size: 106
95680 ATAATAATCA
* * * **
95690 TATTTTAAATATTTATATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCCTT
1 TATTTTAAATATTTATATTTTTTAATATTAAGAAAGGAGCTGTCTTAAAGCACATAGAAACCCTT
*
95755 TTTTGATATTCTTAAATAAATTTTTATAAACTATACTAATT
66 TTATGATATTCTTAAATAAATTTTTATAAACTATACTAATT
95796 TATTTTATTAATATTTATTTATTTTTTAATATTAAGAAAGGAGCTGTCTTAAAGCACATAGAAAC
1 TATTTTA--AATATTTA--TATTTTTTAATATTAAGAAAGGAGCTGTCTTAAAGCACATAGAAAC
*
95861 CCTTTTATGATATTTTTAAATAAAT
62 CCTTTTATGATATTCTTAAATAAAT
95886 AAATATCTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
106 7 0.09
108 8 0.10
110 64 0.81
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (106 bp):
TATTTTAAATATTTATATTTTTTAATATTAAGAAAGGAGCTGTCTTAAAGCACATAGAAACCCTT
TTATGATATTCTTAAATAAATTTTTATAAACTATACTAATT
Found at i:96391 original size:11 final size:11
Alignment explanation
Indices: 96375--96400 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
96365 TTTTTGCACG
96375 CCAACCCCTTT
1 CCAACCCCTTT
96386 CCAACCCCTTT
1 CCAACCCCTTT
96397 CCAA
1 CCAA
96401 AGAATACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (11 bp):
CCAACCCCTTT
Found at i:100115 original size:2 final size:2
Alignment explanation
Indices: 100108--100151 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
100098 TTTCCAAATA
100108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
100150 AT
1 AT
100152 TCAATGAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104573 original size:3 final size:3
Alignment explanation
Indices: 104565--104658 Score: 174
Period size: 3 Copynumber: 32.0 Consensus size: 3
104555 GTTTACAACT
104565 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
104612 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
104659 TTATTATTAT
Statistics
Matches: 89, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.04
3 85 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:104663 original size:3 final size:3
Alignment explanation
Indices: 104657--104685 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
104647 AATAAAATAA
104657 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
104686 ACCTTTACCA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:109831 original size:26 final size:24
Alignment explanation
Indices: 109802--109851 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
109792 TAGCTTAAAT
*
109802 AATATAACTTGAATAAAACATTGAAA
1 AATATAACAT-AATAAAA-ATTGAAA
*
109828 AATATAACATAATAGAAATTGAAA
1 AATATAACATAATAAAAATTGAAA
109852 GGTTTTCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (24 bp):
AATATAACATAATAAAAATTGAAA
Found at i:110207 original size:17 final size:18
Alignment explanation
Indices: 110170--110209 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
110160 TCCATTCTAT
*
110170 GGTATCGATACCCACTTC
1 GGTATCAATACCCACTTC
*
110188 GGTATCAATA-CCATTTC
1 GGTATCAATACCCACTTC
110205 GGTAT
1 GGTAT
110210 TCTAGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (18 bp):
GGTATCAATACCCACTTC
Found at i:114169 original size:3 final size:3
Alignment explanation
Indices: 114161--114200 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
114151 TAGGTTCAAC
* *
114161 AAT AAT AAT AAT AATT GAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
114201 TATTATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:122036 original size:21 final size:21
Alignment explanation
Indices: 122012--122056 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
122002 TTTAATTATA
122012 TAATAAACATTGAGAAAATTG
1 TAATAAACATTGAGAAAATTG
122033 TAATAAACATTGAGAAAATTG
1 TAATAAACATTGAGAAAATTG
122054 TAA
1 TAA
122057 GCCCTAAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.29
Consensus pattern (21 bp):
TAATAAACATTGAGAAAATTG
Found at i:122852 original size:2 final size:2
Alignment explanation
Indices: 122845--122873 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
122835 AAGCATTGCT
122845 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
122874 ATTTTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:128898 original size:3 final size:3
Alignment explanation
Indices: 128884--128951 Score: 100
Period size: 3 Copynumber: 22.0 Consensus size: 3
128874 CAGTTTGTTT
* *
128884 TTA TTT TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
128930 TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA
128952 AATAAATATT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:140665 original size:138 final size:138
Alignment explanation
Indices: 140417--140693 Score: 554
Period size: 138 Copynumber: 2.0 Consensus size: 138
140407 CCACAAGAAT
140417 GAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATATTATTTAAAAAAACAATGAGAAA
1 GAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATATTATTTAAAAAAACAATGAGAAA
140482 ACGCTTTCCTAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTGTTGAATAGTAAGAAAACGA
66 ACGCTTTCCTAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTGTTGAATAGTAAGAAAACGA
140547 TTTTCGTA
131 TTTTCGTA
140555 GAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATATTATTTAAAAAAACAATGAGAAA
1 GAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATATTATTTAAAAAAACAATGAGAAA
140620 ACGCTTTCCTAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTGTTGAATAGTAAGAAAACGA
66 ACGCTTTCCTAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTGTTGAATAGTAAGAAAACGA
140685 TTTTCGTA
131 TTTTCGTA
140693 G
1 G
140694 TTTCTTACTT
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (138 bp):
GAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATATTATTTAAAAAAACAATGAGAAA
ACGCTTTCCTAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTGTTGAATAGTAAGAAAACGA
TTTTCGTA
Found at i:140915 original size:45 final size:45
Alignment explanation
Indices: 140720--141389 Score: 998
Period size: 45 Copynumber: 14.8 Consensus size: 45
140710 CTATTTCCCA
140720 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC--AAAACCTTCGGGT
140767 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC--AAAACCTTCGGGT
*
140814 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * *
140860 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
140905 CATCTTTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
140950 CATCTGTAAGTCATTCAGTGCTTGATGTCTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
140995 CATCTGTAAGTCCTTCAGTGCCTGATGTCTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
141040 CATCTGTAAGCCCTTTAGTTCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
141085 CATCTGTAAGCCCTTCAGTGCTTAATGTCTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
141130 CATCTGTAAGTCCTTCAGTGCTTGATGTCTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * * *
141175 CATCTATAAGTCATTCATTGCTTGATATTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
141220 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
141265 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
141310 AATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
141355 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
141390 CATTTCCATC
Statistics
Matches: 579, Mismatches: 44, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
45 458 0.79
46 43 0.07
47 78 0.13
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:141512 original size:3 final size:3
Alignment explanation
Indices: 141504--141555 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
141494 CAGTTTGTTT
*
141504 TTA TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
141550 TTA TTA
1 TTA TTA
141556 AATAAATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:141974 original size:18 final size:18
Alignment explanation
Indices: 141951--142002 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
141941 CGGTTCACCT
*
141951 GCAAACAAGAAGAAGTCA
1 GCAAACAAGAAGAAGGCA
141969 GCAAACAAGAAGAAGGCA
1 GCAAACAAGAAGAAGGCA
* *
141987 GCGAGCAAGAACGAAG
1 GCAAACAAGAA-GAAG
142003 AACATAGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.52, C:0.17, G:0.29, T:0.02
Consensus pattern (18 bp):
GCAAACAAGAAGAAGGCA
Found at i:143010 original size:2 final size:2
Alignment explanation
Indices: 143003--143034 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
142993 TATTTTAGTA
143003 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
143035 TGTTTAATTG
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:143451 original size:2 final size:2
Alignment explanation
Indices: 143407--143440 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
143397 ATAAATATCT
143407 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
143441 AACTAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:152289 original size:10 final size:11
Alignment explanation
Indices: 152274--152303 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
152264 GATTTGATAA
152274 TTTAATTTA-T
1 TTTAATTTATT
152284 TTTAATTTATT
1 TTTAATTTATT
152295 TTTAATTTA
1 TTTAATTTA
152304 ATAAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTAATTTATT
Found at i:152425 original size:29 final size:29
Alignment explanation
Indices: 152392--152546 Score: 195
Period size: 29 Copynumber: 5.3 Consensus size: 29
152382 ATTTATGTAA
*
152392 TAAGTTAAGATAAAAATAGAATATATTTT
1 TAAGTTAAGATAAAAATAAAATATATTTT
* *
152421 TAAGTTAAGATAAAGACTAAAATA-AATTT
1 TAAGTTAAGATAAA-AATAAAATATATTTT
*
152450 TAAGTTAAAATAAAAATAAAATATATTTT
1 TAAGTTAAGATAAAAATAAAATATATTTT
* * *
152479 TAGGTTAAGATAAGAATAAAATATATTTAA
1 TAAGTTAAGATAAAAATAAAATATATTT-T
* *
152509 TAAGTCAATATAAAAATAAAATATATTTT
1 TAAGTTAAGATAAAAATAAAATATATTTT
152538 TAATGTTAA
1 TAA-GTTAA
152547 AATGTAAAAT
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
28 8 0.08
29 63 0.59
30 35 0.33
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.36
Consensus pattern (29 bp):
TAAGTTAAGATAAAAATAAAATATATTTT
Found at i:152463 original size:58 final size:58
Alignment explanation
Indices: 152391--152546 Score: 215
Period size: 58 Copynumber: 2.7 Consensus size: 58
152381 AATTTATGTA
* * *
152391 ATAAGTTAAGATAAAAATAGAATATATTTTTAAGTTAAGATAAAGACTAAAATAAATTT
1 ATAAGTTAAAATAAAAATAAAATATATTTTTAAGTTAAGAT-AAGAATAAAATAAATTT
* *
152450 -TAAGTTAAAATAAAAATAAAATATATTTTTAGGTTAAGATAAGAATAAAATATATTT
1 ATAAGTTAAAATAAAAATAAAATATATTTTTAAGTTAAGATAAGAATAAAATAAATTT
* *
152507 AATAAGTCAATATAAAAATAAAATATATTTTTAATGTTAA
1 -ATAAGTTAAAATAAAAATAAAATATATTTTTAA-GTTAA
152547 AATGTAAAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
57 15 0.17
58 37 0.43
59 29 0.34
60 5 0.06
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.36
Consensus pattern (58 bp):
ATAAGTTAAAATAAAAATAAAATATATTTTTAAGTTAAGATAAGAATAAAATAAATTT
Found at i:152577 original size:18 final size:19
Alignment explanation
Indices: 152536--152577 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
152526 AAAATATATT
152536 TTTAATGTTAAAATGTAAA
1 TTTAATGTTAAAATGTAAA
* * *
152555 ATTAAT-TTAATATGTGAA
1 TTTAATGTTAAAATGTAAA
152573 TTTAA
1 TTTAA
152578 GATATATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTAATGTTAAAATGTAAA
Found at i:155480 original size:6 final size:6
Alignment explanation
Indices: 155469--155493 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
155459 TTCATTGCGA
155469 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
155494 GAAATTCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:155789 original size:15 final size:14
Alignment explanation
Indices: 155769--155811 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
155759 AAACAAAGAT
155769 ACAAAAAAATGAAAA
1 ACAAAAAAAT-AAAA
155784 AC--AAAAATAAAA
1 ACAAAAAAATAAAA
155796 ACAAAACAAATAAAA
1 ACAAAA-AAATAAAA
155811 A
1 A
155812 ATGACATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.24
13 6 0.24
14 2 0.08
15 11 0.44
ACGTcount: A:0.81, C:0.09, G:0.02, T:0.07
Consensus pattern (14 bp):
ACAAAAAAATAAAA
Found at i:155795 original size:12 final size:13
Alignment explanation
Indices: 155773--155801 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
155763 AAAGATACAA
155773 AAAAATGAAAAAC
1 AAAAATGAAAAAC
155786 AAAAAT-AAAAAC
1 AAAAATGAAAAAC
155798 AAAA
1 AAAA
155802 CAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (13 bp):
AAAAATGAAAAAC
Found at i:158818 original size:45 final size:45
Alignment explanation
Indices: 158767--158938 Score: 202
Period size: 45 Copynumber: 3.8 Consensus size: 45
158757 TATAACATCT
* * * * *
158767 CTTACCATT-TATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTAT-TTCCATAAGCTCATAAGCTTATTTTTCCTATATA
* *
158812 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCA-TT-ATTTCCATAAGCTCATAAGCTTATTTTTCCTATATA
* * *
158859 CTTGCCATTATTTTCGTAAGCTCATAAGCTTATTTTTCCTATATA
1 CTTACCATTATTTCCATAAGCTCATAAGCTTATTTTTCCTATATA
* *
158904 CTTGCCATTATTTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTATTTCCATAAGCTCATAAGCTTATTT
158939 GCATGGTTAC
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
45 73 0.65
46 4 0.04
47 36 0.32
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (45 bp):
CTTACCATTATTTCCATAAGCTCATAAGCTTATTTTTCCTATATA
Found at i:159104 original size:40 final size:40
Alignment explanation
Indices: 159043--159124 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
159033 ACCATAGTGC
*
159043 TACACATAAGGTCTTGTCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCTTGCCCACCATATACACCGAAGTGTAT
* *
159083 TACACTTAAGGT-TGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCT-TGCCCACCATATACACCGAAGTGTAT
159123 TA
1 TA
159125 TAAACCTGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.03
40 37 0.97
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (40 bp):
TACACATAAGGTCTTGCCCACCATATACACCGAAGTGTAT
Found at i:161467 original size:85 final size:84
Alignment explanation
Indices: 161313--161726 Score: 494
Period size: 85 Copynumber: 4.9 Consensus size: 84
161303 TACTATGCGG
* * * * * *
161313 TTGATATGTCATCGAGCTGAATGGAATCAAACT-AACAGTTTTTGGTT-ATAGATAGCCCTTCTC
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCAA-GGTTTTT-GTTGACAGATAGCCCTTCTC
** * ** **
161376 AACTTGAGCTATGATGCAAGC
64 GCCTTGAGCTATGTTATAAAT
* * *
161397 TTGATATGTCCTTGAGCTGAATGTAATCCAACTCAATGGTTTTTATTGACAGATAACCCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCAA-GGTTTTTGTTGACAGATAGCCCTTCTCG
* *
161462 CCTTGAGTTATGTTGTAAAT
65 CCTTGAGCTATGTTATAAAT
* *
161482 TTGATATGTCTTTGAGTTGAATGTAATCGAACTCGAAGG--TTTGTTGACAGATAGCCCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTC-AAGGTTTTTGTTGACAGATAGCCCTTCTCG
*
161545 CCTTGAGCTATGCTATAAAT
65 CCTTGAGCTATGTTATAAAT
* * *
161565 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCAAAGGTTTTTATTGACAGATAACCCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTC-AAGGTTTTTGTTGACAGATAGCCCTTCTCG
* *
161630 CCTTGAGTTATTTTATAAAT
65 CCTTGAGCTATGTTATAAAT
* *
161650 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCTCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTC-AAGGTTTTTGTTGACAGATAGCCCTTCTCG
161715 CCTTGAGCTATG
65 CCTTGAGCTATG
161727 CTGCGAACAA
Statistics
Matches: 284, Mismatches: 41, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
83 74 0.26
84 31 0.11
85 177 0.62
86 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (84 bp):
TTGATATGTCCTTGAGCTGAATGTAATCGAACTCAAGGTTTTTGTTGACAGATAGCCCTTCTCGC
CTTGAGCTATGTTATAAAT
Found at i:161640 original size:168 final size:170
Alignment explanation
Indices: 161313--161728 Score: 597
Period size: 168 Copynumber: 2.5 Consensus size: 170
161303 TACTATGCGG
* * * * * * *
161313 TTGATATGTCATCGAGCTGAATGGAATCAAACT-AACAGTTTTTGGTT-ATAGATAGCCCTTCTC
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGA-AGGTTTTGGTTGACAGATAGCCCTTCTC
** * * * * *
161376 AACTTGAGCTATGATGCAAGCTTGATATGTCCTTGAGCTGAATGTAATCCAACTCAATGGTTTTT
65 GCCTTGAGCTATGCTACAAACTTGATATGCCCTTGAGCTGAATGTAATCCAACTCAAAGGTTTTT
*
161441 ATTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAAT
130 ATTGACAGATAACCCTTCTCGCCTTGAGTTATGTTATAAAT
* *
161482 TTGATATGTCTTTGAGTTGAATGTAATCGAACTCGAAGG-TTT-GTTGACAGATAGCCCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCCTTCTCG
* * *
161545 CCTTGAGCTATGCTATAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCAAAGGTTTTTA
66 CCTTGAGCTATGCTACAAACTTGATATGCCCTTGAGCTGAATGTAATCCAACTCAAAGGTTTTTA
*
161610 TTGACAGATAACCCTTCTCGCCTTGAGTTATTTTATAAAT
131 TTGACAGATAACCCTTCTCGCCTTGAGTTATGTTATAAAT
*
161650 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCTCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCCTTCTCG
161715 CCTTGAGCTATGCT
66 CCTTGAGCTATGCT
161729 GCGAACAATT
Statistics
Matches: 220, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
167 3 0.01
168 149 0.68
169 33 0.15
170 35 0.16
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (170 bp):
TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAGCCCTTCTCG
CCTTGAGCTATGCTACAAACTTGATATGCCCTTGAGCTGAATGTAATCCAACTCAAAGGTTTTTA
TTGACAGATAACCCTTCTCGCCTTGAGTTATGTTATAAAT
Found at i:167024 original size:2 final size:2
Alignment explanation
Indices: 167019--167053 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
167009 GACAAAAATA
167019 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 A
167054 CCCCAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:167305 original size:6 final size:6
Alignment explanation
Indices: 167296--167352 Score: 53
Period size: 6 Copynumber: 8.7 Consensus size: 6
167286 TAGAAAATAA
167296 AAAAAG AAAAACATG AAAAAAG GAAAAAG AAAAAAG AAAAAG AAAAAG
1 AAAAAG -AAAA-A-G AAA-AAG -AAAAAG -AAAAAG AAAAAG AAAAAG
167344 -AAAAG AAAA
1 AAAAAG AAAA
167353 TATATATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
5 5 0.11
6 15 0.34
7 14 0.32
8 8 0.18
9 2 0.05
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:167305 original size:7 final size:7
Alignment explanation
Indices: 167295--167347 Score: 65
Period size: 7 Copynumber: 7.6 Consensus size: 7
167285 GTAGAAAATA
167295 AAAAAAG
1 AAAAAAG
167302 AAAAACATG
1 AAAAA-A-G
167311 AAAAAAG
1 AAAAAAG
*
167318 GAAAAAG
1 AAAAAAG
167325 AAAAAAG
1 AAAAAAG
167332 -AAAAAG
1 AAAAAAG
167338 -AAAAAG
1 AAAAAAG
167344 AAAA
1 AAAA
167348 GAAAATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 12 0.29
7 21 0.51
8 2 0.05
9 6 0.15
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:167335 original size:5 final size:6
Alignment explanation
Indices: 167312--167352 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
167302 AAAAACATGA
167312 AAAAAGG AAAAAG AAAAAAG AAAAAG AAAAAG -AAAAG AAAA
1 AAAAA-G AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAA
167353 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.16
6 16 0.50
7 11 0.34
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:168017 original size:3 final size:3
Alignment explanation
Indices: 167998--168044 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
167988 GTTTTTCTAT
* *
167998 TTA TTT TTA TCTA TTA TTA TTA TTA TTA TTA TTAA CTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
168045 ATACAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:168486 original size:19 final size:19
Alignment explanation
Indices: 168459--168501 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
168449 TTACCTACTG
168459 AATCAGAAACCCATTCCCA
1 AATCAGAAACCCATTCCCA
* * *
168478 AATCTGAAACCCGTTCCTA
1 AATCAGAAACCCATTCCCA
168497 AATCA
1 AATCA
168502 TCAACCCACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.21
Consensus pattern (19 bp):
AATCAGAAACCCATTCCCA
Found at i:169515 original size:30 final size:30
Alignment explanation
Indices: 169481--169547 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
169471 ATTTTTTCTA
*
169481 TTTAGTCCTTCTAGTGTCTGTTAATACCAG
1 TTTAGTCCTTCTAGTGTATGTTAATACCAG
169511 TTTAGTCCTTCTAGTGTATGTTAATACCAG
1 TTTAGTCCTTCTAGTGTATGTTAATACCAG
169541 TTTAGTC
1 TTTAGTC
169548 ATTTAAACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (30 bp):
TTTAGTCCTTCTAGTGTATGTTAATACCAG
Found at i:169619 original size:30 final size:30
Alignment explanation
Indices: 169549--169622 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
169539 AGTTTAGTCA
* *
169549 TTTAAACTTCTGTTTTTGCTGTTTTAACCC
1 TTTAAATTTCTGTTTTTGCTATTTTAACCC
* * * **
169579 TTTGAGTTTCTGTTTTTGCTATTTTGATTC
1 TTTAAATTTCTGTTTTTGCTATTTTAACCC
169609 TTTAAATTTCTGTT
1 TTTAAATTTCTGTT
169623 AATCATATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.15, C:0.14, G:0.12, T:0.59
Consensus pattern (30 bp):
TTTAAATTTCTGTTTTTGCTATTTTAACCC
Found at i:175171 original size:4 final size:4
Alignment explanation
Indices: 175152--175273 Score: 203
Period size: 4 Copynumber: 31.0 Consensus size: 4
175142 GATTGAGAAA
* *
175152 ACAT ACAA ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
175200 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
175248 ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT
175274 GATACATAAA
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.02
4 108 0.98
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:175917 original size:36 final size:36
Alignment explanation
Indices: 175858--175961 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
175848 GAGATCATTT
*
175858 TCTCAAAAACAAACTTT-GTCTCGCTTAAGACAATATA
1 TCTC-AAAGCAAA-TTTCGTCTCGCTTAAGACAATATA
175895 TCTCAAAGCAAATTTCGTCTCGCTTAAGACAATATA
1 TCTCAAAGCAAATTTCGTCTCGCTTAAGACAATATA
* *
175931 TCTCAAAGCAAATTTCATCTCGCTTGAGACA
1 TCTCAAAGCAAATTTCGTCTCGCTTAAGACA
175962 TTTTTTTCTC
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
35 3 0.05
36 56 0.89
37 4 0.06
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.30
Consensus pattern (36 bp):
TCTCAAAGCAAATTTCGTCTCGCTTAAGACAATATA
Found at i:176192 original size:28 final size:28
Alignment explanation
Indices: 176151--176254 Score: 102
Period size: 28 Copynumber: 3.6 Consensus size: 28
176141 TCTTGAGATA
* *
176151 GTTTCTCTTGAAACAAATCTTTGAGTTT
1 GTTTCTTTTAAAACAAATCTTTGAGTTT
* *
176179 GTTCCTTTTAAAACAAATTTTTGAGTTT
1 GTTTCTTTTAAAACAAATCTTTGAGTTT
* *
176207 GTTTCTATTAACAA-AATCATCTTTGAGTAT
1 GTTTCTTTTAA-AACAA--ATCTTTGAGTTT
* *
176237 ATTTCTTTAAAAACAAAT
1 GTTTCTTTTAAAACAAAT
176255 TTTATCTCTC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 37 0.61
29 4 0.07
30 20 0.33
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (28 bp):
GTTTCTTTTAAAACAAATCTTTGAGTTT
Found at i:176486 original size:33 final size:33
Alignment explanation
Indices: 176443--176505 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
176433 CAACATTTAC
176443 CATCTGTGAGTCTATTTCCCTTGAAACAAAACT
1 CATCTGTGAGTCTATTTCCCTTGAAACAAAACT
* * * **
176476 CATCTTTGAGTGTTTTTCTTTTGAAACAAA
1 CATCTGTGAGTCTATTTCCCTTGAAACAAA
176506 GTTTTGTCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (33 bp):
CATCTGTGAGTCTATTTCCCTTGAAACAAAACT
Found at i:176784 original size:31 final size:30
Alignment explanation
Indices: 176749--176855 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 30
176739 CCTTGAGGCA
* *
176749 GTTTCTATGGAAACATAAAATCATTGAGTCT
1 GTTTCTATTGAAACA-AAAATCTTTGAGTCT
*
176780 GTTTCTCTTGAAACAAAACCATCTTTGAGTC-
1 GTTTCTATTGAAACAAAA--ATCTTTGAGTCT
* **
176811 GTTTCTTTTGAAACACCATTATCTTTGAGTCT
1 GTTTCTATTGAAACA--AAAATCTTTGAGTCT
*
176843 GTTTCTTTTGAAA
1 GTTTCTATTGAAA
176856 AATCACCTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
30 3 0.05
31 38 0.58
32 23 0.35
33 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (30 bp):
GTTTCTATTGAAACAAAAATCTTTGAGTCT
Found at i:176794 original size:67 final size:65
Alignment explanation
Indices: 176563--176796 Score: 188
Period size: 65 Copynumber: 3.6 Consensus size: 65
176553 TTTCTTTAAG
* * * * * *
176563 AACAAAAATCTTTGAGTATGTTCCTCTTAAAACAATTTTTTTGTCT-CATGAGACAATTTCTGTG
1 AACAAAAATCTTTGAGTCTGTTTCTCTTGAAACAA--ATTTTGTCTCCTTGAGACAATTTCTATG
176627 GA
64 GA
* * * * *
176629 AA-AAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCT-CTCGAGACAAATTCTTTTG
1 AACAAAAATCTTTGAGTCTGTTTCTCTTGAAAC-AAATTTTGTCTCCTTGAGACAATTTC-TATG
*
176692 AA
64 GA
*** * * * * *
176694 AACATCTATCTTTGAGATC-ATTTCTATTTAAACAAATTTTGTCTCCCTTGAGGCAGTTTCTATG
1 AACAAAAATCTTTGAG-TCTGTTTCTCTTGAAACAAATTTTGTCT-CCTTGAGACAATTTCTATG
176758 GA
64 GA
*
176760 AACATAAAATCATTGAGTCTGTTTCTCTTGAAACAAA
1 AACA-AAAATCTTTGAGTCTGTTTCTCTTGAAACAAA
176797 ACCATCTTTG
Statistics
Matches: 130, Mismatches: 30, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
64 19 0.15
65 43 0.33
66 35 0.27
67 33 0.25
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (65 bp):
AACAAAAATCTTTGAGTCTGTTTCTCTTGAAACAAATTTTGTCTCCTTGAGACAATTTCTATGGA
Found at i:176852 original size:32 final size:32
Alignment explanation
Indices: 176772--176855 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 32
176762 CATAAAATCA
*
176772 TTGAGTCTGTTTCTCTTGAAACAAAACCATCT
1 TTGAGTCTGTTTCTTTTGAAACAAAACCATCT
** **
176804 TTGAGTC-GTTTCTTTTGAAACACCATTATCT
1 TTGAGTCTGTTTCTTTTGAAACAAAACCATCT
176835 TTGAGTCTGTTTCTTTTGAAA
1 TTGAGTCTGTTTCTTTTGAAA
176856 AATCACCTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 26 0.57
32 20 0.43
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (32 bp):
TTGAGTCTGTTTCTTTTGAAACAAAACCATCT
Found at i:176875 original size:29 final size:30
Alignment explanation
Indices: 176772--176885 Score: 97
Period size: 31 Copynumber: 3.7 Consensus size: 30
176762 CATAAAATCA
* * * *
176772 TTGAGTCTGTTTCTCTTGAAACAAAACCATCT
1 TTGAGTC-GTTTCTTTTGAAAC-ACATCACCT
* *
176804 TTGAGTCGTTTCTTTTGAAACACCATTATCT
1 TTGAGTCGTTTCTTTTGAAACA-CATCACCT
176835 TTGAGTCTGTTTCTTTTGAAA-A-ATCACCT
1 TTGAGTC-GTTTCTTTTGAAACACATCACCT
**
176864 TTGAGTCAGTTTCCCTTGAAAC
1 TTGAGTC-GTTTCTTTTGAAAC
176886 CATTATACCT
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
29 23 0.33
30 1 0.01
31 26 0.37
32 20 0.29
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (30 bp):
TTGAGTCGTTTCTTTTGAAACACATCACCT
Found at i:177204 original size:133 final size:132
Alignment explanation
Indices: 176898--177219 Score: 360
Period size: 133 Copynumber: 2.4 Consensus size: 132
176888 TTATACCTAA
*
176898 AGATAACCAACCGTCCTCATCGCGTAAGAACCGAGTTATCACCCTCCCTAAAGATGGCCAATCAT
1 AGATAACCAA-CGTCCTCATCGCGT-AGAACCGAGTTATCACCCTCCCTAAAGATGGCCAAACAT
* * * * * *
176963 CCTCATTATGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAACCGTGTCAC
64 CCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCATCATCACGTAGGAACCGTGTCAC
*
177028 CCCT
129 CCAT
* * ** * * * *
177032 AGATAACTAGTCGTCCTCATCGTATAGGAACTGATTTATCACTCT-CTTAAAGATGGCCAGAAC-
1 AGATAACCA-ACGTCCTCATCGCGTA-GAACCGAGTTATCACCCTCCCTAAAGATGGCCA-AACA
* * ** *
177095 TCTTCATCACGTATGAGTCATGTCATCCCCCGACCAGACCTCATCATCACGTAGGAGCCGTGTCA
63 TCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCATCATCACGTAGGAACCGTGTCA
177160 CCCAT
128 CCCAT
* *
177165 AGATAACCAACAGTCCTCATCGCGTAGTAACCGAGTTATCACCCTTCCTAGAGAT
1 AGATAACCAAC-GTCCTCATCGCGTAG-AACCGAGTTATCACCCTCCCTAAAGAT
177220 TGTAACACCC
Statistics
Matches: 152, Mismatches: 30, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
132 2 0.01
133 106 0.70
134 44 0.29
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (132 bp):
AGATAACCAACGTCCTCATCGCGTAGAACCGAGTTATCACCCTCCCTAAAGATGGCCAAACATCC
TCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCATCATCACGTAGGAACCGTGTCACCC
AT
Found at i:178042 original size:30 final size:31
Alignment explanation
Indices: 178003--178069 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
177993 GAATGACCTA
* * * *
178003 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
*
178033 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
178064 TCCATA
1 TCCATA
178070 TGTTTCTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:178144 original size:63 final size:62
Alignment explanation
Indices: 178031--178152 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 62
178021 CCTCGGCAAC
* * *
178031 TGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCCATATGTTTCTTAGAACATAGGTATAT
1 TGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAT
*
178093 TGTCCATATGTCCCAAA-AGACATAGGTAATTA-TGTCCATATGTTCCGTAGAACATAGGTA
1 TGTCCATAGGTCCCAAAGA-ACATAGGTAA--ACTGTCCATATGTTCCGTAGAACATAGGTA
178153 AACCCTCGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
61 1 0.02
62 25 0.47
63 26 0.49
64 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (62 bp):
TGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAT
Found at i:178148 original size:32 final size:32
Alignment explanation
Indices: 178047--178153 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 32
178037 TAGGTCCCAA
* * * *
178047 AGAACCTAGGTAA-ACTGTCCATATGTTTCTT
1 AGAACATAGGTAATATTGTCCATATGTTCCCT
*
178078 AGAACATAGGT-ATATTGTCCATATG-TCCCA
1 AGAACATAGGTAATATTGTCCATATGTTCCCT
* *
178108 AAAGACATAGGTAAT-TATGTCCATATGTTCCGT
1 AGA-ACATAGGTAATAT-TGTCCATATGTTCCCT
178141 AGAACATAGGTAA
1 AGAACATAGGTAA
178154 ACCCTCGACT
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
30 5 0.08
31 30 0.48
32 22 0.35
33 5 0.08
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (32 bp):
AGAACATAGGTAATATTGTCCATATGTTCCCT
Found at i:179027 original size:64 final size:65
Alignment explanation
Indices: 178944--179101 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 65
178934 TAACATGTGC
* * * *
178944 ATCGATGCACTACCCATGCATCGATACACAT-ATCACCTTCGATGTTT-TAATCTTAAGGAGGTG
1 ATCGATGCACTTCCTATGCATCGATACACATAATCACATTCGATGTTTCCAATCTTAAGG-GGTG
179007 T
65 T
* * ** * *
179008 ATTGATGCAC-TCCTTATGCATCGATGCAC-TAATTGCATTCGATGTTTCCATTTTTAAGGGGTG
1 ATCGATGCACTTCC-TATGCATCGATACACATAATCACATTCGATGTTTCCAATCTTAAGGGGTG
179071 T
65 T
*
179072 ATCGATGCACTTCCTGTGCATCGATACACA
1 ATCGATGCACTTCCTATGCATCGATACACA
179102 CTGAACAATT
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
63 3 0.04
64 62 0.82
65 11 0.14
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (65 bp):
ATCGATGCACTTCCTATGCATCGATACACATAATCACATTCGATGTTTCCAATCTTAAGGGGTGT
Found at i:180161 original size:3 final size:3
Alignment explanation
Indices: 180153--180191 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
180143 TATTTTAATA
* *
180153 TAT TAT TAT TAT TAT TAT GAT TAT TAAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA
180192 ATACGAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:180575 original size:21 final size:21
Alignment explanation
Indices: 180549--180598 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
180539 ACCAACATCA
180549 CCAAGTCAGAGAAAATAATGG
1 CCAAGTCAGAGAAAATAATGG
180570 CCAAGTCAGAGAAAATAATGG
1 CCAAGTCAGAGAAAATAATGG
180591 CCAAGTCA
1 CCAAGTCA
180599 TAAACCCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (21 bp):
CCAAGTCAGAGAAAATAATGG
Found at i:183491 original size:20 final size:21
Alignment explanation
Indices: 183441--183503 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
183431 AATACATACA
183441 ATATATATATATA-TATATAT
1 ATATATATATATATTATATAT
183461 ATATATATATATATTATATA-
1 ATATATATATATATTATATAT
* *
183481 ATGTA-AGTATATATTATAAAT
1 ATATATA-TATATATTATATAT
183502 AT
1 AT
183504 GTTTGTACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.76
21 8 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
ATATATATATATATTATATAT
Found at i:183494 original size:2 final size:2
Alignment explanation
Indices: 183441--183480 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
183431 AATACATACA
183441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
183481 ATGTAAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:187454 original size:41 final size:41
Alignment explanation
Indices: 187288--187458 Score: 109
Period size: 41 Copynumber: 4.2 Consensus size: 41
187278 CAAAATCCTA
* *
187288 CTTTAGTGGCGTTTCTAAA-AAAAGCCGCAAAAGAATCATT
1 CTTTAGTGGCGTTTCTAAACAAATGCCGCAAAAGAATCAAT
* * * * * * *
187328 CTTTAGTGCCATTTTTAAACAAATGCCGTAATATG-GTAAAT
1 CTTTAGTGGCGTTTCTAAACAAATGCCGCAA-AAGAATCAAT
* * ** * * * *
187369 ATTT-GTGGCGTTTTTTGACAAATGCCGC--TACAACCTAGAA
1 CTTTAGTGGCGTTTCTAAACAAATGCCGCAAAAGAATC-A-AT
* *
187409 CTTTAGTGGCGTTTCTAAACAAACGCCGCAAAAGAATCATT
1 CTTTAGTGGCGTTTCTAAACAAATGCCGCAAAAGAATCAAT
187450 CTTTAGTGG
1 CTTTAGTGG
187459 GATTTTTGAA
Statistics
Matches: 91, Mismatches: 32, Indels: 15
0.66 0.23 0.11
Matches are distributed among these distances:
39 1 0.01
40 39 0.43
41 44 0.48
42 3 0.03
43 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (41 bp):
CTTTAGTGGCGTTTCTAAACAAATGCCGCAAAAGAATCAAT
Found at i:187506 original size:122 final size:120
Alignment explanation
Indices: 187287--187507 Score: 293
Period size: 122 Copynumber: 1.8 Consensus size: 120
187277 ACAAAATCCT
*
187287 ACTTTAGTGGCGTTTCTAAAAAAAGCCGCAAAAGAATCATTCTTTAGTGCCATTTTTAAACAAAT
1 ACTTTAGTGGCGTTTCTAAAAAAAGCCGCAAAAGAATCATTCTTTAGTGCCATTTTTAAACAAAC
* * *
187352 GCCGTAATATGGTAAATATTTGTGGCGTTTTTTGACAAATGCCGCTACAACCTAGA
66 GCCGCAATATGG-AAACATTTGTGACGTTTTTTGACAAATGCCGCTACAACCTAGA
* ** *
187408 ACTTTAGTGGCGTTTCTAAACAAACGCCGCAAAAGAATCATTCTTTAGTGGGATTTTTGAAA-AT
1 ACTTTAGTGGCGTTTCTAAA-AAAAGCCGCAAAAGAATCATTCTTTAGTGCCATTTTT-AAACAA
*
187472 ACGCCGCAATAGTTCGG-AACATTTGTGATGTTTTTT
64 ACGCCGCAATA--T-GGAAACATTTGTGACGTTTTTT
187508 TAAAAAACAC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
121 20 0.23
122 44 0.51
123 19 0.22
124 1 0.01
125 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (120 bp):
ACTTTAGTGGCGTTTCTAAAAAAAGCCGCAAAAGAATCATTCTTTAGTGCCATTTTTAAACAAAC
GCCGCAATATGGAAACATTTGTGACGTTTTTTGACAAATGCCGCTACAACCTAGA
Found at i:193803 original size:24 final size:23
Alignment explanation
Indices: 193755--193837 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
193745 TTCCCCTGTG
193755 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
193778 GGGGGGAATTGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
193801 AGGGGGAATCGGCT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
193822 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
193838 TCTGCACCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 5 0.10
21 11 0.21
22 3 0.06
23 33 0.63
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.20
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:193837 original size:20 final size:20
Alignment explanation
Indices: 193800--193839 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
193790 TTCCCCTTCA
*
193800 AAGGGGGAATCGGCTCCCTC
1 AAGGGGGAATCGACTCCCTC
* *
193820 AAGGGGGGATCGATTCCCTC
1 AAGGGGGAATCGACTCCCTC
193840 TGCACCAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (20 bp):
AAGGGGGAATCGACTCCCTC
Found at i:195629 original size:183 final size:183
Alignment explanation
Indices: 195294--195662 Score: 697
Period size: 183 Copynumber: 2.0 Consensus size: 183
195284 TTCTCTCAAA
195294 TTGATTTAACTCTTCTTGCATAGCCATAATCTAATGTTCATCATTTAATGCTTCTTTAATATTCT
1 TTGATTTAACTCTTCTTGCATAGCCATAATCTAATGTTCATCATTTAATGCTTCTTTAATATTCT
195359 TAGGCTCTATGCATGAGATAAATGCAACATAATTACAAATATTTCTAAGAGAAGATCGAGTTGTT
66 TAGGCTCTATGCATGAGATAAATGCAACATAATTACAAATATTTCTAAGAGAAGATCGAGTTGTT
195424 ACCCCTTTTGATGGAAACCTATAATTTCACCATCCTTGACATAGTTGTACTCTC
131 ACCCCTTTTGATGGAAACCTATAATTTCACCATCC-TGACATAGTTGTACTCTC
195478 TTGATTTAACTCTTCTTGCATAGCCATAATCTAATG-TCATCATTTAATGCTTCTTTAATATTCT
1 TTGATTTAACTCTTCTTGCATAGCCATAATCTAATGTTCATCATTTAATGCTTCTTTAATATTCT
195542 TAGGCTCTATGCATGAGATAAATGCAACATAATTACAAAT-TTTCTAAGAGAAGATCGAGTTGTT
66 TAGGCTCTATGCATGAGATAAATGCAACATAATTACAAATATTTCTAAGAGAAGATCGAGTTGTT
*
195606 ACCCCTTTTGATGGATCACCTATAATTTCACCATCCTGACATAGTTGTACTCTC
131 ACCCCTTTTGATGGA-AACCTATAATTTCACCATCCTGACATAGTTGTACTCTC
195660 TTG
1 TTG
195663 GATAAGATAC
Statistics
Matches: 183, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
182 60 0.33
183 87 0.48
184 36 0.20
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (183 bp):
TTGATTTAACTCTTCTTGCATAGCCATAATCTAATGTTCATCATTTAATGCTTCTTTAATATTCT
TAGGCTCTATGCATGAGATAAATGCAACATAATTACAAATATTTCTAAGAGAAGATCGAGTTGTT
ACCCCTTTTGATGGAAACCTATAATTTCACCATCCTGACATAGTTGTACTCTC
Found at i:196027 original size:16 final size:16
Alignment explanation
Indices: 196006--196037 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
195996 AAAGGATGAA
196006 AATAACTAATGTTAGG
1 AATAACTAATGTTAGG
196022 AATAACTAATGTTAGG
1 AATAACTAATGTTAGG
196038 CTTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
AATAACTAATGTTAGG
Found at i:196883 original size:15 final size:16
Alignment explanation
Indices: 196843--196877 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
196833 GAGAACATGC
*
196843 AAAAAGTTATGCATTG
1 AAAATGTTATGCATTG
196859 AAAATGTTATGCATT-
1 AAAATGTTATGCATTG
196874 AAAA
1 AAAA
196878 CTTTATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (16 bp):
AAAATGTTATGCATTG
Found at i:201787 original size:21 final size:21
Alignment explanation
Indices: 201763--201802 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
201753 AAATGATGCT
201763 TCTCCCTACTTCTCTCGCTGC
1 TCTCCCTACTTCTCTCGCTGC
* * *
201784 TCTCTCTGCTTCTTTCGCT
1 TCTCCCTACTTCTCTCGCT
201803 TCAGCTTCGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.42, G:0.10, T:0.45
Consensus pattern (21 bp):
TCTCCCTACTTCTCTCGCTGC
Found at i:205259 original size:21 final size:21
Alignment explanation
Indices: 205233--205272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
205223 TAGAACCCCA
*
205233 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
205254 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
205273 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:208328 original size:2 final size:2
Alignment explanation
Indices: 208321--208349 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
208311 ATGCATCATT
208321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
208350 CCCTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:218267 original size:22 final size:22
Alignment explanation
Indices: 218242--218287 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
218232 TGTCATGAGG
218242 TTTCCCATTTTCCAGTCCAAAC
1 TTTCCCATTTTCCAGTCCAAAC
218264 TTTCCCATTTTCCAGTCCAAAC
1 TTTCCCATTTTCCAGTCCAAAC
218286 TT
1 TT
218288 CTTGAGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.35, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTCCCATTTTCCAGTCCAAAC
Found at i:225441 original size:18 final size:18
Alignment explanation
Indices: 225398--225443 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
225388 TTTAAGGGGG
**
225398 TGCATCGATGCACTCTTA
1 TGCATCGATGCACTAATA
225416 TGCATCGATGCACTAAT-
1 TGCATCGATGCACTAATA
225433 TGCATTCGATG
1 TGCA-TCGATG
225444 TTCATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (18 bp):
TGCATCGATGCACTAATA
Found at i:225441 original size:63 final size:65
Alignment explanation
Indices: 225333--225454 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 65
225323 TCTTTAACAT
* *
225333 GTGCATCGATGCATTACCCATGCATCGATACACAAATCACCTTCGATGTT-TTTATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTATTTATTTTAAGGGG
** * * **
225397 GTGCATCGATGCACT-CTTATGCATCGATGCACTAATTGCATTCGATGTTCATTTATTT
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTT-ATTTATTT
225455 GAGAGTGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 27 0.56
64 14 0.29
65 7 0.15
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (65 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTATTTATTTTAAGGGG
Found at i:226364 original size:24 final size:20
Alignment explanation
Indices: 226306--226352 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
226296 TCATGTTGCC
226306 TCCTTTACTTAACTTTTCCT
1 TCCTTTACTTAACTTTTCCT
226326 TCCTTTACTTAACTTTTCCT
1 TCCTTTACTTAACTTTTCCT
226346 TCCTTTA
1 TCCTTTA
226353 GTTTTTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.55
Consensus pattern (20 bp):
TCCTTTACTTAACTTTTCCT
Found at i:230266 original size:21 final size:21
Alignment explanation
Indices: 230232--230273 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
230222 ATTCATTTAT
230232 TTGAAAATGAATCGATGCACA
1 TTGAAAATGAATCGATGCACA
* *
230253 TTGAAGATGCATCGATGCACA
1 TTGAAAATGAATCGATGCACA
230274 GAACCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (21 bp):
TTGAAAATGAATCGATGCACA
Found at i:237594 original size:19 final size:20
Alignment explanation
Indices: 237561--237605 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
237551 AACCACATTG
* *
237561 AAAGAAAACGAAAGAGATGA
1 AAAGAAAAAGAAAGAGACGA
237581 AAAGAAAAAG-AAGAGACGA
1 AAAGAAAAAGAAAGAGACGA
237600 AAAGAA
1 AAAGAA
237606 GGGAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.69, C:0.04, G:0.24, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAGACGA
Found at i:239727 original size:21 final size:21
Alignment explanation
Indices: 239683--239737 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
239673 ATTATGACTA
239683 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
239704 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
239725 TCGCAATGCGATT
1 TCGCAATGCGATT
239738 CTGACTTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:239749 original size:20 final size:20
Alignment explanation
Indices: 239724--239776 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
239714 ATTTTCCCAA
*
239724 TTCGCAATGCGATTCTGACT
1 TTCGCAATGAGATTCTGACT
*
239744 TTCGCAACGAGATTCTGACT
1 TTCGCAATGAGATTCTGACT
*
239764 ATCGCAATGAGAT
1 TTCGCAATGAGAT
239777 AATACATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (20 bp):
TTCGCAATGAGATTCTGACT
Found at i:239950 original size:12 final size:12
Alignment explanation
Indices: 239931--239964 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
239921 CTCTCCGGCG
239931 ACATCCGTTCCT
1 ACATCCGTTCCT
*
239943 ATATCCGTTCCT
1 ACATCCGTTCCT
239955 ACATCC-TTCC
1 ACATCCGTTCC
239965 CCATTCGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:240545 original size:24 final size:24
Alignment explanation
Indices: 240518--240571 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
240508 GTATTCGAAA
*
240518 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
240542 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
240566 TTTGAT
1 TTTGAT
240572 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:240763 original size:12 final size:12
Alignment explanation
Indices: 240746--240770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
240736 ATATAATCCT
240746 GAAGAAGAAAAA
1 GAAGAAGAAAAA
240758 GAAGAAGAAAAA
1 GAAGAAGAAAAA
240770 G
1 G
240771 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:243112 original size:19 final size:20
Alignment explanation
Indices: 243070--243113 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
243060 CAATCATCTT
*
243070 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
*
243090 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
243109 AATGA
1 AATGA
243114 AAATTGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:243122 original size:19 final size:19
Alignment explanation
Indices: 243077--243220 Score: 111
Period size: 19 Copynumber: 8.3 Consensus size: 19
243067 CTTAATGTCT
* **
243077 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
243097 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
243116 ATTGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
243130 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
243149 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
*
243163 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
243182 ATCGCAA--CG-AATG--A
1 ATCGCAATGCGAAATGAAA
*
243196 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
243215 ATCGCA
1 ATCGCA
243221 GCACGAATTT
Statistics
Matches: 100, Mismatches: 9, Indels: 31
0.71 0.06 0.22
Matches are distributed among these distances:
14 28 0.28
15 2 0.02
16 9 0.09
17 9 0.09
18 2 0.02
19 41 0.41
20 9 0.09
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:243134 original size:33 final size:33
Alignment explanation
Indices: 243097--243220 Score: 187
Period size: 33 Copynumber: 3.8 Consensus size: 33
243087 GGAAATGACT
* *
243097 ATCGCAATGCGAAATGAAAATTGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
243130 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
243163 ATTGCAATGCGAAATGAAAATCGCAACGA-ATGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA-GA
*
243196 ATCGCAAAGCGAAATGAAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCA
243221 GCACGAATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 1 0.01
33 82 0.99
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:243275 original size:33 final size:33
Alignment explanation
Indices: 243233--243312 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
243223 ACGAATTTAG
* *
243233 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
243266 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
243299 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
243313 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:243276 original size:19 final size:19
Alignment explanation
Indices: 243252--243312 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
243242 GCGATTTTGT
243252 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
243271 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
243285 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
243304 CATTGCGAT
1 CGTTGCGAT
243313 AGTCATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:243438 original size:14 final size:14
Alignment explanation
Indices: 243419--243455 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
243409 CATCAATTAA
243419 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
243433 ACAAATCATCTTTT
1 ACAAATCAACTTTT
243447 ACAAATCAA
1 ACAAATCAA
243456 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:244879 original size:21 final size:21
Alignment explanation
Indices: 244813--244879 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
244803 GTGAATCGGG
*
244813 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
244833 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
244855 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
244876 CTCT
1 CTCT
244880 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Done.