Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008773.1 Hibiscus syriacus cultivar Beakdansim tig00111881_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: 1239499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:380377 original size:30 final size:30
Alignment explanation
Indices: 380341--380399 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
380331 GCCCACCATA
*
380341 TGCACTAAGTGCCCTTACAAACTAAAGTGT
1 TGCACTAAATGCCCTTACAAACTAAAGTGT
* * *
380371 TGCACTAAATGTCCTTACACACTATAGTG
1 TGCACTAAATGCCCTTACAAACTAAAGTG
380400 CTAATCTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (30 bp):
TGCACTAAATGCCCTTACAAACTAAAGTGT
Found at i:390537 original size:167 final size:166
Alignment explanation
Indices: 390262--390595 Score: 659
Period size: 167 Copynumber: 2.0 Consensus size: 166
390252 AAGAAGGATT
390262 AGATGGTGGAAACATCAACACTGAGGACTGCTCCAAATCCACTAATTTTTCAGACTTAAGAACTG
1 AGATGGTGGAAACATCAACACTGAGGACTGCTCCAAATCCACTAATTTTTCAGACTTAAGAACTG
390327 GAAAGAGGAAAAAGTATATGAGAGTGTTCGTGATCGTTTCACCACTGGTGATTGGTCTAAGGGTG
66 GAAAGAGGAAAAAGTATATGAGAGTGTTCGTGATCGTTTCACCACTGGTGATTGGTCTAAGGGTG
390392 CCCTCAGGAATCAAATGTCAGAAGCTATAACCGAAG
131 CCCTCAGGAATCAAATGTCAGAAGCTATAACCGAAG
390428 AGATGGTGGAAACATCAACACTGAGGACTGCTCCAAATCCACTAATTTTTCAGAACTTAAGAACT
1 AGATGGTGGAAACATCAACACTGAGGACTGCTCCAAATCCACTAATTTTTCAG-ACTTAAGAACT
390493 GGAAAGAGGAAAAAGTATATGAGAGTGTTCGTGATCGTTTCACCACTGGTGATTGGTCTAAGGGT
65 GGAAAGAGGAAAAAGTATATGAGAGTGTTCGTGATCGTTTCACCACTGGTGATTGGTCTAAGGGT
390558 GCCCTCAGGAATCAAATGTCAGAAGCTATAACCGAAG
130 GCCCTCAGGAATCAAATGTCAGAAGCTATAACCGAAG
390595 A
1 A
390596 AGAAGATGAT
Statistics
Matches: 167, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
166 53 0.32
167 114 0.68
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (166 bp):
AGATGGTGGAAACATCAACACTGAGGACTGCTCCAAATCCACTAATTTTTCAGACTTAAGAACTG
GAAAGAGGAAAAAGTATATGAGAGTGTTCGTGATCGTTTCACCACTGGTGATTGGTCTAAGGGTG
CCCTCAGGAATCAAATGTCAGAAGCTATAACCGAAG
Found at i:394809 original size:35 final size:35
Alignment explanation
Indices: 394760--394826 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
394750 GGGTTAAAGG
* * *
394760 CATTAAACTCTATTTAGGGTTAAAAACAAATTATA
1 CATTAAAATATATTTAGAGTTAAAAACAAATTATA
*
394795 CATTAAAATATATTTAGAGTTAAAGACAAATT
1 CATTAAAATATATTTAGAGTTAAAAACAAATT
394827 CCAACTCTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (35 bp):
CATTAAAATATATTTAGAGTTAAAAACAAATTATA
Found at i:399910 original size:21 final size:21
Alignment explanation
Indices: 399884--399941 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
399874 ATGGTGTCAA
399884 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
399905 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACCCCTGC
399926 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
399942 TACCACTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:400450 original size:34 final size:33
Alignment explanation
Indices: 400410--400480 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
400400 TTTTGTAAAG
* * *
400410 GGGAAAGGTTCTAGTTTATCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCGGA-AAAAACTA
400444 GGGAAAGGTTCTAGTTTAGCCCGGAAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCGGAAAAAACTA
400477 GGGA
1 GGGA
400481 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGTTTAGCCCGGAAAAAACTA
Found at i:403149 original size:21 final size:21
Alignment explanation
Indices: 403123--403162 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
403113 AAACAATTGG
403123 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
403144 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
403163 CATTAAACAT
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:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:403665 original size:20 final size:22
Alignment explanation
Indices: 403627--403666 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
403617 TTTTAGTAGA
403627 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
403649 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
403667 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:404802 original size:19 final size:19
Alignment explanation
Indices: 404780--404821 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
404770 TAAGAAATTT
*
404780 TTTTATTTTTTAAAATAAA
1 TTTTATTTTTAAAAATAAA
404799 TTTTATTTTTAAAAATAAA
1 TTTTATTTTTAAAAATAAA
404818 TTTT
1 TTTT
404822 TAAATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATTTTTAAAAATAAA
Found at i:404967 original size:26 final size:26
Alignment explanation
Indices: 404938--404997 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
404928 ATTTAAGAAA
404938 ATTTAAATTTTTTAAAAGAATTTTTT
1 ATTTAAATTTTTTAAAAGAATTTTTT
* *
404964 ATTT--TTTATTTTAAAATAATTTTTT
1 ATTTAAATT-TTTTAAAAGAATTTTTT
*
404989 -TATAAATTT
1 ATTTAAATTT
404998 AACATATGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
24 4 0.15
25 17 0.63
26 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTAAATTTTTTAAAAGAATTTTTT
Found at i:405011 original size:160 final size:162
Alignment explanation
Indices: 404728--405032 Score: 368
Period size: 160 Copynumber: 1.9 Consensus size: 162
404718 AAGTAAAAGG
* **
404728 ATTTGGAATTAGGGATTTTAGAAATTTGAGTGTTTTTAGATTTAAGAAATTTTTTTATTTTTTAA
1 ATTTGGAATTAGGGATTTTAGAAATTTGAGTGTTTTTAGATTTAAGAAATATTTAAATTTTTTAA
* * * * *
404793 AATAAATTTTATTTTTAAAAATAAATTTTTAAATTTTTATAATTTGATATGTGTCAATTAACAAT
66 AAGAAATTTTATTTTTAAAAATAAA--TATAAATTTTTATAATTTAACATATGTCAATTAACAAT
404858 CAAATTTAAC-GACAGATCAATGTAGGTAAAAAT
129 CAAATTTAACTGACAGATCAATGTAGGTAAAAAT
* *
404891 ATTTGGAATTAGGGATTTTAG-ATTTTGTGT-TTTTTAGATTTAAGAAA-ATTTAAATTTTTTAA
1 ATTTGGAATTAGGGATTTTAGAAATTTGAGTGTTTTTAGATTTAAGAAATATTTAAATTTTTTAA
* * *** * * *
404953 AAGAATTTTTTATTTTTTATTTTAAA-ATAATTTTTTTATAAATTTAACATATGTCAATTAGCAG
66 AAGAA-ATTTTATTTTTAAAAATAAATATAA-ATTTTTAT-AATTTAACATATGTCAATTAACAA
405017 TCAAATTTAACTGACA
128 TCAAATTTAACTGACA
405033 TACACTTAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
158 3 0.03
159 7 0.06
160 46 0.38
161 36 0.30
162 7 0.06
163 21 0.17
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (162 bp):
ATTTGGAATTAGGGATTTTAGAAATTTGAGTGTTTTTAGATTTAAGAAATATTTAAATTTTTTAA
AAGAAATTTTATTTTTAAAAATAAATATAAATTTTTATAATTTAACATATGTCAATTAACAATCA
AATTTAACTGACAGATCAATGTAGGTAAAAAT
Found at i:406097 original size:3 final size:3
Alignment explanation
Indices: 406089--406122 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
406079 ATCAGAAAAT
406089 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
406123 TTCGGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:409827 original size:3 final size:3
Alignment explanation
Indices: 409819--409852 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
409809 ATTTAATTTA
409819 ATT ATT ATT ATT ATTT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT A
409853 ATACAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:409836 original size:13 final size:13
Alignment explanation
Indices: 409820--409852 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
409810 TTTAATTTAA
409820 TTATTATTATTAT
1 TTATTATTATTAT
409833 TTATTATTATTAT
1 TTATTATTATTAT
409846 TATATTA
1 T-TATTA
409853 ATACAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:409838 original size:16 final size:16
Alignment explanation
Indices: 409800--409848 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
409790 GGGTCCTCTT
* *
409800 TTTATTTTTATT-TAA
1 TTTATTATTATTATTA
409815 TTTAATTATTATTATTA
1 TTT-ATTATTATTATTA
409832 TTTATTATTATTATTA
1 TTTATTATTATTATTA
409848 T
1 T
409849 ATTAATACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 3 0.10
16 22 0.73
17 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:415866 original size:14 final size:14
Alignment explanation
Indices: 415847--415876 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
415837 AAGAATTATA
415847 GATTTTTGACACAT
1 GATTTTTGACACAT
415861 GATTTTTGACACAT
1 GATTTTTGACACAT
415875 GA
1 GA
415877 CAAGATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
GATTTTTGACACAT
Found at i:416638 original size:14 final size:14
Alignment explanation
Indices: 416619--416671 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
416609 GAGAAAAGAA
416619 AAACAAAGAGAAAG
1 AAACAAAGAGAAAG
*
416633 AAACAAAGTGAAA-
1 AAACAAAGAGAAAG
*
416646 AAAAAGAAGAGAAAG
1 AAACA-AAGAGAAAG
*
416661 AGGACAAAGAG
1 A-AACAAAGAG
416672 CACATACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.13
14 19 0.61
15 6 0.19
16 2 0.06
ACGTcount: A:0.68, C:0.06, G:0.25, T:0.02
Consensus pattern (14 bp):
AAACAAAGAGAAAG
Found at i:417827 original size:4 final size:4
Alignment explanation
Indices: 417818--417863 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
417808 GATCGAGAAA
*
417818 ACAT ACAT ACAT ACAT ACAT ATAT ACAT --AT ACAT ACAT A-AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
417863 A
1 A
417864 AAATTTGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (4 bp):
ACAT
Found at i:417851 original size:18 final size:17
Alignment explanation
Indices: 417828--417863 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
417818 ACATACATAC
417828 ATACATACATATATACAT
1 ATACATACATA-ATACAT
417846 ATACATACATAATACAT
1 ATACATACATAATACAT
417863 A
1 A
417864 AAATTTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (17 bp):
ATACATACATAATACAT
Found at i:418356 original size:104 final size:102
Alignment explanation
Indices: 418248--418480 Score: 303
Period size: 104 Copynumber: 2.3 Consensus size: 102
418238 AAATTCTCTT
* * *
418248 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATAC-AAATTTTGAATTTGATTCAC
1 AAAACAAACTTTGTCTCGCTTGAGACATTTTCCCTTTGAGAT-CTAAATTTCGAATTTGATTCAC
*
418312 -TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTCTTTC-
65 ATT-AAACAAAATTAATCTCA-CTTGAGATCGTT-TTC--TCA
* * *
418352 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCTAAATTTCGAATTTGTTTCACA
1 AAAACAAACTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATCTAAATTTCGAATTTGATTCACA
* *
418417 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TTAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
418454 AAAACAAACTTTGTCTCGCTTGAGACA
1 AAAACAAACTTTGTCTCGCTTGAGACA
418481 ATTGCTCTAA
Statistics
Matches: 114, Mismatches: 11, Indels: 10
0.84 0.08 0.07
Matches are distributed among these distances:
101 2 0.02
102 25 0.22
103 7 0.06
104 78 0.68
105 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (102 bp):
AAAACAAACTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATCTAAATTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:418493 original size:36 final size:34
Alignment explanation
Indices: 418453--418550 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 34
418443 TCGTTTTCTC
418453 AAAAACAAACTTTGTCTCGCTTGAGACAAT-TGCTCT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATAT-CT-T
** *
418489 AAAAACAAATTTTGTCTCATTTGAGACTATATCTT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCTT
*
418524 -AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTT-GTCTCGCTTGAGACA
418551 TCATTTTCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 3 0.06
34 19 0.37
35 1 0.02
36 28 0.54
37 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (34 bp):
AAAAACAAATTTGTCTCGCTTGAGACAATATCTT
Found at i:418862 original size:56 final size:55
Alignment explanation
Indices: 418800--418926 Score: 179
Period size: 56 Copynumber: 2.3 Consensus size: 55
418790 TTCTTTTGAG
418800 GAAAAAATCTTTGAGTTTGTTCCTCTTG-A-AAAAATCTTTGAGTT-TGTTCTTTTT
1 GAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTGT-TTC-TTTT
* *
418854 GAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAAATCTTTGAGTTGTTTCTTTT
1 G-A-AAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTGTTTCTTTT
418911 GAAAAAATCTTTGAGT
1 GAAAAAATCTTTGAGT
418927 CTATTTATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
54 1 0.02
55 14 0.22
56 25 0.38
57 6 0.09
58 18 0.28
59 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (55 bp):
GAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTGTTTCTTTT
Found at i:418871 original size:29 final size:27
Alignment explanation
Indices: 418800--418926 Score: 175
Period size: 29 Copynumber: 4.6 Consensus size: 27
418790 TTCTTTTGAG
*
418800 GAAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAATCTTTGAGTTTGTTCCTTTT
*
418827 GAAAAAATCTTTGAGTTTGTTCTTTTT
1 GAAAAAATCTTTGAGTTTGTTCCTTTT
*
418854 GAATAAAAATCTTGGAGTTTGTTCCTTTT
1 G-A-AAAAATCTTTGAGTTTGTTCCTTTT
*
418883 GAATAAAAATCTTTGAG-TTGTTTCTTTT
1 G-A-AAAAATCTTTGAGTTTGTTCCTTTT
418911 GAAAAAATCTTTGAGT
1 GAAAAAATCTTTGAGT
418927 CTATTTATTT
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
26 13 0.14
27 27 0.30
28 12 0.13
29 39 0.43
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (27 bp):
GAAAAAATCTTTGAGTTTGTTCCTTTT
Found at i:418937 original size:27 final size:27
Alignment explanation
Indices: 418800--418941 Score: 162
Period size: 27 Copynumber: 5.1 Consensus size: 27
418790 TTCTTTTGAG
* *
418800 GAAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAATCTTTGAGTTTGTTTCTTTT
418827 GAAAAAATCTTTGAGTTTG-TTCTTTTT
1 GAAAAAATCTTTGAGTTTGTTTC-TTTT
* *
418854 GAATAAAAATCTTGGAGTTTGTTCCTTTT
1 G-A-AAAAATCTTTGAGTTTGTTTCTTTT
418883 GAATAAAAATCTTTGAG-TTGTTTCTTTT
1 G-A-AAAAATCTTTGAGTTTGTTTCTTTT
* * *
418911 GAAAAAATCTTTGAGTCTATTTATTTT
1 GAAAAAATCTTTGAGTTTGTTTCTTTT
418938 GAAA
1 GAAA
418942 CGAAGTTTTG
Statistics
Matches: 101, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.15
27 36 0.36
28 12 0.12
29 36 0.36
30 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (27 bp):
GAAAAAATCTTTGAGTTTGTTTCTTTT
Found at i:419066 original size:30 final size:30
Alignment explanation
Indices: 419025--419093 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
419015 ACAATTTTGC
419025 GGAAA-AAAAATCTTTGAGAT-TGTTTCTTT
1 GGAAACAAAAATCTTTGAG-TCTGTTTCTTT
*
419054 TGAAACAAAAATCTTTGAGTCTGTTTCTTT
1 GGAAACAAAAATCTTTGAGTCTGTTTCTTT
419084 GGAAACAAAA
1 GGAAACAAAA
419094 TTTTGTCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (30 bp):
GGAAACAAAAATCTTTGAGTCTGTTTCTTT
Found at i:419496 original size:63 final size:63
Alignment explanation
Indices: 419370--419495 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
419360 GATGTGATCC
* *
419370 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
* * **
419433 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC-TCGAGACAACTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
419495 A
1 A
419496 AAAACATCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 21 0.37
63 36 0.63
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
Found at i:420137 original size:28 final size:28
Alignment explanation
Indices: 420066--420147 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
420056 TAAAAATATC
* * *
420066 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
**
420094 ATCTTTGGGTTTGTTTCT-TTCGAAACAA
1 ATCTTTGAATTTGTTTCTCTT-GAAACAA
420122 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
420148 CATAACTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 5 0.11
28 39 0.85
29 2 0.04
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.49
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:420312 original size:46 final size:45
Alignment explanation
Indices: 420206--420576 Score: 149
Period size: 46 Copynumber: 8.4 Consensus size: 45
420196 CATCCCCAGA
* * * * **
420206 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTTATCACCTTAGATGG
* * *
420249 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTTATCACC-TTAGATGG
* * *
420295 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC-CA-A---
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTTA-TCACCTTAGATGG
* * * **
420335 CCAGATCTCTTCATCACGTATGAGCCGTG---TCACCCTAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTTATCACCTTAGATGG
* * * *
420377 CCAG-CCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTTATCACC-TTAGATGG
* * * * *
420423 CCATAACTATTCATCACGTATGAGCCGTGTCATTC-CC--CGA---
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTTA-TCACCTTAGATGG
* * * **
420463 CCAGATCTCTTCACCACGTAGGAGCC--G-TATCACCCCTAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTTATCA-CCTTAGATGG
* * *
420506 CCAG-ACGTCCTCATCACGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGG
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTTATC-ACC-T--T--AGATGG
420557 CCAGAACTCTTCATCACGTA
1 CCAGAACTCTTCATCACGTA
420577 TGAGTAATGT
Statistics
Matches: 244, Mismatches: 47, Indels: 66
0.68 0.13 0.18
Matches are distributed among these distances:
36 4 0.02
37 3 0.01
38 4 0.02
39 1 0.00
40 51 0.21
41 1 0.00
42 24 0.10
43 50 0.20
44 1 0.00
45 9 0.04
46 67 0.27
47 6 0.02
49 1 0.00
51 20 0.08
52 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (45 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTTATCACCTTAGATGG
Found at i:420436 original size:128 final size:129
Alignment explanation
Indices: 420176--420761 Score: 764
Period size: 134 Copynumber: 4.5 Consensus size: 129
420166 CCAGCTGTCC
* * * *
420176 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
420241 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC-ACCTTTAGATGGCCAGAACTCT
65 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGACCTTTAGATGGCCAGAACTCT
* *
420305 TCATCACGTATGAGCCGTGTCATTCCCCAACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCA-TCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
* * * *
420369 CTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATC-ACCTTTAGATGGCCATAACTAT
65 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGACCTTTAGATGGCCAGAACTCT
* * *
420433 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCACCACGTAGGAGCCGTATCACCC
1 TCATCACGTATGAGCCGTGTCA-TCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
* * *
420498 CTAGATAACCAGACGTCCTCATCACGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAGAA
65 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGACCTT--T--AGATGGCCAGAA
420563 CTCT
126 CTCT
*** * * * *
420567 TCATCACGTATGAGTAATGTCATCCCTCGACCTGATCTCCTCATCACGTAGGAACTGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCC-CGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
* **
420632 ATAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGGCCAGAA
65 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCG----ACCTTTAGATGGCCAGAA
420697 CTCT
126 CTCT
* * * *
420701 TCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCTTCATCGCGTATGAGCAGTGTC
1 TCATCACGTATGAGCCGTGTCATCCCC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTC
420762 GTCCCCAACA
Statistics
Matches: 401, Mismatches: 43, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
128 120 0.30
129 91 0.23
130 9 0.02
132 1 0.00
133 5 0.01
134 172 0.43
138 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCA
TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGACCTTTAGATGGCCAGAACTCT
Found at i:420751 original size:40 final size:40
Alignment explanation
Indices: 420691--420767 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
420681 CTAAAGATGG
420691 CCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGA
1 CCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGA
* * *
420731 CCAGATCTCTTCATCGCGTATGAGCAGTGTCGTCCCC
1 CCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
420768 AACAACCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGA
Found at i:420939 original size:3 final size:3
Alignment explanation
Indices: 420931--420966 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
420921 TATTTTAATT
420931 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
420967 ATACAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:420949 original size:16 final size:16
Alignment explanation
Indices: 420930--420962 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
420920 TTATTTTAAT
420930 TTTATTATTATTATTA
1 TTTATTATTATTATTA
420946 TTTATTATTATTATTA
1 TTTATTATTATTATTA
420962 T
1 T
420963 ATTAATACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:424732 original size:190 final size:190
Alignment explanation
Indices: 424404--424748 Score: 530
Period size: 190 Copynumber: 1.8 Consensus size: 190
424394 AAAGATGATT
* * * *
424404 TTTAATTTGAATATTAATAGGATAATTACTCTTTTAATAAGTTAATTTAAAAAGGTATTTGTTAT
1 TTTAATTTGAATATTAATAGGATAATTACTCTTTGAATAAGTCAATTTAAAAAGATATTTATTAT
*
424469 ATTTTTAATTTTAAATATTAAAAGATAATTATATACTTTTATATATTTCAAATTAAAATAATATA
66 ATTTTTAACTTTAAATATTAAAAGATAATTATATACTTTTATATATTTCAAATTAAAATAATATA
*
424534 TGTTTAAGTTTGAATAGTAAAAGGAATTTACCTTTTGACCATTCTAAATTAAATATATTA
131 TATTTAAGTTTGAATAGTAAAAGGAATTTACCTTTTGACCATTCTAAATTAAATATATTA
* * **
424594 TTTAATTTGATTATTAGTAGGATAATTACTCTTTGAATGTGTCAATTTAAAAAGATATTTATTAT
1 TTTAATTTGAATATTAATAGGATAATTACTCTTTGAATAAGTCAATTTAAAAAGATATTTATTAT
* * * * *
424659 CTTTTTTAACTTTGAATGTT-AAAGATAATTATATACTTTTGTATGTTTCAAATTAAAATAATAT
66 -ATTTTTAACTTTAAATATTAAAAGATAATTATATACTTTTATATATTTCAAATTAAAATAATAT
*
424723 ATATTTAAGTTTGAATGGTAAAAGGA
130 ATATTTAAGTTTGAATAGTAAAAGGA
424749 GTTTTATCTT
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
190 123 0.89
191 15 0.11
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (190 bp):
TTTAATTTGAATATTAATAGGATAATTACTCTTTGAATAAGTCAATTTAAAAAGATATTTATTAT
ATTTTTAACTTTAAATATTAAAAGATAATTATATACTTTTATATATTTCAAATTAAAATAATATA
TATTTAAGTTTGAATAGTAAAAGGAATTTACCTTTTGACCATTCTAAATTAAATATATTA
Found at i:428234 original size:25 final size:25
Alignment explanation
Indices: 428187--428234 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
428177 TTTGAGTTGA
* *
428187 AAATAAAAATATATATTTTTAATCT
1 AAATAAAAATATATATCTATAATCT
428212 AAATAAAAAT-TAATATCTATAAT
1 AAATAAAAATAT-ATATCTATAAT
428235 AAAATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATAAAAATATATATCTATAATCT
Found at i:428663 original size:10 final size:10
Alignment explanation
Indices: 428648--428703 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
428638 TTAATAAATG
428648 AACGAACATA
1 AACGAACATA
**
428658 AACGAACACG
1 AACGAACATA
*
428668 AAC-ATAAATGA
1 AACGA-ACAT-A
428679 ACACGAACATA
1 A-ACGAACATA
428690 AACGAACATA
1 AACGAACATA
428700 AACG
1 AACG
428704 TTGGAGACCC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
9 1 0.03
10 26 0.72
11 3 0.08
12 5 0.14
13 1 0.03
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
AACGAACATA
Found at i:428670 original size:16 final size:16
Alignment explanation
Indices: 428649--428697 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
428639 TAATAAATGA
428649 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
428665 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
428681 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
428697 A
1 A
428698 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:430110 original size:16 final size:16
Alignment explanation
Indices: 430091--430123 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
430081 GTTTAAAAAA
430091 TAAAAATAA-AAAAACT
1 TAAAAA-AACAAAAACT
430107 TAAAAAAACAAAAACT
1 TAAAAAAACAAAAACT
430123 T
1 T
430124 TGAAAACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (16 bp):
TAAAAAAACAAAAACT
Found at i:430962 original size:14 final size:13
Alignment explanation
Indices: 430939--431050 Score: 50
Period size: 14 Copynumber: 9.2 Consensus size: 13
430929 ATATTTGATT
430939 TTAA-TTTTAATA
1 TTAATTTTTAATA
430951 TTAATGTTTTAA-A
1 TTAAT-TTTTAATA
* *
430964 -TAA-ATTAAATA
1 TTAATTTTTAATA
430975 TTAATTTTTTAATA
1 TTAA-TTTTTAATA
*
430989 TT-ATATTATAGATA
1 TTAAT-TTTTA-ATA
*
431003 TTAA-TATTAAT-
1 TTAATTTTTAATA
431014 TT--TTTTTAA-A
1 TTAATTTTTAATA
* *
431024 -TAA-ATTAAATA
1 TTAATTTTTAATA
431035 TTAATTTTTAATA
1 TTAATTTTTAATA
431048 TTA
1 TTA
431051 TATTATAGAT
Statistics
Matches: 72, Mismatches: 12, Indels: 31
0.63 0.10 0.27
Matches are distributed among these distances:
9 1 0.01
10 13 0.18
11 4 0.06
12 16 0.22
13 18 0.25
14 19 0.26
15 1 0.01
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TTAATTTTTAATA
Found at i:431014 original size:34 final size:34
Alignment explanation
Indices: 430967--431063 Score: 122
Period size: 26 Copynumber: 3.1 Consensus size: 34
430957 TTTTAAATAA
430967 ATTAAATATTAATTTTTTAATATTATATTATAGAT
1 ATTAAATATTAA-TTTTTAATATTATATTATAGAT
431002 ATT-AATATTAATTTTT--T-TTA-A--ATA-A-
1 ATTAAATATTAATTTTTAATATTATATTATAGAT
431027 ATTAAATATTAATTTTTAATATTATATTATAGAT
1 ATTAAATATTAATTTTTAATATTATATTATAGAT
431061 ATT
1 ATT
431064 TAATTTTATA
Statistics
Matches: 53, Mismatches: 0, Indels: 19
0.74 0.00 0.26
Matches are distributed among these distances:
25 3 0.06
26 14 0.26
27 3 0.06
28 1 0.02
29 4 0.08
30 4 0.08
31 1 0.02
32 3 0.06
33 6 0.11
34 11 0.21
35 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (34 bp):
ATTAAATATTAATTTTTAATATTATATTATAGAT
Found at i:431022 original size:60 final size:57
Alignment explanation
Indices: 430945--431063 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 57
430935 GATTTTAATT
430945 TTAATATTAATGTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
1 TTAATATTAATGTTTTAAATAAATTAAATATTAA-TTTTTAATATTATATTATAGATA
*
431003 TTAATATTAATTTTTTTTAAATAAATTAAATATTAATTTTTAATATTATATTATAGATA
1 TTAATATTAA--TGTTTTAAATAAATTAAATATTAATTTTTAATATTATATTATAGATA
431062 TT
1 TT
431064 TAATTTTATA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
58 10 0.17
59 25 0.43
60 23 0.40
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (57 bp):
TTAATATTAATGTTTTAAATAAATTAAATATTAATTTTTAATATTATATTATAGATA
Found at i:431055 original size:64 final size:65
Alignment explanation
Indices: 430915--431057 Score: 199
Period size: 60 Copynumber: 2.3 Consensus size: 65
430905 AGGTTTTATA
* * *
430915 TTTAATTTTATATTATATTTGATTTTAATTTTAATATTAATGTTTTAAATAAATTAAATATTAAT
1 TTTAATATTATATTATATTTGATATTAATATTAATATT-ATGTTTTAAATAAATTAAATATTAA-
430980 TT
64 TT
430982 TTTAATATTATATTATA---GATATTAATATTAAT-TT-T-TTTTAAATAAATTAAATATTAATT
1 TTTAATATTATATTATATTTGATATTAATATTAATATTATGTTTTAAATAAATTAAATATTAATT
431041 TTTAATATTATATTATA
1 TTTAATATTATATTATA
431058 GATATTTAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
59 19 0.26
60 22 0.30
61 1 0.01
63 2 0.03
64 13 0.18
67 16 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (65 bp):
TTTAATATTATATTATATTTGATATTAATATTAATATTATGTTTTAAATAAATTAAATATTAATT
Found at i:431067 original size:60 final size:59
Alignment explanation
Indices: 430944--431067 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 59
430934 TGATTTTAAT
430944 TTTAATATTAATGTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
1 TTTAATATTAATGTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
*
431003 -TTAATATTAATTTTTTTTAAATAAATTAAATATTAA-TTTTTAATATTATATTATAGATA
1 TTTAATATTAA--TGTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
431062 TTTAAT
1 TTTAAT
431068 TTTATATCAT
Statistics
Matches: 61, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
58 10 0.16
59 23 0.38
60 28 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (59 bp):
TTTAATATTAATGTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
Found at i:431097 original size:60 final size:60
Alignment explanation
Indices: 430960--431083 Score: 180
Period size: 59 Copynumber: 2.1 Consensus size: 60
430950 ATTAATGTTT
* ** *
430960 TAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTAATATTAATTTTTTT
1 TAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTAATATTAATATCATA
*
431020 TAAATAAATTAAATATTAA-TTTTTAATATTATATTATAGATATTTAAT-TTTATATCATA
1 TAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA-TTAATATTAATATCATA
431079 TAAAT
1 TAAAT
431084 TATTTTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
59 34 0.59
60 24 0.41
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (60 bp):
TAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTAATATTAATATCATA
Found at i:431126 original size:20 final size:19
Alignment explanation
Indices: 431066--431127 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
431056 TAGATATTTA
*
431066 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
431085 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
431103 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
431123 ATTTT
1 ATTTT
431128 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:431739 original size:8 final size:9
Alignment explanation
Indices: 431714--431746 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
431704 GAATTTGGTT
431714 AATTAACCG
1 AATTAACCG
431723 AATTAACCG
1 AATTAACCG
431732 AA-TAACCG
1 AATTAACCG
431740 AAATTAA
1 -AATTAA
431747 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.27
9 13 0.59
10 3 0.14
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:432117 original size:21 final size:20
Alignment explanation
Indices: 432074--432117 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
432064 TTTTATTTTA
*
432074 TAATTATATATTATTTAAAT
1 TAATTATAAATTATTTAAAT
* *
432094 TAATTATAAACTTTTTTGAAT
1 TAATTATAAA-TTATTTAAAT
432115 TAA
1 TAA
432118 AAAATATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTATAAATTATTTAAAT
Found at i:432118 original size:184 final size:183
Alignment explanation
Indices: 431752--432138 Score: 636
Period size: 184 Copynumber: 2.1 Consensus size: 183
431742 ATTAAATTTT
* *
431752 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAAAATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
* * *
431817 TTTAAGATCCAATAACTTTTAAACTTAAATTAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAAATCCAATAACTTTTAAACTTAAATAAATATTAATTAATTAAAAAATTATATAAAATTTT
* *
431882 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTGAATTAAA
431935 AAATATTAAATATATTATATATAAAAATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAAT
1 AAATATTAAATATATTATATAT-AAAATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAAT
*
431999 AATTTAAAATCCAATAACTTTTAAACTTAAATAAATATTAATTAATTAAAAAATTTATCTAAAAT
64 AATTTAAAATCCAATAACTTTTAAACTTAAATAAATATTAATTAATTAAAAAA-TTATATAAAAT
432064 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTGAATTAAA
128 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTGAATTAAA
* *
432119 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
432139 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
183 32 0.17
184 109 0.57
185 50 0.26
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAAAATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAAATCCAATAACTTTTAAACTTAAATAAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTGAATTAAA
Found at i:432395 original size:31 final size:31
Alignment explanation
Indices: 432358--432417 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
432348 TAGTTGTATG
* *
432358 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
432389 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
432418 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:441264 original size:14 final size:14
Alignment explanation
Indices: 441247--441284 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
441237 TAGGAAATAT
*
441247 AATTTATTTTACGG
1 AATTTATTTTACGA
*
441261 AATTTATTTTTCGA
1 AATTTATTTTACGA
441275 AATTTATTTT
1 AATTTATTTT
441285 CCGTGAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (14 bp):
AATTTATTTTACGA
Found at i:441460 original size:22 final size:22
Alignment explanation
Indices: 441435--441481 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
441425 ACAGTAGCAT
441435 CAGCTACCAAAAGATAAACCAG
1 CAGCTACCAAAAGATAAACCAG
441457 CAGCTACCAAAAGATAAACCAG
1 CAGCTACCAAAAGATAAACCAG
441479 CAG
1 CAG
441482 TAGGTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.28, G:0.15, T:0.09
Consensus pattern (22 bp):
CAGCTACCAAAAGATAAACCAG
Found at i:443700 original size:25 final size:26
Alignment explanation
Indices: 443671--443724 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
443661 ACAAAGTACG
443671 AAAAA-TATATATATATAAAATAAATA
1 AAAAAGTATATATATA-AAAATAAATA
*
443697 AAAAAGTATATATATAAAAATTAATA
1 AAAAAGTATATATATAAAAATAAATA
443723 AA
1 AA
443725 TTAAATGACG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAAAGTATATATATAAAAATAAATA
Found at i:443701 original size:27 final size:26
Alignment explanation
Indices: 443605--443724 Score: 84
Period size: 27 Copynumber: 4.5 Consensus size: 26
443595 TAGTAAGTAG
*
443605 AAAAATAATAATAATAAAATATATATAT
1 AAAAAT-A-AATAAAAAAATATATATAT
* * * *
443633 AAAAA-AAGA-AAATAAATA-AAACAA
1 AAAAATAA-ATAAAAAAATATATATAT
* *
443657 AAAAACAAAGTACGAAAAATATATATAT
1 AAAAATAAA-TA-AAAAAATATATATAT
*
443685 ATAAAATAAATAAAAAAGTATATATAT
1 A-AAAATAAATAAAAAAATATATATAT
*
443712 AAAAATTAATAAA
1 AAAAATAAATAAA
443725 TTAAATGACG
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
24 9 0.13
25 10 0.14
26 14 0.20
27 20 0.28
28 11 0.15
29 7 0.10
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (26 bp):
AAAAATAAATAAAAAAATATATATAT
Found at i:444008 original size:2 final size:2
Alignment explanation
Indices: 443958--443994 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
443948 CTTGTGTAGA
443958 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
443995 ATAAAAAATA
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:444049 original size:10 final size:10
Alignment explanation
Indices: 443992--444063 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
443982 ATATATATAT
443992 ATAATAAAAA
1 ATAATAAAAA
*
444002 AT-ATATAAA
1 ATAATAAAAA
* *
444011 ATAATATAAT
1 ATAATAAAAA
* *
444021 ATAATATAAT
1 ATAATAAAAA
444031 A-AAT-AAAA
1 ATAATAAAAA
444039 ATAATAAAAA
1 ATAATAAAAA
444049 ATTAATAGAAAA
1 A-TAATA-AAAA
444061 ATA
1 ATA
444064 TATGTATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
8 3 0.06
9 14 0.26
10 24 0.45
11 7 0.13
12 5 0.09
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:444210 original size:12 final size:11
Alignment explanation
Indices: 444182--444222 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
444172 TAACAAAATA
* *
444182 AATAATATAAA
1 AATAATACAAG
444193 AATAATACAAG
1 AATAATACAAG
444204 TAATAATACAAG
1 -AATAATACAAG
444216 AATAATA
1 AATAATA
444223 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:444327 original size:12 final size:12
Alignment explanation
Indices: 444305--444343 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
444295 GAATAAAAGG
444305 AAAATATAATAGT
1 AAAA-ATAATAGT
*
444318 AAAAATAATAAT
1 AAAAATAATAGT
*
444330 AAATATAATAGT
1 AAAAATAATAGT
444342 AA
1 AA
444344 TAAAAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:444951 original size:37 final size:37
Alignment explanation
Indices: 444910--445006 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
444900 GGATCATATC
*
444910 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
* * *
444947 TTTAGGAGTTTAAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
*
444984 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTAAATCCTAGTAG
445007 GACAAAAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
Found at i:446085 original size:106 final size:106
Alignment explanation
Indices: 445738--447324 Score: 2305
Period size: 106 Copynumber: 15.0 Consensus size: 106
445728 ACATTGTTCT
* * ** * *
445738 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * *
445802 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
445844 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
445903 TCAGCCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
445945 G-GTTCAAGATCCTTCGCTGAGAAGTTGAATTTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
446009 CCAGCGGTCCCTTCTTCGTTAAGTTGAACTTGCGTTATCAT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
** ** *
446050 GAGTCCAATATCCTAAGCTACGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
446115 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
446156 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
446221 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
446262 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
446327 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
446368 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
446433 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
446474 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
446539 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
446580 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
446645 CCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
446686 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
446751 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
446792 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** * * **
446857 CCAGTAGTCCCTTCGTTGTGAAGTTGAACCTATGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
446898 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGATCTGAAATTAGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
446963 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
447004 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
447069 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
447110 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
447175 CCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
447216 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** * * * *
447280 CCAGCCATCCCTTCGTTGTGAAGTCGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
447321 GAGT
1 GAGT
447325 GGCACGATAT
Statistics
Matches: 1341, Mismatches: 128, Indels: 25
0.90 0.09 0.02
Matches are distributed among these distances:
99 2 0.00
100 75 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 52 0.04
106 1197 0.89
107 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:448827 original size:14 final size:13
Alignment explanation
Indices: 448810--448863 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 13
448800 TTCTTTTTGA
448810 TTTTTGTTATTTCT
1 TTTTTGTT-TTTCT
*
448824 TTTTTGTTCTTCTT
1 TTTTTGTTTTTC-T
448838 TTTTTGTTCTTTTCT
1 TTTTTG-T-TTTTCT
448853 TTTTTGTTTTT
1 TTTTTGTTTTT
448864 GCCCTTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 7 0.20
14 16 0.46
15 8 0.23
16 4 0.11
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.81
Consensus pattern (13 bp):
TTTTTGTTTTTCT
Found at i:448862 original size:7 final size:7
Alignment explanation
Indices: 448803--448863 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
448793 TCCCTTTTTC
*
448803 TTTTTGA
1 TTTTTGT
448810 TTTTTGT
1 TTTTTGT
* *
448817 TATTTCT
1 TTTTTGT
448824 TTTTTGT
1 TTTTTGT
*
448831 TCTTCT-T
1 T-TTTTGT
448838 TTTTTGT
1 TTTTTGT
*
448845 TCTTTTCT
1 T-TTTTGT
448853 TTTTTGT
1 TTTTTGT
448860 TTTT
1 TTTT
448864 GCCCTTTTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
6 3 0.07
7 30 0.71
8 9 0.21
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.80
Consensus pattern (7 bp):
TTTTTGT
Found at i:462434 original size:29 final size:29
Alignment explanation
Indices: 462376--462431 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
462366 TAAGAAAGAG
* *
462376 CAGGAGAAGGTAATCTATTTATTATGTTA
1 CAGGAGAAGGTAATCTATTCATAATGTTA
462405 CAGGAGAAGGTAATCTATTCA-AATGTT
1 CAGGAGAAGGTAATCTATTCATAATGTT
462432 TACCAAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (29 bp):
CAGGAGAAGGTAATCTATTCATAATGTTA
Found at i:466425 original size:32 final size:32
Alignment explanation
Indices: 466384--466450 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
466374 TACTAGGTTT
466384 TTCAACCTGCATACTAGGTTTTTCTTGTCTTC
1 TTCAACCTGCATACTAGGTTTTTCTTGTCTTC
466416 TTCAACCTGCATACTAGGTTTTTCTTGTCTTC
1 TTCAACCTGCATACTAGGTTTTTCTTGTCTTC
466448 TTC
1 TTC
466451 TATGAAGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.48
Consensus pattern (32 bp):
TTCAACCTGCATACTAGGTTTTTCTTGTCTTC
Found at i:486477 original size:15 final size:15
Alignment explanation
Indices: 486449--486481 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
486439 GCTACAAGCT
486449 AACAAACTATTCTAG
1 AACAAACTATTCTAG
486464 AACAACACTA-TCTAG
1 AACAA-ACTATTCTAG
486479 AAC
1 AAC
486482 TCACAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.21
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:491781 original size:16 final size:15
Alignment explanation
Indices: 491755--491788 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
491745 GCTACAAGCT
491755 AACAAACTATTCTAG
1 AACAAACTATTCTAG
491770 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
491786 AAC
1 AAC
491789 TCACAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:496560 original size:163 final size:163
Alignment explanation
Indices: 496374--496668 Score: 418
Period size: 163 Copynumber: 1.8 Consensus size: 163
496364 ATTTAATATT
* ** * *
496374 TTTTATATTTTAATATTAATTAGGTGATGATACATGTAAATCTT-AAAATATAAAAATATTATTG
1 TTTTATATTTTAATATCAATTAGGCAATGATACATCTAAAT-TTAAAAATATAAAAATATTATTA
*
496438 CAAATCTTAGATTTGATATTTATT-TA-T-TTTTTATAATTTCATTTTTTGTAGTTTAAAATTAA
65 CAAAT-TTAGATTTAATATTT-TTATACTATTTTTATAATTTCATTTTTT-TAGTTTAAAATTAA
496500 ATATTTTATAATATTTTTAATATTTTAAAACTTAAGA
127 ATATTTTATAATATTTTTAATATTTTAAAACTTAAGA
* * *
496537 TTTTATATTTTAATATCAATTAGGCAATGATACTTCTAAATTTAAAAATTTAAAAATATTATTAT
1 TTTTATATTTTAATATCAATTAGGCAATGATACATCTAAATTTAAAAATATAAAAATATTATTAC
* *
496602 AAATTTAGATTTAATATTTTTATACTTATTTTTATAATTTCATTTTTTTATTTTAAAATTAAGTA
66 AAATTTAGATTTAATATTTTTATAC-TATTTTTATAATTTCATTTTTTTAGTTTAAAATTAAATA
496667 TT
130 TT
496669 AAATTTAATA
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
161 2 0.02
162 18 0.16
163 58 0.50
164 18 0.16
165 20 0.17
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (163 bp):
TTTTATATTTTAATATCAATTAGGCAATGATACATCTAAATTTAAAAATATAAAAATATTATTAC
AAATTTAGATTTAATATTTTTATACTATTTTTATAATTTCATTTTTTTAGTTTAAAATTAAATAT
TTTATAATATTTTTAATATTTTAAAACTTAAGA
Found at i:505123 original size:30 final size:28
Alignment explanation
Indices: 505067--505133 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
505057 TCACTGATCT
505067 TTTAATTTTATCAATCAACTATCTAACTA
1 TTTAATTTTATCAATCAACTATCTAAC-A
* *
505096 TTTAATTATTATCAATTAAGTCA-CTAACA
1 TTTAATT-TTATCAATCAACT-ATCTAACA
*
505125 ATTAATTTT
1 TTTAATTTT
505134 TCTTTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 14 0.42
30 16 0.48
31 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.46
Consensus pattern (28 bp):
TTTAATTTTATCAATCAACTATCTAACA
Found at i:505144 original size:70 final size:70
Alignment explanation
Indices: 505064--505204 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
505054 TTGTCACTGA
505064 TCTTTTAATTTTATCAATCAACTATCTAACTATTTAATTATTATCAATTAAGTCACTAACAATTA
1 TCTTTTAATTTTATCAATCAACTATCTAACTATTTAATTATTATCAATTAAGTCACTAACAATTA
505129 ATTTT
66 ATTTT
* *
505134 TCTTTTAATTTTATCAATCAACTATCTAATTATTTAATTATTATCAATTAAGTCACTAATAATTA
1 TCTTTTAATTTTATCAATCAACTATCTAACTATTTAATTATTATCAATTAAGTCACTAACAATTA
505199 ATTTT
66 ATTTT
505204 T
1 T
505205 TTGATAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (70 bp):
TCTTTTAATTTTATCAATCAACTATCTAACTATTTAATTATTATCAATTAAGTCACTAACAATTA
ATTTT
Found at i:505193 original size:30 final size:28
Alignment explanation
Indices: 505137--505203 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
505127 TAATTTTTCT
505137 TTTAATTTTATCAATCAACTATCTAATTA
1 TTTAATTTTATCAATCAACTATCTAA-TA
* *
505166 TTTAATTATTATCAATTAAGTCA-CTAATA
1 TTTAATT-TTATCAATCAACT-ATCTAATA
*
505195 ATTAATTTT
1 TTTAATTTT
505204 TTTGATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 15 0.45
30 15 0.45
31 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (28 bp):
TTTAATTTTATCAATCAACTATCTAATA
Found at i:508742 original size:17 final size:15
Alignment explanation
Indices: 508708--508916 Score: 51
Period size: 15 Copynumber: 13.2 Consensus size: 15
508698 AATTGAAAAA
508708 ATATAATATATATAT
1 ATATAATATATATAT
*
508723 ATATAATATAAGTTTAT
1 ATATAATAT-A-TATAT
*
508740 ATATAAACTATATTTAT
1 ATAT-AA-TATATATAT
*
508757 ATTATAA-ACGATATAATT
1 A-TATAATA-TATAT-A-T
508775 ATTATAAGT-TATATAT
1 A-TATAA-TATATATAT
* *
508791 ATA-AAT-TATGTTT
1 ATATAATATATATAT
*
508804 ATATGAACTATATATAA
1 ATAT-AA-TATATATAT
* *
508821 ACTAT-ATATGTAAACT
1 A-TATAATATATATA-T
*
508837 ATAT-ATATATAAACT
1 ATATAATATATATA-T
*
508852 ATA-AAAAGTATATAGT
1 ATATAATA-TATATA-T
* *
508868 TTATAA-ACTATAATTT
1 ATATAATA-TAT-ATAT
508884 ATATTAATATAGTATAT
1 ATA-TAATATA-TATAT
508901 ATAT-ATATAT-TAT
1 ATATAATATATATAT
508914 ATA
1 ATA
508917 AAGTGAGTGG
Statistics
Matches: 150, Mismatches: 21, Indels: 48
0.68 0.10 0.22
Matches are distributed among these distances:
13 15 0.10
14 3 0.02
15 43 0.29
16 25 0.17
17 38 0.25
18 23 0.15
19 3 0.02
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.44
Consensus pattern (15 bp):
ATATAATATATATAT
Found at i:508771 original size:20 final size:17
Alignment explanation
Indices: 508713--508770 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
508703 AAAAAATATA
*
508713 ATATATATATATATAA-T
1 ATATTTATATATA-AACT
508730 ATAAGTTTATATATAAACT
1 AT-A-TTTATATATAAACT
*
508749 ATATTTATATTATAAACG
1 ATATTTATA-TATAAACT
508767 ATAT
1 ATAT
508771 AATTATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 8 0.23
18 15 0.43
19 12 0.34
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATTTATATATAAACT
Found at i:508776 original size:20 final size:17
Alignment explanation
Indices: 508718--508781 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 17
508708 ATATAATATA
508718 TATATATATAA-TATAAGTT
1 TATATATA-AACTATAA--T
*
508737 TATATATAAACTATATT
1 TATATATAAACTATAAT
508754 TATATTATAAACGATATAAT
1 TATA-TATAAAC--TATAAT
508774 TAT-TATAA
1 TATATATAA
508782 GTTATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.13
18 14 0.36
19 12 0.31
20 8 0.21
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TATATATAAACTATAAT
Found at i:508854 original size:11 final size:11
Alignment explanation
Indices: 508803--508843 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
508793 AAATTATGTT
*
508803 TATATGAACTA
1 TATATAAACTA
508814 TATATAAACTA
1 TATATAAACTA
508825 TATATGTAAACTA
1 TATA--TAAACTA
508838 TATATA
1 TATATA
508844 TATAAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 16 0.59
13 11 0.41
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (11 bp):
TATATAAACTA
Found at i:508863 original size:24 final size:25
Alignment explanation
Indices: 508812--508881 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 25
508802 TTATATGAAC
508812 TATATATAAACTATATATGTAAACTATA
1 TATATATAAACTATA-A--TAAACTATA
*
508840 TATATATAAACTATAA-AAAGTATA
1 TATATATAAACTATAATAAACTATA
*
508864 TAGTTTATAAACTATAAT
1 TA-TATATAAACTATAAT
508882 TTATATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 9 0.24
25 13 0.34
27 1 0.03
28 15 0.39
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (25 bp):
TATATATAAACTATAATAAACTATA
Found at i:509038 original size:46 final size:46
Alignment explanation
Indices: 508985--509078 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 46
508975 TTATTTTATT
** *
508985 TTGAGAATTTATTGGGAAATTGGAAAATTTTGAT-AATATAGAAAAA
1 TTGAGAATTTAGAGGGAAATTGGAAAATTTAGATGAA-ATAGAAAAA
* *
509031 TTGAGAATTTAGAGGGAAATTGGGAAATTTAGATGGAATAGAAAAA
1 TTGAGAATTTAGAGGGAAATTGGAAAATTTAGATGAAATAGAAAAA
509077 TT
1 TT
509079 TGGAGGGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 41 0.98
47 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (46 bp):
TTGAGAATTTAGAGGGAAATTGGAAAATTTAGATGAAATAGAAAAA
Found at i:509050 original size:19 final size:19
Alignment explanation
Indices: 509028--509097 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
509018 TAATATAGAA
509028 AAATTGAGAATTTAGAGGG
1 AAATTGAGAATTTAGAGGG
* *
509047 AAATTGGGAAATTTAGATGG
1 AAATTGAG-AATTTAGAGGG
* * *
509067 -AATAGAAAAATTTGGAGGG
1 AAATTG-AGAATTTAGAGGG
509086 AAATTGAGAATT
1 AAATTGAGAATT
509098 GAAATTTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 25 0.64
20 14 0.36
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (19 bp):
AAATTGAGAATTTAGAGGG
Found at i:509061 original size:20 final size:20
Alignment explanation
Indices: 509036--509092 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
509026 AAAAATTGAG
**
509036 AATTTAGAGGGAAATTGGGA
1 AATTTAGAGGGAAATTGAAA
* *
509056 AATTTAGATGG-AATAGAAA
1 AATTTAGAGGGAAATTGAAA
*
509075 AATTTGGAGGGAAATTGA
1 AATTTAGAGGGAAATTGA
509093 GAATTGAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (20 bp):
AATTTAGAGGGAAATTGAAA
Found at i:509347 original size:6 final size:6
Alignment explanation
Indices: 509333--509383 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
509323 GCGTACGCGT
509333 GTGTCGC GTGTGC GTGTGC GTGTGC GTGT-- GT-TGC GTGTGC GTGTGC
1 GTGT-GC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
509379 GTGTG
1 GTGTG
509384 TGTAAACTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
3 1 0.02
4 2 0.05
5 2 0.05
6 32 0.78
7 4 0.10
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
GTGTGC
Found at i:509353 original size:21 final size:20
Alignment explanation
Indices: 509329--509385 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
509319 GCGCGCGTAC
*
509329 GCGTGTGTCGCGTGTGCGTGT
1 GCGTGTG-CGTGTGTGCGTGT
509350 GCGTGTGCGTGTGTTGCGTGT
1 GCGTGTGCGTGTG-TGCGTGT
509371 GCGTGTGCGTGTGTG
1 GCGTGTGCGTGTGTG
509386 TAAACTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (20 bp):
GCGTGTGCGTGTGTGCGTGT
Found at i:509353 original size:27 final size:27
Alignment explanation
Indices: 509323--509380 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
509313 GCGCGTGCGC
509323 GCGTACGCGTGTGTCGCGTGTGCGTGT
1 GCGTACGCGTGTGTCGCGTGTGCGTGT
** *
509350 GCGTGTGCGTGTGTTGCGTGTGCGTGT
1 GCGTACGCGTGTGTCGCGTGTGCGTGT
509377 GCGT
1 GCGT
509381 GTGTGTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.02, C:0.19, G:0.47, T:0.33
Consensus pattern (27 bp):
GCGTACGCGTGTGTCGCGTGTGCGTGT
Found at i:509381 original size:27 final size:27
Alignment explanation
Indices: 509329--509383 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
509319 GCGCGCGTAC
509329 GCGTGTGTCGCGTGTGCGTGTGCGTGT
1 GCGTGTGTCGCGTGTGCGTGTGCGTGT
*
509356 GCGTGTGTTGCGTGTGCGTGTGCGTGT
1 GCGTGTGTCGCGTGTGCGTGTGCGTGT
509383 G
1 G
509384 TGTAAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (27 bp):
GCGTGTGTCGCGTGTGCGTGTGCGTGT
Found at i:509473 original size:17 final size:17
Alignment explanation
Indices: 509453--509495 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
509443 ATGTATGTAT
509453 AACTA-ATATAAGTAATA
1 AACTATATA-AAGTAATA
509470 AACTATATAAAGTAATA
1 AACTATATAAAGTAATA
*
509487 AAGTATATA
1 AACTATATA
509496 GTTTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (17 bp):
AACTATATAAAGTAATA
Found at i:509548 original size:14 final size:14
Alignment explanation
Indices: 509504--509538 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
509494 TAGTTTATAA
* *
509504 AAACTCTAAACCCT
1 AAACTATAAACACT
509518 AAACTATAAACACT
1 AAACTATAAACACT
509532 AAACTAT
1 AAACTAT
509539 GAACTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACTATAAACACT
Found at i:509562 original size:14 final size:14
Alignment explanation
Indices: 509516--509563 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
509506 ACTCTAAACC
*
509516 CTAAACTATAAACA
1 CTAAACTATGAACA
*
509530 CTAAACTATGAACT
1 CTAAACTATGAACA
*
509544 TTAAA-TCATGAACA
1 CTAAACT-ATGAACA
509558 CTAAAC
1 CTAAAC
509564 CTTAAACCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 1 0.04
14 26 0.96
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.25
Consensus pattern (14 bp):
CTAAACTATGAACA
Found at i:510071 original size:14 final size:14
Alignment explanation
Indices: 510052--510104 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
510042 ATTGAAACCT
*
510052 TAAACCCTAAATCA
1 TAAACCTTAAATCA
510066 TAAACCTTAAATCA
1 TAAACCTTAAATCA
* *
510080 TAAACTTTAAACCA
1 TAAACCTTAAATCA
510094 TAAACACTTAA
1 TAAAC-CTTAA
510105 CACTAAACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 30 0.88
15 4 0.12
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCTTAAATCA
Found at i:510072 original size:21 final size:20
Alignment explanation
Indices: 510046--510124 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 20
510036 TAGTTTATTG
*
510046 AAACCTTAAACCCTAAATCAT
1 AAACCATAAACCCTAAA-CAT
* * * *
510067 AAACCTTAAATCATAAACTTT
1 AAACCATAAACCCTAAAC-AT
* *
510088 AAACCATAAACACTTAACACT
1 AAACCATAAACCCTAAACA-T
510109 AAACCATAAACCCTAA
1 AAACCATAAACCCTAA
510125 TATAAATAGA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.23
Consensus pattern (20 bp):
AAACCATAAACCCTAAACAT
Found at i:510124 original size:14 final size:14
Alignment explanation
Indices: 510046--510120 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 14
510036 TAGTTTATTG
*
510046 AAACCTTAAACCCT
1 AAACCATAAACCCT
* *
510060 AAATCATAAACCTT
1 AAACCATAAACCCT
* **
510074 AAATCATAAACTTT
1 AAACCATAAACCCT
*
510088 AAACCATAAACACT
1 AAACCATAAACCCT
* *
510102 TAA-CACTAAACCAT
1 AAACCA-TAAACCCT
510116 AAACC
1 AAACC
510121 CTAATATAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
13 2 0.04
14 45 0.94
15 1 0.02
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:513705 original size:35 final size:34
Alignment explanation
Indices: 513620--513706 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
513610 ATTTGATATT
*
513620 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
513654 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
513692 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
513707 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:515956 original size:111 final size:111
Alignment explanation
Indices: 515819--516040 Score: 365
Period size: 111 Copynumber: 2.0 Consensus size: 111
515809 ATTACAAAAA
* *
515819 TTAATTCTTAATCTAATAATCATGCAT-TAAATGAATCAACTAATTATTACTAATAATTTAAATT
1 TTAATTCTTAATCTAATAATCATGCATAT-AATAAATCAACTAAATATTACTAATAATTTAAATT
* ** * *
515883 AAATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
65 AAATTAAAACATTAAAATACTACCGTATCAGCAAAGTGTAGAGATAT
515930 TTAATTCTTAATCTAATAATCATGCATATAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATATAATAAATCAACTAAATATTACTAATAATTTAAATTA
515995 AATTAAAACATTAAAATACTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATACTACCGTATCAGCAAAGTGTAGAGATAT
516041 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 102 0.99
112 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATATAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATACTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:516183 original size:10 final size:10
Alignment explanation
Indices: 516164--516194 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
516154 ATCTTAAAAA
*
516164 GAGAGTATTT
1 GAGAGAATTT
516174 GAGAGAATTT
1 GAGAGAATTT
516184 GAGAGAATTT
1 GAGAGAATTT
516194 G
1 G
516195 GTGTGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:516436 original size:29 final size:29
Alignment explanation
Indices: 516402--516471 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
516392 TTCTGCTAAG
*
516402 GGTGTTAGATCGGGAAATATATTCTGACC
1 GGTGTTAGATCGGGAAATATAGTCTGACC
*
516431 GGTGTTAGATCAGGAAATATAGTCTGACC
1 GGTGTTAGATCGGGAAATATAGTCTGACC
516460 GGTGTTAGATCG
1 GGTGTTAGATCG
516472 ATAATAATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAGTCTGACC
Found at i:517889 original size:31 final size:31
Alignment explanation
Indices: 517854--517918 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
517844 TGATTTTTTT
* *
517854 TTACAAATAGATAACGTTAGTGATCAATTTG
1 TTACAAATAGATAACATTAGTGACCAATTTG
517885 TTACAAATAGATAACATTAGTGACCAATTTG
1 TTACAAATAGATAACATTAGTGACCAATTTG
517916 TTA
1 TTA
517919 TTTTTGAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (31 bp):
TTACAAATAGATAACATTAGTGACCAATTTG
Found at i:518348 original size:41 final size:40
Alignment explanation
Indices: 518302--518380 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
518292 TATTATTAAC
*
518302 ATTCAAAGACTAAAATAATTAGGTTAAATATTTTAAAATAT
1 ATTC-AAGACTAAAATAATTAGGTTAAATATTTAAAAATAT
** *
518343 ATTCAAGTGTAAAATAATTAGGTTAACTATTTAAAAAT
1 ATTCAAGACTAAAATAATTAGGTTAAATATTTAAAAAT
518381 CAAATTATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (40 bp):
ATTCAAGACTAAAATAATTAGGTTAAATATTTAAAAATAT
Found at i:525242 original size:9 final size:9
Alignment explanation
Indices: 525230--525278 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
525220 GGACGATGAT
525230 GACGACAAC
1 GACGACAAC
*
525239 GACGACGAC
1 GACGACAAC
525248 GACGACAAC
1 GACGACAAC
*
525257 GACGACGAC
1 GACGACAAC
*
525266 GACGACAAT
1 GACGACAAC
525275 GACG
1 GACG
525279 GTGATGATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.39, C:0.31, G:0.29, T:0.02
Consensus pattern (9 bp):
GACGACAAC
Found at i:525243 original size:3 final size:3
Alignment explanation
Indices: 525230--525271 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
525220 GGACGATGAT
* *
525230 GAC GAC AAC GAC GAC GAC GAC GAC AAC GAC GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
525272 AATGACGGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.38, C:0.33, G:0.29, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:525251 original size:18 final size:18
Alignment explanation
Indices: 525230--525278 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
525220 GGACGATGAT
525230 GACGACAACGACGACGAC
1 GACGACAACGACGACGAC
525248 GACGACAACGACGACGAC
1 GACGACAACGACGACGAC
*
525266 GACGACAATGACG
1 GACGACAACGACG
525279 GTGATGATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.39, C:0.31, G:0.29, T:0.02
Consensus pattern (18 bp):
GACGACAACGACGACGAC
Found at i:530340 original size:134 final size:132
Alignment explanation
Indices: 530191--530440 Score: 351
Period size: 134 Copynumber: 1.9 Consensus size: 132
530181 AAGTAAAAAA
* **
530191 ATATAAAATCATTAATAAAAATTTTAAAATTATTACTCAAA-TTAAAAAAATTAATTTAATGATT
1 ATATAAAATCATTAATAAAAAGTTTAAAATTATTACT-AAAGTTAAAAAAATTAAAGTAATGATT
*
530255 ATATATATAAATTATTGTTAAATTTATCAGAA-AATTTAAGGTTTTTAAATAATTTTGAATTAAA
65 ATATATATAAATTATTGTTAAATTTATCA-AATAATTTAA--ATTTTAAATAATTTTGAATTAAA
530319 ATATAT
127 ATATAT
* * * * * *
530325 ATATGAAATTATTAATAAAAAGTTTAAAATTATTACTAAAGTTAAACAATTTAAAGTGATGATTG
1 ATATAAAATCATTAATAAAAAGTTTAAAATTATTACTAAAGTTAAAAAAATTAAAGTAATGATTA
*
530390 TATATATAAATTATTGTTAACTTTATCAAATAATTTAAATTTTAAATAATT
66 TATATATAAATTATTGTTAAATTTATCAAATAATTTAAATTTTAAATAATT
530441 CATAATTTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
132 12 0.12
133 5 0.05
134 86 0.83
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (132 bp):
ATATAAAATCATTAATAAAAAGTTTAAAATTATTACTAAAGTTAAAAAAATTAAAGTAATGATTA
TATATATAAATTATTGTTAAATTTATCAAATAATTTAAATTTTAAATAATTTTGAATTAAAATAT
AT
Found at i:530438 original size:16 final size:17
Alignment explanation
Indices: 530417--530455 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
530407 TAACTTTATC
*
530417 AAATAATTTA-AATTTT
1 AAATAATTCATAATTTT
530433 AAATAATTCATAATTTT
1 AAATAATTCATAATTTT
*
530450 TAATAA
1 AAATAA
530456 AATAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATAATTCATAATTTT
Found at i:530476 original size:2 final size:2
Alignment explanation
Indices: 530469--530536 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
530459 AAATAAATTG
530469 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
530511 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
530537 GAATTTATTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533298 original size:22 final size:22
Alignment explanation
Indices: 533270--533321 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
533260 TAATCAATTA
533270 TCGAGTTGTAGTATTTACCTAG
1 TCGAGTTGTAGTATTTACCTAG
*
533292 TCGAGTTGTTGTATTTACCTAG
1 TCGAGTTGTAGTATTTACCTAG
*
533314 TCGTGTTG
1 TCGAGTTG
533322 AACTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.44
Consensus pattern (22 bp):
TCGAGTTGTAGTATTTACCTAG
Found at i:533720 original size:6 final size:6
Alignment explanation
Indices: 533704--533744 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
533694 GCGGGTATTA
533704 AAACA- AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT
1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT
533745 TAGGTATGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.68, C:0.17, G:0.00, T:0.15
Consensus pattern (6 bp):
AAACAT
Found at i:533958 original size:33 final size:33
Alignment explanation
Indices: 533912--533988 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
533902 TTTCAAAATA
* *
533912 AAAGTAATTTTAAGAAAAACCTAACGTGGGGAT
1 AAAGAAATCTTAAGAAAAACCTAACGTGGGGAT
533945 AAAGAAATCTTAAGAAAAACCTAACGTGGGGAT
1 AAAGAAATCTTAAGAAAAACCTAACGTGGGGAT
533978 AAAGAAATCTT
1 AAAGAAATCTT
533989 TTATTGATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (33 bp):
AAAGAAATCTTAAGAAAAACCTAACGTGGGGAT
Found at i:535038 original size:16 final size:16
Alignment explanation
Indices: 535017--535062 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
535007 AATATTGAAA
535017 CTTGAACTCAAAAAGG
1 CTTGAACTCAAAAAGG
535033 CTTGAACTCAAAAAGG
1 CTTGAACTCAAAAAGG
535049 CTTGAACTCAAAAA
1 CTTGAACTCAAAAA
535063 AAAATTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (16 bp):
CTTGAACTCAAAAAGG
Found at i:535862 original size:26 final size:26
Alignment explanation
Indices: 535826--535886 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
535816 CAAAAGAAAA
*
535826 TCGGTGCAATAATGCACCGAATTGAT
1 TCGGTGCAATAATGCACCAAATTGAT
*
535852 TCGGTGCAATAATGCACCAAATTTAT
1 TCGGTGCAATAATGCACCAAATTGAT
535878 TCGGTGCAA
1 TCGGTGCAA
535887 ATGGTCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (26 bp):
TCGGTGCAATAATGCACCAAATTGAT
Found at i:543245 original size:63 final size:63
Alignment explanation
Indices: 543171--543364 Score: 327
Period size: 63 Copynumber: 3.1 Consensus size: 63
543161 GACTAGGATT
*
543171 TAATAAAATAATATTAAATGAAACCCAAATCCAATTAGAAAATCTATTAAATATATGTATAAA
1 TAATAAAATAATATTAAATGAAATCCAAATCCAATTAGAAAATCTATTAAATATATGTATAAA
543234 TAATAAAATAATATTAAATGAAATCCAAATCCAATTAGAAAAAT-TATTAAATATATGTATAAA
1 TAATAAAATAATATTAAATGAAATCCAAATCCAATTAG-AAAATCTATTAAATATATGTATAAA
* * * *
543297 TAATAAAATCATATTAAAAGAAATCCGAATCCAATTAGAAAATCTGTTAAATATATGTATAAA
1 TAATAAAATAATATTAAATGAAATCCAAATCCAATTAGAAAATCTATTAAATATATGTATAAA
543360 TAATA
1 TAATA
543365 CAACATGCAT
Statistics
Matches: 124, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
62 5 0.04
63 114 0.92
64 5 0.04
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (63 bp):
TAATAAAATAATATTAAATGAAATCCAAATCCAATTAGAAAATCTATTAAATATATGTATAAA
Found at i:543251 original size:30 final size:30
Alignment explanation
Indices: 543215--543314 Score: 89
Period size: 30 Copynumber: 3.2 Consensus size: 30
543205 TTAGAAAATC
543215 TATTAAATATATGTATAAATAATAAAATAA
1 TATTAAATATATGTATAAATAATAAAATAA
* **
543245 TATTAAATGA-A-ATCCAAATCCAATTAGAAA-AA
1 TATTAAAT-ATATGTATAAAT--AA-TA-AAATAA
*
543277 TTATTAAATATATGTATAAATAATAAAATCA
1 -TATTAAATATATGTATAAATAATAAAATAA
543308 TATTAAA
1 TATTAAA
543315 AGAAATCCGA
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
29 5 0.09
30 19 0.35
31 6 0.11
32 7 0.13
33 12 0.22
34 5 0.09
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (30 bp):
TATTAAATATATGTATAAATAATAAAATAA
Found at i:543282 original size:33 final size:33
Alignment explanation
Indices: 543182--543285 Score: 87
Period size: 33 Copynumber: 3.2 Consensus size: 33
543172 AATAAAATAA
*
543182 TATTAAATGAAACCCAAATCCAATTAG-AAAAT
1 TATTAAATGAAATCCAAATCCAATTAGAAAAAT
* **
543214 CTATTAAAT-ATATGTATAAAT--AA-TA-AAATAA-
1 -TATTAAATGA-A-ATCCAAATCCAATTAGAAA-AAT
543245 TATTAAATGAAATCCAAATCCAATTAGAAAAAT
1 TATTAAATGAAATCCAAATCCAATTAGAAAAAT
543278 TATTAAAT
1 TATTAAAT
543286 ATATGTATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 20
0.67 0.09 0.25
Matches are distributed among these distances:
29 5 0.09
30 9 0.17
31 7 0.13
32 9 0.17
33 20 0.37
34 4 0.07
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (33 bp):
TATTAAATGAAATCCAAATCCAATTAGAAAAAT
Found at i:546003 original size:15 final size:15
Alignment explanation
Indices: 545983--546013 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
545973 TATACAATTA
545983 ATAAAATAGTTTTAT
1 ATAAAATAGTTTTAT
*
545998 ATAAAATATTTTTAT
1 ATAAAATAGTTTTAT
546013 A
1 A
546014 GTATTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATAAAATAGTTTTAT
Found at i:547506 original size:19 final size:20
Alignment explanation
Indices: 547476--547513 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
547466 ATTTGTGTCA
547476 TTACTATTATTTATTATTAT
1 TTACTATTATTTATTATTAT
*
547496 TTACT-TTATTTGTTATTA
1 TTACTATTATTTATTATTA
547514 GTGTTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTACTATTATTTATTATTAT
Found at i:554211 original size:200 final size:200
Alignment explanation
Indices: 553836--554340 Score: 567
Period size: 200 Copynumber: 2.5 Consensus size: 200
553826 TTAAGGTGAG
* * * *
553836 AAGAGCTATCTGTCGACCAAAGTTTTTGAGTTCAATTCCACTCAGCTCGAGAGCACGTCGAAC-G
1 AAGAGCTATTTGTCGACCAAAGTTTTTGAGTTCAATTCCACTCAGCTCGATAGCGCATCG-ACTG
* * * * * *
553900 CATGGTAGCAGTGAGGAACTACCTTCTAGTTAAATTTTAAATCAAAGTTCTTAAGCCAAGAAGAA
65 CATGGTAGCAGCGAGGAACTACCTTCTGGTCAAATTTCAAATCAAAGTCCTTAAGCCAAAAAGAA
* * * *
553965 GACCTATATTGATTGCGATTTAACAAAAAGGAAACACTTCCCAGTCAAATTTCGACATAG-CTTA
130 AACCTAGATTGACTGCAATTTAACAAAAAGGAAACACTTCCCAGTCAAATTTCGACATAGTCTTA
554029 CGGCGAA-
195 -GGC-AAT
*
554036 AAGAGCTATTTGTC-AGCCAAAGTTTTTGAGTTCGATTCCACTCAGCTCGATAGCGCATCGACTG
1 AAGAGCTATTTGTCGA-CCAAAGTTTTTGAGTTCAATTCCACTCAGCTCGATAGCGCATCGACTG
* * * * **
554100 TATGGTAGTAGCAAGGAACTACCTTCCGGTCAAATTTCAAA-CCGAGTCCTTTAAGCCAAAAAGA
65 CATGGTAGCAGCGAGGAACTACCTTCTGGTCAAATTTCAAATCAAAGTCC-TTAAGCCAAAAAGA
* * * * * * *
554164 AAACCTAGGTTGACTGCAATTTGATAATAAA-GAACCTA-TTTCCAGTCAAATTTTGACATAGTT
129 AAACCTAGATTGACTGCAATTTAACAA-AAAGGAAAC-ACTTCCCAGTCAAATTTCGACATAGTC
554227 TTAGGCAAT
192 TTAGGCAAT
* * *
554236 AAGAGTTATTTGTCGACCAAAGCTTTCGAGTTCAATTCCACTCAGCTCGATAGCGCATCGA-TCG
1 AAGAGCTATTTGTCGACCAAAGTTTTTGAGTTCAATTCCACTCAGCTCGATAGCGCATCGACT-G
* * * *
554300 CATGGTACCAACGAGGAATTACCTTCTGGTCAAATTCCAAA
65 CATGGTAGCAGCGAGGAACTACCTTCTGGTCAAATTTCAAA
554341 GCTTTCAAGT
Statistics
Matches: 256, Mismatches: 40, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
199 11 0.04
200 237 0.93
201 8 0.03
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (200 bp):
AAGAGCTATTTGTCGACCAAAGTTTTTGAGTTCAATTCCACTCAGCTCGATAGCGCATCGACTGC
ATGGTAGCAGCGAGGAACTACCTTCTGGTCAAATTTCAAATCAAAGTCCTTAAGCCAAAAAGAAA
ACCTAGATTGACTGCAATTTAACAAAAAGGAAACACTTCCCAGTCAAATTTCGACATAGTCTTAG
GCAAT
Found at i:556535 original size:27 final size:28
Alignment explanation
Indices: 556498--556553 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
556488 TAGAGAGAAG
* * *
556498 AGAGTTTCTCTCTGTAAA-AAAATGAAA
1 AGAGCTTCTCTATATAAAGAAAATGAAA
556525 AGAGCTTCTCTATATAAAGAAAATGAAA
1 AGAGCTTCTCTATATAAAGAAAATGAAA
556553 A
1 A
556554 TGAAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (28 bp):
AGAGCTTCTCTATATAAAGAAAATGAAA
Found at i:558203 original size:24 final size:24
Alignment explanation
Indices: 558171--558218 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
558161 TCTCAACATG
558171 CTCAATTAAAGTAAATAAAACCTT
1 CTCAATTAAAGTAAATAAAACCTT
*
558195 CTCAGTTAAAGTAAATAAAACCTT
1 CTCAATTAAAGTAAATAAAACCTT
558219 GGAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.29
Consensus pattern (24 bp):
CTCAATTAAAGTAAATAAAACCTT
Found at i:565196 original size:5 final size:5
Alignment explanation
Indices: 565186--565216 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
565176 TGTGTGTTTT
565186 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC C
1 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC C
565217 ATCTCCTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (5 bp):
CCCTC
Found at i:566170 original size:14 final size:13
Alignment explanation
Indices: 566140--566175 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
566130 CATTTTTAGA
566140 TTTAAAAAATATT
1 TTTAAAAAATATT
*
566153 TTTAAATAATATT
1 TTTAAAAAATATT
*
566166 TTTTAAAAAT
1 TTTAAAAAAT
566176 CAGAACGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:570201 original size:3 final size:3
Alignment explanation
Indices: 570193--570241 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
570183 TCTTTTTTAA
** * *
570193 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
570240 TA
1 TA
570242 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:573759 original size:30 final size:30
Alignment explanation
Indices: 573723--573782 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
573713 ATTATCTTAC
* *
573723 TTGTACTAACTAATTTCTTTTCTTTTGTTT
1 TTGTACTAACTAATTTCTTCTCTCTTGTTT
* *
573753 TTGTACTAATTTATTTCTTCTCTCTTGTTT
1 TTGTACTAACTAATTTCTTCTCTCTTGTTT
573783 GTGTCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (30 bp):
TTGTACTAACTAATTTCTTCTCTCTTGTTT
Found at i:575839 original size:19 final size:21
Alignment explanation
Indices: 575815--575959 Score: 111
Period size: 21 Copynumber: 6.7 Consensus size: 21
575805 AATCAAAACA
*
575815 AAGAAAAAG-AGAA-ACAAAG
1 AAGAAAAAGCAAAAGACAAAG
575834 AAGAAAAAGCAAAAGACAAAG
1 AAGAAAAAGCAAAAGACAAAG
* * *
575855 AAAAAAGCAAAGAAAAAAAACAAAG
1 -AAGAA--AAAG-CAAAAGACAAAG
575880 AAGAAAAAGCAAAAGACAAAG
1 AAGAAAAAGCAAAAGACAAAG
*
575901 AA-AAAAAGCAAAGAAAAAAAACAAAG
1 AAGAAAAAGC------AAAAGACAAAG
575927 AAGAAAAAGCAAAAGACAAAG
1 AAGAAAAAGCAAAAGACAAAG
*
575948 --CAAAAAGCAAAA
1 AAGAAAAAGCAAAA
575960 AGAAAACAAG
Statistics
Matches: 103, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
19 20 0.19
20 10 0.10
21 28 0.27
22 8 0.08
24 8 0.08
25 10 0.10
26 12 0.12
27 7 0.07
ACGTcount: A:0.75, C:0.09, G:0.16, T:0.00
Consensus pattern (21 bp):
AAGAAAAAGCAAAAGACAAAG
Found at i:575871 original size:13 final size:13
Alignment explanation
Indices: 575844--575939 Score: 89
Period size: 13 Copynumber: 7.7 Consensus size: 13
575834 AAGAAAAAGC
575844 AAAAGACAAAG-AA
1 AAAAG-CAAAGAAA
575857 AAAAGCAAAGAAA
1 AAAAGCAAAGAAA
*
575870 AAAAACAAAGAAGA
1 AAAAGCAAAGAA-A
575884 AAAAGC-----AA
1 AAAAGCAAAGAAA
*
575892 AAGA-CAAAGAAA
1 AAAAGCAAAGAAA
575904 AAAAGCAAAGAAA
1 AAAAGCAAAGAAA
*
575917 AAAAACAAAGAAGA
1 AAAAGCAAAGAA-A
575931 AAAAGCAAA
1 AAAAGCAAA
575940 AGACAAAGCA
Statistics
Matches: 68, Mismatches: 6, Indels: 17
0.75 0.07 0.19
Matches are distributed among these distances:
7 1 0.01
8 4 0.06
9 1 0.01
12 10 0.15
13 37 0.54
14 15 0.22
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAGCAAAGAAA
Found at i:575905 original size:34 final size:32
Alignment explanation
Indices: 575815--575921 Score: 119
Period size: 34 Copynumber: 3.2 Consensus size: 32
575805 AATCAAAACA
*
575815 AAGAAAAAGAGAAACAAAGAAGAAAAAGC-AA-
1 AAGAAAAAGAAAAACAAAGAA-AAAAAGCAAAG
* *
575846 AAGACAAAGAAAAAAGCAAAGAAAAAAAACAAAG
1 AAGAAAAAG-AAAAA-CAAAGAAAAAAAGCAAAG
575880 AAGAAAAAGCAAAAGACAAAGAAAAAAAGCAAAG
1 AAGAAAAAG-AAAA-ACAAAGAAAAAAAGCAAAG
*
575914 AAAAAAAA
1 AAGAAAAA
575922 CAAAGAAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
31 8 0.12
32 10 0.16
33 9 0.14
34 36 0.56
35 1 0.02
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (32 bp):
AAGAAAAAGAAAAACAAAGAAAAAAAGCAAAG
Found at i:575924 original size:47 final size:46
Alignment explanation
Indices: 575809--575958 Score: 248
Period size: 47 Copynumber: 3.2 Consensus size: 46
575799 AGATCCAATC
575809 AAAA-CAAAGAAAAAGAGAAACAAAGAAGAAAAAGCAAAAGACAAAGAA
1 AAAAGCAAAG-AAAA-A-AAACAAAGAAGAAAAAGCAAAAGACAAAGAA
575857 AAAAGCAAAGAAAAAAAACAAAGAAGAAAAAGCAAAAGACAAAGAAA
1 AAAAGCAAAGAAAAAAAACAAAGAAGAAAAAGCAAAAGACAAAG-AA
*
575904 AAAAGCAAAGAAAAAAAACAAAGAAGAAAAAGCAAAAGACAAAGCA
1 AAAAGCAAAGAAAAAAAACAAAGAAGAAAAAGCAAAAGACAAAGAA
575950 AAAAGCAAA
1 AAAAGCAAA
575959 AAGAAAACAA
Statistics
Matches: 99, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
46 39 0.39
47 47 0.47
48 8 0.08
49 5 0.05
ACGTcount: A:0.75, C:0.09, G:0.15, T:0.00
Consensus pattern (46 bp):
AAAAGCAAAGAAAAAAAACAAAGAAGAAAAAGCAAAAGACAAAGAA
Found at i:577187 original size:20 final size:20
Alignment explanation
Indices: 577123--577187 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
577113 ATCGAGAAAA
577123 ACATACATCA-ATACATATAT
1 ACATACAT-ATATACATATAT
* *
577143 GCATACATACT-TACATCA-AC
1 ACATACATA-TATACAT-ATAT
*
577163 CCATACATATATACATATAT
1 ACATACATATATACATATAT
577183 ACATA
1 ACATA
577188 ACACATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
19 3 0.09
20 31 0.89
21 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (20 bp):
ACATACATATATACATATAT
Found at i:577567 original size:35 final size:35
Alignment explanation
Indices: 577526--577630 Score: 129
Period size: 35 Copynumber: 3.0 Consensus size: 35
577516 TCTTCTTTTG
*
577526 AAAAACAAATTTTGTCTCGCTTGAGACAGTTTTCT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATTTTCT
* * * *
577561 AAAAACAAATTTTGTCTCGTTTAAGGCAATTTCTTT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATTT-TCT
* * *
577597 CAAAACAAATTTCGTCTCGCTTGAGACATTTTTC
1 AAAAACAAATTTTGTCTCGCTTGAGACAATTTTC
577631 CTTTGAGATA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 29 0.51
36 28 0.49
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (35 bp):
AAAAACAAATTTTGTCTCGCTTGAGACAATTTTCT
Done.