Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009203.1 Hibiscus syriacus cultivar Beakdansim tig00112789_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: 338692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:125 original size:32 final size:33
Alignment explanation
Indices: 77--140 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
67 ACCCAAACCC
77 TAAAATATTTATATATAATTAATATAAAAAATA
1 TAAAATATTTATATATAATTAATATAAAAAATA
110 TAAAATA-TTATATATAATTAATATAAAAAAT
1 TAAAATATTTATATATAATTAATATAAAAAAT
141 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAATATTTATATATAATTAATATAAAAAATA
Found at i:154 original size:23 final size:22
Alignment explanation
Indices: 93--154 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
83 ATTTATATAT
*
93 AATTA-ATATAAAAAATATAAAA
1 AATTATATAT-AATAATATAAAA
*
115 TATTATATATAATTAATATAAAA
1 AATTATATATAA-TAATATAAAA
138 AATTATATATATATAAT
1 AATTATATATA-ATAAT
155 CGGGGCGGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 6 0.18
23 27 0.79
24 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTATATATAATAATATAAAA
Found at i:2095 original size:309 final size:308
Alignment explanation
Indices: 1520--2140 Score: 1201
Period size: 309 Copynumber: 2.0 Consensus size: 308
1510 AACAATTGCC
1520 TTACTCCCTCTTCTTACTTTTCACAGGATTTAAAAATAAGGATAATCAAATGAACTGCTTAGATT
1 TTACTCCCTCTTCTTACTTTTCACAGGATTTAAAAATAAGGATAATCAAATGAACTGCTTAGATT
1585 CTCATTTTATTCTAACAGTGATCTGTTGTGCAGTGCTTATATATATATATATATATATATTAGAA
66 CTCATTTTATTCTAACAGTGATCTGTTGTGCAGTGCTTATATATATATATATATATATATTAGAA
1650 TTAATGTATTCACTTAAAGGAAATTTTATTGAAAAATTGAATCTCCCAAATGTTTATTTGATAGC
131 TTAATGTATTCACTTAAAGGAAATTTTATTGAAAAATTGAATCTCCCAAATGTTTATTTGATAGC
1715 AGTTAAGGTCAAGCCAAGAGTTTTCACTACAATCCCCCCTCTTTTGCAGCCCATGCTTTGTGTCA
196 AGTTAAGGTCAAGCCAAGAGTTTTCACTACAATCCCCCCTCTTTTGCAGCCCATGCTTTGTGTCA
1780 GTGCAGTTAATCCCTTCCTGTTTTCAAAGGTTCCAGCTTTGAACCATG
261 GTGCAGTTAATCCCTTCCTGTTTTCAAAGGTTCCAGCTTTGAACCATG
1828 TTACTCCCTCTTCTTAC-TTTCACAGGATTTAAAAATAAGGATAATCAAATGAACTGCTTAGATT
1 TTACTCCCTCTTCTTACTTTTCACAGGATTTAAAAATAAGGATAATCAAATGAACTGCTTAGATT
1892 CTCATTTTATTCTAACAGTGATCTGTTGTGCAGTGCTTATATATATATATATATTATATATATTA
66 CTCATTTTATTCTAACAGTGATCTGTTGTGCAGTGC-T-TATATATATATATA-TATATATATTA
1957 GAATTAATGTATTCACTTAAAGGAAATTTTATTGAAAAA-TGAATCTCCCAAATGTTTATTTGAT
128 GAATTAATGTATTCACTTAAAGGAAATTTTATTGAAAAATTGAATCTCCCAAATGTTTATTTGAT
2021 AGCAGTTAAGGTCAAGCCAAGAGTTTTCACTACAATCCCCCCTCTTTTGCAGCCCATGCTTTGTG
193 AGCAGTTAAGGTCAAGCCAAGAGTTTTCACTACAATCCCCCCTCTTTTGCAGCCCATGCTTTGTG
2086 TCAGTGCAGTTAATCCCTTCCTGTTTTCAAAGGTTCCAGCTTTGAACCATG
258 TCAGTGCAGTTAATCCCTTCCTGTTTTCAAAGGTTCCAGCTTTGAACCATG
2137 TTAC
1 TTAC
2141 GGGCATCAGA
Statistics
Matches: 310, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
307 83 0.27
308 18 0.06
309 159 0.51
310 50 0.16
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (308 bp):
TTACTCCCTCTTCTTACTTTTCACAGGATTTAAAAATAAGGATAATCAAATGAACTGCTTAGATT
CTCATTTTATTCTAACAGTGATCTGTTGTGCAGTGCTTATATATATATATATATATATATTAGAA
TTAATGTATTCACTTAAAGGAAATTTTATTGAAAAATTGAATCTCCCAAATGTTTATTTGATAGC
AGTTAAGGTCAAGCCAAGAGTTTTCACTACAATCCCCCCTCTTTTGCAGCCCATGCTTTGTGTCA
GTGCAGTTAATCCCTTCCTGTTTTCAAAGGTTCCAGCTTTGAACCATG
Found at i:16740 original size:36 final size:36
Alignment explanation
Indices: 16693--16809 Score: 198
Period size: 36 Copynumber: 3.2 Consensus size: 36
16683 TCCTTGGCGG
*
16693 GGAGATGAAGGGTGAAGAATTGGTAATCCATGGTGA
1 GGAGATGAAGGGTGAAGAATTCGTAATCCATGGTGA
* *
16729 GGAGATGAAGGGTGAAGAATTCGAAATCCATGATGA
1 GGAGATGAAGGGTGAAGAATTCGTAATCCATGGTGA
*
16765 GGAGATGAAGGGTGAAGAATTCGTAATCCATGGCGA
1 GGAGATGAAGGGTGAAGAATTCGTAATCCATGGTGA
16801 GGAGATGAA
1 GGAGATGAA
16810 AGGTAATCCA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 75 1.00
ACGTcount: A:0.36, C:0.08, G:0.37, T:0.20
Consensus pattern (36 bp):
GGAGATGAAGGGTGAAGAATTCGTAATCCATGGTGA
Found at i:21134 original size:21 final size:21
Alignment explanation
Indices: 21108--21168 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
21098 TTGAGGGTTA
*
21108 TATGTGGTCATTCGGGACATC
1 TATGTGGTCATTCGAGACATC
*
21129 TATGTGGTCATTTGAGACATC
1 TATGTGGTCATTCGAGACATC
* * *
21150 TATATGGTTATTCAAGACA
1 TATGTGGTCATTCGAGACA
21169 AATTTTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TATGTGGTCATTCGAGACATC
Found at i:22850 original size:21 final size:22
Alignment explanation
Indices: 22824--22880 Score: 80
Period size: 21 Copynumber: 2.5 Consensus size: 22
22814 TGATATTTTA
22824 TATATTAACTTTAAA-ATAATT
1 TATATTAACTTTAAATATAATT
22845 TATATTAACTTATTAAATATAATT
1 TATATTAAC-T-TTAAATATAATT
22869 TATTATTAACTT
1 TA-TATTAACTT
22881 ATTTTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 9 0.28
22 1 0.03
23 6 0.19
24 9 0.28
25 7 0.22
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTAACTTTAAATATAATT
Found at i:22881 original size:25 final size:24
Alignment explanation
Indices: 22820--22883 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 24
22810 GTCATGATAT
22820 TTTATATATTAAC-T-TTAAAATAA
1 TTTAT-TATTAACTTATTAAAATAA
22843 TTTA-TATTAACTTATTAAATATAA
1 TTTATTATTAACTTATTAAA-ATAA
22867 TTTATTATTAACTTATT
1 TTTATTATTAACTTATT
22884 TTTAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.19
22 1 0.03
23 9 0.24
24 8 0.22
25 12 0.32
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTATTATTAACTTATTAAAATAA
Found at i:22932 original size:17 final size:18
Alignment explanation
Indices: 22896--22936 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
22886 TAAAAATATT
22896 TATATTTTCATTTAAAAA
1 TATATTTTCATTTAAAAA
22914 TATATTTT-ATGTT-AAAA
1 TATATTTTCAT-TTAAAAA
22931 TATATT
1 TATATT
22937 CAAAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TATATTTTCATTTAAAAA
Found at i:27694 original size:24 final size:24
Alignment explanation
Indices: 27662--27710 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
27652 AACTTGAATA
27662 CCTCTTTTTCAGTTAATTCTTTGT
1 CCTCTTTTTCAGTTAATTCTTTGT
27686 CCTCTTTTTCAGTTAATTCTTTGT
1 CCTCTTTTTCAGTTAATTCTTTGT
27710 C
1 C
27711 TTGTGTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.22, G:0.08, T:0.57
Consensus pattern (24 bp):
CCTCTTTTTCAGTTAATTCTTTGT
Found at i:27719 original size:24 final size:24
Alignment explanation
Indices: 27662--27720 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
27652 AACTTGAATA
*
27662 CCTCTTTTTCAGTTAATTCTTTGT
1 CCTCTGTTTCAGTTAATTCTTTGT
*
27686 CCTCTTTTTCAGTTAATTCTTTGT
1 CCTCTGTTTCAGTTAATTCTTTGT
* *
27710 CTTGTGTTTCA
1 CCTCTGTTTCA
27721 TTCATTATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.58
Consensus pattern (24 bp):
CCTCTGTTTCAGTTAATTCTTTGT
Found at i:30287 original size:1 final size:1
Alignment explanation
Indices: 30281--30309 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
30271 GAGTTGAGGA
30281 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30310 ATAGTTGGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:48728 original size:17 final size:17
Alignment explanation
Indices: 48694--48752 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
48684 TATAATAATT
48694 ATATAGTTTATAATATAA
1 ATATAGTTTAT-ATATAA
48712 ATATAGTTTATATATAA
1 ATATAGTTTATATATAA
*
48729 ACTTATA-TTATATATATAT
1 A--TATAGTT-TATATATAA
48748 ATATA
1 ATATA
48753 TATTATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 11 0.30
18 13 0.35
19 13 0.35
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATAGTTTATATATAA
Found at i:48753 original size:17 final size:17
Alignment explanation
Indices: 48701--48758 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 17
48691 ATTATATAGT
48701 TTATA-ATATAAATATA
1 TTATATATATAAATATA
48717 GTT-TATATATAAACTTATA
1 -TTATATATATAAA--TATA
48736 TTATATATATATATATATA
1 TTATATATATA-A-ATATA
48755 TTAT
1 TTAT
48759 TTTTTTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 2 0.06
19 20 0.57
20 1 0.03
21 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTATATATATAAATATA
Found at i:66830 original size:22 final size:22
Alignment explanation
Indices: 66804--66883 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
66794 TAAATTTACA
*
66804 CTCTCTAAAGATGATATATTTT
1 CTCTCTAAAGATGATAGATTTT
*
66826 CTCTCTAAAGATGATAGATTTC
1 CTCTCTAAAGATGATAGATTTT
* *
66848 CTCTCCAAAGATGATAGATTCT
1 CTCTCTAAAGATGATAGATTTT
* *
66870 CTTTTTAAAGATGA
1 CTCTCTAAAGATGA
66884 AAGTTTTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
CTCTCTAAAGATGATAGATTTT
Found at i:67432 original size:113 final size:112
Alignment explanation
Indices: 67242--67908 Score: 881
Period size: 113 Copynumber: 5.9 Consensus size: 112
67232 GATTTGAATC
* * * * **
67242 CATCATTCAATGGATCAACATTTCCA-GAAGAGTTCATAATGAGAATTACTCATCTGAAGAAAGA
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* *
67306 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT-GCTTAAATT
* * *
67354 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
67419 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGCTTAAATT
* *
67467 CATCATTCGATGGATCAACATTGCTAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
67532 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTAAATT
* * * * * * *
67580 CATCACTCGGTGGATCAGCAGTGCCAGTTAGTGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * *
67645 AGAAGAAGTTCATAATAAGAAGAATTTTTTTCAACCTTTTGCTTTAATT
66 AGAAGAAGTTCATAATGAGAAGAA-CTTGTTCAA-CTTTTGCTTAAATT
* * * *
67694 CATCACTCGATGGATTATCATTGCCAGTTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAAGA
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * *
67759 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTCGCTTTAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTAAATT
* * * * * * *
67807 CATCACTCGATGG-TTAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAG-AAGA
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* *
67870 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTG
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTG
67909 TATGACTCTA
Statistics
Matches: 506, Mismatches: 45, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
110 4 0.01
111 34 0.07
112 65 0.13
113 295 0.58
114 108 0.21
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (112 bp):
CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTGCTTAAATT
Found at i:67668 original size:226 final size:225
Alignment explanation
Indices: 67242--68027 Score: 936
Period size: 226 Copynumber: 3.5 Consensus size: 225
67232 GATTTGAATC
* * * **
67242 CATCATTCAATGGATCAACATTTCCA-GAAGAGTTCATAATGAGAATTACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * *
67306 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGGATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTTAAATTCATCACTCGATGGATC
* * * *
67370 AACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
130 AGCATTGCCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAAT
67435 GAGAAGAACTTGTTCAACTTTTTGCTTAAATT
195 GAGAAGAACTTGTTCAACTTTTTGCTT-AATT
*
67467 CATCATTCGATGGATCAACATTGCTAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* *
67532 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTCGGTGGATCA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATCA
* * * *
67597 GCAGTGCCAGTTAGTGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATA
131 GCATTGCCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * *
67662 AGAAGAATTTTTTTCAACCTTTTGCTTTAATT
196 AGAAGAA-CTTGTTCAACTTTTTGC-TTAATT
* * * * *
67694 CATCACTCGATGGATTATCATTGCCAGTTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * * *
67759 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTCGCTTTAATTCATCACTCGATGG-TTA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATCA
* * *
67823 GCTTTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAGAAGTTCATAATG
131 GCATTGCCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
67887 AGAAGAGCTTGTTCAACCTTTGTATGACTCT-ATCA
196 AGAAGAACTTGTTCAA-CTTT-T-TG-CT-TAAT-T
** *** * **** **
67922 CAGAAGGAGATAGATCAACATCAATATTTTCAGAAGTATTCATAATGAGAAGAACTCATCTGAA-
1 CATCATTCGATGGATCAACATTGCCA-GGT-AG-AG--TTCATAATGAGAAGAACTCATCTGAAG
* *
67986 TAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
61 AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
68028 AATTTAATTC
Statistics
Matches: 482, Mismatches: 64, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
224 7 0.01
225 50 0.10
226 196 0.41
227 142 0.29
228 18 0.04
229 2 0.00
230 2 0.00
231 2 0.00
232 38 0.08
233 25 0.05
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (225 bp):
CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATCA
GCATTGCCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACTTTTTGCTTAATT
Found at i:68021 original size:20 final size:20
Alignment explanation
Indices: 67960--68022 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 20
67950 TTCAGAAGTA
*
67960 TTCATAATGAGAAGAACTCATC
1 TTCATAATGAGAAGAACT--TG
** *
67982 TGAATAAGGAGAAGAA---G
1 TTCATAATGAGAAGAACTTG
67999 TTCATAATGAGAAGAACTTG
1 TTCATAATGAGAAGAACTTG
68019 TTCA
1 TTCA
68023 ACCTTAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
17 13 0.42
20 5 0.16
22 13 0.42
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTTG
Found at i:68404 original size:3 final size:3
Alignment explanation
Indices: 68396--68440 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
68386 TTTGTTTCAT
*
68396 TTA TTA TTA TTA TT- TTA TT- TTA TT- TTA ATA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
68440 T
1 T
68441 ATTTATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 8 0.22
3 28 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:68422 original size:24 final size:23
Alignment explanation
Indices: 68394--68448 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
68384 CATTTGTTTC
* *
68394 ATTTATTATTATTATTTTATTTT
1 ATTTATTATTATTATTATATTAT
*
68417 ATTTTAATATTATTATTATATTAT
1 A-TTTATTATTATTATTATATTAT
68441 ATTTATTA
1 ATTTATTA
68449 AATAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTATTATTATTATTATATTAT
Found at i:68429 original size:11 final size:10
Alignment explanation
Indices: 68403--68446 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
68393 CATTTATTAT
68403 TATTATTTTA
1 TATTATTTTA
*
68413 TTTTATTTTAA
1 TATTATTTT-A
68424 TATTATTATTA
1 TATTATT-TTA
68435 TATTATATTTA
1 TATTAT-TTTA
68446 T
1 T
68447 TAAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 8 0.28
11 18 0.62
12 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTATTTTA
Found at i:68452 original size:27 final size:27
Alignment explanation
Indices: 68397--68452 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
68387 TTGTTTCATT
* *
68397 TATTATTATTATTTTATTTTATTTTAA
1 TATTATTATTATATTATTTTATTTAAA
68424 TATTATTATTATATTATATTTA-TTAAA
1 TATTATTATTATATTAT-TTTATTTAAA
68451 TA
1 TA
68453 ATTAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTATTATTATATTATTTTATTTAAA
Found at i:68525 original size:14 final size:14
Alignment explanation
Indices: 68501--68534 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
68491 GGCCCGATTA
68501 CAAACCAGACTGGCC
1 CAAA-CAGACTGGCC
68516 CAAACAGACTGGCC
1 CAAACAGACTGGCC
68530 CAAAC
1 CAAAC
68535 CTAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.38, C:0.38, G:0.18, T:0.06
Consensus pattern (14 bp):
CAAACAGACTGGCC
Found at i:71529 original size:16 final size:16
Alignment explanation
Indices: 71508--71549 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
71498 TTACTATTCA
71508 CGTGAATAGTGAATTT
1 CGTGAATAGTGAATTT
71524 CGTGAATAGTGAATTT
1 CGTGAATAGTGAATTT
71540 CGTGAATAGT
1 CGTGAATAGT
71550 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (16 bp):
CGTGAATAGTGAATTT
Found at i:87371 original size:2 final size:2
Alignment explanation
Indices: 87364--87402 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
87354 TTTTAATTAG
87364 AT 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 AT A
87403 ATTCTAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:92455 original size:23 final size:24
Alignment explanation
Indices: 92429--92494 Score: 91
Period size: 23 Copynumber: 2.8 Consensus size: 24
92419 CTAGCCAGTG
*
92429 CTGATGTGGCGATGACATGGA-AA
1 CTGATGTGGTGATGACATGGACAA
* *
92452 CTGACGTGGTGATGACAT-GACAT
1 CTGATGTGGTGATGACATGGACAA
92475 CTGATGTGGTGATGACATGG
1 CTGATGTGGTGATGACATGG
92495 CAGATGACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.05
23 34 0.92
24 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.35, T:0.26
Consensus pattern (24 bp):
CTGATGTGGTGATGACATGGACAA
Found at i:92558 original size:22 final size:22
Alignment explanation
Indices: 92524--92565 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
92514 CATGGTGCCT
*
92524 AGTCAACAACTTCTAGAAGACC
1 AGTCAACAACTTCTAAAAGACC
* *
92546 AGTCAGCAGCTTCTAAAAGA
1 AGTCAACAACTTCTAAAAGA
92566 TTGATAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (22 bp):
AGTCAACAACTTCTAAAAGACC
Found at i:93510 original size:26 final size:26
Alignment explanation
Indices: 93472--93521 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
93462 GTTTCCTTAG
*
93472 TCTCTGTGGGATCGACCCTTATTTAA
1 TCTCTGTGAGATCGACCCTTATTTAA
*
93498 TCTCTGTGAGATCTACCCTTATTT
1 TCTCTGTGAGATCGACCCTTATTT
93522 CTCTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (26 bp):
TCTCTGTGAGATCGACCCTTATTTAA
Found at i:98544 original size:2 final size:2
Alignment explanation
Indices: 98537--98576 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
98527 GAATTTACCC
98537 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
98577 GGTCATTACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100061 original size:21 final size:21
Alignment explanation
Indices: 100037--100078 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
100027 TTAACCCTAG
*
100037 AATTTTAGTTCGTCCCCTTAA
1 AATTTTAGTTCATCCCCTTAA
100058 AATTTTAGTTCATCCCCTTAA
1 AATTTTAGTTCATCCCCTTAA
100079 GTTTAAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (21 bp):
AATTTTAGTTCATCCCCTTAA
Found at i:119694 original size:31 final size:31
Alignment explanation
Indices: 119658--119717 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
119648 AACTTAAAAG
* *
119658 AGTTTTACAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
119689 AGTTTTACAATACTAAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
119718 CATTCAACTA
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:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:120287 original size:12 final size:12
Alignment explanation
Indices: 120270--120352 Score: 78
Period size: 12 Copynumber: 6.7 Consensus size: 12
120260 ATTTATTTAA
120270 AAAATTAATATT
1 AAAATTAATATT
120282 AAAATTAATATCT
1 AAAATTAATAT-T
*
120295 ATAATATAATATT
1 AAAAT-TAATATT
120308 AAAAATTAATATT
1 -AAAATTAATATT
* * * *
120321 TAATTTATTCA-A
1 AAAATTAAT-ATT
120333 AAAATTAATATT
1 AAAATTAATATT
120345 AAAATTAA
1 AAAATTAA
120353 AATCAAATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
11 1 0.02
12 31 0.55
13 14 0.25
14 10 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:120335 original size:63 final size:64
Alignment explanation
Indices: 120216--120367 Score: 247
Period size: 63 Copynumber: 2.4 Consensus size: 64
120206 TTATATGCTA
*
120216 TAAAATTAAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTCAAAAAATTAATAT
*
120281 TAAAATTAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTCAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTCAAAAAATTAATAT
*
120344 TAAAATTAAAATC-A-AATATAATAT
1 TAAAATTAATATCTATAATATAATAT
120368 AATATAAAAT
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
61 10 0.12
62 1 0.01
63 46 0.55
64 20 0.24
65 7 0.08
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (64 bp):
TAAAATTAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTCAAAAAATTAATAT
Found at i:120936 original size:19 final size:19
Alignment explanation
Indices: 120912--120952 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
120902 AAAACATCGA
120912 ATGCACACTTGGTGCACCG
1 ATGCACACTTGGTGCACCG
120931 ATGCACACTTGGTGCACCG
1 ATGCACACTTGGTGCACCG
120950 ATG
1 ATG
120953 TACTAAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (19 bp):
ATGCACACTTGGTGCACCG
Found at i:123156 original size:23 final size:22
Alignment explanation
Indices: 123126--123230 Score: 128
Period size: 23 Copynumber: 4.8 Consensus size: 22
123116 ATTGCGATAG
123126 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGATTTAT
*
123149 TCCAAGTT-CGTTGCGA--TAG
1 TCCAAGTTCCGTTGCGATTTAT
*
123168 TCGAAGTTCACGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGATTTAT
*
123191 TCCAAATTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGATTTAT
123214 TCCAAGTT-CGTTGCGAT
1 TCCAAGTTCCGTTGCGAT
123231 AGTCCAAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
19 9 0.13
21 25 0.35
23 37 0.52
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (22 bp):
TCCAAGTTCCGTTGCGATTTAT
Found at i:123168 original size:42 final size:42
Alignment explanation
Indices: 123117--123230 Score: 142
Period size: 42 Copynumber: 2.6 Consensus size: 42
123107 CATATTCGCA
*
123117 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT-CG
1 TTGCGATAGTCCAAGTTC-CGTTGCGATTTATTCCAAATTCCG
*
123159 TTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGCG
1 TTGCGATAGTCCAAGTTC-CGTTGCGATTTATTCCAAATTC-CG
*
123203 TTGCGATTTATTCCAAGTT-CGTTGCGAT
1 TTGCGA--TAGTCCAAGTTCCGTTGCGAT
123231 AGTCCAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
42 37 0.59
44 17 0.27
46 9 0.14
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCCGTTGCGATTTATTCCAAATTCCG
Found at i:123354 original size:10 final size:11
Alignment explanation
Indices: 123323--123356 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
123313 GACACGTATT
123323 ACCACGACCACG
1 ACCACGACC-CG
123335 ACCACGACCCG
1 ACCACGACCCG
123346 ACC-CGACCCG
1 ACCACGACCCG
123356 A
1 A
123357 GAAGAGACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:123984 original size:21 final size:21
Alignment explanation
Indices: 123960--124049 Score: 108
Period size: 21 Copynumber: 4.3 Consensus size: 21
123950 CACCAGTCGT
* *
123960 TGCGATTTTGGACTATCGTAA
1 TGCGATCTTGGACTATCGCAA
*
123981 TGCGAACTTGGACTATCGCAA
1 TGCGATCTTGGACTATCGCAA
** *
124002 TGCGATAGTCGACTATCGCAA
1 TGCGATCTTGGACTATCGCAA
* *
124023 TGCGAACTTGGACTATCGCAT
1 TGCGATCTTGGACTATCGCAA
124044 TGCGAT
1 TGCGAT
124050 TTACATATTC
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCGATCTTGGACTATCGCAA
Found at i:124007 original size:42 final size:42
Alignment explanation
Indices: 123960--124051 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
123950 CACCAGTCGT
* *
123960 TGCGATTTTGGACTATCGTAATGCGAACTTGGACTATCGCAA
1 TGCGATTTTCGACTATCGCAATGCGAACTTGGACTATCGCAA
** *
124002 TGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAT
1 TGCGATTTTCGACTATCGCAATGCGAACTTGGACTATCGCAA
124044 TGCGATTT
1 TGCGATTT
124052 ACATATTCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (42 bp):
TGCGATTTTCGACTATCGCAATGCGAACTTGGACTATCGCAA
Found at i:124114 original size:21 final size:21
Alignment explanation
Indices: 124088--124310 Score: 84
Period size: 21 Copynumber: 10.8 Consensus size: 21
124078 ATCGCAATTG
124088 GACTATCGCAATGCGATAGTC
1 GACTATCGCAATGCGATAGTC
124109 GACTATCGCAATGCGAT--T-
1 GACTATCGCAATGCGATAGTC
*
124127 TACATATTCGCATTACGATAGCGATAGTCC
1 GAC-TA-TCGC---A--AT-GCGATAGT-C
* * *
124157 AAGT-TCGCATTGCGATAGTC
1 GACTATCGCAATGCGATAGTC
*
124177 GACTATCGCATTGCGAT--T-
1 GACTATCGCAATGCGATAGTC
* * * *
124195 TACATATTCGCATTACGATAGCC
1 GAC-TA-TCGCAATGCGATAGTC
124218 GACTATCGCAAT----T-G--
1 GACTATCGCAATGCGATAGTC
*
124232 GACTATCGTAATGCGATAGTC
1 GACTATCGCAATGCGATAGTC
124253 GACTATCGCAATGCGAT--T-
1 GACTATCGCAATGCGATAGTC
* * *
124271 TACATATTCGCATTGCGATAGCC
1 GAC-TA-TCGCAATGCGATAGTC
*
124294 GACTATCGCATTGCGAT
1 GACTATCGCAATGCGAT
124311 TTACATATTC
Statistics
Matches: 155, Mismatches: 17, Indels: 60
0.67 0.07 0.26
Matches are distributed among these distances:
14 11 0.07
16 1 0.01
17 1 0.01
18 7 0.05
19 10 0.06
20 29 0.19
21 71 0.46
22 5 0.03
23 5 0.03
24 1 0.01
25 2 0.01
26 5 0.03
27 4 0.03
28 1 0.01
29 1 0.01
30 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (21 bp):
GACTATCGCAATGCGATAGTC
Found at i:124138 original size:76 final size:76
Alignment explanation
Indices: 124012--124303 Score: 424
Period size: 76 Copynumber: 3.9 Consensus size: 76
124002 TGCGATAGTC
* * * *
124012 GACTATCGCAATGCGA-ACTTGGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCCGA
1 GACTATCGCAATGCGATA-GTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGCCGA
124076 CTATCGCAATTG
65 CTATCGCAATTG
124088 GACTATCGCAATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAG-CGA-
1 GACTATCGCAATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGCCGAC
124151 TAGTC-CAA---
66 TA-TCGCAATTG
* *
124159 G--T-TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTACGATAGCCGAC
1 GACTATCGCAATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGCCGAC
124221 TATCGCAATTG
66 TATCGCAATTG
* *
124232 GACTATCGTAATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTGCGATAGCCGAC
1 GACTATCGCAATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGCCGAC
124297 TATCGCA
66 TATCGCA
124304 TTGCGATTTA
Statistics
Matches: 195, Mismatches: 10, Indels: 22
0.86 0.04 0.10
Matches are distributed among these distances:
68 53 0.27
69 6 0.03
70 5 0.03
71 1 0.01
73 1 0.01
74 5 0.03
75 6 0.03
76 117 0.60
77 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (76 bp):
GACTATCGCAATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGCCGAC
TATCGCAATTG
Found at i:124197 original size:144 final size:144
Alignment explanation
Indices: 124033--124292 Score: 493
Period size: 144 Copynumber: 1.8 Consensus size: 144
124023 TGCGAACTTG
*
124033 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCCGACTATCGCAATTGGACTATCGCA
1 GACTATCGCATTGCGATTTACATATTCGCATTACGATAGCCGACTATCGCAATTGGACTATCGCA
124098 ATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGCGATAGTCCAAGTTC
66 ATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGCGATAGTCCAAGTTC
124163 GCATTGCGATAGTC
131 GCATTGCGATAGTC
*
124177 GACTATCGCATTGCGATTTACATATTCGCATTACGATAGCCGACTATCGCAATTGGACTATCGTA
1 GACTATCGCATTGCGATTTACATATTCGCATTACGATAGCCGACTATCGCAATTGGACTATCGCA
*
124242 ATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTGCGATAGC
66 ATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGC
124293 CGACTATCGC
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 113 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (144 bp):
GACTATCGCATTGCGATTTACATATTCGCATTACGATAGCCGACTATCGCAATTGGACTATCGCA
ATGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCATTACGATAGCGATAGTCCAAGTTC
GCATTGCGATAGTC
Found at i:124205 original size:41 final size:41
Alignment explanation
Indices: 124160--124375 Score: 225
Period size: 41 Copynumber: 5.4 Consensus size: 41
124150 ATAGTCCAAG
124160 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
* *
124201 TTCGCATTACGATAGCCGACTATCGCAATTG-G----AC-TA
1 TTCGCATTGCGATAGTCGACTATCGC-ATTGCGATTTACATA
* * *
124237 -TCGTAATGCGATAGTCGACTATCGCAATGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
*
124277 TTCGCATTGCGATAGCCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
* * * * * *
124318 TTCGCATTGTGATTGTCTAAGT-TCGCATTGCGATAGTCCA-A
1 TTCGCATTGCGATAGTC-GACTATCGCATTGCGAT-TTACATA
124359 GTTCGCATTGCGATAGT
1 -TTCGCATTGCGATAGT
124376 TGAAGTTCGC
Statistics
Matches: 144, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
34 3 0.02
35 22 0.15
36 2 0.01
37 2 0.01
39 2 0.01
40 2 0.01
41 88 0.61
42 23 0.16
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
Found at i:124287 original size:20 final size:20
Alignment explanation
Indices: 124258--124331 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
124248 TAGTCGACTA
*
124258 TCGCAATGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
***
124278 TCGCATTGCGATAGCCGACTA-
1 TCGCATTGCGATTTAC-A-TAT
124299 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
124319 TCGCATTGTGATT
1 TCGCATTGCGATT
124332 GTCTAAGTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 14 0.33
22 2 0.05
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:124344 original size:21 final size:21
Alignment explanation
Indices: 124318--124392 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
124308 GATTTACATA
* *
124318 TTCGCATTGTGATTGTCTAAG
1 TTCGCATTGCGATAGTCTAAG
*
124339 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCTAAG
124360 TTCGCATTGCGATAGT-TGAAG
1 TTCGCATTGCGATAGTCT-AAG
*
124381 TTCGCGTTGCGA
1 TTCGCATTGCGA
124393 ATCTAGAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCTAAG
Found at i:132972 original size:16 final size:16
Alignment explanation
Indices: 132953--133001 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
132943 TATTATTTAC
* *
132953 TTATTTTATTTATATG
1 TTATATTATATATATG
*
132969 TTATATTATATATATA
1 TTATATTATATATATG
132985 TATATATATATATATAT
1 T-TATAT-TATATATAT
133002 ATATTACGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.50
17 5 0.18
18 9 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATATTATATATATG
Found at i:132982 original size:2 final size:2
Alignment explanation
Indices: 132970--133005 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
132960 ATTTATATGT
132970 TA TA T- 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 TA TA T
133006 TACGTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:133108 original size:4 final size:4
Alignment explanation
Indices: 133099--133199 Score: 50
Period size: 4 Copynumber: 24.5 Consensus size: 4
133089 CTTCGTTTTG
* * *
133099 TTTA TTTA TTT- TATT- TTTA TTTTA TTTA TTCA TTGA TTCA TTT- TTCCTA
1 TTTA TTTA TTTA T-TTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TT--TA
*
133148 TTTTA TTTA TTTA TTTA TCTTA TTCTA TTGTC TTTA TTT- TTT- TTTA
1 -TTTA TTTA TTTA TTTA T-TTA TT-TA TT-TA TTTA TTTA TTTA TTTA
*
133194 TATA TT
1 TTTA TT
133200 CCTTTTATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
3 11 0.14
4 47 0.60
5 18 0.23
7 2 0.03
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:133113 original size:9 final size:9
Alignment explanation
Indices: 133099--133187 Score: 56
Period size: 9 Copynumber: 9.3 Consensus size: 9
133089 CTTCGTTTTG
133099 TTTATTTAT
1 TTTATTTAT
133108 TTTATTTTTAT
1 TTTA--TTTAT
133119 TTTATTTAT
1 TTTATTTAT
*
133128 TCATTGATTCAT
1 T--TT-ATTTAT
*
133140 TTT-TCCTAT
1 TTTAT-TTAT
133149 TTTATTTA-
1 TTTATTTAT
133157 TTTATTTAT
1 TTTATTTAT
*
133166 CTTATTCTAT
1 TTTATT-TAT
* *
133176 TGTCTTTAT
1 TTTATTTAT
133185 TTT
1 TTT
133188 TTTTTATATA
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
8 9 0.15
9 27 0.44
10 9 0.15
11 11 0.18
12 6 0.10
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTATTTAT
Found at i:137706 original size:15 final size:15
Alignment explanation
Indices: 137668--137720 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
137658 GGATTCAATC
*
137668 AGAACAAAAAAGAAA
1 AGAAAAAAAAAGAAA
*
137683 AGGAGAAAAAAAGAAA
1 A-GAAAAAAAAAGAAA
*
137699 AGAAAAAAATCA-AAA
1 AGAAAAAAA-AAGAAA
137714 AGAAAAA
1 AGAAAAA
137721 GGGACAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 18 0.56
16 14 0.44
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (15 bp):
AGAAAAAAAAAGAAA
Found at i:137707 original size:16 final size:16
Alignment explanation
Indices: 137673--137720 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
137663 CAATCAGAAC
* *
137673 AAAAAAGAAAAGGAGA
1 AAAAAAGAAAAGAAAA
137689 AAAAAAGAAAAGAAAA
1 AAAAAAGAAAAGAAAA
**
137705 AAATCA-AAAAGAAAA
1 AAAAAAGAAAAGAAAA
137720 A
1 A
137721 GGGACAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAAGAAAA
Found at i:138770 original size:18 final size:18
Alignment explanation
Indices: 138736--138771 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
138726 TCAACATCAA
* *
138736 ATATTGGGGTATTTTTGG
1 ATATTGGGGCATCTTTGG
138754 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
138772 TGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:139316 original size:33 final size:32
Alignment explanation
Indices: 139280--139342 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
139270 CCCTTGGAAA
** *
139280 AAAAACCTTTGAAATTGTTTCTGTTGAAACAC
1 AAAAACCTTTGAAAAAGTTTCTCTTGAAACAC
139312 AAAAACCTTTGAAAAAGTTTCTCTTGAAACA
1 AAAAACCTTTGAAAAAGTTTCTCTTGAAACA
139343 TAAACATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (32 bp):
AAAAACCTTTGAAAAAGTTTCTCTTGAAACAC
Found at i:139547 original size:37 final size:37
Alignment explanation
Indices: 139477--139548 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
139467 TGGAACTAAG
* * * *
139477 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCTCATAAAACAAAA
* *
139514 TTTTGTCTCCCTTAAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCTCATAAAACAA
139549 CAGATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCTCATAAAACAAAA
Found at i:140322 original size:106 final size:106
Alignment explanation
Indices: 140168--140593 Score: 690
Period size: 106 Copynumber: 4.0 Consensus size: 106
140158 TCGCGCCACC
*
140168 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
140233 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * *
140274 CAAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCTCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * **
140339 TTCAGAGCCAATTTCACCTTCACAGCGAAGGGCATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* *
140380 CGAGACAGCACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
140445 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * *
140486 CGAGACAACATAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
140551 TCCAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
140592 CG
1 CG
140594 GAACAATACA
Statistics
Matches: 297, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 297 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:142043 original size:16 final size:16
Alignment explanation
Indices: 142006--142064 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
141996 CATGTATCAT
*
142006 TATTATTTTAT-TATT
1 TATTATTTTATCTATA
*
142021 TACTTATTTTATTTATA
1 TA-TTATTTTATCTATA
* *
142038 TGTTATATTATCTATA
1 TATTATTTTATCTATA
142054 TATATATTTTA
1 TAT-TATTTTA
142065 CGTTATTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 2 0.06
16 23 0.66
17 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTATTTTATCTATA
Found at i:142907 original size:20 final size:20
Alignment explanation
Indices: 142878--142933 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
142868 TTTCAAAGTG
*
142878 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
142898 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
*
142918 ATGCATCAATGCACCA
1 ATGCATCGATGCACCA
142934 TGGAATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.36, G:0.14, T:0.18
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:143040 original size:46 final size:45
Alignment explanation
Indices: 142955--143041 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
142945 GAACATCGAA
* *
142955 TGCATTTTATGCATCGATGTACATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAG
143000 TGCATTTGATGCATCGATGCACAATACCATGCATCGATGCAC
1 TGCATTTGATGCATCGATGCAC-ATACCATGCATCGATGCAC
143042 AACATCGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAG
Found at i:143070 original size:51 final size:48
Alignment explanation
Indices: 142946--143072 Score: 179
Period size: 51 Copynumber: 2.6 Consensus size: 48
142936 GAATTAATTG
*
142946 AACATCGAATGCATTTTATGCATCGATGTACATACCATGCATCGATGC
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGC
* *
142994 -AC-TC-AGTGCATTTGATGCATCGATGCACAATACCATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC-ATACCATGCATCGATG--C
143042 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
143073 TAAGTATTCC
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
45 21 0.31
46 18 0.26
47 2 0.03
48 1 0.01
49 2 0.03
50 2 0.03
51 22 0.32
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (48 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGC
Found at i:158442 original size:29 final size:29
Alignment explanation
Indices: 158287--158435 Score: 253
Period size: 29 Copynumber: 5.1 Consensus size: 29
158277 CATAAATTAA
* *
158287 TTACGAAACTAAGACCCTTTTAAAAATAC
1 TTACGAAACTAACACCCTTTTAAAAATAT
158316 TTACGAAACTAACACCCTTTTAAAAATAT
1 TTACGAAACTAACACCCTTTTAAAAATAT
158345 TTACGAAACTAACACCCTTTTAAAAATAT
1 TTACGAAACTAACACCCTTTTAAAAATAT
158374 TTACGAAACTAACACCCTTTTAAAAATAT
1 TTACGAAACTAACACCCTTTTAAAAATAT
* * *
158403 TTACAAAAATAATACCCTTTTAAAAATAT
1 TTACGAAACTAACACCCTTTTAAAAATAT
158432 TTAC
1 TTAC
158436 AAAAATAGCA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 115 1.00
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (29 bp):
TTACGAAACTAACACCCTTTTAAAAATAT
Found at i:158465 original size:87 final size:86
Alignment explanation
Indices: 158256--158498 Score: 254
Period size: 87 Copynumber: 2.8 Consensus size: 86
158246 ACAGTCAACT
* * * *
158256 TTTACAAAAATAGCAACTTAACATAAATTAATTACGAAACTAAGACCCTTTTAAAAATACTTACG
1 TTTACAAAAATAGC-ACCTAACA-AAATTAATTACGAAACTAACACCCTTTTAAAAATATTTACA
*
158321 AAACTAACACCCTTTTAAAAATA
64 AAAATAACACCCTTTTAAAAATA
* * * *** * *
158344 TTTACGAAACTAACACCCTTTTAAAAATATTTACGAAACTAACACCCTTTTAAAAATATTTACAA
1 TTTACAAAAATAGCA-CCTAACAAAATTAATTACGAAACTAACACCCTTTTAAAAATATTTACAA
*
158409 AAATAATACCCTTTTAAAAATA
65 AAATAACACCCTTTTAAAAATA
* * * * *
158431 TTTACAAAAATAGCACCGAACAGAAATTAATTACG-TATTAGGCACTCTTTTTAAAAATATTTAC
1 TTTACAAAAATAGCACCTAACA-AAATTAATTACGAAACTA-ACAC-CCTTTTAAAAATATTTAC
158495 AAAA
63 AAAA
158499 TAGCACCAAA
Statistics
Matches: 124, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
86 6 0.05
87 83 0.67
88 35 0.28
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (86 bp):
TTTACAAAAATAGCACCTAACAAAATTAATTACGAAACTAACACCCTTTTAAAAATATTTACAAA
AATAACACCCTTTTAAAAATA
Found at i:158481 original size:58 final size:58
Alignment explanation
Indices: 158419--158563 Score: 256
Period size: 58 Copynumber: 2.5 Consensus size: 58
158409 AAATAATACC
*
158419 CTTTTAAAAATATTTACAAAAATAGCACCGAACAGAAATTAATTACGTATTAGGCACT
1 CTTTTAAAAATATTTACAAAAATAGCACCAAACAGAAATTAATTACGTATTAGGCACT
158477 CTTTTTAAAAATATTTAC-AAAATAGCACCAAACAGAAATTAATTACGTATTAGGCACT
1 C-TTTTAAAAATATTTACAAAAATAGCACCAAACAGAAATTAATTACGTATTAGGCACT
*
158535 CTTTTAAAAATATTTACAAAAATATCACC
1 CTTTTAAAAATATTTACAAAAATAGCACC
158564 CGAATGTTTT
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
57 16 0.19
58 51 0.61
59 16 0.19
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.31
Consensus pattern (58 bp):
CTTTTAAAAATATTTACAAAAATAGCACCAAACAGAAATTAATTACGTATTAGGCACT
Found at i:158618 original size:12 final size:13
Alignment explanation
Indices: 158591--158619 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
158581 TCTCTAGTCA
158591 GGTCAACGGATCG
1 GGTCAACGGATCG
158604 GGTCAACGG-TCG
1 GGTCAACGGATCG
158616 GGTC
1 GGTC
158620 GGGTCAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (13 bp):
GGTCAACGGATCG
Found at i:159447 original size:31 final size:31
Alignment explanation
Indices: 159388--159447 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
159378 GCCCCCATTA
* * *
159388 TCTGATAGGTTCAGTCGCTGTTGGTAATTCC
1 TCTGATAGGTTCAGTCACCGTTGATAATTCC
159419 TCTGATAGGTTCAG-CACCGATTGATAATT
1 TCTGATAGGTTCAGTCACCG-TTGATAATT
159448 TCTTATGGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (31 bp):
TCTGATAGGTTCAGTCACCGTTGATAATTCC
Found at i:160464 original size:11 final size:11
Alignment explanation
Indices: 160450--160476 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
160440 AATATATTTT
160450 AATAATATAAA
1 AATAATATAAA
160461 AATAATATAAA
1 AATAATATAAA
160472 AATAA
1 AATAA
160477 AAATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAATATAAA
Found at i:160478 original size:17 final size:17
Alignment explanation
Indices: 160448--160493 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
160438 CTAATATATT
160448 TTAATAATATAAAAATAA
1 TTAA-AATATAAAAATAA
*
160466 TATAAAA-ATAAAAATTA
1 T-TAAAATATAAAAATAA
160483 TTAAAATATAA
1 TTAAAATATAA
160494 TATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.20
17 14 0.56
18 3 0.12
19 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATATAAAAATAA
Found at i:161465 original size:41 final size:41
Alignment explanation
Indices: 161408--161491 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
161398 AACAATCTGT
* *
161408 TTTGGTCTCGATCGAGGCATTAATAATCTTCACCGCACTGG
1 TTTGGTCTCGATCGAGGCATAAATAATCTTCACCGCAATGG
161449 TTTGGTCTCGATCGAGGCATAAATAATCTTCACCGCAATGG
1 TTTGGTCTCGATCGAGGCATAAATAATCTTCACCGCAATGG
161490 TT
1 TT
161492 GGAGCACCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (41 bp):
TTTGGTCTCGATCGAGGCATAAATAATCTTCACCGCAATGG
Found at i:162842 original size:23 final size:23
Alignment explanation
Indices: 162816--162874 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
162806 TCGTATAAAA
162816 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
162839 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
162861 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
162875 ATATAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:164543 original size:21 final size:21
Alignment explanation
Indices: 164519--164563 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
164509 TCTTGTTCGT
* *
164519 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
164540 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
164561 TTG
1 TTG
164564 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:168778 original size:21 final size:24
Alignment explanation
Indices: 168762--168809 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
168752 TTTTTCTAAA
168762 TTAAAGATTATTTTTTCTCATAAG
1 TTAAAGATTATTTTTTCTCATAAG
*
168786 TTAGAGATTATTTTTTTCTCATAA
1 TTAAAGATTA-TTTTTTCTCATAA
168810 TAAATTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (24 bp):
TTAAAGATTATTTTTTCTCATAAG
Found at i:173472 original size:20 final size:20
Alignment explanation
Indices: 173447--173497 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
173437 CACGGAATGT
173447 AAGATTACCAGTCGA-AATAA
1 AAGATTACCAGT-GAGAATAA
**
173467 AAGATTATAAGTGAGAATAA
1 AAGATTACCAGTGAGAATAA
173487 AAGATTACCAG
1 AAGATTACCAG
173498 GGAATAGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:177417 original size:2 final size:2
Alignment explanation
Indices: 177410--177444 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
177400 AAGGTACGAG
177410 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
177445 ATTTCCAGTT
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:182007 original size:2 final size:2
Alignment explanation
Indices: 182000--182028 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
181990 TTTTCAGAAT
182000 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
182029 TCGTCGGAAT
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:198382 original size:3 final size:3
Alignment explanation
Indices: 198374--198398 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
198364 AAATTAAATA
198374 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
198399 TTCAGATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:198951 original size:26 final size:28
Alignment explanation
Indices: 198922--198985 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
198912 TATTAACTTA
*
198922 TTAGATATATTTTA-TTATT-TTTTAAT
1 TTAGAAATATTTTATTTATTATTTTAAT
*
198948 TTAGAAATATTTTATTTTTTATTTTAAT
1 TTAGAAATATTTTATTTATTATTTTAAT
*
198976 TTAAAAATAT
1 TTAGAAATAT
198986 ATATTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 4 0.12
28 16 0.48
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (28 bp):
TTAGAAATATTTTATTTATTATTTTAAT
Found at i:207138 original size:2 final size:2
Alignment explanation
Indices: 207131--207155 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
207121 ACATACATAC
207131 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
207156 CACACATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:212319 original size:20 final size:20
Alignment explanation
Indices: 212296--212347 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
212286 CAGTTTCCAG
* *
212296 AATCGCAATGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
212316 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
212336 AATCGCAACGCG
1 AATCGCAACGCG
212348 TATTCGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:212357 original size:20 final size:20
Alignment explanation
Indices: 212334--212814 Score: 327
Period size: 20 Copynumber: 23.6 Consensus size: 20
212324 CGCGAACATA
*
212334 TAAATCGCAACGCGTATTCG
1 TAAATCGCAACGCGTATCCG
212354 TAAAAATCGCAACGCGTATCCG
1 T--AAATCGCAACGCGTATCCG
* *
212376 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
*
212396 TAAAGTCGCAACACGTATCCG
1 TAAA-TCGCAACGCGTATCCG
* *
212417 TAAATCGCAACGAGTATTCG
1 TAAATCGCAACGCGTATCCG
*
212437 TAAAAATCACAACGCGTATCCG
1 T--AAATCGCAACGCGTATCCG
* *
212459 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
212479 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
* * *
212500 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGCGTATCCG
*
212520 TAAATCGCAACGCG-ATTC-
1 TAAATCGCAACGCGTATCCG
* *
212538 TGACTATCGCAACGAGTATCCG
1 T-A-AATCGCAACGCGTATCCG
*
212560 TAAAATCGCAACGTGTATCCG
1 T-AAATCGCAACGCGTATCCG
* *
212581 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
* *
212601 TAAAATCACAACGTGTATCCG
1 T-AAATCGCAACGCGTATCCG
* *
212622 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
212642 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
* * * * *
212663 TAAATCGTAATGAGAATACG
1 TAAATCGCAACGCGTATCCG
* *
212683 TAAAATCGCAACACG-ATTC-
1 T-AAATCGCAACGCGTATCCG
* * *
212702 TGATTATCGCAAC-CAGAATACG
1 T-A-AATCGCAACGC-GTATCCG
* * * *
212724 TTAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
212744 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
*
212764 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
212784 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
212804 TAAATCGCAAC
1 TAAATCGCAAC
212815 ACTTAAATTT
Statistics
Matches: 367, Mismatches: 66, Indels: 56
0.75 0.13 0.11
Matches are distributed among these distances:
18 1 0.00
19 7 0.02
20 224 0.61
21 96 0.26
22 39 0.11
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:212417 original size:41 final size:41
Alignment explanation
Indices: 212334--212814 Score: 532
Period size: 41 Copynumber: 11.8 Consensus size: 41
212324 CGCGAACATA
* * *
212334 TAAATCGCAACGCGTATTCGTAAAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGAATACGT-AAAATCGCAACGCGTATCCG
* * *
212376 TAAATCGCAACGACAATACGTAAAGTCGCAACACGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * *
212417 TAAATCGCAACGAGTATTCGTAAAAATCACAACGCGTATCCG
1 TAAATCGCAACGAGAATACGT-AAAATCGCAACGCGTATCCG
*
212459 TAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
*
212500 TAAATCGCAACGAGAATACGT-AAATCGCAACGCG-ATTC-
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * * *
212538 TGACTATCGCAACGAGTATCCGTAAAATCGCAACGTGTATCCG
1 T-A-AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * *
212581 TAAATCGCAACGACAATACGTAAAATCACAACGTGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
*
212622 TAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * * *
212663 TAAATCGTAATGAGAATACGTAAAATCGCAACACG-ATTC-
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * * * * *
212702 TGATTATCGCAACCAGAATACGT-TAATCGCAACGAGAATCTG
1 T-A-AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * *
212744 TAAATCGCAACGATAATCCGT-AAATCGCAACG-ATAATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGT-ATCCG
212784 TAAATCGCAACGAGAAT-CTGT-AAATCGCAAC
1 TAAATCGCAACGAGAATAC-GTAAAATCGCAAC
212815 ACTTAAATTT
Statistics
Matches: 374, Mismatches: 53, Indels: 26
0.83 0.12 0.06
Matches are distributed among these distances:
38 1 0.00
39 6 0.02
40 100 0.27
41 209 0.56
42 57 0.15
43 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (41 bp):
TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
Found at i:212659 original size:163 final size:164
Alignment explanation
Indices: 212379--212814 Score: 589
Period size: 163 Copynumber: 2.7 Consensus size: 164
212369 GTATCCGTAA
* * ** *
212379 ATCGCAACGACAATACGTAAAGTCGCAAC-ACGTATCCGTAAATCGCAACGAGTATTCGTAAAAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGA-GTATCCGTAAATCGCAACGACAATACGT-AAAA
*
212443 TCACAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGC
64 TCACAACGTGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGC
*
212508 AACGAGAATACGT-AAATCGCAACGCGATTCTGACT
129 AACGAGAATACGTAAAATCGCAACACGATTCTGACT
* * *
212543 ATCGCAACGAGTATCCGTAAAATCGCAACGTGTATCCGTAAATCGCAACGACAATACGTAAAATC
1 ATCGCAACGAGAATACGTAAAATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAAATC
*
212608 ACAACGTGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGTAA
66 ACAACGTGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAA
* *
212673 TGAGAATACGTAAAATCGCAACACGATTCTGATT
131 CGAGAATACGTAAAATCGCAACACGATTCTGACT
* * * * * *
212707 ATCGCAACCAGAATACGT-TAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT-AAATC
1 ATCGCAACGAGAATACGTAAAATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAAATC
* * *
212770 GCAACGAT-AATCCGTAAATCGCAACGAGAAT-CTGT-AAATCGCAAC
66 ACAACG-TGTATCCGTAAATCGCAACGACAATAC-GTAAAATCGCAAC
212815 ACTTAAATTT
Statistics
Matches: 243, Mismatches: 25, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
161 11 0.05
162 33 0.14
163 114 0.47
164 85 0.35
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (164 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAAATC
ACAACGTGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAA
CGAGAATACGTAAAATCGCAACACGATTCTGACT
Found at i:213497 original size:12 final size:12
Alignment explanation
Indices: 213476--213509 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
213466 ACCACATTTC
*
213476 CAATACCAAACA
1 CAATATCAAACA
213488 CAATATCAAACA
1 CAATATCAAACA
*
213500 CAATCTCAAA
1 CAATATCAAA
213510 ACCTACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:216217 original size:33 final size:33
Alignment explanation
Indices: 216161--216431 Score: 470
Period size: 33 Copynumber: 8.2 Consensus size: 33
216151 TCATTTTACT
* * *
216161 ATCGCAACGCGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
216195 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
216228 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
216261 ATCGCAATGCGAAATGAAAATCGCAACGCGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
216294 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
216327 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
216360 ATCGTAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
216393 ATCGCAATGCGAAATGAAAATCTCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
216426 ATCGCA
1 ATCGCA
216432 CTCGTTGTGA
Statistics
Matches: 227, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
33 218 0.96
34 9 0.04
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:216587 original size:14 final size:14
Alignment explanation
Indices: 216568--216604 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
216558 CATCAATTAA
216568 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
216582 ACAAATCATCTTTT
1 ACAAATCAACTTTT
216596 ACAAATCAA
1 ACAAATCAA
216605 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:216745 original size:82 final size:84
Alignment explanation
Indices: 216571--216747 Score: 331
Period size: 83 Copynumber: 2.1 Consensus size: 84
216561 CAATTAAACA
216571 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
216636 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
*
216655 AATCAACTTTTACAAATCATCTTTTAC-AATGAATTAAACAATCAAAAAATAAGCAATAATTC-T
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
216718 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
216737 AATCAACTTTT
1 AATCAACTTTT
216748 GCAGCCATAC
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
82 31 0.34
83 34 0.37
84 27 0.29
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (84 bp):
AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
ATTTCCTCATCTACTATTG
Found at i:218123 original size:42 final size:41
Alignment explanation
Indices: 218038--218160 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
218028 GTGAATCGGG
* * * *
218038 CTCTTGAATGGTGGGA-GGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
218080 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
218122 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
218161 CGAGTCGAGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:218548 original size:21 final size:20
Alignment explanation
Indices: 218524--218570 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
218514 GCAGAAGAAA
218524 CGCAACGAGAGAAATGAAAAT
1 CGCAACG-GAGAAATGAAAAT
*
218545 CGCAAC-GCGAAATGAAAAT
1 CGCAACGGAGAAATGAAAAT
*
218564 CACAACG
1 CGCAACG
218571 CGAAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 17 0.74
21 6 0.26
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (20 bp):
CGCAACGGAGAAATGAAAAT
Found at i:218556 original size:19 final size:19
Alignment explanation
Indices: 218534--218586 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
218524 CGCAACGAGA
218534 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
218553 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
**
218572 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
218587 TTGCGATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.51, C:0.23, G:0.17, T:0.09
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:218604 original size:19 final size:19
Alignment explanation
Indices: 218582--218697 Score: 90
Period size: 19 Copynumber: 6.6 Consensus size: 19
218572 GAAACCAAAA
*
218582 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
218601 TCGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
218615 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
218634 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
218648 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
218667 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
218687 TCGTGTTGCGA
1 TCGCGTTGCGA
218698 AAGTAAACTA
Statistics
Matches: 75, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
14 18 0.24
16 6 0.08
17 6 0.08
19 33 0.44
20 12 0.16
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:218629 original size:33 final size:33
Alignment explanation
Indices: 218587--218679 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
218577 CAAAATCGCA
*
218587 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
218620 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
218653 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
218680 TTAAGTTTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:218972 original size:94 final size:92
Alignment explanation
Indices: 218808--218999 Score: 321
Period size: 94 Copynumber: 2.1 Consensus size: 92
218798 GAATACACAG
* * *
218808 TTTAGTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATATACAGTT
1 TTTACTTCAACCAAAAGACAAAACAAAGACAAATACTACTTCACAGTGTTAAAGAATAAACAGTT
*
218873 TAGCAGAATTGGTAGCAACCGAATAAA
66 TAGCAGAATTGGCAGCAACCGAATAAA
218900 TTTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTTACTTCAACCAAAAGACAAAAC-AAAGACAAATACT-ACTTCACAGTGTTAAAGAATAAACAG
*
218965 TTTAGCAGTATTGGCAGCAACCGAATAAA
64 TTTAGCAGAATTGGCAGCAACCGAATAAA
218994 TTTACT
1 TTTACT
219000 AAGCAATCTA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 23 0.25
93 13 0.14
94 57 0.61
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (92 bp):
TTTACTTCAACCAAAAGACAAAACAAAGACAAATACTACTTCACAGTGTTAAAGAATAAACAGTT
TAGCAGAATTGGCAGCAACCGAATAAA
Found at i:220678 original size:14 final size:14
Alignment explanation
Indices: 220659--220715 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
220649 TTGAAATGAA
220659 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
220673 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
220692 AATCGCAACGAGAG
1 AATCGCAACGAGAG
220706 AATCGCAACG
1 AATCGCAACG
220716 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:220691 original size:33 final size:33
Alignment explanation
Indices: 220651--220732 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
220641 TCTTTTGGTT
220651 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
220684 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
220717 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
220733 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:220697 original size:19 final size:19
Alignment explanation
Indices: 220673--220737 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
220663 GCAACGAGAG
220673 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
220692 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
220706 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
220725 AATCGCAATGCGA
1 AATCGCAACGCGA
220738 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:220798 original size:21 final size:19
Alignment explanation
Indices: 220733--220785 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
220723 AAAATCGCAA
**
220733 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
220752 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
220771 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
220786 TCTCGTTGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:221383 original size:42 final size:42
Alignment explanation
Indices: 221311--221409 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
221301 GTGTTTTAAA
** * *
221311 AATCGCGTTGCGA-TTTTACGTATTGTCGTTGCGAT-TTATG
1 AATCGCGTTGCGATTTTTACGTATACTCGTTGCGATAGTAAG
*
221351 GATACGCGTTGCGATTTTTACAG-ATACTCGTTGCGATAGTAAG
1 AAT-CGCGTTGCGATTTTTAC-GTATACTCGTTGCGATAGTAAG
221394 AATCGCGTTGCGATTT
1 AATCGCGTTGCGATTT
221410 ATATGTTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 2 0.04
41 10 0.20
42 31 0.63
43 6 0.12
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.37
Consensus pattern (42 bp):
AATCGCGTTGCGATTTTTACGTATACTCGTTGCGATAGTAAG
Found at i:221438 original size:20 final size:20
Alignment explanation
Indices: 221313--221448 Score: 82
Period size: 20 Copynumber: 6.7 Consensus size: 20
221303 GTTTTAAAAA
*
221313 TCGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CATAT
221334 T-GTCGTTGCGA-TTT-ATGGAT
1 TCG-CGTTGCGATTTTCAT--AT
* *
221354 ACGCGTTGCGATTTTTACAGAT
1 TCGCGTTGCGA-TTTT-CATAT
* * ** * * *
221376 ACTCGTTGCGATAGTAAGAA
1 TCGCGTTGCGATTTTCATAT
*
221396 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
221416 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
221436 TCGCGTTGCGATT
1 TCGCGTTGCGATT
221449 CTGGAAAATC
Statistics
Matches: 89, Mismatches: 16, Indels: 21
0.71 0.13 0.17
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 58 0.65
21 13 0.15
22 15 0.17
24 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:222544 original size:23 final size:23
Alignment explanation
Indices: 222515--222559 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
222505 ACACAAGTAC
*
222515 ACATTTATTGCTTTGGTTTTGCT
1 ACATTTATTGCTTTGATTTTGCT
222538 ACATTTATTGCTTTGATTTTGC
1 ACATTTATTGCTTTGATTTTGC
222560 CGAATTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.56
Consensus pattern (23 bp):
ACATTTATTGCTTTGATTTTGCT
Found at i:228800 original size:9 final size:9
Alignment explanation
Indices: 228786--228812 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
228776 GAGCAAAACA
228786 ACAACCAGT
1 ACAACCAGT
228795 ACAACCAGT
1 ACAACCAGT
228804 ACAACCAGT
1 ACAACCAGT
228813 TCGGTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.33, G:0.11, T:0.11
Consensus pattern (9 bp):
ACAACCAGT
Found at i:231601 original size:25 final size:25
Alignment explanation
Indices: 231570--231618 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
231560 GTATACAATG
231570 ATAAACCTTAATCCAATGAAAAACA
1 ATAAACCTTAATCCAATGAAAAACA
231595 ATAAACCTTAATCCAATGAAAAAC
1 ATAAACCTTAATCCAATGAAAAAC
231619 TTAGTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.20, G:0.04, T:0.20
Consensus pattern (25 bp):
ATAAACCTTAATCCAATGAAAAACA
Found at i:234422 original size:3 final size:3
Alignment explanation
Indices: 234414--234504 Score: 74
Period size: 3 Copynumber: 27.3 Consensus size: 3
234404 TGATTGCTTT
*
234414 GAA GAA GAA GAA GAA GAAA GAA TGAA GAA GAA AAA GGAA GGAA GGAA
1 GAA GAA GAA GAA GAA G-AA GAA -GAA GAA GAA GAA -GAA -GAA -GAA
* *
234461 GAA GGAG GAA GGGA GAA GAA GGAA GAA GGAA GAA GAA GAA GAA G
1 GAA -GAA GAA -GAA GAA GAA -GAA GAA -GAA GAA GAA GAA GAA G
234505 CTGTCACGTT
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
3 49 0.65
4 26 0.35
ACGTcount: A:0.59, C:0.00, G:0.40, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:234441 original size:7 final size:6
Alignment explanation
Indices: 234414--234504 Score: 74
Period size: 7 Copynumber: 13.7 Consensus size: 6
234404 TGATTGCTTT
* *
234414 GAAGAA GAAGAA GAAGAAA GAATGAA GAAGAA AAAGGAA GGAAGGAA GAAGGAG
1 GAAGAA GAAGAA GAAG-AA GAA-GAA GAAGAA GAA-GAA -GAA-GAA GAA-GAA
*
234468 GAAGGGA GAAGAA GGAAGAA GGAAGAA GAAGAA GAAG
1 GAA-GAA GAAGAA -GAAGAA -GAAGAA GAAGAA GAAG
234505 CTGTCACGTT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
6 27 0.36
7 40 0.54
8 7 0.09
ACGTcount: A:0.59, C:0.00, G:0.40, T:0.01
Consensus pattern (6 bp):
GAAGAA
Found at i:234442 original size:17 final size:17
Alignment explanation
Indices: 234415--234504 Score: 96
Period size: 17 Copynumber: 5.4 Consensus size: 17
234405 GATTGCTTTG
234415 AAGAA-GAAGAAGAAGA
1 AAGAAGGAAGAAGAAGA
*
234431 AAGAATGAAGAAGAA-A
1 AAGAAGGAAGAAGAAGA
*
234447 AAGGAAGGAAGGAAGAAGG
1 AA-GAAGGAA-GAAGAAGA
* * *
234466 AGGAAGGGAGAAGAAGG
1 AAGAAGGAAGAAGAAGA
234483 AAGAAGGAAGAAGAAG-
1 AAGAAGGAAGAAGAAGA
234499 AAGAAG
1 AAGAAG
234505 CTGTCACGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
16 14 0.22
17 37 0.58
18 12 0.19
19 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.39, T:0.01
Consensus pattern (17 bp):
AAGAAGGAAGAAGAAGA
Found at i:238921 original size:21 final size:21
Alignment explanation
Indices: 238883--238922 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
238873 AATGTCTATT
238883 ATATTATTATCTTGAAGTTGG
1 ATATTATTATCTTGAAGTTGG
*
238904 ATATTTTTCATCTT-AAGTT
1 ATATTATT-ATCTTGAAGTT
238923 CTAACACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (21 bp):
ATATTATTATCTTGAAGTTGG
Found at i:243585 original size:60 final size:60
Alignment explanation
Indices: 243515--243698 Score: 196
Period size: 60 Copynumber: 3.1 Consensus size: 60
243505 TGCATCATAT
* *
243515 ATCCCCAAACTATAACCCTCATT-TCAAATTAGTCCTTAAACTTTTAAATATTCTAATTTC
1 ATCCCCAAACTATGACTCTCATTCT-AAATTAGTCCTTAAACTTTTAAATATTCTAATTTC
* * * * *
243575 ATCCCCAAACTATGTCTCTCATTCTAAATTAGCCCTTAAA-TTTTAAACATTCCAATTTT
1 ATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTCTAATTTC
* * ** * *
243634 ATCCCTAAAATATGGA-TCTCATTCTAAATTAGTCCCCAAACTTTTGAAT-TTTTCAATTTC
1 ATCCCCAAACTAT-GACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTCT-AATTTC
243694 ATCCC
1 ATCCC
243699 TAAATTTATC
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
59 50 0.49
60 51 0.50
61 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (60 bp):
ATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTCTAATTTC
Found at i:243654 original size:59 final size:60
Alignment explanation
Indices: 243532--243698 Score: 178
Period size: 59 Copynumber: 2.8 Consensus size: 60
243522 AACTATAACC
* * * * **
243532 CTCATT-TCAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATCCCCAAACTATGTCT
1 CTCATTCT-AAATTAGCCCTTAAACTTTTAAACATTCCAATTTCATCCCCAAAATATGGAT
* *
243592 CTCATTCTAAATTAGCCCTTAAA-TTTTAAACATTCCAATTTTATCCCTAAAATATGGAT
1 CTCATTCTAAATTAGCCCTTAAACTTTTAAACATTCCAATTTCATCCCCAAAATATGGAT
* * ** *
243651 CTCATTCTAAATTAGTCCC-CAAACTTTTGAATTTTTCAATTTCATCCC
1 CTCATTCTAAATTAG-CCCTTAAACTTTTAAACATTCCAATTTCATCCC
243699 TAAATTTATC
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 47 0.52
60 42 0.47
61 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (60 bp):
CTCATTCTAAATTAGCCCTTAAACTTTTAAACATTCCAATTTCATCCCCAAAATATGGAT
Found at i:244553 original size:31 final size:31
Alignment explanation
Indices: 244496--244561 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
244486 TACTAATCTA
*
244496 AGAATTTTTTTAAAGTTTAAGTACCAATTTG
1 AGAATTTTTTTAAAGTTTAAGAACCAATTTG
244527 AGAATTTGTTTT-AA-TTTAAGGAACCAATTTG
1 AGAATTT-TTTTAAAGTTTAA-GAACCAATTTG
244558 AGAA
1 AGAA
244562 AAAAAAGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 5 0.16
31 23 0.72
32 4 0.12
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (31 bp):
AGAATTTTTTTAAAGTTTAAGAACCAATTTG
Found at i:248928 original size:32 final size:33
Alignment explanation
Indices: 248855--248929 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 33
248845 TCATAAACCT
* *
248855 TTTATTAAA-TTTATTAAACTATTATAAAACTA
1 TTTATTAAATTTTATCAAACTATTACAAAACTA
*
248887 -TCATTAAATTTTATCAAACTATTACAAAA-TA
1 TTTATTAAATTTTATCAAACTATTACAAAACTA
*
248918 TTTATCAAATTT
1 TTTATTAAATTT
248930 AGTGAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (33 bp):
TTTATTAAATTTTATCAAACTATTACAAAACTA
Found at i:250914 original size:3 final size:3
Alignment explanation
Indices: 250908--250939 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
250898 TAAAAAAAAG
*
250908 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
250940 AAGACTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:251731 original size:3 final size:3
Alignment explanation
Indices: 251723--251816 Score: 125
Period size: 3 Copynumber: 30.7 Consensus size: 3
251713 TCATTTAAAT
** *
251723 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
251771 TAA TTA TTA TTTA TTA TTA TTA TTA CTA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
251817 TAATAAATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 73 0.92
4 6 0.08
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:253463 original size:2 final size:2
Alignment explanation
Indices: 253458--253493 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
253448 AATTATTTTA
253458 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
253494 CAAAGAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:254077 original size:20 final size:21
Alignment explanation
Indices: 254054--254105 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
254044 AGAAATTAAA
254054 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
254074 AATTCTTTTTTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
254096 -ATT-ATTTATT
1 AATTCATTTATT
254106 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:258203 original size:14 final size:14
Alignment explanation
Indices: 258163--258211 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
258153 GCAAAGAAAG
258163 AAGAAAAAAAAAAC
1 AAGAAAAAAAAAAC
* *
258177 AA-ACAAACAAAA-
1 AAGAAAAAAAAAAC
258189 AAGAAAAAAAGAAA-
1 AAGAAAAAAA-AAAC
258203 AAGAAAAAA
1 AAGAAAAAA
258212 TTGAATCAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 13 0.45
14 14 0.48
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAAC
Found at i:260394 original size:93 final size:93
Alignment explanation
Indices: 260230--260509 Score: 420
Period size: 93 Copynumber: 3.0 Consensus size: 93
260220 AGAAGACCCA
* *
260230 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
260295 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGGAAGATGAATGTGCTC
* *
260323 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTATGAAACCACAGAACCGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
260388 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGGAAGATGAATGTGCTC
* * * * *
260416 ATAGCATCTTCTGGAAGTGTTATTTGAATTATCTGATCTGATTTGGTATG-AACTC-CAAAATCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAAC-CACAGAACCA
* ** *
260479 ATCATTGGATTTAAAAGATGAATTTGCTC
65 ATCATTGAATTTGGAAGATGAATGTGCTC
260508 AT
1 AT
260510 GGTAGAAATA
Statistics
Matches: 171, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
92 35 0.20
93 136 0.80
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
TCATTGAATTTGGAAGATGAATGTGCTC
Found at i:260616 original size:114 final size:114
Alignment explanation
Indices: 260416--260728 Score: 441
Period size: 114 Copynumber: 2.7 Consensus size: 114
260406 GAATGTGCTC
* * * * *
260416 ATAGCATCTTCTGGAAGTGTTATTTGAATTATCTGATCTGATTTGGTATGAA-CTCCAAAATCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCTCCAAACT-AA
* * * * **
260480 TCATTGGATTTAAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTTA
65 TCATTGGATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACCCA
*
260530 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCCCCAAACTAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCTCCAAACTAAT
260595 CATTGGATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACCCA
66 CATTGGATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACCCA
** *
260644 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AGAACCTTAAAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATA-AACCTCCAAACTAA
* *
260708 TCATTGGATTAGGAAGATGAA
65 TCATTGGATTTGAAAGATGAA
260729 CTACATGATC
Statistics
Matches: 179, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
113 1 0.01
114 171 0.96
115 7 0.04
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.34
Consensus pattern (114 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCTCCAAACTAAT
CATTGGATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACCCA
Found at i:262899 original size:54 final size:52
Alignment explanation
Indices: 262794--262903 Score: 166
Period size: 54 Copynumber: 2.1 Consensus size: 52
262784 CAATGATTGA
***
262794 GAACATCTGAGCAGAAGCCACAAAAAAATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAATGAATGCACTGTCAAATGTTTTAC
*
262846 GAACATCTGAGCAGAAGCCACAGGAAAAGATGAATGCACTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACA--AAAAAATGAATGCACTGTCAAATGTTTTAC
262900 GAAC
1 GAAC
262904 CTGTTATTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 22 0.42
54 30 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (52 bp):
GAACATCTGAGCAGAAGCCACAAAAAAATGAATGCACTGTCAAATGTTTTAC
Found at i:263300 original size:22 final size:22
Alignment explanation
Indices: 263271--263325 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
263261 ATCTACACTC
*
263271 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
263293 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
263315 TTCAAAGATGA
1 TTCAAAGATGA
263326 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:264162 original size:76 final size:76
Alignment explanation
Indices: 264009--264197 Score: 324
Period size: 76 Copynumber: 2.5 Consensus size: 76
263999 CTATTTCCTA
*
264009 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
264074 AAACCTTAGGGT
65 AAACCTTAGGGT
*
264086 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
* *
264151 AGCCTTCGGGT
66 AACCTTAGGGT
*
264162 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAA
264198 CCTTAGGGTC
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 76 0.71
77 31 0.29
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:264192 original size:45 final size:45
Alignment explanation
Indices: 264139--264252 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
264129 GGGAGCTTTT
264139 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
264184 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
264229 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
264253 AGCTTTTTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 52 0.84
47 10 0.16
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:264277 original size:121 final size:121
Alignment explanation
Indices: 264063--264439 Score: 711
Period size: 121 Copynumber: 3.1 Consensus size: 121
264053 GGGAGCTTTT
264063 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264128 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
264184 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264249 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
264305 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
264370 CGGGAGCTTTTTGATGTTTTCAAAGCC-TCAGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTC-GGGTCATCTGTAAGTCCTTCAGTGCA
*
264426 TGATGTTTCCAAAA
1 TGATGTTTTCAAAA
264440 AGCCTTCGGG
Statistics
Matches: 252, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
120 2 0.01
121 250 0.99
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:264313 original size:45 final size:45
Alignment explanation
Indices: 264260--264373 Score: 192
Period size: 45 Copynumber: 2.5 Consensus size: 45
264250 GGGAGCTTTT
264260 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
264305 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
264350 TGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
264374 AGCTTTTTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 53 0.84
47 10 0.16
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:264387 original size:197 final size:195
Alignment explanation
Indices: 264009--265158 Score: 1432
Period size: 197 Copynumber: 5.8 Consensus size: 195
263999 CTATTTCCTA
* *
264009 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* *
264074 AAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
264139 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTAG
130 TGATGTTTTC--AGGCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTAG
264204 GGT
193 GGT
264207 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * * * *
264272 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTTAGGG-TC-ATCT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * * * ** *** *** *
264333 GTAAGTCCTTCAGTGCAT-GATGTTTTCAAAAAG-CCTTCGGGAGCTTTTTGATGTTTTCAAAGC
131 G-ATGT-TTTCAG-GCTTCG-GGTCATCTGTAAGTCCTTC---AG-TGCATGATGTTTTCAAAAC
*
264396 CTCAGGGT
188 CTTAGGGT
*
264404 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
264469 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * * *
264534 GATGTTTTAAAGCCTTCGGGTCATCTGTAAGTCTTTCAGTGCATGATGTTTTCAAAACCTTCGGG
131 GATGTTTT-CAGGCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTAGGG
264599 T
195 T
264600 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
264665 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * * *
264730 GATGTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCA
131 GATGTTTT-CAGGCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTT-A
264795 GGAG-
192 GG-GT
* * * * ** * ** *** ***
264799 C-TTTTTGATGT-TTTCAAAGCCT--TCGGGTCATCTGTAAGTCCTTC---AG-TGCATGATGTT
1 CATCTGT-AAGTCCTTCAGTGCATGAT-GTTTC--CAAAAAG-CCTTCGGGAGCTTTTTGATGTT
* *
264856 TTCAAAACCTTCGGGTCATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC
61 TTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC
*
264921 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
126 TTTTTGATGTTTTC--AGGCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
*
264986 TTCGGGT
189 TTAGGGT
*
264993 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-A
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* *
265057 AAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTTGGGAGCTTT
65 AAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTT
* *
265122 TTGATGTTTTAAAGCCTTCGGGTCATCTGTAAGTCCT
129 TTGATGTTTT-CAGGCTTCGGGTCATCTGTAAGTCCT
265159 ACAATGTATG
Statistics
Matches: 819, Mismatches: 95, Indels: 77
0.83 0.10 0.08
Matches are distributed among these distances:
193 12 0.01
194 23 0.03
195 28 0.03
196 296 0.36
197 319 0.39
198 93 0.11
199 28 0.03
200 17 0.02
201 3 0.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (195 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAGGCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTAGGGT
Done.