Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008686.1 Hibiscus syriacus cultivar Beakdansim tig00111710_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: 137094
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9927 original size:39 final size:39
Alignment explanation
Indices: 9868--10108 Score: 315
Period size: 39 Copynumber: 6.2 Consensus size: 39
9858 TCAACAACAA
*
9868 CAGACTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
1 CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
**
9907 CAGATTTTGAAGAATCAGTTGCTGCATTAACCTCTCCCT
1 CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
* *
9946 TAGATTTTGAAGAATCAGATGCCACATTAACCTCTCCCT
1 CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
*
9985 CAGATTTTGAAGAATCAGTTGCTC-TATTAACCTCTCCCT
1 CAGATTTTGAAGAATCAGTTGC-CACATTAACCTCTCCCT
* * * *
10024 CAGATTTTGTAGAATCAGTTTCCACATTAACCTCTTCGT
1 CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
* * * * *
10063 CATATTTTGAAGAAT-TGATTGCAACATTAACCACTCCCA
1 CAGATTTTGAAGAATCAG-TTGCCACATTAACCTCTCCCT
10102 CAGATTT
1 CAGATTT
10109 AGCGACAGAT
Statistics
Matches: 174, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
38 2 0.01
39 171 0.98
40 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (39 bp):
CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
Found at i:10492 original size:53 final size:53
Alignment explanation
Indices: 10412--10517 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
10402 CAAATTATAT
10412 ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
1 ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
10465 ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
1 ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
10518 GCTCCCTCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (53 bp):
ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
Found at i:12693 original size:242 final size:243
Alignment explanation
Indices: 12265--12747 Score: 842
Period size: 242 Copynumber: 2.0 Consensus size: 243
12255 GAACAAAGTA
12265 ATAAATGAATTGACAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
1 ATAAATGAATTGACAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
* * *
12330 TAGAAGAGGGAGGAAACTGAACAACATAACTTCTCAGAGGAATCATAACTGATTAATCCAGGGGA
66 TAGAAGAGGGAGGAAACTG-A-AACATAACTCCTCAGAGAAATCATAACTGATTAATCCAGAGGA
*
12395 AACAGAAAATATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAA
129 AACAGAAAAGATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAA
*
12460 GGAACACTAACATGTGAAAGCACTCAGGATCAGTCGGTTTTATAGGCAAC
194 GGAACACTAACATGTGAAAGCACTCAGGATCAGTCGGATTTATAGGCAAC
*
12510 ATAAATGAATTGATAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
1 ATAAATGAATTGACAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
* * *
12575 TAGATGAGGGAGGAAACTG-AACATAACTCCTCAGAGAAATCATAACTGATTATTCCAGAGGCAA
66 TAGAAGAGGGAGGAAACTGAAACATAACTCCTCAGAGAAATCATAACTGATTAATCCAGAGGAAA
12639 CAGAAAAGATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAAGG
131 CAGAAAAGATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAAGG
* *
12704 AACACTAACATGTGAAAGCACTCGGGATCAGTTGGATTTATAGG
196 AACACTAACATGTGAAAGCACTCAGGATCAGTCGGATTTATAGG
12748 TGGTATACAT
Statistics
Matches: 227, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
242 145 0.64
245 82 0.36
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (243 bp):
ATAAATGAATTGACAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
TAGAAGAGGGAGGAAACTGAAACATAACTCCTCAGAGAAATCATAACTGATTAATCCAGAGGAAA
CAGAAAAGATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAAGG
AACACTAACATGTGAAAGCACTCAGGATCAGTCGGATTTATAGGCAAC
Found at i:13959 original size:22 final size:21
Alignment explanation
Indices: 13931--13973 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
13921 AGAAGAATCA
13931 GCTTTTGCAATACAACAATACT
1 GCTTTTGCAATACAAC-ATACT
*
13953 GCTTTTGCAATGCAACATACT
1 GCTTTTGCAATACAACATACT
13974 TAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (21 bp):
GCTTTTGCAATACAACATACT
Found at i:20843 original size:23 final size:23
Alignment explanation
Indices: 20813--20863 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
20803 AAAGTTTCGC
*
20813 TTCAAATGCGTATTAAATCGTGG
1 TTCAAATGCATATTAAATCGTGG
20836 TTCAAATGCATATTAAATCGTGG
1 TTCAAATGCATATTAAATCGTGG
20859 TTCAA
1 TTCAA
20864 GGTAGTCGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (23 bp):
TTCAAATGCATATTAAATCGTGG
Found at i:20903 original size:26 final size:26
Alignment explanation
Indices: 20874--20929 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
20864 GGTAGTCGTC
*
20874 ATCAATCTTTATAAGGATGTGATTGA
1 ATCAATCATTATAAGGATGTGATTGA
* *
20900 ATCACTCATTATAAGGTTGTGATTGA
1 ATCAATCATTATAAGGATGTGATTGA
20926 ATCA
1 ATCA
20930 CTCAAAGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (26 bp):
ATCAATCATTATAAGGATGTGATTGA
Found at i:20930 original size:26 final size:26
Alignment explanation
Indices: 20882--20933 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
20872 TCATCAATCT
20882 TTATAAGGATGTGATTGAATCACTCA
1 TTATAAGGATGTGATTGAATCACTCA
*
20908 TTATAAGGTTGTGATTGAATCACTCA
1 TTATAAGGATGTGATTGAATCACTCA
20934 AAGCTAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (26 bp):
TTATAAGGATGTGATTGAATCACTCA
Found at i:25950 original size:24 final size:24
Alignment explanation
Indices: 25918--25967 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
25908 AATTCCAACC
25918 ATCATATTATAATAGGATGATTAA
1 ATCATATTATAATAGGATGATTAA
*
25942 ATCATATTATAGTAGGATGATTAA
1 ATCATATTATAATAGGATGATTAA
25966 AT
1 AT
25968 TCGAGACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (24 bp):
ATCATATTATAATAGGATGATTAA
Found at i:27080 original size:12 final size:12
Alignment explanation
Indices: 27065--27089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27055 TATATATATA
27065 ATTTTTGAAAAC
1 ATTTTTGAAAAC
27077 ATTTTTGAAAAC
1 ATTTTTGAAAAC
27089 A
1 A
27090 CATATATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:27095 original size:35 final size:35
Alignment explanation
Indices: 27024--27193 Score: 194
Period size: 35 Copynumber: 4.9 Consensus size: 35
27014 TATATATATA
27024 ATATATAATTTTT-AAAATCATTTTGAAAA-ATTAT
1 ATATATAATTTTTGAAAA-CATTTTGAAAACATTAT
*
27058 ATATATAATTTTTGAAAACATTTTTGAAAACA-CAT
1 ATATATAATTTTTGAAAACA-TTTTGAAAACATTAT
*
27093 ATAT-TATAGTTTTGAAAACATTTTGAAAACATTTAT
1 ATATATA-ATTTTTGAAAACATTTTGAAAACA-TTAT
* *
27129 ATATATAGTTTTT-AAAACGTTTTTGAAAAC-TTAT
1 ATATATAATTTTTGAAAAC-ATTTTGAAAACATTAT
*
27163 ATA-AT-ATTTTTGAAAACATGTTGAAAACATT
1 ATATATAATTTTTGAAAACATTTTGAAAACATT
27194 CGTATATTAT
Statistics
Matches: 117, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
32 14 0.12
33 9 0.08
34 35 0.30
35 36 0.31
36 21 0.18
37 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (35 bp):
ATATATAATTTTTGAAAACATTTTGAAAACATTAT
Found at i:27118 original size:11 final size:11
Alignment explanation
Indices: 27102--27126 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27092 TATATTATAG
27102 TTTTGAAAACA
1 TTTTGAAAACA
27113 TTTTGAAAACA
1 TTTTGAAAACA
27124 TTT
1 TTT
27127 ATATATATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:27187 original size:68 final size:71
Alignment explanation
Indices: 27024--27210 Score: 228
Period size: 68 Copynumber: 2.7 Consensus size: 71
27014 TATATATATA
*
27024 ATATAT-A-ATTTTT-AAAATCATTTTGAAAA-A-TTATATATATAATTTTTGAAAACATTTTTG
1 ATATATAATATTTTTGAAAA-CATTTTGAAAACATTTATATATATAGTTTTTGAAAACATTTTTG
27084 AAAACAC
65 AAAACAC
* * *
27091 ATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATATAGTTTTT-AAAACGTTTTTG-
1 ATATATAATATTTTTGAAAACATTTTGAAAACATTTATATATATAGTTTTTGAAAACATTTTTGA
27154 AAA-AC
66 AAACAC
* *
27159 TTATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATATAGTTT
1 ATATATAATATTTTTGAAAACATTTTGAAAACATT--TATA-TATATAGTTT
27211 AAGAAAAAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
67 6 0.06
68 34 0.32
69 19 0.18
70 20 0.19
71 26 0.25
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (71 bp):
ATATATAATATTTTTGAAAACATTTTGAAAACATTTATATATATAGTTTTTGAAAACATTTTTGA
AAACAC
Found at i:27283 original size:3 final size:3
Alignment explanation
Indices: 27275--27309 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
27265 TATATATATA
27275 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
27310 TTTCATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:31629 original size:24 final size:24
Alignment explanation
Indices: 31597--31646 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
31587 AATTCCAACC
31597 ATCATATTATAATAGGATGATTAA
1 ATCATATTATAATAGGATGATTAA
*
31621 ATCATATTATAGTAGGATGATTAA
1 ATCATATTATAATAGGATGATTAA
31645 AT
1 AT
31647 TCGAGACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (24 bp):
ATCATATTATAATAGGATGATTAA
Found at i:32742 original size:34 final size:34
Alignment explanation
Indices: 32699--32869 Score: 165
Period size: 35 Copynumber: 4.9 Consensus size: 34
32689 TATATATATA
32699 ATATATAATTTTTAAAATCATTTTGAAAA-ATTAT
1 ATATATAATTTTTAAAA-CATTTTGAAAACATTAT
*
32733 ATATATAATTTTTGAAAACATTTTTGAAAACA-CAT
1 ATATATAATTTTT-AAAACA-TTTTGAAAACATTAT
* *
32768 ATATTATAGTTTTGAAAACATTTTGAAAACATTTAT
1 ATA-TATAATTTTTAAAACATTTTGAAAACA-TTAT
*
32804 ATATTATATAGTTTTTAAAACGTTTTTGAAAAC-TTAT
1 ATA-TATA-A-TTTTTAAAAC-ATTTTGAAAACATTAT
* *
32841 A-ATAT--TTTTGAAAACATGTTGAAAACATT
1 ATATATAATTTTTAAAACATTTTGAAAACATT
32870 CGTATATTAT
Statistics
Matches: 117, Mismatches: 10, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
30 9 0.08
31 11 0.09
34 26 0.22
35 27 0.23
36 20 0.17
37 5 0.04
38 9 0.08
39 10 0.09
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (34 bp):
ATATATAATTTTTAAAACATTTTGAAAACATTAT
Found at i:32755 original size:12 final size:12
Alignment explanation
Indices: 32740--32764 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32730 TATATATATA
32740 ATTTTTGAAAAC
1 ATTTTTGAAAAC
32752 ATTTTTGAAAAC
1 ATTTTTGAAAAC
32764 A
1 A
32765 CATATATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:32793 original size:11 final size:11
Alignment explanation
Indices: 32777--32801 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
32767 TATATTATAG
32777 TTTTGAAAACA
1 TTTTGAAAACA
32788 TTTTGAAAACA
1 TTTTGAAAACA
32799 TTT
1 TTT
32802 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:32793 original size:69 final size:69
Alignment explanation
Indices: 32702--32880 Score: 197
Period size: 69 Copynumber: 2.6 Consensus size: 69
32692 ATATATAATA
*
32702 TATAATTTTTAAAATCATTTTGAAAA-A-TTATATA-TATA-A-TTTTTGAAAACATTTTTGAAA
1 TATAATTTTGAAAA-CATTTTGAAAACATTTATATATTATATAGTTTTT-AAAACATTTTTG-AA
32762 ACACATATAT
63 A-AC-T-TAT
* *
32772 TATAGTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACGTTTTTGAAAAC
1 TATAATTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTTGAAAAC
32837 TTAT
66 TTAT
* * * **
32841 AATATTTTTGAAAACATGTTGAAAACATTCGTATATTATA
1 TATAATTTTGAAAACATTTTGAAAACATTTATATATTATA
32881 GTTTAAGAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
69 49 0.51
70 14 0.15
71 9 0.09
72 7 0.07
73 12 0.12
74 5 0.05
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (69 bp):
TATAATTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTTGAAAAC
TTAT
Found at i:32957 original size:3 final size:3
Alignment explanation
Indices: 32949--32979 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
32939 TATATATATA
32949 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
32980 TCATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39105 original size:166 final size:163
Alignment explanation
Indices: 38834--39649 Score: 1301
Period size: 166 Copynumber: 5.0 Consensus size: 163
38824 TGCAGCTTAG
* * *
38834 CTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCA
1 CTCAAGGCAAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
38899 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACA
66 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACA
38964 CTCAGCTTCGAGGGCACATCATTTACAGCATAA
131 CTCAGCTTCGAGGGCACATCATTTACAGCATAA
* *
38997 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAG
1 CTCAAGGCAAGAAGGGTTATC--TG-CCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
39062 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
63 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
39127 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
128 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* *
39163 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAG
1 CTCAAGGCAAGAAGGGTTATC--TG-CCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
39228 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
63 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
* *
39293 ACACTCAGCTTCGAGGGCACACCATTTGCAGCATAA
128 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* *
39329 CTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCAAGAAGGGTTATCTGCC-ACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * *
39394 CATATCATTTGCAGTATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
64 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
* *
39459 CACTCAGCTTCGAGGGCACACCATTTGCAGCATAA
129 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* *
39494 CTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCAAGAAGGGTTATCTGCC-ACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * * *
39559 CATATCATTTGCAGTATAGCTTAAGTCAAGAAGGGCTATCTGCC-AAGACTCCCGAGTTCGATTA
64 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
* * * *
39623 CACTCAACTTCGAAGTCATATCATTTA
129 CACTCAGCTTCGAGGGCACATCATTTA
39650 TCATGGCAAG
Statistics
Matches: 628, Mismatches: 20, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
163 21 0.03
164 45 0.07
165 242 0.39
166 320 0.51
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (163 bp):
CTCAAGGCAAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACA
CTCAGCTTCGAGGGCACATCATTTACAGCATAA
Found at i:40399 original size:34 final size:34
Alignment explanation
Indices: 40356--40528 Score: 176
Period size: 34 Copynumber: 4.9 Consensus size: 34
40346 TATATATATA
40356 ATATATAATTTTTAAAATCATTTTGAAAA-ATTAT
1 ATATATAATTTTTAAAA-CATTTTGAAAACATTAT
*
40390 ATATATAATTTTTGAAAACATTTTTGAAAACA-CAT
1 ATATATAATTTTT-AAAACA-TTTTGAAAACATTAT
* *
40425 ATATTATAGTTTTGAAAACATTTTGAAAACATTTAT
1 ATA-TATAATTTTTAAAACATTTTGAAAACA-TTAT
*
40461 ATATTATATAGTTTTTAAAACGTTTTTGAAAAC-TTAT
1 ATA-TATA-A-TTTTTAAAAC-ATTTTGAAAACATTAT
*
40498 ATA-AT-ATTTTTGAAAACATGTTGAAAACATT
1 ATATATAATTTTT-AAAACATTTTGAAAACATT
40529 CGTATATTAT
Statistics
Matches: 119, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
32 14 0.12
33 8 0.07
34 26 0.22
35 26 0.22
36 19 0.16
37 7 0.06
38 9 0.08
39 10 0.08
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (34 bp):
ATATATAATTTTTAAAACATTTTGAAAACATTAT
Found at i:40412 original size:12 final size:12
Alignment explanation
Indices: 40397--40421 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40387 TATATATATA
40397 ATTTTTGAAAAC
1 ATTTTTGAAAAC
40409 ATTTTTGAAAAC
1 ATTTTTGAAAAC
40421 A
1 A
40422 CATATATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:40450 original size:11 final size:11
Alignment explanation
Indices: 40434--40458 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40424 TATATTATAG
40434 TTTTGAAAACA
1 TTTTGAAAACA
40445 TTTTGAAAACA
1 TTTTGAAAACA
40456 TTT
1 TTT
40459 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:40515 original size:71 final size:74
Alignment explanation
Indices: 40356--40545 Score: 231
Period size: 71 Copynumber: 2.7 Consensus size: 74
40346 TATATATATA
40356 ATATAT-A-ATTTTT-AAAATCATTTTGAAAA-A-TTATATA-TATA-A-TTTTTGAAAACATTT
1 ATATATAATATTTTTGAAAA-CATTTTGAAAACATTTATATATTATATAGTTTTTGAAAACATTT
40413 TTGAAAACAC
65 TTGAAAACAC
* * *
40423 ATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTT-AAAACGTTTT
1 ATATATAATATTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTGAAAACATTTT
40487 TG-AAA-AC
66 TGAAAACAC
* * **
40494 TTATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATATAGTTT
1 ATATATAATATTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTT
40546 AAGAAAAAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
67 6 0.06
68 1 0.01
69 16 0.15
70 5 0.05
71 55 0.51
72 7 0.07
73 12 0.11
74 5 0.05
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (74 bp):
ATATATAATATTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTGAAAACATTTT
TGAAAACAC
Found at i:40576 original size:71 final size:70
Alignment explanation
Indices: 40356--40575 Score: 175
Period size: 71 Copynumber: 3.1 Consensus size: 70
40346 TATATATATA
* * **
40356 ATATATAATTTTT-AAAATCATTTTGAAAA-ATT-ATATA-TATA-ATTTTTGAAAAC-ATTTTT
1 ATATAT-ATTTTTGAAAA-CATGTTGAAAACATTCATATATTATATAGTTTAAAAAACGA-TTTT
*
40415 GAAAACACAT
63 G-AAA-ACTT
* * * ** *
40425 ATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACGTTTTTGA
1 ATA-TATATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTTAAAAAACGATTTTGA
40490 AAACTT
65 AAACTT
*
40496 ATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATATAGTTTAAGAAAAAAAC-ATT
1 ATAT-ATATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTT----AAAAAACGATT
*
40560 TTGAAAATTT
61 TTGAAAACTT
40570 ATATAT
1 ATATAT
40576 TATATGTTTT
Statistics
Matches: 126, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
69 19 0.15
70 11 0.09
71 52 0.41
72 7 0.06
73 17 0.13
74 15 0.12
75 5 0.04
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.43
Consensus pattern (70 bp):
ATATATATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTTAAAAAACGATTTTGAA
AACTT
Found at i:40621 original size:3 final size:3
Alignment explanation
Indices: 40613--40638 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40603 ATATATATAT
40613 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40639 TTTCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:44602 original size:2 final size:2
Alignment explanation
Indices: 44589--44621 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
44579 ACCATTTGGC
*
44589 AT AT AC 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 A
44622 GCTTCAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:45809 original size:20 final size:20
Alignment explanation
Indices: 45784--45837 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
45774 TGGAAGCTCG
*
45784 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
45804 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
45824 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
45838 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:48927 original size:13 final size:13
Alignment explanation
Indices: 48909--48939 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
48899 GAAACTAACC
48909 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
48922 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
48935 TTTTT
1 TTTTT
48940 GCATCTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:51637 original size:148 final size:148
Alignment explanation
Indices: 51369--51665 Score: 594
Period size: 148 Copynumber: 2.0 Consensus size: 148
51359 AACCCAATCA
51369 GCATACTATCAGAGAGATTATGATGGACTACTTGCTGGTAACACAACAGCATTAGAAAGTGAGAC
1 GCATACTATCAGAGAGATTATGATGGACTACTTGCTGGTAACACAACAGCATTAGAAAGTGAGAC
51434 TGGGTTGTCTGTCTTCGAGTAATCCGTCTGGAAATGAAGGGTACGATGATCTTCACATTGTTTAC
66 TGGGTTGTCTGTCTTCGAGTAATCCGTCTGGAAATGAAGGGTACGATGATCTTCACATTGTTTAC
51499 CCATGGGATTATGGACGT
131 CCATGGGATTATGGACGT
51517 GCATACTATCAGAGAGATTATGATGGACTACTTGCTGGTAACACAACAGCATTAGAAAGTGAGAC
1 GCATACTATCAGAGAGATTATGATGGACTACTTGCTGGTAACACAACAGCATTAGAAAGTGAGAC
51582 TGGGTTGTCTGTCTTCGAGTAATCCGTCTGGAAATGAAGGGTACGATGATCTTCACATTGTTTAC
66 TGGGTTGTCTGTCTTCGAGTAATCCGTCTGGAAATGAAGGGTACGATGATCTTCACATTGTTTAC
51647 CCATGGGATTATGGACGT
131 CCATGGGATTATGGACGT
51665 G
1 G
51666 TCACCGAGCG
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 149 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (148 bp):
GCATACTATCAGAGAGATTATGATGGACTACTTGCTGGTAACACAACAGCATTAGAAAGTGAGAC
TGGGTTGTCTGTCTTCGAGTAATCCGTCTGGAAATGAAGGGTACGATGATCTTCACATTGTTTAC
CCATGGGATTATGGACGT
Found at i:53589 original size:123 final size:122
Alignment explanation
Indices: 53349--53576 Score: 307
Period size: 123 Copynumber: 1.9 Consensus size: 122
53339 TTGAATTTTT
* * ** * *
53349 TTGAAAGTTTAGGTACTAAAACAGACCAAATTTGATAGTTTAGGTACTAAATGCGTTAAATTTTT
1 TTGAAAGTGTAGATACTAAAACAGACCAAAAATGATAATTTAGGTACTAAATGCATTAAATTTTT
** *
53414 AATGGTAGGGTACGAAAATGAAACTAAAACTAAATGTTAGGTATGATTTTAAAAAAA
66 AATGACAGGGTACGAAAATGAAACTAAAACTAAACGTTAGGTATGATTTTAAAAAAA
*
53471 TTGAAAGTGTAGATACTAAAA-ATGGACCAAAAATGATAATTTAGGTACTAAATGCATTAAGTTT
1 TTGAAAGTGTAGATACTAAAACA--GACCAAAAATGATAATTTAGGTACTAAATGCATTAAATTT
* *
53535 TTAATGACAGTGTACTAAAATGAAA-TAAAAACTAAACGTTAG
64 TTAATGACAGGGTACGAAAATGAAACT-AAAACTAAACGTTAG
53577 TCATTGTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
121 1 0.01
122 20 0.22
123 70 0.77
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (122 bp):
TTGAAAGTGTAGATACTAAAACAGACCAAAAATGATAATTTAGGTACTAAATGCATTAAATTTTT
AATGACAGGGTACGAAAATGAAACTAAAACTAAACGTTAGGTATGATTTTAAAAAAA
Found at i:60780 original size:12 final size:12
Alignment explanation
Indices: 60765--60791 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
60755 TAAAAAGCTC
60765 AAAAAAATATCA
1 AAAAAAATATCA
60777 AAAAAAATATCA
1 AAAAAAATATCA
60789 AAA
1 AAA
60792 TGAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAATATCA
Found at i:69407 original size:16 final size:15
Alignment explanation
Indices: 69386--69419 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
69376 TATGTTGTGA
69386 GTTCTAGAATAGTGTT
1 GTTCTAGAATAGT-TT
69402 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
69417 GTT
1 GTT
69420 AGATTGTAGC
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:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:72313 original size:30 final size:30
Alignment explanation
Indices: 72277--72344 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
72267 ACTGCAAGTC
* *
72277 CCATCAATGTGCGTTCCACCAGTGCCTGCT
1 CCATCAACGTGCGTTCCACCAGTACCTGCT
*
72307 CCATCAACGTGTGTTCCACCAGTACCTGCT
1 CCATCAACGTGCGTTCCACCAGTACCTGCT
72337 CCATCAAC
1 CCATCAAC
72345 ACATCTGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (30 bp):
CCATCAACGTGCGTTCCACCAGTACCTGCT
Found at i:72356 original size:30 final size:29
Alignment explanation
Indices: 72292--72378 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 29
72282 AATGTGCGTT
*** * *
72292 CCACCAGTGCCTGCTCCATCAACGTGTGTT
1 CCACCAGT-CCTGCTCCATCAACACATCTG
72322 CCACCAGTACCTGCTCCATCAACACATCTG
1 CCACCAGT-CCTGCTCCATCAACACATCTG
* *
72352 CCACCATGTGCTTCTCCATCAACACAT
1 CCACCA-GTCCTGCTCCATCAACACAT
72379 GACTCATCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 46 0.96
31 2 0.04
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.24
Consensus pattern (29 bp):
CCACCAGTCCTGCTCCATCAACACATCTG
Found at i:75035 original size:16 final size:15
Alignment explanation
Indices: 75014--75047 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
75004 TATGTTGTGA
75014 GTTCTAGAATAGTGTT
1 GTTCTAGAATAGT-TT
75030 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
75045 GTT
1 GTT
75048 AGATTGTAGC
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:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:77941 original size:27 final size:27
Alignment explanation
Indices: 77889--77941 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
77879 TATTAGAAAC
* * *
77889 ATTATTATTTTTATCGATTTTGTTATT
1 ATTATTATTTTTATCGAGTATATTATT
77916 ATTATGTA-TTTTATCGAGTATATTAT
1 ATTAT-TATTTTTATCGAGTATATTAT
77942 CAAAACCGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.60
Consensus pattern (27 bp):
ATTATTATTTTTATCGAGTATATTATT
Found at i:78884 original size:17 final size:18
Alignment explanation
Indices: 78851--78884 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
78841 CCGCTACTAG
78851 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
78869 TGAACCGGTC-GAACCG
1 TGAACCGGTCAGAACCG
78885 GACCGGCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.32, G:0.29, T:0.12
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:90602 original size:13 final size:13
Alignment explanation
Indices: 90586--90610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
90576 TATTTAATAA
90586 TAATATCATTTTT
1 TAATATCATTTTT
90599 TAATATCATTTT
1 TAATATCATTTT
90611 AATAAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATATCATTTTT
Found at i:90627 original size:15 final size:15
Alignment explanation
Indices: 90609--90639 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
90599 TAATATCATT
90609 TTAATAAATAAAATA
1 TTAATAAATAAAATA
*
90624 TTAATTAATAAAATA
1 TTAATAAATAAAATA
90639 T
1 T
90640 ATTTATCAAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAATAAATAAAATA
Found at i:93712 original size:12 final size:12
Alignment explanation
Indices: 93695--93719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
93685 TAACAAAAAT
93695 ATCAAATTTATC
1 ATCAAATTTATC
93707 ATCAAATTTATC
1 ATCAAATTTATC
93719 A
1 A
93720 GGTCTGAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCAAATTTATC
Found at i:102669 original size:2 final size:2
Alignment explanation
Indices: 102662--102697 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
102652 TTCTCGATGC
102662 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
102698 TAAAGAGCCC
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:105829 original size:12 final size:12
Alignment explanation
Indices: 105814--105848 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
105804 CGATCAGAAT
105814 GACGAAGATGAA
1 GACGAAGATGAA
*
105826 GACGATGATGAA
1 GACGAAGATGAA
*
105838 GATGAAGATGA
1 GACGAAGATGA
105849 TGATGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.34, T:0.14
Consensus pattern (12 bp):
GACGAAGATGAA
Found at i:105838 original size:18 final size:18
Alignment explanation
Indices: 105812--105853 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
105802 GACGATCAGA
*
105812 ATGACGAAGATGAAGACG
1 ATGATGAAGATGAAGACG
*
105830 ATGATGAAGATGAAGATG
1 ATGATGAAGATGAAGACG
105848 ATGATG
1 ATGATG
105854 GAAAAGGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.33, T:0.19
Consensus pattern (18 bp):
ATGATGAAGATGAAGACG
Found at i:108663 original size:21 final size:21
Alignment explanation
Indices: 108637--108676 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
108627 ATTTTTTAAA
108637 ATTTTTAATAATA-AAAATATT
1 ATTTTTAA-AATATAAAATATT
108658 ATTTTTAAAATATAAAATA
1 ATTTTTAAAATATAAAATA
108677 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTTAAAATATAAAATATT
Found at i:110003 original size:14 final size:14
Alignment explanation
Indices: 109984--110025 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
109974 TTTTAGGATT
*
109984 AGGTTTAAGATTTA
1 AGGTTTATGATTTA
*
109998 AGGTTTATGATATA
1 AGGTTTATGATTTA
*
110012 GGGTTTATGATTTA
1 AGGTTTATGATTTA
110026 TGATTCGGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (14 bp):
AGGTTTATGATTTA
Found at i:110369 original size:16 final size:18
Alignment explanation
Indices: 110348--110384 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
110338 TTTATTTATC
*
110348 TAAAATTATTA-A-AATA
1 TAAAATAATTATATAATA
110364 TAAAATAATTATATAATA
1 TAAAATAATTATATAATA
110382 TAA
1 TAA
110385 TTGTATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATAATTATATAATA
Found at i:110803 original size:15 final size:16
Alignment explanation
Indices: 110783--110823 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
110773 GTTTACTTCA
*
110783 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
110798 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
110814 GAATGATTCA
1 GAATGATTCA
110824 GAGACTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:114155 original size:35 final size:35
Alignment explanation
Indices: 114116--114185 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
114106 TTTTTTAGCT
* * * *
114116 TCAATTCATGATTTCGAGTTCGAGTCGAGCTTGAA
1 TCAATTCATAATTTCAAGTTCGAGTCAAACTTGAA
*
114151 TCAATTCATAATTTCAATTTCGAGTCAAACTTGAA
1 TCAATTCATAATTTCAAGTTCGAGTCAAACTTGAA
114186 AATTTTAGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (35 bp):
TCAATTCATAATTTCAAGTTCGAGTCAAACTTGAA
Found at i:116393 original size:12 final size:12
Alignment explanation
Indices: 116378--116441 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
116368 TATTTAAACG
116378 GGTATTGGGCCA
1 GGTATTGGGCCA
* *
116390 GGTATTGGGTCG
1 GGTATTGGGCCA
*
116402 GGTATTGGGTC-
1 GGTATTGGGCCA
**
116413 GGTATTGGGCTG
1 GGTATTGGGCCA
* *
116425 GGAATCGGGCCA
1 GGTATTGGGCCA
116437 GGTAT
1 GGTAT
116442 ATATATATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 9 0.21
12 33 0.79
ACGTcount: A:0.14, C:0.12, G:0.45, T:0.28
Consensus pattern (12 bp):
GGTATTGGGCCA
Found at i:116418 original size:11 final size:12
Alignment explanation
Indices: 116378--116421 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
116368 TATTTAAACG
*
116378 GGTATTGGGCCA
1 GGTATTGGGTCA
*
116390 GGTATTGGGTCG
1 GGTATTGGGTCA
116402 GGTATTGGGTC-
1 GGTATTGGGTCA
116413 GGTATTGGG
1 GGTATTGGG
116422 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:116420 original size:23 final size:24
Alignment explanation
Indices: 116376--116441 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
116366 ATTATTTAAA
116376 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
116400 CGGGTATTGGGTC-GGTATTGGG-
1 CGGGTATTGGGCCAGGTATTGGGT
* *
116422 CTGGGAATCGGGCCAGGTAT
1 C-GGGTATTGGGCCAGGTAT
116442 ATATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 18 0.50
24 17 0.47
ACGTcount: A:0.14, C:0.14, G:0.45, T:0.27
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:116903 original size:2 final size:2
Alignment explanation
Indices: 116898--116935 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
116888 TGTGTGTATG
*
116898 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116936 CCATTTAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:123240 original size:20 final size:20
Alignment explanation
Indices: 123195--123240 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
123185 GACCAACAAA
* *
123195 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
123215 -TCGCAACGCGATCTCCATT
1 ATCGCAACGCGATCTCCAAT
123234 ATCGCAA
1 ATCGCAA
123241 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:123351 original size:20 final size:20
Alignment explanation
Indices: 123326--123392 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
123316 AATTCACAAT
123326 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
123346 GCGAATTGGGAAAATCGCAAT
1 GCGAA-TAAGTAAATCGCAAC
*
123367 GCGAATAAGTAAATTGCAAC
1 GCGAATAAGTAAATCGCAAC
123387 GCGAAT
1 GCGAAT
123393 TGGGAAAATC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:123362 original size:21 final size:21
Alignment explanation
Indices: 123336--123411 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
123326 GCGAATAAGT
123336 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
123357 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
123377 AAATTGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
123398 AAATCGCAATGCGA
1 AAATCGCAACGCGA
123412 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:123367 original size:41 final size:41
Alignment explanation
Indices: 123322--123411 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
123312 TCCCAATTCA
123322 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
*
123363 CAATGCGAATAAGTAAATTGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
123404 CAATGCGA
1 CAATGCGA
123412 TACTGACTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (41 bp):
CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
Found at i:123425 original size:20 final size:20
Alignment explanation
Indices: 123400--123494 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
123390 AATTGGGAAA
*
123400 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
123420 ATCGCAATGCGATAATAAAAAA
1 ATCGCAACGCGATACT--GACT
* *
123442 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
123462 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
123482 TTCGCAACGCGAT
1 ATCGCAACGCGAT
123495 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 46 0.77
22 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:124069 original size:19 final size:19
Alignment explanation
Indices: 124047--124091 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
124037 GCGACCAGAC
*
124047 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
124066 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
124085 AATCGCA
1 AATCGCA
124092 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:124109 original size:19 final size:19
Alignment explanation
Indices: 124087--124232 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
124077 GAAACCAAAA
*
124087 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
124106 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
124125 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
124141 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
124158 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
124172 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
124191 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
124211 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
124231 TC
1 TC
124233 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 19 0.19
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 42 0.42
20 30 0.30
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:124157 original size:33 final size:33
Alignment explanation
Indices: 124120--124207 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
124110 GTTGCGATTT
* **
124120 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
124153 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
124186 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
124208 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:124209 original size:20 final size:20
Alignment explanation
Indices: 124186--124232 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
124176 ATTGCGATAG
124186 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
124206 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
124226 TCATTTC
1 TCATTTC
124233 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:126294 original size:21 final size:21
Alignment explanation
Indices: 126270--126336 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
126260 TCATTCCTCG
126270 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
126291 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
126312 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
126333 AGAG
1 AGAG
126337 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:126294 original size:42 final size:42
Alignment explanation
Indices: 126214--126336 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
126204 GCTCGACTCG
* * * * * * *
126214 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
126256 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
126298 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
126337 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:127715 original size:14 final size:14
Alignment explanation
Indices: 127696--127731 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
127686 ATTGTTTAAT
127696 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
127710 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
127724 TGATTTGT
1 TGATTTGT
127732 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:127932 original size:19 final size:19
Alignment explanation
Indices: 127910--128060 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
127900 CGAAATTAAA
127910 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
127929 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
127944 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
127962 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
127976 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
127995 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
128010 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
128028 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
128047 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
128061 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:127956 original size:33 final size:32
Alignment explanation
Indices: 127914--128040 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
127904 ATTAAATTCG
127914 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
127947 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
127980 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
128013 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
128041 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:128003 original size:66 final size:66
Alignment explanation
Indices: 127907--128039 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
127897 ACGCGAAATT
*
127907 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
127972 G
66 G
*
127973 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
128038 G
66 G
128039 A
1 A
128040 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:130345 original size:12 final size:12
Alignment explanation
Indices: 130328--130352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
130318 TCTTCGGGGA
130328 CTTTTTCTTCTT
1 CTTTTTCTTCTT
130340 CTTTTTCTTCTT
1 CTTTTTCTTCTT
130352 C
1 C
130353 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:130561 original size:24 final size:24
Alignment explanation
Indices: 130527--130580 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
130517 CTGAAACATC
* *
130527 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
130551 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
130575 ATCAAA
1 ATCAAA
130581 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:131659 original size:20 final size:20
Alignment explanation
Indices: 131634--131691 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
131624 CATTCATTGA
131634 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
131654 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
131674 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
131692 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:131751 original size:19 final size:19
Alignment explanation
Indices: 131710--131777 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
131700 GAAATGAAAA
131710 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
131726 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
131743 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
131762 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
131778 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:133805 original size:20 final size:19
Alignment explanation
Indices: 133770--133835 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
133760 GAAACTTAAA
133770 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
133789 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
133809 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
133828 ATCGCAAC
1 ATCGCAAC
133836 AACAAAATCG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:133875 original size:31 final size:33
Alignment explanation
Indices: 133817--133886 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 33
133807 CTATCGCAAT
133817 GCGAAATGAAAATCGCAACAACAAAATCGAAAC
1 GCGAAATGAAAATCGCAACAACAAAATCGAAAC
* *
133850 GCGAAATG-AAATCGC-ACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACAACAAAATCGAAAC
133881 GCGAAA
1 GCGAAA
133887 CACAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 20 0.57
32 7 0.20
33 8 0.23
ACGTcount: A:0.50, C:0.23, G:0.19, T:0.09
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACAACAAAATCGAAAC
Found at i:133946 original size:32 final size:33
Alignment explanation
Indices: 133896--133988 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 33
133886 ACACAAATCG
*
133896 CATTGCGATTTTCATTTCGCGTTGCGATTTTAT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTAT
*
133929 CATTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTAT
* *
133961 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
133989 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.53
33 26 0.47
ACGTcount: A:0.15, C:0.18, G:0.19, T:0.47
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTAT
Found at i:133996 original size:19 final size:20
Alignment explanation
Indices: 133974--134016 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
133964 TGCGATTTTT
133974 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
133993 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
134013 ATTT
1 ATTT
134017 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:134007 original size:20 final size:20
Alignment explanation
Indices: 133982--134027 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
133972 TTATTTCGCA
133982 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
134002 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
134022 TTGCGA
1 TTGCGA
134028 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:135864 original size:20 final size:20
Alignment explanation
Indices: 135839--135876 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
135829 AATAGTTTCT
135839 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
135859 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
135877 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:136165 original size:22 final size:22
Alignment explanation
Indices: 136140--136183 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
136130 GATTTAGATA
136140 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
136162 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
136184 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:136396 original size:20 final size:20
Alignment explanation
Indices: 136371--136423 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
136361 GATTATATAT
*
136371 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
136391 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
136411 TATCTCGTTGCGA
1 TATCGCGTTGCGA
136424 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:136436 original size:41 final size:41
Alignment explanation
Indices: 136391--136468 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
136381 CGAAAGTCAG
* * *
136391 TATCGCGTTGCGAAAGT-AAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTCAA-TATCGCATTGCGATTTTTTAT
*
136432 TATCGCATTGCGATAGTCAATATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT
136469 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTTTAT
Found at i:136483 original size:21 final size:21
Alignment explanation
Indices: 136449--136546 Score: 101
Period size: 20 Copynumber: 4.7 Consensus size: 21
136439 TTGCGATAGT
136449 CAATATCGCATTGCGATTTTCC
1 CAAT-TCGCATTGCGATTTTCC
* *
136471 CAATTCGCGTTGCGA-TTTAC
1 CAATTCGCATTGCGATTTTCC
**
136491 TTATTCGCATTGCGATTTTCC
1 CAATTCGCATTGCGATTTTCC
* *
136512 CAATTCGCGTTGCGA-TTTAC
1 CAATTCGCATTGCGATTTTCC
**
136532 TTATTCGCATTGCGA
1 CAATTCGCATTGCGA
136547 ATTGGAAAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 32 0.52
21 26 0.42
22 4 0.06
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.39
Consensus pattern (21 bp):
CAATTCGCATTGCGATTTTCC
Found at i:136484 original size:41 final size:41
Alignment explanation
Indices: 136454--136546 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
136444 ATAGTCAATA
* *
136454 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACATAT
* *
136495 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACATAT
136536 TCGCATTGCGA
1 TCGCATTGCGA
136547 ATTGGAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACATAT
Done.