Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000495.1 Hibiscus syriacus cultivar Beakdansim tig00000942_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: 75518
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1936 original size:12 final size:12
Alignment explanation
Indices: 1919--1960 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1909 AGGTTTACGG
1919 GAAGCTGCAAAA
1 GAAGCTGCAAAA
1931 GAAGCTGCAAAA
1 GAAGCTGCAAAA
* *
1943 GAACCCGCAAAAA
1 GAAGCTGC-AAAA
1956 GAAGC
1 GAAGC
1961 CCAAGGAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.50, C:0.21, G:0.24, T:0.05
Consensus pattern (12 bp):
GAAGCTGCAAAA
Found at i:3260 original size:33 final size:33
Alignment explanation
Indices: 3217--3282 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
3207 AGATACCAAC
* ** *
3217 TTATATAAAGGTTATCATTTGTTATTGTTTAAT
1 TTATAAAAAGGTTATCATTCATTATTATTTAAT
*
3250 TTATAAAAAGGTTATTATTCATTATTATTTAAT
1 TTATAAAAAGGTTATCATTCATTATTATTTAAT
3283 AACAAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (33 bp):
TTATAAAAAGGTTATCATTCATTATTATTTAAT
Found at i:4503 original size:36 final size:36
Alignment explanation
Indices: 4383--4558 Score: 203
Period size: 36 Copynumber: 4.8 Consensus size: 36
4373 AGTCACTATT
*
4383 TGTAAACCATAATTCACACCCAAAAAAAGCTTCATATG
1 TGTAAACCATAATTCACACCCAAAAAAAGC--CACATG
* * * *
4421 TGTAAACCATAGTTCACACCGGAAAAAAGATCCATATG
1 TGTAAACCATAATTCACACC-CAAAAAA-AGCCACATG
4459 TGTAAACCATAATTCACACCCAAAATAAAGCC-CATG
1 TGTAAACCATAATTCACACCCAAAA-AAAGCCACATG
*
4495 TGTAAACCATAATTCACTCCCAAAATAAAGCC-CATG
1 TGTAAACCATAATTCACACCCAAAA-AAAGCCACATG
* * *
4531 TGTAAACCATATTTCGCACCAAAAAAAA
1 TGTAAACCATAATTCACACCCAAAAAAA
4559 AAACTCGAAG
Statistics
Matches: 123, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
35 3 0.02
36 59 0.48
37 7 0.06
38 46 0.37
39 6 0.05
40 2 0.02
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.22
Consensus pattern (36 bp):
TGTAAACCATAATTCACACCCAAAAAAAGCCACATG
Found at i:9190 original size:20 final size:19
Alignment explanation
Indices: 9165--9215 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
9155 GAAATCCCTT
*
9165 TGAAAATACATGATTTTTAA
1 TGAAAATACATGA-CTTTAA
* *
9185 TGAAAAAACAAGACTTTAA
1 TGAAAATACATGACTTTAA
*
9204 TGAACATACATG
1 TGAAAATACATG
9216 CTCTTGGTCG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (19 bp):
TGAAAATACATGACTTTAA
Found at i:10990 original size:2 final size:2
Alignment explanation
Indices: 10983--11011 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10973 AGAAGGGATT
10983 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
11012 TGGCTCCACG
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:12126 original size:24 final size:25
Alignment explanation
Indices: 12099--12145 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
12089 ACAATCCAGG
12099 TATGTGGATTA-ATGAAAA-TGATTA
1 TATGT-GATTATATGAAAAGTGATTA
*
12123 TATGTGTTTATATGAAAAGTGAT
1 TATGTGATTATATGAAAAGTGAT
12146 GAAAGAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (25 bp):
TATGTGATTATATGAAAAGTGATTA
Found at i:12269 original size:18 final size:18
Alignment explanation
Indices: 12246--12318 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
12236 AGGGATTATC
12246 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
12264 AGTGGTTCTTTGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
12283 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
12302 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGGGACA
12319 AATACTCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:17849 original size:2 final size:2
Alignment explanation
Indices: 17842--17940 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
17832 AAAAGGGATT
17842 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17926 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
17941 TGGCTCCACG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19056 original size:24 final size:25
Alignment explanation
Indices: 19029--19075 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
19019 ACAATCCAGG
19029 TATGTGGATTA-ATGAAAA-TGATTA
1 TATGT-GATTATATGAAAAGTGATTA
*
19053 TATGTGTTTATATGAAAAGTGAT
1 TATGTGATTATATGAAAAGTGAT
19076 GAAAGAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (25 bp):
TATGTGATTATATGAAAAGTGATTA
Found at i:19199 original size:18 final size:18
Alignment explanation
Indices: 19176--19248 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
19166 AGGGATTATC
19176 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
19194 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
19213 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
19232 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGGGACA
19249 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 30 0.62
19 4 0.08
20 14 0.29
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:20071 original size:19 final size:19
Alignment explanation
Indices: 20047--20091 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
20037 TGGGTTGCAT
20047 CTAAGAATGTCATGGTTCA
1 CTAAGAATGTCATGGTTCA
20066 CTAAGAATGTCATGGTTCA
1 CTAAGAATGTCATGGTTCA
20085 CTAAGAA
1 CTAAGAA
20092 ATATGTTGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (19 bp):
CTAAGAATGTCATGGTTCA
Found at i:20149 original size:96 final size:96
Alignment explanation
Indices: 19979--20168 Score: 299
Period size: 96 Copynumber: 2.0 Consensus size: 96
19969 TAAAAATATA
* * * *
19979 TCATAGTTCATTAAGAAATATGTTGTGATATGGAATGTTAATATTTTTATTAATAAAATGGGTTG
1 TCATAGTTCACTAAGAAATATGTTGCGATATGGAATGTTAATATTTTTATAAATAAAATGGGATG
* * *
20044 CATCTAAGAATGTCATGGTTCACTAAGAATG
66 CACCCAAGAATGTCATAGTTCACTAAGAATG
*
20075 TCATGGTTCACTAAGAAATATGTTGCGATATGGAATGTTAATATTTTTATAAATAAAATGGGATG
1 TCATAGTTCACTAAGAAATATGTTGCGATATGGAATGTTAATATTTTTATAAATAAAATGGGATG
*
20140 CGCCCAAGAATGTCATAGTTCACTAAGAA
66 CACCCAAGAATGTCATAGTTCACTAAGAA
20169 ACAGGTTGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (96 bp):
TCATAGTTCACTAAGAAATATGTTGCGATATGGAATGTTAATATTTTTATAAATAAAATGGGATG
CACCCAAGAATGTCATAGTTCACTAAGAATG
Found at i:20253 original size:76 final size:77
Alignment explanation
Indices: 20068--20424 Score: 443
Period size: 76 Copynumber: 4.7 Consensus size: 77
20058 ATGGTTCACT
* *
20068 AAGAATGTCATGGTTCACTAAGAAATATGTTGCGATATGGAATGTTAATATTTTTATAAATAAAA
1 AAGAATGTCATGGTTCACTAAGAAATATGTTGTGATATGGAATGTTAATATTTTTATTAATAAAA
* * *
20133 TGGGATGCGCCC
66 TAGGTTGCACCC
* * * * *
20145 AAGAATGTCATAGTTCACTAAGAAACAGGTTGTGATCTCGAATGTTAATATTTTTATTAATAAAA
1 AAGAATGTCATGGTTCACTAAGAAATATGTTGTGATATGGAATGTTAATATTTTTATTAATAAAA
* *
20210 TGGGTTG-ATCC
66 TAGGTTGCACCC
* *
20221 AAGAATGTCACGGTTCACTGAGAAATATGTTGTGATATGGAATGTTAATA-TTTTATTAATAAAA
1 AAGAATGTCATGGTTCACTAAGAAATATGTTGTGATATGGAATGTTAATATTTTTATTAATAAAA
*
20285 TAGGTTGCGCCC
66 TAGGTTGCACCC
** *
20297 AAGAATGTCATGGTTCACTAA-AAATAAATTGCGATATGGAATGTTAATATTTTTATTAATAAAA
1 AAGAATGTCATGGTTCACTAAGAAATATGTTGTGATATGGAATGTTAATATTTTTATTAATAAAA
* **
20361 TAAGTTATACCC
66 TAGGTTGCACCC
* * * * * *
20373 GAGAATGTCATGATTCATTAAGAAATATGTTGTCATCTAGAATGTTAA-ATTT
1 AAGAATGTCATGGTTCACTAAGAAATATGTTGTGATATGGAATGTTAATATTT
20425 ATTGTTATAA
Statistics
Matches: 239, Mismatches: 38, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
75 45 0.19
76 110 0.46
77 84 0.35
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (77 bp):
AAGAATGTCATGGTTCACTAAGAAATATGTTGTGATATGGAATGTTAATATTTTTATTAATAAAA
TAGGTTGCACCC
Found at i:20805 original size:21 final size:22
Alignment explanation
Indices: 20781--20824 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
20771 AGAGAGAATC
*
20781 GAATCAACAAA-AAAAACTTTT
1 GAATCAAAAAAGAAAAACTTTT
*
20802 GAATTAAAAAAGGAAAAACTTTT
1 GAATCAAAAAA-GAAAAACTTTT
20825 TGGGAAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (22 bp):
GAATCAAAAAAGAAAAACTTTT
Found at i:20970 original size:71 final size:69
Alignment explanation
Indices: 20841--20971 Score: 185
Period size: 71 Copynumber: 1.9 Consensus size: 69
20831 AGTTAAAATA
* *
20841 TCATTTTCTATTTTTTTAAATTCGAAAGAATCGATATTTTTGGGAAAGTATCGATACTTTGTAGC
1 TCATTTTCTATTTTTTTAAATTCGAAAGAATCGATATTTTTGGAAAAATATCGATACTTTGTAGC
20906 CTTC
66 CTTC
*
20910 TCATTTTCTATTTTTTTTAAAATTCGAAAGTATCGATATTTGTT-GAAAAATATTCG-TACTTT
1 TCATTTTCTA-TTTTTTT-AAATTCGAAAGAATCGATATTT-TTGGAAAAATA-TCGATACTTT
20972 TGAACCTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
69 10 0.18
70 7 0.13
71 33 0.60
72 5 0.09
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.47
Consensus pattern (69 bp):
TCATTTTCTATTTTTTTAAATTCGAAAGAATCGATATTTTTGGAAAAATATCGATACTTTGTAGC
CTTC
Found at i:21763 original size:20 final size:20
Alignment explanation
Indices: 21734--21806 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
21724 AGTGAGTTTT
*
21734 GGATCGATCCTTTAGGCAAA
1 GGATCAATCCTTTAGGCAAA
21754 GGATCAATCCTTTAGGCAAA
1 GGATCAATCCTTTAGGCAAA
* *
21774 GGATCAATCCTTTAGGGAAG
1 GGATCAATCCTTTAGGCAAA
*
21794 GGATCAATTCTTT
1 GGATCAATCCTTT
21807 TAATGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (20 bp):
GGATCAATCCTTTAGGCAAA
Found at i:22859 original size:42 final size:42
Alignment explanation
Indices: 22812--22916 Score: 165
Period size: 42 Copynumber: 2.5 Consensus size: 42
22802 CGAAGTAAAA
** *
22812 CTCAACACATTAACCTTGCCCCATGATCTTCTTGGAGCTAAG
1 CTCAACACACCAACCTTACCCCATGATCTTCTTGGAGCTAAG
*
22854 CTCAACGCACCAACCTTACCCCATGATCTTCTTGGAGCTAAG
1 CTCAACACACCAACCTTACCCCATGATCTTCTTGGAGCTAAG
*
22896 CTCAACGCACCAACCTTACCC
1 CTCAACACACCAACCTTACCC
22917 TGTATATTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (42 bp):
CTCAACACACCAACCTTACCCCATGATCTTCTTGGAGCTAAG
Found at i:23176 original size:28 final size:26
Alignment explanation
Indices: 23126--23178 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
23116 CAACCTAAAT
*
23126 TGGATAGTAAGTTGCTCACTCATCCA
1 TGGATAGGAAGTTGCTCACTCATCCA
*
23152 TGGATAGCGAAGTTGTTCCACTCATCC
1 TGGATAG-GAAGTTGCT-CACTCATCC
23179 CATAACATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 7 0.30
28 9 0.39
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (26 bp):
TGGATAGGAAGTTGCTCACTCATCCA
Found at i:23484 original size:18 final size:18
Alignment explanation
Indices: 23461--23496 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
23451 CGGCAAATTA
23461 TTTTACCCCAACATACAT
1 TTTTACCCCAACATACAT
23479 TTTTACCCCAACATACAT
1 TTTTACCCCAACATACAT
23497 CTACCAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTTACCCCAACATACAT
Found at i:24743 original size:77 final size:77
Alignment explanation
Indices: 24622--24991 Score: 293
Period size: 77 Copynumber: 4.7 Consensus size: 77
24612 GTATGCAACC
* * * * * * *
24622 CATTTTATTAATAAAATTAATAACATTCCAGATCACAACATATTTCTTAGTGAACCATGACATTC
1 CATTTTATTAATAAAAATATTAACATTTCAGATCATAACTTATTTCTTAATGAACCATGACATTA
24687 TT-GG-ATGCAAAT
66 TTAGGCA--CAAAT
* * * * *
24699 CATTTTATTAATAAAAATATTAAAATTTCATATCGTAACCTATTTCTTAATGAAACATGACATTA
1 CATTTTATTAATAAAAATATTAACATTTCAGATCATAACTTATTTCTTAATGAACCATGACATTA
** **
24764 TTGGGTATTGGGTGCAACC
66 -T---TA---GGCACAAAT
* * ** * **
24783 CATTTTATTAATAAAAATATTAACATTTAACATTTTAACTTATTTCTTAGTGAATTATGACATTA
1 CATTTTATTAATAAAAATATTAACATTTCAGATCATAACTTATTTCTTAATGAACCATGACATTA
24848 TT-GG-ACACAAT
66 TTAGGCACA-AAT
* * *
24859 CCATTTTATTAATAAAAATATTAACA-TTCTAGATCACAACTTATTTTTTAATAAACCATGACA-
1 -CATTTTATTAATAAAAATATTAACATTTC-AGATCATAACTTATTTCTTAATGAACCATGACAT
*
24922 TACTTAGGCACAACT
64 TA-TTAGGCACAAAT
* * * * *
24937 CATTTTATTAATAAAATTATTAATATTTCATATCATAACTTATTTATTACTGAAC
1 CATTTTATTAATAAAAATATTAACATTTCAGATCATAACTTATTTCTTAATGAAC
24992 TATAAATTTT
Statistics
Matches: 233, Mismatches: 44, Indels: 32
0.75 0.14 0.10
Matches are distributed among these distances:
75 2 0.01
76 7 0.03
77 149 0.64
78 8 0.03
79 3 0.01
80 1 0.00
81 1 0.00
83 1 0.00
84 59 0.25
85 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (77 bp):
CATTTTATTAATAAAAATATTAACATTTCAGATCATAACTTATTTCTTAATGAACCATGACATTA
TTAGGCACAAAT
Found at i:24921 original size:161 final size:160
Alignment explanation
Indices: 24615--24922 Score: 388
Period size: 161 Copynumber: 1.9 Consensus size: 160
24605 GGACGTTGTA
* * *
24615 TGCAACCCATTTTATTAATAAAATTAATAACATTCCAGATCACAACATATTTCTTAGTGAACCAT
1 TGCAACCCATTTTATTAATAAAAATAATAACATTCAACATCACAACATATTTCTTAGTGAACCAT
* * **
24680 GACATTCTTGGATGCAAATCATTTTATTAATAAAAATATTAAAATTTCATATCGTAACCTATTTC
66 GACATTATTGGA-GCAAATCATTTTATTAATAAAAATATTAAAATTTCAGATCACAACCTATTTC
24745 TTAATGAAACATGACATTATTGGGTATTGGG
130 TTAATGAAACATGACATTATTGGGTATTGGG
* * *** * **
24776 TGCAACCCATTTTATTAATAAAAATATTAACATTTAACATTTTAACTTATTTCTTAGTGAATTAT
1 TGCAACCCATTTTATTAATAAAAATAATAACATTCAACATCACAACATATTTCTTAGTGAACCAT
* *
24841 GACATTATTGGA-CACAATCCATTTTATTAATAAAAATATTAACA-TTCTAGATCACAACTTATT
66 GACATTATTGGAGCA-AAT-CATTTTATTAATAAAAATATTAAAATTTC-AGATCACAACCTATT
*
24904 TTTTAAT-AAACCATGACAT
128 TCTTAATGAAA-CATGACAT
24923 ACTTAGGCAC
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
159 2 0.02
160 9 0.07
161 114 0.91
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (160 bp):
TGCAACCCATTTTATTAATAAAAATAATAACATTCAACATCACAACATATTTCTTAGTGAACCAT
GACATTATTGGAGCAAATCATTTTATTAATAAAAATATTAAAATTTCAGATCACAACCTATTTCT
TAATGAAACATGACATTATTGGGTATTGGG
Found at i:26536 original size:18 final size:20
Alignment explanation
Indices: 26513--26550 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
26503 GTCCAAACCC
26513 AAAATA-TTAAAA-CTAAAA
1 AAAATATTTAAAATCTAAAA
26531 AAAATATTTAAAATCTAAAA
1 AAAATATTTAAAATCTAAAA
26551 CATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATATTTAAAATCTAAAA
Found at i:28334 original size:21 final size:22
Alignment explanation
Indices: 28310--28365 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
28300 TATTTTAATG
*
28310 ATTAAAATTAAATTTTTTA-AA
1 ATTAAAATTAAATTATTTATAA
* * *
28331 ATTAAAATCAAGTTATTTATAT
1 ATTAAAATTAAATTATTTATAA
*
28353 ATAAAAATTAAAT
1 ATTAAAATTAAAT
28366 ATTAAATGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTAAAATTAAATTATTTATAA
Found at i:29305 original size:19 final size:19
Alignment explanation
Indices: 29268--29340 Score: 110
Period size: 19 Copynumber: 3.7 Consensus size: 19
29258 AACACATAAG
29268 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
29289 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
29308 TCAAATTCGCAACTCAATT
1 TCAAATTCGCAACTGAATT
*
29327 TCGAATTCGCAACT
1 TCAAATTCGCAACT
29341 CGATTTTTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 39 0.78
20 1 0.02
21 10 0.20
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:29312 original size:40 final size:40
Alignment explanation
Indices: 29189--29339 Score: 175
Period size: 40 Copynumber: 3.8 Consensus size: 40
29179 ACCCAGTTTC
*
29189 CAAATTCGCAACACGAATTTGTAAA-TCGCAACACATAAGT
1 CAAATTCGCAACACGAATTT-CAAATTCGCAACACATAAGT
*
29229 CAAATTCGCAACACGAATTTGTAAA-TCGCAACACATAAGT
1 CAAATTCGCAACACGAATTT-CAAATTCGCAACACATAAGT
** **
29269 CAAATTCGCAACACTGAATTTCAAATTCGCAACTGA-ATTT
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACACATAAGT
* *
29309 CAAATTCGCAACTC-AATTTCGAATTCGCAAC
1 CAAATTCGCAACACGAATTTCAAATTCGCAAC
29340 TCGATTTTTG
Statistics
Matches: 102, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
38 16 0.16
40 72 0.71
41 14 0.14
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (40 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACACATAAGT
Found at i:29341 original size:19 final size:19
Alignment explanation
Indices: 29149--29346 Score: 112
Period size: 20 Copynumber: 10.0 Consensus size: 19
29139 AAATGACCAA
* * *
29149 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACTC-AATTT
* * *
29169 CAATTTCGCAACCCAGTTT
1 CAAATTCGCAACTCAATTT
*
29188 CCAAATTCGCAACACGAATTT
1 -CAAATTCGCAACTC-AATTT
* * **
29209 GTAAA-TCGCAACACATAAGT
1 -CAAATTCGCAACTCA-ATTT
*
29229 CAAATTCGCAACACGAATTT
1 CAAATTCGCAACTC-AATTT
* * **
29249 GTAAA-TCGCAACACATAAGT
1 -CAAATTCGCAACTCA-ATTT
*
29269 CAAATTCGCAACACTGAATTT
1 CAAATTCGC-A-ACTCAATTT
*
29290 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACTCAATTT
29309 CAAATTCGCAACTCAATTT
1 CAAATTCGCAACTCAATTT
* *
29328 CGAATTCGCAACTCGATTT
1 CAAATTCGCAACTCAATTT
29347 TTGAATTTGC
Statistics
Matches: 142, Mismatches: 26, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
19 54 0.38
20 62 0.44
21 23 0.16
22 3 0.02
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (19 bp):
CAAATTCGCAACTCAATTT
Found at i:30344 original size:24 final size:24
Alignment explanation
Indices: 30312--30365 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
30302 GTATTCAAAA
30312 TTTGATCTTGGTAAATACCCGGAC
1 TTTGATCTTGGTAAATACCCGGAC
* * *
30336 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTAAATACCCGGAC
30360 TTTGAT
1 TTTGAT
30366 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTAAATACCCGGAC
Found at i:33127 original size:25 final size:25
Alignment explanation
Indices: 33089--33138 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
33079 AAATCAATTA
*
33089 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
33114 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
33139 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:33545 original size:18 final size:18
Alignment explanation
Indices: 33524--33560 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
33514 GTAATTGGAG
33524 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
33542 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
33560 T
1 T
33561 ATATATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:34722 original size:29 final size:29
Alignment explanation
Indices: 34661--34722 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
34651 ATTTTTTGTT
** ****
34661 GCGATTGTTGCGAAAGTCAAATTCGCGTT
1 GCGATTGTTGCGAAAGTCAAATAAGAAAC
34690 GCGATTGTTGCGAAAGTCAAATAAGAAAC
1 GCGATTGTTGCGAAAGTCAAATAAGAAAC
34719 GCGA
1 GCGA
34723 AATCGTAACG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (29 bp):
GCGATTGTTGCGAAAGTCAAATAAGAAAC
Found at i:34760 original size:20 final size:20
Alignment explanation
Indices: 34735--34836 Score: 123
Period size: 20 Copynumber: 5.1 Consensus size: 20
34725 TCGTAACGCC
* *
34735 AATTTGACTTTCGCGTTGTG
1 AATTTGACTATCGCGTTGCG
*
34755 AATTTGACTATCGCGTTGCA
1 AATTTGACTATCGCGTTGCG
* *
34775 AATTTGACTATCACGTTGTG
1 AATTTGACTATCGCGTTGCG
***
34795 AATTTGACTATCGCAACGCG
1 AATTTGACTATCGCGTTGCG
*
34815 AATTTGACTTTCGCGTTGCG
1 AATTTGACTATCGCGTTGCG
34835 AA
1 AA
34837 AGTGCACTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
AATTTGACTATCGCGTTGCG
Found at i:34819 original size:40 final size:40
Alignment explanation
Indices: 34724--34832 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
34714 GAAACGCGAA
* *
34724 ATCGTAACGCCAATTTGACTTTCGCGTTGTGAATTTGACT
1 ATCGCAACGCAAATTTGACTTTCGCGTTGTGAATTTGACT
*** * *
34764 ATCGCGTTGCAAATTTGACTATCACGTTGTGAATTTGACT
1 ATCGCAACGCAAATTTGACTTTCGCGTTGTGAATTTGACT
*
34804 ATCGCAACGCGAATTTGACTTTCGCGTTG
1 ATCGCAACGCAAATTTGACTTTCGCGTTG
34833 CGAAAGTGCA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (40 bp):
ATCGCAACGCAAATTTGACTTTCGCGTTGTGAATTTGACT
Found at i:34955 original size:37 final size:37
Alignment explanation
Indices: 34905--35022 Score: 112
Period size: 37 Copynumber: 3.5 Consensus size: 37
34895 CAAATCAACT
34905 TTTACAAATCAATTAAACAAGCAAAAAATAATACTTA
1 TTTACAAATCAATTAAACAAGCAAAAAATAATACTTA
* *
34942 TTTACACATCAATT--A-AA-C---AAATCA-AC-T-
1 TTTACAAATCAATTAAACAAGCAAAAAATAATACTTA
*
34969 TTTACAAATCAATTAAACAAGCAAAAAATAATTCTTA
1 TTTACAAATCAATTAAACAAGCAAAAAATAATACTTA
* **
35006 TTTCCTCATCAATTAAA
1 TTTACAAATCAATTAAA
35023 AAATCAACTT
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
27 13 0.21
28 1 0.02
29 3 0.05
30 7 0.11
31 1 0.02
33 1 0.02
34 7 0.11
35 2 0.03
36 1 0.02
37 27 0.43
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.31
Consensus pattern (37 bp):
TTTACAAATCAATTAAACAAGCAAAAAATAATACTTA
Found at i:35038 original size:63 final size:64
Alignment explanation
Indices: 34893--35049 Score: 271
Period size: 64 Copynumber: 2.5 Consensus size: 64
34883 GAAATTTAAC
34893 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATACTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATACTTATTTACACATCAATTA
* * *
34957 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATACTTATTTACACATCAATTA
35021 AA-AAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
35050 ATTCAATTAA
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
63 22 0.25
64 67 0.75
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATACTTATTTACACATCAATTA
Found at i:36433 original size:21 final size:21
Alignment explanation
Indices: 36407--36525 Score: 123
Period size: 21 Copynumber: 5.7 Consensus size: 21
36397 GTGAATCGGG
* * *
36407 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGGC
* *
36428 CTCTTGAACGATGACAGAGGC
1 CTCTTGAACGATGAGAGGGGC
* *
36449 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
36470 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
36491 CTCTTGAATGAT-AGGAGGCGT
1 CTCTTGAACGATGA-GAGGGGC
*
36512 CTCTTGAACAATGA
1 CTCTTGAACGATGA
36526 CAGGTGAATT
Statistics
Matches: 80, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
20 1 0.01
21 78 0.98
22 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:36466 original size:42 final size:42
Alignment explanation
Indices: 36407--36498 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
36397 GTGAATCGGG
36407 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGAGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGAGGC
* * *
36449 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGAGGC
36491 CTCTTGAA
1 CTCTTGAA
36499 TGATAGGAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.22, C:0.21, G:0.37, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGAGGC
Found at i:36508 original size:42 final size:42
Alignment explanation
Indices: 36407--36528 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
36397 GTGAATCGGG
* * *
36407 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGAGGC
1 CTCTTGAACGATAGGAGGGGCCTCTTGAACGATGACAGAGGC
* * * *
36449 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATAGGAGGGGCCTCTTGAACGATGACAGAGGC
* * * *
36491 CTCTTGAATGATAGGAGGCGTCTCTTGAACAATGACAG
1 CTCTTGAACGATAGGAGGGGCCTCTTGAACGATGACAG
36529 GTGAATTGGG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGATAGGAGGGGCCTCTTGAACGATGACAGAGGC
Found at i:36961 original size:21 final size:21
Alignment explanation
Indices: 36860--36975 Score: 76
Period size: 21 Copynumber: 5.5 Consensus size: 21
36850 CGCAGCATTG
*
36860 TCATCACGTAAAACATCC-ACC
1 TCATCACGTAAAGCA-CCGACC
* *
36881 TCACCATGTAAAG-ACCGTACC
1 TCATCACGTAAAGCACCG-ACC
* * * **
36902 TCATCACGTCATGCA-CTATTG
1 TCATCACGTAAAGCACCGA-CC
* * *
36923 TCTTCACGTACAGTACCGACC
1 TCATCACGTAAAGCACCGACC
*
36944 TCATGACGTAAAGCACCGACC
1 TCATCACGTAAAGCACCGACC
36965 TCATCACGTAA
1 TCATCACGTAA
36976 CTCCCCTAAC
Statistics
Matches: 67, Mismatches: 23, Indels: 10
0.67 0.23 0.10
Matches are distributed among these distances:
19 2 0.03
20 2 0.03
21 60 0.90
22 3 0.04
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.22
Consensus pattern (21 bp):
TCATCACGTAAAGCACCGACC
Found at i:38697 original size:20 final size:20
Alignment explanation
Indices: 38672--38753 Score: 105
Period size: 20 Copynumber: 4.2 Consensus size: 20
38662 AAACTTAAAT
38672 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
38692 TCGCAACGC-AAACATGAAAA
1 TCGCAACGCGAAA-ATGAAAA
*
38712 TCGTAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* **
38732 TCGTAACGTAAAAAT-AAAA
1 TCGCAACGCGAAAATGAAAA
38751 TCG
1 TCG
38754 TGTTGCAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
19 10 0.18
20 44 0.77
21 3 0.05
ACGTcount: A:0.50, C:0.18, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:38720 original size:40 final size:39
Alignment explanation
Indices: 38667--38754 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
38657 TTCTAAAACT
* * *
38667 TAAATTCGCAACGCGAAAATGAAAATCGCAACGCAAACA
1 TAAAATCGTAACGCGAAAATGAAAATCGCAACGCAAAAA
* *
38706 TGAAAATCGTAACGCGAAAATGAAAATCGTAACGTAAAAA
1 T-AAAATCGTAACGCGAAAATGAAAATCGCAACGCAAAAA
38746 TAAAATCGT
1 TAAAATCGT
38755 GTTGCAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 9 0.21
40 34 0.79
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.17
Consensus pattern (39 bp):
TAAAATCGTAACGCGAAAATGAAAATCGCAACGCAAAAA
Found at i:38792 original size:20 final size:20
Alignment explanation
Indices: 38751--38792 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
38741 AAAAATAAAA
* *
38751 TCGTGTTGCAATTTTCATTT
1 TCGTGTTGCAATTTTAAGTT
38771 TCGTGTTGCGAA-TTTAAGTT
1 TCGTGTTGC-AATTTTAAGTT
38791 TC
1 TC
38793 AAAAACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (20 bp):
TCGTGTTGCAATTTTAAGTT
Found at i:39156 original size:22 final size:22
Alignment explanation
Indices: 39126--39176 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
39116 GATGGAGATA
39126 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* * *
39148 GATGGATTTTGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
39170 GACGGAT
1 GACGGAT
39177 GTCACCGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.45, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:39359 original size:20 final size:20
Alignment explanation
Indices: 39331--39416 Score: 145
Period size: 20 Copynumber: 4.3 Consensus size: 20
39321 TAAACGCGCT
*
39331 TTGCAAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
39351 TTGCGAATTTAACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
39371 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
39391 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
39411 TTGCGA
1 TTGCGA
39417 TTTACAAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:39434 original size:40 final size:40
Alignment explanation
Indices: 39331--39481 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
39321 TAAACGCGCT
* * *
39331 TTGCAAATTTGAC-TTCTGTGTTGCGAATTTAACTTCTGTG
1 TTGCGAATTTGACATTC-GCGTTGCGAATTTGACTTCTGTG
* * *
39371 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACATTCGCGTTGCGAATTTGACTTCTGTG
** *
39411 TTGCG-ATTT-ACAAATTCGCGTTGCGAATTTGGA-AACTGGG
1 TTGCGAATTTGAC--ATTCGCGTTGCGAATTT-GACTTCTGTG
* *
39451 TTGCGAAATTGGA-GTTCGCGTTGCGAATTTG
1 TTGCG-AATTTGACATTCGCGTTGCGAATTTG
39482 TTGGTCATTT
Statistics
Matches: 93, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
38 2 0.02
39 5 0.05
40 78 0.84
41 4 0.04
42 3 0.03
43 1 0.01
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (40 bp):
TTGCGAATTTGACATTCGCGTTGCGAATTTGACTTCTGTG
Found at i:39454 original size:60 final size:60
Alignment explanation
Indices: 39331--39480 Score: 146
Period size: 60 Copynumber: 2.5 Consensus size: 60
39321 TAAACGCGCT
* * * *** *
39331 TTGCAAATTTGACTTCTGTGTTGCGAATTTAACTTCTGTGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTGTTGCGAATTTAAATTCTGCGTTGCGAATTTGACAACTGGG
39391 TTGCGAATTTGACTTCTGTGTTGCG-ATTTACAAATTC-GCGTTGCGAATTTGGA-AACTGGG
1 TTGCGAATTTGACTTCTGTGTTGCGAATTT--AAATTCTGCGTTGCGAATTT-GACAACTGGG
* * *
39451 TTGCGAAATTGGAGTTC-GCGTTGCGAATTT
1 TTGCG-AATTTGACTTCTGTGTTGCGAATTT
39481 GTTGGTCATT
Statistics
Matches: 75, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
59 4 0.05
60 51 0.68
61 20 0.27
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (60 bp):
TTGCGAATTTGACTTCTGTGTTGCGAATTTAAATTCTGCGTTGCGAATTTGACAACTGGG
Found at i:41616 original size:100 final size:100
Alignment explanation
Indices: 41492--41671 Score: 272
Period size: 100 Copynumber: 1.8 Consensus size: 100
41482 TTTAAATTAT
* * * * * *
41492 AATTATTAGATTATTTATTTTTATTTTACATATTAAGTTGTATTTAAGTAGTTTGATAAGTTTAG
1 AATTATTAGACTAATTATTTTTATTTTACAGATTAAATCGTATTTAAGCAGTTTGATAAGTTTAG
41557 TTTAAAT-TATATTTTCATTTTTATTGAGTAATATA
66 TTTAAATCT-TATTTTCATTTTTATTGAGTAATATA
* *
41592 AATTATTAGACTAATTATTTTTATTTTACAGATTAAATCGTATTTGAGCGGTTTGATAAGTTTAG
1 AATTATTAGACTAATTATTTTTATTTTACAGATTAAATCGTATTTAAGCAGTTTGATAAGTTTAG
41657 TTTAAATCTTATTTT
66 TTTAAATCTTATTTT
41672 TTTTTTGTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 70 0.99
101 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (100 bp):
AATTATTAGACTAATTATTTTTATTTTACAGATTAAATCGTATTTAAGCAGTTTGATAAGTTTAG
TTTAAATCTTATTTTCATTTTTATTGAGTAATATA
Found at i:43939 original size:27 final size:27
Alignment explanation
Indices: 43907--43979 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
43897 ACAAATATCC
* **
43907 ATCACATTAATTTATCTATTGATATTA
1 ATCACATTAATTCAAATATTGATATTA
*
43934 ATCACATTCATTCAAATATTGATATTA
1 ATCACATTAATTCAAATATTGATATTA
* *
43961 ATCATATTCATTCAAATAT
1 ATCACATTAATTCAAATAT
43980 AACATCAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.44
Consensus pattern (27 bp):
ATCACATTAATTCAAATATTGATATTA
Found at i:45431 original size:23 final size:23
Alignment explanation
Indices: 45400--45466 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
45390 CACCGAAGTG
*
45400 CCACATAGATTTGTCCCAAAGGA
1 CCACATAGAATTGTCCCAAAGGA
* * * *
45423 CCGCGTAGAATTGTCCTAAACGA
1 CCACATAGAATTGTCCCAAAGGA
*
45446 CCACATAGAATTGTCACAAAG
1 CCACATAGAATTGTCCCAAAG
45467 ACCTAGGTAG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (23 bp):
CCACATAGAATTGTCCCAAAGGA
Found at i:51958 original size:24 final size:25
Alignment explanation
Indices: 51911--51970 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
51901 CAGTCAAAAC
* * *
51911 TGTCGCGTAGAATTTTGCATCGAAG
1 TGTCACGTAGAATTATGCACCGAAG
51936 TGTCACGTAGAA-TATGCACCGAAG
1 TGTCACGTAGAATTATGCACCGAAG
* *
51960 TGCCACATAGA
1 TGTCACGTAGA
51971 TTTGTCCCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (25 bp):
TGTCACGTAGAATTATGCACCGAAG
Found at i:51993 original size:23 final size:23
Alignment explanation
Indices: 51965--52041 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
51955 CGAAGTGCCA
*
51965 CATAGATTTGTCCCGAAGGACCG
1 CATAGAATTGTCCCGAAGGACCG
* * * *
51988 CGTAGAATTGTCCCAAAAGACCA
1 CATAGAATTGTCCCGAAGGACCG
*
52011 CATGGAATTGTCCCGAAGGACCG
1 CATAGAATTGTCCCGAAGGACCG
52034 CATAGAAT
1 CATAGAAT
52042 CCCTCTACTC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CATAGAATTGTCCCGAAGGACCG
Found at i:56421 original size:22 final size:22
Alignment explanation
Indices: 56393--56437 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
56383 AACATCAGTT
56393 TTTTATGCAATGATTTCAAGAC
1 TTTTATGCAATGATTTCAAGAC
56415 TTTTATGCAATGATTTCAAGAC
1 TTTTATGCAATGATTTCAAGAC
56437 T
1 T
56438 ACAAGAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTTATGCAATGATTTCAAGAC
Found at i:57600 original size:59 final size:59
Alignment explanation
Indices: 57507--57624 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
57497 GGGTTGTTAG
* * *
57507 AGCCATATTATTGAGTTTACCTTTTCATTACGACTAGGAGGGTTCGATAGGATACTTAT
1 AGCCATATTATCGAGTTTACCTTTTCATTACGACTAGGACGGTTCGATAGGACACTTAT
* * *
57566 AGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGACGGTTTGATAGGACACTTAT
1 AGCCATATTATCGAGTTTACCTTTTCATTACGACTAGGACGGTTCGATAGGACACTTAT
57625 TTTCCACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (59 bp):
AGCCATATTATCGAGTTTACCTTTTCATTACGACTAGGACGGTTCGATAGGACACTTAT
Found at i:62694 original size:14 final size:14
Alignment explanation
Indices: 62677--62705 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62667 TAACAAAAAC
62677 TAATTATATAACTA
1 TAATTATATAACTA
62691 TAATTATATAACTA
1 TAATTATATAACTA
62705 T
1 T
62706 TCTTTCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATTATATAACTA
Found at i:65058 original size:3 final size:3
Alignment explanation
Indices: 65050--65074 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
65040 ATAAATGTAA
65050 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
65075 TAACTAATTA
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:66332 original size:10 final size:10
Alignment explanation
Indices: 66317--66347 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
66307 CTAAGGATTC
66317 GGATTTTGGT
1 GGATTTTGGT
66327 GGATTTTGGT
1 GGATTTTGGT
*
66337 AGATTTTGGT
1 GGATTTTGGT
66347 G
1 G
66348 TAAATTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (10 bp):
GGATTTTGGT
Found at i:73869 original size:13 final size:13
Alignment explanation
Indices: 73853--73877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73843 ATAATAGTTT
73853 AATATATATATAA
1 AATATATATATAA
73866 AATATATATATA
1 AATATATATATA
73878 TAAACAAGGT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATATATATAA
Done.