Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007540.1 Hibiscus syriacus cultivar Beakdansim tig00021125_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: 74189
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4257 original size:14 final size:14
Alignment explanation
Indices: 4238--4274 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
4228 TTTAGCTCAT
4238 GTTATGCAAATGCA
1 GTTATGCAAATGCA
4252 GTTATGCAAATGCA
1 GTTATGCAAATGCA
4266 GTTATGCAA
1 GTTATGCAA
4275 TGTATGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (14 bp):
GTTATGCAAATGCA
Found at i:16760 original size:3 final size:3
Alignment explanation
Indices: 16754--16786 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
16744 GTATTATTTG
*
16754 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16787 ATATAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17509 original size:24 final size:24
Alignment explanation
Indices: 17477--17533 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
17467 TTTCGCTTCA
* *
17477 TTCCCTGTCTCCTAACTTTCCATC
1 TTCCATGTCTCCTAACTTTCCACC
*
17501 TTCCATGTCTCCTACCTTTCCACC
1 TTCCATGTCTCCTAACTTTCCACC
17525 TTCCATGTC
1 TTCCATGTC
17534 AACCAAGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.12, C:0.42, G:0.05, T:0.40
Consensus pattern (24 bp):
TTCCATGTCTCCTAACTTTCCACC
Found at i:28025 original size:34 final size:36
Alignment explanation
Indices: 27979--28078 Score: 134
Period size: 37 Copynumber: 2.8 Consensus size: 36
27969 TCGTCCTACT
* *
27979 AGGATTCGAACTCCTAAAAATATGATAGAA-TT-TC
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
*
28013 AGGATTCAAACTCCTAAAAATAGGAT-GAAATTTTGTT
1 AGGATTCAAACTCCTAAAAATAGGATAG-AA-TTTGTC
28050 AGGATTCAAACTCCTAAAAATAGGATAGA
1 AGGATTCAAACTCCTAAAAATAGGATAGA
28079 GTTACACTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
33 1 0.02
34 26 0.45
36 2 0.03
37 28 0.48
38 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (36 bp):
AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
Found at i:28506 original size:34 final size:34
Alignment explanation
Indices: 28462--28542 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
28452 TTATTCTTGT
28462 TATATATACATAT-TATTTTCTATTAAAT-TTATTA
1 TATATATACATATGT-TTTTCTATT-AATGTTATTA
* * *
28496 TATATGTACATATGTTTTTTTATTAGTGTTATTA
1 TATATATACATATGTTTTTCTATTAATGTTATTA
*
28530 TATATATATATAT
1 TATATATACATAT
28543 ATATATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 2 0.05
34 37 0.93
35 1 0.03
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.57
Consensus pattern (34 bp):
TATATATACATATGTTTTTCTATTAATGTTATTA
Found at i:28533 original size:2 final size:2
Alignment explanation
Indices: 28528--28552 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28518 TTAGTGTTAT
28528 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 T
28553 TTCCTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28635 original size:20 final size:20
Alignment explanation
Indices: 28610--28647 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28600 TCTTTTTTTA
28610 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
28630 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
28648 TTTCATTTAT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:28676 original size:16 final size:18
Alignment explanation
Indices: 28655--28689 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
28645 TATTTTCATT
28655 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
28671 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
28689 T
1 T
28690 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:31907 original size:16 final size:16
Alignment explanation
Indices: 31881--31914 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
31871 ACATCCAATC
31881 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
31896 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
31913 AA
1 AA
31915 AAAACAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:32638 original size:22 final size:22
Alignment explanation
Indices: 32610--32655 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
32600 CCCCATCAAT
32610 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
32632 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
32654 CC
1 CC
32656 CTTAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:33076 original size:18 final size:18
Alignment explanation
Indices: 33053--33088 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33043 TCAACATCAA
* *
33053 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
33071 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
33089 GGATTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:33609 original size:71 final size:73
Alignment explanation
Indices: 33526--33849 Score: 239
Period size: 72 Copynumber: 4.6 Consensus size: 73
33516 GTTTTTCTTA
* ** * * * *
33526 AAACAAGA-TTTGTCTCGCTTGAGACCTTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
33588 TTTCCCTTG
65 TTTCCCTTG
* *
33597 AAACAAATTTTGTCTCTCTTGAGA-CAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
33661 TTCCCTTG
66 TTCCCTTG
* * * * *
33669 AAATAAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
33725 TTTTCTTTG
65 TTTCCCTTG
* * ** * * * * *
33734 AAACAAATTTCGTCTCCCTTGAGA-CAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
33798 TTTCTCTTG
65 TTTCCCTTG
* * *
33807 AAAC-AATTTTCGTCTATCTTGAGA-CAGTTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACCAGTTTCACTAGAAACAAA
33850 ATCTTTGAAT
Statistics
Matches: 204, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
64 2 0.01
65 46 0.23
66 5 0.02
70 9 0.04
71 23 0.11
72 78 0.38
73 39 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:33611 original size:36 final size:36
Alignment explanation
Indices: 33568--33849 Score: 321
Period size: 36 Copynumber: 8.0 Consensus size: 36
33558 ACTAGAAGAG
33568 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
33604 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
33640 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
33676 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
33712 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
33741 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
33778 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
33813 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
33850 ATCTTTGAAT
Statistics
Matches: 206, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 142 0.69
37 35 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:33809 original size:102 final size:102
Alignment explanation
Indices: 33624--33812 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
33614 CTTGAGACAG
*
33624 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
33689 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
33726 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
33790 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
33813 TTTTCGTCTA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 34 0.43
102 45 0.57
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:33841 original size:138 final size:137
Alignment explanation
Indices: 33588--33912 Score: 463
Period size: 138 Copynumber: 2.4 Consensus size: 137
33578 CTTGAGACAG
*
33588 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
*
33653 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
*
33718 GAATATG
131 GAATATA
* * * * * * * *
33725 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
33790 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATAT
*
33854 TTGAATTTA
129 TTGAATATA
* * *
33863 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
33913 CAAAATCTTC
Statistics
Matches: 163, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
137 50 0.31
138 113 0.69
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:33911 original size:65 final size:65
Alignment explanation
Indices: 33807--33981 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 65
33797 GTTTCTCTTG
** * **
33807 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCT
33871 A
65 A
* *
33872 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
33937 TA
64 TA
* * *
33939 AAACACAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
33982 CAGATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 25 0.26
66 12 0.13
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:33912 original size:174 final size:168
Alignment explanation
Indices: 33572--33878 Score: 397
Period size: 174 Copynumber: 1.8 Consensus size: 168
33562 GAAGAGTTTT
*
33572 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* *
33637 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCC
66 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA-----TATCTCTTGAGACAGTTTCCC
* * * *
33702 TTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAATTTC
126 CTAAAACAAAATATTTGAACATGTTCTCTTTGAAACAAATTTC
** * *
33745 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
* *
33810 CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA-ATCT-TTGA-ATTTA-TTTCCCCT
65 CAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATATCTCTTGAGA--CAGTTTCCCCT
33871 AAAACAAA
128 AAAACAAA
33879 TTTTGTCTCC
Statistics
Matches: 120, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
166 1 0.01
167 18 0.15
168 4 0.03
173 25 0.21
174 72 0.60
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (168 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATATCTCTTGAGACAGTTTCCCCTAAA
ACAAAATATTTGAACATGTTCTCTTTGAAACAAATTTC
Found at i:33941 original size:67 final size:67
Alignment explanation
Indices: 33798--33980 Score: 219
Period size: 68 Copynumber: 2.7 Consensus size: 67
33788 CTTGAGACAG
* * ** * **
33798 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
33860 TTA
65 TTA
* *
33863 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
33928 TA
66 TA
* * *
33930 TTTCCCTTAAAACACAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
33981 ACAGATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 31 0.31
66 8 0.08
67 29 0.29
68 32 0.32
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:34814 original size:105 final size:105
Alignment explanation
Indices: 34585--35245 Score: 963
Period size: 105 Copynumber: 6.3 Consensus size: 105
34575 GCCATCCGCG
* * * * * * *
34585 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGACACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
34650 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
34694 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
34759 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
34799 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
34864 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
34904 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
34969 ACCGCTGCTTGTCAACAACAATTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
35009 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAATTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
35074 ACCGCTGCTTGTCAATAA-AA-TT-CC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
35109 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
35174 ACAGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
35215 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
35246 TGGAACAATG
Statistics
Matches: 512, Mismatches: 34, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
100 81 0.16
101 3 0.01
102 4 0.01
103 4 0.01
104 4 0.01
105 308 0.60
106 83 0.16
107 3 0.01
109 22 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:35841 original size:34 final size:36
Alignment explanation
Indices: 35795--35894 Score: 143
Period size: 37 Copynumber: 2.8 Consensus size: 36
35785 TCGTCCTACT
*
35795 AGGATTCGAACTCCTAAAAATAGGATAGAA-TT-TC
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
*
35829 AGGATTCAAACTCCTAAAAATAGGAT-GAAATTTTGTT
1 AGGATTCAAACTCCTAAAAATAGGATAG-AA-TTTGTC
35866 AGGATTCAAACTCCTAAAAATAGGATAGA
1 AGGATTCAAACTCCTAAAAATAGGATAGA
35895 GTTACACTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
33 1 0.02
34 27 0.46
36 2 0.03
37 28 0.47
38 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (36 bp):
AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
Found at i:36336 original size:34 final size:35
Alignment explanation
Indices: 36278--36362 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
36268 TTATTCTTGT
36278 TATATATACATAT-TATTTTCTATTAAAT-TTATTA
1 TATATATACATATATATTTTCTATT-AATGTTATTA
* * *
36312 TATATGTACATATAT-TTTTTTATTAGTGTTATTA
1 TATATATACATATATATTTTCTATTAATGTTATTA
*
36346 TATATATATATATATAT
1 TATATATACATATATAT
36363 ATATTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 2 0.05
34 39 0.91
35 2 0.05
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (35 bp):
TATATATACATATATATTTTCTATTAATGTTATTA
Found at i:36349 original size:2 final size:2
Alignment explanation
Indices: 36344--36374 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
36334 TTAGTGTTAT
*
36344 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36375 TTCCTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:36494 original size:16 final size:18
Alignment explanation
Indices: 36475--36509 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
36465 TATTTTCATT
36475 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
36491 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
36509 T
1 T
36510 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:36514 original size:26 final size:26
Alignment explanation
Indices: 36459--36520 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
36449 TGCTTTTACT
* *
36459 TTTTTATATTTTCATTTATTTATCTA
1 TTTTTATATTTTCATATATTTATATA
* *
36485 TTTTTATATTTATCCTATATTT-TATG
1 TTTTTATATTT-TCATATATTTATATA
36511 TTTTTATATT
1 TTTTTATATT
36521 CTTTACTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTTATATTTTCATATATTTATATA
Found at i:43916 original size:37 final size:37
Alignment explanation
Indices: 43866--43970 Score: 125
Period size: 37 Copynumber: 3.0 Consensus size: 37
43856 TAACTAGTAC
43866 AATATTTTGAAATTAAAATATGAACTTTATCAATTGT
1 AATATTTTGAAATTAAAATATGAACTTTATCAATTGT
* ***
43903 AATATTTTGAAATTAAAAT-T---C-CTAT-AA-AAA
1 AATATTTTGAAATTAAAATATGAACTTTATCAATTGT
43933 AATATTTTGAAATTAAAATATGAACTTTATCAATTGT
1 AATATTTTGAAATTAAAATATGAACTTTATCAATTGT
43970 A
1 A
43971 CCTGGAACTG
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
30 19 0.36
31 3 0.06
32 3 0.06
33 1 0.02
34 1 0.02
35 3 0.06
36 3 0.06
37 20 0.38
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.41
Consensus pattern (37 bp):
AATATTTTGAAATTAAAATATGAACTTTATCAATTGT
Found at i:47529 original size:19 final size:20
Alignment explanation
Indices: 47505--47558 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
47495 AATGACCAAC
*
47505 AAAATCGCAATGCGAA-ATA
1 AAAATCGCAACGCGAACATA
47524 AAAATCGCAACGCGAACATA
1 AAAATCGCAACGCGAACATA
*
47544 TAAATCGCAACGCGA
1 AAAATCGCAACGCGA
47559 TTCTGACTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGCGAACATA
Found at i:47611 original size:20 final size:20
Alignment explanation
Indices: 47567--47780 Score: 198
Period size: 20 Copynumber: 10.6 Consensus size: 20
47557 GATTCTGACT
*
47567 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
47588 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
47608 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
47629 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
47649 ATCACAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
47669 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
47689 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
**
47709 ATCGCAATACGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
47729 ATCGCAACGAC-AATACATAAA
1 ATCGCAACG-CGTATCCGT-AA
* *
47750 ATCACAACACGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
47770 ATCGCAACGCG
1 ATCGCAACGCG
47781 ATTTTTAAAG
Statistics
Matches: 150, Mismatches: 37, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
20 103 0.69
21 47 0.31
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:47682 original size:40 final size:41
Alignment explanation
Indices: 47567--47778 Score: 302
Period size: 41 Copynumber: 5.2 Consensus size: 41
47557 GATTCTGACT
* *
47567 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
47608 ATCGCAACGACAATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
47649 ATCACAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
**
47689 ATCGCAACGAGAATACGT-AAATCGCAATACGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
47729 ATCGCAACGACAATACATAAAATCACAACACGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
47770 ATCGCAACG
1 ATCGCAACG
47779 CGATTTTTAA
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 72 0.47
41 82 0.53
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:48366 original size:20 final size:19
Alignment explanation
Indices: 48341--48412 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
48331 TTCTAAACTT
*
48341 AAAATCGCAATATGAAAATG
1 AAAATCGCAACA-GAAAATG
48361 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
48381 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
48402 AAAATCGCAAC
1 AAAATCGCAAC
48413 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:48402 original size:21 final size:21
Alignment explanation
Indices: 48356--48419 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
48346 CGCAATATGA
48356 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAATCGCAACGA-GAG
**
48376 AAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
48397 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
48418 AA
1 AA
48420 TCGCAACGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:48423 original size:14 final size:14
Alignment explanation
Indices: 48401--48465 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
48391 CGAGAGAAAT
48401 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
48415 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
48433 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
48448 GATAATCGCAACGC
1 GAAAATCGCAACGA
48462 GAAA
1 GAAA
48466 CCAAAATTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:48437 original size:33 final size:33
Alignment explanation
Indices: 48396--48465 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
48386 CGCAACGAGA
48396 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
48429 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
48462 GAAA
1 GAAA
48466 CCAAAATTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:48499 original size:19 final size:19
Alignment explanation
Indices: 48477--48564 Score: 105
Period size: 19 Copynumber: 4.8 Consensus size: 19
48467 CAAAATTGCA
48477 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
48496 TTGCGATTCTC--TT---G
1 TTGCGATTTTCATTTCGCG
*
48510 TTGCGATTTTAATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
48529 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
48549 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
48565 AACCAAAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 10 0.17
16 2 0.03
17 2 0.03
19 26 0.45
20 18 0.31
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:48519 original size:33 final size:37
Alignment explanation
Indices: 48477--48564 Score: 121
Period size: 33 Copynumber: 2.4 Consensus size: 37
48467 CAAAATTGCA
48477 TTGCGATTTTCATTTCGCGTTGCGA-TTC-TCT-T-G
1 TTGCGATTTTCATTTCGCGTTGCGATTTCATCTCTCG
*
48510 TTGCGATTTTAATTTCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TTTCA-TCTCTCG
48549 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
48565 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 24 0.51
35 3 0.06
37 3 0.06
38 1 0.02
39 16 0.34
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.50
Consensus pattern (37 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCATCTCTCG
Found at i:48552 original size:20 final size:20
Alignment explanation
Indices: 48501--48562 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
48491 TCGCGTTGCG
* *
48501 ATTCTCTTGTTGCGATTTTA
1 ATTCTCTCGTTGCGATTTTC
*
48521 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
48540 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
48560 ATT
1 ATT
48563 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:49001 original size:19 final size:19
Alignment explanation
Indices: 48947--49026 Score: 98
Period size: 19 Copynumber: 4.4 Consensus size: 19
48937 TGATGGAGTG
*
48947 TTGCGATTTTCATTTTTGCA
1 TTGCGATTTTCA-TTTCGCA
*
48967 TTGCGA--TTCA---CTCA
1 TTGCGATTTTCATTTCGCA
48981 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
49000 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
49019 TTGCGATT
1 TTGCGATT
49027 CTCTCGTTGC
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
14 8 0.15
16 4 0.08
18 4 0.08
19 30 0.58
20 6 0.12
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:49037 original size:52 final size:53
Alignment explanation
Indices: 48947--49079 Score: 160
Period size: 52 Copynumber: 2.5 Consensus size: 53
48937 TGATGGAGTG
* **
48947 TTGCGATTTTCATTTTTGCATTGCGATTCACTCATTGCGATTTTCATTT-CGCA
1 TTGCGATTTTCA-TTTCGCATTGCGATTCACTCATTGCGATAGTCATTTCCGCA
* * *
49000 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCACTCATTGCGATAGTCATTTCCGCA
** *
49053 TTGCGATAGTCAATTCCGCATTGCGAT
1 TTGCGATTTTC-ATTTCGCATTGCGAT
49080 AGTCAAATGA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
52 31 0.45
53 24 0.35
54 14 0.20
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATTCACTCATTGCGATAGTCATTTCCGCA
Found at i:49056 original size:20 final size:20
Alignment explanation
Indices: 49031--49085 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
49021 GCGATTCTCT
*
49031 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
49051 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
49071 CATTGCGATAGTCAA
1 CGTTGCGATAGTCAA
49086 ATGAATGTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:50024 original size:20 final size:19
Alignment explanation
Indices: 50003--50242 Score: 137
Period size: 20 Copynumber: 11.9 Consensus size: 19
49993 GCGATAGTCA
50003 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
50022 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
50042 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* * *
50062 GGATACGCATTGCGATTTAC
1 GAAT-CTCGTTGCGATTTAC
*
50082 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
*
50102 -AGATACGCGTTGCGATTTAC
1 GA-AT-CTCGTTGCGATTTAC
*
50122 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
50142 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
50163 GTATTGTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
*
50183 -AGATACGCGTTGCGATTTTAC
1 GA-AT-CTCGTTGCGA-TTTAC
* *
50204 GGATACTCGTTGCGATAGT-C
1 GAAT-CTCGTTGCGAT-TTAC
*
50224 AGAATCACGTTGCGATTTA
1 -GAATCTCGTTGCGATTTA
50243 TATGTTCGCG
Statistics
Matches: 167, Mismatches: 34, Indels: 38
0.70 0.14 0.16
Matches are distributed among these distances:
18 3 0.02
19 6 0.04
20 118 0.71
21 37 0.22
22 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:50037 original size:40 final size:40
Alignment explanation
Indices: 50006--50219 Score: 311
Period size: 40 Copynumber: 5.3 Consensus size: 40
49996 ATAGTCAGAA
*
50006 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCATTGCGATTTACGTAT
* * *
50046 TCGCATTGCGATTTACGGATACGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCATTGCGATTTACGTAT
*
50086 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCATTGCGATTTACGTAT
* *
50126 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCATTGCGA-TTTACGTAT
* * *
50167 TGTCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGAT
1 TCTCGTTGCGATTTACAGATACGCATTGCGA-TTTACGTAT
*
50208 ACTCGTTGCGAT
1 TCTCGTTGCGAT
50220 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 102 0.64
41 57 0.36
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (40 bp):
TCTCGTTGCGATTTACAGATACGCATTGCGATTTACGTAT
Found at i:50075 original size:60 final size:59
Alignment explanation
Indices: 50009--50219 Score: 228
Period size: 60 Copynumber: 3.5 Consensus size: 59
49999 GTCAGAATCT
* *
50009 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
* * * * * *
50069 CATTGCGATTTACGTATTCTCGTTGCGATTTACAG-ATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCGCGTTGCGATTTAC-GTATTCGCGTTGCGATTTACGGATACG
* *
50129 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTAC-GATTCGCGTTGCGA-TTTACGTATTCG-CGTTGCGATTTACGGATACG
* *
50190 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGA-TTTAC-GATTCGCGTTGCGAT
50220 AGTCAGAATC
Statistics
Matches: 127, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
59 1 0.01
60 73 0.57
61 34 0.27
62 19 0.15
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (59 bp):
CGTTGCGATTTACGATTCGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
Found at i:50254 original size:20 final size:20
Alignment explanation
Indices: 50231--50280 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
50221 GTCAGAATCA
*
50231 CGTTGCGATTTAT-ATGTTCG
1 CGTTGCGATTT-TCATATTCG
50251 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCG
50271 CGTTGCGATT
1 CGTTGCGATT
50281 ATAGAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCG
Found at i:50275 original size:40 final size:40
Alignment explanation
Indices: 50009--50280 Score: 271
Period size: 40 Copynumber: 6.8 Consensus size: 40
49999 GTCAGAATCT
* * *
50009 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCG
* * * * *
50049 CATTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCG
* *
50089 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCG
* *
50129 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-G
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACATATTCG
** * *
50169 TCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATACT
1 -CGTTGCGATTTACAGATACGCGTTGCGA-TTTACATATTCG
* * * *
50211 CGTTGCGATAGT-CAGA-ATCACGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACATATTCG
* * *
50251 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
50281 ATAGAAAATC
Statistics
Matches: 200, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.00
40 130 0.65
41 68 0.34
42 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCG
Found at i:50379 original size:20 final size:20
Alignment explanation
Indices: 50332--50383 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
50322 TCTTCATAAT
50332 TGCGTTGCGATTCTGGGAAA
1 TGCGTTGCGATTCTGGGAAA
** *
50352 TGATTTGCGATTCT-GGAGA
1 TGCGTTGCGATTCTGGGAAA
50371 TCGCGTTGCGATT
1 T-GCGTTGCGATT
50384 TTTATTTCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.17, C:0.15, G:0.33, T:0.35
Consensus pattern (20 bp):
TGCGTTGCGATTCTGGGAAA
Found at i:58919 original size:6 final size:6
Alignment explanation
Indices: 58910--58940 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
58900 ACATTGAAAC
58910 TGAACA TGAACA TGAACA TGAACA TG-ACA TG
1 TGAACA TGAACA TGAACA TGAACA TGAACA TG
58941 CTTCCAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAACA
Found at i:60792 original size:2 final size:2
Alignment explanation
Indices: 60785--60814 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60775 GATCATCACT
60785 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
60815 AATTCTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61596 original size:60 final size:59
Alignment explanation
Indices: 61523--61667 Score: 204
Period size: 59 Copynumber: 2.4 Consensus size: 59
61513 TTTTTAGGGT
*
61523 AAAG-TACACAAATGGTCCCCCGACTAT-AGGGCATTACTTTGTTGAGTCTATCGACTATTA
1 AAAGTTACA-AAATGGT-CTCCGACTATGAGGGCATTACTTTGTTGAGTCT-TCGACTATTA
* * * *
61583 AAAGTTACAAAATGATCTTCGAATATGGGGGCATTACTTTGTTGAGTCTTCGACTATTA
1 AAAGTTACAAAATGGTCTCCGACTATGAGGGCATTACTTTGTTGAGTCTTCGACTATTA
61642 AAAGTTACAAAATGGTCTCCGACTAT
1 AAAGTTACAAAATGGTCTCCGACTAT
61668 TCATATGTTC
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 40 0.53
60 31 0.41
61 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCTCCGACTATGAGGGCATTACTTTGTTGAGTCTTCGACTATTA
Done.