Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005273.1 Hibiscus syriacus cultivar Beakdansim tig00011921_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: 92762
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4362 original size:106 final size:104
Alignment explanation
Indices: 4193--5176 Score: 1376
Period size: 106 Copynumber: 9.4 Consensus size: 104
4183 TTCCAATTTC
* * * * * * *
4193 ATTCAGAGTCTATTTCAACTTCGCAGCGAAGAAAATTGGACTCCAGACAACGCAAGTTAAACTTC
1 ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
* * *
4258 ACGACGAAGGGACCGCTGGTTGTTAATAAACAATTTTCCA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAA-CTTCCA
* * * *
4298 ATACAAGAGCCAATTTCAACTTCACAGCGAAGGATAGTGGACTCCAGACAACACAAGTTCAACTT
1 ATTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
*
4363 CACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCTA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC-A
*
4404 ATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
4469 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC-CA
*
4510 GTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
1 -ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
4575 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC-CA
* * *
4616 ATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
* *
4681 CACGACGAAGGGATCGCTGGTTGTCAATAAACAACTTCCCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT-CCA
* * *
4722 ATTTCATAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAATGCATGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
*
4787 CACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC-CA
*
4828 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAAAACGCATGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
*
4893 CACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTCA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC-CA
* * *
4934 ATTTTAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCATGTTCAACTT
1 A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTT
4999 CACGACGAAGGGACCGCTGGTTGTCAACAAACAA--T---
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCA
* * * * *
5034 -TTC----CCAATTTCAACTTCACAACGAAGGACATTGGACTTCAGACAACACAAGTTCAACTTC
1 ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
* *
5094 ACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT-CCA
* * * *
5134 GTTCCAAAGCCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 ATT-CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
5177 TGGAACAATA
Statistics
Matches: 805, Mismatches: 54, Indels: 39
0.90 0.06 0.04
Matches are distributed among these distances:
94 84 0.10
96 1 0.00
98 2 0.00
101 2 0.00
102 1 0.00
104 1 0.00
105 8 0.01
106 702 0.87
107 4 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (104 bp):
ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCA
Found at i:5104 original size:94 final size:94
Alignment explanation
Indices: 4943--5133 Score: 328
Period size: 94 Copynumber: 2.0 Consensus size: 94
4933 AATTTTAGAG
* * * *
4943 CCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
5008 GGGACCGCTGGTTGTCAACAAACAATTTC
66 GGGACCGCTGGTTGTCAACAAACAATTTC
*
5037 CCAATTTCAACTTCACAACGAAGGACATTGGACTTCAGACAACACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
*
5102 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAACAAACAATTTC
5131 CCA
1 CCA
5134 GTTCCAAAGC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (94 bp):
CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAATTTC
Found at i:5632 original size:164 final size:163
Alignment explanation
Indices: 5297--5900 Score: 637
Period size: 164 Copynumber: 3.6 Consensus size: 163
5287 AATCGTTCCA
* * *
5297 ACCAAAGACCTTCGAGTCCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* * * * * *
5362 CTAGAAGGGTTGA-CTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
66 CTAGAAGGGCT-ATCTGC---CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAAATC
5426 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-
127 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
*
5462 -CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATATCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* * * * *
5526 CAAGAAGGGCTATCTGCC-AAAGACAC-CCGAGTTCGATTACACTCAGCTTCGAGGGCATATCAT
66 CTAGAAGGGCTATCTGCCAAAAGAC-CTTCGAGTTCGATTACACTCAGC-TCAAAGGCAAATCAT
* * * * * * *
5589 TTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
129 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C
* * * *
5625 ACCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCGTTTGCAGCATAACTTAGGG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
5690 CTAGAAGGGTTATCTACCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAAT-A
66 CTAGAAGGGCTATCTGCCAA--AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA-AATCA
* * * *
5754 TTTGTAGCATAGCTTAAATCGAGAAGAGCTATCTACC
128 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-GC
* * * * * * *
5791 ATCCAAAAGACCCTCGAGTTCGATTACACTCAGCTCCGAGGCACATCATTTGTAGTATAGCTTAA
1 A-CC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
*
5856 GT-TGAGAAGGGCTATCTGCCAGCCAAAGACCTGACGAGTTCGATT
64 GTCT-AGAAGGGCTATCTGCCA---AAAGACCT-TCGAGTTCGATT
5901 TTATTCAGCT
Statistics
Matches: 363, Mismatches: 57, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
160 23 0.06
161 41 0.11
163 1 0.00
164 147 0.40
165 1 0.00
166 35 0.10
167 30 0.08
168 66 0.18
169 7 0.02
170 11 0.03
171 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (163 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CTAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAAATCATTT
GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
Found at i:5693 original size:83 final size:83
Alignment explanation
Indices: 5297--5898 Score: 598
Period size: 83 Copynumber: 7.3 Consensus size: 83
5287 AATCGTTCCA
* * *
5297 ACCAAAGACCTTCGAGTCCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
5362 CTAGAAGGGTTGA-CTGCTA
66 CTAGAAGGGCT-ATCTGC-C
* * *
5381 ACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAG
*
5445 TCGAGAAGGGCTATCTG--
65 TCTAGAAGGGCTATCTGCC
*
5462 -CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATATCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
5526 CAAGAAGGGCTATCTG--
66 CTAGAAGGGCTATCTGCC
* * * * * * * * *
5542 -CCAAAGACAC-CCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAACATAACTCAA
1 ACCAAAGAC-CTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAA
* * *
5605 GGCTAGAAGGGTTATCTGTC
64 GTCTAGAAGGGCTATCTGCC
* * * *
5625 ACCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCGTTTGCAGCATAACTTAGGG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
5690 CTAGAAGGGTTATCTACC
66 CTAGAAGGGCTATCTGCC
* * * * *
5708 AACC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAAT-ATTTGTAGCATAGCTTAA
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC-ATCATTTGCAGCATAACTTAA
* * * *
5771 ATCGAGAAGAGCTATCTACC
64 GTCTAGAAGGGCTATCTGCC
* * * * * * *
5791 ATCCAAAAGACCCTCGAGTTCGATTACACTCAGCTCCGAGGCACATCATTTGTAGTATAGCTTAA
1 A-CC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
5856 GT-TGAGAAGGGCTATCTGCC
64 GTCT-AGAAGGGCTATCTGCC
*
5876 AGCCAAAGACCTGACGAGTTCGA
1 A-CCAAAGACCT-TCGAGTTCGA
5899 TTTTATTCAG
Statistics
Matches: 438, Mismatches: 63, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
80 98 0.22
81 43 0.10
82 1 0.00
83 111 0.25
84 106 0.24
85 79 0.18
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (83 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CTAGAAGGGCTATCTGCC
Found at i:6131 original size:6 final size:6
Alignment explanation
Indices: 6120--6175 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
6110 CGGGTTTTAC
* * **
6120 ATTTTT ATTTTT ATTATT ATTATTT ATTTATT ATTATT ATTAAT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATT-TTT ATTT-TT ATTTTT ATTTTT ATTTTT
6170 ATTTTT
1 ATTTTT
6176 TCAGGTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
6 32 0.76
7 10 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:6138 original size:3 final size:3
Alignment explanation
Indices: 6124--6172 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
6114 TTTTACATTT
* * *
6124 TTA TTT TTA TTA TTA TTA TTTA TTTA TTA TTA TTA TTA ATA TTT TTA
1 TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA
6171 TT
1 TT
6173 TTTTCAGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 32 0.82
4 7 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:6156 original size:23 final size:23
Alignment explanation
Indices: 6123--6167 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6113 GTTTTACATT
* *
6123 TTTATTTTTATTATTATTATTTA
1 TTTATTATTATTATTAATATTTA
6146 TTTATTATTATTATTAATATTT
1 TTTATTATTATTATTAATATTT
6168 TTATTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTATTATTATTATTAATATTTA
Found at i:7830 original size:2 final size:2
Alignment explanation
Indices: 7823--7874 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
7813 TGTCGTAAAT
7823 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
7865 TA TA TA TA TA
1 TA TA TA TA TA
7875 GATTAACAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8633 original size:18 final size:18
Alignment explanation
Indices: 8610--8647 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
8600 ATGTTGTCTA
8610 AATCATACTAGAAGTTAG
1 AATCATACTAGAAGTTAG
* *
8628 AATCATATTAGAATTTAG
1 AATCATACTAGAAGTTAG
8646 AA
1 AA
8648 AAAGTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (18 bp):
AATCATACTAGAAGTTAG
Found at i:10191 original size:85 final size:85
Alignment explanation
Indices: 10087--10248 Score: 306
Period size: 85 Copynumber: 1.9 Consensus size: 85
10077 AATTCAAAAA
* *
10087 AAGAATCAAAATAATTCAATTAACTCTATCTCAAGAAAAGAACAGTGGATTTGATACTTGATATG
1 AAGAATCAAAATAATTCAATTAACTCTACCTCAAGAAAAGAACAGTGGATTTGATACTTGAGATG
10152 TTTATCAGCATGTCAAAACT
66 TTTATCAGCATGTCAAAACT
10172 AAGAATCAAAATAATTCAATTAACTCTACCTCAAGAAAAGAACAGTGGATTTGATACTTGAGATG
1 AAGAATCAAAATAATTCAATTAACTCTACCTCAAGAAAAGAACAGTGGATTTGATACTTGAGATG
10237 TTTATCAGCATG
66 TTTATCAGCATG
10249 CTTAATTTGC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (85 bp):
AAGAATCAAAATAATTCAATTAACTCTACCTCAAGAAAAGAACAGTGGATTTGATACTTGAGATG
TTTATCAGCATGTCAAAACT
Found at i:12437 original size:31 final size:30
Alignment explanation
Indices: 12380--12443 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
12370 ATAAATAATT
12380 AATATAATTAATCATAATCTTAATTTAATAA
1 AATATAATTAATCATAATCTTAATTT-ATAA
* * *
12411 AATATAA-TAATCTTAATATTTTATTTATAA
1 AATATAATTAATCATAAT-CTTAATTTATAA
12441 AAT
1 AAT
12444 TATAGACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (30 bp):
AATATAATTAATCATAATCTTAATTTATAA
Found at i:12469 original size:24 final size:23
Alignment explanation
Indices: 12432--12478 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
12422 CTTAATATTT
12432 TATTTATAAAATTA-TAGACATAA
1 TATTTATAAAATTATTAG-CATAA
*
12455 TATTTAATAATATTATTAGCATAA
1 TATTT-ATAAAATTATTAGCATAA
12479 ATAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 13 0.62
25 3 0.14
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (23 bp):
TATTTATAAAATTATTAGCATAA
Found at i:16311 original size:11 final size:10
Alignment explanation
Indices: 16280--16322 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
16270 CCCTTCAAAT
16280 AAATAAATAA
1 AAATAAATAA
16290 AAATAAATAA
1 AAATAAATAA
* *
16300 AAATTAAT-T
1 AAATAAATAA
16309 AAATAAATAA
1 AAATAAATAA
16319 AAAT
1 AAAT
16323 TACATCCGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAATAAATAA
Found at i:22337 original size:2 final size:2
Alignment explanation
Indices: 22330--22371 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
22320 TTAGAAATAG
*
22330 TA TA TA TA TA TA TA TA TA TA TA TA TA TG T- TA T- 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
22370 TA
1 TA
22372 GACACTTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30159 original size:49 final size:45
Alignment explanation
Indices: 30057--30177 Score: 125
Period size: 49 Copynumber: 2.6 Consensus size: 45
30047 GTAACCATGC
*
30057 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
* * * * **
30102 AAAAAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAA
* *
30151 AAATAAGCTTATAAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
30178 AAGGTAAGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
45 23 0.38
46 1 0.02
48 1 0.02
49 36 0.59
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
Found at i:42018 original size:17 final size:17
Alignment explanation
Indices: 41996--42030 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41986 AACGTGCATA
41996 TAAATATA-ATACTAATG
1 TAAATATATATA-TAATG
42013 TAAATATATATATAATG
1 TAAATATATATATAATG
42030 T
1 T
42031 GAACTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (17 bp):
TAAATATATATATAATG
Found at i:43566 original size:3 final size:3
Alignment explanation
Indices: 43560--43593 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
43550 GATGATGATG
43560 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
43594 AACCTGAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:47758 original size:21 final size:21
Alignment explanation
Indices: 47732--47802 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
47722 TAAATATGAC
47732 ATCCATAACAACAAACTTGAA
1 ATCCATAACAACAAACTTGAA
47753 ATCCATAACAACAAACTTGAA
1 ATCCATAACAACAAACTTGAA
* * *
47774 GTACATAACAACCAACTTGAA
1 ATCCATAACAACAAACTTGAA
47795 ATCCATAA
1 ATCCATAA
47803 TAATAAATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.51, C:0.24, G:0.06, T:0.20
Consensus pattern (21 bp):
ATCCATAACAACAAACTTGAA
Found at i:53604 original size:54 final size:54
Alignment explanation
Indices: 53522--53777 Score: 397
Period size: 54 Copynumber: 4.7 Consensus size: 54
53512 TTGACATATT
*
53522 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGTAACCCACCGAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACCGAA
*
53576 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGCGTGCAACCCACCGAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACCGAA
* *
53630 TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCA-TGAAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACCG-AA
* * * **
53684 TTCATAATGAGTTTGTGAATTATCGTATCGACACTATGTGTACAACCCATGGAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACCGAA
* *
53738 TTCATAATGAGTTTATGAATTACTGTATCGGCACTATGTG
1 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTG
53778 CACTTAGGTG
Statistics
Matches: 188, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.01
54 186 0.99
55 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (54 bp):
TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACCGAA
Found at i:56180 original size:41 final size:41
Alignment explanation
Indices: 56095--56180 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
56085 AGTACAAATC
* * * * *
56095 AAGTACAAATCTATAGCGACGTTTGTATAAAAATGCCCCTA
1 AAGTACAAATCTACAACGACGTTTGTATAAAAACGCCACAA
* * *
56136 AAGTACAAGTCTACAACGATGTTTGTATACAAACGCCACAA
1 AAGTACAAATCTACAACGACGTTTGTATAAAAACGCCACAA
56177 AAGT
1 AAGT
56181 CTTAGCCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (41 bp):
AAGTACAAATCTACAACGACGTTTGTATAAAAACGCCACAA
Found at i:56455 original size:41 final size:41
Alignment explanation
Indices: 56340--56475 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 41
56330 ACTCATTGTG
** * *
56340 GCATTTGTATAAAAATGCCACTAAAATAC-TACCCTATTG-T
1 GCATTTGTATAAAAACACCACT-ATATACGAACCCTATTGCT
* * *
56380 GGCATTTTTGGA-AAAAACACCACTATAGATGAACCCTATTGCT
1 -GCA--TTTGTATAAAAACACCACTATATACGAACCCTATTGCT
*
56423 GCATTTGTATAAAAACACCACTATATACGAACCCTATTGCG
1 GCATTTGTATAAAAACACCACTATATACGAACCCTATTGCT
*
56464 GCGTTTGTATAA
1 GCATTTGTATAA
56476 CAACGACGCT
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
40 5 0.06
41 45 0.58
42 22 0.28
43 6 0.08
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (41 bp):
GCATTTGTATAAAAACACCACTATATACGAACCCTATTGCT
Found at i:58971 original size:29 final size:30
Alignment explanation
Indices: 58922--58989 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
58912 ACATTTCTAA
* *
58922 AAATTTTGAGGTGGCTAAATTA-ATTTTTTT
1 AAATTTT-AGGAGGCTAAATTATAATTTTTT
*
58952 AAATTTTAGGAGTCTAAATTATAATTTTTT
1 AAATTTTAGGAGGCTAAATTATAATTTTTT
58982 AAATTTTA
1 AAATTTTA
58990 TTGATCCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 12 0.35
30 22 0.65
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (30 bp):
AAATTTTAGGAGGCTAAATTATAATTTTTT
Found at i:59270 original size:14 final size:15
Alignment explanation
Indices: 59251--59279 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59241 AATCCGACGA
59251 TTTTAAAAT-TTATT
1 TTTTAAAATATTATT
59265 TTTTAAAATATTATT
1 TTTTAAAATATTATT
59280 ATATTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAATATTATT
Found at i:60644 original size:20 final size:21
Alignment explanation
Indices: 60619--60711 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
60609 TTTTCCCAAT
*
60619 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
60639 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
60660 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
60680 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
60701 TCGCAATGCGA
1 TCGCAATGCGA
60712 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:60725 original size:20 final size:20
Alignment explanation
Indices: 60700--60834 Score: 90
Period size: 20 Copynumber: 6.7 Consensus size: 20
60690 AATTGGGAAA
* *
60700 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTAACT
* * **
60720 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-AACT
* *
60741 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTAACT
* * * **
60761 TTCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-AACT
* *
60782 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTAACT
* *
60802 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTAACT
*
60822 TTCGCAACGCGAT
1 ATCGCAACGCGAT
60835 TTACATAGCG
Statistics
Matches: 86, Mismatches: 27, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
20 59 0.69
21 27 0.31
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTAACT
Found at i:60726 original size:41 final size:41
Alignment explanation
Indices: 60619--60711 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
60609 TTTTCCCAAT
60619 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
60660 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
60701 TCGCAATGCGA
1 TCGCAATGCGA
60712 TACTGACTAT
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:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:60742 original size:41 final size:41
Alignment explanation
Indices: 60697--60815 Score: 193
Period size: 41 Copynumber: 2.9 Consensus size: 41
60687 GCGAATTGGG
* * * *
60697 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTTACTTTCGCAATGCGATAATAA
60738 AAAATCGCAACGAGATACTTACTTTCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTTACTTTCGCAATGCGATAATAA
*
60779 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTTTCGCAATGCGATA
60816 CTGACTTTCG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTTTCGCAATGCGATAATAA
Found at i:60795 original size:21 final size:21
Alignment explanation
Indices: 60720--60795 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 21
60710 GATACTGACT
* *
60720 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGAGATAATAAAAA
* * **
60741 ATCGCAACGAGATACT-TACT
1 ATCGCAACGAGATAATAAAAA
* * *
60761 TTCGCAATGCGATAATAAAAA
1 ATCGCAACGAGATAATAAAAA
60782 ATCGCAACGAGATA
1 ATCGCAACGAGATA
60796 CTTACTTTCG
Statistics
Matches: 38, Mismatches: 16, Indels: 2
0.68 0.29 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAGATAATAAAAA
Found at i:61412 original size:18 final size:18
Alignment explanation
Indices: 61353--61432 Score: 78
Period size: 18 Copynumber: 4.5 Consensus size: 18
61343 TGCGAGAATG
61353 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGC-GAAAT
* *
61372 AACTATCGCAA--CGAGAT
1 AA-AATCGCAACGCGAAAT
61389 --AATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAAT
*
61405 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-T
61424 AAAATCGCA
1 AAAATCGCA
61433 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 16 0.32
19 11 0.22
20 7 0.14
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:61450 original size:19 final size:19
Alignment explanation
Indices: 61428--61611 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
61418 GAAACCAAAA
*
61428 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
61447 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
61466 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
61485 TCGCGGTTGCGA-TTTCATT
1 TCGC-GTTGCGATTTTCATT
*
61504 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
61520 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
61537 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
61551 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
61570 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
61590 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
61610 TC
1 TC
61612 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 15, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 8 0.06
19 62 0.46
20 38 0.28
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:61581 original size:34 final size:33
Alignment explanation
Indices: 61490--61586 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
61480 TTATTTCGCG
* * *
61490 GTTGCGAT-TTCATTTCGCGTTGCGATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
*
61522 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
61555 GTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTT-CGCGTTGCGATTCTC
61587 ATTATCTCGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 7 0.12
33 36 0.62
34 15 0.26
ACGTcount: A:0.11, C:0.24, G:0.26, T:0.39
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
Found at i:61588 original size:20 final size:20
Alignment explanation
Indices: 61554--61611 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
61544 GCGATTCTCT
**
61554 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
61574 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
61594 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
61612 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:62538 original size:20 final size:20
Alignment explanation
Indices: 62513--62550 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62503 AATAGTTTCT
62513 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
62533 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
62551 GAGAGAATCA
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:62839 original size:22 final size:22
Alignment explanation
Indices: 62814--62857 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
62804 GATTTAGATA
62814 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
62836 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
62858 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:63055 original size:21 final size:22
Alignment explanation
Indices: 63025--63120 Score: 69
Period size: 20 Copynumber: 4.6 Consensus size: 22
63015 CGCTTTGAAA
*
63025 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGATTATGTAAGT
* *
63046 ATCGCGTTGCGA--AAGTAAGT
1 ATCGCATTGCGATTATGTAAGT
* * * * *
63066 ATCTCGTTGCGATT-TTTTATT
1 ATCGCATTGCGATTATGTAAGT
*
63087 ATCGCATTGCGA-TA-GTCAGT
1 ATCGCATTGCGATTATGTAAGT
63107 ATCGCATTGCGATT
1 ATCGCATTGCGATT
63121 TTCCCAATTC
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
19 3 0.05
20 29 0.51
21 25 0.44
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (22 bp):
ATCGCATTGCGATTATGTAAGT
Found at i:63088 original size:41 final size:41
Alignment explanation
Indices: 63025--63122 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
63015 CGCTTTGAAA
* *
63025 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
* * * * *
63066 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
63107 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
63123 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
Found at i:63137 original size:21 final size:21
Alignment explanation
Indices: 63108--63241 Score: 139
Period size: 20 Copynumber: 6.5 Consensus size: 21
63098 ATAGTCAGTA
63108 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
63129 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
63149 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
63170 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
63190 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
63211 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
63231 TCGCATTGCGA
1 TCGCATTGCGA
63242 ATTGGGAAAA
Statistics
Matches: 90, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
20 48 0.53
21 42 0.47
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:63138 original size:41 final size:41
Alignment explanation
Indices: 63108--63241 Score: 241
Period size: 41 Copynumber: 3.3 Consensus size: 41
63098 ATAGTCAGTA
*
63108 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
*
63149 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
*
63190 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
63231 TCGCATTGCGA
1 TCGCATTGCGA
63242 ATTGGGAAAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
Found at i:63162 original size:82 final size:82
Alignment explanation
Indices: 63088--63241 Score: 249
Period size: 82 Copynumber: 1.9 Consensus size: 82
63078 TTTTTTATTA
63088 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
1 TCGCATTGCGAT--TCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
63151 GCATTGCGATTTTCCCAAT
64 GCATTGCGATTTTCCCAAT
* * *
63170 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
1 TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
63235 ATTGCGA
66 ATTGCGA
63242 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
80 2 0.03
81 2 0.03
82 63 0.94
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (82 bp):
TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
ATTGCGATTTTCCCAAT
Found at i:63581 original size:3 final size:3
Alignment explanation
Indices: 63575--63599 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
63565 ATTATTATTA
63575 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
63600 ATGATGTGGT
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:66014 original size:27 final size:27
Alignment explanation
Indices: 65982--66049 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
65972 TTATTATCTC
65982 TACCGATTTTGTTATTATTGGACATTT
1 TACCGATTTTGTTATTATTGGACATTT
*
66009 TACCGATTTTGTTATTATTGGACGTTT
1 TACCGATTTTGTTATTATTGGACATTT
*
66036 TACCGGTTTTGTTA
1 TACCGATTTTGTTA
66050 ACATATACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (27 bp):
TACCGATTTTGTTATTATTGGACATTT
Found at i:66156 original size:21 final size:21
Alignment explanation
Indices: 66131--66171 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
66121 AAATTTTAAA
*
66131 AAATATTAATGTTTTAGGTAG
1 AAATAATAATGTTTTAGGTAG
66152 AAATAATAATGTTTTAGGTA
1 AAATAATAATGTTTTAGGTA
66172 TTTTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (21 bp):
AAATAATAATGTTTTAGGTAG
Found at i:67421 original size:29 final size:29
Alignment explanation
Indices: 67389--67492 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 29
67379 GCCTACTTGA
67389 TTTTTTAGAAAATTTAAGAACTTAATTAT
1 TTTTTTAGAAAATTTAAGAACTTAATTAT
** * * * *
67418 TTTTTT-CTAAGTTTGAGGACCTAATTGAT
1 TTTTTTAGAAAATTTAAGAACTTAATT-AT
* * * *
67447 TCTTTTAGAAAGTTTAAGTACTTAATTAA
1 TTTTTTAGAAAATTTAAGAACTTAATTAT
*
67476 TTTTTTATAAAATTTAA
1 TTTTTTAGAAAATTTAA
67493 AATATTCTTT
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
28 14 0.25
29 28 0.49
30 15 0.26
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTTTTAGAAAATTTAAGAACTTAATTAT
Found at i:67447 original size:57 final size:58
Alignment explanation
Indices: 67362--67481 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 58
67352 TTGATTTTTA
* * * *
67362 TTTTACTAAGTTCGAGGGCCTACTTGATT-TTTTAGAAAATTTAAGAACTTAATTATT
1 TTTTTCTAAGTTCGAGGACCTAATTGATTCTTTTAGAAAATTTAAGAACTTAATTAAT
* * *
67419 TTTTTCTAAGTTTGAGGACCTAATTGATTCTTTTAGAAAGTTTAAGTACTTAATTAAT
1 TTTTTCTAAGTTCGAGGACCTAATTGATTCTTTTAGAAAATTTAAGAACTTAATTAAT
67477 TTTTT
1 TTTTT
67482 ATAAAATTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 25 0.45
58 30 0.55
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.47
Consensus pattern (58 bp):
TTTTTCTAAGTTCGAGGACCTAATTGATTCTTTTAGAAAATTTAAGAACTTAATTAAT
Found at i:67473 original size:30 final size:29
Alignment explanation
Indices: 67385--67492 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 29
67375 GAGGGCCTAC
67385 TTGATTTTTTAGAAAATTTAAGAACTTAA
1 TTGATTTTTTAGAAAATTTAAGAACTTAA
*** * * * *
67414 TT-ATTTTTTTCTAAGTTTGAGGACCTAA
1 TTGATTTTTTAGAAAATTTAAGAACTTAA
* *
67442 TTGATTCTTTTAGAAAGTTTAAGTACTTAA
1 TTGATT-TTTTAGAAAATTTAAGAACTTAA
* *
67472 TTAATTTTTTATAAAATTTAA
1 TTGATTTTTTAGAAAATTTAA
67493 AATATTCTTT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
28 21 0.34
29 18 0.30
30 22 0.36
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (29 bp):
TTGATTTTTTAGAAAATTTAAGAACTTAA
Found at i:80035 original size:20 final size:19
Alignment explanation
Indices: 80010--80050 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
80000 CGGTTGACTA
80010 ACATTGACCGTTGACTGTTG
1 ACATTGACCGTTGACT-TTG
80030 ACATTGACCGTTGACTTTG
1 ACATTGACCGTTGACTTTG
80049 AC
1 AC
80051 CAAAAAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (19 bp):
ACATTGACCGTTGACTTTG
Found at i:82543 original size:44 final size:44
Alignment explanation
Indices: 82460--82910 Score: 563
Period size: 44 Copynumber: 10.3 Consensus size: 44
82450 TCATCTACTA
* *
82460 TGTGCAAGGGTAAGTCCTTACTGTTT--CCCAGGCTCCTTTGTTG
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCCAGGTTCCTTTGTTG
* *
82503 TGTACAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGATG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
*
82547 TGTGTAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
* * *
82591 TGTGCAAGGGTAAGCCATACAGTTTTCCTCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
*
82635 TGTGCAAGGGTAAGCCTTACAGTTTCCCCTAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
* * *
82679 TATGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
* * * * *
82723 TGTGCAAGGGTAAGTCTAACAGTTTCCCCCAGGTACATTTATTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
*
82767 TGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
* * * ** *
82810 TGTGCAAGGGTAATACCTTATAGTTT--CCCAGGCTCCTTTCCTA
1 TGTGCAAGGGTAA-GCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
* * * * *
82853 TGTGCAAGGGTAAGACCTTACCGTTT-CCCCAGGCTCTTTTGCTA
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCCAGGTTCCTTTGTTG
*
82897 TGTGAAAGGGTAAG
1 TGTGCAAGGGTAAG
82911 AACTTACCGT
Statistics
Matches: 359, Mismatches: 44, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
42 10 0.03
43 76 0.21
44 273 0.76
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (44 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
Found at i:87418 original size:82 final size:85
Alignment explanation
Indices: 87222--87421 Score: 291
Period size: 82 Copynumber: 2.4 Consensus size: 85
87212 CTTACAGTCA
*
87222 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAAGTTCCTTTGTTGTGTGCAAGAGTAAGCCTTA
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAAG---CATTGTTGTGTGCAAGAGTAAGCCTTA
*
87287 CAGTTCTCCCCAGGTTCCTTTGT
63 CAATTCTCCCCAGGTTCCTTTGT
* *
87310 TGTGTGTAAGGGTAAGCCTTACAGTTTCCCCC-AG-ATT-TTGTGTGCAAGGGTAAGCCTTACAA
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAAGCATTGTTGTGTGCAAGAGTAAGCCTTACAA
87372 TT-TCCCCAGGTTCCTTTGT
66 TTCTCCCCAGGTTCCTTTGT
*
87391 TGTGTGCAAGGGTAAGACCTTATAGTTTCCC
1 TGTGTGCAAGGGTAAG-CCTTACAGTTTCCC
87422 AGGCTCCTTT
Statistics
Matches: 105, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
81 32 0.30
82 38 0.36
83 2 0.02
87 2 0.02
88 31 0.30
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (85 bp):
TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAAGCATTGTTGTGTGCAAGAGTAAGCCTTACAA
TTCTCCCCAGGTTCCTTTGT
Found at i:87455 original size:125 final size:126
Alignment explanation
Indices: 87222--87465 Score: 368
Period size: 125 Copynumber: 1.9 Consensus size: 126
87212 CTTACAGTCA
*
87222 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAAGTTCCTTTGTTGTGTGCAAGAGTAAGCCTTA
1 TGTGTGCAAGGGTAAGCCTTACAATTTCCCCCAAGTTCCTTTGTTGTGTGCAAGAGTAAGCCTTA
* * * *
87287 CAGTTCTCCCCAGGTTCCTTTGTTGTGTGTAAGGGTAAGCCTTACAGTTTCCCCCAGATTT
66 CAGTTCTCCCCAGGCTCCTTTGATATGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGATTT
* *
87348 TGTGTGCAAGGGTAAGCCTTACAATTT-CCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGACCTT
1 TGTGTGCAAGGGTAAGCCTTACAATTTCCCCCAAGTTCCTTTGTTGTGTGCAAGAGTAAG-CCTT
* *
87412 ATAGTT-T-CCCAGGCTCCTTTGATATGTGCAAGGGTAAGACCTTACCGTTTCCCC
65 ACAGTTCTCCCCAGGCTCCTTTGATATGTGCAAGGGTAAG-CCTTACAGTTTCCCC
87466 AGGCTCTTTT
Statistics
Matches: 107, Mismatches: 9, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
124 27 0.25
125 45 0.42
126 35 0.33
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (126 bp):
TGTGTGCAAGGGTAAGCCTTACAATTTCCCCCAAGTTCCTTTGTTGTGTGCAAGAGTAAGCCTTA
CAGTTCTCCCCAGGCTCCTTTGATATGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGATTT
Found at i:87483 original size:44 final size:43
Alignment explanation
Indices: 87222--87468 Score: 310
Period size: 44 Copynumber: 5.8 Consensus size: 43
87212 CTTACAGTCA
*
87222 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAAGTTCCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGT
*
87266 TGTGTGCAAGAGTAAGCCTTACAGTTCTCCCCAGGTTCCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTT-TCCCCAGGTTCCTTTGT
* *
87310 TGTGTGTAAGGGTAAGCCTTACAGTTTCCCCCA-G----ATT-T
1 TGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGT
*
87348 TGTGTGCAAGGGTAAGCCTTACAATTTCCCCAGGTTCCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGT
* * *
87391 TGTGTGCAAGGGTAAGACCTTATAGTTT-CCCAGGCTCCTTTGA
1 TGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGT
* *
87434 TATGTGCAAGGGTAAGACCTTACCGTTTCCCCAGG
1 TGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGG
87469 CTCTTTTTCT
Statistics
Matches: 178, Mismatches: 15, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
37 5 0.03
38 27 0.15
39 2 0.01
42 2 0.01
43 57 0.32
44 84 0.47
45 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (43 bp):
TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGT
Done.