Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005750.1 Hibiscus syriacus cultivar Beakdansim tig00013449_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: 148084
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:4516 original size:55 final size:55
Alignment explanation
Indices: 4294--4505 Score: 334
Period size: 55 Copynumber: 3.9 Consensus size: 55
4284 ATTATATGTT
* * *
4294 CAAATCCACAGAATTCATCAAGAGTTGGTGAATAACCGTACATGCACTATGTGTG
1 CAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTG
*
4349 CAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTG
1 CAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTG
* * ** *
4404 CAAATCCATGAAATTCATCATGAGTTGATGAATAACCGTACAAACACTATATGTG
1 CAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTG
*
4459 CAAATCCACGGAATTCATCATGAGTTAATGAATAACCGTACATGCAC
1 CAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGCAC
4506 GAGTTGTGCA
Statistics
Matches: 143, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 143 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (55 bp):
CAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTG
Found at i:10460 original size:55 final size:54
Alignment explanation
Indices: 10372--10610 Score: 343
Period size: 55 Copynumber: 4.4 Consensus size: 54
10362 CTAAGTGTAC
10372 TACAGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCG
1 TACAGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCG
* * * *
10426 TACATGCACTATGTGTTCAATTCTACGAAATTCATCATGAGTTGATGAATAATCG
1 TACA-GCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCG
* * *
10481 TACAGACACTATATGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACAG
1 TACAG-CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCG
* *
10536 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCA
1 TACA-GCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCG
* *
10591 TACATGCACGATATGTGCAA
1 TACA-GCACTATGTGTGCAA
10611 CCCTATTAGC
Statistics
Matches: 165, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
54 5 0.03
55 159 0.96
56 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (54 bp):
TACAGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCG
Found at i:11819 original size:17 final size:17
Alignment explanation
Indices: 11797--11836 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
11787 TAGGATTAAA
11797 AGTTGGGAGAAAGAATC
1 AGTTGGGAGAAAGAATC
11814 AGTTGGGAGAAAGAATC
1 AGTTGGGAGAAAGAATC
11831 AGTTGG
1 AGTTGG
11837 TAGCAAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.38, T:0.20
Consensus pattern (17 bp):
AGTTGGGAGAAAGAATC
Found at i:26034 original size:26 final size:26
Alignment explanation
Indices: 26004--26070 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
25994 GTCATAAATC
**
26004 TATGACTTGCATTGATGACACGCATT
1 TATGACTCACATTGATGACACGCATT
* **
26030 TATGACTCACATTTATGATGCGCATT
1 TATGACTCACATTGATGACACGCATT
26056 TATGA-TGCACATTGA
1 TATGACT-CACATTGA
26071 GCATCATTGC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 1 0.03
26 33 0.97
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (26 bp):
TATGACTCACATTGATGACACGCATT
Found at i:26042 original size:13 final size:13
Alignment explanation
Indices: 26026--26068 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
26016 TGATGACACG
26026 CATTTATGACT-CA
1 CATTTATGA-TGCA
*
26039 CATTTATGATGCG
1 CATTTATGATGCA
26052 CATTTATGATGCA
1 CATTTATGATGCA
26065 CATT
1 CATT
26069 GAGCATCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 1 0.04
13 26 0.96
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (13 bp):
CATTTATGATGCA
Found at i:27004 original size:19 final size:19
Alignment explanation
Indices: 26980--27035 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
26970 CATCAAATGC
26980 AAGTAGTGCATCGATGCAT
1 AAGTAGTGCATCGATGCAT
26999 AAGTAGTGCATCGATGCAT
1 AAGTAGTGCATCGATGCAT
*
27018 AAGTAGTACATCGATGCA
1 AAGTAGTGCATCGATGCA
27036 CCCCCTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (19 bp):
AAGTAGTGCATCGATGCAT
Found at i:28688 original size:23 final size:23
Alignment explanation
Indices: 28661--28751 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
28651 GACATTATAT
28661 GGCACTACGGTGCATTTATACGC
1 GGCACTACGGTGCATTTATACGC
* * * *
28684 GGCACTTCGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTATACGC
* * *
28707 GACATTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTATACGC
*
28730 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTATACG
28752 AGCTGTGGTG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTACGGTGCATTTATACGC
Found at i:32214 original size:19 final size:19
Alignment explanation
Indices: 32190--32226 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
32180 CATCAAATGC
32190 AAGTAGTGCATCGATGCAT
1 AAGTAGTGCATCGATGCAT
32209 AAGTAGTGCATCGATGCA
1 AAGTAGTGCATCGATGCA
32227 CCCCCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (19 bp):
AAGTAGTGCATCGATGCAT
Found at i:33884 original size:23 final size:23
Alignment explanation
Indices: 33857--33940 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
33847 TATGGTACTA
33857 CGGTGCATTTCTACGCGGCACTT
1 CGGTGCATTTCTACGCGGCACTT
* * * * *
33880 TGGTGTAATTCTACGTGGCACTA
1 CGGTGCATTTCTACGCGGCACTT
33903 CGGTGCATTTCTACGCGGCACTT
1 CGGTGCATTTCTACGCGGCACTT
*
33926 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
33941 AGCTGTGGTG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTT
Found at i:37985 original size:29 final size:29
Alignment explanation
Indices: 37943--38014 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
37933 AAATAGCATT
* * *
37943 TTTTTTAAATAATTACCAAAATAGCACCC
1 TTTTTGAATTAATTACCAAAATAGCACCA
*
37972 TTTTTGAATTAATTCCCAAAATAGCACCA
1 TTTTTGAATTAATTACCAAAATAGCACCA
* *
38001 ATTTCGAATTAATT
1 TTTTTGAATTAATT
38015 CCTAGAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.38
Consensus pattern (29 bp):
TTTTTGAATTAATTACCAAAATAGCACCA
Found at i:38015 original size:29 final size:29
Alignment explanation
Indices: 37952--38113 Score: 114
Period size: 29 Copynumber: 5.7 Consensus size: 29
37942 TTTTTTTAAA
* ** *
37952 TAATTACCAAAATAGCACCCTTTTTGAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
37981 TAATTCCCAAAATAGCACCAATTTCGAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
* * * * * *
38010 TAATTCCTAGAATATCA-C-TTTTCAAAAC
1 TAATTCCCAAAATAGCACCAATTTC-GAAT
* * *
38038 AAATTACCAAAATAGCACCTATTTCGAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
*** * **
38067 TAATTCCCCGTATAGCACTAA-ACCGAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
*
38095 TAATTCCCAAAATAACACC
1 TAATTCCCAAAATAGCACC
38114 GGTCAACGGT
Statistics
Matches: 98, Mismatches: 32, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
27 4 0.04
28 34 0.35
29 56 0.57
30 4 0.04
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCAATTTCGAAT
Found at i:38105 original size:57 final size:57
Alignment explanation
Indices: 37977--38113 Score: 148
Period size: 57 Copynumber: 2.4 Consensus size: 57
37967 CACCCTTTTT
* * ***
37977 GAATTAATTCCCAAAATAGCACCAATTTCGAATTAATTCCTAGAATATCACTTTTCA
1 GAATTAATTCCCAAAATAGCACCAATTTCGAATTAATTCCCAGAATAGCACTAAACA
* ** * * * * *
38034 AAACAAATTACCAAAATAGCACCTATTTCGAATTAATTCCCCGTATAGCACTAAACC
1 GAATTAATTCCCAAAATAGCACCAATTTCGAATTAATTCCCAGAATAGCACTAAACA
*
38091 GAATTAATTCCCAAAATAACACC
1 GAATTAATTCCCAAAATAGCACC
38114 GGTCAACGGT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.28
Consensus pattern (57 bp):
GAATTAATTCCCAAAATAGCACCAATTTCGAATTAATTCCCAGAATAGCACTAAACA
Found at i:38159 original size:12 final size:13
Alignment explanation
Indices: 38121--38186 Score: 80
Period size: 13 Copynumber: 4.8 Consensus size: 13
38111 ACCGGTCAAC
38121 GGTCAACGGGTCG
1 GGTCAACGGGTCG
38134 GGTCAACGGGTCG
1 GGTCAACGGGTCG
38147 GGTCAACGGTCGGGTCG
1 GGTCAA----CGGGTCG
38164 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
38176 GGTAAACGGGT
1 GGTCAACGGGT
38187 AAACGGGTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
12 11 0.23
13 23 0.49
17 13 0.28
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:38162 original size:17 final size:17
Alignment explanation
Indices: 38140--38178 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
38130 GTCGGGTCAA
38140 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
38157 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
38174 CGGGT
1 CGGGT
38179 AAACGGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:45361 original size:29 final size:28
Alignment explanation
Indices: 45223--45365 Score: 108
Period size: 29 Copynumber: 4.9 Consensus size: 28
45213 AAATAGCATT
* *
45223 TTTTTAAATAATTACCAAAATAGCACCC
1 TTTTTAATTAATTCCCAAAATAGCACCC
* * *
45251 TTTTCGAATTAATTCCCAAAATAACACCAA
1 TTTT-TAATTAATTCCCAAAATAGCACC-C
* * *
45281 TTTTGAATTAATTCCCAGAATATCA-CC
1 TTTTTAATTAATTCCCAAAATAGCACCC
** *
45308 TTTTTCAAAAAAAATTACCAAAATAGCACCC
1 TTTTT---AATTAATTCCCAAAATAGCACCC
**
45339 ATTTTTAATTAATTCCCCGAATAGCAC
1 -TTTTTAATTAATTCCCAAAATAGCAC
45366 TAAACCGAAT
Statistics
Matches: 89, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
27 4 0.04
28 5 0.06
29 54 0.61
30 19 0.21
31 2 0.02
32 5 0.06
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (28 bp):
TTTTTAATTAATTCCCAAAATAGCACCC
Found at i:45429 original size:25 final size:26
Alignment explanation
Indices: 45395--45469 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 26
45385 AAATAACACC
45395 GGTCAAC-GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAACGGGTCGGGTCG
45420 GGTCAACGGTCGGGTCAAC-GGTCGGGTCG
1 GGTCAA----CGGGTCAACGGGTCGGGTCG
*
45449 GGTCAACGGGTAAACGGGTCG
1 GGTCAACGGGTCAACGGGTCG
45470 TGACCGGTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
25 14 0.33
26 5 0.12
29 17 0.40
30 7 0.16
ACGTcount: A:0.17, C:0.23, G:0.44, T:0.16
Consensus pattern (26 bp):
GGTCAACGGGTCAACGGGTCGGGTCG
Found at i:45432 original size:12 final size:12
Alignment explanation
Indices: 45415--45447 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
45405 CAACGGGTCG
45415 GGTCGGGTCAAC
1 GGTCGGGTCAAC
45427 GGTCGGGTCAAC
1 GGTCGGGTCAAC
45439 GGTCGGGTC
1 GGTCGGGTC
45448 GGGTCAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.18
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:45432 original size:17 final size:17
Alignment explanation
Indices: 45402--45457 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
45392 ACCGGTCAAC
45402 GGTCAACGGGTCGGGTCG
1 GGTCAAC-GGTCGGGTCG
45420 GGTCAA----C-GGTCG
1 GGTCAACGGTCGGGTCG
45432 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
45449 GGTCAACGG
1 GGTCAACGG
45458 GTAAACGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 11 0.33
13 1 0.03
16 1 0.03
17 14 0.42
18 6 0.18
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.16
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:45486 original size:9 final size:10
Alignment explanation
Indices: 45472--45526 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
45462 ACGGGTCGTG
45472 ACCGGTC-AA
1 ACCGGTCAAA
45481 ACCGGTCAAA
1 ACCGGTCAAA
45491 ACCGGTTCAAA
1 ACCGG-TCAAA
*
45502 ACCGGT-TAA
1 ACCGGTCAAA
*
45511 ACCAGTCAAA
1 ACCGGTCAAA
45521 ACCGGT
1 ACCGGT
45527 TTTCAGCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 14 0.36
10 15 0.38
11 10 0.26
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:45494 original size:19 final size:20
Alignment explanation
Indices: 45472--45526 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
45462 ACGGGTCGTG
45472 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGTCAAA
*
45491 ACCGGTTCAAAACCGGT-TAA
1 ACCGG-TCAAAACCGGTCAAA
*
45511 ACCAGTCAAAACCGGT
1 ACCGGTCAAAACCGGT
45527 TTTCAGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.50
20 8 0.25
21 8 0.25
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.15
Consensus pattern (20 bp):
ACCGGTCAAAACCGGTCAAA
Found at i:50876 original size:8 final size:8
Alignment explanation
Indices: 50853--50882 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
50843 TAAGCACAAA
50853 ATTATAAT
1 ATTATAAT
50861 ATTTATAAT
1 A-TTATAAT
50870 ATTATAAT
1 ATTATAAT
50878 ATTAT
1 ATTAT
50883 TTGATTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATTATAAT
Found at i:52824 original size:40 final size:39
Alignment explanation
Indices: 52754--52842 Score: 124
Period size: 40 Copynumber: 2.3 Consensus size: 39
52744 TATTTTAGGG
* * *
52754 ACCAAAGATGAAATTCCCATGTGCACAAGTTGGCCACCT
1 ACCAAAGATGAAATTCCAATGTGCACAAGTTAGCCACCA
* *
52793 ACCAAAGATGAATTTTCCAATGTGTACAAGTTAGCCACCA
1 ACCAAAGATGAA-ATTCCAATGTGCACAAGTTAGCCACCA
52833 ACCAAAGATG
1 ACCAAAGATG
52843 TCAACTTTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 12 0.27
40 32 0.73
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (39 bp):
ACCAAAGATGAAATTCCAATGTGCACAAGTTAGCCACCA
Found at i:57552 original size:40 final size:39
Alignment explanation
Indices: 57474--57563 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 39
57464 ATATTTTAGG
*
57474 GACCAAAGATGAAATTCCCATGTGCACAAGTTAGCCACC
1 GACCAAAGATGAAATTCCAATGTGCACAAGTTAGCCACC
* * * * *
57513 TACCAAAGATGAATTTTCCAATGTGTATAAGTTATCCACC
1 GACCAAAGATGAA-ATTCCAATGTGCACAAGTTAGCCACC
57553 GACCAAAGATG
1 GACCAAAGATG
57564 TCAACTTTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 12 0.28
40 31 0.72
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (39 bp):
GACCAAAGATGAAATTCCAATGTGCACAAGTTAGCCACC
Found at i:69712 original size:81 final size:81
Alignment explanation
Indices: 69576--69770 Score: 249
Period size: 81 Copynumber: 2.5 Consensus size: 81
69566 AAGTCGACAA
* * *
69576 AAAATAAAAAAAGAGAAA-AGAAAAGAACAAAAAAAAGAAAAAACGTTTAGGGTGAAAACCTGAA
1 AAAATAAAAAAAGAAAAAGAGAAAAGAACAAAAAAAAGAAAAAACATTTAGGGTGAAAACCCGAA
69640 AAGGCACCCTAAATTG
66 AAGGCACCCTAAATTG
* *
69656 AAAATAATAAAAGAGAAAAAGAGAAAAGAA-AAGAACAA-AAAAAACATTTAGGGTGAAAACCCG
1 AAAATAA-AAAA-AGAAAAAGAGAAAAGAACAAAAAAAAGAAAAAACATTTAGGGTGAAAACCCG
* *
69719 AAAGGGCACCCTTAATTG
64 AAAAGGCACCCTAAATTG
* *
69737 -AAA-AAAAAAAGAAAAAGAGCAAA-AATAAAAAAAA
1 AAAATAAAAAAAGAAAAAGAGAAAAGAACAAAAAAAA
69771 TAAGGTGGGT
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
76 2 0.02
77 19 0.19
78 4 0.04
79 2 0.02
80 10 0.10
81 43 0.43
82 12 0.12
83 9 0.09
ACGTcount: A:0.64, C:0.09, G:0.16, T:0.10
Consensus pattern (81 bp):
AAAATAAAAAAAGAAAAAGAGAAAAGAACAAAAAAAAGAAAAAACATTTAGGGTGAAAACCCGAA
AAGGCACCCTAAATTG
Found at i:72946 original size:2 final size:2
Alignment explanation
Indices: 72939--72970 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
72929 GTATTATTAA
72939 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72971 TAATTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73151 original size:20 final size:20
Alignment explanation
Indices: 73122--73160 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
73112 TACGATTAAC
* *
73122 ATTTTCTTTGTTTTTTACTG
1 ATTTTATTTGTTATTTACTG
73142 ATTTTATTTGTTATTTACT
1 ATTTTATTTGTTATTTACT
73161 TTGTATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (20 bp):
ATTTTATTTGTTATTTACTG
Found at i:73373 original size:12 final size:12
Alignment explanation
Indices: 73358--73400 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
73348 GTTATTTAAA
73358 CGGGTATCGGGC
1 CGGGTATCGGGC
* *
73370 CGGGTAACGAGC
1 CGGGTATCGGGC
*
73382 CGAGTATCGGGC
1 CGGGTATCGGGC
*
73394 TGGGTAT
1 CGGGTAT
73401 ATATATATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:73447 original size:36 final size:35
Alignment explanation
Indices: 73398--73476 Score: 124
Period size: 36 Copynumber: 2.3 Consensus size: 35
73388 TCGGGCTGGG
73398 TATATATA-TATTTAAATTAAATATATAAATATTA
1 TATATATATTATTTAAATTAAATATATAAATATTA
* *
73432 TATATATATTAATTTAAATTAAATTTATTAATATTA
1 TATATATATT-ATTTAAATTAAATATATAAATATTA
73468 TATATATAT
1 TATATATAT
73477 ATATAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 8 0.20
35 1 0.02
36 32 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TATATATATTATTTAAATTAAATATATAAATATTA
Found at i:79322 original size:90 final size:89
Alignment explanation
Indices: 79170--79342 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
79160 ACACACCCTT
79170 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATTTA
* *
79235 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
79259 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATATATTT
79324 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
79343 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:85323 original size:10 final size:10
Alignment explanation
Indices: 85292--85366 Score: 59
Period size: 9 Copynumber: 7.7 Consensus size: 10
85282 GTCGGGTCAG
85292 ACCGG-TCAA
1 ACCGGTTCAA
* *
85301 ACCTGTTCGA
1 ACCGGTTCAA
*
85311 ACCGGTTGAA
1 ACCGGTTCAA
85321 ACCGG-TCAA
1 ACCGGTTCAA
85330 ACCGG-TCAGA
1 ACCGGTTCA-A
*
85340 ACCGGTTGAAA
1 ACCGGTT-CAA
*
85351 ACTGGTT-AA
1 ACCGGTTCAA
85360 ACCGGTT
1 ACCGGTT
85367 TCCAGCAGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
9 23 0.43
10 21 0.40
11 8 0.15
12 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.20
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:85341 original size:29 final size:29
Alignment explanation
Indices: 85292--85365 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
85282 GTCGGGTCAG
*
85292 ACCGGTCAAACCTGTTCGAACCGGTTG-AA
1 ACCGGTCAAACC-GGTCGAACCGGTTGAAA
85321 ACCGGTCAAACCGGTCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTC-GAACCGGTTGAAA
* *
85351 ACTGGTTAAACCGGT
1 ACCGGTCAAACCGGT
85366 TTCCAGCAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.08
29 22 0.55
30 15 0.38
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (29 bp):
ACCGGTCAAACCGGTCGAACCGGTTGAAA
Found at i:92544 original size:7 final size:7
Alignment explanation
Indices: 92531--92561 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
92521 GTCAAAGAAA
92531 GTCAACG
1 GTCAACG
*
92538 ATCAACG
1 GTCAACG
92545 GTCAACG
1 GTCAACG
92552 GTCAACG
1 GTCAACG
92559 GTC
1 GTC
92562 GGGTCGGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:92579 original size:22 final size:22
Alignment explanation
Indices: 92551--92599 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
92541 AACGGTCAAC
92551 GGTCAACGGTCGGGTCGGATCG
1 GGTCAACGGTCGGGTCGGATCG
*
92573 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGATCG
92595 GGTCA
1 GGTCA
92600 GATCGGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGATCG
Found at i:92625 original size:19 final size:19
Alignment explanation
Indices: 92603--92731 Score: 122
Period size: 19 Copynumber: 6.7 Consensus size: 19
92593 CGGGTCAGAT
92603 CGGTTCAGACCGGTCAAAC
1 CGGTTCAGACCGGTCAAAC
92622 CGGTTC-GAACCGGTCAAAC
1 CGGTTCAG-ACCGGTCAAAC
* *
92641 CGG-TCAAACCGGTTCGAAC
1 CGGTTCAGACCGG-TCAAAC
* *
92660 CGGTTGAAACCGGTCAAAC
1 CGGTTCAGACCGGTCAAAC
*
92679 CGG-TCAGAACCGGTTCGAAC
1 CGGTTCAG-ACCGG-TCAAAC
* *
92699 CGGTTGAAACCGGTCAAAC
1 CGGTTCAGACCGGTCAAAC
92718 CGG-TCAGAACCGGT
1 CGGTTCAG-ACCGGT
92732 TGAAAAACGG
Statistics
Matches: 90, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
18 12 0.13
19 55 0.61
20 21 0.23
21 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.16
Consensus pattern (19 bp):
CGGTTCAGACCGGTCAAAC
Found at i:92632 original size:10 final size:9
Alignment explanation
Indices: 92611--92731 Score: 116
Period size: 10 Copynumber: 12.7 Consensus size: 9
92601 ATCGGTTCAG
*
92611 ACCGGTCAA
1 ACCGGTCGA
92620 ACCGGTTCGA
1 ACCGG-TCGA
*
92630 ACCGGTCAA
1 ACCGGTCGA
*
92639 ACCGGTCAA
1 ACCGGTCGA
92648 ACCGGTTCGA
1 ACCGG-TCGA
*
92658 ACCGGTTGAA
1 ACCGGTCG-A
*
92668 ACCGGTCAA
1 ACCGGTCGA
92677 ACCGGTCAGA
1 ACCGGTC-GA
92687 ACCGGTTCGA
1 ACCGG-TCGA
*
92697 ACCGGTTGAA
1 ACCGGTCG-A
*
92707 ACCGGTCAA
1 ACCGGTCGA
92716 ACCGGTCAGA
1 ACCGGTC-GA
92726 ACCGGT
1 ACCGGT
92732 TGAAAAACGG
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
9 42 0.45
10 50 0.53
11 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:92635 original size:29 final size:28
Alignment explanation
Indices: 92603--92731 Score: 138
Period size: 29 Copynumber: 4.5 Consensus size: 28
92593 CGGGTCAGAT
92603 CGGTTCAGACCGGTCAAACCGGTTCGAAC
1 CGGTTCAGACCGGTCAAACCGG-TCGAAC
*
92632 CGG-TCAAACCGGTCAAACCGGTTCGAAC
1 CGGTTCAGACCGGTCAAACCGG-TCGAAC
* *
92660 CGGTTGAAACCGGTCAAACCGGTCAGAAC
1 CGGTTCAGACCGGTCAAACCGGTC-GAAC
* *
92689 CGGTTC-GAACCGGTTGAAACCGGTCAAAC
1 CGGTTCAG-ACCGG-TCAAACCGGTCGAAC
92718 CGG-TCAGAACCGGT
1 CGGTTCAG-ACCGGT
92732 TGAAAAACGG
Statistics
Matches: 89, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
28 32 0.36
29 47 0.53
30 10 0.11
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.16
Consensus pattern (28 bp):
CGGTTCAGACCGGTCAAACCGGTCGAAC
Found at i:92751 original size:39 final size:39
Alignment explanation
Indices: 92607--92732 Score: 206
Period size: 39 Copynumber: 3.3 Consensus size: 39
92597 TCAGATCGGT
*
92607 TCAG-ACCGG-TCAAACCGGTTCG-AACCGGTCAAACCGG
1 TCAGAACCGGTTCGAACCGGTT-GAAACCGGTCAAACCGG
92644 TCA-AACCGGTTCGAACCGGTTGAAACCGGTCAAACCGG
1 TCAGAACCGGTTCGAACCGGTTGAAACCGGTCAAACCGG
92682 TCAGAACCGGTTCGAACCGGTTGAAACCGGTCAAACCGG
1 TCAGAACCGGTTCGAACCGGTTGAAACCGGTCAAACCGG
92721 TCAGAACCGGTT
1 TCAGAACCGGTT
92733 GAAAAACGGT
Statistics
Matches: 84, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
37 9 0.11
38 28 0.33
39 47 0.56
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.16
Consensus pattern (39 bp):
TCAGAACCGGTTCGAACCGGTTGAAACCGGTCAAACCGG
Found at i:94733 original size:43 final size:43
Alignment explanation
Indices: 94663--94761 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
94653 AAGGTAATTA
* * *
94663 GCGGTGTTTGTTT-TAAAATGCCCCTATAGAACTTGACTATTT
1 GCGGCGTTTGTTTCCAAAATGCCCCTATAGAACTTGACTACTT
* *
94705 GTGGCGTTTGTTTCCAAAATGCCGCTATAGAACTTGACTACTT
1 GCGGCGTTTGTTTCCAAAATGCCCCTATAGAACTTGACTACTT
*
94748 GCGGTGTTTGTTTC
1 GCGGCGTTTGTTTC
94762 TAAGACACCG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 11 0.22
43 38 0.78
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (43 bp):
GCGGCGTTTGTTTCCAAAATGCCCCTATAGAACTTGACTACTT
Found at i:94777 original size:43 final size:43
Alignment explanation
Indices: 94686--94785 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
94676 TAAAATGCCC
* * **
94686 CTATAGAACTTGACTATTTGTGGCGTTTGTTTCCAAAATGCCG
1 CTATAGAACTTGACTACTTGCGGCGTTTGTTTCCAAAACACCG
* * *
94729 CTATAGAACTTGACTACTTGCGGTGTTTGTTTCTAAGACACCG
1 CTATAGAACTTGACTACTTGCGGCGTTTGTTTCCAAAACACCG
* *
94772 TTATAGATCTTGAC
1 CTATAGAACTTGAC
94786 CTTTTGTAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (43 bp):
CTATAGAACTTGACTACTTGCGGCGTTTGTTTCCAAAACACCG
Found at i:96715 original size:64 final size:65
Alignment explanation
Indices: 96646--96801 Score: 242
Period size: 65 Copynumber: 2.4 Consensus size: 65
96636 ACACCCTATT
*
96646 TCGAATGCATTTTGTGTACCGATGCACA-ACCATGCATCGATGCACTCTTGAATATATTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATATTGAAACA
** *
96710 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTATTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATATTGAAACA
* * *
96775 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
96802 TAGGTCTTAT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 28 0.33
65 56 0.67
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATATTGAAACA
Found at i:107297 original size:194 final size:193
Alignment explanation
Indices: 106948--107297 Score: 515
Period size: 194 Copynumber: 1.8 Consensus size: 193
106938 TATTGGTGAC
*
106948 GTTATGCATAATCATCATTCATAATATTATTAGGTAACGATATATTATGTCACTAAAAATGTGAC
1 GTTATGCATAAACATCATTCATAATATTATTAGGTAACGATATATTATGTCACTAAAAATGTGAC
* * * * *
107013 AATATCTCCTTTGTCACATATAAGTTGATTTTAATGCATTATTTTTTACAATATAAATTATCAAT
66 AATATCTCCTTTGTCACATATAAGTTGATTTTAATGCATTATCTGTGACAATATAAATCATCAAA
* ** *
107078 AATGAAATCTTATTTAATTTAGTGACGTAACCAATTGTCATAAAATATAAATTATAAAGTGGT
131 AACGAAATCTTACATAATCTAGTGACGTAACCAATTGTCATAAAATATAAATTATAAAGTGGT
* *
107141 GTTATGCATAAACGTCATTCATAATATTATTAGGTAAC-ATTTATATTATGTCACTAAAAATTTG
1 GTTATGCATAAACATCATTCATAATATTATTAGGTAACGA--TATATTATGTCACTAAAAATGTG
* * *
107205 ACAATATCT-CTTTCGTCACATATAGGTTGATTTTAATGTATTATCTGTGACGATATAAATCATC
64 ACAATATCTCCTTT-GTCACATATAAGTTGATTTTAATGCATTATCTGTGACAATATAAATCATC
*
107269 AAAAACGAAATTTTACATAATCTAGTGAC
128 AAAAACGAAATCTTACATAATCTAGTGAC
107298 ATAATTAGTT
Statistics
Matches: 138, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
192 1 0.01
193 40 0.29
194 97 0.70
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (193 bp):
GTTATGCATAAACATCATTCATAATATTATTAGGTAACGATATATTATGTCACTAAAAATGTGAC
AATATCTCCTTTGTCACATATAAGTTGATTTTAATGCATTATCTGTGACAATATAAATCATCAAA
AACGAAATCTTACATAATCTAGTGACGTAACCAATTGTCATAAAATATAAATTATAAAGTGGT
Found at i:109015 original size:64 final size:65
Alignment explanation
Indices: 108946--109101 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 65
108936 ACACCCTATT
* *
108946 TCGAATGCATTTTGTGTACCGATGCATAG-CCATGCATCGATGCACTCTTGAATATATTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATATTGAAACA
* ** *
109010 TCGAATGCATTTTGTGTACCGATGCACAGACTATGCATCGATGCACTCCTGGCTATTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATATTGAAACA
* * * *
109075 TCGAATGTAATTAGTGTAACGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
109102 CTCAGGTGTA
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
64 28 0.35
65 53 0.65
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATATTGAAACA
Found at i:111241 original size:20 final size:20
Alignment explanation
Indices: 111218--111267 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
111208 CAGATACTGT
* *
111218 AAGAACAATACATGTATTAC
1 AAGAACAATAAAGGTATTAC
* **
111238 AAGAACAGTAAAGGTATTGT
1 AAGAACAATAAAGGTATTAC
111258 AAGAACAATA
1 AAGAACAATA
111268 TTGATATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (20 bp):
AAGAACAATAAAGGTATTAC
Found at i:111316 original size:52 final size:50
Alignment explanation
Indices: 111257--111412 Score: 170
Period size: 52 Copynumber: 3.2 Consensus size: 50
111247 AAAGGTATTG
111257 TAAGAACAATATTGATATTATTATTGATACGAAAAGAATAGTAACGATACTA
1 TAAGAACAATA-TGATATTATTATTGATAC-AAAAGAATAGTAACGATACTA
* * * *
111309 TAAGAAC---A--ATA-T-CTA-TGTTAC--AAGAATAGTATCAATACTA
1 TAAGAACAATATGATATTATTATTGATACAAAAGAATAGTAACGATACTA
111349 TAAGAACAATATCGATATTATTATTGATACTAAAAGAATAGTAACGATACTA
1 TAAGAACAATAT-GATATTATTATTGATAC-AAAAGAATAGTAACGATACTA
111401 TAAGAACAATAT
1 TAAGAACAATAT
111413 CGATGTTACA
Statistics
Matches: 84, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
40 24 0.29
43 6 0.07
44 2 0.02
45 1 0.01
46 6 0.07
47 1 0.01
48 2 0.02
49 6 0.07
52 36 0.43
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.30
Consensus pattern (50 bp):
TAAGAACAATATGATATTATTATTGATACAAAAGAATAGTAACGATACTA
Found at i:111331 original size:92 final size:90
Alignment explanation
Indices: 111210--111461 Score: 364
Period size: 92 Copynumber: 2.7 Consensus size: 90
111200 GTATAATACA
* * * * *
111210 GATACTGTAAGAACAATA-CATGTATTACAAGAACAGTA-AAGGTATTGTAAGAACAATATTGAT
1 GATACTATAAGAACAATATCATG--TTACAAGAATAGTACAA--TACTATAAGAACAATATCGAT
111273 ATTATTATTGATACGAAAAGAATAGTAAC
62 ATTATTATTGATACGAAAAGAATAGTAAC
111302 GATACTATAAGAACAATATCTATGTTACAAGAATAGTATCAATACTATAAGAACAATATCGATAT
1 GATACTATAAGAACAATATC-ATGTTACAAGAATAGTA-CAATACTATAAGAACAATATCGATAT
*
111367 TATTATTGATACTAAAAGAATAGTAAC
64 TATTATTGATACGAAAAGAATAGTAAC
111394 GATACTATAAGAACAATATCGATGTTACAAGAATAGTATCAATACTATAAGAACAATATCGATAT
1 GATACTATAAGAACAATATC-ATGTTACAAGAATAGTA-CAATACTATAAGAACAATATCGATAT
111459 TAT
64 TAT
111462 AACCCAGAAA
Statistics
Matches: 149, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
92 143 0.96
93 1 0.01
94 5 0.03
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.29
Consensus pattern (90 bp):
GATACTATAAGAACAATATCATGTTACAAGAATAGTACAATACTATAAGAACAATATCGATATTA
TTATTGATACGAAAAGAATAGTAAC
Found at i:111347 original size:40 final size:40
Alignment explanation
Indices: 111290--111453 Score: 166
Period size: 40 Copynumber: 3.8 Consensus size: 40
111280 TTGATACGAA
*
111290 AAGAATAGTAACGATACTATAAGAACAATATCTATGTTAC
1 AAGAATAGTAACAATACTATAAGAACAATATCTATGTTAC
* *
111330 AAGAATAGTATCAATACTATAAGAACAATATCGATATTATTATTGATACTAA
1 AAGAATAGTAACAATACTATAAGAACAATATC--------TA-TG-T--TAC
* *
111382 AAGAATAGTAACGATACTATAAGAACAATATCGATGTTAC
1 AAGAATAGTAACAATACTATAAGAACAATATCTATGTTAC
*
111422 AAGAATAGTATCAATACTATAAGAACAATATC
1 AAGAATAGTAACAATACTATAAGAACAATATC
111454 GATATTATAA
Statistics
Matches: 103, Mismatches: 9, Indels: 24
0.76 0.07 0.18
Matches are distributed among these distances:
40 62 0.60
42 1 0.01
43 2 0.02
44 1 0.01
48 2 0.02
49 2 0.02
50 1 0.01
52 32 0.31
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (40 bp):
AAGAATAGTAACAATACTATAAGAACAATATCTATGTTAC
Found at i:111353 original size:20 final size:20
Alignment explanation
Indices: 111290--111354 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
111280 TTGATACGAA
* *
111290 AAGAATAGTAACGATACTAT
1 AAGAATAGTATCAATACTAT
* * * ** *
111310 AAGAACAATATCTATGTTAC
1 AAGAATAGTATCAATACTAT
111330 AAGAATAGTATCAATACTAT
1 AAGAATAGTATCAATACTAT
111350 AAGAA
1 AAGAA
111355 CAATATCGAT
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (20 bp):
AAGAATAGTATCAATACTAT
Found at i:111361 original size:20 final size:20
Alignment explanation
Indices: 111303--111361 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
111293 AATAGTAACG
*
111303 ATACTATAAGAACAATATCT
1 ATACTATAAGAACAATATCA
** * * *
111323 ATGTTACAAGAATAGTATCA
1 ATACTATAAGAACAATATCA
111343 ATACTATAAGAACAATATC
1 ATACTATAAGAACAATATC
111362 GATATTATTA
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (20 bp):
ATACTATAAGAACAATATCA
Found at i:111416 original size:20 final size:20
Alignment explanation
Indices: 111374--111463 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
111364 TATTATTATT
* * * *
111374 GATACTAAAAGAATAGTAAC
1 GATACTATAAGAACAATATC
111394 GATACTATAAGAACAATATC
1 GATACTATAAGAACAATATC
** * * *
111414 GATGTTACAAGAATAGTATC
1 GATACTATAAGAACAATATC
*
111434 AATACTATAAGAACAATATC
1 GATACTATAAGAACAATATC
*
111454 GATATTATAA
1 GATACTATAA
111464 CCCAGAAAAC
Statistics
Matches: 53, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (20 bp):
GATACTATAAGAACAATATC
Found at i:122607 original size:44 final size:44
Alignment explanation
Indices: 122544--122646 Score: 152
Period size: 44 Copynumber: 2.3 Consensus size: 44
122534 TATACTATTT
122544 TATTAAATGATATTCAGATGATTTGAGTATAAATTACTCAATAC
1 TATTAAATGATATTCAGATGATTTGAGTATAAATTACTCAATAC
* * *
122588 TATTAAATGGTATTTAGATGATTTGTGTATAAATTACTCAATAC
1 TATTAAATGATATTCAGATGATTTGAGTATAAATTACTCAATAC
* *
122632 ATTTTATATGATATT
1 -TATTAAATGATATT
122647 TTATAAAATG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 41 0.79
45 11 0.21
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.44
Consensus pattern (44 bp):
TATTAAATGATATTCAGATGATTTGAGTATAAATTACTCAATAC
Found at i:128800 original size:4 final size:4
Alignment explanation
Indices: 128783--128815 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
128773 ATATCTAAAC
128783 ATTT ATTAT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT
128816 TGTGTGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:133678 original size:22 final size:22
Alignment explanation
Indices: 133664--133708 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
133654 GCATCAGCAT
133664 TGATACGAAAGTGCATTCGCAC
1 TGATACGAAAGTGCATTCGCAC
* * *
133686 TGATACTAAAGTGCTTTAGCAC
1 TGATACGAAAGTGCATTCGCAC
133708 T
1 T
133709 ACTGTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (22 bp):
TGATACGAAAGTGCATTCGCAC
Done.