Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005784.1 Hibiscus syriacus cultivar Beakdansim tig00013552_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: 148243
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2240 original size:22 final size:25
Alignment explanation
Indices: 2189--2241 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 25
2179 TTTCTTTTCT
2189 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
2214 TTTCTT-CTTTTT-AGTGCTTT-AA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
2236 TTTCTT
1 TTTCTT
2242 TGTTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.29
23 8 0.29
24 6 0.21
25 6 0.21
ACGTcount: A:0.11, C:0.17, G:0.09, T:0.62
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:5329 original size:22 final size:25
Alignment explanation
Indices: 5281--5333 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 25
5271 TTTCTTTTAT
5281 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
5306 TTTCTT-CTTTTT-AGTGC-TTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
5328 TTTCTT
1 TTTCTT
5334 TACTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.39
23 5 0.18
24 6 0.21
25 6 0.21
ACGTcount: A:0.11, C:0.19, G:0.09, T:0.60
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:8405 original size:23 final size:22
Alignment explanation
Indices: 8379--8422 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8369 ATTTTATTTT
*
8379 TTTTTAGTGTTTTCAATTTCTTC
1 TTTTTAGTG-CTTCAATTTCTTC
*
8402 TTTTTGGTGCTTCAATTTCTT
1 TTTTTAGTGCTTCAATTTCTT
8423 TACTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.64
Consensus pattern (22 bp):
TTTTTAGTGCTTCAATTTCTTC
Found at i:10229 original size:24 final size:23
Alignment explanation
Indices: 10202--10279 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 23
10192 AACGTCAATG
10202 GACATAACTATTGGATCTTCAAAA
1 GACATAACTATTGGATC-TCAAAA
** *
10226 GACATGTCT-TGTGGATCACAAAA
1 GACATAACTAT-TGGATCTCAAAA
* * *
10249 GGTCATGACTATTGGTTCCTCAAAA
1 -GACATAACTATTGGAT-CTCAAAA
10274 GACATA
1 GACATA
10280 TTTCTTGAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
23 6 0.15
24 28 0.68
25 7 0.17
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (23 bp):
GACATAACTATTGGATCTCAAAA
Found at i:11501 original size:22 final size:25
Alignment explanation
Indices: 11453--11505 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 25
11443 TTTCTTTTAT
11453 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
11478 TTTCTT-CTTTTT-AGTGC-TTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
11500 TTTCTT
1 TTTCTT
11506 TACTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.39
23 5 0.18
24 6 0.21
25 6 0.21
ACGTcount: A:0.11, C:0.19, G:0.09, T:0.60
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:14558 original size:23 final size:22
Alignment explanation
Indices: 14532--14575 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
14522 TATTTTTTTT
*
14532 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAATGC-TTCAATTTCTTC
*
14555 TTTTTAATGCTTCAATTTCTT
1 TTTTGAATGCTTCAATTTCTT
14576 TGTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.59
Consensus pattern (22 bp):
TTTTGAATGCTTCAATTTCTTC
Found at i:17641 original size:22 final size:25
Alignment explanation
Indices: 17593--17645 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
17583 TTTCTTTTAT
*
17593 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAATGCTTTCAA
17618 TTTCTT-CTTTTT-AATGC-TTCAA
1 TTTCTTCCTTTTTGAATGCTTTCAA
17640 TTTCTT
1 TTTCTT
17646 TGCTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.41
23 4 0.15
24 6 0.22
25 6 0.22
ACGTcount: A:0.13, C:0.19, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAATGCTTTCAA
Found at i:20758 original size:22 final size:25
Alignment explanation
Indices: 20710--20762 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
20700 TTTCTTTTAT
*
20710 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAATGCTTTCAA
20735 TTTCTT-CTTTTT-AATGC-TTCAA
1 TTTCTTCCTTTTTGAATGCTTTCAA
20757 TTTCTT
1 TTTCTT
20763 TGCTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.41
23 4 0.15
24 6 0.22
25 6 0.22
ACGTcount: A:0.13, C:0.19, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAATGCTTTCAA
Found at i:23878 original size:22 final size:25
Alignment explanation
Indices: 23830--23882 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
23820 TTTCTTTTAT
*
23830 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAATGCTTTCAA
23855 TTTCTT-CTTTTT-AATGC-TTCAA
1 TTTCTTCCTTTTTGAATGCTTTCAA
23877 TTTCTT
1 TTTCTT
23883 TGCTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.41
23 4 0.15
24 6 0.22
25 6 0.22
ACGTcount: A:0.13, C:0.19, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAATGCTTTCAA
Found at i:26992 original size:22 final size:25
Alignment explanation
Indices: 26944--26996 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
26934 TTTCTTTTAT
*
26944 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAATGCTTTCAA
26969 TTTCTT-CTTTTT-AATGC-TTCAA
1 TTTCTTCCTTTTTGAATGCTTTCAA
26991 TTTCTT
1 TTTCTT
26997 TGCTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.41
23 4 0.15
24 6 0.22
25 6 0.22
ACGTcount: A:0.13, C:0.19, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAATGCTTTCAA
Found at i:29966 original size:22 final size:25
Alignment explanation
Indices: 29914--29966 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 25
29904 TATCTTTTCT
29914 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
29939 TTTCTT-CTTTTT-AGTTC-TTCGA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
29961 TTTCTT
1 TTTCTT
29967 TTCTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 4 0.15
24 6 0.23
25 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.09, T:0.62
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:36464 original size:21 final size:21
Alignment explanation
Indices: 36438--36484 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
36428 ATTTTGGGGA
36438 TGAATCTAGACAATTTTAAAC
1 TGAATCTAGACAATTTTAAAC
36459 TGAATCTAGACAATTTTAAAC
1 TGAATCTAGACAATTTTAAAC
36480 TGAAT
1 TGAAT
36485 TTGACCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (21 bp):
TGAATCTAGACAATTTTAAAC
Found at i:37235 original size:17 final size:17
Alignment explanation
Indices: 37213--37263 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
37203 AATTAATAGT
*
37213 TAGTTTAATAAATGAAC
1 TAGTTTAATTAATGAAC
* *
37230 TAGTTTGATTAATGAAA
1 TAGTTTAATTAATGAAC
37247 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
37264 AAACTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:37382 original size:17 final size:17
Alignment explanation
Indices: 37360--37420 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
37350 ACTTGATGCT
37360 TTAAATGCAATGCATGA
1 TTAAATGCAATGCATGA
* *
37377 TTAAATG-AATAACACACTTA
1 TTAAATGCAAT---GCA-TGA
*
37397 TTAAATGCAATGCATGC
1 TTAAATGCAATGCATGA
37414 TTAAATG
1 TTAAATG
37421 AATAACACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
16 3 0.09
17 15 0.44
18 2 0.06
19 2 0.06
20 9 0.26
21 3 0.09
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (17 bp):
TTAAATGCAATGCATGA
Found at i:37401 original size:20 final size:20
Alignment explanation
Indices: 37376--37474 Score: 77
Period size: 20 Copynumber: 5.2 Consensus size: 20
37366 GCAATGCATG
37376 ATTAAATGAATAACACACTT
1 ATTAAATGAATAACACACTT
* *
37396 ATTAAATGCAAT---GCA-TG
1 ATTAAATG-AATAACACACTT
*
37413 CTTAAATGAATAACACACTT
1 ATTAAATGAATAACACACTT
** *
37433 ATTAAATG-A-AATGCA-TG
1 ATTAAATGAATAACACACTT
*
37450 CTTAAATGAATAACACACTT
1 ATTAAATGAATAACACACTT
37470 ATTAA
1 ATTAA
37475 TTGCAATGAA
Statistics
Matches: 57, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
16 3 0.05
17 16 0.28
18 7 0.12
19 7 0.12
20 21 0.37
21 3 0.05
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.30
Consensus pattern (20 bp):
ATTAAATGAATAACACACTT
Found at i:37404 original size:37 final size:37
Alignment explanation
Indices: 37360--37482 Score: 219
Period size: 37 Copynumber: 3.3 Consensus size: 37
37350 ACTTGATGCT
*
37360 TTAAATGCAATGCATGATTAAATGAATAACACACTTA
1 TTAAATGCAATGCATGCTTAAATGAATAACACACTTA
37397 TTAAATGCAATGCATGCTTAAATGAATAACACACTTA
1 TTAAATGCAATGCATGCTTAAATGAATAACACACTTA
*
37434 TTAAATGAAATGCATGCTTAAATGAATAACACACTTA
1 TTAAATGCAATGCATGCTTAAATGAATAACACACTTA
*
37471 TTAATTGCAATG
1 TTAAATGCAATG
37483 AATGTCATTC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 82 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (37 bp):
TTAAATGCAATGCATGCTTAAATGAATAACACACTTA
Found at i:51883 original size:24 final size:24
Alignment explanation
Indices: 51842--51892 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
51832 ACTAACAAAT
*
51842 AAATTGAAGCACTCAAAA-GAAGA
1 AAATTGAAGAACTCAAAAGGAAGA
51865 AAATTGCAAGAACTCAAAAGGAAGA
1 AAATTG-AAGAACTCAAAAGGAAGA
51890 AAA
1 AAA
51893 AGAAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.24
24 11 0.44
25 8 0.32
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.12
Consensus pattern (24 bp):
AAATTGAAGAACTCAAAAGGAAGA
Found at i:78845 original size:23 final size:24
Alignment explanation
Indices: 78796--78848 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
78786 TTTCTTTTAT
* *
78796 TTTCTTCTTTTTGAGTGCCTGACA
1 TTTCTTCTTTTGGAGTGCCTCACA
*
78820 TTTCTTCTTTTGGAGTGCTTCA-A
1 TTTCTTCTTTTGGAGTGCCTCACA
78843 TTTCTT
1 TTTCTT
78849 TGCTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (24 bp):
TTTCTTCTTTTGGAGTGCCTCACA
Found at i:87188 original size:18 final size:18
Alignment explanation
Indices: 87116--87192 Score: 56
Period size: 18 Copynumber: 4.5 Consensus size: 18
87106 TTGGAGTGCA
* *
87116 AAAAAGAAAGAAAAAGAC
1 AAAAAGAAAAAAAAAGTC
*
87134 AAAAAGAAGAAAATAA-TC
1 AAAAAGAA-AAAAAAAGTC
* * *
87152 AGAAA-ATAAGAAAAG--
1 AAAAAGAAAAAAAAAGTC
87167 -AAAAGAAAAAAAAAGTC
1 AAAAAGAAAAAAAAAGTC
87184 AAAAAGAAA
1 AAAAAGAAA
87193 GCAAGCCAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
14 3 0.07
15 8 0.19
16 5 0.12
17 1 0.02
18 21 0.49
19 5 0.12
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAGTC
Found at i:91183 original size:32 final size:32
Alignment explanation
Indices: 91142--91205 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
91132 TATACTTAGT
91142 TTATTTCTTATGTTATGCATGTAGGCACATTC
1 TTATTTCTTATGTTATGCATGTAGGCACATTC
91174 TTATTTCTTATGTTATGCATGTAGGCACATTC
1 TTATTTCTTATGTTATGCATGTAGGCACATTC
91206 GGCCAATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (32 bp):
TTATTTCTTATGTTATGCATGTAGGCACATTC
Found at i:92466 original size:61 final size:61
Alignment explanation
Indices: 92391--92520 Score: 233
Period size: 61 Copynumber: 2.1 Consensus size: 61
92381 TATTTATTTC
*
92391 ATTTATTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATAATTAATTCAT
1 ATTTCTTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATAATTAATTCAT
*
92452 ATTTCTTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATCATTAATTCAT
1 ATTTCTTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATAATTAATTCAT
*
92513 TTTTCTTT
1 ATTTCTTT
92521 CTTATTTTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (61 bp):
ATTTCTTTTCATTTTCAGTGTTTATATTATTATTCATTTCTTAAACCTATAATTAATTCAT
Found at i:92964 original size:20 final size:21
Alignment explanation
Indices: 92939--92983 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
92929 ATTCATTAAG
92939 TCATGTCATG-TTAT-TCTAGC
1 TCATGTCATGTTTATAT-TAGC
*
92959 TCATGTTATGTTTATATTAGC
1 TCATGTCATGTTTATATTAGC
92980 TCAT
1 TCAT
92984 TAGCTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 12 0.55
22 1 0.05
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (21 bp):
TCATGTCATGTTTATATTAGC
Found at i:98979 original size:38 final size:38
Alignment explanation
Indices: 98937--99014 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
98927 TAAGGCTATC
* *
98937 TACTCTTTTCACTAGAGCGTGTAGATCACCTTACATCA
1 TACTCTTTTCACCAAAGCGTGTAGATCACCTTACATCA
98975 TACTCTTTTCACCAAAGCGTGTAGATCACCTTACATCA
1 TACTCTTTTCACCAAAGCGTGTAGATCACCTTACATCA
99013 TA
1 TA
99015 TAAAGTCTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (38 bp):
TACTCTTTTCACCAAAGCGTGTAGATCACCTTACATCA
Found at i:105424 original size:17 final size:16
Alignment explanation
Indices: 105404--105437 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
105394 AAAAGAAAAG
*
105404 AAGAAAATTCAAAGCAA
1 AAGAAAAGTC-AAGCAA
105421 AAGAAAAGTCAAGCAA
1 AAGAAAAGTCAAGCAA
105437 A
1 A
105438 GTTTCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.12, G:0.15, T:0.09
Consensus pattern (16 bp):
AAGAAAAGTCAAGCAA
Found at i:107622 original size:23 final size:24
Alignment explanation
Indices: 107596--107642 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
107586 AAAGTCAGCA
107596 AAGAAAATAG-AAGCACTCAAAAG
1 AAGAAAATAGCAAGCACTCAAAAG
* *
107619 AAGAAAATTGCAAGCACTCCAAAG
1 AAGAAAATAGCAAGCACTCAAAAG
107643 GAATAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.11
Consensus pattern (24 bp):
AAGAAAATAGCAAGCACTCAAAAG
Found at i:126103 original size:21 final size:21
Alignment explanation
Indices: 126064--126103 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
126054 TTTGAAAATT
126064 AAAGAAATGAAATGGAAATGG
1 AAAGAAATGAAATGGAAATGG
*
126085 AAAGAATTGAAATGGAAAT
1 AAAGAAATGAAATGGAAAT
126104 AAATGTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (21 bp):
AAAGAAATGAAATGGAAATGG
Found at i:126235 original size:11 final size:11
Alignment explanation
Indices: 126200--126228 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
126190 GAATATCTTG
126200 ATGATGATTGA
1 ATGATGATTGA
126211 ATGATGATTGA
1 ATGATGATTGA
126222 ATGATGA
1 ATGATGA
126229 ATAAATGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (11 bp):
ATGATGATTGA
Found at i:126353 original size:36 final size:35
Alignment explanation
Indices: 126253--126364 Score: 127
Period size: 35 Copynumber: 3.2 Consensus size: 35
126243 ATTGGGGGTT
* * * * *
126253 TTATAGGCGTGAAATCGTGGTAGAAGATGGTTAGG
1 TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
* * *
126288 ATATAGGCGTGCAATAGTAATGGAAGATGGTGATG
1 TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
*
126323 TTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 TTATAGGCGTG-AAATAGTGATGGAAGATGGTGATG
126359 TT-TAGG
1 TTATAGG
126365 TAATATCTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.29
Consensus pattern (35 bp):
TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
Found at i:131343 original size:15 final size:16
Alignment explanation
Indices: 131316--131345 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
131306 GTAAGAAAAG
131316 ATGAAAGAATAAAGAA
1 ATGAAAGAATAAAGAA
131332 ATGAAA-AATAAAGA
1 ATGAAAGAATAAAGA
131346 TAACTTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (16 bp):
ATGAAAGAATAAAGAA
Found at i:132031 original size:36 final size:35
Alignment explanation
Indices: 131932--132042 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
131922 TTGGGGGTAA
* * * *
131932 TATAGGCGTGAAATAGTGATAGAAGATGGTTAGGA
1 TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
* * *
131967 TATAGGTGTGCAATAGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
*
132002 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATAGTGATGGAAGATGGTGATGT
132038 T-TAGG
1 TATAGG
132043 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
Found at i:133756 original size:2 final size:2
Alignment explanation
Indices: 133749--133781 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
133739 AGTTATATTC
133749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
133782 GTTATTATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134536 original size:48 final size:46
Alignment explanation
Indices: 134480--134592 Score: 136
Period size: 46 Copynumber: 2.4 Consensus size: 46
134470 TGAGAGCATT
** *
134480 TGGTGCCAACATGAGGAAGCACATCACCATTCGACCAAGTGGAGAAAA
1 TGGTGCCAACATGAACAAG--CATCACCATTCGACCAAGGGGAGAAAA
* *
134528 TGGTGCCAAGATGAACAAGCATCACCATTCGGCCAAGGGGAGAAAA
1 TGGTGCCAACATGAACAAGCATCACCATTCGACCAAGGGGAGAAAA
* * *
134574 TGGCGCCAATATTAACAAG
1 TGGTGCCAACATGAACAAG
134593 AATTGCCATT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 41 0.72
48 16 0.28
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (46 bp):
TGGTGCCAACATGAACAAGCATCACCATTCGACCAAGGGGAGAAAA
Found at i:134564 original size:46 final size:46
Alignment explanation
Indices: 134501--134608 Score: 144
Period size: 46 Copynumber: 2.3 Consensus size: 46
134491 TGAGGAAGCA
* * *
134501 CATCACCATTCGACCAAGTGGAGAAAATGGTGCCAAGATGAACAAG
1 CATCACCATTCGGCCAAGGGGAGAAAATGGCGCCAAGATGAACAAG
* *
134547 CATCACCATTCGGCCAAGGGGAGAAAATGGCGCCAATATTAACAAG
1 CATCACCATTCGGCCAAGGGGAGAAAATGGCGCCAAGATGAACAAG
* **
134593 AATTGCCATTCGGCCA
1 CATCACCATTCGGCCA
134609 TGGGAGATGC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (46 bp):
CATCACCATTCGGCCAAGGGGAGAAAATGGCGCCAAGATGAACAAG
Found at i:148210 original size:23 final size:23
Alignment explanation
Indices: 148181--148228 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
148171 CACTTGGATT
148181 TGATGAATGAGTTTGAAAAATAA
1 TGATGAATGAGTTTGAAAAATAA
148204 TGATGAATGAGTTTGAAAAATAA
1 TGATGAATGAGTTTGAAAAATAA
148227 TG
1 TG
148229 CATCCATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (23 bp):
TGATGAATGAGTTTGAAAAATAA
Done.