Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001001.1 Hibiscus syriacus cultivar Beakdansim tig00002001_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: 63384
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2926 original size:30 final size:30
Alignment explanation
Indices: 2892--2953 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
2882 AGTCAAGCAC
*
2892 AAGAGTGATTATCGATTAAGATTCTGAACA
1 AAGAGTGATTATCGATTAAGATTCCGAACA
*
2922 AAGAGTGATTATTGATTAAGATTCCGAACA
1 AAGAGTGATTATCGATTAAGATTCCGAACA
2952 AA
1 AA
2954 CTCTTGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (30 bp):
AAGAGTGATTATCGATTAAGATTCCGAACA
Found at i:10476 original size:2 final size:2
Alignment explanation
Indices: 10471--10498 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10461 AGGTTTTAAT
10471 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
10499 AATAGATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11666 original size:16 final size:17
Alignment explanation
Indices: 11647--11679 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11637 AAACATCATT
11647 AATTT-AATTTATAAAA
1 AATTTAAATTTATAAAA
*
11663 AATTTAAATTTCTAAAA
1 AATTTAAATTTATAAAA
11680 GACTCCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTATAAAA
Found at i:12148 original size:22 final size:23
Alignment explanation
Indices: 12118--12172 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
12108 TTCAATTTTT
*
12118 TATTATTATATTAACT-TAAAATA
1 TATT-TTATATTAACTAAAAAATA
*
12141 TATTTTATTTTAACTACAAAAATA
1 TATTTTATATTAACTA-AAAAATA
12165 TATTTTAT
1 TATTTTAT
12173 TTTTATCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 10 0.36
23 4 0.14
24 14 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTATATTAACTAAAAAATA
Found at i:12433 original size:29 final size:29
Alignment explanation
Indices: 12400--12532 Score: 119
Period size: 29 Copynumber: 4.5 Consensus size: 29
12390 AATATAAATA
*
12400 TTTAAGTTAAGATAAGAATAAATTATAGT
1 TTTAAGTTAAGATAAGAATAAAATATAGT
* **
12429 TTTAATTTAAGATAAGGTTAAAATATATGT
1 TTTAAGTTAAGATAAGAATAAAATATA-GT
* *
12459 TTT-AGATTAAAATAAGAATAAAATATATT
1 TTTAAG-TTAAGATAAGAATAAAATATAGT
* * *
12488 TTTAGGTTACA-AAAAGAATAAAACATA-T
1 TTTAAGTTA-AGATAAGAATAAAATATAGT
12516 TTAATAAGTTAAGATAA
1 TT--TAAGTTAAGATAA
12533 AAAATATTTT
Statistics
Matches: 83, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.04
29 46 0.55
30 34 0.41
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (29 bp):
TTTAAGTTAAGATAAGAATAAAATATAGT
Found at i:12532 original size:24 final size:25
Alignment explanation
Indices: 12505--12555 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
12495 TACAAAAAGA
*
12505 ATAAAACATATTTAATAA-GTTAAG
1 ATAAAAAATATTTAATAATGTTAAG
**
12529 ATAAAAAATATTTTTTAATGTTAAG
1 ATAAAAAATATTTAATAATGTTAAG
12554 AT
1 AT
12556 GTAAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (25 bp):
ATAAAAAATATTTAATAATGTTAAG
Found at i:16239 original size:13 final size:13
Alignment explanation
Indices: 16221--16246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16211 ATTGTTCCTC
16221 TTGAAGACTACAT
1 TTGAAGACTACAT
16234 TTGAAGACTACAT
1 TTGAAGACTACAT
16247 CATCCACATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TTGAAGACTACAT
Found at i:26161 original size:7 final size:7
Alignment explanation
Indices: 26149--26173 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26139 TAAAAATTTT
26149 ATTTAAA
1 ATTTAAA
26156 ATTTAAA
1 ATTTAAA
26163 ATTTAAA
1 ATTTAAA
26170 ATTT
1 ATTT
26174 TATTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTAAA
Found at i:28991 original size:23 final size:22
Alignment explanation
Indices: 28965--29028 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
28955 CAGCTCATAT
28965 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
28988 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
29011 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
29029 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:29169 original size:103 final size:103
Alignment explanation
Indices: 29044--29364 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
29034 TAATGTCCAT
29044 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
29109 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * **
29147 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGGTCAAGTATGTGTCTCACTT
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
29212 GACCTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
29250 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
29315 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
29353 AAGGACCACATA
1 AAGGACCACATA
29365 GACCCTCTAC
Statistics
Matches: 204, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 204 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:29935 original size:21 final size:21
Alignment explanation
Indices: 29911--29953 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29901 TCATATTCGT
*
29911 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
29932 TTGAAGTGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
29953 T
1 T
29954 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:33081 original size:23 final size:22
Alignment explanation
Indices: 33055--33118 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
33045 CAGCTCATAT
33055 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
33078 AATTACACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
33101 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
33119 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:33262 original size:103 final size:103
Alignment explanation
Indices: 33134--33450 Score: 589
Period size: 103 Copynumber: 3.1 Consensus size: 103
33124 TAATGTCCAT
*
33134 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
33199 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
33237 AATGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* * *
33302 GACCTCATACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
33340 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
33405 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
33443 AAGGACCA
1 AAGGACCA
33451 TATAGACCCT
Statistics
Matches: 205, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 205 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:36289 original size:34 final size:34
Alignment explanation
Indices: 36250--36320 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
36240 TCGGTAATCC
* * *
36250 GTTTGTTTATGTTCGTCTATTGATGTCCTTTTAT
1 GTTTGTTTATGTTCGTCCATTGATGTCCGTGTAT
36284 GTTTGTTTATGTTCGTCCATTGATGTCCGTGTAT
1 GTTTGTTTATGTTCGTCCATTGATGTCCGTGTAT
36318 GTT
1 GTT
36321 CTTTATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (34 bp):
GTTTGTTTATGTTCGTCCATTGATGTCCGTGTAT
Found at i:36347 original size:37 final size:37
Alignment explanation
Indices: 36255--36361 Score: 103
Period size: 37 Copynumber: 3.0 Consensus size: 37
36245 AATCCGTTTG
* * * *
36255 TTTATGTTCGTCTATTGATGTCCTTTTATG---TTTG
1 TTTATGTTCGTCCATTGATGTCCGTATATGTTCTTTA
*
36289 TTTATGTTCGTCCATTGATGTCCGTGTATGTTCTTTA
1 TTTATGTTCGTCCATTGATGTCCGTATATGTTCTTTA
* * * * *
36326 TTTATGTTTGTTCATTTATGTCTGTATTTGTTCTTT
1 TTTATGTTCGTCCATTGATGTCCGTATATGTTCTTT
36362 TATATTCAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 27 0.45
37 33 0.55
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (37 bp):
TTTATGTTCGTCCATTGATGTCCGTATATGTTCTTTA
Found at i:36569 original size:23 final size:23
Alignment explanation
Indices: 36543--36599 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
36533 TTTTATGTGG
*
36543 TTATTGT-TGTTGTTTACGTTCAT
1 TTATTGTGT-TTGATTACGTTCAT
*
36566 TTATTGTGTTTGATTATGTTCAT
1 TTATTGTGTTTGATTACGTTCAT
* *
36589 TTGTTATGTTT
1 TTATTGTGTTT
36600 ATGCAGGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.14, C:0.05, G:0.18, T:0.63
Consensus pattern (23 bp):
TTATTGTGTTTGATTACGTTCAT
Found at i:36733 original size:57 final size:57
Alignment explanation
Indices: 36606--36733 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 57
36596 GTTTATGCAG
** * * *
36606 GTTCGTTTATGTTATTTTATGTTCATTTATTGTGTTCATTTATGTTCGTTTACATTC
1 GTTCGTTTATGTTCGTTTACGTTCATTTATTGTGTTCATTTATGTTCATTTACATCC
* * ** *
36663 ATTTGTTTATGTTCGTTTACGTTTGTTTATTGTGTT-AGTTTATGTTCATTTATATCC
1 GTTCGTTTATGTTCGTTTACGTTCATTTATTGTGTTCA-TTTATGTTCATTTACATCC
36720 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
36734 ATTCATTTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
56 1 0.02
57 57 0.98
ACGTcount: A:0.15, C:0.10, G:0.16, T:0.59
Consensus pattern (57 bp):
GTTCGTTTATGTTCGTTTACGTTCATTTATTGTGTTCATTTATGTTCATTTACATCC
Found at i:36747 original size:24 final size:24
Alignment explanation
Indices: 36643--36753 Score: 98
Period size: 24 Copynumber: 4.7 Consensus size: 24
36633 TATTGTGTTC
**
36643 ATTTATGTTCGTTTACATTCATTT
1 ATTTATGTTCGTTTATGTTCATTT
* * **
36667 GTTTATGTTCGTTTACGTTTGTTT
1 ATTTATGTTCGTTTATGTTCATTT
* *
36691 A-TTGTGTTAGTTTATGTTCATTT
1 ATTTATGTTCGTTTATGTTCATTT
* ** *
36714 ATATCCGTTCGTTTATGTTCATTC
1 ATTTATGTTCGTTTATGTTCATTT
*
36738 ATTTATGTTCTTTTAT
1 ATTTATGTTCGTTTAT
36754 CATTTAAATG
Statistics
Matches: 67, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
23 18 0.27
24 49 0.73
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (24 bp):
ATTTATGTTCGTTTATGTTCATTT
Found at i:38385 original size:17 final size:18
Alignment explanation
Indices: 38359--38392 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38349 ATATGAAACC
38359 TTTCAAAACT-CCAAAAT
1 TTTCAAAACTCCCAAAAT
*
38376 TTTCATAACTCCCAAAA
1 TTTCAAAACTCCCAAAA
38393 CTTGATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (18 bp):
TTTCAAAACTCCCAAAAT
Found at i:40436 original size:17 final size:17
Alignment explanation
Indices: 40394--40438 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
40384 ATAATGTTAA
40394 AATTTGTTTAAATTATT
1 AATTTGTTTAAATTATT
** *
40411 AATAAGTTTTAATTATT
1 AATTTGTTTAAATTATT
40428 AATTTGTTTAA
1 AATTTGTTTAA
40439 GTTGTCATTC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (17 bp):
AATTTGTTTAAATTATT
Found at i:43372 original size:26 final size:26
Alignment explanation
Indices: 43336--43395 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
43326 TACTGTCCAG
43336 GGAGCTGTGCGGCAAATATAGATTCT
1 GGAGCTGTGCGGCAAATATAGATTCT
43362 GGAGCTGTGCGGCAAATATAGATTCT
1 GGAGCTGTGCGGCAAATATAGATTCT
43388 GGAGCTGT
1 GGAGCTGT
43396 TTGGATTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (26 bp):
GGAGCTGTGCGGCAAATATAGATTCT
Found at i:51392 original size:20 final size:20
Alignment explanation
Indices: 51358--51398 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
51348 ATACTTCTTT
*
51358 ATTTATATTTTTTAATTAAA
1 ATTTATATTTTTTAAATAAA
51378 ATTTA-ATTTTATTAAATAAA
1 ATTTATATTTT-TTAAATAAA
51398 A
1 A
51399 ATGATTACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTATATTTTTTAAATAAA
Found at i:55229 original size:39 final size:38
Alignment explanation
Indices: 55147--55369 Score: 295
Period size: 39 Copynumber: 6.1 Consensus size: 38
55137 AGGATTAAGT
55147 TGACAAATTCAGCACAAGAGTTGGTACTTTGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGGTACTTTGACTGTTA
* *
55185 CGACAAATTCAGCACAAGAATTGGTACTTTTGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGGTAC-TTTGACTGTTA
* *
55224 TGACAAACTCAGCAGAAGAGTTGG-----TGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGGTACTTTGACTGTTA
55257 TGACAAATTCAGCACAAGAGTTGG-----TGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGGTACTTTGACTGTTA
55290 TGACAAATTCAGCACAAGAGTTGGTACTTTTGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGGTAC-TTTGACTGTTA
* * *
55329 AGACAAATTCAGCACAAGAGTTGGTACTTCGACTATTA
1 TGACAAATTCAGCACAAGAGTTGGTACTTTGACTGTTA
55367 TGA
1 TGA
55370 TCTTCATGGT
Statistics
Matches: 166, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
33 64 0.39
38 36 0.22
39 66 0.40
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (38 bp):
TGACAAATTCAGCACAAGAGTTGGTACTTTGACTGTTA
Found at i:55257 original size:33 final size:33
Alignment explanation
Indices: 55147--55353 Score: 216
Period size: 33 Copynumber: 5.8 Consensus size: 33
55137 AGGATTAAGT
55147 TGACAAATTCAGCACAAGAGTTGGTACTTTGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGG-----TGACTGTTA
* *
55185 CGACAAATTCAGCACAAGAATTGGTACTTTTGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGG------TGACTGTTA
* *
55224 TGACAAACTCAGCAGAAGAGTTGGTGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGGTGACTGTTA
55257 TGACAAATTCAGCACAAGAGTTGGTGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGGTGACTGTTA
55290 TGACAAATTCAGCACAAGAGTTGGTACTTTTGACTGTTA
1 TGACAAATTCAGCACAAGAGTTGG------TGACTGTTA
*
55329 AGACAAATTCAGCACAAGAGTTGGT
1 TGACAAATTCAGCACAAGAGTTGGT
55354 ACTTCGACTA
Statistics
Matches: 150, Mismatches: 12, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
33 65 0.43
38 22 0.15
39 63 0.42
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (33 bp):
TGACAAATTCAGCACAAGAGTTGGTGACTGTTA
Found at i:55334 original size:105 final size:106
Alignment explanation
Indices: 55147--55353 Score: 326
Period size: 105 Copynumber: 1.9 Consensus size: 106
55137 AGGATTAAGT
55147 TGACAAATTCAGCACAAGAGTTGGTACTTTGACTGTTACGACAAATTCAGCACAAGAATTGGTAC
1 TGACAAATTCAGCACAAGAGTTGG----TTGACTGTTACGACAAATTCAGCACAAGAATTGGTAC
* *
55212 TTTTGACTGTTATGACAAACTCAGCAGAAGAGTTGGTGACTGTTA
62 TTTTGACTGTTAAGACAAACTCAGCACAAGAGTTGGTGACTGTTA
* *
55257 TGACAAATTCAGCACAAGAGTTGG-TGACTGTTATGACAAATTCAGCACAAGAGTTGGTACTTTT
1 TGACAAATTCAGCACAAGAGTTGGTTGACTGTTACGACAAATTCAGCACAAGAATTGGTACTTTT
*
55321 GACTGTTAAGACAAATTCAGCACAAGAGTTGGT
66 GACTGTTAAGACAAACTCAGCACAAGAGTTGGT
55354 ACTTCGACTA
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
105 68 0.74
110 24 0.26
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (106 bp):
TGACAAATTCAGCACAAGAGTTGGTTGACTGTTACGACAAATTCAGCACAAGAATTGGTACTTTT
GACTGTTAAGACAAACTCAGCACAAGAGTTGGTGACTGTTA
Found at i:56015 original size:42 final size:40
Alignment explanation
Indices: 55956--56044 Score: 151
Period size: 42 Copynumber: 2.2 Consensus size: 40
55946 TATAATTCTA
55956 TTTATAAAATAATTAAATCATGCTATTGAATGAAAATTTTGT
1 TTTATAAAATAATTAAATCATGCTATTGAATG--AATTTTGT
*
55998 TTTATAAAATAATTAAATCATGCTATTGAATGAATTTTTT
1 TTTATAAAATAATTAAATCATGCTATTGAATGAATTTTGT
56038 TTTATAA
1 TTTATAA
56045 TATTTTGGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 14 0.30
42 32 0.70
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (40 bp):
TTTATAAAATAATTAAATCATGCTATTGAATGAATTTTGT
Done.