Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002627.1 Hibiscus syriacus cultivar Beakdansim tig00005355_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: 98508
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11697 original size:19 final size:19
Alignment explanation
Indices: 11652--11705 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
11642 CTATTCCCTA
*
11652 GTAATCTTACATTCTCACT
1 GTAATCTTACATTCCCACT
*
11671 GATAATCTTTCATTCCCACT
1 G-TAATCTTACATTCCCACT
11691 GTAATCTTACATTCC
1 GTAATCTTACATTCC
11706 GTGAACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.41
Consensus pattern (19 bp):
GTAATCTTACATTCCCACT
Found at i:11866 original size:29 final size:29
Alignment explanation
Indices: 11834--11906 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
11824 CCCTCAATTC
* **
11834 TTTTATATTTTATAATTACTGTC-CTTAAT
1 TTTTATATTTTATAATGA-TAACTCTTAAT
11863 TTTTATA-TTTATAATGATAACTCTTAAT
1 TTTTATATTTTATAATGATAACTCTTAAT
11891 TTTTATAATTTTATAA
1 TTTTAT-ATTTTATAA
11907 AATTTTTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 2 0.05
28 21 0.55
29 8 0.21
30 7 0.18
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTATATTTTATAATGATAACTCTTAAT
Found at i:12458 original size:17 final size:18
Alignment explanation
Indices: 12419--12468 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
12409 TCTTTTATCG
* *
12419 TGTTATAATATTATTTGT
1 TGTTATTATATTATTTCT
12437 T-TTATTAT-TTATTTCT
1 TGTTATTATATTATTTCT
12453 TGTTATTACTATTATT
1 TGTTATTA-TATTATT
12469 AACATCCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 12 0.44
18 2 0.07
19 5 0.19
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (18 bp):
TGTTATTATATTATTTCT
Found at i:18067 original size:15 final size:15
Alignment explanation
Indices: 18049--18079 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18039 AAATTCTAAA
18049 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
18064 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
18079 T
1 T
18080 TTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:35022 original size:13 final size:14
Alignment explanation
Indices: 35002--35042 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
34992 CACCAAAACC
35002 ACGAGCAAGCAACG
1 ACGAGCAAGCAACG
35016 A-GAGCAAGCAACG
1 ACGAGCAAGCAACG
*
35029 ACGACCAA-CAACG
1 ACGAGCAAGCAACG
35042 A
1 A
35043 AAAGAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.46, C:0.29, G:0.24, T:0.00
Consensus pattern (14 bp):
ACGAGCAAGCAACG
Found at i:36189 original size:126 final size:125
Alignment explanation
Indices: 36076--36299 Score: 317
Period size: 126 Copynumber: 1.8 Consensus size: 125
36066 AAAAATAATC
* *
36076 ATATTTT-GATATTTATTTATTTTT-AATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTATTAAGGCACCTAGAAGC
** *
36139 CCTTTTCTGATATTTTTAAATAAATAAATACCTTATTAAAATAAATTTTTATTTTAAGAAA
66 CCTTTTCTGATATTTTTAAATAAATAAATACCTTATTAAAATAAATTTTTA-TAGAAAAAA
* * * *
36200 ATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGTTGTATTAAGGTACCTAGAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTATTAAGGCACCTAGAAGC
* * *
36265 TCTTTTCTGATATTTTTGAATAAATAAATATCTTA
66 CCTTTTCTGATATTTTTAAATAAATAAATACCTTA
36300 CTATATTAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 6 0.07
125 16 0.18
126 67 0.75
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (125 bp):
ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTATTAAGGCACCTAGAAGC
CCTTTTCTGATATTTTTAAATAAATAAATACCTTATTAAAATAAATTTTTATAGAAAAAA
Found at i:36329 original size:115 final size:115
Alignment explanation
Indices: 36197--36414 Score: 337
Period size: 115 Copynumber: 1.9 Consensus size: 115
36187 TTATTTTAAG
* * * *
36197 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGTTGTATTAAGGTACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTATTAAAGCACCTAGA
* * *
36262 AGCTCTTTTCTGATATTTTTGAATAAATAAATATCTTACTATATTAAAAT
66 AGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
* * *
36312 AAAATGTTTTTGATATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTATTAAAGCACCTAGA
*
36377 AGCCCTTTTCTGATATTTCTAAATAAGTAAATATCTTA
66 AGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTA
36415 TTTATGTATA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
115 92 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (115 bp):
AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTATTAAAGCACCTAGA
AGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
Found at i:37432 original size:28 final size:27
Alignment explanation
Indices: 37378--37435 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
37368 TTAAACATAT
* *
37378 AAATTAAAATATATTTAAACAATAATA
1 AAATTAAAATAAATATAAACAATAATA
37405 AAATTAAAACTAAATATAAA-AAGTAATA
1 AAATTAAAA-TAAATATAAACAA-TAATA
37433 AAA
1 AAA
37436 CTTGTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (27 bp):
AAATTAAAATAAATATAAACAATAATA
Found at i:38720 original size:3 final size:3
Alignment explanation
Indices: 38714--38761 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
38704 TTTTTTTATT
*
38714 TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38762 AACAAAAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39053 original size:76 final size:76
Alignment explanation
Indices: 38927--39993 Score: 1938
Period size: 76 Copynumber: 14.0 Consensus size: 76
38917 GGTCTTATGA
* * *
38927 ATGACCCCG-AGGGTTTAAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGA-CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
38991 AAGGACTTACAG
65 AAGGACTTACAG
** * * *
39003 ATGACCTTAAGGCTTTGAAAACATCAAAAAGATCCCAAAGGCTTTTTGGAAACATCCTGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39068 AGGACTTACAG
66 AGGACTTACAG
*
39079 ATGATCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39144 AGGACTTACAG
66 AGGACTTACAG
*
39155 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGTCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39220 AGGACTTACAG
66 AGGACTTACAG
*
39231 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39296 AGGACTTACAG
66 AGGACTTACAG
39307 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39372 AGGACTTACAG
66 AGGACTTACAG
*
39383 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39448 AGGACTTACAG
66 AGGACTTACAG
*
39459 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39524 AGGACTTACAG
66 AGGACTTACAG
*
39535 ATGACCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39600 AGGACTTACAG
66 AGGACTTACAG
*
39611 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39676 AGGACTTACAG
66 AGGACTTACAG
* *
39687 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCTGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39752 AGGACTTACAG
66 AGGACTTACAG
*
39763 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCAGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39828 AGGACTTACAG
66 AGGACTTACAG
*
39839 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCAGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
39904 AGGGCTTACAG
66 AGGACTTACAG
39915 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
39980 AGGACTTACAG
66 AGGACTTACAG
39991 ATG
1 ATG
39994 TGAGAAATAG
Statistics
Matches: 960, Mismatches: 30, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 2 0.00
76 958 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:40693 original size:22 final size:22
Alignment explanation
Indices: 40668--40722 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
40658 CATAAAGTTT
*
40668 TCATCTTTGAAAAGAGAATATG
1 TCATCTTTGAAAAGAGAATATA
* *
40690 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
40712 TCATCTTTGAA
1 TCATCTTTGAA
40723 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:41219 original size:54 final size:53
Alignment explanation
Indices: 41095--41295 Score: 232
Period size: 54 Copynumber: 3.8 Consensus size: 53
41085 CACTAGTTCA
* * *
41095 TAAAACATTTGACAATATATTCAT-CTTTTCCTGTGGTTTCTG-TC-GAG-ATG
1 TAAAACATTTGACAACACATTCATCCTTTT-CTGTGGTTTCTGCTCAGAGTTTG
*
41145 TAAAACACTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGA-GTTTG
* **
41199 TAAAACATTTGACAACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTCA
1 TAAAACATTTGACAACACATTCATCCTTTTC-TGTGGTTTCTGCTCAGA-GTTTG
* * * *
41253 TAAAGCGTTTGACAACACATTTATCCTTTTCTGTGGCTTCTGC
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGC
41296 CAAGATTTCT
Statistics
Matches: 130, Mismatches: 14, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
50 33 0.25
51 7 0.05
52 2 0.02
53 5 0.04
54 79 0.61
55 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (53 bp):
TAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGAGTTTG
Found at i:41294 original size:108 final size:104
Alignment explanation
Indices: 41095--41295 Score: 260
Period size: 104 Copynumber: 1.9 Consensus size: 104
41085 CACTAGTTCA
* * * *
41095 TAAAACATTTGACAATATATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTTGACAA
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
*
41160 CACATTCATCCTTTTCTGTGGTTTCTGCTCAGATGTTTG
66 CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
* * **
41199 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTC-AGACGTTCATAAAGCGTTT
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTG-TCGAGACG-T-A-AAA-CACTT
*
41263 GACAACACATTTATCCTTTTCTGTGGCTTCTGC
61 GACAACACATTCATCCTTTTCTGTGGCTTCTGC
41296 CAAGATTTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
104 41 0.50
105 3 0.04
106 1 0.01
107 3 0.04
108 34 0.41
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (104 bp):
TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
Found at i:51229 original size:22 final size:25
Alignment explanation
Indices: 51193--51258 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 25
51183 AAAATAAAAT
*
51193 AATAATACTAATTAAAATA-TTAAAC
1 AATAATA-AAATTAAAATATTTAAAC
51218 -AT-ATAAAATTAAAATATATTTAAAC
1 AATAATAAAATT-AAA-ATATTTAAAC
51243 AATAATAAAATTAAAA
1 AATAATAAAATTAAAA
51259 CTAAATATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 4 0.11
23 6 0.17
24 5 0.14
25 7 0.20
26 5 0.14
27 8 0.23
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAATAAAATTAAAATATTTAAAC
Found at i:51255 original size:27 final size:28
Alignment explanation
Indices: 51207--51280 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
51197 ATACTAATTA
51207 AAATATTAAAC-AT-ATAAAATTAAAA-T
1 AAAT-TTAAACAATAATAAAATTAAAACT
*
51233 ATATTTAAACAATAATAAAATTAAAACT
1 AAATTTAAACAATAATAAAATTAAAACT
*
51261 AAATATAAA-AAGTAATAAAA
1 AAATTTAAACAA-TAATAAAA
51281 CTTGTAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.15
26 5 0.12
27 14 0.34
28 16 0.39
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.28
Consensus pattern (28 bp):
AAATTTAAACAATAATAAAATTAAAACT
Found at i:51868 original size:13 final size:13
Alignment explanation
Indices: 51850--51878 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
51840 CCACCGTACT
51850 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
51863 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
51876 CCG
1 CCG
51879 TAACGGTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:52565 original size:3 final size:3
Alignment explanation
Indices: 52557--52604 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
52547 TATTTTTATT
* *
52557 TAA TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52605 AACAAAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55085 original size:52 final size:52
Alignment explanation
Indices: 55021--55131 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 52
55011 TAATCCTGTC
* * *
55021 TATATCAAAGTTTAAAATGATTGTCGAAATATATATTCTTAGAAATTTC-ATT
1 TATATCAAAGTTTAAAATGATTGTCAAAATATATATGCATAG-AATTTCAATT
* * *
55073 TATATCAGAGTTTAAAATGATTTTCAAAATATTTATGCATAGAATTTCAATT
1 TATATCAAAGTTTAAAATGATTGTCAAAATATATATGCATAGAATTTCAATT
55125 TATATCA
1 TATATCA
55132 TAGTAGAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 6 0.12
52 46 0.88
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (52 bp):
TATATCAAAGTTTAAAATGATTGTCAAAATATATATGCATAGAATTTCAATT
Found at i:59254 original size:34 final size:35
Alignment explanation
Indices: 59201--59280 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 35
59191 TTAATACGAT
*
59201 TAATAACAGTCATTTGAAGAACTAACTACCCACTC
1 TAATAACAGTCATTGGAAGAACTAACTACCCACTC
* * * *
59236 TAAT-ACAGTGATTGGAAGAACTAAGTACCTACTT
1 TAATAACAGTCATTGGAAGAACTAACTACCCACTC
*
59270 TAATGACAGTC
1 TAATAACAGTC
59281 GTTCCACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 29 0.76
35 9 0.24
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (35 bp):
TAATAACAGTCATTGGAAGAACTAACTACCCACTC
Found at i:59780 original size:18 final size:19
Alignment explanation
Indices: 59746--59784 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
59736 GTAAATATAA
*
59746 AACATTTTATTATAAAATT
1 AACATTTAATTATAAAATT
59765 AACATTTAATTA-AAAATT
1 AACATTTAATTATAAAATT
59783 AA
1 AA
59785 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AACATTTAATTATAAAATT
Found at i:61956 original size:31 final size:26
Alignment explanation
Indices: 61885--61960 Score: 134
Period size: 26 Copynumber: 2.9 Consensus size: 26
61875 TTAATAATTT
61885 TCAAATAAATTTCGATTCGATTAACGG
1 TCAAAT-AATTTCGATTCGATTAACGG
61912 TCAAATAATTTCGATTCGATTAACGG
1 TCAAATAATTTCGATTCGATTAACGG
*
61938 TCAAATAATTTCGGTTCGATTAA
1 TCAAATAATTTCGATTCGATTAA
61961 TGGTTAAAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 42 0.88
27 6 0.12
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (26 bp):
TCAAATAATTTCGATTCGATTAACGG
Found at i:62038 original size:120 final size:119
Alignment explanation
Indices: 61819--62039 Score: 315
Period size: 120 Copynumber: 1.8 Consensus size: 119
61809 TAAATAATTT
* *
61819 TCAAATAAATTTCGGTTCGATTAACTGTTAAGGAAAAAATAATTTATTTTATTCGGTTAATAATT
1 TCAAATAAATTTCGGTTCGATTAACTGTTAAAGAAAAAATAATTTATTTGATTCGGTTAATAATT
61884 TTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGATTCGATTAACGG
66 TTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGATTCGATTAACGG
*
61938 TCAAAT-AATTTCGGTTCGATTAA-TGGTTAAAG-AAAAA-AATTGGCTAATTTGGTTCGGTTAA
1 TCAAATAAATTTCGGTTCGATTAACT-GTTAAAGAAAAAATAATT---T-ATTTGATTCGGTTAA
* * *
61999 TAATTTTCAAATAAATTTCGGTTCGATTAACTGTTAAATAA
61 TAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAA
62040 AAATAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
116 4 0.04
117 6 0.07
118 23 0.25
119 7 0.08
120 51 0.56
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.38
Consensus pattern (119 bp):
TCAAATAAATTTCGGTTCGATTAACTGTTAAAGAAAAAATAATTTATTTGATTCGGTTAATAATT
TTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGATTCGATTAACGG
Found at i:62087 original size:65 final size:66
Alignment explanation
Indices: 61938--62104 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 66
61928 CGATTAACGG
* *
61938 TCAAAT-AATTTCGGTTCGATTAA-TGGTTAAAGAAAAAAATTGGCTAATTTGGTTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAACT-GTTAAATAAAAAAATT-G-TAATTTGATTCGGTTAATA
62001 ATTT
63 ATTT
*
62005 TCAAATAAATTTCGGTTCGATTAACTGTTAAATAAAAATAATT-T-ATTTTATTCGGTTAATAAT
1 TCAAATAAATTTCGGTTCGATTAACTGTTAAATAAAAA-AATTGTAATTTGATTCGGTTAATAAT
62068 TT
65 TT
* * *
62070 TCAAATAAATTTGGGTTCGATTAACGGTCAAATAA
1 TCAAATAAATTTCGGTTCGATTAACTGTTAAATAA
62105 TTTTGGTTCG
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
65 51 0.56
66 1 0.01
67 6 0.07
68 28 0.31
69 5 0.05
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (66 bp):
TCAAATAAATTTCGGTTCGATTAACTGTTAAATAAAAAAATTGTAATTTGATTCGGTTAATAATT
T
Found at i:62100 original size:27 final size:27
Alignment explanation
Indices: 62070--62200 Score: 110
Period size: 26 Copynumber: 4.9 Consensus size: 27
62060 TTAATAATTT
*
62070 TCAAATAAATTTGGGTTCGATTAACGG
1 TCAAATAAATTTCGGTTCGATTAACGG
* *
62097 TCAAAT-AATTTTGGTTCGATTAATGG
1 TCAAATAAATTTCGGTTCGATTAACGG
* * * * * *
62123 TTAAAGAAAAAAATAT-GGTT--AATAAAGT
1 -T---CAAATAAATTTCGGTTCGATTAACGG
62151 TCAAATAAATTTCGGTTCGATTAACGG
1 TCAAATAAATTTCGGTTCGATTAACGG
62178 TCAAAT-AATTTCGGTTCGATTAA
1 TCAAATAAATTTCGGTTCGATTAA
62201 TGTTAAAGAA
Statistics
Matches: 82, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
24 8 0.10
25 4 0.05
26 35 0.43
27 19 0.23
28 5 0.06
30 7 0.09
31 4 0.05
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (27 bp):
TCAAATAAATTTCGGTTCGATTAACGG
Found at i:62194 original size:81 final size:80
Alignment explanation
Indices: 62054--62225 Score: 283
Period size: 81 Copynumber: 2.1 Consensus size: 80
62044 AATTTATTTT
** * *
62054 ATTCGGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTA
1 ATTCGGTTAATAAAGTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTA
62119 ATGGTTAAAGAAAAAA
66 AT-GTTAAAGAAAAAA
62135 ATAT-GGTTAATAAAGTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
1 AT-TCGGTTAATAAAGTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
62199 AATGTTAAAGAAAAAA
65 AATGTTAAAGAAAAAA
62215 ATTCGGTTAAT
1 ATTCGGTTAAT
62226 TTGTTTTGGT
Statistics
Matches: 85, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
79 1 0.01
80 22 0.26
81 61 0.72
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (80 bp):
ATTCGGTTAATAAAGTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTA
ATGTTAAAGAAAAAA
Found at i:62345 original size:93 final size:94
Alignment explanation
Indices: 62139--62365 Score: 348
Period size: 94 Copynumber: 2.4 Consensus size: 94
62129 AAAAAAATAT
**
62139 GGTTAATAAAGTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
1 GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
* *
62204 TAAAGAAAAAAATTCGGTTAATTTGTTTT
66 TAAAGAAAAAAATTCGGTTAATTTGGTTC
* * *
62233 GGTTAATAATTTTCAAATAATTTTTGGTTTGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
1 GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
*** *
62298 TAAAG-AAATTTTTTGGTTAATTTGGTTC
66 TAAAGAAAAAAATTCGGTTAATTTGGTTC
62326 GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
1 GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
62366 TAAAGAAAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 54 0.45
94 65 0.55
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (94 bp):
GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
TAAAGAAAAAAATTCGGTTAATTTGGTTC
Found at i:62681 original size:30 final size:30
Alignment explanation
Indices: 62646--62702 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
62636 ATAATATGTA
*
62646 AATATTAAGGACCAAATGTATAATTATTCC
1 AATATTAAGGACCAAATATATAATTATTCC
*
62676 AATATTAAGGATCAAATATATAATTAT
1 AATATTAAGGACCAAATATATAATTAT
62703 GTCAGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (30 bp):
AATATTAAGGACCAAATATATAATTATTCC
Found at i:71340 original size:2 final size:2
Alignment explanation
Indices: 71333--71368 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
71323 ATATGAAAGA
71333 AT AT 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 AT AT
71369 TATGGTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71471 original size:14 final size:14
Alignment explanation
Indices: 71452--71481 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
71442 ATAGAAATTT
71452 GAATAACTCGACTC
1 GAATAACTCGACTC
*
71466 GAATAACTCTACTC
1 GAATAACTCGACTC
71480 GA
1 GA
71482 TTCAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (14 bp):
GAATAACTCGACTC
Found at i:74153 original size:32 final size:30
Alignment explanation
Indices: 74116--74213 Score: 106
Period size: 32 Copynumber: 3.1 Consensus size: 30
74106 CTAAGGTAAA
74116 CCTTGGGTAGGCTCTCAGGCCCCAAGGTACTC
1 CCTTGGGTAGGCTCT-AGGCCCCAAGGTA-TC
*** *
74148 CCTTGGGTAGGCTCTAAAACCCAAGGTATT
1 CCTTGGGTAGGCTCTAGGCCCCAAGGTATC
* *
74178 CCTTAGGTAGGCTCTAAGGCCCCAAGGCATTC
1 CCTTGGGTAGGCTCT-AGGCCCCAAGGTA-TC
74210 CCTT
1 CCTT
74214 ATATTGGCTC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
30 15 0.28
31 19 0.35
32 20 0.37
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (30 bp):
CCTTGGGTAGGCTCTAGGCCCCAAGGTATC
Found at i:74189 original size:30 final size:31
Alignment explanation
Indices: 74136--74194 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
74126 GCTCTCAGGC
*
74136 CCCAAGGTACTCCCTTGGGTAGGCTCTAAAA
1 CCCAAGGTACTCCCTTAGGTAGGCTCTAAAA
*
74167 CCCAAGGTA-TTCCTTAGGTAGGCTCTAA
1 CCCAAGGTACTCCCTTAGGTAGGCTCTAA
74195 GGCCCCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (31 bp):
CCCAAGGTACTCCCTTAGGTAGGCTCTAAAA
Found at i:74202 original size:31 final size:31
Alignment explanation
Indices: 74116--74210 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
74106 CTAAGGTAAA
* *
74116 CCTTGGGTAGGCTCTCAGGCCCCAAGGTACTC
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTA-TT
**
74148 CCTTGGGTAGGCTCTAA-AACCCAAGGTATT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATT
* *
74178 CCTTAGGTAGGCTCTAAGGCCCCAAGGCATT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATT
74209 CC
1 CC
74211 CTTATATTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 17 0.31
31 21 0.39
32 16 0.30
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGTATT
Found at i:76668 original size:13 final size:13
Alignment explanation
Indices: 76650--76674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76640 GGGTCTTTAC
76650 TTGTAAATGGGCT
1 TTGTAAATGGGCT
76663 TTGTAAATGGGC
1 TTGTAAATGGGC
76675 CTCCGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (13 bp):
TTGTAAATGGGCT
Found at i:77314 original size:30 final size:29
Alignment explanation
Indices: 77258--77331 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
77248 TACATAATAA
77258 ACAAATAAATAAATAAAATAAGAAGAAAAT
1 ACAAATAAATAAA-AAAATAAGAAGAAAAT
* *
77288 ACAAATAAATAAAACAAATGTA-AAGAAGAT
1 ACAAATAAATAAAA-AAAT-AAGAAGAAAAT
77318 A-AAA-AAATAAAAAA
1 ACAAATAAATAAAAAA
77332 TGAAGATAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 2 0.05
28 8 0.20
29 4 0.10
30 25 0.62
31 1 0.03
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (29 bp):
ACAAATAAATAAAAAAATAAGAAGAAAAT
Found at i:77329 original size:8 final size:8
Alignment explanation
Indices: 77253--77331 Score: 50
Period size: 8 Copynumber: 9.1 Consensus size: 8
77243 ATATATACAT
*
77253 AATAAACA
1 AATAAAAA
*
77261 AATAAATA
1 AATAAAAA
*
77269 AATAAAAT
1 AATAAAAA
* *
77277 AAGAAGAA
1 AATAAAAA
77285 AATACAAATA
1 AATA-AAA-A
77295 AATAAAACA
1 AATAAAA-A
77304 AATGTAAAGAA
1 AA--TAAA-AA
*
77315 GATAAAAA
1 AATAAAAA
77323 AATAAAAA
1 AATAAAAA
77331 A
1 A
77332 TGAAGATAAG
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
8 31 0.56
9 12 0.22
10 5 0.09
11 6 0.11
12 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:77407 original size:3 final size:3
Alignment explanation
Indices: 77401--77441 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
77391 AATAAAATAG
77401 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
77442 AAACAGTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:77503 original size:29 final size:30
Alignment explanation
Indices: 77469--77531 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
77459 TAATAAAATA
77469 AAATAAAAATAGAAGGATATAAG-AATAAT
1 AAATAAAAATAGAAGGATATAAGTAATAAT
* * * *
77498 AAAT-AAAATATATGTATATATGTAATAAT
1 AAATAAAAATAGAAGGATATAAGTAATAAT
77527 AAATA
1 AAATA
77532 TAATATTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (30 bp):
AAATAAAAATAGAAGGATATAAGTAATAAT
Found at i:77909 original size:21 final size:21
Alignment explanation
Indices: 77883--78019 Score: 147
Period size: 21 Copynumber: 6.6 Consensus size: 21
77873 GTTTCCAGAT
*
77883 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
77904 TCGCAATGCGAACTTTGACTA
1 TCGCAATGCGAACTTCGACTA
* *
77925 TCGCAATACGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
77946 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
77966 TCACAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
77987 TCGCAATGCGATCTTCGACTA
1 TCGCAATGCGAACTTCGACTA
78008 TCGCAATGCGAA
1 TCGCAATGCGAA
78020 TTTGTGAACT
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
20 15 0.15
21 82 0.85
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:78065 original size:20 final size:20
Alignment explanation
Indices: 78036--78149 Score: 119
Period size: 20 Copynumber: 5.6 Consensus size: 20
78026 AACTTGGACT
78036 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
78056 ATCACAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
78077 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
78097 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
78118 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
78138 ATCGCAATGCGA
1 ATCGCAATGCGA
78150 TAGTCGAAGT
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.05
19 6 0.08
20 35 0.45
21 23 0.29
22 6 0.08
23 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:78086 original size:21 final size:21
Alignment explanation
Indices: 78063--78301 Score: 155
Period size: 21 Copynumber: 11.6 Consensus size: 21
78053 TAAATCACAA
*
78063 TGCGATAGTCGACTATCGCAA
1 TGCGATAGTCGACTATCGCAT
* *
78084 TGCGAATA-T-GTA-AATCGCAA
1 TGCG-ATAGTCG-ACTATCGCAT
*
78104 TGCGATAGTCGACTATCGCAA
1 TGCGATAGTCGACTATCGCAT
* *
78125 TGCGAATA-T-GTA-AATCGCAA
1 TGCG-ATAGTCG-ACTATCGCAT
* *
78145 TGCGATAGTCGAAGT-TCGCGT
1 TGCGATAGTCG-ACTATCGCAT
78166 TGCGATAGTCGACTATCGCAT
1 TGCGATAGTCGACTATCGCAT
* * *
78187 TGCGAT-TTAC-ATTTTCGCAT
1 TGCGATAGT-CGACTATCGCAT
* *
78207 TGCGATAGTCCAAGT-TCGCAT
1 TGCGATAGT-CGACTATCGCAT
78228 TGCGATAGTCGACTATCGCAT
1 TGCGATAGTCGACTATCGCAT
*
78249 TGCGAT--T-TACATATTCGCAT
1 TGCGATAGTCGAC-TA-TCGCAT
*
78269 TGCGATAGTCGAAGT-TCGCAT
1 TGCGATAGTCG-ACTATCGCAT
78290 TGCGATAGTCGA
1 TGCGATAGTCGA
78302 AGTTCGCGTT
Statistics
Matches: 177, Mismatches: 20, Indels: 43
0.74 0.08 0.18
Matches are distributed among these distances:
18 2 0.01
19 9 0.05
20 60 0.34
21 95 0.54
22 9 0.05
23 1 0.01
24 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCGACTATCGCAT
Found at i:78170 original size:41 final size:41
Alignment explanation
Indices: 78032--78156 Score: 241
Period size: 41 Copynumber: 3.0 Consensus size: 41
78022 TGTGAACTTG
*
78032 GACTATCGCAATGCGAATATGTAAATCACAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
78073 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
78114 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
78155 GA
1 GA
78157 AGTTCGCGTT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (41 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
Found at i:78170 original size:62 final size:61
Alignment explanation
Indices: 78098--78319 Score: 297
Period size: 62 Copynumber: 3.6 Consensus size: 61
78088 AATATGTAAA
* * *
78098 TCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTA-A-ATCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGACTATCGCATTGCG-AT-T-TACATATCGCATTGCGATAGTCGAAGT
* * *
78160 TCGCGTTGCGATAGTCGACTATCGCATTGCGATTTACATTTTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACA-TATCGCATTGCGATAGTCGAAGT
78222 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA-TCGCATTGCGATAGTCGAAGT
* *
78284 TCGCATTGCGATAGTCGAAGT-TCGCGTTGCGATTTA
1 TCGCATTGCGATAGTCG-ACTATCGCATTGCGATTTA
78320 TTCCAAATTC
Statistics
Matches: 144, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
59 2 0.01
60 2 0.01
61 3 0.02
62 135 0.94
63 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (61 bp):
TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATCGCATTGCGATAGTCGAAGT
Found at i:78266 original size:41 final size:40
Alignment explanation
Indices: 78032--78296 Score: 186
Period size: 41 Copynumber: 6.5 Consensus size: 40
78022 TGTGAACTTG
* * *
78032 GACTATCGCAATGCGAATATGTA-AATCACAATGCGATAGTC
1 GACTATCGCATTGCG-ATAT-TACAATCGCATTGCGATAGTC
* *
78073 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGATAGTC
1 GACTATCGCATTGCG-ATAT-TACAATCGCATTGCGATAGTC
* *
78114 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGATAGTC
1 GACTATCGCATTGCG-ATAT-TACAATCGCATTGCGATAGTC
* * * * *
78155 GAAGT-TCGCGTTGCGATAGTCGACTATCGCATTGCGAT-TTAC
1 G-ACTATCGCATTGCGATA-T-TACAATCGCATTGCGATAGT-C
* * * *
78197 -ATTTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 GACTATCGCATTGCGATATTACAA--TCGCATTGCGATAGTC
78238 GACTATCGCATTGCGAT-TTACATATTCGCATTGCGATAGTC
1 GACTATCGCATTGCGATATTACA-A-TCGCATTGCGATAGTC
*
78279 GAAGT-TCGCATTGCGATA
1 G-ACTATCGCATTGCGATA
78297 GTCGAAGTTC
Statistics
Matches: 191, Mismatches: 21, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 151 0.79
42 33 0.17
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (40 bp):
GACTATCGCATTGCGATATTACAATCGCATTGCGATAGTC
Found at i:78302 original size:21 final size:21
Alignment explanation
Indices: 78139--78316 Score: 172
Period size: 21 Copynumber: 8.6 Consensus size: 21
78129 AATATGTAAA
*
78139 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
78160 TCGCGTTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
* **
78180 ATCGCATTGCGAT-TTAC-ATTT
1 -TCGCATTGCGATAGT-CGAAGT
*
78201 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
78222 TCGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
78242 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
78263 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
78284 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
78305 TCGCGTTGCGAT
1 TCGCATTGCGAT
78317 TTATTCCAAA
Statistics
Matches: 130, Mismatches: 15, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
20 33 0.25
21 96 0.74
22 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:79197 original size:21 final size:21
Alignment explanation
Indices: 79171--79331 Score: 197
Period size: 21 Copynumber: 7.7 Consensus size: 21
79161 CCAAGTTCGC
*
79171 AAGTTCGCATTGCAATAGTCG
1 AAGTTCGCATTGCGATAGTCG
*
79192 AAGTTCGCGTTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
79213 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
* *
79234 ACTA-TT-GTATTGCGAT-TTAC-
1 A--AGTTCGCATTGCGATAGT-CG
*
79254 ATA-TTCGCATTGCGATAGTCC
1 A-AGTTCGCATTGCGATAGTCG
79275 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
*
79296 AAATTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
79317 AAGTTCGCATTGCGA
1 AAGTTCGCATTGCGA
79332 ATCTGGAAAC
Statistics
Matches: 123, Mismatches: 10, Indels: 14
0.84 0.07 0.10
Matches are distributed among these distances:
19 4 0.03
20 13 0.11
21 103 0.84
22 2 0.02
23 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (21 bp):
AAGTTCGCATTGCGATAGTCG
Found at i:79308 original size:62 final size:62
Alignment explanation
Indices: 79195--79311 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 62
79185 ATAGTCGAAG
* * * *
79195 TTCGCGTTGCGATAGTCGAAGTTCGCATTGCGATAGTCGACTATTGTATTGCGATTTACATA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACAATTGCATTGCGATTTACATA
79257 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGA-AATTCGCATTGCGAT
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACAATT-GCATTGCGAT
79312 AGTCGAAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
61 3 0.06
62 47 0.94
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACAATTGCATTGCGATTTACATA
Found at i:79329 original size:83 final size:82
Alignment explanation
Indices: 79174--79331 Score: 237
Period size: 83 Copynumber: 1.9 Consensus size: 82
79164 AGTTCGCAAG
* * *
79174 TTCGCATTGCAATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCATTGCGATAGTCGACTAT
1 TTCGCATTGCAATAGTCCAAGTTCGCATTGCGATAGTCGAAATTCGCATTGCGATAGTCGAC-AT
*
79239 TGTATTGCGATTTACATA
65 TGCATTGCGATTTACATA
*
79257 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAATTCGCATTGCGATAGTCGA-AGT
1 TTCGCATTGCAATAGTCCAAGTTCGCATTGCGATAGTCGAAATTCGCATTGCGATAGTCGACA-T
79321 TCGCATTGCGA
65 T-GCATTGCGA
79332 ATCTGGAAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
81 1 0.01
82 2 0.03
83 65 0.96
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (82 bp):
TTCGCATTGCAATAGTCCAAGTTCGCATTGCGATAGTCGAAATTCGCATTGCGATAGTCGACATT
GCATTGCGATTTACATA
Found at i:80110 original size:37 final size:37
Alignment explanation
Indices: 80060--80167 Score: 153
Period size: 37 Copynumber: 2.9 Consensus size: 37
80050 TTATGAATCC
* * *
80060 TATTTTTAGGAGTTTGAACCGTAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATAA
* *
80097 TATTTTTAAGAGTTTGAATCATAATAAAACTCTATAA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATAA
* *
80134 TAATTTTAGGAGTTTAAATCATAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
80168 ATGTTAAGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATAA
Found at i:80254 original size:3 final size:3
Alignment explanation
Indices: 80246--80286 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
80236 TATGTTGACA
80246 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
80287 TAGATTATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:80270 original size:22 final size:22
Alignment explanation
Indices: 80245--80286 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
80235 ATATGTTGAC
80245 AAATAATAATAATAATAATAAT
1 AAATAATAATAATAATAATAAT
80267 AAATAATAATAATAATAATA
1 AAATAATAATAATAATAATA
80287 TAGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAATAATAATAATAATAAT
Found at i:80273 original size:19 final size:19
Alignment explanation
Indices: 80249--80286 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
80239 GTTGACAAAT
80249 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
80268 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
80287 TAGATTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATAATAATAATAATA
Found at i:83066 original size:14 final size:14
Alignment explanation
Indices: 83047--83078 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
83037 CGTTCGTGAA
83047 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
83061 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
83075 CGTT
1 CGTT
83079 TATTTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:83973 original size:12 final size:11
Alignment explanation
Indices: 83948--83988 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
83938 TAGGGCAATG
83948 TCGAGCTTGAA
1 TCGAGCTTGAA
83959 TCGAGCTTAGAA
1 TCGAGCTT-GAA
83971 TCGAGCTTGAA
1 TCGAGCTTGAA
83982 TCGAGCT
1 TCGAGCT
83989 CGAGTCTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:84249 original size:16 final size:16
Alignment explanation
Indices: 84224--84288 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
84214 CCAACGTTTA
*
84224 TGTTCGTTTATATTCG
1 TGTTCGTTTATGTTCG
*
84240 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
84256 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
84272 TGTTCTTTTATGTTCG
1 TGTTCGTTTATGTTCG
84288 T
1 T
84289 ACATGAACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.20, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:92183 original size:31 final size:31
Alignment explanation
Indices: 92124--92183 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
92114 ACTTACCACA
*
92124 AATACTAATTTAAACCAAAATATGAAATTTT
1 AATACTAATTTAAACCAAAATATCAAATTTT
*
92155 AATACTAATTTAAATCAACAA-ATCAAATT
1 AATACTAATTTAAACCAA-AATATCAAATT
92184 CAAGACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (31 bp):
AATACTAATTTAAACCAAAATATCAAATTTT
Found at i:92372 original size:2 final size:2
Alignment explanation
Indices: 92365--92394 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
92355 CCCTCAACTT
92365 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92395 TCAAGTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:98490 original size:2 final size:2
Alignment explanation
Indices: 98477--98508 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
98467 TGGCTGGTCC
*
98477 AT AT AC 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
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.