Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005133.1 Hibiscus syriacus cultivar Beakdansim tig00011556_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: 89711
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:389 original size:10 final size:10
Alignment explanation
Indices: 374--423 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
364 GTCTCCAACG
374 TTATGTTCGT
1 TTATGTTCGT
384 TTATGTTCGT
1 TTATGTTCGT
394 TTATGTTCG-
1 TTATGTTCGT
403 ---TGTTCGT
1 TTATGTTCGT
410 TTATGTTCGT
1 TTATGTTCGT
420 TTAT
1 TTAT
424 TATTAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.17
10 30 0.83
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.60
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:408 original size:16 final size:16
Alignment explanation
Indices: 387--419 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
377 TGTTCGTTTA
387 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
403 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
419 T
1 T
420 TTATTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:452 original size:28 final size:27
Alignment explanation
Indices: 420--473 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
410 TTATGTTCGT
420 TTATT-ATTAAATGAACAACATGAACAAG
1 TTATTCATT-AATGAACAA-ATGAACAAG
* *
448 TTATTCCTTAATGAACGAATGAACAA
1 TTATTCATTAATGAACAAATGAACAA
474 AAAAATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 13 0.57
29 2 0.09
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (27 bp):
TTATTCATTAATGAACAAATGAACAAG
Found at i:1311 original size:24 final size:24
Alignment explanation
Indices: 1283--1335 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1273 TGAGATCCAA
* *
1283 ATAAACGAGTCAATAAATGAACTT
1 ATAAACAAGTCAATAAACGAACTT
* *
1307 ATAAATAAGTTAATAAACGAACTT
1 ATAAACAAGTCAATAAACGAACTT
1331 ATAAA
1 ATAAA
1336 AGATTCGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.26
Consensus pattern (24 bp):
ATAAACAAGTCAATAAACGAACTT
Found at i:6578 original size:35 final size:35
Alignment explanation
Indices: 6514--6613 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 35
6504 TTTCGTCCTA
* *
6514 CTAGGATTCAAACTCTCAAAAATATGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
6551 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
6586 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
6614 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.38
36 18 0.33
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:6776 original size:11 final size:11
Alignment explanation
Indices: 6760--6787 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
6750 AGGTAGCATC
6760 TTTTTTATCTT
1 TTTTTTATCTT
6771 TTTTTTATCTT
1 TTTTTTATCTT
6782 TTTTTT
1 TTTTTT
6788 GCATGTGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTATCTT
Found at i:7251 original size:72 final size:72
Alignment explanation
Indices: 7175--7324 Score: 175
Period size: 72 Copynumber: 2.1 Consensus size: 72
7165 TTCTAACATC
* * *
7175 TATTTACGTATATTACCTTTTATCATTATTATA-TATA-TATTA-TTGCT-TCATTTTCTTTATG
1 TATTTACATATATTACCTTTT-T-ATT-TTATATTATACTATTATTTACTATCATTTT-TCTATG
7236 -TGTATTTTATT
62 CTGTA-TTTATT
* *
7247 TATTTATATATATTACCTTTTTATTTTATATTATACTATTATTTACTATCATTTTTCTATGCTTT
1 TATTTACATATATTACCTTTTTATTTTATATTATACTATTATTTACTATCATTTTTCTATGCTGT
7312 ATTTATT
66 ATTTATT
7319 TATTTA
1 TATTTA
7325 TTATTTTATT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
69 5 0.07
70 7 0.10
71 6 0.09
72 40 0.59
73 10 0.15
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.61
Consensus pattern (72 bp):
TATTTACATATATTACCTTTTTATTTTATATTATACTATTATTTACTATCATTTTTCTATGCTGT
ATTTATT
Found at i:7291 original size:22 final size:22
Alignment explanation
Indices: 7242--7291 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 22
7232 TATGTGTATT
*
7242 TTATTTATTTATATATATTACC
1 TTATTTATTTATATATATTACA
7264 TT-TTTATTT-TATAT-TATACTA
1 TTATTTATTTATATATAT-TAC-A
7285 TTATTTA
1 TTATTTA
7292 CTATCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
21 9 0.38
22 6 0.25
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTTATTTATATATATTACA
Found at i:7325 original size:72 final size:69
Alignment explanation
Indices: 7183--7348 Score: 173
Period size: 72 Copynumber: 2.4 Consensus size: 69
7173 TCTATTTACG
* *
7183 TATATTACCTTTTATCATTATTATA-TATATATTATTGCTTCATTTTCTTTATGTGTATTTTATT
1 TATATTACCTTTT-T-ATT-TTATATTATATATTATTACTTCATTTTCTCTATGTGTATTTTATT
7247 TATTTAT
63 TATTTAT
*
7254 ATATATTACCTTTTTATTTTATATTATACTATTATTTACTATCATTTT-TCTATGCTTTA-TTTA
1 -TATATTACCTTTTTATTTTATATTATA-TATTA-TTACT-TCATTTTCTCTATG-TGTATTTTA
7317 TTTATTTAT
61 TTTATTTAT
* *
7326 TATTTTA---TTTTATTTTATTTTAT
1 TATATTACCTTTTTATTTTATATTAT
7349 TTCTTTTTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 14
0.82 0.05 0.14
Matches are distributed among these distances:
68 15 0.18
69 5 0.06
70 7 0.08
71 12 0.14
72 35 0.42
73 10 0.12
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.64
Consensus pattern (69 bp):
TATATTACCTTTTTATTTTATATTATATATTATTACTTCATTTTCTCTATGTGTATTTTATTTAT
TTAT
Found at i:7328 original size:15 final size:14
Alignment explanation
Indices: 7309--7397 Score: 74
Period size: 15 Copynumber: 6.1 Consensus size: 14
7299 TTTTCTATGC
7309 TTTA-TTTATTTATT
1 TTTATTTTATTT-TT
7323 TATTATTTTATTTTAT
1 T-TTATTTTATTTT-T
7339 TTTATTTTATTTCTT
1 TTTATTTTATTT-TT
* ***
7354 TTTATTTTGGTTGAA
1 TTTATTTT-ATTTTT
*
7369 TTTATTTT-TTTAT
1 TTTATTTTATTTTT
7382 TTTATTTTATTTTT
1 TTTATTTTATTTTT
7396 TT
1 TT
7398 ATATCTAACA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
13 11 0.18
14 7 0.11
15 32 0.52
16 12 0.19
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTATTTTATTTTT
Found at i:7335 original size:5 final size:5
Alignment explanation
Indices: 7325--7394 Score: 74
Period size: 5 Copynumber: 14.4 Consensus size: 5
7315 TATTTATTTA
** * *
7325 TTATT TTATT TTATT TTATT TTATT TCT-TT TTATT TTGGT TGAAT TTA-T
1 TTATT TTATT TTATT TTATT TTATT T-TATT TTATT TTATT TTATT TTATT
7374 TT-TT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TT
7395 TTTATATCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
4 7 0.13
5 47 0.85
6 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.04, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:10458 original size:31 final size:32
Alignment explanation
Indices: 10397--10470 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 32
10387 ATTCAATCAG
*
10397 AACAAAAAGGGCAAAAAGAAAAAAAGAAAAGA
1 AACAAAAAGGGAAAAAAGAAAAAAAGAAAAGA
*
10429 AACAAAAAGGAAAAAATAAGAACAAAAA-AGAAAG-
1 AACAAAAAGG-GAAAA-AAGAA-AAAAAGA-AAAGA
10463 AACAAAAA
1 AACAAAAA
10471 TAAAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 10 0.28
33 3 0.08
34 14 0.39
35 9 0.25
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (32 bp):
AACAAAAAGGGAAAAAAGAAAAAAAGAAAAGA
Found at i:12022 original size:36 final size:37
Alignment explanation
Indices: 11975--12079 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 37
11965 GTGCTCGCCA
11975 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-CT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
* *
12011 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAATTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
* * *
12048 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
12080 TAAACATTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 33 0.53
37 29 0.47
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
Found at i:13015 original size:106 final size:105
Alignment explanation
Indices: 12733--13597 Score: 912
Period size: 106 Copynumber: 8.3 Consensus size: 105
12723 TCGAGAGTGG
** * *
12733 ATTTCAACTTCACAATGAAGGATATTGGACTTC-AGACAACGCAAGCTCAACTTCACAGCGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAGCGAAGG
* * * *
12797 GGCGGCTGACTGTCGACAAGCAATTT-C-G-----GAGCCA
65 GACGGCTGATTGTCAACAAACAATTTCCAGTTTCAGAGCCA
*
12831 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
* * *
12896 ACGGCTGGTTGTCAATAAACAATTTCCCAGTTTCAGGGCCA
66 ACGGCTGATTGTCAACAAACAATTT-CCAGTTTCAGAGCCA
* * * *
12937 ATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
* * *
13002 GCGGCTGACTGTCAACAAGCAATTT-C-G-----GAGCCA
66 ACGGCTGATTGTCAACAAACAATTTCCAGTTTCAGAGCCA
*
13035 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
* * * *
13100 ACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCG
66 ACGGCTGATTGTCAACAAACAATTT-CCAGTTTCAGAGCCA
* * * * *
13141 ATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAGCGA
* * ** *
13205 AGGGACGGCTGGTTGTCAACAAACAACTTTTCAGTTTCA-TCCGCG
62 AGGGACGGCTGATTGTCAACAAACAA-TTTCCAGTTTCAGAGC-CA
* * * *
13250 ATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAGCGA
* * *
13314 AGGGACGGCTGATTGTCAACAAACATTTTTCAAATTTCAGAGCCA
62 AGGGACGGCTGATTGTCAACAAACA-ATTTCCAGTTTCAGAGCCA
** *
13359 ATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
* *
13424 ACGGCTGATTGTCAAC-AA-GATTT-C-G-TTCAGAGTCA
66 ACGGCTGATTGTCAACAAACAATTTCCAGTTTCAGAGCCA
* * * * *
13459 ATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCAAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
* * * * *
13524 GCGACTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCA
66 ACGGCTGATTGTCAACAAACAATTT-CCAGTTTCAGAGCCA
* *
13565 ATTTCAACTTCACATCGGAGGATATTGGACTCG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
13598 GAACAATATT
Statistics
Matches: 651, Mismatches: 84, Indels: 56
0.82 0.11 0.07
Matches are distributed among these distances:
97 2 0.00
98 162 0.25
100 81 0.12
101 3 0.00
102 4 0.01
103 4 0.01
104 2 0.00
105 4 0.01
106 199 0.31
107 2 0.00
108 3 0.00
109 180 0.28
110 5 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (105 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
ACGGCTGATTGTCAACAAACAATTTCCAGTTTCAGAGCCA
Found at i:13022 original size:204 final size:205
Alignment explanation
Indices: 12733--13594 Score: 1000
Period size: 204 Copynumber: 4.1 Consensus size: 205
12723 TCGAGAGTGG
** * * *
12733 ATTTCAACTTCACAATGAAGGATATTGGACTTC-AGACAACGCAAGCTCAACTTCACAGCGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGAC-CCGAGACAACACAAGCTCAACTTCACAACGAAGG
* *
12797 GGCGGCTGACTGTCGACAAGCAATTTCG-GAGCCAATCTCAACTTCACAGCGAAGGATATTGGAC
65 GACGGCTGACTGTCAACAAGCAATTTCGTGAGCCAATCTCAACTTCACAGCGAAGGATATTGGAC
* * *
12861 TCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAATAAACAATTTCCCAG
130 TCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGATTGTCAACAAACAATTTCCCAA
* *
12926 TTTCAGGGCCA
195 TTCCAGAGCCA
* * *
12937 ATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACAACGAAGGG
*
13002 GCGGCTGACTGTCAACAAGCAATTTCG-GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACT
66 ACGGCTGACTGTCAACAAGCAATTTCGTGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACT
*
13066 CGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
131 CGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGATTGTCAACAAACAATTTCCCAAT
*
13131 TCCAGAGCCG
196 TCCAGAGCCA
* * * *
13141 ATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACCCGAGACAACACAAGCTCAACTTCACAACGA
** * * * * * * *
13205 AGGGACGGCTGGTTGTCAACAAACAACTTTTCAGTTTCATCCGCGATTTCAACTCCAC-GACGGA
62 AGGGACGGCTGACTGTCAACAAGCAA--TTTC-G--TGA-GC-CAATCTCAACTTCACAG-CGAA
* *
13269 GGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC
119 GGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGATTGTCAAC
* * * *
13334 AAACATTTTTCAAATTTCAGAGCCA
181 AAACAATTTCCCAATTCCAGAGCCA
** * *
13359 ATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACAACGAAGGG
* * * * *
13424 ACGGCTGATTGTCAACAAG--ATTTCGTTCAGAGTCAATTTCATCTTCACAGCGAAGGATATTAG
66 ACGGCTGACTGTCAACAAGCAATTTCG-T--GAGCCAATCTCAACTTCACAGCGAAGGATATTGG
* * * * * *
13487 ACTCGAGACAGCACAAGCTCAACTTCACAGCAAAGGGGCGACTGACTGTCAACAAACAATTTCCC
128 ACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGATTGTCAACAAACAATTTCCC
* *
13552 AGTTCCAGAACCA
193 AATTCCAGAGCCA
* *
13565 ATTTCAACTTCACATCGGAGGATATTGGAC
1 ATTTCAACTTCACAGCGAAGGATATTGGAC
13595 TCGGAACAAT
Statistics
Matches: 567, Mismatches: 70, Indels: 40
0.84 0.10 0.06
Matches are distributed among these distances:
203 2 0.00
204 212 0.37
206 93 0.16
207 52 0.09
209 27 0.05
210 3 0.01
211 5 0.01
213 2 0.00
214 2 0.00
215 74 0.13
216 2 0.00
217 2 0.00
218 90 0.16
219 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (205 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACAACGAAGGG
ACGGCTGACTGTCAACAAGCAATTTCGTGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACT
CGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGATTGTCAACAAACAATTTCCCAAT
TCCAGAGCCA
Found at i:14122 original size:35 final size:35
Alignment explanation
Indices: 14058--14157 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 35
14048 TTTCGTCCTA
* *
14058 CTAGGATTCAAACTCTCAAAAATATGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
14095 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
14130 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
14158 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.38
36 18 0.33
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:14321 original size:12 final size:12
Alignment explanation
Indices: 14304--14333 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
14294 AGGTAGCATC
14304 TTTTTTTATCTT
1 TTTTTTTATCTT
14316 TTTTTTTATCTT
1 TTTTTTTATCTT
14328 TTTTTT
1 TTTTTT
14334 GCATGTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTATCTT
Found at i:14887 original size:15 final size:14
Alignment explanation
Indices: 14868--14956 Score: 74
Period size: 15 Copynumber: 6.1 Consensus size: 14
14858 TTTTCTATGC
14868 TTTA-TTTATTTATT
1 TTTATTTTATTT-TT
14882 TATTATTTTATTTTAT
1 T-TTATTTTATTTT-T
14898 TTTATTTTATTTCTT
1 TTTATTTTATTT-TT
* ***
14913 TTTATTTTGGTTGAA
1 TTTATTTT-ATTTTT
*
14928 TTTATTTT-TTTAT
1 TTTATTTTATTTTT
14941 TTTATTTTATTTTT
1 TTTATTTTATTTTT
14955 TT
1 TT
14957 ATATCTAACA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
13 11 0.18
14 7 0.11
15 32 0.52
16 12 0.19
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTATTTTATTTTT
Found at i:14894 original size:5 final size:5
Alignment explanation
Indices: 14884--14953 Score: 74
Period size: 5 Copynumber: 14.4 Consensus size: 5
14874 TATTTATTTA
** * *
14884 TTATT TTATT TTATT TTATT TTATT TCT-TT TTATT TTGGT TGAAT TTA-T
1 TTATT TTATT TTATT TTATT TTATT T-TATT TTATT TTATT TTATT TTATT
14933 TT-TT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TT
14954 TTTATATCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
4 7 0.13
5 47 0.85
6 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.04, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:14902 original size:30 final size:30
Alignment explanation
Indices: 14796--14953 Score: 92
Period size: 30 Copynumber: 5.0 Consensus size: 30
14786 TCTTTATGTG
14796 TATTTTATTTATTTATATATATTACCTTTTTATTT
1 TATTTTATTTATTTAT-T-TATTA---TTTTATTT
* * *
14831 TATATTTATACTA-TTATTTACTATCATTT-TTC
1 TAT-TTTAT-TTATTTATTTATTAT--TTTATTT
14863 TATGCTTTATTTATTTATTTATTATTTTATTT
1 TAT--TTTATTTATTTATTTATTATTTTATTT
* **
14895 TATTTTATTTTATTTCTTT-TTATTTTGGTT
1 TATTTTA-TTTATTTATTTATTATTTTATTT
* * *
14925 GAATTTATTTTTTTA-TT-TTATTTTATTT
1 TATTTTATTTATTTATTTATTATTTTATTT
14953 T
1 T
14954 TTTATATCTA
Statistics
Matches: 98, Mismatches: 17, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
28 11 0.11
29 6 0.06
30 18 0.18
31 14 0.14
32 12 0.12
33 18 0.18
34 4 0.04
35 4 0.04
36 9 0.09
37 2 0.02
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (30 bp):
TATTTTATTTATTTATTTATTATTTTATTT
Found at i:27214 original size:2 final size:2
Alignment explanation
Indices: 27207--27239 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27197 ACAGAGAAAA
27207 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
27240 ACTTATCCTA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:28922 original size:48 final size:48
Alignment explanation
Indices: 28870--29061 Score: 289
Period size: 48 Copynumber: 4.0 Consensus size: 48
28860 AAGAACTTCC
28870 ACTCCAACTGCAAGAGGAGCCAGTCATACTTCAAGGGGAGTCAGTCCA
1 ACTCCAACTGCAAGAGGAGCCAGTCATACTTCAAGGGGAGTCAGTCCA
* *
28918 ACTCCAACTGCGAGAGGATCCAGTCATACTTCAAGGGGAGTCAGTCCA
1 ACTCCAACTGCAAGAGGAGCCAGTCATACTTCAAGGGGAGTCAGTCCA
*
28966 ACTCCAACTGCAAGAGGAGCCAGT-AGTACTTCAAGGGGAGTCGGTCCA
1 ACTCCAACTGCAAGAGGAGCCAGTCA-TACTTCAAGGGGAGTCAGTCCA
* * * *
29014 ACTCCAACTGCAAGGGGAGTCAGTCCA-ACTCCAAGGGTAGTCAGTCCA
1 ACTCCAACTGCAAGAGGAGCCAGT-CATACTTCAAGGGGAGTCAGTCCA
29062 GCTCGGATGA
Statistics
Matches: 131, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
47 1 0.01
48 129 0.98
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.17
Consensus pattern (48 bp):
ACTCCAACTGCAAGAGGAGCCAGTCATACTTCAAGGGGAGTCAGTCCA
Found at i:28979 original size:27 final size:27
Alignment explanation
Indices: 28901--29047 Score: 122
Period size: 27 Copynumber: 5.9 Consensus size: 27
28891 AGTCATACTT
28901 CAAGGGGAGTCAGTCCAACTCCAACTG
1 CAAGGGGAGTCAGTCCAACTCCAACTG
* * *
28928 CGAGAGGA-TCCAGT-C-A-T---ACTT
1 CAAGGGGAGT-CAGTCCAACTCCAACTG
28949 CAAGGGGAGTCAGTCCAACTCCAACTG
1 CAAGGGGAGTCAGTCCAACTCCAACTG
* * * *
28976 CAAGAGGAGCCAGT---AGT---ACTT
1 CAAGGGGAGTCAGTCCAACTCCAACTG
*
28997 CAAGGGGAGTCGGTCCAACTCCAACTG
1 CAAGGGGAGTCAGTCCAACTCCAACTG
29024 CAAGGGGAGTCAGTCCAACTCCAA
1 CAAGGGGAGTCAGTCCAACTCCAA
29048 GGGTAGTCAG
Statistics
Matches: 90, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
21 27 0.30
22 2 0.02
23 1 0.01
24 6 0.07
25 1 0.01
26 2 0.02
27 51 0.57
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (27 bp):
CAAGGGGAGTCAGTCCAACTCCAACTG
Found at i:29042 original size:21 final size:21
Alignment explanation
Indices: 29016--29061 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
29006 TCGGTCCAAC
*
29016 TCCAACTGCAAGGGGAGTCAG
1 TCCAACTCCAAGGGGAGTCAG
*
29037 TCCAACTCCAAGGGTAGTCAG
1 TCCAACTCCAAGGGGAGTCAG
29058 TCCA
1 TCCA
29062 GCTCGGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (21 bp):
TCCAACTCCAAGGGGAGTCAG
Found at i:29179 original size:84 final size:84
Alignment explanation
Indices: 29033--29195 Score: 254
Period size: 84 Copynumber: 1.9 Consensus size: 84
29023 GCAAGGGGAG
* * * * * *
29033 TCAGTCCAACTCCAAGGGTAGTCAGTCCAGCTCGGATGAGGATATCCACCTCATCGAGTCAATCT
1 TCAGTCCAACTCCAAGGATAGTCAGTCCAACTCGGATGAGGACATCCACCTCATCCAATCAATCC
29098 CATAGCTCAACATCAGTTC
66 CATAGCTCAACATCAGTTC
* *
29117 TCAGTTCAACTCCAAGGATAGTCAGTCCAACTCGGATTAGGACATCCACCTCATCCAATCAATCC
1 TCAGTCCAACTCCAAGGATAGTCAGTCCAACTCGGATGAGGACATCCACCTCATCCAATCAATCC
29182 CATAGCTCAACATC
66 CATAGCTCAACATC
29196 CACCTCATCC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.23
Consensus pattern (84 bp):
TCAGTCCAACTCCAAGGATAGTCAGTCCAACTCGGATGAGGACATCCACCTCATCCAATCAATCC
CATAGCTCAACATCAGTTC
Found at i:29200 original size:33 final size:33
Alignment explanation
Indices: 29158--29221 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
29148 TCGGATTAGG
29158 ACATCCACCTCATCCAATCAATCCCATAGCTCA
1 ACATCCACCTCATCCAATCAATCCCATAGCTCA
**
29191 ACATCCACCTCATCCAATCAATTTCATAGCT
1 ACATCCACCTCATCCAATCAATCCCATAGCT
29222 TAACTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.39, G:0.03, T:0.25
Consensus pattern (33 bp):
ACATCCACCTCATCCAATCAATCCCATAGCTCA
Found at i:29235 original size:117 final size:117
Alignment explanation
Indices: 29076--29309 Score: 312
Period size: 117 Copynumber: 2.0 Consensus size: 117
29066 GGATGAGGAT
* * *
29076 ATCCACCTCATCGAGTCAATCTCATAGCTCAACATCAGTTCTCAGTTCAACTCCAAG-GATAGTC
1 ATCCACCTCATCCAATCAATCTCATAGCTCAACATCAATTCTCAGTTCAACTCCAAGAG-TAGTC
* * *
29140 AGTCCAACTCGGAT-TAGGACATCCACCTCATCCAA-TCAATCCCATAGCTCAAC
65 AGTCCAACTCGAATGAAGG-CATCCACCTCA-CAAAGTCAATCCCATAGCTCAAC
* * * *
29193 ATCCACCTCATCCAATCAATTTCATAGCTTAACTTCAATTCTCAGTTCAACTCCAATAGTAGTCA
1 ATCCACCTCATCCAATCAATCTCATAGCTCAACATCAATTCTCAGTTCAACTCCAAGAGTAGTCA
* *
29258 GTCCCACTCGAATGAAGGCATCCACCTCAGAAAGTCAATCCCATAGCTCAAC
66 GTCCAACTCGAATGAAGGCATCCACCTCACAAAGTCAATCCCATAGCTCAAC
29310 TTCAGTTCTT
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
116 2 0.02
117 96 0.94
118 4 0.04
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.25
Consensus pattern (117 bp):
ATCCACCTCATCCAATCAATCTCATAGCTCAACATCAATTCTCAGTTCAACTCCAAGAGTAGTCA
GTCCAACTCGAATGAAGGCATCCACCTCACAAAGTCAATCCCATAGCTCAAC
Found at i:29345 original size:84 final size:84
Alignment explanation
Indices: 29215--29393 Score: 204
Period size: 84 Copynumber: 2.1 Consensus size: 84
29205 CAATCAATTT
* *
29215 CATAGCTTAACTTCAATTCTCAGTTCAACTCCAATAGTAGTCAGTCC-CACTC-GAATGAAGG-C
1 CATAGCTCAACTTCAATTCTCAGTTCAACTACAATAGTAGTCAGTCCAC-CTCAG-ATG-AGGAC
29277 ATCCACCTCAGAAAGTCAATCC
63 ATCCACCTCAGAAAGTCAATCC
* * * *
29299 CATAGCTCAACTTCAGTTCTTAGTTCAACTACAA-GGCTAGTTAGTCCACCTCAGATGAGGACAT
1 CATAGCTCAACTTCAATTCTCAGTTCAACTACAATAG-TAGTCAGTCCACCTCAGATGAGGACAT
***
29363 CCACCTCATCCAGTCAATCC
65 CCACCTCAGAAAGTCAATCC
*
29383 CATTGCTCAAC
1 CATAGCTCAAC
29394 ATCCGCCTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
83 4 0.05
84 75 0.93
85 2 0.02
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (84 bp):
CATAGCTCAACTTCAATTCTCAGTTCAACTACAATAGTAGTCAGTCCACCTCAGATGAGGACATC
CACCTCAGAAAGTCAATCC
Found at i:29384 original size:201 final size:201
Alignment explanation
Indices: 29033--29413 Score: 541
Period size: 201 Copynumber: 1.9 Consensus size: 201
29023 GCAAGGGGAG
* * * *** *
29033 TCAGTCCAACTCCAAGGGTAGTCAGTCCAGCTCGGATGAGGATATCCACCTCATCGAGTCAATCT
1 TCAGTCCAACTCCAAGAGTAGTCAGTCCAGCTCGAATGAGGACATCCACCTCAGAAAGTCAATCC
* * *
29098 CATAGCTCAACATCAGTTCTCAGTTCAACTCCAAGGATAGTCAGTCCAACTCGGATTAGGACATC
66 CATAGCTCAACATCAGTTCTCAGTTCAACTACAAGGATAGTCAGTCCAACTCAGATGAGGACATC
29163 CACCTCATCCAATCAATCCCATAGCTCAACATCCACCTCATCCAATCAATTTCATAGCTTAACTT
131 CACCTCATCCAATCAATCCCATAGCTCAACATCCACCTCATCCAATCAATTTCATAGCTTAACTT
29228 CAATTC
196 CAATTC
* *
29234 TCAGTTCAACTCCAATAGTAGTCAGTCCCA-CTCGAATGAAGG-CATCCACCTCAGAAAGTCAAT
1 TCAGTCCAACTCCAAGAGTAGTCAGT-CCAGCTCGAATG-AGGACATCCACCTCAGAAAGTCAAT
* * * * *
29297 CCCATAGCTCAACTTCAGTTCTTAGTTCAACTACAAGGCTAGTTAGTCCACCTCAGATGAGGACA
64 CCCATAGCTCAACATCAGTTCTCAGTTCAACTACAAGGATAGTCAGTCCAACTCAGATGAGGACA
* * * *
29362 TCCACCTCATCCAGTCAATCCCATTGCTCAACATCCGCCTCATCCAGTCAAT
129 TCCACCTCATCCAATCAATCCCATAGCTCAACATCCACCTCATCCAATCAAT
29414 CCCATTGCTC
Statistics
Matches: 157, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
201 151 0.96
202 6 0.04
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.25
Consensus pattern (201 bp):
TCAGTCCAACTCCAAGAGTAGTCAGTCCAGCTCGAATGAGGACATCCACCTCAGAAAGTCAATCC
CATAGCTCAACATCAGTTCTCAGTTCAACTACAAGGATAGTCAGTCCAACTCAGATGAGGACATC
CACCTCATCCAATCAATCCCATAGCTCAACATCCACCTCATCCAATCAATTTCATAGCTTAACTT
CAATTC
Found at i:29478 original size:66 final size:66
Alignment explanation
Indices: 29359--29492 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 66
29349 TCAGATGAGG
* * *
29359 ACATCCACCTCATCCAGTCAATCCCATTGCTCAACATCCGCCTCATCCAGTCAATCCCAT-TGCT
1 ACATCCACCTCATCCAGCCAATCCCATAGCTCAACATCCACCTCATCCAGTCAATCCCATGT-CT
29423 CA
65 CA
* * ** *
29425 ACATCCGCCTCATCCAGCCAGTCCCATAGCTCAACATCCACCTCATCTTGTCAATTCCATGTCTC
1 ACATCCACCTCATCCAGCCAATCCCATAGCTCAACATCCACCTCATCCAGTCAATCCCATGTCTC
29490 A
66 A
29491 AC
1 AC
29493 TTCAGTTCTC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
66 58 0.98
67 1 0.02
ACGTcount: A:0.25, C:0.42, G:0.08, T:0.25
Consensus pattern (66 bp):
ACATCCACCTCATCCAGCCAATCCCATAGCTCAACATCCACCTCATCCAGTCAATCCCATGTCTC
A
Found at i:29492 original size:33 final size:33
Alignment explanation
Indices: 29359--29471 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
29349 TCAGATGAGG
29359 ACATCCACCTCATCCAGTCAATCCCATTGCTCA
1 ACATCCACCTCATCCAGTCAATCCCATTGCTCA
*
29392 ACATCCGCCTCATCCAGTCAATCCCATTGCTCA
1 ACATCCACCTCATCCAGTCAATCCCATTGCTCA
* * * *
29425 ACATCCGCCTCATCCAGCCAGTCCCATAGCTCA
1 ACATCCACCTCATCCAGTCAATCCCATTGCTCA
29458 ACATCCACCTCATC
1 ACATCCACCTCATC
29472 TTGTCAATTC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.26, C:0.44, G:0.08, T:0.22
Consensus pattern (33 bp):
ACATCCACCTCATCCAGTCAATCCCATTGCTCA
Found at i:29576 original size:84 final size:84
Alignment explanation
Indices: 29458--29642 Score: 257
Period size: 84 Copynumber: 2.2 Consensus size: 84
29448 CCATAGCTCA
** * * *
29458 ACATCCACCTCATCTTGTCAATTCCATGTCTCAACTTCAGTTCTCAGTTCAACTCCGAGAGTAGT
1 ACATCCACCTCATCAAGTCAATCCCATGTCTCAACTTCAGTTCTCAGTTCAACTCCAAGAGTACT
* *
29523 TAGTCCAATTC-GAGTGAGG
66 TAGTCCAACTCGGA-CGAGG
* *
29542 ACATCCACCTCATCAAGTCAATCCCATAGT-TCAACTTCAGTTGTCAGTTCAACTCCAAGGGTAC
1 ACATCCACCTCATCAAGTCAATCCCAT-GTCTCAACTTCAGTTCTCAGTTCAACTCCAAGAGTAC
29606 TTAGTCCAACTCGGACGAGG
65 TTAGTCCAACTCGGACGAGG
29626 ACATCCACCTCATCAAG
1 ACATCCACCTCATCAAG
29643 AAGAACCCAT
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 86 0.96
85 4 0.04
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (84 bp):
ACATCCACCTCATCAAGTCAATCCCATGTCTCAACTTCAGTTCTCAGTTCAACTCCAAGAGTACT
TAGTCCAACTCGGACGAGG
Found at i:29715 original size:21 final size:21
Alignment explanation
Indices: 29689--29734 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29679 TCTTGGTTCT
*
29689 ACTCCAAGAGGT-GTCAGTCCG
1 ACTCCAAG-GGTAGGCAGTCCG
*
29710 ACTCCAAGGGTAGGCAGTCCT
1 ACTCCAAGGGTAGGCAGTCCG
29731 ACTC
1 ACTC
29735 GGATGAGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.20
Consensus pattern (21 bp):
ACTCCAAGGGTAGGCAGTCCG
Found at i:29843 original size:84 final size:84
Alignment explanation
Indices: 29710--29875 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 84
29700 TGTCAGTCCG
* *
29710 ACTCCAAGGGTAGGCAGTCCTACTCGGATGAGAACATCCACCTCTTCGAGTCAATTCCATAGCTC
1 ACTCCAAGGGTAGGCAGTCCTACTCGGATGAGAACATCCACCTCATCGAGTCAATCCCATAGCTC
29775 AACTTCAGTTCTCAGTTCA
66 AACTTCAGTTCTCAGTTCA
* * * *
29794 ACTCCAAGGGTAGTCAGTCCTACTCGGATGAGGATATCCACCTCATCGAGTCAATCCCATGGCTC
1 ACTCCAAGGGTAGGCAGTCCTACTCGGATGAGAACATCCACCTCATCGAGTCAATCCCATAGCTC
29859 AACTTCAGTTCTCAGTT
66 AACTTCAGTTCTCAGTT
29876 TTGTCACAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (84 bp):
ACTCCAAGGGTAGGCAGTCCTACTCGGATGAGAACATCCACCTCATCGAGTCAATCCCATAGCTC
AACTTCAGTTCTCAGTTCA
Found at i:32112 original size:29 final size:29
Alignment explanation
Indices: 32070--32144 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
32060 AACCCAACCA
**
32070 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
32099 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
32128 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
32145 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:32150 original size:29 final size:29
Alignment explanation
Indices: 32071--32158 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
32061 ACCCAACCAT
* * ****
32071 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
32100 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
32129 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
32158 A
1 A
32159 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:32388 original size:10 final size:10
Alignment explanation
Indices: 32375--32432 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
32365 CAGGGCATGG
32375 ATGGGCGTGC
1 ATGGGCGTGC
32385 ATGGGCGTGCTCC
1 ATGGGCGTG---C
* * *
32398 TTTGGCGAG-
1 ATGGGCGTGC
32407 ATGGGCGTGC
1 ATGGGCGTGC
32417 ATGGGCGTGC
1 ATGGGCGTGC
32427 ATGGGC
1 ATGGGC
32433 ATGGAGGTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 6 0.16
10 25 0.66
13 7 0.18
ACGTcount: A:0.10, C:0.21, G:0.47, T:0.22
Consensus pattern (10 bp):
ATGGGCGTGC
Found at i:32487 original size:29 final size:29
Alignment explanation
Indices: 32452--32538 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
32442 GTTGGCTGGT
*
32452 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
32481 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
32510 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
32539 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:46536 original size:18 final size:18
Alignment explanation
Indices: 46489--46530 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
46479 TTCATGAATG
46489 CATACATGCATATACATA
1 CATACATGCATATACATA
46507 CATACATGCATATACATA
1 CATACATGCATATACATA
46525 CATACA
1 CATACA
46531 GTCATAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (18 bp):
CATACATGCATATACATA
Found at i:51151 original size:23 final size:23
Alignment explanation
Indices: 51092--51152 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
51082 ACATATTATA
* *
51092 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCGACG
** *
51115 CAGCACTACGGTGCAATTCGACG
1 TGGCACTTCGGTGCAATTCGACG
*
51138 TGGCACTTCAGTGCA
1 TGGCACTTCGGTGCA
51153 TTTATACGAG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCGACG
Found at i:57218 original size:21 final size:21
Alignment explanation
Indices: 57192--57236 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57182 GATTTCTGGG
* *
57192 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
57213 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
57234 CAA
1 CAA
57237 ACAACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:57837 original size:18 final size:18
Alignment explanation
Indices: 57814--57848 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57804 CTAGGAGATT
57814 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
57832 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
57849 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:57934 original size:21 final size:22
Alignment explanation
Indices: 57905--57948 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
57895 GTTGTATGAT
57905 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
57926 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
57948 A
1 A
57949 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:58179 original size:2 final size:2
Alignment explanation
Indices: 58172--58215 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
58162 GAACATGTGA
58172 AT AT AT 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 AT AT AT
58214 AT
1 AT
58216 GTCTAAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59323 original size:149 final size:149
Alignment explanation
Indices: 58860--59312 Score: 861
Period size: 149 Copynumber: 3.0 Consensus size: 149
58850 GAGTCGAGGG
* *
58860 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
58925 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
58990 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
59009 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
59074 ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
59139 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
59158 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
59223 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
59288 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
59307 TCTACG
1 TCTACG
59313 GGGCACTTCG
Statistics
Matches: 298, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 298 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:59335 original size:23 final size:23
Alignment explanation
Indices: 59291--59335 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
59281 ATCATTATAT
*
59291 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
59314 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
59336 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:63194 original size:18 final size:18
Alignment explanation
Indices: 63171--63205 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
63161 CTAGGAGATT
63171 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
63189 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
63206 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:63291 original size:21 final size:22
Alignment explanation
Indices: 63262--63305 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
63252 GTTGTATGAT
63262 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
63283 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
63305 A
1 A
63306 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:63539 original size:2 final size:2
Alignment explanation
Indices: 63532--63557 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63522 GAACATGTGA
63532 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
63558 GTCTAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64664 original size:149 final size:149
Alignment explanation
Indices: 64201--64653 Score: 843
Period size: 149 Copynumber: 3.0 Consensus size: 149
64191 GAGTCGAGGG
* * *
64201 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTTTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
64266 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
64331 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
64350 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
64415 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
*
64480 TATGTCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
64499 TCTACGCGGTTCTTCGGGTCATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
64564 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
64629 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
64648 TCTACG
1 TCTACG
64654 GGGCACTTCG
Statistics
Matches: 296, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 296 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:64676 original size:23 final size:23
Alignment explanation
Indices: 64632--64676 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
64622 ATCATTATAT
*
64632 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
64655 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
64677 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:67255 original size:2 final size:2
Alignment explanation
Indices: 67248--67312 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
67238 CAGCTTAAGC
67248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67290 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
67313 TAATCAATTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67418 original size:33 final size:33
Alignment explanation
Indices: 67380--67456 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
67370 ATTTAACAAA
67380 AAGGGGGAGAAATATTAAGTGTTAAAATATTTT
1 AAGGGGGAGAAATATTAAGTGTTAAAATATTTT
*
67413 AAGGGGGAGAAATATTAAGTGTTAAAATGTTTT
1 AAGGGGGAGAAATATTAAGTGTTAAAATATTTT
*
67446 AAAGGGGAGAA
1 AAGGGGGAGAA
67457 GTGTTAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (33 bp):
AAGGGGGAGAAATATTAAGTGTTAAAATATTTT
Found at i:67955 original size:64 final size:64
Alignment explanation
Indices: 67850--68008 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 64
67840 GGAATAAATT
* * * * *
67850 AAACATTGAATGCATTTCATGCAACGATGCA-CATACTATGCATCGATGCACTCAGAG-T-TTTA
1 AAACATCGAATGCATTTCATACATCGATGCATCA-GCCATGCATCGATGCACTCAG-GCTATTT-
67912 TG
63 TG
* *
67914 AAAACATCGAATGCATTT-GTACATCGATGCATCAGCCATGCATCGATGCACTCTGGCTATTTTG
1 -AAACATCGAATGCATTTCATACATCGATGCATCAGCCATGCATCGATGCACTCAGGCTATTTTG
*
67978 AAACATCGAATGCATTTCATGCATCGATGCA
1 AAACATCGAATGCATTTCATACATCGATGCA
68009 CTAAGGGTCC
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
63 18 0.22
64 42 0.52
65 21 0.26
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (64 bp):
AAACATCGAATGCATTTCATACATCGATGCATCAGCCATGCATCGATGCACTCAGGCTATTTTG
Found at i:83539 original size:15 final size:16
Alignment explanation
Indices: 83501--83541 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
83491 ATTCAGTCTC
* *
83501 TGAATCATTCAACATT
1 TGAATCATTCAAAACT
83517 TGAATCATTCAAAACT
1 TGAATCATTCAAAACT
83533 T-AATCATTC
1 TGAATCATTC
83542 TGAAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAAAACT
Found at i:83855 original size:23 final size:23
Alignment explanation
Indices: 83786--83914 Score: 123
Period size: 24 Copynumber: 5.5 Consensus size: 23
83776 CATTTAAATT
* *
83786 ATAAACAAACACAATTGAACGAAC
1 ATAAACGAACACAA-TAAACGAAC
* *
83810 ATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACACA-ATAAACGAAC
*
83834 ATAAACGAACACAATAAACGAAT
1 ATAAACGAACACAATAAACGAAC
* * *
83857 GTAAACAAACACAAATAAATGAAC
1 ATAAACGAACAC-AATAAACGAAC
* * *
83881 GTAAACGAACACGATAAATGAAC
1 ATAAACGAACACAATAAACGAAC
*
83904 GTAAACGAACA
1 ATAAACGAACA
83915 TAAATGAAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
23 39 0.43
24 51 0.57
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.12
Consensus pattern (23 bp):
ATAAACGAACACAATAAACGAAC
Found at i:83886 original size:47 final size:47
Alignment explanation
Indices: 83786--83919 Score: 133
Period size: 47 Copynumber: 2.8 Consensus size: 47
83776 CATTTAAATT
* * * * * **
83786 ATAAACAAACACAATTGAACGAACATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACACAA-TAAACGAACGTAAACAAACACAAATAAACGAAC
* *
83834 ATAAACGAACACAATAAACGAATGTAAACAAACACAAATAAATGAAC
1 ATAAACGAACACAATAAACGAACGTAAACAAACACAAATAAACGAAC
* * * * *
83881 GTAAACGAACACGATAAATGAACGTAAACGAACATAAAT
1 ATAAACGAACACAATAAACGAACGTAAACAAACACAAAT
83920 GAAAATAGAT
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
47 58 0.82
48 13 0.18
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.13
Consensus pattern (47 bp):
ATAAACGAACACAATAAACGAACGTAAACAAACACAAATAAACGAAC
Found at i:84123 original size:14 final size:14
Alignment explanation
Indices: 84086--84129 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
84076 GATTGGGCTA
84086 AACATAAATGAACG
1 AACATAAATGAACG
*
84100 CACAT--A--AACG
1 AACATAAATGAACG
84110 AACATAAATGAACG
1 AACATAAATGAACG
84124 AACATA
1 AACATA
84130 TTACCAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 8 0.33
12 2 0.08
14 14 0.58
ACGTcount: A:0.57, C:0.18, G:0.11, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACG
Done.