Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003043.1 Hibiscus syriacus cultivar Beakdansim tig00006333_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: 78240
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:16440 original size:29 final size:28
Alignment explanation
Indices: 16397--16527 Score: 101
Period size: 29 Copynumber: 4.7 Consensus size: 28
16387 ATCTACTGTA
* *
16397 TTTTTCTTCAATGTTCGAACCAAATCAGT
1 TTTTTCTGCACTGTTCGAACCAAATCA-T
** *
16426 TTTTTCTGCACTGTTCTG-TTCGAA-C--
1 TTTTTCTGCACTGTTC-GAACCAAATCAT
* * *
16451 -TTTTCAGCACAGTTCGAACCAAGTCTAT
1 TTTTTCTGCACTGTTCGAACCAAATC-AT
*
16479 TTTTTCTGCACTGTTCGAACCAAGTCAGT
1 TTTTTCTGCACTGTTCGAACCAAATCA-T
*
16508 TTTTTTTGCACTGTTCGAAC
1 TTTTTCTGCACTGTTCGAAC
16528 AATGTATTTC
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
23 1 0.01
24 15 0.19
25 1 0.01
28 2 0.03
29 60 0.75
30 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (28 bp):
TTTTTCTGCACTGTTCGAACCAAATCAT
Found at i:16729 original size:13 final size:14
Alignment explanation
Indices: 16713--16760 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
16703 TAAAAAAAAA
16713 AAAAAT-AAAATTG
1 AAAAATAAAAATTG
16726 -AAAATAAAAATTG
1 AAAAATAAAAATTG
16739 AACAAATGAAAAA-T-
1 AA-AAAT-AAAAATTG
16753 AAAAATAA
1 AAAAATAA
16761 TAATGGGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 7 0.23
13 11 0.35
14 3 0.10
15 5 0.16
16 5 0.16
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAAATAAAAATTG
Found at i:16735 original size:6 final size:6
Alignment explanation
Indices: 16698--16760 Score: 51
Period size: 6 Copynumber: 10.3 Consensus size: 6
16688 GGCGTACCTA
* *
16698 AAAAAT -AAAA- AAAAA- AAAAAT AAAATT GAAAAT AAAAATT GAACAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA-T -AA-AAAT
16746 GAAAAAT AAAAAT AA
1 -AAAAAT AAAAAT AA
16761 TAATGGGTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
5 13 0.27
6 21 0.44
7 5 0.10
8 6 0.12
9 3 0.06
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:18191 original size:21 final size:21
Alignment explanation
Indices: 18163--18215 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18153 TCGACTTTGG
*
18163 AACTTTTCTTGGGATGCAACT
1 AACTTTTCTTGGGATGCAACC
* * * *
18184 AGCTTTTCCTAGGATGTAACC
1 AACTTTTCTTGGGATGCAACC
18205 AACTTTTCTTG
1 AACTTTTCTTG
18216 TGATATTGCT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
AACTTTTCTTGGGATGCAACC
Found at i:19671 original size:8 final size:8
Alignment explanation
Indices: 19643--19691 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
19633 GATAGAACAA
19643 AATAAAAT
1 AATAAAAT
19651 AA-AAAA-
1 AATAAAAT
19657 AGA-AAAAT
1 A-ATAAAAT
19665 AATAAAAT
1 AATAAAAT
*
19673 AATAAACT
1 AATAAAAT
19681 AATAAAAT
1 AATAAAAT
19689 AAT
1 AAT
19692 GATTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 1 0.03
7 10 0.28
8 25 0.69
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (8 bp):
AATAAAAT
Found at i:19683 original size:16 final size:15
Alignment explanation
Indices: 19647--19691 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
19637 GAACAAAATA
* *
19647 AAATAAAAAAAGAA-
1 AAATAATAAAATAAT
19661 AAATAATAAAATAAT
1 AAATAATAAAATAAT
19676 AAACTAATAAAATAAT
1 AAA-TAATAAAATAAT
19692 GATTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 12 0.44
15 3 0.11
16 12 0.44
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:22338 original size:19 final size:18
Alignment explanation
Indices: 22310--22345 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22300 CATTTTCCTT
22310 TTTCACTTTCATATTCAC
1 TTTCACTTTCATATTCAC
*
22328 TTTCACATTTCATTTTCA
1 TTTCAC-TTTCATATTCA
22346 TAATCCATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTCACTTTCATATTCAC
Found at i:26443 original size:25 final size:25
Alignment explanation
Indices: 26385--26510 Score: 175
Period size: 25 Copynumber: 5.1 Consensus size: 25
26375 TGCACAATAT
* *
26385 GCAGTTGTAACTGCTTAAACTGAAC
1 GCAGTCGTAACTGCTAAAACTGAAC
* * * *
26410 ACAGCCGTAACTGCTAAAATTAAAC
1 GCAGTCGTAACTGCTAAAACTGAAC
*
26435 GCAGTCGTAACTGTTAAAACTGAAC
1 GCAGTCGTAACTGCTAAAACTGAAC
26460 GCAGTCGTAACTGC-AAAACTGAAC
1 GCAGTCGTAACTGCTAAAACTGAAC
26484 GCAGTCGTAACTGC-AAAACTGAAC
1 GCAGTCGTAACTGCTAAAACTGAAC
26508 GCA
1 GCA
26511 CCCTTGGTGC
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
24 37 0.42
25 52 0.58
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (25 bp):
GCAGTCGTAACTGCTAAAACTGAAC
Found at i:36421 original size:30 final size:32
Alignment explanation
Indices: 36387--36451 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
36377 GGAGCAGGGT
*
36387 GCATGAGCTGTTGCT-CG-TGGGAACGGTGAA
1 GCATGAGCTGCTGCTCCGTTGGGAACGGTGAA
*
36417 GCATGAGTTGCTGCTCCGTTGGGAACGGTGAA
1 GCATGAGCTGCTGCTCCGTTGGGAACGGTGAA
36449 GCA
1 GCA
36452 CGGGTAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 13 0.42
31 2 0.06
32 16 0.52
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.23
Consensus pattern (32 bp):
GCATGAGCTGCTGCTCCGTTGGGAACGGTGAA
Found at i:37193 original size:41 final size:41
Alignment explanation
Indices: 37138--37249 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 41
37128 ATCCTGCCCG
* * * *
37138 AAGGTCTTATGGATGGCCTGAAGGACTTATCATCC-TGCTCTA
1 AAGG-CTTACGGATGGCCCGAAGGACTTAGCA-CCATGCTCGA
* *
37180 AAGGCTTACGGATGACCCGAAGGATTTAAGCACCATGCTCGA
1 AAGGCTTACGGATGGCCCGAAGGACTT-AGCACCATGCTCGA
* *
37222 AAGACTTACTGATGGCCCGAAGGACTTA
1 AAGGCTTACGGATGGCCCGAAGGACTTA
37250 CAAATCGTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 22 0.38
42 36 0.62
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (41 bp):
AAGGCTTACGGATGGCCCGAAGGACTTAGCACCATGCTCGA
Found at i:37472 original size:42 final size:42
Alignment explanation
Indices: 37365--37473 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
37355 GGTCTTATGA
* * * *
37365 ATGGCCCGAAGGACTT-ATCATCCTGCTCTAAAGGCTTACGG
1 ATGGCCCGAAGGACTTAAACATCATGCTCGAAAGACTTACGG
* * * *
37406 ATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTAAACATCATGCTCGAAAGACTTACGG
*
37448 ATGGCCCGAAGGACTTAAAAATCATG
1 ATGGCCCGAAGGACTTAAACATCATG
37474 AAATTTTGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
41 14 0.25
42 42 0.75
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (42 bp):
ATGGCCCGAAGGACTTAAACATCATGCTCGAAAGACTTACGG
Found at i:37497 original size:215 final size:215
Alignment explanation
Indices: 37119--37781 Score: 1037
Period size: 215 Copynumber: 3.1 Consensus size: 215
37109 TATTATCCTG
* * *
37119 GTGAAACACATCCTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCCTGCTCTAAAGG
1 GTGAAA-ACATCCTACCCGAAGGTCTTATGAATGGCCCGAAGGACTTATCATCCTGCTCTAAAGG
*
37184 CTTACGGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
65 CTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
*
37249 ACAAATCGTGAAATTTTGAAACTCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCA
130 ACAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCA
37314 TTTTTTCATTTTCAAATTCTT
195 TTTTTTCATTTTCAAATTCTT
37335 GTGAAAACATCCTACCCGAAGGTCTTATGAATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGC
1 GTGAAAACATCCTACCCGAAGGTCTTATGAATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGC
37400 TTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
66 TTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
* * * *
37465 AAAATCATGAAATTTTGAAAATAGCATTCTTTGTTTTCAAACATTTCATCTTCTTAAAACATCA-
131 CAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCAT
*
37529 TTTTTCATTTTTAAATTCATT
196 TTTTTCATTTTCAAATTC-TT
* *
37550 -TGAAAACATCCTACCCGAAGGTCTTATGATTGGCCCGAAGGACTTATCATCCTACTCTAAAGGC
1 GTGAAAACATCCTACCCGAAGGTCTTATGAATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGC
* * * *
37614 TTACGGATGACCCGAAGGATTTCAGCATCGTGCTCGAAAGACATACTGAT-TCCCGAAGGACTTT
66 TTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC-TT
*
37678 ACAAATCGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAA--T--TC--C----AACATCA
130 ACAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCA
37733 TTTTTTCATTTTCAAATTCTT
195 TTTTTTCATTTTCAAATTCTT
* *
37754 GTGAAAACATCCTACCTGAAGGTTTTAT
1 GTGAAAACATCCTACCCGAAGGTCTTAT
37782 AGATGGTTTG
Statistics
Matches: 419, Mismatches: 24, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
204 9 0.02
205 42 0.10
208 1 0.00
210 2 0.00
212 1 0.00
213 10 0.02
214 167 0.40
215 181 0.43
216 6 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (215 bp):
GTGAAAACATCCTACCCGAAGGTCTTATGAATGGCCCGAAGGACTTATCATCCTGCTCTAAAGGC
TTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
CAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCAT
TTTTTCATTTTCAAATTCTT
Found at i:39903 original size:2 final size:2
Alignment explanation
Indices: 39892--39936 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
39882 TTGTAATCAC
39892 AT AT -T 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
39933 AT AT
1 AT AT
39937 TATTGGGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:46378 original size:30 final size:32
Alignment explanation
Indices: 46344--46406 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
46334 GGAGCAGGGT
*
46344 GCATGAACTATTGCT-CG-TGGGAACGGTGAA
1 GCATGAACTACTGCTCCGTTGGGAACGGTGAA
** *
46374 GCATGAGTTGCTGCTCCGTTGGGAACGGTGAA
1 GCATGAACTACTGCTCCGTTGGGAACGGTGAA
46406 G
1 G
46407 AACGGGTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 11 0.41
31 2 0.07
32 14 0.52
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (32 bp):
GCATGAACTACTGCTCCGTTGGGAACGGTGAA
Found at i:50422 original size:20 final size:21
Alignment explanation
Indices: 50392--50431 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
50382 AAGAATTCCA
*
50392 TATAGTGTTTAGGGTTTACAG
1 TATAGTGTTTAAGGTTTACAG
50413 TATA-TGTTTAAGGTTTACA
1 TATAGTGTTTAAGGTTTACA
50432 TCTTTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.45
Consensus pattern (21 bp):
TATAGTGTTTAAGGTTTACAG
Found at i:51579 original size:21 final size:20
Alignment explanation
Indices: 51555--51594 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
51545 AGATTGGGGT
51555 AATGCAAGACCAGATATCGTC
1 AATGCAAGACCAGAT-TCGTC
* *
51576 AATGCATGACGAGATTCGT
1 AATGCAAGACCAGATTCGT
51595 TCTGAACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (20 bp):
AATGCAAGACCAGATTCGTC
Found at i:65197 original size:17 final size:18
Alignment explanation
Indices: 65165--65199 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
65155 AACCAGGAAT
*
65165 TGAAGTTTTAATTATTTA
1 TGAAATTTTAATTATTTA
65183 TGAAATTTT-ATTATTTA
1 TGAAATTTTAATTATTTA
65200 AAAGATGCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (18 bp):
TGAAATTTTAATTATTTA
Found at i:69279 original size:50 final size:51
Alignment explanation
Indices: 69219--69329 Score: 138
Period size: 50 Copynumber: 2.2 Consensus size: 51
69209 AGAGATTATC
* * *
69219 AAAATA-ATATTTTTTATT-TAAATTCGTCACATTAAGATGATAAATTTTA
1 AAAATATATATTTTTTATTATAAATTCATCACATTAAAATGATAAATTCTA
* *
69268 AAAATATATA-TTTTTATTATAATTTTATCACATTAAAATGATAAATTCTA
1 AAAATATATATTTTTTATTATAAATTCATCACATTAAAATGATAAATTCTA
*
69318 ATAAAAATATAT
1 A-AAATATATAT
69330 CTTATTGAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
49 14 0.27
50 30 0.58
51 8 0.15
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (51 bp):
AAAATATATATTTTTTATTATAAATTCATCACATTAAAATGATAAATTCTA
Found at i:72360 original size:308 final size:308
Alignment explanation
Indices: 71802--72417 Score: 1232
Period size: 308 Copynumber: 2.0 Consensus size: 308
71792 CGAGACACAG
71802 TCGTACATGTAAATGTGTTACGGTCAAATTTTTGTATAATTGAAGAGTCTGATGCATTTTACAAG
1 TCGTACATGTAAATGTGTTACGGTCAAATTTTTGTATAATTGAAGAGTCTGATGCATTTTACAAG
71867 AAGCAAGCAATGAATTTCGTTGTCAGTGAACGGAGATTTCAAGGCAAGCTATTAAATATCTATTT
66 AAGCAAGCAATGAATTTCGTTGTCAGTGAACGGAGATTTCAAGGCAAGCTATTAAATATCTATTT
71932 ATTGTCTATTAGATATTTTAAAACCCGACCGAAGACGGCTTTTAGGTTTGTTTCAAATAAAAGGA
131 ATTGTCTATTAGATATTTTAAAACCCGACCGAAGACGGCTTTTAGGTTTGTTTCAAATAAAAGGA
71997 AGAAGAAGACAGATTTTAGGTCACGTATTTCGTTAATATCTACTCATGCCTAAGCTCAACCCTAC
196 AGAAGAAGACAGATTTTAGGTCACGTATTTCGTTAATATCTACTCATGCCTAAGCTCAACCCTAC
72062 TTTCTTCTCTTCCAACAATGCTAATGTAAAATCTTGATGTTTGTGGAT
261 TTTCTTCTCTTCCAACAATGCTAATGTAAAATCTTGATGTTTGTGGAT
72110 TCGTACATGTAAATGTGTTACGGTCAAATTTTTGTATAATTGAAGAGTCTGATGCATTTTACAAG
1 TCGTACATGTAAATGTGTTACGGTCAAATTTTTGTATAATTGAAGAGTCTGATGCATTTTACAAG
72175 AAGCAAGCAATGAATTTCGTTGTCAGTGAACGGAGATTTCAAGGCAAGCTATTAAATATCTATTT
66 AAGCAAGCAATGAATTTCGTTGTCAGTGAACGGAGATTTCAAGGCAAGCTATTAAATATCTATTT
72240 ATTGTCTATTAGATATTTTAAAACCCGACCGAAGACGGCTTTTAGGTTTGTTTCAAATAAAAGGA
131 ATTGTCTATTAGATATTTTAAAACCCGACCGAAGACGGCTTTTAGGTTTGTTTCAAATAAAAGGA
72305 AGAAGAAGACAGATTTTAGGTCACGTATTTCGTTAATATCTACTCATGCCTAAGCTCAACCCTAC
196 AGAAGAAGACAGATTTTAGGTCACGTATTTCGTTAATATCTACTCATGCCTAAGCTCAACCCTAC
72370 TTTCTTCTCTTCCAACAATGCTAATGTAAAATCTTGATGTTTGTGGAT
261 TTTCTTCTCTTCCAACAATGCTAATGTAAAATCTTGATGTTTGTGGAT
72418 GAAACAAACT
Statistics
Matches: 308, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
308 308 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (308 bp):
TCGTACATGTAAATGTGTTACGGTCAAATTTTTGTATAATTGAAGAGTCTGATGCATTTTACAAG
AAGCAAGCAATGAATTTCGTTGTCAGTGAACGGAGATTTCAAGGCAAGCTATTAAATATCTATTT
ATTGTCTATTAGATATTTTAAAACCCGACCGAAGACGGCTTTTAGGTTTGTTTCAAATAAAAGGA
AGAAGAAGACAGATTTTAGGTCACGTATTTCGTTAATATCTACTCATGCCTAAGCTCAACCCTAC
TTTCTTCTCTTCCAACAATGCTAATGTAAAATCTTGATGTTTGTGGAT
Found at i:72820 original size:2 final size:2
Alignment explanation
Indices: 72815--72853 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
72805 AAAAAAATTA
* *
72815 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
72854 GCATCATAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:74588 original size:4 final size:4
Alignment explanation
Indices: 74579--74604 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
74569 TTCAGTATCC
74579 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
74605 CTTTTGACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:75803 original size:108 final size:108
Alignment explanation
Indices: 75614--75810 Score: 394
Period size: 108 Copynumber: 1.8 Consensus size: 108
75604 AAGTGACTAC
75614 ATTATAATTTTGGAAAAGTGCAAGGGCTAAGATAAAAATTAGTCAAATAAATGTTGATATTTATA
1 ATTATAATTTTGGAAAAGTGCAAGGGCTAAGATAAAAATTAGTCAAATAAATGTTGATATTTATA
75679 TGATGATGTAAGAATGGTGATGAAAGCATTGAAAAAGTGGTAA
66 TGATGATGTAAGAATGGTGATGAAAGCATTGAAAAAGTGGTAA
75722 ATTATAATTTTGGAAAAGTGCAAGGGCTAAGATAAAAATTAGTCAAATAAATGTTGATATTTATA
1 ATTATAATTTTGGAAAAGTGCAAGGGCTAAGATAAAAATTAGTCAAATAAATGTTGATATTTATA
75787 TGATGATGTAAGAATGGTGATGAA
66 TGATGATGTAAGAATGGTGATGAA
75811 GGTGATAAAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (108 bp):
ATTATAATTTTGGAAAAGTGCAAGGGCTAAGATAAAAATTAGTCAAATAAATGTTGATATTTATA
TGATGATGTAAGAATGGTGATGAAAGCATTGAAAAAGTGGTAA
Found at i:77061 original size:22 final size:22
Alignment explanation
Indices: 77044--77132 Score: 178
Period size: 22 Copynumber: 4.0 Consensus size: 22
77034 CTCGTATAAA
77044 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
77066 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
77088 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
77110 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
77132 T
1 T
77133 ATGTCCATAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:77393 original size:30 final size:31
Alignment explanation
Indices: 77352--77411 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
77342 TAGACATAGT
*
77352 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
77382 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
77412 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:77468 original size:29 final size:29
Alignment explanation
Indices: 77426--77497 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
77416 TTTTCTGCAT
**
77426 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
77455 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
77484 ATTCATGTCATGTA
1 ATTCATGTCATGTA
77498 TCATATGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:77913 original size:67 final size:67
Alignment explanation
Indices: 77797--77967 Score: 199
Period size: 67 Copynumber: 2.6 Consensus size: 67
77787 TTTTTCTCAT
* * *
77797 GGGGA-ATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGATATCGGTTCCCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAA-ATCATATACGA
77861 TG-A
64 TGAA
* * * *
77864 GGGGATATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGATATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
77929 AA
66 AA
*
77931 GGGG-TATCGGTT--CCCCTTGATGGGTACCGATTCCCCT
1 GGGGATATCGGTTCCCCCCCTG--GGGTACCGATTCCCCT
77968 AGCCCGAAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
64 6 0.07
66 34 0.37
67 38 0.41
68 14 0.15
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGATATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
AA
Done.