Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009052.1 Hibiscus syriacus cultivar Beakdansim tig00112466_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: 35513
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:1710 original size:182 final size:182
Alignment explanation
Indices: 1390--1911 Score: 829
Period size: 181 Copynumber: 2.9 Consensus size: 182
1380 TTCAAATTAC
* **
1390 CGACACTTTTTTAAATGGTATCGACACATTTTTATTCCAATGGGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
1455 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCAT-AAACCGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTTG-AGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
1519 ATATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTTAAAATGT
130 ATATTACAAAATTATCTATTACATTATAATTAT-GGTTGCGATGTG-TAAAATGT
*
1574 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCG-CACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
1638 A-TATAAAGTGTCGATATAGGTTGAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
66 ATTATAAAGTGTCGATATAGGTTGAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
1702 TATTACAAAATTATCTATTACATTATAATTATGGTTGCGATGTGTAAAATGT
131 TATTACAAAATTATCTATTACATTATAATTATGGTTGCGATGTGTAAAATGT
* * *
1754 CGACACTTTTTTAAATCGTATCG-CACATTTTTCTTCC-ATATGTACATAAAGTACCGACACACT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
* * * *
1817 ATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTT-GAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
* * * **
1882 ATATTGCAAATTTACCTATTTTATTATAAT
130 ATATTACAAAATTATCTATTACATTATAAT
1912 ATGTTGAAAG
Statistics
Matches: 318, Mismatches: 16, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
178 17 0.05
179 19 0.06
180 51 0.16
181 91 0.29
182 78 0.25
183 7 0.02
184 55 0.17
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (182 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
ATTATAAAGTGTCGATATAGGTTGAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAATTATGGTTGCGATGTGTAAAATGT
Found at i:3347 original size:3 final size:3
Alignment explanation
Indices: 3339--3425 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
3329 ACTTGTTTGG
* * * **
3339 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
3387 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3426 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:3362 original size:18 final size:18
Alignment explanation
Indices: 3339--3440 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
3329 ACTTGTTTGG
3339 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
3357 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
3375 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
3393 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
3411 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
3429 AGCTTCATCTTC
1 ATCATCATCTTC
3441 TGCGACCGCT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:3406 original size:42 final size:42
Alignment explanation
Indices: 3347--3437 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
3337 GGATCATCAT
*
3347 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
3389 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
3431 CTTCATC
1 CTTCATC
3438 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:5501 original size:197 final size:198
Alignment explanation
Indices: 4888--6569 Score: 3145
Period size: 198 Copynumber: 8.5 Consensus size: 198
4878 TTTAAATTAG
*
4888 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
4953 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
5018 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5083 AAA
196 AAA
5086 TATCGAC-CAAACTATATTAGTGTCG--ACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
5148 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
5212 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCCTGTTTTCCATTAATTCTGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCA-CCCTGTTTTCCATTCATTCTGGAAA
5277 AAAA
195 AAAA
5281 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
5346 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5411 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5474 AAAA
195 AAAA
*
5478 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
5543 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5608 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5672 AAAA
195 AAAA
* *
5676 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGCCATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
5741 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5806 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5871 AAAA
195 AAAA
*
5875 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
5940 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
6005 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
6070 AAA
196 AAA
6073 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
6138 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6202 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
6267 AAAA
195 AAAA
*
6271 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
6336 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6399 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTAATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
6463 AAA
196 AAA
6466 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
6530 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA
6570 TGGATCGACA
Statistics
Matches: 1460, Mismatches: 13, Indels: 26
0.97 0.01 0.02
Matches are distributed among these distances:
194 136 0.09
195 146 0.10
196 39 0.03
197 372 0.25
198 435 0.30
199 332 0.23
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:6762 original size:19 final size:19
Alignment explanation
Indices: 6716--6764 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
6706 ATATATTCAC
*
6716 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
6735 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
6754 ATACAAAATTA
1 ATACAAAATTA
6765 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:8590 original size:33 final size:33
Alignment explanation
Indices: 8553--8618 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
8543 CATCTTAATA
*
8553 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
8586 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
8619 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:10962 original size:19 final size:19
Alignment explanation
Indices: 10917--10962 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
10907 TCCGGTATCA
10917 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
10936 TTGATACCGG-TTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
10956 TTTTACC
1 TTTTACC
10963 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:11131 original size:20 final size:20
Alignment explanation
Indices: 11084--11132 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
11074 CACTTTTAAA
*
11084 TTTACC-GGTTTTATCATTT
1 TTTACCTGGTTTTATCATAT
11103 TGTTA-CTGGTTTTATCATAT
1 T-TTACCTGGTTTTATCATAT
11123 TTTACCTGGT
1 TTTACCTGGT
11133 ATATCGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTACCTGGTTTTATCATAT
Found at i:11592 original size:228 final size:228
Alignment explanation
Indices: 11194--11641 Score: 799
Period size: 228 Copynumber: 2.0 Consensus size: 228
11184 TTAAAACTGC
11194 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
11259 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
11324 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
*
11389 GTATGGACACTTTTATAAAAATGATATATATTTT
195 GTATGGACACTTTTATAAAAAGGATATATATTTT
*
11423 TTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTAC-ATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
11487 TTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
11552 TTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
11617 TATGGACACTTTTATAAAAAGGATA
196 TATGGACACTTTTATAAAAAGGATA
11642 GATAATTTAC
Statistics
Matches: 210, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
227 37 0.18
228 113 0.54
229 60 0.29
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATATTTT
Found at i:12203 original size:27 final size:29
Alignment explanation
Indices: 12164--12228 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
12154 CTCCTAAAAC
*
12164 TTAAAAATTATAA-TTAGATCCTTAAAGTT
1 TTAAAAA-TATAATTTAGATCCTAAAAGTT
* *
12193 TTAAAAA-ATAATTTAGCTCCTAAAATTT
1 TTAAAAATATAATTTAGATCCTAAAAGTT
*
12221 TTAGAAAT
1 TTAAAAAT
12229 TCATATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 4 0.13
28 19 0.63
29 7 0.23
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (29 bp):
TTAAAAATATAATTTAGATCCTAAAAGTT
Found at i:14974 original size:2 final size:2
Alignment explanation
Indices: 14967--15038 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
14957 TATAACAGAA
14967 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
15009 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15039 ATAATAGTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17793 original size:28 final size:28
Alignment explanation
Indices: 17748--17805 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
17738 TATTATGGGT
17748 CCTGGGCGGGCGCACCTCCTGCCCCAGC
1 CCTGGGCGGGCGCACCTCCTGCCCCAGC
*
17776 CCTGGGCGGGCG-ACCCTCCTGCCCCGGC
1 CCTGGGCGGGCGCA-CCTCCTGCCCCAGC
17804 CC
1 CC
17806 AGTGCCAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.05, C:0.52, G:0.33, T:0.10
Consensus pattern (28 bp):
CCTGGGCGGGCGCACCTCCTGCCCCAGC
Found at i:19445 original size:43 final size:43
Alignment explanation
Indices: 19368--19473 Score: 151
Period size: 43 Copynumber: 2.5 Consensus size: 43
19358 ATAGGTCAAG
* *
19368 ATCTATAGCGGCG-TTTTGAAACAAACGCCACAAAATGTCGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCGAT
** * *
19410 ATCTATAGCAACGTTTTTGGAACAAACGCCGCAAAAAGTCTAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCGAT
19453 ATCTATAGCGGCGTTTTTGGA
1 ATCTATAGCGGCGTTTTTGGA
19474 GCGAAAGGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 11 0.20
43 44 0.80
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCGAT
Found at i:19694 original size:43 final size:42
Alignment explanation
Indices: 19623--19740 Score: 112
Period size: 43 Copynumber: 2.8 Consensus size: 42
19613 CCGCTAAAGT
* * * *
19623 TAGCGGCGTTTTTTAAAAAATGTCGCAATAGG-TTACAACATA
1 TAGCGGCGTTTTCTGAAAAACGCCGCAATAGGATT-CAACATA
**** *
19665 TAGCGGCGTTTTCTGAACAAACGCCGCAATAGGATTTGTTATT
1 TAGCGGCGTTTTCTGAA-AAACGCCGCAATAGGATTCAACATA
*
19708 TAGCGGCGTTTTTCAGAAAAACGCCGCAATAGG
1 TAGCGGCG-TTTTCTGAAAAACGCCGCAATAGG
19741 CGTTGATGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 15 0.24
43 38 0.60
44 10 0.16
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTTCTGAAAAACGCCGCAATAGGATTCAACATA
Found at i:19758 original size:43 final size:44
Alignment explanation
Indices: 19668--19768 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
19658 CAACATATAG
* * * *
19668 CGGCG-TTTTCTGAACAAACGCCGCAATAGGATTTGTTATTTAG
1 CGGCGTTTTTCAGAACAAACGCCGCAATAGGAGTTGATATTTAA
* *
19711 CGGCGTTTTTCAGAA-AAACGCCGCAATAGGCGTTGATGTTTAA
1 CGGCGTTTTTCAGAACAAACGCCGCAATAGGAGTTGATATTTAA
19754 CGGCGTTTTT-AGAAC
1 CGGCGTTTTTCAGAAC
19769 GCCGCAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 4 0.08
43 38 0.76
44 8 0.16
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (44 bp):
CGGCGTTTTTCAGAACAAACGCCGCAATAGGAGTTGATATTTAA
Found at i:19990 original size:43 final size:42
Alignment explanation
Indices: 19937--20071 Score: 171
Period size: 43 Copynumber: 3.1 Consensus size: 42
19927 TTCTAGTGCA
* * * *
19937 AAACGCCGCAAAAGGTCAAACCTATAACGGCATTTTTGGAAAC
1 AAACG-CGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
* *
19980 AAACGTCGCAAAAGGTCAGATCTAGAGCGGCGTTTTTGGATAC
1 AAACG-CGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
* *
20023 AAATGCTGCAAAAAGTCAGATCTATAGCGGCATTTTTGGATAC
1 AAACGC-GCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
20066 AAACGC
1 AAACGC
20072 CGCTATTTAC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 1 0.01
43 78 0.99
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (42 bp):
AAACGCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
Found at i:20223 original size:26 final size:26
Alignment explanation
Indices: 20194--20250 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
20184 TTTTAATTAA
20194 GACACAAGTTATGCAAAAAAATACTT
1 GACACAAGTTATGCAAAAAAATACTT
20220 GACACAAGTTATGCAAAAAAATACTT
1 GACACAAGTTATGCAAAAAAATACTT
*
20246 AACAC
1 GACAC
20251 GATAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.21
Consensus pattern (26 bp):
GACACAAGTTATGCAAAAAAATACTT
Found at i:22778 original size:21 final size:19
Alignment explanation
Indices: 22752--22790 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
22742 GGGGGTTTTC
22752 AAGGAAGAATTAGGGAAGAAG
1 AAGGAAG-ATT-GGGAAGAAG
22773 AAGGAAGATTGGGAAGAA
1 AAGGAAGATTGGGAAGAA
22791 AGGTTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.38, T:0.10
Consensus pattern (19 bp):
AAGGAAGATTGGGAAGAAG
Found at i:23197 original size:52 final size:52
Alignment explanation
Indices: 23134--23292 Score: 300
Period size: 52 Copynumber: 3.1 Consensus size: 52
23124 TAACAACAAA
23134 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
* *
23186 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAATAGTCTTCAGC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
23238 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
23290 ATA
1 ATA
23293 TTGTTCAGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:24389 original size:42 final size:42
Alignment explanation
Indices: 24355--24449 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
24345 TTTATACAAA
* * * **
24355 AAACGCCGCTAATTTACCACTCTATTGCGACGTTTTTGGTAT
1 AAACGCCGCTAAATTAACACTATATTGCGACGTTTTTACTAT
24397 AAACGCCGCTAAATTAACACTATATTGCGACGTTTTTACTAT
1 AAACGCCGCTAAATTAACACTATATTGCGACGTTTTTACTAT
24439 AAACGCCGCTA
1 AAACGCCGCTA
24450 TTGTTTAACC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (42 bp):
AAACGCCGCTAAATTAACACTATATTGCGACGTTTTTACTAT
Found at i:24784 original size:43 final size:42
Alignment explanation
Indices: 24723--25132 Score: 484
Period size: 43 Copynumber: 9.7 Consensus size: 42
24713 TGCTGTAGTA
* ** *
24723 TATAGCGGCATTTTTGGAACAAACGCCGCGGAAGGTCGAGATC
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-ATATC
* * *
24766 TATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCATAAC
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCATATC
** *
24808 TATAGCAACATTTTTGGATACAAACGCCGCAAAAGGTCATATC
1 TATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCATATC
* * *
24851 TATAGCGACGTTTTTGGAATAAA--CCGCAAAAGGTCAAGATC
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-ATATC
* * *
24892 TATAGCGGCATTTTTGGAATAAACGCCACAAAAGGTCATATC
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCATATC
* * *
24934 AATAGCGACGTTTTTGGAATAAACGCCGC-AAAGGTCATATC
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCATATC
*
24975 TATAGCGGCGTTTTTGGATACAAACGCCGTAAAAGGTCATATC
1 TATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCATATC
* * * * * *
25018 TGTATCTGTGTTTTTGGAACAAACGCCACAAAAAGTCATATC
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCATATC
* *
25060 TATAGCAGCGTTTTTGGATACAAACGCCGCAAAAAGTCATATC
1 TATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCATATC
*
25103 TATAGCAGCGTTTTTGGATACAAACGCCGC
1 TATAGCGGCGTTTTTGGA-ACAAACGCCGC
25133 TAACCTTTCT
Statistics
Matches: 323, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
40 12 0.04
41 53 0.16
42 96 0.30
43 162 0.50
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCATATC
Found at i:24866 original size:85 final size:85
Alignment explanation
Indices: 24723--25132 Score: 476
Period size: 85 Copynumber: 4.8 Consensus size: 85
24713 TGCTGTAGTA
* ** * * *
24723 TATAGCGGCATTTTTGGA-ACAAACGCCGCGGAAGGTCGAGATCTATAGCGGCATTTTTGGAACA
1 TATAGCAGCATTTTTGGATACAAACGCCGCAAAAGGTC-ATATCTATAGCGACGTTTTTGGAACA
*
24787 AACACCGCAAAAGGTCATAAC
65 AACGCCGCAAAAGGTCATAAC
* *
24808 TATAGCAACATTTTTGGATACAAACGCCGCAAAAGGTCATATCTATAGCGACGTTTTTGGAATAA
1 TATAGCAGCATTTTTGGATACAAACGCCGCAAAAGGTCATATCTATAGCGACGTTTTTGGAACAA
24873 A--CCGCAAAAGGTCA-AGATC
66 ACGCCGCAAAAGGTCATA-A-C
* * * * *
24892 TATAGCGGCATTTTTGGA-ATAAACGCCACAAAAGGTCATATCAATAGCGACGTTTTTGGAATAA
1 TATAGCAGCATTTTTGGATACAAACGCCGCAAAAGGTCATATCTATAGCGACGTTTTTGGAACAA
*
24956 ACGCCGC-AAAGGTCATATC
66 ACGCCGCAAAAGGTCATAAC
* * * * * *
24975 TATAGCGGCGTTTTTGGATACAAACGCCGTAAAAGGTCATATCTGTATCTG-TGTTTTTGGAACA
1 TATAGCAGCATTTTTGGATACAAACGCCGCAAAAGGTCATATCTATAGC-GACGTTTTTGGAACA
* * *
25039 AACGCCACAAAAAGTCATATC
65 AACGCCGCAAAAGGTCATAAC
* *
25060 TATAGCAGCGTTTTTGGATACAAACGCCGCAAAAAGTCATATCTATAGC-AGCGTTTTTGGATAC
1 TATAGCAGCATTTTTGGATACAAACGCCGCAAAAGGTCATATCTATAGCGA-CGTTTTTGGA-AC
25124 AAACGCCGC
64 AAACGCCGC
25133 TAACCTTTCT
Statistics
Matches: 281, Mismatches: 32, Indels: 23
0.84 0.10 0.07
Matches are distributed among these distances:
82 1 0.00
83 76 0.27
84 67 0.24
85 110 0.39
86 27 0.10
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (85 bp):
TATAGCAGCATTTTTGGATACAAACGCCGCAAAAGGTCATATCTATAGCGACGTTTTTGGAACAA
ACGCCGCAAAAGGTCATAAC
Found at i:25032 original size:126 final size:127
Alignment explanation
Indices: 24723--25132 Score: 533
Period size: 126 Copynumber: 3.2 Consensus size: 127
24713 TGCTGTAGTA
* ** *
24723 TATAGCGGCATTTTTGGAACAAACGCCGCGGAAGGTCGAGATCTATAGCGGCATTTTTGGAACAA
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAAGATCTATAGCGGCATTTTTGGAACAA
* * * *
24788 ACACCGCAAAAGGTCATAACTATAGCAACATTTTTGGATACAAACGCCGCAAAAGGTCATATC
66 ACGCCACAAAAGGTCATATCTATAGC-ACGTTTTTGGATACAAACGCCGCAAAAGGTCATATC
* * *
24851 TATAGCGACGTTTTTGGAATAAA--CCGCAAAAGGTCAAGATCTATAGCGGCATTTTTGGAATAA
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAAGATCTATAGCGGCATTTTTGGAACAA
* *
24914 ACGCCACAAAAGGTCATATCAATAGCGACGTTTTTGGA-ATAAACGCCGC-AAAGGTCATATC
66 ACGCCACAAAAGGTCATATCTATAGC-ACGTTTTTGGATACAAACGCCGCAAAAGGTCATATC
* * * * * **
24975 TATAGCGGCGTTTTTGGATACAAACGCCGTAAAAGGTC-ATATCTGTATCTGTGTTTTTGGAACA
1 TATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCAAGATCTATAGCGGCATTTTTGGAACA
* *
25039 AACGCCACAAAAAGTCATATCTATAGCAGCGTTTTTGGATACAAACGCCGCAAAAAGTCATATC
65 AACGCCACAAAAGGTCATATCTATAGCA-CGTTTTTGGATACAAACGCCGCAAAAGGTCATATC
*
25103 TATAGCAGCGTTTTTGGATACAAACGCCGC
1 TATAGCGGCGTTTTTGGA-ACAAACGCCGC
25133 TAACCTTTCT
Statistics
Matches: 246, Mismatches: 30, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
124 29 0.12
125 15 0.06
126 122 0.50
127 21 0.09
128 59 0.24
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (127 bp):
TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAAGATCTATAGCGGCATTTTTGGAACAA
ACGCCACAAAAGGTCATATCTATAGCACGTTTTTGGATACAAACGCCGCAAAAGGTCATATC
Found at i:29329 original size:84 final size:83
Alignment explanation
Indices: 29214--29410 Score: 213
Period size: 84 Copynumber: 2.4 Consensus size: 83
29204 ACATTTTTTG
* * * * * *
29214 CGGCGTTTGT--AAAATGCCGCTACAGTTCTAATCTTTTGCGGCATTTGTT-G-GAAAAAATGCC
1 CGGCGTTTGTAAAAAATGCCGCTAAAGTACTAATCTATTACGGCATTT-TTCGAAAAAAAACGCC
*
29275 ACTATAGGTGAACCCTATTA
65 ACTATAGATGAA-CCTATTA
* * * *
29295 TGGTGTTTTTATAAAAATGCCGCTAAAGTACTAATCTATTATGGCATTTTTCGAAAAAAAACGCC
1 CGGCGTTTGTA-AAAAATGCCGCTAAAGTACTAATCTATTACGGCATTTTTCGAAAAAAAACGCC
* *
29360 ACTATAGATGGACCTATTG
65 ACTATAGATGAACCTATTA
*
29379 CGGCGTTTGTAAAAAACGCCGCTAAAGTACTA
1 CGGCGTTTGTAAAAAATGCCGCTAAAGTACTA
29411 CTTTTTTTAT
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
81 7 0.07
83 22 0.23
84 46 0.49
85 19 0.20
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (83 bp):
CGGCGTTTGTAAAAAATGCCGCTAAAGTACTAATCTATTACGGCATTTTTCGAAAAAAAACGCCA
CTATAGATGAACCTATTA
Found at i:29475 original size:80 final size:80
Alignment explanation
Indices: 29302--29489 Score: 218
Period size: 80 Copynumber: 2.3 Consensus size: 80
29292 TTATGGTGTT
* * *
29302 TTTATAAAAATGCCGCTAAAGTACTAATCTATTATGGCATTTTTCGAAAAAAAACGCCACTATAG
1 TTTATAAAAACGCCGCTAAAGTACTAATCTATTATAGCATTTTTC--AAAAAAACGCCACTAAAG
29367 ATGGACCTATTGCGGCG
64 ATGGACCTATTGCGGCG
* * * * * *
29384 TTTGTAAAAAACGCCGCTAAAGTACTACTTTTTTTATAGC-TTTTTC-AAAAAATGCCACTAAAT
1 TTTAT-AAAAACGCCGCTAAAGTACTA-ATCTATTATAGCATTTTTCAAAAAAACGCCACTAAAG
*
29447 ATGTACCTATTGCGGCG
64 ATGGACCTATTGCGGCG
*
29464 TTTATATAAAACGCCACTAAAGTACT
1 TTTATA-AAAACGCCGCTAAAGTACT
29490 CTCTTTACGG
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 52 0.57
82 4 0.04
83 26 0.29
84 8 0.09
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (80 bp):
TTTATAAAAACGCCGCTAAAGTACTAATCTATTATAGCATTTTTCAAAAAAACGCCACTAAAGAT
GGACCTATTGCGGCG
Done.