Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005047.1 Hibiscus syriacus cultivar Beakdansim tig00011334_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: 68266
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:525 original size:90 final size:90
Alignment explanation
Indices: 372--543 Score: 308
Period size: 90 Copynumber: 1.9 Consensus size: 90
362 CCTAACACAC
* * *
372 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
437 ATTTAATTAATTGAAATTTAATAAT
66 ATTTAATTAATTGAAATTTAATAAT
*
462 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
527 ATTTAATTAATTGAAAT
66 ATTTAATTAATTGAAAT
544 AAATTCGGGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTTAATAAT
Found at i:4432 original size:28 final size:27
Alignment explanation
Indices: 4383--4437 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
4373 CATTAATTAC
* *
4383 CACTCATCTTCCCTCACTCATCTTCCCT
1 CACTCATCTTCCCCCACCCATC-TCCCT
*
4411 CACTCATCTTCCCCCTCCCATCTCCCT
1 CACTCATCTTCCCCCACCCATCTCCCT
4438 ATAAATACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.13, C:0.55, G:0.00, T:0.33
Consensus pattern (27 bp):
CACTCATCTTCCCCCACCCATCTCCCT
Found at i:4433 original size:14 final size:14
Alignment explanation
Indices: 4383--4423 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
4373 CATTAATTAC
4383 CACTCATCTTCCCT
1 CACTCATCTTCCCT
4397 CACTCATCTTCCCT
1 CACTCATCTTCCCT
4411 CACTCATCTTCCC
1 CACTCATCTTCCC
4424 CCTCCCATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.15, C:0.51, G:0.00, T:0.34
Consensus pattern (14 bp):
CACTCATCTTCCCT
Found at i:5028 original size:133 final size:133
Alignment explanation
Indices: 4737--5410 Score: 827
Period size: 134 Copynumber: 5.0 Consensus size: 133
4727 TTCATTTCGA
* * * * *
4737 TGCTCTTCTGGGAAGATTGAATCAAATTTGATTTGTTTCGCTGCTCTTCAGGAAA-ACCAAATCT
1 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTCA-GAAAGATCAAATCT
* *
4801 GAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGGAAAAAAATTGATTC
65 GAAAGAA-AAAAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGA-G-AAAAATTTGATTC
*
4866 ACTCAAC
127 ACTCCAC
* * * * * *
4873 TGTTCTTCATGGAAGATTGAATCGAATGTGATTTACTTCACTACTCTTCAGAAAGATCAAATTTG
1 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTG
* *
4938 AAAGAAAAAAATATGCTCCGCTACTCTTTAGGGGAGGTCAGACCCGAGAAAAATTTGATTCACTC
66 AAAGAAAAAAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTGATTCACTC
*
5003 CAT
131 CAC
* * *
5006 TGCTCTTCAGGGAAGATTGAATCTAACGTGATTTGCTTCACTGCTTTTTCATG-AAGATCAAATC
1 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGC-TCTTCA-GAAAGATCAAATC
*
5070 TGAAAGAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTTAGACTCGAG-AAAATTTGAT
64 TGAAAG-A-AA-AA-AATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTGAT
5134 TCACTCCAC
125 TCACTCCAC
* * * * * *
5143 TGCTCTTCAGGGAAGATTGAATCGAATTTGATTTGC-TCTGCTGCTCTTCAGGATGACCAAATCT
1 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTC-ACTGCTCTTCAGAAAGATCAAATCT
* *
5207 GAAAGAAGAAAAATATGCTCCGCTACTCTTTAGGGGAGGTCATACTCGAGAAAAATTTGATTCAC
65 GAAAGAA-AAAAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTGATTCAC
5272 TCCAC
129 TCCAC
* * * *
5277 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGTTTCACTGCTCTTCAGGAAGATAAAATATG
1 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTG
* * * * *
5342 AGAGAATAAGAAGAATCTACTCCACTACTTTTTAGGGGAGGTCAGACTCAAG-AAAATTTGATTC
66 AAAG-A-AA-AA-AATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTGATTC
5406 ACTCC
127 ACTCC
5411 TCCACTCTTT
Statistics
Matches: 468, Mismatches: 54, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
133 91 0.19
134 101 0.22
135 51 0.11
136 99 0.21
137 90 0.19
138 36 0.08
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (133 bp):
TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTG
AAAGAAAAAAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTGATTCACTC
CAC
Found at i:5212 original size:270 final size:269
Alignment explanation
Indices: 4737--5410 Score: 960
Period size: 270 Copynumber: 2.5 Consensus size: 269
4727 TTCATTTCGA
* * * * *
4737 TGCTCTTCTGGGAAGATTGAATCAAATTTGATTTGTTTCGCTGCTCTTCAGGAAAACCAAATCTG
1 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGTTTCACTGCTCTTCAGGAAGATCAAATCTG
*
4802 -A-AAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGGAAAAAAATTGATT
66 AAGAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGA-G--AAAATTTGATT
* * * *
4865 CACTCAACTGTTCTTCATGGAAGATTGAATCGAATGTGATTTACTTCACTACTCTTCAGAAAGAT
128 CACTCCACTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTACTTCACTACTCTTCAGAAAGAC
*
4930 CAAATTTGAAAGAA-AAAAATATGCTCCGCTACTCTTTAGGGGAGGTCAGACCCGAGAAAAATTT
193 CAAATCTGAAAGAAGAAAAATATGCTCCGCTACTCTTTAGGGGAGGTCAGACCCGAGAAAAATTT
*
4994 GATTCACTCCAT
258 GATTCACTCCAC
* * * * *
5006 TGCTCTTCAGGGAAGATTGAATCTAACGTGATTTGCTTCACTGCTTTTTCATGAAGATCAAATCT
1 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGTTTCACTGC-TCTTCAGGAAGATCAAATCT
*
5071 GAAAGAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTTAGACTCGAGAAAATTTGATTC
65 G-AAGAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAATTTGATTC
* * * * * *
5136 ACTCCACTGCTCTTCAGGGAAGATTGAATCGAATTTGATTTGC-TCTGCTGCTCTTCAGGATGAC
129 ACTCCACTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTACTTC-ACTACTCTTCAGAAAGAC
* *
5200 CAAATCTGAAAGAAGAAAAATATGCTCCGCTACTCTTTAGGGGAGGTCATACTCGAGAAAAATTT
193 CAAATCTGAAAGAAGAAAAATATGCTCCGCTACTCTTTAGGGGAGGTCAGACCCGAGAAAAATTT
5265 GATTCACTCCAC
258 GATTCACTCCAC
* *
5277 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGTTTCACTGCTCTTCAGGAAGATAAAATATG
1 TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGTTTCACTGCTCTTCAGGAAGATCAAATCTG
* * * * *
5342 AGAGAATAAGAAGAATCTACTCCACTACTTTTTAGGGGAGGTCAGACTCAAGAAAATTTGATTCA
66 A-AGAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAATTTGATTCA
5407 CTCC
130 CTCC
5411 TCCACTCTTT
Statistics
Matches: 359, Mismatches: 39, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
269 41 0.11
270 170 0.47
271 100 0.28
272 2 0.01
273 46 0.13
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (269 bp):
TGCTCTTCAGGGAAGATTGAATCAAATGTGATTTGTTTCACTGCTCTTCAGGAAGATCAAATCTG
AAGAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAATTTGATTCAC
TCCACTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTACTTCACTACTCTTCAGAAAGACCAA
ATCTGAAAGAAGAAAAATATGCTCCGCTACTCTTTAGGGGAGGTCAGACCCGAGAAAAATTTGAT
TCACTCCAC
Found at i:6776 original size:7 final size:7
Alignment explanation
Indices: 6766--6813 Score: 96
Period size: 7 Copynumber: 6.9 Consensus size: 7
6756 TATTTCTTCT
6766 TTTTTCC
1 TTTTTCC
6773 TTTTTCC
1 TTTTTCC
6780 TTTTTCC
1 TTTTTCC
6787 TTTTTCC
1 TTTTTCC
6794 TTTTTCC
1 TTTTTCC
6801 TTTTTCC
1 TTTTTCC
6808 TTTTTC
1 TTTTTC
6814 TTCTTTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCC
Found at i:6824 original size:7 final size:7
Alignment explanation
Indices: 6742--6862 Score: 73
Period size: 7 Copynumber: 16.3 Consensus size: 7
6732 TTTTTTTTTA
6742 TTTTTCT
1 TTTTTCT
*
6749 TCTTTCTT
1 TTTTTC-T
6757 ATTTCTTCT
1 -TTT-TTCT
6766 TTTTTCCT
1 TTTTT-CT
*
6774 TTTTCCT
1 TTTTTCT
*
6781 TTTTCCT
1 TTTTTCT
*
6788 TTTTCCT
1 TTTTTCT
*
6795 TTTTCCT
1 TTTTTCT
*
6802 TTTTCCTT
1 TTTTTC-T
6810 TTTCTTCT
1 TTT-TTCT
6818 TTTTTCT
1 TTTTTCT
*
6825 TTCTTCTAT
1 TT-TT-TCT
*
6834 TTTTTAT
1 TTTTTCT
6841 TTTTTCT
1 TTTTTCT
**
6848 TTCCT-T
1 TTTTTCT
6854 TTTTTCT
1 TTTTTCT
6861 TT
1 TT
6863 ATTTTCTCCT
Statistics
Matches: 95, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
6 4 0.04
7 57 0.60
8 22 0.23
9 9 0.09
10 3 0.03
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCT
Found at i:6844 original size:24 final size:24
Alignment explanation
Indices: 6817--6867 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
6807 CTTTTTCTTC
6817 TTTTTTCTTT-CTTCTATTT-TTTA
1 TTTTTTCTTTCCTT-TATTTCTTTA
*
6840 TTTTTTCTTTCCTTTTTTTCTTTA
1 TTTTTTCTTTCCTTTATTTCTTTA
6864 TTTT
1 TTTT
6868 CTCCTCAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTCTTTCCTTTATTTCTTTA
Found at i:6867 original size:23 final size:23
Alignment explanation
Indices: 6794--6867 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
6784 TCCTTTTTCC
6794 TTTTTCCTTT-TTCCTTTTTCTTCT-
1 TTTTT-CTTTCTT-CTTTTTCTT-TA
*
6818 TTTTTCTTTCTTCTATTT-TTTA
1 TTTTTCTTTCTTCTTTTTCTTTA
6840 TTTTTTCTTTCCTT-TTTTTCTTTA
1 -TTTTTCTTT-CTTCTTTTTCTTTA
6864 TTTT
1 TTTT
6868 CTCCTCAGGC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
21 1 0.02
22 2 0.05
23 26 0.60
24 14 0.33
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTCTTCTTTTTCTTTA
Found at i:6869 original size:9 final size:8
Alignment explanation
Indices: 6731--6869 Score: 50
Period size: 9 Copynumber: 16.1 Consensus size: 8
6721 CCCTACTTTA
*
6731 TTTTTTTT
1 TTTTTTTC
6739 TTATTTTTC
1 TT-TTTTTC
*
6748 -TTCTTTC
1 TTTTTTTC
6755 TTATTTCTTC
1 TT-TTT-TTC
*
6765 TTTTTTCC
1 TTTTTTTC
*
6773 TTTTTCCTTT
1 TTTTT--TTC
6783 TTCCTTTTTC
1 TT--TTTTTC
*
6793 -CTTTTTC
1 TTTTTTTC
* *
6800 CTTTTTCC
1 TTTTTTTC
6808 TTTTTCTTC
1 TTTTT-TTC
6817 -TTTTTTC
1 TTTTTTTC
* *
6824 TTTCTTCTA
1 TTT-TTTTC
*
6833 TTTTTTATT
1 TTTTTT-TC
6842 TTTTCTTTCC
1 TTTT-TTT-C
6852 TTTTTTTC
1 TTTTTTTC
6860 TTTATTTTC
1 TTT-TTTTC
6869 T
1 T
6870 CCTCAGGCAA
Statistics
Matches: 98, Mismatches: 17, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
7 14 0.14
8 32 0.33
9 33 0.34
10 16 0.16
12 3 0.03
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTTC
Found at i:14604 original size:45 final size:45
Alignment explanation
Indices: 14548--14693 Score: 195
Period size: 45 Copynumber: 3.2 Consensus size: 45
14538 AATAATGCAC
*
14548 CCTTTTATGCCGATAATGCACTCATATGCATTTCAATTATGGCAT
1 CCTTTCATGCCGATAATGCACTCATATGCATTTCAATTATGGCAT
* * * *
14593 CATTTCATGCCGATAATGGACCCATATGCATTTCAATTATGGCAC
1 CCTTTCATGCCGATAATGCACTCATATGCATTTCAATTATGGCAT
* * * *
14638 CCTTTCATGCTGATAATGCA-TCCCTATACATTTCATTTATGGCAT
1 CCTTTCATGCCGATAATGCACT-CATATGCATTTCAATTATGGCAT
14683 CCTTTCATGCC
1 CCTTTCATGCC
14694 CTTTTATACG
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (45 bp):
CCTTTCATGCCGATAATGCACTCATATGCATTTCAATTATGGCAT
Found at i:14858 original size:67 final size:67
Alignment explanation
Indices: 14711--15100 Score: 537
Period size: 67 Copynumber: 5.8 Consensus size: 67
14701 ACGCTATTAA
* * * * * *
14711 CCTTTCATCTAACTGTCATGATTGACACCTTTCTGTCAAATACATAGCTAGGTCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AATGCACAGTTAGGCCTCAAAGGCACT
14776 TAG
65 TAG
* * * *
14779 CCTTTCATCTAACTAGCATAATTGACACCTTTCCGTCAATGCATAGTTAAGCCTCAAAGGCACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
14844 AG
66 AG
* * * *
14846 CCTTTAATCTAACTGGCATAATTGACACGTTTTTGTCAATGCACAGTTAGACCTCAAAGGCACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
14911 AG
66 AG
* * * *
14913 CCTTGCATCTAACTGGCATAATTGACACCTTTTTGTCAATGCACAGTTAGGCATCAAAGACACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
14978 AG
66 AG
** * * *
14980 CCTTTCATCTAACTGGCATAATTGACATATTTTTGTCAATGCACAGTTAGGTCTCAAAGGCACTA
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
15045 AG
66 AG
* * *
15047 CCTTTCATCTAACTGGCATAATTGACACCATTCTGTCAATACAAAGTTAGGCCT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCT
15101 TTTAATCTTT
Statistics
Matches: 286, Mismatches: 36, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
67 253 0.88
68 33 0.12
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (67 bp):
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
AG
Found at i:15366 original size:57 final size:57
Alignment explanation
Indices: 15305--15418 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
15295 ATAAAGTTCT
15305 TATACGAAAATTAAAAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGCC
1 TATACGAAAATTAAAAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGCC
* * *
15362 TATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGCC
1 TATACGAAAATTAAAAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGCC
15419 ATTATGTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (57 bp):
TATACGAAAATTAAAAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGCC
Found at i:16775 original size:31 final size:31
Alignment explanation
Indices: 16737--16858 Score: 217
Period size: 31 Copynumber: 3.9 Consensus size: 31
16727 AATGCCCTTT
16737 CATTAATCTATCTCTTACACATTGGTCTTGC
1 CATTAATCTATCTCTTACACATTGGTCTTGC
16768 CATTAATCTATCTCTTACACATTGGTCTTGC
1 CATTAATCTATCTCTTACACATTGGTCTTGC
* * *
16799 CATTAATCTATCTCTTACACATTGATCCTGT
1 CATTAATCTATCTCTTACACATTGGTCTTGC
16830 CATTAATCTATCTCTTACACATTGGTCTT
1 CATTAATCTATCTCTTACACATTGGTCTT
16859 ACTTAAGTCA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.43
Consensus pattern (31 bp):
CATTAATCTATCTCTTACACATTGGTCTTGC
Found at i:23176 original size:3 final size:3
Alignment explanation
Indices: 23148--23198 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
23138 GTGCAATCAT
* * *
23148 ATA AT- ATA AAA ATGA ATA ATA CTA ATA ATA ATA CTA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
23193 ACA ATA
1 ATA ATA
23199 TAAATAAAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:23198 original size:12 final size:12
Alignment explanation
Indices: 23162--23192 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
23152 TATAAAAATG
23162 AATAATACTAAT
1 AATAATACTAAT
23174 AATAATACTAAT
1 AATAATACTAAT
23186 AATAATA
1 AATAATA
23193 ACAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATACTAAT
Found at i:23447 original size:22 final size:22
Alignment explanation
Indices: 23353--23465 Score: 117
Period size: 22 Copynumber: 5.1 Consensus size: 22
23343 ATTTAAAAAA
* *
23353 TATATTATATACATTTTAAAC-
1 TATACTATATATATTTTAAACT
*
23374 TATACTATATATATTATT--TCT
1 TATACTATATATATT-TTAAACT
**
23395 CTA-AAAACTATATATTTTAAACT
1 -TATACTA-TATATATTTTAAACT
23418 ATATACTATATATATTTTAAACT
1 -TATACTATATATATTTTAAACT
23441 TATACTATATATATTTTAAACT
1 TATACTATATATATTTTAAACT
23463 TAT
1 TAT
23466 TTTAAATTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
20 1 0.01
21 17 0.22
22 37 0.49
23 19 0.25
24 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.49
Consensus pattern (22 bp):
TATACTATATATATTTTAAACT
Found at i:23501 original size:13 final size:15
Alignment explanation
Indices: 23440--23504 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
23430 TATTTTAAAC
*
23440 TTATACTATATATATT
1 TTATACTATATAT-TA
* *
23456 TTAAACT-TATTTTAAA
1 TTATACTATATATT--A
23472 TTATACTATATATTA
1 TTATACTATATATTA
23487 TTATA-TATA-ATTA
1 TTATACTATATATTA
23500 TTATA
1 TTATA
23505 AAAATAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 9 0.22
14 5 0.12
15 10 0.24
16 12 0.29
17 5 0.12
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATACTATATATTA
Found at i:25189 original size:17 final size:17
Alignment explanation
Indices: 25167--25200 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25157 TTCTACTTTT
*
25167 CGAGGAAGCATGAGGCG
1 CGAGGAAGCACGAGGCG
25184 CGAGGAAGCACGAGGCG
1 CGAGGAAGCACGAGGCG
25201 GGAGCATCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.47, T:0.03
Consensus pattern (17 bp):
CGAGGAAGCACGAGGCG
Found at i:25479 original size:21 final size:21
Alignment explanation
Indices: 25358--25479 Score: 70
Period size: 21 Copynumber: 5.9 Consensus size: 21
25348 CGCAGTCGTT
* *
25358 TCAGATG-CACCACAACCATA
1 TCAGATGCCACCGCAGCCATA
** * *
25378 TCAGATGGTACCGCAACCATT
1 TCAGATGCCACCGCAGCCATA
* *
25399 TCAGATGTCACAGCAG-C-TGA
1 TCAGATGCCACCGCAGCCAT-A
* ***
25419 GTCAGACGCCACCGCTTTCATA
1 -TCAGATGCCACCGCAGCCATA
* * *
25441 TCAGATGTCACTGTAGCCATA
1 TCAGATGCCACCGCAGCCATA
25462 TCAGATGCCACCGCAGCC
1 TCAGATGCCACCGCAGCC
25480 GGGTCAGATG
Statistics
Matches: 74, Mismatches: 23, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
19 1 0.01
20 8 0.11
21 62 0.84
22 2 0.03
23 1 0.01
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (21 bp):
TCAGATGCCACCGCAGCCATA
Found at i:28859 original size:33 final size:30
Alignment explanation
Indices: 28780--28867 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 30
28770 TTAGTATTTT
* *
28780 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTT-TATTAATATA
* *
28812 ATTATATAAATATTATTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTATT--AAT-ATA
28845 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
28868 GAATTATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
30 4 0.09
31 4 0.09
32 15 0.33
33 19 0.41
34 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TTTATATAATTATTATTTTTTATTAATATA
Found at i:28894 original size:17 final size:19
Alignment explanation
Indices: 28874--28908 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
28864 TTTAGAATTA
28874 TTAATTAT-TT-TTTTGTG
1 TTAATTATATTGTTTTGTG
28891 TTAATTATATTGTTTTGT
1 TTAATTATATTGTTTTGT
28909 CTACAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (19 bp):
TTAATTATATTGTTTTGTG
Found at i:29032 original size:17 final size:16
Alignment explanation
Indices: 29010--29063 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
29000 TAATGTTAAT
29010 ATTTAAATTTATTTTTA
1 ATTTAAA-TTATTTTTA
* *
29027 ATTTAAAGTTATTATGA
1 ATTTAAA-TTATTTTTA
* *
29044 ATTTATATTAATTTTA
1 ATTTAAATTATTTTTA
29060 ATTT
1 ATTT
29064 TTTATAATGC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTTA
Found at i:34728 original size:12 final size:12
Alignment explanation
Indices: 34711--34735 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34701 CCAGCGCGAT
34711 TCCACCACCATC
1 TCCACCACCATC
34723 TCCACCACCATC
1 TCCACCACCATC
34735 T
1 T
34736 TAGGAAGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.56, G:0.00, T:0.20
Consensus pattern (12 bp):
TCCACCACCATC
Found at i:37125 original size:16 final size:16
Alignment explanation
Indices: 37097--37129 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37087 CACGTGAGGA
37097 TTATCTTATTTTTATT
1 TTATCTTATTTTTATT
37113 TTAT-TTATCTTTTATT
1 TTATCTTAT-TTTTATT
37129 T
1 T
37130 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATCTTATTTTTATT
Found at i:37960 original size:21 final size:21
Alignment explanation
Indices: 37930--37977 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
37920 GCAGGGGTAC
* *
37930 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
*
37951 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCACTTCAT
37972 ATGCCA
1 ATGCCA
37978 TATTCGTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:38052 original size:42 final size:42
Alignment explanation
Indices: 37987--38075 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
37977 ATATTCGTAG
* *
37987 GGTTACATTCCGAGACCGCAGGGTTACATTCCTAGCCTGTCA
1 GGTTACATTCCGAGACCGCAGGGTTACATTCCTAGCCCGCCA
* * *
38029 GGTTACATTTCGAGCCCGTAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCGAGACCGCAGGGTTACATTCCTAGCCCGCCA
38071 GGTTA
1 GGTTA
38076 TATGCCTAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (42 bp):
GGTTACATTCCGAGACCGCAGGGTTACATTCCTAGCCCGCCA
Found at i:38066 original size:21 final size:21
Alignment explanation
Indices: 37982--38092 Score: 109
Period size: 21 Copynumber: 5.3 Consensus size: 21
37972 ATGCCATATT
* *
37982 CGTAGGGTTACATTCCGAGAC
1 CGTAGGGTTACATTCCTAGCC
*
38003 CGCAGGGTTACATTCCTAGCC
1 CGTAGGGTTACATTCCTAGCC
* * *
38024 TGTCA-GGTTACATTTCGAGCC
1 CGT-AGGGTTACATTCCTAGCC
38045 CGTAGGGTTACATTCCTAGCC
1 CGTAGGGTTACATTCCTAGCC
* * *
38066 CGCCA-GGTTATATGCCTAGCC
1 CG-TAGGGTTACATTCCTAGCC
38087 CGTAGG
1 CGTAGG
38093 ATTTTATACC
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
20 2 0.03
21 68 0.94
22 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (21 bp):
CGTAGGGTTACATTCCTAGCC
Found at i:38087 original size:42 final size:42
Alignment explanation
Indices: 37987--38092 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
37977 ATATTCGTAG
* * * * *
37987 GGTTACATTCCGAGACCGCAGGGTTACATTCCTAGCCTGTCA
1 GGTTACATGCCGAGCCCGTAGGGTTACATTCCTAGCCCGCCA
**
38029 GGTTACATTTCGAGCCCGTAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATGCCGAGCCCGTAGGGTTACATTCCTAGCCCGCCA
* *
38071 GGTTATATGCCTAGCCCGTAGG
1 GGTTACATGCCGAGCCCGTAGG
38093 ATTTTATACC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.26
Consensus pattern (42 bp):
GGTTACATGCCGAGCCCGTAGGGTTACATTCCTAGCCCGCCA
Found at i:38658 original size:34 final size:34
Alignment explanation
Indices: 38606--38705 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 34
38596 TAAATGTTTT
* *
38606 TAAAAATACAAATTATATTATTTGAAATTTAAAA
1 TAAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
38640 TAAAAATAAAAATAATATTATTCAAAATTTAAAT
1 TAAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
38674 TTAAAATATAAATTATAGTATTCGAAATTTAA
1 TAAAAATAAAAATTATATTATTCGAAATTTAA
38706 CATTAAATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (34 bp):
TAAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:39566 original size:126 final size:126
Alignment explanation
Indices: 39118--39584 Score: 792
Period size: 127 Copynumber: 3.7 Consensus size: 126
39108 CTATAGTTCT
*
39118 CGAGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATGGAAGGCGC
1 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC
* * *
39183 CCCCCCGGGAACGTGCCTTCAAGTCCCCTAAGAAATAATAGGTACTGATATGAATAGTGTCCC
66 GCCCCCGGGAACGCGCCTTCAAGTCCCCTGAG-AA-AATAGGTACTGATATGAATAGTGTCCC
39246 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC
1 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC
*
39311 -CCCCTGGGAACGCGCCTTCAAGTCCCCTGAGAAATTATAGGTACTGATATGAATAGTGTCCC
66 GCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAA--ATAGGTACTGATATGAATAGTGTCCC
*
39373 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGAGC
1 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC
39438 GCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAAATAGGTACTGATATGAATAGTGTCCC
66 GCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAAATAGGTACTGATATGAATAGTGTCCC
** * *
39499 CGAGAAACATGAGTGACATAATAGGGCAATGATAACATATTCTTTGATAAAATAATGGAAGGCGC
1 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC
*
39564 GCCCCCGAGAACGCGCCTTCA
66 GCCCCCGGGAACGCGCCTTCA
39585 TGTGAATAGT
Statistics
Matches: 324, Mismatches: 12, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
125 1 0.00
126 108 0.33
127 118 0.36
128 97 0.30
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (126 bp):
CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC
GCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAAATAGGTACTGATATGAATAGTGTCCC
Found at i:39678 original size:8 final size:8
Alignment explanation
Indices: 39665--39705 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
39655 TCACAAGCTT
39665 TCAAATTC
1 TCAAATTC
39673 TCAAATTC
1 TCAAATTC
* *
39681 CCAAACTC
1 TCAAATTC
39689 T-AAATTC
1 TCAAATTC
39696 TCAAATTC
1 TCAAATTC
39704 TC
1 TC
39706 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:65637 original size:64 final size:63
Alignment explanation
Indices: 65564--65688 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 63
65554 ATGTACCAAT
65564 CCATGCATCGATGCAC-CATGG-AATT-AATTGAACATCAAATGCATTTTATGCATCGATGCACA
1 CCATGCATCGATGCACTCA-GGCAATTCAA---AACATCAAATGCATTTTATGCATCGATGCACA
65626 TA
62 TA
* *
65628 CCATGCATCGATGCACTCAGGCTATTTCAAAACATCGAATGCATTTTATGCATCGATGCAC
1 CCATGCATCGATGCACTCAGGC-AATTCAAAACATCAAATGCATTTTATGCATCGATGCAC
65689 TCTTAGTGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
64 48 0.87
65 2 0.04
66 3 0.05
67 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (63 bp):
CCATGCATCGATGCACTCAGGCAATTCAAAACATCAAATGCATTTTATGCATCGATGCACATA
Found at i:68123 original size:13 final size:13
Alignment explanation
Indices: 68105--68129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68095 TTAAAGTAAA
68105 TAAAAAAGGAATT
1 TAAAAAAGGAATT
68118 TAAAAAAGGAAT
1 TAAAAAAGGAAT
68130 AAAATTAGGG
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:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (13 bp):
TAAAAAAGGAATT
Done.