Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006966.1 Hibiscus syriacus cultivar Beakdansim tig00017927_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: 74290
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4001 original size:10 final size:11
Alignment explanation
Indices: 3976--4000 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3966 ATCATTTAAG
3976 TTTTAAGTTTT
1 TTTTAAGTTTT
3987 TTTTAAGTTTT
1 TTTTAAGTTTT
3998 TTT
1 TTT
4001 ACTTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTAAGTTTT
Found at i:4159 original size:16 final size:17
Alignment explanation
Indices: 4127--4171 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
4117 TATTTTTGTG
4127 AAAAAAATTAAATATAA
1 AAAAAAATTAAATATAA
* *
4144 TAAAATATTAAA-ATAA
1 AAAAAAATTAAATATAA
*
4160 AAAAAGATTAAA
1 AAAAAAATTAAA
4172 GATTCTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAAAATTAAATATAA
Found at i:7771 original size:28 final size:28
Alignment explanation
Indices: 7738--7792 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
7728 CCGCCATTCC
* * *
7738 TTTTAAGGATTAGCTTGACAACATAATG
1 TTTTAAGCACTAGCTCGACAACATAATG
7766 TTTTAAGCACTAGCTCGACAACATAAT
1 TTTTAAGCACTAGCTCGACAACATAAT
7793 ATAAACGGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (28 bp):
TTTTAAGCACTAGCTCGACAACATAATG
Found at i:8168 original size:66 final size:66
Alignment explanation
Indices: 8084--8212 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
8074 CCAATCTTTT
* * * *
8084 ATTTTATATAAAATAATATCCATAAATAATAACATGACATGTGATTAATATTATATGCATGAATA
1 ATTTTATATAAAATAATATCCACAAATAATAACATGAAATGTGATAAATATTATATACATGAATA
8149 A
66 A
** * **
8150 ATTTTAT-TCAAAATAATATCCACGTATGATAATGTGAAATGTGATAAATATTATATACATGAA
1 ATTTTATAT-AAAATAATATCCACAAATAATAACATGAAATGTGATAAATATTATATACATGAA
8213 CAGACAGACA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (66 bp):
ATTTTATATAAAATAATATCCACAAATAATAACATGAAATGTGATAAATATTATATACATGAATA
A
Found at i:12620 original size:28 final size:22
Alignment explanation
Indices: 12555--12606 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
12545 ATTCCGTTTT
12555 TCGAAATTCGAACCCGAAGACC
1 TCGAAATTCGAACCCGAAGACC
12577 TCGAAATTCGAACCCGAAGACC
1 TCGAAATTCGAACCCGAAGACC
12599 TCGAAATT
1 TCGAAATT
12607 TTCAGTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (22 bp):
TCGAAATTCGAACCCGAAGACC
Found at i:17088 original size:23 final size:23
Alignment explanation
Indices: 17058--17130 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
17048 ATAATTTACA
*
17058 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
17081 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
17104 ATATAAACGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
17127 ATAT
1 ATAT
17131 TTTTACCTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:17582 original size:23 final size:23
Alignment explanation
Indices: 17549--17621 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
17539 ATACTTTACA
*
17549 ATATAAGCACTACCTATTACATT
1 ATATAAACACTACCTATTACATT
17572 ATATAAACACTACCTATTACATT
1 ATATAAACACTACCTATTACATT
* *
17595 ATATAAACGCTACCTATTACATC
1 ATATAAACACTACCTATTACATT
17618 ATAT
1 ATAT
17622 TTTTACCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATT
Found at i:18003 original size:487 final size:488
Alignment explanation
Indices: 16656--18232 Score: 2908
Period size: 491 Copynumber: 3.2 Consensus size: 488
16646 TTATAATATG
16656 TTGAAAGTGTCCATACTTTTTTATAAAAA-GAATCGATACTTTTTTTAAAGTTATGTAATTTATG
1 TTGAAAGTGTCCATAC-TTTTTATAAAAATG-ATCGATACTTTTTTTAAAGTTATGTAATTTATG
* *
16720 TTTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
64 TTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
* *
16784 ACAAACAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
129 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
* *
16849 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTTTTGTTTTTAATTTAATAATAATATA
194 TTAACCAAAGATAATAAAAAATATGTAATATATATGTTTATT-TTTTTAATTTAATAATAATATA
*
16914 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
258 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
*
16979 TCAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
323 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
* *
17044 ATAGATAATTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
388 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
17109 AACGCTACCTATTACATCATATTTTTACCTATTATA
453 AACGCTACCTATTACATCATATTTTTACCTATTATA
17145 TTGAAAGTGTCCATACTTTTTATAAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTAT-AAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
17210 TTCAATTTTTTTTAACAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTAC
65 TTCAA-TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
17275 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
129 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
17340 TTAACCAAAGATAATAAAAAAATATGTAATATATATGTTTATTTTTTTAATTTAATAATAATATA
194 TTAACCAAAGATAAT-AAAAAATATGTAATATATATGTTTATTTTTTTAATTTAATAATAATATA
17405 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
258 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
17470 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
323 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
*
17535 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATATA
388 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
17600 AACGCTACCTATTACATCATATTTTTACCTATTATA
453 AACGCTACCTATTACATCATATTTTTACCTATTATA
*
17636 TTGAAAGTATCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
17701 TCAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
17765 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
17830 AACCAAAGATAATAAAAAATATGTAATATATATGTTTATTTTTTTAATTTAATAATAATATATAC
196 AACCAAAGATAATAAAAAATATGTAATATATATGTTTATTTTTTTAATTTAATAATAATATATAC
17895 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
261 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
17960 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
326 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
* *
18025 TATACTTTACAATATAAGCACTACTTATTACATTATATAAACGCTACCTATTACATTATATAAAC
391 GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAAC
*
18090 GCTACCTATTACATCATATTTTTACTTATTATA
456 GCTACCTATTACATCATATTTTTACCTATTATA
*
18123 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
18188 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
66 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAA
18233 AACTCGTCTG
Statistics
Matches: 1061, Mismatches: 21, Indels: 13
0.97 0.02 0.01
Matches are distributed among these distances:
487 343 0.32
488 183 0.17
489 60 0.06
490 47 0.04
491 403 0.38
492 25 0.02
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (488 bp):
TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAAAAAATATGTAATATATATGTTTATTTTTTTAATTTAATAATAATATATAC
CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAAC
GCTACCTATTACATCATATTTTTACCTATTATA
Found at i:18071 original size:23 final size:23
Alignment explanation
Indices: 18036--18108 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
18026 ATACTTTACA
* * *
18036 ATATAAGCACTACTTATTACATT
1 ATATAAACGCTACCTATTACATT
18059 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
18082 ATATAAACGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
18105 ATAT
1 ATAT
18109 TTTTACTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:18946 original size:200 final size:200
Alignment explanation
Indices: 18622--20385 Score: 3179
Period size: 200 Copynumber: 8.8 Consensus size: 200
18612 AACATTAAAC
* * * *
18622 AGTGTCGATACA-TATTATATACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
18686 AAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
*
18751 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTATGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
18816 TACAAA
195 TACAAA
* * *
18822 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGATATACTTGTACAGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
18887 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
18952 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTTGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
19017 ACAAA
196 ACAAA
* *
19022 AGTGTCGATACATTATTTAGACCTATTCTCTTATAAAACCGGTATAATTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
19087 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
19152 GATAGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTAGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
19217 ACAAA
196 ACAAA
* *
19222 AGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
19287 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
19352 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
19417 ACAAA
196 ACAAA
19422 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
19487 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
19552 GATCGACACTTTACTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
19617 ACAAA
196 ACAAA
19622 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
19687 AAAATTACCTATTACATTATACTTATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATA
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
19752 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
19817 ACAAA
196 ACAAA
*
19822 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
19887 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
19952 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
20017 ACAAA
196 ACAAA
*
20022 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
20087 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGAGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
20152 GATCAACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
20217 ACAAA
196 ACAAA
* * ** *
20222 ATTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGATATACTTGTATAGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
20287 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
20352 GATCGACACTTTATGGTTGCACACTATTTGCCAT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
20386 ATTGTAAATT
Statistics
Matches: 1510, Mismatches: 53, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
200 1506 1.00
201 4 0.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:20630 original size:18 final size:18
Alignment explanation
Indices: 20607--20667 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
20597 TCTCATTCAT
*
20607 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
20625 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
20644 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
20663 AATTA
1 AATTA
20668 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:20643 original size:19 final size:19
Alignment explanation
Indices: 20619--20667 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
20609 TTATATTCAC
20619 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
20638 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
20657 ATACAAAATTA
1 ATACAAAATTA
20668 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:22495 original size:33 final size:33
Alignment explanation
Indices: 22458--22523 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
22448 CATCTTAATA
*
22458 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
22491 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
22524 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:22586 original size:21 final size:21
Alignment explanation
Indices: 22557--22621 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
22547 CCCCTTATGC
* *
22557 CTATCAAGTGTATCTTCGACT
1 CTATCAAGTTTCTCTTCGACT
*
22578 CTCTCAAGTTTCTCTTCGACT
1 CTATCAAGTTTCTCTTCGACT
22599 CTATCAAGTTTCTCTTCGACT
1 CTATCAAGTTTCTCTTCGACT
22620 CT
1 CT
22622 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
CTATCAAGTTTCTCTTCGACT
Found at i:24897 original size:20 final size:19
Alignment explanation
Indices: 24851--24897 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
24841 TCCGGTATCG
*
24851 TTTTACTGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
24870 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
24891 TTTTACC
1 TTTTACC
24898 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:25148 original size:161 final size:161
Alignment explanation
Indices: 24874--25210 Score: 514
Period size: 161 Copynumber: 2.1 Consensus size: 161
24864 ATCATTTTGA
* * *
24874 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTAAAGTATCGA
1 TACCGGTTTTATCATATTTTTACCTGGTATATCGTTGTGGATCGATAATTTTTTAAAAGTATCGA
* *
24939 CACATTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTGTA-TAAAGT
66 CACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGT
* * * *
25003 ATCGACACTTTCAATATATCCGGTAATGTTT
131 ACCGACACTTTAAATATATCCGGTAACGCTT
*
25034 TACCGGTTTTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGGTATATCGTTGTGGATCGATA-ATTTTTTAAAAGTATCG
* ** *
25099 ACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAG
65 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
* *
25164 TACCGACACTTTAAATGTATCCGGTAGCGCTT
130 TACCGACACTTTAAATATATCCGGTAACGCTT
25196 TACCGGTTTTATCAT
1 TACCGGTTTTATCAT
25211 TTCAATACCG
Statistics
Matches: 159, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
160 45 0.28
161 68 0.43
162 46 0.29
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (161 bp):
TACCGGTTTTATCATATTTTTACCTGGTATATCGTTGTGGATCGATAATTTTTTAAAAGTATCGA
CACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGT
ACCGACACTTTAAATATATCCGGTAACGCTT
Found at i:25262 original size:161 final size:158
Alignment explanation
Indices: 24874--25266 Score: 353
Period size: 161 Copynumber: 2.4 Consensus size: 158
24864 ATCATTTTGA
** * * * ** ** * *
24874 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTAAAGTATCGA
1 TACCGGTTTTATCATATTAATACCTGGTATATAGTTTTACATCGATACATGTTTT--AGGATCGA
* *
24939 CACATTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTGTATAAAGTA
64 CACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGTA
* * * *
25004 TCGACACTTTCAATATATCCGGTAATGTTT
129 CCGACACTTTAAATATATCCGGTAACGCTT
** * ** * *
25034 TACCGGTTTTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
1 TACCGGTTTTATCATATTAATACCTGGTATATAGTTTTACATCGATACATGTTTT---AGGATCG
* ** *
25099 ACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAG
63 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAG
* *
25164 TACCGACACTTTAAATGTATCCGGTAGCGCTT
127 TACCGACACTTTAAATATATCCGGTAACGCTT
* * *
25196 TACCGGTTTTATCAT-TTCAATACC-GGTTTTGTTATAGTTTTACAT-GTTATATCGTTTT-GGA
1 TACCGGTTTTATCATATT-AATACCTGG---T-ATATAGTTTTACATCGATACAT-GTTTTAGGA
25257 TCGACACATT
60 TCGACACATT
25267 TTTAATTTGG
Statistics
Matches: 198, Mismatches: 27, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
160 51 0.26
161 77 0.39
162 50 0.25
164 6 0.03
165 14 0.07
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.42
Consensus pattern (158 bp):
TACCGGTTTTATCATATTAATACCTGGTATATAGTTTTACATCGATACATGTTTTAGGATCGACA
CATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGTACC
GACACTTTAAATATATCCGGTAACGCTT
Found at i:35972 original size:2 final size:2
Alignment explanation
Indices: 35965--36009 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
35955 TCGGATATGA
35965 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
36007 AT A
1 AT A
36010 AGCAGTTTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36527 original size:5 final size:5
Alignment explanation
Indices: 36519--36545 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
36509 GCAAAAAGAA
36519 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
36546 GGGGTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:38914 original size:37 final size:39
Alignment explanation
Indices: 38864--38949 Score: 140
Period size: 39 Copynumber: 2.3 Consensus size: 39
38854 TTCAAAAATC
*
38864 GTTTTAAAAACTATA-TA-ACATATATATATATATATAT
1 GTTTTCAAAACTATATTATACATATATATATATATATAT
*
38901 GTTTTCAAAACTATATTATATATATATATATATATATAT
1 GTTTTCAAAACTATATTATACATATATATATATATATAT
38940 GTTTTCAAAA
1 GTTTTCAAAA
38950 TATGTTTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 14 0.31
38 2 0.04
39 29 0.64
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (39 bp):
GTTTTCAAAACTATATTATACATATATATATATATATAT
Found at i:38929 original size:35 final size:36
Alignment explanation
Indices: 38864--38937 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
38854 TTCAAAAATC
38864 GTTTTAAAAACTATATAACATATATATATATATATAT
1 GTTTTAAAAACTATAT-ACATATATATATATATATAT
* *
38901 GTTTTCAAAACTATATTATATATATATATATATATAT
1 GTTTTAAAAACTATA-TACATATATATATATATATAT
38938 ATGTTTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 33 0.97
38 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (36 bp):
GTTTTAAAAACTATATACATATATATATATATATAT
Found at i:38954 original size:13 final size:13
Alignment explanation
Indices: 38936--38962 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38926 ATATATATAT
38936 ATATGTTTTCAAA
1 ATATGTTTTCAAA
38949 ATATGTTTTCAAA
1 ATATGTTTTCAAA
38962 A
1 A
38963 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:38968 original size:35 final size:34
Alignment explanation
Indices: 38929--39117 Score: 175
Period size: 36 Copynumber: 5.3 Consensus size: 34
38919 TATATATATA
38929 TATATATATATGTTTTCAAAATATGTTTTCAAAAC
1 TATATATATATGTTTTCAAAA-ATGTTTTCAAAAC
** * *
38964 TATATTATATACATTTTTAAAAACTGTTTT-TAAAC
1 TATA-TATATATGTTTTCAAAAA-TGTTTTCAAAAC
*
38999 TATATATTATACGTTTTCAAAAATGTGTTTTCAAAAC
1 TATATA-TATATGTTTTCAAAAA--TGTTTTCAAAAC
* * *
39036 CATAT-TATATGCTTTCAAAAACCGTTTTCTAAAAAC
1 TATATATATATGTTTTCAAAAA-TGTTTTC--AAAAC
*
39072 TATATATTATATGTTTTCAAAAATATTTTCAAAAAC
1 TATATA-TATATGTTTTCAAAAATGTTTTC-AAAAC
39108 TATACTATAT
1 TATA-TATAT
39118 TATTATATAT
Statistics
Matches: 127, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
34 8 0.06
35 41 0.32
36 48 0.38
37 15 0.12
38 15 0.12
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (34 bp):
TATATATATATGTTTTCAAAAATGTTTTCAAAAC
Found at i:38968 original size:37 final size:36
Alignment explanation
Indices: 38888--39117 Score: 163
Period size: 35 Copynumber: 6.2 Consensus size: 36
38878 ATAACATATA
* * * **
38888 TATATATATATATGTTTTCAAAACTATATTAT-ATATA
1 TATATATATATATGTTTTCAAAA--ATGTTTTCAAAAC
38925 TATATATATATATATGTTTTCAAAATATGTTTTCAAAAC
1 TATATATAT--ATATGTTTTCAAAA-ATGTTTTCAAAAC
* *
38964 TATATTATATACAT-TTTT-AAAAACTGTTTT-TAAAC
1 TATA-TATATATATGTTTTCAAAAA-TGTTTTCAAAAC
*
38999 TATATAT-TATACGTTTTCAAAAATGTGTTTTCAAAAC
1 TATATATATATATGTTTTCAAAAA--TGTTTTCAAAAC
* * *
39036 --CATAT-TATATGCTTTCAAAAACCGTTTTCTAAAAAC
1 TATATATATATATGTTTTCAAAAA-TGTTTTC--AAAAC
*
39072 TATATAT-TATATGTTTTCAAAAATATTTTCAAAAAC
1 TATATATATATATGTTTTCAAAAATGTTTTC-AAAAC
39108 TATACTATAT
1 TATA-TATAT
39118 TATTATATAT
Statistics
Matches: 158, Mismatches: 20, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
33 3 0.02
34 13 0.08
35 32 0.20
36 31 0.20
37 25 0.16
38 29 0.18
39 20 0.13
40 5 0.03
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATATATATGTTTTCAAAAATGTTTTCAAAAC
Found at i:39009 original size:89 final size:87
Alignment explanation
Indices: 38835--39003 Score: 209
Period size: 89 Copynumber: 1.9 Consensus size: 87
38825 AATTTAAAAT
* * *
38835 TATATATATTATATATGTTTTCAAAAATCGTTTTAAAAACTATATAACATATATATATATATATA
1 TATATATATTATATATGTTTTCAAAAATCGTTTTAAAAACTATAT-ACATATACATATATAAAAA
38900 TGTTTTCAAAACTATATTATATA
65 TGTTTTCAAAACTATATTATATA
* * * *
38923 TATATATATATATATATGTTTTCAAAATAT-GTTTTCAAAACTATAT-TATATACATTTTTAAAA
1 TATATATAT-TATATATGTTTTCAAAA-ATCGTTTTAAAAACTATATACATATACATATATAAAA
*
38986 ACTGTTTT-TAAACTATAT
64 A-TGTTTTCAAAACTATAT
39004 ATTATACGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
87 21 0.30
88 15 0.21
89 32 0.46
90 2 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.47
Consensus pattern (87 bp):
TATATATATTATATATGTTTTCAAAAATCGTTTTAAAAACTATATACATATACATATATAAAAAT
GTTTTCAAAACTATATTATATA
Found at i:39028 original size:36 final size:35
Alignment explanation
Indices: 38927--39111 Score: 164
Period size: 35 Copynumber: 5.1 Consensus size: 35
38917 TATATATATA
*
38927 TATATATATATATGTTTTCAAAATATGTTTTCAAAAC
1 TATATAT-TATATGTTTTCAAAA-ATGTTTTTAAAAC
*
38964 TATATTATATACAT-TTTT-AAAAACTGTTTTT-AAAC
1 TATA-TAT-TATATGTTTTCAAAAA-TGTTTTTAAAAC
*
38999 TATATATTATACGTTTTCAAAAATGTGTTTTCAAAAC
1 TATATATTATATGTTTTCAAAAATGT-TTTT-AAAAC
* * *
39036 --CATATTATATGCTTTCAAAAACCGTTTTCTAAAAAC
1 TATATATTATATGTTTTCAAAAA-TGTTTT-T-AAAAC
* *
39072 TATATATTATATGTTTTCAAAAATATTTTCAAAAAC
1 TATATATTATATGTTTTCAAAAATGTTTT-TAAAAC
39108 TATA
1 TATA
39112 CTATATTATT
Statistics
Matches: 123, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
33 3 0.02
34 10 0.08
35 39 0.32
36 27 0.22
37 17 0.14
38 27 0.22
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.44
Consensus pattern (35 bp):
TATATATTATATGTTTTCAAAAATGTTTTTAAAAC
Found at i:39028 original size:72 final size:71
Alignment explanation
Indices: 38927--39117 Score: 228
Period size: 72 Copynumber: 2.6 Consensus size: 71
38917 TATATATATA
* *
38927 TATATATATATATGTTTTC-AAAATATGTTTTCAAAACTATATTATATACATTTTTAAAAACTGT
1 TATATAT-TATATGTTTTCAAAAAT-TGTTTTCAAAACTATATTATATAC--TTTCAAAAACCGT
38991 TTT-T-AAAC
62 TTTCTAAAAC
* * *
38999 TATATATTATACGTTTTCAAAAATGTGTTTTCAAAACCATATTATATGCTTTCAAAAACCGTTTT
1 TATATATTATATGTTTTCAAAAAT-TGTTTTCAAAACTATATTATATACTTTCAAAAACCGTTTT
39064 CTAAAAAC
65 CT-AAAAC
* *
39072 TATATATTATATGTTTTCAAAAA-TATTTTCAAAAACTATACTATAT
1 TATATATTATATGTTTTCAAAAATTGTTTTC-AAAACTATATTATAT
39118 TATTATATAT
Statistics
Matches: 104, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
70 14 0.13
71 17 0.16
72 47 0.45
73 26 0.25
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (71 bp):
TATATATTATATGTTTTCAAAAATTGTTTTCAAAACTATATTATATACTTTCAAAAACCGTTTTC
TAAAAC
Found at i:42828 original size:28 final size:30
Alignment explanation
Indices: 42759--42829 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
42749 TAAAAATGAA
42759 AATAAATAAATAAATAAATAATAATATAATCT
1 AATAAA-AAATAAATAAATAATAATATAA-CT
*
42791 AATATAAAAAT-AATAAATGATAATAT-A-T
1 AATA-AAAAATAAATAAATAATAATATAACT
42819 AATTAAAAAAT
1 AA-TAAAAAAT
42830 TATATAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
28 9 0.25
29 2 0.06
30 1 0.03
31 14 0.39
32 8 0.22
33 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (30 bp):
AATAAAAAATAAATAAATAATAATATAACT
Found at i:42829 original size:21 final size:21
Alignment explanation
Indices: 42790--42829 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42780 TAATATAATC
*
42790 TAATATAAAAATAATAAATGA
1 TAATATAAAAATAAAAAATGA
* *
42811 TAATATATAATTAAAAAAT
1 TAATATAAAAATAAAAAAT
42830 TATATAACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
TAATATAAAAATAAAAAATGA
Found at i:42863 original size:22 final size:22
Alignment explanation
Indices: 42838--42879 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42828 ATTATATAAC
*
42838 ATATATTATATTTTCAAAAACT
1 ATATAATATATTTTCAAAAACT
*
42860 ATATAATATGTTTTCAAAAA
1 ATATAATATATTTTCAAAAA
42880 TCGTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATAATATATTTTCAAAAACT
Found at i:43000 original size:37 final size:37
Alignment explanation
Indices: 42848--43112 Score: 198
Period size: 38 Copynumber: 7.2 Consensus size: 37
42838 ATATATTATA
* *
42848 TTTTCAAAAACTATATA--ATATGTTTTCAAAAAT-CG
1 TTTTC-AAAACTATATATTATATGTTTTCAAAACTGTG
* * *
42883 TTTTAAAAACTATATA-TATA--TATTCAAAA-TATG
1 TTTTCAAAACTATATATTATATGTTTTCAAAACTGTG
*
42916 TTTTCAAAACTATAT-TATATACGTTTTCAAAAACCTCGT-
1 TTTTCAAAACTATATAT-TATATGTTTTC-AAAA-CT-GTG
*
42955 TTTT-AAAACTATATATTATACGTTTTCAAAACTGTG
1 TTTTCAAAACTATATATTATATGTTTTCAAAACTGTG
* * *
42991 TTTTCAAAACCATAT-TATATATGTTTTCAAAAACCGATT
1 TTTTCAAAACTATATAT-TATATGTTTTC-AAAACTG-TG
* * *
43030 TTTTAAAAAACTATATATTATATGCTTTTAAAAACCGT-
1 TTTT-CAAAACTATATATTATATG-TTTTCAAAACTGTG
* *
43068 TTTCTAAAAACTATATATTATATGTTTTCAAAA-T-TA
1 TTT-TCAAAACTATATATTATATGTTTTCAAAACTGTG
43104 TTTTCAAAA
1 TTTTCAAAA
43113 ACTCTACACT
Statistics
Matches: 193, Mismatches: 16, Indels: 42
0.77 0.06 0.17
Matches are distributed among these distances:
32 1 0.01
33 23 0.12
34 15 0.08
35 15 0.08
36 14 0.07
37 35 0.18
38 49 0.25
39 13 0.07
40 23 0.12
41 5 0.03
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.43
Consensus pattern (37 bp):
TTTTCAAAACTATATATTATATGTTTTCAAAACTGTG
Found at i:43265 original size:13 final size:13
Alignment explanation
Indices: 43247--43298 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
43237 GTCATAAATC
43247 TATGACGCGCATT
1 TATGACGCGCATT
43260 TATGACGCGCATT
1 TATGACGCGCATT
* *
43273 TATGATGCTCATT
1 TATGACGCGCATT
*
43286 TATGACGCACATT
1 TATGACGCGCATT
43299 GCGCGTCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:45733 original size:2 final size:2
Alignment explanation
Indices: 45726--45850 Score: 250
Period size: 2 Copynumber: 62.5 Consensus size: 2
45716 CAAAGACAAT
45726 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
45768 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
45810 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
45851 TATATATATA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 123 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:45855 original size:2 final size:2
Alignment explanation
Indices: 45850--45897 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
45840 ACACACACAC
45850 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
45892 AT AT AT
1 AT AT AT
45898 CACCAAGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47128 original size:20 final size:20
Alignment explanation
Indices: 47104--47151 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
47094 TGTATATAAT
47104 ATAAAAAATA-TAATAAGATA
1 ATAAAAAATAGTAAT-AGATA
* *
47124 CTAAAAAGTAGTAATAGATA
1 ATAAAAAATAGTAATAGATA
47144 ATAAAAAA
1 ATAAAAAA
47152 CAGAAAGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (20 bp):
ATAAAAAATAGTAATAGATA
Found at i:49698 original size:14 final size:14
Alignment explanation
Indices: 49679--49705 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49669 TGGTTGCTTG
49679 TCTGGAATCTTGAT
1 TCTGGAATCTTGAT
49693 TCTGGAATCTTGA
1 TCTGGAATCTTGA
49706 AGGTCTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
TCTGGAATCTTGAT
Found at i:53710 original size:18 final size:19
Alignment explanation
Indices: 53683--53767 Score: 64
Period size: 23 Copynumber: 4.2 Consensus size: 19
53673 AAAACCAGAA
*
53683 CCCC-AGGGGGTATCGATT
1 CCCCTAGGGGGAATCGATT
*
53701 CCCCTAGGGGGAATCGGTT
1 CCCCTAGGGGGAATCGATT
*
53720 CCCCTTCAAAGGGGGAATCGGTT
1 CCCC-T---AGGGGGAATCGATT
*
53743 CCCCTTCAAGGGGGTATCGATT
1 CCCC-T--AGGGGGAATCGATT
53765 CCC
1 CCC
53768 TCTGCCCTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
18 4 0.07
19 16 0.28
20 1 0.02
22 16 0.28
23 20 0.35
ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22
Consensus pattern (19 bp):
CCCCTAGGGGGAATCGATT
Found at i:53753 original size:22 final size:23
Alignment explanation
Indices: 53706--53767 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
53696 CGATTCCCCT
53706 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
53729 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
53751 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
53768 TCTGCCCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:59976 original size:19 final size:19
Alignment explanation
Indices: 59939--59976 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
59929 ACCCTAAACA
*
59939 TTTTTCTCTTTTTTGTTCT
1 TTTTTCTCTTTTTTCTTCT
59958 TTTTTC-CTTTTCTTCTTCT
1 TTTTTCTCTTTT-TTCTTCT
59977 ACTTAGGACG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTTCTCTTTTTTCTTCT
Found at i:66433 original size:21 final size:21
Alignment explanation
Indices: 66409--66448 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
66399 CCCCTTGACC
*
66409 ATCTTCATCTGATCTTCCAAT
1 ATCTTAATCTGATCTTCCAAT
**
66430 ATCTTAATCTTCTCTTCCA
1 ATCTTAATCTGATCTTCCA
66449 TCTTATTTGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.45
Consensus pattern (21 bp):
ATCTTAATCTGATCTTCCAAT
Found at i:67025 original size:8 final size:7
Alignment explanation
Indices: 66995--67025 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
66985 TATAAAATAT
66995 AAAATGC
1 AAAATGC
67002 AAAATGC
1 AAAATGC
67009 AAAATGC
1 AAAATGC
67016 AAATATGC
1 AAA-ATGC
67024 AA
1 AA
67026 TGCATGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (7 bp):
AAAATGC
Found at i:69194 original size:18 final size:18
Alignment explanation
Indices: 69171--69223 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
69161 ACTGTATATT
69171 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
69189 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
69207 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
69224 CCTTAAGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:69905 original size:20 final size:20
Alignment explanation
Indices: 69876--69919 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
69866 GGTTTGAAAT
69876 TCTC-ATGCATCGATGCACC
1 TCTCAATGCATCGATGCACC
69895 TCTCAATGCATCGATGCACC
1 TCTCAATGCATCGATGCACC
69915 T-TCAA
1 TCTCAA
69920 AATTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27
Consensus pattern (20 bp):
TCTCAATGCATCGATGCACC
Found at i:72871 original size:26 final size:26
Alignment explanation
Indices: 72842--72901 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
72832 AAGTGAATCG
*
72842 AAAATAAA-GACAATAAGAAAATAAAT
1 AAAATAAACGA-AAAAAGAAAATAAAT
* *
72868 AAAACAAACGAAAAAATAAAATAAAT
1 AAAATAAACGAAAAAAGAAAATAAAT
*
72894 AAAGTAAA
1 AAAATAAA
72902 TGTATGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.13
Consensus pattern (26 bp):
AAAATAAACGAAAAAAGAAAATAAAT
Found at i:73003 original size:3 final size:3
Alignment explanation
Indices: 72997--73117 Score: 61
Period size: 3 Copynumber: 38.3 Consensus size: 3
72987 ATGTATAAAG
* *
72997 ATA ATA ATA ATA AGA GAAA ACTA TATA AT- ATA TATA CATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA A-TA -ATA ATA ATA -ATA -ATA ATA ATA
* * *
73043 GTAA ATA ATA ATA ATA AT- ATA TATT ATA TTA AT- ATA A-A ATA ATA
1 AT-A ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
73087 ATA GATA CTA AAA ATTA ATA ATA GATA ATA A
1 ATA -ATA ATA ATA A-TA ATA ATA -ATA ATA A
73118 AAAACAGAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
2 8 0.09
3 59 0.65
4 23 0.25
5 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:73042 original size:16 final size:15
Alignment explanation
Indices: 73018--73117 Score: 64
Period size: 16 Copynumber: 6.7 Consensus size: 15
73008 AAGAGAAAAC
73018 TATATAAT-AT-ATA
1 TATATAATAATAATA
* *
73031 TACATAATAATAGTA
1 TATATAATAATAATA
*
73046 AATAATAATAATAATA
1 TAT-ATAATAATAATA
* *
73062 TATATTATATTAATA
1 TATATAATAATAATA
73077 TA-A-AATAATAATA
1 TATATAATAATAATA
* *
73090 GATACTAAAAATTAATAA
1 TATA-TAATAA-TAAT-A
*
73108 TAGATAATAA
1 TATATAATAA
73118 AAAACAGAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
13 16 0.25
14 4 0.06
15 15 0.23
16 17 0.27
17 9 0.14
18 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (15 bp):
TATATAATAATAATA
Found at i:73088 original size:13 final size:14
Alignment explanation
Indices: 73034--73116 Score: 66
Period size: 13 Copynumber: 6.1 Consensus size: 14
73024 ATATATATAC
*
73034 ATAATAATAGTAA-
1 ATAATAATAATAAT
73047 ATAATAATAATAAT
1 ATAATAATAATAAT
* *
73061 ATATATTATATTAAT
1 ATA-ATAATAATAAT
73076 ATAA-AATAATAAT
1 ATAATAATAATAAT
* * *
73089 A-GATACTAAAAAT
1 ATAATAATAATAAT
73102 -TAATAATAGATAAT
1 ATAATAATA-ATAAT
73116 A
1 A
73117 AAAAACAGAA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
12 1 0.02
13 32 0.60
14 8 0.15
15 12 0.23
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:73107 original size:20 final size:19
Alignment explanation
Indices: 73072--73120 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
73062 TATATTATAT
73072 TAATATAAAATAATAATAGA
1 TAATA-AAAATAATAATAGA
*
73092 TACTAAAAATTAATAATAGA
1 TAATAAAAA-TAATAATAGA
73112 TAATAAAAA
1 TAATAAAAA
73121 ACAGAAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
TAATAAAAATAATAATAGA
Found at i:73117 original size:10 final size:9
Alignment explanation
Indices: 72997--73117 Score: 61
Period size: 10 Copynumber: 12.8 Consensus size: 9
72987 ATGTATAAAG
72997 ATAATAATA
1 ATAATAATA
* *
73006 ATAAGAGAAA
1 ATAATA-ATA
73016 ACTATATAAT-
1 A-TA-ATAATA
73026 ATATATACATA
1 ATA-ATA-ATA
*
73037 ATAATAGTAA
1 ATAATAAT-A
73047 ATAATAATA
1 ATAATAATA
73056 ATAAT-ATA
1 ATAATAATA
* *
73064 TATTATATTA
1 -ATAATAATA
73074 AT-ATAA-A
1 ATAATAATA
73081 ATAATAATA
1 ATAATAATA
* *
73090 GATACTAAAA
1 -ATAATAATA
73100 ATTAATAATA
1 A-TAATAATA
73110 GATAATAA
1 -ATAATAA
73118 AAAACAGAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 25
0.69 0.10 0.20
Matches are distributed among these distances:
7 3 0.03
8 10 0.12
9 26 0.30
10 38 0.44
11 7 0.08
12 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (9 bp):
ATAATAATA
Done.