Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 66 of 344
Found at i:21391084 original size:24 final size:24
Alignment explanation
Indices: 21391057--21391108 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
21391047 TTAGTAAGTC
* *
21391057 AAATAAACTATACTAATGAATGCT
1 AAATAAACTATACTAATAAATACT
* *
21391081 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
21391105 AAAT
1 AAAT
21391109 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:21395771 original size:30 final size:30
Alignment explanation
Indices: 21395733--21395807 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
21395723 ACTTTTTCCC
*
21395733 AAAA-TTTTACTCTCTCCCA-CTTTCACCCT
1 AAAACTTTTACTCCCTCCCATCTTTC-CCCT
* *
21395762 AAAACTTTTACTCCCTCCTATTTTTCCCCT
1 AAAACTTTTACTCCCTCCCATCTTTCCCCT
*
21395792 AAAACTTTTAATCCCT
1 AAAACTTTTACTCCCT
21395808 TCCAATCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.10
30 32 0.80
31 4 0.10
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAACTTTTACTCCCTCCCATCTTTCCCCT
Found at i:21397664 original size:16 final size:15
Alignment explanation
Indices: 21397622--21397670 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
21397612 AGAAAATTGA
21397622 AAAGATAAAAAAT-T
1 AAAGATAAAAAATAT
21397636 AAAGGGATAAAAAAATAT
1 AAA--GAT-AAAAAATAT
*
21397654 AAAGATGAAAAATAT
1 AAAGATAAAAAATAT
21397669 AA
1 AA
21397671 TTTTTCTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 6 0.20
17 7 0.23
18 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.18
Consensus pattern (15 bp):
AAAGATAAAAAATAT
Found at i:21402583 original size:7 final size:7
Alignment explanation
Indices: 21402571--21402619 Score: 98
Period size: 7 Copynumber: 7.0 Consensus size: 7
21402561 ATTCAAAATG
21402571 AATGTGT
1 AATGTGT
21402578 AATGTGT
1 AATGTGT
21402585 AATGTGT
1 AATGTGT
21402592 AATGTGT
1 AATGTGT
21402599 AATGTGT
1 AATGTGT
21402606 AATGTGT
1 AATGTGT
21402613 AATGTGT
1 AATGTGT
21402620 TTGAAGTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (7 bp):
AATGTGT
Found at i:21411512 original size:11 final size:11
Alignment explanation
Indices: 21411496--21411521 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21411486 CAAGAAGAAA
21411496 ATTTTAAAATT
1 ATTTTAAAATT
21411507 ATTTTAAAATT
1 ATTTTAAAATT
21411518 ATTT
1 ATTT
21411522 CTATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTAAAATT
Found at i:21412677 original size:19 final size:20
Alignment explanation
Indices: 21412646--21412712 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
21412636 TAGAGTTTTC
*
21412646 ATTT-ATTTGTTTTATTTAT
1 ATTTAATTTCTTTTATTTAT
21412665 ATTTAATTT-TTTTACTTT-T
1 ATTTAATTTCTTTTA-TTTAT
*
21412684 ATTTAATTTCTATTATTTAT
1 ATTTAATTTCTTTTATTTAT
21412704 -TTTAGATTT
1 ATTTA-ATTT
21412713 AATCCCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 26 0.62
20 16 0.38
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (20 bp):
ATTTAATTTCTTTTATTTAT
Found at i:21413967 original size:40 final size:40
Alignment explanation
Indices: 21413912--21413992 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
21413902 TATCCAACGT
*
21413912 TCAAAGCTACTATTTATTAGGACACTTATATACATTAAAC
1 TCAAAGCTACTATTTATTAGAACACTTATATACATTAAAC
21413952 TCAAAGCTACTATTTATTAGAACACTTATATACATTAAAC
1 TCAAAGCTACTATTTATTAGAACACTTATATACATTAAAC
21413992 T
1 T
21413993 AACCTCAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (40 bp):
TCAAAGCTACTATTTATTAGAACACTTATATACATTAAAC
Found at i:21415204 original size:42 final size:42
Alignment explanation
Indices: 21415140--21415381 Score: 227
Period size: 42 Copynumber: 5.7 Consensus size: 42
21415130 TCGTGTTTAC
* * * *
21415140 TTTCCGTTTAGCTCTCACGAGCTTCTATTTAACTCATATGAG
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTCAACTCATATGAG
* *
21415182 TTTCCGTTTAGCT-GTATTGAGCTTCTGTTCAACTCTTATGAG
1 TTTCCGTTTAGCTCTTA-TGAGCTTCTGTTCAACTCATATGAG
** * * * *
21415224 TTTTTGTTCAGCTCTTCTGAGCTTTTGTTCAACTCTTATGAG
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTCAACTCATATGAG
* ** *
21415266 TTTTCGTCCAACTCTTATGAGCTTCTGTTTCAACTCATATGAG
1 TTTCCGTTTAGCTCTTATGAGCTTCTG-TTCAACTCATATGAG
* * * *
21415309 CTTCCGTTTAGCTCTTATGAGCTCCTGTTCAACCCTTAT-AGG
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTCAACTCATATGA-G
* * * *
21415351 TTTCTGTTTAGCTCTCATAAGCTTCTATTCA
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTCA
21415382 GCCTTAGGGC
Statistics
Matches: 164, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.01
42 126 0.77
43 36 0.22
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTTATGAGCTTCTGTTCAACTCATATGAG
Found at i:21415231 original size:21 final size:21
Alignment explanation
Indices: 21415199--21415347 Score: 147
Period size: 21 Copynumber: 7.0 Consensus size: 21
21415189 TTAGCTGTAT
*
21415199 TGAGCTTCTGTTCAACTCTTA
1 TGAGCTTTTGTTCAACTCTTA
* * *
21415220 TGAGTTTTTGTTCAGCTCTTC
1 TGAGCTTTTGTTCAACTCTTA
21415241 TGAGCTTTTGTTCAACTCTTA
1 TGAGCTTTTGTTCAACTCTTA
*
21415262 TGAG-TTTTCGTCCAACTCTTA
1 TGAGCTTTT-GTTCAACTCTTA
* *
21415283 TGAGCTTCTGTTTCAACTCATA
1 TGAGCTTTTG-TTCAACTCTTA
** * *
21415305 TGAGCTTCCGTTTAGCTCTTA
1 TGAGCTTTTGTTCAACTCTTA
** *
21415326 TGAGCTCCTGTTCAACCCTTA
1 TGAGCTTTTGTTCAACTCTTA
21415347 T
1 T
21415348 AGGTTTCTGT
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.04
21 80 0.76
22 21 0.20
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.44
Consensus pattern (21 bp):
TGAGCTTTTGTTCAACTCTTA
Found at i:21415374 original size:85 final size:84
Alignment explanation
Indices: 21415201--21415381 Score: 193
Period size: 85 Copynumber: 2.1 Consensus size: 84
21415191 AGCTGTATTG
* * ** * ** *
21415201 AGCTTCTGTTCAACTCTTATGAGTTTTTGTTCAGCTCTTCTGAGCTTTTGTTCAACTCTTATGAG
1 AGCTTCTGTTCAACTCATATGAGCTTCCGTTCAGCTCTTATGAGCTCCTGTTCAACCCTTATGAG
* * *
21415266 TTTTCGTCCAACTCTTATG
66 GTTTCGTCCAACTCTCATA
*
21415285 AGCTTCTGTTTCAACTCATATGAGCTTCCGTTTAGCTCTTATGAGCTCCTGTTCAACCCTTAT-A
1 AGCTTCTG-TTCAACTCATATGAGCTTCCGTTCAGCTCTTATGAGCTCCTGTTCAACCCTTATGA
** *
21415349 GGTTTCTGTTTAGCTCTCATA
65 GGTTTC-GTCCAACTCTCATA
*
21415370 AGCTTCTATTCA
1 AGCTTCTGTTCA
21415382 GCCTTAGGGC
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
84 18 0.23
85 61 0.77
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (84 bp):
AGCTTCTGTTCAACTCATATGAGCTTCCGTTCAGCTCTTATGAGCTCCTGTTCAACCCTTATGAG
GTTTCGTCCAACTCTCATA
Found at i:21415376 original size:21 final size:21
Alignment explanation
Indices: 21415201--21415376 Score: 84
Period size: 21 Copynumber: 8.3 Consensus size: 21
21415191 AGCTGTATTG
* *
21415201 AGCTTCTGTTCAACTCTTATG
1 AGCTTCTGTTTAACTCTTATA
* * * * * *
21415222 AGTTTTTGTTCAGCTCTTCTG
1 AGCTTCTGTTTAACTCTTATA
* * *
21415243 AGCTTTTGTTCAACTCTTATG
1 AGCTTCTGTTTAACTCTTATA
* ** *
21415264 AG-TTTTCGTCCAACTCTTATG
1 AGCTTCT-GTTTAACTCTTATA
* *
21415285 AGCTTCTGTTTCAACTCATATG
1 AGCTTCTGTTT-AACTCTTATA
* * *
21415307 AGCTTCCGTTTAGCTCTTATG
1 AGCTTCTGTTTAACTCTTATA
* * *
21415328 AGCTCCTGTTCAACCCTTATA
1 AGCTTCTGTTTAACTCTTATA
* * * *
21415349 GGTTTCTGTTTAGCTCTCATA
1 AGCTTCTGTTTAACTCTTATA
21415370 AGCTTCT
1 AGCTTCT
21415377 ATTCAGCCTT
Statistics
Matches: 122, Mismatches: 30, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
20 4 0.03
21 96 0.79
22 22 0.18
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (21 bp):
AGCTTCTGTTTAACTCTTATA
Found at i:21418665 original size:26 final size:24
Alignment explanation
Indices: 21418621--21418669 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
21418611 ATTTGTTTTA
*
21418621 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
21418645 ATATTTGATTTATTATATTTTTAAA
1 ATATTTG-TTT-TTATATTTTTAAA
21418670 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:21422315 original size:487 final size:487
Alignment explanation
Indices: 21421395--21422371 Score: 1918
Period size: 487 Copynumber: 2.0 Consensus size: 487
21421385 GTAACACCCC
* *
21421395 TAACCTGTATCCATTGTCGAAACAGGGTTTCAGAGCATTACTAGAATTTGCAGATCACCTAAAAA
1 TAACCTATATCCATTATCGAAACAGGGTTTCAGAGCATTACTAGAATTTGCAGATCACCTAAAAA
21421460 AATTTAAATACTTACCGATTCAATGCATCATATAAATAAATATATTACCATTCAATCAACAGTTT
66 AATTTAAATACTTACCGATTCAATGCATCATATAAATAAATATATTACCATTCAATCAACAGTTT
21421525 GGCACTTATATAAGCATCAAACAGCAACATTGTTAGTATACTTGCACATATCTCATATAAATTCA
131 GGCACTTATATAAGCATCAAACAGCAACATTGTTAGTATACTTGCACATATCTCATATAAATTCA
21421590 ACATTGATATATCTATTTTCTCGACATATCGCACTTGAGTTTAATAATAGTCTCAACTTACATAA
196 ACATTGATATATCTATTTTCTCGACATATCGCACTTGAGTTTAATAATAGTCTCAACTTACATAA
21421655 TTTCCTTGTATCAACATATCAAAGATAATCATATATGTACATGTCATGAAACATATCATGCTCTA
261 TTTCCTTGTATCAACATATCAAAGATAATCATATATGTACATGTCATGAAACATATCATGCTCTA
21421720 ACCATTTCTTCATAAGCATAAATCATTCATTTCATTATATCAATATTTCATGCTCCATCATTTCC
326 ACCATTTCTTCATAAGCATAAATCATTCATTTCATTATATCAATATTTCATGCTCCATCATTTCC
21421785 ATATATTTTATGTATATTTATTCCGGTAATAGTTTATATCAAACTTAACATAAATTATATTCCAT
391 ATATATTTTATGTATATTTATTCCGGTAATAGTTTATATCAAACTTAACATAAATTATATTCCAT
21421850 GTACTTATACTTATTTCGTTTATCTATCTTCA
456 GTACTTATACTTATTTCGTTTATCTATCTTCA
21421882 TAACCTATATCCATTATCGAAACAGGGTTTCAGAGCATTACTAGAATTTGCAGATCACCTAAAAA
1 TAACCTATATCCATTATCGAAACAGGGTTTCAGAGCATTACTAGAATTTGCAGATCACCTAAAAA
21421947 AATTTAAATACTTACCGATTCAATGCATCATATAAATAAATATATTACCATTCAATCAACAGTTT
66 AATTTAAATACTTACCGATTCAATGCATCATATAAATAAATATATTACCATTCAATCAACAGTTT
*
21422012 GGCACTTGTATAAGCATCAAACAGCAACATTGTTAGTATACTTGCACATATCTCATATAAATTCA
131 GGCACTTATATAAGCATCAAACAGCAACATTGTTAGTATACTTGCACATATCTCATATAAATTCA
21422077 ACATTGATATATCTATTTTCTCGACATATCGCACTTGAGTTTAATAATAGTCTCAACTTACATAA
196 ACATTGATATATCTATTTTCTCGACATATCGCACTTGAGTTTAATAATAGTCTCAACTTACATAA
21422142 TTTCCTTGTATCAACATATCAAAGATAATCATATATGTACATGTCATGAAACATATCATGCTCTA
261 TTTCCTTGTATCAACATATCAAAGATAATCATATATGTACATGTCATGAAACATATCATGCTCTA
*
21422207 ACCATTTCTTCATAAGCATATATCATTCATTTCATTATATCAATATTTCATGCTCCATCATTTCC
326 ACCATTTCTTCATAAGCATAAATCATTCATTTCATTATATCAATATTTCATGCTCCATCATTTCC
21422272 ATATATTTTATGTATATTTATTCCGGTAATAGTTTATATCAAACTTAACATAAATTATATTCCAT
391 ATATATTTTATGTATATTTATTCCGGTAATAGTTTATATCAAACTTAACATAAATTATATTCCAT
21422337 GTACTTATACTTATTTCGTTTATCTATCTTCA
456 GTACTTATACTTATTTCGTTTATCTATCTTCA
21422369 TAA
1 TAA
21422372 TTATTTCATA
Statistics
Matches: 486, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
487 486 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (487 bp):
TAACCTATATCCATTATCGAAACAGGGTTTCAGAGCATTACTAGAATTTGCAGATCACCTAAAAA
AATTTAAATACTTACCGATTCAATGCATCATATAAATAAATATATTACCATTCAATCAACAGTTT
GGCACTTATATAAGCATCAAACAGCAACATTGTTAGTATACTTGCACATATCTCATATAAATTCA
ACATTGATATATCTATTTTCTCGACATATCGCACTTGAGTTTAATAATAGTCTCAACTTACATAA
TTTCCTTGTATCAACATATCAAAGATAATCATATATGTACATGTCATGAAACATATCATGCTCTA
ACCATTTCTTCATAAGCATAAATCATTCATTTCATTATATCAATATTTCATGCTCCATCATTTCC
ATATATTTTATGTATATTTATTCCGGTAATAGTTTATATCAAACTTAACATAAATTATATTCCAT
GTACTTATACTTATTTCGTTTATCTATCTTCA
Found at i:21422625 original size:46 final size:45
Alignment explanation
Indices: 21422517--21422625 Score: 110
Period size: 46 Copynumber: 2.4 Consensus size: 45
21422507 CGTCTCCTAT
* * *
21422517 CCACGGTCTTATTTATCTTCGACATGATGCCATAGTGTCTTTCAA
1 CCACGGTCTTATTCATTTTCGACATGATGCCATAGTATCTTTCAA
* * ** * * *
21422562 CTATGGTCTTACCCATTTTCTGTCATGTTGCCATGGTATCTTTCAA
1 CCACGGTCTTATTCATTTTC-GACATGATGCCATAGTATCTTTCAA
*
21422608 CCACAGTCTTATTCATTT
1 CCACGGTCTTATTCATTT
21422626 CTTGTCAAGA
Statistics
Matches: 48, Mismatches: 15, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
45 14 0.29
46 34 0.71
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (45 bp):
CCACGGTCTTATTCATTTTCGACATGATGCCATAGTATCTTTCAA
Found at i:21422688 original size:46 final size:46
Alignment explanation
Indices: 21422637--21422787 Score: 241
Period size: 46 Copynumber: 3.3 Consensus size: 46
21422627 TTGTCAAGAT
21422637 ACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCA
1 ACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCA
*
21422683 ACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTTTCA
1 ACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCA
* * *
21422729 ACCATGGTCTTATTCATTT-CTCGTCATATTGCCATAGTATCTTTCA
1 ACCATGGTCTTACTCATTTCCT-GTCATGTTGCCATGGTATCTTTCA
*
21422775 ACTATGGTCTTAC
1 ACCATGGTCTTAC
21422788 ACATCTGAAT
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 2 0.02
46 97 0.98
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (46 bp):
ACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCA
Found at i:21422720 original size:76 final size:76
Alignment explanation
Indices: 21422564--21422708 Score: 245
Period size: 76 Copynumber: 1.9 Consensus size: 76
21422554 TCTTTCAACT
* *
21422564 ATGGTCTTACCCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCACAGTCTTATTCATTTCTT
1 ATGGTCTTACCCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCACAGTCTTATTCATTTCCT
21422629 GTCAAGATACC
66 GTCAAGATACC
* **
21422640 ATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCT
1 ATGGTCTTACCCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCACAGTCTTATTCATTTCCT
21422705 GTCA
66 GTCA
21422709 TGTTGCCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (76 bp):
ATGGTCTTACCCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCACAGTCTTATTCATTTCCT
GTCAAGATACC
Found at i:21422878 original size:45 final size:45
Alignment explanation
Indices: 21422758--21422881 Score: 194
Period size: 45 Copynumber: 2.8 Consensus size: 45
21422748 CTCGTCATAT
* * *
21422758 TGCCATAGTATCTTTCAACTATGGTCTTACACATCTGAATCGCGA
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATCTGAATCGCGA
* *
21422803 TGCCATAGCATCTTTCAGCTATGGTCTTACTCGTCTGAATCGTGA
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATCTGAATCGCGA
*
21422848 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCAT
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCAT
21422882 TCCTGGTATG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (45 bp):
TGCCATAGCATCTTTCAGCTATGGTCTTACTCATCTGAATCGCGA
Found at i:21422897 original size:45 final size:45
Alignment explanation
Indices: 21422640--21422901 Score: 212
Period size: 46 Copynumber: 5.8 Consensus size: 45
21422630 TCAAGATACC
* * *
21422640 ATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACC
1 ATGGTCTTACTCA-TTCCTGTCATGGTGCCATAGTATCTTTCAACT
* * * *
21422686 ATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACC
1 ATGGTCTTACTCA-TTCCTGTCATGGTGCCATAGTATCTTTCAACT
* * **
21422732 ATGGTCTTATTCATTTCTCGTCATATTGCCATAGTATCTTTCAACT
1 ATGGTCTTACTCATTCCT-GTCATGGTGCCATAGTATCTTTCAACT
* * * *
21422778 ATGGTCTTACACA-T-CTG-AATCGCGATGCCATAGCATCTTTCAGCT
1 ATGGTCTTACTCATTCCTGTCAT-G-G-TGCCATAGTATCTTTCAACT
* * * ** *
21422823 ATGGTCTTACTC-GT-CTGAATCGTGATGCCATAGCGTCTTTCAGCT
1 ATGGTCTTACTCATTCCTG--TCATGGTGCCATAGTATCTTTCAACT
21422868 ATGGTCTTACTCATTCCTGGT-ATGGTGCCATAGT
1 ATGGTCTTACTCATTCCT-GTCATGGTGCCATAGT
21422902 CCAACTATGG
Statistics
Matches: 184, Mismatches: 21, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.01
43 1 0.01
44 2 0.01
45 79 0.43
46 95 0.52
47 3 0.02
48 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.39
Consensus pattern (45 bp):
ATGGTCTTACTCATTCCTGTCATGGTGCCATAGTATCTTTCAACT
Found at i:21424584 original size:34 final size:34
Alignment explanation
Indices: 21424541--21424609 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
21424531 AAAGAAAGTT
21424541 TCTTTCTTTCTTTTCTCTTCATACGTTGGGTGCA
1 TCTTTCTTTCTTTTCTCTTCATACGTTGGGTGCA
21424575 TCTTTCTTTCTTTTCTCTTCATACGTTGGGTGCA
1 TCTTTCTTTCTTTTCTCTTCATACGTTGGGTGCA
21424609 T
1 T
21424610 GGGAAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.09, C:0.23, G:0.14, T:0.54
Consensus pattern (34 bp):
TCTTTCTTTCTTTTCTCTTCATACGTTGGGTGCA
Found at i:21425127 original size:25 final size:25
Alignment explanation
Indices: 21425099--21425150 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
21425089 CTAATGTTGA
21425099 CATAACTCAAAATTTCCCCTTTTGT
1 CATAACTCAAAATTTCCCCTTTTGT
*
21425124 CATAACTCAAAATTTCCCTTTTTGT
1 CATAACTCAAAATTTCCCCTTTTGT
21425149 CA
1 CA
21425151 ATTTATTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (25 bp):
CATAACTCAAAATTTCCCCTTTTGT
Found at i:21435385 original size:6 final size:6
Alignment explanation
Indices: 21435374--21435399 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21435364 ATGGGAAAAC
21435374 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
21435400 TGGACTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:21437211 original size:14 final size:15
Alignment explanation
Indices: 21437183--21437229 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
21437173 TATATATATT
*
21437183 TATTAGTAATAAATTA
1 TATTA-TAATTAATTA
21437199 TATTA-AATTAATT-
1 TATTATAATTAATTA
21437212 TATTATAATTATATTA
1 TATTATAATTA-ATTA
21437228 TA
1 TA
21437230 AGATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.19
14 12 0.44
15 3 0.11
16 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TATTATAATTAATTA
Found at i:21437649 original size:3 final size:3
Alignment explanation
Indices: 21437637--21437668 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
21437627 TTAATATAGA
21437637 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21437669 ATAGTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:21437703 original size:13 final size:13
Alignment explanation
Indices: 21437678--21437711 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
21437668 TATAGTAAAT
21437678 AAAGAAA-AAAGA
1 AAAGAAACAAAGA
*
21437690 AATGAAACAAAGA
1 AAAGAAACAAAGA
21437703 AAAGAAACA
1 AAAGAAACA
21437712 GAATAGGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAGAAACAAAGA
Found at i:21438870 original size:51 final size:54
Alignment explanation
Indices: 21438784--21438899 Score: 141
Period size: 51 Copynumber: 2.2 Consensus size: 54
21438774 AAGTGTCGCC
* * * **
21438784 TTACTATTACTGTTCCGGATTCGTTCTGAATAGGTACT-T-TGTA-CTTTACTG
1 TTACTGTTACTGTTCCAGATTCGTTCCGAATAGGTACTCTGTGTACCGCTACTG
*
21438835 TTACTGTTACTGTTCCAGATTTGTTCCG-ATGAGGTACTCTGTGTACCGCTACTG
1 TTACTGTTACTGTTCCAGATTCGTTCCGAAT-AGGTACTCTGTGTACCGCTACTG
21438889 TTACTGTTACT
1 TTACTGTTACT
21438900 ATTACTGTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
50 2 0.04
51 31 0.56
52 1 0.02
53 4 0.07
54 17 0.31
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (54 bp):
TTACTGTTACTGTTCCAGATTCGTTCCGAATAGGTACTCTGTGTACCGCTACTG
Found at i:21439047 original size:18 final size:18
Alignment explanation
Indices: 21439024--21439130 Score: 108
Period size: 18 Copynumber: 5.9 Consensus size: 18
21439014 TAAATAAATG
* * *
21439024 TACTGAATGATTGTCTGC
1 TACTGAATAACTGACTGC
*
21439042 TACTGAATAACTGACTGT
1 TACTGAATAACTGACTGC
*
21439060 TACTGGATAACTGACTGC
1 TACTGAATAACTGACTGC
* *
21439078 TACTGAATAATTGACTGT
1 TACTGAATAACTGACTGC
* * *
21439096 TACTGAATAATTTA-TCGT
1 TACTGAATAACTGACT-GC
21439114 TACTGAATAACTGACTG
1 TACTGAATAACTGACTG
21439131 TTAAAGCGTG
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
17 1 0.01
18 73 0.97
19 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (18 bp):
TACTGAATAACTGACTGC
Found at i:21439078 original size:36 final size:36
Alignment explanation
Indices: 21439024--21439133 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 36
21439014 TAAATAAATG
* * *
21439024 TACTGAATGATTGTCTGCTACTGAATAACTGACTGT
1 TACTGAATAACTGACTGCTACTGAATAACTGACTGT
* *
21439060 TACTGGATAACTGACTGCTACTGAATAATTGACTGT
1 TACTGAATAACTGACTGCTACTGAATAACTGACTGT
* * *
21439096 TACTGAATAATTTA-TCGTTACTGAATAACTGACTGT
1 TACTGAATAACTGACT-GCTACTGAATAACTGACTGT
21439132 TA
1 TA
21439134 AAGCGTGACT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 1 0.02
36 62 0.98
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (36 bp):
TACTGAATAACTGACTGCTACTGAATAACTGACTGT
Found at i:21439083 original size:54 final size:54
Alignment explanation
Indices: 21439024--21439130 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
21439014 TAAATAAATG
* * *
21439024 TACTGAATGATTGTCTGCTACTGAATAACTGA-CTGTTACTGGATAACTGACTGC
1 TACTGAATAATTGACTGCTACTGAATAACTGATC-GTTACTGAATAACTGACTGC
* * *
21439078 TACTGAATAATTGACTGTTACTGAATAATTTATCGTTACTGAATAACTGACTG
1 TACTGAATAATTGACTGCTACTGAATAACTGATCGTTACTGAATAACTGACTG
21439131 TTAAAGCGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 45 0.98
55 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (54 bp):
TACTGAATAATTGACTGCTACTGAATAACTGATCGTTACTGAATAACTGACTGC
Found at i:21439133 original size:18 final size:18
Alignment explanation
Indices: 21439042--21439133 Score: 123
Period size: 18 Copynumber: 5.1 Consensus size: 18
21439032 GATTGTCTGC
21439042 TACTGAATAACTGACTGT
1 TACTGAATAACTGACTGT
* *
21439060 TACTGGATAACTGACTGC
1 TACTGAATAACTGACTGT
*
21439078 TACTGAATAATTGACTGT
1 TACTGAATAACTGACTGT
* *
21439096 TACTGAATAATTTA-TCGT
1 TACTGAATAACTGACT-GT
21439114 TACTGAATAACTGACTGT
1 TACTGAATAACTGACTGT
21439132 TA
1 TA
21439134 AAGCGTGACT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
17 1 0.02
18 62 0.97
19 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (18 bp):
TACTGAATAACTGACTGT
Found at i:21439160 original size:18 final size:18
Alignment explanation
Indices: 21439139--21439195 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
21439129 TGTTAAAGCG
*
21439139 TGACTGAATATTATTGAA
1 TGACTGAATGTTATTGAA
21439157 TGACT-AATTGTTATTGAA
1 TGACTGAA-TGTTATTGAA
* *
21439175 TGATTGAATGTTACTGAA
1 TGACTGAATGTTATTGAA
21439193 TGA
1 TGA
21439196 AACTGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.06
18 30 0.88
19 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (18 bp):
TGACTGAATGTTATTGAA
Found at i:21453567 original size:31 final size:30
Alignment explanation
Indices: 21453526--21453586 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
21453516 TTTAAATTAA
*
21453526 TTAATTAGATAAATATTATTTTATTAATATT
1 TTAATGAGATAAATATTATTTT-TTAATATT
** *
21453557 TTAATGAGATATTTATTATTTTTTATTATT
1 TTAATGAGATAAATATTATTTTTTAATATT
21453587 ATTTATTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (30 bp):
TTAATGAGATAAATATTATTTTTTAATATT
Found at i:21453748 original size:20 final size:20
Alignment explanation
Indices: 21453725--21453774 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
21453715 AAATCCAAAT
21453725 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
* *
21453745 TAAAATCCTGAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
21453765 TAATAATACT
1 TAA-AATACT
21453775 GATGTGGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
TAAAATACTAAAATTCAGGA
Found at i:21456102 original size:46 final size:46
Alignment explanation
Indices: 21455937--21456474 Score: 773
Period size: 46 Copynumber: 11.8 Consensus size: 46
21455927 AATTATATGT
21455937 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAAT--
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
*
21455981 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
* *
21456027 GTAAGA-CATGGTTGAAAGATACCATGGCAACGTG-TCATGAAATAA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGAT-ATGAAATGA
* * *
21456072 ATAAGACCTTGGTTGAAAGATACCATGGCAACATGATATGAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
*
21456118 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
* *
21456164 GTAAGACCATGGTTGAAAGATACCATGGCAACGTG-TCATGAAATAA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGAT-ATGAAATGA
* * *
21456210 ATAAGACCTTGGTTGAAAGATACCATGGCAACATGATATGAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
*
21456256 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
**
21456302 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATGGGAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
* * * *
21456348 ATAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATGAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
** *
21456394 ACAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG-AAATGA
* * * *
21456440 GTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATG
21456475 TCAAAGATAA
Statistics
Matches: 448, Mismatches: 38, Indels: 14
0.90 0.08 0.03
Matches are distributed among these distances:
44 45 0.10
45 41 0.09
46 360 0.80
47 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGA
Found at i:21456224 original size:138 final size:138
Alignment explanation
Indices: 21455938--21456492 Score: 865
Period size: 138 Copynumber: 4.1 Consensus size: 138
21455928 ATTATATGTG
21455938 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAA--TGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
*
21456001 TACCATGGCAACATGATATGAAATGTGTAAGA-CATGGTTGAAAGATACCATGGCAACGTGTCAT
66 TACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGTCAT
21456065 GAAATAAA
131 GAAATAAA
*
21456073 TAAGACCTTGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
*
21456138 TACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGTCAT
66 TACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGTCAT
21456203 GAAATAAA
131 GAAATAAA
*
21456211 TAAGACCTTGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
21456276 TACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG--AT
66 TACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGTCAT
*
21456339 GGGAAATGAA
131 --GAAATAAA
* * * ***
21456349 TAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATGAAATGAACAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
* * * * * *
21456414 TACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATGTCA
66 TACCATGGCAACATGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGTCA
21456478 --AAGATAAA
130 TGAA-ATAAA
21456486 TAAGACC
1 TAAGACC
21456493 GTGGATGGGA
Statistics
Matches: 394, Mismatches: 17, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
135 41 0.10
136 4 0.01
137 65 0.16
138 283 0.72
140 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.22
Consensus pattern (138 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
TACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGTCAT
GAAATAAA
Found at i:21457366 original size:23 final size:22
Alignment explanation
Indices: 21457323--21457368 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
21457313 TACTTTAGCC
*
21457323 ATTTTTATTTTTATTGCAATTT
1 ATTTTTATTTTTATTGAAATTT
* *
21457345 ATTTTTGTTTTTATTTTAAATTT
1 ATTTTTATTTTTA-TTGAAATTT
21457368 A
1 A
21457369 CTAATTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTTATTTTTATTGAAATTT
Found at i:21462216 original size:29 final size:29
Alignment explanation
Indices: 21462141--21462250 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 29
21462131 AATTTCACAT
* *
21462141 ACCTGTATCTGGCCCATTAAGCCC-AATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
* * *
21462169 A--TATCATATAGCTCATTAGGCCCAAATC
1 ACCTGT-ATATGGCCCATTAGGCCCAAATC
21462197 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
* * *
21462226 ACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAGGCCCA
21462251 GTCACATTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 2 0.03
27 14 0.21
28 6 0.09
29 43 0.64
30 2 0.03
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (29 bp):
ACCTGTATATGGCCCATTAGGCCCAAATC
Found at i:21464067 original size:29 final size:28
Alignment explanation
Indices: 21464012--21464115 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 28
21464002 GTGAGCATGA
* * *
21464012 ATATGAATGTGAATGGGCCTAACGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
*
21464040 ATATAAATGTGATTTGGGCTTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * *
21464069 AGATACAGGTGATTTGGGCCTAATGGGTC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* *
21464098 ATATGAATATGATTGGGC
1 ATATAAATGTGATTGGGC
21464116 TTAGTAGGCC
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 17 0.28
29 44 0.72
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.29
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:21464132 original size:57 final size:58
Alignment explanation
Indices: 21464025--21464135 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
21464015 TGAATGTGAA
* * *
21464025 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCTTAATGGGCCAGATACAGGTGATT
1 TGGGCCTAACGGGCCATATAAATATGATTTGGGCTTAATAGGCCAAATACAGGTGATT
* * * *
21464083 TGGGCCTAATGGGTCATATGAATATGA-TTGGGCTTAGTAGGCCAAATACAGGT
1 TGGGCCTAACGGGCCATATAAATATGATTTGGGCTTAATAGGCCAAATACAGGT
21464136 ATGTGAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 23 0.50
58 23 0.50
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (58 bp):
TGGGCCTAACGGGCCATATAAATATGATTTGGGCTTAATAGGCCAAATACAGGTGATT
Found at i:21468473 original size:29 final size:29
Alignment explanation
Indices: 21468433--21468531 Score: 119
Period size: 29 Copynumber: 3.4 Consensus size: 29
21468423 ATGTGACTGA
*
21468433 GCCTAACGGGCCATATAAATGTGATTTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* *
21468462 GCCTAATGGGCCATATACAGGTGATTTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* * *
21468491 GCCTAATGGGCCATCTGAATATGA-TTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* *
21468519 GCTTAGTGGGCCA
1 GCCTAATGGGCCA
21468532 GATACAGGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 15 0.25
29 45 0.75
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (29 bp):
GCCTAATGGGCCATATAAATGTGATTTGG
Found at i:21476977 original size:3 final size:3
Alignment explanation
Indices: 21476971--21476998 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
21476961 TGATGATGAT
21476971 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
21476999 AAGAATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:21478745 original size:5 final size:5
Alignment explanation
Indices: 21478735--21478760 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21478725 ATAAAAGTAT
21478735 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
21478761 AAATAGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:21482428 original size:27 final size:26
Alignment explanation
Indices: 21482396--21482446 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
21482386 AAAATAAATT
21482396 ATAATTATTT-TTAAATATATAATTATC
1 ATAATT-TTTATTAAAT-TATAATTATC
21482423 ATAATTTTTATTAAATTATAATTA
1 ATAATTTTTATTAAATTATAATTA
21482447 CTTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
ATAATTTTTATTAAATTATAATTATC
Found at i:21482485 original size:44 final size:44
Alignment explanation
Indices: 21482375--21482495 Score: 149
Period size: 44 Copynumber: 2.7 Consensus size: 44
21482365 ACTTTATTAA
*
21482375 ATCATAATTTTAAAATAAATTATAATTATTTTTAAATATATAATT
1 ATCATAA-TTTAAATTAAATTATAATTATTTTTAAATATATAATT
** *
21482420 ATCATAATTTTTATTAAATTATAATTACTTTTAAATATATAA-T
1 ATCATAATTTAAATTAAATTATAATTATTTTTAAATATATAATT
21482463 -T-ATAATTCTAAATTAAATATTATAATTATTTTT
1 ATCATAATT-TAAATT-AA-ATTATAATTATTTTT
21482496 CAAAATGTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
41 6 0.09
42 5 0.08
43 3 0.05
44 45 0.68
45 7 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (44 bp):
ATCATAATTTAAATTAAATTATAATTATTTTTAAATATATAATT
Found at i:21482501 original size:26 final size:25
Alignment explanation
Indices: 21482450--21482501 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
21482440 ATAATTACTT
*
21482450 TTAAATATATAATTATAATTCTAAA
1 TTAAATATATAATTATAATTCAAAA
**
21482475 TTAAATATTATAATTATTTTTCAAAA
1 TTAAATA-TATAATTATAATTCAAAA
21482501 T
1 T
21482502 GTCAATTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAAATATATAATTATAATTCAAAA
Found at i:21488275 original size:5 final size:5
Alignment explanation
Indices: 21488265--21488315 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
21488255 ATTTAAGTAA
21488265 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
21488315 A
1 A
21488316 AAATATAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:21488384 original size:18 final size:19
Alignment explanation
Indices: 21488340--21488385 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
21488330 TAAAAGAAAT
21488340 GAAATA-AAAGAAACAAAA
1 GAAATAGAAAGAAACAAAA
*
21488358 GAAAAAGAAAG-AACAAACA
1 GAAATAGAAAGAAACAAA-A
21488377 G-AATAGAAA
1 GAAATAGAAA
21488386 ACGAAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.74, C:0.07, G:0.15, T:0.04
Consensus pattern (19 bp):
GAAATAGAAAGAAACAAAA
Found at i:21489880 original size:4 final size:4
Alignment explanation
Indices: 21489871--21489900 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
21489861 TGGTTGATTA
21489871 TATG TATG TATG TATG TATG TATG TTATG T
1 TATG TATG TATG TATG TATG TATG -TATG T
21489901 TAAGGATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:21493349 original size:46 final size:45
Alignment explanation
Indices: 21493296--21493471 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
21493286 TATTTGGGCA
*
21493296 TCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
21493342 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
21493389 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
21493435 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21493472 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.61
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:21493451 original size:93 final size:93
Alignment explanation
Indices: 21493292--21493463 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
21493282 AGGATATTTG
* *
21493292 GGCATCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
21493357 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
21493385 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
21493450 TTGAGTCTGAGTTC
66 TTGAGTCCGAGTTC
21493464 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:21495856 original size:16 final size:15
Alignment explanation
Indices: 21495811--21495863 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
21495801 ATAAAAATAT
21495811 AAATATAAATATTCTAA
1 AAATATAAA-ATTC-AA
*
21495828 AAAGTATACAATTCAA
1 AAA-TATAAAATTCAA
21495844 AAATAATAAAATTTCAA
1 AAAT-ATAAAA-TTCAA
21495861 AAA
1 AAA
21495864 AAGTTACAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 1 0.03
16 10 0.32
17 15 0.48
18 5 0.16
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATATAAAATTCAA
Found at i:21498154 original size:19 final size:18
Alignment explanation
Indices: 21498103--21498155 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
21498093 TTTAAATTAT
* *
21498103 TATTAATGTTAAATTTTA
1 TATTAAAGTAAAATTTTA
*
21498121 TGTTAAAGTAAAATTTTAA
1 TATTAAAGTAAAATTTT-A
21498140 TATTAAA-TAATAATTT
1 TATTAAAGTAA-AATTT
21498156 ATTATATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
TATTAAAGTAAAATTTTA
Found at i:21499428 original size:22 final size:22
Alignment explanation
Indices: 21499398--21499441 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
21499388 TTTTATGTAT
*
21499398 TATTTTTTTCATAAATTT-AAAA
1 TATTATTTTCA-AAATTTCAAAA
*
21499420 TATTATTTTTAAAATTTCAAAA
1 TATTATTTTCAAAATTTCAAAA
21499442 CACATAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTATTTTCAAAATTTCAAAA
Found at i:21525039 original size:29 final size:31
Alignment explanation
Indices: 21525005--21525083 Score: 81
Period size: 34 Copynumber: 2.5 Consensus size: 31
21524995 TAAATTCAAA
21525005 TGTATACAT-TATATA-ATACCGAATTGAAT
1 TGTATACATATATATAGATACCGAATTGAAT
* *
21525034 TGTATATATAAATATATATGTTACCGAATTGAAT
1 TGTATACAT--ATATATA-GATACCGAATTGAAT
* *
21525068 TGTATATATAAATATA
1 TGTATACATATATATA
21525084 TATGTTGCCG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 8 0.19
32 12 0.29
34 22 0.52
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (31 bp):
TGTATACATATATATAGATACCGAATTGAAT
Found at i:21525059 original size:34 final size:34
Alignment explanation
Indices: 21525021--21525102 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
21525011 CATTATATAA
21525021 TACCGAATTGAATTGTATATATAAATATATATGT
1 TACCGAATTGAATTGTATATATAAATATATATGT
21525055 TACCGAATTGAATTGTATATATAAATATATATGT
1 TACCGAATTGAATTGTATATATAAATATATATGT
* *
21525089 TGCCGAATTTAATT
1 TACCGAATTGAATT
21525103 AAGCATTGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (34 bp):
TACCGAATTGAATTGTATATATAAATATATATGT
Found at i:21539775 original size:19 final size:20
Alignment explanation
Indices: 21539709--21539775 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
21539699 AGTGCTTATG
*
21539709 GAGGCACCAAAGATA-AATTA
1 GAGGCACCAAAG-TACAATCA
* * *
21539729 GGGGAACAAAAGTACAATCA
1 GAGGCACCAAAGTACAATCA
*
21539749 GAGGCACCAAAGTGCAATCA
1 GAGGCACCAAAGTACAATCA
21539769 G-GGCACC
1 GAGGCACC
21539776 GTAGTGCAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 8 0.21
20 30 0.79
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.10
Consensus pattern (20 bp):
GAGGCACCAAAGTACAATCA
Found at i:21539823 original size:20 final size:20
Alignment explanation
Indices: 21539800--21539910 Score: 69
Period size: 20 Copynumber: 5.5 Consensus size: 20
21539790 AGCATGGATA
21539800 TGCTATCAAGAGCACCATAG
1 TGCTATCAAGAGCACCATAG
* * * *
21539820 TGCTAACAAGAGTACGAAAG
1 TGCTATCAAGAGCACCATAG
* ***
21539840 TGCTATCAGGAGCATTTTAG
1 TGCTATCAAGAGCACCATAG
* * ** *
21539860 TGCTATCAGGAGTATGAAAG
1 TGCTATCAAGAGCACCATAG
* * * *
21539880 TACTGTCAGGAGCACCGTAG
1 TGCTATCAAGAGCACCATAG
21539900 TGCTATCAAGA
1 TGCTATCAAGA
21539911 ATATGAAAAT
Statistics
Matches: 66, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (20 bp):
TGCTATCAAGAGCACCATAG
Found at i:21539844 original size:40 final size:40
Alignment explanation
Indices: 21539809--21540025 Score: 247
Period size: 40 Copynumber: 5.4 Consensus size: 40
21539799 ATGCTATCAA
* * * *
21539809 GAGCACCATAGTGCTAACAAGAGTACGAAAGTGCTATCAG
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
*** * *
21539849 GAGCATTTTAGTGCTATCAGGAGTATGAAAGTACTGTCAG
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
* * *
21539889 GAGCACCGTAGTGCTATCAAGAATATGAAAATACTGTCAG
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
* * * *
21539929 GAGCACCGTAATGCTATCAGGAATACGAAAGTACTGTCAA
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
* *
21539969 GAGCACCGTTGTGCTATCAAGAGTACGAAAGTA-TGGTTAG
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACT-GTCAG
*
21540009 GAGCACCATAGTGCTAT
1 GAGCACCGTAGTGCTAT
21540026 TAGAAGCACT
Statistics
Matches: 149, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 148 0.99
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (40 bp):
GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
Found at i:21541071 original size:54 final size:54
Alignment explanation
Indices: 21540981--21541095 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 54
21540971 TTTAATACCT
* *
21540981 ACAAATAAAGATTGAAAATAATAATAACAATGTCTTTATTAATAAACTAAATAA
1 ACAAATAAAGACTGAAAATAATAATAACAATGTCTTTAATAATAAACTAAATAA
* * * * *
21541035 AGAAATAAAGACTGAAAATAATAATAGCAATTTCTTTAATAATAAATTAGATAA
1 ACAAATAAAGACTGAAAATAATAATAACAATGTCTTTAATAATAAACTAAATAA
21541089 ACAAATA
1 ACAAATA
21541096 TGTAATTACA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (54 bp):
ACAAATAAAGACTGAAAATAATAATAACAATGTCTTTAATAATAAACTAAATAA
Found at i:21542154 original size:21 final size:21
Alignment explanation
Indices: 21542130--21542170 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21542120 AGAAATTAAT
*
21542130 TAAAAG-ATTAAATAAAAAATA
1 TAAAAGTA-TAAAAAAAAAATA
21542151 TAAAAGTATAAAAAAAAAAT
1 TAAAAGTATAAAAAAAAAAT
21542171 TATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (21 bp):
TAAAAGTATAAAAAAAAAATA
Found at i:21561099 original size:19 final size:20
Alignment explanation
Indices: 21561033--21561099 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
21561023 AGTGCTTATG
*
21561033 GAGGCACCAAAGATA-AATTA
1 GAGGCACCAAAG-TACAATCA
* * *
21561053 GGGGAACAAAAGTACAATCA
1 GAGGCACCAAAGTACAATCA
*
21561073 GAGGCACCAAAGTGCAATCA
1 GAGGCACCAAAGTACAATCA
21561093 G-GGCACC
1 GAGGCACC
21561100 GTAGTGCAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 8 0.21
20 30 0.79
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.10
Consensus pattern (20 bp):
GAGGCACCAAAGTACAATCA
Found at i:21561147 original size:20 final size:20
Alignment explanation
Indices: 21561124--21561234 Score: 69
Period size: 20 Copynumber: 5.5 Consensus size: 20
21561114 AGCATGGATA
21561124 TGCTATCAAGAGCACCATAG
1 TGCTATCAAGAGCACCATAG
* * * *
21561144 TGCTAACAAGAGTACGAAAG
1 TGCTATCAAGAGCACCATAG
* ***
21561164 TGCTATCAGGAGCATTTTAG
1 TGCTATCAAGAGCACCATAG
* * ** *
21561184 TGCTATCAGGAGTATGAAAG
1 TGCTATCAAGAGCACCATAG
* * * *
21561204 TACTGTCAGGAGCACCGTAG
1 TGCTATCAAGAGCACCATAG
21561224 TGCTATCAAGA
1 TGCTATCAAGA
21561235 ATATGAAAAT
Statistics
Matches: 66, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (20 bp):
TGCTATCAAGAGCACCATAG
Found at i:21561168 original size:40 final size:40
Alignment explanation
Indices: 21561133--21561349 Score: 247
Period size: 40 Copynumber: 5.4 Consensus size: 40
21561123 ATGCTATCAA
* * * *
21561133 GAGCACCATAGTGCTAACAAGAGTACGAAAGTGCTATCAG
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
*** * *
21561173 GAGCATTTTAGTGCTATCAGGAGTATGAAAGTACTGTCAG
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
* * *
21561213 GAGCACCGTAGTGCTATCAAGAATATGAAAATACTGTCAG
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
* * * *
21561253 GAGCACCGTAATGCTATCAGGAATACGAAAGTACTGTCAA
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
* *
21561293 GAGCACCGTTGTGCTATCAAGAGTACGAAAGTA-TGGTTAG
1 GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACT-GTCAG
*
21561333 GAGCACCATAGTGCTAT
1 GAGCACCGTAGTGCTAT
21561350 TAGAAGCACT
Statistics
Matches: 149, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 148 0.99
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (40 bp):
GAGCACCGTAGTGCTATCAAGAGTACGAAAGTACTGTCAG
Found at i:21562406 original size:54 final size:54
Alignment explanation
Indices: 21562316--21562430 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 54
21562306 TTTAATACCT
* *
21562316 ACAAATAAAGATTGAAAATAATAATAACAATGTCTTTATTAATAAACTAAATAA
1 ACAAATAAAGACTGAAAATAATAATAACAATGTCTTTAATAATAAACTAAATAA
* * * * *
21562370 AGAAATAAAGACTGAAAATAATAATAGCAATTTCTTTAATAATAAATTAGATAA
1 ACAAATAAAGACTGAAAATAATAATAACAATGTCTTTAATAATAAACTAAATAA
21562424 ACAAATA
1 ACAAATA
21562431 TGTAATTACA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (54 bp):
ACAAATAAAGACTGAAAATAATAATAACAATGTCTTTAATAATAAACTAAATAA
Found at i:21563512 original size:24 final size:25
Alignment explanation
Indices: 21563485--21563547 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
21563475 CTAAAAAAGG
*
21563485 AAATTAATTTAAAAG-AT-TAAATAA
1 AAATT-ATTTAAAAGTATAAAAATAA
21563509 AAA-TATGTATAAAAGTATAAAAATAA
1 AAATTAT-T-TAAAAGTATAAAAATAA
21563535 AAATTATTTAAAA
1 AAATTATTTAAAA
21563548 AAAATTCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
22 2 0.06
23 2 0.06
24 9 0.27
25 7 0.21
26 10 0.30
27 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (25 bp):
AAATTATTTAAAAGTATAAAAATAA
Found at i:21580756 original size:25 final size:27
Alignment explanation
Indices: 21580696--21580756 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
21580686 CCAGGTAAGG
*
21580696 CTTCTTCTCCTTCATCCGTTCTTCATTC
1 CTTC-TCTTCTTCATCCGTTCTTCATTC
*
21580724 CTT-T-TTCTTCTTCCGTTCTTCA-T-
1 CTTCTCTTCTTCATCCGTTCTTCATTC
21580747 CTTCTCTTCT
1 CTTCTCTTCT
21580757 CAGCATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 3 0.10
24 2 0.07
25 20 0.69
26 1 0.03
28 3 0.10
ACGTcount: A:0.05, C:0.36, G:0.03, T:0.56
Consensus pattern (27 bp):
CTTCTCTTCTTCATCCGTTCTTCATTC
Found at i:21581272 original size:12 final size:13
Alignment explanation
Indices: 21581249--21581274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21581239 TCAATGAACC
21581249 CTTAATTTTTTTG
1 CTTAATTTTTTTG
21581262 CTTAATTTTTTTG
1 CTTAATTTTTTTG
21581275 GTACTCAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
CTTAATTTTTTTG
Found at i:21584683 original size:21 final size:21
Alignment explanation
Indices: 21584657--21584709 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
21584647 CGCTGTTTCT
*
21584657 AATCTCACCGCTACAATATCC
1 AATCTCACCGCTACAATAACC
* *
21584678 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAATAACC
21584699 AATCTCACCGC
1 AATCTCACCGC
21584710 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:21601356 original size:35 final size:35
Alignment explanation
Indices: 21601310--21601379 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
21601300 CTTGGAAGGG
21601310 AGATTAAAGCCATTTGAAGCGGGTTCTGGGTTTAT
1 AGATTAAAGCCATTTGAAGCGGGTTCTGGGTTTAT
*
21601345 AGATTAAAGCCATTTGAAGGGGGTTCTGGGTTTAT
1 AGATTAAAGCCATTTGAAGCGGGTTCTGGGTTTAT
21601380 CTTGTTTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.34
Consensus pattern (35 bp):
AGATTAAAGCCATTTGAAGCGGGTTCTGGGTTTAT
Found at i:21604048 original size:6 final size:6
Alignment explanation
Indices: 21604037--21604062 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21604027 TGCCCCCTCA
21604037 CGATAT CGATAT CGATAT CGATAT CG
1 CGATAT CGATAT CGATAT CGATAT CG
21604063 CGATACCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (6 bp):
CGATAT
Found at i:21606598 original size:29 final size:31
Alignment explanation
Indices: 21606551--21606614 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
21606541 TTTTTAACTA
* *
21606551 AATTTGACTCACAACTTTTT-AAAGGAGTTG
1 AATTTGACTCACAACTTTTTCAAAAGAGTTC
21606581 AATTTGA-TCACTAA-TTTTTCAAAAGAGTTC
1 AATTTGACTCAC-AACTTTTTCAAAAGAGTTC
21606611 AATT
1 AATT
21606615 GTTGTTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (31 bp):
AATTTGACTCACAACTTTTTCAAAAGAGTTC
Found at i:21606741 original size:21 final size:22
Alignment explanation
Indices: 21606717--21606761 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
21606707 ATAATTTTAA
* *
21606717 TTTTTTATAATTTTTGAA-TAT
1 TTTTTTATAAATTTTAAATTAT
21606738 TTTTTTATAAATTTTAAATTAT
1 TTTTTTATAAATTTTAAATTAT
21606760 TT
1 TT
21606762 ATTGACGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTATAAATTTTAAATTAT
Found at i:21617275 original size:3 final size:3
Alignment explanation
Indices: 21617267--21617293 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21617257 GGTTTCTGAA
21617267 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
21617294 TGAAAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:21620554 original size:9 final size:9
Alignment explanation
Indices: 21620540--21620568 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
21620530 TCAACAACCC
21620540 TTTTTTCTT
1 TTTTTTCTT
21620549 TTTTTTCTT
1 TTTTTTCTT
21620558 TTTTTT-TT
1 TTTTTTCTT
21620566 TTT
1 TTT
21620569 GAGAGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:21620560 original size:16 final size:15
Alignment explanation
Indices: 21620539--21620568 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
21620529 CTCAACAACC
21620539 CTTTTTTCTTTTTTTT
1 CTTTTTT-TTTTTTTT
21620555 CTTTTTTTTTTTTT
1 CTTTTTTTTTTTTT
21620569 GAGAGTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
CTTTTTTTTTTTTTT
Found at i:21623161 original size:21 final size:22
Alignment explanation
Indices: 21623135--21623177 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
21623125 TCAGGGTGAT
*
21623135 TTAAAAAAAT-AAATTTAAATA
1 TTAAAAAAATAAAAATTAAATA
21623156 TTAAAAAAATAAAAATTAAATA
1 TTAAAAAAATAAAAATTAAATA
21623178 AAGTGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAAAAAAATAAAAATTAAATA
Found at i:21626461 original size:21 final size:21
Alignment explanation
Indices: 21626435--21626475 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21626425 AGACGAGCAA
* *
21626435 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
21626456 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
21626476 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:21630183 original size:19 final size:19
Alignment explanation
Indices: 21630159--21630198 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
21630149 ATGAAATGAA
21630159 TGATTTCAAGCAAATAGGT
1 TGATTTCAAGCAAATAGGT
21630178 TGATTTCAAGCAAATAGGT
1 TGATTTCAAGCAAATAGGT
21630197 TG
1 TG
21630199 GCAATCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (19 bp):
TGATTTCAAGCAAATAGGT
Found at i:21631094 original size:19 final size:20
Alignment explanation
Indices: 21631061--21631100 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
21631051 AATTATGTAT
21631061 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
21631080 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
21631100 A
1 A
21631101 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:21631367 original size:18 final size:17
Alignment explanation
Indices: 21631344--21631383 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
21631334 AGAGGTTAGG
21631344 TTTTTTCTTTTTCTTCAT
1 TTTTTTCTTTTT-TTCAT
*
21631362 TTTTTTCTTTTTTTTAT
1 TTTTTTCTTTTTTTCAT
21631379 TTTTT
1 TTTTT
21631384 ATTTTGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTTTTTTTCAT
Found at i:21631373 original size:9 final size:9
Alignment explanation
Indices: 21631344--21631383 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
21631334 AGAGGTTAGG
21631344 TTTTTTCTT
1 TTTTTTCTT
* *
21631353 TTTCTTCAT
1 TTTTTTCTT
21631362 TTTTTTCTT
1 TTTTTTCTT
*
21631371 TTTTTTATT
1 TTTTTTCTT
21631380 TTTT
1 TTTT
21631384 ATTTTGGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:21635029 original size:23 final size:21
Alignment explanation
Indices: 21634994--21635036 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
21634984 TTCTGTCACA
*
21634994 ATTTATCACAATACTTTATTTTG
1 ATTTATCAAAATA--TTATTTTG
*
21635017 ATTTATTAAAATATTATTTT
1 ATTTATCAAAATATTATTTT
21635037 TTTAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTATCAAAATATTATTTTG
Found at i:21652810 original size:13 final size:13
Alignment explanation
Indices: 21652771--21652831 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
21652761 AGTTTGACAA
21652771 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
21652784 TGCTGTGGAAAAG
1 TGCTTTTGAGAAG
21652797 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
21652810 TGTTTTTAAGAAG
1 TGCTTTTGAGAAG
*
21652823 TACTTTTGA
1 TGCTTTTGA
21652832 AAATTTTAAG
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:21654972 original size:72 final size:71
Alignment explanation
Indices: 21654848--21655018 Score: 236
Period size: 72 Copynumber: 2.4 Consensus size: 71
21654838 AAAATCATAT
** *
21654848 ATAAACAACTATTGATAAAACTAATTTAGTATAAATAAGTAGAACATAAATTCAATAACCAAAGA
1 ATAAACAACTATTGATAAAACTAATTTAACATAAATAAGTAGAACATAAATTCAATAACCAAAAA
21654913 CCAAAC
66 CCAAAC
* * * *
21654919 ATAAACAACTATTAATAAAAGTAGA-TTACACATAGATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTA-ATTTA-ACATAAATAAGTAGAACATAAATTCAATAACCAAA
21654983 AACCAAAC
64 AACCAAAC
* *
21654991 ATAAATAACTATTGATAAAACTAGTTTA
1 ATAAACAACTATTGATAAAACTAATTTA
21655019 GGATTTTTGT
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
71 24 0.28
72 62 0.72
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.25
Consensus pattern (71 bp):
ATAAACAACTATTGATAAAACTAATTTAACATAAATAAGTAGAACATAAATTCAATAACCAAAAA
CCAAAC
Found at i:21655464 original size:18 final size:18
Alignment explanation
Indices: 21655443--21655508 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
21655433 TCCATCAATT
21655443 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
21655461 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
21655479 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
*
21655497 CGAACATCATTT
1 TGAACATCATTT
21655509 CTCAATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:21659112 original size:22 final size:21
Alignment explanation
Indices: 21659082--21659137 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
21659072 GAACAGTACC
* *
21659082 ACACGCCCGTGTGGCTTATGTG
1 ACACACCCGTGTGGC-TACGTG
* *
21659104 ACACACCCGTGTGTCTCCGTG
1 ACACACCCGTGTGGCTACGTG
21659125 ACACACCCGTGTG
1 ACACACCCGTGTG
21659138 TCTCCGTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.16, C:0.34, G:0.27, T:0.23
Consensus pattern (21 bp):
ACACACCCGTGTGGCTACGTG
Found at i:21659127 original size:21 final size:21
Alignment explanation
Indices: 21659101--21659145 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
21659091 TGTGGCTTAT
21659101 GTGACACACCCGTGTGTCTCC
1 GTGACACACCCGTGTGTCTCC
21659122 GTGACACACCCGTGTGTCTCC
1 GTGACACACCCGTGTGTCTCC
21659143 GTG
1 GTG
21659146 TAGCTCACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.27, T:0.24
Consensus pattern (21 bp):
GTGACACACCCGTGTGTCTCC
Found at i:21660186 original size:28 final size:28
Alignment explanation
Indices: 21660150--21660206 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
21660140 AATACTTTTT
* *
21660150 AATATCAATCAATTTATCATTATCATTC
1 AATAGCAATCAATTGATCATTATCATTC
* *
21660178 AATAGCAATCAATTGATCTTTATTATTC
1 AATAGCAATCAATTGATCATTATCATTC
21660206 A
1 A
21660207 GTAATATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.42
Consensus pattern (28 bp):
AATAGCAATCAATTGATCATTATCATTC
Found at i:21660258 original size:18 final size:18
Alignment explanation
Indices: 21660237--21660277 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21660227 ACAATCAGTA
21660237 ATTCAATAACAGTCAAAT
1 ATTCAATAACAGTCAAAT
* * *
21660255 ATTCAGTAGCAGTCAATT
1 ATTCAATAACAGTCAAAT
21660273 ATTCA
1 ATTCA
21660278 GTACCTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (18 bp):
ATTCAATAACAGTCAAAT
Found at i:21660278 original size:18 final size:18
Alignment explanation
Indices: 21660246--21660280 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21660236 AATTCAATAA
21660246 CAGTCAAATATTCAGTAG
1 CAGTCAAATATTCAGTAG
*
21660264 CAGTCAATTATTCAGTA
1 CAGTCAAATATTCAGTA
21660281 CCTTTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (18 bp):
CAGTCAAATATTCAGTAG
Found at i:21661673 original size:9 final size:9
Alignment explanation
Indices: 21661649--21661677 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
21661639 TCTTTCTTTT
21661649 ATTTATTTA
1 ATTTATTTA
21661658 A-TTATTTA
1 ATTTATTTA
21661666 ATTTATTTA
1 ATTTATTTA
21661675 ATT
1 ATT
21661678 AATATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTATTTA
Found at i:21668778 original size:48 final size:48
Alignment explanation
Indices: 21668726--21668835 Score: 193
Period size: 48 Copynumber: 2.3 Consensus size: 48
21668716 AGTTGCTCCT
* *
21668726 ATTTTATTGTTATTATTTGGATATTGTATAAAACTTATTTTATTATTA
1 ATTTTGTTATTATTATTTGGATATTGTATAAAACTTATTTTATTATTA
*
21668774 ATTTTGTTATTATTATTTGTATATTGTATAAAACTTATTTTATTATTA
1 ATTTTGTTATTATTATTTGGATATTGTATAAAACTTATTTTATTATTA
21668822 ATTTTGTTATTATT
1 ATTTTGTTATTATT
21668836 TTAAAGGCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (48 bp):
ATTTTGTTATTATTATTTGGATATTGTATAAAACTTATTTTATTATTA
Found at i:21668785 original size:15 final size:15
Alignment explanation
Indices: 21668765--21668835 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 15
21668755 AAAACTTATT
21668765 TTATTATTAATTTTG
1 TTATTATTAATTTTG
21668780 TTATTATT-A-TTTG
1 TTATTATTAATTTTG
*
21668793 TATATTGTATAAAACTTATT-
1 T-TA-T-TAT-TAA-TT-TTG
21668813 TTATTATTAATTTTG
1 TTATTATTAATTTTG
21668828 TTATTATT
1 TTATTATT
21668836 TTAAAGGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 19 0.42
16 5 0.11
17 3 0.07
18 2 0.04
19 2 0.04
20 2 0.04
21 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (15 bp):
TTATTATTAATTTTG
Found at i:21670379 original size:18 final size:18
Alignment explanation
Indices: 21670356--21670392 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
21670346 TTTATTGTTT
*
21670356 TCCATTGTTTAATAGGTC
1 TCCATTGTTTAAAAGGTC
21670374 TCCATTGTTTAAAAGGTC
1 TCCATTGTTTAAAAGGTC
21670392 T
1 T
21670393 TTACTTGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (18 bp):
TCCATTGTTTAAAAGGTC
Found at i:21672106 original size:17 final size:17
Alignment explanation
Indices: 21672084--21672139 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
21672074 ATTAATTAAT
21672084 AAAATTATAAAAATATA
1 AAAATTATAAAAATATA
**
21672101 AAAATTAT-ATTATATTA
1 AAAATTATAAAAATA-TA
21672118 AAAA-T-TAAAAATATA
1 AAAATTATAAAAATATA
21672133 AAAATTA
1 AAAATTA
21672140 AATCTCAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 7 0.23
16 10 0.32
17 14 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATATA
Found at i:21672136 original size:8 final size:8
Alignment explanation
Indices: 21672082--21672141 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
21672072 GAATTAATTA
*
21672082 ATAAAATT
1 ATAAAAAT
21672090 ATAAAAAT
1 ATAAAAAT
21672098 ATAAAAAT
1 ATAAAAAT
**
21672106 -TATATTAT
1 ATA-AAAAT
21672114 ATTAAAAAT
1 A-TAAAAAT
21672123 -TAAAAAT
1 ATAAAAAT
21672130 ATAAAAAT
1 ATAAAAAT
21672138 -TAAA
1 ATAAA
21672142 TCTCAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 13 0.30
8 25 0.58
9 3 0.07
10 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
ATAAAAAT
Found at i:21678429 original size:18 final size:17
Alignment explanation
Indices: 21678404--21678437 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21678394 TTCTATTATT
21678404 TATAATTTTTAAAAATA
1 TATAATTTTTAAAAATA
*
21678421 TATATATTTTTATAAAT
1 TATA-ATTTTTAAAAAT
21678438 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAATTTTTAAAAATA
Found at i:21678444 original size:27 final size:28
Alignment explanation
Indices: 21678397--21678452 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
21678387 AAATATTTTC
* *
21678397 TATTATTTATAATTTTTAAAAATATATA
1 TATTATTTATAAATTTAAAAAATATATA
21678425 TATT-TTTATAAATTTAAAAAATATATA
1 TATTATTTATAAATTTAAAAAATATATA
21678452 T
1 T
21678453 TAAAATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTATTTATAAATTTAAAAAATATATA
Found at i:21681175 original size:66 final size:65
Alignment explanation
Indices: 21681100--21681230 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 65
21681090 GTACAGTTAA
* *
21681100 AATAATTATAATTAAAGTAAAAGTTGATATAATCTTTTTTTTACAATTACAATCATTTTAAAATA
1 AATAATTATAATTAAAGTAAAAGTTGATATAA-ATTTTTTTTACAATTACAATCATTTAAAAATA
21681165 T
65 T
21681166 AATAATTATAATTAAAGTAAAAGTTGATATAAATTTTTTTTACAATTACAATCATTTAAAAATAT
1 AATAATTATAATTAAAGTAAAAGTTGATATAAATTTTTTTTACAATTACAATCATTTAAAAATAT
21681231 TTTTCTATAT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 31 0.49
66 32 0.51
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (65 bp):
AATAATTATAATTAAAGTAAAAGTTGATATAAATTTTTTTTACAATTACAATCATTTAAAAATAT
Found at i:21681986 original size:22 final size:23
Alignment explanation
Indices: 21681961--21682013 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
21681951 AAATTAATAT
21681961 ATTAAAAAAATTAAAA-AAATTA
1 ATTAAAAAAATTAAAATAAATTA
* * *
21681983 ATTACAATAATTAAAATATATTA
1 ATTAAAAAAATTAAAATAAATTA
*
21682006 TTTAAAAA
1 ATTAAAAA
21682014 TTAAACTCGT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
ATTAAAAAAATTAAAATAAATTA
Found at i:21682221 original size:29 final size:30
Alignment explanation
Indices: 21682171--21682229 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
21682161 AAATACTCAA
21682171 TTTACTACGTGTAAGTCAGTTTATTAACATG
1 TTTACTACG-GTAAGTCAGTTTATTAACATG
* *
21682202 TTTACTAC-GTAAGTCTGTTTATTGACAT
1 TTTACTACGGTAAGTCAGTTTATTAACAT
21682230 ATTTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (30 bp):
TTTACTACGGTAAGTCAGTTTATTAACATG
Found at i:21685323 original size:53 final size:55
Alignment explanation
Indices: 21685235--21685363 Score: 131
Period size: 54 Copynumber: 2.4 Consensus size: 55
21685225 CTGATGCTAA
* * * *
21685235 AGCCCAGCTGTGGTCTTATAC-GGATCGCTTGTATCACTT-TAATCCAAAGCTAT
1 AGCCCAACTATGGTCTTATACGGGATCGATTGTATCACTTGTAATCCAAAGCCAT
* ** * *
21685288 AGCCTAACTATGGTCTTATACGGGAATC-ATT-TATCACTTGTTTTCCTATGCCAT
1 AGCCCAACTATGGTCTTATACGGG-ATCGATTGTATCACTTGTAATCCAAAGCCAT
*
21685342 AGCCCAACTATAGTCTTATACG
1 AGCCCAACTATGGTCTTATACG
21685364 AATATCGCTT
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
53 26 0.42
54 33 0.53
55 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (55 bp):
AGCCCAACTATGGTCTTATACGGGATCGATTGTATCACTTGTAATCCAAAGCCAT
Found at i:21714306 original size:31 final size:30
Alignment explanation
Indices: 21714271--21714329 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
21714261 TAATAATTTA
21714271 ATTTTTACTATCGTAAAAATGATAAAATTAT
1 ATTTTTACTATCGTAAAAAT-ATAAAATTAT
*
21714302 ATTTTTACTATCGTAAAAATATACAATT
1 ATTTTTACTATCGTAAAAATATAAAATT
21714330 TAATTTCAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (30 bp):
ATTTTTACTATCGTAAAAATATAAAATTAT
Found at i:21719145 original size:124 final size:124
Alignment explanation
Indices: 21718976--21719249 Score: 320
Period size: 124 Copynumber: 2.2 Consensus size: 124
21718966 GACGCCACTT
* * * **
21718976 GTTTTATTTAAAGTAAAATATTTTTTGCTGCGTTTTTTACATAGCGCTTCTAATGCTCGATCTAT
1 GTTTGATTTAAAGTAAAATGTTTTTTACTGCGTTTTTTACATAGCGCCGCTAATGCTCGATCTAT
** * * * *
21719041 TGCAGAGTTTTTTGCCTAGCGCCGCTAATGCCATTAAAGGCGCAACTTAAAGCGGTC-CC
66 TGCAGAGTTTTTCACCTAGCGCCGCTAATGCCACTAAAGACGCAACTAAAAACGG-CACC
* * * *
21719100 GTTTGATTTAAAGTAAAATGTTTTTTAC-GACTTTTTTTCCGTAGCGCCGCTGATGCTCGATCTA
1 GTTTGATTTAAAGTAAAATGTTTTTTACTG-CGTTTTTTACATAGCGCCGCTAATGCTCGATCTA
** * *
21719164 TTGTGGCGTTTTTCACCTAGCGCCGCTAATGCCACTAAAGACGCCACTAAAAACGGCACC
65 TTGCAGAGTTTTTCACCTAGCGCCGCTAATGCCACTAAAGACGCAACTAAAAACGGCACC
*
21719224 GTTTTG-TTTAAAGCAAAATGTTTTTT
1 G-TTTGATTTAAAGTAAAATGTTTTTT
21719250 TTGCGGCGTT
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
123 2 0.02
124 121 0.95
125 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (124 bp):
GTTTGATTTAAAGTAAAATGTTTTTTACTGCGTTTTTTACATAGCGCCGCTAATGCTCGATCTAT
TGCAGAGTTTTTCACCTAGCGCCGCTAATGCCACTAAAGACGCAACTAAAAACGGCACC
Found at i:21719712 original size:14 final size:14
Alignment explanation
Indices: 21719693--21719731 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
21719683 CATAACTATA
21719693 AAACACTAAACACC
1 AAACACTAAACACC
*
21719707 AAACACCAAACACC
1 AAACACTAAACACC
*
21719721 AAACCCTAAAC
1 AAACACTAAAC
21719732 CTTAAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.38, G:0.00, T:0.05
Consensus pattern (14 bp):
AAACACTAAACACC
Found at i:21719812 original size:7 final size:7
Alignment explanation
Indices: 21719770--21719810 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
21719760 TACAAAATAT
21719770 TAAACCA
1 TAAACCA
*
21719777 TAAACAA
1 TAAACCA
*
21719784 TAAACCC
1 TAAACCA
21719791 TAAACCA
1 TAAACCA
*
21719798 TAAACCT
1 TAAACCA
21719805 TAAACC
1 TAAACC
21719811 TTTAAATCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCA
Found at i:21725071 original size:40 final size:39
Alignment explanation
Indices: 21724996--21725079 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 39
21724986 ACGACTTATC
***
21724996 GGCTAAAATGGCACTTAGTGTGTGGTTCGAAATAGCTTT
1 GGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTT
* * *
21725035 GGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCTTT
1 GGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCTTT
21725075 GGCTA
1 GGCTA
21725080 TATATATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (39 bp):
GGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTT
Found at i:21728267 original size:38 final size:35
Alignment explanation
Indices: 21728185--21728267 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
21728175 ATTATTAAGT
**
21728185 TAGATTATTAAATACTGATAGGTTAATAAGGTTTA
1 TAGATTATTAAATACTGATAGGTTAATAACCTTTA
21728220 TAGATTATTAAATACTGATAGGTTCATATGAACCTTTA
1 TAGATTATTAAATACTGATAGGTT-A-AT-AACCTTTA
21728258 TA-ATATATTA
1 TAGAT-TATTA
21728268 TTTTCAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
35 24 0.57
36 1 0.02
37 4 0.10
38 13 0.31
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (35 bp):
TAGATTATTAAATACTGATAGGTTAATAACCTTTA
Found at i:21728841 original size:51 final size:51
Alignment explanation
Indices: 21728779--21728908 Score: 170
Period size: 55 Copynumber: 2.5 Consensus size: 51
21728769 AAAATAGTTG
* *
21728779 AAAGCTACAAAAGAGCTAATATATCAATATTTGATACTATAAAATTAGATA
1 AAAGCTCCAAAAGAGCTAATATATCAATATTTGATACTACAAAATTAGATA
* * *
21728830 AAAGCTCCAAAAGAGCTAGCTAATAAATCAATATTTGGTACTACAAAATTAGATG
1 AAAGCTCC-AAA-AG--AGCTAATATATCAATATTTGATACTACAAAATTAGATA
*
21728885 AAAGCTCCAGAAGAGCTAATATAT
1 AAAGCTCCAAAAGAGCTAATATAT
21728909 TAGTATCTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
51 17 0.25
52 3 0.04
53 4 0.06
54 2 0.03
55 42 0.62
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (51 bp):
AAAGCTCCAAAAGAGCTAATATATCAATATTTGATACTACAAAATTAGATA
Found at i:21728864 original size:55 final size:55
Alignment explanation
Indices: 21728792--21728902 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
21728782 GCTACAAAAG
* *
21728792 AGCTAATATATCAATATTTGATACTATAAAATTAGATAAAAGCTCCAAAAGAGCT
1 AGCTAATAAATCAATATTTGATACTACAAAATTAGATAAAAGCTCCAAAAGAGCT
* * *
21728847 AGCTAATAAATCAATATTTGGTACTACAAAATTAGATGAAAGCTCCAGAAGAGCT
1 AGCTAATAAATCAATATTTGATACTACAAAATTAGATAAAAGCTCCAAAAGAGCT
21728902 A
1 A
21728903 ATATATTAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (55 bp):
AGCTAATAAATCAATATTTGATACTACAAAATTAGATAAAAGCTCCAAAAGAGCT
Found at i:21732508 original size:10 final size:10
Alignment explanation
Indices: 21732495--21732537 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
21732485 AGGATTTAAT
21732495 TTTATTTATC
1 TTTATTTATC
*
21732505 TTTAATTATC
1 TTTATTTATC
21732515 TTTATTTAT-
1 TTTATTTATC
21732524 TTGTATTTATC
1 TT-TATTTATC
21732535 TTT
1 TTT
21732538 TAGAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.07
10 25 0.86
11 2 0.07
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTATTTATC
Found at i:21742735 original size:30 final size:30
Alignment explanation
Indices: 21742675--21742735 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
21742665 ATGTCTATGT
* **
21742675 AAATTATCATTGGTTTGGGATTTTTCTGGA
1 AAATTATCATTGGTCTGGGATTTTGATGGA
21742705 AAATTAAT-ATTGGTCTGGGATTTTGATGGA
1 AAATT-ATCATTGGTCTGGGATTTTGATGGA
21742735 A
1 A
21742736 GAGTATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.43
Consensus pattern (30 bp):
AAATTATCATTGGTCTGGGATTTTGATGGA
Found at i:21743067 original size:28 final size:28
Alignment explanation
Indices: 21743027--21743082 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
21743017 ACTACAAGAG
21743027 ATAGGACTGGTTGTCATCAGCAATTTTT
1 ATAGGACTGGTTGTCATCAGCAATTTTT
* *
21743055 ATAGGATTGGTTGTCATCGGCAATTTTT
1 ATAGGACTGGTTGTCATCAGCAATTTTT
21743083 CTAATATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.41
Consensus pattern (28 bp):
ATAGGACTGGTTGTCATCAGCAATTTTT
Found at i:21748115 original size:45 final size:45
Alignment explanation
Indices: 21748051--21748138 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
21748041 AACCTAACCT
21748051 CTATATAAGTACACCTATATAGGTGCAAGATTAGATGCAATGCCC
1 CTATATAAGTACACCTATATAGGTGCAAGATTAGATGCAATGCCC
* *
21748096 CTATATAAGTCCACCTATATAGGTGCATGATTAGATGCAATGC
1 CTATATAAGTACACCTATATAGGTGCAAGATTAGATGCAATGC
21748139 AGGTTAAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (45 bp):
CTATATAAGTACACCTATATAGGTGCAAGATTAGATGCAATGCCC
Found at i:21755060 original size:5 final size:5
Alignment explanation
Indices: 21755047--21755079 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
21755037 AAGATTTGAT
21755047 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
21755080 TAAATTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:21755063 original size:15 final size:16
Alignment explanation
Indices: 21755040--21755081 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
21755030 AAATAGGAAG
*
21755040 ATTTGATTTTTA-TTT
1 ATTTTATTTTTATTTT
21755055 ATTTTA-TTTTATTTT
1 ATTTTATTTTTATTTT
21755070 ATTTTATTTTTA
1 ATTTTATTTTTA
21755082 AATTAGTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
ATTTTATTTTTATTTT
Found at i:21758708 original size:20 final size:20
Alignment explanation
Indices: 21758683--21758722 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21758673 TACTAAAATG
21758683 TAAAGATGCTATAGAGTGCT
1 TAAAGATGCTATAGAGTGCT
21758703 TAAAGATGCTATAGAGTGCT
1 TAAAGATGCTATAGAGTGCT
21758723 CGAAAGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
TAAAGATGCTATAGAGTGCT
Found at i:21760950 original size:45 final size:45
Alignment explanation
Indices: 21760901--21760995 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 45
21760891 GTAGCAAGGA
*
21760901 AGCAGA-CTAAAAATTACAGA-TCTTATCTTCATGTATCGGCTATGG
1 AGCAGATC-AAAAA-TACAGAGTCTTATCTCCATGTATCGGCTATGG
* **
21760946 AGCAGATCGAAAATAGTGAGTCTTATCTCCATGTATCGGCTATGG
1 AGCAGATCAAAAATACAGAGTCTTATCTCCATGTATCGGCTATGG
21760991 AGCAG
1 AGCAG
21760996 GTTTTAACCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 4 0.09
45 39 0.89
46 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (45 bp):
AGCAGATCAAAAATACAGAGTCTTATCTCCATGTATCGGCTATGG
Found at i:21761180 original size:178 final size:178
Alignment explanation
Indices: 21760871--21761308 Score: 662
Period size: 178 Copynumber: 2.5 Consensus size: 178
21760861 CAGTGAATTC
*
21760871 ACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAAATTACAGATCTTATCTTCATGTA
1 ACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTA
* * *
21760936 TCGGCTATGGAGCAGATCGAAAATAGTGAGTCTTATCTCCATGTATCGGCTATGGAGCAGGTTTT
66 TCGGCTATGGAGCAGATCGAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGAAGCAAGTTTT
21761001 AACCACCAGCCTTATCTCTCTAACGTAGCAAGAGAGCAGGTTGAAGAT
131 AACCACCAGCCTTATCTCTCTAACGTAGCAAGAGAGCAGGTTGAAGAT
* * * *
21761049 ACACGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTAAAAATTACAAATCTTATCTCCATTTA
1 ACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTA
* * * *
21761114 TCGGTTATGGGGCAGATCTG-AAATGGCGAGTTTTATCTCCATGTATCGGCTATGAAGCAAGTTT
66 TCGGCTATGGAGCAGATC-GAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGAAGCAAGTTT
* * * * * *
21761178 TAACCACTAGCTTTGTCTCTCTGAGGTAGCAAGAGAGCATGTTGAAGAT
130 TAACCACCAGCCTTATCTCTCTAACGTAGCAAGAGAGCAGGTTGAAGAT
* * * *
21761227 ACAAGTCTTATCTTCCTGAAGTAGCAAGTAAGCAGACTGAAAATTACAGATCTTATCTCTATGTA
1 ACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTA
21761292 TCGGCTATGGAGCAGAT
66 TCGGCTATGGAGCAGAT
21761309 TTTAGCCACC
Statistics
Matches: 231, Mismatches: 28, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
178 230 1.00
179 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (178 bp):
ACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTA
TCGGCTATGGAGCAGATCGAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGAAGCAAGTTTT
AACCACCAGCCTTATCTCTCTAACGTAGCAAGAGAGCAGGTTGAAGAT
Found at i:21761239 original size:133 final size:131
Alignment explanation
Indices: 21761146--21761441 Score: 382
Period size: 133 Copynumber: 2.2 Consensus size: 131
21761136 ATGGCGAGTT
* * *
21761146 TTATCTCCATGTATCGGCTATGAAGCA-AGTTTTAACCACTAGCTTTGTCTCTCTGAGGTAGCAA
1 TTATCTCCATGTATCGGCTATGAAGCAGA-TTTTAACCACCAGCCTTATCTCTCTGAGGTAGCAA
* *
21761210 GAGAGCATGTTGAAGATACAAGTCTTATCTTCCTGAAGTAGCAAGTAAGCAGACTGAAAATTACA
65 GAGAGCAGGTTGAAGATACAAGTCTTATC-TCC-GAAGTAGCAAGTAAGCAGACTGAAAATGACA
21761275 GATC
128 GATC
* * * *
21761279 TTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTGAGGTAGCAAG
1 TTATCTCCATGTATCGGCTATGAAGCAGATTTTAACCACCAGCCTTATCTCTCTGAGGTAGCAAG
* * * * *
21761344 AGTGCAGGTTGAAGATACAAGTCTTATCTTTCTGAGGTAGCAA-TGAAGTAGACTGAAAATTACA
66 AGAGCAGGTTGAAGATACAAGTCTTATC--TCCGAAGTAGCAAGT-AAGCAGACTGAAAATGACA
21761408 GATC
128 GATC
21761412 TTATCTCCATGTATCGGCTAT-AGAGCAGAT
1 TTATCTCCATGTATCGGCTATGA-AGCAGAT
21761442 CGAAAATGGC
Statistics
Matches: 145, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
132 1 0.01
133 140 0.97
134 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (131 bp):
TTATCTCCATGTATCGGCTATGAAGCAGATTTTAACCACCAGCCTTATCTCTCTGAGGTAGCAAG
AGAGCAGGTTGAAGATACAAGTCTTATCTCCGAAGTAGCAAGTAAGCAGACTGAAAATGACAGAT
C
Found at i:21761416 original size:178 final size:179
Alignment explanation
Indices: 21761232--21761595 Score: 515
Period size: 178 Copynumber: 2.0 Consensus size: 179
21761222 AAGATACAAG
* *
21761232 TCTTATCTTCC-TGAAGT-AGCAAGTA-AGCAGA-CTGAAAATTAC-AGATCTTATCTCTATGTA
1 TCTTATCTTCCATGAA-TCAGCAA-TAGAGCAGATC-GAAAATGACGAG-TCTTATCTCCATGTA
* **
21761292 TCGGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGTGCAGGTTGAA
62 TCGGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTCAAA
* * *
21761357 GATACAAGTCTTATCTTTCTGAGGTAGCAATGAAGTAGACTGAAAATTACAGA
127 GATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAAATTACAGA
* * * *
21761410 TCTTATC-TCCATGTATCGGCTATAGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATCGG
1 TCTTATCTTCCATGAATCAGCAATAGAGCAGATCGAAAATGACGAGTCTTATCTCCATGTATCGG
*
21761474 CTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTTTGAGGTAGCAAGAGAGCAGGTCAAAGATA
66 CTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTCAAAGATA
* *
21761539 CAAGTCTTATCTTCCTGAGGTAGTAAGGAAGCAGACTGAAAATTTCAGA
131 CAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAAATTACAGA
21761588 TCTTATCT
1 TCTTATCT
21761596 CCCTAAATAG
Statistics
Matches: 165, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
177 6 0.04
178 156 0.95
179 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (179 bp):
TCTTATCTTCCATGAATCAGCAATAGAGCAGATCGAAAATGACGAGTCTTATCTCCATGTATCGG
CTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTCAAAGATA
CAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAAATTACAGA
Done.