Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003170.1 Hibiscus syriacus cultivar Beakdansim tig00006666_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: 749787
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:529547 original size:19 final size:20
Alignment explanation
Indices: 529509--529547 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
529499 GTGCACGCAT
*
529509 AAATGTCGATACATTTATAAA
1 AAATCTCGATACA-TTATAAA
529530 AAATCTCGATAC-TTATAA
1 AAATCTCGATACATTATAA
529548 TGTAATAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (20 bp):
AAATCTCGATACATTATAAA
Found at i:529844 original size:23 final size:23
Alignment explanation
Indices: 529808--529855 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
529798 AAATAGGTCA
*
529808 ATATAAACGCTACCTATTATATT
1 ATATAAACGCTACCTAATATATT
* * *
529831 ATATAAGCGTTACCTAATATGTT
1 ATATAAACGCTACCTAATATATT
529854 AT
1 AT
529856 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATAAACGCTACCTAATATATT
Found at i:531933 original size:22 final size:24
Alignment explanation
Indices: 531906--531951 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
531896 AAAATAGTAT
531906 TTTAATA-TT-ATA-TGAATTGAAA
1 TTTAATAGTTAATATTG-ATTGAAA
531928 TTTAATAGTTAATATTGATTGAAA
1 TTTAATAGTTAATATTGATTGAAA
531952 ATTTGTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.33
23 2 0.10
24 10 0.48
25 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (24 bp):
TTTAATAGTTAATATTGATTGAAA
Found at i:534886 original size:35 final size:35
Alignment explanation
Indices: 534815--534889 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
534805 TGGTGTGGCG
* * * * *
534815 AAAGTTTAATGAAATTGTAAAAGTGTGTTGAGGCA
1 AAAGTTTAATGAAATTGAAAAAGTATGCTAAAGCA
534850 AAAGTTTAA-GTAAATTGAAAAAGTATGCTAAAGCA
1 AAAGTTTAATG-AAATTGAAAAAGTATGCTAAAGCA
534885 AAAGT
1 AAAGT
534890 AAATTGAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.47, C:0.04, G:0.21, T:0.28
Consensus pattern (35 bp):
AAAGTTTAATGAAATTGAAAAAGTATGCTAAAGCA
Found at i:536492 original size:2 final size:2
Alignment explanation
Indices: 536485--536514 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
536475 TGTTATTATT
536485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
536515 ATTTTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:544017 original size:22 final size:21
Alignment explanation
Indices: 543975--544014 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
543965 AAGACTATTT
543975 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
543996 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
544015 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:552272 original size:20 final size:18
Alignment explanation
Indices: 552230--552273 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
552220 ATATTGCTAC
* *
552230 CACATTTCACATTGCCAT
1 CACATTTCACAATACCAT
552248 CACATTTCCACAATACCATT
1 CACATTT-CACAATACCA-T
552268 CACATT
1 CACATT
552274 CGCTCCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 8 0.36
20 7 0.32
ACGTcount: A:0.32, C:0.34, G:0.02, T:0.32
Consensus pattern (18 bp):
CACATTTCACAATACCAT
Found at i:555537 original size:8 final size:8
Alignment explanation
Indices: 555524--555550 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
555514 GTGTTTGAGG
555524 GAAAAAAT
1 GAAAAAAT
555532 GAAAAAAT
1 GAAAAAAT
555540 GAAAAAAT
1 GAAAAAAT
555548 GAA
1 GAA
555551 GAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (8 bp):
GAAAAAAT
Found at i:555590 original size:4 final size:4
Alignment explanation
Indices: 555581--555614 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
555571 ATAAAAGGAA
555581 AAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
555615 TTAAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:555626 original size:2 final size:2
Alignment explanation
Indices: 555619--555651 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
555609 GAAATATTAA
555619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
555652 ATGAGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:555928 original size:2 final size:2
Alignment explanation
Indices: 555923--555954 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
555913 TTTAAAAAAG
555923 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
555955 GTATTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:556521 original size:37 final size:37
Alignment explanation
Indices: 556480--556584 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
556470 GTGCTTGTGG
* * *
556480 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
556517 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
556554 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
556585 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:557613 original size:106 final size:106
Alignment explanation
Indices: 557295--558770 Score: 2106
Period size: 106 Copynumber: 14.0 Consensus size: 106
557285 GCATTGTTCC
* *** *
557295 GAGTCCAATATCC-TC-CATCGTGAAGTTGAAATTGGCTCTGGAACCAGGAAATTGTTTATTGAC
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAC
* * * *
557358 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
557401 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * * *
557460 TCAGTC-GCCCCTTCATTGTGAAGTTGATCTTGTGTTGTCTTG
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
557502 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
557566 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
557607 GAGTCCAATATCCTACGGTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
557672 CCAGCGGTCCCTTTGTCGTGAAATTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
557713 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
557778 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
557819 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
557884 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
557925 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGG-AGTTGTTTGTTAACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GGAAGTTGTTTATTGACA
*
557989 ACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
558031 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
558096 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCG-T-TCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
558135 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
558200 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
558241 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
558306 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
558347 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
558412 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
558453 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
558518 CCAGCGGT--CTTCATCGTGAAGTTAAACTTGTGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
558557 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
558622 CCAGTGGTCCATTCGTCGTGAATTTGAACTTTCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
558663 GAGTCCAATATCCTTCGCTATGAAGTT-AAATTGGCTCCGAAATTGGAAAATT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
558726 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
558767 GAGT
1 GAGT
558771 GGCACGATAT
Statistics
Matches: 1248, Mismatches: 103, Indels: 40
0.90 0.07 0.03
Matches are distributed among these distances:
100 79 0.06
101 6 0.00
102 4 0.00
104 242 0.19
105 33 0.03
106 878 0.70
107 5 0.00
108 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:558331 original size:422 final size:422
Alignment explanation
Indices: 557295--558770 Score: 2145
Period size: 422 Copynumber: 3.5 Consensus size: 422
557285 GCATTGTTCC
* * * * ** *
557295 GAGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTGGAA-CCAGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTATTTATTGACA
* * * *
557359 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGA
* * * * *
557424 AGTTGAAATTGACTCTG-AA-T--GAAA-TTTTATTGACAATCAGTCGCCCCTTCATTGTGAAGT
130 AGTTGAAATTGGCTCTGAAATTGGGAAATTTTTATTGACAACCAGTCGTCCCTTCGTCGTGAAGT
* * * *
557484 TGATCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTG-
195 TGAACTTGTGTTGTC-TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* * * *
557547 GGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTC
259 GG-AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
* *
557612 CAATATCCTACGGTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGC
323 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGC
* * *
557677 GGTCCCTTTGTCGTGAAATTGAACTTGCATTGTCTG
388 GGTCCCTTCGTCGTGAAGTTGAACTTGC-GTGTCTG
* *
557713 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTATTGACAA
* *
557778 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * *
557843 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTAACAACCAG-CGGTCCATTCGTCGTGAAG
131 GTTGAAATTGGCTCTGAAATTGGGAAATT-TTTATTGACAACCAGTC-GTCCCTTCGTCGTGAAG
557907 TTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
194 TTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
557972 GGAGTTGTTTGTTAACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
259 GGAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
558037 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTGTTTATTGACAACCAGCA
324 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCG
558102 GTCCCTTCGTCGTGAAGTTGAACTTGCGT-TCTG
389 GTCCCTTCGTCGTGAAGTTGAACTTGCGTGTCTG
* * *
558135 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTATTGACAA
*
558200 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* *
558265 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGATAACCAG-CGGTCCCTTCGTCGTGAAG
131 GTTGAAATTGGCTCTGAAATTGGGAAATT-TTTATTGACAACCAGTC-GTCCCTTCGTCGTGAAG
*
558329 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
194 TTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
558394 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCC
259 GGAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
558459 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAGTTGTTTATTGACAACCAGC
324 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTATTGACAACCAGC
* * * *
558523 GGT--CTTCATCGTGAAGTTAAACTTGTGTTGTTTG
388 GGTCCCTTCGTCGTGAAGTTGAACTTGCG-TGTCTG
* * *
558557 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTATTGACAA
* * * * *
558622 CCAGTGGTCCATTCGTCGTGAATTTGAACTTTCGTTGTCTGGAGTCCAATATCCTTCGCTATGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * * * *
558687 GTT-AAATTGGCTCCGAAATTGGAAAATTATTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTT
131 GTTGAAATTGGCTCTGAAATTGGGAAATTTTTATTGACAACCAGTCGTCCCTTCGTCGTGAAGTT
*
558751 GAACTTGTGTTGTCTTGAGT
196 GAACTTGTGTTGTCTGGAGT
558771 GGCACGATAT
Statistics
Matches: 960, Mismatches: 84, Indels: 26
0.90 0.08 0.02
Matches are distributed among these distances:
418 129 0.13
419 2 0.00
420 70 0.07
421 28 0.03
422 499 0.52
423 6 0.01
424 224 0.23
425 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (422 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGGGAAATTTTTATTGACAACCAGTCGTCCCTTCGTCGTGAAGTT
GAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGG
AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
CCCTTCGTCGTGAAGTTGAACTTGCGTGTCTG
Found at i:559623 original size:22 final size:22
Alignment explanation
Indices: 559597--559671 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
559587 ATGTTTGGTA
559597 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
*
559619 AAAGGTTTGGCATTTGATACTC
1 AAAGGTTTGGCATTTGATGCTC
*
559641 ATAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
*
559663 AACGGTTTG
1 AAAGGTTTG
559672 ATGAGGTAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (22 bp):
AAAGGTTTGGCATTTGATGCTC
Found at i:563293 original size:4 final size:4
Alignment explanation
Indices: 563284--563438 Score: 63
Period size: 4 Copynumber: 37.8 Consensus size: 4
563274 ATAAAAGGAA
* * *
563284 AAAT AAAT AAAT AAAT AAAT AAAT GAAAT ATTAAT -AAT ATAT ATAT ATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A--AAT AAAT AAAT AAAT AAAT
* * * *
563334 ATAT ATAT ATAT ATAT ATAAT -AAT -AAT -AAT AAAAT AATAGT AATAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT -AAAT AA-A-T AA-AT
* * *
563380 AAA- ATAAT AACAT AATAT AAAT AAAT AAA- AAAA AAAC AAA- AAAA AAAT
1 AAAT A-AAT AA-AT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
563428 AAAT ATAT AAA
1 AAAT AAAT AAA
563439 CCAAATATAA
Statistics
Matches: 130, Mismatches: 7, Indels: 28
0.79 0.04 0.17
Matches are distributed among these distances:
3 19 0.15
4 81 0.62
5 22 0.17
6 8 0.06
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:563327 original size:2 final size:2
Alignment explanation
Indices: 563320--563352 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
563310 AATATTAATA
563320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
563353 ATAATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:563359 original size:6 final size:6
Alignment explanation
Indices: 563310--563389 Score: 51
Period size: 6 Copynumber: 12.8 Consensus size: 6
563300 AAATAAATGA
*
563310 AATATT AATAAT -ATATAT ATATATAT ATATATAT ATATATAT AATAAT
1 AATAAT AATAAT AATA-AT A-ATA-AT A-ATA-AT A-ATA-AT AATAAT
*
563358 AATAAT AA-AAT AATAGT AAT-AT AA-AAT AATAA
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAA
563390 CATAATATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
5 15 0.23
6 24 0.37
7 3 0.05
8 23 0.35
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (6 bp):
AATAAT
Found at i:563369 original size:14 final size:14
Alignment explanation
Indices: 563352--563389 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
563342 ATATATATAT
563352 AATAATAATAATAA
1 AATAATAATAATAA
* *
563366 AATAATAGTAATAT
1 AATAATAATAATAA
563380 AA-AATAATAA
1 AATAATAATAA
563390 CATAATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:563372 original size:17 final size:17
Alignment explanation
Indices: 563350--563403 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
563340 ATATATATAT
563350 ATAATAATAATAATAAA
1 ATAATAATAATAATAAA
*
563367 ATAATAGTAAT-ATAAA
1 ATAATAATAATAATAAA
*
563383 ATAATAA-CATAATATAA
1 ATAATAATAATAATA-AA
563400 ATAA
1 ATAA
563404 ATAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 14 0.44
17 16 0.50
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAATAATAATAATAAA
Found at i:563386 original size:24 final size:22
Alignment explanation
Indices: 563346--563412 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 22
563336 ATATATATAT
563346 ATATATAATAATAATAATAAAATA
1 ATATA-AATAA-AATAATAAAATA
*
563370 ATAGTAATATAAAATAATAACATA
1 ATA-TAA-ATAAAATAATAAAATA
*
563394 ATATAAAT-AAATAAAAAAA
1 ATATAAATAAAATAATAAAA
563413 AAACAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 9 0.24
22 2 0.05
23 3 0.08
24 18 0.47
25 6 0.16
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (22 bp):
ATATAAATAAAATAATAAAATA
Found at i:564249 original size:37 final size:37
Alignment explanation
Indices: 564157--564258 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
564147 GTGCTTGTGG
* * * * *
564157 ATCCTATCTTTAGGAGTTCAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
564194 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
564231 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
564259 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:566636 original size:21 final size:21
Alignment explanation
Indices: 566605--566664 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
566595 TAGAATTTGT
* *
566605 CCCAAATGACCACATAGATAT
1 CCCAAAGGACCACATAGATAC
* * *
566626 CCCGAAGGACCACATATATGC
1 CCCAAAGGACCACATAGATAC
*
566647 CCCAAATGACCACATAGA
1 CCCAAAGGACCACATAGA
566665 AATCTCCTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.32, G:0.13, T:0.15
Consensus pattern (21 bp):
CCCAAAGGACCACATAGATAC
Found at i:574202 original size:161 final size:161
Alignment explanation
Indices: 573937--574258 Score: 644
Period size: 161 Copynumber: 2.0 Consensus size: 161
573927 AGAGCGAGGA
573937 GTTGGCGAGGAAGACGGTGGAAACCAGGGCGGCTTAGACGCCATTGGAGAGAAAGCGTTTAGTGA
1 GTTGGCGAGGAAGACGGTGGAAACCAGGGCGGCTTAGACGCCATTGGAGAGAAAGCGTTTAGTGA
574002 ATTGGAGCATGGGATTAATGTGACCTTGACCGGGGAAAAGGAAAGATCAAAACATGAAGTTTTCT
66 ATTGGAGCATGGGATTAATGTGACCTTGACCGGGGAAAAGGAAAGATCAAAACATGAAGTTTTCT
574067 AGGGTTTTGTTCCACCCCCATTGATTCTCCG
131 AGGGTTTTGTTCCACCCCCATTGATTCTCCG
574098 GTTGGCGAGGAAGACGGTGGAAACCAGGGCGGCTTAGACGCCATTGGAGAGAAAGCGTTTAGTGA
1 GTTGGCGAGGAAGACGGTGGAAACCAGGGCGGCTTAGACGCCATTGGAGAGAAAGCGTTTAGTGA
574163 ATTGGAGCATGGGATTAATGTGACCTTGACCGGGGAAAAGGAAAGATCAAAACATGAAGTTTTCT
66 ATTGGAGCATGGGATTAATGTGACCTTGACCGGGGAAAAGGAAAGATCAAAACATGAAGTTTTCT
574228 AGGGTTTTGTTCCACCCCCATTGATTCTCCG
131 AGGGTTTTGTTCCACCCCCATTGATTCTCCG
574259 ATCACCGTTC
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 161 1.00
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (161 bp):
GTTGGCGAGGAAGACGGTGGAAACCAGGGCGGCTTAGACGCCATTGGAGAGAAAGCGTTTAGTGA
ATTGGAGCATGGGATTAATGTGACCTTGACCGGGGAAAAGGAAAGATCAAAACATGAAGTTTTCT
AGGGTTTTGTTCCACCCCCATTGATTCTCCG
Found at i:580993 original size:29 final size:29
Alignment explanation
Indices: 580951--581046 Score: 174
Period size: 29 Copynumber: 3.3 Consensus size: 29
580941 ATGATCACAA
* *
580951 GCATATGATGATCAGGATCTATATTACTT
1 GCATATGACGATCAAGATCTATATTACTT
580980 GCATATGACGATCAAGATCTATATTACTT
1 GCATATGACGATCAAGATCTATATTACTT
581009 GCATATGACGATCAAGATCTATATTACTT
1 GCATATGACGATCAAGATCTATATTACTT
581038 GCATATGAC
1 GCATATGAC
581047 TACAAATTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (29 bp):
GCATATGACGATCAAGATCTATATTACTT
Found at i:589491 original size:31 final size:31
Alignment explanation
Indices: 589439--589499 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
589429 TGATCACATA
*
589439 TTAATTAAATAAAATCGAAAGTGACCAAATC
1 TTAATTAAATAAAATCAAAAGTGACCAAATC
589470 TTAATTAAATAAAAAT-AAAAGTGACCAAAT
1 TTAATTAAAT-AAAATCAAAAGTGACCAAAT
589500 ATTATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (31 bp):
TTAATTAAATAAAATCAAAAGTGACCAAATC
Found at i:590861 original size:19 final size:17
Alignment explanation
Indices: 590794--590861 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 17
590784 ATAAAACAAG
590794 AAAAA-TAAAAAATAAT
1 AAAAATTAAAAAATAAT
*
590810 AAAACACGTAAAAAATAAT
1 AAAA-A-TTAAAAAATAAT
*
590829 AAAAATAAACAAAATGAAT
1 AAAAATTAA-AAAAT-AAT
590848 AAAATATTAAAAAA
1 AAAA-ATTAAAAAA
590862 CAAAGACAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
16 4 0.09
17 3 0.07
18 6 0.14
19 26 0.60
20 4 0.09
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATTAAAAAATAAT
Found at i:590937 original size:20 final size:18
Alignment explanation
Indices: 590896--590944 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
590886 ATTAATGAAG
*
590896 TAAAAAAATAAAAAAAGG
1 TAAAAAAATAAAAAAAGA
*
590914 TAAAAGAAATTAAAAAAGAA
1 TAAAA-AAATAAAAAAAG-A
590934 TAAAAATAATA
1 TAAAAA-AATA
590945 TGTACATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 5 0.20
19 12 0.48
20 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (18 bp):
TAAAAAAATAAAAAAAGA
Found at i:590939 original size:36 final size:34
Alignment explanation
Indices: 590818--590942 Score: 87
Period size: 36 Copynumber: 3.6 Consensus size: 34
590808 ATAAAACACG
*
590818 TAAAAAA-TAATAAAAATAAACAAAATGAATAAAATAT
1 TAAAAAAGTAA-AAAAATAAA-AAAAGGAA-AAAA-AT
* * * *
590855 TAAAAAA-CAAAGACAA-AGATAAAGGAAAAAAAT
1 TAAAAAAGTAAA-AAAATAAAAAAAGGAAAAAAAT
**
590888 TAATGAAGTAAAAAAATAAAAAAAGGTAAAAGAAAT
1 TAAAAAAGTAAAAAAATAAAAAAAGG-AAAA-AAAT
590924 TAAAAAAG-AATAAAAATAA
1 TAAAAAAGTAA-AAAAATAA
590943 TATGTACATA
Statistics
Matches: 69, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
33 10 0.14
34 14 0.20
35 12 0.17
36 21 0.30
37 12 0.17
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (34 bp):
TAAAAAAGTAAAAAAATAAAAAAAGGAAAAAAAT
Found at i:591077 original size:16 final size:17
Alignment explanation
Indices: 591045--591100 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
591035 TATTAAGAAA
591045 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
591062 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
* *
591078 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAA-AAAT
591097 AAAA
1 AAAA
591101 ATAGAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 3 0.10
19 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:591148 original size:37 final size:36
Alignment explanation
Indices: 591080--591162 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 36
591070 GTAAAAATAT
591080 AATATATATAAATAAATAAAAATAGAATATTAAGAA
1 AATATATATAAATAAATAAAAATAGAATATTAAGAA
* *
591116 AATATATATAAA-AACGTATAAAATATAATATTAAGAA
1 AATATATATAAATAA-ATA-AAAATAGAATATTAAGAA
*
591153 AAAATATATA
1 AATATATATA
591163 TATAGTAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 2 0.05
36 14 0.33
37 26 0.62
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (36 bp):
AATATATATAAATAAATAAAAATAGAATATTAAGAA
Found at i:591204 original size:2 final size:2
Alignment explanation
Indices: 591192--591240 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
591182 TTAATACATC
* *
591192 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
591233 TA TA TA TA
1 TA TA TA TA
591241 ATAAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:591303 original size:21 final size:20
Alignment explanation
Indices: 591240--591303 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
591230 AGATATATAT
*
591240 AATAAAAATAAA-ATAATATA
1 AATAAAAAAAAATATAAT-TA
*
591260 AATAAAAAAAGGAATAT-AGTA
1 AATAAAAAAA--AATATAATTA
591281 AATAAATAAAAAATATAATTA
1 AATAAA-AAAAAATATAATTA
591302 AA
1 AA
591304 AATATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 14 0.39
21 13 0.36
22 7 0.19
23 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
AATAAAAAAAAATATAATTA
Found at i:592829 original size:109 final size:107
Alignment explanation
Indices: 592635--592889 Score: 340
Period size: 109 Copynumber: 2.4 Consensus size: 107
592625 TATTGTTCCG
*
592635 AGTCCAATAT-CCTC-CGTCGTGAAGTTGAAATTGGCTCTG--GAACTGGAAATTGTTTGTTGAC
1 AGTCCAATATCCCTCAC-T-GTGAAGTTGAAATTGGCTCTGAAGAACTGAAAATTGTTTGTTGAC
*
592696 AGTCAGCCGCCCCTTCGTTGTGAAGTTGAGATTGTGTTGTCTCA
64 AATCAGCCGCCCCTTCGTTGTGAAGTTGAGATTGTGTTGTCTCA
* * *
592740 AGTTCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTT-TTGA
1 AGTCCAATATCCCTCACTGTGAAGTTGAAATTGGCTCTGAA-G-AACTGAAAA-TTGTTTGTTGA
* * **
592804 CAATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
63 CAATCAGCCGCCCCTTCGTTGTGAAGTTGAGATTGTGTTGTCTCA
*
592849 AGTCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 AGTCCAATATCCCTCACTGTGAAGTTGAAATTGGCTCTGAA
592890 ACTGGGAAGC
Statistics
Matches: 130, Mismatches: 13, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
105 29 0.22
106 4 0.03
107 1 0.01
108 1 0.01
109 89 0.68
110 6 0.05
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (107 bp):
AGTCCAATATCCCTCACTGTGAAGTTGAAATTGGCTCTGAAGAACTGAAAATTGTTTGTTGACAA
TCAGCCGCCCCTTCGTTGTGAAGTTGAGATTGTGTTGTCTCA
Found at i:593773 original size:65 final size:66
Alignment explanation
Indices: 593593--593788 Score: 218
Period size: 65 Copynumber: 2.9 Consensus size: 66
593583 GGAAACGATC
* * * *
593593 TCAAAGATATCTGTTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAA-TTTGTTTTAAGGGAAA
593657 TAAAT
62 TAAAT
** * *
593662 TTGAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGGAAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGG-AGACAAAATTTGTTTTAAGGGAAATAA
593727 AT
65 AT
* * *
593729 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAATTTGTTTTAAGGGAAA
593789 CTGTCTCAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
65 43 0.39
66 4 0.04
67 36 0.33
68 20 0.18
69 6 0.06
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (66 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGAGACAAAATTTGTTTTAAGGGAAATAAA
T
Found at i:593789 original size:36 final size:36
Alignment explanation
Indices: 593737--594049 Score: 255
Period size: 36 Copynumber: 9.0 Consensus size: 36
593727 ATTCAAAGAT
593737 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
593773 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * **
593809 CTTAGTTCCAAAAGAAACTGTCTTAAGAGAGATGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*** * *
593846 TTTGTTTCAAATAAAACATAT-TC-----A-A-ATAA
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
593875 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
593911 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
593947 TTTATTTCAAGGGAAA-TGTTTTC-A-A-TG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
593975 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
594012 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
594049 T
1 T
594050 CTTTTTTTTA
Statistics
Matches: 220, Mismatches: 35, Indels: 44
0.74 0.12 0.15
Matches are distributed among these distances:
28 4 0.02
29 33 0.15
30 4 0.02
31 1 0.00
32 1 0.00
33 1 0.00
34 2 0.01
35 4 0.02
36 106 0.48
37 62 0.28
38 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:593982 original size:101 final size:102
Alignment explanation
Indices: 593771--594043 Score: 343
Period size: 101 Copynumber: 2.7 Consensus size: 102
593761 AGAGAGACAA
* * ** *
593771 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
* * *
593836 AGAGATGAAATTTGTTTCAAATAAAACATATTCAAAT
66 AGAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
*
593873 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
* * ** *
593937 AGAGACGAAATTTATTTCAAGGGAAATGTTTTC-AAT
66 AGAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
** * * *
593973 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAA
*
594038 GCGAGA
65 GAGAGA
594044 TAAAATCTTT
Statistics
Matches: 149, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
100 5 0.03
101 78 0.52
102 66 0.44
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (102 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
AGAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
Found at i:594029 original size:37 final size:37
Alignment explanation
Indices: 593978--594049 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
593968 TCAATGTTTA
* *
593978 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
* *
594015 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
594050 CTTTTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
Found at i:595732 original size:13 final size:14
Alignment explanation
Indices: 595703--595754 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 14
595693 TTTTTCTTCA
595703 ATTTTC-CTTTATT
1 ATTTTCTCTTTATT
595716 -TTTTCTCTTT-TT
1 ATTTTCTCTTTATT
595728 ATTTTCTCTTTACTTT
1 ATTTTCTCTTTA--TT
*
595744 TTTTTCTCTTT
1 ATTTTCTCTTT
595755 TGTTCTGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
16 12 0.36
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTTCTCTTTATT
Found at i:598868 original size:20 final size:19
Alignment explanation
Indices: 598821--598875 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
598811 GGAAAAAATT
598821 AAGAAGTAAAAAAATAAAAA
1 AAGAA-TAAAAAAATAAAAA
* *
598841 AAG-GTAAAAGAAATTAAAA
1 AAGAATAAAA-AAATAAAAA
598860 AAGAATAAAAATAATA
1 AAGAATAAAAA-AATA
598876 TGTACAATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 5 0.18
19 12 0.43
20 11 0.39
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.15
Consensus pattern (19 bp):
AAGAATAAAAAAATAAAAA
Found at i:600285 original size:45 final size:44
Alignment explanation
Indices: 600177--600304 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 44
600167 CACAAACGCT
* * * *
600177 GCTATATAACATGAATGTTGTGGTGTTTGTATAAAAAAAATGCC
1 GCTATAAAACCTGAATGTTGCGGCGTTTGTATAAAAAAAATGCC
* * * *
600221 GCTATAAAACCTGATTGTTGCGGCTTTTGTACAAAAAAAATGCT
1 GCTATAAAACCTGAATGTTGCGGCGTTTGTATAAAAAAAATGCC
* * *
600265 GTTATAGAATCTGACATGTTGCGGCGTTTGTATAAAAAAA
1 GCTATAAAACCTGA-ATGTTGCGGCGTTTGTATAAAAAAA
600305 TGTCACTATA
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
44 47 0.68
45 22 0.32
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (44 bp):
GCTATAAAACCTGAATGTTGCGGCGTTTGTATAAAAAAAATGCC
Found at i:602852 original size:3 final size:3
Alignment explanation
Indices: 602846--602903 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
602836 ATTTATTATT
* * *
602846 TAA TAA TAA TAA T-G TAA TAA TAA TAT TAA TAA TAA AAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
602892 TAA TAA AAA TAA
1 TAA TAA TAA TAA
602904 AGTCGGGACA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:602891 original size:26 final size:26
Alignment explanation
Indices: 602845--602896 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
602835 TATTTATTAT
* *
602845 TTAATAATAATAATGTAATAATAATA
1 TTAATAATAAAAATATAATAATAATA
602871 TTAATAATAAAAATA-ATATAATAATA
1 TTAATAATAAAAATATA-ATAATAATA
602897 AAAATAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
TTAATAATAAAAATATAATAATAATA
Found at i:602892 original size:17 final size:18
Alignment explanation
Indices: 602864--602903 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
602854 ATAATGTAAT
602864 AATAATATTAATAATAAA
1 AATAATATTAATAATAAA
602882 AATAATA-TAATAATAAA
1 AATAATATTAATAATAAA
602899 AATAA
1 AATAA
602904 AGTCGGGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAATATTAATAATAAA
Found at i:602902 original size:26 final size:28
Alignment explanation
Indices: 602848--602903 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
602838 TTATTATTTA
* * *
602848 ATAATAATAATGTAATAATAATATTAAT
1 ATAATAATAATATAATAATAAAAATAAT
*
602876 AATAAAAATAATATAATAATAAAAATAA
1 -ATAATAATAATATAATAATAAAAATAA
602904 AGTCGGGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
ATAATAATAATATAATAATAAAAATAAT
Found at i:603489 original size:112 final size:113
Alignment explanation
Indices: 603247--604040 Score: 1001
Period size: 112 Copynumber: 7.0 Consensus size: 113
603237 GAATCAAATT
* * *
603247 AAGGTTGAACAAGTTCTTCTTATTATAAACTTCTTC-TCATTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *** ** *
603311 TGAACACTT-CTGGAAATGTCGATGTTGATCTATCTCCTTTTGTAA-TAGAGTCATGCA
66 TGAACTCTTCCTGGAAA-----A-GCTGATCCATCGAGTGATG-AATTCGAG-CA---A
* *
603368 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
603432 TGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTTGAGCAA
66 TGAACTCTTC-CTGGAAAAGCTGATCCATCGAGTGATGAATTCGAGCAA
* *
603480 AAGGTTGAACAAGTTTTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
603545 TGAACTCTTCC-AGAAATGCTGATCCATCGAGTGATGAATTCGAGCAA
66 TGAACTCTTCCTGGAAAAGCTGATCCATCGAGTGATGAATTCGAGCAA
603592 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *
603657 TGAACTCTACCTGGAAATA-TTGATCCATCGAATGATGGATTCGAACAA
66 TGAACTCTTCCTGGAAA-AGCTGATCCATCGAGTGATGAATTCGAGCAA
*
603705 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * ** *
603770 TGAACTCTACCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGTAA
66 TGAACTCTTCCTGGAAAAGCTGATCCATCGAGTGATGAATTCGAGCAA
*
603818 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *
603883 TGAACTCGTCC-GGAAATGCTGATCCATTGAGTGATGAATTTGAGAAA
66 TGAACTCTTCCTGGAAAAGCTGATCCATCGAGTGATGAATTCGAGCAA
*
603930 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
603995 TGAACTCTTCCTGGAAAAGTGTTGACCCATCGAGTGATGGATTCGA
66 TGAACTCTTCCTGGAAAA--GCTGATCCATCGAGTGATGAATTCGA
604041 ATCTTTGCTG
Statistics
Matches: 599, Mismatches: 62, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
112 245 0.41
113 236 0.39
114 3 0.01
115 25 0.04
116 17 0.03
117 1 0.00
120 2 0.00
121 61 0.10
122 9 0.02
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (113 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTTCCTGGAAAAGCTGATCCATCGAGTGATGAATTCGAGCAA
Found at i:603807 original size:338 final size:338
Alignment explanation
Indices: 603247--604041 Score: 1094
Period size: 338 Copynumber: 2.3 Consensus size: 338
603237 GAATCAAATT
* * *
603247 AAGGTTGAACAAGTTCTTCTTATTATAAACTTCTTC-TCATTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *** ** * * * *
603311 TGAACACTTCTGGAAATGTCGATGTTGATCTATCTCCTTTTGTAATAGAGTCATGCAAAGGTTGA
66 TGAACTCTCCTGGAAA-GT--A--TTGATCCATCGAATGATGGATTCGA-ACA--CAAAGGTTGA
*
603376 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTC
123 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTAC
* * ** *
603441 TCTGGAAAAGTTGATCCATCGAGTGATGAATTTGAGCAAAAGGTTGAACAAGTTTTTCTCATTAT
188 TCTGGAAAAGCTAATCCATCGAGTGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTCTCATTAT
* * *
603506 GAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCAGAAATGCTGATCCA
253 GAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCGTCCAGAAATGCTGATCCA
*
603571 TCGAGTGATGAATTCGAGCAA
318 TCGAGTGATGAATTCGAGAAA
603592 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
603657 TGAACTCTACCTGGAAA-TATTGATCCATCGAATGATGGATTCGAACA-AAAGGTTGAACAAGTT
66 TGAACTCT-CCTGGAAAGTATTGATCCATCGAATGATGGATTCGAACACAAAGGTTGAACAAATT
* *
603720 CTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGG
130 CTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-TACTCTGG
* * * *
603784 CAATGCTAATCCATCGGGTGATGAATTAAAGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACT
193 AAAAGCTAATCCATCGAGTGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACT
* *
603849 TCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCGTCCGGAAATGCTGATCCATTGAG
258 TCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCGTCCAGAAATGCTGATCCATCGAG
*
603914 TGATGAATTTGAGAAA
323 TGATGAATTCGAGAAA
*
603930 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
603995 TGAACTCTTCCTGGAAAAGTGTTGACCCATCGAGTGATGGATTCGAA
66 TGAACTC-TCCTGG-AAAGTATTGATCCATCGAATGATGGATTCGAA
604042 TCTTTGCTGA
Statistics
Matches: 404, Mismatches: 39, Indels: 19
0.87 0.08 0.04
Matches are distributed among these distances:
337 39 0.10
338 239 0.59
339 6 0.01
340 27 0.07
341 16 0.04
343 1 0.00
345 35 0.09
346 34 0.08
347 7 0.02
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (338 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTCCTGGAAAGTATTGATCCATCGAATGATGGATTCGAACACAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTACTCTGGAAA
AGCTAATCCATCGAGTGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCGTCCAGAAATGCTGATCCATCGAGTGA
TGAATTCGAGAAA
Found at i:604255 original size:22 final size:22
Alignment explanation
Indices: 604221--604349 Score: 213
Period size: 22 Copynumber: 5.9 Consensus size: 22
604211 AAATCTAATA
* * *
604221 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
*
604243 AACCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
604265 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
*
604287 AATCTATCATATTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
604309 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
604331 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
604350 ATGTAGATGT
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 100 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:604725 original size:20 final size:20
Alignment explanation
Indices: 604702--604739 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
604692 ATTTGTTCGG
604702 CACCATAATTACTGGTTCAA
1 CACCATAATTACTGGTTCAA
604722 CACCATAATTACTGGTTC
1 CACCATAATTACTGGTTC
604740 GTAAAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (20 bp):
CACCATAATTACTGGTTCAA
Found at i:607803 original size:14 final size:14
Alignment explanation
Indices: 607780--607813 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
607770 ATTTTTCCCC
607780 TTTTTT-TTGTTGG
1 TTTTTTATTGTTGG
*
607793 TTTTTTATTGTTGT
1 TTTTTTATTGTTGG
607807 TTTTTTA
1 TTTTTTA
607814 CTGATGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.06, C:0.00, G:0.15, T:0.79
Consensus pattern (14 bp):
TTTTTTATTGTTGG
Found at i:611056 original size:13 final size:15
Alignment explanation
Indices: 611038--611072 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
611028 AAATAAACAT
611038 AAATGCAAA-ATG-A
1 AAATGCAAAGATGCA
611051 AAATGCAAAGATGCA
1 AAATGCAAAGATGCA
611066 AAATGCA
1 AAATGCA
611073 TGTATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 3 0.15
15 8 0.40
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.14
Consensus pattern (15 bp):
AAATGCAAAGATGCA
Found at i:611226 original size:43 final size:43
Alignment explanation
Indices: 611146--611230 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
611136 CCGTGCATCA
*
611146 AACAAAACTTTACATATAGGGGACATATTTCAGTCCTAACTTC
1 AACAAAACTTTACATATAGGGGACATATTTCACTCCTAACTTC
* * *
611189 AACAAAACTTTACATATATGGGATA-ACTTTCCCTCCTAACTT
1 AACAAAACTTTACATATAGGGGACATA-TTTCACTCCTAACTT
611231 TTCTAAAGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.32
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGACATATTTCACTCCTAACTTC
Found at i:612623 original size:26 final size:28
Alignment explanation
Indices: 612565--612622 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
612555 AACATTAATA
* *
612565 AAAATAATATATATATATAAATATTATG
1 AAAATAATATATATATAAAAAAATTATG
612593 AAAATAATA-AGTATATAAAAAAATT-TG
1 AAAATAATATA-TATATAAAAAAATTATG
612620 AAA
1 AAA
612623 TGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATAATATATATATAAAAAAATTATG
Found at i:626945 original size:20 final size:20
Alignment explanation
Indices: 626906--626946 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
626896 CATTGCAGGA
*
626906 ATTTATGGCCTCGACGAAAG
1 ATTTATGGCCTCCACGAAAG
626926 ATTTCATGGCCTCCAC-AAAG
1 ATTT-ATGGCCTCCACGAAAG
626946 A
1 A
626947 CCTTGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
ATTTATGGCCTCCACGAAAG
Found at i:649584 original size:48 final size:48
Alignment explanation
Indices: 649497--649594 Score: 108
Period size: 48 Copynumber: 2.0 Consensus size: 48
649487 GCAACAAAGA
** ** **
649497 GAAAGGGAGGAGGAAGAGAGAGAGTAAAGGAGACGTGAAATGGAGAGG
1 GAAAGGGAGGAGGAAGAGAGAGAACAAAAAAGACGTGAAAAAGAGAGG
* *
649545 GAAAGGGAGGA-GAAGGAGAGAGAACAAAAAAGGCTTGAAAAAGAGAGG
1 GAAAGGGAGGAGGAA-GAGAGAGAACAAAAAAGACGTGAAAAAGAGAGG
649593 GA
1 GA
649595 GCGAGTCAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
47 3 0.07
48 38 0.93
ACGTcount: A:0.48, C:0.03, G:0.44, T:0.05
Consensus pattern (48 bp):
GAAAGGGAGGAGGAAGAGAGAGAACAAAAAAGACGTGAAAAAGAGAGG
Found at i:653555 original size:44 final size:44
Alignment explanation
Indices: 653492--653616 Score: 234
Period size: 44 Copynumber: 2.8 Consensus size: 44
653482 ATAAGTAAAC
653492 CCAATGGCTTAG-AAGGCAAGCAATCATATCTATAGAACAAAATG
1 CCAATGGCTTAGCAA-GCAAGCAATCATATCTATAGAACAAAATG
653536 CCAATGGCTTAGCAAGCAAGCAATCATATCTATAGAACAAAATG
1 CCAATGGCTTAGCAAGCAAGCAATCATATCTATAGAACAAAATG
653580 CCAATGGCTTAGCAAGCAAGCAATCATATCTATAGAA
1 CCAATGGCTTAGCAAGCAAGCAATCATATCTATAGAA
653617 AACCATAAAG
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
44 78 0.98
45 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (44 bp):
CCAATGGCTTAGCAAGCAAGCAATCATATCTATAGAACAAAATG
Found at i:656478 original size:10 final size:11
Alignment explanation
Indices: 656455--656495 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
656445 AAATTAAGAG
*
656455 TATATATAAAT
1 TATATCTAAAT
656466 TATATCT-AAT
1 TATATCTAAAT
656476 TATA-CTAAAT
1 TATATCTAAAT
*
656486 TATATATAAA
1 TATATCTAAA
656496 ATGTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 2 0.08
10 14 0.54
11 10 0.38
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATCTAAAT
Found at i:657861 original size:15 final size:15
Alignment explanation
Indices: 657840--657886 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
657830 TTTAATAATA
657840 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGG
*
657855 TGGGCGGATGCGGGG
1 CGGGCGGATGCGGGG
* *
657870 CGGACGGATACGGGG
1 CGGGCGGATGCGGGG
657885 CG
1 CG
657887 AGTAAGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.11, C:0.19, G:0.62, T:0.09
Consensus pattern (15 bp):
CGGGCGGATGCGGGG
Found at i:660211 original size:3 final size:3
Alignment explanation
Indices: 660205--660300 Score: 135
Period size: 3 Copynumber: 33.0 Consensus size: 3
660195 TCATTTGGTT
660205 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
660252 TTA -TA TTA TAA TTA -TA ATA TTA TTA ATA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
660298 TTA
1 TTA
660301 CAATCTCAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
2 6 0.07
3 77 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:661651 original size:17 final size:18
Alignment explanation
Indices: 661629--661662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
661619 GTCACTACTT
*
661629 ATTTA-TATTTTAATTTA
1 ATTTATTATTTAAATTTA
661646 ATTTATTATTTAAATTT
1 ATTTATTATTTAAATTT
661663 CAATATGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATTATTTAAATTTA
Found at i:661713 original size:17 final size:16
Alignment explanation
Indices: 661693--661755 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
661683 TCTAATTATT
661693 ATTTTATTATTATTTTA
1 ATTTTA-TATTATTTTA
* **
661710 ATTTTATAATA-AATA
1 ATTTTATATTATTTTA
661725 ATATTTAT-TTATTTTA
1 AT-TTTATATTATTTTA
*
661741 ATTTTTTATTATTTT
1 ATTTTATATTATTTT
661756 TATATTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
15 10 0.28
16 20 0.56
17 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTATATTATTTTA
Found at i:661716 original size:11 final size:12
Alignment explanation
Indices: 661642--661716 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 12
661632 TATATTTTAA
661642 TTTAATTTATTAT
1 TTTAA-TTATTAT
* *
661655 TTAAATTTCAATAT
1 TTTAA-TT-ATTAT
*
661669 GTTTAATTCAATAT
1 -TTTAATT-ATTAT
*
661683 TCTAATTATTAT
1 TTTAATTATTAT
661695 TTT-ATTATTAT
1 TTTAATTATTAT
661706 TTTAATT-TTAT
1 TTTAATTATTAT
661717 AATAAATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
11 15 0.28
12 9 0.17
13 13 0.25
14 12 0.23
15 4 0.08
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (12 bp):
TTTAATTATTAT
Found at i:661809 original size:15 final size:16
Alignment explanation
Indices: 661778--661810 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
661768 AAATCCTATT
661778 TATAAATTTAATTTTA
1 TATAAATTTAATTTTA
*
661794 TATAAA-TTACTTTTA
1 TATAAATTTAATTTTA
661809 TA
1 TA
661811 AACATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAAATTTAATTTTA
Found at i:661987 original size:43 final size:43
Alignment explanation
Indices: 661940--662024 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
661930 AATTAATTTA
661940 AAATATTTTATTAATATTTTATTTA-TTTTTAATATTAAGAAAG
1 AAATATTTTATTAATA-TTTATTTATTTTTTAATATTAAGAAAG
661983 AAATATTTTATTAATATTTATTTATTTTTTAATATTAAGAAA
1 AAATATTTTATTAATATTTATTTATTTTTTAATATTAAGAAA
662025 ATGATTGTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 8 0.20
43 33 0.80
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (43 bp):
AAATATTTTATTAATATTTATTTATTTTTTAATATTAAGAAAG
Found at i:671911 original size:19 final size:19
Alignment explanation
Indices: 671881--671943 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
671871 TATTATGCTT
* * *
671881 AAAGAAGAAAAAAAAGAATA
1 AAAGAATAAAAGAAA-AAGA
671901 AAAGAATAAAAGAAAAAGA
1 AAAGAATAAAAGAAAAAGA
671920 AAAGAA-AAAGTAGAAAAA-A
1 AAAGAATAAA--AGAAAAAGA
671939 AAAGA
1 AAAGA
671944 GGGTCAAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 3 0.08
19 15 0.39
20 20 0.53
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAGAATAAAAGAAAAAGA
Found at i:672313 original size:18 final size:18
Alignment explanation
Indices: 672287--672324 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
672277 CAAGTTCATC
*
672287 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
*
672305 TTTTCGAAATTTAATTTA
1 TTTTCGAAATTCAATTTA
672323 TT
1 TT
672325 CTTTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:673009 original size:22 final size:22
Alignment explanation
Indices: 672947--673020 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
672937 ACATCTACAT
* *
672947 TCTTCAAAAATGATAGATACAT-
1 TCTTCAAAGATGATAGATTC-TC
672969 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
672991 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
673013 TTTTCAAA
1 TCTTCAAA
673021 TAAGAAAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:673030 original size:22 final size:22
Alignment explanation
Indices: 672969--673031 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
672959 ATAGATACAT
* *
672969 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGAAGAAAGATTCTC
* *
672991 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGAAGAAAGATTCTC
* *
673013 TTTTCAAATAAGAAAGATT
1 TCTTCAAAGAAGAAAGATT
673032 TATTGGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGAAGAAAGATTCTC
Found at i:673031 original size:44 final size:44
Alignment explanation
Indices: 672947--673031 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
672937 ACATCTACAT
* *
672947 TCTTCAAAAATGATAGATACATTCTTCAAAGATGATAGATTCTC
1 TCTTCAAAAATGATAGATACATTCTTCAAAGAAGAAAGATTCTC
* * * *
672991 TCTTCAAAGATGATAGATTC-TCTTTTCAAATAAGAAAGATT
1 TCTTCAAAAATGATAGATACAT-TCTTCAAAGAAGAAAGATT
673032 TATTGGATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 1 0.03
44 33 0.97
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (44 bp):
TCTTCAAAAATGATAGATACATTCTTCAAAGAAGAAAGATTCTC
Found at i:673904 original size:123 final size:122
Alignment explanation
Indices: 673675--673970 Score: 398
Period size: 123 Copynumber: 2.4 Consensus size: 122
673665 AAGCTCATAA
673675 TCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGCTTCTAT
1 TCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGCTTCTAT
* * * * * * *
673740 CACAGAAGGAGATAGATCATCATCAAATTTTGCAGAAAAAGTTCATAATGAGAAGAAC
66 CACAGAAAGAGATAGATCAACACCAAAGTTTCCAGAAAAAGTTCATAAT-AAAAAAAC
* * * *
673798 TCATATGAAGAAGGAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGGC-TCTA
1 TCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCAT-GCTTCTA
* *
673862 TCACAGAAAGAGATAGATCAACACCAACGTTTCCAGATAAAGTTCATAATAAAAAAAC
65 TCACAGAAAGAGATAGATCAACACCAAAGTTTCCAGAAAAAGTTCATAATAAAAAAAC
* * * *
673920 TTATCTGAAG-AGGAAGAAGAAGTTCGTAATGAGAATAACTTGTTCGACCTT
1 TCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
673971 AGCTTGATTC
Statistics
Matches: 151, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
121 3 0.02
122 46 0.30
123 100 0.66
124 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
TCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGCTTCTAT
CACAGAAAGAGATAGATCAACACCAAAGTTTCCAGAAAAAGTTCATAATAAAAAAAC
Found at i:674053 original size:17 final size:17
Alignment explanation
Indices: 674031--674063 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
674021 GATCAATGTT
*
674031 TTCATAATGAGAAGAAG
1 TTCATAATAAGAAGAAG
674048 TTCATAATAAGAAGAA
1 TTCATAATAAGAAGAA
674064 CTTATTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
TTCATAATAAGAAGAAG
Found at i:674281 original size:3 final size:3
Alignment explanation
Indices: 674275--674370 Score: 103
Period size: 3 Copynumber: 33.0 Consensus size: 3
674265 TCATTTGGTT
674275 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * * *
674319 TTA TT- TTA TT- TTA TAA TTA -TA ATA ATA TTA TTA TTA ATA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
674362 TTA TTA TTA
1 TTA TTA TTA
674371 CAGGCCCAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
2 10 0.12
3 66 0.81
4 5 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:676187 original size:17 final size:18
Alignment explanation
Indices: 676167--676206 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
676157 ATAAATATCT
676167 TATTTATAAAAATT-ATA
1 TATTTATAAAAATTAATA
*
676184 TATTTATAAAAGTTAATA
1 TATTTATAAAAATTAATA
676202 TATTT
1 TATTT
676207 TTCTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTTATAAAAATTAATA
Found at i:676810 original size:194 final size:193
Alignment explanation
Indices: 676464--676852 Score: 655
Period size: 194 Copynumber: 2.0 Consensus size: 193
676454 TATTTGACCT
676464 ACCTAACCTAAAAAGGTCAATGGCGACTCCCAAAACATTTTTTAAATCAAAAATTATTTATTATC
1 ACCTAACCTAAAAAGGTCAATGGCGACTCCCAAAACATTTTTTAAATC-AAAATTATTTATTATC
676529 ATTTTATTTTTCCCGCCAAATAAAAATTCTACCGGGCAAAAACGGTTACGACAGAAAATATAACA
65 ATTTTATTTTTCCCGCCAAATAAAAATTCTACCGGGCAAAAACGGTTACGACAGAAAATATAACA
676594 CTTACCCTTCCCGATTTTGTTCCATGG-TGAAACTTCGG-TTTCTACAAAGATTACAAACCGTAA
130 CTTACCCTTCCCGATTTTGTTCC-TGGTTGAAACTTCGGTTTTCTACAAAGATTAC-AACCGTAA
676657 A
193 A
676658 ACCTAACCT-AAAAGGTCAATGGCGACTCCCAAAACA-TTTTTAAATC-AAATTATTTATTTATT
1 ACCTAACCTAAAAAGGTCAATGGCGACTCCCAAAACATTTTTTAAATCAAAATTATTTA-TTA-T
*
676720 CATTTTTATTTTTCCCGCCAAATAAAAATTCGTACCGGGCAAAAACCGGTTACGACAGAACATAT
64 CA-TTTTATTTTTCCCGCCAAATAAAAATTC-TACCGGGCAAAAA-CGGTTACGACAGAAAATAT
676785 AACACTT-CCCTTCCCGATTTTGTTCCTGGTTGAAACTTCGGTTTTCTACAAAGATTACAACCGT
126 AACACTTACCCTTCCCGATTTTGTTCCTGGTTGAAACTTCGGTTTTCTACAAAGATTACAACCGT
676849 AAA
191 AAA
676852 A
1 A
676853 ACCTGGGCCT
Statistics
Matches: 187, Mismatches: 1, Indels: 14
0.93 0.00 0.07
Matches are distributed among these distances:
190 10 0.05
191 3 0.02
192 13 0.07
193 58 0.31
194 62 0.33
195 41 0.22
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (193 bp):
ACCTAACCTAAAAAGGTCAATGGCGACTCCCAAAACATTTTTTAAATCAAAATTATTTATTATCA
TTTTATTTTTCCCGCCAAATAAAAATTCTACCGGGCAAAAACGGTTACGACAGAAAATATAACAC
TTACCCTTCCCGATTTTGTTCCTGGTTGAAACTTCGGTTTTCTACAAAGATTACAACCGTAAA
Found at i:679123 original size:15 final size:15
Alignment explanation
Indices: 679091--679137 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
679081 AGTTAAAATA
*
679091 AATTAA-TTTTTAATT
1 AATTAATTTTTTTA-T
679106 AATTAATTTTTTTAT
1 AATTAATTTTTTTAT
*
679121 AATGAAATTTTTTTAT
1 AAT-TAATTTTTTTAT
679137 A
1 A
679138 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
AATTAATTTTTTTAT
Found at i:685759 original size:2 final size:2
Alignment explanation
Indices: 685752--685781 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
685742 CAATTTTGTA
685752 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
685782 TATGAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:685988 original size:18 final size:19
Alignment explanation
Indices: 685965--686007 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
685955 CAGTAATCCT
685965 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
685983 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
686003 ATTCC
1 ATTCC
686008 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:685995 original size:20 final size:20
Alignment explanation
Indices: 685970--686007 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
685960 ATCCTATTCC
685970 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
685990 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
686008 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:700027 original size:17 final size:18
Alignment explanation
Indices: 699986--700024 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
699976 ATTATATAAG
699986 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
700003 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
700021 TAAA
1 TAAA
700025 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:700096 original size:10 final size:10
Alignment explanation
Indices: 700083--700128 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
700073 AGAGTATTTA
*
700083 AGAGAAGTTG
1 AGAGAAATTG
700093 AGAGAAATTG
1 AGAGAAATTG
*
700103 AGAGAATTTG
1 AGAGAAATTG
700113 AGAGAAATTG
1 AGAGAAATTG
700123 AGAGAA
1 AGAGAA
700129 TTTGGTGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.20
Consensus pattern (10 bp):
AGAGAAATTG
Found at i:700129 original size:20 final size:20
Alignment explanation
Indices: 700083--700132 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
700073 AGAGTATTTA
*
700083 AGAGAAGTTGAGAGAAATTG
1 AGAGAATTTGAGAGAAATTG
700103 AGAGAATTTGAGAGAAATTG
1 AGAGAATTTGAGAGAAATTG
700123 AGAGAATTTG
1 AGAGAATTTG
700133 GTGTGATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (20 bp):
AGAGAATTTGAGAGAAATTG
Found at i:705039 original size:18 final size:19
Alignment explanation
Indices: 705008--705047 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
704998 CTATTAAAAG
705008 TTATAAAATAATTATTTGA
1 TTATAAAATAATTATTTGA
*
705027 TTATAAAAT-ATTATTTTA
1 TTATAAAATAATTATTTGA
705045 TTA
1 TTA
705048 AGTCACTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTATAAAATAATTATTTGA
Found at i:705531 original size:2 final size:2
Alignment explanation
Indices: 705514--705558 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
705504 TTCTAAAACA
* *
705514 AT AT AT AC AT AC 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
705556 AT A
1 AT A
705559 AGTTTTTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:716224 original size:62 final size:62
Alignment explanation
Indices: 716126--716316 Score: 303
Period size: 62 Copynumber: 3.1 Consensus size: 62
716116 AGAGTCATTG
* *
716126 AATTCTAGAT-CCTTAAGCAAGATTAAGAGTTCGAATCATGACATTTGTGAATGGAGCAAATT
1 AATTCTAGATCCCTTAAG-AATATTAAGAGTTCGAATCATAACATTTGTGAATGGAGCAAATT
*
716188 AATTCTAGATCCCTTAAGAATATTAAGAGTTTGAATCATAACATTTGTGAATGGAGCAAATT
1 AATTCTAGATCCCTTAAGAATATTAAGAGTTCGAATCATAACATTTGTGAATGGAGCAAATT
* * *
716250 AATTCTAGATCCCTTAAGAATATTAAGAGTTCGAATCCTAACATTTGTGAATTGAACAAATT
1 AATTCTAGATCCCTTAAGAATATTAAGAGTTCGAATCATAACATTTGTGAATGGAGCAAATT
716312 GAATT
1 -AATT
716317 AAAACAGTTG
Statistics
Matches: 120, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
62 109 0.91
63 11 0.09
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (62 bp):
AATTCTAGATCCCTTAAGAATATTAAGAGTTCGAATCATAACATTTGTGAATGGAGCAAATT
Found at i:718322 original size:276 final size:251
Alignment explanation
Indices: 717746--718362 Score: 808
Period size: 276 Copynumber: 2.4 Consensus size: 251
717736 CTCCATCCGA
*
717746 GACCCGACCCGACCAAAATAAAGTTTCACCTGACCCGACCCGAATATATGAATTAGAAACCCGA-
1 GACCCGACCCGA-CAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
**
717810 -C-CCGAAATAATAAAAATTTTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAATTATA
65 CCACCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAATTATA
*
717873 TATAGAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTGGGTCGGG
130 TATAGAGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTGGGTCGGG
*
717938 TCGGGTATTTTTCACCCTAAACTCGAACCCGACCCGAATATCACACTTAAAAAAACC
195 TCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTTAAAAAAACC
*
717995 GACCTGA--C--CAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
1 GACCCGACCCGACAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
*
718056 CGACTCGAAATAATAAAAAAATTATTTTTATTCAATAAAAA-AGTGACTTAATTGAAAAAAAATT
66 C-AC-CGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTG--AAAAAATT
*
718120 ATTTATAGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATATATATAT
127 ATATATAGA-GGGTATTATTATAATTATTCCTAAATATATAAGGT--AA--A-AT-TATATAT-T
*
718185 ATATTCGGGTCGTGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACTCGACTCGAATAT
184 -T-TT---G--G-GTCGGGTCGGGTATTTTTCACCCTAAACCCGAA--C--C-CGACCCGAATAT
718250 CACACTTAAAAAAACC
236 CACACTTAAAAAAACC
* *
718266 GACCCGACCCGATCAAAATAAAGTTCCACCCAACCCGACCCGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGA-CAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
718331 CCA---AAATAATAAAAAAA-TATTTTTATTCAATA
65 CCACCGAAATAATAAAAAAATTATTTTTATTCAATA
718363 TATGAATAAA
Statistics
Matches: 323, Mismatches: 12, Indels: 45
0.85 0.03 0.12
Matches are distributed among these distances:
244 50 0.15
246 1 0.00
247 1 0.00
248 13 0.04
249 40 0.12
250 16 0.05
251 34 0.11
253 2 0.01
255 1 0.00
256 2 0.01
257 7 0.02
258 1 0.00
259 1 0.00
260 2 0.01
263 1 0.00
265 1 0.00
266 32 0.10
268 1 0.00
270 16 0.05
271 47 0.15
273 1 0.00
275 1 0.00
276 52 0.16
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (251 bp):
GACCCGACCCGACAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
CACCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAATTATAT
ATAGAGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTGGGTCGGGT
CGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTTAAAAAAACC
Found at i:721627 original size:30 final size:30
Alignment explanation
Indices: 721593--721649 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
721583 CTGATTATGT
**
721593 ATGGGATTTATTCTTCGTCCTAATTCTACA
1 ATGGGATTTATTCCCCGTCCTAATTCTACA
*
721623 ATGGGATTTATTCCCCGTCCTGATTCT
1 ATGGGATTTATTCCCCGTCCTAATTCT
721650 GCATGAGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (30 bp):
ATGGGATTTATTCCCCGTCCTAATTCTACA
Found at i:721698 original size:30 final size:29
Alignment explanation
Indices: 721664--721747 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
721654 GAGCTTAGTC
* *
721664 CCCGTTCTGACATCTATATGGGATAAACTT
1 CCCGTTCTGACATCTACATGAGATAAA-TT
* * *
721694 CCCGTTTTGACATATGCATGAGATAAATT
1 CCCGTTCTGACATCTACATGAGATAAATT
* *
721723 CCTCGTTCTGACATCTGCACGAGAT
1 CC-CGTTCTGACATCTACATGAGAT
721748 TATATCTTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 4 0.09
30 41 0.91
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (29 bp):
CCCGTTCTGACATCTACATGAGATAAATT
Found at i:731607 original size:31 final size:32
Alignment explanation
Indices: 731572--731747 Score: 143
Period size: 31 Copynumber: 5.6 Consensus size: 32
731562 CTGTCTATAG
*
731572 GTTCCGAT-GAACCTAGGTAAACTATCCATAT
1 GTTCCGATAGAACATAGGTAAACTATCCATAT
* *
731603 GTTCC-TTAGAACATAGGTATACTATCCATAT
1 GTTCCGATAGAACATAGGTAAACTATCCATAT
* * * *
731634 G-TCTCAAAAG-ACATAGGTAATTCTGTCCATAT
1 GTTC-CGATAGAACATAGGTAA-ACTATCCATAT
* *
731666 GTTCCG-TAGAACATAGGTATACTGTCCATAT
1 GTTCCGATAGAACATAGGTAAACTATCCATAT
* * * *
731697 G-TCTCAAAAG-ACATAGGTAATTCTGTCCATAT
1 GTTC-CGATAGAACATAGGTAA-ACTATCCATAT
731729 GTTCCG-TAGAACATAGGTA
1 GTTCCGATAGAACATAGGTA
731748 TACCCTCGAC
Statistics
Matches: 116, Mismatches: 18, Indels: 21
0.75 0.12 0.14
Matches are distributed among these distances:
30 5 0.04
31 62 0.53
32 45 0.39
33 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (32 bp):
GTTCCGATAGAACATAGGTAAACTATCCATAT
Found at i:731667 original size:32 final size:31
Alignment explanation
Indices: 731613--731730 Score: 148
Period size: 32 Copynumber: 3.7 Consensus size: 31
731603 GTTCCTTAGA
*
731613 ACATAGGTATACTATCCATATGTCTCAAAAG
1 ACATAGGTATACTGTCCATATGTCTCAAAAG
* ***
731644 ACATAGGTAATTCTGTCCATATGT-TCCGTAG
1 ACATAGGT-ATACTGTCCATATGTCTCAAAAG
731675 AACATAGGTATACTGTCCATATGTCTCAAAAG
1 -ACATAGGTATACTGTCCATATGTCTCAAAAG
*
731707 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
731731 TCCGTAGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 34 0.47
32 39 0.53
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCAAAAG
Found at i:731683 original size:63 final size:63
Alignment explanation
Indices: 731596--731750 Score: 292
Period size: 63 Copynumber: 2.5 Consensus size: 63
731586 AGGTAAACTA
*
731596 TCCATATGTTCCTTAGAACATAGGTATACTATCCATATGTCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTATCCATATGTCTCAAAAGACATAGGTAATTCTG
*
731659 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTATCCATATGTCTCAAAAGACATAGGTAATTCTG
731722 TCCATATGTTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
731751 CCTCGACTCT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 90 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (63 bp):
TCCATATGTTCCGTAGAACATAGGTATACTATCCATATGTCTCAAAAGACATAGGTAATTCTG
Found at i:732909 original size:64 final size:64
Alignment explanation
Indices: 732757--732913 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
732747 CAATAAGGGT
* * ** *
732757 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATACATTCGATGTTCTATTATTAAAGAG
* * * *
732821 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCGATG-TTCTATTATTAAAG
732882 AG
63 AG
732884 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
732914 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
63 3 0.04
64 62 0.82
65 11 0.14
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTCTATTATTAAAGAG
Found at i:736457 original size:32 final size:31
Alignment explanation
Indices: 736405--736520 Score: 153
Period size: 32 Copynumber: 3.7 Consensus size: 31
736395 GTTCCTTAGA
736405 ACATAGGTATACTGTCCATATGTCTCAAAAG
1 ACATAGGTATACTGTCCATATGTCTCAAAAG
* ***
736436 ACATAGGTAATTCTGTCCATATGT-TCCGTAG
1 ACATAGGT-ATACTGTCCATATGTCTCAAAAG
736467 AACATAGGTATACTGTCCATATGTCTCAAAAG
1 -ACATAGGTATACTGTCCATATGTCTCAAAAG
*
736499 ACATAGGTAATTCTGTCCATAT
1 ACATAGGT-ATACTGTCCATAT
736521 ATTCCGTAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
31 34 0.47
32 38 0.53
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCAAAAG
Found at i:736468 original size:63 final size:63
Alignment explanation
Indices: 736388--736542 Score: 292
Period size: 63 Copynumber: 2.5 Consensus size: 63
736378 AGGTAAACTA
*
736388 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
736451 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
*
736514 TCCATATATTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
736543 CCTCGACTCT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 90 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (63 bp):
TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATTCTG
Found at i:736535 original size:32 final size:32
Alignment explanation
Indices: 736353--736539 Score: 179
Period size: 31 Copynumber: 5.9 Consensus size: 32
736343 ATCCTCGGTA
* * *
736353 ACTGTCTATAGGTTCCGAT-GAACCTAGGTAA-
1 ACTGTCCATATGTTCC-ATAGAACATAGGTAAT
* *
736384 ACTATCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCATAGAACATAGGTAAT
* *
736415 ACTGTCCATATGTCTCAAAAG-ACATAGGTAAT
1 ACTGTCCATATGT-TCCATAGAACATAGGTAAT
* *
736447 TCTGTCCATATGTTCCGTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCATAGAACATAGGTAAT
* *
736478 ACTGTCCATATGTCTCAAAAG-ACATAGGTAAT
1 ACTGTCCATATGT-TCCATAGAACATAGGTAAT
* * *
736510 TCTGTCCATATATTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCATAGAACATAGGTA
736540 TACCCTCGAC
Statistics
Matches: 126, Mismatches: 22, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
30 2 0.02
31 72 0.57
32 52 0.41
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (32 bp):
ACTGTCCATATGTTCCATAGAACATAGGTAAT
Found at i:740800 original size:16 final size:16
Alignment explanation
Indices: 740779--740818 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
740769 TGTTGGTTGA
740779 ACACGTGTACTTTGTG
1 ACACGTGTACTTTGTG
740795 ACACGTGTACTTTGTG
1 ACACGTGTACTTTGTG
740811 ACACGTGT
1 ACACGTGT
740819 TTAAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (16 bp):
ACACGTGTACTTTGTG
Found at i:743893 original size:58 final size:59
Alignment explanation
Indices: 743820--743999 Score: 163
Period size: 60 Copynumber: 3.1 Consensus size: 59
743810 GCAGCATATG
* * **
743820 TCCCTAAACTATGACTCTCTTTTTAAATTGATTCATAAAC-TTTGAACATTCCAATTTCA
1 TCCCTAAACTATGAC-CTCTTTATAAATTAACCCATAAACTTTTGAACATTCCAATTTCA
* * * *
743879 TCCC-AAACTATGA-CTCATTATAAATTAACCCTTAAACTTTTGAACATTCTAATTTTA
1 TCCCTAAACTATGACCTCTTTATAAATTAACCCATAAACTTTTGAACATTCCAATTTCA
* * * * * *
743936 TCCCTAAAATATGACCCTCTTTCA-AATTTAGTCCC-CAAACTTTTAAATATTCCAATTTCA
1 TCCCTAAACTATGA-CCTCTTT-ATAAATTA-ACCCATAAACTTTTGAACATTCCAATTTCA
743996 TCCC
1 TCCC
744000 CAAATTCATC
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
56 18 0.18
57 21 0.21
58 17 0.17
59 4 0.04
60 34 0.35
61 4 0.04
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (59 bp):
TCCCTAAACTATGACCTCTTTATAAATTAACCCATAAACTTTTGAACATTCCAATTTCA
Found at i:743943 original size:29 final size:28
Alignment explanation
Indices: 743855--743943 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
743845 AATTGATTCA
* *
743855 TAAACTTTGAACATTCCAATTTCATCCC
1 TAAACTTTGAACATTCTAATTTTATCCC
* * * * *
743883 -AAACTATGACTCATTATAA-ATTAACCC
1 TAAACTTTGA-ACATTCTAATTTTATCCC
743910 TTAAACTTTTGAACATTCTAATTTTATCCC
1 -TAAAC-TTTGAACATTCTAATTTTATCCC
743940 TAAA
1 TAAA
743944 ATATGACCCT
Statistics
Matches: 44, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
27 13 0.30
28 6 0.14
29 15 0.34
30 10 0.23
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (28 bp):
TAAACTTTGAACATTCTAATTTTATCCC
Found at i:744245 original size:59 final size:58
Alignment explanation
Indices: 744126--744264 Score: 156
Period size: 59 Copynumber: 2.3 Consensus size: 58
744116 TATACGTATT
* * *
744126 GTTTGGGATAAAATTGGAATGTTCAAAAAGTTTGGGACTAATTTAGAATCAATGCCATA
1 GTTTGGGATGAAATTGAAATGTTCAAAAAGTTTGGGACTAATTTAGAATCAAT-CAATA
* * * *
744185 GTTTGGGATGTAATTGAAATGTTC-AAATGTTTGATGACTAATTTAGAATTATAAT-AATA
1 GTTTGGGATGAAATTGAAATGTTCAAAAAGTTTG-GGACTAATTTAGAA-T-CAATCAATA
744244 GTTTAGGGATGAAATTGAAAT
1 GTTT-GGGATGAAATTGAAAT
744265 ATTTAAAATT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
58 8 0.12
59 41 0.60
60 16 0.24
61 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.36
Consensus pattern (58 bp):
GTTTGGGATGAAATTGAAATGTTCAAAAAGTTTGGGACTAATTTAGAATCAATCAATA
Found at i:747176 original size:17 final size:17
Alignment explanation
Indices: 747154--747186 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
747144 CCGGTTTCGG
747154 TTTTAAAAAACCGGTTT
1 TTTTAAAAAACCGGTTT
747171 TTTTAAAAAACCGGTT
1 TTTTAAAAAACCGGTT
747187 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAACCGGTTT
Found at i:747398 original size:21 final size:21
Alignment explanation
Indices: 747374--747425 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
747364 ACACTTAGGG
747374 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
747395 AACCGATT-CCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
747415 TACCGATTCCC
1 AACCGATTCCC
747426 CCACGCTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:747640 original size:13 final size:13
Alignment explanation
Indices: 747619--747673 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
747609 AAGTTCGATA
*
747619 AATTCAAATACTT
1 AATTGAAATACTT
747632 AATTGAAATACTT
1 AATTGAAATACTT
* *
747645 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
747659 AATTGAAATACTT
1 AATTGAAATACTT
747672 AA
1 AA
747674 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:747755 original size:32 final size:33
Alignment explanation
Indices: 747659--747757 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
747649 AACTCAACAT
* * *
747659 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
747692 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
747725 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
747757 A
1 A
747758 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:747776 original size:21 final size:21
Alignment explanation
Indices: 747752--747791 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
747742 ACTTCAAGTT
747752 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
747773 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
747792 ATAAATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:747799 original size:21 final size:21
Alignment explanation
Indices: 747754--747799 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
747744 TTCAAGTTCG
*
747754 ATAATTGAAACAAAGTTTACG
1 ATAATTGAAACAAAGTTTACA
*
747775 ATAATTGAAATAAAGTTATA-A
1 ATAATTGAAACAAAGTT-TACA
747796 ATAA
1 ATAA
747800 ACTACATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.30
Consensus pattern (21 bp):
ATAATTGAAACAAAGTTTACA
Done.