Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 124 of 345
Found at i:41753888 original size:16 final size:16
Alignment explanation
Indices: 41753867--41753899 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41753857 AATTGAGTTG
41753867 AGAAATTTATTTAATT
1 AGAAATTTATTTAATT
41753883 AGAAATTTATTTAATT
1 AGAAATTTATTTAATT
41753899 A
1 A
41753900 AATTAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
AGAAATTTATTTAATT
Found at i:41757213 original size:40 final size:40
Alignment explanation
Indices: 41757131--41757282 Score: 182
Period size: 40 Copynumber: 3.8 Consensus size: 40
41757121 GAATATGCCC
* * * * * *
41757131 CTGGCTTGAAGGCCCTTCGAAACTGAGTTCGGTCATGA-CA
1 CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGGTTAT-ATCA
* *
41757171 CTGG-TTCGAAAGTCCTTCGGAACTAAGTCCGGTTATATCA
1 CTGGCTT-AAAAGCCCTTCGGAACTAAGTCCGGTTATATCA
* *
41757211 CTGGCTTAAAAGCCCTTCAGAACTAAGTCCGATTATATCA
1 CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGGTTATATCA
41757251 CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGG
1 CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGG
41757283 ATTTTAAATC
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 92 0.95
41 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (40 bp):
CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGGTTATATCA
Found at i:41760784 original size:29 final size:29
Alignment explanation
Indices: 41760751--41760859 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 29
41760741 CAGAAAATGA
41760751 TAAAAATTATAAAAATATTTAAATTTTAT
1 TAAAAATTATAAAAATATTTAAATTTTAT
** *
41760780 TAAAAATTATAAATTTATTTAAAATTATAT
1 TAAAAATTATAAAAATATTT-AAATTTTAT
* * * *
41760810 AAAAAAATATAAAAAAATATTAAA-ATTAT
1 TAAAAATTATAAAAATAT-TTAAATTTTAT
*
41760839 ATAAAATTTAATATAAAATAT
1 -TAAAAATT-ATA-AAAATAT
41760860 AAATATAAAG
Statistics
Matches: 61, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
29 21 0.34
30 29 0.48
31 5 0.08
32 6 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAAAATTATAAAAATATTTAAATTTTAT
Found at i:41760798 original size:18 final size:19
Alignment explanation
Indices: 41760760--41760808 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
41760750 ATAAAAATTA
*
41760760 TAAAAATATTTAAATTTTAT
1 TAAAAAT-TATAAATTTTAT
41760780 TAAAAATTATAAA-TTTAT
1 TAAAAATTATAAATTTTAT
*
41760798 TTAAAATTATA
1 TAAAAATTATA
41760809 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 15 0.56
19 5 0.19
20 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAAATTATAAATTTTAT
Found at i:41760845 original size:10 final size:10
Alignment explanation
Indices: 41760744--41760857 Score: 67
Period size: 10 Copynumber: 11.5 Consensus size: 10
41760734 CACGTGGCAG
*
41760744 AAAATGATA-
1 AAAATTATAT
41760753 AAAATTATA-
1 AAAATTATAT
41760762 AAAA-TAT-T
1 AAAATTATAT
* *
41760770 TAAATTTTATT
1 AAAATTATA-T
*
41760781 AAAAAT-TAT
1 AAAATTATAT
* *
41760790 AAATTTATTT
1 AAAATTATAT
41760800 AAAATTATAT
1 AAAATTATAT
**
41760810 AAAAAAATAT
1 AAAATTATAT
**
41760820 AAAAAAATATT
1 AAAATTATA-T
41760831 AAAATTATAT
1 AAAATTATAT
41760841 AAAATTTAATAT
1 AAAA-TT-ATAT
41760853 AAAAT
1 AAAAT
41760858 ATAAATATAA
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
8 6 0.07
9 19 0.23
10 34 0.41
11 16 0.19
12 8 0.10
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (10 bp):
AAAATTATAT
Found at i:41760866 original size:13 final size:12
Alignment explanation
Indices: 41760806--41760868 Score: 57
Period size: 10 Copynumber: 5.6 Consensus size: 12
41760796 ATTTAAAATT
41760806 ATATAAAA--AA
1 ATATAAAATTAA
41760816 ATATAAAA--AA
1 ATATAAAATTAA
41760826 ATATTAAAATT--
1 ATA-TAAAATTAA
*
41760837 ATATAAAATTTA
1 ATATAAAATTAA
41760849 ATATAAAATATAA
1 ATATAAAAT-TAA
41760862 ATATAAA
1 ATATAAA
41760869 GAGAAACATA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
10 20 0.43
11 8 0.17
12 9 0.20
13 9 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATAAAATTAA
Found at i:41762308 original size:34 final size:34
Alignment explanation
Indices: 41762265--41762340 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
41762255 GATTTCAGAG
*
41762265 TGTGATGAATCAGTTGCTTGGTATGGGTGTCAAA
1 TGTGATGAATCAGTTACTTGGTATGGGTGTCAAA
*
41762299 TGTGATGAATTAGTTACTTGGTATGGGTGTCAAA
1 TGTGATGAATCAGTTACTTGGTATGGGTGTCAAA
*
41762333 TTTGATGA
1 TGTGATGA
41762341 CGCGATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.38
Consensus pattern (34 bp):
TGTGATGAATCAGTTACTTGGTATGGGTGTCAAA
Found at i:41767275 original size:131 final size:133
Alignment explanation
Indices: 41766973--41767441 Score: 369
Period size: 133 Copynumber: 3.5 Consensus size: 133
41766963 TTCCAAAGAA
* * * * * * ** *
41766973 ATATCCGATTGTTTTGAACAAACGAGAGATTGCAA-CCAAGTACGACAGGGCACGATT-CTCGAA
1 ATATTCGATTATTTTGAGCAAACGAGAAATTACAACCCAA-CACGTTAGGGCACGATTCCGCGAA
* * * * * * ** * **
41767036 TTGCCAAACATCGAACATAGCCTTTGTTTTAAAGGGTTTTCTTAAGAA-ACATGAGTGAAA-ACC
65 TGGCCAAACATCAAACTTTGCCTTCGCTTTAAAGAATTTT-TTAA-AAGACATGAATGAAAGTTC
* *
41767099 TAAAGGA
128 -GAAGGG
* * * * * * * * *
41767106 ATATTCGATCATTTTGAACAAACAAGAAATCACAACCCAGCACGATAGGGCATGATTTC-TGAAT
1 ATATTCGATTATTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCCGCGAAT
* * * * * * * * *
41767170 TGTCAAACATC-GAGTATTGCCTTCGCTTTAGAGGA-TTTTTAGAAGACCTGAATGGAA-TCTCG
66 GGCCAAACATCAAACT-TTGCCTTCGCTTTAAAGAATTTTTTAAAAGACATGAATGAAAGT-TCG
41767232 AAGGG
129 AAGGG
*
41767237 ATATTTGATTATTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCCGCGAAT
1 ATATTCGATTATTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCCGCGAAT
* * * * *
41767302 GGCCAAATATCAAACTTTGCCTTCGTTTTAAAGAATTTTTTAAAAGGCATGAGTGAAAGTTTGAA
66 GGCCAAACATCAAACTTTGCCTTCGCTTTAAAGAATTTTTTAAAAGACATGAATGAAAGTTCGAA
41767367 GGG
131 GGG
* * * *
41767370 ATATTCGATTATTTCGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACTATTCCGCGAAT
1 ATATTCGATTATTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCCGCGAAT
*
41767435 TGCCAAA
66 GGCCAAA
41767442 TATCGAATCT
Statistics
Matches: 268, Mismatches: 59, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
130 2 0.01
131 66 0.25
132 33 0.12
133 162 0.60
134 5 0.02
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (133 bp):
ATATTCGATTATTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCCGCGAAT
GGCCAAACATCAAACTTTGCCTTCGCTTTAAAGAATTTTTTAAAAGACATGAATGAAAGTTCGAA
GGG
Found at i:41767389 original size:133 final size:133
Alignment explanation
Indices: 41767231--41767474 Score: 382
Period size: 133 Copynumber: 1.8 Consensus size: 133
41767221 ATGGAATCTC
* *
41767231 GAAGGGATATTTGATTATTTTGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCC
1 GAAGGGATATTCGATTATTTCGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCC
*
41767296 GCGAATGGCCAAATATCAAA-CTTTGCCTTCGTTTTAAAGAATTTTTTAAAAGGCATGAGTGAAA
66 GCGAATGGCCAAATATCAAATC-TCGCCTTCGTTTTAAAGAATTTTTTAAAAGGCATGAGTGAAA
41767360 GTTT
130 GTTT
* * *
41767364 GAAGGGATATTCGATTATTTCGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACTATTCC
1 GAAGGGATATTCGATTATTTCGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCC
* * * *
41767429 GCGAATTGCCAAATATCGAATCTCGTCTTCTTTTTAAAGAATTTTT
66 GCGAATGGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTT
41767475 AAATGAATAC
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
133 99 0.99
134 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (133 bp):
GAAGGGATATTCGATTATTTCGAGCAAACGAGAAATTACAACCCAACACGTTAGGGCACGATTCC
GCGAATGGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTTAAAAGGCATGAGTGAAAG
TTT
Found at i:41771067 original size:20 final size:19
Alignment explanation
Indices: 41771030--41771081 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
41771020 TTCTATACTT
*
41771030 TTATATTTTATAACAATTT-
1 TTATATTTT-TAAAAATTTA
41771049 TATATATTTTTAATAAATTTA
1 T-TATATTTTTAA-AAATTTA
41771070 TTATAATTTTTA
1 TTAT-ATTTTTA
41771082 TATTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTTTTAAAAATTTA
Found at i:41771150 original size:46 final size:46
Alignment explanation
Indices: 41771028--41771169 Score: 125
Period size: 46 Copynumber: 3.1 Consensus size: 46
41771018 TATTCTATAC
* *
41771028 TTTTATATTTTATAACAATTTTATATATTTTTAAT-AAATTTATTATAAT
1 TTTTATATTTTAT-A-AATTTTATATATTTTT-ATCTAATTT-TTATATT
* * *
41771077 TTTTATA--TTAAAATATTTTAAATATTTTTCTCTAATTTTTATATT
1 TTTTATATTTTATAA-ATTTTATATATTTTTATCTAATTTTTATATT
*
41771122 TGTTTATATTTTATAAATTTTATA-ATTTTTTTCT--TTTTTATCATT
1 T-TTTATATTTTATAAATTTTATATATTTTTATCTAATTTTTAT-ATT
41771167 TTT
1 TTT
41771170 CCATTATGTG
Statistics
Matches: 79, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
44 9 0.11
45 13 0.16
46 35 0.44
47 10 0.13
48 5 0.06
49 7 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.64
Consensus pattern (46 bp):
TTTTATATTTTATAAATTTTATATATTTTTATCTAATTTTTATATT
Found at i:41771169 original size:27 final size:26
Alignment explanation
Indices: 41771109--41771169 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
41771099 TATTTTTCTC
41771109 TAATTTTTATATTTGTTTATATTTTA
1 TAATTTTTATATTTGTTTATATTTTA
* * * *
41771135 TAAATTTTATAATTTTTTTCTTTTTTA
1 TAATTTTTAT-ATTTGTTTATATTTTA
*
41771162 TCATTTTT
1 TAATTTTT
41771170 CCATTATGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (26 bp):
TAATTTTTATATTTGTTTATATTTTA
Found at i:41771528 original size:23 final size:24
Alignment explanation
Indices: 41771493--41771544 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
41771483 TTAAATTCAA
**
41771493 ATTT-AATATATAATTTAAATATT
1 ATTTAAATATATAAGGTAAATATT
*
41771516 ATTTAAATA-ATAAGGTAATTATT
1 ATTTAAATATATAAGGTAAATATT
41771539 ATTTAA
1 ATTTAA
41771545 CTTTATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
ATTTAAATATATAAGGTAAATATT
Found at i:41772767 original size:9 final size:9
Alignment explanation
Indices: 41772755--41772792 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
41772745 TATATATAAG
41772755 ATATTTAAA
1 ATATTTAAA
41772764 ATATTTAAA
1 ATATTTAAA
* *
41772773 ATATTGATA
1 ATATTTAAA
41772782 A-ATTTAAA
1 ATATTTAAA
41772790 ATA
1 ATA
41772793 ATACACGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (9 bp):
ATATTTAAA
Found at i:41773773 original size:20 final size:20
Alignment explanation
Indices: 41773711--41773784 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
41773701 TTATAGTTTT
*
41773711 AAAAATTAT-TAAATTT-TA
1 AAAAATTATAAAAATTTGTA
* * *
41773729 ATAAAAATATTAAAAATTAGAA
1 A-AAAATTA-TAAAAATTTGTA
41773751 AAAAATTATAAAAATTTGTA
1 AAAAATTATAAAAATTTGTA
**
41773771 AAATTTTATAAAAA
1 AAAAATTATAAAAA
41773785 ATCATAATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.02
19 6 0.14
20 23 0.53
21 11 0.26
22 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAAATTATAAAAATTTGTA
Found at i:41781821 original size:35 final size:35
Alignment explanation
Indices: 41781770--41781846 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
41781760 CAATATTATG
**
41781770 ATGAATTGACGAATATTAAGTCTTGGTTAAACCTT
1 ATGAATTGACGAATATTAAGTCCCGGTTAAACCTT
* *
41781805 ATGAATTGACGGATATTAAGTCCCGGTTGAACCTT
1 ATGAATTGACGAATATTAAGTCCCGGTTAAACCTT
*
41781840 AGGAATT
1 ATGAATT
41781847 CTTATGATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (35 bp):
ATGAATTGACGAATATTAAGTCCCGGTTAAACCTT
Found at i:41785444 original size:21 final size:21
Alignment explanation
Indices: 41785419--41785462 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
41785409 TTTACCTCTC
41785419 TTCGTCTTTAAACTTATACTT
1 TTCGTCTTTAAACTTATACTT
* *
41785440 TTCGTCTTTAAATTTGTACTT
1 TTCGTCTTTAAACTTATACTT
41785461 TT
1 TT
41785463 AGTTAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.16, G:0.07, T:0.57
Consensus pattern (21 bp):
TTCGTCTTTAAACTTATACTT
Found at i:41787489 original size:136 final size:129
Alignment explanation
Indices: 41787230--41787566 Score: 417
Period size: 136 Copynumber: 2.5 Consensus size: 129
41787220 GCAAGAGCTT
* * *
41787230 AAGCTAGCAGAGAAGAAGTATGAGAGAGTCTAGAG-AGAGTTACTCGGGTATTTATACCTAGCCT
1 AAGCTAGCAGAGAAGAAGTA-GAGAGAG---AGAGTTG-G-TACTTGGATATTTATACCTAGCCT
* * *
41787294 TGGGGGCATCAATGCTCCAGAGTGCTATCTGATGCTTAAGTTAGCAAAGGAGATTGTGTAATGGA
60 T-GGGGCATCAATGCTCCAGAATGCTATCTGATGCTTAAGTTAGAAAAGGAGATAGTGTAATGGA
41787359 TAAAAAAAGAGC
124 T-----AA-AGC
*
41787371 TTAAGCTAGCAGAGAAGAAGT-GTGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGG
1 --AAGCTAGCAGAGAAGAAGTAGAGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGG
* * *
41787435 GCATCAATGCTCCAGAATGCTCTTTGATGCTTAAGTTAGAAAAGGAGATAGTGTAATGGGTAAAG
64 GCATCAATGCTCCAGAATGCTATCTGATGCTTAAGTTAGAAAAGGAGATAGTGTAATGGATAAAG
41787500 C
129 C
*
41787501 AAGCTAGCAGAGAAGAAGTAAGAGAGAGAGAGTTGGTACTTGGGTATTTATACCTAGCCTTGGGG
1 AAGCTAGCAGAGAAGAAGT-AGAGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGG
41787566 C
65 C
41787567 TGCCTGTTGC
Statistics
Matches: 179, Mismatches: 12, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
128 19 0.11
130 46 0.26
131 2 0.01
136 58 0.32
137 23 0.13
138 5 0.03
139 1 0.01
141 6 0.03
143 19 0.11
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (129 bp):
AAGCTAGCAGAGAAGAAGTAGAGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGGC
ATCAATGCTCCAGAATGCTATCTGATGCTTAAGTTAGAAAAGGAGATAGTGTAATGGATAAAGC
Found at i:41790647 original size:20 final size:22
Alignment explanation
Indices: 41790608--41790649 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
41790598 ACGAAGTAGG
41790608 AAAGTGATTATGAATATTAAAT
1 AAAGTGATTATGAATATTAAAT
*
41790630 AAAGT-ATT-TGATTATTAAAT
1 AAAGTGATTATGAATATTAAAT
41790650 TTTCTATCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (22 bp):
AAAGTGATTATGAATATTAAAT
Found at i:41791493 original size:2 final size:2
Alignment explanation
Indices: 41791488--41791514 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41791478 CAAGTAAAAC
41791488 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 A
41791515 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41795052 original size:42 final size:42
Alignment explanation
Indices: 41794954--41795108 Score: 145
Period size: 42 Copynumber: 3.6 Consensus size: 42
41794944 TACCAACGTA
* * * *
41794954 CCAGACGTGGTCTTACATGT-AATCAAATATTGATGCCACTGTC
1 CCAGACATGGTCTTACACGTAAATC-AA-ATCGATGCCAATGTC
***
41794997 CCAGACA-GAGTCTTACACG-AAATCAAATACGATGTTGATGTC
1 CCAGACATG-GTCTTACACGTAAATCAAAT-CGATGCCAATGTC
* *
41795039 CCAAACATGGTCTTACACGTAAATCTCAAATCGATGCCAACGTC
1 CCAGACATGGTCTTACACGTAAA--TCAAATCGATGCCAATGTC
*
41795083 CTAGACATGGTCTTACACGTAAATCA
1 CCAGACATGGTCTTACACGTAAATCA
41795109 CATATAGGAA
Statistics
Matches: 91, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 30 0.33
43 23 0.25
44 30 0.33
45 6 0.07
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (42 bp):
CCAGACATGGTCTTACACGTAAATCAAATCGATGCCAATGTC
Found at i:41798626 original size:21 final size:21
Alignment explanation
Indices: 41798600--41798639 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
41798590 CACGTAAAAA
41798600 GAAATTTCTCTAAATCCTGAT
1 GAAATTTCTCTAAATCCTGAT
41798621 GAAATTTCTCTAAATCCTG
1 GAAATTTCTCTAAATCCTG
41798640 TGGTTCCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (21 bp):
GAAATTTCTCTAAATCCTGAT
Found at i:41804193 original size:43 final size:43
Alignment explanation
Indices: 41804074--41804185 Score: 122
Period size: 42 Copynumber: 2.6 Consensus size: 43
41804064 TCGATTTGAT
* *
41804074 AATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATCTG
1 AATTACGTGTAAGACCACGTCTGGGACATAGGCATCGTATCTG
** * *
41804117 -ATTTTGTGTAAGACC-CTATCTGGGACAAAGGCATCG-ATACTG
1 AATTACGTGTAAGACCAC-GTCTGGGACATAGGCATCGTAT-CTG
*
41804159 AATTACATGTAAGACCACGTCTGGGAC
1 AATTACGTGTAAGACCACGTCTGGGAC
41804186 GTCGGCATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
41 2 0.04
42 32 0.58
43 20 0.36
44 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
AATTACGTGTAAGACCACGTCTGGGACATAGGCATCGTATCTG
Found at i:41804488 original size:26 final size:26
Alignment explanation
Indices: 41804459--41804511 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
41804449 GTACTTTATA
41804459 TGATTTAGTAGTTAGAGAAATTGTAT
1 TGATTTAGTAGTTAGAGAAATTGTAT
41804485 TGATTTAGTAGTTAGAGAAATTGTAT
1 TGATTTAGTAGTTAGAGAAATTGTAT
41804511 T
1 T
41804512 TGGCTTACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (26 bp):
TGATTTAGTAGTTAGAGAAATTGTAT
Found at i:41814971 original size:19 final size:19
Alignment explanation
Indices: 41814935--41814971 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41814925 AGTAGTGTGT
* *
41814935 TTAATTAGGTGAATTTAGC
1 TTAATTAGGAGAAATTAGC
41814954 TTAATTAGGAGAAATTAG
1 TTAATTAGGAGAAATTAG
41814972 GAAAAATGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (19 bp):
TTAATTAGGAGAAATTAGC
Found at i:41816204 original size:3 final size:3
Alignment explanation
Indices: 41816196--41816243 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
41816186 AATGAGAATT
41816196 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41816244 AAGAGCTAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41816393 original size:10 final size:10
Alignment explanation
Indices: 41816378--41816412 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
41816368 TCAGAAAATG
41816378 AATAATAATA
1 AATAATAATA
41816388 AATAATAATA
1 AATAATAATA
41816398 AATAATAATA
1 AATAATAATA
41816408 AATAA
1 AATAA
41816413 ATAAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAATAATA
Found at i:41816423 original size:14 final size:14
Alignment explanation
Indices: 41816373--41816417 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
41816363 GAAGATCAGA
41816373 AAATGAATAAT-AAT
1 AAAT-AATAATAAAT
41816387 AAATAATAATAAAT
1 AAATAATAATAAAT
41816401 -AATAATAAATAAAT
1 AAATAAT-AATAAAT
41816415 AAA
1 AAA
41816418 ATTAAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.43
14 14 0.50
15 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:41816771 original size:14 final size:14
Alignment explanation
Indices: 41816752--41816778 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41816742 AGAGCCTAGA
41816752 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
41816766 AAAAAAATAAAAA
1 AAAAAAATAAAAA
41816779 AAATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:41817654 original size:19 final size:19
Alignment explanation
Indices: 41817618--41817654 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41817608 TAATTAGGAT
* *
41817618 TTAATTAGGTGAATTTAGC
1 TTAATTAGGAGAAATTAGC
41817637 TTAATTAGGAGAAATTAG
1 TTAATTAGGAGAAATTAG
41817655 GAAAAAGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (19 bp):
TTAATTAGGAGAAATTAGC
Found at i:41818274 original size:7 final size:7
Alignment explanation
Indices: 41818264--41818303 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
41818254 TATTATGTTT
41818264 TATTATA
1 TATTATA
41818271 TATTATA
1 TATTATA
41818278 TATTATA
1 TATTATA
*
41818285 TTCTTATTA
1 -TATTA-TA
41818294 TATTATA
1 TATTATA
41818301 TAT
1 TAT
41818304 ATAAAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 19 0.66
8 8 0.28
9 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTATA
Found at i:41818293 original size:25 final size:26
Alignment explanation
Indices: 41818222--41818306 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 26
41818212 TTTAAGTTTA
* * *
41818222 ATATATATTATATTATTA-AATAATAAA
1 ATATATATTATATT-TTATTAT-ATTAT
* *
41818249 ATATTTATTATGTTTTATTATA-TAT
1 ATATATATTATATTTTATTATATTAT
41818274 -TATATATTATATTCTTATTATATTAT
1 ATATATATTATATT-TTATTATATTAT
41818300 ATATATA
1 ATATATA
41818307 AAGTAAAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 11 0.23
25 9 0.19
26 7 0.15
27 20 0.43
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (26 bp):
ATATATATTATATTTTATTATATTAT
Found at i:41819195 original size:70 final size:75
Alignment explanation
Indices: 41819116--41819282 Score: 191
Period size: 78 Copynumber: 2.2 Consensus size: 75
41819106 AATTGGAAAT
** *
41819116 TAAAAGTGATTTGAATT-AAGTAATTGAATT-AT-G-AATTATGTGAATATTTGAAA-GTATATT
1 TAAAAGTGATTTGAATTAAACAAATTGAATTAATAGAAAATATGTGAATATTTGAAATGTATATT
*
41819176 GACTGAAAAC
66 GACTGAAAAA
*
41819186 TAAAAGTGATTTGAATTGAAACAAATTGAATTGAATGAAGAAAATATGTGAGTATTTGAAATGTA
1 TAAAAGTGATTTGAATT-AAACAAATTGAATT-AAT--AGAAAATATGTGAATATTTGAAATGTA
*
41819251 TATTGATTGAAAAA
62 TATTGACTGAAAAA
*
41819265 TAATTAGTGATTTGAATT
1 TAA-AAGTGATTTGAATT
41819283 TGATTGGAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
70 17 0.21
72 11 0.14
74 2 0.03
77 1 0.01
78 18 0.22
79 18 0.22
80 13 0.16
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.37
Consensus pattern (75 bp):
TAAAAGTGATTTGAATTAAACAAATTGAATTAATAGAAAATATGTGAATATTTGAAATGTATATT
GACTGAAAAA
Found at i:41819314 original size:29 final size:28
Alignment explanation
Indices: 41819252--41819338 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
41819242 TGAAATGTAT
**
41819252 ATTGATTGAAAAAT-AATTAGTGATT-TGA
1 ATTGATTG-AAAATGAATTA-AAATTATGA
41819280 ATTTGATTGGAAAATGAATTAAAATTATGA
1 A-TTGATT-GAAAATGAATTAAAATTATGA
*
41819310 ATTGAAT-AAAAGTGAATT-AAATTATGA
1 ATTGATTGAAAA-TGAATTAAAATTATGA
41819337 AT
1 AT
41819339 ATGTGTGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
27 15 0.29
28 7 0.14
29 19 0.37
30 10 0.20
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (28 bp):
ATTGATTGAAAATGAATTAAAATTATGA
Found at i:41821843 original size:5 final size:5
Alignment explanation
Indices: 41821833--41821867 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
41821823 TTGTATGTTC
41821833 TTTAT TTTAT TTTAT TTTATTT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTA--T TTTAT TTTAT TTT
41821868 TCACAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 23 0.82
7 5 0.18
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:41829191 original size:61 final size:57
Alignment explanation
Indices: 41829066--41829208 Score: 171
Period size: 61 Copynumber: 2.4 Consensus size: 57
41829056 TTTAATTCAT
* * *
41829066 ATAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTTTAAAATTGTATTTA
1 ATAATAATTATATTAA-AATATAATTAAATTATATATTATTTTTTAAAATTATATTTA
*
41829124 ATAATAATTATGTTAAAATATAATTAAATTATTTATTATTATTTTTAATAAAA-TATATTTA
1 ATAATAATTATATTAAAATATAATTAAATTA--TA-TATTATTTTT--TAAAATTATATTTA
* *
41829185 ATAATAATTTTATTAAAATTTAAT
1 ATAATAATTATATTAAAATATAAT
41829209 AATAATAACA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
57 13 0.18
58 15 0.21
59 2 0.03
60 10 0.14
61 28 0.38
62 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATAATTAAATTATATATTATTTTTTAAAATTATATTTA
Found at i:41829195 original size:26 final size:25
Alignment explanation
Indices: 41829144--41829204 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
41829134 TGTTAAAATA
* * * *
41829144 TAATTAAATTATTTATTATTATTTT
1 TAATAAAATTATTTAATAATAATTT
41829169 TAATAAAATATATTTAATAATAATTT
1 TAATAAAAT-TATTTAATAATAATTT
*
41829195 TATTAAAATT
1 TAATAAAATT
41829205 TAATAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATAAAATTATTTAATAATAATTT
Found at i:41829400 original size:23 final size:24
Alignment explanation
Indices: 41829374--41829429 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
41829364 AACTGATTAC
41829374 AACT-TTACTTCATCACAATTCTA
1 AACTATTACTTCATCACAATTCTA
** *
41829397 AACTATTAC-TCATTGCCATTCTA
1 AACTATTACTTCATCACAATTCTA
*
41829420 AACTGTTACT
1 AACTATTACT
41829430 GCTCTATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (24 bp):
AACTATTACTTCATCACAATTCTA
Found at i:41832767 original size:27 final size:26
Alignment explanation
Indices: 41832714--41832771 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
41832704 GAACAGAATT
* * * *
41832714 GAATTGAATAGACTAAAAATTACACC
1 GAATTAAACAGACTAAAAATAAAACC
41832740 GAATTAAACAGACTAAAAATAAAAACC
1 GAATTAAACAGACTAAAAAT-AAAACC
41832767 GAATT
1 GAATT
41832772 GATAGTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (26 bp):
GAATTAAACAGACTAAAAATAAAACC
Found at i:41844644 original size:44 final size:43
Alignment explanation
Indices: 41844581--41844732 Score: 152
Period size: 43 Copynumber: 3.5 Consensus size: 43
41844571 TATGTATTAT
*
41844581 CGTGTAAGACCACGTCTGGGACGTTAGCATCGATTTGTGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTT-TGATTTA
* * * *
41844625 CGTGTAAGACCATGTCTGGGACATTGGCGTCG-TATATGATTT-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTTGATTTA
*
41844667 CGTGTAAGACC-CTGTCTGGGTCAG-TGGCATCGATATTTGA-TTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TTTGATTTA
* *
41844710 CATGTAAGACCACGTTTGGGACG
1 CGTGTAAGACCACGTCTGGGACG
41844733 CTTGCATTGT
Statistics
Matches: 89, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
42 29 0.33
43 30 0.34
44 30 0.34
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTTGATTTA
Found at i:41844677 original size:86 final size:87
Alignment explanation
Indices: 41844570--41844731 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 87
41844560 TAGGATTCCG
*
41844570 ATATGTATTATCGTGTAAGACCAC-GTCTGGGAC-GTTAGCATCGAT-TTGTGATTTACGTGTAA
1 ATATGTATTATCGTGTAAGACC-CTGTCTGGGACAG-TAGCATCGATATT-TGA-TTACATGTAA
*
41844632 GACCATGTCTGGGACATTGGCGTCGT
62 GACCACGTCTGGGACATTGGCGTCGT
* *
41844658 ATATG-ATT-TCGTGTAAGACCCTGTCTGGGTCAGTGGCATCGATATTTGATTACATGTAAGACC
1 ATATGTATTATCGTGTAAGACCCTGTCTGGGACAGTAGCATCGATATTTGATTACATGTAAGACC
*
41844721 ACGTTTGGGAC
66 ACGTCTGGGAC
41844732 GCTTGCATTG
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
85 23 0.35
86 32 0.48
87 6 0.09
88 5 0.08
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (87 bp):
ATATGTATTATCGTGTAAGACCCTGTCTGGGACAGTAGCATCGATATTTGATTACATGTAAGACC
ACGTCTGGGACATTGGCGTCGT
Found at i:41844683 original size:42 final size:43
Alignment explanation
Indices: 41844570--41844720 Score: 153
Period size: 44 Copynumber: 3.5 Consensus size: 43
41844560 TAGGATTCCG
* *
41844570 ATATGTATTATCGTGTAAGACCAC-GTCTGGGACGTTAGCATCGAT
1 ATATG-ATT-TCGTGTAAGACC-CTGTCTGGGACATTGGCATCGAT
* * * *
41844615 TTGTGATTTACGTGTAAGACCATGTCTGGGACATTGGCGTCG-T
1 ATATGATTT-CGTGTAAGACCCTGTCTGGGACATTGGCATCGAT
* *
41844658 ATATGATTTCGTGTAAGACCCTGTCTGGGTCAGTGGCATCGAT
1 ATATGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCGAT
* * *
41844701 ATTTGATTACATGTAAGACC
1 ATATGATTTCGTGTAAGACC
41844721 ACGTTTGGGA
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 28 0.32
43 27 0.31
44 30 0.34
45 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
ATATGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCGAT
Found at i:41846414 original size:21 final size:22
Alignment explanation
Indices: 41846389--41846429 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41846379 TGTTGATATC
41846389 TGAC-TTTGA-TGTGATAATGTA
1 TGACTTTTGATTGTGA-AATGTA
41846410 TGACTTTTGATTGTGAAATG
1 TGACTTTTGATTGTGAAATG
41846430 ATTGCGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (22 bp):
TGACTTTTGATTGTGAAATGTA
Found at i:41861274 original size:42 final size:42
Alignment explanation
Indices: 41861200--41861281 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
41861190 GTGTCCTCAA
*
41861200 CCGTGTAACTCACTGAGATGCCCCACACGCCCATGTGCCAAG
1 CCGTGTAACTCACTGAGATGCCACACACGCCCATGTGCCAAG
* * *
41861242 CCGTGTAACTCTCTGAGTTGCCACACATGCCCATGTGCCA
1 CCGTGTAACTCACTGAGATGCCACACACGCCCATGTGCCA
41861282 GACCGTTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.21
Consensus pattern (42 bp):
CCGTGTAACTCACTGAGATGCCACACACGCCCATGTGCCAAG
Found at i:41868815 original size:33 final size:32
Alignment explanation
Indices: 41868717--41868827 Score: 134
Period size: 32 Copynumber: 3.4 Consensus size: 32
41868707 TAAATGAATA
*
41868717 TTGTTATCATTT-AACAAAATTAAAGTTGATAT
1 TTGTTATCATTTCAA-AAAATTAAAGTTGAAAT
* * *
41868749 TTGTTATCATTTTACAAAATTAAAGTTGTAAT
1 TTGTTATCATTTCAAAAAATTAAAGTTGAAAT
* *
41868781 TTATTATCATTTCAAAAAATGAAAAGTTGAAAT
1 TTGTTATCATTTCAAAAAAT-TAAAGTTGAAAT
*
41868814 TTGTTACCATTTCA
1 TTGTTATCATTTCA
41868828 CAGAACCACA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
32 44 0.66
33 23 0.34
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (32 bp):
TTGTTATCATTTCAAAAAATTAAAGTTGAAAT
Found at i:41869781 original size:17 final size:17
Alignment explanation
Indices: 41869732--41869785 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
41869722 GATAGTGTCG
*
41869732 ATTACATATCAAAGAAT
1 ATTACAAATCAAAGAAT
* *
41869749 A-TAAAAATGAATAGAAT
1 ATTACAAATCAA-AGAAT
41869766 ATTACAAATCAAAGAAT
1 ATTACAAATCAAAGAAT
41869783 ATT
1 ATT
41869786 GGTCAATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 7 0.23
17 15 0.50
18 8 0.27
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.28
Consensus pattern (17 bp):
ATTACAAATCAAAGAAT
Found at i:41872094 original size:45 final size:45
Alignment explanation
Indices: 41872043--41872134 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
41872033 AATTCTAACC
41872043 CATAACCATTTTTGTACAATTTTTAGTGATTTTCCAAAGTTGAGA
1 CATAACCATTTTTGTACAATTTTTAGTGATTTTCCAAAGTTGAGA
41872088 CATAACCATTTTTGTACAATTTTTAGTGATTTTCCAAAGTTGAGA
1 CATAACCATTTTTGTACAATTTTTAGTGATTTTCCAAAGTTGAGA
41872133 CA
1 CA
41872135 GGGGAGCCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (45 bp):
CATAACCATTTTTGTACAATTTTTAGTGATTTTCCAAAGTTGAGA
Found at i:41872725 original size:48 final size:47
Alignment explanation
Indices: 41872654--41872823 Score: 191
Period size: 48 Copynumber: 3.6 Consensus size: 47
41872644 TAAAGTACCA
* * * *
41872654 ATGCCATGTCCCCAACACGGTCTTACAT-GAATTCACATATCATTGCTG
1 ATGCCATGTCCCGAACATGGTCTTACATGGCA--CACATATCATCGCTG
* *
41872702 ATGCCATGTCCCGAACATGGTCTTACATAGGCACACAAATCATCGCCG
1 ATGCCATGTCCCGAACATGGTCTTACAT-GGCACACATATCATCGCTG
* * * *
41872750 ATGCCATGTCTCGGACATGGTCCTACACTGGCACACATATCATCACTG
1 ATGCCATGTCCCGAACATGGTCTTACA-TGGCACACATATCATCGCTG
41872798 ATGCCATGTCCC-AGACATGGTCTTAC
1 ATGCCATGTCCCGA-ACATGGTCTTAC
41872824 CCAGTCCCAG
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
48 100 0.97
49 1 0.01
50 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (47 bp):
ATGCCATGTCCCGAACATGGTCTTACATGGCACACATATCATCGCTG
Found at i:41875224 original size:29 final size:27
Alignment explanation
Indices: 41875174--41875227 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
41875164 GATTTTTAGT
*
41875174 GAAAATGTCAATTAGGGATTAAATTAA
1 GAAAATGTAAATTAGGGATTAAATTAA
*
41875201 GAAAAGTGTAAATTGAGGGGTTAAATT
1 GAAAA-TGTAAATT-AGGGATTAAATT
41875228 GTGAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 7 0.30
29 11 0.48
ACGTcount: A:0.44, C:0.02, G:0.24, T:0.30
Consensus pattern (27 bp):
GAAAATGTAAATTAGGGATTAAATTAA
Found at i:41875233 original size:29 final size:27
Alignment explanation
Indices: 41875172--41875233 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
41875162 GTGATTTTTA
*
41875172 GTGAAAATGTCAATTAGGGATTAAATT
1 GTGAAAATGTAAATTAGGGATTAAATT
** *
41875199 AAGAAAAGTGTAAATTGAGGGGTTAAATT
1 GTGAAAA-TGTAAATT-AGGGATTAAATT
41875228 GTGAAA
1 GTGAAA
41875234 TAAATGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
27 5 0.19
28 7 0.26
29 15 0.56
ACGTcount: A:0.44, C:0.02, G:0.26, T:0.29
Consensus pattern (27 bp):
GTGAAAATGTAAATTAGGGATTAAATT
Found at i:41875840 original size:47 final size:47
Alignment explanation
Indices: 41875777--41875895 Score: 211
Period size: 47 Copynumber: 2.5 Consensus size: 47
41875767 GTGCGAATAA
*
41875777 TACCTTGATTTGGCTACGGGCCATGATATAGGTATTTTGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGATATAAGTATTTTGAGAGGAGT
* *
41875824 TACCTTGATATAGCTACGGGCCATGATATAAGTATTTTGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGATATAAGTATTTTGAGAGGAGT
41875871 TACCTTGATTTGGCTACGGGCCATG
1 TACCTTGATTTGGCTACGGGCCATG
41875896 GTATGGATAC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGATATAAGTATTTTGAGAGGAGT
Found at i:41891668 original size:29 final size:27
Alignment explanation
Indices: 41891615--41891674 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
41891605 GATTTCTAGT
* *
41891615 GAAAATGTCAATTAGGGATTCAATTGA
1 GAAAATGTAAATTAGGGATTAAATTGA
* *
41891642 GAAAAGTGTAAATTGAGGGGTTAAATTGT
1 GAAAA-TGTAAATT-AGGGATTAAATTGA
41891671 GAAA
1 GAAA
41891675 TAAATGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 7 0.26
29 15 0.56
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.28
Consensus pattern (27 bp):
GAAAATGTAAATTAGGGATTAAATTGA
Found at i:41898782 original size:17 final size:17
Alignment explanation
Indices: 41898762--41898817 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
41898752 TATATGCATT
41898762 TAAAAAATCAAATAACA
1 TAAAAAATCAAATAACA
* **
41898779 TAAACAAA-GAAATAGATT
1 TAAA-AAATCAAATA-ACA
41898797 TAAAAAATCAAATAACA
1 TAAAAAATCAAATAACA
41898814 TAAA
1 TAAA
41898818 CAAAGGAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.68, C:0.09, G:0.04, T:0.20
Consensus pattern (17 bp):
TAAAAAATCAAATAACA
Found at i:41898846 original size:35 final size:35
Alignment explanation
Indices: 41898759--41898831 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
41898749 AAATATATGC
41898759 ATTTAAAAAATCAAATAACATAAACAAAGAAATAG
1 ATTTAAAAAATCAAATAACATAAACAAAGAAATAG
*
41898794 ATTTAAAAAATCAAATAACATAAACAAAGGAATAG
1 ATTTAAAAAATCAAATAACATAAACAAAGAAATAG
41898829 ATT
1 ATT
41898832 GTAAGTTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.63, C:0.08, G:0.07, T:0.22
Consensus pattern (35 bp):
ATTTAAAAAATCAAATAACATAAACAAAGAAATAG
Found at i:41909209 original size:29 final size:29
Alignment explanation
Indices: 41909175--41909248 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
41909165 TAATCAACCG
*
41909175 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
41909204 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
41909233 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
41909249 ATCCTCACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:41917357 original size:29 final size:29
Alignment explanation
Indices: 41917323--41917396 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
41917313 TAATCAACCG
*
41917323 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
41917352 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
41917381 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
41917397 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:41920641 original size:29 final size:29
Alignment explanation
Indices: 41920577--41920642 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
41920567 CTTTCATTTA
* * *
41920577 TTTCACAATTTAACTCCTTAATTTACAGT
1 TTTCTCAATTTAACTCCCTAATATACAGT
* *
41920606 TTTCTCAATTTAA-TCCCTAATATGCATT
1 TTTCTCAATTTAACTCCCTAATATACAGT
41920634 TTTACTCAA
1 TTT-CTCAA
41920643 AATCACTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTCTCAATTTAACTCCCTAATATACAGT
Found at i:41922524 original size:18 final size:18
Alignment explanation
Indices: 41922485--41922527 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
41922475 GCAATTATAA
*
41922485 CCAAAGAAAATTAAAATC
1 CCAAAGAAAAATAAAATC
41922503 CCAAATGAAAAATAAAAT-
1 CCAAA-GAAAAATAAAATC
41922521 CCAAAGA
1 CCAAAGA
41922528 GGCCGTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 10 0.43
19 11 0.48
ACGTcount: A:0.63, C:0.16, G:0.07, T:0.14
Consensus pattern (18 bp):
CCAAAGAAAAATAAAATC
Found at i:41930330 original size:18 final size:18
Alignment explanation
Indices: 41930291--41930333 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
41930281 GCAGTTATAA
*
41930291 CCAAAGAAAATTAAAATC
1 CCAAAGAAAAATAAAATC
41930309 CCAAATGAAAAATAAAAT-
1 CCAAA-GAAAAATAAAATC
41930327 CCAAAGA
1 CCAAAGA
41930334 GGCCGTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 10 0.43
19 11 0.48
ACGTcount: A:0.63, C:0.16, G:0.07, T:0.14
Consensus pattern (18 bp):
CCAAAGAAAAATAAAATC
Found at i:41939176 original size:16 final size:16
Alignment explanation
Indices: 41939155--41939189 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
41939145 CAGCAGCTGC
41939155 GTCAACCATTTGCCGA
1 GTCAACCATTTGCCGA
41939171 GTCAACCATTTGCCGA
1 GTCAACCATTTGCCGA
41939187 GTC
1 GTC
41939190 GAATTCAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (16 bp):
GTCAACCATTTGCCGA
Found at i:41941265 original size:49 final size:49
Alignment explanation
Indices: 41941208--41941309 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
41941198 ATTTCATATA
41941208 CCATAGTTTCCATGTATTCCACATATATTTATTTTCCTCCTCCTCCTCT
1 CCATAGTTTCCATGTATTCCACATATATTTATTTTCCTCCTCCTCCTCT
41941257 CCATAGTTTCCATGTATTCCACATATATTTATTTTCCTCCTCCTCCTCT
1 CCATAGTTTCCATGTATTCCACATATATTTATTTTCCTCCTCCTCCTCT
41941306 CCAT
1 CCAT
41941310 TCCACATCCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.19, C:0.33, G:0.04, T:0.44
Consensus pattern (49 bp):
CCATAGTTTCCATGTATTCCACATATATTTATTTTCCTCCTCCTCCTCT
Found at i:41967348 original size:20 final size:20
Alignment explanation
Indices: 41967323--41967365 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41967313 TTGTGGTCAC
* *
41967323 ACACACCCGTATGGCTTGGG
1 ACACACCCATATGGCTTAGG
*
41967343 ACACACCCATGTGGCTTAGG
1 ACACACCCATATGGCTTAGG
41967363 ACA
1 ACA
41967366 TGCCCGTGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (20 bp):
ACACACCCATATGGCTTAGG
Found at i:41969167 original size:50 final size:50
Alignment explanation
Indices: 41969102--41969299 Score: 236
Period size: 50 Copynumber: 3.9 Consensus size: 50
41969092 ACCGAAGCTC
* *
41969102 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAA
* * * * *
41969152 TTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGCTA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCT-AA-CAA
* * *
41969203 TCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAA
* * * * *
41969253 TCTGATACACGTACTAGCCTGCAATTAGTACTACACACGTGACCTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAA
41969300 AACCGTCTTA
Statistics
Matches: 122, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 1 0.01
50 80 0.66
51 40 0.33
52 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAA
Found at i:41969240 original size:101 final size:101
Alignment explanation
Indices: 41969095--41969294 Score: 346
Period size: 101 Copynumber: 2.0 Consensus size: 101
41969085 TCTTGTAACC
* * * *
41969095 GAAGCTCTCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATTTGGTAC
1 GAAGCTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATAC
* *
41969160 ACGTAGTAGCCTGCACTTAGTACTACACACGTGATT
66 ACGTACTAGCCTGCAATTAGTACTACACACGTGATT
41969196 GAAGCTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATAC
1 GAAGCTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATAC
41969261 ACGTACTAGCCTGCAATTAGTACTACACACGTGA
66 ACGTACTAGCCTGCAATTAGTACTACACACGTGA
41969295 CCTAAAACCG
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 93 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (101 bp):
GAAGCTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATAC
ACGTACTAGCCTGCAATTAGTACTACACACGTGATT
Found at i:41973180 original size:19 final size:20
Alignment explanation
Indices: 41973143--41973197 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
41973133 AATTAAAATT
41973143 CATAATTTTAA-TATTTT-TAA
1 CATAA-TTTAATTATTTTAT-A
41973163 CATAATTTAATTATTTTATA
1 CATAATTTAATTATTTTATA
41973183 -AT-ATTTAATTATTTT
1 CATAATTTAATTATTTT
41973198 TTGACAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 13 0.39
19 7 0.21
20 12 0.36
21 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
CATAATTTAATTATTTTATA
Found at i:41973198 original size:19 final size:19
Alignment explanation
Indices: 41973144--41973198 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
41973134 ATTAAAATTC
41973144 ATAAT-TTTAA-TATTTTT
1 ATAATATTTAATTATTTTT
41973161 A-ACATAATTTAATTA-TTTT
1 ATA-AT-ATTTAATTATTTTT
41973180 ATAATATTTAATTATTTTT
1 ATAATATTTAATTATTTTT
41973199 TGACAAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
16 1 0.03
17 3 0.09
18 9 0.28
19 16 0.50
20 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATAATATTTAATTATTTTT
Found at i:41993647 original size:6 final size:6
Alignment explanation
Indices: 41993633--41993691 Score: 64
Period size: 6 Copynumber: 9.5 Consensus size: 6
41993623 ATTGAAACGT
* * *
41993633 AAATAA AAATCA AAAGAA AAATAA AAATAA AATAAAGA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA-ATA-A AAATAA AAATAA
*
41993683 GAATAA AAA
1 AAATAA AAA
41993692 ATAGGAGGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 36 0.84
7 4 0.09
8 3 0.07
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:41993671 original size:21 final size:21
Alignment explanation
Indices: 41993645--41993689 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 21
41993635 ATAAAAATCA
41993645 AAAGAAAAATAAAAATAA-AAT
1 AAAG-AAAATAAAAATAAGAAT
41993666 AAAGAAAATAAAAATAAGAAT
1 AAAGAAAATAAAAATAAGAAT
41993687 AAA
1 AAA
41993690 AAATAGGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (21 bp):
AAAGAAAATAAAAATAAGAAT
Found at i:42006101 original size:46 final size:46
Alignment explanation
Indices: 42006048--42006183 Score: 200
Period size: 46 Copynumber: 3.0 Consensus size: 46
42006038 ATATATACAA
* * *
42006048 ATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATCC
1 ATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATATCC
* * *
42006094 ATCTCATACATGTTTCGCATTAGCCATTCGGCTTTACCTCATATCT
1 ATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATATCC
* *
42006140 ATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 ATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATAT
42006184 ATACATGTTC
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (46 bp):
ATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATATCC
Found at i:42006222 original size:47 final size:47
Alignment explanation
Indices: 42006157--42006398 Score: 322
Period size: 47 Copynumber: 5.1 Consensus size: 47
42006147 ACACATTTCG
* *
42006157 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* * *
42006204 CATTGGCCATTCGACCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* **
42006251 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
*
42006298 CATTGGCCATTCGGCCTTATCATGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C--ATATATACATGTTCACATTCATCA
** * **
42006349 CATTTTCCATTCGGCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
42006396 CAT
1 CAT
42006399 AAAATCCTAA
Statistics
Matches: 173, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
47 132 0.76
49 2 0.01
51 39 0.23
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
Found at i:42006285 original size:94 final size:97
Alignment explanation
Indices: 42006157--42006398 Score: 337
Period size: 98 Copynumber: 2.5 Consensus size: 97
42006147 ACACATTTCG
*
42006157 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCACATTGGCCATTCGACCTT
1 CATTAGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGACCTT
* *
42006222 ATC-T-C-ATATATGCATGTTCACATTCATCA
66 ATCATGCAATATATACAGGTTCACATTCATCA
* * ** *
42006251 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGACCTT
42006316 ATCATGCATATATATACAGGTTCACATTCATCA
66 ATCATGCA-ATATATACAGGTTCACATTCATCA
** * **
42006349 CATTTTCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CATTAGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACAT
42006399 AAAATCCTAA
Statistics
Matches: 128, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
94 62 0.48
95 1 0.01
96 1 0.01
98 64 0.50
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (97 bp):
CATTAGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGACCTT
ATCATGCAATATATACAGGTTCACATTCATCA
Found at i:42006320 original size:25 final size:25
Alignment explanation
Indices: 42006245--42006320 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
42006235 ATGTTCACAT
42006245 TCATCACATTGGCCATTCGGCCTTA
1 TCATCACATTGGCCATTCGGCCTTA
** * *
42006270 TCA-CACATACG-CATGTTC--ACAT-
1 TCATCACATTGGCCA--TTCGGCCTTA
42006292 TCATCACATTGGCCATTCGGCCTTA
1 TCATCACATTGGCCATTCGGCCTTA
42006317 TCAT
1 TCAT
42006321 GCATATATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.32
Consensus pattern (25 bp):
TCATCACATTGGCCATTCGGCCTTA
Found at i:42010120 original size:40 final size:40
Alignment explanation
Indices: 42010050--42010326 Score: 414
Period size: 40 Copynumber: 7.0 Consensus size: 40
42010040 CCTCATAATT
* * *
42010050 CTAGCATGAATGC-CTTCGAGG-TTTAACCCGGATATATCA
1 CTAGCACGAATGCTCTTCG-GGACTTAGCCCGGATATATCA
*
42010089 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGTTATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
42010129 CTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
42010169 CTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
* * *
42010209 CTAGCACGAATGCTCTTCGGAACTTAGCCCGGACATATTA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
* * *
42010249 CCAGCACGGATGCTCTTCGGGACTTAGCCCGGATATAACA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
42010289 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
42010327 AACTCTCAGT
Statistics
Matches: 220, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 14 0.06
40 206 0.94
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
Found at i:42011862 original size:46 final size:46
Alignment explanation
Indices: 42011809--42011945 Score: 202
Period size: 46 Copynumber: 3.0 Consensus size: 46
42011799 TATATATACA
* * * *
42011809 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
42011855 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
42011901 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
42011946 ATACATGTTC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:42011984 original size:47 final size:47
Alignment explanation
Indices: 42011919--42012207 Score: 362
Period size: 47 Copynumber: 6.1 Consensus size: 47
42011909 ACACATTTCG
* * *
42011919 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACACATGTTCACATTCATCA
* * *
42011966 CATTGGCCATTCGACCTTATCTCATATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACACATGTTCACATTCATCA
* * * *
42012013 CATTGGCCATTCGGCCTTATCACACATGCGCATGTTCACATTCATAA
1 CATTGGCCATTCGGCCTTATCACATATACACATGTTCACATTCATCA
* * *
42012060 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACACATGTTCACATTCATCA
* *
42012107 CATTGGCCATTCGGCCTTATCACGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C--ATATACACATGTTCACATTCATCA
* * * **
42012158 CATTTGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACACATGTTCACATTCATCA
42012205 CAT
1 CAT
42012208 AAAATCCTAA
Statistics
Matches: 215, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
47 173 0.80
49 2 0.01
51 40 0.19
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATACACATGTTCACATTCATCA
Found at i:42012086 original size:24 final size:24
Alignment explanation
Indices: 42012011--42012086 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
42012001 TCACATTCAT
*
42012011 CACATTGGCCATTCGGCCTTATCA
1 CACATTGGCCATTCAGCCTTATCA
*
42012035 CACA-T-GCGCATGTTCA-CATTCAT-A
1 CACATTGGC-CA--TTCAGCCTT-ATCA
42012059 -ACATTGGCCATTCAGCCTTATCA
1 CACATTGGCCATTCAGCCTTATCA
42012082 CACAT
1 CACAT
42012087 ACGCATGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 18
0.66 0.05 0.30
Matches are distributed among these distances:
22 8 0.20
23 10 0.25
24 15 0.38
25 7 0.17
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (24 bp):
CACATTGGCCATTCAGCCTTATCA
Found at i:42012106 original size:25 final size:25
Alignment explanation
Indices: 42012031--42012108 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
42012021 ATTCGGCCTT
*
42012031 ATCACACATGCGCATGTTCACATTC
1 ATCACACATACGCATGTTCACATTC
** *
42012056 AT-A-ACATTGGCCA--TTCAGCCTT-
1 ATCACACATACG-CATGTTCA-CATTC
42012078 ATCACACATACGCATGTTCACATTC
1 ATCACACATACGCATGTTCACATTC
42012103 ATCACA
1 ATCACA
42012109 TTGGCCATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 6 0.15
23 11 0.28
24 11 0.28
25 12 0.30
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.28
Consensus pattern (25 bp):
ATCACACATACGCATGTTCACATTC
Found at i:42020658 original size:46 final size:48
Alignment explanation
Indices: 42020600--42020730 Score: 164
Period size: 46 Copynumber: 2.8 Consensus size: 48
42020590 ATGGTTGAGC
* *
42020600 ATCCGAATTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-ATG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACAGG
* *
42020647 -TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAC-AGG
*
42020692 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42020731 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
43 6 0.08
45 4 0.06
46 29 0.41
47 29 0.41
48 2 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (48 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACAGG
Found at i:42022509 original size:37 final size:37
Alignment explanation
Indices: 42022468--42022547 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
42022458 GTGACACGGA
42022468 TTTAGCCTGAACTAGTAATTTGTTGT-GATTTTAAAGG
1 TTTAGCCTGAACTAGTAATTTGTTGTCG-TTTTAAAGG
42022505 TTTAGCCTGAACTAGTAATTTGTTGTCGTTTTAAAGG
1 TTTAGCCTGAACTAGTAATTTGTTGTCGTTTTAAAGG
42022542 TTTAGC
1 TTTAGC
42022548 TTGGACTGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 41 0.98
38 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (37 bp):
TTTAGCCTGAACTAGTAATTTGTTGTCGTTTTAAAGG
Found at i:42024886 original size:3 final size:3
Alignment explanation
Indices: 42024878--42024911 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42024868 GTAGGCCAGC
42024878 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42024912 TTTTGGGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42024997 original size:20 final size:20
Alignment explanation
Indices: 42024968--42025012 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
42024958 CAAAATAGTT
* *
42024968 ACCTATGTTTTATTTCAGTC
1 ACCTAGGTTTCATTTCAGTC
42024988 ACCTAGGTTTCATTTCAGTC
1 ACCTAGGTTTCATTTCAGTC
42025008 ACCTA
1 ACCTA
42025013 ACTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (20 bp):
ACCTAGGTTTCATTTCAGTC
Found at i:42025058 original size:19 final size:19
Alignment explanation
Indices: 42025029--42025072 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
42025019 GAAAAATAAC
*
42025029 AAAACAGTCACTAACGTTAT
1 AAAA-AGTCACTAACCTTAT
42025049 AAAAAGTCACTAACCTTAT
1 AAAAAGTCACTAACCTTAT
42025068 AAAAA
1 AAAAA
42025073 AGTGACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.23
Consensus pattern (19 bp):
AAAAAGTCACTAACCTTAT
Found at i:42025227 original size:3 final size:3
Alignment explanation
Indices: 42025219--42025265 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
42025209 CATTTAACAG
*
42025219 AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
42025266 CAGCAGCAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42026281 original size:21 final size:21
Alignment explanation
Indices: 42026242--42026282 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42026232 CAACGTGGCA
* *
42026242 AGTTAACTGGTCACGTCAGCT
1 AGTTAACTGGCCACATCAGCT
*
42026263 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
42026283 GGTTCTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:42026402 original size:20 final size:20
Alignment explanation
Indices: 42026377--42026425 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
42026367 TTTCAAAAGT
42026377 TAGGTGACTGAAATGAAACC
1 TAGGTGACTGAAATGAAACC
*
42026397 TAGGTGACTGAAATGAAACT
1 TAGGTGACTGAAATGAAACC
42026417 TAGGTGACT
1 TAGGTGACT
42026426 ATTTTGTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (20 bp):
TAGGTGACTGAAATGAAACC
Found at i:42030775 original size:25 final size:24
Alignment explanation
Indices: 42030747--42030824 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
42030737 CTATATAATA
*
42030747 GGAAGCTCATGTGAGCCATGTAACG
1 GGAAGCTCATGAGAGCCAT-TAACG
* *
42030772 GGAAACTCCA-GAGAGCCATTAATG
1 GGAAGCT-CATGAGAGCCATTAACG
* *
42030796 GGAAGCTCAT-ACGAGCCAATATCG
1 GGAAGCTCATGA-GAGCCATTAACG
42030820 GGAAG
1 GGAAG
42030825 TTTAAGCAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
23 3 0.07
24 24 0.56
25 14 0.33
26 2 0.05
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (24 bp):
GGAAGCTCATGAGAGCCATTAACG
Found at i:42034219 original size:20 final size:20
Alignment explanation
Indices: 42034194--42034234 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
42034184 TGTGATATGT
42034194 TGACACTACTAAGTCATAAA
1 TGACACTACTAAGTCATAAA
42034214 TGACACTACTAAGTCATAAA
1 TGACACTACTAAGTCATAAA
42034234 T
1 T
42034235 TAACCATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (20 bp):
TGACACTACTAAGTCATAAA
Found at i:42047782 original size:44 final size:44
Alignment explanation
Indices: 42047733--42047822 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
42047723 ATTCATGAGG
42047733 GTATGATCATGTTTTACTTTGTTTTTAATAATCGTTAAGTATAA
1 GTATGATCATGTTTTACTTTGTTTTTAATAATCGTTAAGTATAA
42047777 GTATGATCATGTTTTACTTTGTTTTTAATAATCGTTAAGTATAA
1 GTATGATCATGTTTTACTTTGTTTTTAATAATCGTTAAGTATAA
42047821 GT
1 GT
42047823 GTTAAAAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (44 bp):
GTATGATCATGTTTTACTTTGTTTTTAATAATCGTTAAGTATAA
Found at i:42058337 original size:47 final size:47
Alignment explanation
Indices: 42058283--42058440 Score: 262
Period size: 47 Copynumber: 3.4 Consensus size: 47
42058273 TTAGGATTTT
** * **
42058283 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGAAA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
42058330 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
*
42058377 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
42058424 ATGTGATGAATGTGAAC
1 ATGTGATGAATGTGAAC
42058441 CGAATGGCCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 105 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
Found at i:42058449 original size:74 final size:74
Alignment explanation
Indices: 42058366--42058514 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
42058356 TGAGATAAGG
*
42058366 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGAT
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGAT
42058431 GAATGTGAA
66 GAATGTGAA
42058440 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGAT
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGAT
42058505 GAATGTGAA
66 GAATGTGAA
42058514 C
1 C
42058515 ATGCGTATGT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (74 bp):
CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGAT
GAATGTGAA
Found at i:42058454 original size:121 final size:121
Alignment explanation
Indices: 42058319--42058702 Score: 444
Period size: 121 Copynumber: 3.0 Consensus size: 121
42058309 TGAGATAAGG
*
42058319 CCGAATGGAAAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGAT
1 CCGAATGGAAAATGTGATGAATGTGAACATGCATATATGAGATAAGACCGAATGGCCAATGTGAT
42058384 GAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
66 GAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
** *
42058440 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGAT
1 CCGAATGGAAAATGTGATGAATGTGAACATGCATATATGAGATAAGACCGAATGGCCAATGTGAT
* *
42058505 GAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
66 GAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* * * * * *
42058561 CATGCGTATGTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAA
1 C---CG-A-ATG-GAAAATG-TG-AT-G--AA--TG-------TGAACATGCATATATGAGATAA
* * * *
42058626 GGCCGAATGGCCAATGTGATGAATGCGAACATGCATATATGTGATAAGGCCGAATGGTCAATGTC
46 GACCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTG
42058691 ATGAATGTGAA
111 ATGAATGTGAA
42058702 C
1 C
42058703 ATGCATATAT
Statistics
Matches: 225, Mismatches: 18, Indels: 20
0.86 0.07 0.08
Matches are distributed among these distances:
121 116 0.52
124 2 0.01
125 1 0.00
126 2 0.01
127 4 0.02
128 2 0.01
129 2 0.01
130 1 0.00
132 2 0.01
134 2 0.01
141 91 0.40
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (121 bp):
CCGAATGGAAAATGTGATGAATGTGAACATGCATATATGAGATAAGACCGAATGGCCAATGTGAT
GAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
Found at i:42058478 original size:168 final size:168
Alignment explanation
Indices: 42058283--42058608 Score: 535
Period size: 168 Copynumber: 1.9 Consensus size: 168
42058273 TTAGGATTTT
** * *
42058283 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGAAAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGACCGAATGGAAAATGTGATGAATGTGAACA
42058348 TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
66 TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
42058413 CCGAATGGCCAATGTGATGAATGTGAACCGAATGGCCA
131 CCGAATGGCCAATGTGATGAATGTGAACCGAATGGCCA
* **
42058451 ATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGACCGAATGGAAAATGTGATGAATGTGAACA
* * * * *
42058516 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
66 TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
*
42058581 CTGAATGGCCAATGTGATGAATGTGAAC
131 CCGAATGGCCAATGTGATGAATGTGAAC
42058609 ATGCGTATGT
Statistics
Matches: 145, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
168 145 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (168 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGACCGAATGGAAAATGTGATGAATGTGAACA
TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
CCGAATGGCCAATGTGATGAATGTGAACCGAATGGCCA
Found at i:42058645 original size:22 final size:22
Alignment explanation
Indices: 42058618--42058689 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
42058608 CATGCGTATG
42058618 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
42058640 TGTGATGAATG-CGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
42058665 TGTGATAAGGCCGAATGGTCAA
1 TGTGATAAGGCCGAATGGCCAA
42058687 TGT
1 TGT
42058690 CATGAATGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
22 12 0.32
23 9 0.24
24 8 0.21
25 9 0.24
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:42058667 original size:25 final size:25
Alignment explanation
Indices: 42058639--42058716 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
42058629 CGAATGGCCA
42058639 ATGTGATGAATGCGAACATGCATAT
1 ATGTGATGAATGCGAACATGCATAT
* *
42058664 ATGTGAT-AAGGCCG-A-ATG-GTCA-
1 ATGTGATGAATG-CGAACATGCAT-AT
* *
42058686 ATGTCATGAATGTGAACATGCATAT
1 ATGTGATGAATGCGAACATGCATAT
42058711 ATGTGA
1 ATGTGA
42058717 CAAGGCAGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 14
0.65 0.12 0.23
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 8 0.21
25 15 0.38
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.28
Consensus pattern (25 bp):
ATGTGATGAATGCGAACATGCATAT
Found at i:42058775 original size:94 final size:94
Alignment explanation
Indices: 42058440--42058782 Score: 485
Period size: 94 Copynumber: 3.6 Consensus size: 94
42058430 TGAATGTGAA
42058440 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGAT-AAGACCGAATGGCCAATGTGA
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAAG-CCGAATGGCCAATGTGA
42058504 TGAATGTGAACATGCGTATGTGTGATAAGG
65 TGAATGTGAACATGCGTATGTGTGATAAGG
* * * *
42058534 CCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCAATGTGAT
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGAT
42058599 GAATGTGAACATGCGTATGTGTGATAAGG
66 GAATGTGAACATGCGTATGTGTGATAAGG
* * * *
42058628 CCGAATGGCCAATGTGATGAATGCGAACATGCATATATGTGATAAGGCCGAATGGTCAATGTCAT
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGAT
* * *
42058693 GAATGTGAACATGCATATATGTGACAAGG
66 GAATGTGAACATGCGTATGTGTGATAAGG
* * * * * *
42058722 CAGAATGGCCAATGTGATGAACATG-GAA-GTGTATATATGTGGTAAAGCTGAATGGCTAATG
1 CCGAATGGCCAATGTGATG-A-ATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATG
42058783 CGAAATGTGT
Statistics
Matches: 225, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
94 216 0.96
95 6 0.03
96 3 0.01
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (94 bp):
CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGAT
GAATGTGAACATGCGTATGTGTGATAAGG
Found at i:42058775 original size:141 final size:141
Alignment explanation
Indices: 42058442--42058782 Score: 481
Period size: 141 Copynumber: 2.4 Consensus size: 141
42058432 AATGTGAACC
42058442 GAATGGCCAATGTGATGAATGTGAACATGCATATATGTGAT-AAGACCGAATGGCCAATGTGATG
1 GAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAAG-CCGAATGGCCAATGTGATG
* * * * * *
42058506 AATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATG
65 AATGCGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTCATGAATGTGAACATGCATATA
* *
42058571 TGTGATAAGGCT
130 TGTGACAAGGCA
* * *
42058583 GAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGA
1 GAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATGA
*
42058648 ATGCGAACATGCATATATGTGATAAGGCCGAATGGTCAATGTCATGAATGTGAACATGCATATAT
66 ATGCGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTCATGAATGTGAACATGCATATAT
42058713 GTGACAAGGCA
131 GTGACAAGGCA
* * * * *
42058724 GAATGGCCAATGTGATGAACATG-GAA-GTGTATATATGTGGTAAAGCTGAATGGCTAATG
1 GAATGGCCAATGTGATG-A-ATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATG
42058783 CGAAATGTGT
Statistics
Matches: 177, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
141 168 0.95
142 6 0.03
143 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (141 bp):
GAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATGA
ATGCGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTCATGAATGTGAACATGCATATAT
GTGACAAGGCA
Found at i:42058777 original size:47 final size:47
Alignment explanation
Indices: 42058440--42058742 Score: 489
Period size: 47 Copynumber: 6.4 Consensus size: 47
42058430 TGAATGTGAA
*
42058440 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGA
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
* *
42058487 CCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
* *
42058534 CCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
* * *
42058581 CTGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
*
42058628 CCGAATGGCCAATGTGATGAATGCGAACATGCATATATGTGATAAGG
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
* * *
42058675 CCGAATGGTCAATGTCATGAATGTGAACATGCATATATGTGACAAGG
1 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
*
42058722 CAGAATGGCCAATGTGATGAA
1 CCGAATGGCCAATGTGATGAA
42058743 CATGGAAGTG
Statistics
Matches: 241, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 241 1.00
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (47 bp):
CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
Found at i:42058812 original size:46 final size:46
Alignment explanation
Indices: 42058756--42058892 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
42058746 GGAAGTGTAT
* *
42058756 ATATGTGGTAAAGCTGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
*
42058802 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * * * * *
42058848 ACATGCGGTAAAGCCAAATGGCTAATGTGAGATATGTATAAGATG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
42058893 TGTATATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.35, C:0.09, G:0.31, T:0.25
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:42075552 original size:39 final size:39
Alignment explanation
Indices: 42075429--42075648 Score: 273
Period size: 40 Copynumber: 5.6 Consensus size: 39
42075419 ACTCGCTCAA
* *
42075429 ATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCACA-
1 ATGCCTTCGGGACTTAGCCCGGATT--AGTAACTAGCACAG
* * *
42075468 ATTGCCTTCGGGACTTAGCCCGAATTTAGTAACTCGCACAA
1 A-TGCCTTCGGGACTTAGCCCGGA-TTAGTAACTAGCACAG
* *
42075509 ATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGTACAG
1 ATGCCTTCGGGACTTAGCCCGGATTAGTAACTAGCACAG
* *
42075548 ATGCCTTCGGGACTTAGCCCGGGTTTAGTAACTTGCACAG
1 ATGCCTTCGGGACTTAGCCC-GGATTAGTAACTAGCACAG
* **
42075588 ATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGTGCAG
1 ATGCCTTCGGGACTTAGCCCGGATTAGTAACTAGCACAG
42075627 ATGCCTTCGGGACTTAGCCCGG
1 ATGCCTTCGGGACTTAGCCCGG
42075649 TTTTCATCCA
Statistics
Matches: 160, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 69 0.43
40 88 0.55
41 1 0.01
42 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (39 bp):
ATGCCTTCGGGACTTAGCCCGGATTAGTAACTAGCACAG
Found at i:42075580 original size:79 final size:79
Alignment explanation
Indices: 42075419--42075648 Score: 329
Period size: 79 Copynumber: 2.9 Consensus size: 79
42075409 GGATATAACT
* * * * *
42075419 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCACA-ATTGCCTTCGGGAC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT--AGTCACTAGTACAGA-TGCCTTCGGGAC
*
42075482 TTAGCCCGAATTTAGTA
63 TTAGCCCGGATTTAGTA
42075499 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGTACAGATGCCTTCGGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGTACAGATGCCTTCGGGACTTA
*
42075564 GCCCGGGTTTAGTA
66 GCCCGGATTTAGTA
* * *
42075578 ACTTGCACAGATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGTGCAGATGCCTTCGGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGTACAGATGCCTTCGGGACTTA
42075643 GCCCGG
66 GCCCGG
42075649 TTTTCATCCA
Statistics
Matches: 138, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
79 105 0.76
80 31 0.22
81 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (79 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGTACAGATGCCTTCGGGACTTA
GCCCGGATTTAGTA
Found at i:42099767 original size:40 final size:41
Alignment explanation
Indices: 42099723--42099800 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
42099713 ACCAGCATTT
** *
42099723 AGCCTGCTAGGTTTTAAACCTGAATTCA-TCACCGGCACGA
1 AGCCTGCTAGACTTTAAACCTGAACTCATTCACCGGCACGA
**
42099763 AGCCTGCTAGACTTTAAGTCTGAACTCATTCACCGGCA
1 AGCCTGCTAGACTTTAAACCTGAACTCATTCACCGGCA
42099801 TTTCGTCTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 23 0.72
41 9 0.28
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACTTTAAACCTGAACTCATTCACCGGCACGA
Found at i:42099867 original size:43 final size:42
Alignment explanation
Indices: 42099818--42099961 Score: 130
Period size: 43 Copynumber: 3.3 Consensus size: 42
42099808 TACTAGGCTT
*
42099818 GAAGCCCGATATCATTTCACCGGCATTATAGCCTGCTAGGTCC
1 GAAGCCCGATATCATTTCACCAGCATTATAGCCTGCTAGG-CC
* * * *
42099861 GAAGCCCGATATTATCTCACTAGTATTATAGCCTGCTAGGCCC
1 GAAGCCCGATATCATTTCACCAGCATTATAGCCTGCTAGG-CC
* * * *
42099904 TAAGCCTGATAAT-ATTATTCACCAGC-TTAAAGCTTGCTAGGCC
1 GAAGCCCGAT-ATCA-T-TTCACCAGCATTATAGCCTGCTAGGCC
*
42099947 GAGGCCCGAATATCA
1 GAAGCCCG-ATATCA
42099962 CATTTCGATA
Statistics
Matches: 80, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
43 55 0.69
44 19 0.24
45 6 0.08
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (42 bp):
GAAGCCCGATATCATTTCACCAGCATTATAGCCTGCTAGGCC
Found at i:42106740 original size:41 final size:41
Alignment explanation
Indices: 42106682--42106812 Score: 192
Period size: 41 Copynumber: 3.2 Consensus size: 41
42106672 ACAACATTTC
*
42106682 CATTTGTTATCCTTTACGGATAAC-TCCTTTTTTGACCTTTT
1 CATTTGTTATCCTTTACGGATAACTTCC-TTTTTAACCTTTT
* * *
42106723 CATTTGTTATCCATTACGAAGAACTTCCTTTTTAACCTTTT
1 CATTTGTTATCCTTTACGGATAACTTCCTTTTTAACCTTTT
* *
42106764 CATTTGTTATCCTTTACGGATAACTTCCTTTTCAACCTTTC
1 CATTTGTTATCCTTTACGGATAACTTCCTTTTTAACCTTTT
42106805 CATTTGTT
1 CATTTGTT
42106813 CAAAAATACC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 77 0.96
42 3 0.04
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.49
Consensus pattern (41 bp):
CATTTGTTATCCTTTACGGATAACTTCCTTTTTAACCTTTT
Found at i:42113399 original size:31 final size:30
Alignment explanation
Indices: 42113344--42113416 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
42113334 TTGTATACCT
* *
42113344 AAACTATAATTTGGTGCAATTATATACGTG
1 AAACTCTAATTTGGTGCAAATATATACGTG
* * *
42113374 AAGCTCTAATTGTGGTTCAAATATATACTTG
1 AAACTCTAATT-TGGTGCAAATATATACGTG
*
42113405 AAACTTTAATTT
1 AAACTCTAATTT
42113417 TGATTTAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (30 bp):
AAACTCTAATTTGGTGCAAATATATACGTG
Found at i:42117927 original size:16 final size:17
Alignment explanation
Indices: 42117906--42117937 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42117896 ATAACAATAA
42117906 TTTAATCAT-CAAAAAG
1 TTTAATCATCCAAAAAG
42117922 TTTAATCATCCAAAAA
1 TTTAATCATCCAAAAA
42117938 TCATACATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (17 bp):
TTTAATCATCCAAAAAG
Found at i:42121751 original size:40 final size:42
Alignment explanation
Indices: 42121680--42121776 Score: 130
Period size: 40 Copynumber: 2.4 Consensus size: 42
42121670 TCGACTATGC
42121680 TGGCACTAAGTGTGC-AGTTCGAAATAACTTCGGCTACAA-A
1 TGGCACTAAGTGTGCGAGTTCGAAATAACTTCGGCTACAAGA
* * * *
42121720 TGGCACTAAGTGTGCGAGTT-GGAATAGCTTCGGTTATAAGA
1 TGGCACTAAGTGTGCGAGTTCGAAATAACTTCGGCTACAAGA
42121761 -GGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
42121777 TACCGAGATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 46 0.90
41 5 0.10
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (42 bp):
TGGCACTAAGTGTGCGAGTTCGAAATAACTTCGGCTACAAGA
Found at i:42124859 original size:24 final size:23
Alignment explanation
Indices: 42124824--42124868 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
42124814 CTGTTACGTA
42124824 GCTCTTTGTGAGCAATCCTGATAG
1 GCTCTTTGTGAGC-ATCCTGATAG
*
42124848 GCTCTTCT-TGAGCTTCCTGAT
1 GCTCTT-TGTGAGCATCCTGAT
42124869 TAAAAGTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 11 0.58
25 1 0.05
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (23 bp):
GCTCTTTGTGAGCATCCTGATAG
Found at i:42131551 original size:25 final size:25
Alignment explanation
Indices: 42131523--42131570 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
42131513 CACAGAGTAA
* *
42131523 GGATATGTTCGATTTTTGAACCTAG
1 GGATATATTCAATTTTTGAACCTAG
42131548 GGATATATTCAATTTTTGAACCT
1 GGATATATTCAATTTTTGAACCT
42131571 GAATTGTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (25 bp):
GGATATATTCAATTTTTGAACCTAG
Found at i:42138912 original size:19 final size:17
Alignment explanation
Indices: 42138889--42138954 Score: 71
Period size: 17 Copynumber: 3.6 Consensus size: 17
42138879 CGATTTTTTA
42138889 TAATTTTTATAAAATTT
1 TAATTTTTATAAAATTT
*
42138906 TACAATTTTTTATAAAAAATT
1 T--AA-TTTTTAT-AAAATTT
42138927 TAATTTTTA-ATAAATTT
1 TAATTTTTATA-AAATTT
42138944 TAATTTTTATA
1 TAATTTTTATA
42138955 TTTTTACTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.02
17 15 0.37
18 7 0.17
19 4 0.10
20 7 0.17
21 7 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTTTTATAAAATTT
Found at i:42138934 original size:20 final size:20
Alignment explanation
Indices: 42138892--42138940 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
42138882 TTTTTTATAA
*
42138892 TTTTTATAAAATTTTACAAT
1 TTTTTATAAAAATTTACAAT
42138912 TTTTTATAAAAAATTT--AAT
1 TTTTTAT-AAAAATTTACAAT
*
42138931 TTTTAATAAA
1 TTTTTATAAA
42138941 TTTTAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 7 0.27
21 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTTATAAAAATTTACAAT
Found at i:42138965 original size:25 final size:25
Alignment explanation
Indices: 42138925--42139018 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 25
42138915 TTATAAAAAA
*
42138925 TTTA-ATTTTTAATAAATTTTAATT
1 TTTATATTTTTACTAAATTTTAATT
*
42138949 TTTATATTTTTACTAAAATTTAA--
1 TTTATATTTTTACTAAATTTTAATT
*
42138972 --TAT-TTTTT-CTAAAATTTTTATT
1 TTTATATTTTTACT-AAATTTTAATT
* *
42138994 TTTATATTTTTTTCTAATTTTTAAT
1 TTTATA-TTTTTACTAAATTTTAAT
42139019 AAAAGCAGGG
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
19 2 0.04
20 12 0.22
21 3 0.05
24 7 0.13
25 16 0.29
26 13 0.24
27 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTATATTTTTACTAAATTTTAATT
Found at i:42138976 original size:19 final size:18
Alignment explanation
Indices: 42138949--42138997 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
42138939 AATTTTAATT
42138949 TTTATATTTTTACTAAAA
1 TTTATATTTTTACTAAAA
*
42138967 TTTAATATTTTTTCTAAAA
1 TTT-ATATTTTTACTAAAA
*
42138986 TTTTTATTTTTA
1 TTTATATTTTTA
42138998 TATTTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATTTTTACTAAAA
Found at i:42140180 original size:41 final size:41
Alignment explanation
Indices: 42140106--42140186 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
42140096 GACTTAGTTT
* * *
42140106 ATTTAGTGGGTAAAAAATATGTTTTTGCCGTGAAGAATATA
1 ATTTAGTGGGTAAAAAATATGTTTCTACAGTGAAGAATATA
* * *
42140147 ATTTGGTGGGTAAAAATTATGTTTCTATAGTGAAGAATAT
1 ATTTAGTGGGTAAAAAATATGTTTCTACAGTGAAGAATAT
42140187 GAGAAGAGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (41 bp):
ATTTAGTGGGTAAAAAATATGTTTCTACAGTGAAGAATATA
Found at i:42144838 original size:45 final size:44
Alignment explanation
Indices: 42144786--42145048 Score: 219
Period size: 45 Copynumber: 5.8 Consensus size: 44
42144776 GCAAACTTGA
*
42144786 AGAAGAAGATTCATAGATATGGTGAACTTATACATGCGGTTTCAT
1 AGAAGAAGATTCATAGATAT-GTGAACTTATACATGCGGATTCAT
* * ** * *
42144831 GGTAGAAGATTCAT-GAATATGGTGAACTCGTATATGTGGATTCAT
1 AGAAGAAGATTCATAG-ATAT-GTGAACTTATACATGCGGATTCAT
* * * *
42144876 AGTAGAAGATTCATAGATAT-TACAGACTCATACATGTGGATTCAT
1 AGAAGAAGATTCATAGATATGT-GA-ACTTATACATGCGGATTCAT
* ** *
42144921 AGAAGAAGATTAATAGATATGACAGA-TTCATACATGCTGATTCAT
1 AGAAGAAGATTCATAGATATGTGA-ACTT-ATACATGCGGATTCAT
* * *
42144966 AGAAGAAGATTAATAGATATG-GAAGATTCATACATGCAGATTCAT
1 AGAAGAAGATTCATAGATATGTGAA-CTT-ATACATGCGGATTCAT
* * *
42145011 AGAAGAAGATTCATAAATATGGTGGACTAATACATGCG
1 AGAAGAAGATTCATAGATAT-GTGAACTTATACATGCG
42145049 AACTGTGTTG
Statistics
Matches: 183, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
43 2 0.01
44 4 0.02
45 172 0.94
46 3 0.02
47 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (44 bp):
AGAAGAAGATTCATAGATATGTGAACTTATACATGCGGATTCAT
Found at i:42144888 original size:14 final size:15
Alignment explanation
Indices: 42144869--42145025 Score: 76
Period size: 14 Copynumber: 10.5 Consensus size: 15
42144859 CGTATATGTG
42144869 GATTCATAGTA-GAA
1 GATTCATAGTATGAA
*
42144883 GATTCATAGATATTACA
1 GATTCATAG-TATGA-A
* * **
42144900 GACTCATA-CATGTG
1 GATTCATAGTATGAA
*
42144914 GATTCATAG-AAGAA
1 GATTCATAGTATGAA
*
42144928 GATTAATAGATATGACA
1 GATTCATAG-TATGA-A
* **
42144945 GATTCATA-CATGCT
1 GATTCATAGTATGAA
*
42144959 GATTCATAG-AAGAA
1 GATTCATAGTATGAA
*
42144973 GATTAATAGATATGGAA
1 GATTCATAG-TAT-GAA
* *
42144990 GATTCATA-CATGCA
1 GATTCATAGTATGAA
*
42145004 GATTCATAG-AAGAA
1 GATTCATAGTATGAA
42145018 GATTCATA
1 GATTCATA
42145026 AATATGGTGG
Statistics
Matches: 105, Mismatches: 26, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
14 65 0.62
15 9 0.09
16 5 0.05
17 26 0.25
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (15 bp):
GATTCATAGTATGAA
Found at i:42144920 original size:90 final size:90
Alignment explanation
Indices: 42144786--42145047 Score: 266
Period size: 90 Copynumber: 2.9 Consensus size: 90
42144776 GCAAACTTGA
* * * * *
42144786 AGAAGAAGATTCATAGATATGGTGA-ACTTATACATGCGGTTTCATGGTAGAAGATTCATGAATA
1 AGAAGAAGATTCATAGATAT-GTAAGACTCATACATGCGGATTCATAGAAGAAGATTCAT-AATA
* *
42144850 TGGTGA-ACTCGTATATG-TGGATTCAT
64 TGGTGAGACTCATACATGCT-GATTCAT
* * *
42144876 AGTAGAAGATTCATAGATAT-TACAGACTCATACATGTGGATTCATAGAAGAAGATTAATAGATA
1 AGAAGAAGATTCATAGATATGTA-AGACTCATACATGCGGATTCATAGAAGAAGATTCATA-ATA
** *
42144940 T-GACAGATTCATACATGCTGATTCAT
64 TGGTGAGACTCATACATGCTGATTCAT
* * * *
42144966 AGAAGAAGATTAATAGATATGGAAGATTCATACATGCAGATTCATAGAAGAAGATTCATAAATAT
1 AGAAGAAGATTCATAGATATGTAAGACTCATACATGCGGATTCATAGAAGAAGATTCAT-AATAT
*
42145031 GGTG-GACTAATACATGC
65 GGTGAGACTCATACATGC
42145048 GAACTGTGTT
Statistics
Matches: 140, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
88 1 0.01
89 4 0.03
90 131 0.94
91 4 0.03
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (90 bp):
AGAAGAAGATTCATAGATATGTAAGACTCATACATGCGGATTCATAGAAGAAGATTCATAATATG
GTGAGACTCATACATGCTGATTCAT
Found at i:42152876 original size:20 final size:20
Alignment explanation
Indices: 42152853--42152891 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
42152843 TTTACTCTGA
42152853 TTTAA-TATAATATATATTTT
1 TTTAATTATAATAT-TATTTT
42152873 TTTAATTTATAATATTATT
1 TTTAA-TTATAATATTATT
42152892 AGTAACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 4 0.24
22 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAATTATAATATTATTTT
Found at i:42158478 original size:19 final size:20
Alignment explanation
Indices: 42158454--42158493 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
42158444 CAATAAATGA
*
42158454 ATACACATGTAT-AAATAAT
1 ATACACATATATAAAATAAT
42158473 ATACACATATATAAAATAAT
1 ATACACATATATAAAATAAT
42158493 A
1 A
42158494 AATAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (20 bp):
ATACACATATATAAAATAAT
Found at i:42158607 original size:25 final size:25
Alignment explanation
Indices: 42158557--42158608 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
42158547 AATAATAAAG
*
42158557 TAAATAAAAGAATAAACAAAGTAAA
1 TAAATAAAAGAATAAACAAAGAAAA
*
42158582 TAAATAAAAGAA-AAAGAATAGAAAA
1 TAAATAAAAGAATAAACAA-AGAAAA
42158607 TA
1 TA
42158609 GAAAGAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (25 bp):
TAAATAAAAGAATAAACAAAGAAAA
Found at i:42164165 original size:41 final size:40
Alignment explanation
Indices: 42164117--42164203 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
42164107 TCAAATACAT
*
42164117 TTAAAACAAATATTAAAATAAGAAACAAATAAAAAATTATA
1 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAA-TATA
* * * * *
42164158 TTAAAACAATTCTTAAAACAATACACAAATTAAAAATATA
1 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATATA
*
42164198 ATAAAA
1 TTAAAA
42164204 AGTGATTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 9 0.23
41 30 0.77
ACGTcount: A:0.66, C:0.08, G:0.01, T:0.25
Consensus pattern (40 bp):
TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATATA
Done.