Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 96 of 147
Found at i:17620192 original size:15 final size:16
Alignment explanation
Indices: 17620150--17620191 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
17620140 TTTTCTCATC
*
17620150 TTTAATTTTTTT-CTT
1 TTTAATTTTTTTAATT
17620165 TTTAATTTTTTTAATT
1 TTTAATTTTTTTAATT
17620181 TTTATATTTTT
1 TTTA-ATTTTT
17620192 ATCTGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.50
16 6 0.25
17 6 0.25
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTAATTTTTTTAATT
Found at i:17624412 original size:18 final size:18
Alignment explanation
Indices: 17624369--17624412 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
17624359 GGAATGTATA
*
17624369 AATATATAAATATATATTT
1 AATA-ATAAATAAATATTT
17624388 -ATAAATAAATAAATATTT
1 AAT-AATAAATAAATATTT
17624406 AATAATA
1 AATAATA
17624413 CTAAATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAATAAATAAATATTT
Found at i:17624646 original size:14 final size:14
Alignment explanation
Indices: 17624627--17624655 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17624617 ATTAACATAA
17624627 TAATACATGAATAT
1 TAATACATGAATAT
17624641 TAATACATGAATAT
1 TAATACATGAATAT
17624655 T
1 T
17624656 GTGATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
TAATACATGAATAT
Found at i:17626173 original size:3 final size:3
Alignment explanation
Indices: 17626165--17626206 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
17626155 CAATTTTTCC
17626165 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
17626207 AAGGAAAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17636889 original size:15 final size:16
Alignment explanation
Indices: 17636865--17636900 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
17636855 TTTGCCTAAG
*
17636865 AAAAAGATAAAA-AAA
1 AAAAACATAAAACAAA
17636880 AAAAACATAAAACAAA
1 AAAAACATAAAACAAA
17636896 AAAAA
1 AAAAA
17636901 AGGAAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.86, C:0.06, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAACATAAAACAAA
Found at i:17637955 original size:54 final size:49
Alignment explanation
Indices: 17637665--17637967 Score: 285
Period size: 49 Copynumber: 6.1 Consensus size: 49
17637655 TTCTTTTAAT
* *
17637665 AGATTTTAAAGTTTCAAA-ACTTATATTTAGG-GGTAGCCATTTGT-AAACA
1 AGATTTTAAAGTTTCAAAGCCTT-TGTTTAGGAGG-AGCCATTT-TCAAACA
* * *
17637714 AAATTTT-AAGTTTTAAAGCCTTTGTTTA-AAGGGAGCCATTTTCAAACA
1 AGATTTTAAAGTTTCAAAGCCTTTGTTTAGGA-GGAGCCATTTTCAAACA
* * * * * * ** *
17637762 AAATTTTAAAGCTTCAAAGCCTCTATTTCGAAAAAGCCATTTTCAGACA
1 AGATTTTAAAGTTTCAAAGCCTTTGTTTAGGAGGAGCCATTTTCAAACA
* *
17637811 AGATTTTAAAGTTTCAAAGCCTTTATTTAGGATGAGCCATTTTCAAACA
1 AGATTTTAAAGTTTCAAAGCCTTTGTTTAGGAGGAGCCATTTTCAAACA
* * *
17637860 AGATTTTAAAGTTTTAAAGCCTCTGTTTGGGAGGAGCCATTTTCAAACA
1 AGATTTTAAAGTTTCAAAGCCTTTGTTTAGGAGGAGCCATTTTCAAACA
* *
17637909 ATATTTTTTTTAAAAGATTCAAAGCCTTTGTTTAAGG-GGAGCCATTTTCAAACA
1 AGA----TTTT-AAAGTTTCAAAGCCTTTGTTT-AGGAGGAGCCATTTTCAAACA
17637963 AGATT
1 AGATT
17637968 AAAAAAATTA
Statistics
Matches: 210, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
47 1 0.00
48 34 0.16
49 128 0.61
50 4 0.02
53 4 0.02
54 37 0.18
55 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (49 bp):
AGATTTTAAAGTTTCAAAGCCTTTGTTTAGGAGGAGCCATTTTCAAACA
Found at i:17640878 original size:33 final size:32
Alignment explanation
Indices: 17640759--17640879 Score: 120
Period size: 33 Copynumber: 3.7 Consensus size: 32
17640749 TCATGTTTCA
*
17640759 ATACCTCTGGTTAGAGGAA-CATTTCAAATCCC
1 ATACCTCTGGTTAGAGGAATC-TTTCAAATCTC
* *
17640791 ATTACCTCTGGTTAGAGGAAT-ATTCTAAATTTC
1 A-TACCTCTGGTTAGAGGAATCTTTC-AAATCTC
*
17640824 ATGGCCTCTGGTTAGAGGAATCTTTCAAATCTC
1 AT-ACCTCTGGTTAGAGGAATCTTTCAAATCTC
* * *
17640857 ACTACCTTTGGTTAAAAGAATCT
1 A-TACCTCTGGTTAGAGGAATCT
17640880 CTATATTGCC
Statistics
Matches: 73, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
32 5 0.07
33 64 0.88
34 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (32 bp):
ATACCTCTGGTTAGAGGAATCTTTCAAATCTC
Found at i:17641042 original size:68 final size:69
Alignment explanation
Indices: 17640887--17641147 Score: 233
Period size: 68 Copynumber: 3.7 Consensus size: 69
17640877 TCTCTATATT
* * * * *
17640887 GCCTCAAGTTAGAGGAATTTTTTC-AAGTATCATTA-CCTCTAATCAAAGGAGTTTTTTTAAAAA
1 GCCTCTAGTTAGATGAATTTTTTCAAAGTTTCA-TAGCCTCTAGTCAGAGGAG-TTTTTT----A
**
17640950 AAGTTTCATA
60 AAGTGCCATA
* * *
17640960 GCCTCTGGTTAGATGAATTTTTTCAAAGTTTCATAGCTTTTAGTCAGAGGAG-TTTTTAAAGTGC
1 GCCTCTAGTTAGATGAATTTTTTCAAAGTTTCATAGCCTCTAGTCAGAGGAGTTTTTTAAAGTGC
17641024 CATA
66 CATA
* * * * * * *
17641028 GCCTCTAGTTAGATGAGTTTTCTTAAAAGTGTCATTGCCTCTAGTTAGATGAGTTTTTTCAAGTG
1 GCCTCTAGTTAGATGAATTTT-TTCAAAGTTTCATAGCCTCTAGTCAGAGGAGTTTTTTAAAGTG
17641093 CCATA
65 CCATA
* * * * *
17641098 GCCTTTTGTTAGAT-AAGTTTTTCAAAGTTTCATAGCCTCTGGTTAGAGGA
1 GCCTCTAGTTAGATGAATTTTTTCAAAGTTTCATAGCCTCTAGTCAGAGGA
17641148 ACTCATTAAT
Statistics
Matches: 155, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
68 53 0.34
69 28 0.18
70 27 0.17
72 5 0.03
73 23 0.15
74 19 0.12
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (69 bp):
GCCTCTAGTTAGATGAATTTTTTCAAAGTTTCATAGCCTCTAGTCAGAGGAGTTTTTTAAAGTGC
CATA
Found at i:17641085 original size:104 final size:104
Alignment explanation
Indices: 17640948--17641144 Score: 254
Period size: 104 Copynumber: 1.9 Consensus size: 104
17640938 TTTTTTTAAA
* * ** *
17640948 AAAAGTTTCATAGCCTCTGGTTAGATGAATTTTTTCAAAGTTTCATAG-CTTTTAGTCAGAGGAG
1 AAAAGTGTCATAGCCTCTAGTTAGATGAATTTTTTC-AAGTGCCATAGCCTTTT-GTCAGAGAAG
17641012 TTTTT-AAAGTGCCATAGCCTCTAGTTAGATGAGTTTTCTT
64 TTTTTCAAAGTGCCATAGCCTCTAGTTAGATGAGTTTTCTT
* * * *
17641052 AAAAGTGTCATTGCCTCTAGTTAGATGAGTTTTTTCAAGTGCCATAGCCTTTTGTTAGATAAGTT
1 AAAAGTGTCATAGCCTCTAGTTAGATGAATTTTTTCAAGTGCCATAGCCTTTTGTCAGAGAAGTT
** *
17641117 TTTCAAAGTTTCATAGCCTCTGGTTAGA
66 TTTCAAAGTGCCATAGCCTCTAGTTAGA
17641145 GGAACTCATT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
103 21 0.27
104 58 0.73
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (104 bp):
AAAAGTGTCATAGCCTCTAGTTAGATGAATTTTTTCAAGTGCCATAGCCTTTTGTCAGAGAAGTT
TTTCAAAGTGCCATAGCCTCTAGTTAGATGAGTTTTCTT
Found at i:17641132 original size:34 final size:34
Alignment explanation
Indices: 17640949--17641144 Score: 189
Period size: 34 Copynumber: 5.7 Consensus size: 34
17640939 TTTTTTAAAA
* * *
17640949 AAAGTTTCATAGCCTCTGGTTAGATGAATTTTTTC
1 AAAGTGTCATAGCCTCTAGTTAGATG-AGTTTTTC
* * * * *
17640984 AAAGTTTCATAGCTTTTAGTCAGAGGAGTTTTT-
1 AAAGTGTCATAGCCTCTAGTTAGATGAGTTTTTC
* *
17641017 AAAGTGCCATAGCCTCTAGTTAGATGAGTTTTCTTA
1 AAAGTGTCATAGCCTCTAGTTAGATGAG-TTT-TTC
*
17641053 AAAGTGTCATTGCCTCTAGTTAGATGAGTTTTTTC
1 AAAGTGTCATAGCCTCTAGTTAGATGAG-TTTTTC
* * * *
17641088 -AAGTGCCATAGCCTTTTGTTAGATAAGTTTTTC
1 AAAGTGTCATAGCCTCTAGTTAGATGAGTTTTTC
* *
17641121 AAAGTTTCATAGCCTCTGGTTAGA
1 AAAGTGTCATAGCCTCTAGTTAGA
17641145 GGAACTCATT
Statistics
Matches: 133, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
33 28 0.21
34 50 0.38
35 25 0.19
36 30 0.23
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (34 bp):
AAAGTGTCATAGCCTCTAGTTAGATGAGTTTTTC
Found at i:17641336 original size:36 final size:36
Alignment explanation
Indices: 17641287--17641357 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
17641277 AGATGAGTTA
* * *
17641287 TTTAAAGTTTCATAGCCTTTAGTTAAAAGAGTTTTC
1 TTTAAAGTGTCATAGCCTCTAATTAAAAGAGTTTTC
*
17641323 TTTAAAGTGTCATAGCCTCTAATTAGAAGAGTTTT
1 TTTAAAGTGTCATAGCCTCTAATTAAAAGAGTTTT
17641358 ATAAGCACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.42
Consensus pattern (36 bp):
TTTAAAGTGTCATAGCCTCTAATTAAAAGAGTTTTC
Found at i:17641501 original size:273 final size:269
Alignment explanation
Indices: 17641000--17641611 Score: 683
Period size: 273 Copynumber: 2.3 Consensus size: 269
17640990 TCATAGCTTT
* * ** * * * * *
17641000 TAGTCAGAGGAGTT-TTTAAAGTGCCATAGCCTCTAGTTAGATGAGTTTTCTTAAAAGTGTCATT
1 TAGTTAGATGAGTTATTTAAAGTTTCATAGCCTTTAGTTAAAAGAGTTTTCTTTAAAGTGTCATA
* * * ** * *
17641064 GCCTCTAGTTAGATGAGTTTTTTCAAGTGCCATAGCCTTTTGTTAGATAAGTTTTTCAAAGTTTC
66 GCCTCTAATTAGAAGAGTTTTATCAAGCACCATAGCCTTTTGCTAGAGAAGTTTTTCAAAGTTTC
* *
17641129 ATAGCCTCTGGTTAGAGGAACTCATTAATTTTAAAAACCTCTAAATAGAAGACTCTTTCAAAATT
131 ATAGCCTCTGGTTAAAGGAACTCATTAATTTTAAAAACCTCTAAATAGAAGACTCCTTCAAAATT
* *
17641194 AGGCATGATTTGTAAGACTAAAAAGCATAATCTATAAGACCTCTTAGATTTTTAATTTCAAGTAT
196 AGGCATGATTCGTAAGACCAAAAAGCATAATCTATAAGACCTCTTAGATTTTTAATTTCAAGTAT
*
17641259 CATTGTCTGCCTT
261 CA---T-TGCCTC
*
17641272 TGGTTAGATGAGTTATTTAAAGTTTCATAGCCTTTAGTTAAAAGAGTTTTCTTTAAAGTGTCATA
1 TAGTTAGATGAGTTATTTAAAGTTTCATAGCCTTTAGTTAAAAGAGTTTTCTTTAAAGTGTCATA
*
17641337 GCCTCTAATTAGAAGAGTTTTAT-AAGCACCATAGCCTTTTGCTAGAGGAGTTCGTTTCAAAGTT
66 GCCTCTAATTAGAAGAGTTTTATCAAGCACCATAGCCTTTTGCTAGAGAAGTT--TTTCAAAGTT
* * ** ** * * *** *
17641401 TCATAGCTTCTGGTTAAAGG-AGTTTTTAATTTTACGAGCCTTTGGTTAGATGACTCCTTCAAAA
129 TCATAGCCTCTGGTTAAAGGAACTCATTAATTTTAAAAACCTCTAAATAGAAGACTCCTTCAAAA
* ** * *
17641465 TTAGGCATTATTCGTAAGACCAAAGGGTATAATCTATAAGACCTTTTAGATTTTTAATTTCAAGT
194 TTAGGCATGATTCGTAAGACCAAAAAGCATAATCTATAAGACCTCTTAGATTTTTAATTTCAAGT
*
17641530 TTCATTGCCTC
259 ATCATTGCCTC
* * * * * * * * *
17641541 TAGTTAGATAAGTTATTTAAAGTTTGACAACATTTGGTT-AGAGAAGTTTTATTTAAAGTTTCAT
1 TAGTTAGATGAGTTATTTAAAGTTTCATAGCCTTTAGTTAAAAG-AGTTTTCTTTAAAGTGTCAT
17641605 AGCCTCT
65 AGCCTCT
17641612 GGTTAGAGAA
Statistics
Matches: 285, Mismatches: 51, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
268 3 0.01
269 62 0.22
270 1 0.00
272 35 0.12
273 156 0.55
274 28 0.10
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (269 bp):
TAGTTAGATGAGTTATTTAAAGTTTCATAGCCTTTAGTTAAAAGAGTTTTCTTTAAAGTGTCATA
GCCTCTAATTAGAAGAGTTTTATCAAGCACCATAGCCTTTTGCTAGAGAAGTTTTTCAAAGTTTC
ATAGCCTCTGGTTAAAGGAACTCATTAATTTTAAAAACCTCTAAATAGAAGACTCCTTCAAAATT
AGGCATGATTCGTAAGACCAAAAAGCATAATCTATAAGACCTCTTAGATTTTTAATTTCAAGTAT
CATTGCCTC
Found at i:17641564 original size:34 final size:34
Alignment explanation
Indices: 17641521--17641624 Score: 109
Period size: 36 Copynumber: 3.0 Consensus size: 34
17641511 TAGATTTTTA
* * * *
17641521 ATTTCAAGTTTCATTGCCTCTAGTTAGATAAGTT
1 ATTTAAAGTTTCATAGCCTCTGGTTAGAGAAGTT
* * * * *
17641555 ATTTAAAGTTTGACAACATTTGGTTAGAGAAGTTTT
1 ATTTAAAGTTTCATAGCCTCTGGTTAGAGAAG--TT
17641591 ATTTAAAGTTTCATAGCCTCTGGTTAGAGAAGTT
1 ATTTAAAGTTTCATAGCCTCTGGTTAGAGAAGTT
17641625 TTCTTTAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
34 25 0.46
36 29 0.54
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (34 bp):
ATTTAAAGTTTCATAGCCTCTGGTTAGAGAAGTT
Found at i:17641599 original size:36 final size:36
Alignment explanation
Indices: 17641553--17641633 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
17641543 GTTAGATAAG
* *
17641553 TTATTTAAAGTTTGACAACATTTGGTTAGAGAAGTT
1 TTATTTAAAGTTTCACAACATCTGGTTAGAGAAGTT
* * *
17641589 TTATTTAAAGTTTCATAGCCTCTGGTTAGAGAAGTT
1 TTATTTAAAGTTTCACAACATCTGGTTAGAGAAGTT
*
17641625 TTCTTTAAA
1 TTATTTAAA
17641634 ATGTCATAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (36 bp):
TTATTTAAAGTTTCACAACATCTGGTTAGAGAAGTT
Found at i:17642658 original size:9 final size:10
Alignment explanation
Indices: 17642634--17642659 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
17642624 ATTCTAGGAT
17642634 ATTTTTGGAA
1 ATTTTTGGAA
17642644 ATTTTTGGAA
1 ATTTTTGGAA
17642654 ATTTTT
1 ATTTTT
17642660 TAGAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (10 bp):
ATTTTTGGAA
Found at i:17643105 original size:14 final size:16
Alignment explanation
Indices: 17643086--17643121 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
17643076 TTTTTTAGGA
17643086 TTTTTATAAT-T-TAT
1 TTTTTATAATATATAT
17643100 TTTTTATAATATATAT
1 TTTTTATAATATATAT
17643116 TTTTTA
1 TTTTTA
17643122 ACTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
15 1 0.05
16 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTATAATATATAT
Found at i:17643695 original size:7 final size:7
Alignment explanation
Indices: 17643683--17643717 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
17643673 AAAATGATGA
17643683 AAATAAT
1 AAATAAT
17643690 AAATAAT
1 AAATAAT
17643697 AAATAAT
1 AAATAAT
17643704 AAATAAAT
1 AAAT-AAT
17643712 AAATAA
1 AAATAA
17643718 CAATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:17643722 original size:18 final size:18
Alignment explanation
Indices: 17643687--17643724 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17643677 TGATGAAAAT
*
17643687 AATAAATAATAAATAATA
1 AATAAATAATAAACAATA
17643705 AATAAATAA-ATAACAATA
1 AATAAATAATA-AACAATA
17643723 AA
1 AA
17643725 AATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAAATAATAAACAATA
Found at i:17644047 original size:3 final size:3
Alignment explanation
Indices: 17644041--17644072 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17644031 AGAATTTATT
17644041 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17644073 GTTTTTCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17647395 original size:13 final size:13
Alignment explanation
Indices: 17647379--17647428 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
17647369 TTCACATATA
17647379 TATAAATTAAAAT
1 TATAAATTAAAAT
*
17647392 TATAAATT-ATAT
1 TATAAATTAAAAT
*
17647404 ATATAAATTAAAAA
1 -TATAAATTAAAAT
*
17647418 TAAAAATTAAA
1 TATAAATTAAA
17647429 TTTAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 3 0.10
13 26 0.84
14 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATAAATTAAAAT
Found at i:17647403 original size:26 final size:26
Alignment explanation
Indices: 17647374--17647426 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
17647364 TTCAATTCAC
* *
17647374 ATATATATAAATTAAAATTATAAATT
1 ATATATATAAATTAAAAATAAAAATT
17647400 ATATATATAAATTAAAAATAAAAATT
1 ATATATATAAATTAAAAATAAAAATT
17647426 A
1 A
17647427 AATTTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATATATAAATTAAAAATAAAAATT
Found at i:17652664 original size:13 final size:13
Alignment explanation
Indices: 17652646--17652671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17652636 AAAGTAAACT
17652646 AAACTAATACTAA
1 AAACTAATACTAA
17652659 AAACTAATACTAA
1 AAACTAATACTAA
17652672 TGAATGGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
AAACTAATACTAA
Found at i:17656275 original size:3 final size:3
Alignment explanation
Indices: 17656267--17656300 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
17656257 AAGCAAATTT
*
17656267 TAA TAA TAA TAA TAA TAA TAA GAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17656301 TTCATTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:17657390 original size:30 final size:30
Alignment explanation
Indices: 17657345--17657427 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
17657335 TCAAAAATAA
* * *
17657345 AAAATAAATTATTTTACTCATTTCATGTTAT
1 AAAAT-AATCATTTTACTCATTTAATATTAT
* * *
17657376 ATAATAATCATTTTATTCTTTTAATATTAT
1 AAAATAATCATTTTACTCATTTAATATTAT
*
17657406 AAAATAATTATTTTACTC-TTTA
1 AAAATAATCATTTTACTCATTTA
17657428 TCAAAAAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
29 4 0.09
30 35 0.81
31 4 0.09
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (30 bp):
AAAATAATCATTTTACTCATTTAATATTAT
Found at i:17657850 original size:20 final size:20
Alignment explanation
Indices: 17657806--17657850 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
17657796 TTAAGAAGTT
*
17657806 TAAAGGCTTGAAAATTAGGA
1 TAAAGGCTTGAAAAGTAGGA
*
17657826 GAAAGGCTTG-AAAGTAGAGA
1 TAAAGGCTTGAAAAGTAG-GA
17657846 TAAAG
1 TAAAG
17657851 ATAATTACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.47, C:0.04, G:0.29, T:0.20
Consensus pattern (20 bp):
TAAAGGCTTGAAAAGTAGGA
Found at i:17658209 original size:6 final size:6
Alignment explanation
Indices: 17658198--17658244 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
17658188 GTTGAGTTTC
17658198 TTTATT TTTATT TTTATT TATT-TT TTTATAT TTTATAT TTTATT TTT
1 TTTATT TTTATT TTTATT T-TTATT TTTAT-T TTTAT-T TTTATT TTT
17658245 TCAAACCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.05
6 21 0.55
7 15 0.39
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:17663600 original size:23 final size:22
Alignment explanation
Indices: 17663556--17663613 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
17663546 TCTTCAAGCC
*
17663556 CTCTTTTTTTTTCATCTCTTCT
1 CTCTTTTTTTCTCATCTCTTCT
* *
17663578 CTCTTTTTTTGCTCCTCTTTTCT
1 CTCTTTTTTT-CTCATCTCTTCT
17663601 CTTCATTTTTTTC
1 C-TC-TTTTTTTC
17663614 GGTAGACCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 3 0.10
25 7 0.23
ACGTcount: A:0.03, C:0.28, G:0.02, T:0.67
Consensus pattern (22 bp):
CTCTTTTTTTCTCATCTCTTCT
Found at i:17664179 original size:144 final size:144
Alignment explanation
Indices: 17663926--17664331 Score: 455
Period size: 144 Copynumber: 2.8 Consensus size: 144
17663916 TTTAAAACAC
* * * * * *
17663926 CAAAAATCATGAAATATTATTAAATTGAGATCTGAAAAGTTTCATGAAAATCCAAGTTCGAGAAT
1 CAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAGCTCAAGAAG
*
17663991 GTCAAATTATGAAAATACCCTTATAAGGGTATTTT-GATAATTTCATACTTTTCAG-GGTATTGC
66 GT-AAATTATGAAAATACCCTTATAAGGGTATTTTAG-TAATTTCATACTTTTCAGAGGTACTGC
17664054 TGTGATTTCAAATGCA
129 TGTGATTTCAAATGCA
* * * * * *
17664070 TTAAAAATCATAAAATATTATGAAATTAAAATCTAAAAATTTTCAT-AAAATACGAGCTCAAGAA
1 -CAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAGCTCAAGAA
** * * * * *
17664134 GGCTAAATTACAAAAATACCCTTATAAGGGTATTTTAGTAGTTTCACAATTTT-TGAGGTGCTGC
65 GG-TAAATTATGAAAATACCCTTATAAGGGTATTTTAGTAATTTCATACTTTTCAGAGGTACTGC
* *
17664198 TGTGATTTTAAATGTA
129 TGTGATTTCAAATGCA
* *
17664214 CCAAAATTATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAGCTCAA-AAG
1 CAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAGCTCAAGAA-
* * **
17664278 GGTTAAATTATGAAAATAACCTT-TAAAAGGTATTTTAGTAATTTTGTACTTTTC
65 GG-TAAATTATGAAAATACCCTTAT-AAGGGTATTTTAGTAATTTCATACTTTTC
17664332 TCAGTGCAAT
Statistics
Matches: 214, Mismatches: 40, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
143 43 0.20
144 131 0.61
145 40 0.19
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (144 bp):
CAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAGCTCAAGAAG
GTAAATTATGAAAATACCCTTATAAGGGTATTTTAGTAATTTCATACTTTTCAGAGGTACTGCTG
TGATTTCAAATGCA
Found at i:17667590 original size:44 final size:44
Alignment explanation
Indices: 17667488--17667617 Score: 136
Period size: 44 Copynumber: 2.9 Consensus size: 44
17667478 CTTTGAAGAT
17667488 TTACATTCGAAAAATCTTAAAGATTCAAATCCAAGACTCAAAGGC
1 TTACATTC-AAAAATCTTAAAGATTCAAATCCAAGACTCAAAGGC
* * * * *
17667533 TTATATTCAAAAATCTTAAAGGTTTACATCTAAGACTCAAAGG-
1 TTACATTCAAAAATCTTAAAGATTCAAATCCAAGACTCAAAGGC
** * * * *
17667576 TTCACATTTGAAAATCTTAGAGATTCACATCCTAGATTCAAA
1 TT-ACATTCAAAAATCTTAAAGATTCAAATCCAAGACTCAAA
17667618 TATTCACATT
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
43 2 0.03
44 61 0.87
45 7 0.10
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (44 bp):
TTACATTCAAAAATCTTAAAGATTCAAATCCAAGACTCAAAGGC
Found at i:17667635 original size:34 final size:34
Alignment explanation
Indices: 17667592--17667658 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
17667582 TTTGAAAATC
17667592 TTAGAGATTCACATCCT-AGATTCAAATATTCACA
1 TTAGAGATTCACAT-CTAAGATTCAAATATTCACA
*
17667626 TTAGAGATTCATATCTAAGATTCAAATATTCAC
1 TTAGAGATTCACATCTAAGATTCAAATATTCAC
17667659 TTTTGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 2 0.06
34 29 0.94
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (34 bp):
TTAGAGATTCACATCTAAGATTCAAATATTCACA
Found at i:17667799 original size:21 final size:21
Alignment explanation
Indices: 17667744--17667784 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17667734 AATTTTAGAA
*
17667744 ATTCACATCTAAAATTCAAAG
1 ATTCACATCTGAAATTCAAAG
17667765 ATTCACATCTGAAATTCAAA
1 ATTCACATCTGAAATTCAAA
17667785 TATTTTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (21 bp):
ATTCACATCTGAAATTCAAAG
Found at i:17667889 original size:21 final size:23
Alignment explanation
Indices: 17667853--17667907 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
17667843 AATATTTTAG
17667853 AGATTCACA-TCTAAAA-TTCAA
1 AGATTCACATTCTAAAAGTTCAA
*
17667874 ATATTCACATTC-AAAAGGTTCAA
1 AGATTCACATTCTAAAA-GTTCAA
*
17667897 AGATTCTCATT
1 AGATTCACATT
17667908 TGAAAGATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 12 0.43
22 2 0.07
23 14 0.50
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (23 bp):
AGATTCACATTCTAAAAGTTCAA
Found at i:17667913 original size:23 final size:23
Alignment explanation
Indices: 17667868--17667935 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
17667858 CACATCTAAA
* * **
17667868 ATTCAAATATTCACATTCAAAAG
1 ATTCAAAAATTCTCATTTGAAAG
* *
17667891 GTTCAAAGATTCTCATTTGAAAG
1 ATTCAAAAATTCTCATTTGAAAG
*
17667914 ATTAAAAAATTCTCATTTGAAA
1 ATTCAAAAATTCTCATTTGAAA
17667936 AATTTAGAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (23 bp):
ATTCAAAAATTCTCATTTGAAAG
Found at i:17667948 original size:23 final size:23
Alignment explanation
Indices: 17667895--17667952 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
17667885 CAAAAGGTTC
*
17667895 AAAGATTCTCATTTGAAAGATTA
1 AAAGATTCTCATTTGAAAAATTA
* *
17667918 AAAAATTCTCATTTGAAAAATTT
1 AAAGATTCTCATTTGAAAAATTA
*
17667941 AGAGATTCTCAT
1 AAAGATTCTCAT
17667953 CCAAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (23 bp):
AAAGATTCTCATTTGAAAAATTA
Found at i:17669384 original size:21 final size:21
Alignment explanation
Indices: 17669358--17669397 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
17669348 TTTTAACCCA
17669358 TTTTTT-CATTTTCTTTTATAT
1 TTTTTTCCATTTT-TTTTATAT
17669379 TTTTTTCCATTTTTTTTAT
1 TTTTTTCCATTTTTTTTAT
17669398 TTCTTCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTCCATTTTTTTTATAT
Found at i:17669393 original size:19 final size:20
Alignment explanation
Indices: 17669371--17669419 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
17669361 TTTCATTTTC
*
17669371 TTTTATATTTTTTTC-CATT
1 TTTTATATTTTCTTCACATT
*
17669390 TTTTTTA-TTTCTTCACATT
1 TTTTATATTTTCTTCACATT
17669409 TTTTAT-TTTTC
1 TTTTATATTTTC
17669420 ATTATTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTATATTTTCTTCACATT
Found at i:17669426 original size:17 final size:17
Alignment explanation
Indices: 17669380--17669427 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
17669370 CTTTTATATT
17669380 TTTTTCCATT-TTTTTTA
1 TTTTT-CATTATTTTTTA
*
17669397 TTTCTTCA-CATTTTTTA
1 TTT-TTCATTATTTTTTA
17669414 TTTTTCATTATTTT
1 TTTTTCATTATTTT
17669428 CTTTTTAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.15
17 20 0.77
18 2 0.08
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTCATTATTTTTTA
Found at i:17676339 original size:13 final size:13
Alignment explanation
Indices: 17676321--17676347 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17676311 GACTCTTCCT
17676321 TAAATCCGTGACA
1 TAAATCCGTGACA
17676334 TAAATCCGTGACA
1 TAAATCCGTGACA
17676347 T
1 T
17676348 TCTTCCCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (13 bp):
TAAATCCGTGACA
Found at i:17678772 original size:2 final size:2
Alignment explanation
Indices: 17678765--17678793 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17678755 CAAATTAAAA
17678765 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
17678794 AAAGAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17686073 original size:3 final size:3
Alignment explanation
Indices: 17686065--17686130 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
17686055 TAAAACATCA
17686065 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17686113 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
17686131 TTCTTATATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17686478 original size:14 final size:15
Alignment explanation
Indices: 17686455--17686489 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
17686445 TACTTATTTT
*
17686455 TAAAACTAAAA-AAA
1 TAAAAATAAAAGAAA
17686469 TAAAAATAAAAGAAA
1 TAAAAATAAAAGAAA
17686484 TAAAAA
1 TAAAAA
17686490 ATAATAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (15 bp):
TAAAAATAAAAGAAA
Found at i:17687077 original size:174 final size:174
Alignment explanation
Indices: 17686766--17687079 Score: 400
Period size: 174 Copynumber: 1.8 Consensus size: 174
17686756 TTTGTGGTGC
* * * *
17686766 TATGATTAAATTTGAAAAGAAAAGATAAATTATGATTTAATATATTTAAATTCAAAATTTCTGTA
1 TATGATTAAATTTGAAAAGAAAAGATAAATTATAATTTAATACATTTAAATTCAAAATTTATGCA
* * *
17686831 AAATTTCAATTTTTGATAGAGTTTGATTCAAATTTGAATAGTTACCCAAAAATATTAAATTTAGA
66 AAATTTAAATTTTTGATAGAGTTTGATTCAAATTTAAATAGTTACCCAAAAATATTAAATTTAAA
17686896 TAATTTATTAAATAGAATTATTTGATAGCATATATATTTCAAAT
131 TAATTTATTAAATAGAATTATTTGATAGCATATATATTTCAAAT
* * *
17686940 TATGATTAAATTT-AAAA-ACAAAGGTAAATTATAATTTAATACATTTGAATTTAAAATTTATGC
1 TATGATTAAATTTGAAAAGA-AAAGATAAATTATAATTTAATACATTTAAATTCAAAATTTATGC
* * ** * * ** * *
17687003 AAAATTTTAAATATTTT-ATAGATTTTGTTTTGAATTTAAATAGTTATCTAAACTTGTTAATTTT
65 AAAA-TTTAAAT-TTTTGATAGAGTTTGATTCAAATTTAAATAGTTACCCAAAAATATTAAATTT
17687067 AAATAATTTATTA
128 AAATAATTTATTA
17687080 TTAATAAAGT
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
172 1 0.01
173 45 0.38
174 67 0.57
175 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (174 bp):
TATGATTAAATTTGAAAAGAAAAGATAAATTATAATTTAATACATTTAAATTCAAAATTTATGCA
AAATTTAAATTTTTGATAGAGTTTGATTCAAATTTAAATAGTTACCCAAAAATATTAAATTTAAA
TAATTTATTAAATAGAATTATTTGATAGCATATATATTTCAAAT
Found at i:17688674 original size:31 final size:32
Alignment explanation
Indices: 17688639--17688704 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
17688629 TTGTTAATGC
17688639 AAAGAAAT-TT-TCTATATGTAAAATTAATAAA
1 AAAGAAATATTATCTATATG-AAAATTAATAAA
17688670 AAAGAAATATTGATCTATATGAAAATTAATAAA
1 AAAGAAATATT-ATCTATATGAAAATTAATAAA
17688703 AA
1 AA
17688705 TTAATTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 8 0.25
32 2 0.06
33 14 0.44
34 8 0.25
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (32 bp):
AAAGAAATATTATCTATATGAAAATTAATAAA
Found at i:17691533 original size:82 final size:82
Alignment explanation
Indices: 17691304--17691507 Score: 302
Period size: 82 Copynumber: 2.5 Consensus size: 82
17691294 AAACTATTTT
* * *
17691304 TTAAAATTCAAC-AAAGATGCTATTTTTAAGATTAAAAATGTGGTCCTTATTGAAAATTTGGAAA
1 TTAAATTTCAACGAAA-ATGATATTTTTAAAATTAAAAATGTGGTCCTTATTGAAAATTTGGAAA
*
17691368 AATTACTTTTCAAAATTG
65 AATTACTTTTCAAAATTC
* * * *
17691386 TTAAATTTCAACGAAAATGACATTTTTAAAATTAAAAACGTGGTCCTCATTCAAAATTTGGAAAA
1 TTAAATTTCAACGAAAATGATATTTTTAAAATTAAAAATGTGGTCCTTATTGAAAATTTGGAAAA
*
17691451 ATTATTTTTCAAAATTC
66 ATTACTTTTCAAAATTC
*
17691468 TTAAATTTCAATGAAAATGATATTTTTAAAATTAAAAATG
1 TTAAATTTCAACGAAAATGATATTTTTAAAATTAAAAATG
17691508 CAATCTTTGT
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
82 106 0.97
83 3 0.03
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (82 bp):
TTAAATTTCAACGAAAATGATATTTTTAAAATTAAAAATGTGGTCCTTATTGAAAATTTGGAAAA
ATTACTTTTCAAAATTC
Found at i:17695210 original size:33 final size:30
Alignment explanation
Indices: 17695105--17695214 Score: 86
Period size: 30 Copynumber: 3.7 Consensus size: 30
17695095 AATAAATCTA
* * *
17695105 TAAAAACAACCCAAC-AAATCTCAACAATAC
1 TAAAAAAAAACCAACAAAAT-TGAACAATAC
*
17695135 TA--AAAAAA--AATAAAATTGAACAATAC
1 TAAAAAAAAACCAACAAAATTGAACAATAC
* *
17695161 TAAAAAAAAACCAACAAAATTTAATAATAC
1 TAAAAAAAAACCAACAAAATTGAACAATAC
*
17695191 TCAACAAAAAAATCTAACAAAATT
1 T-AA-AAAAAAA-CCAACAAAATT
17695215 AAACTACAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
26 13 0.20
27 4 0.06
28 10 0.16
30 18 0.28
31 2 0.03
32 7 0.11
33 10 0.16
ACGTcount: A:0.64, C:0.17, G:0.01, T:0.18
Consensus pattern (30 bp):
TAAAAAAAAACCAACAAAATTGAACAATAC
Found at i:17695633 original size:16 final size:17
Alignment explanation
Indices: 17695600--17695632 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17695590 TTTTTTTAAT
17695600 TTTTTTATGGATAAAAA
1 TTTTTTATGGATAAAAA
*
17695617 TTTTTTATTGATAAAA
1 TTTTTTATGGATAAAA
17695633 TAATTACCAA
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:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
TTTTTTATGGATAAAAA
Found at i:17696206 original size:26 final size:27
Alignment explanation
Indices: 17696170--17696221 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
17696160 ATCATCATTG
17696170 AAGAAATATATTTTTGATT-ATATATT
1 AAGAAATATATTTTTGATTCATATATT
17696196 AAGAAATATATTTTTGATTCATATAT
1 AAGAAATATATTTTTGATTCATATAT
17696222 AAACATAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (27 bp):
AAGAAATATATTTTTGATTCATATATT
Found at i:17699479 original size:16 final size:16
Alignment explanation
Indices: 17699445--17699478 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
17699435 CTTTCAGTTC
17699445 TTTGTTTTTTGCTTTT
1 TTTGTTTTTTGCTTTT
17699461 TTTGTTTTTTG-TTTT
1 TTTGTTTTTTGCTTTT
17699476 TTT
1 TTT
17699479 TATTGGACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (16 bp):
TTTGTTTTTTGCTTTT
Found at i:17707167 original size:509 final size:507
Alignment explanation
Indices: 17706206--17707225 Score: 1623
Period size: 509 Copynumber: 2.0 Consensus size: 507
17706196 TTCATTAAAC
* * *
17706206 ATGTACAAGTTATTTCAGACCCTATTCTCTTGTAGAATCACACCATCATTCTTATATACTTTGCA
1 ATGTACAAGTTATTTCAGACCATATTCCCTTGTAGAATCACACCATCATTCTTATACACTTTGCA
*
17706271 TCAATCATTTCATACATAGTATATATATCCATGAGAAGCTAATTCACCTAAAACTATCAAATTGT
66 TCAATCATTTCATACATAATATATATATCCATGAGAAGCTAATTCACCTAAAACTATCAAATTGT
* *
17706336 AGCTAAAACTCAAAGCATACCTTACATGATGAAGAGTCATAATAATATCATTATGAGATCTAAGG
131 AGCTAAAACTCAAAGCATACCTTACATGATGAAGAGTCATAACAATACCATTATGAGATCTAAGG
* *
17706401 CAAATACTCCAAATGCTTTGAATCTGCACATTTTCATTATTGGTAACCATAATATCCTTATACTT
196 CAAACACTCCAAATACTTTGAATCTGCACATTTTCATTATTGGTAACCATAATATCCTTATACTT
* * * *
17706466 CTCATTCTCTTTTAACTCCATAAAGTAACTCTTATCATTGTAGACATGGACATTAGTAGCTGAAT
261 CTCATTCTCTTCTAACTCCACAAAGTAACTCTTAGCATTGCAGACATGGACATTAGTAGCTGAAT
* * * * * ** * *
17706531 CTAAAACTCATCCTTTATCACCTTTGAAAGTTTGAGTTTTTTCTACATAAGTAATCAAAAGGACA
326 CTAAAACTCATACTTTATCACCTTTGAAACTCTGAATCTCATATACATAAGTAATCAAAAGAACA
17706596 TCATCATCATCAAACATAATAGCAATAGTATCACTTTTTCTCATCCAATTTTTTATTGTCATTTG
391 TCATCATCATCAAACATAATAGCAATAGTATCACTTTTTCTCATCCAATTTTTTATTGTCATTTG
*
17706661 -CCTTTTGAAAGTAGCCATATTCCTTCTCAACTTTTTGTAGTGCACTTGGAT
456 CCCTTTTGAAAGTAGCCATATTCCTTCTCAACTTCTTGTAGTGCACTTGGAT
* * *
17706712 ATGTACAAAGTTATTTTAGACCATATTCCCTTGTAGAATCATACTATCATTCTTATACACTTTGC
1 ATGTAC-AAGTTATTTCAGACCATATTCCCTTGTAGAATCACACCATCATTCTTATACACTTTGC
17706777 ATCAATCATTTCATACATAATATATATATATCCATGAGAAGCTAATTCACCTAAAA-TAATCAAA
65 ATCAATCATTTCATACAT-A-ATATATATATCCATGAGAAGCTAATTCACCTAAAACT-ATCAAA
* * * *
17706841 TTGTAGTTACAACTCAAAGCATACCTTACGTGATGAAGAGTCCTAACAATACCATTATGAGATCT
127 TTGTAGCTAAAACTCAAAGCATACCTTACATGATGAAGAGTCATAACAATACCATTATGAGATCT
*
17706906 AAGGCAAACACTCTC-AATACTTTGAATCTGCACATTTTCATTATTGGTAACCGTAATATCCTTA
192 AAGGCAAACACTC-CAAATACTTTGAATCTGCACATTTTCATTATTGGTAACCATAATATCCTTA
* *
17706970 TACTTCTCATTCTCTTCTAACTCCACAAAGTAACTCTTAGCATTGCAGATATGGACATTAGTAGT
256 TACTTCTCATTCTCTTCTAACTCCACAAAGTAACTCTTAGCATTGCAGACATGGACATTAGTAGC
* *
17707035 TGAATCTAAAACTCATACTTTATCACCTTTGAAACTCTGAATCTCATATGCATAAGTCATCAAAA
321 TGAATCTAAAACTCATACTTTATCACCTTTGAAACTCTGAATCTCATATACATAAGTAATCAAAA
* *
17707100 GAATATCATCATCATCAAACATAATAGCAATAGTATCACTTTTTTTCATCCAATTTTTTATTGTC
386 GAACATCATCATCATCAAACATAATAGCAATAGTATCACTTTTTCTCATCCAATTTTTTATTGTC
* * *
17707165 ATTTGCCCTTTTGAAAGTAGCCTTATTCTTTTTCAACTTCTTGTAGTGCACTTGGAT
451 ATTTGCCCTTTTGAAAGTAGCCATATTCCTTCTCAACTTCTTGTAGTGCACTTGGAT
17707222 ATGT
1 ATGT
17707226 TATTTTTTAT
Statistics
Matches: 469, Mismatches: 39, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
506 6 0.01
507 70 0.15
508 2 0.00
509 339 0.72
510 52 0.11
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.36
Consensus pattern (507 bp):
ATGTACAAGTTATTTCAGACCATATTCCCTTGTAGAATCACACCATCATTCTTATACACTTTGCA
TCAATCATTTCATACATAATATATATATCCATGAGAAGCTAATTCACCTAAAACTATCAAATTGT
AGCTAAAACTCAAAGCATACCTTACATGATGAAGAGTCATAACAATACCATTATGAGATCTAAGG
CAAACACTCCAAATACTTTGAATCTGCACATTTTCATTATTGGTAACCATAATATCCTTATACTT
CTCATTCTCTTCTAACTCCACAAAGTAACTCTTAGCATTGCAGACATGGACATTAGTAGCTGAAT
CTAAAACTCATACTTTATCACCTTTGAAACTCTGAATCTCATATACATAAGTAATCAAAAGAACA
TCATCATCATCAAACATAATAGCAATAGTATCACTTTTTCTCATCCAATTTTTTATTGTCATTTG
CCCTTTTGAAAGTAGCCATATTCCTTCTCAACTTCTTGTAGTGCACTTGGAT
Found at i:17724507 original size:16 final size:14
Alignment explanation
Indices: 17724479--17724519 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
17724469 ATTGCATAAC
*
17724479 TTTTTTTTCTTTGT
1 TTTTTTTTTTTTGT
17724493 TTTGTTTTGTTTTTGT
1 TTT-TTTT-TTTTTGT
17724509 TTTTTTTTTTT
1 TTTTTTTTTTT
17724520 GCCCTTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 8 0.33
16 9 0.38
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTGT
Found at i:17730654 original size:13 final size:13
Alignment explanation
Indices: 17730636--17730669 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
17730626 TTATCATGCA
17730636 AATAATATCATAC
1 AATAATATCATAC
17730649 AATAATATCATAC
1 AATAATATCATAC
*
17730662 CATAATAT
1 AATAATAT
17730670 AATATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAATATCATAC
Found at i:17731869 original size:30 final size:30
Alignment explanation
Indices: 17731833--17731892 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
17731823 AGTGCCGTTC
*
17731833 TTTGCATAATTTTTATGAAACAGGAATTAT
1 TTTGCATAATTTTTATGAAACAAGAATTAT
17731863 TTTGCATAATTTTTATGAAACAAGAATTAT
1 TTTGCATAATTTTTATGAAACAAGAATTAT
17731893 ATAAAGACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (30 bp):
TTTGCATAATTTTTATGAAACAAGAATTAT
Found at i:17732311 original size:18 final size:18
Alignment explanation
Indices: 17732288--17732326 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17732278 TCAAGTTTTG
*
17732288 TAAAAATT-TGAAAAGATT
1 TAAAAATTCT-AAAAAATT
17732306 TAAAAATTCTAAAAAATT
1 TAAAAATTCTAAAAAATT
17732324 TAA
1 TAA
17732327 GATTGCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (18 bp):
TAAAAATTCTAAAAAATT
Found at i:17732371 original size:18 final size:18
Alignment explanation
Indices: 17732334--17732404 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
17732324 TAAGATTGCA
* *
17732334 AAGGTTTGCAAAAATGCC
1 AAGGTTTGCAAAGATTCC
17732352 AAGGTTTGCAAAGATTCC
1 AAGGTTTGCAAAGATTCC
* *
17732370 AA-ATTTGC-AAGATTTC
1 AAGGTTTGCAAAGATTCC
*
17732386 AAGTTTTGCAGAAG-TTCC
1 AAGGTTTGCA-AAGATTCC
17732404 A
1 A
17732405 GATTTGTAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 9 0.20
17 10 0.23
18 22 0.50
19 3 0.07
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (18 bp):
AAGGTTTGCAAAGATTCC
Found at i:17732378 original size:17 final size:17
Alignment explanation
Indices: 17732356--17732410 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
17732346 AATGCCAAGG
17732356 TTTGCAAAGATTCCAAA
1 TTTGCAAAGATTCCAAA
* *
17732373 TTTGC-AAGATTTCAAGT
1 TTTGCAAAGATTCCAA-A
*
17732390 TTTGCAGAAG-TTCCAGA
1 TTTGCA-AAGATTCCAAA
17732407 TTTG
1 TTTG
17732411 TAAGGTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.30
17 14 0.47
18 4 0.13
19 3 0.10
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (17 bp):
TTTGCAAAGATTCCAAA
Found at i:17732404 original size:34 final size:33
Alignment explanation
Indices: 17732351--17732462 Score: 107
Period size: 34 Copynumber: 3.2 Consensus size: 33
17732341 GCAAAAATGC
* *
17732351 CAAGGTTTGCAAAGATTCCAAATTTGCAAGATTT
1 CAAGTTTTGCAAAG-TTCCAGATTTGCAAGATTT
* *
17732385 CAAGTTTTGCAGAAGTTCCAGATTTGTAAGGTTT
1 CAAGTTTTGCA-AAGTTCCAGATTTGCAAGATTT
* * * *
17732419 TAAGTTTCGCAAAAGTTCTAGATTTGCAAGGATTC
1 CAAGTTTTGC-AAAGTTCCAGATTTGCAA-GATTT
17732454 CAAGGTTTT
1 CAA-GTTTT
17732463 AGAGGTTCTA
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
34 49 0.79
35 9 0.15
36 4 0.06
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (33 bp):
CAAGTTTTGCAAAGTTCCAGATTTGCAAGATTT
Found at i:17732487 original size:34 final size:35
Alignment explanation
Indices: 17732449--17732523 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 35
17732439 GATTTGCAAG
*
17732449 GATTCCAAGGTTT-TAGAGG-TTCTAAA-TTCACAAA
1 GATTCCAAGATTTGTA-AGGTTTC-AAATTTCACAAA
17732483 GATTCC-AGATTTGTAAGGTTTCAAATTTCACAAA
1 GATTCCAAGATTTGTAAGGTTTCAAATTTCACAAA
*
17732517 GGTTCCA
1 GATTCCA
17732524 GATACGCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
33 11 0.31
34 24 0.69
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (35 bp):
GATTCCAAGATTTGTAAGGTTTCAAATTTCACAAA
Found at i:17732593 original size:18 final size:18
Alignment explanation
Indices: 17732566--17732603 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17732556 ATTTGCAAAG
17732566 ATTTTCAAATTCACAAGA
1 ATTTTCAAATTCACAAGA
* *
17732584 ATTTTTAAATTCCCAAGA
1 ATTTTCAAATTCACAAGA
17732602 AT
1 AT
17732604 GAAAAATTTG
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:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (18 bp):
ATTTTCAAATTCACAAGA
Found at i:17732630 original size:16 final size:17
Alignment explanation
Indices: 17732609--17732642 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17732599 AGAATGAAAA
*
17732609 ATTTGCAAGAA-TTCAG
1 ATTTGCAAAAATTTCAG
17732625 ATTTGCAAAAATTTCAG
1 ATTTGCAAAAATTTCAG
17732642 A
1 A
17732643 CTCATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (17 bp):
ATTTGCAAAAATTTCAG
Found at i:17732923 original size:17 final size:17
Alignment explanation
Indices: 17732903--17732935 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17732893 GAACTTAAGG
17732903 TTTGTAAGAATTTCAGA
1 TTTGTAAGAATTTCAGA
*
17732920 TTTGTAAGAGTTTCAG
1 TTTGTAAGAATTTCAG
17732936 TTTCACAAAA
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:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (17 bp):
TTTGTAAGAATTTCAGA
Found at i:17733013 original size:17 final size:17
Alignment explanation
Indices: 17732993--17733035 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
17732983 TCATATTCGA
* *
17732993 AAGAAATTTAGTTTCAT
1 AAGAAATTTAGATTCAC
*
17733010 AAGAATTTTTAGATTCAC
1 AAGAA-ATTTAGATTCAC
17733028 AAGAAATT
1 AAGAAATT
17733036 CAATTTCGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (17 bp):
AAGAAATTTAGATTCAC
Found at i:17733208 original size:202 final size:201
Alignment explanation
Indices: 17732856--17733264 Score: 746
Period size: 202 Copynumber: 2.0 Consensus size: 201
17732846 AATTTCTAGT
* *
17732856 TCACAAGAAATCATAGATTCGAATTTTAGATTCGCAAGAACTTAAGGTTTGTAAGAATTTCAGAT
1 TCACAAGAAATCAAAGATTCGAATTTTAGATTCGCAAGAACTTAAAGTTTGTAAGAATTTCAGAT
17732921 TTGTAAGAGTTTCAGTTTCACAAAAATGAAAGATTCGCAAAAACTTTAGATTTGTAAGAATTTCA
66 TTGTAAGAGTTTCAGTTTCACAAAAATGAAAGATTCGCAAAAACTTTAGATTTGTAAGAATTTCA
17732986 TATTCGAAAGAAATTTAGTTTCATAAGAATTTTTAGATTCACAAGAAATTCAATTTCGTCATTGT
131 TATTCGAAAGAAATTTAGTTTCATAAGAATTTTTAGATTCACAAGAAATTCAATTTCGTCATTGT
17733051 AAAGAC
196 AAAGAC
* * * *
17733057 TCACAAGAAATTAAAGATTTGAATTTTAGATTCGTAAGAACTTAAAGTTTGTAAGAATTTCATAT
1 TCACAAGAAATCAAAGATTCGAATTTTAGATTCGCAAGAACTTAAAGTTTGTAAGAATTTCAGAT
17733122 TTGTAAGAGTTTCAGTTTTCACAAAAATGAAAGATTCGCAAAAACTTTAGATTTGTAAGAATTTC
66 TTGTAAGAGTTTCAG-TTTCACAAAAATGAAAGATTCGCAAAAACTTTAGATTTGTAAGAATTTC
17733187 ATATTCGAAAGAAATTTAGTTTCATAAGAATTTTTAGATTCACAAGAAATTCAATTTCGTCATTG
130 ATATTCGAAAGAAATTTAGTTTCATAAGAATTTTTAGATTCACAAGAAATTCAATTTCGTCATTG
*
17733252 TAAAGAT
195 TAAAGAC
17733259 TCACAA
1 TCACAA
17733265 ATTGTAATGC
Statistics
Matches: 200, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
201 74 0.37
202 126 0.63
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (201 bp):
TCACAAGAAATCAAAGATTCGAATTTTAGATTCGCAAGAACTTAAAGTTTGTAAGAATTTCAGAT
TTGTAAGAGTTTCAGTTTCACAAAAATGAAAGATTCGCAAAAACTTTAGATTTGTAAGAATTTCA
TATTCGAAAGAAATTTAGTTTCATAAGAATTTTTAGATTCACAAGAAATTCAATTTCGTCATTGT
AAAGAC
Found at i:17733215 original size:17 final size:17
Alignment explanation
Indices: 17733195--17733237 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
17733185 TCATATTCGA
* *
17733195 AAGAAATTTAGTTTCAT
1 AAGAAATTTAGATTCAC
*
17733212 AAGAATTTTTAGATTCAC
1 AAGAA-ATTTAGATTCAC
17733230 AAGAAATT
1 AAGAAATT
17733238 CAATTTCGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (17 bp):
AAGAAATTTAGATTCAC
Found at i:17733508 original size:46 final size:46
Alignment explanation
Indices: 17733315--17733710 Score: 252
Period size: 45 Copynumber: 8.8 Consensus size: 46
17733305 TTGTTAGTTA
* * *
17733315 TTCACATCCAAAATTT-AAAGAATT-TCATTCAAAAAAATTT-AAGGA
1 TTCACATCCAAAATTTCAAAG-ATTCTCATT-AAAAAACTTTCATGGT
* * *
17733360 TTCACAT-CAAAATGTCAAAGATTCACATTCAAAAAA-TTT-AT-AT
1 TTCACATCCAAAATTTCAAAGATTCTCATT-AAAAAACTTTCATGGT
* * ** * *
17733403 ATTCACATCCAAAGTTTCAAAAATTCTTGTTAAAAAACTTTAAT-AT
1 -TTCACATCCAAAATTTCAAAGATTCTCATTAAAAAACTTTCATGGT
** *
17733449 TTCACAAGCAAAATTTCAAAGATTCTCATATGAAAAA-TTTCATGGT
1 TTCACATCCAAAATTTCAAAGATTCTCAT-TAAAAAACTTTCATGGT
* * *
17733495 TTCACCTCAAAAATTTCAAAGATTCAT-ATTCAAAAAATTTTTCAAT--T
1 TTCACATCCAAAATTTCAAAGATTC-TCATT-AAAAAA-CTTTC-ATGGT
* * * *
17733542 TT-GCATCTAAAATTT--AAGATTCACATTAAAAAAACTTTAAT-GT
1 TTCACATCCAAAATTTCAAAGATTCTCATT-AAAAAACTTTCATGGT
* * * * *
17733585 TTTACAT-CTAAATTTCAAAGGTTCTCATTCAAAAACTTT-ATGAT
1 TTCACATCCAAAATTTCAAAGATTCTCATTAAAAAACTTTCATGGT
* ** * * *
17733629 TTCACATCCAAAATTTCAAACATTCTCATTTGAAAATTTTTAGGGT
1 TTCACATCCAAAATTTCAAAGATTCTCATTAAAAAACTTTCATGGT
* * *
17733675 TTCACATCCAAAATTTCAAAGTTTCACATCAAAAAA
1 TTCACATCCAAAATTTCAAAGATTCTCATTAAAAAA
17733711 TTTTAAGGAT
Statistics
Matches: 276, Mismatches: 54, Indels: 41
0.74 0.15 0.11
Matches are distributed among these distances:
42 2 0.01
43 14 0.05
44 62 0.22
45 106 0.38
46 82 0.30
47 4 0.01
48 4 0.01
49 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (46 bp):
TTCACATCCAAAATTTCAAAGATTCTCATTAAAAAACTTTCATGGT
Found at i:17733520 original size:22 final size:22
Alignment explanation
Indices: 17733347--17733530 Score: 65
Period size: 22 Copynumber: 8.2 Consensus size: 22
17733337 TTTCATTCAA
*
17733347 AAAAATTT-AAGGATTCACATC
1 AAAAATTTCAAAGATTCACATC
*
17733368 -AAAATGTCAAAGATTCACATTC
1 AAAAATTTCAAAGATTCACA-TC
* *
17733390 AAAAAATTT-ATATATTCACATC
1 -AAAAATTTCAAAGATTCACATC
* * * *** *
17733412 CAAAGTTTCAAAAATTCTTGTTA
1 AAAAATTTCAAAGATTC-ACATC
* *
17733435 AAAAACTTT-AATA-TTTCACAAGC
1 AAAAA-TTTCAA-AGATTCAC-ATC
* *
17733458 -AAAATTTCAAAGATTCTCATATG
1 AAAAATTTCAAAGA-T-TCACATC
** * *
17733481 AAAAATTTCATGGTTTCACCTC
1 AAAAATTTCAAAGATTCACATC
*
17733503 AAAAATTTCAAAGATTCATATTC
1 AAAAATTTCAAAGATTCACA-TC
17733526 AAAAA
1 AAAAA
17733531 ATTTTTCAAT
Statistics
Matches: 112, Mismatches: 36, Indels: 28
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.05
21 20 0.18
22 35 0.31
23 28 0.25
24 23 0.21
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.33
Consensus pattern (22 bp):
AAAAATTTCAAAGATTCACATC
Found at i:17733633 original size:180 final size:179
Alignment explanation
Indices: 17733377--17733714 Score: 439
Period size: 180 Copynumber: 1.9 Consensus size: 179
17733367 CAAAATGTCA
* **
17733377 AAGATTCACATTCAAAAAATTTATATATTCACATCCAAAGTTTCAAAAATTCTTGTTAAAAAACT
1 AAGATTCACATTAAAAAAATTTATATATTCACATCCAAAGTTTCAAAAATTCTCATTAAAAAACT
* * * *
17733442 TTAATATTTCACAAGCAAAATTTCAAAGATTCTCATATGAAAAATTTCATGGTTTCACCTCAAAA
66 TTAATATTTCACAACCAAAATTTCAAACATTCTCATATGAAAAATTTCAGGGTTTCACATCAAAA
*
17733507 ATTTCAAAGATTCATATTCAAAAAATTTTTCAATTTTGCATCTAAAATTT
131 ATTTCAAAGATTCACA-TCAAAAAATTTTTCAATTTTGCATCTAAAATTT
* * * ** *
17733557 AAGATTCACATTAAAAAAACTTTA-ATGTTTTACATCTAAA-TTTCAAAGGTTCTCATTCAAAAA
1 AAGATTCACATTAAAAAAA-TTTATAT-ATTCACATCCAAAGTTTCAAAAATTCTCATTAAAAAA
* * * * *
17733620 CTTT-ATGATTTCACATCCAAAATTTCAAACATTCTCATTTGAAAATTTTTAGGGTTTCACATCC
64 CTTTAAT-ATTTCACAACCAAAATTTCAAACATTCTCATATGAAAAATTTCAGGGTTTCACATCA
*
17733684 AAAATTTCAAAGTTTCACATCAAAAAATTTT
128 AAAATTTCAAAGATTCACATCAAAAAATTTT
17733715 AAGGATTATG
Statistics
Matches: 135, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
179 14 0.10
180 107 0.79
181 14 0.10
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (179 bp):
AAGATTCACATTAAAAAAATTTATATATTCACATCCAAAGTTTCAAAAATTCTCATTAAAAAACT
TTAATATTTCACAACCAAAATTTCAAACATTCTCATATGAAAAATTTCAGGGTTTCACATCAAAA
ATTTCAAAGATTCACATCAAAAAATTTTTCAATTTTGCATCTAAAATTT
Found at i:17733701 original size:22 final size:22
Alignment explanation
Indices: 17733628--17733709 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
17733618 AACTTTATGA
*
17733628 TTTCACATCCAAAATTTCAAAC
1 TTTCACATCCAAAATTTCAAAG
* * ** * **
17733650 ATTCTCATTTGAAAATTTTTAGGG
1 TTTCACA-TCCAAAA-TTTCAAAG
17733674 TTTCACATCCAAAATTTCAAAG
1 TTTCACATCCAAAATTTCAAAG
*
17733696 TTTCACATCAAAAA
1 TTTCACATCCAAAA
17733710 ATTTTAAGGA
Statistics
Matches: 42, Mismatches: 16, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
22 23 0.55
23 10 0.24
24 9 0.21
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (22 bp):
TTTCACATCCAAAATTTCAAAG
Found at i:17736036 original size:14 final size:15
Alignment explanation
Indices: 17736012--17736040 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17736002 TTGGCTTACA
17736012 AAAAAATTTTCAAAC
1 AAAAAATTTTCAAAC
17736027 AAAAAA-TTTCAAAC
1 AAAAAATTTTCAAAC
17736041 TTCATTGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAAATTTTCAAAC
Found at i:17736336 original size:20 final size:19
Alignment explanation
Indices: 17736302--17736342 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
17736292 TTTTTATTGT
*
17736302 CAAACAATTCAAATAAATG
1 CAAAAAATTCAAATAAATG
*
17736321 CAAAAAATTACAAATACATG
1 CAAAAAATT-CAAATAAATG
17736341 CA
1 CA
17736343 TGCGAATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.59, C:0.17, G:0.05, T:0.20
Consensus pattern (19 bp):
CAAAAAATTCAAATAAATG
Found at i:17737884 original size:20 final size:21
Alignment explanation
Indices: 17737846--17737886 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
17737836 TAATATTATG
* *
17737846 TAATAATATCATGCCATAATA
1 TAATAATATCATACAATAATA
17737867 TAAT-ATATCATACAATAATA
1 TAATAATATCATACAATAATA
17737887 ATATAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (21 bp):
TAATAATATCATACAATAATA
Found at i:17737909 original size:23 final size:24
Alignment explanation
Indices: 17737883--17737935 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
17737873 ATCATACAAT
*
17737883 AATAATA-TAATTA-AAATATGCAA
1 AATAATATTAAATAGAAATATGC-A
*
17737906 AATAA-ATTAAATAGAATTATGCA
1 AATAATATTAAATAGAAATATGCA
17737929 AATAATA
1 AATAATA
17737936 AATAAACCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.04
23 16 0.64
24 8 0.32
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (24 bp):
AATAATATTAAATAGAAATATGCA
Found at i:17739491 original size:18 final size:19
Alignment explanation
Indices: 17739440--17739492 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
17739430 TAATAAAACT
*
17739440 AAAATTAAAGACCAAAAATC
1 AAAATT-AAGAACAAAAATC
17739460 AAAATT-AGAACAAAAATC
1 AAAATTAAGAACAAAAATC
*
17739478 -AAATTAAGATCAAAA
1 AAAATTAAGAACAAAA
17739493 TTAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 19 0.63
20 6 0.20
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAATTAAGAACAAAAATC
Found at i:17739499 original size:18 final size:18
Alignment explanation
Indices: 17739434--17739499 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
17739424 TAAAAATAAT
* *
17739434 AAAACTAAAATTAAAGACC
1 AAAATTAAAATT-AAGAAC
*
17739453 AAAAATCAAAATT-AGAAC
1 -AAAATTAAAATTAAGAAC
* * *
17739471 AAAAATCAAATTAAGATC
1 AAAATTAAAATTAAGAAC
17739489 AAAATTAAAAT
1 AAAATTAAAAT
17739500 ATTTTGGGCT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
17 9 0.25
18 17 0.47
20 10 0.28
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAATTAAAATTAAGAAC
Found at i:17740865 original size:42 final size:42
Alignment explanation
Indices: 17740802--17740881 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
17740792 TTTTTGTTAG
17740802 AACATTGTGTTTGATTGTGTTG-GCAAATTTTAGTGTAGTCGA
1 AACATTGTGTTTGATTGTGTTGTG-AAATTTTAGTGTAGTCGA
* *
17740844 AACATTGTGTTTGATTTTGTTGTGAAATTTTGGTGTAG
1 AACATTGTGTTTGATTGTGTTGTGAAATTTTAGTGTAG
17740882 CCAATTTAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (42 bp):
AACATTGTGTTTGATTGTGTTGTGAAATTTTAGTGTAGTCGA
Found at i:17742175 original size:21 final size:21
Alignment explanation
Indices: 17742110--17742177 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
17742100 AACTTCTCAT
*
17742110 TTTCAACCCTTAGCTCCTTAT-
1 TTTCAACCCTTAGCTTCTT-TG
17742131 TTT-AACCCTTAG--T-TTTG
1 TTTCAACCCTTAGCTTCTTTG
17742148 CCTTTTCAACCCTTAGCTTCTTTG
1 ---TTTCAACCCTTAGCTTCTTTG
17742172 TTTCAA
1 TTTCAA
17742178 TCTCTCTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 16
0.69 0.02 0.29
Matches are distributed among these distances:
16 1 0.03
17 2 0.05
20 12 0.32
21 18 0.47
23 1 0.03
24 4 0.11
ACGTcount: A:0.18, C:0.28, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTCAACCCTTAGCTTCTTTG
Found at i:17747999 original size:22 final size:22
Alignment explanation
Indices: 17747970--17748038 Score: 77
Period size: 23 Copynumber: 3.1 Consensus size: 22
17747960 ATTTGTTATT
*
17747970 AAATAAAATAAATAAATATTTA
1 AAATAAAATAAATAAATATTAA
** *
17747992 ATGTAAAAAATAATAAATATTAA
1 AAATAAAATA-AATAAATATTAA
17748015 AAATAAAATGAAA-AAATATTAA
1 AAATAAAAT-AAATAAATATTAA
17748037 AA
1 AA
17748039 TTATAGTGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 18 0.47
23 19 0.50
24 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (22 bp):
AAATAAAATAAATAAATATTAA
Found at i:17748015 original size:7 final size:7
Alignment explanation
Indices: 17747999--17748110 Score: 59
Period size: 6 Copynumber: 17.3 Consensus size: 7
17747989 TTAATGTAAA
17747999 AAATAAT
1 AAATAAT
*
17748006 AAATATT
1 AAATAAT
17748013 AAA-AAT
1 AAATAAT
*
17748019 AAAATGAAA
1 -AAAT-AAT
*
17748028 AAATATT
1 AAATAAT
*
17748035 AAA-ATT
1 AAATAAT
* *
17748041 ATAGTGAT
1 A-AATAAT
17748049 AA-TAAT
1 AAATAAT
17748055 -AATAAT
1 AAATAAT
17748061 -AATAAT
1 AAATAAT
17748067 -AATAAT
1 AAATAAT
17748073 -AATAAT
1 AAATAAT
17748079 -AATAAT
1 AAATAAT
17748085 -AATAAT
1 AAATAAT
17748091 -AATAAT
1 AAATAAT
17748097 -AATAAT
1 AAATAAT
17748103 -AATAAT
1 AAATAAT
17748109 AA
1 AA
17748111 TAAAATTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 14
0.79 0.08 0.12
Matches are distributed among these distances:
5 1 0.01
6 61 0.69
7 19 0.21
8 6 0.07
9 2 0.02
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (7 bp):
AAATAAT
Found at i:17748021 original size:23 final size:23
Alignment explanation
Indices: 17747970--17748038 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 23
17747960 ATTTGTTATT
* *
17747970 AAATAAAATA-AATAAATATTTA
1 AAATAAAAAATAATAAATATTAA
**
17747992 ATGTAAAAAATAATAAATATTAA
1 AAATAAAAAATAATAAATATTAA
*
17748015 AAAT--AAAATGAAAAAATATTAA
1 AAATAAAAAAT-AATAAATATTAA
17748037 AA
1 AA
17748039 TTATAGTGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 5 0.13
22 20 0.53
23 13 0.34
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (23 bp):
AAATAAAAAATAATAAATATTAA
Found at i:17748055 original size:3 final size:3
Alignment explanation
Indices: 17748047--17748113 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
17748037 AATTATAGTG
17748047 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17748095 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
17748114 AATTTAACAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17748837 original size:18 final size:19
Alignment explanation
Indices: 17748797--17748839 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17748787 TTAATTAAAC
*
17748797 AAAAAATGTAATAAAAATT
1 AAAAAATGTAATAAAAATA
17748816 AAAAAAT-TAATTAAAAA-A
1 AAAAAATGTAA-TAAAAATA
17748834 AAAAAA
1 AAAAAA
17748840 CAAAAGGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAAATGTAATAAAAATA
Found at i:17749035 original size:23 final size:22
Alignment explanation
Indices: 17748999--17749049 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
17748989 GTCGTCAAAC
* * *
17748999 CAGCCAGTGCTACAGACACTTA
1 CAGCCAGCGCTACAAACACCTA
17749021 CAGCCATGCGCTACAAACACCTA
1 CAGCCA-GCGCTACAAACACCTA
*
17749044 CTGCCA
1 CAGCCA
17749050 CCCCCTATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.31, C:0.37, G:0.16, T:0.16
Consensus pattern (22 bp):
CAGCCAGCGCTACAAACACCTA
Found at i:17750454 original size:36 final size:37
Alignment explanation
Indices: 17750414--17750483 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
17750404 CCCAAACCCT
*
17750414 AAAATCTAAAATCTCAAA-CCTCAAAA-CCAAAACTCG
1 AAAATCCAAAATCTCAAACCCT-AAAATCCAAAACTCG
*
17750450 AAAATCCAAAATCTCGAACCCTAAAATCCAAAAC
1 AAAATCCAAAATCTCAAACCCTAAAATCCAAAAC
17750484 CTTAAAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.53, C:0.29, G:0.03, T:0.16
Consensus pattern (37 bp):
AAAATCCAAAATCTCAAACCCTAAAATCCAAAACTCG
Found at i:17750458 original size:15 final size:15
Alignment explanation
Indices: 17750421--17750467 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
17750411 CCTAAAATCT
*
17750421 AAAATCTCAAACCTC-
1 AAAATC-CAAAACTCG
17750436 AAAA-CCAAAACTCG
1 AAAATCCAAAACTCG
17750450 AAAATCCAAAATCTCG
1 AAAATCCAAAA-CTCG
17750466 AA
1 AA
17750468 CCCTAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 10 0.36
16 6 0.21
ACGTcount: A:0.53, C:0.28, G:0.04, T:0.15
Consensus pattern (15 bp):
AAAATCCAAAACTCG
Found at i:17758069 original size:70 final size:70
Alignment explanation
Indices: 17757987--17758138 Score: 277
Period size: 70 Copynumber: 2.2 Consensus size: 70
17757977 TTACGGCTAC
17757987 TGATAAAAAAAAACATAATACTGGAAAAGAAAGAAAAGAGAATGGCACGTCTCAAAGGGCAAGAC
1 TGATAAAAAAAAACATAATACTGGAAAAGAAAGAAAAGAGAATGGCACGTCTCAAAGGGCAAGAC
17758052 TTGAT
66 TTGAT
* * *
17758057 TGATAAAAAAAAACATAATGCTGGAAAAGAAAGAAAGGAGAATGGCATGTCTCAAAGGGCAAGAC
1 TGATAAAAAAAAACATAATACTGGAAAAGAAAGAAAAGAGAATGGCACGTCTCAAAGGGCAAGAC
17758122 TTGAT
66 TTGAT
17758127 TGATAAAAAAAA
1 TGATAAAAAAAA
17758139 TGGTGTTCCC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 79 1.00
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.16
Consensus pattern (70 bp):
TGATAAAAAAAAACATAATACTGGAAAAGAAAGAAAAGAGAATGGCACGTCTCAAAGGGCAAGAC
TTGAT
Found at i:17761391 original size:19 final size:19
Alignment explanation
Indices: 17761367--17761413 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
17761357 ATATTTTACT
*
17761367 TAAAAAAATAAAA-AAAATG
1 TAAAAAAA-AAAAGAAAAAG
17761386 TAAAAAAAAAAAGAAAAAG
1 TAAAAAAAAAAAGAAAAAG
17761405 -AAAAAAAAA
1 TAAAAAAAAA
17761414 GAGATGATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (19 bp):
TAAAAAAAAAAAGAAAAAG
Found at i:17761414 original size:10 final size:10
Alignment explanation
Indices: 17761368--17761415 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
17761358 TATTTTACTT
*
17761368 AAAAAAATAA
1 AAAAAAAGAA
* *
17761378 AAAAAATGTA
1 AAAAAAAGAA
17761388 AAAAAAA-AA
1 AAAAAAAGAA
*
17761397 AGAAAAAGAA
1 AAAAAAAGAA
17761407 AAAAAAAGA
1 AAAAAAAGA
17761416 GATGATTCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.06
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:17762539 original size:36 final size:35
Alignment explanation
Indices: 17762475--17762552 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
17762465 CTTGCGATTT
* **
17762475 AATCCCGATCTCTTTATTTTCTTAACTCGTGGTTC
1 AATCCCAATCTCTTTATCCTCTTAACTCGTGGTTC
* *
17762510 AGTCCCAATCATCTTTATCCTCTTGACTCGTGGTTC
1 AATCCCAATC-TCTTTATCCTCTTAACTCGTGGTTC
17762546 AATCCCA
1 AATCCCA
17762553 GTCTTCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 8 0.22
36 28 0.78
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (35 bp):
AATCCCAATCTCTTTATCCTCTTAACTCGTGGTTC
Found at i:17762995 original size:9 final size:10
Alignment explanation
Indices: 17762968--17762992 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17762958 ATGGTAACGA
17762968 AAAAAATAAC
1 AAAAAATAAC
17762978 AAAAAATAAC
1 AAAAAATAAC
17762988 AAAAA
1 AAAAA
17762993 TAAAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAC
Found at i:17764981 original size:15 final size:15
Alignment explanation
Indices: 17764963--17764993 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17764953 CAAAATCCCG
17764963 AACCCTAAAATTCAA
1 AACCCTAAAATTCAA
*
17764978 AACCTTAAAATTCAA
1 AACCCTAAAATTCAA
17764993 A
1 A
17764994 TCCAAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (15 bp):
AACCCTAAAATTCAA
Found at i:17770514 original size:24 final size:25
Alignment explanation
Indices: 17770487--17770538 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
17770477 GGGTTTAATC
17770487 TAGGGTTT-AGTTTATGGTTTT-GGT
1 TAGGGTTTCAGTTTA-GGTTTTGGGT
*
17770511 TAGGGTTTCATTTTAGGTTTTGGGT
1 TAGGGTTTCAGTTTAGGTTTTGGGT
17770536 TAG
1 TAG
17770539 AATTAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.13, C:0.02, G:0.33, T:0.52
Consensus pattern (25 bp):
TAGGGTTTCAGTTTAGGTTTTGGGT
Found at i:17780924 original size:27 final size:27
Alignment explanation
Indices: 17780883--17780945 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
17780873 AGGTTAGGTA
* *
17780883 GGTTGAGAATTTAGTTTTGAAGGGGCT
1 GGTTGGGAATCTAGTTTTGAAGGGGCT
*
17780910 GGTTGGGAATCTAGTTTTGAAGGGGTT
1 GGTTGGGAATCTAGTTTTGAAGGGGCT
17780937 GGTTGGGAA
1 GGTTGGGAA
17780946 ATTGGCAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.03, G:0.41, T:0.35
Consensus pattern (27 bp):
GGTTGGGAATCTAGTTTTGAAGGGGCT
Found at i:17785040 original size:5 final size:5
Alignment explanation
Indices: 17785024--17785076 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
17785014 TGCATTTAAA
* * * *
17785024 AAAAT AACAT AAAAT AAGAT AAAA- AAAAA AAAAT AACAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
17785073 AAAA
1 AAAA
17785077 AACAGAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:17785058 original size:19 final size:21
Alignment explanation
Indices: 17785024--17785077 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 21
17785014 TGCATTTAAA
* *
17785024 AAAATAACAT-AAAATAAGAT
1 AAAATAAAATAAAAATAACAT
17785044 AAAA-AAAA-AAAAATAACAT
1 AAAATAAAATAAAAATAACAT
17785063 AAAATAAAATAAAAA
1 AAAATAAAATAAAAA
17785078 ACAGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 16 0.55
20 8 0.28
21 5 0.17
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.15
Consensus pattern (21 bp):
AAAATAAAATAAAAATAACAT
Found at i:17785059 original size:24 final size:24
Alignment explanation
Indices: 17785021--17785078 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
17785011 AATTGCATTT
* * *
17785021 AAAAAAATAACATAAAATAAGATA
1 AAAAAAAAAAAATAAAATAAAATA
*
17785045 AAAAAAAAAAAATAACATAAAATA
1 AAAAAAAAAAAATAAAATAAAATA
*
17785069 AAATAAAAAA
1 AAAAAAAAAA
17785079 CAGAGAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.81, C:0.03, G:0.02, T:0.14
Consensus pattern (24 bp):
AAAAAAAAAAAATAAAATAAAATA
Found at i:17785061 original size:29 final size:30
Alignment explanation
Indices: 17785021--17785092 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
17785011 AATTGCATTT
*
17785021 AAAAAAATAACATAAAATAAGATAAAAAA-
1 AAAAAAATAACATAAAATAAAATAAAAAAC
17785050 AAAAAAATAACATAAAATAAAATAAAAAAC
1 AAAAAAATAACATAAAATAAAATAAAAAAC
*
17785080 AGAGAAAATAACA
1 A-AAAAAATAACA
17785093 AGAAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 28 0.72
30 1 0.03
31 10 0.26
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (30 bp):
AAAAAAATAACATAAAATAAAATAAAAAAC
Found at i:17785100 original size:29 final size:27
Alignment explanation
Indices: 17785021--17785103 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 27
17785011 AATTGCATTT
17785021 AAAAAAATAACATAAAATAAGATAAAAAA
1 AAAAAAATAACATAAAA-AA-ATAAAAAA
17785050 AAAAAAATAACATAAAATAAAATAAAAAA
1 AAAAAAATAACAT-AAA-AAAATAAAAAA
*
17785079 CAGAGAAAATAACA-AGAAAAAATAA
1 -A-AAAAAATAACATA-AAAAAATAA
17785104 CATATAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
29 29 0.60
30 8 0.17
31 11 0.23
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (27 bp):
AAAAAAATAACATAAAAAAATAAAAAA
Found at i:17811087 original size:27 final size:24
Alignment explanation
Indices: 17811056--17811130 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
17811046 GTTAGGAATT
17811056 AGGTTAGGGTTTTGATTTTGGTGTTC
1 AGGTTAGGGTTTTGA-TTTGG-GTTC
*
17811082 GAGGTT-TGGTTTGTGATTTGGGTTC
1 -AGGTTAGGGTTT-TGATTTGGGTTC
* * *
17811107 AGTTTAGGGGTTTGGTTTAGGGTT
1 AGGTTAGGGTTTTGATTT-GGGTT
17811131 TAAAGGTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
24 9 0.22
25 13 0.32
26 10 0.25
27 8 0.20
ACGTcount: A:0.11, C:0.03, G:0.39, T:0.48
Consensus pattern (24 bp):
AGGTTAGGGTTTTGATTTGGGTTC
Found at i:17811138 original size:20 final size:20
Alignment explanation
Indices: 17811108--17811548 Score: 334
Period size: 20 Copynumber: 22.2 Consensus size: 20
17811098 TTTGGGTTCA
*
17811108 GTTTAGGGGTTTGGTTTAGG
1 GTTTAAGGGTTTGGTTTAGG
* *
17811128 GTTTAAAGGTTTGGCTT-GG
1 GTTTAAGGGTTTGGTTTAGG
* * *
17811147 GTTTAAGGAATTTGATTTGGG
1 GTTTAAGG-GTTTGGTTTAGG
***
17811168 GTTTAA-GGTGTCAATTTA-G
1 GTTTAAGGGT-TTGGTTTAGG
* *
17811187 GTTT-TGGGACTTAGG-TTAGG
1 GTTTAAGGG--TTTGGTTTAGG
17811207 GTTT-AGCGGTTTGGTTTAGG
1 GTTTAAG-GGTTTGGTTTAGG
*
17811227 GTTTAAGGGTTTGGTTT-TG
1 GTTTAAGGGTTTGGTTTAGG
17811246 GTTTAAGGGATTTGGTTT-GG
1 GTTTAAGGG-TTTGGTTTAGG
*
17811266 GTCTAAGGGTTTTGGTTTAGG
1 GTTTAAGGG-TTTGGTTTAGG
*
17811287 GTTTAAGGGTTTGGTTT-TG
1 GTTTAAGGGTTTGGTTTAGG
* * *
17811306 GTTTAAGGTTTTAGTTT-CG
1 GTTTAAGGGTTTGGTTTAGG
* * *
17811325 GTTTAAGGGTTTGCTTTCGA
1 GTTTAAGGGTTTGGTTTAGG
* * * *
17811345 GTCTAAAGGTTTCAGTTTGGG
1 GTTTAAGGGTTT-GGTTTAGG
* *
17811366 GTTGAAGGGTTTGGTTT-TG
1 GTTTAAGGGTTTGGTTTAGG
17811385 GTTTAAGGGTTTGGTTT-GG
1 GTTTAAGGGTTTGGTTTAGG
* *
17811404 TGTCTAAAGGTTTGGTTTAGG
1 -GTTTAAGGGTTTGGTTTAGG
** *
17811425 GTCCAAGGGTTTGGTTTAAG
1 GTTTAAGGGTTTGGTTTAGG
** * *
17811445 GTCAAAGGTTTTGGTTTGGG
1 GTTTAAGGGTTTGGTTTAGG
* *
17811465 GTTTAAGAGTTTGGTTTAAG
1 GTTTAAGGGTTTGGTTTAGG
17811485 GTTTAAGGGTTTTGG-TTATGG
1 GTTTAAGGG-TTTGGTTTA-GG
17811506 GTTTAAGGGTTTGGTTT-GG
1 GTTTAAGGGTTTGGTTTAGG
* *
17811525 GTTTAAGGATTTGGTTTGGG
1 GTTTAAGGGTTTGGTTTAGG
17811545 GTTT
1 GTTT
17811549 GGCTTAGGGC
Statistics
Matches: 339, Mismatches: 62, Indels: 40
0.77 0.14 0.09
Matches are distributed among these distances:
19 101 0.30
20 183 0.54
21 55 0.16
ACGTcount: A:0.15, C:0.03, G:0.37, T:0.45
Consensus pattern (20 bp):
GTTTAAGGGTTTGGTTTAGG
Found at i:17811229 original size:26 final size:26
Alignment explanation
Indices: 17811204--17811316 Score: 82
Period size: 26 Copynumber: 4.0 Consensus size: 26
17811194 GACTTAGGTT
17811204 AGGGTTTAGCGGTTTGGTTTAGGGTTTA
1 AGGGTTT-G-GGTTTGGTTTAGGGTTTA
* *
17811232 AGGGTTTGGTTTTGGTTTAAGGGATTTGGTT
1 AGGGTTTGGGTTTGGTTT-AGGG--TT--TA
* *
17811263 TGGGTCTAAGGGTTTTGGTTTAGGGTTTA
1 AGGGT-T-TGGGTTT-GGTTTAGGGTTTA
* *
17811292 AGGGTTTGGTTTTGGTTTAAGGTTT
1 AGGGTTTGGGTTTGGTTTAGGGTTT
17811317 TAGTTTCGGT
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
26 20 0.30
27 10 0.15
28 8 0.12
29 7 0.10
31 7 0.10
32 1 0.01
33 9 0.13
34 5 0.07
ACGTcount: A:0.13, C:0.02, G:0.38, T:0.47
Consensus pattern (26 bp):
AGGGTTTGGGTTTGGTTTAGGGTTTA
Found at i:17811235 original size:8 final size:7
Alignment explanation
Indices: 17811202--17811298 Score: 50
Period size: 8 Copynumber: 14.3 Consensus size: 7
17811192 GGGACTTAGG
17811202 TTAGGGT
1 TTAGGGT
17811209 TTAGCGGT
1 TTAG-GGT
17811217 TT--GGT
1 TTAGGGT
17811222 TTAGGGT
1 TTAGGGT
17811229 TTAAGGGT
1 TT-AGGGT
17811237 TT--GGT
1 TTAGGGT
*
17811242 TT-TGGT
1 TTAGGGT
17811248 TTAAGGGAT
1 TT-AGGG-T
17811257 TT--GGT
1 TTAGGGT
17811262 TT-GGGT
1 TTAGGGT
*
17811268 CTAAGGGT
1 -TTAGGGT
*
17811276 TT-TGGT
1 TTAGGGT
17811282 TTAGGGT
1 TTAGGGT
17811289 TTAAGGGT
1 TT-AGGGT
17811297 TT
1 TT
17811299 GGTTTTGGTT
Statistics
Matches: 72, Mismatches: 5, Indels: 25
0.71 0.05 0.25
Matches are distributed among these distances:
5 13 0.18
6 15 0.21
7 16 0.22
8 25 0.35
9 3 0.04
ACGTcount: A:0.13, C:0.02, G:0.38, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:17813326 original size:143 final size:143
Alignment explanation
Indices: 17813023--17813460 Score: 418
Period size: 144 Copynumber: 3.0 Consensus size: 143
17813013 ATTCTTGTGA
* * * * ** *
17813023 TTTTAATACATCAAAATTCATAAAATAATATT-TAATCATGATCTGGAGCATTTCATGAAAAACC
1 TTTTAATACATCAAAATTCATAAAATAA-ATTCAAAACATGATTTGGAGCTTTTCACAAAAAACT
* * * * * * * * *
17813087 AACTTTGGAAAGGTTAAATTAAAAAATATCACTAAAGGGCATTTTGATCATTTCAACCTTTTCGA
65 AACATTGAAAAGGTCAAATTAGAAAATACCATTAAAGGGCATTTTGATAATTTCAAACTTTTTGA
** *
17813152 GGTGTTATCAGGGC
130 GGTGCAATCAGGGT
* * *
17813166 TTTTAATGCATCAAAATTCATAAAATAAATTCAAAACATGATTTAGAGCTTTTCACAAAAAACTG
1 TTTTAATACATCAAAATTCATAAAATAAATTCAAAACATGATTTGGAGCTTTTCACAAAAAACTA
* * *
17813231 ACATTAAAAAGGTCAAATTATGAAAATACCATTAGAA-GGCATTTTGTTAATTTCAAACTTTTTA
66 ACATTGAAAAGGTCAAATTA-GAAAATACCATTA-AAGGGCATTTTGATAATTTCAAACTTTTTG
* *
17813295 AGGTGCCATCAAGGT
129 AGGTGCAATCAGGGT
* * * * *
17813310 TTTTAATATATC-AAATTCATGAAAT-AATATCAAAGCATGATTTGGAGCATTTTTACAAAAAAT
1 TTTTAATACATCAAAATTCATAAAATAAAT-TCAAAACATGATTTGGAGC-TTTTCACAAAAAAC
* * * * * * *
17813373 TAACCTCGAGAAGATCAAATTACGAAAATACC-TCTAAAGGGTATTTTAATAATTTTAAACTTTT
64 TAACATTGAAAAGGTCAAATTA-GAAAATACCAT-TAAAGGGCATTTTGATAATTTCAAACTTTT
*
17813437 TGATGTGCAATCAGGGT
127 TGAGGTGCAATCAGGGT
17813454 TTTTAAT
1 TTTTAAT
17813461 GCATTAAAGT
Statistics
Matches: 240, Mismatches: 48, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
142 6 0.03
143 99 0.41
144 133 0.55
145 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (143 bp):
TTTTAATACATCAAAATTCATAAAATAAATTCAAAACATGATTTGGAGCTTTTCACAAAAAACTA
ACATTGAAAAGGTCAAATTAGAAAATACCATTAAAGGGCATTTTGATAATTTCAAACTTTTTGAG
GTGCAATCAGGGT
Found at i:17813368 original size:144 final size:144
Alignment explanation
Indices: 17813023--17813599 Score: 445
Period size: 143 Copynumber: 4.0 Consensus size: 144
17813013 ATTCTTGTGA
** * * ** *
17813023 TTTTAATACATCAAAATTCATAAAATAATATTTAATCATGATCTGGAGCA-TTTCATGAAAAACC
1 TTTTAATACATCAAAATTCATAAAATAATATCAAAGCATGATTTGGAGCATTTTCACAAAAAACT
* * * * * * * * *
17813087 AACTTTGGAAAGGTTAAATTAAAAAATATCACTAAAGGGCATTTTGATCATTTCAACCTTTTCGA
66 AACATTGAAAAGGTCAAATTAGAAAATACCATTAAAGGGCATTTTGATAATTTCAAACTTTTTGA
** *
17813152 GGTGTTATCAGGGC
131 GGTGCAATCAGGGT
* * *
17813166 TTTTAATGCATCAAAATTCATAAAATAA-ATTCAAAACATGATTTAGAGC-TTTTCACAAAAAAC
1 TTTTAATACATCAAAATTCATAAAATAATA-TCAAAGCATGATTTGGAGCATTTTCACAAAAAAC
* * *
17813229 TGACATTAAAAAGGTCAAATTATGAAAATACCATTAGAA-GGCATTTTGTTAATTTCAAACTTTT
65 TAACATTGAAAAGGTCAAATTA-GAAAATACCATTA-AAGGGCATTTTGATAATTTCAAACTTTT
* * *
17813293 TAAGGTGCCATCAAGGT
128 TGAGGTGCAATCAGGGT
* * * *
17813310 TTTTAATATATC-AAATTCATGAAATAATATCAAAGCATGATTTGGAGCATTTTTACAAAAAATT
1 TTTTAATACATCAAAATTCATAAAATAATATCAAAGCATGATTTGGAGCATTTTCACAAAAAACT
* * * * * * *
17813374 AACCTCGAGAAGATCAAATTACGAAAATACC-TCTAAAGGGTATTTTAATAATTTTAAACTTTTT
66 AACATTGAAAAGGTCAAATTA-GAAAATACCAT-TAAAGGGCATTTTGATAATTTCAAACTTTTT
*
17813438 GATGTGCAATCAGGGT
129 GAGGTGCAATCAGGGT
* * * * * * * * ** *
17813454 TTTTAATGCATTAAAGTTTATGAAATAATATCAAAGTATAATATAAAGC-TTTTCATAAAAAA--
1 TTTTAATACATCAAAATTCATAAAATAATATCAAAGCATGATTTGGAGCATTTTCACAAAAAACT
** * * * * * * * **
17813516 ATGATCTCAAAAGATCAAATTACAAAAATATCC-TTAAAGGGTATTTTGGTCATTTTATTCTTTT
66 AACAT-TGAAAAGGTCAAATTA-GAAAATA-CCATTAAAGGGCATTTTGATAATTTCAAACTTTT
*
17813580 TGAGGTGCAATCATGGT
128 TGAGGTGCAATCAGGGT
17813597 TTT
1 TTT
17813600 CATTGCCTCA
Statistics
Matches: 349, Mismatches: 74, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
142 3 0.01
143 165 0.47
144 150 0.43
145 31 0.09
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (144 bp):
TTTTAATACATCAAAATTCATAAAATAATATCAAAGCATGATTTGGAGCATTTTCACAAAAAACT
AACATTGAAAAGGTCAAATTAGAAAATACCATTAAAGGGCATTTTGATAATTTCAAACTTTTTGA
GGTGCAATCAGGGT
Found at i:17813561 original size:143 final size:140
Alignment explanation
Indices: 17813102--17813599 Score: 446
Period size: 144 Copynumber: 3.5 Consensus size: 140
17813092 TGGAAAGGTT
* * * **
17813102 AAATTA-AAAAATATCAC-TAAAGGGCATTTTGATCATTTCAACCTTTTCGAGGTGTTATCAGGG
1 AAATTACAAAAATA-C-CTTAAAGGGCATTTTGATAATTTCAAACTTTTTGAGGTGCAATCAGGG
* * * *
17813165 CTTTTAATGCATCAAAATTCATAAAATAA-ATTCAAAACATGATTTAGAGCTTTTCACAAAAAAC
64 TTTTTAATGCATC-AAATTCATGAAATAATA-TCAAAGCATGATTTAGAGCTTTTCACAAAAAAA
* *
17813229 TGACATTAAAAAGGTC
127 TGAC--TCAAAAGATC
** * * * *
17813245 AAATTATGAAAATACCATTAGAA-GGCATTTTGTTAATTTCAAACTTTTTAAGGTGCCATCAAGG
1 AAATTACAAAAATACC-TTA-AAGGGCATTTTGATAATTTCAAACTTTTTGAGGTGCAATCAGGG
** * * *
17813309 TTTTTAATATATCAAATTCATGAAATAATATCAAAGCATGATTTGGAGCATTTTTACAAAAAATT
64 TTTTTAATGCATCAAATTCATGAAATAATATCAAAGCATGATTTAGAGC-TTTTCACAAAAAAAT
* *
17813374 AACCTCGAGAAGATC
128 GA-CTC-AAAAGATC
* * * * *
17813389 AAATTACGAAAATACCTCTAAAGGGTATTTTAATAATTTTAAACTTTTTGATGTGCAATCAGGGT
1 AAATTACAAAAATACCT-TAAAGGGCATTTTGATAATTTCAAACTTTTTGAGGTGCAATCAGGGT
* * * * * * *
17813454 TTTTAATGCATTAAAGTTTATGAAATAATATCAAAGTATAATATAAAGCTTTTCATAAAAAAATG
65 TTTTAATGCATCAAA-TTCATGAAATAATATCAAAGCATGATTTAGAGCTTTTCACAAAAAAATG
17813519 ATCTCAAAAGATC
129 A-CTCAAAAGATC
* * * * ** *
17813532 AAATTACAAAAATATCCTTAAAGGGTATTTTGGTCATTTTATTCTTTTTGAGGTGCAATCATGGT
1 AAATTACAAAAATA-CCTTAAAGGGCATTTTGATAATTTCAAACTTTTTGAGGTGCAATCAGGGT
17813597 TTT
65 TTT
17813600 CATTGCCTCA
Statistics
Matches: 290, Mismatches: 53, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
142 1 0.00
143 105 0.36
144 154 0.53
145 30 0.10
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (140 bp):
AAATTACAAAAATACCTTAAAGGGCATTTTGATAATTTCAAACTTTTTGAGGTGCAATCAGGGTT
TTTAATGCATCAAATTCATGAAATAATATCAAAGCATGATTTAGAGCTTTTCACAAAAAAATGAC
TCAAAAGATC
Found at i:17820150 original size:1 final size:1
Alignment explanation
Indices: 17820114--17820141 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
17820104 TTTTTTTTTT
17820114 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
17820142 AGGAGGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:17820697 original size:39 final size:39
Alignment explanation
Indices: 17820653--17820736 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
17820643 AATTACATAT
*
17820653 TTGAATACATATGAATGAGATACAAAGAATAATATACAA
1 TTGAATACATACGAATGAGATACAAAGAATAATATACAA
* *
17820692 TTGAATATATACGAATGAGATACAAAGAATAGTATACAA
1 TTGAATACATACGAATGAGATACAAAGAATAATATACAA
*
17820731 ATGAAT
1 TTGAAT
17820737 TTAAATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.26
Consensus pattern (39 bp):
TTGAATACATACGAATGAGATACAAAGAATAATATACAA
Found at i:17827040 original size:17 final size:17
Alignment explanation
Indices: 17827018--17827089 Score: 77
Period size: 17 Copynumber: 4.6 Consensus size: 17
17827008 GACTTAGGTT
17827018 GGTTTGGTTTAGCTAGA
1 GGTTTGGTTTAGCTAGA
17827035 GGTTT-GTTT---TAG-
1 GGTTTGGTTTAGCTAGA
*
17827047 GG-TTGGTTTTAGGTAGA
1 GGTTTGG-TTTAGCTAGA
17827064 GGTTTGGTTTAGCTAGA
1 GGTTTGGTTTAGCTAGA
17827081 GG-TTGGTTT
1 GGTTTGGTTT
17827090 GGTTTGGGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
11 2 0.04
12 3 0.06
13 6 0.13
16 14 0.30
17 18 0.38
18 4 0.09
ACGTcount: A:0.14, C:0.03, G:0.38, T:0.46
Consensus pattern (17 bp):
GGTTTGGTTTAGCTAGA
Found at i:17827063 original size:29 final size:28
Alignment explanation
Indices: 17827021--17827075 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
17827011 TTAGGTTGGT
*
17827021 TTGGTTTAGCTAGAGGTTTGTTTTAGGG
1 TTGGTTTAGCTAGAGGTTTGGTTTAGGG
*
17827049 TTGGTTTTAGGTAGAGGTTTGGTTTAG
1 TTGG-TTTAGCTAGAGGTTTGGTTTAG
17827076 CTAGAGGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.15, C:0.02, G:0.36, T:0.47
Consensus pattern (28 bp):
TTGGTTTAGCTAGAGGTTTGGTTTAGGG
Found at i:17827141 original size:23 final size:23
Alignment explanation
Indices: 17827085--17827149 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
17827075 GCTAGAGGTT
*
17827085 GGTTT-GGTTT-GGG-TTAGTTT
1 GGTTTAGGTTTGGGGTTTAGTTA
*
17827105 GATTTGAGGCTTTGGGGTTTAGTTA
1 GGTTT-AGG-TTTGGGGTTTAGTTA
17827130 GGTTTAGGTTTGGGGTTTAG
1 GGTTTAGGTTTGGGGTTTAG
17827150 GGTTTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.11
22 2 0.05
23 15 0.41
24 6 0.16
25 10 0.27
ACGTcount: A:0.11, C:0.02, G:0.40, T:0.48
Consensus pattern (23 bp):
GGTTTAGGTTTGGGGTTTAGTTA
Found at i:17827212 original size:20 final size:20
Alignment explanation
Indices: 17827169--17827235 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
17827159 TAGGGTTTGT
** *
17827169 GGTTTGAGTTTGGAATTTAG
1 GGTTTGAGTTTGGGGTCTAG
*
17827189 GGTTTGAGTTTGGGGTCTAA
1 GGTTTGAGTTTGGGGTCTAG
*
17827209 GGTTTGAGTTTAGGGTCTAG
1 GGTTTGAGTTTGGGGTCTAG
17827229 GGTTTGA
1 GGTTTGA
17827236 ATGGAGTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.03, G:0.39, T:0.42
Consensus pattern (20 bp):
GGTTTGAGTTTGGGGTCTAG
Found at i:17828376 original size:16 final size:17
Alignment explanation
Indices: 17828347--17828381 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
17828337 GAATAGTTTC
17828347 ATGGCTTAAAAAAAATA
1 ATGGCTTAAAAAAAATA
17828364 ATGGCTT-AAAAAAATA
1 ATGGCTTAAAAAAAATA
17828380 AT
1 AT
17828382 ATAAATAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (17 bp):
ATGGCTTAAAAAAAATA
Found at i:17828996 original size:3 final size:3
Alignment explanation
Indices: 17828990--17829055 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
17828980 TACTTTAAAA
* * *
17828990 AAT AAT AAT AAT AAT AAT AAT AAT AAG AGT AAAT AAT AA- ATAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT AAT
17829036 AAT AAT AAT -AT AAAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AA
17829056 AAAAATCCCT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 3 0.06
3 45 0.87
4 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17829407 original size:28 final size:28
Alignment explanation
Indices: 17829376--17829440 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
17829366 CCTAAAATTG
*
17829376 AAATCTTAAAATCAAAACCCCAATGTTA
1 AAATCCTAAAATCAAAACCCCAATGTTA
*
17829404 AAATCCTAAAATCGAAACCCCAATGTTA
1 AAATCCTAAAATCAAAACCCCAATGTTA
*
17829432 AAACCCTAA
1 AAATCCTAA
17829441 TTAAAATCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.22
Consensus pattern (28 bp):
AAATCCTAAAATCAAAACCCCAATGTTA
Found at i:17829448 original size:68 final size:67
Alignment explanation
Indices: 17829322--17829460 Score: 154
Period size: 68 Copynumber: 2.0 Consensus size: 67
17829312 TGAAAACCTG
** ** * *
17829322 AAACCCCAATGTTAAAATCCTAAATGAAACCTTAAAATCAATGCCCTAAAATTGAAATCTTAAAA
1 AAACCCCAATGTTAAAATCCTAAATGAAACCCCAAAATCAAAACCCT-AAATTAAAATCCTAAAA
17829387 TCA
65 TCA
** *
17829390 AAACCCCAATGTTAAAATCCTAAAATCGAAACCCCAATGTTAAAACCCT-AATTAAAATCCTAAA
1 AAACCCCAATGTTAAAATCCT-AAAT-GAAACCCCAAAATCAAAACCCTAAATTAAAATCCTAAA
*
17829454 ATTA
64 ATCA
17829458 AAA
1 AAA
17829461 TCCTAAAACC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
68 40 0.68
69 4 0.07
70 15 0.25
ACGTcount: A:0.50, C:0.22, G:0.05, T:0.24
Consensus pattern (67 bp):
AAACCCCAATGTTAAAATCCTAAATGAAACCCCAAAATCAAAACCCTAAATTAAAATCCTAAAAT
CA
Found at i:17829456 original size:14 final size:14
Alignment explanation
Indices: 17829366--17829468 Score: 66
Period size: 14 Copynumber: 7.5 Consensus size: 14
17829356 AAATCAATGC
*
17829366 CCTAAAATTGAAAT
1 CCTAAAATTAAAAT
* * *
17829380 CTTAAAATCAAAAC
1 CCTAAAATTAAAAT
* **
17829394 CCCAATGTTAAAAT
1 CCTAAAATTAAAAT
** *
17829408 CCTAAAATCGAAAC
1 CCTAAAATTAAAAT
* ** *
17829422 CCCAATGTTAAAAC
1 CCTAAAATTAAAAT
17829436 CCT--AATTAAAAT
1 CCTAAAATTAAAAT
17829448 CCTAAAATTAAAAT
1 CCTAAAATTAAAAT
17829462 CCTAAAA
1 CCTAAAA
17829469 CCCTAAAGCA
Statistics
Matches: 62, Mismatches: 25, Indels: 4
0.68 0.27 0.04
Matches are distributed among these distances:
12 9 0.15
14 53 0.85
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.24
Consensus pattern (14 bp):
CCTAAAATTAAAAT
Found at i:17829723 original size:3 final size:3
Alignment explanation
Indices: 17829715--17829763 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
17829705 TCATAATTTA
*
17829715 AAT AAT AAT AA- AAT TA- AAT AAAT AATT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT -AAT AA-T AAT AAT AAT AAT AAT AAT
17829759 AAT AA
1 AAT AA
17829764 GATTTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 5 0.13
3 28 0.72
4 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17829763 original size:24 final size:20
Alignment explanation
Indices: 17829713--17829759 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
17829703 TTTCATAATT
*
17829713 TAAATAATAATAAAATTAAA
1 TAAATAATAATAAAATAAAA
17829733 TAAATAATTAATAATAATAATAA
1 TAAATAA-TAATAA-AATAA-AA
17829756 TAAA
1 TAAA
17829760 ATAAGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 4 0.17
23 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATAATAATAAAATAAAA
Found at i:17837452 original size:3 final size:3
Alignment explanation
Indices: 17837444--17837552 Score: 119
Period size: 3 Copynumber: 36.3 Consensus size: 3
17837434 CATGTCATAA
* * * *
17837444 ACT ACT ACT ACT ACC ACT ACT ACT ACT ACT ATT ACC ACC ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
* * * * * * *
17837492 GCT ACT ACC ACC ACC ACC ACA ACC ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
17837540 ACT ACT ACT ACT A
1 ACT ACT ACT ACT A
17837553 TTATTATTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.34, C:0.39, G:0.01, T:0.26
Consensus pattern (3 bp):
ACT
Found at i:17837557 original size:3 final size:3
Alignment explanation
Indices: 17837551--17837587 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
17837541 CTACTACTAC
17837551 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17837588 GATGCAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17846797 original size:13 final size:13
Alignment explanation
Indices: 17846779--17846807 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17846769 ATTCTTGATA
17846779 TGAGAAATGGATG
1 TGAGAAATGGATG
17846792 TGAGAAATGGATG
1 TGAGAAATGGATG
17846805 TGA
1 TGA
17846808 TTGGGCCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (13 bp):
TGAGAAATGGATG
Found at i:17848811 original size:35 final size:35
Alignment explanation
Indices: 17848766--17849211 Score: 142
Period size: 35 Copynumber: 12.5 Consensus size: 35
17848756 GGTTATCCCC
* *
17848766 GTCATCTTTATTTTTGGACCTATGGTGTTGTTTCG
1 GTCATCTTTATTTTTTGACCTATGGTGTTGTTCCG
* * * *
17848801 GTCATTTTTATTTTTCTGATC-ATGGTGTTGTCCCA
1 GTCATCTTTATTTTT-TGACCTATGGTGTTGTTCCG
* *
17848836 GTCATCTTTATTTTTTCAGCTAATGGTGTTG-TCCTG
1 GTCATCTTTATTTTTTGACCT-ATGGTGTTGTTCC-G
* * * * ** *
17848872 ATCATTTTTATTTTTTTTGACCTACGGTATT-AACTG
1 GTCATCTTTA--TTTTTTGACCTATGGTGTTGTTCCG
* * * * *
17848908 GATCATCTTTGTTTTCTCGA-CTGTTGGTGTTGTCCCA
1 G-TCATCTTTATTTT-TTGACCT-ATGGTGTTGTTCCG
* * **
17848945 GTCATTTTTACTTTTTGA-CT-TGCAGTGTTGTTCTA
1 GTCATCTTTATTTTTTGACCTATG--GTGTTGTTCCG
* * ** * *
17848980 ATCATATTTATTTTCTTGACCTACAGTGTTGTCCCA
1 GTCATCTTTATTTT-TTGACCTATGGTGTTGTTCCG
* * * *
17849016 GTCATTTTTGTTTTTTGACCTGAT-GCGTTGTTCTG
1 GTCATCTTTATTTTTTGACCT-ATGGTGTTGTTCCG
* * * *
17849051 GTCATATTTATTTTTTCGACC-ATTAGTGTT-ATCCTA
1 GTCATCTTTATTTTTT-GACCTA-TGGTGTTGTTCC-G
* * * * * *
17849087 GTCATCTTT-TTTTTTTACCTATAGTATTATCCCA
1 GTCATCTTTATTTTTTGACCTATGGTGTTGTTCCG
* * *
17849121 GTCATCTTTGATTTCTTGATC-ATTGGTGTTG-TCCTA
1 GTCATCTTT-ATTTTTTGACCTA-TGGTGTTGTTCC-G
* * * ** * *
17849157 GTTAACTTTATTTTTTTAACCTACAGTGTTGTTTCA
1 GTCATCTTTA-TTTTTTGACCTATGGTGTTGTTCCG
*
17849193 GTTATCTTTATTTTTTGAC
1 GTCATCTTTATTTTTTGAC
17849212 TTGCGATGTT
Statistics
Matches: 302, Mismatches: 79, Indels: 60
0.68 0.18 0.14
Matches are distributed among these distances:
33 2 0.01
34 23 0.08
35 124 0.41
36 123 0.41
37 21 0.07
38 9 0.03
ACGTcount: A:0.16, C:0.17, G:0.16, T:0.51
Consensus pattern (35 bp):
GTCATCTTTATTTTTTGACCTATGGTGTTGTTCCG
Done.