Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000520.1 Hibiscus syriacus cultivar Beakdansim tig00000991_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1956684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:772060 original size:30 final size:30
Alignment explanation
Indices: 772026--772141 Score: 155
Period size: 30 Copynumber: 3.9 Consensus size: 30
772016 ATGGTTCAGT
* *
772026 CCTTAAGTTTCTATTTTTGCAATTTTATTC
1 CCTTAAGTTTCTATTTTTGCTATTTTAGTC
*
772056 CCTTAAGTTTCTATTTTTGTTATTTTAGTC
1 CCTTAAGTTTCTATTTTTGCTATTTTAGTC
*
772086 CCTTAAGTTTCTATTTTTTCTATTTTAGTC
1 CCTTAAGTTTCTATTTTTGCTATTTTAGTC
*
772116 CTTTAAG-TTC-ATGGTTTTGCTATTTT
1 CCTTAAGTTTCTAT--TTTTGCTATTTT
772142 GGTTCTTTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
28 2 0.03
29 3 0.04
30 72 0.94
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (30 bp):
CCTTAAGTTTCTATTTTTGCTATTTTAGTC
Found at i:776645 original size:2 final size:2
Alignment explanation
Indices: 776640--776668 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
776630 ATATATACCC
776640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
776669 AGTATACAAT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:779784 original size:131 final size:129
Alignment explanation
Indices: 779584--780033 Score: 528
Period size: 131 Copynumber: 3.4 Consensus size: 129
779574 GTGTAGAAAC
* * * ** * * *
779584 CGTGTCATCCCCCGACCATACTTTTTCATCACGTAGGAGTCGAGTCACCCTTAGATAACCAGTTG
1 CGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAG-CGTGTCACCCTTAGATAACCAGCTA
779649 TCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGGTTATCATCCTTATCACGTAGGAA
65 TCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGGTTATCATCCTTATCACGTAGGAA
* * * *
779714 TCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCAGCGTCACCCTTAGATAACTAGCC
1 -CGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGC-GTGTCACCCTTAGATAACCAGCT
* * *
779779 ATCCTCATCACGTAGGAACCATGTTATCATCCCTAAAGAT-CGTCTATCATCCTCATCACGTAGG
64 ATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGGT-TATCATCCTTATCACGTAGG
779843 AA
128 AA
* *
779845 CAGTGTCATCCACCGACTAGACCTCCTCATCACGTAGGAGCCGTGTCACCCATAGATAACCAGCT
1 C-GTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAG-CGTGTCACCCTTAGATAACCAGCT
* * *** * *
779910 ATCCTCATCACGTAGAAACCGTGTTATCACCATTCCTAAAGATGGCAGAAC-T-CTTAATCATGT
64 ATCCTCATCACGTAGGAACCGTGTTAT---CATCCCTAAAGATGGGTTATCATCCTT-ATCACGT
*
779973 ATGAGA
125 AGGA-A
* *
779979 CGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCTGTGTCACCCTTAGA
1 CGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGC-GTGTCACCCTTAGA
780034 AGACCATAAC
Statistics
Matches: 275, Mismatches: 33, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
130 4 0.01
131 193 0.70
132 4 0.01
133 58 0.21
134 16 0.06
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (129 bp):
CGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCGTGTCACCCTTAGATAACCAGCTAT
CCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGGTTATCATCCTTATCACGTAGGAA
Found at i:781800 original size:30 final size:29
Alignment explanation
Indices: 781760--781890 Score: 151
Period size: 30 Copynumber: 4.4 Consensus size: 29
781750 ATATTTGTGG
781760 TTTAGT-CCTTAAGTTTTTGTTTTTTCTAT
1 TTTAGTCCCTTAAGTTTTTG-TTTTTCTAT
* *
781789 TTAAGTCCCTTAAG-TTTTGTTTTTGTAGT
1 TTTAGTCCCTTAAGTTTTTGTTTTTCTA-T
781818 TTTAGTCCCTTAAGTTTCTAT-TTTTTCTAT
1 TTTAGTCCCTTAAGTTT-T-TGTTTTTCTAT
* *
781848 TTTAGTCCTTTAAGTTCCTTGTTTTTCTAT
1 TTTAGTCCCTTAAGTT-TTTGTTTTTCTAT
*
781878 TTTAGTCCTTTAA
1 TTTAGTCCCTTAA
781891 ATCGAATATG
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.08
29 25 0.28
30 48 0.54
31 8 0.09
32 1 0.01
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.60
Consensus pattern (29 bp):
TTTAGTCCCTTAAGTTTTTGTTTTTCTAT
Found at i:781834 original size:59 final size:59
Alignment explanation
Indices: 781760--781890 Score: 176
Period size: 59 Copynumber: 2.2 Consensus size: 59
781750 ATATTTGTGG
* * *
781760 TTTAGT-CCTTAAGTTTTTGTTTTTTCTATTTAAGTCCCTTAAGTT-TTGTTTTTGTAGT
1 TTTAGTCCCTTAAGTTTCTATTTTTTCTATTTAAGTCCCTTAAGTTCTTGTTTTTCTA-T
* *
781818 TTTAGTCCCTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTCCTTGTTTTTCTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTTCTATTTAAGTCCCTTAAGTT-CTTGTTTTTCTAT
*
781878 TTTAGTCCTTTAA
1 TTTAGTCCCTTAA
781891 ATCGAATATG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
58 6 0.09
59 35 0.55
60 13 0.20
61 10 0.16
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.60
Consensus pattern (59 bp):
TTTAGTCCCTTAAGTTTCTATTTTTTCTATTTAAGTCCCTTAAGTTCTTGTTTTTCTAT
Found at i:782500 original size:20 final size:20
Alignment explanation
Indices: 782393--782505 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
782383 ACAGGTTCCA
* *
782393 AAATCGCAATGTGAATATGT
1 AAATCGCAACGCGAATATGT
**
782413 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATATGT
* *
782433 AAATCGCAACGCGCGAT-TTT
1 AAATCGCAACGCG-AATATGT
* *
782453 CCAAAATCGCAATGCTAATATGT
1 ---AAATCGCAACGCGAATATGT
* *
782476 TAATCGCAACGCGAATTTGT
1 AAATCGCAACGCGAATATGT
*
782496 AAATCCCAAC
1 AAATCGCAAC
782506 ACAGAAGCCA
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
20 54 0.76
21 2 0.03
22 2 0.03
23 13 0.18
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:782691 original size:57 final size:57
Alignment explanation
Indices: 782620--782778 Score: 248
Period size: 57 Copynumber: 2.8 Consensus size: 57
782610 GAATTTTGAT
* *
782620 TTCGCAATGGTAATTACCGATATAGGTAAACAGTACTATCGCAATGC-AGTTTTCAAA
1 TTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATGCGA-TTTTCAAA
* *
782677 TTCGCAACGCTAATTACCGATATAGGAAAACAGTACTATCGCAATGCGATTTTTAAA
1 TTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATGCGATTTTCAAA
* *
782734 TTCGCAACGCTAATTACCGATATAGGTAAATAGTACTATTGCAAT
1 TTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAT
782779 ATAAACAGTA
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
57 93 0.99
58 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (57 bp):
TTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATGCGATTTTCAAA
Found at i:783258 original size:24 final size:23
Alignment explanation
Indices: 783226--783293 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
783216 TTTTTCTTTT
783226 TTTTCATGTAATATTTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTTAC
783250 ATTTTATGT-AT-TTTATTTTTTAC
1 -TTTTATGTAATATTT-TTTTTTAC
783273 -TTTA-GTATATATTTTTATTTT
1 TTTTATGTA-ATATTTTT-TTTT
783294 TTTAGATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
20 2 0.05
21 4 0.11
22 7 0.18
23 17 0.45
24 4 0.11
25 4 0.11
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTATGTAATATTTTTTTTTAC
Found at i:783288 original size:25 final size:25
Alignment explanation
Indices: 783242--783322 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
783232 TGTAATATTT
*
783242 TTTTTTACATT-T-TATGTATTTTA
1 TTTTTTACATTATATATATATTTTA
*
783265 TTTTTTACTTTAGTATATAT-TTTTA
1 TTTTTTACATTA-TATATATATTTTA
* *
783290 TTTTTTTAGATTATATATATATATTA
1 -TTTTTTACATTATATATATATTTTA
783316 TTTTTTA
1 TTTTTTA
783323 TTATCAGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
23 10 0.21
25 20 0.42
26 18 0.38
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTTTTACATTATATATATATTTTA
Found at i:783294 original size:26 final size:26
Alignment explanation
Indices: 783241--783321 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
783231 ATGTAATATT
*
783241 TTTTTTTACATT-T-TATGTATTTTA
1 TTTTTTTACATTATATATATATTTTA
*
783265 -TTTTTTACTTTAGTATATAT-TTTTA
1 TTTTTTTACATTA-TATATATATTTTA
* *
783290 TTTTTTTAGATTATATATATATATTA
1 TTTTTTTACATTATATATATATTTTA
783316 TTTTTT
1 TTTTTT
783322 ATTATCAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
23 10 0.21
25 13 0.28
26 24 0.51
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTTTTACATTATATATATATTTTA
Found at i:783325 original size:23 final size:25
Alignment explanation
Indices: 783258--783400 Score: 70
Period size: 24 Copynumber: 5.8 Consensus size: 25
783248 ACATTTTATG
783258 TATT-TTATTTTTTACTT-TAGTATA
1 TATTATTATTTTTTA-TTATAGTATA
*
783282 TATTTTTATTTTTTTAGATTATA-TATA
1 TATTATTA-TTTTTT--ATTATAGTATA
*
783309 TA-TATTATTTTTTATTATCAGT-TT
1 TATTATTATTTTTTATTAT-AGTATA
* * * * *
783333 TATTAATA-TATATA-TATACTATT
1 TATTATTATTTTTTATTATAGTATA
* *
783356 TTTTATTTTTTTATTTATTATA-TATA
1 TATTA-TTATTT-TTTATTATAGTATA
783382 TATATATTA-TTTTTATTAT
1 TAT-TATTATTTTTTATTAT
783401 TTATTTATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
22 2 0.02
23 14 0.15
24 21 0.23
25 17 0.19
26 20 0.22
27 14 0.15
28 3 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
TATTATTATTTTTTATTATAGTATA
Found at i:783374 original size:4 final size:4
Alignment explanation
Indices: 783352--783461 Score: 64
Period size: 4 Copynumber: 26.5 Consensus size: 4
783342 ATATATATAC
* * * *
783352 TATT T-TT TATT TTTT TATT TATT ATATA TATA TATAT TATT TTTAT TATT
1 TATT TATT TATT TATT TATT TATT -TATT TATT TAT-T TATT TAT-T TATT
* * *
783402 TATT TATT TATT TGTTT TATT TATAT TTTT TCATT T-TT TCCTT TATT
1 TATT TATT TATT T-ATT TATT TAT-T TATT T-ATT TATT T-ATT TATT
*
783449 TA-T TATT TTTT TA
1 TATT TATT TATT TA
783462 CTTACTATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
3 9 0.11
4 53 0.64
5 21 0.25
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:783385 original size:35 final size:33
Alignment explanation
Indices: 783278--783394 Score: 130
Period size: 38 Copynumber: 3.4 Consensus size: 33
783268 TTTACTTTAG
*
783278 TATATA-TTTTTATTTTTTTA-GATTATATATA
1 TATATATTTTTTATTTTTTTATTATTATATATA
*
783309 TATATTATTTTTTATTATCAGTTTTATTAATATATATA
1 TATA-TATTTTTTATT-T---TTTTATTATTATATATA
783347 TATACTATTTTTTATTTTTTTATTTATTATATATA
1 TATA-TATTTTTTATTTTTTTA-TTATTATATATA
783382 TATATATTATTTT
1 TATATATT-TTTT
783395 TATTATTTAT
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
31 4 0.05
32 2 0.03
33 8 0.11
34 10 0.14
35 19 0.26
37 6 0.08
38 24 0.33
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (33 bp):
TATATATTTTTTATTTTTTTATTATTATATATA
Found at i:783404 original size:35 final size:37
Alignment explanation
Indices: 783301--783409 Score: 143
Period size: 38 Copynumber: 2.9 Consensus size: 37
783291 TTTTTTAGAT
*
783301 TATATATATATATTATTTTTTATTA-TCAGTTTTATTAA
1 TATATATATATATTATTTTTTATTATTTA--TTTATTAA
* *
783339 TATATATATATACTATTTTTTATTTTTTTATTTATT-A
1 TATATATATATATTATTTTTTA-TTATTTATTTATTAA
783376 TATATATATATATTA-TTTTTATTATTTATTTATT
1 TATATATATATATTATTTTTTATTATTTATTTATT
783410 TATTTGTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
35 12 0.19
36 6 0.09
37 15 0.23
38 27 0.42
39 2 0.03
40 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (37 bp):
TATATATATATATTATTTTTTATTATTTATTTATTAA
Found at i:783427 original size:39 final size:38
Alignment explanation
Indices: 783301--783454 Score: 120
Period size: 38 Copynumber: 4.0 Consensus size: 38
783291 TTTTTTAGAT
* *
783301 TATATATATATATTATTTT-TTA-TTA-TCAGTTTTATTAA
1 TATATATATATATTTTTTTATTATTTATTTA--TTTATT-A
* * *
783339 TATATATATATACTATTTT-TTATTTTTTTATTTATTA
1 TATATATATATATTTTTTTATTATTTATTTATTTATTA
783376 TATATATATATATTATTTTTATTATTTATTTATTTATT-
1 TATATATATATATT-TTTTTATTATTTATTTATTTATTA
* * * * * *
783414 TGTTTTATTTATATTTTTTCATTTTTTCCTTTATTTATTA
1 T-ATATATATATATTTTTTTATTATTT-ATTTATTTATTA
783454 T
1 T
783455 TTTTTTACTT
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
37 14 0.14
38 42 0.43
39 38 0.39
40 3 0.03
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (38 bp):
TATATATATATATTTTTTTATTATTTATTTATTTATTA
Found at i:783427 original size:43 final size:42
Alignment explanation
Indices: 783311--783461 Score: 112
Period size: 43 Copynumber: 3.6 Consensus size: 42
783301 TATATATATA
** * **
783311 TATTATTT-TTTATTATCAGTTTTATTAATATATA-TATATAC
1 TATTATTTATTTATTATTTGTTTTATTTATATATATTAT-TTT
* * * * *
783352 TATTTTTTATTTTTTTATTTATTATATATATATATATTATTTT
1 TATTATTTA-TTTATTATTTGTTTTATTTATATATATTATTTT
* *
783395 TATTATTTATTTATTTATTTGTTTTATTTATATTTTTTCATTTT
1 TATTATTTATTTA-TTATTTGTTTTATTTATATATATT-ATTTT
**
783439 T-TCCTTTATTTATTATTT-TTTTA
1 TATTATTTATTTATTATTTGTTTTA
783462 CTTACTATTT
Statistics
Matches: 86, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
41 12 0.14
42 9 0.10
43 56 0.65
44 9 0.10
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (42 bp):
TATTATTTATTTATTATTTGTTTTATTTATATATATTATTTT
Found at i:783455 original size:27 final size:27
Alignment explanation
Indices: 783393--783459 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
783383 ATATATTATT
**
783393 TTTATTATTTATTTATTTATTTGTTTTA
1 TTTATTATTT-TTTATTTATTTCCTTTA
783421 TTTA-TATTTTTTCATTT-TTTCCTTTA
1 TTTATTATTTTTT-ATTTATTTCCTTTA
783447 TTTATTATTTTTT
1 TTTATTATTTTTT
783460 TACTTACTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 14 0.40
27 17 0.49
28 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (27 bp):
TTTATTATTTTTTATTTATTTCCTTTA
Found at i:785347 original size:25 final size:25
Alignment explanation
Indices: 785309--785358 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
785299 ATACCTCGAA
785309 CATCTCATGCATTTTT-GCATTTTG
1 CATCTCATGCATTTTTAGCATTTTG
*
785333 CATCTACATTCATTTTTAAGCATTTT
1 CATCT-CATGCATTTTT-AGCATTTT
785359 CATAAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 10 0.45
27 7 0.32
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.50
Consensus pattern (25 bp):
CATCTCATGCATTTTTAGCATTTTG
Found at i:786625 original size:19 final size:19
Alignment explanation
Indices: 786585--786625 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
786575 AAAGAGGAAA
*
786585 AAAGAGAAAATAAAAAGAG
1 AAAGAGAAAAAAAAAAGAG
786604 AAAGAGAAAAAAACAAAG-G
1 AAAGAGAAAAAAA-AAAGAG
786623 AAA
1 AAA
786626 ATTGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAGAGAAAAAAAAAAGAG
Found at i:786810 original size:69 final size:69
Alignment explanation
Indices: 786699--786833 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
786689 GATTCAAACT
* *
786699 ATGAGATTGATCAAGCATAATCATTTTCGAATCACTGAATCACTTCACTCAAAGATCATAGAGCA
1 ATGAGATTGATCAAACACAATCATTTTCGAATCACTGAATCACTTCACTCAAAGATCATAGAGCA
786764 TTAA
66 TTAA
*
786768 ATGAGATTGATCAAACACAATCA-TTTCTGAATCACTGAATCACTTCACTCGAAGATCATAGAGC
1 ATGAGATTGATCAAACACAATCATTTTC-GAATCACTGAATCACTTCACTCAAAGATCATAGAGC
786832 AT
65 AT
786834 CAAGAGAGAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 4 0.06
69 58 0.94
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATCAAACACAATCATTTTCGAATCACTGAATCACTTCACTCAAAGATCATAGAGCA
TTAA
Found at i:787777 original size:32 final size:32
Alignment explanation
Indices: 787741--787845 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 32
787731 GGAACAATGA
* *
787741 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGTAGATTCAACATCAAATATTG
** * *
787773 GGGCAT-TTT-TTTATTTAATATCAAATATTG
1 GGGCATCTTTGTAGATTCAACATCAAATATTG
* * * *
787803 GGGCGTTTTTTTAGATTCAACATCGAATATTG
1 GGGCATCTTTGTAGATTCAACATCAAATATTG
*
787835 GGGAATCTTTG
1 GGGCATCTTTG
787846 GGAATTAAAC
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
30 20 0.36
31 6 0.11
32 29 0.53
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (32 bp):
GGGCATCTTTGTAGATTCAACATCAAATATTG
Found at i:788724 original size:105 final size:106
Alignment explanation
Indices: 788433--788752 Score: 392
Period size: 106 Copynumber: 3.0 Consensus size: 106
788423 ATATCGTGCC
* * * * *
788433 ACTCGAGACAACACAAGTTCAACTCCACAAAGAAGGGATGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAGCACAAGTTCAACTTCACAAAGAAGGGACGGCTGGCTGTCAACAAACAATTTCTC
* *
788498 AATTTCAAAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 AATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
788539 ACTCGAGACATCACAAGTTCAACTTCACAACGAAGGGACGGCT-GCTTGTCAACAAACAGTTTCT
1 ACTCGAGACAGCACAAGTTCAACTTCACAAAGAAGGGACGGCTGGC-TGTCAACAAACAATTTCT
**
788603 CAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
788645 ACTCGAG-CAGCCCAAGCTCAACTTCACAATGAAGGGGCGGCTGGCTGTCAACAAACAATTTCTT
1 ACTCGAGACAGCACAAGTTCAACTTCACAAAGAAGGGACGGCTGGCTGTCAACAAACAATTTCTC
* * * * * * * *
788709 AGTTCCATAGTCAATTTTAACTTCACGGAGGAGGATATTGG
66 AATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
788750 ACT
1 ACT
788753 TGGAACAATA
Statistics
Matches: 185, Mismatches: 27, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
105 83 0.45
106 102 0.55
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAGCACAAGTTCAACTTCACAAAGAAGGGACGGCTGGCTGTCAACAAACAATTTCTC
AATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:789107 original size:86 final size:87
Alignment explanation
Indices: 789009--789186 Score: 304
Period size: 87 Copynumber: 2.1 Consensus size: 87
788999 AGACTTTTCT
*
789009 CTTGAAACATAAACATTGAAAACATTT-CCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
*
789073 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
* * *
789095 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
789160 CTTGAAACAAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
789182 CTTGA
1 CTTGA
789187 GACAATTTCT
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
86 27 0.31
87 59 0.69
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCC
Found at i:789209 original size:102 final size:102
Alignment explanation
Indices: 789095--789330 Score: 373
Period size: 102 Copynumber: 2.3 Consensus size: 102
789085 TTTTGTCTCC
* *
789095 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
789160 CTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCT
* * * * *
789197 GTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
* *
789262 CTTGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCT
* *
789299 CTTGAAACATAAACCTTGAAAACGTTTCCCTT
1 CTTGAAACATAAACATTGAAAACATTTCCCTT
789331 AAAACACAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 121 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCT
Found at i:789282 original size:37 final size:37
Alignment explanation
Indices: 789235--789307 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
789225 CTTTGAAATT
*
789235 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
*
789272 AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
789308 TAAACCTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
Found at i:789518 original size:37 final size:36
Alignment explanation
Indices: 789453--789567 Score: 140
Period size: 36 Copynumber: 3.2 Consensus size: 36
789443 TATCTTTTCC
* * * *
789453 TTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTT
1 TTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTT
* * *
789489 TTAGAACTAAGTTTTGTCTCTCTTAAGACAGTTTCTT
1 TT-GAAATAAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
789526 TTGAAATAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTT
789562 TTGAAA
1 TTGAAA
789568 CACAAAAAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 37 0.56
37 29 0.44
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (36 bp):
TTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:789632 original size:38 final size:38
Alignment explanation
Indices: 789567--789642 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
789557 TTCTCTTGAA
* *
789567 ACACAAAAAAACCCTCGAAATTATTTCTTTTGAAACAC
1 ACACAAAAAAACCCTCGAAAATATTTCTCTTGAAACAC
* * *
789605 ACACAAAAAAACCTTTGAAAATGTTTCTCTTGAAACAC
1 ACACAAAAAAACCCTCGAAAATATTTCTCTTGAAACAC
789643 CAAACCCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (38 bp):
ACACAAAAAAACCCTCGAAAATATTTCTCTTGAAACAC
Found at i:790682 original size:14 final size:14
Alignment explanation
Indices: 790629--790682 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
790619 TACATTTACG
* *
790629 TTTTAATTATTATTA
1 TTTTATTTA-TATAA
*
790644 TTTTATTTATTTAA
1 TTTTATTTATATAA
790658 TTTTATTTATATAA
1 TTTTATTTATATAA
790672 TTTTATTTATA
1 TTTTATTTATA
790683 CGCACATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
14 27 0.77
15 8 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTATATAA
Found at i:790830 original size:39 final size:38
Alignment explanation
Indices: 790787--790960 Score: 117
Period size: 38 Copynumber: 4.5 Consensus size: 38
790777 TTTACTTTAG
**
790787 TATA-TATTTTTATTTTTTTAGATTAGATATATATATATA
1 TATATTATTTTTATTTTTTTAG-TTTTAT-TATATATATA
* *
790826 TATATTATTTTT-TTATTATCAGTTTTATTA-ATATATA
1 TATATTATTTTTATT-TTTTTAGTTTTATTATATATATA
* *
790863 TATA-TATATTTACTATTTTTTATTTTTTATT-TATTATATA
1 TATATTATTTTTA-T-TTTTTTA-GTTTTATTATA-TATATA
* * * *
790903 TATATTATTTTTACTTTTTTA-TTATTATTTTATTTATT
1 TATATTATTTTTATTTTTTTAGTT-TTATTATATATATA
* * *
790941 TGTTTTATTTATATTTTTTT
1 TATATTATTTTTATTTTTTT
790961 CTTCTTTTTC
Statistics
Matches: 108, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
36 6 0.06
37 13 0.12
38 32 0.30
39 28 0.26
40 22 0.20
41 7 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (38 bp):
TATATTATTTTTATTTTTTTAGTTTTATTATATATATA
Found at i:790888 original size:6 final size:6
Alignment explanation
Indices: 790879--790988 Score: 50
Period size: 6 Copynumber: 18.2 Consensus size: 6
790869 TATTTACTAT
* * * *
790879 TTTTTA TTTTT- TATTTA TTATATA TATATTA TTTTTA CTTTTTTA TTATTA
1 TTTTTA TTTTTA TTTTTA TT-TTTA T-TTTTA TTTTTA --TTTTTA TTTTTA
* * * * *
790930 -TTTTA TTTATT- TGTTTTA TTTATA TTTTT- TTCTTC TTTTTC TTTAT-
1 TTTTTA TTT-TTA T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
790976 TTTTTA TTTTTA T
1 TTTTTA TTTTTA T
790989 ACTTACTATT
Statistics
Matches: 79, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
5 16 0.20
6 44 0.56
7 12 0.15
8 7 0.09
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:790897 original size:25 final size:24
Alignment explanation
Indices: 790869--790959 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 24
790859 TATATATATA
790869 TATTTACTATTTTTTATTTTTTATT
1 TATTTA-TATTTTTTATTTTTTATT
* *
790894 TATTATATATATATTA-TTTTTACTT
1 TATT-TATATTTTTTATTTTTTA-TT
*
790919 T-TTTATTATTATTTTATTTATTTGTTT
1 TATTTA-TATT-TTTTATTT-TTT-ATT
790946 TATTTATATTTTTT
1 TATTTATATTTTTT
790960 TCTTCTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
23 2 0.04
24 11 0.21
25 18 0.34
26 8 0.15
27 10 0.19
28 4 0.08
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (24 bp):
TATTTATATTTTTTATTTTTTATT
Found at i:790947 original size:32 final size:31
Alignment explanation
Indices: 790865--790930 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
790855 AATATATATA
* *
790865 TATATATTTACTATTTTTTATTTTTTATTTAT
1 TATATATATATTA-TTTTTATTTTTTATTTAT
790897 TATATATATATTATTTTTACTTTTTTA-TTAT
1 TATATATATATTATTTTTA-TTTTTTATTTAT
790928 TAT
1 TAT
790931 TTTATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (31 bp):
TATATATATATTATTTTTATTTTTTATTTAT
Found at i:790954 original size:47 final size:47
Alignment explanation
Indices: 790849--790984 Score: 117
Period size: 47 Copynumber: 3.0 Consensus size: 47
790839 TATTATCAGT
* *
790849 TTTATTAATATATATATATATATT-TACTATTT-TTTA---TTT-TTTA
1 TTTATT-ATATATATAT-TATTTTCTACTTTTTCTTTATTTTTTATTTA
790892 TTTATTATATATATATTATTTT-TACTTTTT-TATTATTATTTTATTTA
1 TTTATTATATATATATTATTTTCTACTTTTTCT-TTATT-TTTTATTTA
* * * * *
790939 TTTGTTTTATTTATATTTTTTTCTTCTTTTTCTTTATTTTTTATTT
1 TTTATTATATATATATTATTTTCTACTTTTTCTTTATTTTTTATTT
790985 TTATACTTAC
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
41 13 0.17
42 13 0.17
43 6 0.08
46 3 0.04
47 30 0.38
48 12 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.72
Consensus pattern (47 bp):
TTTATTATATATATATTATTTTCTACTTTTTCTTTATTTTTTATTTA
Found at i:791451 original size:20 final size:20
Alignment explanation
Indices: 791426--791474 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
791416 TACGACACTA
*
791426 TCGCAATGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
*
791446 TCGCAACGGGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
791466 TCGCAACGC
1 TCGCAACGC
791475 TAATTACCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:791519 original size:20 final size:20
Alignment explanation
Indices: 791490--791530 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
791480 ACCGATTTAG
791490 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
791510 GTAAATAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
791530 G
1 G
791531 CGATTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:791536 original size:77 final size:77
Alignment explanation
Indices: 791422--791662 Score: 297
Period size: 77 Copynumber: 3.1 Consensus size: 77
791412 CGGTTACGAC
** * * * *
791422 ACTATCGCAATGCGATTTTCAAATTCGCAACGGGATTTTCAAATTCGCAACGCTAATTACCGATT
1 ACTATCGCAATGAAATGTACAAATTCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATA
791487 TAGGTAAACAGT
66 TAGGTAAACAGT
* * *
791499 ACTATCGCAATGTAAATAGTAC-TA-TCGCAATGCGATTTTCAAATTTGCAACGCTAATTACCGA
1 ACTATCGCAATG-AAAT-GTACAAATTCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGA
791562 TATAGGTAAACAGT
64 TATAGGTAAACAGT
** * * * *
791576 ACTATCGCAATGCGATTTTCAAATTCGCAACGTGATTTTCAAATTCGCAACGCTAATTACCGATG
1 ACTATCGCAATGAAATGTACAAATTCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATA
**
791641 TAGGTAAACAAA
66 TAGGTAAACAGT
791653 ACTATCGCAA
1 ACTATCGCAA
791663 CGCGAATTTC
Statistics
Matches: 140, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
75 2 0.01
76 3 0.02
77 130 0.93
78 3 0.02
79 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (77 bp):
ACTATCGCAATGAAATGTACAAATTCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATA
TAGGTAAACAGT
Found at i:791605 original size:20 final size:20
Alignment explanation
Indices: 791580--791628 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
791570 AACAGTACTA
*
791580 TCGCAATGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
*
791600 TCGCAACGTGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
791620 TCGCAACGC
1 TCGCAACGC
791629 TAATTACCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:791716 original size:19 final size:20
Alignment explanation
Indices: 791664--791716 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
791654 CTATCGCAAC
791664 GCGAATTTCTGAAACTGAGTT
1 GCGAATTT-TGAAACTGAGTT
* *
791685 GCGAATTTAGAAACTGTGTT
1 GCGAATTTTGAAACTGAGTT
*
791705 GTG-ATTTTGAAA
1 GCGAATTTTGAAA
791717 ATCGCGTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.29
20 12 0.43
21 8 0.29
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (20 bp):
GCGAATTTTGAAACTGAGTT
Found at i:791737 original size:21 final size:20
Alignment explanation
Indices: 791702--791752 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
791692 TAGAAACTGT
*
791702 GTTGTGATTTTGAAAATCGC
1 GTTGTGATTTGGAAAATCGC
*
791722 GTTGTGAATTTGGAAAATTGC
1 GTTGTG-ATTTGGAAAATCGC
*
791743 GTTGCGATTT
1 GTTGTGATTT
791753 ACATACTCGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (20 bp):
GTTGTGATTTGGAAAATCGC
Found at i:792400 original size:21 final size:22
Alignment explanation
Indices: 792367--792410 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
792357 AAATCACTTC
792367 AAAATCACCAATT-TTTTCAAAA
1 AAAATCACCAATTGTTTT-AAAA
*
792389 AAAATCA-TAATTGTTTTAAAA
1 AAAATCACCAATTGTTTTAAAA
792410 A
1 A
792411 TAATATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATCACCAATTGTTTTAAAA
Found at i:793015 original size:14 final size:12
Alignment explanation
Indices: 792981--793012 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
792971 ATCACATGTA
792981 AAATATATGAAG
1 AAATATATGAAG
792993 AAATATATGAAG
1 AAATATATGAAG
793005 AAATATAT
1 AAATATAT
793013 ATGTATATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (12 bp):
AAATATATGAAG
Found at i:793834 original size:65 final size:64
Alignment explanation
Indices: 793705--793857 Score: 202
Period size: 65 Copynumber: 2.4 Consensus size: 64
793695 CTGGGGTGCA
* * *
793705 CATCGGTGCAC-AAAT-CTACTTTGATGTTTCAAAATAGCTGGGGTGCATCGATGCATGTCTTGT
1 CATCGGTGCACTAAATGC-A-TTCGATGTTTCAAAATAGCAGGGGTGCATCGATGCATGACTTGT
793768 G
64 G
* * * *
793769 CATCGGTGCATTGAATGCATTCGATGTTTCAAAATATTCAGGGGTGCATTGATGCATGACTTGTG
1 CATCGGTGCACTAAATGCATTCGATGTTTCAAAATA-GCAGGGGTGCATCGATGCATGACTTGTG
793834 CATCGGTGCACTAAATGCATTCGA
1 CATCGGTGCACTAAATGCATTCGA
793858 AATTCAATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 26 0.34
65 50 0.65
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (64 bp):
CATCGGTGCACTAAATGCATTCGATGTTTCAAAATAGCAGGGGTGCATCGATGCATGACTTGTG
Found at i:796626 original size:23 final size:23
Alignment explanation
Indices: 796478--796625 Score: 173
Period size: 23 Copynumber: 6.7 Consensus size: 23
796468 AAAATCCGAT
* *
796478 GAGTGTATCGATGCACA-GC-A-
1 GAGTGCATCGATGCACATTCAAG
796498 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
*
796521 GAGTGCGTCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
*
796544 GAGTGCGTCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
796567 GAGTGCATCGGTGCACCTTCAA-
1 GAGTGCATCGATGCACATTCAAG
* *
796589 G-GTGTATCGATGCATATTCAAAG
1 GAGTGCATCGATGCACATTC-AAG
796612 GA-TGCATCGATGCA
1 GAGTGCATCGATGCA
796626 TTGTTTAGTG
Statistics
Matches: 111, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
20 16 0.14
21 15 0.14
22 4 0.04
23 76 0.68
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:800492 original size:22 final size:21
Alignment explanation
Indices: 800450--800489 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
800440 AAGATTATTT
800450 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
800471 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
800490 ATAAATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:800501 original size:21 final size:21
Alignment explanation
Indices: 800460--800502 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
800450 TCATTTTTCA
* *
800460 ATTTTGAAATATCATTTTTAT
1 ATTTTGAAATATAATTCTTAT
800481 ATTTTGAAA-ATAAATTCTTAT
1 ATTTTGAAATAT-AATTCTTAT
800502 A
1 A
800503 ATCCTAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTTGAAATATAATTCTTAT
Found at i:802421 original size:64 final size:65
Alignment explanation
Indices: 802351--802506 Score: 196
Period size: 64 Copynumber: 2.4 Consensus size: 65
802341 TACACTGGGG
* *
802351 TGTGCATCGGTGCAC-AAATCTGC-TTCGATGTTTCAAAATAGTC-GGGGTGCATCAATGCATGT
1 TGTGCATCGGTGCACTAAAT-TGCATTCGATGTTT-AAAATAGTCAGGGGTACATCAATGCATGG
802413 CT
64 CT
* * ** *
802415 TGTGCATCGGTGCACTGAA-TGCATTCGATGTTTTAAATTTTCAGGGGTACATCGATGCATGGCT
1 TGTGCATCGGTGCACTAAATTGCATTCGATGTTTAAAATAGTCAGGGGTACATCAATGCATGGCT
802479 TGTGCATCGGTGCACTAAA-TGCATTCGA
1 TGTGCATCGGTGCACTAAATTGCATTCGA
802507 AATTCAATTT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
63 9 0.11
64 70 0.86
65 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (65 bp):
TGTGCATCGGTGCACTAAATTGCATTCGATGTTTAAAATAGTCAGGGGTACATCAATGCATGGCT
Found at i:808734 original size:20 final size:22
Alignment explanation
Indices: 808704--808748 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
808694 ATCAAAAAAA
808704 TAAAGATTTAGTATAT-TATTT
1 TAAAGATTTAGTATATATATTT
*
808725 TAAA-ATTTAGTCTATATATTT
1 TAAAGATTTAGTATATATATTT
808746 TAA
1 TAA
808749 TTTTGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (22 bp):
TAAAGATTTAGTATATATATTT
Found at i:810407 original size:418 final size:418
Alignment explanation
Indices: 809625--810460 Score: 1636
Period size: 418 Copynumber: 2.0 Consensus size: 418
809615 AAGGGCTGAC
809625 AGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAAATACCTTACAGAGAGGAGCCTA
1 AGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAAATACCTTACAGAGAGGAGCCTA
809690 ATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAATAGGACCTCATAATAGAGCATC
66 ATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAATAGGACCTCATAATAGAGCATC
809755 TCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAAACTCCTCTAAGACACAAGTAAC
131 TCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAAACTCCTCTAAGACACAAGTAAC
809820 TCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGATTATCTGCAAAGTAAAAGTGGG
196 TCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGATTATCTGCAAAGTAAAAGTGGG
809885 CGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCTCTTTTCCACAGCTAAGTCTAAG
261 CGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCTCTTTTCCACAGCTAAGTCTAAG
809950 ATTTTTTAGAGAACATTCACCGCAAGGAAAAACAAATAGGGGGATAGGGGATCCCTTACATGATG
326 ATTTTTTAGAGAACATTCACCGCAAGGAAAAACAAATAGGGGGATAGGGGATCCCTTACATGATG
810015 CCTCTAGCCCCTTCAAAAAAACTAACGT
391 CCTCTAGCCCCTTCAAAAAAACTAACGT
810043 AGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAAATACCTTACAGAGAGGAGCCTA
1 AGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAAATACCTTACAGAGAGGAGCCTA
*
810108 ATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAATATGACCTCATAATAGAGCATC
66 ATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAATAGGACCTCATAATAGAGCATC
810173 TCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAAACTCCTCTAAGACACAAGTAAC
131 TCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAAACTCCTCTAAGACACAAGTAAC
810238 TCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGATTATCTGCAAAGTAAAAGTGGG
196 TCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGATTATCTGCAAAGTAAAAGTGGG
810303 CGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCTCTTTTCCACAGCTAAGTCTAAG
261 CGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCTCTTTTCCACAGCTAAGTCTAAG
* *
810368 ATTTTTTAGAGAACATTCACCGCAAGGAAAAATAAATAGGGGGATAGGGGATCCCTTATATGATG
326 ATTTTTTAGAGAACATTCACCGCAAGGAAAAACAAATAGGGGGATAGGGGATCCCTTACATGATG
*
810433 CCTCTAGCCCCTTCAAAAAAACTCACGT
391 CCTCTAGCCCCTTCAAAAAAACTAACGT
810461 GACTATCATT
Statistics
Matches: 414, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
418 414 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (418 bp):
AGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAAATACCTTACAGAGAGGAGCCTA
ATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAATAGGACCTCATAATAGAGCATC
TCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAAACTCCTCTAAGACACAAGTAAC
TCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGATTATCTGCAAAGTAAAAGTGGG
CGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCTCTTTTCCACAGCTAAGTCTAAG
ATTTTTTAGAGAACATTCACCGCAAGGAAAAACAAATAGGGGGATAGGGGATCCCTTACATGATG
CCTCTAGCCCCTTCAAAAAAACTAACGT
Found at i:811878 original size:955 final size:954
Alignment explanation
Indices: 810022--811929 Score: 3744
Period size: 955 Copynumber: 2.0 Consensus size: 954
810012 ATGCCTCTAG
810022 CCCCTTCAAAAAAACTAACGTAGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAAA
1 CCCCTTCAAAAAAACTAACGTAGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAAA
810087 TACCTTACAGAGAGGAGCCTAATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAAT
66 TACCTTACAGAGAGGAGCCTAATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAAT
810152 ATGACCTCATAATAGAGCATCTCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAAA
131 ATGACCTCATAATAGAGCATCTCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAAA
810217 CTCCTCTAAGACACAAGTAACTCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGAT
196 CTCCTCTAAGACACAAGTAACTCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGAT
810282 TATCTGCAAAGTAAAAGTGGGCGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCTC
261 TATCTGCAAAGTAAAAGTGGGCGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCTC
* *
810347 TTTTCCACAGCTAAGTCTAAGATTTTTTAGAGAACATTCACCGCAAGGAAAAATAAATAGGGGGA
326 TTTTCCACAACTAAGTCTAAGATTTTTTAGAGAACATTCACCGCAAGGAAAAACAAATAGGGGGA
*
810412 TAGGGGATCCCTTATATGATGCCTCTAGCCCCTTCAAAAAAACTCACGTGACTATCATTAAACGA
391 TAGGGGATCCCTTACATGATGCCTCTAGCCCCTTCAAAAAAACTCACGTGACTATCATTAAACGA
*
810477 GATAAAAAAATCGGGGAAAGTTAACCAAGCTTCAATCCAACCACGAAAAGCATTAGACAGGCCTA
456 GATAAAAAAATCGGGGAAAGTTAACCAAGCTTCAATCCAACCACGAAAAGCATTAGACAGACCTA
810542 TAACCTCTAAAACAGTCAGAATGAAGTCCCAATTCAAAAAATTAAGGGCCTTTTGAGGGTCAATC
521 TAACCTCTAAAACAGTCAGAATGAAGTCCCAATTCAAAAAATTAAGGGCCTTTTGAGGGTCAATC
810607 TTAAGAGCAATCATAGAGGATAAGGTGGTCTTCCTAGCATAGCCCTTGACAATTTCCTTAGCTAA
586 TTAAGAGCAATCATAGAGGATAAGGTGGTCTTCCTAGCATAGCCCTTGACAATTTCCTTAGCTAA
*
810672 TAAGGTGTAACCCACAATGCATCTCCCTTTAATAAATACAATTTGTTTGTGGGAGACCATGCTCG
651 TAAGGTGTAACCCACAATGCATATCCCTTTAATAAATACAATTTGTTTGTGGGAGACCATGCTCG
810737 GGAAGAAAAGTGCAAGTCTTCGCACAAGGATCCTAGGGACGGTCTTGTAAATCACATAGCAACAA
716 GGAAGAAAAGTGCAAGTCTTCGCACAAGGATCCTAGGGACGGTCTTGTAAATCACATAGCAACAA
*
810802 GAGATGGGATGAAAATCCTTAGTCGAACTTAGATTATGGGACTTAGGCACCAACACTATAGTAGT
781 GAGATGGGATGAAAATCCTTAGCCGAACTTAGATTATGGGACTTAGGCACCAACACTATAGTAGT
810867 CAAATTGAAAGCATGGGACATCATAGAGGAATAAAAGAAGTACTTTACATCAACAATAAAGTTCT
846 CAAATTGAAAGCATGGGACATCATAGAGGAATAAAAGAAGTACTTTACATCAACAATAAAGTTCT
810932 GCCCAACAATAGACTAGGTAGACTTGAAAAAATGGGAAGTATAT
911 GCCCAACAATAGACTAGGTAGACTTGAAAAAATGGGAAGTATAT
810976 CCCCTTCAAAAAAAACTAACGTAGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAA
1 CCCCTTC-AAAAAAACTAACGTAGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAA
811041 ATACCTTACAGAGAGGAGCCTAATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAA
65 ATACCTTACAGAGAGGAGCCTAATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAA
811106 TATGACCTCATAATAGAGCATCTCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAA
130 TATGACCTCATAATAGAGCATCTCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAA
811171 ACTCCTCTAAGACACAAGTAACTCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGA
195 ACTCCTCTAAGACACAAGTAACTCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGA
811236 TTATCTGCAAAGTAAAAGTGGGCGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCT
260 TTATCTGCAAAGTAAAAGTGGGCGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCT
811301 CTTTTCCACAACTAAGTCTAAGATTTTTTAGAGAACATTCACCGCAAGGAAAAACAAATAGGGGG
325 CTTTTCCACAACTAAGTCTAAGATTTTTTAGAGAACATTCACCGCAAGGAAAAACAAATAGGGGG
811366 ATAGGGGATCCCTTACATGATGCCTCTAGCCCCTTCAAAAAAACTCACGTGACTATCATTAAACG
390 ATAGGGGATCCCTTACATGATGCCTCTAGCCCCTTCAAAAAAACTCACGTGACTATCATTAAACG
811431 AGATAAAAAAATCGGGGAAAGTTAACCAAGCTTCAATCCAACCACGAAAAGCATTAGACAGACCT
455 AGATAAAAAAATCGGGGAAAGTTAACCAAGCTTCAATCCAACCACGAAAAGCATTAGACAGACCT
811496 ATAACCTCTAAAACAGTCAGAATGAAGTCCCAATTCAAAAAATTAAGGGCCTTTTGAGGGTCAAT
520 ATAACCTCTAAAACAGTCAGAATGAAGTCCCAATTCAAAAAATTAAGGGCCTTTTGAGGGTCAAT
811561 CTTAAGAGCAATCATAGAGGATAAGGTGGTCTTCCTAGCATAGCCCTTGACAATTTCCTTAGCTA
585 CTTAAGAGCAATCATAGAGGATAAGGTGGTCTTCCTAGCATAGCCCTTGACAATTTCCTTAGCTA
811626 ATAAGGTGTAACCCACAATGCATATCCCTTTAATAAATACAATTTGTTTGTGGGAGACCATGCTC
650 ATAAGGTGTAACCCACAATGCATATCCCTTTAATAAATACAATTTGTTTGTGGGAGACCATGCTC
*
811691 GGGAAGAAAAGTGGAAGTCTTCGCACAAGGATCCTAGGGACGGTCTTGTAAATCACATAGCAACA
715 GGGAAGAAAAGTGCAAGTCTTCGCACAAGGATCCTAGGGACGGTCTTGTAAATCACATAGCAACA
811756 AGAGATGGGATGAAAATCCTTAGCCGAACTTAGATTATGGGACTTAGGCACCAACACTATAGTAG
780 AGAGATGGGATGAAAATCCTTAGCCGAACTTAGATTATGGGACTTAGGCACCAACACTATAGTAG
811821 TCAAATTGAAAGCATGGGACATCATAGAGGAATAAAAGAAGTACTTTACATCAACAATAAAGTTC
845 TCAAATTGAAAGCATGGGACATCATAGAGGAATAAAAGAAGTACTTTACATCAACAATAAAGTTC
811886 TGCCCAACAATAGACTAGGTAGACTTGAAAAAATGGGAAGTATA
910 TGCCCAACAATAGACTAGGTAGACTTGAAAAAATGGGAAGTATA
811930 CCCATTAGGC
Statistics
Matches: 946, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
954 7 0.01
955 939 0.99
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (954 bp):
CCCCTTCAAAAAAACTAACGTAGTCCTTTTTAGAGAGATTGTGGGTCATAAGTGAAACACCTAAA
TACCTTACAGAGAGGAGCCTAATCCTAAAACCAGAAGCCTCATGAATCGTAACCAACAGATTAAT
ATGACCTCATAATAGAGCATCTCGCTCTTAGCAACATTTATCTTTTGGCCAAAAATACAGTAAAA
CTCCTCTAAGACACAAGTAACTCCTATCATCGAGTCAAGAGAACCCTTACAGAGGATAAATAGAT
TATCTGCAAAGTAAAAGTGGGCGACACAGATCTTTCTATGCTTGGGGTAAAATTAACAAATCCTC
TTTTCCACAACTAAGTCTAAGATTTTTTAGAGAACATTCACCGCAAGGAAAAACAAATAGGGGGA
TAGGGGATCCCTTACATGATGCCTCTAGCCCCTTCAAAAAAACTCACGTGACTATCATTAAACGA
GATAAAAAAATCGGGGAAAGTTAACCAAGCTTCAATCCAACCACGAAAAGCATTAGACAGACCTA
TAACCTCTAAAACAGTCAGAATGAAGTCCCAATTCAAAAAATTAAGGGCCTTTTGAGGGTCAATC
TTAAGAGCAATCATAGAGGATAAGGTGGTCTTCCTAGCATAGCCCTTGACAATTTCCTTAGCTAA
TAAGGTGTAACCCACAATGCATATCCCTTTAATAAATACAATTTGTTTGTGGGAGACCATGCTCG
GGAAGAAAAGTGCAAGTCTTCGCACAAGGATCCTAGGGACGGTCTTGTAAATCACATAGCAACAA
GAGATGGGATGAAAATCCTTAGCCGAACTTAGATTATGGGACTTAGGCACCAACACTATAGTAGT
CAAATTGAAAGCATGGGACATCATAGAGGAATAAAAGAAGTACTTTACATCAACAATAAAGTTCT
GCCCAACAATAGACTAGGTAGACTTGAAAAAATGGGAAGTATAT
Found at i:821777 original size:21 final size:21
Alignment explanation
Indices: 821753--821802 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
821743 TTCTTACTAA
*
821753 TTAGTTAGAAACAGTTTTGAG
1 TTAGTTAGAAACAATTTTGAG
821774 TTAGTTAGAAACAATTTTGAG
1 TTAGTTAGAAACAATTTTGAG
821795 TTAGTTAG
1 TTAGTTAG
821803 GTGGTTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (21 bp):
TTAGTTAGAAACAATTTTGAG
Found at i:824116 original size:37 final size:38
Alignment explanation
Indices: 824049--824120 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 38
824039 CATTTAAATG
*
824049 ATAAACGAACACAAATGAATGAACATAAACGAACGGTT
1 ATAAACGAACACAAATAAATGAACATAAACGAACGGTT
824087 ATAAACGAACAC-AATAAATGAACATAAACGAACG
1 ATAAACGAACACAAATAAATGAACATAAACGAACG
824121 TAACCGAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 21 0.64
38 12 0.36
ACGTcount: A:0.56, C:0.17, G:0.14, T:0.14
Consensus pattern (38 bp):
ATAAACGAACACAAATAAATGAACATAAACGAACGGTT
Found at i:824330 original size:14 final size:14
Alignment explanation
Indices: 824307--824371 Score: 76
Period size: 14 Copynumber: 4.6 Consensus size: 14
824297 TGGGCTAAAT
* * *
824307 ATAAATGAACACAC
1 ATAAACGAACATAA
824321 ATAAACGAACATAA
1 ATAAACGAACATAA
*
824335 ACAAACGAACATAA
1 ATAAACGAACATAA
*
824349 ATGAACGAACATAA
1 ATAAACGAACATAA
*
824363 ACAAACGAA
1 ATAAACGAA
824372 TTACCGAACC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.11
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:829859 original size:15 final size:15
Alignment explanation
Indices: 829839--829867 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
829829 ATCTGTTTGA
829839 ATTCAATTAATTTAT
1 ATTCAATTAATTTAT
829854 ATTCAATTAATTTA
1 ATTCAATTAATTTA
829868 CAAATAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTCAATTAATTTAT
Found at i:832682 original size:2 final size:2
Alignment explanation
Indices: 832675--832699 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
832665 ATACAAATTC
832675 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 A
832700 GTTATGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:833456 original size:23 final size:23
Alignment explanation
Indices: 833429--833508 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
833419 CTTTAAATCT
833429 AACTTATTTCACTTATTACATTA
1 AACTTATTTCACTTATTACATTA
* *
833452 AACTTTTACGAATTTGACTCT-TTAAATCTA
1 AAC--TT----ATTTCACT-TATTACAT-TA
833482 -ACTTATTTCACTTATTACATTA
1 AACTTATTTCACTTATTACATTA
833504 AACTT
1 AACTT
833509 TTACTCATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 20
0.64 0.06 0.30
Matches are distributed among these distances:
22 3 0.07
23 19 0.44
25 2 0.05
27 2 0.05
29 14 0.33
30 3 0.07
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (23 bp):
AACTTATTTCACTTATTACATTA
Found at i:833485 original size:29 final size:29
Alignment explanation
Indices: 833399--833485 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
833389 TATTACATTA
833399 AACTTTTACGAATTTCGACTCTTTAAATCT
1 AACTTTTACGAATTT-GACTCTTTAAATCT
* *
833429 AAC--TT----ATTTCACT-TATTACAT-T
1 AACTTTTACGAATTTGACTCT-TTAAATCT
833451 AAACTTTTACGAATTTGACTCTTTAAATCT
1 -AACTTTTACGAATTTGACTCTTTAAATCT
833481 AACTT
1 AACTT
833486 ATTTCACTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 21
0.63 0.06 0.31
Matches are distributed among these distances:
22 2 0.05
23 11 0.26
24 4 0.09
25 2 0.05
28 2 0.05
29 17 0.40
30 5 0.12
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (29 bp):
AACTTTTACGAATTTGACTCTTTAAATCT
Found at i:833493 original size:52 final size:53
Alignment explanation
Indices: 833354--833512 Score: 302
Period size: 53 Copynumber: 3.0 Consensus size: 53
833344 CGACAGAGAT
*
833354 CGAATTTCGACTCTTTCAATCTAACTTATTTCACTTATTACATTAAACTTTTA
1 CGAATTTCGACTCTTTAAATCTAACTTATTTCACTTATTACATTAAACTTTTA
833407 CGAATTTCGACTCTTTAAATCTAACTTATTTCACTTATTACATTAAACTTTTA
1 CGAATTTCGACTCTTTAAATCTAACTTATTTCACTTATTACATTAAACTTTTA
833460 CGAATTT-GACTCTTTAAATCTAACTTATTTCACTTATTACATTAAACTTTTA
1 CGAATTTCGACTCTTTAAATCTAACTTATTTCACTTATTACATTAAACTTTTA
833512 C
1 C
833513 TCATGAATAT
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 46 0.44
53 59 0.56
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.45
Consensus pattern (53 bp):
CGAATTTCGACTCTTTAAATCTAACTTATTTCACTTATTACATTAAACTTTTA
Found at i:838599 original size:12 final size:11
Alignment explanation
Indices: 838573--838612 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
838563 GATAATGATA
*
838573 ATTTAAATAAC
1 ATTTGAATAAC
*
838584 ATTTGATATAAA
1 ATTTGA-ATAAC
838596 ATTTGAATAAC
1 ATTTGAATAAC
838607 ATTTGA
1 ATTTGA
838613 GTTAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:839191 original size:13 final size:14
Alignment explanation
Indices: 839167--839217 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
839157 TATTAAATAA
839167 TAATTGCATGTTAT
1 TAATTGCATGTTAT
839181 TAATT-CATG-T-T
1 TAATTGCATGTTAT
**
839192 GCATTGCATGTTAT
1 TAATTGCATGTTAT
839206 TAATT-CATGTTA
1 TAATTGCATGTTA
839218 CATTAGGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 4 0.13
12 5 0.17
13 12 0.40
14 9 0.30
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (14 bp):
TAATTGCATGTTAT
Found at i:839229 original size:25 final size:25
Alignment explanation
Indices: 839169--839221 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
839159 TTAAATAATA
*
839169 ATTGCATGTTATTAATTCATGTTGC
1 ATTGCATGTTATTAATTCATGTTAC
839194 ATTGCATGTTATTAATTCATGTTAC
1 ATTGCATGTTATTAATTCATGTTAC
839219 ATT
1 ATT
839222 AGGTGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (25 bp):
ATTGCATGTTATTAATTCATGTTAC
Found at i:839993 original size:2 final size:2
Alignment explanation
Indices: 839982--840143 Score: 121
Period size: 2 Copynumber: 84.0 Consensus size: 2
839972 ATAGTATTTC
839982 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
840023 TA TA TA TA TA TA TA TA -A TC TA TA GA T- TA CT- TA TA T- TA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * *
840062 TA TA CA TA TA TA TA CTA TA T- TA -A TA TA AA T- TA TA -A TT TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
840101 TA AA CTA TA TA T- TT TA TA TA GTT TA TA CA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
840144 AAAGTTAAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
1 11 0.09
2 110 0.87
3 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:840466 original size:2 final size:2
Alignment explanation
Indices: 840459--840624 Score: 129
Period size: 2 Copynumber: 86.0 Consensus size: 2
840449 ACTCACTTGA
840459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
840501 AT AT AT AT AT AT AT AT -T AT -T AT AT AT AGT -T CAT AT AA AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT AT
* * * *
840542 A- AT TT AT AT AT AG CT -T AT A- AT A- AT -T AT AT AGT TT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
840579 AT AT AA AT AT AGT TT AT AT AT AA ACT -T AT AT AT AT AT AT -T AT
1 AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
840621 AT AT
1 AT AT
840625 TTTTTTCCAA
Statistics
Matches: 132, Mismatches: 16, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
1 11 0.08
2 117 0.89
3 4 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:842420 original size:29 final size:29
Alignment explanation
Indices: 842386--842444 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
842376 CCTAAATTAA
842386 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
842415 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
842444 T
1 T
842445 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:847090 original size:28 final size:29
Alignment explanation
Indices: 847035--847092 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
847025 ACCTAATTAA
847035 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
847064 TTTGATGTCATTGC-TACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
847092 T
1 T
847093 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:848475 original size:26 final size:28
Alignment explanation
Indices: 848415--848476 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
848405 GAGTATTGCT
*
848415 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
848446 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
848472 GAGCT
1 GAGCT
848477 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:851295 original size:48 final size:48
Alignment explanation
Indices: 851224--851326 Score: 170
Period size: 48 Copynumber: 2.1 Consensus size: 48
851214 CCTAAATTTT
* *
851224 CAGGATTTAACTTCACTAAATAACGAAGAAAATCAACAAGAGGACAAA
1 CAGGATTTAACTTCACCAAATAACAAAGAAAATCAACAAGAGGACAAA
* *
851272 CAGGATTTCACTTCACCAAATAACAAAGAAAATCAACAAGAGGACAAT
1 CAGGATTTAACTTCACCAAATAACAAAGAAAATCAACAAGAGGACAAA
851320 CAGGATT
1 CAGGATT
851327 CGGTGGAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (48 bp):
CAGGATTTAACTTCACCAAATAACAAAGAAAATCAACAAGAGGACAAA
Found at i:852005 original size:14 final size:14
Alignment explanation
Indices: 851986--852030 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
851976 CGTTCATTTA
*
851986 TATTTATGTCCATT
1 TATTTATGTTCATT
*
852000 TATTTATGTTCGTT
1 TATTTATGTTCATT
*
852014 CATTTATGTTCATT
1 TATTTATGTTCATT
852028 TAT
1 TAT
852031 GTTCGAACAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (14 bp):
TATTTATGTTCATT
Found at i:852026 original size:10 final size:10
Alignment explanation
Indices: 851951--852034 Score: 50
Period size: 10 Copynumber: 8.4 Consensus size: 10
851941 GTGCTTGTTC
*
851951 GTTCATTTAC
1 GTTCATTTAT
851961 GTTCGATTATAT
1 GTTC-ATT-TAT
* *
851973 GTTCGTTCAT
1 GTTCATTTAT
*
851983 -TTATATTTAT
1 GTT-CATTTAT
*
851993 GTCCATTTAT
1 GTTCATTTAT
*
852003 -TT-ATGTT-C
1 GTTCAT-TTAT
852011 GTTCATTTAT
1 GTTCATTTAT
852021 GTTCATTTAT
1 GTTCATTTAT
852031 GTTC
1 GTTC
852035 GAACAGAGGG
Statistics
Matches: 55, Mismatches: 11, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
8 2 0.04
9 9 0.16
10 32 0.58
11 6 0.11
12 6 0.11
ACGTcount: A:0.19, C:0.13, G:0.12, T:0.56
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:852330 original size:23 final size:22
Alignment explanation
Indices: 852298--852346 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
852288 GTGTTTGTGT
* *
852298 TGTTCGTTTATATTCATTTATTG
1 TGTTCCTTTATATTCA-TTATTA
*
852321 TGTTCCTTTATGTTCATTATTA
1 TGTTCCTTTATATTCATTATTA
852343 TGTT
1 TGTT
852347 ATGTTCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.16, C:0.10, G:0.12, T:0.61
Consensus pattern (22 bp):
TGTTCCTTTATATTCATTATTA
Found at i:852383 original size:74 final size:70
Alignment explanation
Indices: 852276--852429 Score: 204
Period size: 74 Copynumber: 2.2 Consensus size: 70
852266 TGTTCGAATA
* *
852276 AGTTTGTTT-TTTGTGTTTGTGTTGTTCGTTTATATTCATTTATTGTGTTCCTTTATGTTCATTA
1 AGTTCGTTTGTTTGTGTTTGTGTTGTTCGTTTATATTCATTTATTGTGTTCCTTTATGTT-AAT-
852340 TTATGTT
64 TTATGTT
** *
852347 ATGTTCGTTTGTTTGTGTTTGT-TTACGTTCGTTTATATTTGTTTATTGTGTTCGTTTATGTTAA
1 A-GTTCGTTTGTTTGTGTTTGTGTT--GTTCGTTTATATTCATTTATTGTGTTCCTTTATGTTAA
852411 TTTATGTT
63 TTTATGTT
852419 AGTTCGTTTGT
1 AGTTCGTTTGT
852430 GTTCGTTTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
71 11 0.15
72 17 0.23
73 13 0.18
74 33 0.45
ACGTcount: A:0.12, C:0.06, G:0.19, T:0.62
Consensus pattern (70 bp):
AGTTCGTTTGTTTGTGTTTGTGTTGTTCGTTTATATTCATTTATTGTGTTCCTTTATGTTAATTT
ATGTT
Found at i:852390 original size:10 final size:10
Alignment explanation
Indices: 852353--852418 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
852343 TGTTATGTTC
*
852353 GTTTGTTTGT
1 GTTTGTTTAT
*
852363 GTTTGTTTAC
1 GTTTGTTTAT
*
852373 GTTCGTTTAT
1 GTTTGTTTAT
*
852383 ATTTGTTTATT
1 GTTTGTTTA-T
852394 GTGTTCGTTTAT
1 GT-TT-GTTTAT
**
852406 GTTAATTTAT
1 GTTTGTTTAT
852416 GTT
1 GTT
852419 AGTTCGTTTG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 31 0.70
11 3 0.07
12 5 0.11
13 5 0.11
ACGTcount: A:0.12, C:0.05, G:0.20, T:0.64
Consensus pattern (10 bp):
GTTTGTTTAT
Found at i:852415 original size:33 final size:33
Alignment explanation
Indices: 852358--852438 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
852348 TGTTCGTTTG
* ** *
852358 TTTGTGTTTGTTTACGTTCGTTTATATTTGTT-
1 TTTGTGTTCGTTTACGTTAATTTATATTAGTTC
* *
852390 TATTGTGTTCGTTTATGTTAATTTATGTTAGTTC
1 T-TTGTGTTCGTTTACGTTAATTTATATTAGTTC
852424 GTTTGTGTTCGTTTA
1 -TTTGTGTTCGTTTA
852439 ATTTCGTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 1 0.03
33 25 0.62
34 13 0.32
35 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.20, T:0.62
Consensus pattern (33 bp):
TTTGTGTTCGTTTACGTTAATTTATATTAGTTC
Found at i:852438 original size:24 final size:24
Alignment explanation
Indices: 852340--852438 Score: 57
Period size: 24 Copynumber: 4.1 Consensus size: 24
852330 ATGTTCATTA
* *
852340 TTATGTTATGTTCGTTTGT-TTGT
1 TTATGTTACGTTCGTTTATGTTGT
*
852363 GTT-TGTTTACGTTCGTTTATATTTGT
1 -TTATG-TTACGTTCGTTTAT-GTTGT
*
852389 TTAT-TGT--GTTCGTTTATGTTAAT
1 TTATGT-TACGTTCGTTTATGTT-GT
*
852412 TTATGTTA-GTTCGTTTGTGTTCGT
1 TTATGTTACGTTCGTTTATGTT-GT
852436 TTA
1 TTA
852439 ATTTCGTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
22 2 0.03
23 18 0.30
24 32 0.53
25 3 0.05
26 5 0.08
ACGTcount: A:0.12, C:0.06, G:0.20, T:0.62
Consensus pattern (24 bp):
TTATGTTACGTTCGTTTATGTTGT
Found at i:853102 original size:22 final size:23
Alignment explanation
Indices: 853067--853116 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
853057 CATTTTATCG
*
853067 CATTTCAACAAAATTAC-TTAAA
1 CATTTTAACAAAATTACTTTAAA
*
853089 CATTTTAACCAAATTACTTTAAA
1 CATTTTAACAAAATTACTTTAAA
853112 -ATTTT
1 CATTTT
853117 TAGATGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (23 bp):
CATTTTAACAAAATTACTTTAAA
Found at i:859989 original size:3 final size:3
Alignment explanation
Indices: 859981--860019 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
859971 AACATTAAAT
*
859981 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA
860020 TTTTTTCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:860476 original size:128 final size:128
Alignment explanation
Indices: 860302--860935 Score: 560
Period size: 128 Copynumber: 5.0 Consensus size: 128
860292 TTAGGATTGA
* * * * * *
860302 TGATAACTCAGTTCTTACGTGATGAGGACGGCTGGTTATCTAGGTTGAAATAGCTCCTACACAAT
1 TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGAAACAGCTCCTACATAAT
* * * * * *
860367 GAAGAGATATGGTCGGGTGATGACACGACTCATACGTGATGAAGAGTTCTGGCCATTTAAAAG
66 GAGGAGATCTGGTCAGGTGATGACACGATTCATACGTGATGAAGAGTTCTGGCCATCTAAAGG
* * * * * *
860430 TGATAACACGGTTCCTACGTGATAAAGACAGTTGGCTATCTGGGTTGACACAGCTCCTACATAAT
1 TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGAAACAGCTCCTACATAAT
* * * * * * * * ** *
860495 GAGGAAATCGGGTCTGGTGATGACAC-AGTTCCTGCGCGATGAGGA-TGGCAAGCCATCTAAGGG
66 GAGGAGATCTGGTCAGGTGATGACACGA-TTCATACGTGATGAAGAGT-TCTGGCCATCTAAAGG
* * * **
860558 TGATAACACGGTTCCTACGTGATGAAGATGGCTGGTTATCTAGGATTGACTCAGCTCCTACATAA
1 TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT-GGGTTGAAACAGCTCCTACATAA
* * * * * *
860623 TGAGGAAATCTGGCCAGTTGATGTCACGACTCATACGTGATGAAGAGTTATGGCCATCTAAAGG
65 TGAGGAGATCTGGTCAGGTGATGACACGATTCATACGTGATGAAGAGTTCTGGCCATCTAAAGG
* * * * * ** * * *
860687 TGATAACACGTTTCTTACATGACGAGGACGACTGACTATCTGGGTTGATACAACTCTTACATAAT
1 TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGAAACAGCTCCTACATAAT
* * * * * *
860752 GAGGAGATATGGTCA-GTGATGACA-TAGTTCTTACGTGATGAGGACG-ACAT-GCCATCTAAGG
66 GAGGAGATCTGGTCAGGTGATGACACGA-TTCATACGTGATGAAGA-GTTC-TGGCCATCTAAAG
860813 G
128 G
* * * * * * *
860814 TGATAACACGGTTCCTACGTGATGAGGACGGTTGATTATATGGATTGACACAACTCCAACATAAT
1 TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGAAACAGCTCCTACATAAT
* * * * *
860879 GAGGAGACCTGGTCAGGTGATGACATGATTCATACGTGGTGAAGAGTTTTGGTCATC
66 GAGGAGATCTGGTCAGGTGATGACACGATTCATACGTGATGAAGAGTTCTGGCCATC
860936 CTTAGGGATT
Statistics
Matches: 397, Mismatches: 97, Indels: 24
0.77 0.19 0.05
Matches are distributed among these distances:
126 1 0.00
127 102 0.26
128 193 0.49
129 99 0.25
130 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (128 bp):
TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGAAACAGCTCCTACATAAT
GAGGAGATCTGGTCAGGTGATGACACGATTCATACGTGATGAAGAGTTCTGGCCATCTAAAGG
Found at i:861050 original size:66 final size:66
Alignment explanation
Indices: 860979--861106 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
860969 GGAGATGATG
* * *
860979 CTTCAAAAGAAGCTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 CTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGATTTT
861044 T
66 T
* * * ** * * *
861045 CTTCAACAGAAATTGTCTCGATTGAGACGATACTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 CTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGAT
861107 GGTCAATAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (66 bp):
CTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGATTTT
T
Found at i:861216 original size:32 final size:32
Alignment explanation
Indices: 861175--861262 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
861165 TTCGCATCAG
861175 GATGTTGAATCCCTAAAGATGCCCCAATATTC
1 GATGTTGAATCCCTAAAGATGCCCCAATATTC
*
861207 GATGTTGAATCTCC-AAAGATGCCCCAATATTT
1 GATGTTGAATC-CCTAAAGATGCCCCAATATTC
*
861239 GATGTTGAAT-CTTCAAAGATGCCC
1 GATGTTGAATCCCT-AAAGATGCCC
861263 TCTATTGCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
30 1 0.02
32 48 0.94
33 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCCCTAAAGATGCCCCAATATTC
Found at i:862342 original size:3 final size:3
Alignment explanation
Indices: 862330--862359 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
862320 TTTCTCTTTG
862330 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
862360 AAGTGTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:866714 original size:63 final size:63
Alignment explanation
Indices: 866545--866715 Score: 209
Period size: 63 Copynumber: 2.7 Consensus size: 63
866535 TATGATGATC
* * *
866545 ATGCAGAATGCGAAGATGCAAATGTTGATGCAAAATTGACGATCCTATAAAATGCAATGCATA
1 ATGCAGAATGCGAAGATGCAAATGTAGATGCAAAAATGATGATCCTATAAAATGCAATGCATA
* * * * * *
866608 ATGC-GAAATACGAAGATGCAAATGTAGATGTAAAAGTGATGATCCTATGAAATGTATTGCATA
1 ATGCAG-AATGCGAAGATGCAAATGTAGATGCAAAAATGATGATCCTATAAAATGCAATGCATA
* * * *
866671 ATGCAGAATGCGAAGATGCAGATGCAAATGCAAAAATGTTGATCC
1 ATGCAGAATGCGAAGATGCAAATGTAGATGCAAAAATGATGATCC
866716 CAGTGATGGA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
62 1 0.01
63 89 0.98
64 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (63 bp):
ATGCAGAATGCGAAGATGCAAATGTAGATGCAAAAATGATGATCCTATAAAATGCAATGCATA
Found at i:886128 original size:60 final size:59
Alignment explanation
Indices: 885982--886128 Score: 170
Period size: 60 Copynumber: 2.4 Consensus size: 59
885972 AATTATGGGT
* *
885982 AAAG-TACACAAATGGTCCCCTGACTATATGATACTGCTTTATTAAGTCCATCGACTATTA
1 AAAGTTACA-AAATGGT-CCCTGACTATATAATACTACTTTATTAAGTCCATCGACTATTA
* * * ** * *
886042 AAAGTTACAAAATGATCCTTTAACTATATAATGTTACTTTGTTAAGTCCCTCGACTATTA
1 AAAGTTACAAAATGGTCC-CTGACTATATAATACTACTTTATTAAGTCCATCGACTATTA
886102 AAAGTTACAAAATGGTCACCTGACTAT
1 AAAGTTACAAAATGGTC-CCTGACTAT
886129 TTATTATATT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
59 2 0.03
60 65 0.90
61 5 0.07
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCCCTGACTATATAATACTACTTTATTAAGTCCATCGACTATTA
Found at i:888850 original size:21 final size:22
Alignment explanation
Indices: 888825--888866 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
888815 TTTGTTTTAT
888825 AATTGACTCGAATTT-TAAAAA
1 AATTGACTCGAATTTATAAAAA
* *
888846 AATTGAGTCGAGTTTATAAAA
1 AATTGACTCGAATTTATAAAA
888867 TTACGTGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (22 bp):
AATTGACTCGAATTTATAAAAA
Found at i:889445 original size:18 final size:16
Alignment explanation
Indices: 889404--889436 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
889394 GGGGTTCTTC
889404 GGGTGGTTGTGTCATT
1 GGGTGGTTGTGTCATT
889420 GGGTGGTTGTGTCATT
1 GGGTGGTTGTGTCATT
889436 G
1 G
889437 ATGGTGGTTA
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:0.06, C:0.06, G:0.45, T:0.42
Consensus pattern (16 bp):
GGGTGGTTGTGTCATT
Found at i:890436 original size:101 final size:100
Alignment explanation
Indices: 890245--890446 Score: 388
Period size: 99 Copynumber: 2.0 Consensus size: 100
890235 ATTTATTCAA
890245 TCTCTAACTTAATAAGGAGATATTGTGGTATTGATATCATATATATATATATATATAAGGGATTG
1 TCTCTAACTTAATAAGGAGATATTGTGGTATTGATATCA-ATATATATATATATATAAGGGATTG
890310 ATATCTAAATGAAATAGGAAAGTGTGTGACAATTTC
65 ATATCTAAATGAAATAGGAAAGTGTGTGACAATTTC
890346 TCTCTAACTTAATAAGGAGATATTGTGGTATTGATATC-ATATATATATATATATAAGGGATTGA
1 TCTCTAACTTAATAAGGAGATATTGTGGTATTGATATCAATATATATATATATATAAGGGATTGA
890410 TATCTAAATGAAATAGGAAAGTGTGTGACAATTTC
66 TATCTAAATGAAATAGGAAAGTGTGTGACAATTTC
890445 TC
1 TC
890447 ATAATATCAA
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
99 63 0.62
101 38 0.38
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (100 bp):
TCTCTAACTTAATAAGGAGATATTGTGGTATTGATATCAATATATATATATATATAAGGGATTGA
TATCTAAATGAAATAGGAAAGTGTGTGACAATTTC
Found at i:891692 original size:24 final size:23
Alignment explanation
Indices: 891665--891713 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
891655 AAAAACCATA
*
891665 AAATCAAGTAAAACAAAATGATTT
1 AAATCAACTAAAACAAAAT-ATTT
* *
891689 AAATCAACTACAACATAATATTT
1 AAATCAACTAAAACAAAATATTT
891712 AA
1 AA
891714 GGTAAAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (23 bp):
AAATCAACTAAAACAAAATATTT
Found at i:892064 original size:36 final size:36
Alignment explanation
Indices: 892014--892089 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
892004 TTATAGCAAA
*
892014 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
892050 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
892086 AAAA
1 AAAA
892090 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:896590 original size:15 final size:15
Alignment explanation
Indices: 896572--896601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
896562 CCACGGTGCT
*
896572 CCCGGAATCCTGCGC
1 CCCGAAATCCTGCGC
896587 CCCGAAATCCTGCGC
1 CCCGAAATCCTGCGC
896602 GATTGTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (15 bp):
CCCGAAATCCTGCGC
Found at i:897077 original size:36 final size:36
Alignment explanation
Indices: 897027--897102 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
897017 TTATAGCAAA
* *
897027 AAAAATCGTCTTTATTTGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
897063 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
897099 AAAA
1 AAAA
897103 TCCCGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:897980 original size:30 final size:30
Alignment explanation
Indices: 897913--897980 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
897903 AGTGAACCGG
* *
897913 CGGTTCAAACCGGTTTTGCCGGTTTTCAGC
1 CGGTTCATACCGGTTTTACCGGTTTTCAGC
*
897943 CGGTTCATCCCGGTTTTACCGGTTTTCAGC
1 CGGTTCATACCGGTTTTACCGGTTTTCAGC
897973 CGGTTCAT
1 CGGTTCAT
897981 TGCCAGACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.12, C:0.28, G:0.25, T:0.35
Consensus pattern (30 bp):
CGGTTCATACCGGTTTTACCGGTTTTCAGC
Found at i:905598 original size:24 final size:24
Alignment explanation
Indices: 905547--905599 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
905537 TTCCTCGTTG
* *
905547 GTTCCCTGGTCGATTTCTTCATCG
1 GTTCCCTGGTCGATTTCCTCATCA
* *
905571 GTTCCCTGGTCGGTTTCCTCCTCA
1 GTTCCCTGGTCGATTTCCTCATCA
905595 GTTCC
1 GTTCC
905600 TGCATTAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.34, G:0.21, T:0.40
Consensus pattern (24 bp):
GTTCCCTGGTCGATTTCCTCATCA
Found at i:913852 original size:19 final size:17
Alignment explanation
Indices: 913820--913859 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
913810 ATATTACCGC
*
913820 TATTATTATAATATTAT
1 TATTATTATAATATTAA
913837 TATTATTAATTAATATTAA
1 TATTATT-A-TAATATTAA
913856 TATT
1 TATT
913860 TATTTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATTATAATATTAA
Found at i:913952 original size:23 final size:23
Alignment explanation
Indices: 913926--913982 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
913916 TTTACCTAAA
913926 AACCTAAACCCTAATTACAATCT
1 AACCTAAACCCTAATTACAATCT
913949 AACCTAAACCCTAATTACAATCT
1 AACCTAAACCCTAATTACAATCT
*
913972 AACCCAAACCC
1 AACCTAAACCC
913983 AAAGGCCTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (23 bp):
AACCTAAACCCTAATTACAATCT
Found at i:915344 original size:28 final size:26
Alignment explanation
Indices: 915313--915383 Score: 61
Period size: 29 Copynumber: 2.6 Consensus size: 26
915303 AAATATGTTA
* *
915313 TTTATTTATTTTTATTCGGCCATATAAT
1 TTTATTTATTTTTATTCAGCC-CAT-AT
* * * *
915341 TTTAATATATTTTAATTTAGCCCATGT
1 TTT-ATTTATTTTTATTCAGCCCATAT
915368 TTTATTTATTTTTATT
1 TTTATTTATTTTTATT
915384 TTAGCACGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
26 11 0.32
27 4 0.12
28 5 0.15
29 14 0.41
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTATTTATTTTTATTCAGCCCATAT
Found at i:927145 original size:43 final size:43
Alignment explanation
Indices: 927098--927200 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
927088 AATAGGTAAC
* *
927098 GATATATAGAGGCGTTTGT-TTAACAAACGACGTAATAGGTGTT
1 GATATTTAGCGGCGTTTGTCTTAA-AAACGACGTAATAGGTGTT
* *
927141 GATATTTAGCGACGTTTGTCTTAAAAACGCCGTAATAGGTGTT
1 GATATTTAGCGGCGTTTGTCTTAAAAACGACGTAATAGGTGTT
*
927184 GAGATTTAGCGGCGTTT
1 GATATTTAGCGGCGTTT
927201 TTATCACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 49 0.92
44 4 0.08
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (43 bp):
GATATTTAGCGGCGTTTGTCTTAAAAACGACGTAATAGGTGTT
Found at i:927229 original size:43 final size:41
Alignment explanation
Indices: 927182--927303 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 41
927172 GTAATAGGTG
*
927182 TTGAGATTTAGCGGCGTTTTTATCACAAATGCCGC-AATAAGTT
1 TTGAGATTTAGCGGCGTTTTTAT-ACAAACGCCGCTAA-AA-TT
* * *
927225 TTGAGATTTAGTGGCATTTTTTATGCAAACGCCGCTAAAATT
1 TTGAGATTTAGCGGC-GTTTTTATACAAACGCCGCTAAAATT
*
927267 CTG-GTATTTAGCGGCGTTTTTAGGATACAAACGCCGC
1 TTGAG-ATTTAGCGGCGTTTTT---ATACAAACGCCGC
927304 GATAGGTCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
41 6 0.09
42 13 0.20
43 25 0.38
44 21 0.32
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (41 bp):
TTGAGATTTAGCGGCGTTTTTATACAAACGCCGCTAAAATT
Found at i:927287 original size:42 final size:44
Alignment explanation
Indices: 927165--927287 Score: 114
Period size: 43 Copynumber: 2.9 Consensus size: 44
927155 TTTGTCTTAA
* *
927165 AAACGCCGTAATAGGTGT-TGAGATTTAGCGGCG-TTTTTATCAC
1 AAACGCCGCAATAAGT-TCTGAGATTTAGCGGCGTTTTTTATCAC
* * * * *
927208 AAATGCCGCAATAAGTTTTGAGATTTAGTGGCATTTTTTAT-GC
1 AAACGCCGCAATAAGTTCTGAGATTTAGCGGCGTTTTTTATCAC
927251 AAACGCCGCTAA-AA-TTCTG-GTATTTAGCGGCGTTTTT
1 AAACGCCGC-AATAAGTTCTGAG-ATTTAGCGGCGTTTTT
927288 AGGATACAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
41 1 0.02
42 19 0.29
43 37 0.56
44 9 0.14
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (44 bp):
AAACGCCGCAATAAGTTCTGAGATTTAGCGGCGTTTTTTATCAC
Found at i:928594 original size:22 final size:22
Alignment explanation
Indices: 928569--928612 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
928559 AATAAATAAT
928569 TAAA-ATAAAAAAAGTCATGGTA
1 TAAATATAAAAAAAGTCA-GGTA
* *
928591 TAAATGTAAATAAAGTCAGGTA
1 TAAATATAAAAAAAGTCAGGTA
928613 AATTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.25
Consensus pattern (22 bp):
TAAATATAAAAAAAGTCAGGTA
Found at i:929433 original size:83 final size:83
Alignment explanation
Indices: 929303--929528 Score: 253
Period size: 83 Copynumber: 2.7 Consensus size: 83
929293 TTTGTAGGAC
* * * ** * *
929303 AAACGCCGCTATATTA-TTACTCTATTGTGGCATTTTTTGCCCTAACGCCACTATAAACAATACT
1 AAACGCCGCTAAATTACTTACTCTATTGCGGCATTTGTTGAACAAACGCCACTATAAACAACACT
** * *
929367 ATTGCAGCGTTTGTTTGAT
66 ATAACAGCGTTTGTGT-AA
* *
929386 AAACGCCGCTAAATTACTTA-TCTATTGCGTCATTTGTTGAACAAACGCCATTATAAACAACACT
1 AAACGCCGCTAAATTACTTACTCTATTGCGGCATTTGTTGAACAAACGCCACTATAAACAACACT
929450 ATAACAGCGTTTGTGTAA
66 ATAACAGCGTTTGTGTAA
* * * *
929468 AAATGCCGCTAAATTAC-CACTCTATTGCGGCGTTTGTTGAAACAAA-GCTACTATAAACAAC
1 AAACGCCGCTAAATTACTTACTCTATTGCGGCATTTGTTG-AACAAACGCCACTATAAACAAC
929529 TTTATTGTGG
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
81 1 0.01
82 47 0.39
83 70 0.58
84 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (83 bp):
AAACGCCGCTAAATTACTTACTCTATTGCGGCATTTGTTGAACAAACGCCACTATAAACAACACT
ATAACAGCGTTTGTGTAA
Found at i:929542 original size:82 final size:83
Alignment explanation
Indices: 929303--929563 Score: 208
Period size: 83 Copynumber: 3.2 Consensus size: 83
929293 TTTGTAGGAC
* * * * ** * *
929303 AAACGCCGCTATATTA-TTACTCTATTGTGGCATTTTTTGCCCTAACGCCACTATAAACAATACT
1 AAACGCCGCTAAATTACTCA-TCTATTGCGGCATTTGTTGAACAAACGCCACTATAAACAACACT
** ** *
929367 ATTGCAGCGTTTG-TTTGAT
65 ATAACAGCGTTTGAGCT-AA
* * *
929386 AAACGCCGCTAAATTACTTATCTATTGCGTCATTTGTTGAACAAACGCCATTATAAACAACACTA
1 AAACGCCGCTAAATTACTCATCTATTGCGGCATTTGTTGAACAAACGCCACTATAAACAACACTA
*
929451 TAACAGCGTTTGTG-TAA
66 TAACAGCGTTTGAGCTAA
* * * **
929468 AAATGCCGCTAAATTAC-CACTCTATTGCGGCGTTTGTTGAAACAAA-GCTACTATAAACAACTT
1 AAACGCCGCTAAATTACTCA-TCTATTGCGGCATTTGTTG-AACAAACGCCACTATAAACAACAC
**** *
929531 TATTGTGGCGTTTGAGCTAT
64 TATAACAGCGTTTGAGCTAA
929551 AAACGCCGCTAAA
1 AAACGCCGCTAAA
929564 GTATCATTTT
Statistics
Matches: 145, Mismatches: 28, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
81 1 0.01
82 58 0.40
83 83 0.57
84 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (83 bp):
AAACGCCGCTAAATTACTCATCTATTGCGGCATTTGTTGAACAAACGCCACTATAAACAACACTA
TAACAGCGTTTGAGCTAA
Found at i:931275 original size:32 final size:31
Alignment explanation
Indices: 931233--931305 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
931223 CATCGGATAG
931233 GTTGATTTTTAAATCGGGTCAATACCGGATCA
1 GTTGA-TTTTAAATCGGGTCAATACCGGATCA
** * *
931265 GTTAGATTTTAGGTCGGGTCAATATCGGATCG
1 GTT-GATTTTAAATCGGGTCAATACCGGATCA
931297 GTTGATTTT
1 GTTGATTTT
931306 CAGTTTAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 6 0.17
32 28 0.78
33 2 0.06
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.38
Consensus pattern (31 bp):
GTTGATTTTAAATCGGGTCAATACCGGATCA
Found at i:942422 original size:21 final size:21
Alignment explanation
Indices: 942398--942438 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
942388 TTTTAAAAAA
* *
942398 ATATGGTTTTGAGAACAATAT
1 ATATAGTTTTCAGAACAATAT
*
942419 ATATAGTTTTCATAACAATA
1 ATATAGTTTTCAGAACAATA
942439 ACATAATTTA
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:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (21 bp):
ATATAGTTTTCAGAACAATAT
Found at i:942913 original size:20 final size:21
Alignment explanation
Indices: 942859--942921 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
942849 ACAGAACCCC
942859 AGGGGGGTATCGGTTCCCCTTCAA
1 AGGGGGG-ATCGGTT-CCC-TCAA
*
942883 AGGGGGAATCGGTTCCCTC-A
1 AGGGGGGATCGGTTCCCTCAA
* *
942903 TGGGGGGATCGATTCCCTC
1 AGGGGGGATCGGTTCCCTC
942922 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 7 0.20
24 6 0.17
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
AGGGGGGATCGGTTCCCTCAA
Found at i:946772 original size:22 final size:21
Alignment explanation
Indices: 946730--946769 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
946720 GAGTTTGTTT
*
946730 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
946751 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
946770 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:950632 original size:95 final size:95
Alignment explanation
Indices: 950522--950720 Score: 337
Period size: 95 Copynumber: 2.1 Consensus size: 95
950512 AGATTATAAT
*
950522 ATTAT-ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
950586 AGATAAGATTCAGCTAGCCTGATAAAGATG
66 AGATAAGATTCAGCTAGCCTGATAAAGATG
* * *
950616 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGGAATTGGTTAAACGCCGCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
950681 AGATAAGATTTAGCTAGCCTGATAAAGGTG
66 AGATAAGATTCAGCTAGCCTGATAAAGATG
950711 ATTATAATAT
1 ATTATAATAT
950721 TAAGCTGTCC
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 5 0.05
95 93 0.95
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
AGATAAGATTCAGCTAGCCTGATAAAGATG
Found at i:952434 original size:85 final size:84
Alignment explanation
Indices: 952187--952600 Score: 497
Period size: 85 Copynumber: 4.9 Consensus size: 84
952177 CTATTATATT
* * *
952187 ATAGCTCAAGGCGAGAAGGGCTATATGTCAACCAAAACCTTCGAATTCGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAA-CAAAAACTTCGAGTTCGATTACATTCAGCTCAA
*
952252 GGACATATCAAATTTATAGC
65 GGACATATCAAATTTACAGC
* * * ** * * *
952272 ATAGCTCGAGGAGAGAAGGCCTATCACTCAACCAAAACTTCGAGTTCGATTACAATCAGCT-TAG
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTCGAGTTCGATTACATTCAGCTCAAG
952336 GACATATCAAATTTACAGC
66 GACATATCAAATTTACAGC
* * * * * * **
952355 ATAACTCAAGGCAAGAAGGGTTATCTGTCAATAAAAATCTTCGATTTTGATTTGATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAA-CTTCGAGTTCGATTACATTCAGCTCAA
* *
952420 GGGCATATCAAATTTACAAC
65 GGACATATCAAATTTACAGC
* * * *
952440 ATAGCTTAAGGCGAGAAGGGCTATCTGTTAATAAAAACCTTCGAGTTCGATTATATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAA-CTTCGAGTTCGATTACATTCAGCTCAA
*
952505 GGGCATATCAAATTTACAGC
65 GGACATATCAAATTTACAGC
* * * *
952525 ATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACTCTCGAGTTTGATTCCATTCAGCTCGA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACT-TCGAGTTCGATTACATTCAGCTCAA
*
952590 TGACATATCAA
65 GGACATATCAA
952601 CCGCATGGTA
Statistics
Matches: 275, Mismatches: 51, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
83 47 0.17
84 47 0.17
85 181 0.66
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (84 bp):
ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTCGAGTTCGATTACATTCAGCTCAAG
GACATATCAAATTTACAGC
Found at i:954968 original size:15 final size:16
Alignment explanation
Indices: 954934--954970 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
954924 CATACCAGTT
954934 TTTTGTCTTAAAAATGA
1 TTTT-TCTTAAAAATGA
954951 TTTTTCTTAAAAAT-A
1 TTTTTCTTAAAAATGA
954966 TTTTT
1 TTTTT
954971 AAAAGACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 10 0.50
17 4 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTTTCTTAAAAATGA
Found at i:955567 original size:4 final size:4
Alignment explanation
Indices: 955558--955595 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
955548 GCTAACAACC
955558 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CT
1 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CT
955596 GCAGTAACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CTAA
Found at i:956342 original size:16 final size:16
Alignment explanation
Indices: 956321--956355 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
956311 ATTTCAATAT
* *
956321 GTTCGGGTTGTTTTTG
1 GTTCGGGTTATTTTCG
956337 GTTCGGGTTATTTTCG
1 GTTCGGGTTATTTTCG
956353 GTT
1 GTT
956356 TTGGATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.09, G:0.34, T:0.54
Consensus pattern (16 bp):
GTTCGGGTTATTTTCG
Found at i:958006 original size:24 final size:24
Alignment explanation
Indices: 957979--958236 Score: 123
Period size: 24 Copynumber: 10.8 Consensus size: 24
957969 TTTCTTATCA
*
957979 GTTTCCTGGTTGGTTCCCTCGACG
1 GTTTCCTCGTTGGTTCCCTCGACG
* * * * *
958003 GTTTTCTTGCTAGTTCTCTC-ATCG
1 GTTTCCTCGTTGGTTCCCTCGA-CG
* * *
958027 GTTTCTTCATTTGTTCCCTC-ACCG
1 GTTTCCTCGTTGGTTCCCTCGA-CG
* * * **
958051 GTTTCCTCATTGATTCCCTTGATA
1 GTTTCCTCGTTGGTTCCCTCGACG
* *
958075 GTTTCCTCGCTGGTTCCCTCAACG
1 GTTTCCTCGTTGGTTCCCTCGACG
* * *
958099 GTTTCCTCTTTGTTTCCCTCGCCG
1 GTTTCCTCGTTGGTTCCCTCGACG
* * *
958123 G-TTCCTTCGTTGATTGCCTCGCCG
1 GTTTCC-TCGTTGGTTCCCTCGACG
* *
958147 GTTCCCTCGTTGGTTCTCTC-ATCG
1 GTTTCCTCGTTGGTTCCCTCGA-CG
* ** * *
958171 G-TTCCTTTGCCGGTTCCCT-TATTG
1 GTTTCC-TCGTTGGTTCCCTCGA-CG
* * *
958195 ATTTCCTCATTGGTTCCCTCGCCG
1 GTTTCCTCGTTGGTTCCCTCGACG
*
958219 GTTTCCTCGTCGGTTCCC
1 GTTTCCTCGTTGGTTCCC
958237 CAGTCTGTGT
Statistics
Matches: 169, Mismatches: 56, Indels: 18
0.70 0.23 0.07
Matches are distributed among these distances:
23 8 0.05
24 153 0.91
25 8 0.05
ACGTcount: A:0.06, C:0.33, G:0.19, T:0.42
Consensus pattern (24 bp):
GTTTCCTCGTTGGTTCCCTCGACG
Found at i:958183 original size:36 final size:37
Alignment explanation
Indices: 958139--958234 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 37
958129 TCGTTGATTG
958139 CCTCGCCGGTTCCCTCGTTGGTTCT-CTCATCGGTTC
1 CCTCGCCGGTTCCCTCGTTGGTTCTCCTCATCGGTTC
* * ** * *
958175 CTTTGCCGGTTCCCTTATTGATT-TCCTCATTGGTTC
1 CCTCGCCGGTTCCCTCGTTGGTTCTCCTCATCGGTTC
* *
958211 CCTCGCCGGTTTCCTCGTCGGTTC
1 CCTCGCCGGTTCCCTCGTTGGTTC
958235 CCCAGTCTGT
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
35 1 0.02
36 44 0.98
ACGTcount: A:0.04, C:0.35, G:0.21, T:0.40
Consensus pattern (37 bp):
CCTCGCCGGTTCCCTCGTTGGTTCTCCTCATCGGTTC
Found at i:958258 original size:24 final size:24
Alignment explanation
Indices: 958231--958281 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
958221 TTCCTCGTCG
*
958231 GTTCCCCAGTCTGTGTCCACATCA
1 GTTCCCCAGTCGGTGTCCACATCA
*
958255 GTTCCCCAGTCGGTGTCCACGTCA
1 GTTCCCCAGTCGGTGTCCACATCA
958279 GTT
1 GTT
958282 TCGGCATGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.35, G:0.22, T:0.29
Consensus pattern (24 bp):
GTTCCCCAGTCGGTGTCCACATCA
Found at i:958333 original size:36 final size:36
Alignment explanation
Indices: 958292--958366 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
958282 TCGGCATGGA
958292 TTCCCTGGCCAGTTC-GTCCACTGGTTCCCGCAGTGG
1 TTCCCTGGCCAGTTCGGT-CACTGGTTCCCGCAGTGG
*** * *
958328 TTCCCTGGTTGGTTCGGTCACTGGTTCCCTCATTGG
1 TTCCCTGGCCAGTTCGGTCACTGGTTCCCGCAGTGG
958364 TTC
1 TTC
958367 GCTGTCTGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 31 0.94
37 2 0.06
ACGTcount: A:0.07, C:0.32, G:0.27, T:0.35
Consensus pattern (36 bp):
TTCCCTGGCCAGTTCGGTCACTGGTTCCCGCAGTGG
Found at i:958375 original size:24 final size:24
Alignment explanation
Indices: 958325--958383 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
958315 GTTCCCGCAG
** *
958325 TGGTTCCCTGGTTGGTTCGGTCAC
1 TGGTTCCCTCATTGGTTCGCTCAC
**
958349 TGGTTCCCTCATTGGTTCGCTGTC
1 TGGTTCCCTCATTGGTTCGCTCAC
*
958373 TGGTTTCCTCA
1 TGGTTCCCTCA
958384 CCTGGCCATG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.05, C:0.27, G:0.27, T:0.41
Consensus pattern (24 bp):
TGGTTCCCTCATTGGTTCGCTCAC
Found at i:960903 original size:21 final size:21
Alignment explanation
Indices: 960879--960919 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
960869 TTGTTAGATC
960879 TTTTACGACTTTACCCCTACA
1 TTTTACGACTTTACCCCTACA
***
960900 TTTTTTTACTTTACCCCTAC
1 TTTTACGACTTTACCCCTAC
960920 TTTAAGCTTA
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:0.20, C:0.32, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTACGACTTTACCCCTACA
Found at i:962700 original size:33 final size:34
Alignment explanation
Indices: 962646--962710 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
962636 TACCTAACTC
* *
962646 TCACCTAACTAATTTGATGTAAGCAATGACATCT
1 TCACCTAACTAAATTGATGTAAGCAATAACATCT
962680 TCACCTAAC-AAATTGATGTAAGCAATAACAT
1 TCACCTAACTAAATTGATGTAAGCAATAACAT
962711 GAAATTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (34 bp):
TCACCTAACTAAATTGATGTAAGCAATAACATCT
Found at i:964498 original size:12 final size:12
Alignment explanation
Indices: 964481--964506 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
964471 AGTTTCAAGC
964481 TCTTGTTGAGGT
1 TCTTGTTGAGGT
964493 TCTTGTTGAGGT
1 TCTTGTTGAGGT
964505 TC
1 TC
964507 ACCTAGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.12, G:0.31, T:0.50
Consensus pattern (12 bp):
TCTTGTTGAGGT
Found at i:971220 original size:16 final size:16
Alignment explanation
Indices: 971188--971235 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
971178 GACTTTGGAC
*
971188 CTAAAATAAAATGAAAA
1 CTAAAAT-AAATAAAAA
971205 -TGAAAATAAATAAAAA
1 CT-AAAATAAATAAAAA
*
971221 CTAAACTAAATAAAA
1 CTAAAATAAATAAAA
971236 TAAAATAGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (16 bp):
CTAAAATAAATAAAAA
Found at i:971372 original size:28 final size:28
Alignment explanation
Indices: 971340--971400 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
971330 AAATATACAT
*
971340 TATATGTTTTCAAAAACTGCATA-TTATA
1 TATAT-TTTTCAAAAACTACATAGTTATA
*
971368 TATATTTTTTAAAAACTACATAGTTATA
1 TATATTTTTCAAAAACTACATAGTTATA
971396 TATAT
1 TATAT
971401 ATATATATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (28 bp):
TATATTTTTCAAAAACTACATAGTTATA
Found at i:992156 original size:19 final size:19
Alignment explanation
Indices: 992132--992256 Score: 89
Period size: 21 Copynumber: 6.3 Consensus size: 19
992122 ATAAAGTCAT
992132 ATATATTTTAAAATATATA
1 ATATATTTTAAAATATATA
992151 ATATATATTTCAAAACTATAT-
1 ATATAT-TTT-AAAA-TATATA
* *
992172 ATAT-TTTCCAAAACATAT-
1 ATATATTT-TAAAATATATA
*
992190 ATATATTTCAAAA-ATATA
1 ATATATTTTAAAATATATA
992208 ATAT-TTTTCAAAAATATAATA
1 ATATATTTT--AAAATAT-ATA
*
992229 TATATTTTTTAAAACTATATA
1 -ATATATTTTAAAA-TATATA
992250 TATATAT
1 -ATATAT
992257 ATATTTAAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
17 7 0.08
18 17 0.19
19 19 0.21
20 6 0.07
21 24 0.27
22 12 0.13
23 4 0.04
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATTTTAAAATATATA
Found at i:992198 original size:37 final size:38
Alignment explanation
Indices: 992130--992252 Score: 144
Period size: 37 Copynumber: 3.2 Consensus size: 38
992120 GAATAAAGTC
*
992130 ATATATATTTT-AAAATATATAATATATATTTCAAAACT
1 ATATATATTTTCAAAA-ACATAATATATATTTCAAAACT
* *
992168 ATATATATTTTCCAAAACAT-ATATATATTTCAAAAAT
1 ATATATATTTTCAAAAACATAATATATATTTCAAAACT
* *
992205 ATA-ATATTTTTCAAAAATATAATATATATTTTTTAAAACT
1 ATATATA-TTTTCAAAAACATAATATATA--TTTCAAAACT
992245 ATATATAT
1 ATATATAT
992253 ATATATATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
36 3 0.04
37 30 0.42
38 21 0.29
39 3 0.04
40 12 0.17
41 3 0.04
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.45
Consensus pattern (38 bp):
ATATATATTTTCAAAAACATAATATATATTTCAAAACT
Done.