Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003924.1 Hibiscus syriacus cultivar Beakdansim tig00008483_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: 1466330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 5
Found at i:341119 original size:20 final size:20
Alignment explanation
Indices: 341094--341136 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
341084 ATTTTTTTTC
**
341094 AAAAAAAAGGAAAAAAAACA
1 AAAAAAAACCAAAAAAAACA
*
341114 AAAAAAAACCAAAAAAACCA
1 AAAAAAAACCAAAAAAAACA
341134 AAA
1 AAA
341137 TTTCAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAAACCAAAAAAAACA
Found at i:350835 original size:21 final size:19
Alignment explanation
Indices: 350809--350858 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
350799 GAAACCCCTT
350809 TGAAAATACAGGACTTTTAAA
1 TGAAAATACAGGA-TTTT-AA
*
350830 TGAAAATACATGATTTTAA
1 TGAAAATACAGGATTTTAA
*
350849 TGAATATACA
1 TGAAAATACA
350859 TGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (19 bp):
TGAAAATACAGGATTTTAA
Found at i:350852 original size:19 final size:21
Alignment explanation
Indices: 350809--350860 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
350799 GAAACCCCTT
*
350809 TGAAAATACAGGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
350830 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
350849 TGAATATACATG
1 TGAAAATACATG
350861 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:354039 original size:34 final size:31
Alignment explanation
Indices: 353982--354053 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
353972 CTTGGCTTGC
*
353982 TTTCTTTTTTAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTTAATTTCTTCTTCTTTT-TGTCT
354013 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-T-AA-TTTCTTCTTCTTTTTGTCT
354047 TTTCTTT
1 TTTCTTT
354054 ATTTTTGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
32 1 0.03
33 3 0.08
34 23 0.64
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (31 bp):
TTTCTTTTTTAATTTCTTCTTCTTTTTGTCT
Found at i:354761 original size:21 final size:19
Alignment explanation
Indices: 354735--354784 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
354725 GAAACCCCTT
354735 TGAAAATACAGGACTTTTAAA
1 TGAAAATACAGGA-TTTT-AA
*
354756 TGAAAATACATGATTTTAA
1 TGAAAATACAGGATTTTAA
*
354775 TGAAGATACA
1 TGAAAATACA
354785 TGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (19 bp):
TGAAAATACAGGATTTTAA
Found at i:354778 original size:19 final size:21
Alignment explanation
Indices: 354735--354786 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
354725 GAAACCCCTT
*
354735 TGAAAATACAGGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
354756 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
354775 TGAAGATACATG
1 TGAAAATACATG
354787 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:357314 original size:35 final size:37
Alignment explanation
Indices: 357268--357347 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
357258 TTTGAGAATT
*
357268 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
357303 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
357340 TGGGGATG
1 TGGTGATG
357348 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:361444 original size:19 final size:20
Alignment explanation
Indices: 361424--361459 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
361414 CTTTCTTTAT
361424 TTTA-TTTCATT-CTTATTA
1 TTTATTTTCATTACTTATTA
361442 TTTATTTTCATTACTTAT
1 TTTATTTTCATTACTTAT
361460 ATTATTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTTCATTACTTATTA
Found at i:361462 original size:19 final size:17
Alignment explanation
Indices: 361420--361462 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
361410 TATCCTTTCT
361420 TTAT-TTTATTTCATTC
1 TTATATTTATTTCATTC
361436 TTATTATTTATTTTCATTAC
1 TTA-TATTTA-TTTCATT-C
361456 TTATATT
1 TTATATT
361463 ATTATCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 1 0.04
18 4 0.17
19 11 0.48
20 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTTATTTCATTC
Found at i:361742 original size:6 final size:6
Alignment explanation
Indices: 361727--361781 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
361717 ATTAGAGTGC
* * ** *
361727 AAAAAG -AAAAG AAAAAG ACAAA- AAGAAG AATCAG AAAAAA AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
361773 AAAAAG AAA
1 AAAAAG AAA
361782 TTCAAAAGAG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
5 8 0.21
6 30 0.79
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:369344 original size:5 final size:5
Alignment explanation
Indices: 369334--369386 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
369324 CGGTCAAAGA
* * *
369334 TCGGG TCGGG TCAATGG TCGGG TCGGA TCGGG TC-AG TCGGG TCGGG TCGGG
1 TCGGG TCGGG TC--GGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
369385 TC
1 TC
369387 AGACCGGTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 32 0.82
7 4 0.10
ACGTcount: A:0.08, C:0.21, G:0.49, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:369347 original size:17 final size:17
Alignment explanation
Indices: 369325--369359 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
369315 AAAGGGCAAC
369325 GGTCAAAGATCGGGTCG
1 GGTCAAAGATCGGGTCG
* *
369342 GGTCAATGGTCGGGTCG
1 GGTCAAAGATCGGGTCG
369359 G
1 G
369360 ATCGGGTCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.46, T:0.20
Consensus pattern (17 bp):
GGTCAAAGATCGGGTCG
Found at i:369374 original size:19 final size:19
Alignment explanation
Indices: 369350--369388 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
369340 CGGGTCAATG
369350 GTCGGGTCGGATCGGGTCA
1 GTCGGGTCGGATCGGGTCA
*
369369 GTCGGGTCGGGTCGGGTCA
1 GTCGGGTCGGATCGGGTCA
369388 G
1 G
369389 ACCGGTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.08, C:0.21, G:0.51, T:0.21
Consensus pattern (19 bp):
GTCGGGTCGGATCGGGTCA
Found at i:369395 original size:19 final size:19
Alignment explanation
Indices: 369354--369395 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
369344 TCAATGGTCG
* *
369354 GGTCGGATCGGGTCAGTCG
1 GGTCGGATCGGGTCAGACC
*
369373 GGTCGGGTCGGGTCAGACC
1 GGTCGGATCGGGTCAGACC
369392 GGTC
1 GGTC
369396 AAAACCGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.19
Consensus pattern (19 bp):
GGTCGGATCGGGTCAGACC
Found at i:377708 original size:13 final size:13
Alignment explanation
Indices: 377690--377716 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
377680 AGTGGTCAAC
377690 GGTCAACGGGTCG
1 GGTCAACGGGTCG
377703 GGTCAACGGGTCG
1 GGTCAACGGGTCG
377716 G
1 G
377717 TCGGGTAAAC
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:0.15, C:0.22, G:0.48, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:377720 original size:17 final size:17
Alignment explanation
Indices: 377698--377733 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
377688 ACGGTCAACG
*
377698 GGTCGGGTCAACGGGTC
1 GGTCGGGTAAACGGGTC
377715 GGTCGGGTAAACGGGTC
1 GGTCGGGTAAACGGGTC
377732 GG
1 GG
377734 GTCGAGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.17
Consensus pattern (17 bp):
GGTCGGGTAAACGGGTC
Found at i:381083 original size:21 final size:21
Alignment explanation
Indices: 381057--381096 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
381047 AAAACCTTAC
381057 TATTTC-TAAATTTTTGTAAAA
1 TATTTCTTAAA-TTTTGTAAAA
381078 TATTTCTTAAATTTTGTAA
1 TATTTCTTAAATTTTGTAA
381097 CCCCTAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (21 bp):
TATTTCTTAAATTTTGTAAAA
Found at i:382574 original size:7 final size:7
Alignment explanation
Indices: 382562--382605 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
382552 GTCAAAGGAA
382562 GTCAACG
1 GTCAACG
382569 GTCAACG
1 GTCAACG
382576 GTC-ACG
1 GTCAACG
382582 GTCAACG
1 GTCAACG
*
382589 GTCAACA
1 GTCAACG
382596 GTCAACG
1 GTCAACG
382603 GTC
1 GTC
382606 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:382587 original size:20 final size:21
Alignment explanation
Indices: 382563--382605 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
382553 TCAAAGGAAG
*
382563 TCAACGGTCAACGGTC-ACGG
1 TCAACGGTCAACAGTCAACGG
382583 TCAACGGTCAACAGTCAACGG
1 TCAACGGTCAACAGTCAACGG
382604 TC
1 TC
382606 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
TCAACGGTCAACAGTCAACGG
Found at i:382640 original size:19 final size:19
Alignment explanation
Indices: 382618--382681 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
382608 GTCGGGTCAG
*
382618 ACCGGTCAAATTGGTTC-A
1 ACCGGTCAAATCGGTTCGA
*
382636 TACCGATCAAATCGGTTCGA
1 -ACCGGTCAAATCGGTTCGA
*
382656 ACCGGTCGAAACCGG-TCAGA
1 ACCGGTC-AAATCGGTTC-GA
382676 ACCGGT
1 ACCGGT
382682 TTCCAGCCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (19 bp):
ACCGGTCAAATCGGTTCGA
Found at i:389821 original size:5 final size:5
Alignment explanation
Indices: 389811--389843 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
389801 GGAAGTCAAC
*
389811 GGTCG GGTCG GGTC- AGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
389844 AGTCGAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.03, C:0.21, G:0.55, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:389835 original size:19 final size:19
Alignment explanation
Indices: 389811--389848 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
389801 GGAAGTCAAC
389811 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGTCG
389830 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGTCG
389849 AGTTGGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.21, G:0.53, T:0.21
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGTCG
Found at i:389848 original size:14 final size:14
Alignment explanation
Indices: 389812--389838 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
389802 GAAGTCAACG
389812 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
389826 GTCGGGTCGGGTC
1 GTCGGGTCGGGTC
389839 GGGTCAGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:389856 original size:19 final size:19
Alignment explanation
Indices: 389812--389856 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
389802 GAAGTCAACG
*
389812 GTCGGGTCGGGTCAGTCGG
1 GTCGGGTCGGGTCAGTCGA
389831 GTCGGGTCGGGTCAGTCGA
1 GTCGGGTCGGGTCAGTCGA
*
389850 GTTGGGT
1 GTCGGGT
389857 TAGACCGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.07, C:0.18, G:0.51, T:0.24
Consensus pattern (19 bp):
GTCGGGTCGGGTCAGTCGA
Found at i:389882 original size:19 final size:19
Alignment explanation
Indices: 389854--389905 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
389844 AGTCGAGTTG
389854 GGTT-AGACCGGTCAAACC
1 GGTTCAGACCGGTCAAACC
389872 GGTTCAGACCGGTCAAACC
1 GGTTCAGACCGGTCAAACC
*
389891 GATTC-GAACCGGTCA
1 GGTTCAG-ACCGGTCA
389906 GAACTGGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (19 bp):
GGTTCAGACCGGTCAAACC
Found at i:391797 original size:24 final size:24
Alignment explanation
Indices: 391787--391898 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
391777 CATAATTCAC
* * *
391787 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
391811 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
391835 GTCAAGTATTAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
391859 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
391883 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
391899 TAAATCAAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:394356 original size:7 final size:7
Alignment explanation
Indices: 394344--394383 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
394334 TGGTCAACGC
394344 CGGTCAA
1 CGGTCAA
394351 CGGTCAA
1 CGGTCAA
*
394358 TGGGTCAA
1 -CGGTCAA
394366 CGGTCAA
1 CGGTCAA
394373 CGGGTCAA
1 C-GGTCAA
394381 CGG
1 CGG
394384 GTCGGGTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:394365 original size:8 final size:8
Alignment explanation
Indices: 394325--394386 Score: 65
Period size: 8 Copynumber: 7.5 Consensus size: 8
394315 TCAAAGTTTT
394325 GGTCAACAG
1 GGTCAAC-G
394334 TGGTCAACG
1 -GGTCAACG
394343 CCGGTCAAC-
1 --GGTCAACG
*
394352 GGTCAATG
1 GGTCAACG
394360 GGTCAAC-
1 GGTCAACG
394367 GGTCAACG
1 GGTCAACG
394375 GGTCAACG
1 GGTCAACG
394383 GGTC
1 GGTC
394387 GGGTCGGGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
7 13 0.28
8 18 0.39
9 1 0.02
10 14 0.30
ACGTcount: A:0.24, C:0.26, G:0.34, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:394365 original size:15 final size:15
Alignment explanation
Indices: 394335--394383 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
394325 GGTCAACAGT
394335 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
*
394352 GGTCAATGGGTCAAC
1 GGTCAACGGGTCAAC
394367 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
394382 GG
1 GG
394384 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 23 0.77
17 7 0.23
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.14
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:394396 original size:18 final size:18
Alignment explanation
Indices: 394386--394436 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
394376 GTCAACGGGT
394386 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
* **
394404 TGGGTCGGGAAGGGTCAA
1 CGGGTCGGGTCGGGTCAA
*
394422 CGGGTTGGGTCGGGT
1 CGGGTCGGGTCGGGT
394437 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.12, C:0.16, G:0.53, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTCAA
Found at i:394418 original size:23 final size:23
Alignment explanation
Indices: 394373--394419 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
394363 CAACGGTCAA
**
394373 CGGGTCAACGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGGGAAGGGT
*
394396 CGGGTCAATGGGTCGGGAAGGGT
1 CGGGTCAACGGGTCGGGAAGGGT
394419 C
1 C
394420 AACGGGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (23 bp):
CGGGTCAACGGGTCGGGAAGGGT
Found at i:404694 original size:30 final size:30
Alignment explanation
Indices: 404653--404710 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
404643 GCTGTTTGTT
*
404653 AGTTGTTTATGTCTCCCAAATGCTCCACCA
1 AGTTGTATATGTCTCCCAAATGCTCCACCA
*
404683 AGTTGTATATGTCTTCCAAATGCTCCAC
1 AGTTGTATATGTCTCCCAAATGCTCCAC
404711 TAAGCTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (30 bp):
AGTTGTATATGTCTCCCAAATGCTCCACCA
Found at i:404722 original size:30 final size:30
Alignment explanation
Indices: 404660--404722 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
404650 GTTAGTTGTT
* *
404660 TATGTCTCCCAAATGCTCCACCAAGTTGTA
1 TATGTCTCCCAAATGCTCCACCAAGCTATA
* *
404690 TATGTCTTCCAAATGCTCCACTAAGCTATA
1 TATGTCTCCCAAATGCTCCACCAAGCTATA
404720 TAT
1 TAT
404723 TTATGATTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (30 bp):
TATGTCTCCCAAATGCTCCACCAAGCTATA
Found at i:405342 original size:12 final size:12
Alignment explanation
Indices: 405325--405393 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 12
405315 ACAGAGATAT
*
405325 CAGAAATTAGAA
1 CAGAAATCAGAA
*
405337 CAGAAATCAGAG
1 CAGAAATCAGAA
* *
405349 CAGAATTCATAA
1 CAGAAATCAGAA
* * *
405361 TAGAATTCAGAG
1 CAGAAATCAGAA
*
405373 TAGAAATCAGAA
1 CAGAAATCAGAA
405385 CAGAAATCA
1 CAGAAATCA
405394 TATAAAATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.17
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:405365 original size:24 final size:24
Alignment explanation
Indices: 405325--405393 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
405315 ACAGAGATAT
*
405325 CAGAAATTAGAACAGAAATCAGAG
1 CAGAAATCAGAACAGAAATCAGAG
* * * *
405349 CAGAATTCATAATAGAATTCAGAG
1 CAGAAATCAGAACAGAAATCAGAG
*
405373 TAGAAATCAGAACAGAAATCA
1 CAGAAATCAGAACAGAAATCA
405394 TATAAAATAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAAATCAGAG
Found at i:409055 original size:12 final size:12
Alignment explanation
Indices: 409038--409128 Score: 65
Period size: 12 Copynumber: 7.6 Consensus size: 12
409028 ATAGAGATAT
*
409038 CAGAAATTAGAA
1 CAGAAATCAGAA
*
409050 CAGAAATCAGAG
1 CAGAAATCAGAA
*
409062 CAGAAATCATAA
1 CAGAAATCAGAA
* * * *
409074 CATAATTAAGAG
1 CAGAAATCAGAA
*
409086 CAGAAATCATAA
1 CAGAAATCAGAA
* *
409098 CAGAATTCAGAG
1 CAGAAATCAGAA
* *
409110 CATAAATCAAAA
1 CAGAAATCAGAA
*
409122 CAAAAAT
1 CAGAAAT
409129 TAGATAAAAT
Statistics
Matches: 57, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 57 1.00
ACGTcount: A:0.56, C:0.14, G:0.13, T:0.16
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:409075 original size:24 final size:24
Alignment explanation
Indices: 409038--409128 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
409028 ATAGAGATAT
* *
409038 CAGAAATTAGAACAGAAATCAGAG
1 CAGAAATCATAACAGAAATCAGAG
* * *
409062 CAGAAATCATAACATAATTAAGAG
1 CAGAAATCATAACAGAAATCAGAG
*
409086 CAGAAATCATAACAGAATTCAGAG
1 CAGAAATCATAACAGAAATCAGAG
* * *
409110 CATAAATCAAAACAAAAAT
1 CAGAAATCATAACAGAAAT
409129 TAGATAAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.56, C:0.14, G:0.13, T:0.16
Consensus pattern (24 bp):
CAGAAATCATAACAGAAATCAGAG
Found at i:409114 original size:36 final size:35
Alignment explanation
Indices: 409042--409114 Score: 83
Period size: 36 Copynumber: 2.1 Consensus size: 35
409032 AGATATCAGA
* *
409042 AATTAGAACAGAAATCAGAGCAGAAATCATAACAT
1 AATTAGAACAGAAATCAGAACAGAAATCAGAACAT
* * * *
409077 AATTAAGAGCAGAAATCATAACAGAATTCAGAGCAT
1 AATT-AGAACAGAAATCAGAACAGAAATCAGAACAT
409113 AA
1 AA
409115 ATCAAAACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
35 4 0.13
36 27 0.87
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.18
Consensus pattern (35 bp):
AATTAGAACAGAAATCAGAACAGAAATCAGAACAT
Found at i:412624 original size:12 final size:12
Alignment explanation
Indices: 412607--412671 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
412597 ACAGAGATAT
412607 CAGAAATTAGAA
1 CAGAAATTAGAA
* *
412619 CAGAAATCAGAG
1 CAGAAATTAGAA
* *
412631 CATAAATTATAA
1 CAGAAATTAGAA
*
412643 CAG-AATTCAGAG
1 CAGAAATT-AGAA
* *
412655 CAGAAATAATAA
1 CAGAAATTAGAA
412667 CAGAA
1 CAGAA
412672 TTCAAATAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 4 0.10
12 32 0.82
13 3 0.08
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.17
Consensus pattern (12 bp):
CAGAAATTAGAA
Found at i:412672 original size:24 final size:24
Alignment explanation
Indices: 412607--412675 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
412597 ACAGAGATAT
* *
412607 CAGAAATTAGAACAGAAATCAGAG
1 CAGAAATTATAACAGAATTCAGAG
*
412631 CATAAATTATAACAGAATTCAGAG
1 CAGAAATTATAACAGAATTCAGAG
*
412655 CAGAAATAATAACAGAATTCA
1 CAGAAATTATAACAGAATTCA
412676 AATAAAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.54, C:0.13, G:0.14, T:0.19
Consensus pattern (24 bp):
CAGAAATTATAACAGAATTCAGAG
Found at i:416230 original size:24 final size:24
Alignment explanation
Indices: 416171--416241 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
416161 AAAGAGATAT
* * * *
416171 CAGAAATGAGAACAAAAATCAAAG
1 CAGAAATCATAACAAAATTCAGAG
*
416195 CAGAAATTATAACAAAATTCAGAG
1 CAGAAATCATAACAAAATTCAGAG
416219 CAGAAATCATAA-AAGAATTCAGA
1 CAGAAATCATAACAA-AATTCAGA
416242 TAAAATATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 39 0.95
ACGTcount: A:0.58, C:0.13, G:0.14, T:0.15
Consensus pattern (24 bp):
CAGAAATCATAACAAAATTCAGAG
Found at i:419888 original size:12 final size:12
Alignment explanation
Indices: 419873--419940 Score: 73
Period size: 12 Copynumber: 5.7 Consensus size: 12
419863 AAATTAGAAT
419873 AGAAATCAGAGC
1 AGAAATCAGAGC
* *
419885 AGAAATCATAAC
1 AGAAATCAGAGC
*
419897 AGAATTCAGAGC
1 AGAAATCAGAGC
* *
419909 AGAAATCATAAC
1 AGAAATCAGAGC
* *
419921 AGAATTCAGAGT
1 AGAAATCAGAGC
419933 AGAAATCA
1 AGAAATCA
419941 AAACATAAAT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.16
Consensus pattern (12 bp):
AGAAATCAGAGC
Found at i:419888 original size:24 final size:24
Alignment explanation
Indices: 419873--419945 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
419863 AAATTAGAAT
*
419873 AGAAATCAGAGCAGAAATCATAAC
1 AGAATTCAGAGCAGAAATCATAAC
419897 AGAATTCAGAGCAGAAATCATAAC
1 AGAATTCAGAGCAGAAATCATAAC
* *
419921 AGAATTCAGAGTAGAAATCAAAAC
1 AGAATTCAGAGCAGAAATCATAAC
419945 A
1 A
419946 TAAATCAGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.53, C:0.15, G:0.16, T:0.15
Consensus pattern (24 bp):
AGAATTCAGAGCAGAAATCATAAC
Found at i:421700 original size:19 final size:19
Alignment explanation
Indices: 421678--421718 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
421668 AGACCGATAA
421678 GGGTTACCAGATCCGATCC
1 GGGTTACCAGATCCGATCC
421697 GGGTTACCAGATCCGATCC
1 GGGTTACCAGATCCGATCC
421716 GGG
1 GGG
421719 GTGTTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.29, G:0.32, T:0.20
Consensus pattern (19 bp):
GGGTTACCAGATCCGATCC
Found at i:422243 original size:2 final size:2
Alignment explanation
Indices: 422236--422260 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
422226 TTTTTAAAAC
422236 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
422261 CCCCCATCCG
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:422486 original size:24 final size:24
Alignment explanation
Indices: 422469--422580 Score: 172
Period size: 24 Copynumber: 4.7 Consensus size: 24
422459 ATCAAAACAT
422469 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
422493 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
*
422517 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTA-TCAGATCAA
* *
422541 AATCCAGGTCAAGTATCCGATCAC
1 AATCCAGGTCAAGTATCAGATCAA
*
422565 AATCCAGGTCATGTAT
1 AATCCAGGTCAAGTAT
422581 TATAATAGAA
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:422504 original size:12 final size:13
Alignment explanation
Indices: 422469--422575 Score: 68
Period size: 12 Copynumber: 8.8 Consensus size: 13
422459 ATCAAAACAT
422469 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
422482 TAT-CAGATCAA-
1 AATCCAGGTCAAG
422493 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
422506 TAT-CAGATCAA-
1 AATCCAGGTCAAG
422517 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
422530 TATTC-GATC-AG
1 AATCCAGGTCAAG
422541 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
422554 TATCC-GATC-AC
1 AATCCAGGTCAAG
422565 AATCCAGGTCA
1 AATCCAGGTCA
422576 TGTATTATAA
Statistics
Matches: 67, Mismatches: 19, Indels: 16
0.66 0.19 0.16
Matches are distributed among these distances:
11 14 0.21
12 40 0.60
13 13 0.19
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:425616 original size:23 final size:23
Alignment explanation
Indices: 425586--425662 Score: 136
Period size: 23 Copynumber: 3.3 Consensus size: 23
425576 TTGGCTCGTC
*
425586 GATCGGAGGTCAGACGACGAGTA
1 GATCGGAGGTCGGACGACGAGTA
*
425609 GATCGGAGATCGGACGACGAGTA
1 GATCGGAGGTCGGACGACGAGTA
425632 GATCGGAGGTCGGACGACGAGTA
1 GATCGGAGGTCGGACGACGAGTA
425655 GATCGGAG
1 GATCGGAG
425663 TTGAAAGGAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.29, C:0.17, G:0.42, T:0.13
Consensus pattern (23 bp):
GATCGGAGGTCGGACGACGAGTA
Found at i:427941 original size:24 final size:24
Alignment explanation
Indices: 427921--428029 Score: 146
Period size: 24 Copynumber: 4.5 Consensus size: 24
427911 AAAAAATTAG
* *
427921 AACAGAAATCATAGCAGAAATCAT
1 AACAGAATTCAGAGCAGAAATCAT
* *
427945 AATAGAATTCAGAGCATAAATCAT
1 AACAGAATTCAGAGCAGAAATCAT
*
427969 AACAGAATTCAGAGCAGAAAACAT
1 AACAGAATTCAGAGCAGAAATCAT
*
427993 AACAGAATTCAGAGCAGAAATCAG
1 AACAGAATTCAGAGCAGAAATCAT
* *
428017 AACAAAAATCAGA
1 AACAGAATTCAGA
428030 TAAATATTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.54, C:0.16, G:0.15, T:0.16
Consensus pattern (24 bp):
AACAGAATTCAGAGCAGAAATCAT
Found at i:428016 original size:12 final size:12
Alignment explanation
Indices: 427914--428029 Score: 88
Period size: 12 Copynumber: 9.7 Consensus size: 12
427904 TAGATATAAA
*
427914 AAATTAGAACAG
1 AAATCAGAACAG
* *
427926 AAATCATAGCAG
1 AAATCAGAACAG
* *
427938 AAATCATAATAG
1 AAATCAGAACAG
* * *
427950 AATTCAGAGCAT
1 AAATCAGAACAG
*
427962 AAATCATAACAG
1 AAATCAGAACAG
* *
427974 AATTCAGAGCAG
1 AAATCAGAACAG
* *
427986 AAAACATAACAG
1 AAATCAGAACAG
* *
427998 AATTCAGAGCAG
1 AAATCAGAACAG
*
428010 AAATCAGAACAA
1 AAATCAGAACAG
428022 AAATCAGA
1 AAATCAGA
428030 TAAATATTCA
Statistics
Matches: 76, Mismatches: 28, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 76 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.16
Consensus pattern (12 bp):
AAATCAGAACAG
Found at i:435044 original size:19 final size:19
Alignment explanation
Indices: 435020--435062 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
435010 AGACATCTTC
435020 AGATCTTTATATTGAGCGA
1 AGATCTTTATATTGAGCGA
435039 AGATCTTTATATTGAGCGA
1 AGATCTTTATATTGAGCGA
435058 AGATC
1 AGATC
435063 CTACTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (19 bp):
AGATCTTTATATTGAGCGA
Found at i:435404 original size:31 final size:31
Alignment explanation
Indices: 435333--435407 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
435323 GGGGCATACG
* * * *
435333 AGCCTACCCAAGAAAAGTCTCGGGGCCATAA
1 AGCCTACCCAAGAAAAATATCAGGGCCACAA
* *
435364 AGGCCTACCCAAGAAAAATATCAGGGTCGCAA
1 A-GCCTACCCAAGAAAAATATCAGGGCCACAA
435396 AGCCTACCCAAG
1 AGCCTACCCAAG
435408 GGTCGCCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 12 0.32
32 25 0.68
ACGTcount: A:0.37, C:0.29, G:0.21, T:0.12
Consensus pattern (31 bp):
AGCCTACCCAAGAAAAATATCAGGGCCACAA
Found at i:435579 original size:24 final size:24
Alignment explanation
Indices: 435551--435604 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
435541 CAGATATATT
435551 AGAAATCATAACAAAAATCAGAGC
1 AGAAATCATAACAAAAATCAGAGC
** *
435575 AGAAATCATAACAGGATTCAGAGC
1 AGAAATCATAACAAAAATCAGAGC
435599 AGAAAT
1 AGAAAT
435605 AAAATAGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.15
Consensus pattern (24 bp):
AGAAATCATAACAAAAATCAGAGC
Found at i:437808 original size:49 final size:48
Alignment explanation
Indices: 437737--437835 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 48
437727 CCATTATCGG
437737 ACCCCAATAAATCTCCTTTTTCTCTTCTACATCAGTGAAACAAACCTT
1 ACCCCAATAAATCTCCTTTTTCTCTTCTACATCAGTGAAACAAACCTT
437785 ACCCCAATAAAATCTCCTTTTTCTCTTCTACATCAGTGAAACAAACCTT
1 ACCCCAAT-AAATCTCCTTTTTCTCTTCTACATCAGTGAAACAAACCTT
437834 AC
1 AC
437836 AATTTCTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 8 0.16
49 42 0.84
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.32
Consensus pattern (48 bp):
ACCCCAATAAATCTCCTTTTTCTCTTCTACATCAGTGAAACAAACCTT
Found at i:443328 original size:7 final size:7
Alignment explanation
Indices: 443316--443341 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
443306 ATTGCTAGAA
443316 TTAAATG
1 TTAAATG
443323 TTAAATG
1 TTAAATG
443330 TTAAATG
1 TTAAATG
443337 TTAAA
1 TTAAA
443342 GGTACTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (7 bp):
TTAAATG
Found at i:445145 original size:17 final size:18
Alignment explanation
Indices: 445112--445148 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
445102 TATTACCTAA
445112 ATTTTGTTCTGATTTCTG
1 ATTTTGTTCTGATTTCTG
445130 ATTTGTGTTCT-A-TTCTG
1 ATTT-TGTTCTGATTTCTG
445147 AT
1 AT
445149 ATATGATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (18 bp):
ATTTTGTTCTGATTTCTG
Found at i:445173 original size:48 final size:48
Alignment explanation
Indices: 445075--445179 Score: 111
Period size: 48 Copynumber: 2.2 Consensus size: 48
445065 ATTTTATCTA
* * * * *
445075 ATTTCTGACTTGAATTCTGTTCTGATATATTACCTAAATTTTGTTCTG
1 ATTTCTGATTTGAATTCTATTCTGATATATGACATAAATTCTGTTCTG
** * * *
445123 ATTTCTGATTTGTGTTCTATTCTGATATATGATATGAATTCTGTTTTG
1 ATTTCTGATTTGAATTCTATTCTGATATATGACATAAATTCTGTTCTG
*
445171 ATTTATGAT
1 ATTTCTGAT
445180 ATCTCCGTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.52
Consensus pattern (48 bp):
ATTTCTGATTTGAATTCTATTCTGATATATGACATAAATTCTGTTCTG
Found at i:449808 original size:24 final size:24
Alignment explanation
Indices: 449750--449822 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
449740 ATACATTACC
* *
449750 TGAATTTTGTTCTGATTTTTGATT
1 TGAATTTTGTTCTGATTTATGATA
* * * *
449774 TGGATTCTGTTCTGATATCTGATA
1 TGAATTTTGTTCTGATTTATGATA
*
449798 TGAATTTTGTTTTGATTTATGATA
1 TGAATTTTGTTCTGATTTATGATA
449822 T
1 T
449823 ATCCGTTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (24 bp):
TGAATTTTGTTCTGATTTATGATA
Found at i:449994 original size:2 final size:2
Alignment explanation
Indices: 449982--450020 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
449972 CGAATGGGGG
*
449982 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
450021 GTTTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:458165 original size:29 final size:29
Alignment explanation
Indices: 458103--458169 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
458093 ATAGAAATTA
*
458103 ATTACAAAACTAACAACCTTTTAAAAAAT
1 ATTACGAAACTAACAACCTTTTAAAAAAT
*
458132 ATTACGAAACTAACACCCTTTT-AAAAAT
1 ATTACGAAACTAACAACCTTTTAAAAAAT
458160 ATTTACGAAA
1 A-TTACGAAA
458170 ATAGCACCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 7 0.20
29 28 0.80
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (29 bp):
ATTACGAAACTAACAACCTTTTAAAAAAT
Found at i:458177 original size:29 final size:29
Alignment explanation
Indices: 458103--458177 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
458093 ATAGAAATTA
*
458103 ATTAC-AAAACTAACAACCTTTTAAAAAAT
1 ATTACGAAAA-TAACACCCTTTTAAAAAAT
*
458132 ATTACGAAACTAACACCCTTTT-AAAAAT
1 ATTACGAAAATAACACCCTTTTAAAAAAT
*
458160 ATTTACGAAAATAGCACC
1 A-TTACGAAAATAACACC
458178 TGGGTTAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 7 0.17
29 30 0.75
30 3 0.08
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (29 bp):
ATTACGAAAATAACACCCTTTTAAAAAAT
Found at i:461086 original size:18 final size:18
Alignment explanation
Indices: 461063--461098 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
461053 TGGGGGTTTG
*
461063 GTAAAATGAAATTAAATA
1 GTAAAAAGAAATTAAATA
*
461081 GTAAAAAGAGATTAAATA
1 GTAAAAAGAAATTAAATA
461099 AATAAAGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (18 bp):
GTAAAAAGAAATTAAATA
Found at i:467361 original size:28 final size:28
Alignment explanation
Indices: 467322--467375 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
467312 TAGCAAATAA
*
467322 AAAAAAAGTTGAAAA-TAAAAGTAAAAAC
1 AAAAAAACTTGAAAAGTAAAA-TAAAAAC
467350 AAAAAAACTTGAAAAGTAAAATAAAA
1 AAAAAAACTTGAAAAGTAAAATAAAA
467376 GAGAAAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (28 bp):
AAAAAAACTTGAAAAGTAAAATAAAAAC
Found at i:473558 original size:18 final size:18
Alignment explanation
Indices: 473511--473559 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
473501 TTGACCCAAT
**
473511 TTGACCCAACCTAACCCG
1 TTGACCCAACCCGACCCG
* * *
473529 TTCACTCGACCCGACCCG
1 TTGACCCAACCCGACCCG
473547 TTGACCCAACCCG
1 TTGACCCAACCCG
473560 TTGACTATTG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.47, G:0.14, T:0.16
Consensus pattern (18 bp):
TTGACCCAACCCGACCCG
Found at i:475040 original size:32 final size:32
Alignment explanation
Indices: 474938--475058 Score: 104
Period size: 31 Copynumber: 3.8 Consensus size: 32
474928 TCGACAACTG
* * *
474938 TCCATAGGTCCCGAAGAACCTAGGT-ATACTG
1 TCCATATGTCCCGAAGAACATAGGTAATACTA
* * * **
474969 TACATATATTCCTTAGAACATAGGT-ATACTA
1 TCCATATGTCCCGAAGAACATAGGTAATACTA
* *
475000 TCCATATGTCCCGAA-AGACATAGGTAATTCTG
1 TCCATATGTCCCGAAGA-ACATAGGTAATACTA
* *
475032 TCCATATGTTCCGTAGAACATAGGTAA
1 TCCATATGTCCCGAAGAACATAGGTAA
475059 ACCCTCGACT
Statistics
Matches: 70, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
30 1 0.01
31 41 0.59
32 27 0.39
33 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (32 bp):
TCCATATGTCCCGAAGAACATAGGTAATACTA
Found at i:480097 original size:30 final size:30
Alignment explanation
Indices: 480036--480119 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
480026 CCCGAAGGAC
* *
480036 CTATCCAGAGGTCACAAGGAACCTTGATAA
1 CTATCCAGAGGTCACAAAGAACCTCGATAA
* * *
480066 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGATAA
* *
480096 CTGTCCATAGGTC-CAGAAGAACCT
1 CTATCCAGAGGTCACA-AAGAACCT
480120 AGGTATACTG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 1 0.02
30 43 0.98
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGATAA
Found at i:480219 original size:32 final size:31
Alignment explanation
Indices: 480091--480218 Score: 109
Period size: 31 Copynumber: 4.1 Consensus size: 31
480081 AAAGATCCTC
* * * * *
480091 GGTA-ACTGTCCATAGGTCCAGAAGAACCTA
1 GGTATACTGTCCATATGTTCTGTAGAACATA
*
480121 GGTATACTGTCCATATATTCCT-TAGAACATA
1 GGTATACTGTCCATATGTT-CTGTAGAACATA
* * * *
480152 GGTATACTATCCATATGTCCCG-AAAGACATA
1 GGTATACTGTCCATATGTTCTGTAGA-ACATA
*
480183 GGTAATTCTGTCCATATGTTCTGTAGAACATA
1 GGT-ATACTGTCCATATGTTCTGTAGAACATA
480215 GGTA
1 GGTA
480219 AACCCTCGAC
Statistics
Matches: 76, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
30 7 0.09
31 43 0.57
32 24 0.32
33 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
GGTATACTGTCCATATGTTCTGTAGAACATA
Found at i:484016 original size:17 final size:18
Alignment explanation
Indices: 483981--484017 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
483971 GGATTAATAA
483981 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
483999 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
484016 AT
1 AT
484018 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Found at i:488844 original size:31 final size:31
Alignment explanation
Indices: 488809--488932 Score: 117
Period size: 31 Copynumber: 4.0 Consensus size: 31
488799 ATCCTCGGCA
* *
488809 ACTGTCCATAGGTCCCGAAGAACCTAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
* * * **
488840 ACTGTACATATATTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
*
488871 ACTATCCATATGTCCCGAA-AGACATAGGTAATT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGT-A-T
* *
488904 A-TGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAGAACATAGGTA
488933 AACCCTCGAC
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
30 1 0.01
31 46 0.63
32 23 0.32
33 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (31 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAT
Found at i:494056 original size:31 final size:31
Alignment explanation
Indices: 493969--494092 Score: 133
Period size: 31 Copynumber: 4.0 Consensus size: 31
493959 ATCCTCGGCA
*
493969 ACTGTCCATATGTCCCGAAGAACCTAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
* * * **
494000 ACTGTCTATATATTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
*
494031 ACTATCCATATGTCCCGAA-AGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGT-AT
* * *
494063 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAGAACATAGGTA
494093 AACCCTCGAC
Statistics
Matches: 74, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
30 1 0.01
31 47 0.64
32 25 0.34
33 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (31 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAT
Found at i:495190 original size:64 final size:63
Alignment explanation
Indices: 495038--495190 Score: 143
Period size: 64 Copynumber: 2.4 Consensus size: 63
495028 CAATGAAAGT
* * ** *
495038 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTACTG-TGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* * *
495102 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-
1 ATGCATCGATGCACT-AC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAG
495163 AG
62 AG
495165 AGTGCATCGATGCACTATCTGTGCAT
1 A-TGCATCGATGCACTA-CTGTGCAT
495191 TGATACACCT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
63 3 0.04
64 59 0.82
65 10 0.14
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTGTGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:497916 original size:17 final size:18
Alignment explanation
Indices: 497881--497917 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
497871 GGATTAATAA
497881 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
497899 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
497916 AT
1 AT
497918 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Found at i:499593 original size:12 final size:12
Alignment explanation
Indices: 499578--499625 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
499568 GATACATGAC
499578 CTGAATTCTGTT
1 CTGAATTCTGTT
*
499590 CTGATTTCT-TAT
1 CTGAATTCTGT-T
*
499602 CTGGATTCTGTT
1 CTGAATTCTGTT
*
499614 CTGGATTCTGTT
1 CTGAATTCTGTT
499626 TTGATTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 1 0.03
12 29 0.94
13 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:501907 original size:24 final size:23
Alignment explanation
Indices: 501880--501962 Score: 58
Period size: 24 Copynumber: 3.5 Consensus size: 23
501870 ATTTTTTATT
501880 TGAATTTTGTTCTGACATCTGATA
1 TGAATTTTGTTCTGA-ATCTGATA
* * * * *
501904 TGAAATCTGTTCCGATTCCTGACA
1 TGAATTTTGTTCTGAAT-CTGATA
* * *
501928 TGGATTTTGTTCTGATATATGATC
1 TGAATTTTGTTCTGA-ATCTGATA
*
501952 TGAATTATGTT
1 TGAATTTTGTT
501963 TTTTTAATGA
Statistics
Matches: 42, Mismatches: 15, Indels: 4
0.69 0.25 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.95
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (23 bp):
TGAATTTTGTTCTGAATCTGATA
Found at i:524020 original size:24 final size:24
Alignment explanation
Indices: 523993--524068 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
523983 TATATCAAAA
523993 ATCAAAACATAAAT-AAGGTCAAGT
1 ATCAAAACA-AAATCAAGGTCAAGT
* * *
524017 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCAAGGTCAAGT
* * *
524041 ATCAGATCAGAATCCAA-GTCAAGT
1 ATCAAAACAAAAT-CAAGGTCAAGT
524065 ATCA
1 ATCA
524069 TATCATAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.09
24 38 0.86
25 2 0.05
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCAAGGTCAAGT
Found at i:524073 original size:24 final size:24
Alignment explanation
Indices: 524010--524125 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
524000 CATAAATAAG
* * *
524010 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
524034 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* * *
524058 GTCAAGTATCATATCATAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
524082 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
524106 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
524126 TCAAATCGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:524141 original size:48 final size:48
Alignment explanation
Indices: 524041--524143 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 48
524031 CAGGTCAAGT
* * ** *
524041 ATCAGATCAGAATCCAAGTCAAGTATCATATCATAATCTATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
*
524089 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAT-TCAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAG-AA
524137 ATCAGAT
1 ATCAGAT
524144 AAAATATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.04
48 45 0.96
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
Found at i:528749 original size:24 final size:24
Alignment explanation
Indices: 528722--528797 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
528712 TATATCAAAA
528722 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* **
528746 ATCATATTAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
528770 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
528794 ATCA
1 ATCA
528798 TATCAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.09
24 40 0.91
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:528802 original size:24 final size:24
Alignment explanation
Indices: 528739--528854 Score: 142
Period size: 24 Copynumber: 4.8 Consensus size: 24
528729 CATAAATCAG
* * * *
528739 GTCAAGTATCATATTAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
528763 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* *
528787 GTCAAGTATCATATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
* *
528811 GTCAAATATTAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
528835 GTTAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
528855 TCAAATCGAA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 78 1.00
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:528870 original size:48 final size:48
Alignment explanation
Indices: 528764--528872 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
528754 AAAATCCAGG
* * * **
528764 TCAAGTATCAGATCAGAATCCAAGTCAAGTATCATATCAGAATCTATG
1 TCAAATATTAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAA
* *
528812 TCAAATATTAGATCAGAATCCATGTTAAGTATCAGATCAGAAT-TCAAA
1 TCAAATATTAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAA
528860 TCGAAA-ATTAGAT
1 TC-AAATATTAGAT
528873 AAAATATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 48 0.92
49 3 0.06
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (48 bp):
TCAAATATTAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAA
Found at i:531338 original size:18 final size:18
Alignment explanation
Indices: 531315--531361 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
531305 CAACGATCAA
531315 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
531333 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
531351 CGGGTCGGGTC
1 CGGGTCGGGTC
531362 GGGTTATGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:531409 original size:30 final size:30
Alignment explanation
Indices: 531374--531446 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
531364 GTTATGACCG
*
531374 GTCAAACTGGTCAACTATGCACCATAACTA
1 GTCAAACTGGTCAACTATGCACCAAAACTA
*
531404 GTCAAACCT-GTCAACTATGCACCAAAACTG
1 GTCAAA-CTGGTCAACTATGCACCAAAACTA
*
531434 GTCAAACCGGTCA
1 GTCAAACTGGTCA
531447 TTTGGATCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 1 0.03
30 35 0.92
31 2 0.05
ACGTcount: A:0.36, C:0.29, G:0.15, T:0.21
Consensus pattern (30 bp):
GTCAAACTGGTCAACTATGCACCAAAACTA
Found at i:549878 original size:19 final size:20
Alignment explanation
Indices: 549854--549896 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
549844 AGCATTTATC
*
549854 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
549873 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
549893 TTCA
1 TTCA
549897 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:550666 original size:25 final size:27
Alignment explanation
Indices: 550602--550671 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 27
550592 CAAAAGGAAA
**
550602 AGAAAAGACCAAAAGAAGAAAAAAATTC
1 AGAAAAGAAGAAAAGAA-AAAAAAATTC
* *
550630 AGAAAAGAAGAAAAGAAAAAGAAATTT
1 AGAAAAGAAGAAAAGAAAAAAAAATTC
550657 A-AAAAG-AG-AAAGAAA
1 AGAAAAGAAGAAAAGAAA
550672 GCCAAGGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 7 0.18
25 2 0.05
26 5 0.13
27 9 0.24
28 15 0.39
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.07
Consensus pattern (27 bp):
AGAAAAGAAGAAAAGAAAAAAAAATTC
Found at i:553874 original size:19 final size:20
Alignment explanation
Indices: 553850--553892 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
553840 AGCGTTTATC
*
553850 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
553869 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
553889 TTCA
1 TTCA
553893 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:554628 original size:28 final size:27
Alignment explanation
Indices: 554597--554650 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
554587 CAAAAGGAAA
*
554597 AGAAAAGACCAAAAGAAGAAAAAAATTC
1 AGAAAAGAACAAAAGAA-AAAAAAATTC
* *
554625 AGAAAAGAAGAAAAGAAAAAGAAATT
1 AGAAAAGAACAAAAGAAAAAAAAATT
554651 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.70, C:0.06, G:0.17, T:0.07
Consensus pattern (27 bp):
AGAAAAGAACAAAAGAAAAAAAAATTC
Found at i:558121 original size:19 final size:20
Alignment explanation
Indices: 558097--558139 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
558087 AGCATTTATC
*
558097 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
558116 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
558136 TTCA
1 TTCA
558140 GAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:564823 original size:20 final size:21
Alignment explanation
Indices: 564798--564879 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 21
564788 TTTTGGTGCA
*
564798 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
564818 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
564839 GAAGGGGAACCGATTCCCCCACA-
1 G-A-GGGAACCGATTCCCCC-CAT
* *
564862 G-GGGAATCGATACCCCCC
1 GAGGGAACCGATTCCCCCC
564880 TGGGGTTCTA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
19 1 0.02
20 24 0.47
21 8 0.16
22 1 0.02
23 17 0.33
ACGTcount: A:0.24, C:0.35, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:565357 original size:5 final size:5
Alignment explanation
Indices: 565347--565372 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
565337 CTCAAAACCA
565347 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
565373 GAAGTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:573820 original size:18 final size:15
Alignment explanation
Indices: 573781--573838 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 15
573771 TGGGTTGACC
573781 GATCCGACCCGATTT
1 GATCCGACCCGATTT
*
573796 GAACCGACCCGACCTGTT
1 GATCCGACCCGA--T-TT
573814 GATCCGACCCG--TT
1 GATCCGACCCGATTT
*
573827 GACCCGACCCGA
1 GATCCGACCCGA
573839 CCCGTTGATC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
13 12 0.33
15 11 0.31
17 1 0.03
18 12 0.33
ACGTcount: A:0.21, C:0.40, G:0.22, T:0.17
Consensus pattern (15 bp):
GATCCGACCCGATTT
Found at i:573837 original size:31 final size:32
Alignment explanation
Indices: 573781--573848 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 32
573771 TGGGTTGACC
*
573781 GATCCGACCCGATTTGAACCGACCCGACCTGTT
1 GATCCGACCCGA-TTGAACCGACCCGACCCGTT
*
573814 GATCCGACCCG-TTGACCCGACCCGACCCGTT
1 GATCCGACCCGATTGAACCGACCCGACCCGTT
573845 GATC
1 GATC
573849 GTTGACCACC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 22 0.67
33 11 0.33
ACGTcount: A:0.19, C:0.40, G:0.22, T:0.19
Consensus pattern (32 bp):
GATCCGACCCGATTGAACCGACCCGACCCGTT
Found at i:576396 original size:29 final size:29
Alignment explanation
Indices: 576344--576454 Score: 152
Period size: 29 Copynumber: 3.8 Consensus size: 29
576334 ATAATTACAG
576344 AATAGCACCCTTTTCAAATTAATTCCCAA
1 AATAGCACCCTTTTCAAATTAATTCCCAA
* *
576373 AATAGCA-CATTTTCGAATTAAATTCCCAA
1 AATAGCACCCTTTTCAAATT-AATTCCCAA
* *
576402 AATAACACCTTTTTCAAATTAATTCCCAA
1 AATAGCACCCTTTTCAAATTAATTCCCAA
* *
576431 AATAGAACCCTTTTCGAATTAATT
1 AATAGCACCCTTTTCAAATTAATT
576455 ACTAAAATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
28 10 0.14
29 51 0.72
30 10 0.14
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (29 bp):
AATAGCACCCTTTTCAAATTAATTCCCAA
Found at i:576509 original size:18 final size:18
Alignment explanation
Indices: 576476--576510 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
576466 ACTGGTCAAC
*
576476 GGTCAACGGGTCGGGTCG
1 GGTCAACGAGTCGGGTCG
*
576494 GGTCAACGAGTTGGGTC
1 GGTCAACGAGTCGGGTC
576511 AAAACCGATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.20, G:0.46, T:0.20
Consensus pattern (18 bp):
GGTCAACGAGTCGGGTCG
Found at i:584383 original size:19 final size:20
Alignment explanation
Indices: 584331--584384 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
584321 ACGTGGGGAA
*
584331 GGGTTCGACCAGTGCTGAAACC
1 GGGTT-GACCGGT-CTGAAACC
* *
584353 GGTTTAACCGGTCTGAAA-C
1 GGGTTGACCGGTCTGAAACC
584372 GGGTTGACCGGTC
1 GGGTTGACCGGTC
584385 AAACCCAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
21 5 0.19
22 4 0.15
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.22
Consensus pattern (20 bp):
GGGTTGACCGGTCTGAAACC
Found at i:589745 original size:2 final size:2
Alignment explanation
Indices: 589738--589768 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
589728 GCTTTTTGAA
589738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
589769 CAACTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:611293 original size:13 final size:13
Alignment explanation
Indices: 611275--611300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
611265 ATTGACCGGC
611275 GTTGACCAAAGTT
1 GTTGACCAAAGTT
611288 GTTGACCAAAGTT
1 GTTGACCAAAGTT
611301 TACCATAACT
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTTGACCAAAGTT
Found at i:620128 original size:16 final size:17
Alignment explanation
Indices: 620107--620141 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
620097 ATGAAAAGAT
620107 ACATATCTTTTT-AAAA
1 ACATATCTTTTTCAAAA
*
620123 ACATATTTTTTTCAAAA
1 ACATATCTTTTTCAAAA
620140 AC
1 AC
620142 CATAGTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
ACATATCTTTTTCAAAA
Found at i:620430 original size:156 final size:155
Alignment explanation
Indices: 620129--620440 Score: 407
Period size: 156 Copynumber: 2.0 Consensus size: 155
620119 AAAAACATAT
* * **
620129 TTTTTTCAAAAACCATAGTAATCCCTCCAGCCGTACACACCAAAATGTGTAGGTTCCCCAGAACC
1 TTTTATCAAAAACCATAATAATCCCTCCAGCCCAACACACCAAAATGTGTAGGTTCCCCAGAACC
* * * * *
620194 ATATACCCACCTGAACATCAAGTAAGTCCTTGAGCTCAAAGCCGAGGAGCCTGCGAAAATACTTT
66 ATACACCCACCTGAACATCAAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCGAAAATACTTC
*
620259 CTCCAATAACACCCCAAAATAAAACA
131 CTCCAACAACACCCC-AAATAAAACA
* *
620285 TTTTATCAAAAACCATAATAATCCCTCCAGCCCAACACATCATAATGTGTAGGTTCCCCAGAACC
1 TTTTATCAAAAACCATAATAATCCCTCCAGCCCAACACACCAAAATGTGTAGGTTCCCCAGAACC
* * *
620350 ATACACCCACC-GTCACATCAGGTAAGGCCCTGAGCACAAAG-CGATGG-GCCTGC-AAGTATAC
66 ATACACCCACCTG-AACATCAAGTAAGGCCCTGAGCACAAAGCCGA-GGAGCCTGCGAA-AATAC
*
620411 TTCCTCCAACAATACCCCCAAATAAAACA
128 TTCCTCCAACAACA-CCCCAAATAAAACA
620440 T
1 T
620441 GTTCCATCTG
Statistics
Matches: 136, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
154 2 0.01
155 36 0.26
156 98 0.72
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.21
Consensus pattern (155 bp):
TTTTATCAAAAACCATAATAATCCCTCCAGCCCAACACACCAAAATGTGTAGGTTCCCCAGAACC
ATACACCCACCTGAACATCAAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCGAAAATACTTC
CTCCAACAACACCCCAAATAAAACA
Found at i:624280 original size:24 final size:24
Alignment explanation
Indices: 624253--624300 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
624243 AAACGAATAT
*
624253 ATCAAAAATCAAAACATAATTCAG
1 ATCAAAAATCAAAACAGAATTCAG
* * *
624277 ATCACATATCAGAACAGAATTCAG
1 ATCAAAAATCAAAACAGAATTCAG
624301 TTCATGTATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (24 bp):
ATCAAAAATCAAAACAGAATTCAG
Found at i:624310 original size:24 final size:24
Alignment explanation
Indices: 624260--624320 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
624250 TATATCAAAA
*
624260 ATCAAAACATAATTCAGATCACAT
1 ATCAAAACAGAATTCAGATCACAT
* * **
624284 ATCAGAACAGAATTCAGTTCATGT
1 ATCAAAACAGAATTCAGATCACAT
*
624308 ATCATAACAGAAT
1 ATCAAAACAGAAT
624321 CCAGGTAAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCACAT
Found at i:624333 original size:24 final size:24
Alignment explanation
Indices: 624283--624344 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
624273 TCAGATCACA
* * * * *
624283 TATCAGAACAGAATTCAGTTCATG
1 TATCATAACAGAATCCAGGTAAGG
624307 TATCATAACAGAATCCAGGTAAGG
1 TATCATAACAGAATCCAGGTAAGG
*
624331 TATCATAATAGAAT
1 TATCATAACAGAAT
624345 TGAAATCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (24 bp):
TATCATAACAGAATCCAGGTAAGG
Found at i:626600 original size:24 final size:24
Alignment explanation
Indices: 626541--626609 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
626531 AAATATAATT
** *
626541 CAGGTCAAGTAGAAGATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
626565 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
626589 CAGGTCAAGTATCATATCAAA
1 CAGGTCAAGTATCATATCAAA
626610 GTTCAAATCG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAAAATC
Found at i:629057 original size:17 final size:17
Alignment explanation
Indices: 629035--629072 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
629025 TCAACAGTGA
* *
629035 TCAATGCCGGTCAACGT
1 TCAATGCAGGTCAACGG
629052 TCAATGCAGGTCAACGG
1 TCAATGCAGGTCAACGG
629069 TCAA
1 TCAA
629073 CAGTCGACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (17 bp):
TCAATGCAGGTCAACGG
Found at i:631304 original size:24 final size:24
Alignment explanation
Indices: 631215--631307 Score: 150
Period size: 24 Copynumber: 3.9 Consensus size: 24
631205 AAACATAATT
* * *
631215 CAGGTCAAGTAGCATATTAGAATC
1 CAGGTCAAGTATCATATCAAAATC
*
631239 CAGGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATCAAAATC
631263 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
631287 CAGGTCAAGTATCATATCAAA
1 CAGGTCAAGTATCATATCAAA
631308 GTTCAAATTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAAAATC
Found at i:633458 original size:207 final size:207
Alignment explanation
Indices: 633103--633512 Score: 811
Period size: 207 Copynumber: 2.0 Consensus size: 207
633093 CTGGTTGATT
633103 TCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGTAGAACCCCC
1 TCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGTAGAACCCCC
*
633168 AACCAAAATCTATGTAACCACCTCAGACTGATGCGGGTAACCTGATTCGATTTAGAGTGTCACAT
66 AACCAAAATCTATGTAACCACCTCAGACTGATGCGGGTAACCTGATTCGATCTAGAGTGTCACAT
633233 TAGGGCCACCGGAGCGACCCACTATAAAAGTAGCAGAAAATTTAAAACTTTTATTAAAACATGTA
131 TAGGGCCACCGGAGCGACCCACTATAAAAGTAGCAGAAAATTTAAAACTTTTATTAAAACATGTA
633298 ACTTATAAGATG
196 ACTTATAAGATG
633310 TCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGTAGAACCCCC
1 TCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGTAGAACCCCC
633375 AACCAAAATCTATGTAACCACCTCAGACTGATGCGGGTAACCTGATTCGATCTAGAGTGTCACAT
66 AACCAAAATCTATGTAACCACCTCAGACTGATGCGGGTAACCTGATTCGATCTAGAGTGTCACAT
633440 TAGGGCCACCGGAGCGACCCACTATAAAAGTAGCAGAAAATTTAAAACTTTTATTAAAACATGTA
131 TAGGGCCACCGGAGCGACCCACTATAAAAGTAGCAGAAAATTTAAAACTTTTATTAAAACATGTA
633505 ACTTATAA
196 ACTTATAA
633513 AATGATTTAT
Statistics
Matches: 202, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 202 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (207 bp):
TCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGTAGAACCCCC
AACCAAAATCTATGTAACCACCTCAGACTGATGCGGGTAACCTGATTCGATCTAGAGTGTCACAT
TAGGGCCACCGGAGCGACCCACTATAAAAGTAGCAGAAAATTTAAAACTTTTATTAAAACATGTA
ACTTATAAGATG
Found at i:634438 original size:27 final size:27
Alignment explanation
Indices: 634398--634467 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
634388 TTAGAGATGC
* *
634398 TTTAGGCCCTTTTACACTTTAGGGGCAT
1 TTTA-GCCATTTTACACTTAAGGGGCAT
* * *
634426 TTTGGTCATTTTACACTTAAGGGGTAT
1 TTTAGCCATTTTACACTTAAGGGGCAT
634453 TTTAGCCATTTTACA
1 TTTAGCCATTTTACA
634468 GATACACGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (27 bp):
TTTAGCCATTTTACACTTAAGGGGCAT
Found at i:637587 original size:43 final size:42
Alignment explanation
Indices: 637512--637804 Score: 275
Period size: 43 Copynumber: 6.8 Consensus size: 42
637502 TGCAAAACGG
* * * * *
637512 TAAGGTCTTACTCTTGTACA-ACGCAAAAGAGCCTGTGGAAACA
1 TAAGG-CTTACCCTTGCACACA-GCAAAGGAACCTGGGGAAACA
* *
637555 GCAAGGCTTACCCTTGCACACAGCAAAGGAGCCTGGGGAAACTA
1 -TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAAC-A
* * *
637599 TAAGGGTTACCTTTACACACAGCAAAGGAACCTGGGGAAACTA
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAAC-A
* * * * *
637642 TAAGCCTTACCCTTGTACACAACAAAGGAA-CTTGGGAAATTA
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAA-CA
*
637684 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACAA
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAAC-A
* * * ***
637727 TTAGGCTTACCCTTGCACACAGCAAAGGAACCTGCAGTAATGG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTG-GGGAAACA
* *
637770 TAAGGACTTACCCTTGCACATAGCAAAGGAGCCTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTG
637805 AAATATTTAC
Statistics
Matches: 210, Mismatches: 32, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
42 37 0.18
43 137 0.65
44 36 0.17
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (42 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACA
Found at i:637710 original size:85 final size:85
Alignment explanation
Indices: 637512--637804 Score: 291
Period size: 85 Copynumber: 3.4 Consensus size: 85
637502 TGCAAAACGG
* * * * * ** *
637512 TAAGGTCTTACTCTTGTACA-ACGCAAAAGAGCCTGTGGAAACAGCAAGGCTTACCCTTGCACAC
1 TAAGG-CTTACCCTTGCACACA-GCAAAGGAACCTGGGGAAACAATAAGCCTTACCCTTGCACAC
* * *
637576 AGCAAAGGAGCCTGGGGAAACTA
64 AGCAAAGGA-ACTTGGGAAATTA
* * * * * *
637599 TAAGGGTTACCTTTACACACAGCAAAGGAACCTGGGGAAACTATAAGCCTTACCCTTGTACACAA
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACAATAAGCCTTACCCTTGCACACAG
637664 CAAAGGAACTTGGGAAATTA
66 CAAAGGAACTTGGGAAATTA
* * *
637684 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACAATTAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACAATAAGCCTTACCCTTGCACACAG
* * * **
637749 CAAAGGAACCTGCAGTAATGG
66 CAAAGGAACTTG-GGAAATTA
* *
637770 TAAGGACTTACCCTTGCACATAGCAAAGGAGCCTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTG
637805 AAATATTTAC
Statistics
Matches: 169, Mismatches: 34, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
85 77 0.46
86 60 0.36
87 32 0.19
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (85 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACAATAAGCCTTACCCTTGCACACAG
CAAAGGAACTTGGGAAATTA
Found at i:639022 original size:27 final size:26
Alignment explanation
Indices: 638992--639056 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
638982 TTAGAGATAC
*
638992 TTTAGGTCATTTACACTTTAGGGGCAT
1 TTTA-GTCATTTACAATTTAGGGGCAT
* * *
639019 TTTAGTTATTTTATAATTTAGGGGTAT
1 TTTAGTCA-TTTACAATTTAGGGGCAT
639046 TTTAGTCATTT
1 TTTAGTCATTT
639057 TACTGATACA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 6 0.19
27 26 0.81
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (26 bp):
TTTAGTCATTTACAATTTAGGGGCAT
Found at i:640244 original size:10 final size:10
Alignment explanation
Indices: 640229--640289 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
640219 CAACGGTCGA
*
640229 GTCAAACCGG
1 GTCAAACTGG
*
640239 GTCAAATTGG
1 GTCAAACTGG
640249 GTCAAACGGGTTGG
1 GTCAAAC----TGG
*
640263 GTCAAACCGG
1 GTCAAACTGG
*
640273 GTCAAATTGG
1 GTCAAACTGG
640283 GTCAAAC
1 GTCAAAC
640290 GGTTGGGTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
10 30 0.75
14 10 0.25
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.20
Consensus pattern (10 bp):
GTCAAACTGG
Found at i:640254 original size:20 final size:20
Alignment explanation
Indices: 640229--640289 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
640219 CAACGGTCGA
640229 GTCAAACCGGGTCAAATTGG
1 GTCAAACCGGGTCAAATTGG
640249 GTCAAA-CGGG-----TTGG
1 GTCAAACCGGGTCAAATTGG
640263 GTCAAACCGGGTCAAATTGG
1 GTCAAACCGGGTCAAATTGG
640283 GTCAAAC
1 GTCAAAC
640290 GGTTGGGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
14 10 0.29
15 4 0.11
19 4 0.11
20 17 0.49
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.20
Consensus pattern (20 bp):
GTCAAACCGGGTCAAATTGG
Found at i:640299 original size:33 final size:33
Alignment explanation
Indices: 640215--640310 Score: 149
Period size: 34 Copynumber: 2.9 Consensus size: 33
640205 AGGTCGTGTC
* *
640215 GGGTC-AACGGTCGAGTCAAACCGGGTCAAATT
1 GGGTCAAACGGTTGGGTCAAACCGGGTCAAATT
640247 GGGTCAAACGGGTTGGGTCAAACCGGGTCAAATT
1 GGGTCAAAC-GGTTGGGTCAAACCGGGTCAAATT
*
640281 GGGTCAAACGGTTGGGTCAAACCTGGTCAA
1 GGGTCAAACGGTTGGGTCAAACCGGGTCAA
640311 CTGCCCTAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
32 5 0.08
33 23 0.39
34 31 0.53
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (33 bp):
GGGTCAAACGGTTGGGTCAAACCGGGTCAAATT
Found at i:642246 original size:43 final size:43
Alignment explanation
Indices: 642162--642454 Score: 304
Period size: 43 Copynumber: 6.8 Consensus size: 43
642152 AGAGCATGCA
* * * *
642162 AAACTGTAAGGTCTTACTCTTGCACA-ATGCAAAAGAGCCTGGGG
1 AAACTATAAGG-CTTACCCTTGCACACA-GCAAAGGAACCTGGGG
* * *
642206 AAATTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
1 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
*
642249 AAACTATAAGGCTTACCCTTGCACACAGCAAAGCAACCTGGGG
1 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * * * *
642292 AAATTATAAGGCTCAGCCTTGCACACAACAAAGTAACCT-GGG
1 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * *
642334 AAACTATAATGCTTACCCTTGTACACAACAAAGGAACCTGGGG
1 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
* * * * * *
642377 AAACTATAAGGCTTTCCCTTACACACAGTAAAGAAACATGCGGT
1 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGAACCTG-GGG
** *
642421 AAA-GGTAAGGACTTACCCTTGCACATAGCAAAGG
1 AAACTATAAGG-CTTACCCTTGCACACAGCAAAGG
642455 TGCCTGAAAT
Statistics
Matches: 209, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
42 36 0.17
43 139 0.67
44 34 0.16
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (43 bp):
AAACTATAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
Found at i:642378 original size:85 final size:86
Alignment explanation
Indices: 642199--642403 Score: 295
Period size: 85 Copynumber: 2.4 Consensus size: 86
642189 TGCAAAAGAG
* *
642199 CCTGGGGAAATTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTATAAGGCTTA
1 CCTGGGGAAATTATAAGGCTCACCCTTGCACACAACAAAGGAACCTGGGGAAACTATAAGGCTTA
*
642264 CCCTTGCACACAGCAAAGCAA
66 CCCTTGCACACAACAAAGCAA
* * *
642285 CCTGGGGAAATTATAAGGCTCAGCCTTGCACACAACAAAGTAACCT-GGGAAACTATAATGCTTA
1 CCTGGGGAAATTATAAGGCTCACCCTTGCACACAACAAAGGAACCTGGGGAAACTATAAGGCTTA
* *
642349 CCCTTGTACACAACAAAGGAA
66 CCCTTGCACACAACAAAGCAA
* ** *
642370 CCTGGGGAAACTATAAGGCTTTCCCTTACACACA
1 CCTGGGGAAATTATAAGGCTCACCCTTGCACACA
642404 GTAAAGAAAC
Statistics
Matches: 106, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 64 0.60
86 42 0.40
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (86 bp):
CCTGGGGAAATTATAAGGCTCACCCTTGCACACAACAAAGGAACCTGGGGAAACTATAAGGCTTA
CCCTTGCACACAACAAAGCAA
Found at i:643871 original size:27 final size:27
Alignment explanation
Indices: 643841--643898 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
643831 CTTTAGGCCA
* * *
643841 TTTACACTTTAGGGGCATTTTGGTCAT
1 TTTACAATTTAAGGGCATTTTAGTCAT
*
643868 TTTACAATTTAAGGGTATTTTAGTCAT
1 TTTACAATTTAAGGGCATTTTAGTCAT
643895 TTTA
1 TTTA
643899 TTGATACATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (27 bp):
TTTACAATTTAAGGGCATTTTAGTCAT
Found at i:645047 original size:18 final size:19
Alignment explanation
Indices: 645024--645063 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
645014 TCAAAGTAAA
**
645024 CGGTCAACTGTCAAC-GGT
1 CGGTCAACAATCAACGGGT
645042 CGGTCAACAATCAACGGGT
1 CGGTCAACAATCAACGGGT
645061 CGG
1 CGG
645064 GTCTACAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.17
Consensus pattern (19 bp):
CGGTCAACAATCAACGGGT
Found at i:652059 original size:44 final size:44
Alignment explanation
Indices: 651976--652288 Score: 338
Period size: 44 Copynumber: 7.1 Consensus size: 44
651966 CTGGAGAAAG
* * * *
651976 TTTCCGAATGCTCATCTGTTGTGTGCAAGGGTGATACCTTACCA
1 TTTCTGAAGGCTCCTCTGTTGTGTGCAAGGGTGAGACCTTACCA
* * *
652020 TTTCTGAAGGCTCCTATGTTGTGTGCAAGGGTGAAACCTTGCCA
1 TTTCTGAAGGCTCCTCTGTTGTGTGCAAGGGTGAGACCTTACCA
* * **
652064 TTTCTGAAGGCTCTTTTGTTGTGTGCAATATGTGAGACCTTACCA
1 TTTCTGAAGGCTCCTCTGTTGTGTGCAA-GGGTGAGACCTTACCA
* * * * * * *
652109 TTACAGACGGCTCCTCTGCTATGCGTAAGGGTGAGACCTTACCA
1 TTTCTGAAGGCTCCTCTGTTGTGTGCAAGGGTGAGACCTTACCA
* * *
652153 TTTCTGAAGGCTCCTTTGTTGTGTGTAAGGGTAAGACCTTACCA
1 TTTCTGAAGGCTCCTCTGTTGTGTGCAAGGGTGAGACCTTACCA
* * * *
652197 TTTTTGAAGGCTTCTCTGCTGTGTGCAAGGGTGAGACCTTATCA
1 TTTCTGAAGGCTCCTCTGTTGTGTGCAAGGGTGAGACCTTACCA
* * * * **
652241 TTTTTTAAGGCTCCTCTGCTATGTTAAAGGGTGAGACCTTACCA
1 TTTCTGAAGGCTCCTCTGTTGTGTGCAAGGGTGAGACCTTACCA
652285 TTTC
1 TTTC
652289 CACAGGCTTC
Statistics
Matches: 223, Mismatches: 45, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
44 192 0.86
45 31 0.14
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (44 bp):
TTTCTGAAGGCTCCTCTGTTGTGTGCAAGGGTGAGACCTTACCA
Found at i:652393 original size:39 final size:38
Alignment explanation
Indices: 652336--652413 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
652326 ACCGCTTTCC
* *
652336 GCAGGCTCCTCGGATTTGTTCTCAGGGTAAGTCCTTACT
1 GCAGGCTCCTCGGATTTGTGCACAGGGTAAG-CCTTACT
** *
652375 GCAGGCTCCTTTGCTTTGTGCACAGGGTAAGCCTTACT
1 GCAGGCTCCTCGGATTTGTGCACAGGGTAAGCCTTACT
652413 G
1 G
652414 GGTGTACATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 8 0.24
39 26 0.76
ACGTcount: A:0.15, C:0.26, G:0.27, T:0.32
Consensus pattern (38 bp):
GCAGGCTCCTCGGATTTGTGCACAGGGTAAGCCTTACT
Found at i:658136 original size:88 final size:88
Alignment explanation
Indices: 657984--658220 Score: 307
Period size: 88 Copynumber: 2.7 Consensus size: 88
657974 TTAGAGGAAG
* * * * *
657984 TTTTTGAAGGCTCCTTTGTTGTGTGCAAGGGTGAGACCTTACCATTTCTTAAGGCTCCTTTACTG
1 TTTTTAAAGGCTCCTCTGCTGTGTGCAAGGGTGAGACCTTACCATTTCTGAAGGCTCCTCTACTG
658049 TGTGCAAGGATGAGACCTTACAA
66 TGTGCAAGGATGAGACCTTACAA
* ** *
658072 TTTTTAAAGGCTCCTCTACTGTGTGTTAGGGTG-GAACCTTGCCATTTCTGAAGGCTCCTCTACT
1 TTTTTAAAGGCTCCTCTGCTGTGTGCAAGGGTGAG-ACCTTACCATTTCTGAAGGCTCCTCTACT
* *
658136 GTGTGCAAGGGTGAGACCTTACCA
65 GTGTGCAAGGATGAGACCTTACAA
* * * *
658160 TTTCTAAAGGCTCTTCTGCTGTGTGCAAGGGTGAGACCTTACCGTTTC-CATAGGCTCCTCT
1 TTTTTAAAGGCTCCTCTGCTGTGTGCAAGGGTGAGACCTTACCATTTCTGA-AGGCTCCTCT
658221 TCCATGTGCA
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
87 2 0.02
88 124 0.98
89 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.34
Consensus pattern (88 bp):
TTTTTAAAGGCTCCTCTGCTGTGTGCAAGGGTGAGACCTTACCATTTCTGAAGGCTCCTCTACTG
TGTGCAAGGATGAGACCTTACAA
Found at i:658215 original size:44 final size:44
Alignment explanation
Indices: 658003--658260 Score: 275
Period size: 44 Copynumber: 5.8 Consensus size: 44
657993 GCTCCTTTGT
** *
658003 TGTGTGCAAGGGTGAGACCTTACCATTTCTTAAGGCTCCTTTAC
1 TGTGTGCAAGGGTGAGACCTTACCATTTCCAAAGGCTCCTCTAC
* * **
658047 TGTGTGCAAGGATGAGACCTTACAATTTTTAAAGGCTCCTCTAC
1 TGTGTGCAAGGGTGAGACCTTACCATTTCCAAAGGCTCCTCTAC
** * **
658091 TGTGTGTTAGGGTG-GAACCTTGCCATTTCTGAAGGCTCCTCTAC
1 TGTGTGCAAGGGTGAG-ACCTTACCATTTCCAAAGGCTCCTCTAC
* * *
658135 TGTGTGCAAGGGTGAGACCTTACCATTTCTAAAGGCTCTTCTGC
1 TGTGTGCAAGGGTGAGACCTTACCATTTCCAAAGGCTCCTCTAC
* * *
658179 TGTGTGCAAGGGTGAGACCTTACCGTTTCCATAGGCTCCTCTTC
1 TGTGTGCAAGGGTGAGACCTTACCATTTCCAAAGGCTCCTCTAC
** * * * *
658223 CATGTGCAAGAGTAATACCTTACCACTTTCCACAGGCT
1 TGTGTGCAAGGGTGAGACCTTACCA-TTTCCAAAGGCT
658261 ACTCGGTTTT
Statistics
Matches: 181, Mismatches: 30, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
43 1 0.01
44 168 0.93
45 12 0.07
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (44 bp):
TGTGTGCAAGGGTGAGACCTTACCATTTCCAAAGGCTCCTCTAC
Done.