Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 24
Found at i:2077015 original size:2 final size:2
Alignment explanation
Indices: 2077008--2077037 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
2076998 ATTCAAATTA
2077008 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
2077038 ATTATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2077079 original size:32 final size:32
Alignment explanation
Indices: 2077037--2077102 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
2077027 TATATCATAT
* * *
2077037 AATTATTTATTGTATTTAATGATGAAGAATTA
1 AATTATTTATTGTACTTAACGACGAAGAATTA
* * *
2077069 AATTTTTTATTTTACTTAACGACGAATAATTA
1 AATTATTTATTGTACTTAACGACGAAGAATTA
2077101 AA
1 AA
2077103 ACGAAACTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (32 bp):
AATTATTTATTGTACTTAACGACGAAGAATTA
Found at i:2084280 original size:15 final size:15
Alignment explanation
Indices: 2084260--2084325 Score: 114
Period size: 15 Copynumber: 4.4 Consensus size: 15
2084250 TTCTAGAAAA
2084260 TGAATTACTGGAATT
1 TGAATTACTGGAATT
2084275 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
2084290 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
2084305 TGAATTACTGGAATT
1 TGAATTACTGGAATT
2084320 TGAATT
1 TGAATT
2084326 CTGTAAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:2084294 original size:30 final size:30
Alignment explanation
Indices: 2084260--2084341 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
2084250 TTCTAGAAAA
**
2084260 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
2084290 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
*
2084320 TGAATT-CTGTAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
2084342 ATTTCTGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 15 0.31
30 34 0.69
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:2084339 original size:14 final size:15
Alignment explanation
Indices: 2084255--2084341 Score: 104
Period size: 15 Copynumber: 5.9 Consensus size: 15
2084245 TGGTTTTCTA
2084255 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
2084270 GAATTTGAATTACTG
1 GAAAATGAATTACTG
**
2084285 GAATTTGAATTACTG
1 GAAAATGAATTACTG
2084300 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
2084315 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
*
2084329 TAAAATGAATTAC
1 GAAAATGAATTAC
2084342 ATTTCTGTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.18
15 51 0.82
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.34
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:2084347 original size:20 final size:20
Alignment explanation
Indices: 2084324--2084393 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
2084314 GGAATTTGAA
*
2084324 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
2084344 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2084364 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2084384 TTCTGGAAAA
1 TTCTGGAAAA
2084394 CATCTGGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:2084615 original size:28 final size:27
Alignment explanation
Indices: 2084560--2084624 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
2084550 TTTACTAAAA
*
2084560 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAATATTAT
2084588 TCATTATTAAATATATAAAAAA-ATTTAT
1 T-ATTATTAAATATATAAAAAATA-TTAT
2084616 TATATATTA
1 TAT-TATTA
2084625 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 24 0.73
29 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:2084650 original size:31 final size:31
Alignment explanation
Indices: 2084559--2084651 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 31
2084549 CTTTACTAAA
*
2084559 ATATTATTGAAATATAT--AAATA-ATATTAT
1 ATATTATT-AAATATATAAAAAAATATATTAT
*
2084588 -TCATTATTAAATATATAAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAAAATATATTAT
*
2084619 ATATTATTAAA-ATA-AAAATATAATATCTTAT
1 ATATTATTAAATATATAAAA-A-AATATATTAT
2084650 AT
1 AT
2084652 TATAATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
28 9 0.17
29 10 0.19
30 8 0.15
31 25 0.47
32 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (31 bp):
ATATTATTAAATATATAAAAAAATATATTAT
Found at i:2084729 original size:21 final size:22
Alignment explanation
Indices: 2084673--2084733 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
2084663 TGATTATTTT
* * *
2084673 ATATATATTAAAAATATAATATT
1 ATATATTTTAAATAT-TAATATA
*
2084696 ATATTATTATAAATATTAATA-A
1 ATA-TATTTTAAATATTAATATA
2084718 ATATATTTTAAATATT
1 ATATATTTTAAATATT
2084734 TTAATAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 12 0.38
22 3 0.09
23 8 0.25
24 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATATTTTAAATATTAATATA
Found at i:2084729 original size:45 final size:48
Alignment explanation
Indices: 2084631--2084729 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 48
2084621 ATTATTAAAA
* * **
2084631 TAAAAATATAATATCTTATATTATAATATAATTGATTATTTTATATATAT
1 TAAAAATATAATA-CTTATATTAT-ATATAAATGATTAATAAATATATAT
*
2084681 TAAAAATATAATA-TTATATTAT-TATAAAT-ATTAATAAATATATTT
1 TAAAAATATAATACTTATATTATATATAAATGATTAATAAATATATAT
2084726 TAAA
1 TAAA
2084730 TATTTTAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
45 16 0.36
46 6 0.14
48 9 0.20
50 13 0.30
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (48 bp):
TAAAAATATAATACTTATATTATATATAAATGATTAATAAATATATAT
Found at i:2084981 original size:42 final size:42
Alignment explanation
Indices: 2084922--2085041 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
2084912 ATGAATTACA
*
2084922 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
2084964 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
2085006 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
2085042 TTCGGGGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:2087553 original size:10 final size:10
Alignment explanation
Indices: 2087537--2087592 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
2087527 CTTTACATTC
2087537 TTTTTATTGA
1 TTTTTATTGA
* *
2087547 ATTTTATTCA
1 TTTTTATTGA
* *
2087557 CTTTTAAT-A
1 TTTTTATTGA
2087566 TTTTTATTGCA
1 TTTTTATTG-A
2087577 TTTTTATTGA
1 TTTTTATTGA
2087587 TTTTTA
1 TTTTTA
2087593 AATATATGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
9 7 0.18
10 21 0.55
11 10 0.26
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.66
Consensus pattern (10 bp):
TTTTTATTGA
Found at i:2089861 original size:12 final size:12
Alignment explanation
Indices: 2089844--2089939 Score: 68
Period size: 12 Copynumber: 7.9 Consensus size: 12
2089834 GTGCCTCCCA
2089844 GTTAGTGACAAC
1 GTTAGTGACAAC
** *
2089856 GTTAGTTCTCAAA
1 GTTAG-TGACAAC
2089869 GTTAGTGACAA-
1 GTTAGTGACAAC
* *
2089880 TTTAGTGACCAAA
1 GTTAGTGA-CAAC
*
2089893 GTTAGTGACAAT
1 GTTAGTGACAAC
* *
2089905 GCTAGTAACAAC
1 GTTAGTGACAAC
* *
2089917 TTTGGTGACAAC
1 GTTAGTGACAAC
*
2089929 ATTAGTGACAA
1 GTTAGTGACAA
2089940 ATTTCGTGTG
Statistics
Matches: 64, Mismatches: 17, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
11 7 0.11
12 41 0.64
13 16 0.25
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (12 bp):
GTTAGTGACAAC
Found at i:2089892 original size:24 final size:24
Alignment explanation
Indices: 2089843--2089904 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
2089833 AGTGCCTCCC
* *
2089843 AGTTAGTGACAACGTTAGTTCTCAA
1 AGTTAGTGACAA-TTTAGTACTCAA
2089868 AGTTAGTGACAATTTAGTGAC-CAA
1 AGTTAGTGACAATTTAGT-ACTCAA
2089892 AGTTAGTGACAAT
1 AGTTAGTGACAAT
2089905 GCTAGTAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 21 0.62
25 13 0.38
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (24 bp):
AGTTAGTGACAATTTAGTACTCAA
Found at i:2089899 original size:13 final size:13
Alignment explanation
Indices: 2089843--2089901 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
2089833 AGTGCCTCCC
2089843 AGTTAGTGA-CAA
1 AGTTAGTGACCAA
* *
2089855 CGTTAGT-TCTCAA
1 AGTTAGTGAC-CAA
2089868 AGTTAGTGA-C-A
1 AGTTAGTGACCAA
*
2089879 ATTTAGTGACCAA
1 AGTTAGTGACCAA
2089892 AGTTAGTGAC
1 AGTTAGTGAC
2089902 AATGCTAGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
11 9 0.25
12 8 0.22
13 19 0.53
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (13 bp):
AGTTAGTGACCAA
Found at i:2090958 original size:25 final size:26
Alignment explanation
Indices: 2090924--2090985 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
2090914 AAAAAAGTGA
* * *
2090924 CAAATTTAGTGAG-AACTTTAATTCT
1 CAAAGTTAGTGAGAAAATTTAATTAT
**
2090949 CAAAGTTAGTG-GAAAATTTTGTTAT
1 CAAAGTTAGTGAGAAAATTTAATTAT
2090974 CAAAGTTAGTGA
1 CAAAGTTAGTGA
2090986 CCACGCTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (26 bp):
CAAAGTTAGTGAGAAAATTTAATTAT
Found at i:2091045 original size:37 final size:37
Alignment explanation
Indices: 2091004--2091647 Score: 302
Period size: 37 Copynumber: 17.9 Consensus size: 37
2090994 ATAACAATGC
* *
2091004 TAGTTCTCAAAGTTAGTGACAACTTTAGTGACATCTT
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
* * *
2091041 TAGTTTTCAAATTTAGTGACAAATTTAAG-GACAAATT
1 TAGTTCTCAAAGTTAGTGACAAATTT-AGTGACAACTT
* * * * * **
2091078 T-GTGAC-C-ACGCTAGTGACAACTTTAGTGACCACAC
1 TAGT-TCTCAAAGTTAGTGACAAATTTAGTGACAACTT
** * * * ** *
2091113 TAG-TGACAACGCTAATTTTCAAAGTTAGTGACAACTT
1 TAGTTCTCAAAG-TTAGTGACAAATTTAGTGACAACTT
* * ** * *
2091150 TAGTAACACTTTAGTT-CTTA-AA-TTTAGTGACAACTT
1 TAGT-TCTC-AAAGTTAGTGACAAATTTAGTGACAACTT
* * * *
2091186 TAGTTCTCAGAGTTTGTGTCAAATTTAGTGACAACTC
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
*
2091223 TAGTTCTCAAAGTTAGTGACAAATTTAGTGATAACTT
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
* * * *
2091260 TAGTTCTTAAAGTTAATGACAAAGTTAGTGACAAATT
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
** * *
2091297 TAGTGAT-AATGCTAGTG--------A----CAACTT
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
* * * *
2091321 TAGTTCCCAAAGCTAGTAACAAATTTAGTGACAACAT
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
* *
2091358 TAGTTTC-CAGAGTTAGTAACAAATTTAGTGACAACTT
1 TAG-TTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
2091395 TAGTTCTCAAAGTTAGTGAC-AA---A-T------TT
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
2091421 T-GTTCTCAAAGTTAGTGGA-AAATTTAGTGACAACTT
1 TAGTTCTCAAAGTTAGT-GACAAATTTAGTGACAACTT
** * * * *
2091457 TAGACCTAAAAGTTAGTGACAAATTTGGCGATAACTT
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
* *
2091494 TAGTTCTCAAAGTTAGTCACAAATTT-GATGATAACTT
1 TAGTTCTCAAAGTTAGTGACAAATTTAG-TGACAACTT
* ** * * *
2091531 TAGTTCTC-AACTTAATGTTCTCAAAGTT-GTTGATAAAATT
1 TAGTTCTCAAAGTT-A-G-TGACAAATTTAG-TGA-CAACTT
*
2091571 AGTAACAAGTTCTCAAAGTTAGGGACAAATTTAGTGACAACTT
1 --T----AGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
*
2091614 TAGTTCTCAAAGTTAGTGACATATTTAGTGACAA
1 TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAA
2091648 TGTTGTGACA
Statistics
Matches: 455, Mismatches: 97, Indels: 110
0.69 0.15 0.17
Matches are distributed among these distances:
24 9 0.02
25 23 0.05
26 7 0.02
28 1 0.00
29 1 0.00
30 1 0.00
32 1 0.00
33 2 0.00
34 6 0.01
35 22 0.05
36 48 0.11
37 277 0.61
38 8 0.02
39 15 0.03
40 5 0.01
41 1 0.00
42 1 0.00
43 4 0.01
44 9 0.02
45 2 0.00
46 8 0.02
47 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (37 bp):
TAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACTT
Found at i:2091251 original size:25 final size:25
Alignment explanation
Indices: 2091204--2091448 Score: 110
Period size: 25 Copynumber: 9.9 Consensus size: 25
2091194 AGAGTTTGTG
* * *
2091204 TCAAATTTAGTGACAACTCTAGTTC
1 TCAAAGTTAGTGACAAATTTAGTTC
**
2091229 TCAAAGTTAGTGACAAATTTAGTGA
1 TCAAAGTTAGTGACAAATTTAGTTC
** * * * *
2091254 T-AACTTTAGT-TCTTAAAGTTA-ATG
1 TCAAAGTTAGTGAC--AAATTTAGTTC
* **
2091278 ACAAAGTTAGTGACAAATTTAGTGA
1 TCAAAGTTAGTGACAAATTTAGTTC
* * *
2091303 T-AATGCTAGTGACAACTTTAGTTC
1 TCAAAGTTAGTGACAAATTTAGTTC
* * * *
2091327 CCAAAGCTAGTAACAAATTTAG-TG
1 TCAAAGTTAGTGACAAATTTAGTTC
* ** * * *
2091351 ACAACA-TTAGTTTCCAGAGTTAG-TA
1 TCAA-AGTTAG-TGACAAATTTAGTTC
* * *
2091376 ACAAATTTAGTGACAACTTTAGTTC
1 TCAAAGTTAGTGACAAATTTAGTTC
*
2091401 TCAAAGTTAGTGACAAATTTTGTTC
1 TCAAAGTTAGTGACAAATTTAGTTC
2091426 TCAAAGTTAGTGGA-AAATTTAGT
1 TCAAAGTTAGT-GACAAATTTAGT
2091449 GACAACTTTA
Statistics
Matches: 160, Mismatches: 49, Indels: 22
0.69 0.21 0.10
Matches are distributed among these distances:
23 1 0.01
24 46 0.29
25 110 0.69
26 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (25 bp):
TCAAAGTTAGTGACAAATTTAGTTC
Found at i:2091299 original size:12 final size:12
Alignment explanation
Indices: 2091011--2091459 Score: 108
Period size: 12 Copynumber: 36.8 Consensus size: 12
2091001 TGCTAGTTCT
*
2091011 CAAAGTTAGTGA
1 CAAATTTAGTGA
*
2091023 CAACTTTAGTGA
1 CAAATTTAGTGA
** **
2091035 CATCTTTAGTTTT
1 CAAATTTAG-TGA
2091048 CAAATTTAGTGA
1 CAAATTTAGTGA
2091060 CAAATTTAAG-GA
1 CAAATTT-AGTGA
2091072 CAAATTT-GTGA
1 CAAATTTAGTGA
* ***
2091083 CCACGCTAGTGA
1 CAAATTTAGTGA
*
2091095 CAACTTTAGTGA
1 CAAATTTAGTGA
* *
2091107 CCACA-CTAGTGA
1 -CAAATTTAGTGA
** * * **
2091119 CAACGCTAATTTT
1 CAA-ATTTAGTGA
*
2091132 CAAAGTTAGTGA
1 CAAATTTAGTGA
* *
2091144 CAACTTTAGTAA
1 CAAATTTAGTGA
* *
2091156 C-ACTTTAGT-T
1 CAAATTTAGTGA
2091166 CTTAAATTTAGTGA
1 C--AAATTTAGTGA
* **
2091180 CAACTTTAGTTCT
1 CAAATTTAG-TGA
* *
2091193 CAGAGTTT-GTGT
1 CA-AATTTAGTGA
2091205 CAAATTTAGTGA
1 CAAATTTAGTGA
* * **
2091217 CAACTCTAGTTCT
1 CAAATTTAG-TGA
*
2091230 CAAAGTTAGTGA
1 CAAATTTAGTGA
2091242 CAAATTTAGTGA
1 CAAATTTAGTGA
* * *
2091254 TAACTTTAGT-T
1 CAAATTTAGTGA
* *
2091265 CTTAAAGTTAATGA
1 C--AAATTTAGTGA
*
2091279 CAAAGTTAGTGA
1 CAAATTTAGTGA
2091291 CAAATTTAGTGA
1 CAAATTTAGTGA
* *
2091303 -TAATGCTAGTGA
1 CAAAT-TTAGTGA
* **
2091315 CAACTTTAGTTCC
1 CAAATTTAG-TGA
** *
2091328 CAAAGCTAGTAA
1 CAAATTTAGTGA
2091340 CAAATTTAGTGA
1 CAAATTTAGTGA
**
2091352 CAACA-TTAGTTTC
1 CAA-ATTTAG-TGA
* * *
2091365 CAGAGTTAGTAA
1 CAAATTTAGTGA
2091377 CAAATTTAGTGA
1 CAAATTTAGTGA
* **
2091389 CAACTTTAGTTCT
1 CAAATTTAG-TGA
*
2091402 CAAAGTTAGTGA
1 CAAATTTAGTGA
* **
2091414 CAAATTTTGTTCT
1 CAAATTTAG-TGA
*
2091427 CAAAGTTAGTGGA
1 CAAATTTAGT-GA
2091440 -AAATTTAGTGA
1 CAAATTTAGTGA
*
2091451 CAACTTTAG
1 CAAATTTAG
2091460 ACCTAAAAGT
Statistics
Matches: 304, Mismatches: 105, Indels: 56
0.65 0.23 0.12
Matches are distributed among these distances:
10 2 0.01
11 24 0.08
12 198 0.65
13 74 0.24
14 6 0.02
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (12 bp):
CAAATTTAGTGA
Found at i:2091332 original size:49 final size:49
Alignment explanation
Indices: 2091211--2091351 Score: 135
Period size: 49 Copynumber: 2.9 Consensus size: 49
2091201 GTGTCAAATT
* * *
2091211 TAGTGACAACTCTAGTTCTCAAAGTTAGTGACAAATTTAGTGATAACTT
1 TAGTGACAACTTTAGTTCACAAAGTTAGTGACAAATTTAGTGATAACTC
* ** * *
2091260 TAGT-TCTTAAAGTTA-ATGACAAAGTTAGTGACAAATTTAGTGATAA-TGC
1 TAGTGAC--AACTTTAGTTCACAAAGTTAGTGACAAATTTAGTGATAACT-C
* * *
2091309 TAGTGACAACTTTAGTTCCCAAAGCTAGTAACAAATTTAGTGA
1 TAGTGACAACTTTAGTTCACAAAGTTAGTGACAAATTTAGTGA
2091352 CAACATTAGT
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
48 7 0.10
49 59 0.83
50 5 0.07
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (49 bp):
TAGTGACAACTTTAGTTCACAAAGTTAGTGACAAATTTAGTGATAACTC
Found at i:2091415 original size:62 final size:62
Alignment explanation
Indices: 2091340--2091481 Score: 173
Period size: 62 Copynumber: 2.3 Consensus size: 62
2091330 AAGCTAGTAA
* * **
2091340 CAAATTTAGTGACAACATTAGT-TTC-CAGAGTTAGT-AACAAATTTAGTGACAACTTTAGTTCT
1 CAAAGTTAGTGACAA-ATT-GTGTTCTCAAAGTTAGTGAA-AAATTTAGTGACAACTTTAGACCT
* *
2091402 CAAAGTTAGTGACAAATTTTGTTCTCAAAGTTAGTGGAAAATTTAGTGACAACTTTAGACCT
1 CAAAGTTAGTGACAAATTGTGTTCTCAAAGTTAGTGAAAAATTTAGTGACAACTTTAGACCT
*
2091464 AAAAGTTAGTGACAAATT
1 CAAAGTTAGTGACAAATT
2091482 TGGCGATAAC
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
60 1 0.01
61 6 0.09
62 62 0.89
63 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (62 bp):
CAAAGTTAGTGACAAATTGTGTTCTCAAAGTTAGTGAAAAATTTAGTGACAACTTTAGACCT
Found at i:2091617 original size:12 final size:11
Alignment explanation
Indices: 2091598--2091668 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 11
2091588 GTTAGGGACA
2091598 AATTTAGTGAC
1 AATTTAGTGAC
**
2091609 AACTTTAGTTCTC
1 AA-TTTAG-TGAC
*
2091622 AAAGTTAGTGAC
1 -AATTTAGTGAC
2091634 ATATTTAGTGAC
1 A-ATTTAGTGAC
2091646 AATGTT-GTGAC
1 AAT-TTAGTGAC
2091657 AACTTTAGTGAC
1 AA-TTTAGTGAC
2091669 GTTAGTTCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
11 14 0.30
12 25 0.53
13 6 0.13
14 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (11 bp):
AATTTAGTGAC
Found at i:2091663 original size:23 final size:24
Alignment explanation
Indices: 2091589--2092422 Score: 196
Period size: 25 Copynumber: 34.2 Consensus size: 24
2091579 GTTCTCAAAG
* *
2091589 TTAGGGACAAATTTAGTGACAACT
1 TTAGTGACAAAGTTAGTGACAACT
**
2091613 TTAGTTCTCAAAGTTAGTGACATA-T
1 TTAG-TGACAAAGTTAGTGACA-ACT
*
2091638 TTAGTGACAATGTT-GTGACAACT
1 TTAGTGACAAAGTTAGTGACAACT
* **
2091661 TTAGTGAC---GTTAGT-TCTAAAAA
1 TTAGTGACAAAGTTAGTGAC--AACT
** *
2091683 TTAGTGACAACTTTAGTG---ACG
1 TTAGTGACAAAGTTAGTGACAACT
* *
2091704 TTAGTTTTA-AAAATTAGTGACAACT
1 TTAG--TGACAAAGTTAGTGACAACT
* * *
2091729 TTAGTGACAAATTTAGCGACCA-T
1 TTAGTGACAAAGTTAGTGACAACT
*
2091752 GCTAGTGATCAAAGTTAGTGACAACT
1 -TTAGTGA-CAAAGTTAGTGACAACT
** * * **
2091778 TTAGTTCTCAAATTTACTGATGAC-
1 TTAG-TGACAAAGTTAGTGACAACT
*** *
2091802 TT--TGACCTCGCTAGTGACAACT
1 TTAGTGACAAAGTTAGTGACAACT
* ** * *
2091824 CTAGTTCTCAAAGTTAGTGACATCG
1 TTAG-TGACAAAGTTAGTGACAACT
* ** *
2091849 CTAGTTCTCAAAGTTAGTGACAATT
1 TTAG-TGACAAAGTTAGTGACAACT
** *
2091874 TTAGTTCTCAAATTTAGTGACAACT
1 TTAG-TGACAAAGTTAGTGACAACT
** *
2091899 TTAGTTCTCAAATTTAGTGACAACT
1 TTAG-TGACAAAGTTAGTGACAACT
* ** * *
2091924 TTAATTCTCAAAGTTAGTTACAAAT
1 TT-AGTGACAAAGTTAGTGACAACT
** ** **
2091949 TTAGTGACAACTTTAGTTCTCAAAG
1 TTAGTGACAAAGTTAG-TGACAACT
* *
2091974 TTAGTGACAACTA-TT-GTGATAACG
1 TTAGTGACAA--AGTTAGTGACAACT
* * *
2091998 CTAGTGACAAA-TTGAATGACAACG
1 TTAGTGACAAAGTT-AGTGACAACT
** *
2092022 CGAGTGACAAATTTAGTGACAACT
1 TTAGTGACAAAGTTAGTGACAACT
* ** *
2092046 TTTGTTCCCGAAGTTAGTGACAACT
1 TTAG-TGACAAAGTTAGTGACAACT
** *
2092071 TTAGTTCTCAAAGTTAGTGACAAAT
1 TTAG-TGACAAAGTTAGTGACAACT
* ** * *
2092096 TTTGTTCTCTAAGTTGGTGACAACT
1 TTAG-TGACAAAGTTAGTGACAACT
* *
2092121 TTAGTGACAATGCTAGTGACAACT
1 TTAGTGACAAAGTTAGTGACAACT
** *
2092145 TTAGTTCTCGAAGTTAGTGACAACT
1 TTAG-TGACAAAGTTAGTGACAACT
* * ** **
2092170 TTAGTGACAATGTTACTTCTCAAAG
1 TTAGTGACAAAGTTA-GTGACAACT
* *
2092195 TTAGTGACAAATTTAGTGGCAACT
1 TTAGTGACAAAGTTAGTGACAACT
* ** * *
2092219 TTACTTCTCAAAGTTATTGAAAACT
1 TTA-GTGACAAAGTTAGTGACAACT
* *
2092244 TTAGT-TCTAAACGTTAGTGACAAAT
1 TTAGTGAC-AAA-GTTAGTGACAACT
* ** ** **
2092269 TTGGTGACAACTTTAGTTCTCAAAG
1 TTAGTGACAAAGTTAG-TGACAACT
* *
2092294 TTAGTGACAACGCTAGTGACAACT
1 TTAGTGACAAAGTTAGTGACAACT
*** * *
2092318 TTAGCTTTTAAAGTTGGTGACAAAAT
1 TTAG-TGACAAAGTTAGTGAC-AACT
** *
2092344 TT-GATCTCAAAGTTAGTGACAAAAT
1 TTAG-TGACAAAGTTAGTGAC-AACT
** *
2092369 TT-GATCTCAAAGTTAGTGACAACG
1 TTAG-TGACAAAGTTAGTGACAACT
**
2092393 TTAGTTCTCAAAGTTAGTGACAACT
1 TTAG-TGACAAAGTTAGTGACAACT
2092418 TTAGT
1 TTAGT
2092423 CTACTCTGTT
Statistics
Matches: 605, Mismatches: 163, Indels: 84
0.71 0.19 0.10
Matches are distributed among these distances:
20 4 0.01
21 16 0.03
22 23 0.04
23 22 0.04
24 131 0.22
25 397 0.66
26 12 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (24 bp):
TTAGTGACAAAGTTAGTGACAACT
Found at i:2091693 original size:34 final size:34
Alignment explanation
Indices: 2091652--2091736 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
2091642 TGACAATGTT
2091652 GTGACAACTTTAGTGACGTTAGTTCTAAAAATTA
1 GTGACAACTTTAGTGACGTTAGTTCTAAAAATTA
*
2091686 GTGACAACTTTAGTGACGTTAGTTTTAAAAATTA
1 GTGACAACTTTAGTGACGTTAGTTCTAAAAATTA
2091720 GTGACAACTTTAGTGAC
1 GTGACAACTTTAGTGAC
2091737 AAATTTAGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (34 bp):
GTGACAACTTTAGTGACGTTAGTTCTAAAAATTA
Found at i:2091734 original size:12 final size:12
Alignment explanation
Indices: 2091717--2091782 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
2091707 GTTTTAAAAA
*
2091717 TTAGTGACAACT
1 TTAGTGACAAAT
2091729 TTAGTGACAAAT
1 TTAGTGACAAAT
* *
2091741 TTAGCGAC-CAT
1 TTAGTGACAAAT
* *
2091752 GCTAGTGATCAAAG
1 -TTAGTGA-CAAAT
*
2091766 TTAGTGACAACT
1 TTAGTGACAAAT
2091778 TTAGT
1 TTAGT
2091783 TCTCAAATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
11 2 0.05
12 31 0.76
13 7 0.17
14 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (12 bp):
TTAGTGACAAAT
Found at i:2091782 original size:25 final size:25
Alignment explanation
Indices: 2091717--2092422 Score: 263
Period size: 25 Copynumber: 28.7 Consensus size: 25
2091707 GTTTTAAAAA
* *
2091717 TTAGTGACAACTTTAGTG-ACAAAT
1 TTAGTGACAACTTTAGTGCTCAAAG
* * * *
2091741 TTAGCGACCA-TGCTAGTGATCAAAG
1 TTAGTGACAACT-TTAGTGCTCAAAG
* *
2091766 TTAGTGACAACTTTAGTTCTCAAAT
1 TTAGTGACAACTTTAGTGCTCAAAG
* ** **
2091791 TTACTGATGACTTT-GACCTC---G
1 TTAGTGACAACTTTAGTGCTCAAAG
* * *
2091812 CTAGTGACAACTCTAGTTCTCAAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
* ** *
2091837 TTAGTGACATCGCTAGTTCTCAAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
* * *
2091862 TTAGTGACAATTTTAGTTCTCAAAT
1 TTAGTGACAACTTTAGTGCTCAAAG
* *
2091887 TTAGTGACAACTTTAGTTCTCAAAT
1 TTAGTGACAACTTTAGTGCTCAAAG
* *
2091912 TTAGTGACAACTTTAATTCTCAAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
* * * **
2091937 TTAGTTACAAATTTAGTG-ACAACT
1 TTAGTGACAACTTTAGTGCTCAAAG
** ** *
2091961 TTAGTTCTCAAAGTTAGTG-ACAACTA-
1 TTAG-TGACAACTTTAGTGCTCAA--AG
* ** *
2091987 TT-GTGATAACGCTAGTG-ACAAA-
1 TTAGTGACAACTTTAGTGCTCAAAG
* *** * *
2092009 TTGAATGACAACGCGAGTG-ACAAAT
1 TT-AGTGACAACTTTAGTGCTCAAAG
* * * *
2092034 TTAGTGACAACTTTTGTTCCCGAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
*
2092059 TTAGTGACAACTTTAGTTCTCAAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
* * * *
2092084 TTAGTGACAAATTTTGTTCTCTAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
* * *
2092109 TTGGTGACAACTTTAGTG-ACAATG
1 TTAGTGACAACTTTAGTGCTCAAAG
* * *
2092133 CTAGTGACAACTTTAGTTCTCGAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
* *
2092158 TTAGTGACAACTTTAGTG-ACAATG
1 TTAGTGACAACTTTAGTGCTCAAAG
* ** ** * *
2092182 TTACTTCTCAAAGTTAGTG-ACAAAT
1 TTA-GTGACAACTTTAGTGCTCAAAG
* * *
2092207 TTAGTGGCAACTTTACTTCTCAAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
* * *
2092232 TTATTGAAAACTTTAGTTCT-AAACG
1 TTAGTGACAACTTTAGTGCTCAAA-G
* * * **
2092257 TTAGTGACAAATTTGGTG-ACAACT
1 TTAGTGACAACTTTAGTGCTCAAAG
** ** * *
2092281 TTAGTTCTCAAAGTTAGTG-ACAACG
1 TTAG-TGACAACTTTAGTGCTCAAAG
* * *
2092306 CTAGTGACAACTTTAGCT-TTTAAAG
1 TTAGTGACAACTTTAG-TGCTCAAAG
* *
2092331 TTGGTGACAAAATTT-GAT-CTCAAAG
1 TTAGTGAC-AACTTTAG-TGCTCAAAG
*
2092356 TTAGTGACAAAATTT-GAT-CTCAAAG
1 TTAGTGAC-AACTTTAG-TGCTCAAAG
* *
2092381 TTAGTGACAACGTTAGTTCTCAAAG
1 TTAGTGACAACTTTAGTGCTCAAAG
2092406 TTAGTGACAACTTTAGT
1 TTAGTGACAACTTTAGT
2092423 CTACTCTGTT
Statistics
Matches: 519, Mismatches: 138, Indels: 49
0.74 0.20 0.07
Matches are distributed among these distances:
21 9 0.02
22 7 0.01
23 1 0.00
24 116 0.22
25 378 0.73
26 8 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (25 bp):
TTAGTGACAACTTTAGTGCTCAAAG
Found at i:2091954 original size:37 final size:37
Alignment explanation
Indices: 2091907--2092320 Score: 152
Period size: 37 Copynumber: 11.5 Consensus size: 37
2091897 CTTTAGTTCT
*
2091907 CAAATTTAGTGACAACTTTAATTCTCAAAGTTAGTTA
1 CAAATTTAGTGACAACTTTAATTCTCAAAGTTAGTGA
*
2091944 CAAATTTAGTGACAACTTTAGTTCTCAAAGTTAGTGA
1 CAAATTTAGTGACAACTTTAATTCTCAAAGTTAGTGA
* * ** * ** *
2091981 CAACTATT-GTGATAACGCT-AGTGACAAA-TTGAATGA
1 CAAAT-TTAGTGACAACTTTAATTCTCAAAGTT-AGTGA
**** * * ** ** ** **
2092017 CAACGCGAGTGACAAATTT-AGTGACAACTTTTGTTCC
1 CAAATTTAGTGACAACTTTAATTCTCAA-AGTTAGTGA
* * *
2092054 CGAAGTTAGTGACAACTTTAGTTCTCAAAGTTAGTGA
1 CAAATTTAGTGACAACTTTAATTCTCAAAGTTAGTGA
** * * **
2092091 CAAATTT--TG--TTCTCTAAGTTGGTGACAACTTTAGTGA
1 CAAATTTAGTGACAACTTTAA-TT-CT--CAAAGTTAGTGA
* * *
2092128 C-AATGCTAGTGACAACTTTAGTTCTCGAAGTTAGTGA
1 CAAAT-TTAGTGACAACTTTAATTCTCAAAGTTAGTGA
* *
2092165 CAACTTTAGTGACAA-TGTTACTTCTCAAAGTTAGTGA
1 CAAATTTAGTGACAACT-TTAATTCTCAAAGTTAGTGA
* *
2092202 CAAATTTAGTGGCAACTTTACTTCTCAAAG-T--T--
1 CAAATTTAGTGACAACTTTAATTCTCAAAGTTAGTGA
* * * *
2092234 ---A--T--TGAAAACTTTAGTTCTAAACGTTAGTGA
1 CAAATTTAGTGACAACTTTAATTCTCAAAGTTAGTGA
* *
2092264 CAAATTTGGTGACAACTTTAGTTCTCAAAGTTAGTGA
1 CAAATTTAGTGACAACTTTAATTCTCAAAGTTAGTGA
***
2092301 CAACGCTAGTGACAACTTTA
1 CAAATTTAGTGACAACTTTA
2092321 GCTTTTAAAG
Statistics
Matches: 273, Mismatches: 74, Indels: 60
0.67 0.18 0.15
Matches are distributed among these distances:
25 16 0.06
26 1 0.00
27 1 0.00
28 1 0.00
29 1 0.00
33 5 0.02
34 3 0.01
35 6 0.02
36 33 0.12
37 186 0.68
38 11 0.04
39 3 0.01
40 2 0.01
41 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (37 bp):
CAAATTTAGTGACAACTTTAATTCTCAAAGTTAGTGA
Found at i:2092159 original size:49 final size:49
Alignment explanation
Indices: 2092035--2092181 Score: 204
Period size: 49 Copynumber: 3.0 Consensus size: 49
2092025 GTGACAAATT
* ** * *
2092035 TAGTGACAACTTTTGTTCCCGAAGTTAGTGACAACTTTAGTTCTCAAAGT
1 TAGTGACAACTTTTGTTCTCGAAGTTAGTGACAACTTTAG-TGACAATGC
* * *
2092085 TAGTGACAAATTTTGTTCTCTAAGTTGGTGACAACTTTAGTGACAATGC
1 TAGTGACAACTTTTGTTCTCGAAGTTAGTGACAACTTTAGTGACAATGC
*
2092134 TAGTGACAACTTTAGTTCTCGAAGTTAGTGACAACTTTAGTGACAATG
1 TAGTGACAACTTTTGTTCTCGAAGTTAGTGACAACTTTAGTGACAATG
2092182 TTACTTCTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 49 0.58
50 36 0.42
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (49 bp):
TAGTGACAACTTTTGTTCTCGAAGTTAGTGACAACTTTAGTGACAATGC
Found at i:2092221 original size:12 final size:12
Alignment explanation
Indices: 2091857--2092212 Score: 79
Period size: 12 Copynumber: 28.9 Consensus size: 12
2091847 CGCTAGTTCT
*
2091857 CAAAGTTAGTGA
1 CAAATTTAGTGA
* **
2091869 CAATTTTAGTTCT
1 CAAATTTAG-TGA
2091882 CAAATTTAGTGA
1 CAAATTTAGTGA
* **
2091894 CAACTTTAGTTCT
1 CAAATTTAG-TGA
2091907 CAAATTTAGTGA
1 CAAATTTAGTGA
* * **
2091919 CAACTTTAATTCT
1 CAAATTT-AGTGA
* *
2091932 CAAAGTTAGTTA
1 CAAATTTAGTGA
2091944 CAAATTTAGTGA
1 CAAATTTAGTGA
* **
2091956 CAACTTTAGTTCT
1 CAAATTTAG-TGA
*
2091969 CAAAGTTAGTGA
1 CAAATTTAGTGA
*
2091981 CAACTATT-GTGA
1 CAAAT-TTAGTGA
* ***
2091993 TAACGCTAGTGA
1 CAAATTTAGTGA
* *
2092005 CAAATTGAATGA
1 CAAATTTAGTGA
****
2092017 CAACGCGAGTGA
1 CAAATTTAGTGA
2092029 CAAATTTAGTGA
1 CAAATTTAGTGA
* * **
2092041 CAACTTTTGTTCC
1 CAAATTTAG-TGA
* *
2092054 CGAAGTTAGTGA
1 CAAATTTAGTGA
* **
2092066 CAACTTTAGTTCT
1 CAAATTTAG-TGA
*
2092079 CAAAGTTAGTGA
1 CAAATTTAGTGA
* **
2092091 CAAATTTTGTTCT
1 CAAATTTAG-TGA
* * *
2092104 CTAAGTTGGTGA
1 CAAATTTAGTGA
*
2092116 CAACTTTAGTGA
1 CAAATTTAGTGA
*
2092128 C-AATGCTAGTGA
1 CAAAT-TTAGTGA
* **
2092140 CAACTTTAGTTCT
1 CAAATTTAG-TGA
* *
2092153 CGAAGTTAGTGA
1 CAAATTTAGTGA
*
2092165 CAACTTTAGTGA
1 CAAATTTAGTGA
* **
2092177 C-AATGTTACTTCT
1 CAAAT-TTA-GTGA
*
2092190 CAAAGTTAGTGA
1 CAAATTTAGTGA
2092202 CAAATTTAGTG
1 CAAATTTAGTG
2092213 GCAACTTTAC
Statistics
Matches: 224, Mismatches: 105, Indels: 30
0.62 0.29 0.08
Matches are distributed among these distances:
11 5 0.02
12 147 0.66
13 70 0.31
14 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (12 bp):
CAAATTTAGTGA
Found at i:2092244 original size:99 final size:100
Alignment explanation
Indices: 2092112--2092366 Score: 281
Period size: 99 Copynumber: 2.6 Consensus size: 100
2092102 CTCTAAGTTG
** * * * *
2092112 GTGACAACTTTAG-TGACAATGCTAGTGAC-AACTTTAGTTCTCGAAGTTAGTGACAACTTTAGT
1 GTGACAACTTTAGCTTTCAAAGTTAGTGACAAACTTTAGTTCTCAAAGTTAGTGACAAATTTAGT
**
2092175 GACAA-TGTTACTTCTCAAAGTTAGTGACAAATTTA
66 GACAACT-TTACTTCTCAAAGTTAGTGACAAAGCTA
* * *
2092210 GTGGCAACTTTA-CTTCTCAAAGTTATTGA-AAACTTTAGTTCT-AAACGTTAGTGACAAATTTG
1 GTGACAACTTTAGCTT-TCAAAGTTAGTGACAAACTTTAGTTCTCAAA-GTTAGTGACAAATTTA
* *
2092272 GTGACAACTTTAGTTCTCAAAGTTAGTGACAACGCTA
64 GTGACAACTTTACTTCTCAAAGTTAGTGACAAAGCTA
* * * *
2092309 GTGACAACTTTAGCTTTTAAAGTTGGTGACAAAATTT-GATCTCAAAGTTAGTGACAAA
1 GTGACAACTTTAGCTTTCAAAGTTAGTGACAAACTTTAGTTCTCAAAGTTAGTGACAAA
2092367 ATTTGATCTC
Statistics
Matches: 130, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
98 14 0.11
99 103 0.79
100 13 0.10
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (100 bp):
GTGACAACTTTAGCTTTCAAAGTTAGTGACAAACTTTAGTTCTCAAAGTTAGTGACAAATTTAGT
GACAACTTTACTTCTCAAAGTTAGTGACAAAGCTA
Found at i:2092276 original size:74 final size:73
Alignment explanation
Indices: 2092059--2092422 Score: 245
Period size: 74 Copynumber: 4.9 Consensus size: 73
2092049 GTTCCCGAAG
* * * *
2092059 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAAA-TTTTGTTCTCTAAGTTGGTGACAACTTT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGA-AAACTTTAGTTCT-AAAGTTAGTGACAAATTT
2092123 AGTGAC-AAT
64 AGTGACAAAT
* * * * * * ** *
2092132 GCTAGTGACAACTTTAGTTCTCGAAGTTAGTGACAACTTTAGTGAC-AATGTTACTTCTCAAAGT
1 -TTAGTGACAACTTTAGTTCTCAAAGTTAGTGAAAACTTTAGT-TCTAAAGTTA-GTGACAAATT
2092196 TAGTGACAAAT
63 TAGTGACAAAT
* * * *
2092207 TTAGTGGCAACTTTACTTCTCAAAGTTATTGAAAACTTTAGTTCTAAACGTTAGTGACAAATTTG
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGAAAACTTTAGTTCTAAA-GTTAGTGACAAATTTA
*
2092272 GTGACAACT
65 GTGACAAAT
** ** ** * * * * *
2092281 TTAGTTCTCAAAGTTAG-TGACAACGCTAGTGACAACTTTAGCTTTTAAAGTTGGTGACAAAATT
1 TTAG-TGACAACTTTAGTTCTCAAAGTTAGTGAAAACTTTAG-TTCTAAAGTTAGTGAC-AAATT
** *
2092345 T-GATCTCAAAG
63 TAG-TGACAAAT
* * * * *
2092356 TTAGTGACAAAATTT-GATCTCAAAGTTAGTGACAACGTTAGTTCTCAAAGTTAGTGACAACTTT
1 TTAGTGAC-AACTTTAGTTCTCAAAGTTAGTGAAAACTTTAGTTCT-AAAGTTAGTGACAAATTT
2092420 AGT
64 AGT
2092423 CTACTCTGTT
Statistics
Matches: 221, Mismatches: 55, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
73 7 0.03
74 143 0.65
75 71 0.32
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (73 bp):
TTAGTGACAACTTTAGTTCTCAAAGTTAGTGAAAACTTTAGTTCTAAAGTTAGTGACAAATTTAG
TGACAAAT
Found at i:2092321 original size:37 final size:36
Alignment explanation
Indices: 2092240--2092341 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
2092230 AGTTATTGAA
** *
2092240 AACTTTAGTTCTAAACGTTAGTGACAAATTTGGTGAC
1 AACTTTAGTTCTAAA-GTTAGTGACAAAGCTAGTGAC
*
2092277 AACTTTAGTTCTCAAAGTTAGTGACAACGCTAGTGAC
1 AACTTTAGTTCT-AAAGTTAGTGACAAAGCTAGTGAC
* *
2092314 AACTTTAGCTTTTAAAGTTGGTGACAAA
1 AACTTTAG-TTCTAAAGTTAGTGACAAA
2092342 ATTTGATCTC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 50 0.89
38 6 0.11
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (36 bp):
AACTTTAGTTCTAAAGTTAGTGACAAAGCTAGTGAC
Found at i:2092422 original size:37 final size:37
Alignment explanation
Indices: 2092244--2092422 Score: 114
Period size: 37 Copynumber: 4.8 Consensus size: 37
2092234 ATTGAAAACT
* *
2092244 TTAGTTCT-AAACGTTAGTGACAAATTTGGTGACAACT
1 TTAGTTCTCAAA-GTTAGTGACAAATTTAGTGACAACG
*** *
2092281 TTAGTTCTCAAAGTTAGTGACAACGCTAGTGACAACT
1 TTAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACG
* * ** *
2092318 TTAGCTT-TTAAAGTTGGTGACAAAATTT-GATCTCAAAG
1 TTAG-TTCTCAAAGTTAGTGAC-AAATTTAG-TGACAACG
** * * ** *
2092356 TTAG-TGACAAAATTTGATCTCAAAGTTAGTGACAACG
1 TTAGTTCTCAAAGTTAG-TGACAAATTTAGTGACAACG
*
2092393 TTAGTTCTCAAAGTTAGTGACAACTTTAGT
1 TTAGTTCTCAAAGTTAGTGACAAATTTAGT
2092423 CTACTCTGTT
Statistics
Matches: 103, Mismatches: 31, Indels: 16
0.69 0.21 0.11
Matches are distributed among these distances:
36 1 0.01
37 75 0.73
38 27 0.26
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (37 bp):
TTAGTTCTCAAAGTTAGTGACAAATTTAGTGACAACG
Found at i:2093693 original size:12 final size:12
Alignment explanation
Indices: 2093676--2093741 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
2093666 GTTCTCAAAG
*
2093676 TTAGTGATAACT
1 TTAGTGACAACT
2093688 TTAGTGACAACT
1 TTAGTGACAACT
** **
2093700 TTAGTTCTCAAAG
1 TTAG-TGACAACT
2093713 TTAGTGACAACT
1 TTAGTGACAACT
*
2093725 TTTGTGACAACT
1 TTAGTGACAACT
2093737 TTAGT
1 TTAGT
2093742 TCTCAAAGTT
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 34 0.81
13 8 0.19
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (12 bp):
TTAGTGACAACT
Found at i:2093703 original size:37 final size:37
Alignment explanation
Indices: 2093651--2094376 Score: 339
Period size: 37 Copynumber: 19.1 Consensus size: 37
2093641 ATAAAAAAAG
* * *
2093651 TTAGTGATAAATTTAGTTCTCAAAGTTAGTGATAACT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
2093688 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
* *
2093725 TTTGTGACAACTTTAGTTCTCAAAGTTAGTGAGATCTTTAGTCACGACG
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGT--G------A--CA--ACT
* ** * *
2093774 TTGGTGACAACGCTAGTTCTCAAAGTTGGTGAC-ATT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
* * *
2093810 TTAGTAACAACTTTGGTTCTCAAAGTTGGTGACAACT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
*
2093847 TTAGT------TTTA------AAAGTTAGTGACAAAT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
** * *
2093872 TTGTTGACAACTTTAGTTCTCAAAGTTGGTGACAAAT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
**
2093909 TTAGTGACAACTTTAGTTCTCAAAGTTAGTACGCTAGTCCTCAAAA
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGT--G--A-----CAACT
* *
2093955 TTAGTGACAAATTTAGTAACAACTTTAATTCTTAAA-TCTAGTGAC-ACAT
1 TTAGTG---A---------CAACTTTAGTTCTCAAAGT-TAGTGACAAC-T
* * * *
2094004 TTATTGACAACTTTAGTTCTAAAAGTTAGTGAAAAAT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
* * * * *
2094041 CTGGTCACAACTTTAGTTCTCAAAGTTAATGACAACG
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
* * * *
2094078 TTAGTGATAACATTAGTTCTCAAAGTTTGTGATAAC-
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
** ** ** ** **
2094114 TTAGTTCTCAAAGTTAG-TGACAATTTTAGTTCG-CAAAA
1 TTAG-TGACAACTTTAGTTCTCAAAGTTAG-T-GACAACT
* * *
2094152 TTAGTGACAACTTTAGTTCTAAAAGTTAGTGATAAAT
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
*
2094189 TTAGTGACAACTTTAGTTCTCAAAG--AGTAACAA-T
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
*
2094223 TATAGTGACAACGTTAGTTCTCAAAGTTAGTGACAA-T
1 T-TAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
* *
2094260 GCTAGTGACAACTTTAGTTC-CAAAAGTTAGTGACAAAT
1 -TTAGTGACAACTTTAGTTCTC-AAAGTTAGTGACAACT
* * * * * *
2094298 TTTGTGGCCACTTTAGTTCTCAATGTCAGTGACAACG
1 TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
* * * * *
2094335 CTAGTGACAA-TGATAGTTTTTAAAGTTAGTGATAACT
1 TTAGTGACAACT-TTAGTTCTCAAAGTTAGTGACAACT
2094372 TTAGT
1 TTAGT
2094377 TCTCAATGTC
Statistics
Matches: 522, Mismatches: 103, Indels: 128
0.69 0.14 0.17
Matches are distributed among these distances:
25 17 0.03
31 7 0.01
34 2 0.00
35 29 0.06
36 43 0.08
37 330 0.63
38 16 0.03
39 3 0.01
41 2 0.00
45 1 0.00
46 11 0.02
47 3 0.01
48 1 0.00
49 35 0.07
54 1 0.00
56 1 0.00
57 1 0.00
58 19 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (37 bp):
TTAGTGACAACTTTAGTTCTCAAAGTTAGTGACAACT
Found at i:2093766 original size:49 final size:48
Alignment explanation
Indices: 2093713--2093826 Score: 138
Period size: 49 Copynumber: 2.4 Consensus size: 48
2093703 GTTCTCAAAG
* * ** *
2093713 TTAGTGACAACTTTTGTGACAACTTTAGTTCTCAAAGTTAGTGAGATCT
1 TTAGTAACAACTTTGGTGACAACGCTAGTTCTCAAAGTTAGTGACAT-T
* * * *
2093762 TTAGTCACGACGTTGGTGACAACGCTAGTTCTCAAAGTTGGTGACATT
1 TTAGTAACAACTTTGGTGACAACGCTAGTTCTCAAAGTTAGTGACATT
2093810 TTAGTAACAACTTTGGT
1 TTAGTAACAACTTTGGT
2093827 TCTCAAAGTT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
48 15 0.28
49 39 0.72
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (48 bp):
TTAGTAACAACTTTGGTGACAACGCTAGTTCTCAAAGTTAGTGACATT
Found at i:2093845 original size:25 final size:25
Alignment explanation
Indices: 2093810--2093874 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
2093800 TGGTGACATT
* *
2093810 TTAGTAACAACTTTGGTTCTCAAAG
1 TTAGTGACAACTTTGGTTCTAAAAG
* * *
2093835 TTGGTGACAACTTTAGTTTTAAAAG
1 TTAGTGACAACTTTGGTTCTAAAAG
*
2093860 TTAGTGACAAATTTG
1 TTAGTGACAACTTTG
2093875 TTGACAACTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (25 bp):
TTAGTGACAACTTTGGTTCTAAAAG
Found at i:2093915 original size:12 final size:12
Alignment explanation
Indices: 2093860--2093925 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
2093850 GTTTTAAAAG
2093860 TTAGTGACAAAT
1 TTAGTGACAAAT
*
2093872 TT-GTTGACAACT
1 TTAG-TGACAAAT
** *
2093884 TTAGTTCTCAAAG
1 TTAG-TGACAAAT
*
2093897 TTGGTGACAAAT
1 TTAGTGACAAAT
*
2093909 TTAGTGACAACT
1 TTAGTGACAAAT
2093921 TTAGT
1 TTAGT
2093926 TCTCAAAGTT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 1 0.02
12 31 0.76
13 9 0.22
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (12 bp):
TTAGTGACAAAT
Found at i:2093932 original size:25 final size:25
Alignment explanation
Indices: 2093904--2093971 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 25
2093894 AAGTTGGTGA
*
2093904 CAAATTTAGTGACAACTTTAGTTCT
1 CAAAGTTAGTGACAACTTTAGTTCT
* *
2093929 CAAAGTTAGT-AC-GC--TAGTCCT
1 CAAAGTTAGTGACAACTTTAGTTCT
* *
2093950 CAAAATTAGTGACAAATTTAGT
1 CAAAGTTAGTGACAACTTTAGT
2093972 AACAACTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 15 0.45
22 2 0.06
23 1 0.03
24 2 0.06
25 13 0.39
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (25 bp):
CAAAGTTAGTGACAACTTTAGTTCT
Found at i:2093999 original size:95 final size:96
Alignment explanation
Indices: 2093855--2094033 Score: 256
Period size: 95 Copynumber: 1.9 Consensus size: 96
2093845 CTTTAGTTTT
* * *
2093855 AAAAGTTAGTGACAAATTTGTTGACAACTTTAGTTCTCAAAGTTGGTGACAAATTTAGTGACAAC
1 AAAAGTTAGTGACAAATTTGTTAACAACTTTAATTCTCAAAGTTAGTGACAAATTTAGTGACAAC
*
2093920 TTTAGTTCTCAAAGTTAGTACGCTAGTCCTC
66 TTTAGTTCTAAAAGTTAGTACGCTAGTCCTC
* * *
2093951 AAAA-TTAGTGACAAATTTAG-TAACAACTTTAATTCTTAAA-TCTAGTGACACATTTATTGACA
1 AAAAGTTAGTGACAAATTT-GTTAACAACTTTAATTCTCAAAGT-TAGTGACAAATTTAGTGACA
2094013 ACTTTAGTTCTAAAAGTTAGT
64 ACTTTAGTTCTAAAAGTTAGT
2094034 GAAAAATCTG
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
94 1 0.01
95 68 0.92
96 5 0.07
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (96 bp):
AAAAGTTAGTGACAAATTTGTTAACAACTTTAATTCTCAAAGTTAGTGACAAATTTAGTGACAAC
TTTAGTTCTAAAAGTTAGTACGCTAGTCCTC
Found at i:2094109 original size:25 final size:25
Alignment explanation
Indices: 2094077--2094193 Score: 146
Period size: 25 Copynumber: 4.7 Consensus size: 25
2094067 TAATGACAAC
*
2094077 GTTAGTGATAACATTAGTTCTCAAA
1 GTTAGTGATAACTTTAGTTCTCAAA
*
2094102 GTTTGTGATAAC-TTAGTTCTCAAA
1 GTTAGTGATAACTTTAGTTCTCAAA
* * *
2094126 GTTAGTGACAATTTTAGTTCGCAAA
1 GTTAGTGATAACTTTAGTTCTCAAA
* * *
2094151 ATTAGTGACAACTTTAGTTCTAAAA
1 GTTAGTGATAACTTTAGTTCTCAAA
*
2094176 GTTAGTGATAAATTTAGT
1 GTTAGTGATAACTTTAGT
2094194 GACAACTTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
24 21 0.27
25 58 0.73
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (25 bp):
GTTAGTGATAACTTTAGTTCTCAAA
Found at i:2094131 original size:49 final size:50
Alignment explanation
Indices: 2094077--2094186 Score: 141
Period size: 49 Copynumber: 2.2 Consensus size: 50
2094067 TAATGACAAC
* * * * *
2094077 GTTAGTGATAACATTAGTTCTCAAAGTTTGTGATAAC-TTAGTTCTCAAA
1 GTTAGTGATAACATTAGTTCGCAAAATTAGTGACAACTTTAGTTCTAAAA
* **
2094126 GTTAGTGACAATTTTAGTTCGCAAAATTAGTGACAACTTTAGTTCTAAAA
1 GTTAGTGATAACATTAGTTCGCAAAATTAGTGACAACTTTAGTTCTAAAA
2094176 GTTAGTGATAA
1 GTTAGTGATAA
2094187 ATTTAGTGAC
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
49 30 0.59
50 21 0.41
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (50 bp):
GTTAGTGATAACATTAGTTCGCAAAATTAGTGACAACTTTAGTTCTAAAA
Found at i:2094331 original size:74 final size:72
Alignment explanation
Indices: 2094153--2094344 Score: 199
Period size: 72 Copynumber: 2.6 Consensus size: 72
2094143 TTCGCAAAAT
* * * * ***
2094153 TAGTGACAACTTTAGTTCTAAAAGTTAGTGATAAATTTAGTGACAACTTTAGTTCTCAAAGAGTA
1 TAGTGACAACGTTAGTTCTCAAAGTCAGTGACAACGCTAGTGACAACTTTAGTTCTCAAAGAGTA
2094218 ACAATTA
66 ACAATTA
* *
2094225 TAGTGACAACGTTAGTTCTCAAAGTTAGTGACAATGCTAGTGACAACTTTAGTTC-CAAAAGTTA
1 TAGTGACAACGTTAGTTCTCAAAGTCAGTGACAACGCTAGTGACAACTTTAGTTCTC-AAAG--A
*
2094289 GTGACAAATT-
63 GTAAC-AATTA
* * * * *
2094299 TTGTGGCCACTTTAGTTCTCAATGTCAGTGACAACGCTAGTGACAA
1 TAGTGACAACGTTAGTTCTCAAAGTCAGTGACAACGCTAGTGACAA
2094345 TGATAGTTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
71 1 0.01
72 53 0.52
74 44 0.43
75 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (72 bp):
TAGTGACAACGTTAGTTCTCAAAGTCAGTGACAACGCTAGTGACAACTTTAGTTCTCAAAGAGTA
ACAATTA
Found at i:2094373 original size:62 final size:62
Alignment explanation
Indices: 2094307--2094438 Score: 228
Period size: 62 Copynumber: 2.1 Consensus size: 62
2094297 TTTTGTGGCC
*
2094307 ACTTTAGTTCTCAATGTCAGTGACAACGCTAGTGACAATGATAGTTTTTAAAGTTAGTGATA
1 ACTTTAGTTCTCAATGTCAGTGACAACGCTAGTGACAATGATAGTTTTTAAAGTTAGTGACA
* * *
2094369 ACTTTAGTTCTCAATGTCAGTGACAACTCTAGTGACAATGTTAGTTTTTAAAGTTAGTGACC
1 ACTTTAGTTCTCAATGTCAGTGACAACGCTAGTGACAATGATAGTTTTTAAAGTTAGTGACA
2094431 ACTTTAGT
1 ACTTTAGT
2094439 GACAACACTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (62 bp):
ACTTTAGTTCTCAATGTCAGTGACAACGCTAGTGACAATGATAGTTTTTAAAGTTAGTGACA
Found at i:2094413 original size:37 final size:37
Alignment explanation
Indices: 2094372--2094443 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
2094362 AGTGATAACT
*
2094372 TTAGTTCTCAATGTCAGTGACAACTCTAGTGACAATG
1 TTAGTTCTCAAAGTCAGTGACAACTCTAGTGACAATG
* * * * *
2094409 TTAGTTTTTAAAGTTAGTGACCACTTTAGTGACAA
1 TTAGTTCTCAAAGTCAGTGACAACTCTAGTGACAA
2094444 CACTAGCGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (37 bp):
TTAGTTCTCAAAGTCAGTGACAACTCTAGTGACAATG
Found at i:2094439 original size:12 final size:12
Alignment explanation
Indices: 2094422--2094468 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
2094412 GTTTTTAAAG
*
2094422 TTAGTGACCACT
1 TTAGTGACAACT
*
2094434 TTAGTGACAACA
1 TTAGTGACAACT
* *
2094446 CTAGCGACAACT
1 TTAGTGACAACT
2094458 TTAGTGACAAC
1 TTAGTGACAAC
2094469 GTTTGTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (12 bp):
TTAGTGACAACT
Found at i:2094501 original size:21 final size:21
Alignment explanation
Indices: 2094460--2094504 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2094450 CGACAACTTT
* *
2094460 AGTGACAACGTTTGTTTTCAA
1 AGTGAAAACGTTTGTTCTCAA
2094481 AGTGAAAAC-TTTAGTTCTCAA
1 AGTGAAAACGTTT-GTTCTCAA
2094502 AGT
1 AGT
2094505 TAGTGACAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (21 bp):
AGTGAAAACGTTTGTTCTCAA
Found at i:2094561 original size:25 final size:25
Alignment explanation
Indices: 2094533--2094590 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
2094523 TTAGTAACGG
*
2094533 CTTTAGTTCTCAAAGTTTGTGACAA
1 CTTTAGTTCTCAAAGTTAGTGACAA
2094558 CTTTAGTTCTCAAAGTTAGTGACAA
1 CTTTAGTTCTCAAAGTTAGTGACAA
2094583 CTTTAGTT
1 CTTTAGTT
2094591 GTGACTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (25 bp):
CTTTAGTTCTCAAAGTTAGTGACAA
Found at i:2094668 original size:37 final size:37
Alignment explanation
Indices: 2094606--2094797 Score: 147
Period size: 37 Copynumber: 5.2 Consensus size: 37
2094596 TAATTTGGTT
* *
2094606 ACAACTTTAGTGAC-A-GTTATTTCTCAAAGTTAGTG
1 ACAAATTTAGTGACAACGTTAGTTCTCAAAGTTAGTG
* * *
2094641 ACAAATTTGGTGACAACTTTAGTTCTCAAAGTTGGTG
1 ACAAATTTAGTGACAACGTTAGTTCTCAAAGTTAGTG
* * * ** * ** * *
2094678 ATAATTTTTGTTCCCAAAGTTAG-TGACAACGCTAGTG
1 ACAAATTTAG-TGACAACGTTAGTTCTCAAAGTTAGTG
* * *
2094715 ACAATTTTAGTGACAACGTTCGTTCTTAAAGTTAGTG
1 ACAAATTTAGTGACAACGTTAGTTCTCAAAGTTAGTG
* * * *
2094752 ACAAATTTATTGACAACTTTAGTTCTTAAAGTTAATG
1 ACAAATTTAGTGACAACGTTAGTTCTCAAAGTTAGTG
*
2094789 ACAACTTTA
1 ACAAATTTA
2094798 CTTCTCAAAA
Statistics
Matches: 119, Mismatches: 34, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
35 12 0.10
36 9 0.08
37 90 0.76
38 8 0.07
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (37 bp):
ACAAATTTAGTGACAACGTTAGTTCTCAAAGTTAGTG
Found at i:2094675 original size:25 final size:25
Alignment explanation
Indices: 2094642--2094707 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
2094632 AAGTTAGTGA
* *
2094642 CAAATTTGGTGACAACTTTAGTTCT
1 CAAAGTTGGTGACAACTTTAGTTCC
* * *
2094667 CAAAGTTGGTGATAATTTTTGTTCC
1 CAAAGTTGGTGACAACTTTAGTTCC
*
2094692 CAAAGTTAGTGACAAC
1 CAAAGTTGGTGACAAC
2094708 GCTAGTGACA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (25 bp):
CAAAGTTGGTGACAACTTTAGTTCC
Found at i:2094762 original size:136 final size:136
Alignment explanation
Indices: 2094622--2094916 Score: 317
Period size: 136 Copynumber: 2.2 Consensus size: 136
2094612 TTAGTGACAG
* ** * * * *
2094622 TTATTTCTCAAAGTTAGTGACAAATTTGGTGACAACTTTAGTTCTCAAAGTTGGTGATAATTTTT
1 TTATTTCTCAAAGTTAGTGACAAAGTTAATGACAACTTTACTTCTCAAAATTGGTGACAAATTTT
* *** * * *
2094687 GTTCCCAAAGTTAGTGACAACGCTAGTGACAATTTTAGTGACAACGTTCGTTCTTAAAGTTAGTG
66 GTTACCAAAGTTAGTGACAACGCTAGTGACAACGCTAGTGACAACGTTAGTTCTCAAAGTCAGTG
2094752 ACAAAT
131 ACAAAT
** ** *
2094758 TTA-TTGACAACTTTAGT-TCTTAAAGTTAATGACAACTTTACTTCTCAAAATTGGTGACAAATT
1 TTATTTCTCAAAGTTAGTGAC--AAAGTTAATGACAACTTTACTTCTCAAAATTGGTGACAAATT
* ** ** *
2094821 TTGTTATCAAAGTTAGTGGTAACTTTAGTGACAACGCTAGTGACAACTTTAGTTCTCAAAGTCAG
64 TTGTTACCAAAGTTAGTGACAACGCTAGTGACAACGCTAGTGACAACGTTAGTTCTCAAAGTCAG
2094886 TGACAAAT
129 TGACAAAT
2094894 TT-TGTTCTCAAAGTTAGTGACAA
1 TTAT-TTCTCAAAGTTAGTGACAA
2094917 CGCTACTGAC
Statistics
Matches: 124, Mismatches: 30, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
134 1 0.01
135 10 0.08
136 102 0.82
137 10 0.08
138 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (136 bp):
TTATTTCTCAAAGTTAGTGACAAAGTTAATGACAACTTTACTTCTCAAAATTGGTGACAAATTTT
GTTACCAAAGTTAGTGACAACGCTAGTGACAACGCTAGTGACAACGTTAGTTCTCAAAGTCAGTG
ACAAAT
Found at i:2094791 original size:25 final size:25
Alignment explanation
Indices: 2094753--2094917 Score: 152
Period size: 25 Copynumber: 6.6 Consensus size: 25
2094743 AAGTTAGTGA
* *
2094753 CAAATTTATTGACAACTTTAGTTCT
1 CAAAGTTAGTGACAACTTTAGTTCT
* * *
2094778 TAAAGTTAATGACAACTTTACTTCT
1 CAAAGTTAGTGACAACTTTAGTTCT
* * * * *
2094803 CAAAATTGGTGACAAATTTTGTTAT
1 CAAAGTTAGTGACAACTTTAGTTCT
** **
2094828 CAAAGTTAGTGGTAACTTTAG-TGA
1 CAAAGTTAGTGACAACTTTAGTTCT
* *
2094852 CAACGCTAGTGACAACTTTAGTTCT
1 CAAAGTTAGTGACAACTTTAGTTCT
* * *
2094877 CAAAGTCAGTGACAAATTTTGTTCT
1 CAAAGTTAGTGACAACTTTAGTTCT
2094902 CAAAGTTAGTGACAAC
1 CAAAGTTAGTGACAAC
2094918 GCTACTGACA
Statistics
Matches: 106, Mismatches: 33, Indels: 2
0.75 0.23 0.01
Matches are distributed among these distances:
24 18 0.17
25 88 0.83
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (25 bp):
CAAAGTTAGTGACAACTTTAGTTCT
Found at i:2094927 original size:74 final size:74
Alignment explanation
Indices: 2094787--2094932 Score: 202
Period size: 74 Copynumber: 2.0 Consensus size: 74
2094777 TTAAAGTTAA
** ** ** *
2094787 TGACAACTTTACTTCTCAAAATTGGTGACAAATTTTGTTATCAAAGTTAGTGGTAACTTTAGTGA
1 TGACAACTTTACTTCTCAAAATCAGTGACAAATTTTGTTATCAAAGTTAGTGACAACGCTACTGA
2094852 CAACGCTAG
66 CAACGCTAG
* * *
2094861 TGACAACTTTAGTTCTCAAAGTCAGTGACAAATTTTGTTCTCAAAGTTAGTGACAACGCTACTGA
1 TGACAACTTTACTTCTCAAAATCAGTGACAAATTTTGTTATCAAAGTTAGTGACAACGCTACTGA
2094926 CAACGCT
66 CAACGCT
2094933 GCCTCCTTCC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (74 bp):
TGACAACTTTACTTCTCAAAATCAGTGACAAATTTTGTTATCAAAGTTAGTGACAACGCTACTGA
CAACGCTAG
Found at i:2107003 original size:112 final size:111
Alignment explanation
Indices: 2106806--2107158 Score: 591
Period size: 112 Copynumber: 3.2 Consensus size: 111
2106796 TAGCGCTAAT
* *
2106806 AAAGTGTCGATACTTTATAAAATTGTATTGATCCATAACAATATAACAGGTAAAAAAATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGA-AAA
*
2106871 ATCGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTG
65 ACCGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTG
* *
2106918 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGA-AAA
*
2106983 ACCGGTCTATAAATGACAAAATAGG-AAAAGCGCTACCGGATATATTG
65 ACCGGTCTATAAATGACAAAACAGGTAAAA-CGCTACCGGATATATTG
2107030 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGAAAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGAAAAA
* *
2107095 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTG
66 CCGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTG
*
2107141 ATAGTGTCGATACTTTAT
1 AAAGTGTCGATACTTTAT
2107159 TATAAGTATC
Statistics
Matches: 226, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
111 64 0.28
112 162 0.72
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (111 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGAAAAA
CCGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTG
Found at i:2107336 original size:182 final size:181
Alignment explanation
Indices: 2107030--2107478 Score: 754
Period size: 182 Copynumber: 2.5 Consensus size: 181
2107020 GGATATATTG
*
2107030 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGAAAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAA
** * *
2107095 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATT
66 CCGGTCTCGAAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATT
* * *
2107160 ATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
131 ATAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCTAAT
*
2107211 AAAGTGTCGATACATTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-AAA
* *
2107276 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGTTACCGGATATGTTGAAAGTGTCGATACTTTAT
65 ACCGGTCTCGAAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
2107341 TATAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCTAAT
130 TATAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCTAAT
* *
2107393 AAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-AAA
*
2107458 ATCGGTCTCGAAATGACAAAA
65 ACCGGTCTCGAAATGACAAAA
2107479 TCGATAGTAA
Statistics
Matches: 251, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
181 59 0.24
182 192 0.76
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (181 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAA
CCGGTCTCGAAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATT
ATAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCTAAT
Found at i:2108130 original size:23 final size:23
Alignment explanation
Indices: 2108101--2108148 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2108091 AAATAGGTCA
*
2108101 ATATAAGCGATACCTATTACATT
1 ATATAAGCGATACCTAATACATT
* *
2108124 ATATAAGCGTTACCTAATATATT
1 ATATAAGCGATACCTAATACATT
2108147 AT
1 AT
2108149 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGATACCTAATACATT
Found at i:2111999 original size:20 final size:20
Alignment explanation
Indices: 2111974--2112042 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
2111964 AGTTTTAAAG
2111974 CTTATACATTTCAATTCAAA
1 CTTATACATTTCAATTCAAA
* * * *
2111994 CTTATACATAT-AGTTTTAGA
1 CTTATACATTTCA-ATTCAAA
*
2112014 -TATCTACATTTCAATTCAAA
1 CT-TATACATTTCAATTCAAA
2112034 CTTATACAT
1 CTTATACAT
2112043 ATAGTTTTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (20 bp):
CTTATACATTTCAATTCAAA
Found at i:2112030 original size:40 final size:39
Alignment explanation
Indices: 2111978--2112055 Score: 147
Period size: 40 Copynumber: 2.0 Consensus size: 39
2111968 TTAAAGCTTA
2111978 TACATTTCAATTCAAACTTATACATATAGTTTTAGATATC
1 TACATTTCAATTCAAACTTATACATATAGTTTTA-ATATC
2112018 TACATTTCAATTCAAACTTATACATATAGTTTTAATAT
1 TACATTTCAATTCAAACTTATACATATAGTTTTAATAT
2112056 GATAAAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 4 0.11
40 34 0.89
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (39 bp):
TACATTTCAATTCAAACTTATACATATAGTTTTAATATC
Found at i:2112290 original size:6 final size:6
Alignment explanation
Indices: 2112274--2112395 Score: 237
Period size: 6 Copynumber: 20.5 Consensus size: 6
2112264 TCTCGTCTCG
2112274 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2112321 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2112369 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
2112396 AATACGTGTC
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.04
6 111 0.96
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2112516 original size:20 final size:20
Alignment explanation
Indices: 2112491--2112641 Score: 198
Period size: 20 Copynumber: 7.3 Consensus size: 20
2112481 GAATTTACCC
2112491 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
2112511 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
2112531 ATTTTCTTTCTGAATCGCGTTGCG
1 A---T-TTTCTGAATCGCGTTGCG
2112555 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
2112575 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
2112595 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
2112615 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
2112635 ATTTTCT
1 ATTTTCT
2112642 CAAAATAATA
Statistics
Matches: 115, Mismatches: 8, Indels: 16
0.83 0.06 0.12
Matches are distributed among these distances:
19 4 0.03
20 87 0.76
21 5 0.04
23 1 0.01
24 18 0.16
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:2112597 original size:40 final size:40
Alignment explanation
Indices: 2112498--2112641 Score: 234
Period size: 40 Copynumber: 3.5 Consensus size: 40
2112488 CCCATTTTCT
*
2112498 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTTTCT
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA--TTC-TT-G
*
2112542 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
2112582 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
2112622 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
2112642 CAAAATAATA
Statistics
Matches: 97, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
40 59 0.61
41 2 0.02
42 3 0.03
44 33 0.34
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (40 bp):
GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
Found at i:2115042 original size:36 final size:36
Alignment explanation
Indices: 2114969--2115042 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
2114959 CAAATTGTAA
**
2114969 AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
1 AATATTTATATATTTTCTTTAAAAAATTAAAAACAT
*
2115005 AATATTTATATAATTTT-TTTACAAAATTAAAAACAT
1 AATATTTATAT-ATTTTCTTTAAAAAATTAAAAACAT
2115041 AA
1 AA
2115043 AAAATGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 29 0.85
37 5 0.15
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAAATTAAAAACAT
Found at i:2118616 original size:16 final size:17
Alignment explanation
Indices: 2118585--2118621 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2118575 TTTTCTAAAA
*
2118585 ATTTAAAATTATTATAT
1 ATTTAAAATAATTATAT
2118602 ATTTAAAA-AATTATAT
1 ATTTAAAATAATTATAT
2118618 ATTT
1 ATTT
2118622 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAAATAATTATAT
Found at i:2118618 original size:18 final size:19
Alignment explanation
Indices: 2118589--2118624 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2118579 CTAAAAATTT
2118589 AAAATTATTATATATTTAA
1 AAAATTATTATATATTTAA
*
2118608 AAAATTA-TATATTTTTA
1 AAAATTATTATATATTTA
2118625 TTAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATTATTATATATTTAA
Found at i:2125664 original size:21 final size:21
Alignment explanation
Indices: 2125638--2125677 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2125628 CCCCCTTTGA
*
2125638 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2125659 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2125678 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2129518 original size:5 final size:5
Alignment explanation
Indices: 2129508--2129534 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2129498 TAGGGGTGTA
2129508 TTCGG TTCGG TTCGG TTCGG TTCGG TT
1 TTCGG TTCGG TTCGG TTCGG TTCGG TT
2129535 TTTTACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.37, T:0.44
Consensus pattern (5 bp):
TTCGG
Found at i:2130216 original size:24 final size:23
Alignment explanation
Indices: 2130180--2130251 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
2130170 ATTTAAATTT
2130180 AAACTAATATTTAATATATTATCA
1 AAAC-AATATTTAATATATTATCA
** *
2130204 AAACAATATTTTAATATCACAAACAA
1 AAACAATA-TTTAATAT-ATTATC-A
2130230 AAACAATATTTAA-ATATTATCA
1 AAACAATATTTAATATATTATCA
2130252 TGTCATAAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 1 0.03
23 7 0.18
24 14 0.36
25 8 0.21
26 9 0.23
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (23 bp):
AAACAATATTTAATATATTATCA
Found at i:2140642 original size:63 final size:63
Alignment explanation
Indices: 2140543--2140670 Score: 193
Period size: 63 Copynumber: 2.0 Consensus size: 63
2140533 GAAGAAAAGT
2140543 CTAAGCATGAGAATAACATTATATTACTATTATTAACGACATCAATTTATAACAAAATAACCA
1 CTAAGCATGAGAATAACATTATATTACTATTATTAACGACATCAATTTATAACAAAATAACCA
* * * ** * *
2140606 CTAAGCATGAGAGTAACATTTTATTACTATTATTAACGTCATTGATTTATAACAAGATAATCA
1 CTAAGCATGAGAATAACATTATATTACTATTATTAACGACATCAATTTATAACAAAATAACCA
2140669 CT
1 CT
2140671 TCACCATCGA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (63 bp):
CTAAGCATGAGAATAACATTATATTACTATTATTAACGACATCAATTTATAACAAAATAACCA
Found at i:2141404 original size:2 final size:2
Alignment explanation
Indices: 2141397--2141427 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
2141387 CTAATATGAA
2141397 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
2141428 TATTACATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2143200 original size:2 final size:2
Alignment explanation
Indices: 2143193--2143226 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2143183 GGATGGAGGG
2143193 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
2143227 GTGTGTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2143478 original size:2 final size:2
Alignment explanation
Indices: 2143471--2143502 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2143461 CCGACAGGAA
2143471 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
2143503 CCATTAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2145146 original size:15 final size:15
Alignment explanation
Indices: 2145128--2145157 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2145118 ATTTAAATTT
2145128 AAATTTTATTTTTTA
1 AAATTTTATTTTTTA
2145143 AAATTTTATTTTTTA
1 AAATTTTATTTTTTA
2145158 TAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AAATTTTATTTTTTA
Found at i:2156515 original size:24 final size:24
Alignment explanation
Indices: 2156483--2156530 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2156473 TCAACGAGGC
*
2156483 TTAATATATTTTTTGGTACGTAAA
1 TTAATATATTTTTAGGTACGTAAA
*
2156507 TTAATATATTTTTAGTTACGTAAA
1 TTAATATATTTTTAGGTACGTAAA
2156531 ATAAGGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
TTAATATATTTTTAGGTACGTAAA
Found at i:2157345 original size:20 final size:19
Alignment explanation
Indices: 2157301--2157347 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2157291 TTCCATCTAT
*
2157301 TATTTTTTAATTAAATCAA
1 TATTTTTTAATAAAATCAA
*
2157320 TTTTTTATTGAATAAAAT-AA
1 TATTTT-TT-AATAAAATCAA
2157340 TATTTTTT
1 TATTTTTT
2157348 TATTTCGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 9 0.39
21 7 0.30
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTTTTTAATAAAATCAA
Found at i:2159589 original size:20 final size:20
Alignment explanation
Indices: 2159564--2159736 Score: 242
Period size: 20 Copynumber: 8.6 Consensus size: 20
2159554 GATTTTCCAG
* *
2159564 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2159584 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2159604 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2159624 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2159644 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2159664 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2159684 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
2159705 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2159725 AATCGCAACGCG
1 AATCGCAACGCG
2159737 ATTTTTAAAG
Statistics
Matches: 137, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
20 118 0.86
21 19 0.14
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2160155 original size:33 final size:33
Alignment explanation
Indices: 2160116--2160186 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2160106 TTCACTTAGA
2160116 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2160149 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2160182 TTTCA
1 TTTCA
2160187 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2160292 original size:21 final size:21
Alignment explanation
Indices: 2160266--2160342 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
2160256 TGCAGAAGAG
2160266 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
2160287 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
2160307 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
2160329 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2160343 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:2160346 original size:14 final size:14
Alignment explanation
Indices: 2160327--2160383 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2160317 GAAAAATGAA
2160327 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2160341 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2160360 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2160374 AATCGCAACG
1 AATCGCAACG
2160384 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2160358 original size:33 final size:33
Alignment explanation
Indices: 2160320--2160388 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
2160310 GCAACGAGAA
2160320 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
2160353 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
2160386 AAA
1 AAA
2160389 CCAAAATCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:2160395 original size:33 final size:33
Alignment explanation
Indices: 2160325--2160396 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
2160315 GAGAAAAATG
**
2160325 AAAATCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
2160358 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
2160391 AAAATC
1 AAAATC
2160397 ACATTGCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.47, C:0.24, G:0.21, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:2160436 original size:14 final size:14
Alignment explanation
Indices: 2160417--2160473 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2160407 TTTCATTTCG
2160417 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2160431 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2160450 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2160464 CGTTGCGATT
1 CGTTGCGATT
2160474 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2160442 original size:33 final size:33
Alignment explanation
Indices: 2160400--2160522 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
2160390 CAAAATCACA
2160400 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2160433 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2160466 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
2160507 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2160523 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2160484 original size:21 final size:21
Alignment explanation
Indices: 2160458--2160522 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2160448 CGCGTTGCGA
2160458 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2160479 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2160499 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2160520 TTC
1 TTC
2160523 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2161335 original size:22 final size:22
Alignment explanation
Indices: 2161318--2161384 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
2161308 CTCGTATAAA
2161318 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2161340 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2161362 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2161384 T
1 T
2161385 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2161721 original size:29 final size:29
Alignment explanation
Indices: 2161679--2161748 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
2161669 TTCTGCATAA
**
2161679 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
2161708 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
2161737 TCATGTCATGTA
1 TCATGTCATGTA
2161749 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:2162172 original size:69 final size:69
Alignment explanation
Indices: 2162051--2162205 Score: 213
Period size: 69 Copynumber: 2.2 Consensus size: 69
2162041 TTTTTCTCAT
* *
2162051 GGGGGAATCGGTTCCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATAC
1 GGGGGTATCGGTTCCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TAC
2162116 GATGA
65 GATGA
* ** * *
2162121 GGGGGTATCGGTTCCCCCCCC-TGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCG
1 GGGGGTATCGGTTCCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACG
*
2162185 TTGA
66 ATGA
*
2162189 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
2162206 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
68 22 0.29
69 34 0.45
70 20 0.26
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.28
Consensus pattern (69 bp):
GGGGGTATCGGTTCCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACG
ATGA
Found at i:2162215 original size:21 final size:21
Alignment explanation
Indices: 2162185--2162227 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2162175 ATTCATTTCG
* *
2162185 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2162206 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2162227 T
1 T
2162228 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2168262 original size:22 final size:22
Alignment explanation
Indices: 2168237--2168303 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
2168227 CTCGTATAAA
*
2168237 TGCACCAAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2168259 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2168281 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2168303 T
1 T
2168304 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2168640 original size:29 final size:29
Alignment explanation
Indices: 2168598--2168667 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
2168588 TTCTGCATAA
**
2168598 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
2168627 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
2168656 TCATGTCATGTA
1 TCATGTCATGTA
2168668 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:2169089 original size:69 final size:68
Alignment explanation
Indices: 2168969--2169122 Score: 209
Period size: 69 Copynumber: 2.2 Consensus size: 68
2168959 CTTTTCTCAT
* * *
2168969 GGGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTTCCCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACG
2169034 ATGA
65 ATGA
* ** * * *
2169038 GGGGGTATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGT
1 GGGGGTATCGGTTCCCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGA
2169103 TGA
66 TGA
*
2169106 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
2169123 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 22 0.29
69 53 0.71
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGA
TGA
Found at i:2169132 original size:21 final size:21
Alignment explanation
Indices: 2169102--2169144 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2169092 ATTCATTTCG
* *
2169102 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2169123 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2169144 T
1 T
2169145 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2171553 original size:92 final size:93
Alignment explanation
Indices: 2171320--2171634 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
2171310 TAGATTGCTT
*
2171320 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2171385 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2171413 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2171478 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2171505 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2171570 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2171598 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2171635 AATACCCTGA
Statistics
Matches: 219, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.42
93 128 0.58
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2171769 original size:14 final size:14
Alignment explanation
Indices: 2171750--2171806 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2171740 CGAAACTTAA
2171750 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2171764 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2171783 AATCGCAACGACAG
1 AATCGCAACGAGAG
2171797 AATCGCAACG
1 AATCGCAACG
2171807 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2171788 original size:19 final size:18
Alignment explanation
Indices: 2171764--2171855 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
2171754 GCAACGAGAG
2171764 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
2171783 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
2171797 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
2171816 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
2171830 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
2171849 AATCGCA
1 AATCGCA
2171856 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:2171790 original size:33 final size:33
Alignment explanation
Indices: 2171732--2171855 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
2171722 TAGTTTACTT
* * *
2171732 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
2171766 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
2171799 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
2171832 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
2171856 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:2171832 original size:14 final size:14
Alignment explanation
Indices: 2171781--2171839 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2171771 ACGCGAAATG
2171781 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2171795 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
2171814 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2171828 AAAATCGCAACG
1 AAAATCGCAACG
2171840 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2171873 original size:19 final size:19
Alignment explanation
Indices: 2171851--2172023 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
2171841 GAAACCAAAA
*
2171851 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2171870 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2171884 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2171903 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2171919 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2171936 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
2171955 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
2171974 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
2171993 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2172013 TCGTGTTGCGA
1 TCGCGTTGCGA
2172024 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2171892 original size:14 final size:14
Alignment explanation
Indices: 2171873--2171929 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2171863 TTTCATTTCG
2171873 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2171887 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
2171904 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
2171920 CGTTGCGATT
1 CGTTGCGATT
2171930 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2171981 original size:38 final size:38
Alignment explanation
Indices: 2171851--2172023 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
2171841 GAAACCAAAA
*
2171851 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
2171886 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
2171919 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
2171955 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
2171993 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
2172024 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:2173965 original size:14 final size:14
Alignment explanation
Indices: 2173946--2173981 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2173936 ATTGTTTAAT
2173946 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2173960 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2173974 TGATTTGT
1 TGATTTGT
2173982 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2174104 original size:19 final size:19
Alignment explanation
Indices: 2174088--2174185 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
2174078 AAAAATGACT
2174088 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2174107 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2174126 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2174140 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2174159 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2174179 ATCGCAA
1 ATCGCAA
2174186 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2174217 original size:53 final size:53
Alignment explanation
Indices: 2174088--2174204 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
2174078 AAAAATGACT
2174088 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2174140 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2174193 ATCGCAATGCGA
1 ATCGCAATGCGA
2174205 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:2174276 original size:33 final size:33
Alignment explanation
Indices: 2174218--2174384 Score: 151
Period size: 33 Copynumber: 4.8 Consensus size: 33
2174208 TCATTTCGCA
2174218 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
2174252 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
2174289 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
2174324 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
2174358 TTGCGACTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2174385 TTCATTTCCG
Statistics
Matches: 107, Mismatches: 13, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
31 4 0.04
32 6 0.06
33 34 0.32
34 32 0.30
35 4 0.04
36 3 0.03
37 2 0.02
38 2 0.02
39 8 0.07
40 3 0.03
41 9 0.08
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:2174457 original size:72 final size:71
Alignment explanation
Indices: 2174200--2174509 Score: 304
Period size: 72 Copynumber: 4.4 Consensus size: 71
2174190 AGAATCGCAA
* * *
2174200 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCG-ATTTTC
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATT-T-TCATTTCCGCA-TTGC
* *
2174263 -ATTTCGCAT
62 GATTTCTCGT
*
2174272 TGCGATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
*
2174331 TT-TCATT
65 TTCTC-GT
* * * * *
2174338 TCCGCA-TTGCGATTCTCTCGTTGCGACTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
2174402 ATTCTCTCGT
63 ATT-TCTCGT
2174412 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
2174477 T-TCATGT
66 TCTC--GT
2174484 TG-GTATTTTCATTTCGCATTGCGATT
1 TGCG-ATTTTCATTTCGCATTGCGATT
2174510 CTCTCGTTGC
Statistics
Matches: 202, Mismatches: 16, Indels: 40
0.78 0.06 0.16
Matches are distributed among these distances:
65 8 0.04
66 15 0.07
67 20 0.10
68 1 0.00
69 5 0.02
70 8 0.04
71 5 0.02
72 104 0.51
73 26 0.13
74 8 0.04
75 2 0.01
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (71 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
TCTCGT
Found at i:2174538 original size:53 final size:53
Alignment explanation
Indices: 2174200--2174523 Score: 511
Period size: 53 Copynumber: 6.1 Consensus size: 53
2174190 AGAATCGCAA
2174200 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
2174253 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
2174306 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
2174359 TGCGACTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
2174412 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TCT-CG--T
2174470 TGCGATTTTCA--T-G--TTG-GTATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCG-ATTTTCATTTCCGCATTGCGATTCTCTCGT
2174517 TGCGATT
1 TGCGATT
2174524 GTAATTTCCG
Statistics
Matches: 260, Mismatches: 4, Indels: 20
0.92 0.01 0.07
Matches are distributed among these distances:
47 8 0.03
49 2 0.01
50 2 0.01
51 3 0.01
52 11 0.04
53 213 0.82
54 3 0.01
55 3 0.01
56 3 0.01
58 12 0.05
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:2177030 original size:24 final size:24
Alignment explanation
Indices: 2176996--2177042 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2176986 CTGAAACATC
2176996 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2177020 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2177043 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2177762 original size:20 final size:20
Alignment explanation
Indices: 2177734--2177962 Score: 228
Period size: 20 Copynumber: 11.4 Consensus size: 20
2177724 AAATTTCAGT
* * *
2177734 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2177754 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2177774 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2177794 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2177814 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2177834 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2177854 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
2177874 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
2177894 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATTCGC
*
2177914 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2177934 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2177954 GTTGCGATT
1 GTTGCGATT
2177963 CTGGAAAATC
Statistics
Matches: 182, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 179 0.98
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2178614 original size:2 final size:2
Alignment explanation
Indices: 2178607--2178663 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2178597 GGCATCCATT
2178607 TA TA TA 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
2178649 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2178664 GTGTGCATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2180014 original size:37 final size:37
Alignment explanation
Indices: 2179941--2180015 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
2179931 GTTGGAAAAT
* *
2179941 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
2179978 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
2180015 A
1 A
2180016 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:2180111 original size:80 final size:81
Alignment explanation
Indices: 2180027--2180211 Score: 293
Period size: 80 Copynumber: 2.3 Consensus size: 81
2180017 TGTTTAATGA
2180027 AAGGGTAAAATTTTATTTTAACCCCTAAACTTCACATAAAATTTTAATTATAGA-TTTTTTTTGT
1 AAGGGTAAAATTTTATTTTAACCCCTAAACTTCACATAAAATTTTAATTATAGATTTTTTTTTGT
2180091 AAATCTAAAATAGTTT
66 AAATCTAAAATAGTTT
* *
2180107 AAGGGTAAAATTTTATTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTTT
1 AAGGGTAAAATTTTATTTTAACCCCTAAACTTCACATAAAATTTTAATTATAGA--TTTTTTTTT
2180172 GTAAATCTAAAATAGTTT
64 GTAAATCTAAAATAGTTT
* *
2180190 AAGGAT-AAATTTGTAATTTAAC
1 AAGGGTAAAATTT-TATTTTAAC
2180212 ATTCGTAGAA
Statistics
Matches: 97, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
80 52 0.54
82 6 0.06
83 39 0.40
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (81 bp):
AAGGGTAAAATTTTATTTTAACCCCTAAACTTCACATAAAATTTTAATTATAGATTTTTTTTTGT
AAATCTAAAATAGTTT
Found at i:2181260 original size:14 final size:14
Alignment explanation
Indices: 2181241--2181267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2181231 TGTTAAAATT
2181241 TAGTCCAATTGTAC
1 TAGTCCAATTGTAC
2181255 TAGTCCAATTGTA
1 TAGTCCAATTGTA
2181268 AATCTTATTT
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:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
TAGTCCAATTGTAC
Found at i:2185427 original size:22 final size:22
Alignment explanation
Indices: 2185399--2185440 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2185389 AAGATAATCA
2185399 AACACC-AAAATCAATCCAAAGC
1 AACACCAAAAATCAA-CCAAAGC
2185421 AACACCAAAAATCAACCAAA
1 AACACCAAAAATCAACCAAA
2185441 ACTTACCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.60, C:0.31, G:0.02, T:0.07
Consensus pattern (22 bp):
AACACCAAAAATCAACCAAAGC
Found at i:2188861 original size:6 final size:6
Alignment explanation
Indices: 2188846--2188880 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2188836 ACTCAGCTTA
* *
2188846 TCTCCG TCTCCT TCTCCT TCTCCT TCTCCG TCTCC
1 TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTCC
2188881 CTGCCCCGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.51, G:0.06, T:0.43
Consensus pattern (6 bp):
TCTCCT
Found at i:2188867 original size:12 final size:12
Alignment explanation
Indices: 2188846--2188880 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
2188836 ACTCAGCTTA
2188846 TCTCCGTCTCCT
1 TCTCCGTCTCCT
*
2188858 TCTCCTTCTCCT
1 TCTCCGTCTCCT
2188870 TCTCCGTCTCC
1 TCTCCGTCTCC
2188881 CTGCCCCGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.51, G:0.06, T:0.43
Consensus pattern (12 bp):
TCTCCGTCTCCT
Found at i:2198793 original size:3 final size:3
Alignment explanation
Indices: 2198785--2198815 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2198775 CACCCTTTCC
*
2198785 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2198816 TCAGTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2200730 original size:19 final size:20
Alignment explanation
Indices: 2200694--2200731 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2200684 TTGTTGACAA
* *
2200694 TTTATTTTCAATCTTAAAAT
1 TTTATATTCAATCCTAAAAT
2200714 TTTATATTC-ATCCTAAAA
1 TTTATATTCAATCCTAAAA
2200732 AAAACCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATATTCAATCCTAAAAT
Found at i:2201531 original size:16 final size:16
Alignment explanation
Indices: 2201510--2201549 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2201500 ATCTGATCTG
*
2201510 ATCTAAAAATTTATAT
1 ATCTAAAAATTTAGAT
2201526 ATCTAAAAATTTAGAT
1 ATCTAAAAATTTAGAT
*
2201542 ACCTAAAA
1 ATCTAAAA
2201550 TAATAATTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (16 bp):
ATCTAAAAATTTAGAT
Found at i:2206020 original size:14 final size:14
Alignment explanation
Indices: 2206001--2206030 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2205991 TACGAAGGAA
2206001 TCCATTCTCAAATC
1 TCCATTCTCAAATC
*
2206015 TCCATTGTCAAATC
1 TCCATTCTCAAATC
2206029 TC
1 TC
2206031 AACCATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (14 bp):
TCCATTCTCAAATC
Found at i:2208372 original size:21 final size:21
Alignment explanation
Indices: 2208346--2208419 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
2208336 ACGTTGCATT
2208346 TCGCGTTGCGATAGTTAGAGA
1 TCGCGTTGCGATAGTTAGAGA
** ** **
2208367 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTAGAGA
*
2208387 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTAGAGA
2208408 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2208420 TTTCCATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTAGAGA
Found at i:2208387 original size:41 final size:41
Alignment explanation
Indices: 2208342--2208503 Score: 214
Period size: 41 Copynumber: 4.1 Consensus size: 41
2208332 ATTCACGTTG
*
2208342 CATTTCGCGTTGCGATAGTTAGAGATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTAGAGATCGCGTTGCGATTTTC
*
2208383 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTAGAGATCGCGTTGCGATTTTC
*
2208424 CATTTCGCGTTGCGATAGTT-GAAAATCGCGTT--G----TC
1 CATTTCGCGTTGCGATAGTTAG-AGATCGCGTTGCGATTTTC
*
2208459 CATTTCGCGTTGCGATAGTCTACAG-TCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TAGAGATCGCGTTGCGATTTTC
2208500 CATT
1 CATT
2208504 AAAAAAAAGA
Statistics
Matches: 107, Mismatches: 5, Indels: 18
0.82 0.04 0.14
Matches are distributed among these distances:
35 28 0.26
36 2 0.02
37 1 0.01
39 1 0.01
40 1 0.01
41 74 0.69
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTAGAGATCGCGTTGCGATTTTC
Done.